Publications

Agtuca BJ, Stopka SA, Tuleski TR, do Amaral FP, Evans S, Liu Y, Xu D, Monteiro RA, Koppenaal DW, Paša-Tolić L, Anderton CR, Vertes A and Stacey G (2020). In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria. Molecular plant-microbe interactions: MPMI, 33(2):272-283, 2020.
[Abstract] [DOI] [BibTeX]

Abstract: Over the past decades, crop yields have risen in parallel with increasing use of fossil fuel-derived nitrogen (N) fertilizers but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic, and endophytic plant growth-promoting bacteria (PGPB) are known to stimulate plant growth. However, compared with the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix+) or a fix- mutant strain (SmR54) compared with uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole-root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in-situ laser ablation electrospray ionization mass spectrometry to sample only those root segments at or adjacent to the sites of bacterial colonization. Metabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants, while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix- strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix- strain, perhaps reflecting a plant defense response.

BibTeX:

@article{agtuca_-situ_2020,
author = {Agtuca, Beverly J. and Stopka, Sylwia A. and Tuleski, Thalita R. and do Amaral, Fernanda P. and Evans, Sterling and Liu, Yang and Xu, Dong and Monteiro, Rose Adele and Koppenaal, David W. and Paša-Tolić, Ljiljana and Anderton, Christopher R. and Vertes, Akos and Stacey, Gary},
title = {In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria},
journal = {Molecular plant-microbe interactions: MPMI},
year = {2020},
volume = {33},
number = {2},
pages = {272--283},
doi = {10.1094/MPMI-06-19-0174-R}
}

Kamoun A, de Reyniès A, Allory Y, Sjödahl G, Robertson AG, Seiler R, Hoadley KA, Groeneveld CS, Al-Ahmadie H, Choi W, Castro MAA, Fontugne J, Eriksson P, Mo Q, Kardos J, Zlotta A, Hartmann A, Dinney CP, Bellmunt J, Powles T, Malats N, Chan KS, Kim WY, McConkey DJ, Black PC, Dyrskjøt L, Höglund M, Lerner SP, Real FX, Radvanyi F and Bladder Cancer Molecular Taxonomy Group (2020). A Consensus Molecular Classification of Muscle-invasive Bladder Cancer. European Urology, 77(4):420-433, 2020.
[Abstract] [DOI] [BibTeX]

Abstract: BACKGROUND: Muscle-invasive bladder cancer (MIBC) is a molecularly diverse disease with heterogeneous clinical outcomes. Several molecular classifications have been proposed, but the diversity of their subtype sets impedes their clinical application.
OBJECTIVE: To achieve an international consensus on MIBC molecular subtypes that reconciles the published classification schemes.
DESIGN, SETTING, AND PARTICIPANTS: We used 1750 MIBC transcriptomic profiles from 16 published datasets and two additional cohorts.
OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: We performed a network-based analysis of six independent MIBC classification systems to identify a consensus set of molecular classes. Association with survival was assessed using multivariable Cox models.
RESULTS AND LIMITATIONS: We report the results of an international effort to reach a consensus on MIBC molecular subtypes. We identified a consensus set of six molecular classes: luminal papillary (24, luminal nonspecified (8, luminal unstable (15, stroma-rich (15, basal/squamous (35, and neuroendocrine-like (3. These consensus classes differ regarding underlying oncogenic mechanisms, infiltration by immune and stromal cells, and histological and clinical characteristics, including outcomes. We provide a single-sample classifier that assigns a consensus class label to a tumor sample's transcriptome. Limitations of the work are retrospective clinical data collection and a lack of complete information regarding patient treatment.
CONCLUSIONS: This consensus system offers a robust framework that will enable testing and validation of predictive biomarkers in future prospective clinical trials.
PATIENT SUMMARY: Bladder cancers are heterogeneous at the molecular level, and scientists have proposed several classifications into sets of molecular classes. While these classifications may be useful to stratify patients for prognosis or response to treatment, a consensus classification would facilitate the clinical use of molecular classes. Conducted by multidisciplinary expert teams in the field, this study proposes such a consensus and provides a tool for applying the consensus classification in the clinical setting.

BibTeX:

@article{kamoun_consensus_2020,
author = {Kamoun, Aurélie and de Reyniès, Aurélien and Allory, Yves and Sjödahl, Gottfrid and Robertson, A. Gordon and Seiler, Roland and Hoadley, Katherine A. and Groeneveld, Clarice S. and Al-Ahmadie, Hikmat and Choi, Woonyoung and Castro, Mauro A. A. and Fontugne, Jacqueline and Eriksson, Pontus and Mo, Qianxing and Kardos, Jordan and Zlotta, Alexandre and Hartmann, Arndt and Dinney, Colin P. and Bellmunt, Joaquim and Powles, Thomas and Malats, Núria and Chan, Keith S. and Kim, William Y. and McConkey, David J. and Black, Peter C. and Dyrskjøt, Lars and Höglund, Mattias and Lerner, Seth P. and Real, Francisco X. and Radvanyi, François and Bladder Cancer Molecular Taxonomy Group},
title = {A Consensus Molecular Classification of Muscle-invasive Bladder Cancer},
journal = {European Urology},
year = {2020},
volume = {77},
number = {4},
pages = {420--433},
doi = {10.1016/j.eururo.2019.09.006}
}

Kukolj C, Pedrosa FO, de Souza GA, Sumner LW, Lei Z, Sumner B, do Amaral FP, Juexin W, Trupti J, Huergo LF, Monteiro RA, Valdameri G, Stacey G and de Souza EM (2020). Proteomic and Metabolomic Analysis of Azospirillum brasilensentrC Mutant under High and Low Nitrogen Conditions. Journal of Proteome Research, 19(1):92-105, 2020.
[Abstract] [DOI] [BibTeX]

Abstract: Azospirillum brasilense is a diazotrophic microorganism capable of associating with roots of important grasses and cereals, promoting plant growth and increasing crop yields. Nitrogen levels and the Ntr regulatory system control the nitrogen metabolism in A. brasilense. This system comprises the nitrogen regulatory proteins GlnD, which is capable of adding uridylyl groups to the PII proteins, GlnB (PII-1) and GlnZ (PII-2), under limiting nitrogen levels. Under such conditions, the histidine kinase NtrB (nitrogen regulatory protein B) cannot interact with GlnB and phosphorylate NtrC (nitrogen regulatory protein C). The phosphorylated form of NtrC acts as a transcriptional activator of genes involved in the metabolism of alternative nitrogen sources. Considering the key role of NtrC in nitrogen metabolism in A. brasilense, in this work we evaluated the proteomic and metabolomic profiles of the wild-type FP2 strain and its mutant ntrC grown under high and low nitrogen. Analysis of the integrated data identifies novel NtrC targets, including proteins involved in the response against oxidative stress (i.e., glutathione S-transferase and hydroperoxide resistance protein), underlining the importance of NtrC to bacterial survival under oxidative stress conditions.

BibTeX:

@article{kukolj_proteomic_2020,
author = {Kukolj, Caroline and Pedrosa, Fábio O. and de Souza, Gustavo A. and Sumner, Lloyd W. and Lei, Zhentian and Sumner, Barbara and do Amaral, Fernanda P. and Juexin, Wang and Trupti, Joshi and Huergo, Luciano F. and Monteiro, Rose Adele and Valdameri, Glaucio and Stacey, Gary and de Souza, Emanuel M.},
title = {Proteomic and Metabolomic Analysis of Azospirillum brasilensentrC Mutant under High and Low Nitrogen Conditions},
journal = {Journal of Proteome Research},
year = {2020},
volume = {19},
number = {1},
pages = {92--105},
doi = {10.1021/acs.jproteome.9b00397}
}

Trefflich S, Dalmolin RJS, Ortega JM and Castro MAA (2020). Which came first, the transcriptional regulator or its target genes? An evolutionary perspective into the construction of eukaryotic regulons. Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms, 1863(6):194472, 2020.
[Abstract] [DOI] [BibTeX]

Abstract: Eukaryotic regulons are regulatory units formed by a set of genes under the control of the same transcription factor (TF). Despite the functional plasticity, TFs are highly conserved and recognize the same DNA sequences in different organisms. One of the main factors that confer regulatory specificity is the distribution of the binding sites of the TFs along the genome, allowing the configuration of different transcriptional regulatory networks (TRNs) from the same regulator. A similar scenario occurs between tissues of the same organism, where a TRN can be rewired by epigenetic factors, modulating the accessibility of the TF to its binding sites. In this article we discuss concepts that can help to formulate testable hypotheses about the construction of regulons, exploring the presence and absence of the elements that form a TRN throughout the evolution of an ancestral lineage. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.

BibTeX:

@article{trefflich_which_2020,
author = {Trefflich, Sheyla and Dalmolin, Rodrigo J. S. and Ortega, José Miguel and Castro, Mauro A. A.},
title = {Which came first, the transcriptional regulator or its target genes? An evolutionary perspective into the construction of eukaryotic regulons},
journal = {Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms},
year = {2020},
volume = {1863},
number = {6},
pages = {194472},
doi = {10.1016/j.bbagrm.2019.194472}
}

Tuleski TR, Kimball J, do Amaral FP, Pereira TP, Tadra-Sfeir MZ, de Oliveira Pedrosa F, Maltempi de Souza E, Balint-Kurti P, Monteiro RA and Stacey G (2020). Herbaspirillum rubrisubalbicans as a Phytopathogenic Model to Study the Immune System of Sorghum bicolor. Molecular plant-microbe interactions: MPMI, 33(2):235-246, 2020.
[Abstract] [DOI] [BibTeX]

Abstract: Herbaspirillum rubrisubalbicans is the causal agent of red stripe disease (RSD) and mottle stripe disease of sorghum and sugarcane, respectively. In all, 63 genotypes of Sorghum bicolor were inoculated with H. rubrisubalbicans, with 59 showing RSD symptoms. Quantitative trait loci (QTL) analysis in a recombinant inbred line (RIL) population identified several QTL associated with variation in resistance to RSD. RNA sequencing analysis identified a number of genes whose transcript levels were differentially regulated during H. rubrisubalbicans infection. Among those genes that responded to H. rubrisubalbicans inoculation were many involved in plant-pathogen interactions such as leucine-rich repeat receptors, mitogen-activated protein kinase 1, calcium-binding proteins, transcriptional factors (ethylene-responsive element binding factor), and callose synthase. Pretreatment of sorghum leaves with the pathogen-associated molecular pattern (PAMP) molecules flg22 and chitooctaose provided protection against subsequent challenge with the pathogen, suggesting that PAMP-triggered immunity plays an important role in the sorghum immunity response. These data present baseline information for the use of the genetically tractable H. rubrisubalbicans-sorghum pathosystem for the study of innate immunity and disease resistance in this important grain and bioenergy crop. Information gained from the use of this system is likely to be informative for other monocots, including those more intractable for experimental study (e.g., sugarcane).

BibTeX:

@article{tuleski_herbaspirillum_2020,
author = {Tuleski, Thalita Regina and Kimball, Jennifer and do Amaral, Fernanda P. and Pereira, Tomas P. and Tadra-Sfeir, Michelle Zibetti and de Oliveira Pedrosa, Fabio and Maltempi de Souza, Emanuel and Balint-Kurti, Peter and Monteiro, Rose Adele and Stacey, Gary},
title = {Herbaspirillum rubrisubalbicans as a Phytopathogenic Model to Study the Immune System of Sorghum bicolor},
journal = {Molecular plant-microbe interactions: MPMI},
year = {2020},
volume = {33},
number = {2},
pages = {235--246},
doi = {10.1094/MPMI-06-19-0154-R}
}

Alnoch RC, Cardoso RLA, Guizelini D, Balsanelli E, Tadra-Sfeir MZ, de Oliveira Pedrosa F, Sassaki GL, Cruz LM, Mitchell DA, de Souza EM, Krieger N and Muller-Santos M (2019). Genome sequencing of Burkholderia contaminans LTEB11 reveals a lipolytic arsenal of biotechnological interest. Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology], 50(3):619-624, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: Burkholderia contaminans LTEB11 is a Gram-negative betaproteobacterium isolated as a contaminant of a culture in mineral medium supplemented with vegetable oil. Here, we report the genome sequence of B. contaminans LTEB11, identifying and analyzing the genes involved in its lipolytic machinery and in the production of other biotechnological products.

BibTeX:

@article{alnoch_genome_2019,
author = {Alnoch, Robson Carlos and Cardoso, Rodrigo Luis Alves and Guizelini, Dieval and Balsanelli, Eduardo and Tadra-Sfeir, Michelle Zibetti and de Oliveira Pedrosa, Fábio and Sassaki, Guilherme Lanzi and Cruz, Leonardo Magalhães and Mitchell, David Alexander and de Souza, Emanuel Maltempi and Krieger, Nadia and Muller-Santos, Marcelo},
title = {Genome sequencing of Burkholderia contaminans LTEB11 reveals a lipolytic arsenal of biotechnological interest},
journal = {Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]},
year = {2019},
volume = {50},
number = {3},
pages = {619--624},
doi = {10.1007/s42770-019-00076-4}
}

Andreazza AP, Cardoso RLA, Cocco J, Guizelini D, Faoro H, Tadra-Sfeir MZ, Balsanelli E, Cruz LM, Fadel-Picheth CMT, Donatti L, Souza EM, Foerster LA, Pedrosa FO and Chubatsu LS (2019). Genome Analysis of Entomopathogenic Bacillus sp. ABP14 Isolated from a Lignocellulosic Compost. Genome Biology and Evolution, 11(6):1658-1662, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: We report the complete genome sequence of Bacillus sp. strain ABP14 isolated from lignocellulosic compost and selected by its ability in hydrolyzing carboxymethyl cellulose. This strain does not produce a Cry-like protein but showed an insecticidal activity against larvae of Anticarsia gemmatalis (Lepidoptera). Genome-based taxonomic analysis revealed that the ABP14 chromosome is genetically close to Bacillus thuringiensis serovar finitimus YBT020. ABP14 also carries one plasmid which showed no similarity with those from YBT020. Genome analysis of ABP14 identified unique genes related to cell surface structures, cell wall, metabolic competence, and virulence factors that may contribute for its survival and environmental adaptation, as well as its entomopathogenic activity.

BibTeX:

@article{andreazza_genome_2019,
author = {Andreazza, Ana Paula and Cardoso, Rodrigo L. A. and Cocco, Jessica and Guizelini, Dieval and Faoro, Helisson and Tadra-Sfeir, Michelle Z. and Balsanelli, Eduardo and Cruz, Leonardo M. and Fadel-Picheth, Cyntia M. T. and Donatti, Lucélia and Souza, Emanuel M. and Foerster, Luís A. and Pedrosa, Fabio O. and Chubatsu, Leda S.},
title = {Genome Analysis of Entomopathogenic Bacillus sp. ABP14 Isolated from a Lignocellulosic Compost},
journal = {Genome Biology and Evolution},
year = {2019},
volume = {11},
number = {6},
pages = {1658--1662},
doi = {10.1093/gbe/evz114}
}

Brusamarello-Santos LCC, Alberton D, Valdameri G, Camilios-Neto D, Covre R, Lopes KdP, Zibetti Tadra-Sfeir M, Faoro H, Adele Monteiro R, Barbosa-Silva A, John Broughton W, Oliveira Pedrosa F, Wassem R and Souza EMd (2019). Modulation of defence and iron homeostasis genes in rice roots by the diazotrophic endophyte Herbaspirillum seropedicae. Scientific Reports, 9(1):10573, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: Rice is staple food of nearly half the world's population. Rice yields must therefore increase to feed ever larger populations. By colonising rice and other plants, Herbaspirillum spp. stimulate plant growth and productivity. However the molecular factors involved are largely unknown. To further explore this interaction, the transcription profiles of Nipponbare rice roots inoculated with Herbaspirillum seropedicae were determined by RNA-seq. Mapping the 104 million reads against the Oryza sativa cv. Nipponbare genome produced 65 million unique mapped reads that represented 13,840 transcripts each with at least two-times coverage. About 7.4% (1,014) genes were differentially regulated and of these 255 changed expression levels more than two times. Several of the repressed genes encoded proteins related to plant defence (e.g. a putative probenazole inducible protein), plant disease resistance as well as enzymes involved in flavonoid and isoprenoid synthesis. Genes related to the synthesis and efflux of phytosiderophores (PS) and transport of PS-iron complexes were induced by the bacteria. These data suggest that the bacterium represses the rice defence system while concomitantly activating iron uptake. Transcripts of H. seropedicae were also detected amongst which transcripts of genes involved in nitrogen fixation, cell motility and cell wall synthesis were the most expressed.

BibTeX:

@article{brusamarello-santos_modulation_2019,
author = {Brusamarello-Santos, Liziane Cristina Campos and Alberton, Dayane and Valdameri, Glaucio and Camilios-Neto, Doumit and Covre, Rafael and Lopes, Katia de Paiva and Zibetti Tadra-Sfeir, Michelle and Faoro, Helisson and Adele Monteiro, Rose and Barbosa-Silva, Adriano and John Broughton, William and Oliveira Pedrosa, Fabio and Wassem, Roseli and Souza, Emanuel Maltempi de},
title = {Modulation of defence and iron homeostasis genes in rice roots by the diazotrophic endophyte Herbaspirillum seropedicae},
journal = {Scientific Reports},
year = {2019},
volume = {9},
number = {1},
pages = {10573},
doi = {10.1038/s41598-019-45866-w}
}

Ceccon DM, Faoro H, Lana PdC, Souza EMd and Pedrosa FdO (2019). Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil. The Science of the Total Environment, 694:133609, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (textless5 PSU and textgreater30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.

BibTeX:

@article{ceccon_metataxonomic_2019,
author = {Ceccon, Denny Marcel and Faoro, Helisson and Lana, Paulo da Cunha and Souza, Emanuel Maltempi de and Pedrosa, Fábio de Oliveira},
title = {Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil},
journal = {The Science of the Total Environment},
year = {2019},
volume = {694},
pages = {133609},
doi = {10.1016/j.scitotenv.2019.133609}
}

Chagas VS, Groeneveld CS, Oliveira KG, Trefflich S, de Almeida RC, Ponder BAJ, Meyer KB, Jones SJM, Robertson AG and Castro MAA (2019). RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons. Bioinformatics (Oxford, England), 35(24):5357-5358, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: MOTIVATION: Transcription factors (TFs) are key regulators of gene expression, and can activate or repress multiple target genes, forming regulatory units, or regulons. Understanding downstream effects of these regulators includes evaluating how TFs cooperate or compete within regulatory networks. Here we present RTNduals, an R/Bioconductor package that implements a general method for analyzing pairs of regulons.
RESULTS: RTNduals identifies a dual regulon when the number of targets shared between a pair of regulators is statistically significant. The package extends the RTN (Reconstruction of Transcriptional Networks) package, and uses RTN transcriptional networks to identify significant co-regulatory associations between regulons. The Supplementary Information reports two case studies for TFs using the METABRIC and TCGA breast cancer cohorts.
AVAILABILITY AND IMPLEMENTATION: RTNduals is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNduals/.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BibTeX:

@article{chagas_rtnduals_2019,
author = {Chagas, Vinicius S. and Groeneveld, Clarice S. and Oliveira, Kelin G. and Trefflich, Sheyla and de Almeida, Rodrigo C. and Ponder, Bruce A. J. and Meyer, Kerstin B. and Jones, Steven J. M. and Robertson, A. Gordon and Castro, Mauro A. A.},
title = {RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons},
journal = {Bioinformatics (Oxford, England)},
year = {2019},
volume = {35},
number = {24},
pages = {5357--5358},
doi = {10.1093/bioinformatics/btz534}
}

de Jong JJ, Liu Y, Robertson AG, Seiler R, Groeneveld CS, van der Heijden MS, Wright JL, Douglas J, Dall'Era M, Crabb SJ, van Rhijn BWG, van Kessel KEM, Davicioni E, Castro MAA, Lotan Y, Zwarthoff EC, Black PC, Boormans JL and Gibb EA (2019). Long non-coding RNAs identify a subset of luminal muscle-invasive bladder cancer patients with favorable prognosis. Genome Medicine, 11(1):60, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: BACKGROUND: Muscle-invasive bladder cancer (MIBC) is a heterogeneous disease, and gene expression profiling has identified several molecular subtypes with distinct biological and clinicopathological characteristics. While MIBC subtyping has primarily been based on messenger RNA (mRNA), long non-coding RNAs (lncRNAs) may provide additional resolution.
METHODS: LncRNA expression was quantified from microarray data of a MIBC cohort treated with neoadjuvant chemotherapy (NAC) and radical cystectomy (RC) (n = 223). Unsupervised consensus clustering of highly variant lncRNAs identified a four-cluster solution, which was characterized using a panel of MIBC biomarkers, regulon activity profiles, gene signatures, and survival analysis. The four-cluster solution was confirmed in The Cancer Genome Atlas (TCGA) cohort (n = 405). A single-sample genomic classifier (GC) was trained using ridge-penalized logistic regression and validated in two independent cohorts (n = 255 and n = 94).
RESULTS: NAC and TCGA cohorts both contained an lncRNA cluster (LC3) with favorable prognosis that was enriched with tumors of the luminal-papillary (LP) subtype. In both cohorts, patients with LP tumors in LC3 (LPL-C3) were younger and had organ-confined, node-negative disease. The LPL-C3 tumors had enhanced FGFR3, SHH, and wild-type p53 pathway activity. In the TCGA cohort, LPL-C3 tumors were enriched for FGFR3 mutations and depleted for TP53 and RB1 mutations. A GC trained to identify these LPL-C3 patients showed robust performance in two validation cohorts.
CONCLUSIONS: Using lncRNA expression profiles, we identified a biologically distinct subgroup of luminal-papillary MIBC with a favorable prognosis. These data suggest that lncRNAs provide additional information for higher-resolution subtyping, potentially improving precision patient management.

BibTeX:

@article{de_jong_long_2019,
author = {de Jong, Joep J. and Liu, Yang and Robertson, A. Gordon and Seiler, Roland and Groeneveld, Clarice S. and van der Heijden, Michiel S. and Wright, Jonathan L. and Douglas, James and Dall'Era, Marc and Crabb, Simon J. and van Rhijn, Bas W. G. and van Kessel, Kim E. M. and Davicioni, Elai and Castro, Mauro A. A. and Lotan, Yair and Zwarthoff, Ellen C. and Black, Peter C. and Boormans, Joost L. and Gibb, Ewan A.},
title = {Long non-coding RNAs identify a subset of luminal muscle-invasive bladder cancer patients with favorable prognosis},
journal = {Genome Medicine},
year = {2019},
volume = {11},
number = {1},
pages = {60},
doi = {10.1186/s13073-019-0669-z}
}

de Lima Nichio BT, de Oliveira AMR, de Pierri CR, Santos LGC, Lejambre AQ, Vialle RA, da Rocha Coimbra NA, Guizelini D, Marchaukoski JN, de Oliveira Pedrosa F and Raittz RT (2019). RAFTS3G: an efficient and versatile clustering software to analyses in large protein datasets. BMC bioinformatics, 20(1):392, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: BACKGROUND: Clustering methods are essential to partitioning biological samples being useful to minimize the information complexity in large datasets. Tools in this context usually generates data with greed algorithms that solves some Data Mining difficulties which can degrade biological relevant information during the clustering process. The lack of standardization of metrics and consistent bases also raises questions about the clustering efficiency of some methods. Benchmarks are needed to explore the full potential of clustering methods - in which alignment-free methods stand out - and the good choice of dataset makes it essentials.
RESULTS: Here we present a new approach to Data Mining in large protein sequences datasets, the Rapid Alignment Free Tool for Sequences Similarity Search to Groups (RAFTS3G), a method to clustering aiming of losing less biological information in the processes of generation groups. The strategy developed in our algorithm is optimized to be more astringent which reflects increase in accuracy and sensitivity in the generation of clusters in a wide range of similarity. RAFTS3G is the better choice compared to three main methods when the user wants more reliable result even ignoring the ideal threshold to clustering.
CONCLUSION: In general, RAFTS3G is able to group up to millions of biological sequences into large datasets, which is a remarkable option of efficiency in clustering. RAFTS3G compared to other "standard-gold" methods in the clustering of large biological data maintains the balance between the reduction of biological information redundancy and the creation of consistent groups. We bring the binary search concept applied to grouped sequences which shows maintaining sensitivity/accuracy relation and up to minimize the time of data generated with RAFTS3G process.

BibTeX:

@article{de_lima_nichio_rafts3g_2019,
author = {de Lima Nichio, Bruno Thiago and de Oliveira, Aryel Marlus Repula and de Pierri, Camilla Reginatto and Santos, Leticia Graziela Costa and Lejambre, Alexandre Quadros and Vialle, Ricardo Assunção and da Rocha Coimbra, Nilson Antônio and Guizelini, Dieval and Marchaukoski, Jeroniza Nunes and de Oliveira Pedrosa, Fabio and Raittz, Roberto Tadeu},
title = {RAFTS3G: an efficient and versatile clustering software to analyses in large protein datasets},
journal = {BMC bioinformatics},
year = {2019},
volume = {20},
number = {1},
pages = {392},
doi = {10.1186/s12859-019-2973-4}
}

de Medeiros LM, De Bastiani MA, Rico EP, Schonhofen P, Pfaffenseller B, Wollenhaupt-Aguiar B, Grun L, Barbé-Tuana F, Zimmer ER, Castro MAA, Parsons RB and Klamt F (2019). Cholinergic Differentiation of Human Neuroblastoma SH-SY5Y Cell Line and Its Potential Use as an In vitro Model for Alzheimer's Disease Studies. Molecular Neurobiology, 56(11):7355-7367, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: Cholinergic transmission is critical to high-order brain functions such as memory, learning, and attention. Alzheimer's disease (AD) is characterized by cognitive decline associated with a specific degeneration of cholinergic neurons. No effective treatment to prevent or reverse the symptoms is known. Part of this might be due to the lack of in vitro models that effectively mimic the relevant features of AD. Here, we describe the characterization of an AD in vitro model using the SH-SY5Y cell line. Exponentially growing cells were maintained in DMEM/F12 medium and differentiation was triggered by the combination of retinoic acid (RA) and BDNF. Both acetylcholinesterase (AChE) and choline acetyltransferase (ChAT) enzymatic activities and immunocontent were determined. For mimicking tau and amyloid-β pathology, RA + BDNF-differentiated cells were challenged with okadaic acid (OA) or soluble oligomers of amyloid-β (AβOs) and neurotoxicity was evaluated. RA + BDNF-induced differentiation resulted in remarkable neuronal morphology alterations characterized by increased neurite density. Enhanced expression and enzymatic activities of cholinergic markers were observed compared to RA-differentiation only. Combination of sublethal doses of AβOs and OA resulted in decreased neurite densities, an in vitro marker of synaptopathy. Challenging RA + BDNF-differentiated SH-SY5Y cells with the combination of sublethal doses of OA and AβO, without causing considerable decrease of cell viability, provides an in vitro model which mimics the early-stage pathophysiology of cholinergic neurons affected by AD.

BibTeX:

@article{de_medeiros_cholinergic_2019,
author = {de Medeiros, Liana M. and De Bastiani, Marco A. and Rico, Eduardo P. and Schonhofen, Patrícia and Pfaffenseller, Bianca and Wollenhaupt-Aguiar, Bianca and Grun, Lucas and Barbé-Tuana, Florência and Zimmer, Eduardo R. and Castro, Mauro A. A. and Parsons, Richard B. and Klamt, Fábio},
title = {Cholinergic Differentiation of Human Neuroblastoma SH-SY5Y Cell Line and Its Potential Use as an In vitro Model for Alzheimer's Disease Studies},
journal = {Molecular Neurobiology},
year = {2019},
volume = {56},
number = {11},
pages = {7355--7367},
doi = {10.1007/s12035-019-1605-3}
}

de Santana Lopes A, Gomes Pacheco T, Nascimento da Silva O, Magalhães Cruz L, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F and Rogalski M (2019). The plastomes of Astrocaryum aculeatum G. Mey. and A. murumuru Mart. show a flip-flop recombination between two short inverted repeats. Planta, 250(4):1229-1246, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: MAIN CONCLUSION: The plastomes of Astrocaryum murumuru and A. aculeatum revealed a lineage-specific structural feature originated by flip-flop recombination, non-synonymous substitutions in conserved genes and several molecular markers. Astrocaryum murumuru Mart. and A. aculeatum G.Mey. are two palm species of Amazon forest that are economically important as source of food, oil and raw material for several applications. Genetic studies aiming to establish strategies for conservation and domestication of both species are still in the beginning given that the exploitation is mostly by extractive activity. The identification and characterization of molecular markers are essential to assess the genetic diversity of natural populations of both species. Therefore, we sequenced and characterized in detail the plastome of both species. We compared both species and identified 32 polymorphic SSR loci, 150 SNPs, 46 indels and eight hotspots of nucleotide diversity. Additionally, we reported a specific RNA editing site found in the ccsA gene, which is exclusive to A. murumuru. Moreover, the structural analysis in the plastomes of both species revealed a 4.6-kb inversion encompassing a set of genes involved in chlororespiration and plastid translation. This 4.6-kb inversion is a lineage-specific structural feature of the genus Astrocaryum originated by flip-flop recombination between two short inverted repeats. Furthermore, our phylogenetic analysis using whole plastomes of 39 Arecaceae species placed the Astrocaryum species sister to Acrocomia within the tribe Cocoseae. Finally, our data indicated substantial changes in the plastome structure and sequence of both species of the genus Astrocaryum, bringing new molecular markers, several structural and evolving features, which can be applied in several areas such as genetic, evolution, breeding, phylogeny and conservation strategies for both species.

BibTeX:

@article{de_santana_lopes_plastomes_2019,
author = {de Santana Lopes, Amanda and Gomes Pacheco, Túlio and Nascimento da Silva, Odyone and Magalhães Cruz, Leonardo and Balsanelli, Eduardo and Maltempi de Souza, Emanuel and de Oliveira Pedrosa, Fábio and Rogalski, Marcelo},
title = {The plastomes of Astrocaryum aculeatum G. Mey. and A. murumuru Mart. show a flip-flop recombination between two short inverted repeats},
journal = {Planta},
year = {2019},
volume = {250},
number = {4},
pages = {1229--1246},
doi = {10.1007/s00425-019-03217-z}
}

Faoro H, Oliveira WK, Weiss VA, Tadra-Sfeir MZ, Cardoso RL, Balsanelli E, Brusamarello-Santos LCC, Camilios-Neto D, Cruz LM, Raittz RT, Marques ACQ, LiPuma J, Fadel-Picheth CMT, Souza EM and Pedrosa FO (2019). Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts. BMC genomics, 20(1):630, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: BACKGROUND: Herbaspirillum seropedicae is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. However, strains of H. seropedicae have been isolated from immunocompromised patients and associated with human infections and deaths. In this work, we sequenced the genomes of two clinical strains of H. seropedicae, AU14040 and AU13965, and compared them with the genomes of strains described as having an environmental origin.
RESULTS: Both genomes were closed, indicating a single circular chromosome; however, strain AU13965 also carried a plasmid of 42,977 bp, the first described in the genus Herbaspirillum. Genome comparison revealed that the clinical strains lost the gene sets related to biological nitrogen fixation (nif) and the type 3 secretion system (T3SS), which has been described to be essential for interactions with plants. Comparison of the pan-genomes of clinical and environmental strains revealed different sets of accessorial genes. However, antimicrobial resistance genes were found in the same proportion in all analyzed genomes. The clinical strains also acquired new genes and genomic islands that may be related to host interactions. Among the acquired islands was a cluster of genes related to lipopolysaccharide (LPS) biosynthesis. Although highly conserved in environmental strains, the LPS biosynthesis genes in the two clinical strains presented unique and non-orthologous genes within the genus Herbaspirillum. Furthermore, the AU14040 strain cluster contained the neuABC genes, which are responsible for sialic acid (Neu5Ac) biosynthesis, indicating that this bacterium could add it to its lipopolysaccharide. The Neu5Ac-linked LPS could increase the bacterial resilience in the host aiding in the evasion of the immune system.
CONCLUSIONS: Our findings suggest that the lifestyle transition from environment to opportunist led to the loss and acquisition of specific genes allowing adaptations to colonize and survive in new hosts. It is possible that these substitutions may be the starting point for interactions with new hosts.

BibTeX:

@article{faoro_genome_2019,
author = {Faoro, Helisson and Oliveira, Willian K. and Weiss, Vinicius A. and Tadra-Sfeir, Michelle Z. and Cardoso, Rodrigo L. and Balsanelli, Eduardo and Brusamarello-Santos, Liziane C. C. and Camilios-Neto, Doumit and Cruz, Leonardo M. and Raittz, Roberto T. and Marques, Ana C. Q. and LiPuma, John and Fadel-Picheth, Cyntia M. T. and Souza, Emanuel M. and Pedrosa, Fabio O.},
title = {Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts},
journal = {BMC genomics},
year = {2019},
volume = {20},
number = {1},
pages = {630},
doi = {10.1186/s12864-019-5982-9}
}

Groeneveld CS, Chagas VS, Jones SJM, Robertson AG, Ponder BAJ, Meyer KB and Castro MAA (2019). RTNsurvival: an R/Bioconductor package for regulatory network survival analysis. Bioinformatics (Oxford, England), 35(21):4488-4489, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: MOTIVATION: Transcriptional networks are models that allow the biological state of cells or tumours to be described. Such networks consist of connected regulatory units known as regulons, each comprised of a regulator and its targets. Inferring a transcriptional network can be a helpful initial step in characterizing the different phenotypes within a cohort. While the network itself provides no information on molecular differences between samples, the per-sample state of each regulon, i.e. the regulon activity, can be used for describing subtypes in a cohort. Integrating regulon activities with clinical data and outcomes would extend this characterization of differences between subtypes.
RESULTS: We describe RTNsurvival, an R/Bioconductor package that calculates regulon activity profiles using transcriptional networks reconstructed by the RTN package, gene expression data, and a two-tailed Gene Set Enrichment Analysis. Given regulon activity profiles across a cohort, RTNsurvival can perform Kaplan-Meier analyses and Cox Proportional Hazards regressions, while also considering confounding variables. The Supplementary Information provides two case studies that use data from breast and liver cancer cohorts and features uni- and multivariate regulon survival analysis.
AVAILABILITY AND IMPLEMENTATION: RTNsurvival is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNsurvival/.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BibTeX:

@article{groeneveld_rtnsurvival_2019,
author = {Groeneveld, Clarice S. and Chagas, Vinicius S. and Jones, Steven J. M. and Robertson, A. Gordon and Ponder, Bruce A. J. and Meyer, Kerstin B. and Castro, Mauro A. A.},
title = {RTNsurvival: an R/Bioconductor package for regulatory network survival analysis},
journal = {Bioinformatics (Oxford, England)},
year = {2019},
volume = {35},
number = {21},
pages = {4488--4489},
doi = {10.1093/bioinformatics/btz229}
}

Ibañez IL, Grings FM, Bracalente C, Rinflerch AR, Volonteri V, Castro MAA, Klamt F and Durán H (2019). Potential predictive value of cofilin-1 for metastasis occurrence in a small cohort of Argentinian patients with mid-low Breslow thickness melanoma. Pathology, Research and Practice, 215(10):152582, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: Nowadays, histopathological criteria for melanocytic lesions are the mainstay prognostic factors for melanoma. However, there are cases in which these parameters fall short to predict melanoma spread. We recently demonstrated a correlation of cofilin-1 levels, a key protein for tumor invasion, with different histopathological parameters associated with melanoma malignancy as well as a negative correlation with survival. In order to broaden our previous findings, we aim to estimate the probability of a melanoma to metastasize as a function of both a conventional histopathological parameter (Breslow thickness, BT) and cofilin-1's immunohistochemical expression levels, which we propose as a potential marker for metastasis. We used a Bayesian approach to analyze clinical and cofilin-1 datasets formerly obtained from a patients' small cohort diagnosed with malignant melanocytic lesions since 2000 until 2008; classified at different tumor stages with or without detected metastasis and with at least 5 years of clinical follow-up. Low BT values exhibited wide variance to predict metastasis occurrence, while the differential diagnostic value of cofilin-1 confirmed BT diagnosis or resulted more precise to predict outcome. Particularly, the probability of metastasis estimation improved when cofilin-1 was combined with BT for specific cases, where BT displayed large uncertainties. Our analysis and the cofilin-1 determination provided statistically significant prognostic value in mid-low BT melanomas, which could complement further evaluation criteria to assist diagnosis and treatment decision-making. Moreover, the combined use of cofilin-1 with BT, if validated in follow-up studies, would be feasible to help patients' selection for treatment and optimize health resources.

BibTeX:

@article{ibanez_potential_2019,
author = {Ibañez, Irene L. and Grings, Francisco M. and Bracalente, Candelaria and Rinflerch, Adriana R. and Volonteri, Victoria and Castro, Mauro A. A. and Klamt, Fabio and Durán, Hebe},
title = {Potential predictive value of cofilin-1 for metastasis occurrence in a small cohort of Argentinian patients with mid-low Breslow thickness melanoma},
journal = {Pathology, Research and Practice},
year = {2019},
volume = {215},
number = {10},
pages = {152582},
doi = {10.1016/j.prp.2019.152582}
}

Leite WC, Penteado RF, Gomes F, Iulek J, Etto RM, Saab SC, Steffens MBR and Galvão CW (2019). MAW point mutation impairs H. Seropedicae RecA ATP hydrolysis and DNA repair without inducing large conformational changes in its structure. PloS One, 14(4):e0214601, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: RecA is a multifunctional protein that plays a central role in DNA repair in bacteria. The structural Make ATP Work motif (MAW) is proposed to control the ATPase activity of RecA. In the present work, we report the biochemical activity and structural effects of the L53Q mutation at the MAW motif of the RecA protein from H. seropedicae (HsRecA L53Q). In vitro studies showed that HsRecA L53Q can bind ADP, ATP, and ssDNA, as does wild-type RecA. However, the ATPase and DNA-strand exchange activities were completely lost. In vivo studies showed that the expression of HsRecA L53Q in E. coli recA1 does not change its phenotype when cells were challenged with MMS and UV. Molecular dynamics simulations showed the L53Q point mutation did not cause large conformational changes in the HsRecA structure. However, there is a difference on dynamical cross-correlation movements of the residues involved in contacts within the ATP binding site and regions that hold the DNA binding sites. Additionally, a new hydrogen bond, formed between Q53 and T49, was hypothesized to allow an independent motion of the MAW motif from the hydrophobic core, what could explain the observed loss of activity of HsRecA L53Q.

BibTeX:

@article{leite_maw_2019,
author = {Leite, Wellington C. and Penteado, Renato F. and Gomes, Fernando and Iulek, Jorge and Etto, Rafael M. and Saab, Sérgio C. and Steffens, Maria B. R. and Galvão, Carolina W.},
title = {MAW point mutation impairs H. Seropedicae RecA ATP hydrolysis and DNA repair without inducing large conformational changes in its structure},
journal = {PloS One},
year = {2019},
volume = {14},
number = {4},
pages = {e0214601},
doi = {10.1371/journal.pone.0214601}
}

Martini VP, Krieger N, Glogauer A, Souza EM and Iulek J (2019). Structure solution and analyses of the first true lipase obtained from metagenomics indicate potential for increased thermostability. New Biotechnology, 53:65-72, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: Metagenomics is a modern approach to discovery of new enzymes with novel properties. This article reports the structure of a new lipase, belonging to family I.1, obtained by means of metagenomics. Its structure presents a fold typical of α/β hydrolases, with the lid in closed conformation. The protein was previously shown to present high thermostability and to be stable in aqueous solutions of polar organic solvents at high concentrations [30% (V/V)]. Molecular dynamics studies showed that the protein maintains its structure well in organic solvents. They also suggested that its thermostability might be enhanced if it were mutated to present a disulfide bond similar to that typically found in lipase family I.2. These findings identify this lipase as a good candidate for further improvement through protein engineering.

BibTeX:

@article{martini_structure_2019,
author = {Martini, Viviane Paula and Krieger, Nadia and Glogauer, Arnaldo and Souza, Emanuel Maltempi and Iulek, Jorge},
title = {Structure solution and analyses of the first true lipase obtained from metagenomics indicate potential for increased thermostability},
journal = {New Biotechnology},
year = {2019},
volume = {53},
pages = {65--72},
doi = {10.1016/j.nbt.2019.07.001}
}

Martins da Costa E, Soares de Carvalho T, Azarias Guimarães A, Ribas Leão AC, Magalhães Cruz L, de Baura VA, Lebbe L, Willems A and de Souza Moreira FM (2019). Classification of the inoculant strain of cowpea UFLA03-84 and of other strains from soils of the Amazon region as Bradyrhizobium viridifuturi (symbiovar tropici). Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology], 50(2):335-345, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: Cowpea (Vigna unguiculata L.) is a legume species that considerably benefits from inoculation with nitrogen fixing bacteria of the genus Bradyrhizobium. One of the strains recommended for inoculation in cowpea in Brazil is UFLA03-84 (Bradyrhizobium sp.). The aim of our study was to define the taxonomic position of the UFLA03-84 strain and of two other strains of Bradyrhizobium (UFLA03-144 and INPA237B), all belonging to the same phylogenetic group and isolated from soils of the Brazilian Amazon. Multilocus sequence analysis (MLSA) of the housekeeping genes atpD, gyrB, recA, and rpoB grouped (with similarity higher than 99 the three strains with Bradyrhizobium viridifuturi SEMIA 690T. The analyses of average nucleotide identity and digital DNA-DNA hybridization supported classification of the group as Bradyrhizobium viridifuturi. The three strains exhibited similar behavior in relation to the most of the phenotypic characteristics evaluated. However, some characteristics exhibited variation, indicating phenotypic diversity within the species. Phylogenetic analysis of the nodC and nifH genes showed that the three strains are members of the same symbiovar (tropici) that contains type strains of Bradyrhizobium species coming from tropical soils (SEMIA 690TB. viridifuturi, CNPSo 1112TB. tropiciagri, CNPSo 2833TB. embrapense, and B. brasilense UFLA03-321T).

BibTeX:

@article{martins_da_costa_classification_2019,
author = {Martins da Costa, Elaine and Soares de Carvalho, Teotonio and Azarias Guimarães, Amanda and Ribas Leão, Aniele Carolina and Magalhães Cruz, Leonardo and de Baura, Valter Antonio and Lebbe, Liesbeth and Willems, Anne and de Souza Moreira, Fatima Maria},
title = {Classification of the inoculant strain of cowpea UFLA03-84 and of other strains from soils of the Amazon region as Bradyrhizobium viridifuturi (symbiovar tropici)},
journal = {Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]},
year = {2019},
volume = {50},
number = {2},
pages = {335--345},
doi = {10.1007/s42770-019-00045-x}
}

Nery TGM, Silva EM, Tavares R and Passetti F (2019). The Challenge to Search for New Nervous System Disease Biomarker Candidates: the Opportunity to Use the Proteogenomics Approach. Journal of molecular neuroscience: MN, 67(1):150-164, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: Alzheimer's disease, Parkinson's disease, prion diseases, schizophrenia, and multiple sclerosis are the most common nervous system diseases, affecting millions of people worldwide. The current scientific literature associates these pathological conditions to abnormal expression levels of certain proteins, which in turn improved the knowledge concerning normal and affected brains. However, there is no available cure or preventive therapy for any of these disorders. Proteogenomics is a recent approach defined as the data integration of both nucleotide high-throughput sequencing and protein mass spectrometry technologies. In the last years, proteogenomics studies in distinct diseases have emerged as a strategy for the identification of uncharacterized proteoforms, which are all the different protein forms derived from a single gene. For many of these diseases, at least one protein used as biomarker presents more than one proteoform, which fosters the analysis of publicly available data focusing proteoforms. Given this context, we describe the most important biomarkers for each neurodegenerative disease and how genomics, transcriptomics, and proteomics separately contributed to unveil them. Finally, we present a selection of proteogenomics studies in which the combination of nucleotide and proteome high-throughput data, from cell lines or brain tissue samples, is used to uncover proteoforms not previously described. We believe that this new approach may improve our knowledge about nervous system diseases and brain function and an opportunity to identify new biomarker candidates.

BibTeX:

@article{nery_challenge_2019,
author = {Nery, Thais Guimarães Martins and Silva, Esdras Matheus and Tavares, Raphael and Passetti, Fabio},
title = {The Challenge to Search for New Nervous System Disease Biomarker Candidates: the Opportunity to Use the Proteogenomics Approach},
journal = {Journal of molecular neuroscience: MN},
year = {2019},
volume = {67},
number = {1},
pages = {150--164},
doi = {10.1007/s12031-018-1220-1}
}

Petry VS, Stefenon VM, Machado LO, Klabunde GHF, Pedrosa FO and Nodari RO (2019). Repetitive genomic elements in Campomanesia xanthocarpa: prospection, characterization and cross amplification of molecular markers. 3 Biotech, 9(11):423, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: Repetitive genomic elements were prospected in Campomanesia xanthocarpa, aiming to characterize these elements in a non-model plant species and to develop species-specific microsatellite markers. Approximately 4.12% of the partial genome of C. xanthocarpa is composed of repetitive elements, being retrotransposons the most widely represented. A total of nine polymorphic microsatellite markers were obtained: four nuclear-neutral, two nuclear EST, two plastidial and one mitochondrial. Levels of population genetic diversity of four natural populations of C. xanthocarpa were characterized using these markers. In addition, the cross-species amplification of the microsatellite markers was tested in seven species of tribe Myrteae (Myrtaceae). The characterized microsatellite markers revealed low to moderate levels of genetic diversity (expected heterozygosity range: 0.33-0.57; observed heterozygosity: 0.26-0.74 and number of alleles: 2.25-4.25). Cross-species amplification was successful for all loci, except Cxant76. These nine markers will contribute for studies on genetic diversity, gene flow, plant selection and breeding of this species, towards the conservation of natural populations, as well as its commercial use.

BibTeX:

@article{petry_repetitive_2019,
author = {Petry, Vanessa S. and Stefenon, Valdir Marcos and Machado, Lilian O. and Klabunde, Gustavo H. F. and Pedrosa, Fábio O. and Nodari, Rubens O.},
title = {Repetitive genomic elements in Campomanesia xanthocarpa: prospection, characterization and cross amplification of molecular markers},
journal = {3 Biotech},
year = {2019},
volume = {9},
number = {11},
pages = {423},
doi = {10.1007/s13205-019-1953-8}
}

Prediger KdC, Dallagassa CB, Moriel B, Vizzotto BS, Volanski W, Souza EM, Pedrosa FO, Weiss V, Alberton D, Guizelini D and Fadel-Picheth CMT (2019). Virulence characteristics and antimicrobial resistance of Aeromonas veronii biovar sobria 312M, a clinical isolate. Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology], 2019.
[Abstract] [DOI] [BibTeX]

Abstract: Aeromonas are bacteria widely distributed in the environment, and some species are able to cause infections in humans, of which diarrhea is the most common. The objective of this study was to evaluate the presence of virulence and antimicrobial resistance associated characteristics in A. veronii biovar sobria strain 312M isolated from diarrheal stools. For this, the genome sequencing and phenotypical tests were performed. The draft genome annotation revealed several complete pathways associated with carbon metabolism and a mucin-desulfating sulfatase which may contribute to intestine colonization, and a large number of virulence-associated genes encoding structures associated with adhesion, toxins, and secretion systems. The strain exhibited swimming and swarming motility, biofilm formation, and hemolytic activity. It was resistant to ampicillin, ampicillin/sulbactam, and amoxicillin-clavulanic acid. Although a cphA gene encoding a narrow-spectrum carbapenase was identified in the strain genome, no carbapenemase activity was detected in the antimicrobial susceptibility test. When compared with other A. veronii with complete genomes, the main differences in virulence characteristics are related to lateral flagella and type III and VI secretion systems; the antimicrobial resistance spectrum also varied among strains. The results indicated that A. veronii biovar sobria 312M presents high virulence potential and resistance to limited classes of antimicrobials.

BibTeX:

@article{prediger_virulence_2019,
author = {Prediger, Karoline de C. and Dallagassa, Cibelle B. and Moriel, Bárbara and Vizzotto, Bruno Stefanello and Volanski, Waldemar and Souza, Emanuel M. and Pedrosa, Fábio O. and Weiss, Vinícius and Alberton, Dayane and Guizelini, Dieval and Fadel-Picheth, Cyntia M. T.},
title = {Virulence characteristics and antimicrobial resistance of Aeromonas veronii biovar sobria 312M, a clinical isolate},
journal = {Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]},
year = {2019},
doi = {10.1007/s42770-019-00180-5}
}

Souza FFC, Rissi DV, Pedrosa FO, Souza EM, Baura VA, Monteiro RA, Balsanelli E, Cruz LM, Souza RAF, Andreae MO, Reis RA, Godoi RHM and Huergo LF (2019). Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon forest. The Science of the Total Environment, 688:83-86, 2019.
[Abstract] [DOI] [BibTeX]

Abstract: Biological aerosols (bioaerosol) are atmospheric particles that act as a dispersion unit of living organisms across the globe thereby affecting the biogeographic distribution of organisms. Despite their importance, there is virtually no knowledge about bioaerosols emitted by pristine forests. Here we provide the very first survey of the prokaryotic community of a bioaerosol collected inside pristine Amazon forest at 2 m above ground. Total atmospheric particles were collected at the Amazon Tall Tower Observatory, subjected to metagenomic DNA extraction and the prokaryotic diversity was determined by 16S rRNA gene amplicon sequencing. A total of 271,577 reads of 250 bp of the 16S rRNA gene amplicon were obtained. Only 27% of the reads could be classified using the 16S SILVA database. Most belonged to Proteobacteria, Actinobacteria and Firmicutes which is in good agreement with other bioaerosol studies. Further inspection of the reads using Blast searches and the 18S SILVA database revealed that most of the dataset was composed of Fungi sequences. The identified microbes suggest that the atmosphere may act as an important gateway to interchange bacteria between plants, soil and water ecosystems.

BibTeX:

@article{souza_uncovering_2019,
author = {Souza, Felipe F. C. and Rissi, Daniel V. and Pedrosa, Fabio O. and Souza, Emanuel M. and Baura, Valter A. and Monteiro, Rose A. and Balsanelli, Eduardo and Cruz, Leonardo M. and Souza, Rodrigo A. F. and Andreae, Meinrat O. and Reis, Rodrigo A. and Godoi, Ricardo H. M. and Huergo, Luciano F.},
title = {Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon forest},
journal = {The Science of the Total Environment},
year = {2019},
volume = {688},
pages = {83--86},
doi = {10.1016/j.scitotenv.2019.06.218}
}

West State University of Paraná (UNIOESTE) - Campus Marechal Cândido Rondon – PR, Brazil, Chaves EID, Federal University of Paraná (UFPR) – Campus Palotina – PR, Guimarães VF, West State University of Paraná (UNIOESTE) - Campus Marechal Cândido Rondon – PR, Brazil, Vendruscolo ECG, Federal University of Paraná (UFPR) – Campus Palotina – PR, Santos MFd, Federal University of Paraná (UFPR) – Campus Palotina – PR, Oliveira FFd, Federal University of Paraná (UFPR) – Campus Palotina – PR, Abreu JACd, Federal University of Paraná (UFPR) – Campus Palotina – PR, Camargo MP, Federal University of Paraná (UFPR) – Campus Palotina – PR, Schneider VS, Federal University of Paraná (UFPR) – Campus Palotina – PR, Souza EMd, Federal University of Paraná (UFPR) – Campus Curitiba – PR, Brazil, Cruz LM, Federal University of Paraná (UFPR) – Campus Curitiba – PR, Brazil, Vasconcelos ESd and West State University of Paraná (UNIOESTE) - Campus Marechal Cândido Rondon – PR, Brazil (2019). Interactions between endophytic bacteria and their effects on poaceae growth performance in different inoculation and fertilization conditions. Australian Journal of Crop Science, 13(01):69-79, 2019.
[DOI] [URL] [BibTeX]

Abstract:

BibTeX:

@article{west_state_university_of_parana_unioeste_-_campus_marechal_candido_rondon__pr_brazil_interactions_2019,
author = {West State University of Paraná (UNIOESTE) - Campus Marechal Cândido Rondon – PR, Brazil and Chaves, Elisiane Inês Dall'Óglio and Federal University of Paraná (UFPR) – Campus Palotina – PR and Guimarães, Vandeir Francisco and West State University of Paraná (UNIOESTE) - Campus Marechal Cândido Rondon – PR, Brazil and Vendruscolo, Eliane Cristina Gruszka and Federal University of Paraná (UFPR) – Campus Palotina – PR and Santos, Marise Fonseca dos and Federal University of Paraná (UFPR) – Campus Palotina – PR and Oliveira, Fernanda Freitas de and Federal University of Paraná (UFPR) – Campus Palotina – PR and Abreu, Joel Antônio Cordeiro de and Federal University of Paraná (UFPR) – Campus Palotina – PR and Camargo, Maiara Pasuch and Federal University of Paraná (UFPR) – Campus Palotina – PR and Schneider, Vanessa Suzane and Federal University of Paraná (UFPR) – Campus Palotina – PR and Souza, Emanuel Maltempi de and Federal University of Paraná (UFPR) – Campus Curitiba – PR, Brazil and Cruz, Leonardo Magalhães and Federal University of Paraná (UFPR) – Campus Curitiba – PR, Brazil and Vasconcelos, Edmar Soares de and West State University of Paraná (UNIOESTE) - Campus Marechal Cândido Rondon – PR, Brazil},
title = {Interactions between endophytic bacteria and their effects on poaceae growth performance in different inoculation and fertilization conditions},
journal = {Australian Journal of Crop Science},
year = {2019},
volume = {13},
number = {01},
pages = {69--79},
url = {https://www.cropj.com/chaves_13_1_2019_69_79.pdf},
doi = {10.21475/ajcs.19.13.01.p1249}
}

Antunes HS, Wajnberg G, Pinho MB, Jorge NAN, de Moraes JLM, Stefanoff CG, Herchenhorn D, Araújo CMM, Viégas CMP, Rampini MP, Dias FL, de Araujo-Souza PS, Passetti F and Ferreira CG (2018). cDNA microarray analysis of human keratinocytes cells of patients submitted to chemoradiotherapy and oral photobiomodulation therapy: pilot study. Lasers in Medical Science, 33(1):11-18, 2018.
[Abstract] [DOI] [BibTeX]

Abstract: Oral mucositis is an acute toxicity that occurs in patients submitted to chemoradiotherapy to treat head and neck squamous cell carcinoma. In this study, we evaluated differences in gene expression in the keratinocytes of the oral mucosa of patients treated with photobiomodulation therapy and tried to associate the molecular mechanisms with clinical findings. From June 2009 to December 2010, 27 patients were included in a randomized double-blind pilot study. Buccal smears from 13 patients were obtained at days 1 and 10 of chemoradiotherapy, and overall gene expression of samples from both dates were analyzed by complementary DNA (cDNA) microarray. In addition, samples from other 14 patients were also collected at D1 and D10 of chemoradiotherapy for subsequent validation of cDNA microarray findings by qPCR. The expression array analysis identified 105 upregulated and 60 downregulated genes in our post-treatment samples when compared with controls. Among the upregulated genes with the highest fold change, it was interesting to observe the presence of genes related to keratinocyte differentiation. Among downregulated genes were observed genes related to cytotoxicity and immune response. The results indicate that genes known to be induced during differentiation of human epidermal keratinocytes were upregulated while genes associated with cytotoxicity and immune response were downregulated in the laser group. These results support previous clinical findings indicating that the lower incidence of oral mucositis associated with photobiomodulation therapy might be correlated to the activation of genes involved in keratinocyte differentiation.

BibTeX:

@article{antunes_cdna_2018,
author = {Antunes, Heliton S. and Wajnberg, Gabriel and Pinho, Marcos B. and Jorge, Natasha Andressa Nogueira and de Moraes, Joyce Luana Melo and Stefanoff, Claudio Gustavo and Herchenhorn, Daniel and Araújo, Carlos M. M. and Viégas, Celia Maria Pais and Rampini, Mariana P. and Dias, Fernando L. and de Araujo-Souza, Patricia Savio and Passetti, Fabio and Ferreira, Carlos G.},
title = {cDNA microarray analysis of human keratinocytes cells of patients submitted to chemoradiotherapy and oral photobiomodulation therapy: pilot study},
journal = {Lasers in Medical Science},
year = {2018},
volume = {33},
number = {1},
pages = {11--18},
doi = {10.1007/s10103-017-2313-8}
}

Batista MB, Chandra G, Monteiro RA, De Souza EM and Dixon R (2018). Hierarchical interactions between Fnr orthologs allows fine-tuning of transcription in response to oxygen in Herbaspirillum seropedicae. Nucleic Acids Research, 46(8):3953-3966, 2018.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Bacteria adjust the composition of their electron transport chain (ETC) to efficiently adapt to oxygen gradients. This involves differential expression of various ETC components to optimize energy generation. In Herbaspirillum seropedicae, reprogramming of gene expression in response to oxygen availability is controlled at the transcriptional level by three Fnr orthologs. Here, we characterised Fnr regulons using a combination of RNA-Seq and ChIP-Seq analysis. We found that Fnr1 and Fnr3 directly regulate discrete groups of promoters (Groups I and II, respectively), and that a third group (Group III) is co-regulated by both transcription factors. Comparison of DNA binding motifs between the three promoter groups suggests Group III promoters are potentially co-activated by Fnr3–Fnr1 heterodimers. Specific interaction between Fnr1 and Fnr3, detected in two-hybrid assays, was dependent on conserved residues in their dimerization interfaces, indicative of heterodimer formation in vivo. The requirements for co-activation of the fnr1 promoter, belonging to Group III, suggest either sequential activation by Fnr3 and Fnr1 homodimers or the involvement of Fnr3–Fnr1 heterodimers. Analysis of Fnr proteins with swapped activation domains provides evidence that co-activation by Fnr1 and Fnr3 at Group III promoters optimises interactions with RNA polymerase to fine-tune transcription in response to prevailing oxygen concentrations.

BibTeX:

@article{batista_hierarchical_2018,
author = {Batista, Marcelo Bueno and Chandra, Govind and Monteiro, Rose Adele and De Souza, Emanuel Maltempi and Dixon, Ray},
title = {Hierarchical interactions between Fnr orthologs allows fine-tuning of transcription in response to oxygen in Herbaspirillum seropedicae},
journal = {Nucleic Acids Research},
year = {2018},
volume = {46},
number = {8},
pages = {3953--3966},
url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky142/4909994},
doi = {10.1093/nar/gky142}
}

Batista MB, Teixeira CS, Sfeir MZT, Alves LPS, Valdameri G, Pedrosa FdO, Sassaki GL, Steffens MBR, de Souza EM, Dixon R and Müller-Santos M (2018). PHB Biosynthesis Counteracts Redox Stress in Herbaspirillum seropedicae. Frontiers in Microbiology, 9:472, 2018.
[Abstract] [DOI] [BibTeX]

Abstract: The ability of bacteria to produce polyhydroxyalkanoates such as poly(3-hydroxybutyrate) (PHB) enables provision of a carbon storage molecule that can be mobilized under demanding physiological conditions. However, the precise function of PHB in cellular metabolism has not been clearly defined. In order to determine the impact of PHB production on global physiology, we have characterized the properties of a ΔphaC1 mutant strain of the diazotrophic bacterium Herbaspirillum seropedicae. The absence of PHB in the mutant strain not only perturbs redox balance and increases oxidative stress, but also influences the activity of the redox-sensing Fnr transcription regulators, resulting in significant changes in expression of the cytochrome c-branch of the electron transport chain. The synthesis of PHB is itself dependent on the Fnr1 and Fnr3 proteins resulting in a cyclic dependency that couples synthesis of PHB with redox regulation. Transcriptional profiling of the ΔphaC1 mutant reveals that the loss of PHB synthesis affects the expression of many genes, including approximately 30% of the Fnr regulon.

BibTeX:

@article{batista_phb_2018,
author = {Batista, Marcelo B. and Teixeira, Cícero S. and Sfeir, Michelle Z. T. and Alves, Luis P. S. and Valdameri, Glaucio and Pedrosa, Fabio de Oliveira and Sassaki, Guilherme L. and Steffens, Maria B. R. and de Souza, Emanuel M. and Dixon, Ray and Müller-Santos, Marcelo},
title = {PHB Biosynthesis Counteracts Redox Stress in Herbaspirillum seropedicae},
journal = {Frontiers in Microbiology},
year = {2018},
volume = {9},
pages = {472},
doi = {10.3389/fmicb.2018.00472}
}

Bortoluzzi A, Salum GA, da Rosa ED, Chagas VdS, Castro MAA and Manfro GG (2018). DNA methylation in adolescents with anxiety disorder: a longitudinal study. Scientific Reports, 8(1):13800, 2018.
[Abstract] [DOI] [BibTeX]

Abstract: Anxiety disorders (AD) typically manifest in children and adolescents and might persist into adulthood. However, there are still few data concerning epigenetic mechanisms associated with onset, persistence or remission of AD over time. We investigated a cohort of adolescents and young adults at baseline (age; 13.19 ± 2.38) and after 5 years and classified them according to the AD diagnosis and their longitudinal trajectories into 4 groups: (1) Typically Developing Comparisons (TDC; control group, n = 14); (2) Incident (AD in the second evaluation only, n = 11); (3) Persistent (AD in both evaluations, n = 14) and (4) Remittent (AD in the first evaluation only, n = 8). DNA methylation was evaluated with the Infinium HumanMethylation450 BeadChip from saliva samples collected at both evaluations. Gene set enrichment analysis was applied to consider biological pathways. We found decreased DNA methylation in TDC group while the chronic cases of AD presented hypermethylation in central nervous system development pathways. Moreover, we showed that this persistent group also presented hypermethylation while the other three groups were associated with hypomethylation in nervous system development pathway. Incidence and remission groups were associated with increased and decreased methylation in neuron development pathways, respectively. Larger studies are likely to detect specific genes relevant to AD.

BibTeX:

@article{bortoluzzi_dna_2018,
author = {Bortoluzzi, Andressa and Salum, Giovanni Abrahão and da Rosa, Eduarda Dias and Chagas, Vinicius de Saraiva and Castro, Mauro Antônio Alves and Manfro, Gisele Gus},
title = {DNA methylation in adolescents with anxiety disorder: a longitudinal study},
journal = {Scientific Reports},
year = {2018},
volume = {8},
number = {1},
pages = {13800},
doi = {10.1038/s41598-018-32090-1}
}

Campbell TM, Castro MA, de Oliveira KG, Ponder BA and Meyer KB (2018). Era binding by transcription factors NFIB and YBX1 enables FGFR2 signaling to modulate estrogen responsiveness in breast cancer. Cancer Research, 78(2):410-421, 2018.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Two opposing clusters of transcription factors (TF) have been associated with the differential risks of estrogen receptor positive or negative breast cancers, but the mechanisms underlying the opposing functions of the two clusters are undefined. In this study, we identified NFIB and YBX1 as novel interactors of the estrogen receptor (ESR1). NFIB and YBX1 are both risk TF associated with progression of ESR1-negative disease. Notably, they both interacted with the ESR1-FOXA1 complex and inhibited the transactivational potential of ESR1. Moreover, signaling through FGFR2, a known risk factor in breast cancer development, augmented these interactions and further repressed ESR1 target gene expression. We therefore show that members of two opposing clusters of risk TFs associated with ESR1-positive and -negative breast cancer can physically interact. We postulate that this interaction forms a toggle between two developmental pathways affected by FGFR2 signaling, possibly offering a junction to exploit therapeutically.Significance:Binding of the transcription factors NFIB and YBX1 to the estrogen receptor can promote an estrogen-independent phenotype that can be reverted by inhibiting FGFR2 signaling.Cancer Res; 78(2); 410-21. ©2017 AACR.

BibTeX:

@article{campbell_era_2018,
author = {Campbell, Thomas M. and Castro, Mauro A.A. and de Oliveira, Kelin Gonçalves and Ponder, Bruce A.J. and Meyer, Kerstin B.},
title = {Era binding by transcription factors NFIB and YBX1 enables FGFR2 signaling to modulate estrogen responsiveness in breast cancer},
journal = {Cancer Research},
year = {2018},
volume = {78},
number = {2},
pages = {410--421},
note = {ISBN: 0008-5472},
url = {http://cancerres.aacrjournals.org/lookup/doi/10.1158/0008-5472.CAN-17-1153},
doi = {10.1158/0008-5472.CAN-17-1153}
}

Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C, Cancer Genome Atlas Analysis Network, Greenleaf WJ and Chang HY (2018). The chromatin accessibility landscape of primary human cancers. Science (New York, N.Y.), 362(6413) 2018.
[Abstract] [DOI] [BibTeX]

Abstract: We present the genome-wide chromatin accessibility profiles of 410 tumor samples spanning 23 cancer types from The Cancer Genome Atlas (TCGA). We identify 562,709 transposase-accessible DNA elements that substantially extend the compendium of known cis-regulatory elements. Integration of ATAC-seq (the assay for transposase-accessible chromatin using sequencing) with TCGA multi-omic data identifies a large number of putative distal enhancers that distinguish molecular subtypes of cancers, uncovers specific driving transcription factors via protein-DNA footprints, and nominates long-range gene-regulatory interactions in cancer. These data reveal genetic risk loci of cancer predisposition as active DNA regulatory elements in cancer, identify gene-regulatory interactions underlying cancer immune evasion, and pinpoint noncoding mutations that drive enhancer activation and may affect patient survival. These results suggest a systematic approach to understanding the noncoding genome in cancer to advance diagnosis and therapy.

BibTeX:

@article{corces_chromatin_2018,
author = {Corces, M. Ryan and Granja, Jeffrey M. and Shams, Shadi and Louie, Bryan H. and Seoane, Jose A. and Zhou, Wanding and Silva, Tiago C. and Groeneveld, Clarice and Wong, Christopher K. and Cho, Seung Woo and Satpathy, Ansuman T. and Mumbach, Maxwell R. and Hoadley, Katherine A. and Robertson, A. Gordon and Sheffield, Nathan C. and Felau, Ina and Castro, Mauro A. A. and Berman, Benjamin P. and Staudt, Louis M. and Zenklusen, Jean C. and Laird, Peter W. and Curtis, Christina and Cancer Genome Atlas Analysis Network and Greenleaf, William J. and Chang, Howard Y.},
title = {The chromatin accessibility landscape of primary human cancers},
journal = {Science (New York, N.Y.)},
year = {2018},
volume = {362},
number = {6413},
doi = {10.1126/science.aav1898}
}

da Silva PRA, Simões-Araújo JL, Vidal MS, Cruz LM, de Souza EM and Baldani JI (2018). Draft genome sequence of Paraburkholderia tropica Ppe8 strain, a sugarcane endophytic diazotrophic bacterium. Brazilian Journal of Microbiology, 49(2):210-211, 2018.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Paraburkholderia tropica (syn Burkholderia tropica) are nitrogen-fixing bacteria commonly found in sugarcane. The Paraburkholderia tropica strain Ppe8 is part of the sugarcane inoculant consortium that has a beneficial effect on yield. Here, we report a draft genome sequence of this strain elucidating the mechanisms involved in its interaction mainly with Poaceae. A genome size of approximately 8.75 Mb containing 7844 protein coding genes distributed in 526 subsystems was de novo assembled with ABySS and annotated by RAST. Genes related to the nitrogen fixation process, the secretion systems (I, II, III, IV, and VI), and related to a variety of metabolic traits, such as metabolism of carbohydrates, amino acids, vitamins, and proteins, were detected, suggesting a broad metabolic capacity and possible adaptation to plant association.

BibTeX:

@article{da_silva_draft_2018,
author = {da Silva, Paula Renata Alves and Simões-Araújo, Jean Luiz and Vidal, Márcia Soares and Cruz, Leonardo Magalhães and de Souza, Emanuel Maltempi and Baldani, José Ivo},
title = {Draft genome sequence of Paraburkholderia tropica Ppe8 strain, a sugarcane endophytic diazotrophic bacterium},
journal = {Brazilian Journal of Microbiology},
year = {2018},
volume = {49},
number = {2},
pages = {210--211},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1517838217303027},
doi = {10.1016/j.bjm.2017.07.005}
}

da Silva Filho AC, Raittz RT, Guizelini D, De Pierri CR, Augusto DW, Dos Santos-Weiss ICR and Marchaukoski JN (2018). Comparative Analysis of Genomic Island Prediction Tools. Frontiers in Genetics, 9:619, 2018.
[Abstract] [DOI] [BibTeX]

Abstract: Tools for genomic island prediction use strategies for genomic comparison analysis and sequence composition analysis. The goal of comparative analysis is to identify unique regions in the genomes of related organisms, whereas sequence composition analysis evaluates and relates the composition of specific regions with other regions in the genome. The goal of this study was to qualitatively and quantitatively evaluate extant genomic island predictors. We chose tools reported to produce significant results using sequence composition prediction, comparative genomics, and hybrid genomics methods. To maintain diversity, the tools were applied to eight complete genomes of organisms with distinct characteristics and belonging to different families. Escherichia coli CFT073 was used as a control and considered as the gold standard because its islands were previously curated in vitro. The results of predictions with the gold standard were manually curated, and the content and characteristics of each predicted island were analyzed. For other organisms, we created GenBank (GBK) files using Artemis software for each predicted island. We copied only the amino acid sequences from the coding sequence and constructed a multi-FASTA file for each predictor. We used BLASTp to compare all results and generate hits to evaluate similarities and differences among the predictions. Comparison of the results with the gold standard revealed that GIPSy produced the best results, covering textasciitilde91% of the composition and regions of the islands, followed by Alien Hunter (81, IslandViewer (47.8, Predict Bias (31, GI Hunter (17, and Zisland Explorer (16. The tools with the best results in the analyzes of the set of organisms were the same ones that presented better performance in the tests with the gold standard.

BibTeX:

@article{da_silva_filho_comparative_2018,
author = {da Silva Filho, Antonio Camilo and Raittz, Roberto Tadeu and Guizelini, Dieval and De Pierri, Camilla Reginatto and Augusto, Diônata Willian and Dos Santos-Weiss, Izabella Castilhos Ribeiro and Marchaukoski, Jeroniza Nunes},
title = {Comparative Analysis of Genomic Island Prediction Tools},
journal = {Frontiers in Genetics},
year = {2018},
volume = {9},
pages = {619},
doi = {10.3389/fgene.2018.00619}
}

Dallagassa CB, Surek M, Vizzotto BS, Prediger KC, Moriel B, Wolf S, Weiss V, Cruz LM, Assis FE, Paludo KS, Rego FG, Farah SM, Picheth G, Souza EM, Pedrosa FO, Chubatsu LS and Fadel-Picheth CM (2018). Characteristics of an Aeromonas trota strain isolated from cerebrospinal fluid. Microbial Pathogenesis, 116:109-112, 2018.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Aeromonas are ubiquitous in aquatic habitats. However some species can cause infections in humans, but rarely meningitis. Here we describe the isolation and characterization of an Aeromonas strain from cerebrospinal fluid of a meningitis patient. The isolate, identified as A. trota by biochemical and molecular methods, was susceptible to ampicillin but resistant to cephalothin and cefazolin. Genome sequencing revealed virulence factor genes such as type VI secretion system, aerolysin and lateral flagella. The isolate exhibited swarming motility, hemolytic activity and adhesion and cytotoxicity on HeLa cells. This is the first report of A. trota associated with meningitis and its virulence characteristics.

BibTeX:

@article{dallagassa_characteristics_2018,
author = {Dallagassa, Cibelle B. and Surek, Monica and Vizzotto, Bruno S. and Prediger, Karoline C. and Moriel, Bárbara and Wolf, Suélen and Weiss, Vinícius and Cruz, Leonardo M. and Assis, Flávia E.A. and Paludo, Katia S. and Rego, Fabiane G.M. and Farah, Sônia M.S.S. and Picheth, Geraldo and Souza, Emanuel M. and Pedrosa, Fábio O. and Chubatsu, Leda S. and Fadel-Picheth, Cyntia M.T.},
title = {Characteristics of an Aeromonas trota strain isolated from cerebrospinal fluid},
journal = {Microbial Pathogenesis},
year = {2018},
volume = {116},
pages = {109--112},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0882401016304296},
doi = {10.1016/j.micpath.2018.01.017}
}

de Almeida RC, Chagas VS, Castro MAA and Petzl-Erler ML (2018). Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites. Frontiers in Genetics, 9:139, 2018.
[Abstract] [DOI] [BibTeX]

Abstract: Genome-wide and fine mapping studies have shown that more than 90% of genetic variants associated with autoimmune diseases (AID) are located in non-coding regions of the human genome and especially in regulatory sequences, including microRNAs (miRNA) target sites. MiRNAs are small endogenous noncoding RNAs that modulate gene expression at the post-transcriptional level. Single nucleotide polymorphisms (SNPs) located within the 3' untranslated region of their target mRNAs (miRSNP) can alter miRNA binding sites. Yet, little is known about their effect on regulation by miRNA and the consequences for AID. Conversely, it is well known that two or more AID may share part of their genetic background. Here, we hypothesized that miRSNPs could be associated with more than one AID. To identify miRSNPs associated with AID, we integrated results from three different prediction tools (Polymirts, miRSNP, and miRSNPscore) using a naïve Bayes classifier approach to identify miRSNPs predicted to affect binding sites of miRNAs. Further, to detect miRSNPs associated with two or more AID, we integrated predictions with summary statistics from 12 AID studies. In addition, to prioritize miRSNPs, miRNAs and AID-associated target genes, we used public expression quantitative trait locus (eQTL) data and mRNA-seq and small RNA-seq data. We identified 34 miRNSPs associated with at least two AID. Furthermore, we found 86 miRNAs predicted to target 18 of the associated gene's mRNAs. Our integrative approach revealed new insights into miRNAs and AID associated target genes. Thus, it helped to prioritize AID noncoding risk SNPs that might be involved in the causal mechanisms, providing valuable information for further functional studies.

BibTeX:

@article{de_almeida_integrative_2018,
author = {de Almeida, Rodrigo C. and Chagas, Vinícius S. and Castro, Mauro A. A. and Petzl-Erler, Maria L.},
title = {Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites},
journal = {Frontiers in Genetics},
year = {2018},
volume = {9},
pages = {139},
doi = {10.3389/fgene.2018.00139}
}

de Santana Lopes A, Gomes Pacheco T, Nimz T, do Nascimento Vieira L, Guerra MP, Nodari RO, de Souza EM, de Oliveira Pedrosa F and Rogalski M (2018). The complete plastome of macaw palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] and extensive molecular analyses of the evolution of plastid genes in Arecaceae. Planta, 247(4):1011-1030, 2018.
[Abstract] [DOI] [BibTeX]

Abstract: MAIN CONCLUSION: The plastome of macaw palm was sequenced allowing analyses of evolution and molecular markers. Additionally, we demonstrated that more than half of plastid protein-coding genes in Arecaceae underwent positive selection. Macaw palm is a native species from tropical and subtropical Americas. It shows high production of oil per hectare reaching up to 70% of oil content in fruits and an interesting plasticity to grow in different ecosystems. Its domestication and breeding are still in the beginning, which makes the development of molecular markers essential to assess natural populations and germplasm collections. Therefore, we sequenced and characterized in detail the plastome of macaw palm. A total of 221 SSR loci were identified in the plastome of macaw palm. Additionally, eight polymorphism hotspots were characterized at level of subfamily and tribe. Moreover, several events of gain and loss of RNA editing sites were found within the subfamily Arecoideae. Aiming to uncover evolutionary events in Arecaceae, we also analyzed extensively the evolution of plastid genes. The analyses show that highly divergent genes seem to evolve in a species-specific manner, suggesting that gene degeneration events may be occurring within Arecaceae at the level of genus or species. Unexpectedly, we found that more than half of plastid protein-coding genes are under positive selection, including genes for photosynthesis, gene expression machinery and other essential plastid functions. Furthermore, we performed a phylogenomic analysis using whole plastomes of 40 taxa, representing all subfamilies of Arecaceae, which placed the macaw palm within the tribe Cocoseae. Finally, the data showed here are important for genetic studies in macaw palm and provide new insights into the evolution of plastid genes and environmental adaptation in Arecaceae.

BibTeX:

@article{de_santana_lopes_complete_2018,
author = {de Santana Lopes, Amanda and Gomes Pacheco, Túlio and Nimz, Tabea and do Nascimento Vieira, Leila and Guerra, Miguel P. and Nodari, Rubens O. and de Souza, Emanuel Maltempi and de Oliveira Pedrosa, Fábio and Rogalski, Marcelo},
title = {The complete plastome of macaw palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] and extensive molecular analyses of the evolution of plastid genes in Arecaceae},
journal = {Planta},
year = {2018},
volume = {247},
number = {4},
pages = {1011--1030},
doi = {10.1007/s00425-018-2841-x}
}

de Santana Lopes A, Pacheco TG, dos Santos KG, Vieira LdN, Guerra MP, Nodari RO, de Souza EM, de Oliveira Pedrosa F and Rogalski M (2018). The Linum usitatissimum L. plastome reveals atypical structural evolution, new editing sites, and the phylogenetic position of Linaceae within Malpighiales. Plant Cell Reports, 37(2):307-328, 2018.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: KEY MESSAGE: The plastome of Linum usitatissimum was completely sequenced allowing analyses of evolution of genome structure, RNA editing sites, molecular markers, and indicating the position of Linaceae within Malpighiales. Flax (Linum usitatissimum L.) is an economically important crop used as food, feed, and industrial feedstock. It belongs to the Linaceae family, which is noted by high morphological and ecological diversity. Here, we reported the complete sequence of flax plastome, the first species within Linaceae family to have the plastome sequenced, assembled and characterized in detail. The plastome of flax is a circular DNA molecule of 156,721 bp with a typical quadripartite structure including two IRs of 31,990 bp separating the LSC of 81,767 bp and the SSC of 10,974 bp. It shows two expansion events from IRB to LSC and from IRB to SSC, and a contraction event in the IRA-LSC junction, which changed significantly the size and the gene content of LSC, SSC and IRs. We identified 109 unique genes and 2 pseudogenes (rpl23 and ndhF). The plastome lost the conserved introns of clpP gene and the complete sequence of rps16 gene. The clpP, ycf1, and ycf2 genes show high nucleotide and aminoacid divergence, but they still possibly retain the functionality. Moreover, we also identified 176 SSRs, 20 tandem repeats, and 39 dispersed repeats. We predicted in 18 genes a total of 53 RNA editing sites of which 32 were not found before in other species. The phylogenetic inference based on 63 plastid protein-coding genes of 38 taxa supports three major clades within Malpighiales order. One of these clades has flax (Linaceae) sister to Chrysobalanaceae family, differing from earlier studies that included Linaceae into the euphorbioid clade.

BibTeX:

@article{de_santana_lopes_linum_2018,
author = {de Santana Lopes, Amanda and Pacheco, Túlio Gomes and dos Santos, Karla Gasparini and Vieira, Leila do Nascimento and Guerra, Miguel Pedro and Nodari, Rubens Onofre and de Souza, Emanuel Maltempi and de Oliveira Pedrosa, Fábio and Rogalski, Marcelo},
title = {The Linum usitatissimum L. plastome reveals atypical structural evolution, new editing sites, and the phylogenetic position of Linaceae within Malpighiales},
journal = {Plant Cell Reports},
year = {2018},
volume = {37},
number = {2},
pages = {307--328},
note = {ISBN: 0123456789},
url = {http://link.springer.com/10.1007/s00299-017-2231-z},
doi = {10.1007/s00299-017-2231-z}
}

Gravina F, Sanchuki HS, Rodrigues TE, Gerhardt EC, Pedrosa FO, Souza EM, Valdameri G, de Souza GA and Huergo LF (2018). Proteome analysis of an Escherichia coli ptsN-null strain under different nitrogen regimes. Journal of Proteomics, 174:28-35, 2018.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The carbohydrate-uptake phosphorelay PTS system plays a key role in metabolic regulation in Bacteria controlling the utilization of secondary carbon sources. Some bacteria, such as Escherichia coli, encode a paralogous system named PTSNtr(nitrogen related PTS). PTSNtris composed of EINtr(ptsP), NPr (ptsO), and EIIANtr(ptsN). These proteins act as a phosphorelay system from phosphoenolpyruvate to EINtr, NPr and them to EIIANtr. PTSNtris not involved in carbohydrate uptake and it may be dedicated to performing regulatory functions. The phosphorylation state of EINtris regulated by allosteric binding of glutamine and 2-oxoglutarate, metabolites whose intracellular levels reflect the nitrogen status. Although PTSNtris designated as having nitrogen-sensory properties, no major effect of this system on nitrogen regulation has been described in E. coli. Here we show that an E. coli ptsN deletion mutant has impaired growth in minimal medium. Proteome analysis of the ∆ ptsN strain under different nitrogen regimes revealed no involvement in regulation of the canonical nitrogen regulatory (Ntr) system. The proteomic data support the conclusion that ptsN is required to balance the activities of the sigma factors RpoS and RpoD in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed. Significance The nitrogen related PTSNtrphosphorelay system has been hypothesized to participate in the control of nitrogen metabolism. Here we used a proteomics approach to show that an Escherichia coli ptsN null strain, which misses the final module of PTSNtrphosphorelay, has no significant effects on nitrogen metabolism under different nitrogen regimes. We noted that ptsN is required for fitness under minimal medium and for the proper balance between RpoS and sigma 70 activities in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed.

BibTeX:

@article{gravina_proteome_2018,
author = {Gravina, Fernanda and Sanchuki, Heloisa S. and Rodrigues, Thiago E. and Gerhardt, Edileusa C.M. and Pedrosa, Fábio O. and Souza, Emanuel M. and Valdameri, Gláucio and de Souza, Gustavo A. and Huergo, Luciano F.},
title = {Proteome analysis of an Escherichia coli ptsN-null strain under different nitrogen regimes},
journal = {Journal of Proteomics},
year = {2018},
volume = {174},
pages = {28--35},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1874391917304293},
doi = {10.1016/j.jprot.2017.12.006}
}

Huergo LF, Rissi DV, Elias AS, Gonçalves MV, Gernet MV, Barreto F, Dahmer GW, Reis RA, Pedrosa FO, Souza EM, Monteiro RA, Baura VA, Balsanelli E and Cruz LM (2018). Influence of ancient anthropogenic activities on the mangrove soil microbiome. The Science of the Total Environment, 645:1-9, 2018.
[Abstract] [DOI] [BibTeX]

Abstract: Mangroves are highly productive ecosystems located at the transition between the terrestrial and marine environments. Mangroves play an important role in carbon storage, nutrient cycling and support for the marine food web. Mangrove soils are formed by fine particles rich in organic carbon and are subject to constant fluctuations in oxygen, salinity and nutrient availability due to fresh water flux and tidal variations. Microbes play an important role in nutrient cycling in mangrove soils; however, studies on the mangrove soil microbiome are scarce. Here we compare the microbiome of pristine mangrove soil located in an environmentally protected area in Guaratuba, Southern Brazil, with the microbiome of mangrove soil affected by the presence of carbonaceaous debris eroding from an archeological site known as Sambaqui. We show that although the Sambaqui site has a major effect on soil chemistry, increasing the soil pH by 2.6 units, only minor changes in the soil microbiome were detected indicating resilience of the microbial community to pH variations. The high alpha diversity indexes and predicted metabolic potential suggest that the mangrove soil microbiome not only provides important ecological services but also may host a broad range of microbes and genes of biotechnological interest.

BibTeX:

@article{huergo_influence_2018,
author = {Huergo, Luciano F. and Rissi, Daniel V. and Elias, Andressa S. and Gonçalves, Maria V. and Gernet, Marcos V. and Barreto, Flávio and Dahmer, Gilson W. and Reis, Rodrigo A. and Pedrosa, Fábio O. and Souza, Emanuel M. and Monteiro, Rose A. and Baura, Valter A. and Balsanelli, Eduardo and Cruz, Leonardo M.},
title = {Influence of ancient anthropogenic activities on the mangrove soil microbiome},
journal = {The Science of the Total Environment},
year = {2018},
volume = {645},
pages = {1--9},
doi = {10.1016/j.scitotenv.2018.07.094}
}

Klassen LM, Chequin A, Manica GC, Biembengut IV, Toledo MB, Baura VA, de O. Pedrosa F, Ramos EA, Costa FF, de Souza EM and Klassen G (2018). MMP9 gene expression regulation by intragenic epigenetic modifications in breast cancer. Gene, 642:461-466, 2018.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer death among women worldwide. Metastasis remains a major challenge for the clinical management and prognosis of patients with cancer. The metalloprotease MMP-9 plays a critical role in the first step of metastasis through extracellular matrix degradation. In this study, our goal was to determine the effect of epigenetic mechanisms in the promoter and intragenic region of this gene and to correlate it to the levels of expression of MMP9 in breast cancer cell lines. We have identified that MMP9 was highly expressed in the breast cancer cell lines MCF7 and MDA-MB-436 after 5-aza-2′-deoxycytidine (5-azadC) treatment. Sequencing of the promoter region as well as the CGI intronic CpG islands showed a specific sequence in CGI2, between CpGs 12–30 that was demethylated after 5-azadC treatment. This specific region was studied in breast cancer samples that revealed similar results with demethylation in positive MMP-9 breast cancer samples. Furthermore, the histone methylation marker of open chromatin (H3K4me3) was found in the promoter and intronic regions of MMP9 after 5-azadC treatment. Taken together these results showed a mechanism of DNA methylation and gene expression regulation by epigenetic marks present in the intronic DNA region of MMP9.

BibTeX:

@article{klassen_mmp9_2018,
author = {Klassen, Liliane M.B. and Chequin, Andressa and Manica, Graciele C.M. and Biembengut, Isis V. and Toledo, Mariana B. and Baura, Valter A. and de O. Pedrosa, Fábio and Ramos, Edneia A.S. and Costa, Fabrício F. and de Souza, Emanuel M. and Klassen, Giseli},
title = {MMP9 gene expression regulation by intragenic epigenetic modifications in breast cancer},
journal = {Gene},
year = {2018},
volume = {642},
pages = {461--466},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0378111917310181},
doi = {10.1016/j.gene.2017.11.054}
}

Lammel DR, Barth G, Ovaskainen O, Cruz LM, Zanatta JA, Ryo M, de Souza EM and Pedrosa FO (2018). Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures. Microbiome, 6(1):106, 2018.
[Abstract] [DOI] [BibTeX]

Abstract: BACKGROUND: pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to "spillover effects" on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures.
RESULTS: We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical-chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes.
CONCLUSIONS: Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and "spillover effects" of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.

BibTeX:

@article{lammel_direct_2018,
author = {Lammel, Daniel R. and Barth, Gabriel and Ovaskainen, Otso and Cruz, Leonardo M. and Zanatta, Josileia A. and Ryo, Masahiro and de Souza, Emanuel M. and Pedrosa, Fábio O.},
title = {Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures},
journal = {Microbiome},
year = {2018},
volume = {6},
number = {1},
pages = {106},
doi = {10.1186/s40168-018-0482-8}
}

Ostrensky A, Horodesky A, Faoro H, Balsanelli E, Sfeir MZT, Cozer N, Pie MR, Dal Pont G and Castilho-Westphal GG (2018). Metagenomic evaluation of the effects of storage conditions on the bacterial microbiota of oysters Crassostrea gasar (Adanson, 1757). Journal of Applied Microbiology, 125(5):1435-1443, 2018.
[Abstract] [DOI] [BibTeX]

Abstract: AIMS: To evaluate the influence of storage conditions on the composition of the bacterial microbiota of living oysters Crassostrea gasar.
METHODS AND RESULTS: The oysters used in this study came from marine farms (Guaratuba Bay, Brazil) and were exposed to two conditions that simulated different storage situations: immersion in water (group I) and exposure to air (group II). The animals were subjected to five different temperatures (5-25°C), for 10 days. The 16S rRNA gene from oysters was amplified and sequenced to determine the taxonomic units and bacterial strains present in the samples. Group I showed higher diversity of bacteria (163 genera) rather than group II (104 genera). In all, 59 bacterial genera potentially pathogenic to humans were identified (n = 56 in group I and n = 45 in group II).
CONCLUSIONS: The storage conditions having a direct influence on the oyster microbiota. Live C. gasar should be stored exposed to air at 5-25°C, because it favours a lower prevalence of bacteria potentially pathogenic to humans.
SIGNIFICANCE AND IMPACT OF THE STUDY: During the oyster commercialization process, some conditions of storage, time and temperature must be followed in order to reduce the prevalence of bacteria potentially pathogenic to humans.

BibTeX:

@article{ostrensky_metagenomic_2018,
author = {Ostrensky, A. and Horodesky, A. and Faoro, H. and Balsanelli, E. and Sfeir, M. Z. T. and Cozer, N. and Pie, M. R. and Dal Pont, G. and Castilho-Westphal, G. G.},
title = {Metagenomic evaluation of the effects of storage conditions on the bacterial microbiota of oysters Crassostrea gasar (Adanson, 1757)},
journal = {Journal of Applied Microbiology},
year = {2018},
volume = {125},
number = {5},
pages = {1435--1443},
doi = {10.1111/jam.14045}
}

Pillonetto M, Arend LN, Faoro H, D'Espindula HR, Blom J, Smits TH, Mira MT and Rezzonico F (2018). Emended description of the genus phytobacter, its type species phytobacter diazotrophicus (Zhang 2008) and description of phytobacter ursingii sp. nov. International Journal of Systematic and Evolutionary Microbiology, 68(1):176-184, 2018.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The species Phytobacter diazotrophicus and the associated genus Phytobacter were originally described by Zhanget al. [Arch Microbiol 189 (2008), 431–439] on the basis of few endophytic nitrogen-fixing bacteria isolated from wild rice (Oryza rufipogon) in China. In this study, we demonstrate that a number of clinical isolates that were either described in the literature, preserved in culture collections, or obtained during a 2013 multi-state sepsis outbreak in Brazil also belong to the same genus. 16S rRNA gene sequencing, multilocus sequence analysis based on gyrB, rpoB, atpD and infB genes, as well as digital DNA–DNA hybridization support the existence of a second species within the genus Phytobacter . All isolates from the recent Brazilian outbreak, along with some older American clinical strains, were found to belong to the already described species Phytobacter diazotrophicus , whereas three clinical strains retrieved in the USA over a time span of almost four decades, could be assigned to a new Phytobacter species. Implementation of an extended set of biochemical tests showed that the two Phytobacter species could phenotypically be discriminated from each other by the ability to utilize l-sorbose and d-serine. This feature was limited to the strains of the novel species described herein, for which the name Phytobacter ursingii sp. nov. is proposed, with ATCC 27989T (=CNCTC 5729T) as the designated type strain. An emended description of the species Phytobacter diazotrophicus and of the genus Phytobacter is also provided.

BibTeX:

@article{pillonetto_emended_2018,
author = {Pillonetto, Marcelo and Arend, Lavinia N. and Faoro, Helisson and D'Espindula, Helena R.S. and Blom, Jochen and Smits, Theo H.M. and Mira, Marcelo T. and Rezzonico, Fabio},
title = {Emended description of the genus phytobacter, its type species phytobacter diazotrophicus (Zhang 2008) and description of phytobacter ursingii sp. nov},
journal = {International Journal of Systematic and Evolutionary Microbiology},
year = {2018},
volume = {68},
number = {1},
pages = {176--184},
url = {http://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.002477},
doi = {10.1099/ijsem.0.002477}
}

Santos ARS, Gerhardt ECM, Moure VR, Pedrosa FO, Souza EM, Diamanti R, Högbom M and Huergo LF (2018). Kinetics and structural features of dimeric glutamine-dependent bacterial NAD+ synthetases suggest evolutionary adaptation to available metabolites. The Journal of Biological Chemistry, 293(19):7397-7407, 2018.
[Abstract] [DOI] [BibTeX]

Abstract: NADH (NAD+) and its reduced form NADH serve as cofactors for a variety of oxidoreductases that participate in many metabolic pathways. NAD+ also is used as substrate by ADP-ribosyl transferases and by sirtuins. NAD+ biosynthesis is one of the most fundamental biochemical pathways in nature, and the ubiquitous NAD+ synthetase (NadE) catalyzes the final step in this biosynthetic route. Two different classes of NadE have been described to date: dimeric single-domain ammonium-dependent NadENH3 and octameric glutamine-dependent NadEGln, and the presence of multiple NadE isoforms is relatively common in prokaryotes. Here, we identified a novel dimeric group of NadEGln in bacteria. Substrate preferences and structural analyses suggested that dimeric NadEGln enzymes may constitute evolutionary intermediates between dimeric NadENH3 and octameric NadEGln The characterization of additional NadE isoforms in the diazotrophic bacterium Azospirillum brasilense along with the determination of intracellular glutamine levels in response to an ammonium shock led us to propose a model in which these different NadE isoforms became active accordingly to the availability of nitrogen. These data may explain the selective pressures that support the coexistence of multiple isoforms of NadE in some prokaryotes.

BibTeX:

@article{santos_kinetics_2018,
author = {Santos, Adrian Richard Schenberger and Gerhardt, Edileusa Cristina Marques and Moure, Vivian Rotuno and Pedrosa, Fábio Oliveira and Souza, Emanuel Maltempi and Diamanti, Riccardo and Högbom, Martin and Huergo, Luciano Fernandes},
title = {Kinetics and structural features of dimeric glutamine-dependent bacterial NAD+ synthetases suggest evolutionary adaptation to available metabolites},
journal = {The Journal of Biological Chemistry},
year = {2018},
volume = {293},
number = {19},
pages = {7397--7407},
doi = {10.1074/jbc.RA118.002241}
}

Trovero MF, Scavone P, Platero R, de Souza EM, Fabiano E and Rosconi F (2018). Herbaspirillum seropedicae Differentially Expressed Genes in Response to Iron Availability. Frontiers in Microbiology, 9:1430, 2018.
[Abstract] [DOI] [BibTeX]

Abstract: Herbaspirillum seropedicae Z67 is a nitrogen-fixing endophyte that colonizes many important crops. Like in almost all organisms, vital cellular processes of this endophyte are iron dependent. In order to efficiently acquire iron to fulfill its requirements, this bacterium produces the siderophores serobactins. However, the presence in its genome of many others iron acquisition genes suggests that serobactins are not the only strategy used by H. seropedicae to overcome metal deficiency. The aim of this work was to identify genes and proteins differentially expressed by cells growing in low iron conditions in order to describe H. seropedicae response to iron limitation stress. For this purpose, and by using a transcriptomic approach, we searched and identified a set of genes up-regulated when iron was scarce. One of them, Hsero2337, codes for a TonB-dependent transporter/transducer present in the serobactins biosynthesis genomic locus, with an unknown function. Another TonB-dependent receptor, the one encoded by Hsero1277, and an inner membrane ferrous iron permease, coded by Hsero2720, were also detected. By using a proteomic approach focused in membrane proteins, we identified the specific receptor for iron-serobactin internalization SbtR and two non-characterized TonB-dependent receptors (coded by genes Hsero1277 and Hsero3255). We constructed mutants on some of the identified genes and characterized them by in vitro growth, biofilm formation, and interaction with rice plants. Characterization of mutants in gene Hsero2337 showed that the TonB-dependent receptor coded by this gene has a regulatory role in the biosynthesis of serobactins, probably by interacting with the alternative sigma factor PfrI, coded by gene Hsero2338. Plant colonization of the mutant strains was not affected, since the mutant strain normally colonize the root and aerial part of rice plants. These results suggest that the strategies used by H. seropedicae to acquire iron inside plants are far more diverse than the ones characterized in this work. In vivo expression studies or colonization competition experiments between the different mutant strains could help us in future works to determine the relative importance of the different iron acquisition systems in the interaction of H. seropedicae with rice plants.

BibTeX:

@article{trovero_herbaspirillum_2018,
author = {Trovero, María F. and Scavone, Paola and Platero, Raúl and de Souza, Emanuel M. and Fabiano, Elena and Rosconi, Federico},
title = {Herbaspirillum seropedicae Differentially Expressed Genes in Response to Iron Availability},
journal = {Frontiers in Microbiology},
year = {2018},
volume = {9},
pages = {1430},
doi = {10.3389/fmicb.2018.01430}
}

Alves LP, Almeida AT, Cruz LM, Pedrosa FO, de Souza EM, Chubatsu LS, Müller-Santos M and Valdameri G (2017). A simple and efficient method for poly-3-hydroxybutyrate quantification in diazotrophic bacteria within 5 minutes using flow cytometry. Brazilian Journal of Medical and Biological Research, 50(1) 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Managed landscapes in which non-native ornamental plants are favored over native vegetation now dominate the United States, particularly east of the Mississippi River. We measured how landscaping with native plants affects the avian and lepidopteran communities on 6 pairs of suburban properties in southeastern Pennsylvania. One property in each pair was landscaped entirely with native plants and the other exhibited a more conventional suburban mixture of plants–a native canopy with non-native groundcover and shrubs. Vegetation sampling confirmed that total plant cover and plant diversity did not differ between treatments, but non-native plant cover was greater on the conventional sites and native plant cover was greater on the native sites. Several avian (abundance, species richness, biomass, and breeding-bird abundance) and larval lepidopteran (abundance and species richness) community parameters were measured from June 2006 to August 2006. Native properties supported significantly more caterpillars and caterpillar species and significantly greater bird abundance, diversity, species richness, biomass, and breeding pairs of native species. Of particular importance is that bird species of regional conservation concern were 8 times more abundant and significantly more diverse on native properties. In our study area, native landscaping positively influenced the avian and lepidopteran carrying capacity of suburbia and provided a mechanism for reducing biodiversity losses in human-dominated landscapes.

BibTeX:

@article{alves_simple_2017,
author = {Alves, L. P.S. and Almeida, A. T. and Cruz, L. M. and Pedrosa, F. O. and de Souza, E. M. and Chubatsu, L. S. and Müller-Santos, M. and Valdameri, G.},
title = {A simple and efficient method for poly-3-hydroxybutyrate quantification in diazotrophic bacteria within 5 minutes using flow cytometry},
journal = {Brazilian Journal of Medical and Biological Research},
year = {2017},
volume = {50},
number = {1},
note = {ISBN: 0100-879x},
url = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2017000100606&lng=en&tlng=en},
doi = {10.1590/1414-431X20165492}
}

Anghebem-Oliveira MI, Webber S, Alberton D, de Souza EM, Klassen G, Picheth G and Rego FGdM (2017). The GCKR Gene Polymorphism rs780094 is a Risk Factor for Gestational Diabetes in a Brazilian Population. Journal of Clinical Laboratory Analysis, 31(2):e22035, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: BACKGROUND The glucokinase regulatory protein (GCKR) regulates the activity of the glucokinase (GCK), which plays a key role in glucose homeostasis. Genetic variants in GCK have been associated with diabetes and gestational diabetes (GDM). Due to the relationship between GCKRP and GCK, polymorphisms in GCKR are also candidates for genetic association with GDM. The aim of this study was to evaluate the association between the GCKR rs780094 polymorphism and GDM in a Brazilian population. METHODS 252 unrelated Euro-Brazilian pregnant women were classified as control (healthy pregnant women, n = 125) and GDM (pregnant women with GDM, n = 127) age-matched groups. Clinical and anthropometric data were obtained from all subjects. The GCKR rs780094 polymorphism was genotyped using fluorescent probes (TaqMan® , code C286287310). RESULTS Both groups were in Hardy-Weinberg equilibrium. The GCKR rs780094 polymorphism was associated with GDM in codominant and dominant models (P = 0.022 and P = 0.010, respectively). The minor allele (T) frequency for the control group in the study was 38.4% (95% CI: 32-44, similar to frequencies reported for other Caucasian populations. CONCLUSION Carriers of the C allele of rs780094 were 1.41 (odds ratio, 95% CI, 0.97-2.03) times more likely to develop GDM.

BibTeX:

@article{anghebem-oliveira_gckr_2017,
author = {Anghebem-Oliveira, Mauren Isfer and Webber, Susan and Alberton, Dayane and de Souza, Emanuel Maltempi and Klassen, Giseli and Picheth, Geraldo and Rego, Fabiane Gomes de Moraes},
title = {The GCKR Gene Polymorphism rs780094 is a Risk Factor for Gestational Diabetes in a Brazilian Population},
journal = {Journal of Clinical Laboratory Analysis},
year = {2017},
volume = {31},
number = {2},
pages = {e22035},
url = {http://doi.wiley.com/10.1002/jcla.22035},
doi = {10.1002/jcla.22035}
}

Antunes D, Jorge NAN, Caffarena ER and Passetti F (2017). Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools. Frontiers in Genetics, 8:231, 2017.
[Abstract] [DOI] [BibTeX]

Abstract: RNA molecules are essential players in many fundamental biological processes. Prokaryotes and eukaryotes have distinct RNA classes with specific structural features and functional roles. Computational prediction of protein structures is a research field in which high confidence three-dimensional protein models can be proposed based on the sequence alignment between target and templates. However, to date, only a few approaches have been developed for the computational prediction of RNA structures. Similar to proteins, RNA structures may be altered due to the interaction with various ligands, including proteins, other RNAs, and metabolites. A riboswitch is a molecular mechanism, found in the three kingdoms of life, in which the RNA structure is modified by the binding of a metabolite. It can regulate multiple gene expression mechanisms, such as transcription, translation initiation, and mRNA splicing and processing. Due to their nature, these entities also act on the regulation of gene expression and detection of small metabolites and have the potential to helping in the discovery of new classes of antimicrobial agents. In this review, we describe software and web servers currently available for riboswitch aptamer identification and secondary and tertiary structure prediction, including applications.

BibTeX:

@article{antunes_using_2017,
author = {Antunes, Deborah and Jorge, Natasha A. N. and Caffarena, Ernesto R. and Passetti, Fabio},
title = {Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools},
journal = {Frontiers in Genetics},
year = {2017},
volume = {8},
pages = {231},
doi = {10.3389/fgene.2017.00231}
}

Assis FE, Dallagassa CB, Farah SM, Souza EM, Pedrosa FO, Chubatsu LS and Fadel-Picheth CM (2017). Molecular characterisation of Salmonella strains isolated from outbreaks and sporadic cases of diarrhoea occurred in Paraná State, South of Brazil. Epidemiology and Infection, 145(9):1953-1960, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: \textlessp\textgreater A total of 46 strains of \textlessitalic\textgreaterSalmonella\textless/italic\textgreater isolated from patients with sporadic diarrhoea or involved in foodborne outbreaks were analysed by PCR for genus identification and serotyping. Subtyping was performed using pulsed-field gel electrophoresis (PFGE) and multiple amplification of phage locus typing (MAPLT) for seven variable loci. Bacteria were identified as belonging to serotype Enteritidis (33 strains; 71·7 or Typhimurium (13 strains; 28·3. A high similarity coefficient (94·6 was observed in the \textlessitalic\textgreaterSalmonella\textless/italic\textgreater Enteritidis group for which were found three related PFGE profiles and only one MAPLT; strains representing profile PA/P1/MI were prevalent (27; 81·8. Two \textlessitalic\textgreaterSalmonella\textless/italic\textgreater Typhimurium isolates were untypeable by PFGE. The remaining 11 strains had eight PFGE and three MAPLT profiles. The discriminatory power of MAPLT was lower than that of PFGE. \textlessitalic\textgreaterSalmonella\textless/italic\textgreater Enteritidis of clonal nature is predominant in Paraná State, with the most prevalent profile PA/P1/M1 associated with sporadic diarrhoea and with seven of nine reported outbreaks. In conclusion, PFGE shows higher discriminatory power among \textlessitalic\textgreaterSalmonella\textless/italic\textgreater strains. \textless/p\textgreater

BibTeX:

@article{assis_molecular_2017,
author = {Assis, F. E.A. and Dallagassa, C. B. and Farah, S. M.S.S. and Souza, E. M. and Pedrosa, F. O. and Chubatsu, L. S. and Fadel-Picheth, C. M.T.},
title = {Molecular characterisation of Salmonella strains isolated from outbreaks and sporadic cases of diarrhoea occurred in Paraná State, South of Brazil},
journal = {Epidemiology and Infection},
year = {2017},
volume = {145},
number = {9},
pages = {1953--1960},
url = {https://www.cambridge.org/core/product/identifier/S0950268817000619/type/journal_article},
doi = {10.1017/S0950268817000619}
}

Bach E, Sant'Anna FH, dos Passos JFM, Balsanelli E, de Baura VA, Pedrosa FdO, de Souza EM and Passaglia LMP (2017). Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov.. Pathogens and Disease, 75(6) 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The correct identification of bacteria from the Burkholderia cepacia complex (Bcc) is crucial for epidemiological studies and treatment of cystic fibrosis infections. However, genome-based identification tools are revealing many controversial Bcc species assignments. The aim of this work is to re-examine the taxonomic position of the soil bacterium B. cepacia 89 through polyphasic and genomic approaches. recA and 16S rRNA gene sequence analysis positioned strain 89 inside the Bcc group. However, based on the divergence score of seven concatenated allele sequences, and values of average nucleotide identity, and digital DNA:DNA hybridization, our results suggest that strain 89 is different from other Bcc species formerly described. Thus, we propose to classify Burkholderia sp. 89 as the novel species Burkholderia catarinensis sp. nov. with strain 89T (=DSM 103188T = BR 10601T) as the type strain. Moreover, our results call the attention to some probable misidentifications of Bcc genomes at the National Center for Biotechnology Information database.

BibTeX:

@article{bach_detection_2017,
author = {Bach, Evelise and Sant'Anna, Fernando Hayashi and dos Passos, João Frederico Magrich and Balsanelli, Eduardo and de Baura, Valter Antonio and Pedrosa, Fábio de Oliveira and de Souza, Emanuel Maltempi and Passaglia, Luciane Maria Pereira},
title = {Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov.},
journal = {Pathogens and Disease},
year = {2017},
volume = {75},
number = {6},
url = {https://academic.oup.com/femspd/article-lookup/doi/10.1093/femspd/ftx076},
doi = {10.1093/femspd/ftx076}
}

Dos-Santos CM, de Souza DG, Balsanelli E, Cruz LM, de Souza EM, Baldani JI and Schwab S (2017). A Culture-Independent Approach to Enrich Endophytic Bacterial Cells from Sugarcane Stems for Community Characterization. Microbial Ecology, 74(2):453-465, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Bacterial endophytes constitute a very diverse community and they confer important benefits which help to improve agricultural yield. Some of these benefits remain underexplored or little understood, mainly due to the bottlenecks associated with the plant feature, a low number of endophytic bacterial cells in relation to the plant, and difficulties in accessing these bacteria using cultivation-independent methods. Enriching endophytic bacterial cells from plant tissues, based on a non-biased, cultivation-independent physical enrichment method, may help to circumvent those problems, especially in the case of sugarcane stems, which have a high degree of interfering factors, such as polysaccharides, phenolic compounds, nucleases, and fibers. In the present study, an enrichment approach for endophytic bacterial cells from sugarcane lower stems is described. The results demonstrate that the enriched bacterial cells are suitable for endophytic community characterization. A community analysis revealed the presence of previously well-described but also novel endophytic bacteria in sugarcane tissues which may exert functions such as plant growth promotion and biological control, with a predominance of the Proteobacterial phylum, but also Actinobacteria, Bacteroidetes, and Firmicutes, among others. In addition, by comparing the present and literature data, it was possible to list the most frequently detected bacterial endophyte genera in sugarcane tissues. The presented enrichment approach paves the way for improved future research toward the assessment of endophytic bacterial community in sugarcane and other biofuel crops.

BibTeX:

@article{dos-santos_culture-independent_2017,
author = {Dos-Santos, Carlos M. and de Souza, Daniel G. and Balsanelli, Eduardo and Cruz, Leonardo Magalhães and de Souza, Emanuel M. and Baldani, José I. and Schwab, Stefan},
title = {A Culture-Independent Approach to Enrich Endophytic Bacterial Cells from Sugarcane Stems for Community Characterization},
journal = {Microbial Ecology},
year = {2017},
volume = {74},
number = {2},
pages = {453--465},
note = {ISBN: 0095-3628, 1432-184X},
url = {http://link.springer.com/10.1007/s00248-017-0941-y},
doi = {10.1007/s00248-017-0941-y}
}

Faoro H, Rene Menegazzo R, Battistoni F, Gyaneshwar P, do Amaral FP, Taulé C, Rausch S, Gonçalves Galvão P, de los Santos C, Mitra S, Heijo G, Sheu SY, Chen WM, Mareque C, Zibetti Tadra-Sfeir M, Ivo Baldani J, Maluk M, Paula Guimarães A, Stacey G, de Souza EM, Pedrosa FO, Magalhães Cruz L and James EK (2017). The oil-contaminated soil diazotroph Azoarcus olearius DQS-4Tis genetically and phenotypically similar to the model grass endophyte Azoarcus sp. BH72. Environmental Microbiology Reports, 9(3):223-238, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The genome of Azoarcus olearius DQS-4(T), a N-2-fixing Betaproteobacterium isolated from oil-contaminated soil in Taiwan, was sequenced and compared with other Azoarcus strains. The genome sequence showed high synteny with Azoarcus sp. BH72, a model endophytic diazotroph, but low synteny with five non-plant-associated strains (Azoarcus CIB, Azoarcus EBN1, Azoarcus KH32C, A. toluclasticus MF63(T) and Azoarcus PA01). Average Nucleotide Identity (ANI) revealed that DQS-4(T) shares 98.98% identity with Azoarcus BH72, which should now be included in the species A. olearius. The genome of DQS-4(T) contained several genes related to plant colonization and plant growth promotion, such as nitrogen fixation, plant adhesion and root surface colonization. In accordance with the presence of these genes, DQS-4(T) colonized rice (Oryza sativa) and Setaria viridis, where it was observed within the intercellular spaces and aerenchyma mainly of the roots. Although they promote the growth of grasses, the mechanism(s) of plant growth promotion by A. olearius strains is unknown, as the genomes of DQS-4(T) and BH72 do not contain genes for indole acetic acid (IAA) synthesis nor phosphate solubilization. In spite of its original source, both the genome and behaviour of DQS-4(T) suggest that it has the capacity to be an endophytic, nitrogen-fixing plant growth-promoting bacterium.

BibTeX:

@article{faoro_oil-contaminated_2017,
author = {Faoro, Helisson and Rene Menegazzo, Rodrigo and Battistoni, Federico and Gyaneshwar, Prasad and do Amaral, Fernanda P. and Taulé, Cecilia and Rausch, Sydnee and Gonçalves Galvão, Patricia and de los Santos, Cecilia and Mitra, Shubhajit and Heijo, Gabriela and Sheu, Shih Yi and Chen, Wen Ming and Mareque, Cintia and Zibetti Tadra-Sfeir, Michelle and Ivo Baldani, J. and Maluk, Marta and Paula Guimarães, Ana and Stacey, Gary and de Souza, Emanuel M. and Pedrosa, Fabio O. and Magalhães Cruz, Leonardo and James, Euan K.},
title = {The oil-contaminated soil diazotroph Azoarcus olearius DQS-4Tis genetically and phenotypically similar to the model grass endophyte Azoarcus sp. BH72},
journal = {Environmental Microbiology Reports},
year = {2017},
volume = {9},
number = {3},
pages = {223--238},
url = {http://doi.wiley.com/10.1111/1758-2229.12502},
doi = {10.1111/1758-2229.12502}
}

Gerhardt EC, Moure VR, Souza AW, Pedrosa FO, Souza EM, Diacovich L, Gramajo H and Huergo LF (2017). Expression and purification of untagged Glnk proteins from actinobacteria. EXCLI Journal, 16:949-958, 2017.
[Abstract] [DOI] [BibTeX]

Abstract: The PII protein family constitutes one of the most conserved and well distributed family of signal transduction proteins in nature. These proteins play key roles in nitrogen and carbon metabolism. PII function has been well documented in Gram-negative bacteria. However, there are very few reports describing the in vitro properties and function of PII derived from Gram-positive bacteria. Here we present the heterologous expression and efficient purification protocols for untagged PII from three Actinobacteria of medical and biotechnological interest namely: Mycobacterium tuberculosis, Rhodococcus jostii and Streptomyces coelicolor. Circular dichroism and gel filtration analysis supported that the purified proteins are correctly folded. The purification protocol described here will facilitate biochemical studies and help to uncover the biochemical functions of PII proteins in Actinobacteria.

BibTeX:

@article{gerhardt_expression_2017,
author = {Gerhardt, Edileusa C.M. and Moure, Vivian R. and Souza, Andrey W. and Pedrosa, Fabio O. and Souza, Emanuel M. and Diacovich, Lautaro and Gramajo, Hugo and Huergo, Luciano F.},
title = {Expression and purification of untagged Glnk proteins from actinobacteria},
journal = {EXCLI Journal},
year = {2017},
volume = {16},
pages = {949--958},
doi = {10.17179/excli2017-394}
}

Leao ACR, Weiss VA, Vicente VA, Costa F, Bombassaro A, Raittz RT, Steffens MBR, Pedrosa FO, Gomes RR, Baura V, Faoro H, Sfeir MZT, Balsanelli E, Moreno LF, Najafzadeh MJ, de Hoog S and Souza EM (2017). Genome Sequence of Type Strain \textlessi\textgreaterFonsecaea multimorphosa\textless/i\textgreater CBS 980.96 \textlesssup\textgreaterT\textless/sup\textgreater , a Causal Agent of Feline Cerebral Phaeohyphomycosis. Genome Announcements, 5(7):e01666-16, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: \textlessp\textgreater A draft genome sequence of type strain \textlessitalic\textgreaterFonsecaea multimorphosa\textless/italic\textgreater CBS 980.96 \textlesssup\textgreaterT\textless/sup\textgreater was obtained. This species was first isolated from a cat with cerebral phaeohyphomycosis in Queensland, Australia. \textless/p\textgreater

BibTeX:

@article{leao_genome_2017,
author = {Leao, Aniele C. Ribas and Weiss, Vinicius Almir and Vicente, Vania Aparecida and Costa, Flavia and Bombassaro, Amanda and Raittz, Roberto Tadeu and Steffens, Maria Berenice R. and Pedrosa, Fabio Oliveira and Gomes, Renata R. and Baura, Valter and Faoro, Helisson and Sfeir, Michelle Zibetti Tadra and Balsanelli, Eduardo and Moreno, Leandro F. and Najafzadeh, M. Javad and de Hoog, Sybren and Souza, Emanuel Maltempi},
title = {Genome Sequence of Type Strain \textlessi\textgreaterFonsecaea multimorphosa\textless/i\textgreater CBS 980.96 \textlesssup\textgreaterT\textless/sup\textgreater , a Causal Agent of Feline Cerebral Phaeohyphomycosis},
journal = {Genome Announcements},
year = {2017},
volume = {5},
number = {7},
pages = {e01666--16},
url = {http://genomea.asm.org/lookup/doi/10.1128/genomeA.01666-16},
doi = {10.1128/genomeA.01666-16}
}

Lopes FM, da Motta LL, De Bastiani MA, Pfaffenseller B, Aguiar BW, de Souza LF, Zanatta G, Vargas DM, Schönhofen P, Londero GF, de Medeiros LM, Freire VN, Dafre AL, Castro MA, Parsons RB and Klamt F (2017). RA Differentiation Enhances Dopaminergic Features, Changes Redox Parameters, and Increases Dopamine Transporter Dependency in 6-Hydroxydopamine-Induced Neurotoxicity in SH-SY5Y Cells. Neurotoxicity Research, 31(4):545-559, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Research on Parkinson's disease (PD) and drug development is hampered by the lack of suitable human in vitro models that simply and accurately recreate the disease conditions. To counteract this, many attempts to differentiate cell lines, such as the human SH-SY5Y neuroblastoma, into dopaminergic neurons have been undertaken since they are easier to cultivate when compared with other cellular models. Here, we characterized neuronal features discriminating undifferentiated and retinoic acid (RA)-differentiated SH-SYSY cells and described significant differences between these cell models in 6-hydroxydopamine (6-OHDA) cytotoxicity. In contrast to undifferentiated cells, RA-differentiated SH-SY5Y cells demonstrated low proliferative rate and a pronounced neuronal morphology with high expression of genes related to synapse vesicle cycle, dopamine synthesis/degradation, and of dopamine transporter (DAT). Significant differences between undifferentiated and RA-differentiated SH-SY5Y cells in the overall capacity of antioxidant defenses were found; although RA-differentiated SH-SY5Y cells presented a higher basal antioxidant capacity with high resistance against H2O2 insult, they were twofold more sensitive to 6-OHDA. DAT inhibition by 3α-bis-4-fluorophenyl-methoxytropane and dithiothreitol (a cell-permeable thiol-reducing agent) protected RA-differentiated, but not undifferentiated, SH-SY5Y cells from oxidative damage and cell death caused by 6-OHDA. Here, we demonstrate that undifferentiated and RA-differentiated SH-SY5Y cells are two unique phenotypes and also have dissimilar mechanisms in 6-OHDA cytotoxicity. Hence, our data support the use of RA-differentiated SH-SY5Y cells as an in vitro model of PD. This study may impact our understanding of the pathological mechanisms of PD and the development of new therapies and drugs for the management of the disease.

BibTeX:

@article{lopes_ra_2017,
author = {Lopes, Fernanda M. and da Motta, Leonardo Lisbôa and De Bastiani, Marco A. and Pfaffenseller, Bianca and Aguiar, Bianca W. and de Souza, Luiz F. and Zanatta, Geancarlo and Vargas, Daiani M. and Schönhofen, Patrícia and Londero, Giovana F. and de Medeiros, Liana M. and Freire, Valder N. and Dafre, Alcir L. and Castro, Mauro A.A. and Parsons, Richard B. and Klamt, Fabio},
title = {RA Differentiation Enhances Dopaminergic Features, Changes Redox Parameters, and Increases Dopamine Transporter Dependency in 6-Hydroxydopamine-Induced Neurotoxicity in SH-SY5Y Cells},
journal = {Neurotoxicity Research},
year = {2017},
volume = {31},
number = {4},
pages = {545--559},
note = {ISBN: 1476-3524 (Electronic) 1029-8428 (Linking)},
url = {http://link.springer.com/10.1007/s12640-016-9699-0},
doi = {10.1007/s12640-016-9699-0}
}

Machado LdO, Vieira LdN, Stefenon VM, de Oliveira Pedrosa F, de Souza EM, Guerra MP and Nodari RO (2017). Phylogenomic relationship of feijoa (Acca sellowiana (O.Berg) Burret) with other Myrtaceae based on complete chloroplast genome sequences. Genetica, 145(2):163-174, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Given their distribution, importance, and rich- ness, Myrtaceae species comprise a model system for stud- ying the evolution of tropical plant diversity. In addition, chloroplast (cp) genome sequencing is an e cient tool for phylogenetic relationship studies. Feijoa [Acca sellowiana (O. Berg) Burret; CN: pineapple-guava] is a Myrtaceae species that occurs naturally in southern Brazil and north- ern Uruguay. Feijoa is known for its exquisite perfume and avorful fruits, pharmacological properties, ornamen- tal value and increasing economic relevance. In the pre- sent work, we reported the complete cp genome of feijoa. The feijoa cp genome is a circular molecule of 159,370 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC 88,028 bp) and a Small Single Copy region (SSC 18,598 bp) separated by Inverted Repeat regions (IRs 26,372 bp). The genome structure, gene order, GC content and codon usage are sim- ilar to those of typical angiosperm cp genomes. When com- pared to other cp genome sequences of Myrtaceae, feijoa showed closest relationship with pitanga (Eugenia uni ora L.). Furthermore, a comparison of pitanga synonymous (Ks) and nonsynonymous (Ka) substitution rates revealed extremely low values. Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identi- cal in topology. These trees supported monophyly of three Myrtoideae clades.

BibTeX:

@article{machado_phylogenomic_2017,
author = {Machado, Lilian de Oliveira and Vieira, Leila do Nascimento and Stefenon, Valdir Marcos and de Oliveira Pedrosa, Fábio and de Souza, Emanuel Maltempi and Guerra, Miguel Pedro and Nodari, Rubens Onofre},
title = {Phylogenomic relationship of feijoa (Acca sellowiana (O.Berg) Burret) with other Myrtaceae based on complete chloroplast genome sequences},
journal = {Genetica},
year = {2017},
volume = {145},
number = {2},
pages = {163--174},
note = {ISBN: 0123456789},
url = {http://link.springer.com/10.1007/s10709-017-9954-1},
doi = {10.1007/s10709-017-9954-1}
}

Manica GCM, Ribeiro CF, de Oliveira MAS, Pereira IT, Chequin A, Ramos EAS, Klassen LMB, Sebastião APM, Alvarenga LM, Zanata SM, Noronha LD, Rabinovich I, Costa FF, Souza EM and Klassen G (2017). Down regulation of ADAM33 as a Predictive Biomarker of Aggressive Breast Cancer. Scientific Reports, 7:44414, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: © The Author(s) 2017. Breast cancer is a heterogeneous disease with differences in its clinical, molecular and biological features. Traditionally, immunohistochemical markers together with clinicopathologic parameters are used to classify breast cancer and to predict disease outcome. Triple-negative breast cancer (TNBC) is a particular type of breast cancer that is defined by a lack of expression of hormonal receptors and the HER2 gene. Most cases of TNBC also have a basal-like phenotype (BLBC) with expression of cytokeratin 5/6 and/or EGFR. A basal marker alone is insufficient for a better understanding of the tumor biology of TNBC. In that regard, the ADAM33 gene is silenced by DNA hypermethylation in breast cancer, which suggests that ADAM33 might be useful as a molecular marker. In the present study, we have produced monoclonal antibodies against the ADAM33 protein and have investigated the role of ADAM33 protein in breast cancer. We used 212 breast tumor samples and lower levels of ADAM33 were correlated with TNBC and basal-like markers. A lower level of ADAM33 was also correlated with shorter overall survival and metastasis-free survival and was considered an independent prognostic factor suggesting that ADAM33 is a novel molecular biomarker of TNBC and BLBC that might be useful as a prognostic factor.

BibTeX:

@article{manica_down_2017,
author = {Manica, Graciele C. M. and Ribeiro, Caroline F. and de Oliveira, Marco A. S. and Pereira, Isabela T. and Chequin, Andressa and Ramos, Edneia A. S. and Klassen, Liliane M. B. and Sebastião, Ana Paula M. and Alvarenga, Larissa M. and Zanata, Silvio M. and Noronha, Lucia De and Rabinovich, Iris and Costa, Fabricio F. and Souza, Emanuel M. and Klassen, Giseli},
title = {Down regulation of ADAM33 as a Predictive Biomarker of Aggressive Breast Cancer},
journal = {Scientific Reports},
year = {2017},
volume = {7},
pages = {44414},
url = {http://www.nature.com/articles/srep44414},
doi = {10.1038/srep44414}
}

Mesa D, Lammel DR, Balsanelli E, Sena C, Noseda MD, Caron LF, Cruz LM, Pedrosa FO and Souza EM (2017). Cecal Microbiota in Broilers Fed with Prebiotics. Frontiers in Genetics, 8 2017.
[DOI] [URL] [BibTeX]

Abstract:

BibTeX:

@article{mesa_cecal_2017,
author = {Mesa, Dany and Lammel, Daniel R. and Balsanelli, Eduardo and Sena, Claudia and Noseda, Miguel D. and Caron, Luiz F. and Cruz, Leonardo M. and Pedrosa, Fabio O. and Souza, Emanuel M.},
title = {Cecal Microbiota in Broilers Fed with Prebiotics},
journal = {Frontiers in Genetics},
year = {2017},
volume = {8},
note = {ISBN: 1664-8021 (Print) 1664-8021 (Linking)},
url = {http://journal.frontiersin.org/article/10.3389/fgene.2017.00153/full},
doi = {10.3389/fgene.2017.00153}
}

Nichio BT, Marchaukoski JN and Raittz RT (2017). New tools in orthology analysis: A brief review of promising perspectives. Frontiers in Genetics, 8(OCT) 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques) and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST "all-against-all" methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm); or proteinOrtho (which improves the accuracy of ortholog groups); or ReMark (tackling the integration of the pipeline to turn the entry process automatic); or OrthAgogue (using algorithms developed to minimize processing time); and proteinOrtho (developed for dealing with large amounts of biological data). We made a comparison among the main features of four tool and tested them using four for prokaryotic genomas. We hope that our review can be useful for researchers and will help them in selecting the most appropriate tool for their work in the field of orthology.

BibTeX:

@article{nichio_new_2017,
author = {Nichio, Bruno T.L. and Marchaukoski, Jeroniza Nunes and Raittz, Roberto Tadeu},
title = {New tools in orthology analysis: A brief review of promising perspectives},
journal = {Frontiers in Genetics},
year = {2017},
volume = {8},
number = {OCT},
url = {http://journal.frontiersin.org/article/10.3389/fgene.2017.00165/full},
doi = {10.3389/fgene.2017.00165}
}

Oliveira C, Faoro H, Alves LR and Goldenberg S (2017). RNA-binding proteins and their role in the regulation of gene expression in trypanosoma cruzi and saccharomyces cerevisiae. Genetics and Molecular Biology, 40(1):22-30, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: RNA-binding proteins (RBPs) have important functions in the regulation of gene expression. RBPs play key roles in post-transcriptional processes in all eukaryotes, such as splicing regulation, mRNA transport and modulation of mRNA translation and decay. RBPs assemble into different mRNA-protein complexes, which form messenger ribonucleoprotein complexes (mRNPs). Gene expression regulation in trypanosomatids occurs mainly at the post-transcriptional level and RBPs play a key role in all processes. However, the functional characterization of RBPs in Trypanosoma cruzi has been impaired due to the lack of reliable reverse genetic manipulation tools. The comparison of RBPs from Saccharomyces cerevisiae and T. cruzi might allow inferring on the function of these proteins based on the information available for the orthologous RNA-binding proteins from the S. cerevisiae model organism. In this review, we discuss the role of some RBPs from T. cruzi and their homologues in regulating gene expression in yeast.

BibTeX:

@article{oliveira_rna-binding_2017,
author = {Oliveira, Camila and Faoro, Helisson and Alves, Lysangela Ronalte and Goldenberg, Samuel},
title = {RNA-binding proteins and their role in the regulation of gene expression in trypanosoma cruzi and saccharomyces cerevisiae},
journal = {Genetics and Molecular Biology},
year = {2017},
volume = {40},
number = {1},
pages = {22--30},
url = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000100022&lng=en&tlng=en},
doi = {10.1590/1678-4685-GMB-2016-0258}
}

Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ, Albert M, Alexopoulou I, Ally A, Antic T, Aron M, Balasundaram M, Bartlett J, Baylin SB, Beaver A, Birol I, Boice L, Bootwalla MS, Bowen J, Bowlby R, Brooks D, Broom BM, Bshara W, Burks E, Cárcano FM, Carlsen R, Carvalho BS, Carvalho AL, Castle EP, Castro P, Catto JW, Chesla DW, Chuah E, Chudamani S, Cortessis VK, Cottingham SL, Crain D, Curley E, Daneshmand S, Demchok JA, Dhalla N, Djaladat H, Eckman J, Egea SC, Engel J, Felau I, Ferguson ML, Gardner J, Gastier-Foster JM, Gerken M, Gomez-Fernandez CR, Harr J, Hartmann A, Herbert LM, Ho TH, Holt RA, Hutter CM, Jones SJ, Jorda M, Kahnoski RJ, Kasaian K, Kwiatkowski DJ, Lai PH, Lane BR, Lerner SP, Liu J, Lolla L, Lotan Y, Lucchesi FR, Ma Y, Machado RD, Maglinte DT, Mallery D, Marra MA, Martin SE, Mayo M, Meraney A, Moinzadeh A, Moore RA, Mora Pinero EM, Morris S, Morrison C, Mungall AJ, Myers JB, Naresh R, O'Donnell PH, Parekh DJ, Parfitt J, Paulauskis JD, Sekhar Pedamallu C, Penny RJ, Pihl T, Porten S, Quintero-Aguilo ME, Ramirez NC, Rathmell WK, Rieger-Christ K, Saller C, Salner A, Sandusky G, Scapulatempo-Neto C, Schein JE, Schuckman AK, Shelton C, Shelton T, Simko J, Singh P, Sipahimalani P, Smith ND, Sofia HJ, Sorcini A, Stanton ML, Steinberg GD, Stoehr R, Su X, Sullivan T, Sun Q, Tam A, Tarnuzzer R, Tarvin K, Taubert H, Thiessen N, Thorne L, Tse K, Tucker K, Van Den Berg DJ, van Kessel KE, Wach S, Wan Y, Wang Z, Weinstein JN, Weisenberger DJ, Wise L, Wong T, Wu Y, Yang L, Zach LA, Zenklusen JC, Zhang J(J, Zmuda E and Zwarthoff EC (2017). Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell, 171(3):540-556.e25, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival “neuronal” subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments. A multiplatform analysis of 412 muscle-invasive bladder cancer patients provides insights into mutational profiles with prognostic value and establishes a framework associating distinct tumor subtypes with clinical options.

BibTeX:

@article{robertson_comprehensive_2017,
author = {Robertson, A. Gordon and Kim, Jaegil and Al-Ahmadie, Hikmat and Bellmunt, Joaquim and Guo, Guangwu and Cherniack, Andrew D. and Hinoue, Toshinori and Laird, Peter W. and Hoadley, Katherine A. and Akbani, Rehan and Castro, Mauro A.A. and Gibb, Ewan A. and Kanchi, Rupa S. and Gordenin, Dmitry A. and Shukla, Sachet A. and Sanchez-Vega, Francisco and Hansel, Donna E. and Czerniak, Bogdan A. and Reuter, Victor E. and Su, Xiaoping and de Sa Carvalho, Benilton and Chagas, Vinicius S. and Mungall, Karen L. and Sadeghi, Sara and Pedamallu, Chandra Sekhar and Lu, Yiling and Klimczak, Leszek J. and Zhang, Jiexin and Choo, Caleb and Ojesina, Akinyemi I. and Bullman, Susan and Leraas, Kristen M. and Lichtenberg, Tara M. and Wu, Catherine J. and Schultz, Nikolaus and Getz, Gad and Meyerson, Matthew and Mills, Gordon B. and McConkey, David J. and Albert, Monique and Alexopoulou, Iakovina and Ally, Adrian and Antic, Tatjana and Aron, Manju and Balasundaram, Miruna and Bartlett, John and Baylin, Stephen B. and Beaver, Allison and Birol, Inanc and Boice, Lori and Bootwalla, Moiz S. and Bowen, Jay and Bowlby, Reanne and Brooks, Denise and Broom, Bradley M. and Bshara, Wiam and Burks, Eric and Cárcano, Flavio M. and Carlsen, Rebecca and Carvalho, Benilton S. and Carvalho, Andre L. and Castle, Eric P. and Castro, Patricia and Catto, James W. and Chesla, David W. and Chuah, Eric and Chudamani, Sudha and Cortessis, Victoria K. and Cottingham, Sandra L. and Crain, Daniel and Curley, Erin and Daneshmand, Siamak and Demchok, John A. and Dhalla, Noreen and Djaladat, Hooman and Eckman, John and Egea, Sophie C. and Engel, Jay and Felau, Ina and Ferguson, Martin L. and Gardner, Johanna and Gastier-Foster, Julie M. and Gerken, Mark and Gomez-Fernandez, Carmen R. and Harr, Jodi and Hartmann, Arndt and Herbert, Lynn M. and Ho, Thai H. and Holt, Robert A. and Hutter, Carolyn M. and Jones, Steven J.M. and Jorda, Merce and Kahnoski, Richard J. and Kasaian, Katayoon and Kwiatkowski, David J. and Lai, Phillip H. and Lane, Brian R. and Lerner, Seth P. and Liu, Jia and Lolla, Laxmi and Lotan, Yair and Lucchesi, Fabiano R. and Ma, Yussanne and Machado, Roberto D. and Maglinte, Dennis T. and Mallery, David and Marra, Marco A. and Martin, Sue E. and Mayo, Michael and Meraney, Anoop and Moinzadeh, Alireza and Moore, Richard A. and Mora Pinero, Edna M. and Morris, Scott and Morrison, Carl and Mungall, Andrew J. and Myers, Jerome B. and Naresh, Rashi and O'Donnell, Peter H. and Parekh, Dipen J. and Parfitt, Jeremy and Paulauskis, Joseph D. and Sekhar Pedamallu, Chandra and Penny, Robert J. and Pihl, Todd and Porten, Sima and Quintero-Aguilo, Mario E. and Ramirez, Nilsa C. and Rathmell, W. Kimryn and Rieger-Christ, Kimberly and Saller, Charles and Salner, Andrew and Sandusky, George and Scapulatempo-Neto, Cristovam and Schein, Jacqueline E. and Schuckman, Anne K. and Shelton, Candace and Shelton, Troy and Simko, Jeff and Singh, Parminder and Sipahimalani, Payal and Smith, Norm D. and Sofia, Heidi J. and Sorcini, Andrea and Stanton, Melissa L. and Steinberg, Gary D. and Stoehr, Robert and Su, Xiaoping and Sullivan, Travis and Sun, Qiang and Tam, Angela and Tarnuzzer, Roy and Tarvin, Katherine and Taubert, Helge and Thiessen, Nina and Thorne, Leigh and Tse, Kane and Tucker, Kelinda and Van Den Berg, David J. and van Kessel, Kim E. and Wach, Sven and Wan, Yunhu and Wang, Zhining and Weinstein, John N. and Weisenberger, Daniel J. and Wise, Lisa and Wong, Tina and Wu, Ye and Yang, Liming and Zach, Leigh Anne and Zenklusen, Jean C. and Zhang, Jiashan (Julia) and Zmuda, Erik and Zwarthoff, Ellen C.},
title = {Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer},
journal = {Cell},
year = {2017},
volume = {171},
number = {3},
pages = {540--556.e25},
note = {ISBN: 1097-4172 0092-8674},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867417310565},
doi = {10.1016/j.cell.2017.09.007}
}

Sacomboio ENM, Kim EYS, Correa HLR, Bonato P, Pedrosa FDO, De Souza EM, Chubatsu LS and Müller-Santos M (2017). The transcriptional regulator NtrC controls glucose-6-phosphate dehydrogenase expression and polyhydroxybutyrate synthesis through NADPH availability in Herbaspirillum seropedicae. Scientific Reports, 7(1) 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The NTR system is the major regulator of nitrogen metabolism in Bacteria. Despite its broad and well-known role in the assimilation, biosynthesis and recycling of nitrogenous molecules, little is known about its role in carbon metabolism. In this work, we present a new facet of the NTR system in the control of NADPH concentration and the biosynthesis of molecules dependent on reduced coenzyme in Herbaspirillum seropedicae SmR1. We demonstrated that a ntrC mutant strain accumulated high levels of polyhydroxybutyrate (PHB), reaching levels up to 2-fold higher than the parental strain. In the absence of NtrC, the activity of glucose-6-phosphate dehydrogenase (encoded by zwf) increased by 2.8-fold, consequently leading to a 2.1-fold increase in the NADPH/NADP+ ratio. A GFP fusion showed that expression of zwf is likewise controlled by NtrC. The increase in NADPH availability stimulated the production of polyhydroxybutyrate regardless the C/N ratio in the medium. The mutant ntrC was more resistant to H2O2 exposure and controlled the propagation of ROS when facing the oxidative condition, a phenotype associated with the increase in PHB content.

BibTeX:

@article{sacomboio_transcriptional_2017,
author = {Sacomboio, Euclides Nenga Manuel and Kim, Edson Yu Sin and Correa, Henrique Leonardo Ruchaud and Bonato, Paloma and Pedrosa, Fabio De Oliveira and De Souza, Emanuel Maltempi and Chubatsu, Leda Satie and Müller-Santos, Marcelo},
title = {The transcriptional regulator NtrC controls glucose-6-phosphate dehydrogenase expression and polyhydroxybutyrate synthesis through NADPH availability in Herbaspirillum seropedicae},
journal = {Scientific Reports},
year = {2017},
volume = {7},
number = {1},
url = {http://www.nature.com/articles/s41598-017-12649-0},
doi = {10.1097/SAP.0000000000000962}
}

Saiki FA, Bernardi AP, Reis MS, Faoro H, Souza EM, Pedrosa FO, Mantovani A and Guidolin AF (2017). Development and validation of the first SSR markers for Mimosa scabrella Benth. Genetics and Molecular Research, 16(1) 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: © 2017 The Authors. Mimosa scabrella Benth., popularly known as “bracatinga”, is a pioneer and endemic species of Brazil, occurring in Mixed Ombrophilous Forest associated with Brazilian Atlantic Rainforest biomes. It is a fast-growing tree of the Fabaceae family that facilitates the dynamics of ecological succession. SSR development, when there is no genome sequence, is time and labor intensive and there are no molecular markers for M. scabrella. We developed and validated the first microsate llite markers for this tetraploid species, evaluating mother trees and progenies. Using Illumina sequencing, we identified 290 SSR loci and 211 primer pairs. After 31 SSR loci PCR/agarose electrophoresis selection, a subset of 11 primer pairs was synthetized with fluorescence in the forward primer for PCR and capillary electrophoresis validation with leaf DNA of 33 adult and 411 progeny individuals. Polymorphic locus percentage was 36, 4 in 11 loci, 3 chloroplast SSRs, and 1 nuclear SSR. Allele number of polymorphic loci ranged from 2 to 11 alleles considering all sampling. All 11 primer pairs were also tested for cross-species amplification for five FabaceaeMimosoideae species, ranging from 2 loci transferred to Calliandra tweedii Benth. and all 11 loci transferred to Mimosa taimbensis Burkart. The assessed and validated SSR markers for M. scabrella are suitable and useful for analysis and population genetic studies.

BibTeX:

@article{saiki_development_2017,
author = {Saiki, F. A. and Bernardi, A. P. and Reis, M. S. and Faoro, H. and Souza, E. M. and Pedrosa, F. O. and Mantovani, A. and Guidolin, A. F.},
title = {Development and validation of the first SSR markers for Mimosa scabrella Benth},
journal = {Genetics and Molecular Research},
year = {2017},
volume = {16},
number = {1},
url = {http://www.funpecrp.com.br/gmr/year2017/vol16-1/pdf/gmr-16-01-gmr.16019571.pdf},
doi = {10.4238/gmr16019571}
}

Sanchuki HB, Gravina F, Rodrigues TE, Gerhardt EC, Pedrosa FO, Souza EM, Raittz RT, Valdameri G, de Souza GA and Huergo LF (2017). Dynamics of the Escherichia coli proteome in response to nitrogen starvation and entry into the stationary phase. Biochimica et Biophysica Acta - Proteins and Proteomics, 1865(3):344-352, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Nitrogen is needed for the biosynthesis of biomolecules including proteins and nucleic acids. In the absence of fixed nitrogen prokaryotes such as E. coli immediately ceases growth. Ammonium is the preferred nitrogen source for E. coli supporting the fastest growth rates. Under conditions of ammonium limitation, E. coli can use alternative nitrogen sources to supply ammonium ions and this reprogramming is led by the induction of the NtrC regulon. Here we used label free proteomics to determine the dynamics of E. coli proteins expression in response to ammonium starvation in both the short (30 min) and the longer (60 min) starvation. Protein abundances and post-translational modifications confirmed that activation of the NtrC regulon acts as the first line of defense against nitrogen starvation. The ribosome inactivating protein Rmf was induced shortly after ammonium exhaustion and this was preceded by induction of other ribosome inactivating proteins such as Hpf and RaiA supporting the hypothesis that ribosome shut-down is a key process during nitrogen limitation stress. The proteomic data revealed that growth arrest due to nitrogen starvation correlates with the accumulation of proteins involved in DNA condensation, RNA and protein catabolism and ribosome hibernation. Collectively, these proteome adaptations will result in metabolic inactive cells which are likely to exhibit multidrug tolerance.

BibTeX:

@article{sanchuki_dynamics_2017,
author = {Sanchuki, Heloisa B.S. and Gravina, Fernanda and Rodrigues, Thiago E. and Gerhardt, Edileusa C.M. and Pedrosa, Fábio O. and Souza, Emanuel M. and Raittz, Roberto T. and Valdameri, Glaucio and de Souza, Gustavo A. and Huergo, Luciano F.},
title = {Dynamics of the Escherichia coli proteome in response to nitrogen starvation and entry into the stationary phase},
journal = {Biochimica et Biophysica Acta - Proteins and Proteomics},
year = {2017},
volume = {1865},
number = {3},
pages = {344--352},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1570963916302564},
doi = {10.1016/j.bbapap.2016.12.002}
}

Sant'Anna FH, Ambrosini A, de Souza R, de Carvalho Fernandes G, Bach E, Balsanelli E, Baura V, Brito LF, Wendisch VF, de Oliveira Pedrosa F, de Souza EM and Passaglia LM (2017). Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: Genome-based metrics improve bacterial taxonomic classification. Frontiers in Microbiology, 8(OCT) 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: © 2017 Sant'Anna, Ambrosini, de Souza, de Carvalho Fernandes, Bach, Balsanelli, Baura, Brito, Wendisch, de Oliveira Pedrosa, de Souza and Passaglia. Species from the genus Paenibacillus are widely studied due to their biotechnological relevance. Dozens of novel species descriptions of this genus were published in the last couple of years, but few utilized genomic data as classification criteria. Here, we demonstrate the importance of using genome-based metrics and phylogenetic analyses to identify and classify Paenibacillus strains. For this purpose, Paenibacillus riograndensis SBR5 T , Paenibacillus sonchi X19-5 T , and their close relatives were compared through phenotypic, genotypic, and genomic approaches. With respect to P. sonchi X19-5 T , P. riograndensis SBR5 T , Paenibacillus sp. CAR114, and Paenibacillus sp. CAS34 presented ANI (average nucleotide identity) values ranging from 95.61 to 96.32 gANI (whole-genome average nucleotide identity) values ranging from 96.78 to 97.31 and dDDH (digital DNA-DNA hybridization) values ranging from 68.2 to 73.2%. Phylogenetic analyses of 16S rRNA, gyrB, recA, recN, and rpoB genes and concatenated proteins supported the monophyletic origin of these Paenibacillus strains. Therefore, we propose to assign Paenibacillus sp. CAR114 and Paenibacillus sp. CAS34 to P. sonchi species, and reclassify P. riograndensis SBR5 T as a later heterotypic synonym of P. sonchi (type strain X19-5 T ), with the creation of three novel genomovars, P. sonchi genomovar Sonchi (type strain X19-5 T ), P. sonchi genomovar Riograndensis (type strain SBR5 T ), P. sonchi genomovar Oryzarum (type strain CAS34 T = DSM 102041T; = BR10511T).

BibTeX:

@article{santanna_reclassification_2017,
author = {Sant'Anna, Fernando H. and Ambrosini, Adriana and de Souza, Rocheli and de Carvalho Fernandes, Gabriela and Bach, Evelise and Balsanelli, Eduardo and Baura, Valter and Brito, Luciana F. and Wendisch, Volker F. and de Oliveira Pedrosa, Fábio and de Souza, Emanuel M. and Passaglia, Luciane M.P.},
title = {Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: Genome-based metrics improve bacterial taxonomic classification},
journal = {Frontiers in Microbiology},
year = {2017},
volume = {8},
number = {OCT},
url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.01849/full},
doi = {10.3389/fmicb.2017.01849}
}

Santos ARS, Etto RM, Furmam RW, de Freitas DL, Santos KFdN, de Souza EM, Pedrosa FdO, Ayub RA, Steffens MBR and Galvão CW (2017). Labeled Azospirillum brasilense wild type and excretion-ammonium strains in association with barley roots. Plant Physiology and Biochemistry, 118:422-426, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Soil bacteria colonization in plants is a complex process, which involves interaction between many bacterial characters and plant responses. In this work, we labeled Azospirillum brasilense FP2 (wild type) and HM053 (excretion-ammonium) strains by insertion of the reporter gene gusA-kanamycin into the dinitrogenase reductase coding gene, nifH, and evaluated bacteria colonization in barley (Hordeum vulgare). In addition, we determined inoculation effect based on growth promotion parameters. We report an uncommon endophytic behavior of A. brasilense Sp7 derivative inside the root hair cells of barley and highlight the promising use of A. brasilense HM053 as plant growth-promoting bacterium.

BibTeX:

@article{santos_labeled_2017,
author = {Santos, Adrian Richard Schenberger and Etto, Rafael Mazer and Furmam, Rafaela Wiegand and de Freitas, Denis Leandro and Santos, Karina Freire d.Eça Nogueira and de Souza, Emanuel Maltempi and Pedrosa, Fábio de Oliveira and Ayub, Ricardo Antônio and Steffens, Maria Berenice Reynaud and Galvão, Carolina Weigert},
title = {Labeled Azospirillum brasilense wild type and excretion-ammonium strains in association with barley roots},
journal = {Plant Physiology and Biochemistry},
year = {2017},
volume = {118},
pages = {422--426},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0981942817302255},
doi = {10.1016/j.plaphy.2017.07.003}
}

Santos KF, Moure VR, Hauer V, Santos AR, Donatti L, Galvão CW, Pedrosa FO, Souza EM, Wassem R and Steffens MB (2017). Wheat colonization by an Azospirillum brasilense ammonium-excreting strain reveals upregulation of nitrogenase and superior plant growth promotion. Plant and Soil, 415(1-2):245-255, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: © 2016, Springer International Publishing Switzerland. Aims: In this work, an ammonium-excreting strain (HM053) of A. brasilense was further characterized genetically and biochemically, and its abilities to colonize and promote wheat growth were determined. Methods: Immunoblot, reverse transcription-qPCR, and DNA sequencing were used for HM053 characterization. To analyze wheat-A. brasilense interaction nifH::gusA fusions in the wild-type FP2 (FP2-7) and HM053 (HM053-36) backgrounds were employed. Results: HM053 glutamine synthetase (GS) was not adenylylated in response to an ammonium shock or under any condition tested. Sequencing of the glnA gene revealed a substitution of a proline residue by a leucine at position 347 of the GS. Under axenic growth condition, HM053 was capable of colonizing the surface of wheat roots and increased by 30 and 49% the shoot and root dry weight, respectively, when compared with uninoculated plants, and by 30 and 31% when compared with the parental strain FP2. Although HM053-36 and FP2-7 showed GUS activity located mainly at lateral root emergence points, HM053-36 consistently showed stronger signals and expressed the nifH gene at a level 278 fold higher than strain FP2 in planta, according to qPCR data. Conclusions: HM053, a spontaneous mutant in GS, increased wheat root and shoot dry weight when compared to the wild-type FP2. HM053 ability to excrete ammonium and fix nitrogen constitutively, even in the presence of high NH 4 + concentration, could explain why this mutant has a higher potential to promote plant growth than FP2 and suggests HM053 as a potential nitrogen biofertilizer. However, HM053 should be tested under field conditions to evaluate its abilities to compete with indigenous microflora.

BibTeX:

@article{santos_wheat_2017,
author = {Santos, K. F.D.N. and Moure, V. R. and Hauer, V. and Santos, A. R.S. and Donatti, L. and Galvão, C. W. and Pedrosa, F. O. and Souza, E. M. and Wassem, R. and Steffens, M. B.R.},
title = {Wheat colonization by an Azospirillum brasilense ammonium-excreting strain reveals upregulation of nitrogenase and superior plant growth promotion},
journal = {Plant and Soil},
year = {2017},
volume = {415},
number = {1-2},
pages = {245--255},
url = {http://link.springer.com/10.1007/s11104-016-3140-6},
doi = {10.1007/s11104-016-3140-6}
}

Teixeira MM, Moreno LF, Stielow BJ, Muszewska A, Hainaut M, Gonzaga L, Abouelleil A, Patané JS, Priest M, Souza R, Young S, Ferreira KS, Zeng Q, da Cunha MM, Gladki A, Barker B, Vicente VA, de Souza EM, Almeida S, Henrissat B, Vasconcelos AT, Deng S, Voglmayr H, Moussa TA, Gorbushina A, Felipe MS, Cuomo CA and de Hoog GS (2017). Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota). Studies in Mycology, 86:1-28, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12 817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi.

BibTeX:

@article{teixeira_exploring_2017,
author = {Teixeira, M. M. and Moreno, L. F. and Stielow, B. J. and Muszewska, A. and Hainaut, M. and Gonzaga, L. and Abouelleil, A. and Patané, J. S.L. and Priest, M. and Souza, R. and Young, S. and Ferreira, K. S. and Zeng, Q. and da Cunha, M. M.L. and Gladki, A. and Barker, B. and Vicente, V. A. and de Souza, E. M. and Almeida, S. and Henrissat, B. and Vasconcelos, A. T.R. and Deng, S. and Voglmayr, H. and Moussa, T. A.A. and Gorbushina, A. and Felipe, M. S.S. and Cuomo, C. A. and de Hoog, G. Sybren},
title = {Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota)},
journal = {Studies in Mycology},
year = {2017},
volume = {86},
pages = {1--28},
note = {ISBN: 0166-0616 (Print) 0166-0616 (Linking)},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0166061617300167},
doi = {10.1016/j.simyco.2017.01.001}
}

Thimoteo SS, Glogauer A, Faoro H, de Souza EM, Huergo LF, Moerschbacher BM and Pedrosa FO (2017). A broad pH range and processive chitinase from a metagenome library. Brazilian Journal of Medical and Biological Research, 50(1) 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Chitinases are hydrolases that degrade chitin, a polymer of N-acetylglucosamine linked beta(1-4) present in the exoskeleton of crustaceans, insects, nematodes and fungal cell walls. A metagenome fosmid library from a wastewater-contaminated soil was functionally screened for chitinase activity leading to the isolation and identification of a chitinase gene named metachi18A. The metachi18A gene was subcloned and overexpressed in Escherichia coli BL21 and the MetaChi18A chitinase was purified by affinity chromatography as a 6xHis-tagged fusion protein. The MetaChi18A enzyme is a 92-kDa protein with a conserved active site domain of glycosyl hydrolases family 18. It hydrolyses colloidal chitin with an optimum pH of 5 and temperature of 50 degrees C. Moreover, the enzyme retained at least 80% of its activity in the pH range from 4 to 9 and 98% at 600 mM NaCl. Thin layer chromatography analyses identified chitobiose as the main product of MetaChi18A on chitin polymers as substrate. Kinetic analysis showed inhibition of MetaChi18A activity at high concentrations of colloidal chitin and 4-methylumbelliferyl N,N'-diacetylchitobiose and sigmoid kinetics at low concentrations of colloidal chitin, indicating a possible conformational change to lead the chitin chain from the chitin-binding to the catalytic domain. The observed stability and activity of MetaChi18A over a wide range of conditions suggest that this chitinase, now characterized, may be suitable for application in the industrial processing of chitin.

BibTeX:

@article{thimoteo_broad_2017,
author = {Thimoteo, S. S. and Glogauer, A. and Faoro, H. and de Souza, E. M. and Huergo, L. F. and Moerschbacher, B. M. and Pedrosa, F. O.},
title = {A broad pH range and processive chitinase from a metagenome library},
journal = {Brazilian Journal of Medical and Biological Research},
year = {2017},
volume = {50},
number = {1},
note = {ISBN: 1414-431X (Electronic) 0100-879X (Linking)},
url = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2017000100602&lng=en&tlng=en},
doi = {10.1590/1414-431X20165658}
}

Valdameri G, Alberton D, Moure VR, Kokot TB, Kukolj C, Brusamarello-Santos LCC, Monteiro RA, Pedrosa FdO and de Souza EM (2017). Herbaspirillum rubrisubalbicans, a mild pathogen impairs growth of rice by augmenting ethylene levels. Plant Molecular Biology, 94(6):625-640, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: © 2017, Springer Science+Business Media B.V. Key message: Herbaspirillum rubrisubalbicans decreases growth of rice. Inoculation of rice with H. rubrisubalbicansincreased the ACCO mRNA levels and ethylene production. The H. rubrisubalbicans riceinteractions were further characterized by proteomic approach. Abstract: Herbaspirillum rubrisubalbicans is a well-known growth-promoting rhizobacteria that can also act as a mild phyto-pathogen. During colonisation of rice, RT-qPCR analyses showed that H. rubrisubalbicans up-regulates the methionine recycling pathway as well as phyto-siderophore synthesis genes. mRNA levels of ACC oxidase and ethylene levels also increased in rice roots but inoculation with H. rubrisubalbicans impaired growth of the rice plant. A proteomic approach was used to identify proteins specifically modulated by H. rubrisubalbicans in rice and amongst the differentially expressed proteins a V-ATPase and a 14-3-3 protein were down-regulated. Several proteins of H. rubrisubalbicans were identified, including the type VI secretion system effector Hcp1, suggesting that protein secretion play a role colonisation in rice. Finally, the alkyl hydroperoxide reductase, a primary scavenger of endogenous hydrogen peroxide was also identified. Monitoring the levels of reactive oxygen species in the epiphytic bacteria by flow cytometry revealed that H. rubrisubalbicans is subjected to oxidative stress, suggesting that the alkyl hydroperoxide reductase is an important regulator of redox homeostasis in plant-bacteria interactions.

BibTeX:

@article{valdameri_herbaspirillum_2017,
author = {Valdameri, Glaucio and Alberton, Dayane and Moure, Vivian Rotuno and Kokot, Thiago Borba and Kukolj, Caroline and Brusamarello-Santos, Liziane Cristina Campos and Monteiro, Rose Adele and Pedrosa, Fabio de Oliveira and de Souza, Emanuel Maltempi},
title = {Herbaspirillum rubrisubalbicans, a mild pathogen impairs growth of rice by augmenting ethylene levels},
journal = {Plant Molecular Biology},
year = {2017},
volume = {94},
number = {6},
pages = {625--640},
note = {ISBN: 0123456789},
url = {http://link.springer.com/10.1007/s11103-017-0629-1},
doi = {10.1007/s11103-017-0629-1}
}

Vicente VA, Weiss VA, Bombassaro A, Moreno LF, Costa FF, Raittz RT, Leão AC, Gomes RR, Bocca AL, Fornari G, De Castro RJ, Sun J, Faoro H, Tadra-Sfeir MZ, Baura V, Balsanelli E, Almeida SR, Dos Santos SS, de Melo Teixeira M, Soares Felipe MS, Fidelis do Nascimento MM, Pedrosa FO, Steffens MB, Attili-Angelis D, Najafzadeh MJ, Queiroz-Telles F, Souza EM and Hoog SD (2017). Comparative Genomics of Sibling Species of Fonsecaea Associated with Human Chromoblastomycosis. Frontiers in Microbiology, 8(OCT) 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The final positioning of fibres plays a major role in fibre reinforced concrete (FRC) performance, especially in fracture results used to evaluate the structural competence of the composite material. FRC post-cracking behaviour is related with the number of fibres acting in the cracked surface and the forming angle. This study aims to associate polyolefin fibre orientation and distribution with several external regular and standardised conditions that have been shown to affect steel-rigid fibres positively. The main sources of anisotropy have been addressed: fresh state properties of the concrete, pouring methods, compaction procedures, wall-effects and formwork geometries. The mechanical properties and fracture behaviour showed a remarkably reliable performance of the polyolefin fibre reinforced concrete. While such variations had an equal fibre dosage of 6kg/m3, the results showed narrow scatter. The fracture surface analysis allowed assessment of the differences, obtaining the orientation factor and evaluating wall effects and fibre distribution with each procedure and concrete type.

BibTeX:

@article{vicente_comparative_2017,
author = {Vicente, Vania A. and Weiss, Vinícius A. and Bombassaro, Amanda and Moreno, Leandro F. and Costa, Flávia F. and Raittz, Roberto T. and Leão, Aniele C. and Gomes, Renata R. and Bocca, Anamelia L. and Fornari, Gheniffer and De Castro, Raffael J.A. and Sun, Jiufeng and Faoro, Helisson and Tadra-Sfeir, Michelle Z. and Baura, Valter and Balsanelli, Eduardo and Almeida, Sandro R. and Dos Santos, Suelen S. and de Melo Teixeira, Marcus and Soares Felipe, Maria S. and Fidelis do Nascimento, Mariana Machado and Pedrosa, Fabio O. and Steffens, Maria B. and Attili-Angelis, Derlene and Najafzadeh, Mohammad J. and Queiroz-Telles, Flávio and Souza, Emanuel M. and Hoog, Sybren De},
title = {Comparative Genomics of Sibling Species of Fonsecaea Associated with Human Chromoblastomycosis},
journal = {Frontiers in Microbiology},
year = {2017},
volume = {8},
number = {OCT},
note = {ISBN: 00137944},
url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.01924/full},
doi = {10.3389/fmicb.2017.01924}
}

Wassem R, Marin AM, Daddaoua A, Monteiro RA, Chubatsu LS, Ramos JL, Deakin WJ, Broughton WJ, Pedrosa FO and Souza EM (2017). A NodD-like protein activates transcription of genes involved with naringenin degradation in a flavonoid-dependent manner in Herbaspirillum seropedicae. Environmental Microbiology, 19(3):1030-1040, 2017.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Herbaspirillum seropedicae is an associative, endophytic non-nodulating diazotrophic bacterium that colonises several grasses. An ORF encoding a LysR-type transcriptional regulator, very similar to NodD proteins of rhizobia, was identified in its genome. This nodD-like gene, named fdeR, is divergently transcribed from an operon encoding enzymes involved in flavonoid degradation (fde operon). Apigenin, chrysin, luteolin and naringenin strongly induce transcription of the fde operon, but not that of the fdeR, in an FdeR-dependent manner. The intergenic region between fdeR and fdeA contains several generic LysR consensus sequences (T-N11 -A) and we propose a binding site for FdeR, which is conserved in other bacteria. DNase I foot-printing revealed that the interaction with the FdeR binding site is modified by the four flavonoids that stimulate transcription of the fde operon. Moreover, FdeR binds naringenin and chrysin as shown by isothermal titration calorimetry. Interestingly, FdeR also binds in vitro to the nod-box from the nodABC operon of Rhizobium sp. NGR234 and is able to activate its transcription in vivo. These results show that FdeR exhibits two features of rhizobial NodD proteins: nod-box recognition and flavonoid-dependent transcription activation, but its role in H. seropedicae and related organisms seems to have evolved to control flavonoid metabolism.

BibTeX:

@article{wassem_nodd-like_2017,
author = {Wassem, R. and Marin, A. M. and Daddaoua, A. and Monteiro, R. A. and Chubatsu, L. S. and Ramos, J. L. and Deakin, W. J. and Broughton, W. J. and Pedrosa, F. O. and Souza, E. M.},
title = {A NodD-like protein activates transcription of genes involved with naringenin degradation in a flavonoid-dependent manner in Herbaspirillum seropedicae},
journal = {Environmental Microbiology},
year = {2017},
volume = {19},
number = {3},
pages = {1030--1040},
url = {http://doi.wiley.com/10.1111/1462-2920.13604},
doi = {10.1111/1462-2920.13604}
}

Alemar B, Izetti P, Gregório C, Macedo GS, Castro MAA, Osvaldt AB, Matte U and Ashton-Prolla P (2016). miRNA-21 and miRNA-34a Are Potential Minimally Invasive Biomarkers for the Diagnosis of Pancreatic Ductal Adenocarcinoma. Pancreas, 45(1):84-92, 2016.
[Abstract] [DOI] [BibTeX]

Abstract: OBJECTIVES: Pancreatic ductal adenocarcinoma (PDAC) is one of the most deadly cancers, and its diagnosis often requires invasive procedures. Deregulated miRNA expression has been described in patients with PDAC. In this study, we analyzed the expression levels of 6 miRNAs (miR-21, -34a, -155, -196a, -200b, and -376a involved in PDAC tumorigenesis) in serum and salivary samples to assess their potential role as circulating diagnostics biomarkers.
METHODS: Serum and salivary samples were collected from patients with PDAC and healthy controls, and miRNA levels were quantified using qRT-PCR. Twenty-four patients with PDAC and 10 healthy controls were recruited.
RESULTS: A significant difference between PDAC and healthy groups was observed for the expression of miR-21 and miR-34a (P textless 0.001 and P = 0.001) in serum samples. Both miRNAs accurately discriminated between the 2 groups, with an area under the curve for miR-21 and miR-34a of 0.889 (P = 0.001) and 0.865 (P = 0.002), respectively. In general, the expression of miRNAs between salivary samples did not differ.
CONCLUSIONS: Serum miR-21 and miR-34a are potentially useful diagnostic biomarkers of PDAC. In addition, our results suggest that these miRNAs are not differentially expressed in saliva, making them unsuitable for use as noninvasive biomarkers for diagnostic purposes.

BibTeX:

@article{alemar_mirna-21_2016,
author = {Alemar, Bárbara and Izetti, Patrícia and Gregório, Cleandra and Macedo, Gabriel S. and Castro, Mauro Antonio Alves and Osvaldt, Alessandro Bersch and Matte, Ursula and Ashton-Prolla, Patricia},
title = {miRNA-21 and miRNA-34a Are Potential Minimally Invasive Biomarkers for the Diagnosis of Pancreatic Ductal Adenocarcinoma},
journal = {Pancreas},
year = {2016},
volume = {45},
number = {1},
pages = {84--92},
doi = {10.1097/MPA.0000000000000383}
}

Almeida S, Tiwari S, Mariano D, Souza F, Jamal SB, Coimbra N, Raittz RT, Dorella FA, de Carvalho AF, Pereira FL, Soares SdC, Leal CAG, Barh D, Ghosh P, Figueiredo H, Moura-Costa LF, Portela RW, Meyer R, Silva A and Azevedo V (2016). The genome anatomy of Corynebacterium pseudotuberculosis VD57 a highly virulent strain causing Caseous lymphadenitis. Standards in Genomic Sciences, 11(1) 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Corynebacterium pseudotuberculosis strain VD57 (CpVD57), a highly virulent, nonmotile, non-sporulating, and a mesophilic bacterium, was isolated from a goat's granulomatous lesion in the municipality of Juazeiro, Bahia State, Brazil. Here, we describe a set of features of the strain, together with the details of its complete genome sequence and annotation. The genome comprises of a 2.5 Mbp long, single circular genome with 2,101 protein-coding genes, 12 rRNA, 49 tRNA and 47 pseudogenes and a G + C content of 52.85 %. Genetic variation was detected in CpVD57 using C. pseudotuberculosis strain 1002 as reference, wherein small genomic insertions and deletions were identified. The comparative analysis of the genome sequence provides means to better understand the host pathogen interactions of this strain and can also help us to understand the molecular and genetic basis of virulence of this bacterium.

BibTeX:

@article{almeida_genome_2016,
author = {Almeida, Sintia and Tiwari, Sandeep and Mariano, Diego and Souza, Flávia and Jamal, Syed Babar and Coimbra, Nilson and Raittz, Roberto Tadeu and Dorella, Fernanda Alves and de Carvalho, Alex Fiorine and Pereira, Felipe Luiz and Soares, Siomar de Castro and Leal, Carlos Augusto Gomes and Barh, Debmalya and Ghosh, Preetam and Figueiredo, Henrique and Moura-Costa, Lília Ferreira and Portela, Ricardo Wagner and Meyer, Roberto and Silva, Artur and Azevedo, Vasco},
title = {The genome anatomy of Corynebacterium pseudotuberculosis VD57 a highly virulent strain causing Caseous lymphadenitis},
journal = {Standards in Genomic Sciences},
year = {2016},
volume = {11},
number = {1},
url = {http://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0149-7},
doi = {10.1186/s40793-016-0149-7}
}

Alnoch R, Rodrigues de Melo R, Palomo J, Maltempi de Souza E, Krieger N and Mateo C (2016). New Tailor-Made Alkyl-Aldehyde Bifunctional Supports for Lipase Immobilization. Catalysts, 6(12):191, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: © 2016 by the authors; licensee MDPI, Basel, Switzerland.Immobilized and stabilized lipases are important biocatalytic tools. In this paper, different tailor-made bifunctional supports were prepared for the immobilization of a new metagenomic lipase (LipC12). The new supports contained hydrophobic groups (different alkyl groups) to promote interfacial adsorption of the lipase and aldehyde groups to react covalently with the amino groups of side chains of the adsorbed lipase. The best catalyst was 3.5-fold more active and 5000-fold more stable than the soluble enzyme. It was successfully used in the regioselective deacetylation of peracetylated D-glucal. The PEGylated immobilized lipase showed high regioselectivity, producing high yields of the C-3 monodeacetylated product at pH 5.0 and 4 °C.

BibTeX:

@article{alnoch_new_2016,
author = {Alnoch, Robson and Rodrigues de Melo, Ricardo and Palomo, Jose and Maltempi de Souza, Emanuel and Krieger, Nadia and Mateo, Cesar},
title = {New Tailor-Made Alkyl-Aldehyde Bifunctional Supports for Lipase Immobilization},
journal = {Catalysts},
year = {2016},
volume = {6},
number = {12},
pages = {191},
url = {http://www.mdpi.com/2073-4344/6/12/191},
doi = {10.3390/catal6120191}
}

Alves LP, Teixeira CS, Tirapelle EF, Donatti L, Tadra-Sfeir MZ, Steffens MB, de Souza EM, de Oliveira Pedrosa F, Chubatsu LS and Müller-Santos M (2016). Backup expression of the PhaP2 phasin compensates for phaP1 deletion in Herbaspirillum seropedicae, maintaining fitness and PHB accumulation. Frontiers in Microbiology, 7(MAY) 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Phasins are important proteins controlling poly-3-hydroxybutyrate (PHB) granules formation, their number into the cell and stability. The genome sequencing of the endophytic and diazotrophic bacterium Herbaspirillum seropedicae SmR1 revealed two homologous phasin genes. To verify the role of the phasins on PHB accumulation in the parental strain H. seropedicae SmR1, isogenic strains defective in the expression of phaP1, phaP2 or both genes were obtained by gene deletion and characterized in this work. Despite of the high sequence similarity between PhaP1 and PhaP2, PhaP1 is the major phasin in H. seropedicae, since its deletion reduced PHB accumulation by ≈50% in comparison to the parental and ΔphaP2. Upon deletion of phaP1, the expression of phaP2 was sixfold enhanced in the ΔphaP1 strain. The responsive backup expression of phaP2 partially rescued the ΔphaP1 mutant, maintaining about 50% of the parental PHB level. The double mutant ΔphaP1.2 did not accumulate PHB in any growth stage and showed a severe reduction of growth when glucose was the carbon source, a clear demonstration of negative impact in the fitness. The co-occurrence of phaP1 and phaP2 homologous in bacteria relatives of H. seropedicae, including other endophytes, indicates that the mechanism of phasin compensation by phaP2 expression may be operating in other organisms, showing that PHB metabolism is a key factor to adaptation and efficiency of endophytic bacteria.

BibTeX:

@article{alves_backup_2016,
author = {Alves, Luis P.S. and Teixeira, Cícero S. and Tirapelle, Evandro F. and Donatti, Lucélia and Tadra-Sfeir, Michelle Z. and Steffens, Maria B.R. and de Souza, Emanuel M. and de Oliveira Pedrosa, Fabio and Chubatsu, Leda S. and Müller-Santos, Marcelo},
title = {Backup expression of the PhaP2 phasin compensates for phaP1 deletion in Herbaspirillum seropedicae, maintaining fitness and PHB accumulation},
journal = {Frontiers in Microbiology},
year = {2016},
volume = {7},
number = {MAY},
url = {http://journal.frontiersin.org/Article/10.3389/fmicb.2016.00739/abstract},
doi = {10.3389/fmicb.2016.00739}
}

Anghebem-Oliveira MI, Gobor L, Welter M, da Costa CD, de Souza EM, Alberton D, Picheth G and de Moraes Rego FG (2016). Non-fasting plasma glucose concentration in blood donors. Clinical Chemistry and Laboratory Medicine, 54(4):e135-137, 2016.
[DOI] [BibTeX]

Abstract:

BibTeX:

@article{anghebem-oliveira_non-fasting_2016,
author = {Anghebem-Oliveira, Mauren Isfer and Gobor, Luiza and Welter, Marciane and da Costa, Claudia Dib and de Souza, Emanuel Maltempi and Alberton, Dayane and Picheth, Geraldo and de Moraes Rego, Fabiane Gomes},
title = {Non-fasting plasma glucose concentration in blood donors},
journal = {Clinical Chemistry and Laboratory Medicine},
year = {2016},
volume = {54},
number = {4},
pages = {e135--137},
doi = {10.1515/cclm-2015-0483}
}

Balsanelli E, Tadra-Sfeir MZ, Faoro H, Pankievicz VC, de Baura VA, Pedrosa FO, de Souza EM, Dixon R and Monteiro RA (2016). Molecular adaptations of Herbaspirillum seropedicae during colonization of the maize rhizosphere. Environmental Microbiology, 18(8):2343-2356, 2016.
[Abstract] [DOI] [BibTeX]

Abstract: Molecular mechanisms of plant recognition and colonization by diazotrophic bacteria are barely understood. Herbaspirillum seropedicae is a Betaproteobacterium capable of colonizing epiphytically and endophytically commercial grasses, to promote plant growth. In this study, we utilized RNA-seq to compare the transcriptional profiles of planktonic and maize root-attached H. seropedicae SmR1 recovered 1 and 3 days after inoculation. The results indicated that nitrogen metabolism was strongly activated in the rhizosphere and polyhydroxybutyrate storage was mobilized in order to assist the survival of H. seropedicae during the early stages of colonization. Epiphytic cells showed altered transcription levels of several genes associated with polysaccharide biosynthesis, peptidoglycan turnover and outer membrane protein biosynthesis, suggesting reorganization of cell wall envelope components. Specific methyl-accepting chemotaxis proteins and two-component systems were differentially expressed between populations over time, suggesting deployment of an extensive bacterial sensory system for adaptation to the plant environment. An insertion mutation inactivating a methyl-accepting chemosensor induced in planktonic bacteria, decreased chemotaxis towards the plant and attachment to roots. In summary, analysis of mutant strains combined with transcript profiling revealed several molecular adaptations that enable H. seropedicae to sense the plant environment, attach to the root surface and survive during the early stages of maize colonization.

BibTeX:

@article{balsanelli_molecular_2016,
author = {Balsanelli, Eduardo and Tadra-Sfeir, Michelle Z. and Faoro, Helisson and Pankievicz, Vânia Cs and de Baura, Valter A. and Pedrosa, Fábio O. and de Souza, Emanuel M. and Dixon, Ray and Monteiro, Rose A.},
title = {Molecular adaptations of Herbaspirillum seropedicae during colonization of the maize rhizosphere},
journal = {Environmental Microbiology},
year = {2016},
volume = {18},
number = {8},
pages = {2343--2356},
doi = {10.1111/1462-2920.12887}
}

Bonato P, Alves LR, Osaki JH, Rigo LU, Pedrosa FO, Souza EM, Zhang N, Schumacher J, Buck M, Wassem R and Chubatsu LS (2016). The NtrY–NtrX two-component system is involved in controlling nitrate assimilation in Herbaspirillum seropedicae strain SmR1. FEBS Journal, 283(21):3919-3930, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Herbaspirillum seropedicae is a diazotrophic β-Proteobacterium found endophytically associated with gramineae (Poaceae or graminaceous plants) such as rice, sorghum and sugar cane. In this work we show that nitrate-dependent growth in this organism is regulated by the master nitrogen regulatory two-component system NtrB/NtrC, and by NtrY/NtrX which functions to specifically regulate nitrate metabolism. NtrY is a histidine kinase sensor protein predicted to be associated with the membrane and NtrX is the response regulator partner. The ntrYntrX genes are widely distributed in Proteobacteria. In α-Proteobacteria they are frequently located downstream from ntrBC, whereas in β-Proteobacteria these genes are located downstream from genes encoding a RNA methyltransferase and a proline-rich protein with unknown function. The α-Proteobacteria NtrX protein has an AAA+ domain, absent in those from β-Proteobacteria. An ntrY mutant of H. seropedicae showed wild type fixing nitrogen phenotype, but the nitrate dependent growth was abolished. Gene fusion assays indicated that NtrY is involved in the expression of genes coding for the assimilatory nitrate reductase as well as the nitrate-responsive two-component system NarX/NarL (narK and narX promoters, respectively). The purified NtrX protein was capable of binding the narK and narX promoters, and the binding site at the narX promoter for the NtrX protein was determined by DNA footprinting. In silico analyses revealed similar sequences in other promoter regions of H. seropedicae that are related to nitrate assimilation, supporting the role of the NtrY/NtrX system in regulating nitrate metabolism in H. seropedicae. This article is protected by copyright. All rights reserved.

BibTeX:

@article{bonato_ntryntrx_2016,
author = {Bonato, Paloma and Alves, Lysangela R. and Osaki, Juliana H. and Rigo, Liu U. and Pedrosa, Fabio O. and Souza, Emanuel M. and Zhang, Nan and Schumacher, Jörg and Buck, Martin and Wassem, Roseli and Chubatsu, Leda S.},
title = {The NtrY–NtrX two-component system is involved in controlling nitrate assimilation in Herbaspirillum seropedicae strain SmR1},
journal = {FEBS Journal},
year = {2016},
volume = {283},
number = {21},
pages = {3919--3930},
url = {http://doi.wiley.com/10.1111/febs.13897},
doi = {10.1111/febs.13897}
}

Bonato P, Batista MB, Camilios-Neto D, Pankievicz VC, Tadra-Sfeir MZ, Monteiro RA, Pedrosa FO, Souza EM, Chubatsu LS, Wassem R and Rigo LU (2016). RNA-seq analyses reveal insights into the function of respiratory nitrate reductase of the diazotroph Herbaspirillum seropedicae. Environmental microbiology, 18(8):2677-2688, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Herbaspirillum seropedicae is a nitrogen-fixing β-proteobacterium that associates with roots of gramineous plants. In silico analyses revealed that H. seropedicae genome has genes encoding a putative respiratory (NAR) and an assimilatory nitrate reductase (NAS). To date, little is known about nitrate metabolism in H. seropedicae, and, as this bacterium cannot respire nitrate, the function of NAR remains unknown. This study aimed to investigate the function of NAR in H. seropedicae and how it metabolizes nitrate in a low aerated-condition. RNA-seq transcriptional profiling in the presence of nitrate allowed us to pinpoint genes important for nitrate metabolism in H. seropedicae, including nitrate transporters and regulatory proteins. Additionally, both RNA-seq data and physiological characterization of a mutant in the catalytic subunit of NAR (narG mutant) showed that NAR is not required for nitrate assimilation but is required for: (i) production of high levels of nitrite, (ii) production of NO and (iii) dissipation of redox power, which in turn lead to an increase in carbon consumption. In addition, wheat plants showed an increase in shoot dry weight only when inoculated with H. seropedicae wild type, but not with the narG mutant, suggesting that NAR is important to H. seropedicae-wheat interaction.

BibTeX:

@article{bonato_rna-seq_2016,
author = {Bonato, Paloma and Batista, Marcelo B. and Camilios-Neto, Doumit and Pankievicz, Vânia C.S. and Tadra-Sfeir, Michelle Z. and Monteiro, Rose Adele and Pedrosa, Fabio O. and Souza, Emanuel M. and Chubatsu, Leda S. and Wassem, Roseli and Rigo, Liu Un},
title = {RNA-seq analyses reveal insights into the function of respiratory nitrate reductase of the diazotroph Herbaspirillum seropedicae},
journal = {Environmental microbiology},
year = {2016},
volume = {18},
number = {8},
pages = {2677--2688},
url = {http://doi.wiley.com/10.1111/1462-2920.13422},
doi = {10.1111/1462-2920.13422}
}

Campanerut-Sá PA, Ghiraldi-Lopes LD, Meneguello JE, Fiorini A, Evaristo GP, Siqueira VL, Scodro RB, Patussi EV, Donatti L, Souza EM and Cardoso RF (2016). Proteomic and morphological changes produced by subinhibitory concentration of isoniazid in Mycobacterium tuberculosis. Future Microbiology, 11(9):1123-1132, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: AIM To study the proteomic and morphological changes in Mycobacterium tuberculosis H37Rv exposed to subinhibitory concentration of isoniazid (INH). MATERIALS & METHODS The bacillus was exposed to ½ MIC of INH at 12, 24 and 48 h. The samples' cells were submitted to scanning electron microscopy. The proteins were separated by 2D gel electrophoresis and identified by MS. RESULTS INH exposure was able to alter the format, the multiplication and causing a cell swelling in the bacillus. The major altered proteins were related to the virulence, detoxification, adaptation, intermediary metabolism and lipid metabolism. CONCLUSION The protein and morphological changes in M. tuberculosis induced by ½ MIC INH were related to defense mechanism of the bacillus or the action of INH therein.

BibTeX:

@article{campanerut-sa_proteomic_2016,
author = {Campanerut-Sá, Paula A.Z. and Ghiraldi-Lopes, Luciana D. and Meneguello, Jean E. and Fiorini, Adriana and Evaristo, Geisa P.C. and Siqueira, Vera L.D. and Scodro, Regiane B.L. and Patussi, Eliana V. and Donatti, Lucélia and Souza, Emanuel M. and Cardoso, Rosilene F.},
title = {Proteomic and morphological changes produced by subinhibitory concentration of isoniazid in Mycobacterium tuberculosis},
journal = {Future Microbiology},
year = {2016},
volume = {11},
number = {9},
pages = {1123--1132},
url = {http://www.futuremedicine.com/doi/10.2217/fmb-2016-5000},
doi = {10.2217/fmb-2016-5000}
}

Campbell TM, Castro MA, Ponder BA and Meyer KB (2016). Identification of post-transcriptional modulators of breast cancer transcription factor activity using MINDy. PLoS ONE, 11(12):e0168770, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: We have recently identified transcription factors (TFs) that are key drivers of breast cancer risk. To better understand the pathways or sub-networks in which these TFs mediate their function we sought to identify upstream modulators of their activity. We applied the MINDy (Modulator Inference by Network Dynamics) algorithm to four TFs (ESR1, FOXA1, GATA3 and SPDEF) that are key drivers of estrogen receptor-positive (ER+) breast cancer risk, as well as cancer progression. Our computational analysis identified over 500 potential modulators. We assayed 189 of these and identified 55 genes with functional characteristics that were consistent with a role as TF modulators. In the future, the identified modulators may be tested as potential therapeutic targets, able to alter the activity of TFs that are critical in the development of breast cancer.

BibTeX:

@article{campbell_identification_2016,
author = {Campbell, Thomas M. and Castro, Mauro A.A. and Ponder, Bruce A.J. and Meyer, Kerstin B.},
editor = {Ahmad, Aamir},
title = {Identification of post-transcriptional modulators of breast cancer transcription factor activity using MINDy},
journal = {PLoS ONE},
year = {2016},
volume = {11},
number = {12},
pages = {e0168770},
note = {ISBN: 1111111111},
url = {http://dx.plos.org/10.1371/journal.pone.0168770},
doi = {10.1371/journal.pone.0168770}
}

Castro MAA, de Santiago I, Campbell TM, Vaughn C, Hickey TE, Ross E, Tilley WD, Markowetz F, Ponder BAJ and Meyer KB (2016). Regulators of genetic risk of breast cancer identified by integrative network analysis. Nature Genetics, 48(1):12-21, 2016.
[Abstract] [DOI] [BibTeX]

Abstract: Genetic risk for breast cancer is conferred by a combination of multiple variants of small effect. To better understand how risk loci might combine, we examined whether risk-associated genes share regulatory mechanisms. We created a breast cancer gene regulatory network comprising transcription factors and groups of putative target genes (regulons) and asked whether specific regulons are enriched for genes associated with risk loci via expression quantitative trait loci (eQTLs). We identified 36 overlapping regulons that were enriched for risk loci and formed a distinct cluster within the network, suggesting shared biology. The risk transcription factors driving these regulons are frequently mutated in cancer and lie in two opposing subgroups, which relate to estrogen receptor (ER)(+) luminal A or luminal B and ER(-) basal-like cancers and to different luminal epithelial cell populations in the adult mammary gland. Our network approach provides a foundation for determining the regulatory circuits governing breast cancer, to identify targets for intervention, and is transferable to other disease settings.

BibTeX:

@article{castro_regulators_2016,
author = {Castro, Mauro A. A. and de Santiago, Ines and Campbell, Thomas M. and Vaughn, Courtney and Hickey, Theresa E. and Ross, Edith and Tilley, Wayne D. and Markowetz, Florian and Ponder, Bruce A. J. and Meyer, Kerstin B.},
title = {Regulators of genetic risk of breast cancer identified by integrative network analysis},
journal = {Nature Genetics},
year = {2016},
volume = {48},
number = {1},
pages = {12--21},
doi = {10.1038/ng.3458}
}

Costa FF, de Hoog S, Raittz RT, Weiss VA, Leão ACR, Bombassaro A, Sun J, Moreno LF, Souza EM, Pedrosa FO, Steffens MBR, Baura V, Tadra-Sfeir MZ, Balsanelli E, Najafzadeh MJ, Gomes RR, Felipe MS, Teixeira M, Santos GD, Xi L, Alves de Castro MA and Vicente VA (2016). Draft Genome Sequence of \textlessi\textgreaterFonsecaea nubica\textless/i\textgreater Strain CBS 269.64, Causative Agent of Human Chromoblastomycosis. Genome Announcements, 4(4):e00735-16, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: \textlessp\textgreater On the basis of multilocus phylogenetic data, \textlessitalic\textgreaterFonsecaea nubica\textless/italic\textgreater was described in 2010 as a molecular sibling of \textlessitalic\textgreaterF. monophora\textless/italic\textgreater , an established agent of the human skin disease chomoblastomycosis in tropical zones. Genome analysis of these pathogens is mandatory to identify genes involved in the interaction with host and virulence. \textless/p\textgreater

BibTeX:

@article{costa_draft_2016,
author = {Costa, Flávia F. and de Hoog, Sybren and Raittz, Roberto T. and Weiss, Vinicius A. and Leão, Aniele C. R. and Bombassaro, Amanda and Sun, Jiufeng and Moreno, Leandro F. and Souza, Emanuel M. and Pedrosa, Fabio O. and Steffens, Maria Berenice R. and Baura, Valter and Tadra-Sfeir, Michele Z. and Balsanelli, Eduardo and Najafzadeh, M. Javad and Gomes, Renata R. and Felipe, Maria S. and Teixeira, Marcus and Santos, Germana D. and Xi, Liyan and Alves de Castro, Mauro Antônio and Vicente, Vânia A.},
title = {Draft Genome Sequence of \textlessi\textgreaterFonsecaea nubica\textless/i\textgreater Strain CBS 269.64, Causative Agent of Human Chromoblastomycosis},
journal = {Genome Announcements},
year = {2016},
volume = {4},
number = {4},
pages = {e00735--16},
note = {ISBN: 1369378041},
url = {http://genomea.asm.org/lookup/doi/10.1128/genomeA.00735-16},
doi = {10.1128/genomeA.00735-16}
}

do Amaral FP, Pankievicz VC, Arisi ACM, de Souza EM, Pedrosa F and Stacey G (2016). Differential growth responses of Brachypodium distachyon genotypes to inoculation with plant growth promoting rhizobacteria. Plant Molecular Biology, 90(6):689-697, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Plant growth promoting rhizobacteria (PGPR) can associate and enhance the growth of important crop grasses. However, in most cases, the molecular mecha- nisms responsible for growth promotion are not known. Such research could benefit by the adoption of a grass model species that showed a positive response to bacterial inoculation and was amenable to genetic and molecular research methods. In this work we inoculated different genotypes of the model grass Brachypodium distachyon with two, well-characterized PGPR bacteria, Azospirillum brasilense and Herbaspirillum seropedicae, and evaluated the growth response. Plants were grown in soil under no nitrogen or with low nitrogen (i.e., 0.5 mM KNO3). A variety of growth parameters (e.g., shoot height, root length, number of lateral roots, fresh and dry weight) were measured 35 days after inoculation. The data indicate that plant genotype plays a very important role in determining the plant response to PGPR inoculation. A positive growth response was observed with only four genotypes grown under no nitrogen and three genotypes tested under low nitrogen. However, in contrast, relatively good root colonization was seen with most genotypes, as measured by drop plate counting and direct, microscopic examination of roots. In particular, the endophytic bacteria H. serope- dicae showed strong epiphytic and endophytic colonization of roots.

BibTeX:

@article{do_amaral_differential_2016,
author = {do Amaral, Fernanda P. and Pankievicz, Vânia C.S. and Arisi, Ana Carolina M. and de Souza, Emanuel M. and Pedrosa, Fabio and Stacey, Gary},
title = {Differential growth responses of Brachypodium distachyon genotypes to inoculation with plant growth promoting rhizobacteria},
journal = {Plant Molecular Biology},
year = {2016},
volume = {90},
number = {6},
pages = {689--697},
note = {ISBN: 1573-5028 (Electronic) 0167-4412 (Linking)},
url = {http://link.springer.com/10.1007/s11103-016-0449-8},
doi = {10.1007/s11103-016-0449-8}
}

do Nascimento Vieira L, Rogalski M, Faoro H, Pacheco de Freitas Fraga H, Goulart dos Anjos K, Assine Picchi GF, Onofre Nodari R, de Oliveira Pedrosa F, Maltempi de Souza E and Pedro Guerra M (2016). The plastome sequence of the endemic Amazonian conifer, Retrophyllum piresii (Silba) C.N.Page, reveals different recombination events and plastome isoforms. Tree Genetics and Genomes, 12(1):1-11, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: © 2016, Springer-Verlag Berlin Heidelberg. Retrophyllum piresii (Podocarpaceae) is an endemic conifer species from the Brazilian Amazonian Region, and very few data related to ecological and genetic characteristics of this species are available. Plastome sequencing is an efficient tool to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as to probe the structural and functional evolution of plants. Usually, the plastome of photosynthetic land plants is quadripartite, with two copies of the inverted repeats (IRs) separating the small and large single-copy regions. However, in gymnosperms, IR can vary from large in size to completely absent, being constituted principally by transfer RNA (tRNA) genes, or a part of sequence of other genes. Here, we sequenced and characterized the complete plastome of R. piresii. This plastome was determined to be 133,291 bp (∼480-fold coverage), presenting a total of 120 identified genes, of which 118 were single copy and two genes, trnN-GUU and trnD-GUC, were found to be duplicated and occurring as inverted and directed repeat (DR) sequences, respectively. These repeated regions presented recombinationally active sites, resulting in an IR-mediated inversion and a DR-mediated deletion. However, the isoform resulted from DR-mediated deletion may result in unviable plastome, with deletion of photosynthetic and expression machinery-related genes.

BibTeX:

@article{do_nascimento_vieira_plastome_2016,
author = {do Nascimento Vieira, Leila and Rogalski, Marcelo and Faoro, Helisson and Pacheco de Freitas Fraga, Hugo and Goulart dos Anjos, Karina and Assine Picchi, Gisele Fernanda and Onofre Nodari, Rubens and de Oliveira Pedrosa, Fábio and Maltempi de Souza, Emanuel and Pedro Guerra, Miguel},
title = {The plastome sequence of the endemic Amazonian conifer, Retrophyllum piresii (Silba) C.N.Page, reveals different recombination events and plastome isoforms},
journal = {Tree Genetics and Genomes},
year = {2016},
volume = {12},
number = {1},
pages = {1--11},
url = {http://link.springer.com/10.1007/s11295-016-0968-0},
doi = {10.1007/s11295-016-0968-0}
}

Frigeri HR, Auwerter NC, Koczicki L, Martins LT, de Souza EM, Alberton D, de Moraes Rego FG and Picheth G (2016). Polymorphisms rs144723656, rs2268574, and rs2268575 of the glucokinase gene are not associated with obese women with type 2 diabetes mellitus. Clinical Biochemistry, 49(1):194-195, 2016.
[DOI] [URL] [BibTeX]

Abstract:

BibTeX:

@article{frigeri_polymorphisms_2016,
author = {Frigeri, Henrique Ravanhol and Auwerter, Nathalia Cavalheiro and Koczicki, Letícia and Martins, Laysa Toschi and de Souza, Emanuel Maltempi and Alberton, Dayane and de Moraes Rego, Fabiane Gomes and Picheth, Geraldo},
title = {Polymorphisms rs144723656, rs2268574, and rs2268575 of the glucokinase gene are not associated with obese women with type 2 diabetes mellitus},
journal = {Clinical Biochemistry},
year = {2016},
volume = {49},
number = {1},
pages = {194--195},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0009912015004658},
doi = {10.1016/j.clinbiochem.2015.09.016}
}

Guizelini D, Raittz RT, Cruz LM, Souza EM, Steffens MB and Pedrosa FO (2016). GFinisher: A new strategy to refine and finish bacterial genome assemblies. Scientific Reports, 6(1) 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Despite the development in DNA sequencing technology, improving the number and the length of reads, the process of reconstruction of complete genome sequences, the so called genome assembly, is still complex. Only 13% of the prokaryotic genome sequencing projects have been completed. Draft genome sequences deposited in public databases are fragmented in contigs and may lack the full gene complement. The aim of the present work is to identify assembly errors and improve the assembly process of bacterial genomes. The biological patterns observed in genomic sequences and the application of a priori information can allow the identification of misassembled regions, and the reorganization and improvement of the overall de novo genome assembly. GFinisher starts generating a Fuzzy GC skew graphs for each contig in an assembly and follows breaking down the contigs in critical points in order to reassemble and close them using jFGap. This has been successfully applied to dataset from 96 genome assemblies, decreasing the number of contigs by up to 86%. GFinisher can easily optimize assemblies of prokaryotic draft genomes and can be used to improve the assembly programs based on nucleotide sequence patterns in the genome. The software and source code are available at http://gfinisher.sourceforge.net/.

BibTeX:

@article{guizelini_gfinisher_2016,
author = {Guizelini, Dieval and Raittz, Roberto T. and Cruz, Leonardo M. and Souza, Emanuel M. and Steffens, Maria B.R. and Pedrosa, Fabio O.},
title = {GFinisher: A new strategy to refine and finish bacterial genome assemblies},
journal = {Scientific Reports},
year = {2016},
volume = {6},
number = {1},
url = {http://www.nature.com/articles/srep34963},
doi = {10.1038/srep34963}
}

Hauf W, Schmid K, Gerhardt EC, Huergo LF and Forchhammer K (2016). Interaction of the nitrogen regulatory protein GlnB (PII) with biotin carboxyl carrier protein (BCCP) controls acetyl-Coa levels in the cyanobacterium synechocystis sp. PCC 6803. Frontiers in Microbiology, 7(OCT) 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The family of PII signal transduction proteins (members GlnB, GlnK, NifI) plays key roles in various cellular processes related to nitrogen metabolism at different functional levels. Recent studies implied that PII proteins may also be involved in the regulation of fatty acid metabolism, since GlnB proteins from Proteobacteria and from Arabidopsis thaliana were shown to interact with biotin carboxyl carrier protein (BCCP) of acetyl-CoA carboxylase (ACC). In case of E. coli ACCase, this interaction reduces the kcat of acetyl-CoA carboxylation, which should have a marked impact on the acetyl-CoA metabolism. In this study we show that the PII protein of a unicellular cyanobacterium inhibits the biosynthetic activity of Escherichia coli ACC and also interacts with cyanobacterial BCCP in an ATP and 2-oxoglutarate dependent manner. In a PII mutant strain of Synechocystis strain PCC 6803, the lacking control leads to reduced acetyl-CoA levels, slightly increased levels of fatty acids and formation of lipid bodies as well as an altered fatty acid composition.

BibTeX:

@article{hauf_interaction_2016,
author = {Hauf, Waldemar and Schmid, Katharina and Gerhardt, Edileusa C.M. and Huergo, Luciano F. and Forchhammer, Karl},
title = {Interaction of the nitrogen regulatory protein GlnB (PII) with biotin carboxyl carrier protein (BCCP) controls acetyl-Coa levels in the cyanobacterium synechocystis sp. PCC 6803},
journal = {Frontiers in Microbiology},
year = {2016},
volume = {7},
number = {OCT},
note = {ISBN: 1664-302X (Linking)},
url = {http://journal.frontiersin.org/article/10.3389/fmicb.2016.01700/full},
doi = {10.3389/fmicb.2016.01700}
}

Laskoski K, Santos AR, Bonatto AC, Pedrosa FO, Souza EM and Huergo LF (2016). In vitro characterization of the NAD+synthetase NadE1 from Herbaspirillum seropedicae. Archives of Microbiology, 198(4):307-313, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: © 2016, Springer-Verlag Berlin Heidelberg.Nicotinamide adenine dinucleotide synthetase enzyme (NadE) catalyzes the amination of nicotinic acid adenine dinucleotide (NaAD) to form NAD+. This reaction represents the last step in the majority of the NAD+ biosynthetic routes described to date. NadE enzymes typically use either glutamine or ammonium as amine nitrogen donor, and the reaction is energetically driven by ATP hydrolysis. Given the key role of NAD+ in bacterial metabolism, NadE has attracted considerable interest as a potential target for the development of novel antibiotics. The plant-associative nitrogen-fixing bacteria Herbaspirillum seropedicae encodes two putative NadE, namely nadE1 and nadE2. The nadE1 gene is linked to glnB encoding the signal transduction protein GlnB. Here we report the purification and in vitro characterization of H. seropedicae NadE1. Gel filtration chromatography analysis suggests that NadE1 is an octamer. The NadE1 activity was assayed in vitro, and the Michaelis–Menten constants for substrates NaAD, ATP, glutamine and ammonium were determined. Enzyme kinetic and in vitro substrate competition assays indicate that H. seropedicae NadE1 uses glutamine as a preferential nitrogen donor.

BibTeX:

@article{laskoski_vitro_2016,
author = {Laskoski, Kerly and Santos, Adrian R.S. and Bonatto, Ana C. and Pedrosa, Fábio O. and Souza, Emanuel M. and Huergo, Luciano F.},
title = {In vitro characterization of the NAD+synthetase NadE1 from Herbaspirillum seropedicae},
journal = {Archives of Microbiology},
year = {2016},
volume = {198},
number = {4},
pages = {307--313},
url = {http://link.springer.com/10.1007/s00203-016-1190-z},
doi = {10.1007/s00203-016-1190-z}
}

Leite WC, Galvão CW, Saab SC, Iulek J, Etto RM, Steffens MB, Chitteni-Pattu S, Stanage T, Keck JL and Cox MM (2016). Structural and functional studies of H. seropedicae RecA Protein - Insights into the polymerization of RecA protein as nucleoprotein filament. PLoS ONE, 11(7):e0159871, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: ? 2016 Leite et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 ? resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.

BibTeX:

@article{leite_structural_2016,
author = {Leite, Wellington C. and Galvão, Carolina W. and Saab, Sérgio C. and Iulek, Jorge and Etto, Rafael M. and Steffens, Maria B.R. and Chitteni-Pattu, Sindhu and Stanage, Tyler and Keck, James L. and Cox, Michael M.},
editor = {Spies, Maria},
title = {Structural and functional studies of H. seropedicae RecA Protein - Insights into the polymerization of RecA protein as nucleoprotein filament},
journal = {PLoS ONE},
year = {2016},
volume = {11},
number = {7},
pages = {e0159871},
url = {http://dx.plos.org/10.1371/journal.pone.0159871},
doi = {10.1371/journal.pone.0159871}
}

Maria Marin A, de la Torre J, Ricardo Marques Oliveira A, Barison A, Satie Chubatsu L, Adele Monteiro R, de Oliveira Pedrosa F, Maltempi de Souza E, Wassem R, Duque E and Ramos JL (2016). Genetic and functional characterization of a novel meta-pathway for degradation of naringenin in Herbaspirillum seropedicae SmR1. Environmental Microbiology, 18(12):4653-4661, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.In this study, a random mutant library of Herbaspirillum seropedicae SmR1 was constructed by Tn5 insertion and a mutant incapable of utilizing naringenin as a carbon source was isolated. The Tn5 transposon was found to be inserted in the fdeE gene (Hsero1007), which encodes a monooxygenase. Two other mutant strains in fdeC (Hsero1005) and fdeG (Hsero1009) genes coding for a dioxygenase and a putative cyclase, respectively, were obtained by site-directed mutagenesis and then characterized. Liquid Chromatography coupled to mass spectrometry (LC-MS)/MS analyses of culture supernatant from the fdeE mutant strain revealed that naringenin remained unaltered, suggesting that the FdeE protein is involved in the initial step of naringenin degradation. LC-MS/MS analyses of culture supernatants from the wild-type (SmR1) and FdeC deficient mutant suggested that in H. seropedicae SmR1 naringenin is first mono-oxygenated by the FdeE protein, to produce 5,7,8-trihydroxy-2-(4-hydroxyphenyl)-2,3-dihydro-4H-chromen-4-one, that is subsequently dioxygenated and cleaved at the A-ring by the FdeC dioxygenase, since the latter compound accumulated in the fdeC strain. After meta-cleavage of the A-ring, the subsequent metabolic steps generate oxaloacetic acid that is metabolized via the tricarboxylic acid cycle. This bacterium can also modify naringenin by attaching a glycosyl group to the B-ring or a methoxy group to the A-ring, leading to the generation of dead-end products.

BibTeX:

@article{maria_marin_genetic_2016,
author = {Maria Marin, Anelis and de la Torre, Jésus and Ricardo Marques Oliveira, Alfredo and Barison, Andersson and Satie Chubatsu, Leda and Adele Monteiro, Rose and de Oliveira Pedrosa, Fabio and Maltempi de Souza, Emanuel and Wassem, Roseli and Duque, Estrella and Ramos, Juan Luis},
title = {Genetic and functional characterization of a novel meta-pathway for degradation of naringenin in Herbaspirillum seropedicae SmR1},
journal = {Environmental Microbiology},
year = {2016},
volume = {18},
number = {12},
pages = {4653--4661},
url = {http://doi.wiley.com/10.1111/1462-2920.13313},
doi = {10.1111/1462-2920.13313}
}

Pankievicz VC, Camilios-Neto D, Bonato P, Balsanelli E, Tadra-Sfeir MZ, Faoro H, Chubatsu LS, Donatti L, Wajnberg G, Passetti F, Monteiro RA, Pedrosa FO and Souza EM (2016). RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots. Plant Molecular Biology, 90(6):589-603, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Herbaspirillum seropedicae is a diazotrophic and endophytic bacterium that associates with economi- cally important grasses promoting plant growth and increasing productivity. To identify genes related to bac- terial ability to colonize plants, wheat seedlings growing hydroponically in Hoagland's medium were inoculated with H. seropedicae and incubated for 3 days. Total mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Com- parison of RNA profile of root attached and planktonic bacteria revealed extensive metabolic adaptations to the epiphytic life style. These adaptations include expression of specific adhesins and cell wall re-modeling to attach to the root. Additionally, the metabolism was adapted to the microxic environment and nitrogen-fixation genes were expressed. Polyhydroxybutyrate (PHB) synthesis was activated, and PHB granules were stored as observed by microscopy. Genes related to plant growth promotion, such as auxin production were expressed. Many ABC trans- porter genes were regulated in the bacteria attached to the roots. The results provide new insights into the adaptation of H. seropedicae to the interaction with the plant.

BibTeX:

@article{pankievicz_rna-seq_2016,
author = {Pankievicz, V. C.S. and Camilios-Neto, D. and Bonato, P. and Balsanelli, E. and Tadra-Sfeir, M. Z. and Faoro, H. and Chubatsu, L. S. and Donatti, L. and Wajnberg, G. and Passetti, F. and Monteiro, R. A. and Pedrosa, F. O. and Souza, E. M.},
title = {RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots},
journal = {Plant Molecular Biology},
year = {2016},
volume = {90},
number = {6},
pages = {589--603},
note = {ISBN: 1573-5028 (Electronic) 0167-4412 (Linking)},
url = {http://link.springer.com/10.1007/s11103-016-0430-6},
doi = {10.1007/s11103-016-0430-6}
}

Pfaffenseller B, da Silva Magalhães PV, De Bastiani MA, Castro MA, Gallitano AL, Kapczinski F and Klamt F (2016). Differential expression of transcriptional regulatory units in the prefrontal cortex of patients with bipolar disorder: potential role of early growth response gene 3. Translational psychiatry, 6(5):e805, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Bipolar disorder (BD) is a severe mental illness with a strong genetic component. Despite its high degree of heritability, current genetic studies have failed to reveal individual loci of large effect size. In lieu of focusing on individual genes, we investigated regulatory units (regulons) in BD to identify candidate transcription factors (TFs) that regulate large groups of differentially expressed genes. Network-based approaches should elucidate the molecular pathways governing the pathophysiology of BD and reveal targets for potential therapeutic intervention. The data from a large-scale microarray study was used to reconstruct the transcriptional associations in the human prefrontal cortex, and results from two independent microarray data sets to obtain BD gene signatures. The regulatory network was derived by mapping the significant interactions between known TFs and all potential targets. Five regulons were identified in both transcriptional network models: early growth response 3 (EGR3), TSC22 domain family, member 4 (TSC22D4), interleukin enhancer-binding factor 2 (ILF2), Y-box binding protein 1 (YBX1) and MAP-kinase-activating death domain (MADD). With a high stringency threshold, the consensus across tests was achieved only for the EGR3 regulon. We identified EGR3 in the prefrontal cortex as a potential key target, robustly repressed in both BD signatures. Considering that EGR3 translates environmental stimuli into long-term changes in the brain, disruption in biological pathways involving EGR3 may induce an impaired response to stress and influence on risk for psychiatric disorders, particularly BD.

BibTeX:

@article{pfaffenseller_differential_2016,
author = {Pfaffenseller, B. and da Silva Magalhães, P. V. and De Bastiani, M. A. and Castro, M. A.A. and Gallitano, A. L. and Kapczinski, F. and Klamt, F.},
title = {Differential expression of transcriptional regulatory units in the prefrontal cortex of patients with bipolar disorder: potential role of early growth response gene 3},
journal = {Translational psychiatry},
year = {2016},
volume = {6},
number = {5},
pages = {e805},
note = {ISBN: 2158-3188},
url = {http://www.nature.com/doifinder/10.1038/tp.2016.78},
doi = {10.1038/tp.2016.78}
}

Prediger KdC, Surek M, Dalagassa CDB, de Assis FEA, Piantavini MS, Souza EE, Pedrosa FOFO, Farah SMdSS, Alberton D and Fadel-Picheth CMT (2016). Utilization of carbon sources by clinical isolates of Aeromonas. Canadian Journal of Microbiology, 63(4):cjm-2016-0526, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Bacteria in the genus Aeromonas are primarily aquatic organisms; however, some species can cause diseases in humans, ranging from wound infections to septicemia, of which diarrhea is the most common condition. The ability to use a variety of carbon substrates is advantageous for pathogenic bacteria. Therefore, we used Biolog GN2 microplates to analyze the ability of 103 clinical, predominantly diarrheal, isolates of Aeromonas to use various carbon sources and verified whether among the substrates metabolized by these strains there were some endogenous to the human intestine. Results indicate that Aeromonas present great diversity in the utilization of carbon sources, and that they preferentially use carbohydrates and amino acids as carbon sources. Among the carbon sources metabolized by Aeromonas in vitro, some were found to be components of intestinal mucin including aspartic acid, glutamic acid, L-serine, galactose, N-acetyl-glucosamine, and glucose, which were used by...

BibTeX:

@article{prediger_utilization_2016,
author = {Prediger, Karoline de Campos and Surek, Monica and Dalagassa, Cibelle De Borba and de Assis, Flávia Emanoelli Araújo and Piantavini, Mário Sérgio and Souza, Emanuel E.M. and Pedrosa, Fabio O. F O and Farah, Sônia Maria de Souza Santos and Alberton, Dayane and Fadel-Picheth, Cyntia Maria Telles},
title = {Utilization of carbon sources by clinical isolates of Aeromonas},
journal = {Canadian Journal of Microbiology},
year = {2016},
volume = {63},
number = {4},
pages = {cjm--2016--0526},
url = {http://www.nrcresearchpress.com/doi/10.1139/cjm-2016-0526},
doi = {10.1139/cjm-2016-0526}
}

Rocha IF, Maller A, De Cássia Garcia Simão R, Kadowaki MK, Angeli Alves LF, Huergo LF and Da Conceição Silva JL (2016). Proteomic profile of hemolymph and detection of induced antimicrobial peptides in response to microbial challenge in Diatraea saccharalis (Lepidoptera: Crambidae). Biochemical and Biophysical Research Communications, 473(2):511-516, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Insects are organisms extremely well adapted to diverse habitats, primarily due to their innate immune system, which provides them with a range of cellular and humoral responses against microorganisms. Lepidoptera hemolymph proteins involved in humoral responses are well known; however, there is a lack of knowledge about the sugarcane borer Diatraea saccharalis. In this present work, the hemolymph proteins of this pest insect were studied by applying proteomic methodologies. Two-dimensional electrophoresis (2-DE) gels of proteins extracted from naive larvae and larvae challenged with Escherichia coli (ATCC 11224) and Bacillus subtilis (ATCC 6623) showed an average of 300 spots, and 92 of these spots corresponded in all three 2-DE gels. Forty-one spots were excised and digested with trypsin and analyzed using mass spectrometry. After analysis, 10 proteins were identified, including some proteins of the immune system: β-defensin-like protein, Turandot A-like protein, attacin-like protein, peptidoglycan recognition protein and cyclophilin-like protein. Nine proteins were present in both experimental conditions; however, β-defensin-like protein was present only in hemolymph challenged by B. subtilis. Notably, attacin-like protein was strongly induced by challenge with E. coli, suggesting an immune response against the infection. However, antimicrobial activity was observed in the test zone of microbial growth inhibition of B. subtilis solely with the hemolymph extract of the larvae challenged with B. subtilis. We made for the first time a proteomic profile of the hemolymph of D. saccharalis in which it was possible to identify the presence of important proteins involved in the immune response.

BibTeX:

@article{rocha_proteomic_2016,
author = {Rocha, Iara Fernanda and Maller, Alexandre and De Cássia Garcia Simão, Rita and Kadowaki, Marina Kimiko and Angeli Alves, Luis Francisco and Huergo, Luciano Fernandes and Da Conceição Silva, José Luis},
title = {Proteomic profile of hemolymph and detection of induced antimicrobial peptides in response to microbial challenge in Diatraea saccharalis (Lepidoptera: Crambidae)},
journal = {Biochemical and Biophysical Research Communications},
year = {2016},
volume = {473},
number = {2},
pages = {511--516},
note = {ISBN: 978-0-674-04557-6 eprint: arXiv:1011.1669v3},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0006291X16304028},
doi = {10.1016/j.bbrc.2016.03.091}
}

Rubel ET, Raittz RT, Coimbra NAdR, Gehlen MAC and Pedrosa FdO (2016). ProClaT, a new bioinformatics tool for in silico protein reclassification: Case study of DraB, a protein coded from the draTGB operon in Azospirillum brasilense. BMC Bioinformatics, 17(S18) 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Azopirillum brasilense is a plant-growth promoting nitrogen-fixing bacteria that is used as bio-fertilizer in agriculture. Since nitrogen fixation has a high-energy demand, the reduction of N2 to NH4 + by nitrogenase occurs only under limiting conditions of NH4 + and O2. Moreover, the synthesis and activity of nitrogenase is highly regulated to prevent energy waste. In A. brasilense nitrogenase activity is regulated by the products of draG and draT. The product of the draB gene, located downstream in the draTGB operon, may be involved in the regulation of nitrogenase activity by an, as yet, unknown mechanism. A deep in silico analysis of the product of draB was undertaken aiming at suggesting its possible function and involvement with DraT and DraG in the regulation of nitrogenase activity in A. brasilense. In this work, we present a new artificial intelligence strategy for protein classification, named ProClaT. The features used by the pattern recognition model were derived from the primary structure of the DraB homologous proteins, calculated by a ProClaT internal algorithm. ProClaT was applied to this case study and the results revealed that the A. brasilense draB gene codes for a protein highly similar to the nitrogenase associated NifO protein of Azotobacter vinelandii. This tool allowed the reclassification of DraB/NifO homologous proteins, hypothetical, conserved hypothetical and those annotated as putative arsenate reductase, ArsC, as NifO-like. An analysis of co-occurrence of draB, draT, draG and of other nif genes was performed, suggesting the involvement of draB (nifO) in nitrogen fixation, however, without the definition of a specific function.

BibTeX:

@article{rubel_proclat_2016,
author = {Rubel, Elisa Terumi and Raittz, Roberto Tadeu and Coimbra, Nilson Antonio da Rocha and Gehlen, Michelly Alves Coutinho and Pedrosa, Fábio de Oliveira},
title = {ProClaT, a new bioinformatics tool for in silico protein reclassification: Case study of DraB, a protein coded from the draTGB operon in Azospirillum brasilense},
journal = {BMC Bioinformatics},
year = {2016},
volume = {17},
number = {S18},
note = {ISBN: 1285901613385},
url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1338-5},
doi = {10.1186/s12859-016-1338-5}
}

Sanchuki HB, Valdameri G, Moure VR, Rodriguez JA, Pedrosa FO, Souza EM, Korolik V, Ribeiro RR and Huergo LF (2016). Conserved histidine residues at the ferroxidase centre of the Campylobacter jejuni Dps protein are not strictly required for metal binding and oxidation. Microbiology (United Kingdom), 162(1):156-163, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Iron is an essential micronutrient for living organisms as it is involved in a broad variety of important biological processes. However, free iron inside the cell could be potentially toxic, generating hydroxyl radicals through the Fenton reaction. Dps (DNA-binding protein from starved cells) belongs to a subfamily of ferritins and can store iron atoms inside the dodecamer. The presence of a ferroxidase centre, composed of highly conserved residues, is a signature of this protein family. In this study, we analysed the role of two conserved histidine residues (H25 and H37) located at the ferroxidase centre of the Campylobacter jejuni Dps protein by replacing them with glycine residues. The C. jejuni H25G/H37G substituted variant showed reduced iron binding and ferroxidase activities in comparison with wt Dps, while DNA-binding activity remained unaffected. We also found that both CjDps wt and CjDps H25G/H37G were able to bind manganese atoms. These results indicate that the H25 and H37 residues at the ferroxidase centre of C. jejuni Dps are not strictly required for metal binding and oxidation.

BibTeX:

@article{sanchuki_conserved_2016,
author = {Sanchuki, Heloisa B.S. and Valdameri, Glaucio and Moure, Vivian R. and Rodriguez, Jorge A. and Pedrosa, Fábio O. and Souza, Emanuel M. and Korolik, Victoria and Ribeiro, Ronny Rocha and Huergo, Luciano F.},
title = {Conserved histidine residues at the ferroxidase centre of the Campylobacter jejuni Dps protein are not strictly required for metal binding and oxidation},
journal = {Microbiology (United Kingdom)},
year = {2016},
volume = {162},
number = {1},
pages = {156--163},
note = {Publisher: Microbiology Society},
url = {http://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.000210 http://dx.doi.org/10.1099/mic.0.000210},
doi = {10.1099/mic.0.000210}
}

Sperb ER, Tadra-Sfeir MZ, Sperotto RA, Fernandes GdC, Pedrosa FdO, de Souza EM and Passaglia LMP (2016). Iron deficiency resistance mechanisms enlightened by gene expression analysis in Paenibacillus riograndensis SBR5. Research in Microbiology, 167(6):501-509, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Despite its importance in growth and cell division, iron metabolism is still poorly understood in microorganisms, especially in Gram-positive bacteria. In this work, we used RNA sequencing technology to elucidate global mechanisms involved in iron starvation resistance in Paenibacillus riograndensis SBR5, a potential plant growth-promoting bacterium. Iron deficiency caused several changes in gene expression, and 150 differentially expressed genes were found: 71 genes were overexpressed and 79 genes were underexpressed. Eight genes for which expression was at least twice as high or twice as low in iron-limited condition compared with iron-sufficient condition were chosen for RT-qPCR analysis to validate the RNA seq data. In general, most genes exhibited the same pattern of expression after 24 h of P. riograndensis growth under iron-limiting condition. Our results suggest that, during iron deficiency, bacteria express several genes related to nutrient uptake when they start to grow to obtain all of the molecules necessary for maintaining major cellular processes. However, once iron becomes highly limiting and is no longer able to sustain exponential growth, bacteria begin to express genes related to several processes, like sporulation and DNA protection, as a way of resisting this stress.

BibTeX:

@article{sperb_iron_2016,
author = {Sperb, Edilena Reis and Tadra-Sfeir, Michelle Zibetti and Sperotto, Raul Antônio and Fernandes, Gabriela de Carvalho and Pedrosa, Fábio de Oliveira and de Souza, Emanuel Maltempi and Passaglia, Luciane Maria Pereira},
title = {Iron deficiency resistance mechanisms enlightened by gene expression analysis in Paenibacillus riograndensis SBR5},
journal = {Research in Microbiology},
year = {2016},
volume = {167},
number = {6},
pages = {501--509},
note = {ISBN: 9781479946402},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0923250816300092},
doi = {10.1016/j.resmic.2016.04.007}
}

Vieira LdN, Dos Anjos KG, Faoro H, Fraga HPdF, Greco TM, Pedrosa FdO, de Souza EM, Rogalski M, de Souza RF and Guerra MP (2016). Phylogenetic inference and SSR characterization of tropical woody bamboos tribe Bambuseae (Poaceae: Bambusoideae) based on complete plastid genome sequences. Current Genetics, 62(2):443-453, 2016.
[Abstract] [DOI] [BibTeX]

Abstract: The complete plastome sequencing is an efficient option for increasing phylogenetic resolution and evolutionary studies, as well as may greatly facilitate the use of plastid DNA markers in plant population genetic studies. Merostachys and Guadua stand out as the most common and the highest potential utilization bamboos indigenous of Brazil. Here, we sequenced the complete plastome sequences of the Brazilian Guadua chacoensis and Merostachys sp. to perform full plastome phylogeny and characterize the occurrence, type, and distribution of SRRs using 20 Bambuseae species. The determined plastome sequence of Merostachys sp. and G. chacoensis is 136,334 and 135,403 bp in size, respectively, with an identical gene content and typical quadripartite structure consisting of a pair of IRs separated by the LSC and SSC regions. The Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of Paleotropical and Neotropical Bamboos clades. The Neotropical bamboos segregated into three well-supported lineages, Chusqueinae, Guaduinae, and Arthrostylidiinae, with the last two forming a well-supported sister relationship. Paleotropical bamboos segregated into two well-supported lineages, Hickeliinae and Bambusinae + Melocanninae. We identified 141.8 cpSSR in Bambuseae plastomes and an inferior value (38.15) for plastome coding sequences. Among them, we identified 16 polymorphic SSR loci, with number of alleles varying from 3 to 10. These 16 polymorphic cpSSR loci in Bambuseae plastome can be assessed for the intraspecific level of polymorphism, leading to innovative highly sensitive phylogeographic and population genetics studies for this tribe.

BibTeX:

@article{vieira_phylogenetic_2016,
author = {Vieira, Leila do Nascimento and Dos Anjos, Karina Goulart and Faoro, Helisson and Fraga, Hugo Pacheco de Freitas and Greco, Thiago Machado and Pedrosa, Fábio de Oliveira and de Souza, Emanuel Maltempi and Rogalski, Marcelo and de Souza, Robson Francisco and Guerra, Miguel Pedro},
title = {Phylogenetic inference and SSR characterization of tropical woody bamboos tribe Bambuseae (Poaceae: Bambusoideae) based on complete plastid genome sequences},
journal = {Current Genetics},
year = {2016},
volume = {62},
number = {2},
pages = {443--453},
doi = {10.1007/s00294-015-0549-z}
}

Wollenhaupt-Aguiar B, Pfaffenseller B, Chagas VDS, Castro MA, Passos IC, anna Márcia KS, Kapczinski F and Klamt F (2016). Reduced neurite density in neuronal cell cultures exposed to serum of patients with bipolar disorder. International Journal of Neuropsychopharmacology, 19(10):1-5, 2016.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: BACKGROUND: Increased inflammatory markers and oxidative stress have been reported in serum among patients with bipolar disorder (BD). The aim of this study is to assess whether biochemical changes in serum of patients induces neurotoxicity in neuronal cell cultures. METHODS: We challenged the retinoic acid-differentiated human neuroblastoma SH-SY5Y cells with serum of BD patients at early- and late-stages of illness and assessed neurite density and cell viability as neurotoxic endpoints. RESULTS: Decreased neurite density was found in neurons treated with serum of patients, mostly patients at late-stages of illness. Also, neurons challenged with serum of late-stages patients showed a significant decrease in cell viability. CONCLUSIONS: Our findings showed that serum of patients with bipolar disorder induced a decrease in neurite density and cell viability in neuronal cultures.

BibTeX:

@article{wollenhaupt-aguiar_reduced_2016,
author = {Wollenhaupt-Aguiar, Bianca and Pfaffenseller, Bianca and Chagas, Vinicius De Saraiva and Castro, Mauro A.A. and Passos, Ives Cavalcante and anna Márcia, Kauer Sant and Kapczinski, Flavio and Klamt, Fábio},
title = {Reduced neurite density in neuronal cell cultures exposed to serum of patients with bipolar disorder},
journal = {International Journal of Neuropsychopharmacology},
year = {2016},
volume = {19},
number = {10},
pages = {1--5},
note = {ISBN: 6314449537},
url = {https://academic.oup.com/ijnp/article-lookup/doi/10.1093/ijnp/pyw051},
doi = {10.1093/ijnp/pyw051}
}

Ambrosini A, Sant'Anna FH, de Souza R, Tadra-Sfeir M, Faoro H, Alvarenga SM, Pedrosa FO, Souza EM and Passaglia LMP (2015). Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower. Genome Announcements, 3(2):e00245-15, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Bacillus mycoides B38V is a bacterium isolated from the sunflower rhizosphere that is able to promote plant growth and N uptake. The genome of the isolate has approximately 5.80 Mb and presents sequence codifiers for plant growth-promoting characteristics, such as nitrate reduction and ammonification and iron-siderophore uptake.

BibTeX:

@article{ambrosini_genome_2015,
author = {Ambrosini, Adriana and Sant'Anna, Fernando Hayashi and de Souza, Rocheli and Tadra-Sfeir, Michele and Faoro, Helisson and Alvarenga, Samuel M. and Pedrosa, Fabio Oliveira and Souza, Emanuel Maltempi and Passaglia, Luciane M. P.},
title = {Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower},
journal = {Genome Announcements},
year = {2015},
volume = {3},
number = {2},
pages = {e00245--15},
note = {ISBN: 1471218023 Publisher: American Society for Microbiology},
url = {http://genomea.asm.org/lookup/doi/10.1128/genomeA.00245-15},
doi = {10.1128/genomeA.00245-15}
}

Becker M, De Bastiani MA, Parisi MM, Guma FT, Markoski MM, Castro MA, Kaplan MH, Barbé-Tuana FM and Klamt F (2015). Integrated Transcriptomics Establish Macrophage Polarization Signatures and have Potential Applications for Clinical Health and Disease. Scientific Reports, 5:13351, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Growing evidence defines macrophages (Mϕ) as plastic cells with wide-ranging states of activation and expression of different markers that are time and location dependent. Distinct from the simple M1/M2 dichotomy initially proposed, extensive diversity of macrophage phenotypes have been extensively demonstrated as characteristic features of monocyte-macrophage differentiation, highlighting the difficulty of defining complex profiles by a limited number of genes. Since the description of macrophage activation is currently contentious and confusing, the generation of a simple and reliable framework to categorize major Mϕ phenotypes in the context of complex clinical conditions would be extremely relevant to unravel different roles played by these cells in pathophysiological scenarios. In the current study, we integrated transcriptome data using bioinformatics tools to generate two macrophage molecular signatures. We validated our signatures in in vitro experiments and in clinical samples. More importantly, we were able to attribute prognostic and predictive values to components of our signatures. Our study provides a framework to guide the interrogation of macrophage phenotypes in the context of health and disease. The approach described here could be used to propose new biomarkers for diagnosis in diverse clinical settings including dengue infections, asthma and sepsis resolution.

BibTeX:

@article{becker_integrated_2015,
author = {Becker, Matheus and De Bastiani, Marco A. and Parisi, Mariana M. and Guma, Fátima T.C.R. and Markoski, Melissa M. and Castro, Mauro A.A. and Kaplan, Mark H. and Barbé-Tuana, Florencia M. and Klamt, Fábio},
title = {Integrated Transcriptomics Establish Macrophage Polarization Signatures and have Potential Applications for Clinical Health and Disease},
journal = {Scientific Reports},
year = {2015},
volume = {5},
pages = {13351},
note = {Publisher: Nature Publishing Group},
url = {http://dx.doi.org/10.1038/srep13351},
doi = {10.1038/srep13351}
}

Cosate MRV, Soares SC, Mendes TA, Raittz RT, Moreira EC, Leite R, Fernandes GR, Haddad JPA and Ortega JM (2015). Whole-Genome Sequence of \textlessi\textgreaterLeptospira interrogans\textless/i\textgreater Serovar Hardjo Subtype Hardjoprajitno Strain Norma, Isolated from Cattle in a Leptospirosis Outbreak in Brazil. Genome Announcements, 3(6):e01302-15, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: \textlessp\textgreater Leptospirosis is caused by pathogenic bacteria of the genus \textlessitalic\textgreaterLeptospira\textless/italic\textgreater spp. This neglected re-emergent disease has global distribution and relevance in veterinary production. Here, we report the whole-genome sequence and annotation of \textlessitalic\textgreaterLeptospira interrogans\textless/italic\textgreater serovar Hardjo subtype Hardjoprajitno strain Norma, isolated from cattle in a livestock leptospirosis outbreak in Brazil. \textless/p\textgreater

BibTeX:

@article{cosate_whole-genome_2015,
author = {Cosate, M. R. V. and Soares, S. C. and Mendes, T. A. and Raittz, R. T. and Moreira, E. C. and Leite, R. and Fernandes, G. R. and Haddad, J. P. A. and Ortega, J. Miguel},
title = {Whole-Genome Sequence of \textlessi\textgreaterLeptospira interrogans\textless/i\textgreater Serovar Hardjo Subtype Hardjoprajitno Strain Norma, Isolated from Cattle in a Leptospirosis Outbreak in Brazil},
journal = {Genome Announcements},
year = {2015},
volume = {3},
number = {6},
pages = {e01302--15},
note = {ISBN: 1203800800 Publisher: American Society for Microbiology},
url = {http://genomea.asm.org/lookup/doi/10.1128/genomeA.01302-15},
doi = {10.1128/genomeA.01302-15}
}

de Melo SF, Frigeri HR, dos Santos-Weiss ICR, Réa RR, de Souza EM, Alberton D, de Moraes Rego FG and Picheth G (2015). Polymorphisms in FTO and TCF7L2 genes of Euro-Brazilian women with gestational diabetes. Clinical Biochemistry, 48(16-17):1064-1067, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Objective: To investigate the association between fat mass and obesity-associated (FTO) gene polymorphisms rs8050136C\textgreaterA and rs9939609T\textgreaterA, and transcription factor 7-like 2 (TCF7L2) gene polymorphisms rs12255372G\textgreaterT and rs7903146C\textgreaterT, in a sample group of pregnant Euro-Brazilian women with or without gestational diabetes mellitus (GDM). Methods: Subjects were classified as either healthy pregnant control (n. = 200) or GDM (n. = 200) according to the 2010 criteria of the American Diabetes Association. The polymorphisms were genotyped using fluorescent probes (TaqMan®). Results: All groups were in the Hardy-Weinberg equilibrium. The genotype and allele frequencies of the examined polymorphisms did not exhibit significant difference (P. \textgreater. 0.05) between the groups. In the healthy and GDM pregnant women groups, the A-allele frequencies (95% CI) of FTO polymorphisms rs8050136 and rs9939609 were 39% (34-44; 38% (33-43 and 40% (35-45; 41% (36-46, respectively; and the T-allele frequencies of TCF7L2 polymorphisms rs12255372 and rs7903146 were 30% (26-35, 32% (27-37 and 29% (25-34, 36% (31-41, respectively. Conclusion: The examined polymorphisms were not associated with GDM in the Euro-Brazilian population studied.

BibTeX:

@article{de_melo_polymorphisms_2015,
author = {de Melo, Sandra Fabrico and Frigeri, Henrique Ravanhol and dos Santos-Weiss, Izabella Castilhos Ribeiro and Réa, Rosângela Roginski and de Souza, Emanuel Maltempi and Alberton, Dayane and de Moraes Rego, Fabiane Gomes and Picheth, Geraldo},
title = {Polymorphisms in FTO and TCF7L2 genes of Euro-Brazilian women with gestational diabetes},
journal = {Clinical Biochemistry},
year = {2015},
volume = {48},
number = {16-17},
pages = {1064--1067},
note = {Publisher: Elsevier BV},
url = {http://dx.doi.org/10.1016/j.clinbiochem.2015.06.013},
doi = {10.1016/j.clinbiochem.2015.06.013}
}

de Souza R, Sant'Anna FH, Ambrosini A, Tadra-Sfeir M, Faoro H, Pedrosa FO, Souza EM and Passaglia LMP (2015). Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields. Genome Announcements, 3(2):e00249-15, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences.

BibTeX:

@article{de_souza_genome_2015,
author = {de Souza, Rocheli and Sant'Anna, Fernando Hayashi and Ambrosini, Adriana and Tadra-Sfeir, Michele and Faoro, Helisson and Pedrosa, Fabio Oliveira and Souza, Emanuel Maltempi and Passaglia, Luciane M. P.},
title = {Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields},
journal = {Genome Announcements},
year = {2015},
volume = {3},
number = {2},
pages = {e00249--15},
note = {ISBN: 1471216497 Publisher: American Society for Microbiology},
url = {http://genomea.asm.org/lookup/doi/10.1128/genomeA.00249-15},
doi = {10.1128/genomeA.00249-15}
}

de Souza R, Sant'Anna FH, Ambrosini A, Tadra-Sfeir M, Faoro H, Pedrosa FO, Souza EM and Passaglia LMP (2015). Genome of Pseudomonas sp. FeS53a, a Putative Plant Growth-Promoting Bacterium Associated with Rice Grown in Iron-Stressed Soils. Genome Announcements, 3(2):e00248-15, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Pseudomonas sp. FeS53a was isolated from the roots of rice plants cultivated in one area with a well-established history of iron toxicity. The FeS53a genome sequence provides the genetic basis for understanding its lifestyle and survival in association with rice in conditions of iron toxicity.

BibTeX:

@article{de_souza_genome_2015-1,
author = {de Souza, Rocheli and Sant'Anna, Fernando Hayashi and Ambrosini, Adriana and Tadra-Sfeir, Michele and Faoro, Helisson and Pedrosa, Fabio Oliveira and Souza, Emanuel Maltempi and Passaglia, Luciane M. P.},
title = {Genome of Pseudomonas sp. FeS53a, a Putative Plant Growth-Promoting Bacterium Associated with Rice Grown in Iron-Stressed Soils},
journal = {Genome Announcements},
year = {2015},
volume = {3},
number = {2},
pages = {e00248--15},
note = {ISBN: 1110401214025 Publisher: American Society for Microbiology},
url = {http://genomea.asm.org/lookup/doi/10.1128/genomeA.00248-15},
doi = {10.1128/genomeA.00248-15}
}

Faoro H, de Souza EM and Pedrosa FO (2015). Brazilian Atlantic Forest Soil Metagenome. In Encyclopedia of Metagenomics. New York, NY :54-59, 2015.
[DOI] [URL] [BibTeX]

Abstract:

BibTeX:

@incollection{faoro_brazilian_2015,
author = {Faoro, Helisson and de Souza, Emanuel Maltempi and Pedrosa, Fábio Oliveira},
editor = {Nelson, Karen E},
title = {Brazilian Atlantic Forest Soil Metagenome},
booktitle = {Encyclopedia of Metagenomics},
publisher = {Springer New York},
year = {2015},
pages = {54--59},
url = {http://link.springer.com/10.1007/978-1-4899-7475-4_781},
doi = {10.1007/978-1-4899-7475-4_781}
}

Gaensly F, Agustini BC, da Silva GA, Picheth G and Bonfim TMB (2015). Autochthonous yeasts with β-glucosidase activity increase resveratrol concentration during the alcoholic fermentation of Vitis labrusca grape must. Journal of Functional Foods, 19:288-295, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Since red wine is the main dietary source of resveratrol, a well-known polyphenol that reduces coronary events in humans, different strategies have been employed in winery to achieve resveratrol-enriched wines. Yeasts-endowed β-glucosidase activity enhances free-resveratrol concentration in wine without modifying its composition or sensorial properties. Current assay screened 308 autochthonous yeast strains for β-glucosidase activity employing arbutin, esculin, cellobiose and piceid as substrates. The β-glucosidase-producer yeasts were evaluated in the must of Vitis labrusca Bordô grape to quantify resveratrol concentration before and after alcoholic fermentation. Fourteen yeasts increased the resveratrol concentration up to 102% without any significant difference and nine of these yeast strains also produced high ethanol contents. Four autochthonous Hanseniaspora uvarum β-glucosidase-producer strains showed adequate oenological characteristics and hydrolysed resveratrol-glucosides during the alcoholic fermentation of V. labrusca grape must.

BibTeX:

@article{gaensly_autochthonous_2015,
author = {Gaensly, Fernanda and Agustini, Bruna Carla and da Silva, Gildo Almeida and Picheth, Geraldo and Bonfim, Tania Maria Bordin},
title = {Autochthonous yeasts with β-glucosidase activity increase resveratrol concentration during the alcoholic fermentation of Vitis labrusca grape must},
journal = {Journal of Functional Foods},
year = {2015},
volume = {19},
pages = {288--295},
note = {ISBN: 1756-4646 Publisher: Elsevier BV},
url = {http://dx.doi.org/10.1016/j.jff.2015.09.041},
doi = {10.1016/j.jff.2015.09.041}
}

Gomig F, Galvão CW, De Freitas DL, Labas L, Etto RM, Esmerino LA, De Lima MA, Appel MH, Zanata SM, Steffens MBR, Nader HB and Da Silveira RB (2015). Quinolone resistance and ornithine decarboxylation activity in lactose-negative escherichia coli. Brazilian Journal of Microbiology, 46(3):753-757, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Quinolones and fluoroquinolones are widely used to treat uropathogenic Escherichia coli infections. Bacterial resistance to these antimicrobials primarily involves mutations in gyrA and parC genes. To date, no studies have examined the potential relationship between biochemical characteristics and quinolone resistance in uropathogenic E. coli strains. The present work analyzed the quinolone sensitivity and biochemical activities of fifty-eight lactose-negative uropathogenic E. coli strains. A high percentage of the isolates (48.3 was found to be resistant to at least one of the tested quinolones, and DNA sequencing revealed quinolone resistant determining region gyrA and parC mutations in the multi-resistant isolates. Statistical analyses suggested that the lack of ornithine decarboxylase (ODC) activity is correlated with quinolone resistance. Despite the low number of isolates examined, this is the first study correlating these characteristics in lactose-negative E. coli isolates.

BibTeX:

@article{gomig_quinolone_2015,
author = {Gomig, Franciane and Galvão, Carolina Weigert and De Freitas, Denis Leandro and Labas, Larissa and Etto, Rafael Mazer and Esmerino, Luiz Antonio and De Lima, Marcelo Andrade and Appel, Marcia Helena and Zanata, Silvio Marques and Steffens, Maria Berenice Reynaud and Nader, Helena Bonciani and Da Silveira, Rafael Bertoni},
title = {Quinolone resistance and ornithine decarboxylation activity in lactose-negative escherichia coli},
journal = {Brazilian Journal of Microbiology},
year = {2015},
volume = {46},
number = {3},
pages = {753--757},
note = {ISBN: 1517838246320 Publisher: FapUNIFESP (SciELO)},
url = {http://dx.doi.org/10.1590/s1517-838246320131291},
doi = {10.1590/S1517-838246320131291}
}

Guizelini D, Saizaki PM, Coimbra NAR, Weiss VA, Faoro H, Sfeir MZT, Baura VA, Monteiro RA, Chubatsu LS, Souza EM, Cruz LM, Pedrosa FO, Raittz RT, Marchaukoski JN and Steffens MBR (2015). Complete Genome Sequence of Herbaspirillum hiltneri N3 (DSM 17495), Isolated from Surface-Sterilized Wheat Roots. Genome Announcements, 3(5):e01288-15, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: We report the complete genome sequence of Herbaspirillum hiltneri N3 (DSM 17495), a member of the genus Herbaspirillum of the Betaproteobacteria. The genome is contained in a single chromosome, and analysis revealed that N3 lacks the whole nitrogen fixation (nif) gene cluster, confirming its inability to fix nitrogen.

BibTeX:

@article{guizelini_complete_2015,
author = {Guizelini, Dieval and Saizaki, Paula M. and Coimbra, Nilson A. R. and Weiss, Vinicius A. and Faoro, Helisson and Sfeir, Michelle Z. T. and Baura, Valter A. and Monteiro, Rose A. and Chubatsu, Leda S. and Souza, Emanuel M. and Cruz, Leonardo M. and Pedrosa, Fabio O. and Raittz, Roberto T. and Marchaukoski, Jeroniza N. and Steffens, Maria B. R.},
title = {Complete Genome Sequence of Herbaspirillum hiltneri N3 (DSM 17495), Isolated from Surface-Sterilized Wheat Roots},
journal = {Genome Announcements},
year = {2015},
volume = {3},
number = {5},
pages = {e01288--15},
note = {ISBN: 1471216497 Publisher: American Society for Microbiology},
url = {http://genomea.asm.org/content/3/5/e01288-15.full},
doi = {10.1128/genomeA.01288-15}
}

Huergo LF and Dixon R (2015). The Emergence of 2-Oxoglutarate as a Master Regulator Metabolite. Microbiology and Molecular Biology Reviews, 79(4):419-435, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The metabolite 2-oxoglutarate (also known as α-ketoglutarate, 2-ketoglutaric acid, or oxoglutaric acid) lies at the intersection between the carbon and nitrogen metabolic pathways. This compound is a key intermediate of one of the most fundamental biochemical pathways in carbon metabolism, the tricarboxylic acid (TCA) cycle. In addition, 2-oxoglutarate also acts as the major carbon skeleton for nitrogen-assimilatory reactions. Experimental data support the conclusion that intracellular levels of 2-oxoglutarate fluctuate according to nitrogen and carbon availability. This review summarizes how nature has capitalized on the ability of 2-oxoglutarate to reflect cellular nutritional status through evolution of a variety of 2-oxoglutarate-sensing regulatory proteins. The number of metabolic pathways known to be regulated by 2-oxoglutarate levels has increased significantly in recent years. The signaling properties of 2-oxoglutarate are highlighted by the fact that this metabolite regulates the synthesis of the well-established master signaling molecule, cyclic AMP (cAMP), in Escherichia coli.

BibTeX:

@article{huergo_emergence_2015,
author = {Huergo, Luciano F. and Dixon, Ray},
title = {The Emergence of 2-Oxoglutarate as a Master Regulator Metabolite},
journal = {Microbiology and Molecular Biology Reviews},
year = {2015},
volume = {79},
number = {4},
pages = {419--435},
note = {Publisher: American Society for Microbiology},
url = {http://mmbr.asm.org/lookup/doi/10.1128/MMBR.00038-15},
doi = {10.1128/MMBR.00038-15}
}

Inaba J, Thornton J, Huergo LF, Monteiro RA, Klassen G, Pedrosa FdO, Merrick M and de Souza EM (2015). Mutational analysis of GlnB residues critical for NifA activation in Azospirillum brasilense. Microbiological Research, 171:65-72, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: PII proteins are signal transduction that sense cellular nitrogen status and relay this signals to other targets. Azospirillum brasilense is a nitrogen fixing bacterium, which associates with grasses and cereals promoting beneficial effects on plant growth and crop yields. A. brasilense contains two PII encoding genes, named glnB and glnZ.In this paper, glnB was mutagenised in order to identify amino acid residues involved in GlnB signaling. Two variants were obtained by random mutagenesis, GlnBL13P and GlnBV100A and a site directed mutant, GlnBY51F, was obtained. Their ability to complement nitrogenase activity of glnB mutant strains of A. brasilense were determined. The variant proteins were also overexpressed in Escherichia coli, purified and characterized biochemically. None of the GlnB variant forms was able to restore nitrogenase activity in glnB mutant strains of A. brasilense LFH3 and 7628. The purified GlnBY51F and GlnBL13P proteins could not be uridylylated by GlnD, whereas GlnBV100A was uridylylated but at only 20% of the rate for wild type GlnB. Biochemical and computational analyses suggest that residue Leu13, located in the α helix 1 of GlnB, is important to maintain GlnB trimeric structure and function. The substitution V100A led to a lower affinity for ATP binding. Together the results suggest that NifA activation requires uridylylated GlnB bound to ATP.

BibTeX:

@article{inaba_mutational_2015,
author = {Inaba, Juliana and Thornton, Jeremy and Huergo, Luciano Fernandes and Monteiro, Rose Adele and Klassen, Giseli and Pedrosa, Fábio de Oliveira and Merrick, Mike and de Souza, Emanuel Maltempi},
title = {Mutational analysis of GlnB residues critical for NifA activation in Azospirillum brasilense},
journal = {Microbiological Research},
year = {2015},
volume = {171},
pages = {65--72},
note = {Publisher: Elsevier BV},
url = {http://dx.doi.org/10.1016/j.micres.2014.12.005},
doi = {10.1016/j.micres.2014.12.005}
}

Junior JPL, Frigeri HR, dos Santos-Weiss IC, de Souza EM, Rego FG, Picheth G and Alberton D (2015). The MTNR1B gene polymorphism rs10830963 is associated with gestational diabetes in a Brazilian population. Gene, 568(1):114-115, 2015.
[DOI] [URL] [BibTeX]

Abstract:

BibTeX:

@article{junior_mtnr1b_2015,
author = {Junior, João Paulo Lobo and Frigeri, Henrique R. and dos Santos-Weiss, Izabella C.R. and de Souza, Emanuel M. and Rego, Fabiane G.M. and Picheth, Geraldo and Alberton, Dayane},
title = {The MTNR1B gene polymorphism rs10830963 is associated with gestational diabetes in a Brazilian population},
journal = {Gene},
year = {2015},
volume = {568},
number = {1},
pages = {114--115},
note = {Publisher: Elsevier BV},
url = {http://linkinghub.elsevier.com/retrieve/pii/S037811191500582X},
doi = {10.1016/j.gene.2015.05.024}
}

Kuhring M, Dabrowski PW, Piro VC, Nitsche A and Renard BY (2015). SuRankCo: Supervised ranking of contigs in de novo assemblies. BMC Bioinformatics, 16(1) 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: BACKGROUND: Evaluating the quality and reliability of a de novo assembly and of single contigs in particular is challenging since commonly a ground truth is not readily available and numerous factors may influence results. Currently available procedures provide assembly scores but lack a comparative quality ranking of contigs within an assembly. RESULTS: We present SuRankCo, which relies on a machine learning approach to predict quality scores for contigs and to enable the ranking of contigs within an assembly. The result is a sorted contig set which allows selective contig usage in downstream analysis. Benchmarking on datasets with known ground truth shows promising sensitivity and specificity and favorable comparison to existing methodology. CONCLUSIONS: SuRankCo analyzes the reliability of de novo assemblies on the contig level and thereby allows quality control and ranking prior to further downstream and validation experiments.

BibTeX:

@article{kuhring_surankco_2015,
author = {Kuhring, Mathias and Dabrowski, Piotr Wojtek and Piro, Vitor C. and Nitsche, Andreas and Renard, Bernhard Y.},
title = {SuRankCo: Supervised ranking of contigs in de novo assemblies},
journal = {BMC Bioinformatics},
year = {2015},
volume = {16},
number = {1},
url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0644-7},
doi = {10.1186/s12859-015-0644-7}
}

Lammel DR, Cruz LM, Mescolotti D, Stürmer SL and Cardoso EJ (2015). Woody Mimosa species are nodulated by Burkholderia in ombrophylous forest soils and their symbioses are enhanced by arbuscular mycorrhizal fungi (AMF). Plant and Soil, 393(1-2):123-135, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: © 2015, Springer International Publishing Switzerland.Background and Aims: Mimosa is one of the largest genera in the Fabaceae, and includes several trees. They form symbioses with rhizobia and arbuscular mycorrizhal fungi (AMF), which improve nutrition and growth of host plants. Our objective was to analyze the tripartite symbiosis in two woody Mimosa species, and the natural occurrence of their symbiotic microorganisms in soils. Methods: Mimosa scabrella and M. bimucronata were grown in trap cultures using soils from Araucaria forests under three management systems: native, planted, and regenerating forest. Bacteria and AMF spores were isolated, identified and their symbiotic efficiency tested. Results: The Mimosa species trapped β-rhizobia (Burkholderia), putative endophytic bacteria (Pseudomonas, Herbaspirillum, and Xanthomonas), and AMF (Acaulospora, Ambispora, Gigaspora, Glomus, Paraglomus, Scutellospora, and Racocetra). The soils of the different forest managements led to distinct nodule bacterial diversity and AMF sporulation, but a predominance of Burkholderia and Acaulospora spp. was still observed in all areas. Some isolates showed potential to be used as inoculants, and higher nodulation in the presence of AMF was observed. Conclusions: Since different plant growth rates using different soils and microbial inocula were found, we suggest that the dual inoculation with selected β-rhizobia and AMF is desirable in reforestation projects involving Mimosa spp.

BibTeX:

@article{lammel_woody_2015,
author = {Lammel, Daniel R. and Cruz, Leonardo M. and Mescolotti, Denise and Stürmer, Sidney Luiz and Cardoso, Elke J.B.N.},
title = {Woody Mimosa species are nodulated by Burkholderia in ombrophylous forest soils and their symbioses are enhanced by arbuscular mycorrhizal fungi (AMF)},
journal = {Plant and Soil},
year = {2015},
volume = {393},
number = {1-2},
pages = {123--135},
note = {Publisher: Springer Science Business Media},
url = {http://dx.doi.org/10.1007/s11104-015-2470-0},
doi = {10.1007/s11104-015-2470-0}
}

Lima-Oliveira G, Lippi G, Salvagno GL, Gaino S, Poli G, Gelati M, Picheth G and Guidi GC (2015). Venous stasis and whole blood platelet aggregometry: A question of data reliability and patient safety. Blood Coagulation and Fibrinolysis, 26(6):665-668, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The assessment of platelet function by multiple electrode aggregometry (MEA) (Multiplate, Roche Diagnostics GmbH) is common in laboratory hematology. As regards the ISO 15189:2012 international standard, appropriate use of laboratory equipment requires appropriate pre-examination activities (e.g., blood collection). Venous stasis can influence several blood analytes, but the tourniquet time is rarely regarded as a source of variability. Aim of the present study was to evaluate the impact of venous stasis on platelet function by MEA. A total of 6 ml of blood was collected from 20 volunteers into two 3.0 ml Hirudin vacuum tube (Roche Diagnostics GmbH), and subjected to two procedures: procedure 1 (no stasis) - collection after localization of forearm vein by subcutaneous tissue transilluminator device without tourniquet; procedure 2 (stasis) - collection after localization of vein by prior 60 s tourniquet application. Samples were processed on Multiplate, for: ADP-test (without prostaglandin E1), ADP HS-test (with prostaglandin E1), ASPI-test, COL-test, RISTO H-test (high concentration, 0.77 mg/ml), RISTO L-test (low concentration, 0.20 mg/ml), and TRAP-test. The significance of the differences between samples was assessed by Wilcoxon ranked-pairs test. Surprisingly, the results of ADP HS-test, ASPI-test, COL-test, and RISTO H-test appeared unbiased by venous stasis. RISTO L-test, ADP-test, and TRAP-test were significantly biased; the mean percent difference between stasis and no stasis were S7.2% (PU0.040), S28.4% (PU0.015), and 1.1% (PU0.031), respectively. In conclusion, the tourniquet should be avoided when assessing platelet function by MEA.Copyright © 2015 Wolters Kluwer Health, Inc. All rights reserved.

BibTeX:

@article{lima-oliveira_venous_2015,
author = {Lima-Oliveira, Gabriel and Lippi, Giuseppe and Salvagno, Gian Luca and Gaino, Stefania and Poli, Giovanni and Gelati, Matteo and Picheth, Geraldo and Guidi, Gian Cesare},
title = {Venous stasis and whole blood platelet aggregometry: A question of data reliability and patient safety},
journal = {Blood Coagulation and Fibrinolysis},
year = {2015},
volume = {26},
number = {6},
pages = {665--668},
note = {ISBN: 0000000000000 Publisher: Ovid Technologies (Wolters Kluwer Health)},
url = {http://dx.doi.org/10.1097/mbc.0000000000000342},
doi = {10.1097/MBC.0000000000000342}
}

Marques AC, Paludo KS, Dallagassa CB, Surek M, Pedrosa FO, Souza EM, Cruz LM, LiPuma JJ, Zanata SM, Rego FG and Fadel-Picheth CM (2015). Biochemical characteristics, adhesion, and cytotoxicity of environmental and clinical isolates of Herbaspirillum spp. Journal of Clinical Microbiology, 53(1):302-308, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Herbaspirillum bacteria are best known as plant growth-promoting rhizobacteria but have also been recovered from clinical samples. Here, biochemical tests, matrix-assisted laser deionization-time of flight (MALDI-TOF) mass spectrometry, adherence, and cytotoxicity to eukaryotic cells were used to compare clinical and environmental isolates of Herbaspirillum spp. Discrete biochemical differences were observed between human and environmental strains. All strains adhered to HeLa cells at low densities, and cytotoxic effects were discrete, supporting the view that Herbaspirillum bacteria are opportunists with low virulence potential.

BibTeX:

@article{marques_biochemical_2015,
author = {Marques, Ana C.Q. and Paludo, Katia S. and Dallagassa, Cibelle B. and Surek, Monica and Pedrosa, Fábio O. and Souza, Emanuel M. and Cruz, Leonardo M. and LiPuma, John J. and Zanata, Sílvio M. and Rego, Fabiane G.M. and Fadel-Picheth, Cyntia M.T.},
editor = {Fenwick, B W},
title = {Biochemical characteristics, adhesion, and cytotoxicity of environmental and clinical isolates of Herbaspirillum spp},
journal = {Journal of Clinical Microbiology},
year = {2015},
volume = {53},
number = {1},
pages = {302--308},
note = {Publisher: American Society for Microbiology},
url = {http://dx.doi.org/10.1128/jcm.02192-14},
doi = {10.1128/JCM.02192-14}
}

Moriel B, Cruz LM, Dallagassa CB, Faoro H, de Souza EM, Pedrosa FO, Rego FG, Picheth G and Fadel-Picheth CM (2015). Draft Genome Sequence of Aeromonas caviae 8LM, Isolated from Stool Culture of a Child with Diarrhea. Genome Announc, 3(3):e00524-15, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Aeromonas spp. are Gram-negative rods ubiquitous in aquatic environments; however, some species are able to cause a variety of infections in humans. Here, we report the draft genome sequence of Aeromonas caviae 8LM isolated from stool culture from a child with diarrhea in southern Brazil.

BibTeX:

@article{moriel_draft_2015,
author = {Moriel, B and Cruz, L M and Dallagassa, C B and Faoro, H and de Souza, E M and Pedrosa, F O and Rego, F G and Picheth, G and Fadel-Picheth, C M},
title = {Draft Genome Sequence of Aeromonas caviae 8LM, Isolated from Stool Culture of a Child with Diarrhea},
journal = {Genome Announc},
year = {2015},
volume = {3},
number = {3},
pages = {e00524--15},
note = {ISBN: 2169-8287 (Electronic) Publisher: American Society for Microbiology},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25999559},
doi = {10.1128/genomeA.00524-15}
}

Müller CB, De Bastiani MA, Becker M, França FS, Branco MA, Castro MAA and Klamt F (2015). Potential crosstalk between cofilin-1 and EGFR pathways in cisplatin resistance of non-small-cell lung cancer. Oncotarget, 6(6):3531-9, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Current challenge in oncology is to establish the concept of personalized medicine in clinical practice. In this context, non-small-cell lung cancer (NSCLC) presents clinical, histological and molecular heterogeneity, being one of the most genomically diverse of all cancers. Recent advances added Epidermal Growth Factor Receptor (EGFR) as a predictive biomarker for patients with advanced NSCLC. In tumors with activating EGFR mutations, tyrosine kinase inhibitors (TKI) are indicated as first-line treatment, although restricted to a very small target population. In this context, cofilin-1 (a cytosolic protein involved with actin dynamics) has been widely studied as a biomarker of an aggressive phenotype in tumors, and overexpression of cofilin-1 is associated with cisplatin resistance and poor prognosis in NSCLC. Here, we gather information about the predictive potential of cofilin-1 and reviewed the crosstalk between cofilin-1/EGFR pathways. We aimed to highlight new perspectives of how these interactions might affect cisplatin resistance in NSCLC. We propose that cofilin-1 quantification in clinical samples in combination with presence/absence of EGFR mutation could be used to select patients that would benefit from TKI's treatment. This information is of paramount importance and could result in a possibility of guiding more effective treatments to NSCLC patients.

BibTeX:

@article{muller_potential_2015,
author = {Müller, Carolina Beatriz and De Bastiani, Marco Antônio and Becker, Matheus and França, Fernanda Stapenhorst and Branco, Mariane Araujo and Castro, Mauro Antônio Alves and Klamt, Fabio},
title = {Potential crosstalk between cofilin-1 and EGFR pathways in cisplatin resistance of non-small-cell lung cancer},
journal = {Oncotarget},
year = {2015},
volume = {6},
number = {6},
pages = {3531--9},
note = {ISBN: 1949-2553 Publisher: Impact Journals, LLC},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25784483%5Cnhttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4414134},
doi = {10.18632/oncotarget.3471}
}

Neto MR, Galvão CW, Cruz LM, Guizelini D, Silva LC, Garcia JR and Etto RM (2015). Multiple gene sequence analysis using genes of the bacterial DNA repair pathway. Brazilian Archives of Biology and Technology, 58(3):421-430, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The ability to recognize and repair abnormal DNA structures is common to all forms of life. Physiological studies and genomic sequencing of a variety of bacterial species have identified an incredible diversity of DNA repair pathways. Despite the amount of available genes in public database, the usual method to place genomes in a taxonomic context is based mainly on the 16S rRNA or housekeeping genes. Thus, the relationships among genomes remain poorly understood. In this work, an approach of multiple gene sequence analysis based on genes of DNA repair pathway was used to compare bacterial genomes. Housekeeping and DNA repair genes were searched in 872 completely sequenced bacterial genomes. Seven DNA repair and housekeeping genes from distinct metabolic pathways were selected, aligned, edited and concatenated head-to-tail to form a super-gene. Results showed that the multiple gene sequence analysis using DNA repair genes had better resolution at class level than the housekeeping genes. As housekeeping genes, the DNA repair genes were advantageous to separate bacterial groups at low taxonomic levels and also sensitive to genes derived from horizontal transfer.

BibTeX:

@article{neto_multiple_2015,
author = {Neto, Miguel Rotelok and Galvão, Carolina Weigert and Cruz, Leonardo Magalhães and Guizelini, Dieval and Silva, Leilane Caline and Garcia, Jarem Raul and Etto, Rafael Mazer},
title = {Multiple gene sequence analysis using genes of the bacterial DNA repair pathway},
journal = {Brazilian Archives of Biology and Technology},
year = {2015},
volume = {58},
number = {3},
pages = {421--430},
note = {Publisher: FapUNIFESP (SciELO)},
url = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132015000300421&lng=en&tlng=en http://dx.doi.org/10.1590/S1516-8913201500474},
doi = {10.1590/S1516-8913201500474}
}

Otemaier KR, Steffens M, Raittz RT, Brawerman A and Marchaukoski JN (2015). Biosom: Gene synonym analysis by self-organizing map. Genetics and Molecular Research, 14(1):1461-1468, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: There are several guidelines for gene nomenclature, but they are not always applied to the names of newly identified genes. The lack of standardization in naming genes generates inconsistent databases with errors such as genes with the same function and different names, genes with different functions and the same name, and use of an abbreviated name. This paper presents a methodology for predicting synonyms in a given gene nomenclature, thereby detecting and minimizing naming redundancy and inconsistency and facilitating the annotation of new genes and data mining in public databases. To identify gene synonyms, i.e., gene ambiguity, the methodology proposed begins by grouping genes according to their names using a Kohonen self-organizing map artificial neural network. Afterwards, it identifies the groups generated employing the Matrix-U technique. The employment of such techniques allows one to infer the synonyms of genes, to predict probable hypothetical gene names and to point out possible errors in a database record. Many mistakes related to gene nomenclature were detected in this research, demonstrating the importance of predicting synonyms. The methodology developed is applicable for describing hypothetical, putative and other types of genes without a known function. Moreover, it can also indicate a possible function for genes after grouping them.

BibTeX:

@article{otemaier_biosom_2015,
author = {Otemaier, K. R. and Steffens, M. and Raittz, R. T. and Brawerman, A. and Marchaukoski, J. N.},
title = {Biosom: Gene synonym analysis by self-organizing map},
journal = {Genetics and Molecular Research},
year = {2015},
volume = {14},
number = {1},
pages = {1461--1468},
note = {ISBN: 1676-5680 (Electronic) 1676-5680 (Linking) Publisher: Genetics and Molecular Research},
url = {http://dx.doi.org/10.4238/2015.february.20.1},
doi = {10.4238/2015.February.20.1}
}

Pankievicz VC, Do Amaral FP, Santos KF, Agtuca B, Xu Y, Schueller MJ, Arisi ACM, Steffens MB, De Souza EM, Pedrosa FO, Stacey G and Ferrieri RA (2015). Robust biological nitrogen fixation in a model grass-bacterial association. Plant Journal, 81(6):907-919, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Nitrogen-fixing rhizobacteria can promote plant growth; however, it is controversial whether biological nitrogen fixation (BNF) from associative interaction contributes to growth promotion. The roots of Setaria viridis, a model C4 grass, were effectively colonized by bacterial inoculants resulting in a significant enhancement of growth. Nitrogen-13 tracer studies provided direct evidence for tracer uptake by the host plant and incorporation into protein. Indeed, plants showed robust growth under nitrogen-limiting conditions when inoculated with an ammonium-excreting strain of Azospirillum brasilense. (11) C-labeling experiments showed that patterns in central carbon metabolism and resource allocation exhibited by nitrogen-starved plants were largely reversed by bacterial inoculation, such that they resembled plants grown under nitrogen-sufficient conditions. Adoption of S. viridis as a model should promote research into the mechanisms of associative nitrogen fixation with the ultimate goal of greater adoption of BNF for sustainable crop production.

BibTeX:

@article{pankievicz_robust_2015,
author = {Pankievicz, Vânia C.S. and Do Amaral, Fernanda P. and Santos, Karina F.D.N. and Agtuca, Beverly and Xu, Youwen and Schueller, Michael J. and Arisi, Ana Carolina M. and Steffens, Maria B.R. and De Souza, Emanuel M. and Pedrosa, Fábio O. and Stacey, Gary and Ferrieri, Richard A.},
title = {Robust biological nitrogen fixation in a model grass-bacterial association},
journal = {Plant Journal},
year = {2015},
volume = {81},
number = {6},
pages = {907--919},
note = {ISBN: 1365-313X (Electronic)$\backslash$r0960-7412 (Linking) Publisher: Wiley-Blackwell},
url = {http://dx.doi.org/10.1111/tpj.12777},
doi = {10.1111/tpj.12777}
}

Pereira JQ, Ambrosini A, Sant'Anna FH, Tadra-Sfeir M, Faoro H, Pedrosa FO, Souza EM, Brandelli A and Passaglia LMP (2015). Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment. Genome Announcements, 3(2):e00246-15, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments.

BibTeX:

@article{pereira_whole-genome_2015,
author = {Pereira, Jamile Queiroz and Ambrosini, Adriana and Sant'Anna, Fernando Hayashi and Tadra-Sfeir, Michele and Faoro, Helisson and Pedrosa, Fábio Oliveira and Souza, Emanuel Maltempi and Brandelli, Adriano and Passaglia, Luciane M. P.},
title = {Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment},
journal = {Genome Announcements},
year = {2015},
volume = {3},
number = {2},
pages = {e00246--15},
note = {ISBN: 1471216497 Publisher: American Society for Microbiology},
url = {http://genomea.asm.org/lookup/doi/10.1128/genomeA.00246-15},
doi = {10.1128/genomeA.00246-15}
}

Rodrigues BN, Steffens MB, Raittz RT, Santos-Weiss IC and Marchaukoski JN (2015). Quantitative assessment of protein function prediction programs. Genetics and Molecular Research, 14(4):17555-17566, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Fast prediction of protein function is essential for high-throughput sequencing analysis. Bioinformatic resources provide cheaper and faster techniques for function prediction and have helped to accelerate the process of protein sequence characterization. In this study, we assessed protein function prediction programs that accept amino acid sequences as input. We analyzed the classification, equality, and similarity between programs, and, additionally, compared program performance. The following programs were selected for our assessment: Blast2GO, InterProScan, PANTHER, Pfam, and ScanProsite. This selection was based on the high number of citations (over 500), fully automatic analysis, and the possibility of returning a single best classification per sequence. We tested these programs using 12 gold standard datasets from four different sources. The gold standard classification of the databases was based on expert analysis, the Protein Data Bank, or the Structure-Function Linkage Database. We found that the miss rate among the programs is globally over 50%. Furthermore, we observed little overlap in the correct predictions from each program. Therefore, a combination of multiple types of sources and methods, including experimental data, protein-protein interaction, and data mining, may be the best way to generate more reliable predictions and decrease the miss rate.

BibTeX:

@article{rodrigues_quantitative_2015,
author = {Rodrigues, B. N. and Steffens, M. B.R. and Raittz, R. T. and Santos-Weiss, I. C.R. and Marchaukoski, J. N.},
title = {Quantitative assessment of protein function prediction programs},
journal = {Genetics and Molecular Research},
year = {2015},
volume = {14},
number = {4},
pages = {17555--17566},
note = {Publisher: Genetics and Molecular Research},
url = {http://www.funpecrp.com.br/gmr/year2015/vol14-4/pdf/gmr6593.pdf http://dx.doi.org/10.4238/2015.December.21.28},
doi = {10.4238/2015.December.21.28}
}

Sanchuki HB, Valdameri G, Moure VR, Oliveira MA, Pedrosa FO, Souza EM, Korolik V and Huergo LF (2015). Purification of the Campylobacter jejuni Dps protein assisted by its high melting temperature. Protein Expression and Purification, 111:105-110, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Dps proteins (DNA binding protein from starved cell) form a distinct group within the ferritin superfamily. All Dps members are composed of 12 identical subunits that assemble into a conserved spherical protein shell. Dps oxidize Fe2+in a conserved ferroxidase center located at the interface between monomers, the product of the reaction Fe3+, is then stored inside the protein shell in the form of non-reactive insoluble Fe2O3. The Campylobacter jejuni Dps (CjDps) has been reported to play a plethora of functions, such as DNA binding and protection, iron storage, survival in response to hydrogen peroxide and sulfatide binding. CjDps is also important during biofilm formation and caecal colonization in poultry. In order to facilitate in vitro characterisation of CjDps, it is important to have a simple and reproducible protocol for protein purification. Here we report an observation that CjDps has an unusual high melting temperature. We exploited this property for protein purification by introducing a thermal treatment step which allowed achieving homogeneity by using only two chromatographic steps. Gel filtration chromatography, circular dichroism, mass spectrometry, DNA-binding and iron oxidation analysis confirmed that the CjDps structure and function were unaffected.

BibTeX:

@article{sanchuki_purification_2015,
author = {Sanchuki, Heloisa B.S. and Valdameri, Glaucio and Moure, Vivian R. and Oliveira, Marco A. and Pedrosa, Fábio O. and Souza, Emanuel M. and Korolik, Victoria and Huergo, Luciano F.},
title = {Purification of the Campylobacter jejuni Dps protein assisted by its high melting temperature},
journal = {Protein Expression and Purification},
year = {2015},
volume = {111},
pages = {105--110},
note = {Publisher: Elsevier BV},
url = {http://dx.doi.org/10.1016/j.pep.2014.12.011},
doi = {10.1016/j.pep.2014.12.011}
}

Schönhofen P, de Medeiros LM, Bristot IJ, Lopes FM, De Bastiani MA, Kapczinski F, Crippa JAS, Castro MAA, Parsons RB and Klamt F (2015). Cannabidiol Exposure During Neuronal Differentiation Sensitizes Cells Against Redox-Active Neurotoxins. Molecular Neurobiology, 52(1):26-37, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Cannabidiol (CBD), one of the most abundant Cannabis sativa-derived compds., has been implicated with neuroprotective effect in several human pathologies. Until now, no undesired side effects have been assocd. with CBD. In this study, we evaluated CBD's neuroprotective effect in terminal differentiation (mature) and during neuronal differentiation (neuronal developmental toxicity model) of the human neuroblastoma SH-SY5Y cell line. A dose-response curve was performed to establish a sublethal dose of CBD with antioxidant activity (2.5 μM). In terminally differentiated SH-SY5Y cells, incubation with 2.5 μM CBD was unable to protect cells against the neurotoxic effect of glycolaldehyde, methylglyoxal, 6-hydroxydopamine, and hydrogen peroxide (H2O2). Moreover, no difference in antioxidant potential and neurite d. was obsd. When SH-SY5Y cells undergoing neuronal differentiation were exposed to CBD, no differences in antioxidant potential and neurite d. were obsd. However, CBD potentiated the neurotoxicity induced by all redox-active drugs tested. Our data indicate that 2.5 μM of CBD, the higher dose tolerated by differentiated SH-SY5Y neuronal cells, does not provide neuroprotection for terminally differentiated cells and shows, for the first time, that exposure of CBD during neuronal differentiation could sensitize immature cells to future challenges with neurotoxins. [on SciFinder(R)]

BibTeX:

@article{schonhofen_cannabidiol_2015,
author = {Schönhofen, Patrícia and de Medeiros, Liana M. and Bristot, Ivi Juliana and Lopes, Fernanda M. and De Bastiani, Marco A. and Kapczinski, Flávio and Crippa, José Alexandre S. and Castro, Mauro Antônio A. and Parsons, Richard B. and Klamt, Fábio},
title = {Cannabidiol Exposure During Neuronal Differentiation Sensitizes Cells Against Redox-Active Neurotoxins},
journal = {Molecular Neurobiology},
year = {2015},
volume = {52},
number = {1},
pages = {26--37},
note = {ISBN: 0893-7648 Publisher: Springer Science Business Media},
url = {http://dx.doi.org/10.1007/s12035-014-8843-1},
doi = {10.1007/s12035-014-8843-1}
}

Stets MI, Campbell Alqueres SM, Souza EM, Pedrosa FdO, Schmid M, Hartmann A and Cruz LM (2015). Quantification of Azospirillum brasilense FP2 bacteria in wheat roots by strain-specific quantitative PCR. Applied and Environmental Microbiology, 81(19):6700-6709, 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Azospirillum is a rhizobacterial genus containing plant growth-promoting species associated with different crops worldwide. Azospirillum brasilense strains exhibit a growth-promoting effect by means of phytohormone production and possibly by N2 fixation. However, one of the most important factors for achieving an increase in crop yield by plant growth-promoting rhizobacteria is the survival of the inoculant in the rhizosphere, which is not always achieved. The objective of this study was to develop quantitative PCR protocols for the strain-specific quantification of A. brasilense FP2. A novel approach was applied to identify strain-specific DNA sequences based on a comparison of the genomic sequences within the same species. The draft genome sequences of A. brasilense FP2 and Sp245 were aligned, and FP2-specific regions were filtered and checked for other possible matches in public databases. Strain-specific regions were then selected to design and evaluate strain-specific primer pairs. The primer pairs AzoR2.1, AzoR2.2, AzoR5.1, AzoR5.2, and AzoR5.3 were specific for the A. brasilense FP2 strain. These primer pairs were used to monitor quantitatively the population of A. brasilense in wheat roots under sterile and nonsterile growth conditions. In addition, coinoculations with other plant growth-promoting bacteria in wheat were performed under nonsterile conditions. The results showed that A. brasilense FP2 inoculated into wheat roots is highly competitive and achieves high cell numbers (∼10(7) CFU/g [fresh weight] of root) in the rhizosphere even under nonsterile conditions and when coinoculated with other rhizobacteria, maintaining the population at rather stable levels for at least up to 13 days after inoculation. The strategy used here can be applied to other organisms whose genome sequences are available.

BibTeX:

@article{stets_quantification_2015,
author = {Stets, Maria Isabel and Campbell Alqueres, Sylvia Maria and Souza, Emanuel Maltempi and Pedrosa, Fábio de Oliveira and Schmid, Michael and Hartmann, Anton and Cruz, Leonardo Magalhães},
editor = {Lovell, C R},
title = {Quantification of Azospirillum brasilense FP2 bacteria in wheat roots by strain-specific quantitative PCR},
journal = {Applied and Environmental Microbiology},
year = {2015},
volume = {81},
number = {19},
pages = {6700--6709},
note = {Publisher: American Society for Microbiology},
url = {http://dx.doi.org/10.1128/aem.01351-15},
doi = {10.1128/AEM.01351-15}
}

Tadra-Sfeir MZ, Faoro H, Camilios-Neto D, Brusamarello-Santos L, Balsanelli E, Weiss V, Baura VA, Wassem R, Cruz LM, De Oliveira Pedrosa F, Souza EM and Monteiro RA (2015). Genome wide transcriptional profiling of Herbaspirillum seropedicae SmR1 grown in the presence of naringenin. Frontiers in Microbiology, 6(MAY) 2015.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Herbaspirillum seropedicae is a diazotrophic bacterium which associates endophytically with economically important gramineae. Flavonoids such as naringenin have been shown to have an effect on the interaction between H. seropedicae and its host plants. We used a high-throughput sequencing based method (RNA-Seq) to access the influence of naringenin on the whole transcriptome profile of H. seropedicae. Three hundred and four genes were downregulated and seventy seven were upregulated by naringenin. Data analysis revealed that genes related to bacterial flagella biosynthesis, chemotaxis and biosynthesis of peptidoglycan were repressed by naringenin. Moreover, genes involved in aromatic metabolism and multidrug transport efllux were actived.

BibTeX:

@article{tadra-sfeir_genome_2015,
author = {Tadra-Sfeir, Michelle Z. and Faoro, Helisson and Camilios-Neto, Doumit and Brusamarello-Santos, Liziane and Balsanelli, Eduardo and Weiss, Vinicius and Baura, Valter A. and Wassem, Roseli and Cruz, Leonardo M. and De Oliveira Pedrosa, Fábio and Souza, Emanuel M. and Monteiro, Rose A.},
title = {Genome wide transcriptional profiling of Herbaspirillum seropedicae SmR1 grown in the presence of naringenin},
journal = {Frontiers in Microbiology},
year = {2015},
volume = {6},
number = {MAY},
note = {ISBN: 1664-302X (Electronic)$\backslash$r1664-302X (Linking) Publisher: Frontiers Media SA},
url = {http://dx.doi.org/10.3389/fmicb.2015.00491},
doi = {10.3389/fmicb.2015.00491}
}

Welter M, Frigeri HR, Réa RR, de Souza EM, Alberton D, Picheth G and Rego FGdM (2015). The rs10885122 polymorphism of the adrenoceptor alpha 2A (ADRA2A) gene in Euro-Brazilians with type 2 diabetes mellitus. Archives of Endocrinology and Metabolism, 59(1):29-33, 2015.
[Abstract] [DOI] [BibTeX]

Abstract: OBJECTIVE: To investigate the association of the rs10885122GtextgreaterT polymorphism in the ADRA2A gene in a Euro-Brazilian sample of healthy (controls) and type 2 diabetic (T2D) subjects.
SUBJECTS AND METHODS: We used fluorescent probes (TaqMan) to genotype 241 subjects, that is, 121 healthy and 120 T2D subjects, who were classified based on the Brazilian Diabetes Association (2013) and American Diabetes Association (2014) criteria.
RESULTS: The genotype and allele frequencies showed no significant (P textgreater 0.05) difference between the two studied groups. The minor allele (T) frequencies (95 for rs10885122 were 19% (14-24 and 20% (15-26 for healthy and T2D groups, respectively. Carriers of the T allele (genotypes GT+TT) were significantly associated (P = 0.016) with approximately a 7-kg body weight reduction compared with the genotype GG, which was only found in the T2D group.
CONCLUSION: The rs10885122GtextgreaterT polymorphism of the ADRA2A gene was not associated with T2D in Euro-Brazilians, and carriers of the T allele had lower body weight in the presence of T2D.

BibTeX:

@article{welter_rs10885122_2015,
author = {Welter, Marciane and Frigeri, Henrique Ravanhol and Réa, Rosângela Roginski and de Souza, Emanuel Maltempi and Alberton, Dayane and Picheth, Geraldo and Rego, Fabiane Gomes de Moraes},
title = {The rs10885122 polymorphism of the adrenoceptor alpha 2A (ADRA2A) gene in Euro-Brazilians with type 2 diabetes mellitus},
journal = {Archives of Endocrinology and Metabolism},
year = {2015},
volume = {59},
number = {1},
pages = {29--33},
doi = {10.1590/2359-3997000000006}
}

Assis FE, Wolf S, Surek M, De Toni F, Souza EM, Pedrosa FO, Farah SM, Picheth G and Fadel-Picheth CM (2014). Impact of aeromonas and diarrheagenic escherichia coli screening in patients with diarrhea in Paraná, Southern Brazil. Journal of Infection in Developing Countries, 8(12):1609-1614, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: INTRODUCTION: A wide diversity of bacterial agents may cause diarrhea, presenting challenges to clinical laboratories to define a diagnosis. Considering that most stool cultures are negative, we screened stool samples from patients with diarrhea for the presence of 14 bacterial enteropathogens, aiming to establish which of them should be included in routine stool analysis. METHODOLOGY: Stool samples from 400 patients with diarrhea were analyzed for the presence of Salmonella, Shigella, Campylobacter, Aeromonas, Plesiomonas shigelloides, Vibrio, Yersinia enterocolitica, and diarrheagenic Escherichia coli using conventional microbiological methods and PCR. Two distinct samples were studied; one included predominantly patients involved in outbreaks, and the other patients of low socioeconomic status presenting sporadic cases of diarrhea. RESULTS: In total, 86 cultures (21.5 were positive. Mixed infections were found in five patients, leading to recovery of 91 strains of enteropathogenic bacteria: Salmonella Enteritidis (9.2, Aeromonas (7.2, diarrheagenic E. coli (5.2, and C. jejuni (1. However, Salmonella predominated, with 11.5% frequency in diarrhea outbreaks, while Aeromonas predominated among patients of low socioeconomic status, with 14.6% frequency. CONCLUSION: Aeromonas and diarrheagenic E. coli, which are not routinely screened for, deserve to be included in laboratory screening panels.

BibTeX:

@article{assis_impact_2014,
author = {Assis, Flávia E.A. and Wolf, Suélen and Surek, Monica and De Toni, Fabiana and Souza, Emanuel M. and Pedrosa, Fábio O. and Farah, Sônia M.S.S. and Picheth, Geraldo and Fadel-Picheth, Cyntia M.T.},
title = {Impact of aeromonas and diarrheagenic escherichia coli screening in patients with diarrhea in Paraná, Southern Brazil},
journal = {Journal of Infection in Developing Countries},
year = {2014},
volume = {8},
number = {12},
pages = {1609--1614},
note = {ISBN: 1972-2680 Publisher: Journal of Infection in Developing Countries},
url = {http://dx.doi.org/10.3855/jidc.4434},
doi = {10.3855/jidc.4434}
}

Balsanelli E, De Baura VA, De Oliveira Pedrosa F, De Souza EM and Monteiro RA (2014). Exopolysaccharide biosynthesis enables mature biofilm formation on abiotic surfaces by herbaspirillum seropedicae. PLoS ONE, 9(10):e110392, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: H. seropedicae associates endophytically and epiphytically with important poaceous crops and is capable of promoting their growth. The molecular mechanisms involved in plant colonization by this microrganism are not fully understood. Exopolysaccharides (EPS) are usually necessary for bacterial attachment to solid surfaces, to other bacteria, and to form biofilms. The role of H. seropedicae SmR1 exopolysaccharide in biofilm formation on both inert and plant substrates was assessed by characterization of a mutant in the espB gene which codes for a glucosyltransferase. The mutant strain was severely affected in EPS production and biofilm formation on glass wool. In contrast, the plant colonization capacity of the mutant strain was not altered when compared to the parental strain. The requirement of EPS for biofilm formation on inert surface was reinforced by the induction of eps genes in biofilms grown on glass and polypropylene. On the other hand, a strong repression of eps genes was observed in H. seropedicae cells adhered to maize roots. Our data suggest that H. seropedicae EPS is a structural component of mature biofilms, but this development stage of biofilm is not achieved during plant colonization.

BibTeX:

@article{balsanelli_exopolysaccharide_2014,
author = {Balsanelli, Eduardo and De Baura, Válter Antonio and De Oliveira Pedrosa, Fábio and De Souza, Emanuel Maltempi and Monteiro, Rose Adele},
editor = {Otto, Michael},
title = {Exopolysaccharide biosynthesis enables mature biofilm formation on abiotic surfaces by herbaspirillum seropedicae},
journal = {PLoS ONE},
year = {2014},
volume = {9},
number = {10},
pages = {e110392},
note = {Publisher: Public Library of Science (PLoS)},
url = {http://dx.doi.org/10.1371/journal.pone.0110392},
doi = {10.1371/journal.pone.0110392}
}

Boritza KC, Dos Santos-Weiss ICR, Da Silva Couto Alves A, Réa RR, Pedrosa FO, De Souza EM, Picheth G and De Moraes Rego FG (2014). 1,5 Anhydroglucitol serum concentration as a biomarker for screening gestational diabetes in early pregnancy. 52(8) 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Abstract As a companion to Part I, which discussed the calibration of probabilistic 2-m temperature forecasts using large training datasets, Part II discusses the calibration of probabilistic forecasts of 12-hourly precipitation amounts. Again, large ensemble reforecast datasets from the European Centre for Medium-Range Weather Forecasts (ECMWF) and the Global Forecast System (GFS) were used for testing and calibration. North American Regional Reanalysis (NARR) 12-hourly precipitation analysis data were used for verification and training. Logistic regression was used to perform the calibration, with power-transformed ensemble means and spreads as predictors. Forecasts were produced and validated for every NARR grid point in the conterminous United States (CONUS). Training sample sizes were increased by including data from 10 nearby grid points with similar analyzed climatologies. “Raw” probabilistic forecasts from each system were considered, in which probabilities were set according to ensemble relative ...

BibTeX:

@book{boritza_15_2014,
author = {Boritza, Kátia Cristina and Dos Santos-Weiss, Izabella Castilhos Ribeiro and Da Silva Couto Alves, Alexessander and Réa, Rosângela Roginski and Pedrosa, Fábio Oliveira and De Souza, Emanuel Maltempi and Picheth, Geraldo and De Moraes Rego, Fabiane Gomes},
title = {1,5 Anhydroglucitol serum concentration as a biomarker for screening gestational diabetes in early pregnancy},
publisher = {Walter de Gruyter GmbH},
year = {2014},
volume = {52},
number = {8},
note = {ISSN: 14374331 Publication Title: Clinical Chemistry and Laboratory Medicine},
url = {http://dx.doi.org/10.1515/cclm-2013-1042},
doi = {10.1515/cclm-2013-1042}
}

Brawerman A, Bortoloti C, Guimaraes LB, Granato LC, Aroldi MD and Souza VMD (2014). Educating Through Mobile Devices: The ABC Game, a Study Case. Int. J. Recent Contrib. Eng. Sci. IT, 2(3):4, 2014.
[DOI] [URL] [BibTeX]

Abstract:

BibTeX:

@article{brawerman_educating_2014,
author = {Brawerman, Alessandro and Bortoloti, Cristopher and Guimaraes, Leonardo Basso and Granato, Luca Chamecki and Aroldi, Mauricio Domingues and Souza, Vinicius Mendes De},
title = {Educating Through Mobile Devices: The ABC Game, a Study Case},
journal = {Int. J. Recent Contrib. Eng. Sci. IT},
year = {2014},
volume = {2},
number = {3},
pages = {4},
note = {Publisher: International Association of Online Engineering (IAOE)},
url = {http://dx.doi.org/10.3991/ijes.v2i3.3817},
doi = {10.3991/ijes.v2i3.3817}
}

Camilios-Neto D, Bonato P, Wassem R, Tadra-Sfeir MZ, Brusamarello-Santos LC, Valdameri G, Donatti L, Faoro H, Weiss VA, Chubatsu LS, Pedrosa FO and Souza EM (2014). Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes. BMC Genomics, 15(1):378, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: BACKGROUND: The rapid growth of the world's population demands an increase in food production that no longer can be reached by increasing amounts of nitrogenous fertilizers. Plant growth promoting bacteria (PGPB) might be an alternative to increase nitrogenous use efficiency (NUE) in important crops such wheat. Azospirillum brasilense is one of the most promising PGPB and wheat roots colonized by A. brasilense is a good model to investigate the molecular basis of plant-PGPB interaction including improvement in plant-NUE promoted by PGPB. RESULTS: We performed a dual RNA-Seq transcriptional profiling of wheat roots colonized by A. brasilense strain FP2. cDNA libraries from biological replicates of colonized and non-inoculated wheat roots were sequenced and mapped to wheat and A. brasilense reference sequences. The unmapped reads were assembled de novo. Overall, we identified 23,215 wheat expressed ESTs and 702 A. brasilense expressed transcripts. Bacterial colonization caused changes in the expression of 776 wheat ESTs belonging to various functional categories, ranging from transport activity to biological regulation as well as defense mechanism, production of phytohormones and phytochemicals. In addition, genes encoding proteins related to bacterial chemotaxi, biofilm formation and nitrogen fixation were highly expressed in the sub-set of A. brasilense expressed genes. CONCLUSIONS: PGPB colonization enhanced the expression of plant genes related to nutrient up-take, nitrogen assimilation, DNA replication and regulation of cell division, which is consistent with a higher proportion of colonized root cells in the S-phase. Our data support the use of PGPB as an alternative to improve nutrient acquisition in important crops such as wheat, enhancing plant productivity and sustainability.

BibTeX:

@article{camilios-neto_dual_2014,
author = {Camilios-Neto, Doumit and Bonato, Paloma and Wassem, Roseli and Tadra-Sfeir, Michelle Z. and Brusamarello-Santos, Liziane C.C. and Valdameri, Glaucio and Donatti, Lucélia and Faoro, Helisson and Weiss, Vinicius A. and Chubatsu, Leda S. and Pedrosa, Fábio O. and Souza, Emanuel M.},
title = {Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes},
journal = {BMC Genomics},
year = {2014},
volume = {15},
number = {1},
pages = {378},
note = {ISBN: 1471-2164 Publisher: Springer Science Business Media},
url = {http://dx.doi.org/10.1186/1471-2164-15-378},
doi = {10.1186/1471-2164-15-378}
}

da Franca Aguiar G, Brawerman A, Barbara CXC and Wilhelm VE (2014). A Game Theory Approach Using Excel. Journal of Mechanics Engineering and Automation, 4(9) 2014.
[BibTeX]

Abstract:

BibTeX:

@article{da_franca_aguiar_game_2014,
author = {da Franca Aguiar, Giancarlo and Brawerman, Alessandro and Barbara, C X C and Wilhelm, Volmir E},
title = {A Game Theory Approach Using Excel},
journal = {Journal of Mechanics Engineering and Automation},
year = {2014},
volume = {4},
number = {9},
note = {Publisher: David Publishing Company, Inc.}
}

Dallagassa CB, Huergo LF, Stets MI, Pedrosa FO, Souza EM, Cruz LM, Assis FE, Wolf S, Volanski W, Picheth G, Pigatto-Denardi CP, Farah SM and Fadel-Picheth CM (2014). Matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis of Escherichia coli categories. Genetics and Molecular Research, 13(1):716-722, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The mass profiles of cell-free extracts of 180 commensal and pathogenic strains of Escherichia coli were determined by MALDI-TOF mass spectrometry (MS). While some peaks were highly conserved in all E. coli, several peaks occurred only in some strains, showing heterogeneity among them. We did not detect strain-specific peaks for any of the E. coli categories tested. However, review of the fully conserved and the variable peaks suggested that MALDI-TOF MS has the potential to distinguish commensal and uropathogenic E. coli strains. Additionally, eight Shigella sonnei isolates were tested and found to be indistinguishable from E. coli by MALDI-TOF MS under the test conditions.

BibTeX:

@article{dallagassa_matrix-assisted_2014,
author = {Dallagassa, C. B. and Huergo, L. F. and Stets, M. I. and Pedrosa, F. O. and Souza, E. M. and Cruz, L. M. and Assis, F. E.A. and Wolf, S. and Volanski, W. and Picheth, G. and Pigatto-Denardi, C. P. and Farah, S. M.S.S. and Fadel-Picheth, C. M.T.},
title = {Matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis of Escherichia coli categories},
journal = {Genetics and Molecular Research},
year = {2014},
volume = {13},
number = {1},
pages = {716--722},
note = {ISBN: 1676-5680 (Electronic)$\backslash$r1676-5680 (Linking) Publisher: Genetics and Molecular Research},
url = {http://www.funpecrp.com.br/gmr/year2014/vol13-1/pdf/gmr2752.pdf http://dx.doi.org/10.4238/2014.january.29.2},
doi = {10.4238/2014.January.29.2}
}

D'Oliveira Albanus R, Siqueira Dalmolin RJ, Rybarczyk-Filho JL, Alves Castro MA and Fonseca Moreira JC (2014). Differential evolutionary constraints in the evolution of chemoreceptors: A murine and human case study. The Scientific World Journal, 2014:1-9, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Chemoreception is among the most important sensory modalities in animals. Organisms use the ability to perceive chemical compounds in all major ecological activities. Recent studies have allowed the characterization of chemoreceptor gene families. These genes present strikingly high variability in copy numbers and pseudogenization degrees among different species, but the mechanisms underlying their evolution are not fully understood. We have analyzed the functional networks of these genes, their orthologs distribution, and performed phylogenetic analyses in order to investigate their evolutionary dynamics. We have modeled the chemosensory networks and compared the evolutionary constraints of their genes in Mus musculus, Homo sapiens, and Rattus norvegicus. We have observed significant differences regarding the constraints on the orthologous groups and network topologies of chemoreceptors and signal transduction machinery. Our findings suggest that chemosensory receptor genes are less constrained than their signal transducing machinery, resulting in greater receptor diversity and conservation of information processing pathways. More importantly, we have observed significant differences among the receptors themselves, suggesting that olfactory and bitter taste receptors are more conserved than vomeronasal receptors.

BibTeX:

@article{doliveira_albanus_differential_2014,
author = {D'Oliveira Albanus, Ricardo and Siqueira Dalmolin, Rodrigo Juliani and Rybarczyk-Filho, José Luiz and Alves Castro, Mauro Antônio and Fonseca Moreira, José Cláudio},
title = {Differential evolutionary constraints in the evolution of chemoreceptors: A murine and human case study},
journal = {The Scientific World Journal},
year = {2014},
volume = {2014},
pages = {1--9},
note = {ISBN: 1537-744X (Electronic)$\backslash$r1537-744X (Linking) Publisher: Hindawi Publishing Corporation},
url = {http://dx.doi.org/10.1155/2014/696485},
doi = {10.1155/2014/696485}
}

Etto RM, Cruz LM, Da Conceição Jesus E, Galvão CW, Galvão F, De Souza EM, De Oliveira Pedrosa F and Reynaud Steffens MB (2014). Seasonal changes in dominant bacterial taxa from acidic peatlands of the Atlantic Rain Forest. Research in Microbiology, 165(7):517-525, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The acidic peatlands of southern Brazil are essential for maintenance of the Atlantic Rain Forest, one of the 25 hot-spots of biodiversity in the world. While these ecosystems are closely linked to conservation issues, their microbial community ecology and composition remain unknown. In this work, histosol samples were collected from three acidic peatland regions during dry and rainy seasons and their chemical and microbial characteristics were evaluated. Culturing and culture-independent approaches based on SSU rRNA gene pyrosequencing were used to survey the bacterial community and to identify environmental factors affecting the biodiversity and microbial metabolic potential of the Brazilian peatlands. All acidic peatlands were dominated by the Acidobacteria phylum (56-22 followed by Proteobacteria (28-12. The OTU richness of these phyla and the abundance of their Gp1, Gp2, Gp3, Gp13, Rhodospirillales and Caulobacteriales members varied according to the period of collection and significantly correlated with the rainy season. However, despite changes in acidobacterial and proteobacterial communities, rainfall did not affect the microbial metabolic potential of the southern Brazilian Atlantic Rain Forest peatlands, as judged by the metabolic capabilities of the microbial community.

BibTeX:

@article{etto_seasonal_2014,
author = {Etto, Rafael Mazer and Cruz, Leonardo Magalhães and Da Conceição Jesus, Ederson and Galvão, Carolina Weigert and Galvão, Franklin and De Souza, Emanuel Maltempi and De Oliveira Pedrosa, Fábio and Reynaud Steffens, Maria Berenice},
title = {Seasonal changes in dominant bacterial taxa from acidic peatlands of the Atlantic Rain Forest},
journal = {Research in Microbiology},
year = {2014},
volume = {165},
number = {7},
pages = {517--525},
note = {Publisher: Elsevier BV},
url = {http://dx.doi.org/10.1016/j.resmic.2014.05.036},
doi = {10.1016/j.resmic.2014.05.036}
}

Frigeri HR, Martins LT, Auwerter NC, dos Santos-Weiss ICR, Pedrosa FO, de Souza EM, de Moraes Rego FG and Picheth G (2014). The polymorphism rs2268574 in Glucokinase gene is associated with gestational Diabetes mellitus. Clinical Biochemistry, 47(6):499-500, 2014.
[DOI] [URL] [BibTeX]

Abstract:

BibTeX:

@article{frigeri_polymorphism_2014,
author = {Frigeri, Henrique Ravanhol and Martins, Laysa Toschi and Auwerter, Nathalia Cavalheiro and dos Santos-Weiss, Izabella Castilhos Ribeiro and Pedrosa, Fábio Oliveira and de Souza, Emanuel Maltempi and de Moraes Rego, Fabiane Gomes and Picheth, Geraldo},
title = {The polymorphism rs2268574 in Glucokinase gene is associated with gestational Diabetes mellitus},
journal = {Clinical Biochemistry},
year = {2014},
volume = {47},
number = {6},
pages = {499--500},
note = {ISBN: 1873-2933 (Electronic)$\backslash$r0009-9120 (Linking) Publisher: Elsevier BV},
url = {http://dx.doi.org/10.1016/j.clinbiochem.2014.01.024},
doi = {10.1016/j.clinbiochem.2014.01.024}
}

Lira PHM, Giraldi GA, Neves LAP and Feijóo RA (2014). Dental R-ray image segmentation using texture recognition. IEEE Latin America Transactions, 12(4):694-698, 2014.
[Abstract] [DOI] [BibTeX]

Abstract: Panoramic x-ray images are very popular as a first tool for diagnosis in odontological protocols. Automating the process of analysis of such images is important in order to help dentist procedures. In this process, teeth segmentation of the radiographic images is an essential step. In this paper, we propose a segmentation approach based on a supervised learning technique for texture recognition. Firstly, feature extraction is performed by computing moments and statistical features. The obtained data are the input to a Bayesian classifier that, after training, can distinguish two classes of pixels: active (inside the target texture) or inactive (outside the teeth). In the experimental results we show that the methodology is a promising one for teeth segmentation in panoramic x-ray images and discuss its limitations.

BibTeX:

@article{lira_dental_2014,
author = {Lira, P. H M and Giraldi, G. A. and Neves, L. A P and Feijóo, R. A.},
title = {Dental R-ray image segmentation using texture recognition},
journal = {IEEE Latin America Transactions},
year = {2014},
volume = {12},
number = {4},
pages = {694--698},
note = {ISBN: 1548-0992 Publisher: IEEE},
doi = {10.1109/TLA.2014.6868871}
}

Lisbôa Da Motta L, Müller CB, De Bastiani MA, Behr GA, França FS, Da Rocha RF, Minotto JB, Meurer RT, Fernandes MC, Roehe A, Markoski MM, Andrade CF, Castro MA and Klamt F (2014). Imbalance in redox status is associated with tumor aggressiveness and poor outcome in lung adenocarcinoma patients. Journal of Cancer Research and Clinical Oncology, 140(3):461-470, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: PURPOSE: The expression levels of human antioxidant genes (HAGs) and oxidative markers were investigated in light of lung adenocarcinoma aggressiveness and patient outcome. METHODS: We assayed in vitro the tumoral invasiveness and multidrug resistance in human lung adenocarcinoma (AdC) cell lines (EKVX and A549). Data were associated with several redox parameters and differential expression levels of HAG network. The clinicopathological significance of these findings was investigated using microarray analysis of tumor tissue and by immunohistochemistry in archival collection of biopsies. RESULTS: An overall increased activity (expression) of selected HAG components in the most aggressive cell line (EKVX cells) was observed by bootstrap and gene set enrichment analysis (GSEA). In vitro validation of oxidative markers revealed that EKVX cells had high levels of oxidative stress markers. In AdC cohorts, GSEA of microarray datasets showed significantly high levels of HAG components in lung AdC samples in comparison with normal tissue, in advanced stage compared with early stage and in patients with poor outcome. Cox multivariate regression analysis in a cohort of early pathologic (p)-stage of AdC cases showed that patients with moderate levels of 4-hydroxynonenal, a specific and stable end product of lipid peroxidation, had a significantly less survival rate (hazard ratio of 8.87) (P \textless 0.05). CONCLUSIONS: High levels of oxidative markers are related to tumor aggressiveness and can predict poor outcome of early-stage lung adenocarcinoma patients.

BibTeX:

@article{lisboa_da_motta_imbalance_2014,
author = {Lisbôa Da Motta, Leonardo and Müller, Carolina B. and De Bastiani, Marco A. and Behr, Guilherme A. and França, Fernanda S. and Da Rocha, Ricardo F. and Minotto, Juliane B. and Meurer, Rosalva T. and Fernandes, Marilda C. and Roehe, Adriana and Markoski, Melissa M. and Andrade, Cristiano F. and Castro, Mauro A.A. and Klamt, Fábio},
title = {Imbalance in redox status is associated with tumor aggressiveness and poor outcome in lung adenocarcinoma patients},
journal = {Journal of Cancer Research and Clinical Oncology},
year = {2014},
volume = {140},
number = {3},
pages = {461--470},
note = {ISBN: 1432-1335 (Electronic)$\backslash$r0171-5216 (Linking) Publisher: Springer Science Business Media},
url = {http://dx.doi.org/10.1007/s00432-014-1586-6},
doi = {10.1007/s00432-014-1586-6}
}

Moure VR, Costa FF, Cruz LM, Pedrosa FO, Souza EM, Li XD, Winkler F and Huergo LF (2014). Regulation of nitrogenase by reversible mono-ADP-ribosylation. Current Topics in Microbiology and Immunology, 384:89-106, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Posttranslational modification of proteins plays a key role in the regulation of a plethora of metabolic functions. Protein modification by mono-ADP-ribosylation was first described as a mechanism of action of bacterial toxins. Since these pioneering studies, the number of pathways regulated by ADP-ribosylation in organisms from all domains of life expanded significantly. However, in only a few cases the full regulatory ADP-ribosylation circuit is known. Here, we review the system where mono-ADP-ribosylation regulates the activity of an enzyme: the regulation of nitrogenase in bacteria. When the nitrogenase product, ammonium, becomes available, the ADP-ribosyltransferase (DraT) covalently links an ADP-ribose moiety to a specific arginine residue on nitrogenase switching-off nitrogenase activity. After ammonium exhaustion, the ADP-ribosylhydrolase (DraG) removes the modifying group, restoring nitrogenase activity. DraT and DraG activities are reversibly regulated through interaction with PII signaling proteins . Bioinformatics analysis showed that DraT homologs are restricted to a few nitrogen-fixing bacteria while DraG homologs are widespread in Nature. Structural comparisons indicated that bacterial DraG is closely related to Archaea and mammalian ADP-ribosylhydrolases (ARH). In all available structures, the ARH active site consists of a hydrophilic cleft carrying a binuclear Mg2+ or Mn2+ cluster, which is critical for catalysis.

BibTeX:

@article{moure_regulation_2014,
author = {Moure, Vivian R. and Costa, Flavia F. and Cruz, Leonardo M. and Pedrosa, Fabio O. and Souza, Emanuel M. and Li, Xiao Dan and Winkler, Fritz and Huergo, Luciano F.},
title = {Regulation of nitrogenase by reversible mono-ADP-ribosylation},
journal = {Current Topics in Microbiology and Immunology},
year = {2014},
volume = {384},
pages = {89--106},
note = {ISBN: 0070-217X (Print)$\backslash$r0070-217X (Linking) Publisher: Springer Science Business Media},
url = {http://dx.doi.org/10.1007/82_2014_380},
doi = {10.1007/82_2014_380}
}

Neiverth A, Delai S, Garcia DM, Saatkamp K, de Souza EM, Pedrosa FdO, Guimarães VF, dos Santos MF, Vendruscolo ECG and da Costa ACT (2014). Performance of different wheat genotypes inoculated with the plant growth promoting bacterium Herbaspirillum seropedicae. European Journal of Soil Biology, 64:1-5, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Several diazotrophic bacteria can promote plant growth and increase crop productivity. However, such effects are variable probably due to interaction between the plant genotype and the bacterial strain, soil properties and climatic factors. The aim of this study was to evaluate the performance of wheat genotypes inoculated with Herbaspirillum seropedicae SmR1, an endophytic diazotrophic bacterium. Invitro plantlets of five wheat genotypes were inoculated with H. seropedicae for 7 days. The fresh weight of roots, fresh and dry weight of shoots, total nitrogen, root morphology and bacterial counts were determined. For greenhouse experiments, seeds were inoculated or not with H.seropedicae (106cells/seed) cultivated in the absence or presence of urea. At harvest dry weight of shoots, grain index and grain yield were evaluated. Invitro results showed the presence of epiphytic bacteria on all genotypes and the presence of endophytic bacteria in CD 108 and CD 120. An increase in root hairs in genotypes CD 119 and 120 was observed. Two contrasting genotypes (CD 104 and CD 120) were evaluated under greenhouse conditions. The results showed that cultivar CD 120 inoculated with H.seropedicae had a higher productivity when the plants were not supplemented with urea. Data emphases the potential of H.seropedicae as a biofertilizer, reducing costs and improving agricultural sustainability. © 2014 Elsevier Masson SAS.

BibTeX:

@article{neiverth_performance_2014,
author = {Neiverth, Adeline and Delai, Suellen and Garcia, Dayane M. and Saatkamp, Kleber and de Souza, Emanuel Maltempi and Pedrosa, Fábio de Oliveira and Guimarães, Vandeir Francisco and dos Santos, Marise Fonseca and Vendruscolo, Eliane Cristina Gruszka and da Costa, Antonio Carlos Torres},
title = {Performance of different wheat genotypes inoculated with the plant growth promoting bacterium Herbaspirillum seropedicae},
journal = {European Journal of Soil Biology},
year = {2014},
volume = {64},
pages = {1--5},
note = {ISBN: 1164-5563 Publisher: Elsevier BV},
url = {http://dx.doi.org/10.1016/j.ejsobi.2014.07.001},
doi = {10.1016/j.ejsobi.2014.07.001}
}

Piro VC, Faoro H, Weiss VA, Steffens MBR, Pedrosa FO, Souza EM and Raittz RT (2014). FGAP: An automated gap closing tool. BMC Research Notes, 7(1):371, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: BACKGROUND: The fast reduction of prices of DNA sequencing allowed rapid accumulation of genome data. However, the process of obtaining complete genome sequences is still very time consuming and labor demanding. In addition, data produced from various sequencing technologies or alternative assemblies remain underexplored to improve assembly of incomplete genome sequences. FINDINGS: We have developed FGAP, a tool for closing gaps of draft genome sequences that takes advantage of different datasets. FGAP uses BLAST to align multiple contigs against a draft genome assembly aiming to find sequences that overlap gaps. The algorithm selects the best sequence to fill and eliminate the gap. CONCLUSIONS: FGAP reduced the number of gaps by 78% in an E. coli draft genome assembly using two different sequencing technologies, Illumina and 454. Using PacBio long reads, 98% of gaps were solved. In human chromosome 14 assemblies, FGAP reduced the number of gaps by 35%. All the inserted sequences were validated with a reference genome using QUAST. The source code and a web tool are available at http://www.bioinfo.ufpr.br/fgap/.

BibTeX:

@article{piro_fgap_2014,
author = {Piro, Vitor C. and Faoro, Helisson and Weiss, Vinicius A. and Steffens, Maria B R and Pedrosa, Fabio O. and Souza, Emanuel M. and Raittz, Roberto T.},
title = {FGAP: An automated gap closing tool},
journal = {BMC Research Notes},
year = {2014},
volume = {7},
number = {1},
pages = {371},
note = {ISBN: 1756-0500 Publisher: Springer Science Business Media},
url = {http://dx.doi.org/10.1186/1756-0500-7-371},
doi = {10.1186/1756-0500-7-371}
}

Rocha RA, Frigeri HR, Santos-Weiss IC, Rea RR, Souza EM, Rego FG and Picheth G (2014). Preproghrelin polymorphism Q90L (rs4684677) in gestational diabetes. 58(1) 2014.
[DOI] [URL] [BibTeX]

Abstract:

BibTeX:

@book{ra_preproghrelin_2014,
author = {R.A., Rocha and H.R., Frigeri and I.C., Santos-Weiss and R.R., Rea and E.M., Souza and F.G., Rego and G., Picheth},
title = {Preproghrelin polymorphism Q90L (rs4684677) in gestational diabetes},
publisher = {SciELO Brasil},
year = {2014},
volume = {58},
number = {1},
note = {ISSN: 1677-9487 Publication Title: Arquivos brasileiros de endocrinologia e metabologia},
url = {http://ovidsp.ovid.com/ovidweb.cgi?T=JS&PAGE=reference&D=emed13&NEWS=N&AN=24728171},
doi = {10.1590/0004-2730000003176}
}

Rabello FR, Villeth GR, Rabello AR, Rangel PH, Guimarães CM, Huergo LF, Souza EM, Pedrosa FO, Ferreira ME and Mehta A (2014). Proteomic analysis of upland rice (Oryza sativa L.) exposed to intermittent water deficit. Protein Journal, 33(3):221-230, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Rice is the most important crop consumed all over the world. In Brazil, irrigated rice covers 50 % of the rice producing area and is responsible for 75 % of the national production. Upland rice covers most of the remaining area, and is therefore, a very important production system in the country. In the present study, we have used the drought tolerant upland rice variety Tres Meses Antigo to investigate the proteomic changes that occur during drought stress. Plants were submitted to drought by the reposition of 50 % of the water lost daily. Twenty days after the beginning of the drought stress period, leaves were harvested and used for protein extraction. The 2D maps obtained from treated and control plants revealed 408 reproducible spots, 44 of which were identified by mass spectrometry, including 15 differential proteins. Several unaltered proteins were also identified (39 spots) and were mainly involved in photosynthesis. Taken together, the results obtained suggest that the tolerant upland rice up-regulates anti-oxidant and energy production related proteins in order to cope with water deficit.

BibTeX:

@article{rabello_proteomic_2014,
author = {Rabello, Fernanda R. and Villeth, Gabriela R.C. and Rabello, Aline R. and Rangel, Paulo H.N. and Guimarães, Cleber M. and Huergo, Luciano F. and Souza, Emanuel M. and Pedrosa, Fabio O. and Ferreira, Márcio E. and Mehta, Angela},
title = {Proteomic analysis of upland rice (Oryza sativa L.) exposed to intermittent water deficit},
journal = {Protein Journal},
year = {2014},
volume = {33},
number = {3},
pages = {221--230},
note = {ISBN: 1875-8355 (Electronic)$\backslash$r1572-3887 (Linking) Publisher: Springer Science Business Media},
url = {http://dx.doi.org/10.1007/s10930-014-9554-1},
doi = {10.1007/s10930-014-9554-1}
}

Rodrigues TE, Gerhardt EC, Oliveira MA, Chubatsu LS, Pedrosa FO, Souza EM, Souza GA, Müller-Santos M and Huergo LF (2014). Search for novel targets of the PII signal transduction protein in Bacteria identifies the BCCP component of acetyl-CoA carboxylase as a PII binding partner. Molecular Microbiology, 91(4):751-761, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The PII family comprises a group of widely distributed signal transduction proteins. The archetypal function of PII is to regulate nitrogen metabolism in bacteria. As PII can sense a range of metabolic signals, it has been suggested that the number of metabolic pathways regulated by PII may be much greater than described in the literature. In order to provide experimental evidence for this hypothesis a PII protein affinity column was used to identify PII targets in Azospirillum brasilense. One of the PII partners identified was the biotin carboxyl carrier protein (BCCP), a component of the acetyl-CoA carboxylase which catalyses the committed step in fatty acid biosynthesis. As BCCP had been previously identified as a PII target in Arabidopsis thaliana we hypothesized that the PII -BCCP interaction would be conserved throughout Bacteria. In vitro experiments using purified proteins confirmed that the PII -BCCP interaction is conserved in Escherichia coli. The BCCP-PII interaction required MgATP and was dissociated by increasing 2-oxoglutarate. The interaction was modestly affected by the post-translational uridylylation status of PII ; however, it was completely dependent on the post-translational biotinylation of BCCP.

BibTeX:

@article{rodrigues_search_2014,
author = {Rodrigues, Thiago E. and Gerhardt, Edileusa C.M. and Oliveira, Marco A. and Chubatsu, Leda S. and Pedrosa, Fabio O. and Souza, Emanuel M. and Souza, Gustavo A. and Müller-Santos, Marcelo and Huergo, Luciano F.},
title = {Search for novel targets of the PII signal transduction protein in Bacteria identifies the BCCP component of acetyl-CoA carboxylase as a PII binding partner},
journal = {Molecular Microbiology},
year = {2014},
volume = {91},
number = {4},
pages = {751--761},
note = {Publisher: Wiley-Blackwell},
url = {http://dx.doi.org/10.1111/mmi.12493},
doi = {10.1111/mmi.12493}
}

Stets MI, Etto RM, Galvão CW, Ayub RA, Cruz LM, Steffens MBR and Barana AC (2014). Microbial community and performance of slaughterhouse wastewater treatment filters. Genetics and Molecular Research, 13(2):4444-4455, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The performance of anaerobic filter bioreactors (AFs) is influenced by the composition of the substrate, support medium, and the microbial species present in the sludge. In this study, the efficiency of a slaughterhouse effluent treatment using three AFs containing different support media was tested, and the microbial diversity was investigated by amplified ribosomal DNA restriction analysis and 16S rRNA gene sequencing. The physicochemical analysis of the AF systems tested suggested their feasibility, with rates of chemical oxygen demand removal of 72±8% in hydraulic retention times of 1 day. Analysis of pH, alkalinity, volatile acidity, total solids, total volatile solids, total Kjeldahl nitrogen, and the microbial community structures indicated high similarity among the three AFs. The composition of prokaryotic communities showed a prevalence of Proteobacteria (27.3 and Bacteroidetes (18.4 of the Bacteria domain and Methanomicrobiales (36.4 and Methanosarcinales (35.3 of the Archaea domain. Despite the high similarity of the microbial communities among the AFs, the reactor containing pieces of clay brick as a support medium presented the highest richness and diversity of bacterial and archaeal operational taxonomic units.

BibTeX:

@article{stets_microbial_2014,
author = {Stets, M. I. and Etto, R. M. and Galvão, C. W. and Ayub, R. A. and Cruz, L. M. and Steffens, M. B R and Barana, A. C.},
title = {Microbial community and performance of slaughterhouse wastewater treatment filters},
journal = {Genetics and Molecular Research},
year = {2014},
volume = {13},
number = {2},
pages = {4444--4455},
note = {Publisher: Genetics and Molecular Research},
url = {http://dx.doi.org/10.4238/2014.June.16.3},
doi = {10.4238/2014.June.16.3}
}

Vieira LDN, Faoro H, Rogalski M, De Freitas Fraga HP, Cardoso RLA, De Souza EM, De Oliveira Pedrosa F, Nodari RO and Guerra MP (2014). The complete chloroplast genome sequence of Podocarpus lambertii: Genome structure, evolutionary aspects, gene content and SSR detection. PLoS ONE, 9(3):e84792, 2014.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: BACKGROUND: Podocarpus lambertii (Podocarpaceae) is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp) genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. METHODOLOGY/PRINCIPAL FINDINGS: The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR). It contains 118 unique genes and one duplicated tRNA (trnN-GUU), which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi) and Araucariaceae (Agathis dammara). Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. CONCLUSION: The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of this genus.

BibTeX:

@article{vieira_complete_2014,
author = {Vieira, Leila Do Nascimento and Faoro, Helisson and Rogalski, Marcelo and De Freitas Fraga, Hugo Pacheco and Cardoso, Rodrigo Luis Alves and De Souza, Emanuel Maltempi and De Oliveira Pedrosa, Fábio and Nodari, Rubens Onofre and Guerra, Miguel Pedro},
editor = {Munderloh, Ulrike Gertrud},
title = {The complete chloroplast genome sequence of Podocarpus lambertii: Genome structure, evolutionary aspects, gene content and SSR detection},
journal = {PLoS ONE},
year = {2014},
volume = {9},
number = {3},
pages = {e84792},
note = {Publisher: Public Library of Science (PLoS)},
url = {http://dx.doi.org/10.1371/journal.pone.0090618 http://dx.doi.org/10.1371/journal.pone.0084792},
doi = {10.1371/journal.pone.0090618}
}

Alberton D, Müller-Santos M, Brusamarello-Santos LCC, Valdameri G, Cordeiro FA, Yates MG, De Oliveira Pedrosa F and De Souza EM (2013). Comparative proteomics analysis of the rice roots colonized by Herbaspirillum seropedicae strain SmR1 reveals induction of the methionine recycling in the plant host. Journal of Proteome Research, 12(11):4757-4768, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Although the use of plant growth-promoting bacteria in agriculture is a reality, the molecular basis of plant-bacterial interaction is still poorly understood. We used a proteomic approach to study the mechanisms of interaction of Herbaspirillum seropedicae SmR1 with rice. Root proteins of rice seedlings inoculated or noninoculated with H. seropedicae were separated by 2-D electrophoresis. Differentially expressed proteins were identified by MALDI-TOF/TOF and MASCOT program. Among the identified proteins of H. seropedicae, the dinitrogenase reductase NifH and glutamine synthetase GlnA, which participate in nitrogen fixation and ammonium assimilation, respectively, were the most abundant. The rice proteins up-regulated included the S-adenosylmethionine synthetase, methylthioribose kinase, and acireductone dioxygenase 1, all of which are involved in the methionine recycling. S-Adenosylmethionine synthetase catalyzes the synthesis of S-adenosylmethionine, an intermediate used in transmethylation reactions and in ethylene, polyamine, and phytosiderophore biosynthesis. RT-qPCR analysis also confirmed that the methionine recycling and phytosiderophore biosynthesis genes were up-regulated, while ACC oxidase mRNA level was down-regulated in rice roots colonized by bacteria. In agreement with these results, ethylene production was reduced approximately three-fold in rice roots colonized by H. seropedicae. The results suggest that H. seropedicae stimulates methionine recycling and phytosiderophore synthesis and diminishes ethylene synthesis in rice roots.

BibTeX:

@article{alberton_comparative_2013,
author = {Alberton, Dayane and Müller-Santos, Marcelo and Brusamarello-Santos, Liziane Cristina Campos and Valdameri, Glaucio and Cordeiro, Fabio Aparecido and Yates, Marshall Geoffrey and De Oliveira Pedrosa, Fabio and De Souza, Emanuel Maltempi},
title = {Comparative proteomics analysis of the rice roots colonized by Herbaspirillum seropedicae strain SmR1 reveals induction of the methionine recycling in the plant host},
journal = {Journal of Proteome Research},
year = {2013},
volume = {12},
number = {11},
pages = {4757--4768},
note = {Publisher: American Chemical Society (ACS)},
url = {http://pubs.acs.org/doi/10.1021/pr400425f http://dx.doi.org/10.1021/pr400425f},
doi = {10.1021/pr400425f}
}

Balsanelli E, Tuleski TR, de Baura VA, Yates MG, Chubatsu LS, de Oliveira Pedrosa F, de Souza EM and Monteiro RA (2013). Maize Root Lectins Mediate the Interaction with Herbaspirillum seropedicae via N-Acetyl Glucosamine Residues of Lipopolysaccharides. PLoS ONE, 8(10):e77001, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Herbaspirillum seropedicae is a plant growth-promoting diazotrophic betaproteobacterium which associates with important crops, such as maize, wheat, rice and sugar-cane. We have previously reported that intact lipopolysaccharide (LPS) is required for H. seropedicae attachment and endophytic colonization of maize roots. In this study, we present evidence that the LPS biosynthesis gene waaL (codes for the O-antigen ligase) is induced during rhizosphere colonization by H. seropedicae. Furthermore a waaL mutant strain lacking the O-antigen portion of the LPS is severely impaired in colonization. Since N-acetyl glucosamine inhibits H. seropedicae attachment to maize roots, lectin-like proteins from maize roots (MRLs) were isolated and mass spectrometry (MS) analysis showed that MRL-1 and MRL-2 correspond to maize proteins with a jacalin-like lectin domain, while MRL-3 contains a B-chain lectin domain. These proteins showed agglutination activity against wild type H. seropedicae, but failed to agglutinate the waaL mutant strain. The agglutination reaction was severely diminished in the presence of N-acetyl glucosamine. Moreover addition of the MRL proteins as competitors in H. seropedicae attachment assays decreased 80-fold the adhesion of the wild type to maize roots. The results suggest that N-acetyl glucosamine residues of the LPS O-antigen bind to maize root lectins, an essential step for efficient bacterial attachment and colonization.

BibTeX:

@article{balsanelli_maize_2013,
author = {Balsanelli, Eduardo and Tuleski, Thalita Regina and de Baura, Valter Antonio and Yates, Marshall Geoffrey and Chubatsu, Leda Satie and de Oliveira Pedrosa, Fabio and de Souza, Emanuel Maltempi and Monteiro, Rose Adele},
editor = {Cascales, Eric},
title = {Maize Root Lectins Mediate the Interaction with Herbaspirillum seropedicae via N-Acetyl Glucosamine Residues of Lipopolysaccharides},
journal = {PLoS ONE},
year = {2013},
volume = {8},
number = {10},
pages = {e77001},
note = {ISBN: 9781522540816 Publisher: Public Library of Science (PLoS)},
url = {http://dx.doi.org/10.1371/journal.pone.0077001},
doi = {10.1371/journal.pone.0077001}
}

Bandil GB, Etto RM, Galvão CW, Ramos HJ, Souza EM, Pedrosa FO, Chaves DF, Huergo LF and Ayub RA (2013). Comparative proteomic analysis between early developmental stages of the Coffea arabica fruits. Genetics and Molecular Research, 12(4):5102-5110, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Coffee is one of the most valuable agricultural commodities. There is much agronomic research on coffee, but molecular knowledge of its fruit development and ripening is limited. This study reports a comparative proteomic investigation of immature coffee fruits in two early developmental stages: stage 1, cell division and elongation of the perisperm; and stage 2, early growth of the endosperm progressively replacing the perisperm. Proteins were extracted using a modified SDS-phenol method and two-dimensional electrophoresis gels stained with Coomassie blue revealed about 300 well-resolved polypeptide spots in the pH range of 3 to 10. The differentially expressed polypeptides spots were excised, trypsin-digested, and analyzed by MALDI-TOF mass spectrometry. Peptide MS data were searched against the coffee EST database. Most of the identified protein spots are involved in the glycolytic pathway and energy reserve, and are more highly expressed at stage 2.

BibTeX:

@article{bandil_comparative_2013,
author = {Bandil, G. B. and Etto, R. M. and Galvão, C. W. and Ramos, H. J.O. and Souza, E. M. and Pedrosa, F. O. and Chaves, D. F.S. and Huergo, L. F. and Ayub, R. A.},
title = {Comparative proteomic analysis between early developmental stages of the Coffea arabica fruits},
journal = {Genetics and Molecular Research},
year = {2013},
volume = {12},
number = {4},
pages = {5102--5110},
note = {Publisher: Genetics and Molecular Research},
url = {http://dx.doi.org/10.4238/2013.October.29.4 http://www.funpecrp.com.br/gmr/year2013/vol12-4/pdf/gmr2625.pdf},
doi = {10.4238/2013.October.29.4}
}

Batista MB, Sfeir MZ, Faoro H, Wassem R, Steffens MB, Pedrosa FO, Souza EM, Dixon R and Monteiro RA (2013). The Herbaspirillum seropedicae SmR1 Fnr orthologs controls the cytochrome composition of the electron transport chain. Scientific Reports, 3 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The transcriptional regulatory protein Fnr, acts as an intracellular redox sensor regulating a wide range of genes in response to changes in oxygen levels. Genome sequencing of Herbaspirillum seropedicae SmR1 revealed the presence of three fnr-like genes. In this study we have constructed single, double and triple fnr deletion mutant strains of H. seropedicae. Transcriptional profiling in combination with expression data from reporter fusions, together with spectroscopic analysis, demonstrates that the Fnr1 and Fnr3 proteins not only regulate expression of the cbb3-type respiratory oxidase, but also control the cytochrome content and other component complexes required for the cytochrome c-based electron transport pathway. Accordingly, in the absence of the three Fnr paralogs, growth is restricted at low oxygen tensions and nitrogenase activity is impaired. Our results suggest that the H. seropedicae Fnr proteins are major players in regulating the composition of the electron transport chain in response to prevailing oxygen concentrations.

BibTeX:

@article{batista_herbaspirillum_2013,
author = {Batista, Marcelo B. and Sfeir, Michelle Z.T. and Faoro, Helisson and Wassem, Roseli and Steffens, Maria B.R. and Pedrosa, Fábio O. and Souza, Emanuel M. and Dixon, Ray and Monteiro, Rose A.},
title = {The Herbaspirillum seropedicae SmR1 Fnr orthologs controls the cytochrome composition of the electron transport chain},
journal = {Scientific Reports},
year = {2013},
volume = {3},
note = {Publisher: Nature Publishing Group},
url = {http://dx.doi.org/10.1038/srep02544},
doi = {10.1038/srep02544}
}

Cangahuala-Inocente GC, Plucani do Amaral F, Faleiro AC, Huergo LF and Maisonnave Arisi AC (2013). Identification of six differentially accumulated proteins of Zea mays seedlings (DKB240 variety) inoculated with Azospirillum brasilense strain FP2. European Journal of Soil Biology, 58:45-50, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The plant growth promoting bacteria (PGPB) Azospirillum brasilense has been known to exert beneficial influence on inoculated plants, such as maize and wheat. The successful PGPB-plant association depends on plant and PGPB genotypes and it was not fully understood. In this study we have employed two-dimensional gel electrophoresis and mass spectrometry to analyze the changes in protein profile of maize roots in response to A. brasilense strain FP2 ten days after inoculation and 87 differently expressed protein spots were revealed. We report the identification of six of these proteins in detail: Two down-regulated proteins in inoculated roots, Zea mays annexin2 (2-fold) and Z. mays hypothetical protein LOC100275372 (4-fold), that is 60% similar to an Arabidopsis thaliana hydroxyproline-rich glycoprotein-like protein; two up-regulated proteins in inoculated roots, A.brasilense F-type H+-transporting ATPase beta chain (3-fold) and A.brasilense major outer membrane protein OmaA precursor (14-fold). Two spots exclusively expressed in inoculated roots were identified as A. brasilense malate dehydrogenase. © 2013 Elsevier Masson SAS.

BibTeX:

@article{cangahuala-inocente_identification_2013,
author = {Cangahuala-Inocente, Gabriela Claudia and Plucani do Amaral, Fernanda and Faleiro, Alexandro César and Huergo, Luciano F. and Maisonnave Arisi, Ana Carolina},
title = {Identification of six differentially accumulated proteins of Zea mays seedlings (DKB240 variety) inoculated with Azospirillum brasilense strain FP2},
journal = {European Journal of Soil Biology},
year = {2013},
volume = {58},
pages = {45--50},
note = {Publisher: Elsevier BV},
url = {http://dx.doi.org/10.1016/j.ejsobi.2013.06.002},
doi = {10.1016/j.ejsobi.2013.06.002}
}

Cordeiro FA, Tadra-Sfeir MZ, Huergo LF, De Oliveira Pedrosa F, Monteiro RA and De Souza EM (2013). Proteomic analysis of herbaspirillum seropedicae cultivated in the presence of sugar cane extract. Journal of Proteome Research, 12(3):1142-1150, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Bacterial endophytes of the genus Herbaspirillum colonize sugar cane and can promote plant growth. The molecular mechanisms that mediate plant- H. seropedicae interaction are poorly understood. In this work, we used 2D-PAGE electrophoresis to identify H. seropedicae proteins differentially expressed at the log growth phase in the presence of sugar cane extract. The differentially expressed proteins were validated by RT qPCR. A total of 16 differential spots (1 exclusively expressed, 7 absent, 5 up- and 3 down-regulated) in the presence of 5% sugar cane extract were identified; thus the host extract is able to induce and repress specific genes of H. seropedicae. The differentially expressed proteins suggest that exposure to sugar cane extract induced metabolic changes and adaptations in H. seropedicae presumably in preparation to establish interaction with the plant.

BibTeX:

@article{cordeiro_proteomic_2013,
author = {Cordeiro, Fabio Aparecido and Tadra-Sfeir, Michelle Zibetti and Huergo, Luciano Fernandes and De Oliveira Pedrosa, Fábio and Monteiro, Rose Adele and De Souza, Emanuel Maltempi},
title = {Proteomic analysis of herbaspirillum seropedicae cultivated in the presence of sugar cane extract},
journal = {Journal of Proteome Research},
year = {2013},
volume = {12},
number = {3},
pages = {1142--1150},
note = {Publisher: American Chemical Society (ACS)},
url = {http://dx.doi.org/10.1021/pr300746j http://pubs.acs.org/doi/10.1021/pr300746j},
doi = {10.1021/pr300746j}
}

Da Rocha RA, Weschenfelder TA, De Castilhos F, De Souza EM, Huergo LF and Mitchell DA (2013). Mathematical model of the binding of allosteric effectors to the escherichia coli PII signal transduction protein GlnB. Biochemistry, 52(15):2683-2693, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: PII proteins are important regulators of nitrogen metabolism in a wide variety of organisms: the binding of the allosteric effectors ATP, ADP, and 2-oxoglutarate (2-OG) to PII proteins affects their ability to interact with target proteins. We modeled the simultaneous binding of ATP, ADP, and 2-OG to one PII protein, namely GlnB of Escherichia coli, using a modeling approach that allows the prediction of the proportions of individual binding states. Four models with different binding rules were compared. We selected one of these models (that assumes that the binding of the first nucleotide to GlnB makes it harder for subsequent nucleotides to bind) and used it to explore how physiological concentrations of ATP, ADP, and 2-OG would affect the proportions of those states of GlnB that interact with the target proteins ATase and NtrB. Our simulations indicate that GlnB can, as suggested by previous researchers, act as a sensor of both 2-OG and the ATP:ADP ratio. We conclude that our modeling approach will be an important tool in future studies concerning the PII binding states and their interactions with target proteins.

BibTeX:

@article{da_rocha_mathematical_2013,
author = {Da Rocha, Ricardo Alves and Weschenfelder, Thiago André and De Castilhos, Fernanda and De Souza, Emanuel Maltempi and Huergo, Luciano Fernandes and Mitchell, David Alexander},
title = {Mathematical model of the binding of allosteric effectors to the escherichia coli PII signal transduction protein GlnB},
journal = {Biochemistry},
year = {2013},
volume = {52},
number = {15},
pages = {2683--2693},
note = {ISBN: 1520-4995 (Electronic)$\backslash$r0006-2960 (Linking) Publisher: American Chemical Society (ACS)},
url = {http://dx.doi.org/10.1021/bi301659r http://pubs.acs.org/doi/10.1021/bi301659r},
doi = {10.1021/bi301659r}
}

de Souza V, Piro VC, Faoro H, Tadra-Sfeir MZ, Chicora VK, Guizelini D, Weiss V, Vialle Ra, Monteiro Ra, Steffens MBR, Marchaukoski JN, Pedrosa FO, Cruz LM, Chubatsu LS and Raittz RT (2013). Draft Genome Sequence of Herbaspirillum huttiense subsp. putei IAM 15032, a Strain Isolated from Well Water. Genome announcements, 1(1):1-2, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Here we report the one-scaffold draft genome of Herbaspirillum huttiense subsp. putei strain 7-2 T (IAM 15032), which was iso-lated from well water. LS, Raittz RT. 2013. Draft genome sequence of Herbaspirillum huttiense subsp. putei IAM 15032, a strain isolated from well water. Genome Announc. 1(1):e00252-12. H erbaspirillum huttiense subsp. putei strain 7-2 T (IAM 15032) is a betaproteobacterium isolated from well water in Osaka, Ja-pan. It was first described as a new species, Herbaspirillum putei, closely related to H. huttiense (1). Later, 16S rRNA gene rese-quencing and DNA-DNA hybridization analysis led to the reclas-sification of H. putei as a subspecies of H. huttiense, and it is now named H. huttiense subsp. putei (2). The genome sequence of H. huttiense subsp. putei was deter-mined using mate-paired libraries on a SOLiD4 sequencer (Life Technologies), producing a total of 102,768,904 paired reads of 50 bp. These libraries were used for de novo genome assembly using Velvet v.1.2.03 (3). Gap closure was achieved by using in-house scripts. The H. huttiense subsp. putei draft genome was assembled in one scaffold containing 32 contigs. The estimated genome size is 5.7 Mb with a 62.2% GϩC content. Previously estimated genome size was 3.9 Mb with a 62.1% GϩC content (2). Automatic anno-tation using RAST (4) revealed 5,317 open reading frames (ORFs) covering 86% of the chromosome, 49 tRNA genes, and 2 16S-23S-5S rRNA operons. Our analysis indicated the absence of nif genes, confirming that this species is not a nitrogen fixer. On the other hand, genes in-volved in nitrate/nitrite metabolism were observed. H. huttiense subsp. putei is able to grow using nitrate as the sole nitrogen source (data not shown), and analyses indicated genes with high similar-ity to H. seropedicae nasA, nirD, nirB, narK, and nasFED, whereas genes narG, narH, narI, narU, and narXL are not present, reinforc-ing that this bacterium is capable of reducing nitrate as a nitrogen source (assimilative metabolism) and suggesting that it cannot use nitrate as an electron acceptor in anaerobic respiration (dissimi-lative metabolism). The H. huttiense subsp. putei genome has genes coding for all the enzymes required for the Embden-Meyerhof-Parnas pathway. Genes coding for the Entner-Doudoroff, the pentose phosphate, and the tricarboxylic acid cycle (TCA) pathways were also ob-served. Although H. seropedicae and H. lusitanum show two po-tential pathways for trehalose biosynthesis (5, 6), H. huttiense subsp. putei seems to have only the pathway involving otsA and otsB, which may be related to the differences among the environ-ments from which these species were isolated. Studies on plant interaction of H. huttiense subsp. putei are not available; however, a gene coding for 1-aminocyclopropane-1-carboxylate (ACC) deaminase was observed, which may suggest contributions to plant development under stress conditions (5). Although secretion systems type I, II, and V were observed, the type III secretion system, which was suggested to be involved in plant-bacterium interaction, was not observed in H. huttiense subsp. putei. An interesting feature was the presence of a gene cluster for cellulose biosynthesis (wss) and degradation that was reported only in H. rubrisubalbicans M1 and seems to be involved in enhanced colonization of maize (7).

BibTeX:

@article{de_souza_draft_2013,
author = {de Souza, Vanely and Piro, Vitor C and Faoro, Helisson and Tadra-Sfeir, Michelle Z and Chicora, Vanessa K and Guizelini, Dieval and Weiss, Vinicius and Vialle, Ricardo a and Monteiro, Rose a and Steffens, Maria Berenice R and Marchaukoski, Jeroniza N and Pedrosa, Fabio O and Cruz, Leonardo M and Chubatsu, Leda S and Raittz, Roberto T},
title = {Draft Genome Sequence of Herbaspirillum huttiense subsp. putei IAM 15032, a Strain Isolated from Well Water},
journal = {Genome announcements},
year = {2013},
volume = {1},
number = {1},
pages = {1--2},
note = {ISBN: 0520224108 Publisher: American Society for Microbiology},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3587956&tool=pmcentrez&rendertype=abstract},
doi = {10.1128/genomeA.00252-12}
}

dos Santos-Weiss IC, Réa RR, Fadel-Picheth CM, Rego FG, Pedrosa FdO, Gillery P, Souza EM and Picheth G (2013). The plasma logarithm of the triglyceride/HDL-cholesterol ratio is a predictor of low risk gestational diabetes in early pregnancy. Clinica Chimica Acta, 418:1-4, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Background: The plasma lipid profile changes atherogenically during normal pregnancy. Gestational diabetes mellitus (GDM) can exacerbate the changes in metabolism. The logarithm of the ratio triglycerides/HDL-cholesterol is an atherogenic index of the plasma (AIP) and can be used as a marker for plasma atherogenicity. Methods: Serum of 576 unrelated Euro-Brazilian pregnant women was collected and the subjects were classified as healthy pregnant women (control, n = 288) and gestational diabetic patients (GDM, n = 288) according to the ADA 2010 criteria. Both studied groups were sub classified in 4 gestational periods: (i) 12-23, (ii) 24-28, (iii) 29-32 and (iv) \textgreater 32. weeks of gestation. Results: Except for the AIP, the other parameters showed low discrimination between control and GDM groups (ROC curves). When analyzed by ROC curves the AIP of subjects in the early period of gestation showed sensitivity and specificity of 82.6% and 83.4 respectively, with a cut-off point of 0.099 (AUC 0.886, P \textless 0.0001). Conclusions: The AIP is a valuable index to identify pregnant women with low risk of gestational diabetes before 24. weeks of gestation. © 2012 Elsevier B.V.

BibTeX:

@article{dos_santos-weiss_plasma_2013,
author = {dos Santos-Weiss, Izabella C.R. and Réa, Rosângela R. and Fadel-Picheth, Cyntia M.T. and Rego, Fabiane G.M. and Pedrosa, Fábio de O. and Gillery, Philippe and Souza, Emanuel M. and Picheth, Geraldo},
title = {The plasma logarithm of the triglyceride/HDL-cholesterol ratio is a predictor of low risk gestational diabetes in early pregnancy},
journal = {Clinica Chimica Acta},
year = {2013},
volume = {418},
pages = {1--4},
note = {ISBN: 1873-3492 (Electronic)$\backslash$r0009-8981 (Linking) Publisher: Elsevier BV},
url = {http://dx.doi.org/10.1016/j.cca.2012.12.004 http://linkinghub.elsevier.com/retrieve/pii/S0009898112005748},
doi = {10.1016/j.cca.2012.12.004}
}

Fialho OB, de Souza EM, de Borba Dallagassa C, de Oliveira Pedrosa F, Klassen G, Irino K, Paludo KS, de Assis FEA, Surek M, de Souza Santos Farah SM and Fadel-Picheth CMT (2013). Detection of Diarrheagenic Escherichia coli Using a Two-System Multiplex-PCR Protocol. Journal of Clinical Laboratory Analysis, 27(2):155-161, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: BACKGROUND: Diarrheagenic Escherichia coli (DEC) strains are important causes of diarrhea. However, they cannot be distinguished from E. coli of the intestinal microbiota by conventional microbiological tests. METHODS: This work presents a two-system multiplex PCR for detection of DEC. Primers for 16S rRNA gene were added as internal amplification control to validate negative reactions. The multiplex-PCR system 1 contains primers for detection of Shiga toxin producing E. coli (STEC; stx1, stx2), enteropathogenic E. coli (EPEC; eae, bfpA), atypical enteropathogenic E. coli (aEPEc; eae), enteroinvasive E. coli (ETEC; lt, st), enteroinvasive E. coli (EIEC; ial), and the internal amplification control 16S rRNA. The system 2 contains primers for EIEC (ipaH), enteroaggregative E. coli (CVD432), diffusely adherent E. coli (daaE), and 16S rRNA. The protocol was tested with E. coli reference strains, and also with cultures of fecal specimens of people with diarrhea and healthy controls. RESULTS: The protocol correctly identified the DEC reference strains. No DEC marker was amplified for negative controls; these results were validated by the amplification of a fragment of the 16S rRNA gene. The frequency of DEC was 7.6% for both patients and healthy controls; two Shigella sonnei strains were detected in the group with diarrhea. The identity of the amplicons was confirmed by DNA sequencing. CONCLUSION: The protocol is specific for DEC Shigella and is suitable for clinical laboratories.

BibTeX:

@article{fialho_detection_2013,
author = {Fialho, Octaviana Baccin and de Souza, Emanuel Maltempi and de Borba Dallagassa, Cibelle and de Oliveira Pedrosa, Fábio and Klassen, Giseli and Irino, Kinue and Paludo, Katia Sabrina and de Assis, Flávia Emanoelli Araújo and Surek, Monica and de Souza Santos Farah, Sônia Maria and Fadel-Picheth, Cyntia Maria Telles},
title = {Detection of Diarrheagenic Escherichia coli Using a Two-System Multiplex-PCR Protocol},
journal = {Journal of Clinical Laboratory Analysis},
year = {2013},
volume = {27},
number = {2},
pages = {155--161},
note = {Publisher: Wiley-Blackwell},
url = {http://doi.wiley.com/10.1002/jcla.21578},
doi = {10.1002/jcla.21578}
}

Huergo LF, Chandra G and Merrick M (2013). PIIsignal transduction proteins: Nitrogen regulation and beyond. FEMS Microbiology Reviews, 37(2):251-283, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The P(II) proteins are one of the most widely distributed families of signal transduction proteins in nature. They are pivotal players in the control of nitrogen metabolism in bacteria and archaea, and are also found in the plastids of plants. Quite remarkably, P(II) proteins control the activities of a diverse range of enzymes, transcription factors and membrane transport proteins, and in recent years the extent of these interactions has been recognized to be much greater than heretofore described. Major advances have been made in structural studies of P(II) proteins, including the solution of the first structures of P(II) proteins complexed with their targets. We have also begun to gain insights into how the key effector molecules, 2-oxoglutarate and ATP/ADP, influence the activities of P(II) proteins. In this review, we have set out to summarize our current understanding of P(II) biology and to consider where future studies of these extraordinarily adaptable proteins might lead us.

BibTeX:

@article{huergo_piisignal_2013,
author = {Huergo, Luciano F. and Chandra, Govind and Merrick, Mike},
title = {PIIsignal transduction proteins: Nitrogen regulation and beyond},
journal = {FEMS Microbiology Reviews},
year = {2013},
volume = {37},
number = {2},
pages = {251--283},
note = {Publisher: Oxford University Press (OUP)},
url = {https://academic.oup.com/femsre/article-lookup/doi/10.1111/j.1574-6976.2012.00351.x http://dx.doi.org/10.1111/j.1574-6976.2012.00351.x},
doi = {10.1111/j.1574-6976.2012.00351.x}
}

Lammel DR, Cruz LM, Carrer H and Cardoso EJBN (2013). Diversity and symbiotic effectiveness of beta-rhizobia isolated from sub-tropical legumes of a Brazilian Araucaria Forest. World Journal of Microbiology and Biotechnology, 29(12):2335-2342, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The aim of this work was to simulate in two dimensions the spatio-temporal evolution of the moisture content, the temperature, the solid (dry matter) concentration, the dry product total porosity, the gas porosity, and the mechanical stress within a deformable and unsaturated product during convective drying. The material under study was an elongated cellulose–clay composite sample with a square section placed in hot air flow. Currently, this innovative composite is used in the processing of boxes devoted to the preservation of heritage and precious objects against fire damage and other degradation (moisture, insects, etc.). A comprehensive and rigorous hydrothermal model had been merged with a dynamic linear viscoelasticity model based on Bishop's effective stress theory, assuming that the stress tensor is the sum of solid, liquid, and gas stresses. The material viscoelastic properties were measured by means of stress relaxation tests for different water contents. The viscoelastic behaviour was described by a generalized Maxwell model whose parameters were correlated to the water content. The equations of our model were solved by means of the ‘COMSOL Multiphysics' software. The hydrothermal part of the model was validated by comparison with experimental drying curves obtained in a laboratory hot-air dryer. The simulations of the spatio-temporal distributions of mechanical stress were performed and interpreted in terms of material potential damage. The sample shape was also predicted all over the drying process.

BibTeX:

@article{lammel_diversity_2013,
author = {Lammel, Daniel R. and Cruz, Leonardo M. and Carrer, Helaine and Cardoso, Elke J B N},
title = {Diversity and symbiotic effectiveness of beta-rhizobia isolated from sub-tropical legumes of a Brazilian Araucaria Forest},
journal = {World Journal of Microbiology and Biotechnology},
year = {2013},
volume = {29},
number = {12},
pages = {2335--2342},
note = {ISBN: 1466-5034 (Electronic)$\backslash$n1466-5026 (Linking) Publisher: Springer Science Business Media},
url = {http://dx.doi.org/10.1007/s11274-013-1400-7},
doi = {10.1016/j.crme.2017.02.004}
}

Lima-Oliveira G, Lippi G, Salvagno GL, Danese E, Montagnana M, Brocco G, Voi M, Picheth G and Guidi GC (2013). Does Laboratory Automation for the Preanalytical Phase Improve Data Quality?. Journal of Laboratory Automation, 18(5):375-381, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Our aim was to evaluate whether automation for the preanalytical phase improves data quality. Blood from 100 volunteers was collected into two vacuum tubes. One sample from each volunteer was respectively assigned to (G1) traditional processing, starting with centrifugation at 1200 g for 10 min, and (G2) the MODULAR PRE-ANALYTICALS EVO-MPA system. The routine clinical chemistry tests were performed in duplicate on the same instrument Cobas 6000 \textlessc501\textgreater module. G1 samples were uncapped manually and immediately placed into the instrument. G2 samples were directly fed from the MPA system to the instrument without further staff intervention. At the end, (1) the G1 samples were stored for 6 h at 4 °C as prescribed in our accredited laboratory and (2) the G2 samples were stored for 6 h in the MPA output buffer. Results from G1 and G2, before and after storage, were compared. Significant increases were observed in G1 compared with G2 samples as follows: (1) before storage for alkaline phosphatase (ALP), lactate dehydrogenase (LDH), phosphate (P), magnesium (MG), iron (FE), and hemolysis index and (2) after storage for total cholesterol (COL), triglycerides (TG), total protein (TP), albumin (ALB), blood urea nitrogen (BUN), creatinine (CRE), uric acid (UA), ALP, pancreatic amylase, aspartate aminotransferase (AST), alanine aminotransferase (ALT), g-glutamyltransferase (GGT), LDH, creatine kinase (CK), calcium (CA), FE, sodium (NA), potassium (K), and hemolysis index. Moreover, significant increases were observed in (3) G1-after versus G1-before storage samples for COL, high-density lipoprotein cholesterol, TG, TP, ALB, BUN, CRE, UA, AST, ALT, GGT, LDH, P, CA, MG, FE, NA, K, and hemolysis index and (4) G2-after versus G2-before storage only for BUN, AST, LDH, P, and CA. In conclusion, our results show that the MPA system improves the quality of laboratory testing.

BibTeX:

@article{lima-oliveira_does_2013,
author = {Lima-Oliveira, Gabriel and Lippi, Giuseppe and Salvagno, Gian Luca and Danese, Elisa and Montagnana, Martina and Brocco, Giorgio and Voi, Monica and Picheth, Geraldo and Guidi, Gian Cesare},
title = {Does Laboratory Automation for the Preanalytical Phase Improve Data Quality?},
journal = {Journal of Laboratory Automation},
year = {2013},
volume = {18},
number = {5},
pages = {375--381},
note = {ISBN: 2211068213488 Publisher: SAGE Publications},
url = {http://dx.doi.org/10.1177/2211068213488892},
doi = {10.1177/2211068213488892}
}

Lima-Oliveira G, Lippi G, Salvagno GL, Montagnana M, Gelati M, Volanski W, Boritiza KC, Picheth G and Guidi GC (2013). Effects of vigorous mixing of blood vacuum tubes on laboratory test results. Clinical Biochemistry, 46(3):250-254, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Objective: To evaluate the effect of tubes mixing (gentle vs. vigorous) on diagnostic blood specimens collected in vacuum tube systems by venipuncture. Design and methods: Blood was collected for routine coagulation, immunochemistry and hematological testing from one hundred volunteers into six vacuum tubes: two 3.6mL vacuum tubes containing 0.4mL of buffered sodium citrate (9NC) 0.109mol/L: 3.2W/V two 3.5mL vacuum tubes with clot activator and gel separator; and two 3.0mL vacuum tubes containing 5.9mg K2EDTA (Terumo Europe, Belgium). Immediately after the venipuncture all vacuum tubes (each of one additive type) were processed through two different procedures: i) Standard: blood specimens in K2EDTA- or sodium citrate-vacuum tubes were gently inverted five times whereas the specimens in tubes with clot activator and gel separator were gently inverted ten times, as recommended by the manufacturer; ii) Vigorous mix: all blood specimens were shaken up vigorously during 3-5s independently of the additive type inside the tubes. The significance of the differences between samples was assessed by Student's t-test or Wilcoxon ranked-pairs test after checking for normality. The level of statistical significance was set at P\textless0.05. Results: No significant difference (P\textless0.05) was detected between the procedures for all tested parameters. Surprisingly only a visual alteration (presence of foam on the top) was shown by all the tubes mixed vigorously before centrifugation (Fig. 1 A, B and C). Moreover the serum tubes from vigorous mixing procedure shows a "blood ring" on the tube top after stopper removal (Fig. 1 D). Conclusion: Our results drop out a paradigm suggesting that the incorrect primary blood tubes mixing promotes laboratory variability. We suggest that similar evaluation should be done using other brands of vacuum tubes by each laboratory manager. © 2012 The Canadian Society of Clinical Chemists.

BibTeX:

@article{lima-oliveira_effects_2013,
author = {Lima-Oliveira, Gabriel and Lippi, Giuseppe and Salvagno, Gian Luca and Montagnana, Martina and Gelati, Matteo and Volanski, Waldemar and Boritiza, Katia Cristina and Picheth, Geraldo and Guidi, Gian Cesare},
title = {Effects of vigorous mixing of blood vacuum tubes on laboratory test results},
journal = {Clinical Biochemistry},
year = {2013},
volume = {46},
number = {3},
pages = {250--254},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0009912012006121},
doi = {10.1016/j.clinbiochem.2012.10.033}
}

Magnani GS, Cruz LM, Weber H, Bespalhok JC, Daros E, Baura V, Yates MG, Monteiro RA, Faoro H, Pedrosa FO and Souza EM (2013). Culture-independent analysis of endophytic bacterial communities associated with Brazilian sugarcane. Genetics and Molecular Research, 12(4):4549-4558, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Sugarcane is an economically important culture in Brazil. Endophytic bacteria live inside plants, and can provide many benefits to the plant host. We analyzed the bacterial diversity of sugarcane cultivar RB-72454 by cultivation-independent techniques. Total DNA from sugarcane stems from a commercial plantation located in Paraná State was extracted. Partial 16S rRNA genes were amplified and sequenced for library construction. Of 152 sequences obtained, 52% were similar to 16S rRNA from Pseudomonas sp, and 35.5% to Enterobacter sp. The genera Pantoea, Serratia, Citrobacter, and Klebsiella were also represented. The endophytic communities in these sugarcane samples were dominated by the families Enterobacteriaceae and Pseudomonadaceae (class Gammaproteobacteria).

BibTeX:

@article{magnani_culture-independent_2013,
author = {Magnani, G. S. and Cruz, L. M. and Weber, H. and Bespalhok, J. C. and Daros, E. and Baura, V. and Yates, M. G. and Monteiro, R. A. and Faoro, H. and Pedrosa, F. O. and Souza, E. M.},
title = {Culture-independent analysis of endophytic bacterial communities associated with Brazilian sugarcane},
journal = {Genetics and Molecular Research},
year = {2013},
volume = {12},
number = {4},
pages = {4549--4558},
note = {ISBN: 1676-5680 Publisher: Genetics and Molecular Research},
url = {http://www.funpecrp.com.br/gmr/year2013/vol12-4/pdf/gmr2524.pdf http://dx.doi.org/10.4238/2013.october.15.3},
doi = {10.4238/2013.October.15.3}
}

Manica GCM, Ramos EAS, de Oliveira MAS, Costa FF, Pedrosa FdO, de Souza EM, de Noronha L and Klassen G (2013). ADAM33 as a new biomarker for invasive lobular breast carcinoma. Journal of Cancer Science and Therapy, 5(1):14-17, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Invasive ductal carcinoma (IDC) and invasive lobular breast carcinoma (ILC) are the most common malignancies compromising the breast tissue in women worldwide. ILCs tend to form metastasisin remote locations, such as the gastrointestinal tract, peritoneal surface and retroperitoneum, compared with IDCs that move preferentially to the lymph nodes, lung, pleura, liver, brain and bones. The histological characteristics of these two tumors are very similar and there is no useful molecular marker to differentiate IDC from ILC to date. In this study, we cloned and expressed ADAM33 recombinant protein cystein rich domain in order to produce polyclonal antibodies and used it as a new immnunohistochemical molecular biomarker that specifically recognizes the ILC breast cancer subtype. © 2013 Manica GCM, et al.

BibTeX:

@article{manica_adam33_2013,
author = {Manica, Graciele C M and Ramos, Edneia A S and de Oliveira, Marco Aurelio Schuler and Costa, Fabricio F. and Pedrosa, Fábio de O and de Souza, Emanuel M. and de Noronha, Lúcia and Klassen, Giseli},
title = {ADAM33 as a new biomarker for invasive lobular breast carcinoma},
journal = {Journal of Cancer Science and Therapy},
year = {2013},
volume = {5},
number = {1},
pages = {14--17},
note = {Publisher: OMICS Publishing Group},
url = {http://dx.doi.org/10.4172/1948-5956.1000178 https://www.omicsonline.org/adam33-as-a-new-biomarker-for-invasive-lobular-breast-carcinoma-1948-5956.1000178.php?aid=10272},
doi = {10.4172/1948-5956.1000178}
}

Marin AM, Souza EM, Pedrosa FO, Souza LM, Sassaki GL, Baura VA, Yates MG, Wassem R and Monteiro RA (2013). Naringenin degradation by the endophytic diazotroph Herbaspirillum seropedicae SmR1. Microbiology (United Kingdom), 159(1):167-175, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Several bacteria are able to degrade flavonoids and use them as carbon sources or as a detoxification mechanism. Degradation pathways have been proposed for several bacteria but the genes responsible are not known. We identified in the genome of the endophyte Herbaspirillum seropedicae SmR1 an operon potentially associated with the degradation of aromatic compounds. We show that this operon is involved in naringenin degradation and its expression is induced by naringenin and chrysin, two closely related flavonoids. Mutation of fdeA, the first gene of the operon, and fdeR, its transcriptional activator, abolished the ability of H. seropedicae to degrade naringenin.

BibTeX:

@article{marin_naringenin_2013,
author = {Marin, A. M. and Souza, E. M. and Pedrosa, F. O. and Souza, L. M. and Sassaki, G. L. and Baura, V. A. and Yates, M. G. and Wassem, R. and Monteiro, R. A.},
title = {Naringenin degradation by the endophytic diazotroph Herbaspirillum seropedicae SmR1},
journal = {Microbiology (United Kingdom)},
year = {2013},
volume = {159},
number = {1},
pages = {167--175},
note = {ISBN: 1465-2080 (Electronic)$\backslash$r1350-0872 (Linking) Publisher: Microbiology Society},
url = {http://dx.doi.org/10.1099/mic.0.061135-0},
doi = {10.1099/mic.0.061135-0}
}

Neves LA and Giraldi GA (2013). SVM framework for incorporating content-based image retrieval and data mining into the SBIM image manager. In Lecture Notes in Computational Vision and Biomechanics. Dordrecht 8:49-66, 2013.
[DOI] [URL] [BibTeX]

Abstract:

BibTeX:

@incollection{neves_svm_2013,
author = {Neves, Luiz A.P. and Giraldi, Gilson A.},
editor = {Tavares, João Manuel R S and Natal Jorge, Renato M},
title = {SVM framework for incorporating content-based image retrieval and data mining into the SBIM image manager},
booktitle = {Lecture Notes in Computational Vision and Biomechanics},
publisher = {Springer Netherlands},
year = {2013},
volume = {8},
pages = {49--66},
note = {ISSN: 22129413},
url = {http://link.springer.com/10.1007/978-94-007-0726-9_3},
doi = {10.1007/978-94-007-0726-9_3}
}

Oliveira MIA, de Souza EM, Pedrosa FdO, Réa RR, Alves AdSC, Picheth G and Rego FGdM (2013). RAGE receptor and its soluble isoforms in diabetes mellitus complications. Jornal Brasileiro de Patologia e Medicina Laboratorial, 49(2):97-108, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Chronic hyperglycemia, which is present in all types of diabetes, increases the formation of advanced glycation end-products (AGEs). The interaction of AGEs with receptor of advanced glycation end-products (RAGE) initiates a cascade of pro-inflammatory and pro-coagulant processes that result in oxidative stress, stimulating the formation and accumulation of more AGE molecules. This cyclic process, denominated metabolic memory, may explain the persistency of diabetic vascular complications in patients with satisfactory glycemic control. The RAGE found in several cell membranes is also present in soluble isoforms (esRAGE and cRAGE), which are generated by alternative deoxyribonucleic acid splicing or by proteolytic cleavage. This review focuses on new research into these mediators as potential biomarkers for vascular complications in diabetes.

BibTeX:

@article{oliveira_rage_2013,
author = {Oliveira, Mauren Isfer Anghebem and de Souza, Emanuel Maltempi and Pedrosa, Fábio de Oliveira and Réa, Rosângela Roginski and Alves, Alexessander da Silva Couto and Picheth, Geraldo and Rego, Fabiane Gomes de Moraes},
title = {RAGE receptor and its soluble isoforms in diabetes mellitus complications},
journal = {Jornal Brasileiro de Patologia e Medicina Laboratorial},
year = {2013},
volume = {49},
number = {2},
pages = {97--108},
note = {ISBN: 1676-2444 UL - http://www.scielo.br/scielo.php?script=sciarttext&pid=S1676-24442013000200004&nrm=iso Publisher: FapUNIFESP (SciELO)},
url = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1676-24442013000200004&lng=en&nrm=iso&tlng=en},
doi = {10.1590/S1676-24442013000200004}
}

Ribeiro CG, Reynaud Steffens MBR, Etto RM, Galvão CW, Martins CdC, Pedrosa FdO and Kolm HE (2013). Ardra profiles of bacteria and archaea in mangrove sediments with different levels of contamination in the estuarine complex of paranaguá, brazil. Brazilian Archives of Biology and Technology, 56(2):275-281, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The mangrove's sediments from the coastal areas under human activities may contain significant contaminations by hydrocarbons, even when there are no visual evidences of it. The microorganisms are essential to these ecosystems, especially in the control of their chemical environment. Sediment samples were collected in two regions under different environment conditions (pristine and contaminated) of the Paranagua Estuarine Complex (Paranagua Bay and Laranjeiras Bay), Brazil. Aliphatic hydrocarbons were determined by the GC-FID to assess the status of contamination of the studied areas. The total DNA was extracted from these samples. The 16S rRNA gene was amplified by the PCR reactions with the pair of primers 21F and 958R for the archaeal domain, and 27F and 1492R for the bacterial domain. Comparisons of communities were made by the ARDRA technique, using the HinfI restriction enzyme. The phosphate concentration showed significant differences between the two regions. The aliphatic hydrocarbons analysis showed the presence of unresolved complex mixture (UCM), an indicator of oil contamination, in the samples from the Paranagua Bay, which was corroborated by the concentration of total aliphatic hydrocarbons. The ARDRA profile indicated that the structure of archaeal and bacterial communities of the sampled areas was very similar. Therefore, the anthropogenic influences in the Paranagua Bay showed to be not sufficient to produce disturbances in the prokaryotic dominant groups.

BibTeX:

@article{ribeiro_ardra_2013,
author = {Ribeiro, Catherine Gérikas and Reynaud Steffens, Maria Berenice Reynaud and Etto, Rafael Mazer and Galvão, Carolina Weigert and Martins, César de Castro and Pedrosa, Fábio de Oliveira and Kolm, Hedda Elisabeth},
title = {Ardra profiles of bacteria and archaea in mangrove sediments with different levels of contamination in the estuarine complex of paranaguá, brazil},
journal = {Brazilian Archives of Biology and Technology},
year = {2013},
volume = {56},
number = {2},
pages = {275--281},
note = {ISBN: 1516-8913 Publisher: FapUNIFESP (SciELO)},
url = {http://dx.doi.org/10.1590/S1516-89132013000200013},
doi = {10.1590/S1516-89132013000200013}
}

Ribeiro CB, Sobral MG, Tanaka CL, Dallagassa CB, Picheth G, Rego FG, Alberton D, Huergo LF, Pedrosa FO, Souza EM and Fadel-Picheth CM (2013). Proteins differentially expressed by Shiga toxin-producing Escherichia coli strain M03 due to the biliar salt sodium deoxycholate. Genetics and Molecular Research, 12(4):4909-4917, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Shiga toxin-producing Escherichia coli (STEC) can cause conditions ranging from diarrhea to potentially fatal hemolytic uremic syndrome. Enteropathogen adaptation to the intestinal environment is necessary for the development of infection, and response to bile is an essential characteristic. We evaluated the response of STEC strain M03 to the bile salt sodium deoxycholate through proteomic analysis. Cell extracts of strain M03 grown with and without sodium deoxycholate were analyzed by two-dimensional electrophoresis; the differentially expressed proteins were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Three proteins were found to be differentially expressed due to sodium deoxycholate. Glycerol dehydrogenase and phosphate acetyltransferase, which are involved in carbon metabolism and have been associated with virulence in some bacteria, were downregulated. The elongation factor Tu (TufA) was upregulated. This protein participates in the translation process and also has chaperone activities. These findings help us understand strategies for bacterial survival under these conditions.

BibTeX:

@article{ribeiro_proteins_2013,
author = {Ribeiro, C. B.A. and Sobral, M. G. and Tanaka, C. L. and Dallagassa, C. B. and Picheth, G. and Rego, F. G.M. and Alberton, D. and Huergo, L. F. and Pedrosa, F. O. and Souza, E. M. and Fadel-Picheth, C. M.T.},
title = {Proteins differentially expressed by Shiga toxin-producing Escherichia coli strain M03 due to the biliar salt sodium deoxycholate},
journal = {Genetics and Molecular Research},
year = {2013},
volume = {12},
number = {4},
pages = {4909--4917},
note = {Publisher: Genetics and Molecular Research},
url = {http://dx.doi.org/10.4238/2013.October.24.1},
doi = {10.4238/2013.October.24.1}
}

Stets MI, Pinto AS, Huergo LF, de Souza EM, Guimarães VF, Alves AC, Steffens MBR, Monteiro RA, Pedrosa FdO and Cruz LM (2013). Rapid identification of bacterial isolates from wheat roots by high resolution whole cell MALDI-TOF MS analysis. Journal of Biotechnology, 165(3-4):167-174, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Whole-cell mass spectrometry analysis is a powerful tool to rapidly identify microorganisms. Several studies reported the successful application of this technique to identify a variety of bacterial species with a discriminatory power at the strain level, mainly for bacteria of clinical importance. In this study we used matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) to assess the diversity of wheat-associated bacterial isolates. Wheat plants cultivated in non-sterile vermiculite, under greenhouse conditions were used for bacterial isolation. Total cellular extracts of 138 isolates were analyzed by MALDI-TOF MS and the mass spectra were used to cluster the isolates. Taxonomic identification and phylogenetic reconstruction based on 16S rRNA gene sequences showed the presence of Pseudomonas, Pantoea, Acinetobacter, Enterobacter and Curtobacterium. The 16S rRNA gene sequence analyses were congruent with the clusterization from mass spectra profile. Moreover, MALDI-TOF whole cell mass profiling allowed a finer discrimination of the isolates, suggesting that this technique has the potential of differentiating bacterial isolates at the strain level. © 2013 Elsevier B.V.

BibTeX:

@article{stets_rapid_2013,
author = {Stets, Maria Isabel and Pinto, Artur Soares and Huergo, Luciano Fernandes and de Souza, Emanuel Maltempi and Guimarães, Vandeir Francisco and Alves, Alexessander Couto and Steffens, Maria Berenice Reynaud and Monteiro, Rose Adele and Pedrosa, Fábio de Oliveira and Cruz, Leonardo Magalhães},
title = {Rapid identification of bacterial isolates from wheat roots by high resolution whole cell MALDI-TOF MS analysis},
journal = {Journal of Biotechnology},
year = {2013},
volume = {165},
number = {3-4},
pages = {167--174},
note = {ISBN: 0168-1656 Publisher: Elsevier BV},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0168165613001818 http://dx.doi.org/10.1016/j.jbiotec.2013.04.001},
doi = {10.1016/j.jbiotec.2013.04.001}
}

Tirapelle EF, Müller-Santos M, Tadra-Sfeir MZ, Kadowaki MAS, Steffens MBR, Monteiro RA, Souza EM, Pedrosa FO and Chubatsu LS (2013). Identification of Proteins Associated with Polyhydroxybutyrate Granules from Herbaspirillum seropedicae SmR1 - Old Partners, New Players. PLoS ONE, 8(9):e75066, 2013.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Herbaspirillum seropedicae is a diazotrophic ß-Proteobacterium found associated with important agricultural crops. This bacterium produces polyhydroxybutyrate (PHB), an aliphatic polyester, as a carbon storage and/or source of reducing equivalents. The PHB polymer is stored as intracellular insoluble granules coated mainly with proteins, some of which are directly involved in PHB synthesis, degradation and granule biogenesis. In this work, we have extracted the PHB granules from H. seropedicae and identified their associated-proteins by mass spectrometry. This analysis allowed us to identify the main phasin (PhaP1) coating the PHB granule as well as the PHB synthase (PhbC1) responsible for its synthesis. A phbC1 mutant is impaired in PHB synthesis, confirming its role in H. seropedicae. On the other hand, a phaP1 mutant produces PHB granules but coated mainly with the secondary phasin (PhaP2). Furthermore, some novel proteins not previously described to be involved with PHB metabolism were also identified, bringing new possibilities to PHB function in H. seropedicae.

BibTeX:

@article{tirapelle_identification_2013,
author = {Tirapelle, Evandro F. and Müller-Santos, Marcelo and Tadra-Sfeir, Michelle Z. and Kadowaki, Marco A S and Steffens, Maria B R and Monteiro, Rose A. and Souza, Emanuel M. and Pedrosa, Fabio O. and Chubatsu, Leda S.},
editor = {Desvaux, Mickaël},
title = {Identification of Proteins Associated with Polyhydroxybutyrate Granules from Herbaspirillum seropedicae SmR1 - Old Partners, New Players},
journal = {PLoS ONE},
year = {2013},
volume = {8},
number = {9},
pages = {e75066},
note = {Publisher: Public Library of Science (PLoS)},
url = {http://dx.plos.org/10.1371/journal.pone.0075066 http://dx.doi.org/10.1371/journal.pone.0075066},
doi = {10.1371/journal.pone.0075066}
}

Torda A (2013). Protein Function Prediction. In Methods in Molecular Biology. New York, NY 1611:1-51, 2013.
[DOI] [URL] [BibTeX]

Abstract:

BibTeX:

@incollection{torda_protein_2013,
author = {Torda, Andrew},
editor = {Kaufmann, Michael and Klinger, Claudia and Savelsbergh, Andreas},
title = {Protein Function Prediction},
booktitle = {Methods in Molecular Biology},
publisher = {Springer New York},
year = {2013},
volume = {1611},
pages = {1--51},
note = {ISSN: 10643745},
url = {http://link.springer.com/10.1007/978-1-4939-7231-9_5},
doi = {10.1038/sj.em}
}

Bonatto AC, Souza EM, Oliveira MAS, Monteiro RA, Chubatsu LS, Huergo LF and Pedrosa FO (2012). Uridylylation of herbaspirillum seropedicae glnb and glnk proteins is differentially affected by ATP, ADP and 2-oxoglutarate in vitro. Archives of Microbiology, 194(8):643-652, 2012.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: PII are signal-transducing proteins that integrate metabolic signals and transmit this information to a large number of proteins. In proteobacteria, PII are modified by GlnD (uridylyltransferase/uridylyl-removing enzyme) in response to the nitrogen status. The uridylylation/deuridylylation cycle of PII is also regulated by carbon and energy signals such as ATP, ADP and 2-oxoglutarate (2-OG). These molecules bind to PII proteins and alter their tridimensional structure/conformation and activity. In this work, we determined the effects of ATP, ADP and 2-OG levels on the in vitro uridylylation of Herbaspirillum seropedicae PII proteins, GlnB and GlnK. Both proteins were uridylylated by GlnD in the presence of ATP or ADP, although the uridylylation levels were higher in the presence of ATP and under high 2-OG levels. Under excess of 2-OG, the GlnB uridylylation level was higher in the presence of ATP than with ADP, while GlnK uridylylation was similar with ATP or ADP. Moreover, in the presence of ADP/ATP molar ratios varying from 10/1 to 1/10, GlnB uridylylation level decreased as ADP concentration increased, whereas GlnK uridylylation remained constant. The results suggest that uridylylation of both GlnB and GlnK responds to 2-OG levels, but only GlnB responds effectively to variation on ADP/ATP ratio.

BibTeX:

@article{bonatto_uridylylation_2012,
author = {Bonatto, Ana C. and Souza, Emanuel M. and Oliveira, Marco A S and Monteiro, Rose A. and Chubatsu, Leda S. and Huergo, Luciano F. and Pedrosa, Fábio O.},
title = {Uridylylation of herbaspirillum seropedicae glnb and glnk proteins is differentially affected by ATP, ADP and 2-oxoglutarate in vitro},
journal = {Archives of Microbiology},
year = {2012},
volume = {194},
number = {8},
pages = {643--652},
note = {Publisher: Springer Science Business Media},
url = {http://dx.doi.org/10.1007/s00203-012-0799-9},
doi = {10.1007/s00203-012-0799-9}
}

de Souza JAM, Tieppo E, de Souza Magnani G, Alves LMC, Cardoso RL, Cruz LM, de Oliveira LF, Raittz RT, de Souza EM, de Oliveira Pedrosa F and de Macedo Lemos EG (2012). Draft genome sequence of the nitrogen-fixing symbiotic bacterium Bradyrhizobium elkanii 587. Journal of Bacteriology, 194(13):3547-3548, 2012.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The draft sequence of the genome of Bradyrhizobium elkanii 587 is presented. This was obtained using Illumina Next-Gen DNA sequencing combined with Sanger sequencing. Genes for the pathways involved in biological nitrogen fixation (the nif gene cluster), nod genes including nodABC, and genes for the type III protein secretion system (T3SS) are present.

BibTeX:

@article{de_souza_draft_2012,
author = {de Souza, Jackson Antônio Marcondes and Tieppo, Eduardo and de Souza Magnani, Giovana and Alves, Lucia Maria Carareto and Cardoso, Rodrigo Luís and Cruz, Leonardo Magalhães and de Oliveira, Lucas Ferrari and Raittz, Roberto Tadeu and de Souza, Emanuel Maltempi and de Oliveira Pedrosa, Fábio and de Macedo Lemos, Eliana Gertrudes},
title = {Draft genome sequence of the nitrogen-fixing symbiotic bacterium Bradyrhizobium elkanii 587},
journal = {Journal of Bacteriology},
year = {2012},
volume = {194},
number = {13},
pages = {3547--3548},
note = {ISBN: 0021-9193 Publisher: American Society for Microbiology},
url = {http://jb.asm.org/cgi/doi/10.1128/JB.00563-12 http://dx.doi.org/10.1128/JB.00563-12},
doi = {10.1128/JB.00563-12}
}

Faoro H, Glogauer A, Couto GH, de Souza EM, Rigo LU, Cruz LM, Monteiro RA and de Oliveira Pedrosa F (2012). Characterization of a new Acidobacteria-derived moderately thermostable lipase from a Brazilian Atlantic Forest soil metagenome. FEMS Microbiology Ecology, 81(2):386-394, 2012.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: A clone (LP001) expressing a new lipase gene was isolated from a metagenomic library of the Brazilian Atlantic Forest soil. The DNA insert of LP001 was fully sequenced, and 38 ORFs were identified. Comparison of ORFs, %G + C content and gene organization with sequenced bacterial genomes suggested that the fosmid DNA insert belongs to an organism of the Acidobacteria phylum. Protein domain analysis and inactivation by transposon insertion showed that the protein encoded by ORF29 was responsible for the lipase activity and was named LipAAc. The purified LipAAc lipase was capable of hydrolyzing a broad range of substrates, showing the highest activity against p-nitrophenol (pNP) decanoate. The lipase was active over a pH range of 5.0-10.0 and was insensitive to divalent cations. LipAAc is moderately thermostable with optimum temperature between 50 and 60 °C and was thermally activated (80% activity increase) after 1 h incubation at 50 °C. Phylogenetic analysis suggested that the LipAAc is a member of family I of bacterial lipases and clusters with other moderately thermostable lipases of this group. Comparisons of the DNA insert of fosmid LP001 with other acidobacterial genomes and sequence database suggest that lipAAc gene has a fungal origin and was acquired by horizontal transfer.

BibTeX:

@article{faoro_characterization_2012,
author = {Faoro, Helisson and Glogauer, Arnaldo and Couto, Gustavo Henrique and de Souza, Emanuel Maltempi and Rigo, Liu Un and Cruz, Leonardo Magalhães and Monteiro, Rose Adele and de Oliveira Pedrosa, Fábio},
title = {Characterization of a new Acidobacteria-derived moderately thermostable lipase from a Brazilian Atlantic Forest soil metagenome},
journal = {FEMS Microbiology Ecology},
year = {2012},
volume = {81},
number = {2},
pages = {386--394},
note = {ISBN: 1574-6941 (Electronic)$\backslash$r0168-6496 (Linking) Publisher: Oxford University Press (OUP)},
url = {http://dx.doi.org/10.1111/j.1574-6941.2012.01361.x},
doi = {10.1111/j.1574-6941.2012.01361.x}
}

Monteiro RA, Balsanelli E, Tuleski T, Faoro H, Cruz LM, Wassem R, de Baura VA, Tadra-Sfeir MZ, Weiss V, Darocha WD, Muller-Santos M, Chubatsu LS, Huergo LF, Pedrosa FO and de Souza EM (2012). Genomic comparison of the endophyte Herbaspirillum seropedicae SmR1 and the phytopathogen Herbaspirillum rubrisubalbicans M1 by suppressive subtractive hybridization and partial genome sequencing. FEMS Microbiology Ecology, 80(2):441-451, 2012.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Herbaspirillum rubrisubalbicans M1 causes the mottled stripe disease in sugarcane cv. B-4362. Inoculation of this cultivar with Herbaspirillum seropedicae SmR1 does not produce disease symptoms. A comparison of the genomic sequences of these closely related species may permit a better understanding of contrasting phenotype such as endophytic association and pathogenic life style. To achieve this goal, we constructed suppressive subtractive hybridization (SSH) libraries to identify DNA fragments present in one species and absent in the other. In a parallel approach, partial genomic sequence from H. rubrisubalbicans M1 was directly compared in silico with the H. seropedicae SmR1 genome. The genomic differences between the two organisms revealed by SSH suggested that lipopolysaccharide and adhesins are potential molecular factors involved in the different phenotypic behavior. The cluster wss probably involved in cellulose biosynthesis was found in H. rubrisubalbicans M1. Expression of this gene cluster was increased in H. rubrisubalbicans M1 cells attached to the surface of maize root, and knockout of wssD gene led to decrease in maize root surface attachment and endophytic colonization. The production of cellulose could be responsible for the maize attachment pattern of H. rubrisubalbicans M1 that is capable of outcompeting H. seropedicae SmR1.

BibTeX:

@article{monteiro_genomic_2012,
author = {Monteiro, Rose A. and Balsanelli, Eduardo and Tuleski, Thalita and Faoro, Helison and Cruz, Leonardo M. and Wassem, Roseli and de Baura, Valter A. and Tadra-Sfeir, Michelle Z. and Weiss, Vinícius and Darocha, Wanderson D. and Muller-Santos, Marcelo and Chubatsu, Leda S. and Huergo, Luciano F. and Pedrosa, Fábio O. and de Souza, Emanuel M.},
title = {Genomic comparison of the endophyte Herbaspirillum seropedicae SmR1 and the phytopathogen Herbaspirillum rubrisubalbicans M1 by suppressive subtractive hybridization and partial genome sequencing},
journal = {FEMS Microbiology Ecology},
year = {2012},
volume = {80},
number = {2},
pages = {441--451},
note = {ISBN: 0168-6496 Publisher: Oxford University Press (OUP)},
url = {https://academic.oup.com/femsec/article-lookup/doi/10.1111/j.1574-6941.2012.01309.x http://dx.doi.org/10.1111/j.1574-6941.2012.01309.x},
doi = {10.1111/j.1574-6941.2012.01309.x}
}

Nishikawa CY, Araújo LM, Kadowaki MAS, Monteiro RA, Steffens MBR, Pedrosa FO, Souza EM and Chubatsu LS (2012). Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense. Brazilian Journal of Medical and Biological Research, 45(2):113-117, 2012.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Azospirillumbrasilense is a nitrogen-fixing bacterium associated with important agricultural crops such as rice, wheat and maize. The expression of genes responsible for nitrogen fixation (nif genes) in this bacterium is dependent on the transcriptional activator NifA. This protein contains three structural domains: the N-terminal domain is responsible for the negative control by fixed nitrogen; the central domain interacts with the RNA polymerase σ⁵⁴ factor and the C-terminal domain is involved in DNA binding. The central and C-terminal domains are linked by the interdomain linker (IDL). A conserved four-cysteine motif encompassing the end of the central domain and the IDL is probably involved in the oxygen-sensitivity of NifA. In the present study, we have expressed, purified and characterized an N-truncated form of A. brasilense NifA. The protein expression was carried out in Escherichia coli and the N-truncated NifA protein was purified by chromatography using an affinity metal-chelating resin followed by a heparin-bound resin. Protein homogeneity was determined by densitometric analysis. The N-truncated protein activated in vivo nifH::lacZ transcription regardless of fixed nitrogen concentration (absence or presence of 20 mM NH₄Cl) but only under low oxygen levels. On the other hand, the aerobically purified N-truncated NifA protein bound to the nifB promoter, as demonstrated by an electrophoretic mobility shift assay, implying that DNA-binding activity is not strictly controlled by oxygen levels. Our data show that, while the N-truncated NifA is inactive in vivo under aerobic conditions, it still retains DNA-binding activity, suggesting that the oxidized form of NifA bound to DNA is not competent to activate transcription. (PsycINFO Database Record (c) 2012 APA, all rights reserved). (journal abstract)

BibTeX:

@article{nishikawa_expression_2012,
author = {Nishikawa, C. Y. and Araújo, L. M. and Kadowaki, M. A S and Monteiro, R. A. and Steffens, M. B R and Pedrosa, F. O. and Souza, E. M. and Chubatsu, L. S.},
title = {Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense},
journal = {Brazilian Journal of Medical and Biological Research},
year = {2012},
volume = {45},
number = {2},
pages = {113--117},
note = {Publisher: FapUNIFESP (SciELO)},
url = {http://dx.doi.org/10.1590/S0100-879X2012007500006 http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2012000200004&lng=en&tlng=en},
doi = {10.1590/S0100-879X2012007500006}
}

Nunes GG, Bonatto AC, De Albuquerque CG, Barison A, Ribeiro RR, Back DF, Andrade AVC, De Sá EL, Pedrosa FDO, Soares JF and De Souza EM (2012). Synthesis, characterization and chemoprotective activity of polyoxovanadates against DNA alkylation. In Journal of Inorganic Biochemistry. 108:36-46, 2012.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: The alkylation of pUC19 plasmid DNA has been employed as a model reaction for the first studies on chemoprotective action by a mixed-valence (+ IV/+V) polyoxovanadate. A new, non-hydrothermal route for the high yield preparation of the test compound is described. The deep green, microcrystalline solid A was isolated after a three-day reaction in water at 80 °C and 1 atm, while the reaction at 100 °C gave green crystals of B. Both solids were structurally characterized by X-ray diffractometry and FTIR, EPR, NMR and Raman spectroscopies. Product A was identified as (NH4)2V3O8, while B corresponds to the spherical polyoxoanion [V15O36(Cl)]6-, isolated as the NMe4+salt. The lack of solubility of A in water and buffers prevented its use in DNA interaction studies, which were then carried out with B. Complex B was also tested for its ability to react with DNA alkylating agents by incubation with diethylsulphate (DES) and dimethylsulphate (DMS) in both the absence and presence of pUC19. For DMS, the best results were obtained with 10 mM of B (48% protection); with DES, this percentage increased to 70%. The direct reaction of B with increasing amounts of DMS in both buffered (PIPES 50 mM) and non-buffered aqueous solutions revealed the sequential formation of several vanadium(IV), vanadium(V) and mixed-valence aggregates of different nuclearities, whose relevance to the DNA-protecting activity is discussed. © 2011 Elsevier Inc. All rights reserved.

BibTeX:

@inproceedings{nunes_synthesis_2012,
author = {Nunes, Giovana G. and Bonatto, Ana C. and De Albuquerque, Carla G. and Barison, Andersson and Ribeiro, Ronny R. and Back, Davi F. and Andrade, André Vitor C. and De Sá, Eduardo L. and Pedrosa, Fábio De O. and Soares, Jaísa F. and De Souza, Emanuel M.},
title = {Synthesis, characterization and chemoprotective activity of polyoxovanadates against DNA alkylation},
booktitle = {Journal of Inorganic Biochemistry},
publisher = {Elsevier BV},
year = {2012},
volume = {108},
pages = {36--46},
note = {ISSN: 01620134},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0162013411003667 http://dx.doi.org/10.1016/j.jinorgbio.2011.11.019},
doi = {10.1016/j.jinorgbio.2011.11.019}
}

Oliveira MA, Aquino B, Bonatto AC, Huergo LF, Chubatsu LS, Pedrosa FO, Souza EM, Dixon R and Monteiro RA (2012). Interaction of GlnK with the GAF domain of Herbaspirillum seropedicae NifA mediates NH4+-regulation. Biochimie, 94(4):1041-1047, 2012.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Nitrogen fixation in Herbaspirillum seropedicae is transcriptionally regulated by NifA, a σ54transcriptional activator with three structural domains: an N-terminal GAF domain, a catalytic AAA+ domain and a C-terminal DNA-binding domain. NifA is only active in H. seropedicae when cultures are grown in the absence of fixed nitrogen and at low oxygen tensions. There is evidence that the inactivation of NifA in response to fixed nitrogen is mediated by the regulatory GAF domain. However, the mechanism of NifA repression by the GAF domain, as well as the transduction of nitrogen status to NifA, is not understood. In order to study the regulation of NifA activity by fixed nitrogen independently of oxygen regulation, we constructed a chimeric protein containing the GAF domain of H. seropedicae NifA fused to the AAA+ and C-terminal domains of Azotobacter vinelandii NifA. This chimeric protein (NifAQ1) lacks the cysteine motif found in oxygen sensitive NifA proteins and is not oxygen responsive in vivo. Our results demonstrate that NifAQ1 responds to fixed nitrogen and requires GlnK protein for activity, a behavior similar to H. seropedicae NifA. In addition, protein footprinting analysis indicates that this response probably involves a protein-protein contact between the GAF domain and the GlnK protein. © 2011 Published by Elsevier Masson SAS.

BibTeX:

@article{oliveira_interaction_2012,
author = {Oliveira, Marco A.S. and Aquino, Bruno and Bonatto, Ana Claudia and Huergo, Luciano F. and Chubatsu, Leda S. and Pedrosa, Fábio O. and Souza, Emanuel M. and Dixon, Ray and Monteiro, Rose A.},
title = {Interaction of GlnK with the GAF domain of Herbaspirillum seropedicae NifA mediates NH4+-regulation},
journal = {Biochimie},
year = {2012},
volume = {94},
number = {4},
pages = {1041--1047},
note = {ISBN: 0300-9084 Publisher: Elsevier BV},
url = {http://dx.doi.org/10.1016/j.biochi.2012.01.007},
doi = {10.1016/j.biochi.2012.01.007}
}

Schmidt MA, Balsanelli E, Faoro H, Cruz LM, Wassem R, De Baura VA, Weiss V, Yates MG, Madeira HMF, Pereira-Ferrari L, Fungaro MHP, De Paula FM, Pereira LFP, Vieira LGE, Olivares FL, Pedrosa FO, De Souza EM and Monteiro RA (2012). The type III secretion system is necessary for the development of a pathogenic and endophytic interaction between Herbaspirillum rubrisubalbicans and Poaceae. BMC Microbiology, 12(1):98, 2012.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: BACKGROUND: Herbaspirillum rubrisubalbicans was first identified as a bacterial plant pathogen, causing the mottled stripe disease in sugarcane. H. rubrisubalbicans can also associate with various plants of economic interest in a non pathogenic manner. RESULTS: A 21 kb DNA region of the H. rubrisubalbicans genome contains a cluster of 26 hrp/hrc genes encoding for the type three secretion system (T3SS) proteins. To investigate the contribution of T3SS to the plant-bacterial interaction process we generated mutant strains of H. rubrisubalbicans M1 carrying a Tn5 insertion in both the hrcN and hrpE genes. H. rubrisulbalbicans hrpE and hrcN mutant strains of the T3SS system failed to cause the mottled stripe disease in the sugarcane susceptible variety B-4362. These mutant strains also did not produce lesions on Vigna unguiculata leaves. Oryza sativa and Zea mays colonization experiments showed that mutations in hrpE and hrcN genes reduced the capacity of H. rubrisulbalbicans to colonize these plants, suggesting that hrpE and hrcN genes are involved in the endophytic colonization. CONCLUSIONS: Our results indicate that the T3SS of H. rubrisubalbicans is necessary for the development of the mottled stripe disease and endophytic colonization of rice.

BibTeX:

@article{schmidt_type_2012,
author = {Schmidt, Maria Augusta and Balsanelli, Eduardo and Faoro, Hellison and Cruz, Leonardo M. and Wassem, Roseli and De Baura, Valter A. and Weiss, Vinícius and Yates, Marshall G. and Madeira, Humberto M F and Pereira-Ferrari, Lilian and Fungaro, Maria H P and De Paula, Francine M. and Pereira, Luiz F P and Vieira, Luiz G E and Olivares, Fábio L. and Pedrosa, Fábio O. and De Souza, Emanuel M. and Monteiro, Rose A.},
title = {The type III secretion system is necessary for the development of a pathogenic and endophytic interaction between Herbaspirillum rubrisubalbicans and Poaceae},
journal = {BMC Microbiology},
year = {2012},
volume = {12},
number = {1},
pages = {98},
note = {ISBN: 1471-2180 (Electronic)$\backslash$r1471-2180 (Linking) Publisher: Springer Science Business Media},
url = {http://dx.doi.org/10.1186/1471-2180-12-98},
doi = {10.1186/1471-2180-12-98}
}

Serrato RV, Balsanelli E, Sassaki GL, Carlson RW, Muszynski A, Monteiro RA, Pedrosa FO, Souza EM and Iacomini M (2012). Structural analysis of Herbaspirillum seropedicae lipid-A and of two mutants defective to colonize maize roots. International Journal of Biological Macromolecules, 51(4):384-391, 2012.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Lipid-A was isolated by mild acid hydrolysis from lipopolysaccharides extracted from cells of Herbaspirillum seropedicae, strain SMR1, and from two mutants deficient in the biosynthesis of rhamnose (rmlB-and rmlC-). Structural analyzes were carried out using MALDI-TOF and derivatization by per-O-trimethylsilylation followed by GC-MS in order to determine monosaccharide and fatty acid composition. De-O-acylation was also performed to determine the presence of N-linked fatty acids. Lipid-A from H. seropedicae SMR1 showed a major structure comprising 2-amino-2-deoxy-glucopyranose-(1→6)-2-amino-2-deoxy-glucopyranose phosphorylated at C4' and C1 positions, each carrying a unit of 4-amino-4-deoxy-arabinose. C2 and C2' positions were substituted by amide-linked 3-hydroxy-dodecanoic acids. Both rhamnose-defective mutants showed similar structure for their lipid-A moieties, except for the lack of 4-amino-4-deoxy-arabinose units attached to phosphoryl groups. © 2012 Elsevier B.V.

BibTeX:

@article{serrato_structural_2012,
author = {Serrato, Rodrigo V. and Balsanelli, Eduardo and Sassaki, Guilherme L. and Carlson, Russell W. and Muszynski, Artur and Monteiro, Rose A. and Pedrosa, Fábio O. and Souza, Emanuel M. and Iacomini, Marcello},
title = {Structural analysis of Herbaspirillum seropedicae lipid-A and of two mutants defective to colonize maize roots},
journal = {International Journal of Biological Macromolecules},
year = {2012},
volume = {51},
number = {4},
pages = {384--391},
note = {ISBN: 1024123X (ISSN) Publisher: Elsevier BV},
url = {http://dx.doi.org/10.1016/j.ijbiomac.2012.05.034},
doi = {10.1016/j.ijbiomac.2012.05.034}
}

Silva A, Ramos R, Carneiro A, Pinto A, Soares S, Santos A, Almeida S, Guimarães L, Aburjaile F, Barbosa E, Dorella F, Rocha F, Lopes T, Kawasaki R, Sá P, Coimbra N, Cerdeira L, Barbosa M, Schneider M, Miyoshi A, Selim S, Moawad M and Azevedo V (2012). Complete genome sequence of Corynebacterium pseudotuberculosis Cp31, isolated from an Egyptian buffalo. Journal of Bacteriology, 194(23):6663-6664, 2012.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Corynebacterium pseudotuberculosis is of major veterinary importance because it affects many animal species, causing economically significant livestock diseases and losses. Therefore, the genomic sequencing of various lines of this organism, isolated from different hosts, will aid in the development of diagnostic methods and new prevention and treatment strategies and improve our knowledge of the biology of this microorganism. In this study, we present the genome of C. pseudotuberculosis Cp31, isolated from a buffalo in Egypt. © 2012, American Society for Microbiology.

BibTeX:

@article{silva_complete_2012,
author = {Silva, A. and Ramos, R.T.J. and Carneiro, A.R. and Pinto, A.C. and Soares, S.C. and Santos, A.R. and Almeida, S.S. and Guimarães, L.C. and Aburjaile, F.F. and Barbosa, E.G.V. and Dorella, F.A. and Rocha, F.S. and Lopes, T.S. and Kawasaki, R. and Sá, P.G. and Coimbra, N.A.R. and Cerdeira, L.T. and Barbosa, M.S. and Schneider, M.P.C. and Miyoshi, A. and Selim, S.A.K. and Moawad, M.S. and Azevedo, V.},
title = {Complete genome sequence of Corynebacterium pseudotuberculosis Cp31, isolated from an Egyptian buffalo},
journal = {Journal of Bacteriology},
year = {2012},
volume = {194},
number = {23},
pages = {6663--6664},
url = {http://jb.asm.org/cgi/doi/10.1128/JB.01782-12},
doi = {10.1128/JB.01782-12}
}

Weiss VA, Faoro H, Tadra-Sfeir MZ, Raittz RT, de Souza EM, Monteiro RA, Cardoso RLA, Wassem R, Chubatsu LS, Huergo LF, Müller-Santos M, Steffens MBR, Rigo LU, Pedrosa FdO and Cruz LM (2012). Draft genome sequence of Herbaspirillum lusitanum p6-12, an endophyte isolated from root nodules of Phaseolus vulgaris. Journal of Bacteriology, 194(15):4136-4137, 2012.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Herbaspirillum lusitanum strain P6-12 (DSM 17154) is, so far, the only species of Herbaspirillum isolated from plant root nodules. Here we report a draft genome sequence of this organism.

BibTeX:

@article{weiss_draft_2012,
author = {Weiss, Vinícius Almir and Faoro, Helisson and Tadra-Sfeir, Michelle Zibbetti and Raittz, Roberto Tadeu and de Souza, Emanuel Maltempi and Monteiro, Rose Adele and Cardoso, Rodrigo Luis Alves and Wassem, Roseli and Chubatsu, Leda Satie and Huergo, Luciano Fernandes and Müller-Santos, Marcelo and Steffens, Maria Berenice Reynaud and Rigo, Liu Un and Pedrosa, Fábio de Oliveira and Cruz, Leonardo Magalhães},
title = {Draft genome sequence of Herbaspirillum lusitanum p6-12, an endophyte isolated from root nodules of Phaseolus vulgaris},
journal = {Journal of Bacteriology},
year = {2012},
volume = {194},
number = {15},
pages = {4136--4137},
note = {ISBN: 1471216497},
url = {http://jb.asm.org/cgi/doi/10.1128/JB.00657-12},
doi = {10.1128/JB.00657-12}
}

Beneduzi A, Campos S, Ambrosini A, de Souza R, Granada C, Costa P, Arruda L, Moreira F, Vargas LK, Weiss V, Tieppo E, Faoro H, de Souza EM, Pedrosa FO and Passaglia LM (2011). Genome Sequence of the Diazotrophic Gram-Positive Rhizobacterium Paenibacillus riograndensis SBR5T. Journal of Bacteriology, 193(22):6391-6392, 2011.
[Abstract] [DOI] [URL] [BibTeX]

Abstract: Paenibacillus riograndensis SBR5(T), a nitrogen-fixing Gram-positive rhizobacterium isolated from a wheat field in the south of Brazil, has a great potential for agricultural applications due to its plant growth promotion effects. Here we present the draft genome sequence of P. riograndensis SBR5(T). Its 7.37-Mb genome encodes determinants of the diazotrophic lifestyle and plant growth promotion, such as nitrogen fixation, antibiotic resistance, nitrate utilization, and iron uptake.

BibTeX:

@article{beneduzi_genome_2011,
author = {Beneduzi, Anelise and Campos, Samanta and Ambrosini, Adriana and de Souza, Rocheli and Granada, Camille and Costa, Pedro and Arruda, Letícia and Moreira, Fernanda and Vargas, Luciano K. and Weiss, Vinícius and Tieppo, Eduardo and Faoro, Helisson and de Souza, Emanuel M. and Pedrosa, Fábio O. and Passaglia, Luciane M.P.},
title = {Genome Sequence of the Diazotrophic Gram-Positive Rhizobacterium Paenibacillus riograndensis SBR5T},
journal = {Journal of Bacteriology},
year = {2011},
volume = {193},
number = {22},
pages = {6391--6392},
note = {ISBN: 1098-5530 (Electronic)$\backslash$r0021-9193 (Linking)},
url = {http://jb.asm.org/lookup/doi/10.1128/JB.06100-11},
doi = {10.1128/JB.06100-11}
}

Cerdeira LT, Schneider MPC, Pinto AC, de Almeida SS, dos Santos AR, Barbosa EGV, Ali A, Aburjaile FF, de Abreu VAC, Guimaraes LC, Soares SdC, Dorella FA, Rocha FS, Bol E, de Sa PHC, Lopes TS, Barbosa MS, Carneiro AR, Juca Ramos RT, Coimbra NAdR, Lima ARJ, Barh D, Jain N, Tiwari S, Raja R, Zambare V, Ghosh P, Trost E, Tauch A, Miyoshi A, Azevedo V and Silva A (2011). Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain CIP 52.97, Isolated from a Horse in Kenya. Journal of Bacteriology, 193(24):7025-7026, 2011.
[DOI] [URL] [BibTeX]

Abstract:

BibTeX:

@article{cerdeira_complete_2011,
author = {Cerdeira, L T and Schneider, M P C and Pinto, A C and de Almeida, S S and dos Santos, A R and Barbosa, E G V and Ali, A and Aburjaile, F F and de Abreu, V A C and Guimaraes, L C and Soares, S d. C and Dorella, F A and Rocha, F S and Bol, E and de Sa, P H C and Lopes, T S and Barbosa, M S and Carneiro, A R and Juca Ramos, R T and Coimbra, N A d. R and Lima, A R J and Barh, D and Jain, N and Tiwari, S and Raja, R and Zambare, V and Ghosh, P and Trost, E and Tauch, A and Miyoshi, A and Azevedo, V and Silva, A},
title = {Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain CIP 52.97, Isolated from a Horse in Kenya},
journal = {Journal of Bacteriology},
year = {2011},
volume = {193},
number = {24},
pages = {7025--7026},
url = {http://jb.asm.org/cgi/doi/10.1128/JB.06293-11},
doi = {10.1128/JB.06293-11}
}

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