LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 124

Search options

  1. Article ; Online: Quantitative phylogenomic evidence reveals a spatially structured SARS-CoV-2 diversity.

    Jones, Leandro R / Manrique, Julieta M

    Virology

    2020  Volume 550, Page(s) 70–77

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent RNA virus that spread around the planet in about 4 months. The consequences of this rapid dispersion are under investigation. In this work, we analyzed thousands of genomes and ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent RNA virus that spread around the planet in about 4 months. The consequences of this rapid dispersion are under investigation. In this work, we analyzed thousands of genomes and protein sequences from Africa, America, Asia, Europe, and Oceania. We provide statistically significant evidence that SARS-CoV-2 phylogeny is spatially structured. Remarkably, the virus phylogeographic patterns were correlated with ancestral amino acidic substitutions, suggesting that such mutations emerged along colonization events. We hypothesize that geographic structuring is the result of founder effects occurring as a consequence of, and local evolution occurring after, long-distance dispersion. Based on previous studies, the possibility that this could significantly affect the virus biology is not remote.
    MeSH term(s) Africa/epidemiology ; Americas/epidemiology ; Asia/epidemiology ; Betacoronavirus/classification ; Betacoronavirus/genetics ; Betacoronavirus/pathogenicity ; COVID-19 ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Coronavirus Infections/transmission ; Disease Outbreaks ; Europe/epidemiology ; Evolution, Molecular ; Genetic Variation ; Genome, Viral ; Humans ; Oceania/epidemiology ; Open Reading Frames ; Pandemics ; Phylogeny ; Phylogeography ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/transmission ; SARS-CoV-2 ; Viral Proteins/genetics
    Chemical Substances Viral Proteins
    Keywords covid19
    Language English
    Publishing date 2020-08-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2020.08.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.172: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article ; Online: Quantitative phylogenomic evidence reveals a spatially structured SARS-CoV-2 diversity

    Jones, Leandro R. / Manrique, Julieta M.

    Virology

    2020  Volume 550, Page(s) 70–77

    Keywords Virology ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2020.08.010
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.172: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: Corrigendum to "Are ocean currents to slow to counteract SAR11 evolution? A next-generation sequencing, phylogeographic analysis" [Mol. Phylogenet. Evol. 107 (2017) 324-337].

    Manrique, Julieta M / Jones, Leandro R

    Molecular phylogenetics and evolution

    2017  Volume 110, Page(s) 150

    Language English
    Publishing date 2017-05
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 33610-5
    ISSN 1095-9513 ; 1055-7903
    ISSN (online) 1095-9513
    ISSN 1055-7903
    DOI 10.1016/j.ympev.2017.03.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3644: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article ; Online: Mega-phylogeny sheds light on SARS-CoV-2 spatial phylogenetic structure

    Jones, Leandro R. / Manrique, Julieta Marina

    bioRxiv

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent RNA virus that spread around the planet in about 4 months. The consequences of this rapid dispersion are under investigation. In this work, we analyzed thousands of genomes and ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent RNA virus that spread around the planet in about 4 months. The consequences of this rapid dispersion are under investigation. In this work, we analyzed thousands of genomes and protein sequences from Africa, America, Asia, Europe, and Oceania. We show that the virus is a complex of slightly different variants that are unevenly distributed on Earth, and demonstrate that SARS-CoV-2 phylogeny is spatially structured. Remarkably, the virus phylogeographic patterns were associated with ancestral amino acidic mutations. We hypothesize that geographic structuring is the result of founder effects occurring as a consequence of, and local evolution occurring after, long-distance dispersal. Based on previous studies, the possibility that this could significantly affect the virus phenotype is not remote.
    Keywords covid19
    Publisher BioRxiv; WHO
    Document type Article ; Online
    Note WHO #Covidence: #135954
    DOI 10.1101/2020.06.05.135954
    Database COVID19

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article: Quantitative phylogenomic evidence reveals a spatially structured SARS-CoV-2 diversity

    Jones, Leandro R / Manrique, Julieta M

    Virology

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent RNA virus that spread around the planet in about 4 months. The consequences of this rapid dispersion are under investigation. In this work, we analyzed thousands of genomes and ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent RNA virus that spread around the planet in about 4 months. The consequences of this rapid dispersion are under investigation. In this work, we analyzed thousands of genomes and protein sequences from Africa, America, Asia, Europe, and Oceania. We provide statistically significant evidence that SARS-CoV-2 phylogeny is spatially structured. Remarkably, the virus phylogeographic patterns were correlated with ancestral amino acidic substitutions, suggesting that such mutations emerged along colonization events. We hypothesize that geographic structuring is the result of founder effects occurring as a consequence of, and local evolution occurring after, long-distance dispersion. Based on previous studies, the possibility that this could significantly affect the virus biology is not remote.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #731922
    Database COVID19

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article: Quantitative phylogenomic evidence reveals a spatially structured SARS-CoV-2 diversity

    Jones, Leandro R / Manrique, Julieta M

    Virology. 2020 Nov., v. 550

    2020  

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent RNA virus that spread around the planet in about 4 months. The consequences of this rapid dispersion are under investigation. In this work, we analyzed thousands of genomes and ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent RNA virus that spread around the planet in about 4 months. The consequences of this rapid dispersion are under investigation. In this work, we analyzed thousands of genomes and protein sequences from Africa, America, Asia, Europe, and Oceania. We provide statistically significant evidence that SARS-CoV-2 phylogeny is spatially structured. Remarkably, the virus phylogeographic patterns were correlated with ancestral amino acidic substitutions, suggesting that such mutations emerged along colonization events. We hypothesize that geographic structuring is the result of founder effects occurring as a consequence of, and local evolution occurring after, long-distance dispersion. Based on previous studies, the possibility that this could significantly affect the virus biology is not remote.
    Keywords Severe acute respiratory syndrome coronavirus ; amino acid sequences ; founder effect ; genome ; mutation ; phylogeny ; phylogeography ; virology ; viruses ; Africa ; Asia ; Europe ; Pacific Ocean Islands
    Language English
    Dates of publication 2020-11
    Size p. 70-77.
    Publishing place Elsevier Inc.
    Document type Article
    Note NAL-light
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2020.08.010
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 3686: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: Abundant microbes of surface sea waters of the uncharted Engaño Bay at the Atlantic Patagonian Coast: relevance of bacteria-sized photosynthetic eukaryotes

    Giaccardi, Laura I. / Badenas, Misael A. / Jones, Leandro R. / Manrique, Julieta M.

    Aquat Ecol. 2022 Dec., v. 56, no. 4 p.1217-1230

    2022  

    Abstract: Microorganisms play a central role in the structure and function of marine ecosystems. Its vast diversity makes the disentangling of the microbial taxonomic composition an essential task. Engaño Bay, a highly productive temperate region on the Patagonian ...

    Abstract Microorganisms play a central role in the structure and function of marine ecosystems. Its vast diversity makes the disentangling of the microbial taxonomic composition an essential task. Engaño Bay, a highly productive temperate region on the Patagonian Atlantic Coast, constitutes a remote uncharted area. Here, metabarcoding analyses revealed that the microbiome community (cells < 5 µm) of surface water is dominated by a few bacterial taxa along with diverse low frequency groups. A substantial number of sequences of photosynthetic picoeukaryotes (PPE) were also evidenced, yet no cyanobacterial sequences could be observed. Specific PCR-detection of cyanobacteria, monitoring of viruses specific for cyanobacteria and PPE, microbiological isolation, and molecular diet analyses confirmed these findings. Cyanobacteria were PCR detected in three out of thirteen samples, while virological monitoring indicated the presence of PPE viruses and the absence of cyanobacteria phages. Traditional culture methods allowed the isolation of Ostreococcus and Micromonas spp. from samples belonging to warm and cold seasons, respectively. Molecular diet analyses showed that PPE were grazed by nanoplankters and that grazing pressure on PPE was stronger than on bacteria. Phylogenetic characterization of viral sequences indicated the presence of Ostreococcus virus, four Micromonas virus lineages and a divergent clade of Phycodnavirus belonging to no known viral species, pointing out a complex scenario of its hosts. This work characterizes the marine microbiome from a temperate uncharted region at the Southern Hemisphere, demonstrating the prevalence of PPE as primary producers with a complex scenario which warrant further studies.
    Keywords Cyanobacteria ; DNA barcoding ; coasts ; cold ; diet ; eukaryotic cells ; microbiome ; photosynthesis ; phylogeny ; surface water ; taxonomy ; temperate zones ; viruses
    Language English
    Dates of publication 2022-12
    Size p. 1217-1230.
    Publishing place Springer Netherlands
    Document type Article ; Online
    ZDB-ID 1411979-1
    ISSN 1573-5125 ; 1386-2588
    ISSN (online) 1573-5125
    ISSN 1386-2588
    DOI 10.1007/s10452-022-09962-w
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 7664: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  8. Article ; Online: Are ocean currents to slow to counteract SAR11 evolution? A next-generation sequencing, phylogeographic analysis.

    Manrique, Julieta M / Jones, Leandro R

    Molecular phylogenetics and evolution

    2017  Volume 107, Page(s) 324–337

    Abstract: This work set out to shed light on the phylogeography of the SAR11 clade of Alphaproteobacteria, which is probably the most abundant group of heterotrophic bacteria on Earth. In particular, we assessed the degree to which empirical evidence ( ... ...

    Abstract This work set out to shed light on the phylogeography of the SAR11 clade of Alphaproteobacteria, which is probably the most abundant group of heterotrophic bacteria on Earth. In particular, we assessed the degree to which empirical evidence (environmental DNA sequences) supports the concept that SAR11 lineages evolve faster than they are dispersed thus generating vicariant distributions, as predicted by recent simulation efforts. We generated 16S rRNA gene sequences from surface seawater collected at the South West Atlantic Ocean and combined these data with previously published sequences from similar environments from elsewhere. Altogether, these data consisted in about 1e6 reads, from which we generated 355,306 high quality sequences of which 95,318 corresponded to SAR11. Quantitative phylogeographic analyses supported the existence of a spatially explicit distribution of SAR11 species and provided evidence in favor of the idea that dispersal limitations significantly contribute to SAR11 radiation throughout the world's oceans. Likewise, pairwise phylogenetic distances between the communities studied here were significantly correlated with the genetic divergences predicted by a previously proposed neutral model. As discussed in the paper, these findings are compatible with the concept that the ocean surface constitutes a homogeneous environment for SAR11, in agreement with previous experimental data. We discuss the implications of this hypothesis in a global change scenario. This is the first study combining high throughput sequencing and phylogenic analysis to study bacterial phylogeography and reporting a distance decay pattern of phylogenetic distances for bacteria.
    MeSH term(s) Alphaproteobacteria/classification ; Alphaproteobacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Likelihood Functions ; Oceans and Seas ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Water Movements
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2017-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 33610-5
    ISSN 1095-9513 ; 1055-7903
    ISSN (online) 1095-9513
    ISSN 1055-7903
    DOI 10.1016/j.ympev.2016.11.015
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3644: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  9. Article: Effects of Alcohol Withdrawal on Sleep Macroarchitecture and Microarchitecture in Female and Male Rats.

    Jones, Marissa R / Brandner, Adam J / Vendruscolo, Leandro F / Vendruscolo, Janaina C M / Koob, George F / Schmeichel, Brooke E

    Frontiers in neuroscience

    2022  Volume 16, Page(s) 838486

    Abstract: The prevalence of sleep disruptions is higher among people with alcohol use disorder (AUD), particularly during alcohol withdrawal, compared to non-AUD individuals. Although women generally have a higher risk of developing sleep disorders, few studies ... ...

    Abstract The prevalence of sleep disruptions is higher among people with alcohol use disorder (AUD), particularly during alcohol withdrawal, compared to non-AUD individuals. Although women generally have a higher risk of developing sleep disorders, few studies have investigated sex differences in sleep disruptions following chronic alcohol exposure. The present study examined sleep macroarchitecture (time spent asleep or awake and sleep onset latency) and microarchitecture (bout rate and duration and sleep spindle characterization) prior to alcohol vapor exposure (baseline), during acute withdrawal, and through protracted abstinence in female and male rats. Females and males showed reduced time in rapid eye movement (REM) sleep during acute withdrawal, which returned to baseline levels during protracted abstinence. REM sleep onset latency was decreased during protracted abstinence in females only. Furthermore, there was a sex difference observed in overall REM sleep bout rate. Although there were no changes in non-REM sleep time, or to non-REM sleep bout rate or duration, there was an increase in non-REM sleep intra-spindle frequency during acute withdrawal in both females and males. Finally, there was increased wakefulness time and bout duration during acute withdrawal in both females and males. The results demonstrate both macroarchitectural and microarchitectural changes in sleep following chronic alcohol exposure, particularly during acute withdrawal, suggesting the need for therapeutic interventions for sleep disturbances during withdrawal in individuals with AUD. Furthermore, sex differences were observed in REM sleep, highlighting the importance of including both sexes in future alcohol-related sleep studies.
    Language English
    Publishing date 2022-06-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2411902-7
    ISSN 1662-453X ; 1662-4548
    ISSN (online) 1662-453X
    ISSN 1662-4548
    DOI 10.3389/fnins.2022.838486
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article ; Online: Genetic analysis of the invasive alga Didymosphenia geminata in Southern Argentina: Evidence of a Pleistocene origin of local lineages.

    Jones, Leandro R / Manrique, Julieta M / Uyua, Noelia M / Whitton, Brian A

    Scientific reports

    2019  Volume 9, Issue 1, Page(s) 18706

    Abstract: The diatom Didymosphenia geminata has gained notoriety due to the massive growths which have occurred in recent decades in temperate regions. Different explanations have been proposed for this phenomenon, including the emergence of new invasive strains, ... ...

    Abstract The diatom Didymosphenia geminata has gained notoriety due to the massive growths which have occurred in recent decades in temperate regions. Different explanations have been proposed for this phenomenon, including the emergence of new invasive strains, human dispersion and climate change. Despite the fact in Argentina nuisance growths began in about 2010, historical records suggest that the alga was already present before that date. In addition, preliminary genetic data revealed too high a diversity to be explained by a recent invasion. Here, we estimate the divergence times of strains from southern Argentina. We integrate new genetic data and secondary, fossil and geological calibrations into a Penalized Likelihood model used to infer 18,630 plausible chronograms. These indicate that radiation of the lineages in Argentina began during or before the Pleistocene, which is hard to reconcile with the hypothesis that a new variant is responsible for the local mass growths. Instead, this suggests that important features of present distribution could be the result of multiple recent colonizations or the expansion of formerly rare populations. The text explains how these two possibilities are compatible with the hypothesis that recent nuisance blooms may be a consequence of climate change.
    MeSH term(s) Argentina ; Biological Evolution ; Climate Change ; DNA, Mitochondrial/genetics ; Diatoms/genetics ; Ecosystem ; Evolution, Molecular ; Genetic Testing ; Genetic Variation/genetics ; Introduced Species ; Phylogeny ; Rivers
    Chemical Substances DNA, Mitochondrial
    Language English
    Publishing date 2019-12-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-019-55155-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top