Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics

Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomicand metatranscriptomic-based analyses of a large composting operation in the Sao Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 degrees C to 75 degrees C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the processand that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Provost's Office for Research of the University of Sao PauloCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ Sao Paulo, Inst Quim, Dept Bioquim, Sao Paulo, BrazilUniv Sao Paulo, Programa Pos Graduacao Interunidades Bioinformat, Sao Paulo, BrazilUniv Sao Paulo, Escola Artes Ciencias & Humanidades, Sao Paulo, Brazil|Fundacao Parque Zool Sao Paulo, Sao Paulo, BrazilUniv Fed Sao Paulo, Dept Ciencias Biol, Sao Paulo, BrazilBiocomplex Inst Virginia, Blacksburg, VA USADepartamento de Ciências Biológicas, Universidade Federal de São Paulo, São Paulo, BrazilFAPESP: 2011/50870-6Web of Scienc

Metagenomic analysis of a tropical composting operation at the São Paulo Zoo Park reveals diversity of biomass degradation functions and organisms.

Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the Sao Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.FAPESP 2009/52030-5RCNPqCAPE

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Interaction network and mass spectrometry data of Xanthomonas citri subsp. citri surface proteins from differential proteomic analysis of infectious and non-infectious cells

Here we provide the mass-spectrometry and in silico interaction network dataset of proteins identified on our research article on surface proteomic analysis from Xanthomonas citri subsp. citri (XAC) cells grown in vivo (infectious) and in vitro (non-infectious, control) by 2D-DIGE approach. Fluorescence labeling of proteins were performed on intact cells followed by cellular lysis and labeled spots from 2D gel differing in abundance between the two conditions (ANOVA, p-value<0.05) were analyzed by a nano-electrospray tandem mass spectrometry Q-Tof Ultima API mass spectrometer (MicroMass/Waters) (LC-ESI-MS/MS). This article contains raw data of proteins detected in the 79 spots analyzed by LC-ESI-MS/MS approach and also an enrichment analysis on the resulting protein–protein interaction network performed with the Integrated Interactome System (IIS) platform and Cytoscape software. The data are supplementary to our original research article, “Xanthomonas citri subsp. citri surface proteome by 2D-DIGE: ferric enterobactin receptor and other outer membrane proteins potentially involved in citric host interaction” (Carnielli et al., 2016) [1], and raw data are available via Peptide Atlas (ftp://PASS00850:[email protected]/). Keywords: Interaction network, MS data, Xanthomonas citri, Surface proteome, Citrus canke

Proposta de inclusão do fator “geração elétrica em PCHs” nos critérios de distribuição do ICMS ecológico no estado de Minas Gerais.

Vários mecanismos legais têm sido criados para compensar territórios que promovam ações ambientais. Este trabalho foi desenvolvido com o objetivo de analisar os impactos da inserção do critério “produção de energia elétrica por Pequenas Centrais Hidrelétricas” na distribuição do ICMS Ecológico no Estado de Minas Gerais. Foi realizada uma simulação para verificar o impacto da adoção deste critério para a região de abrangência da Associação dos Municípios da Microrregião do Vale do Rio Piranga. O município de Diogo de Vasconcelos, por exemplo, poderia arrecadar R$199.411,00 por ano com a inclusão do critério “produção de energia elétrica por Pequenas Centrais Hidrelétricas” na legislação estadual. O recurso poderia ser aplicado em ações socioambientais, como plantio de áreas verdes, construção de escolas e investimentos em saúde. Portanto, recomenda-se a inclusão do critério analisado neste trabalho na Lei de ICMS Ecológico no Estado de Minas Gerais.This work was developed with the objective of analysing the impact of the inclusion of the variable "Electricity Production by Small Hydropower Plants" in the distribution of the “Ecological Sales Tax” (ICMS Ecológico) in the State of Minas Gerais. Simulation was performed to verify the impact of adopting this criterion for the region covered by the Association of Municipalities of Piranga River Valley. The municipality of Diogo de Vasconcelos, for example, could raise R$ 199.411 per year with the inclusion of the criterion "Production of electricity for Small Hydropower" in state law. This feature could be applied in environmental initiatives such as plantation of green areas, school construction and health investments. Therefore, the inclusion of the criterion analysed in this work in the “Ecological Sales Tax” law of the State of Minas Gerais is recommended

Análise do perfil de expressão dos genes da cana-de-açúcar envolvidos na interação com Leifsonia xyli subsp: xyli

Utilizando a técnica de macroarranjos de cDNA em membranas de náilon, analisou-se o perfil de expressão de 3.575 ESTs (Expressed Sequence Tags) de cana-de-açúcar, oriundas do projeto SUCEST, em duas variedades, uma tolerante (SP80-0185) e outra suscetível (SP70-3370) ao Raquitismo da Soqueira. Foram analisadas amostras foliares de plantas inoculadas com Leifsonia xyli subsp. xyli., agente etiológico do Raquitismo, contrastadas com plantas não inoculadas (controle), para cada variedade, marcadas com sondas de cDNA e hibridizadas contra os macroarranjos. Após as hibridizações e análises estatísticas dos dados foi possível identificar 49 ESTs com expressão alterada, sendo 44 na variedade tolerante (41 ESTs induzidos e 3 reprimidos) e 5 na variedade suscetível (2 ESTs induzidos e 3 reprimidos). Os resultados obtidos sugerem que a tolerância da variedade SP80-0185 de cana-de-açúcar à bactéria fitopatogênica pode estar relacionada com a percepção de sinais extracelulares, visto que ESTs relacionados a vias de transdução de sinais apresentaram expressão gênica induzida na variedade tolerante, os quais codificam para uma EST com similaridade à H+-ATPase da membrana plasmática, fatores de transcrição G-box, OsNAC6, DNA binding, família MYB e Zinc Finger e ainda uma EST com similaridade ao fator de ligação ao G-Box, o qual corresponde a uma seqüência de DNA cis presente em vários promotores de plantas e requerido para o reconhecimento de muitos estímulos ambientais. Na variedade suscetível foi reprimido uma EST com similaridade à lipase. Esta enzima, também de membrana, faz parte da síntese do jasmonato, o qual ativa as defesas vegetais contra patógenos de plantas. Possíveis funções para os genes induzidos ou reprimidos nas cultivares de cana tolerante ou resistente ao Raquitismo são discutidas neste trabalho.The macroarray nylon membrane technology was used to study the differential gene expression of 3.575 ESTs clones from sugarcane libraries. Total RNA was extracted from two varieties, one known as tolerant (SP80-0185) and another known as susceptible (SP70-3370) to the ratoon stunting disease (RSD), after being inoculated with Lefsonia xyli subsp. xyli bacterial extracts, and used as probe. Out of the 3.575 ESTs, 49 showed differential expression levels. Most of the selected ESTs were found in the resistant variety, 41 being induced and 3 being repressed in response to bacterial inoculation. on the other hand, the susceptible variety showed only 5 differentially expressed genes, 2 being induced and 3 being repressed. These results indicate that the tolerance to bacterial infection could be associated to extracellular signal perception because ESTs associated to signal transduction pathways were induced in the variety SP80-185, e.g. plasma membrane H+ ATPase EST. Also, ESTs related to transcription factor expression, such as G-box, OsNAC6, DNA binding, MYB family, Zinc Finger were induced in the tolerant variety after infection. An EST with high similarity to G-Box binding factor, a cis-DNA sequence present in some plant promoter genes required to signal transduction for environmental signals, was also induced. Even though the susceptible variety had no significant difference in gene expression, a lipase-like EST was repressed when plants were infected. Lipase, a membrane enzyme, is also involved in jasmonate biosynthesis, which plays a major role in plant defense mechanisms. Putative roles for induced and repressed genes in both tolerant and susceptible varieties are discussed here.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

CXCL12 rs1801157 Polymorphism in Patients with Breast Cancer, Hodgkin`s Lymphoma, and Non-Hodgkin`s Lymphoma

Chemokines and their receptors regulate the trafficking of immune cells during their development, inflammation, and tissue repair. The single-nucleotide polymorphism (SNP) rs1801157 (previously known as CXCL12-A/ stromal cell-derived factor-1 (SDF1)-3`A) in CXCL12/SDF1 gene was assessed in breast cancer, Hodgkin`s lymphoma (HL), and non-Hodgkin`s lymphoma (NHL), since the chemokine CXCL12, previously known as SDF1, and its receptor CXCR4 regulate leukocyte trafficking and many essential biological processes, including tumor growth, angiogenesis, and metastasis of different types of tumors. Genotyping was performed by PCR-RFLP (polymerase chain reaction followed by restriction fragment length polymorphism) using a restriction enzyme Hpall cleavage. No significant difference was observed in genotype distribution between breast cancer patients (GG: 57.3%; GA: 39.8%; AA: 2.9%) and healthy female controls (GG: 62.9%; GA: 33%; AA: 4.1%) nor between HL patients (GG: 61.1%; GA:27.8%; AA: 11.1%) and healthy controls (GG: 65.6%; GA: 28.9%; AA: 5.5%), whereas a significant difference was observed in genotype distribution between NHL patients (GG: 51.4%; GA: 47.1%; AA: 1.5%) and healthy controls (GG: 65.6%; GA: 28.9%; AA: 5.5%). Further studies will be necessary to elucidate the cancer chemokine network. However, this study suggests that CXCL12 rs1801157 polymorphism may have important implications in the pathogenesis of NHL. J. Clin. Lab. Anal. 23:387-393, 2009. (C) 2009 Wiley-Liss, Inc.Conselho Nacional de Desenvolvimento Cientifico c Tectiologico (CNPq)Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)Londrina State University Coordination for Postgraduation (PROPPG-UEL

Comparative proteomic analysis reveals that T3SS, Tfp, and xanthan gum are key factors in initial stages of Citrus sinensis infection by Xanthomonas citri subsp. citri.

The bacteria Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker. The disease symptoms are characterized by localized host cell hyperplasia followed by tissue necrosis at the infected area. An arsenal of bacterial pathogenicity- and virulence-related proteins is expressed to ensure a successful infection process. At the post-genomic stage of Xac, we used a proteomic approach to analyze the proteins that are displayed differentially over time when the pathogen attacks the host plant. Protein extracts were prepared from infectious Xac grown in inducing medium (XAM1) for 24 h or from host citrus plants for 3 or 5 days after infection, detached times to evaluate the adaptation and virulence of the pathogen. The protein extracts were proteolyzed, and the peptides derived from tryptic digestion were investigated using liquid chromatography and tandem mass spectrometry. Changes in the protein expression profile were compared with the Xac genome and the proteome recently described under non-infectious conditions. An analysis of the proteome of Xac under infectious conditions revealed proteins directly involved in virulence such as the type III secretion system (T3SS) and effector proteins (T3SS-e), the type IV pilus (Tfp), and xanthan gum biosynthesis. Moreover, four new mutants related to proteins detected in the proteome and with different functions exhibited reduced virulence relative to the wild-type proteins. The results of the proteome analysis of infectious Xac define the processes of adaptation to the host and demonstrate the induction of the virulence factors of Xac involved in plant–pathogen interactions