Details
Name
Nuno FonsecaCluster
Computer ScienceRole
External Research CollaboratorSince
01st June 2009
Nationality
PortugalCentre
Artificial Intelligence and Decision SupportContacts
+351220402963
nuno.fonseca@inesctec.pt
2021
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.
2021
Authors
Egeter, B; Veríssimo, J; Lopes-Lima, M; chaves, c; Pinto, J; Riccardi, N; Beja, P; Fonseca, NA;
Publication
ARPHA Conference Abstracts
Abstract
2021
Authors
Garg, M; Couturier, DL; Nsengimana, J; Fonseca, NA; Wongchenko, M; Yan, YB; Lauss, M; Jonsson, GB; Newton Bishop, J; Parkinson, C; Middleton, MR; Bishop, DT; McDonald, S; Stefanos, N; Tadross, J; Vergara, IA; Lo, S; Newell, F; Wilmott, JS; Thompson, JF; Long, GV; Scolyer, RA; Corrie, P; Adams, DJ; Brazma, A; Rabbie, R;
Publication
NATURE COMMUNICATIONS
Abstract
Adjuvant systemic therapies are now routinely used following resection of stage III melanoma, however accurate prognostic information is needed to better stratify patients. We use differential expression analyses of primary tumours from 204 RNA-sequenced melanomas within a large adjuvant trial, identifying a 121 metastasis-associated gene signature. This signature strongly associated with progression-free (HR=1.63, p=5.24 x 10(-5)) and overall survival (HR=1.61, p=1.67 x 10(-4)), was validated in 175 regional lymph nodes metastasis as well as two externally ascertained datasets. The machine learning classification models trained using the signature genes performed significantly better in predicting metastases than models trained with clinical covariates (p(AUROC) = 7.03 x 10(-4)), or published prognostic signatures (p(AUROC) < 0.05). The signature score negatively correlated with measures of immune cell infiltration (
2021
Authors
Fernandes, C; Martins, L; Teixeira, M; Blom, J; Pothier, JE; Fonseca, NA; Tavares, F;
Publication
MICROORGANISMS
Abstract
The recent report of distinct Xanthomonas lineages of Xanthomonas arboricola pv. juglandis and Xanthomonas euroxanthea within the same walnut tree revealed that this consortium of walnut-associated Xanthomonas includes both pathogenic and nonpathogenic strains. As the implications of this co-colonization are still poorly understood, in order to unveil niche-specific adaptations, the genomes of three X. euroxanthea strains (CPBF 367, CPBF 424(T), and CPBF 426) and of an X. arboricola pv. juglandis strain (CPBF 427) isolated from a single walnut tree in Loures (Portugal) were sequenced with two different technologies, Illumina and Nanopore, to provide consistent single scaffold chromosomal sequences. General genomic features showed that CPBF 427 has a genome similar to other X. arboricola pv. juglandis strains, regarding its size, number, and content of CDSs, while X. euroxanthea strains show a reduction regarding these features comparatively to X. arboricola pv. juglandis strains. Whole genome comparisons revealed remarkable genomic differences between X. arboricola pv. juglandis and X. euroxanthea strains, which translates into different pathogenicity and virulence features, namely regarding type 3 secretion system and its effectors and other secretory systems, chemotaxis-related proteins, and extracellular enzymes. Altogether, the distinct genomic repertoire of X. euroxanthea may be particularly useful to address pathogenicity emergence and evolution in walnut-associated Xanthomonas.
2021
Authors
Teixeira, M; Fernandes, C; Chaves, C; Pinto, J; Tavares, F; Fonseca, NA;
Publication
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
Abstract
We report the genome sequence of Xanthomonas arboricola pv. juglandis strain CPBF 427, which was isolated from early-season buds of a diseased walnut tree, suggesting overwinter potential. This study provides a consistent genomic reference for this pathovar and may contribute to addressing the overwinter survival of these walnut pathogens.
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