Navegando por Assunto "Transcriptoma"

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Acesso aberto (Open Access)
Análise transcriptômica das linhagens celulares B103 e C6 expostas à ação do metilmercúrio
(Universidade Federal do Pará, 2023-04) BONFIM, Laís Teixeira; FERREIRA, Wallax Augusto Silva Ferreira; OLIVEIRA, Edivaldo Herculano Correa de; http://lattes.cnpq.br/009400771470765; https://orcid.org/0000-0001-6315-3352
The intensification of anthropogenic activities produces a high rate of environmental pollution, mainly in water bodies, where the contamination by metals has become an object of great interest, due to their inability to support such load. Mercury (Hg) is a naturally occurring metal that can be used in the manufacture of home products such as fluorescent lamps, fungicides, and germicides. The entry of Hg into the food chain occurs through the methylation of Hg2+ ions into MeHg. After methylation, Hg is considered highly toxic to humans, and among the main target organs of this intoxication we can mention the brain, since MeHg easily crosses the blood-brain barrier and can accumulate in different brain areas. It is known that, once in the CNS, MeHg can cause extensive cellular damage, such as DNA damage, oxidative stress, neuroinflammation and cell death in both neurons and glial cells. Thus, the objective of this study was to analyze the transcriptomic alterations of cell lines B103 and C6, derived from neuroblastoma and glioma of Rattus norvegicus, exposed to the action of methylmercury. For this, the expression microarray technique was used to evaluate the global profile of gene expression after 24h of MeHg exposure. Our results demonstrate that MeHg induces significant alterations in gene expression of the two cell lines evaluated. The alterations were more prominent in the C6 cell line, in which a greater amount of differentially expressed genes was observed. Among the genes differentially expressed of the B103 cells we can highlight the genes Cdc42se2 (log2 FC -4.055713), Dcx (log2 FC 3.618981) and 4930449C09Rik (log2 FC 3.5129156) at a concentration of 0.1 μM. As for the exposure of 2.8 μM, the genes with the highest FC were Crem (log2 FC -4.027875), Otoa (log2 FC 3.501512) and Dcx (log2 FC 3.423433). In addition to the abovementioned genes, the genes Trim14, Gm14169, Gm30871, Otoa and Dcx were shared between the two exposed groups. As for the C6 lineage, ten transcripts with FC above 3 (Aldh1l2, Dac1, Rps4l, Zbtb46, 6430573p05Rik, Tcf12, Awat2, Muc3, Dclre1b, Slc38a6) are highlighted. In the 6.3 μM treatment, only three genes were altered more than 3 times (Rps4l, Ankdr44 and 2610318N02Rik). It is also noteworthy that three genes were shared between treatments (Rps4l, Lamb 3 and Gm 41386).
Acesso aberto (Open Access)
Identificação de polimorfismos de nucleotídeo único com efeitos deletérios em transcriptomas de câncer gástrico
(Universidade Federal do Pará, 2015-09-29) SILVA, Viviane Santos da; DARNET, Sylvain Henri; http://lattes.cnpq.br/4586614214029929
Gastric cancer is one of the leading causes of cancer mortality in the world. Its development is associated with factors related to lifestyle and genetic alterations that can modify genes and important biosynthetic and metabolic pathways that help maintaining cellular and tissue integrity. One of the main cancer research objectives is identify genes and mutations that may be used as genetic markers and potential therapeutic targets. Studies with genes related to the pathway of steroid hormones proteins have already identified polymorphisms that may be related to the risk of cancer. Because it is an important route for physiological and pathological processes identification of genetic polymorphisms in this and cholesterol biosynthesis pathway may contribute to the understanding of gastric carcinogenesis. Therefore, we performed a comprehensive bioinformatics analysis of transcriptome datasets from gastric tissues with and without cancer, in order to identify SNPs in genes associated to enzymes of biosynthetic pathways of steroid hormones, cholesterol and progesterone receptor that may be related to gastric cancer. The analysis was performed using the Galaxy Platform, the Bowtie alignment tool and the Provean software for functional analysis of variations. Deleterious mutations have been identified in CYP51A1, DHCR24 and SQLE genes in the steroid hormone biosynthesis pathway, and in CYP3A5, HSD17B12, UGT1A1, UGT1A5, UGT1A6 and AKR1C3 genes in the cholesterol biosynthetic pathway. The CYP3A5 gene had the highest number of deleterious SNPs. These results indicate a possible participation of genes analyzed in the molecular mechanisms involved in the development of gastric cancer.
Acesso aberto (Open Access)
Método de identificação de genes taxonomicamente restritos em dados de RNA-seq em organismo não modelo
(Universidade Federal do Pará, 2015-09-28) OLIVEIRA, Lorena Silva de; DARNET, Sylvain Henri; http://lattes.cnpq.br/4586614214029929
Black pepper (Piper nigrum) is a biotechnologically interesting plant, research target for both metabolism exploration and improvement related to phytopathological problems, in addition to understanding the evolution of basal angiosperms, ancestral group to which it belongs. With the technological revolution, the next generation sequencing offered access to genetic heritage of non model plants enabling the opening of new biotechnological perspective. The identification of non homologous genes restricted to certain species, called taxonomically restricted genes (TRGs), is a primary biotechnological target, especially in species and groups that are divergent and ancestral. This study aims to establish a method for TRGs identification from RNA-seq data and to validate the approach a dataset for black pepper. The method consists in filtering the transcripts in several stages, so that the annotated transcripts and false positives are removed, and the remaining data without molecular information are classified as potential TRGs. The application of this approach to a black pepper transcriptome dataset (35,631 transcripts) resulted in 22,661 transcripts annotated by similarity. The transcripts that were not annotated in this first analysis were processed in the TRAPID tool, resulting in 12,895 transcripts not annotated. The evaluation of transcripts for false positive detection resulted in 245 true transcripts that were analyzed for the presence of non-coding RNA, resulting in 204 unidentified transcripts. At the end of the method application 71 non annotated transcripts remained with coding regions of protein, indicating potential TRGs. The characterization of these potential TRGs in black pepper can provide new information about the molecular mechanism of this specie and perhaps elucidate pathways for the establishment of cultivars tolerant to disease.
Acesso aberto (Open Access)
Reconstrução e modelagem in silico da via de biossíntese de ácidos graxos da bactéria psicotrófica Exiguobacterium antarticum linhagem B7
(Universidade Federal do Pará, 2016-04-04) FRANCÊS, Regiane Silva Kawasaki; SCHNEIDER, Maria Paula Cruz; http://lattes.cnpq.br/3901112943859155
Mathematical modeling in silico based restrictions is an approach adopted by systems biology to analyze metabolic networks. The Gram-positive bacterium Exiguobacterium antarticum B7 is an extremophile organism able to survive in cold environments as glacial ice and permafrost. The ability of these microorganisms of adaptation to cold attracts great biotechnological interest. An important factor for the understanding of cold adaptation process is related to the chemical modification of fatty acids constituting the cell membrane of psicotrophic bacteria in order to maintain membrane fluidity to avoid freezing ofthe bacteria. In this work, the metabolic pathway of fatty acid biosynthesis of the bacterium E. antarticum B7 was rebuilt from its annotated genome. The software tools KEGG (Kyoto Encyclopedia of Genes and Genomes) and RAST (The Rapid Annotation Server) were used to generate a preliminary network model. The next step was to cure manually the genomic, biochemical and physiological informations available in different databases and specific literature. During this process, the FabZ and DesK enzymes responsible for adding carbon-carbon unsaturations in the fatty acid chain during synthesis have been identified in the genome, though in a truncated form. The fluxome metabolic pathway was defined, describing the routes of the main reactions since the first monomer, Acetyl-CoA, to the final product, the Hexadecenoic acid. A computational modeling was done using the software MATLAB® with toolboxes and specific tools for systems biology. The quantification of metabolites produced via was performed by the method constraint-based Flux Balance Analysis (FBA). To evaluate the influence of the gene expression in the fluxome analysis, the FBA method was also calculated using the log2FC values obtained in the transcriptome analysis at 0ºC and 37ºC. The fatty acid biosynthesis pathway showed a total of 13 elementary flux modes, four of which showed routes for the production of hexadecenoic acid. The reconstructed pathway demonstrated the capacity of E. antarcticum B7 to produce fatty acid molecules. Under the influence of the transcriptome, the fluxome was altered, promoting the production of short-chain fatty acids. The calculated models contributes to better understand the bacterial adaptation at cold environments.