Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences

The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.

The post-transcriptional gene silencing pathway in Eucalyptus

Post-transcriptional gene silencing (PTGS) is a conserved surveillance mechanism that identifies and cleaves double-stranded RNA molecules and their cellular cognate transcripts. The RNA silencing response is actually used as a powerful technique (named RNA interference) for potent and specific inhibition of gene expression in several organisms. To identify gene products in Eucalyptus sharing similarities with enzymes involved in the PTGS pathway, we queried the expressed sequence tag database of the Brazilian Eucalyptus Genome Sequence Project Consortium (FORESTs) with the amino acid sequences of known PTGS-related proteins. Among twenty-six prospected genes, our search detected fifteen assembled sequences encoding products presenting high level of similarity (E value < 10 -40) to proteins involved in PTGS in plants and other organisms. We conclude that most of the genes known to be involved in the PTGS pathway are represented in the FORESTs database. Copyright by the Brazilian Society of Genetics.

Report of a chimeric origin of transposable elements in a bovine-coding gene

Despite the wide distribution of transposable elements (TEs) in mammalian genomes, part of their evolutionary significance remains to be discovered. Today there is a substantial amount of evidence showing that TEs are involved in the generation of new exons in different species. In the present study, we searched 22,805 genes and reported the occurrence of TE-cassettes in coding sequences of 542 cow genes using the RepeatMasker program. Despite the significant number (542) of genes with TE insertions in exons only 14 (2.6%) of them were translated into protein, which we characterized as chimeric genes. From these chimeric genes, only the FAST kinase domains 3 (FASTKD3) gene, present on chromosome BTA 20, is a functional gene and showed evidence of the exaptation event. The genome sequence analysis showed that the last exon coding sequence of bovine FASTKD3 is ∼85% similar to the ART2A retrotransposon sequence. In addition, comparison among FASTKD3 proteins shows that the last exon is very divergent from those of Homo sapiens, Pan troglodytes and Canis familiares. We suggest that the gene structure of bovine FASTKD3 gene could have originated by several ectopic recombinations between TE copies. Additionally, the absence of TE sequences in all other species analyzed suggests that the TE insertion is clade-specific, mainly in the ruminant lineage. ©FUNPEC-RP.

Modelagem molecular da Chiquimato quinase de Mycobacterium leprae

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Bioinformática estrutural aplicada ao estudo de proteínas alvo do genoma do Mycobacterium tuberculosis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Funcionalidade das proteínas ParA e ParB na segregação cromossômica de Xanthomonas citri ssp citri

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Epidemiologia molecular das estirpes LaSota e São João do Meriti do vírus da Doença de Newcastle

Pós-graduação em Microbiologia Agropecuária - FCAV

Molecular and Pathogenic Diversity Among Brazilian Isolates of Xanthomonas albilineans Assessed with SSR Marker Loci

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudo comparativo do genoma e do transcriptoma de Phyllosticta citricarpa (fase sexual Guignardia citricarpa) agente da Mancha Preta dos Citros e Phyllosticta capitalensis

Pós-graduação em Ciências Biológicas (Genética) - IBB

Construction and preliminary characterization of a river buffalo bacterial artificial chromosome library

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Pesquisa de genomas virais em primatas não humanos do novo mundo por metagenômica

Pós-graduação em Medicina Veterinária - FMVZ

Isolation and characterization of mayaro virus from a human in Acre, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Precision of distances and ordering of microsatellite markers in consensus linkage maps of chromosomes 1, 3 and 4 from two reciprocal chicken populations using bootstrap sampling

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

P-220-Escherichia coli displaying virulence features of multiple diarrheogenic pathotypes detected in a Crohn's disease patient

Background: The number of Escherichia coli in the gut of Crohn's disease (CD) patients is higher than that of normal subjects, but the virulence potential of these bacteria is not fully known. Previous studies have shown that these E. coli are closely related to extraintestinal pathogenic categories (ExPEC), are able to invade epithelial cells, and usually do not produce exotoxins. We report here the detection, in a CD patient, of an E. coli which belongs to a classical enteropathogenic (EPEC) serotype and displays virulence markers of enteroinvasive (EIEC), enteroaggregative (EAEC) and enterohemorrhagic (EHEC) pathotypes. Methods: The E. coli strain was isolated, in 2009, by classical bacteriological procedures from a 56 year old woman who underwent ileo-terminal resection 1 year before, due to intestinal obstruction. The bacterial characterization was carried out by in vitro adhesion and invasion assays to cultured epithelial cells and macrophages and screening by PCR to identify virulence genetic markers of diarrheogenic E. coli (DEC) and to detect one of the gene combinations which define the phylogroups of the E. coli reference (EcoR) collection. The strain was also tested for the ability to produce biofilm and shiga cytotoxins and had its whole genome sequenced by Ion Torrent Sequencing Technology. Results: The studied strain, which was detected both in ileum biopsies and the stools of the patient, displayed the aggregative adherence (AA) phenotype to Hep-2 cells and an ability to enter Caco-2 cells 3x as high as that of EIEC reference strain and 89% of that of the prototype AIEC LF82 strain. Although it could invade cultured macrophages, the strain was unable to replicate inside these cells. PCR screening revealed the presence of eae, aggR and stx1. Tests with bacterial culture supernatants in Vero cells demonstrating cytotoxicity suggested the production of Stx1. In addition, the strain revealed to be a strong biofilm producer, belonged to the B2 EcoR phylogroup, to the O126:H27 serogroup and to the multilocus sequencing type (MLST) ST3057. The 2 later features were deduced from the whole genome sequence of the strain. Conclusions: The characterization of this E. coli isolate from a CD patient revealed a combination of virulence markers of distinct DEC pathotypes, namely eae and stx1 of EHEC, AA, aggR and biofilm formation of EAEC, and invasiveness of EIEC. These features along with its serotype and phylogroup identity seem to suggest a potential to be involved in CD, an observation which should be tested with additional studies.

Isolamento de sequências repetitivas do genoma de espécies do gênero Ancistrus (Siluriformes: Loricariidae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)