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Publications

2021

Shedding light on the african enigma: In vitro testing of homo sapiens-helicobacter pylori coevolution

Authors
Cavadas, B; Leite, M; Pedro, N; Magalhaes, AC; Melo, J; Correia, M; Maximo, V; Camacho, R; Fonseca, NA; Figueiredo, C; Pereira, L;

Publication
Microorganisms

Abstract
The continuous characterization of genome-wide diversity in population and case- cohort samples, allied to the development of new algorithms, are shedding light on host ancestry impact and selection events on various infectious diseases. Especially interesting are the longstanding associations between humans and certain bacteria, such as the case of Helicobacter pylori, which could have been strong drivers of adaptation leading to coevolution. Some evidence on admixed gastric cancer cohorts have been suggested as supporting Homo-Helicobacter coevolution, but reliable experimental data that control both the bacterium and the host ancestries are lacking. Here, we conducted the first in vitro coinfection assays with dual humanand bacterium-matched and -mismatched ancestries, in African and European backgrounds, to evaluate the genome wide gene expression host response to H. pylori. Our results showed that: (1) the host response to H. pylori infection was greatly shaped by the human ancestry, with variability on innate immune system and metabolism; (2) African human ancestry showed signs of coevolution with H. pylori while European ancestry appeared to be maladapted; and (3) mismatched ancestry did not seem to be an important differentiator of gene expression at the initial stages of infection as assayed here. © 2021 by the authors.

2020

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci

Authors
Cavadas, B; Camacho, R; Ferreira, JC; Ferreira, RM; Figueiredo, C; Brazma, A; Fonseca, NA; Pereira, L;

Publication
MICROORGANISMS

Abstract
The human gastrointestinal tract harbors approximately 100 trillion microorganisms with different microbial compositions across geographic locations. In this work, we used RNASeq data from stomach samples of non-disease (164 individuals from European ancestry) and gastric cancer patients (137 from Europe and Asia) from public databases. Although these data were intended to characterize the human expression profiles, they allowed for a reliable inference of the microbiome composition, as confirmed from measures such as the genus coverage, richness and evenness. The microbiome diversity (weighted UniFrac distances) in gastric cancer mimics host diversity across the world, with European gastric microbiome profiles clustering together, distinct from Asian ones. Despite the confirmed loss of microbiome diversity from a healthy status to a cancer status, the structured profile was still recognized in the disease condition. In concordance with the parallel host-bacteria population structure, we found 16 human loci (non-synonymous variants) in the European-descendent cohorts that were significantly associated with specific genera abundance. These microbiome quantitative trait loci display heterogeneity between population groups, being mainly linked to the immune system or cellular features that may play a role in enabling microbe colonization and inflammation.

2020

Pan-cancer analysis of whole genomes

Authors
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium,;

Publication
Nature

Abstract

2020

Complete Genome Sequences of Walnut-Associated Xanthomonas euroxanthea Strains CPBF 367 and CPBF 426 Obtained by Illumina/Nanopore Hybrid Assembly

Authors
Teixeira, M; Martins, L; Fernandes, C; Chaves, C; Pinto, J; Tavares, F; Fonseca, NA;

Publication
MICROBIOLOGY RESOURCE ANNOUNCEMENTS

Abstract
We present the complete genome sequences of two Xanthomonas euroxanthea strains isolated from buds of a walnut tree. The whole-genome sequences of strains CPBF 367 and CPBF 426 consist of two circular chromosomes of 4,923,218 bp and 4,883,254 bp and two putative plasmids of 45,241 bp and 17,394 bp, respectively. These data may contribute to the understanding of Xanthomonas species-specific adaptations to walnut.

2020

Expression Atlas update: from tissues to single cells

Authors
Papatheodorou, I; Moreno, P; Manning, J; Fuentes, AMP; George, N; Fexova, S; Fonseca, NA; Fullgrabe, A; Green, M; Huang, N; Huerta, L; Lqbal, H; Jianu, M; Mohammed, S; Zhao, LY; Jarnuczak, AF; Jupp, S; Marioni, J; Meyer, K; Petryszak, R; Medina, CAP; Talavera Lopez, C; Teichmann, S; Vizcaino, JA; Brazma, A;

Publication
NUCLEIC ACIDS RESEARCH

Abstract
Expression Atlas is EMBL-EBI's resource for gene and protein expression. It sources and compiles data on the abundance and localisation of RNA and proteins in various biological systems and contexts and provides open access to this data for the research community. With the increased availability of single cell RNA-Seq datasets in the public archives, we have now extended Expression Atlas with a new added-value service to display gene expression in single cells. Single Cell Expression Atlas was launched in 2018 and currently includes 123 single cell RNA-Seq studies from 12 species. The website can be searched by genes within or across species to reveal experiments, tissues and cell types where this gene is expressed or under which conditions it is a marker gene. Within each study, cells can be visualized using a pre-calculated t-SNE plot and can be coloured by different features or by cell clusters based on gene expression. Within each experiment, there are links to downloadable files, such as RNA quantification matrices, clustering results, reports on protocols and associated metadata, such as assigned cell types.