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Adaptive evolution of HIV at HLA epitopes is associated with ethnicity in Canada.

https://arctichealth.org/en/permalink/ahliterature123483
Source
PLoS One. 2012;7(5):e36933
Publication Type
Article
Date
2012
Author
Manon Ragonnet-Cronin
Stéphane Aris-Brosou
Isabelle Joanisse
Harriet Merks
Dominic Vallee
Kyna Caminiti
Paul Sandstrom
James Brooks
Author Affiliation
National HIV and Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, Canada.
Source
PLoS One. 2012;7(5):e36933
Date
2012
Language
English
Publication Type
Article
Keywords
Adaptation, Physiological - genetics
Adult
Alleles
Canada - ethnology
Epitopes - immunology
Evolution, Molecular
Female
HIV Infections - ethnology - immunology - virology
HIV-1 - genetics - pathogenicity
HLA Antigens - genetics - immunology
Humans
Male
Middle Aged
Selection, Genetic
Young Adult
Abstract
Host immune selection pressure influences the development of mutations that allow for HIV escape. Mutation patterns induced in HIV by the human leukocyte antigen (HLA) are HLA-allele specific. As ethnic groups have distinct and characteristic HLA allele frequencies, we can expect divergent viral evolution within ethnicities. Here, we have sequenced and analyzed the HIV pol gene from 1248 subtype B infected, treatment-na?ve individuals in Canada. Phylogenetic analysis showed no separation between pol sequences from five self-identified ethnic groups, yet fixation index (F(ST)) values showed significant divergence between ethnicities. A total of 17 amino acid sites showed an ethnic-specific fixation pattern (0.015
Notes
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PubMed ID
22693560 View in PubMed
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Genetic diversity as a marker for timing infection in HIV-infected patients: evaluation of a 6-month window and comparison with BED.

https://arctichealth.org/en/permalink/ahliterature122350
Source
J Infect Dis. 2012 Sep 1;206(5):756-64
Publication Type
Article
Date
Sep-1-2012
Author
Manon Ragonnet-Cronin
Stéphane Aris-Brosou
Isabelle Joanisse
Harriet Merks
Dominic Vallée
Kyna Caminiti
Michael Rekart
Mel Krajden
Darrel Cook
John Kim
Laurie Malloch
Paul Sandstrom
James Brooks
Author Affiliation
National HIV and Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, Canada.
Source
J Infect Dis. 2012 Sep 1;206(5):756-64
Date
Sep-1-2012
Language
English
Publication Type
Article
Keywords
Area Under Curve
Base Sequence
Canada - epidemiology
DNA-Directed RNA Polymerases - chemistry - genetics
Genetic Variation
HIV Infections - epidemiology - genetics
HIV-1 - genetics
Humans
Incidence
Molecular Sequence Data
RNA, Viral - chemistry - genetics
ROC Curve
Reverse Transcriptase Polymerase Chain Reaction
Sequence Alignment
Sequence Analysis, DNA
Time Factors
Abstract
It has been reported that the increase in human immunodeficiency virus (HIV) sequence diversity in drug resistance surveillance specimens may be used to classify the duration of HIV infection as 1 year. We describe a mixed base classifier (MBC) optimized to categorize the duration of subtype B infections as 6 months on the basis of sequences for drug resistance surveillance specimens and compared MBC findings with those of serologic methods.
The behavior of the MBC was examined across a range of thresholds for calling mixed bases. MBC performance was then evaluated using either complete pol sequences or sites reflecting evolutionary pressures (HLA selection sites, sites that increased in entropy over the course of infection, and codon positions).
The MBC performance was optimal when secondary peaks on the sequencing chromatogram accounted for at least 15% of the area of primary peaks. A cutoff of
PubMed ID
22826337 View in PubMed
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How the Central American Seaway and an ancient northern passage affected flatfish diversification.

https://arctichealth.org/en/permalink/ahliterature291952
Source
Mol Biol Evol. 2018 May 21; :
Publication Type
Journal Article
Date
May-21-2018
Author
Lisa Byrne
François Chapleau
Stéphane Aris-Brosou
Author Affiliation
Department of Biology, University of Ottawa, Ottawa, ON, CANADA.
Source
Mol Biol Evol. 2018 May 21; :
Date
May-21-2018
Language
English
Publication Type
Journal Article
Abstract
While the natural history of flatfish has been debated for decades, the mode of diversification of this biologically and economically important group has never been elucidated. To address this question, we assembled the largest molecular data set to date, covering > 300 species (out of ca. 800 extant), from 13 of the 14 known families over nine genes, and employed relaxed molecular clocks to uncover their patterns of diversification. As the fossil record of flatfish is contentious, we used sister species distributed on both sides of the American continent to calibrate clock models based on the closure of the Central American Seaway (CAS), and on their current species range. We show that flatfish diversified in two bouts, as species that are today distributed around the Equator diverged during the closure of CAS, while those with a northern range diverged after this, hereby suggesting the existence of a post-CAS closure dispersal for these northern species, most likely along a trans-Arctic northern route, a hypothesis fully compatible with paleogeographic reconstructions.
PubMed ID
29788493 View in PubMed
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How the Central American Seaway and an Ancient Northern Passage Affected Flatfish Diversification.

https://arctichealth.org/en/permalink/ahliterature301162
Source
Mol Biol Evol. 2018 08 01; 35(8):1982-1989
Publication Type
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Date
08-01-2018
Author
Lisa Byrne
François Chapleau
Stéphane Aris-Brosou
Author Affiliation
Department of Biology, University of Ottawa, Ottawa, ON, Canada.
Source
Mol Biol Evol. 2018 08 01; 35(8):1982-1989
Date
08-01-2018
Language
English
Publication Type
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
Flatfishes - genetics
Genetic Speciation
Geological Phenomena
Phylogeny
Phylogeography
Abstract
While the natural history of flatfish has been debated for decades, the mode of diversification of this biologically and economically important group has never been elucidated. To address this question, we assembled the largest molecular data set to date, covering?>?300 species (out of ca. 800 extant), from 13 of the 14 known families over nine genes, and employed relaxed molecular clocks to uncover their patterns of diversification. As the fossil record of flatfish is contentious, we used sister species distributed on both sides of the American continent to calibrate clock models based on the closure of the Central American Seaway (CAS), and on their current species range. We show that flatfish diversified in two bouts, as species that are today distributed around the equator diverged during the closure of CAS, whereas those with a northern range diverged after this, hereby suggesting the existence of a postCAS closure dispersal for these northern species, most likely along a trans-Arctic northern route, a hypothesis fully compatible with paleogeographic reconstructions.
PubMed ID
29788493 View in PubMed
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Microbial community structure in lake and wetland sediments from a high Arctic polar desert revealed by targeted transcriptomics.

https://arctichealth.org/en/permalink/ahliterature259499
Source
PLoS One. 2014;9(3):e89531
Publication Type
Article
Date
2014
Author
Magdalena K Stoeva
Stéphane Aris-Brosou
John Chételat
Holger Hintelmann
Philip Pelletier
Alexandre J Poulain
Source
PLoS One. 2014;9(3):e89531
Date
2014
Language
English
Publication Type
Article
Keywords
Arctic Regions
Base Sequence
Biodiversity
DNA Primers
Ecosystem
Geologic Sediments - microbiology
Lakes
Polymerase Chain Reaction
Transcriptome
Water Microbiology
Wetlands
Abstract
While microbial communities play a key role in the geochemical cycling of nutrients and contaminants in anaerobic freshwater sediments, their structure and activity in polar desert ecosystems are still poorly understood, both across heterogeneous freshwater environments such as lakes and wetlands, and across sediment depths. To address this question, we performed targeted environmental transcriptomics analyses and characterized microbial diversity across three depths from sediment cores collected in a lake and a wetland, located on Cornwallis Island, NU, Canada. Microbial communities were characterized based on 16S rRNA and two functional gene transcripts: mcrA, involved in archaeal methane cycling and glnA, a bacterial housekeeping gene implicated in nitrogen metabolism. We show that methane cycling and overall bacterial metabolic activity are the highest at the surface of lake sediments but deeper within wetland sediments. Bacterial communities are highly diverse and structured as a function of both environment and depth, being more diverse in the wetland and near the surface. Archaea are mostly methanogens, structured by environment and more diverse in the wetland. McrA transcript analyses show that active methane cycling in the lake and wetland corresponds to distinct communities with a higher potential for methane cycling in the wetland. Methanosarcina spp., Methanosaeta spp. and a group of uncultured Archaea are the dominant methanogens in the wetland while Methanoregula spp. predominate in the lake.
Notes
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PubMed ID
24594936 View in PubMed
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Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada.

https://arctichealth.org/en/permalink/ahliterature292428
Source
Front Microbiol. 2018; 9:1138
Publication Type
Journal Article
Date
2018
Author
Matti O Ruuskanen
Kyra A St Pierre
Vincent L St Louis
Stéphane Aris-Brosou
Alexandre J Poulain
Author Affiliation
Department of Biology, University of Ottawa, Ottawa, ON, Canada.
Source
Front Microbiol. 2018; 9:1138
Date
2018
Language
English
Publication Type
Journal Article
Abstract
The Arctic is undergoing rapid environmental change, potentially affecting the physicochemical constraints of microbial communities that play a large role in both carbon and nutrient cycling in lacustrine environments. However, the microbial communities in such Arctic environments have seldom been studied, and the drivers of their composition are poorly characterized. To address these gaps, we surveyed the biologically active surface sediments in Lake Hazen, the largest lake by volume north of the Arctic Circle, and a small lake and shoreline pond in its watershed. High-throughput amplicon sequencing of the 16S rRNA gene uncovered a community dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, similar to those found in other cold and oligotrophic lake sediments. We also show that the microbial community structure in this Arctic polar desert is shaped by pH and redox gradients. This study lays the groundwork for predicting how sediment microbial communities in the Arctic could respond as climate change proceeds to alter their physicochemical constraints.
Notes
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PubMed ID
29922252 View in PubMed
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Swift evolutionary response of microbes to a rise in anthropogenic mercury in the Northern Hemisphere.

https://arctichealth.org/en/permalink/ahliterature307728
Source
ISME J. 2020 03; 14(3):788-800
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
03-2020
Author
Matti O Ruuskanen
Stéphane Aris-Brosou
Alexandre J Poulain
Author Affiliation
Department of Biology, University of Ottawa, Ottawa, ON, Canada.
Source
ISME J. 2020 03; 14(3):788-800
Date
03-2020
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Bacteria - classification - genetics - isolation & purification - metabolism
Bacterial Proteins - genetics - metabolism
Biological Evolution
Canada
Ecosystem
Environmental Pollutants - analysis
Finland
Geologic Sediments - chemistry - microbiology
Mercury - analysis - metabolism
Oxidoreductases - genetics - metabolism
Abstract
Anthropogenic mercury remobilization has considerably increased since the Industrial Revolution in the late 1700s. The Minamata Convention on Mercury is a United Nations treaty (2017) aiming at curbing mercury emissions. Unfortunately, evaluating the effectiveness of such a global treaty is hampered by our inability to determine the lag in aquatic ecosystem responses to a change in atmospheric mercury deposition. Whereas past metal concentrations are obtained from core samples, there are currently no means of tracking historical metal bioavailability or toxicity. Here, we recovered DNA from nine dated sediment cores collected in Canada and Finland, and reconstructed the past demographics of microbes carrying genes coding for the mercuric reductase (MerA)-an enzyme involved in Hg detoxification-using Bayesian relaxed molecular clocks. We found that the evolutionary dynamics of merA exhibited a dramatic increase in effective population size starting from 1783.8?±?3.9 CE, which coincides with both the Industrial Revolution, and with independent measurements of atmospheric Hg concentrations. We show that even low levels of anthropogenic mercury affected the evolutionary trajectory of microbes in the Northern Hemisphere, and that microbial DNA encoding for detoxification determinants stored in environmental archives can be used to track historical pollutant toxicity.
PubMed ID
31831837 View in PubMed
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Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake.

https://arctichealth.org/en/permalink/ahliterature304307
Source
Front Microbiol. 2020; 11:561194
Publication Type
Journal Article
Date
2020
Author
Graham A Colby
Matti O Ruuskanen
Kyra A St Pierre
Vincent L St Louis
Alexandre J Poulain
Stéphane Aris-Brosou
Author Affiliation
Department of Biology, University of Ottawa, Ottawa, ON, Canada.
Source
Front Microbiol. 2020; 11:561194
Date
2020
Language
English
Publication Type
Journal Article
Abstract
Temperatures in the Arctic are expected to increase dramatically over the next century, and transform high latitude watersheds. However, little is known about how microbial communities and their underlying metabolic processes will be affected by these environmental changes in freshwater sedimentary systems. To address this knowledge gap, we analyzed sediments from Lake Hazen, NU Canada. Here, we exploit the spatial heterogeneity created by varying runoff regimes across the watershed of this uniquely large high-latitude lake to test how a transition from low to high runoff, used as one proxy for climate change, affects the community structure and functional potential of dominant microbes. Based on metagenomic analyses of lake sediments along these spatial gradients, we show that increasing runoff leads to a decrease in taxonomic and functional diversity of sediment microbes. Our findings are likely to apply to other, smaller, glacierized watersheds typical of polar or high latitude ecosystems; we can predict that such changes will have far reaching consequences on these ecosystems by affecting nutrient biogeochemical cycling, the direction and magnitude of which are yet to be determined.
PubMed ID
33133035 View in PubMed
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8 records – page 1 of 1.