Navegando por Assunto "Bioinformática"

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Análise de lacases de microrganismos com aplicações em biorremediação usando ferramentas de bioinformática
(2022-10-21) Silva, Andrey Giordane Costa; Buarque, Diego de Souza; http://lattes.cnpq.br/7609652740088882; http://lattes.cnpq.br/8075252796586989
The improper disposal and dumping of household waste, industrial waste, electronic waste, fertilizers, pesticides can elevate environmental concentrations of contaminants that cause significant impacts on human health and biodiversity. Given this problem, the development of technologies that assist in the environmental treatment of sites contaminated by these xenobiotics is of great importance. An applicable method for environmental remediation is biodegradation by enzymatic catalysis. Fungal lacases (in particular those of the genus Trametes) have a great potential for application in the area of wastewater treatment and bioremediation. Thus, a sequence analysis becomes important for the determination of lacases from some microorganisms. For this, we used the 1KYA, which represents the code of an active lacase structure from T. versicolor present in the Protein Data Bank (PDB). This structure is complexed to the ligand 2,5-xylidine, which is derived from commercially used solvents. Through this analysis, it is possible to understand structural factors important for the enzyme to detoxify environmentally harmful compounds, such as 2,5-xylidine. The structures and binding sites were analyzed using the BIOVIA Discovery Studio Visualizer 2021 program, where we were able to identify the amino acid residues and bonds that are part of the lacase 1KYA site that interact with 2,5-xylidine. To identify important structural factors in the sequences of lacases from microorganisms, a comparison was made in the primary sequence of the active lacase (1KYA) with a known sequence of the lacase from Trametes versicolor to determine what would be the degree of homology between them and if all amino acids that are part of the active site identified. By checking the degree of homology between different types of lacases from different organisms, it was possible to identify sequences of 16 microorganisms with a percentage equal to or greater than 79.56%. In addition, it was possible to identify the amino acid residues conserved in lacases from different organisms and the residues that changed among the sequences of this enzyme.
Análise in silico de Polimorfismo de Nucleotídeo Único (SNP) de variantes missense do gene IL17A
(2022-10-06) Silva, João Gabriel da; Maia, Maria de Mascena Diniz; http://lattes.cnpq.br/7051998554981575
Contribuições do uso de ferramentas de bioinformática no ensino e aprendizagem de evolução envolvendo a temática pandemias causadas pela bactéria Yersinia pestis
(2025-08-06) Sousa, Matheus Geovane Gomes de; Freitas, Nara Suzy Aguiar de; Silva, Alexsandro Alberto da; http://lattes.cnpq.br/2011377431714562; http://lattes.cnpq.br/6891650997818766; http://lattes.cnpq.br/7743011824083084
Este trabalho investigou as contribuições do uso de ferramentas de bioinformática de modo lúdico no ensino-aprendizagem da evolução, sob a perspectiva das histórias das pandemias provocadas pela bactéria Yersinia pestis, como modelo evolutivo. Adotou-se uma abordagem quali-quantitativa com metodologia descritiva, aplicando uma sequência de aulas dividida em quatro momentos, que envolveu questionários iniciais e finais. As sequências genéticas e a árvore filogenética gerada nas aulas permitiram aos discentes a visualização de processos históricos das três pandemias de Y. pestis. Inicialmente com visão tipológica, os discentes avançaram para um entendimento atual reconhecendo alterações genéticas ao longo do tempo e correlacionando com as variações do vírus da pandemia de COVID-19. As ferramentas de bioinformática têm papel relevante no ensino de conceitos evolutivos no ensino médio e são facilitadoras da compreensão da diversidade da vida e da história evolutiva das espécies, tornando as aulas mais significativas e facilitadoras do ensino-aprendizagem contribuindo para a alfabetização científica e a capacidade de interpretação crítica baseada em evidências. Essas tecnologias tornam teorias abstratas em representações visuais, facilitando a superação de equívocos sobre mecanismos evolutivos. A integração da bioinformática nas aulas potencializa o ensino de evolução, tornando o ensino mais atual e significativo. No entanto, sua implementação efetiva depende de investimento nas infraestruturas escolares e na formação continuada dos professores. O ensino da evolução, todavia, ainda, necessita enfrentar obstáculos pedagógicos e emocionais.
Desenvolvimento e validação de marcadores moleculares tipo microssatélites a partir do transcriptoma de Vigna unguiculata (L.) Walp.
(2019-07-17) Oliveira, Wilson Dias de; Iseppon, Ana Maria Benko; Araújo, Flávia Czekalski de; http://lattes.cnpq.br/1888011932745430; http://lattes.cnpq.br/7796654028353519; http://lattes.cnpq.br/3544882037972617
Genetic improvement of plants has potentiated continuous gains in the productivity of several crops. In this context, molecular markers stand out as a promising tool, which allows direct access to the genotype of the individual, thus differentiating it self from the morphological markers. Microsatellites (SSR) are codominant markers and are among the most used for this purpose. Thus, the present work aimed to develop and validate SSR markers for use in genetic improvement programs of cowpea [Vigna unguiculata (L.) Walp.]. For this, three transcripts of the species, from experiments by CPSMV (Cowpea Severe Mosaic Virus), CABMV (Cowpea Aphid-born Mosaic Virus) and root dehydration were analyzed. A computational pipeline was used to identify and annotate SSRs. The selection of the candidates for the development of the markers was performed considering the polymorphism of size between the motifs, followed for the design of the primers using the SnapGene tool. 45,776 sequences containing SSRs were identified, among which the di- and trinucleotide motifs prevailed, together representing a total of 60% of the sequences identified. Of these, 3,493 sequences were present in the three transcripts analyzed, where 160 were selected based on the most significant difference in size (12-42) among the motifs, followed by the design of 30 SSRs. In the conventional PCR step, it was observed that 73% of the markers confirmed polymorphism between the BR 14-Mulato and IT85F-2687 accessions, while 57% were polymorphic between Pingo de Ouro and Santo Inácio. A total of 23 markers were transferable to V. unguiculata subsp. sesquipedalis and 16 for V. radiata (L.). Finally, the analysis allowed the identification of SSRs in the transcriptomes of cowpea, submitted to biotic and abiotic stresses, revealing polymorphisms between different accessions. The data identified, analyzed and validated will contribute to studies of genetic diversity and pre-breeding, aiming to broaden the available genetic base of cowpea.
Inferência filogenética de Apoidea (Hymenoptera) a partir da análise do grau de homologia do citocromo c por ferramentas de bioinformática
(2022-06-01) Melo, Ericles Charles Da Silva; Buarque, Diego de Souza; http://lattes.cnpq.br/7609652740088882; http://lattes.cnpq.br/4571885030401284
The Apoidea superfamily (Hymenoptera) is home to about 30,000 recorded species and consists of several subgroups of apoid bees and wasps, with different types of habits from kleptoparist to eusociality. The species of this subfamily can be identified by body division (head, mesosoma and metasoma) and by the presence or absence of hair on the body. Due to the great difficulty in establishing molecular markers that can infer the phylogeny of this group, we aimed in this work to verify if cytochrome c, a protein essential to oxidative metabolism and energy production, highly conserved in species, can satisfactorily fulfill this role. The work consisted of two approaches: 1) the search for the primary sequences of cytochrome c of organisms of the Apoidea superfamily available in biological databases (NCBI Protein), for subsequent multiple alignment and obtaining a phylogenetic tree through the MAFFT program; 2) comparison with the phylogenies present in the literature. FASTA sequences were obtained from 15 species, all containing 108 amino acid residues. The cladogram obtained from the proposed alignment shows that the Bombini and Apini tribes seem to form a sister group. The study also showed that the common ancestor that gives rise to the Euglossini tribe also gives rise to the Bombini, Apini and Meliponini tribes, thus demonstrating that Apini and Euglossini can be paraphyletic groups. Despite the few Apoidea cytochrome c sequences available in the NCBI Protein, it was possible to observe that the cladogram seems to go against some proposals in the literature, suggesting that cytochrome c seems to be promising for this purpose. However, this study does not immediately propose a new classification, as it would be necessary to analyze a greater number of primary sequences from different Apoidea species. Therefore, more studies are needed in different groups among the Hymenoptera so that it is possible to use cytochrome c as a possible marker.
Levantamento e análise da variabilidade genética do gênero Siderastrea Blainville, 1830
(2024-10-04) Lira, Jean Tácio Tôrres de; Amaral, Fernanda Maria Duarte do; http://lattes.cnpq.br/7026011892824176; http://lattes.cnpq.br/0569107903225207
This study aimed to fill gaps in knowledge about the genetic and phylogenetic diversity of the genus Siderastrea (Blainville, 1830), important coral reef-building organisms, with a greater focus on the species Siderastrea stellata (Verrill, 1868). Partially bleached colonies of the species S. stellata were collected on Gaibu beach, from November 2022 to January 2023 and the genomic DNA of the colonies was extracted using the Wizard Genomic DNA Purification Kit. A specific primer pair was designed to confirm the species S. stellata and the identification of the colonies was performed by the conventional PCR technique. The analysis of the variability between the colonies was performed by the RAPD technique using 06 random ITS primers. Furthermore, to analyze whether there was genetic variability among the S. stellata samples in the Genbank genomic database, we downloaded all sequences and performed sequence alignment. Subsequently, phylogenetic analyses were performed among the deposited samples using the Mega platform. Finally, in silico restriction enzyme analyses were performed to search for restriction enzymes that could be used to differentiate between the isolates. The results obtained with the RAPD technique did not provide sufficient data to identify genetic variability among the samples analyzed in the present study. On the other hand, regarding the data from the phylogenetic analysis, it was possible to find differences between the sequences of isolates from different regions. There was greater genetic proximity between S. stellata isolates from Panama and Brazil and less proximity to the isolate from Mexico. Siderastrea savigneana stood out as the most distant ancestor within the genus. In addition, it was possible to detect preliminary genetic variations among the populations evaluated, using data from the in silico restriction analysis. Thus, this study provides a first approach to genetic analysis of variability within the species of S. stellata. However, more in-depth studies are needed and may help to clarify the complexity of the genetic variability of the genus, in addition to assisting in management and conservation strategies for these organisms and the marine ecosystems they support.
Métodos computacionais para a análise de dados de expressão gênica provenientes de uma análise de microarray utilizada para teste farmacológico
(2023-04-28) Costa, Allan Mesquita da; Melo, Jeane Cecília Bezerra de; Costa, Luciana Amaral de Mascena; http://lattes.cnpq.br/2352032088330896; http://lattes.cnpq.br/8499459630583005; http://lattes.cnpq.br/2703136397519338
The advent of the Human Genome Project (HGP), completed in October 2003, propelled the development of techniques for obtaining and analyzing biological data. The need to manage the vast amount of digital genome data was a decisive factor in the growth of a multidisciplinary area of knowledge, Computational Biology. In the two decades following the completion of the HGP, genomes of different organisms were obtained. Regarding mammals, projects such as the 1000 Genomes Project and the Cancer Genome Atlas (TCGA) illustrated the advancement of knowledge in the analysis of complex data. Among the newest techniques, we highlight Microarrays. They provide a significant amount of data in a single experiment, allowing the comparison of complete genomes. The analysis of Microarray data is relatively complex and requires protocols that make this analysis simpler, producing more understandable information. The present study involves the use of computational methods to analyze gene expression data obtained from a Microarray experiment used for pharmacological testing related to breast cancer. To process the raw data, obtained from a spreadsheet containing more than 3216 genes resulting from a Microarray analysis, a script was developed to facilitate the extraction of information from this data and subsequent selection of genes of interest. The program allowed the search for genes involved in the processes of cell death (apoptosis, necrosis, and autophagy), which are determining factors in the success analysis of the tested drug. To categorize the genes involved in the apoptotic, necrotic, and autophagic death cascade, heatmaps were constructed from fold-change values (difference in gene expression for values before and after treatment of cancerous cells with the mesoionic compound), using k-means clustering and hierarchical clustering techniques provided in the Heatmapper program. Results of the study include the development of a script in the R program that resulted in the separation of 20 genes involved in the apoptotic death cascade, six involved in the autophagic death, and seven involved in the necrotic death cascade, as well as the development of three heatmaps, contributing to the biological analysis of data, in addition to making Microarray data processing more accessible.
Predição por análise in silico da consequência de mutação missense no gene IGF2 humano
(2023-09-04) Costa, Karla Roberta Lemos Maul de Souza; Maia, Maria de Mascena Diniz; http://lattes.cnpq.br/7051998554981575; http://lattes.cnpq.br/8727605240852776
Sequenciamento genético de nova geração e sua aplicabilidade na virologia veterinária: revisão de literatura
(2025-07-25) Guaraná, Ayrton Carlos Luz; Pinheiro Júnior, José Wilton; http://lattes.cnpq.br/3931532041328673; http://lattes.cnpq.br/1933294583713129
Objetiva-se com o presente relatório demonstrar as principais atividades exercidas pelo discente Ayrton Carlos Luz Guaraná sob orientação e supervisão, do Professor Dr. José Wilton Pinheiro Junior, da Universidade Federal Rural de Pernambuco e da Professora Dra. Líria Hiromi Okuda do Instituto Biológico, respectivamente. Este trabalho foi dividido em dois capítulos, no primeiro inclui-se uma descrição das atividades realizadas durante o período de vivência do estágio, e o segundo capítulo contém a revisão de literatura sobre Sequenciamento Genético de Nova Geração (NGS) e sua aplicabilidade na virologia veterinária. O Estágio Supervisionado Obrigatório (ESO) ocorreu no período de 14 de abril a 04 de julho de 2025, no Laboratório de Viroses de Bovídeos (LVB), que faz parte do Instituto Biológico (IB), também conhecido como Secretaria da Agricultura e Abastecimento, localizado no município de São Paulo, no bairro da Vila Mariana (Zona Sul). A revisão evidenciou que o NGS supera métodos tradicionais na detecção de vírus emergentes e coinfecções, com aplicações críticas em vigilância genômica (ex.: identificação de novas variantes de Felipivirus e Calicivirus felino). Plataformas como Illumina, Ion Torrent e Oxford Nanopore são eficazes na caracterização de variantes virais e suporte a estratégias profiláticas. Conclui-se que o NGS é indispensável para respostas rápidas a ameaças virais, embora desafios técnicos e econômicos persistam.