Papers by Adriano Velasque Werhli
International Seven Journal of Health Research
The development and application of new molecular tools has shown the real complexity involved in ... more The development and application of new molecular tools has shown the real complexity involved in Mycobacterium Tuberculosis infection. The sequencing of the complete Koch's Bacillus genome can reveal information about the true extent of the point mutations that confer resistance to treatment to these bacteria. Complete genome sequencing techniques and their availability in public databases, have been responsible for the exponential growth of computational tools to extract information about important features encoded in the genomes of Mycobacterium complex species. This is a literature review study, from scientific research platforms, with the aim of discussing how computational tools used for analysis of the complete genome sequencing of M. tuberculosis can identify the genetic relationship between strain mutations and antimicrobial resistance. Whole genome sequencing is considered a surveillance marker of transmission and drug resistance, as well as a strong predictor of the em...
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IEEE Signal Processing Magazine, 2009
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Aquatic Toxicology, 2022
Saxitoxin (STX) is a neurotoxic cyanotoxin that also generate reactive oxygen species, leading to... more Saxitoxin (STX) is a neurotoxic cyanotoxin that also generate reactive oxygen species, leading to a situation of oxidative stress and altered metabolism. The Amazonian fruit açaí Euterpe oleracea possesses a high concentration of antioxidant molecules, a fact that prompted us to evaluate its chemoprotection activity against STX toxicity (obtained from samples of Trichodesmium sp. collected in the environment) in the shrimp Litopenaeus vannamei. For 30 days, shrimps were maintained in 16 aquaria containing 10 shrimps (15% salinity, pH 8.0, 24 °C, 12C/12D photoperiod) and fed twice daily with a diet supplemented with lyophilized açaí pulp (10%), in addition to the control diet. After, shrimps (7.21 ± 0.04 g) were exposed to the toxin added to the feed for 96 h. Four treatments were defined: CTR (control diet), T (lyophilized powder of Trichodesmium sp. 0.8 μg/g), A (10% of açaí) and the combination T + A. HPLC analysis showed predominance of gonyautoxin-1 concentrations (GTX-1) and gonyautoxin-4 concentrations (GTX-4). The results of molecular docking simulations indicated that all variants of STX, including GTX-1, can be a substrate of isoform mu of the glutathione-S-transferase (GST) enzyme since these molecules obtained similar values of estimated Free Energy of Binding (FEB), as well as similar final positions on the binding site. GSH levels were reduced in muscle tissues of shrimp in the T, A, and T + A treatments. Increased GST activity was observed in shrimp hepatopancreas of the T treatment and the gills of the A and T + A treatments. A decrease of protein sulfhydryl groups (P-SH) was observed in gills of shrimps from T + A treatment. A reduction in malondialdehyde (MDA) levels was registered in the hepatopancreas of the T + A treatment in respect to the Control, T, and A treatments. The use of açaí supplements in L. vannamei feed was able to partially mitigate the toxic effects caused by Trichodesmium sp. extracts, and points to mu GST isoform as a key enzyme for saxitoxin detoxification in L. vannamei, an issue that deserves further investigation.
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Lecture Notes in Computer Science, 2022
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CERN European Organization for Nuclear Research - Zenodo, May 17, 2022
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PeerJ, Mar 22, 2022
Background The SARS-CoV-2 pandemic reverberated, posing health and social hygiene obstacles throu... more Background The SARS-CoV-2 pandemic reverberated, posing health and social hygiene obstacles throughout the globe. Mutant lineages of the virus have concerned scientists because of convergent amino acid alterations, mainly on the viral spike protein. Studies have shown that mutants have diminished activity of neutralizing antibodies and enhanced affinity with its human cell receptor, the ACE2 protein. Methods Hence, for real-time measuring of the impacts caused by variant strains in such complexes, we implemented E-Volve, a tool designed to model a structure with a list of mutations requested by users and return analyses of the variant protein. As a proof of concept, we scrutinized the spike-antibody and spike-ACE2 complexes formed in the variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma), by using contact maps depicting the interactions made amid them, along with heat maps to quantify these major interactions. Results The results found in this study depict the highly frequent interface changes made by the entire set of mutations, mainly conducted by N501Y and E484K. In the spike-Antibody complex, we have noticed alterations concerning electrostatic surface complementarity, breaching essential sites in the P17 and BD-368-2 antibodies. Alongside, the spike-ACE2 complex has presented new hydrophobic bonds. Discussion Molecular dynamics simulations followed by Poisson-Boltzmann calculations corroborate the higher complementarity to the receptor and lower to the antibodies for the K417T/E484K/N501Y (Gamma) mutant compared to the wild-type strain, as pointed by E-Volve, as well as an intensification of this effect by changes at the protein conformational equilibrium in solution. A local disorder of the loop α1′/β1′, as well its possible effects on the affinity to the BD-368-2 antibody were also incorporated to the final conclusions after this analysis. Moreover, E-Volve can depict the main alterations in important biological structures, as shown in the SARS-CoV-2 complexes, marking a major step in the real-time tracking of the virus mutant lineages. E-Volve is available at http://bioinfo.dcc.ufmg.br/evolve.
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Computational Biology and Chemistry, 2019
Fluorescent proteins have been applied in a wide variety of fields ranging from basic science to ... more Fluorescent proteins have been applied in a wide variety of fields ranging from basic science to industrial applications. Apart from the naturally occurring fluorescent proteins, there is a growing interest in genetically modified variants that emit light in a specific wavelength. Genetically modifying a protein is not an easy task, especially because the exchange of one residue by other has to achieve the desired property while maintaining protein stability. To help in the choice of residue exchange, computational methods are applied to predict function and stability of proteins. In this work we have prepared a dataset composed by 109 fluorescent proteins and tested four classical supervised classification algorithms: artificial neural networks (ANNs), decision trees (DTs), support vector machines (SVMs) and random forests (RFs). This is the first time that algorithms are compared in this task. Results of comparing the algorithm's performance shows that DT, SVM and RF were significantly better than ANNs, and RF was the best method in all the scenarios. However, the interpretability of DTs is highly relevant and can provide important clues about the mechanisms involved in protein color emission. The results are promising and indicate that the use of in silico methods can greatly reduce the time and cost of the in vitro experiments.
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Science of The Total Environment, 2020
Arsenic (As) is one of the most widespread contaminants; it is found in almost every environment.... more Arsenic (As) is one of the most widespread contaminants; it is found in almost every environment. Its toxic effects on living organisms have been studied for decades, but the interaction of this metalloid with other contaminants is still relatively unknown, mainly whether this interaction occurs with emerging contaminants such as nanomaterials. To examine this relationship, the marine shrimp Litopenaeus vannamei was exposed for 48 h to As, graphene oxide (GO; two different concentrations) or a combination of both, and gills, hepatopancreas and muscle tissues were sampled. Glutathione S-transferase (GST)-omega gene expression and activity were assessed. As accumulation and speciation (metabolisation capacity) were also examined. Finally, a molecular docking simulation was performed to verify the possible interaction between the nanomaterial and GST-omega. The main finding was that GO modulated the As toxic effect: it decreased GST-omega activity, a consequence related to altered As accumulation and metabolism. Besides, the molecular docking simulation confirmed the capacity of GO to interact with the enzyme structure, which also can be related to the decreased GST-omega activity and subsequently to the altered As accumulation and metabolisation pattern.
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ISPRS Journal of Photogrammetry and Remote Sensing, 2019
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Chemical Research in Toxicology, 2019
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Papers by Adriano Velasque Werhli