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Dissertations |
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1
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Felipe Rangel do Vale Lima
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Functional redundancy of microbial communities in diverse terrestrial ecosystems.
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Advisor : PEDRO MILET MEIRELLES
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COMMITTEE MEMBERS :
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RONALDO BASTOS FRANCINI FILHO
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PAULA CARVALHAL LAGE VON BUETTNER RISTOW
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PEDRO MILET MEIRELLES
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Data: Jan 20, 2023
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Show Abstract
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Functional redundancy is a mechanism that guarantees the maintenance of ecological processes that are crucial to the functionality of the ecosystem, even with the loss of species. Although widely studied in animals and plants, little is understood about the functional redundancy in microbial communities despite the importance of these communities for the maintenance of numerous ecosystem services. Rare microorganisms, microbial taxa with relative abundance below 0.01%, play a key role in maintaining ecosystem services, but are generally neglected in studies of functional redundancy in microbial communities. In the present study, we collected 6794 metagenomic samples, obtained from 73 habitats distributed in 9 ecosystems across the planet, from which we calculated the functional redundancy in microbial communities from different ecosystems. To test the relationship between relative abundance and richness of the rare biosphere of the microorganism community and the functional redundancy indices found, we performed a simple linear regression considering significant the analyzes whose P value <0.05. Our findings demonstrate that functional redundancy differs considerably between the studied ecosystems. Data from this study reveal that the functional redundancy of microbial communities is apparently strongly influenced by the lifestyle of microorganisms and the environments in which they are inserted. The analysis carried out revealed that microbial communities with a high richness of rare microorganisms generally have reduced functional redundancy which leads us to believe that rare microorganisms can be important in performing highly specialized and distinct functions in each environment and their extinction can trigger cascading effects reducing the functionality of ecosystems.
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2
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LUCAS BARBOSA DE AMORIM CONCEIÇÃO
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Identification and Characterization of Endogenous Viral Elements in Genomes of Bombus spp.
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Advisor : ERIC ROBERTO GUIMARAES ROCHA AGUIAR
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COMMITTEE MEMBERS :
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RODRIGO ARAÚJO LIMA RODRIGUES
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ERIC ROBERTO GUIMARAES ROCHA AGUIAR
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LUIZ EDUARDO VIEIRA DEL BEM
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Data: Feb 27, 2023
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Show Abstract
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Bee populations are extremely important for the maintenance of pollination-dependent populations of plants, which reflects on a market cap of 24 billion dollars, supporting global food production with more than US$ 200 bilhões. The genus Bombus stands out by comprising efficient pollinator species in commercial crops and their natural habitats. Bee populations have been manifesting a concerning decline due to climate change, the use of pesticides and parasites, especially viruses. Therefore, it is necessary to investigate immunological mechanisms that act on these organisms' immune defenses, decreasing pathogens' influence on the populations. Non-retroviral endogenous elements (EVEs) may be transcribed and processed into small RNAs potentially helping on the antiviral immune response in insect species. Interfering RNAs (RNAi) constitute the main antiviral response path in Arthropoda. The diversity and transcriptional activity of EVEs has already been proven in dipterans, but there is little data about EVEs in bees. The goal of this study is to identify and characterize EVEs in, publicly available, Bombus spp. Genomes. Firstly, the most recent genomes of 30 Bombus species were obtained from Genbank. After a prediction of Open Reading Frames (ORFs) and subsequent sequence similarity analysis against viral sequence databases, using the programs getorf and DIAMOND, respectively, the selected sequences were submitted to manual curation to eliminate repetitions, retrovirus-like sequences, transposons, DNA virus or other non-viral organisms, only mantaining putative non-retroviral RNA EVEs.. The curated sequences were processed again on NCBI, using both blastx and blastn online versions, to guarantee a better robustnessof the results, and aligned among one another for later inferences on the evolutionary history of these EVEs. It is possible to affirm that the EVEs presented similarities, partially, with four known viral families: Partitiviridae, Phasmaviridae, Totiviridae and Virgaviridae; whereas most of them were similar to non-classified viruses Altogether, each species presented between 1-20 EVEs, excluding B. superbus and B. waltoni, which did not manifest any EVEs; and B. terrestris, B. polaris and B. vosnesenskii, which had more robust results, with 32, 27 and 25 respectively. After aligning with one another, the sequences manifested, on the whole, many cases of similarity between different species, which may suggest an old and common evolutionary origin, endorsed by the data obtained from blastn. In future studies, the transcriptional activity of identified EVEs and the possible small-RNA production that might influence on bee’s antiviral response will be tested.
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3
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GRACIETE SOARES LIBORIO VERÍSSIMO
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Genomic and phenotypic analyzes of the surface polysaccharide poly-N-acetylglucosamine (PNAG) in bacteria of the genus Leptospira.
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Advisor : PAULA CARVALHAL LAGE VON BUETTNER RISTOW
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COMMITTEE MEMBERS :
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FLÁVIA FIGUEIRA ABURJAILE
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ANGELA SILVA BARBOSA
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PAULA CARVALHAL LAGE VON BUETTNER RISTOW
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Data: Jun 2, 2023
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Show Abstract
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Poly-β-1,6-N-acetyl-glucosamine (PNAG) is a surface polysaccharide widely expressed and present in the biofilm matrix of different bacterial species. PNAG is a virulence factor, involved in protection against innate host defenses, antibiotic therapy, and environmental stress conditions. Pathogenic leptospires are the etiological agents of leptospirosis, an anthropozoonosis with worldwide distribution that impacts human and animal health. Leptospira forms biofilms in the environment and in the kidneys of the reservoir Rattus norvegicus. However, information about the composition of the exopolymer matrix of Leptospira biofilms, as well as the proteins involved in PNAG expression, are poorly characterized. In this work we evaluated PNAG expression by Leptospira through immunofluorescence (IF), biochemical, and genomic approaches. Through IF, we demonstrated that PNAG is expressed on the cell surface of Leptospira with different degrees of pathogenicity and is present in the exopolymer matrix of the biofilm. Biochemical treatment with sodium metaperiodate cleaved N-acetylglucosamine-β- (1,6) bonds, confirming the presence of PNAG. Through comparative genomic analysis, we identified proteins with similarity to glycosyltransferases and deacetylases related to PNAG expression. In this study, we demonstrated the presence of PNAG in Leptospira in the planktonic phenotype and in the biofilm matrix. Our study expands knowledge about Leptospira biofilm composition and contributes to the understanding of possible Leptospira survival mechanisms in the environment and in the host-pathogen relationship.
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4
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ALICE MARIA ABREU GUSMAO SOARES
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Monitoring antibody production in patients infected with SARS-CoV-2 and vaccinated for SARS-CoV-2, in Salvador, Bahia, Brazil
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Advisor : GUBIO SOARES CAMPOS
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COMMITTEE MEMBERS :
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ELISANGELA DE JESUS CAMPOS
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GUBIO SOARES CAMPOS
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LUANA LEANDRO GOIS
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Data: Jul 10, 2023
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Show Abstract
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SARS-COV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is the virus that causesCOVID-19 (Coronavirus Disease 2019). The reach and negative impact of SARS-CoV-2across the world has placed this pandemic among the most notorious on record. Because it isa global emergency, as well as the growing number of cases and deaths caused and thecharacteristics of SARS-CoV-2, such as the high transmissibility between individuals and thevariability of clinical manifestations associated with the infection, make laboratory diagnosisa tool very important in the fight against the pandemic. Epidemiological screening for SARS-CoV-2 aims to correctly identify patients exposed to the virus to better understand theprevalence, epidemiology and dynamics of the disease. There is a lot to understand about theinteraction between SARS-CoV-2 and its host. With this, the search for a betterunderstanding of the immunological aspects of SARS-CoV-2 has increased. Thus, understanding how the antibody response works during and after natural infection is essentialto better understand the disease, as well as evaluating the immune response induced by thevaccine to understand how the antibody response works during and after infection. In thissense, a long-term follow-up study is important to understand, monitor and investigate IgGantibody levels. This study aimed to evaluate the level of antibodies to SARS-CoV-2 ingroups of infected patients (previously tested by qRT-PCR with detectable results for SARS-CoV2) and subsequently vaccinated in Salvador, Bahia, Brazil. For this, serologicalcollections were carried out from 245 individuals, where six analyzes of the presence ofantibodies of the IgG class were carried out through the enzyme-linked immunoabsorptiontest (ELISA) in the serum samples of these individuals over approximately 1 year, at differenttimes in the Virology Laboratory of the Federal University of Bahia - UFBA. In this work, itis learned that primary vaccination induced a significant increase in SARS-CoV-2 specificantibodies, which was further intensified by the booster dose. However, in individualsrecovered from SARS-CoV2, there was no further increase in antibody levels after thesecond vaccine dose. Notably, IgG levels were similar in individuals who were not infectedwith SARS-CoV-2 and in individuals who recovered from SARS-CoV-2 after a booster dose.
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5
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TACILA ANDER OLIVEIRA ALMEIDA
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BIOTECHNOLOGICAL POTENTIAL OF FRESHWATER MITOSPORY FUNGI
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Advisor : ADRIANA OLIVEIRA MEDEIROS
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COMMITTEE MEMBERS :
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ADRIANA OLIVEIRA MEDEIROS
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RICARDO BIZOGNE SOUTO
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VERA LUCIA COSTA VALE
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Data: Aug 31, 2023
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Show Abstract
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: Fungi that occupy freshwater environments have been reported to produce metabolites with wide chemical diversity and a wide range of biological activities. Among the groups of fungi that occur in these environments are the mitosporic fungi, which consist of asexual states, mainly of ascomycetes and some basidiomycetes. Aquatic hyphomycetes are mitosporic fungi recognized mainly for their role in the decomposition of allochthonous leaf organic matter in lotic environments and for their ability to sporulate below the surface. The main objective of this work is to evaluate the biotechnological potential of freshwater mitosporic fungi. Chapter 1 is an integrative review on the metabolic production of aquatic hyphomycetes and its biotechnological applications. The results showed this group as important producers of several metabolites with applications in several sectors of industry, agriculture and health, mainly enzymes associated with the breakdown of lignocellulolytic compounds and with antimicrobial potential. Chapter 2 is an experimental work that aimed to evaluate the antimicrobial activity of four species of mitosporic fungi isolated in different streams associated with decomposing plant material. The fungi were grown in different culture media and their crude extracts were tested against nine bacterial and fungal pathogens using the broth microdilution technique. The fungi F. curvula, A. penicillioides and P. submersus strain 133057 inhibited most bacterial pathogens, but none showed antifungal activity. Strains of the same species collected from different environments and extracts from cultures in different culture media showed differences in terms of bioactivity, which are important aspects to be considered in the bioprospecting of antimicrobial activity
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6
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THAYRA GOMES DOS SANTOS
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Genomic analysis of Lactiplantibacillus plantarum in the identification of probiotic properties
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Advisor : RODRIGO DIAS DE OLIVEIRA CARVALHO
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COMMITTEE MEMBERS :
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RODRIGO DIAS DE OLIVEIRA CARVALHO
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SANDEEP TIWARI
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WANDERSON MARQUES DA SILVA
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Data: Sep 25, 2023
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Show Abstract
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Probiotics are microorganisms with beneficial properties for the health of the host who consumes them. These can be applied both in industry and in the promotion of human health, such as for the treatment of inflammatory bowel diseases. Currently, it is possible to find several studies on lactobacilli, especially Lactiplantibacillus plantarum, however, due to its great genetic diversity, the species is still little explored. In this sense, the isolation and genomic characterization of new Lb. plantarum of Brazilian biodiversity could allow the discovery of exclusive protective mechanisms and presents potential for the development of alternative therapies to combat inflammation. As a result, a growing line of research, probiogenomics, has provided a more comprehensive and assertive understanding of the molecular bases of these probiotics. In this context, through the application of bioinformatics analyses, this work aimed to taxonomically and functionally characterize the complete genomes of six strains isolated in Brazil. In this way, the taxonomy of the six lineages was confirmed using the Average Nucleotide Identity by BLAST (ANIb), using the genome of the Lb lineage as a reference. plantarum SK151 from the GENBANK database (NCBI). In contrast, a multilocus phylogenetic analysis was performed using 220 complete Lb genomes. plantarum from the aforementioned database, to investigate evolutionary relationships with other probiotic lineages of the same species. Our results suggest high genetic proximity to probiotics already marketed, or that have demonstrated anti-inflammatory effects in clinical trials or preclinical studies of inflammatory diseases. Next, the analysis of antimicrobial peptides in the genomes of Brazilian isolates identified several plantaricin genes, suggesting antimicrobial potential. The presence of the gadB gene was also identified in the six lineages, which may be involved in the production of gamma-aminobutyric acid through the action of the enzyme glutamate decarboxylase, suggesting an important role in the regulation of the intestine-brain axis. Through SNP analyzes and molecular modeling, the lpl4 lineage showed a high degree of genetic and structural conservation of this enzyme when compared to the homologous protein considered functional in the Taj-Apis362 lineage. Furthermore, pangenomic analysis among all strains revealed the presence of exclusive genes in the lpl4 strain, namely, five hypothetical proteins and a sulfotransferase, involved in the synthesis of vitamin B6. To analyze the safety of the strains, the presence of antibiotic resistance genes was investigated, where only one marker was observed in a region of genomic plasticity on the chromosome of the E6 strain. Therefore, it is possible to conclude that the strains evaluated have probiotic properties with therapeutic potential for inflammatory diseases that affect the intestine-brain axis, especially lpl4, and can be considered safe for human and animal use. However, more studies are needed to investigate its therapeutic potential.
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7
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LUIZ RICARDO FRASER SILVA
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A comparative evaluation of automated platforms for assembly and analysis of SARS-CoV-2 genomes
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Advisor : LUIS GUSTAVO CARVALHO PACHECO
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COMMITTEE MEMBERS :
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BRENA MOTA MOITINHO SANT'ANNA
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GUBIO SOARES CAMPOS
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LUIS GUSTAVO CARVALHO PACHECO
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Data: Oct 5, 2023
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Show Abstract
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The COVID-19 pandemic, caused by the SARS-CoV-2 virus (Severe Acute Respiratory Syndrome Coronavirus 2), began in the province of Wuhan in China and quickly spread around the globe, generating socioeconomic and public health impacts. The discovery of the viral agent causing the disease was only possible thanks to new nucleic acid sequencing technologies, collectively known as NGS (Next Generation Sequencing). Currently, these same technologies are being used for genomic surveillance of the virus, including the identification of mutations and determination of new variants. In 2022, the World Health Organization issued a global genomic surveillance strategy for potentially pandemic and epidemic pathogens (2022-2032). In order to contribute to this strategy and improve access to viral detection tools, the main objective of this work is to implement, compare, and validate analysis protocols using only raw NGS data (FASTQ files) for the diagnosis and variant calling of SARS-CoV-2. For this purpose, a total of 15 new SARS-CoV-2 sequencing samples obtained by Ion AmpliSeq targeted methodology (n=10) or metatranscriptomic approach (n=5) were used as the sample universe. These FASTQ files were subjected to assembly using the automated assemblers: PATRIC, BV-BRC, ID-seq, CoronaSPAdes, and Genome Detective. Variant calling was performed using the platforms GISAID, Genome Detective, Nextclade, and BV-BRC, which have an integrated approach to assembly and annotation. The analyses were carried out at two different time points to identify possible changes in the results after platform updates. The generated results were compared, among other aspects, in terms of the ability to call SARS-CoV-2 variants, the average time spent on analysis, identified viral ORFs (Open Reading Frames), and the percentage of G+C content in the assembled genome. Initially, the BV-BRC platform proved to be capable of correctly determining the variant, with the highest number of results generated in the shortest time. ID-seq and Genome Detective were able to perform genome assembly, and from the generated FASTA files, variant calling was performed using the Nextclade platform and Genome Detective itself for annotation. After updates, BV-BRC, despite still producing the highest number of results in the shortest time, showed lower specificity in variant calling. However, Genome Detective presented an integrated approach to assembly and annotation with a greater ability to determine the variant. The assembler PATRIC and the annotation platform GISAID were not able to generate satisfactory results for the evaluated samples.
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8
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JULIA DE MELO JUREMA GUIMARÃES
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Effect of pH on survival and biofilm formation by Leptospira
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Advisor : PAULA CARVALHAL LAGE VON BUETTNER RISTOW
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COMMITTEE MEMBERS :
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LUCIANA DOS SANTOS MEDEIROS
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PAULA CARVALHAL LAGE VON BUETTNER RISTOW
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RODRIGO DIAS DE OLIVEIRA CARVALHO
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Data: Dec 7, 2023
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Show Abstract
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Leptospires are Gram negative bacteria with a wide physical-chemical agents sensibility profile, previous works revealed that Leptospira may survive for months in water and soil. Therefore, leptospires remain as a relevant human and veterinary health issue. Leptopsira form biofilms in vitro, in vivo and on the environment. However, there is no literature to our knowledge describing if continuous exposition to unfavorable temperatures and pHs may or not alter biofilm formation in Leptospira. The aim of this work is to evaluate pH and temperature stress action in biofilm formation and cell survival. Leptospiral biofilm biomass cultivated at 30°C with pHs 5.0; 6.5; 7.5 e 8.5 was quantified using crystal violet stain method. We generated growth curves of planktonic Leptospira at 30 °C with pH 5.0; 7.5 and 8.5. Preliminary results show that pH 5.0 and elevate temperatures cultivation conditions inhibit biofilm formation in Leptospira. The present results alongside our future results may enlighten if physycal-chemical stress exposition interfere in Leptospira biofilm formation
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