A5031688287- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Metabolomics and Mass Spectrometry Studies
- Enzyme Production and Characterization
- Microbial bioremediation and biosurfactants
- Biofuel production and bioconversion
- Bacterial Genetics and Biotechnology
- Microbial Community Ecology and Physiology
- Antibiotic Resistance in Bacteria
- Gut microbiota and health
- Analytical Chemistry and Chromatography
- Microbial Natural Products and Biosynthesis
- Genetics, Bioinformatics, and Biomedical Research
- Computational Drug Discovery Methods
- Bacterial Identification and Susceptibility Testing
- Gene expression and cancer classification
- Bacteriophages and microbial interactions
- Studies on Chitinases and Chitosanases
- Plant Pathogens and Fungal Diseases
- Nematode management and characterization studies
- Plant-Microbe Interactions and Immunity
- Enzyme Catalysis and Immobilization
- Bacterial biofilms and quorum sensing
- Bioinformatics and Genomic Networks
- Science and Education Research
Universidade de São Paulo
2016-2025
Universidade de Ribeirão Preto
2021
Abstract Motivation Annotation of the mass signals is still biggest bottleneck for untargeted spectrometry analysis complex mixtures. Molecular networks are being increasingly adopted by community as a tool to annotate large-scale experiments. We have previously shown that process propagating annotations from spectral library matches on molecular can be automated using Network Propagation (NAP). One limitations NAP information only propagated locally, first neighbor match. Here, we show...
The analysis of the secretome allows us to identify proteins, especially carbohydrate-active enzymes (CAZymes), secreted by different microorganisms cultivated under conditions. CAZymes are divided into five classes containing protein families. Thermothelomyces thermophilus is a thermophilic ascomycete, source many glycoside hydrolases and oxidative that aid in breakdown lignocellulosic materials. T. LMBC 162 with submerged fermentation using tamarind seeds as carbon revealed 79 proteins...
Abstract Background Clustering analysis is a foundational step in exploratory data workflows, with dimensionality reduction methods commonly used to visualize multidimensional lower-dimensional spaces and infer sample clustering. Principal Component Analysis (PCA) widely applied metabolomics but often suboptimal for clustering visualization. Metabolomics require specialized manipulations such as blank removal, quality control adjustments, transformations that demand efficient visualization...
Introduction Exploiting microbial natural products is a key pursuit of the bioactive compound discovery field. Recent advances in modern analytical techniques have increased volume genomes and their encoded biosynthetic measured by mass spectrometry-based metabolomics. However, connecting multi-omics data to uncover metabolic processes interest still challenging. This results large portion genes metabolites remaining unannotated. Further exacerbating annotation challenge, databases tools for...
In response to the escalating demand for sustainable agricultural methodologies, utilization of microbial volatile organic compounds (VOCs) as antagonists against phytopathogens has emerged a viable eco-friendly alternative. Microbial volatiles exhibit rapid diffusion rates, facilitating prompt chemical interactions. Moreover, microorganisms possess capacity emit constitutively, well in biological interactions and environmental stimuli. addition compounds, these bacteria demonstrate ability...
The examination of fungal secretomes has garnered attention for its potential to unveil the repertoire secreted proteins, notably CAZymes (Carbohydrate-Active enzymes), across various microorganisms. This study presents findings on categorizing secretome profile by their function and family, derived from filamentous fungus Trichoderma longibrachiatum LMBC 172. cultivation was performed through submerged fermentation with three distinct carbon sources: sugarcane bagasse, tamarind seeds, a...
(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in several species isolated from intensive care unit Brazil. (2) Methods: We used whole-genome analysis identify genes (ARGs) and plasmids 34 strains Gram-negative Gram-positive bacteria, providing the first genomic description Morganella morganii Ralstonia mannitolilytica clinical isolates South America. (3) Results: identified...
Abstract Surveying antimicrobial resistance (AMR) is essential to track its evolution and spread. Alignment-based annotation tools use strict identity (>80%) cutoffs distinguish between non-resistant (NRP) resistant proteins (ARP) only annotating similar those in their databases. Deep learning Hidden Markov Models (HMM) based also depend on protein alignment at some level. DeepARG filters input data select the um SNP ARG-like HMMs are built multi-sequence (MSA) specific for a given family...
Abstract Exploiting microbial natural products is a key pursuit of the bioactive compound discovery field. Recent advances in modern analytical techniques have increased volume genomes and their encoded biosynthetic measured by mass spectrometry-based metabolomics. However, connecting multi-omics data to uncover metabolic processes interest still challenging. This results large portion genes metabolites remaining unannotated. Further exacerbating annotation challenge, databases tools for...
ABSTRACT This study introduces a low-cost, open-source, semi-automated bioreactor system, developed using Arduino and Raspberry Pi, for longitudinal microbial culture studies. The system protocol includes detailed instructions custom-designed components, specifications easily purchasable parts, open-source code web-based control interface. It was validated sterility tested in case involving the cultivation of Phanerochaete chrysosporium Trichoderma reesei to assess their metabolic dynamics,...
Metagenomics approaches have been of high relevance for providing enzymes used in diverse industrial applications. In the current study, we focused on prospection protease and glycosyl hydrolase activities from a soil sample by using lacZα -based plasmid pSEVA232. For this, functional screen based skimmed milk agar pH indicator dye detection both enzymes, as previously reported literature. Although effectively identified positive clones screenings, subsequent experiments revealed that this...
Abstract The rise of multi-antibiotics resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in several species isolated from intensive care unit Brazil. We used whole-genome analysis identify genes (ARGs) and plasmids 35 strains Gram-negative Gram-positive bacteria, including the first genomic description Morganella morganii Ralstonia mannitolilytica clinical isolates South America. a high abundance beta-lactamase highly...
E se pudéssemos rebobinar a fita da evolução? Se reiniciarmos história terra partir de um certo instante no passado, vida desenvolveria mesma forma? você, assim como eu, é biólogo, então sabe que essas questões propostas por Stephen Jay Gould causam longas discussões durante as aulas evolução. Há quem diga sim pois condições seriam mesmas, há aqueles cuja opinião fruto efeito borboleta (sim, o filme) e argumentam existe componente caótico na “Bastaria uma mutação diferente mudanças...
Abstract The vast biochemical repertoire found in microbial communities from a wide-range of environments allows screening and isolation novel enzymes with improved catalytic features. In this sense, metagenomics approaches have been high relevance for providing used diverse industrial applications. For instance, glycosyl hydrolases, which catalyze the hydrolysis carbohydrates to sugars, are essential bioethanol production renewable resources. current study, we focused on prospection...
Abstract Annotation of the mass signals is still biggest bottleneck for untargeted spectrometry analysis complex mixtures. Molecular networks are being increasingly adopted by community as a tool to annotate large scale experiments. We have previously shown that process propagating annotations from spectral library matches on molecular can be automated using Network Propagation (NAP). One limitations NAP information only propagated locally, first neighbor match. Here we show annotation...