Genomic characterization of orthobunyavirus of veterinary importance in America

During 2013, in Argentina, three new isolates of serogroup Bunyamwera virus (genus Orthobunyavirus, family Peribunyaviridae)were recovered from two horses with encephalitis, and from an aborted equine fetus. In the present study, we report the complete genome sequence, genetic characterization, and phylogenetic analysis of three new strains isolated in Argentina to clarifying their relationship within the Bunyamwera serogroup virus and to investigate the evolutionary history of viruses with segmented genomes.Fil: Tauro, Laura Beatriz. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: de Souza, William Marciel. Universidade de Sao Paulo; BrasilFil: Rivarola, María Elisa. Universidad Nacional de Córdoba. Facultad de Medicina. Laboratorio de Arbovirus y Arenovirus; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: de Oliveira, Rodrigo. Instituto Evandro Chagas; BrasilFil: Konigheim, Brenda Salome. Universidad Nacional de Cordoba. Facultad de Medicina. Instituto de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Patroca Silva, Sandro. Instituto Evandro Chagas; BrasilFil: Lima, Clayton. Instituto Evandro Chagas; BrasilFil: Oliveira, Layanna. Instituto Evandro Chagas; BrasilFil: Vasconcelos, Janaina M.. Instituto Evandro Chagas; BrasilFil: Ferreira Cardoso, Jedson. Instituto Evandro Chagas; BrasilFil: Vianez Júnior, João Lídio. Instituto Evandro Chagas; BrasilFil: Teixeira Nunes, Márcio Roberto. Instituto Evandro Chagas; BrasilFil: Contigiani de Minio, Marta Silvia. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentin

Insights Into Limnothrix sp. Metabolism Based on Comparative Genomics

Currently only four genome sequences for Limnothrix spp. are publicly available, and information on the genetic properties of cyanobacteria belonging to this genus is limited. In this study, we report the draft genome of Limnothrix sp. CACIAM 69d, isolated from the reservoir of a hydroelectric dam located in the Amazon ecosystem, from where cyanobacterial genomic data are still scarce. Comparative genomic analysis of Limnothrix revealed the presence of key enzymes in the cyanobacterial central carbon metabolism and how it is well equipped for environmental sulfur and nitrogen acquisition. Additionally, this work covered the analysis of Limnothrix CRISPR-Cas systems, pathways related to biosynthesis of secondary metabolites and assembly of extracellular polymeric substances and their exportation. A trans-AT PKS gene cluster was identified in two strains, possibly related to the novel toxin Limnothrixin biosynthesis. Overall, the draft genome of Limnothrix sp. CACIAM 69d adds new data to the small Limnothrix genome library and contributes to a growing representativeness of cyanobacterial genomes from the Amazon region. The comparative genomic analysis of Limnothrix made it possible to highlight unique genes for each strain and understand the overall features of their metabolism

Biotecnologia vegetal: introdução

Ensino Fundamental Final::Ciências NaturaisEnsino Médio::BiologiaConceitua a biotecnologia vegetal por meio de uma abordagem histórica. Para isso, apresenta a origem dos produtos agrícolas consumidos pela população, abordando desde a seleção das sementes para o plantio até o controle das pragas e a colheit

Biotecnologia vegetal: introdução

Ensino Fundamental Final::Ciências NaturaisEnsino Médio::BiologiaConceitua a biotecnologia vegetal por meio de uma abordagem histórica. Para isso, apresenta a origem dos produtos agrícolas consumidos pela população, abordando desde a seleção das sementes para o plantio até o controle das pragas e a colheit

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

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

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

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