Transcriptomic analysis of Mucor irregularis containing a negative single-stranded RNA mycovirus

Foundation for Scientific and Technological Development in Health-FIOTEC for a scholarship (project PRES-012-FIO-16)Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovação Tecnológicas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovação Tecnológicas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovação Tecnológicas. Ananindeua, PA, Brasil.The fungus Mucor irregularis is a causative agent of mucormycosis. The transcriptome analysis of the isolated M. irregularis strain C3B revealed the presence of an RNA polymerase domain of a negative-polarity RNA virus. In this work, we describe the gene ontology-based annotation of the Mucor irregularis transcriptome, which includes a putative RNA mycovirus

Single cell multiomic approaches to disentangle T cell heterogeneity

IIGM/CSP, Armenise-Harvard foundation, AIRC IG 2020 ID 24463; Ministero della Salute ‘COVID-2020-12371849’, FPO/Candiolo Advance 5×1000_2018 ‘Im-MEMORY’; Ministero della Salute Ricerca Corrente 2021.University of Bologna. Department of Biological, Geological and Environmental Sciences. Laboratory of Molecular Anthropology. Center for Genome Biology. Bologna, Italy / Italian Institute for Genomic Medicine. Armenise-Harvard Immune Regulation Unit. Turin, ItalyItalian Institute for Genomic Medicine. Armenise-Harvard Immune Regulation Unit. Turin, Italy / Fondazione del Piemonte per l'Oncologia. Candiolo Cancer Institute. Candiolo, Turin, ItalyMinistério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, BrasilItalian Institute for Genomic Medicine. Armenise-Harvard Immune Regulation Unit. Turin, Italy / Fondazione del Piemonte per l'Oncologia. Candiolo Cancer Institute. Candiolo, Turin, ItalySingle-cell multi-omics is a rapidly evolving field, thanks to a fast technological improvement and the growing accuracy of dedicated computational tools for data analysis. Its importance is highlighted by the possibility to distinguish apparently identical cells based on their pattern of gene expression. In this review, the mostly used methodological pipelines for single-cell analysis, as well as the advantages and potential limitations of several analytical steps, are presented and discussed, with specific sections focusing on crucial parts of this procedure, their bioinformatic tools, as well as their advantages and potential drawbacks. The current bioinformatic approaches for T-cell receptor (TCR) reconstruction are also introduced, as well as a comparison of single-cell sequencing technologies. Critical points that may introduce analytical biases and potential inaccuracies in data interpretation are also highlighted

Incidence of viral hepatitis in brazil from 2009 to 2018: an epidemiological study of confirmed cases of viral hepatitis

CAPES and Universidade Federal do ParáMinistério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Programa de Pós-Graduação em Virologia. Ananindeua, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências da Saúde. Especialização em Hematologia e Imunologia. Belém, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências da Saúde. Especialização em Hematologia e Imunologia. Belém, PA, Brasil.Universidade Federal do Pará. Faculdade de Formação e Desenvolvimento do Campo. Abaetetuba, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia e Biomolecular. Belém, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.INTRODUCTION: Viral hepatitis is a major public health problem. It is necessary to understand the epidemic, verifying the combination of biological and demographic characteristics. METHODS: This is an analytical ecological and epidemiological study. Confirmed case data from the Notification Disease Information System (SINAN) were used. RESULTS: From 2009-2018, SINAN confirmed 404,003 viral hepatitis cases in Brazil, with 12.49%, 37.06%, and 48.28% cases of hepatitis A, B, and C, respectively. CONCLUSIONS: In Brazil, 4,296 deaths were associated with viral hepatitis, of which 36.66% were associated with acute hepatitis B. The proportional distribution of cases varied among the five Brazilian regions

Anti-dengue virus activity of scytovirin and evaluation of point mutation effects by molecular dynamics and binding free energy calculations

Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovações Tecnológicas. Ananindeua, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Naturais. Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovações Tecnológicas. Ananindeua, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.The absence of a specific treatment against DENV has led to intensive research into developing strategies for curing the infection. One lectin with high antiviral activity is scytovirin, which was isolated from the cyanobacterium Scytonema varium and has proven activity against HIV and Zaire Ebola Virus. To achieve the results presented here, we tested the affinity of full-length scytovirin, SD1 and SD2 separately, and six SD1 mutants for DENV glycoprotein E carbohydrate by Molecular Dynamics (MD) simulations and binding free energy calculations. It was possible to identify the key residues for protein-ligand interaction such as Glu10, Ala11, Pro17, Ans18, Arg30, Thr41, Ser42 and Arg43, which also has importance action against HIV. All binding free energy calculations showed negative values to ΔGbind of protein-DENV carbohydrate complexation. Additionally, these results are similar to the values of scytovirin and HIV gp120 carbohydrate complexation (-32.20 kcal/mol). Furthermore, we found that SD1 individually has more affinity to the carbohydrate and the Asn9, Glu10, Asn18, Arg30 and Arg43 demonstrated an important role in this matter. We also found that mutant G48R has better affinity (-34.10 kcal/mol) for the DENV carbohydrate than the wild type protein (-27.15 kcal/mol)

Genomic screening of new putative antiviral lectins from Amazonian cyanobacteria based on a bioinformatics approach

Fundação Amazônia Paraense de Amparo à Pesquisa. Grant Number: ICAAF 099/2014; Conselho Nacional de Desenvolvimento Científico e Tecnológico. Grant Number: 311686/2015‐0Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Universidade Federal do Pará. Instituto de Ciências Naturais. Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Lectins are proteins of nonimmune origin, which are capable of recognizing and binding to glycoconjugate moieties. Some of them can block the interaction of viral glycoproteins to the host cell receptors acting as antiviral agents. Although cyanobacterial lectins have presented broad biotechnological potential, little research has been directed to Amazonian Cyanobacterial diversity. In order to identify new antiviral lectins, we performed genomic analysis in seven cyanobacterial strains from Coleção Amazônica de Cianobactérias e Microalgas (CACIAM). We found 75 unique CDS presenting one or more lectin domains. Since almost all were annotated as hypothetical proteins, we used homology modeling and molecular dynamics simulations to evaluate the structural and functional properties of three CDS that were more similar to known antiviral lectins. Nostoc sp. CACIAM 19 as well as Tolypothrix sp. CACIAM 22 strains presented cyanovirin‐N homologues whose function was confirmed by binding free energy calculations. Asn, Glu, Thr, Lys, Leu, and Gly, which were described as binding residues for cyanovirin, were also observed on those structures. As for other known cyanovirins, those residues in both our models also made favorable interactions with dimannose. Finally, Alkalinema sp. CACIAM 70d presented one CDS, which was identified as a seven‐bladed beta‐propeller structure with binding sites predicted for sialic acid and N‐acetylglucosamine. Despite its singular structure, our analysis suggested this molecule as a new putative antiviral lectin. Overall, the identification and the characterization of new lectins and their homologues are a promising area in antiviral research, and Amazonian cyanobacteria present biotechnological potential to be explored in this regard

In silico analysis of the cyanobacterial lectin scytovirin : new insights into binding properties

We acknowledge Fundação Amazônia de Amparo a Estudos e Pesquisas do Pará (FAPESPA) for financially supporting (ICAAF 099/2014) our project. Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) also supported individual authors through Grant 311686/2015-0 (ECG).Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Universidade Federal do Pará. Instituto de Ciências Exatas e Naturais. Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular. Belém, PA, Brazil.Universidade Federal do Pará. Instituto de Ciências Exatas e Naturais. Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Scytovirin is a lectin isolated from the cyanobacterium Scytonema varium that has shown activity against HIV, SARS coronavirus and Zaire Ebola virus. Its 95 amino acids are divided into two structural domains (SD), the first spanning amino acids 1–48 (SD1) and the second 49–95 (SD2). Interestingly, the domains are nearly identical but differ in their affinities for carbohydrates. With the aim of enhancing understanding of the binding properties of scytovirin, we performed molecular dynamics (MD) simulations of scytovirin complexed with Man4. We set up three systems: (i) Man4 bound to both domains (SD1+SD2) using the full-length protein; (ii) Man4 bound to an incomplete protein, containing only SD1 and (iii) Man4 bound to an incomplete protein containing only SD2. Contrary to other reports, binding free energy results suggest that Man4 can bind simultaneously to SD1 and SD2 binding regions, but SD1 individually has the best values of energy and the best affinity for Man4. Decomposition of the binding free energy showed that the residues that interact with Man4 were different in the three systems, suggesting that the binding mechanism of Man4 varies between full-length protein, SD1 and SD2. The results presented here may help to formulate strategies to use scytovirin and promote mutagenesis studies to improve the antiviral activity of scytovirin

Comparative modeling and molecular dynamics suggest high carboxylase activity of the Cyanobium sp. CACIAM14 RbcL protein

Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brasil.Universidade Federal Rural da Amazônia. Belém, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brasil.Rubisco catalyzes the first step reaction in the carbon fixation pathway, bonding atmospheric CO2/O2 to ribulose 1,5-bisphosphate; it is therefore considered one of the most important enzymes in the biosphere. Genetic modifications to increase the carboxylase activity of rubisco are a subject of great interest to agronomy and biotechnology, since this could increase the productivity of biomass in plants, algae and cyanobacteria and give better yields in crops and biofuel production. Thus, the aim of this study was to characterize in silico the catalytic domain of the rubisco large subunit (rbcL gene) of Cyanobium sp. CACIAM14, and identify target sites to improve enzyme affinity for ribulose 1,5-bisphosphate. A three-dimensional model was built using MODELLER 9.14, molecular dynamics was used to generate a 100 ns trajectory by AMBER12, and the binding free energy was calculated using MM-PBSA, MM-GBSA and SIE methods with alanine scanning. The model obtained showed characteristics of form-I rubisco, with 15 beta sheets and 19 alpha helices, and maintained the highly conserved catalytic site encompassing residues Lys175, Lys177, Lys201, Asp203, and Glu204. The binding free energy of the enzyme substrate complexation of Cyanobium sp. CACIAM14 showed values around −10 kcal mol−1 using the SIE method. The most important residues for the interaction with ribulose 1,5-bisphosphate were Arg295 followed by Lys334. The generated model was successfully validated, remaining stable during the whole simulation, and demonstrated characteristics of enzymes with high carboxylase activity. The binding analysis revealed candidates for directed mutagenesis sites to improve rubisco s affinity

Investigating the effects of point mutations on the affinity between the cyanobacterial lectin microvirin and high mannose-type glycans present on the HIV envelope glycoprotein

Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Faculdade Integrada Brasil Amazônia. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Faculdade Integrada Brasil Amazônia. Belém, PA, Brazil / Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Tecnologia Biomolecular. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Human immunodeficiency virus (HIV) infections continue to exert an enormous impact on global human health. This led experts to emphasize the importance of new measures for preventing HIV infections, including the development of vaccines and novel drugs. In this context, a promising approach involves the use of lectins that can bind the surface envelope glycoprotein gp120 of HIV with high affinity, preventing viral entry. The cyanobacterial lectin microvirin (MVN) has been proposed as a candidate for development as a topical microbicide because of its ability to bind to high mannose-type glycans, potently inhibiting HIV-1 entry. Thus, the aim of this computational study was to investigate the effects of four point mutations (D53Q, D53E, D53K, and D53W) on the structure and affinity of MVN with di-mannose (MAN). Molecular dynamics simulations followed by binding free energy calculations using MM-GBSA were employed. The calculated binding free energy of ligand-receptor complexation of MVN with MAN was −26.02 kcal mol-1. We identified in the wild-type protein that residues I45, T59, and Q81 have a major contribution to the binding free energy of di-mannose. Among the investigated mutants, the most promising one was the D53W mutation, with a theoretical binding free energy value of −29.16 kcal mol-1. We suggest that this increased stability is due to the introduction of extra rigidity on the hinge region connecting two key structural elements of the MVN binding site

Analysis of kojic acid derivatives as competitive inhibitors of tyrosinase: a molecular modeling approach

This research received financial support of CAPES and CNPq.Universidade Federal do Pará. Instituto de Ciências Exatas e Naturais. Laboratório de Modelagem Molecular. Belém, PA, Brasil / Universidade Federal do Pará. Instituto de Ciências Exatas e Naturais. Laboratório de Planejamento e Desenvolvimento de Fármacos. Belém, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Exatas e Naturais. Laboratório de Sistemas Moleculares Complexos. Belém, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Exatas e Naturais. Laboratório de Planejamento e Desenvolvimento de Fármacos. Belém, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Exatas e Naturais. Laboratório de Planejamento e Desenvolvimento de Fármacos. Belém, PA, Brasil / Universidade Federal do Oeste do Pará. Instituto de Biodiversidade. Santarém, PA, BrasilUniversidade Federal do Pará. Instituto de Ciências Exatas e Naturais. Laboratório de Modelagem Molecular. Belém, PA, Brasil.Universidade Federal do Pará. Instituto de Ciências Exatas e Naturais. Laboratório de Planejamento e Desenvolvimento de Fármacos. Belém, PA, Brasil.Abstract: Tyrosinases belong to the functional copper-containing proteins family, and their structure contains two copper atoms, in the active site, which are coordinated by three histidine residues. The biosynthesis of melanin in melanocytes has two stages depending on the actions of the natural substrates L-DOPA and L-tyrosine. The dysregulation of tyrosinase is involved in skin cancer initiation. In the present study, using molecular modeling tools, we analyzed the inhibition activity of tyrosinase activity using kojic acid (KA) derivatives designed from aromatic aldehydes and malononitrile. All derivatives showed conformational affinity to the enzyme active site, and a favorable distance to chelate the copper ion, which is essential for enzyme function. Molecular dynamics simulations revealed that the derivatives formed promising complexes, presenting stable conformations with deviations between 0.2 and 0.35 Å. In addition, the investigated KA derivatives showed favorable binding free energies. The most stable KA derivatives showed the following binding free energies: −17.65 kcal mol−1 (D6), −18.07 kcal mol−1 (D2), −18.13 (D5) kcal mol−1, and −10.31 kcal mol−1 (D4). Our results suggest that these derivatives could be potent competitive inhibitors of the natural substrates of L-DOPA (−12.84 kcal mol−1) and L-tyrosine (−9.04 kcal mol−1) in melanogenesi

The genome of Enterobacter hormaechei Strain MG02, a 2,4-Dichlorophenoxyacetic Acid-Degrading Bacterium isolated from Brazilian Soil

Universidade Federal do Rio de Janeiro (UFRJ); Fundação Oswaldo Cruz (FIOCRUZ), Centro Universitário Estadual da Zona Oeste (UEZO); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Capes); Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro(FAPERJ); and the Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos (PBV).Universidade Federal do Rio de Janeiro. Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos. Rio de Janeiro, RJ, BrazilUniversidade Federal do Rio de Janeiro. Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos. Rio de Janeiro, RJ, BrazilUniversidade Federal do Rio de Janeiro. Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos. Rio de Janeiro, RJ, BrazilUniversidade Federal do Rio de Janeiro. Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos. Rio de Janeiro, RJ, Brazil / Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Paulo de Góes. Rio de Janeiro, RJ, BrazilMinistério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, BrasilCentro Universitário Estadual da Zona Oeste. Laboratório de Biotecnologia Ambiental. Rio de Janeiro, RJ, BrazilUniversidade Federal do Rio de Janeiro. Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos. Rio de Janeiro, RJ, Brazil / Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Paulo de Góes. Rio de Janeiro, RJ, BrazilABSTRACTEnterobacter hormaecheistrain MG02 was isolated from a mixed culture col-lected from soil with a history of pesticide application. This strain degrades 2,4-dichloro-phenoxyacetic acid (2,4-D). Here, we report on its genome, which has 4,923,875 bp and55.4% G1C content