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  • 1
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    A multi-decade record of high-quality fCO2 data in version 3 of the Surface Ocean CO2 Atlas (SOCAT) (2016)
    Copernicus Publications
    In:  EPIC3Earth System Science Data Discussions, Copernicus Publications, pp. 1-55, ISSN: 1866-3591
    Details
    Publication Date: 2016-05-26
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , notRev
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    PAPER (OA)
  • 2
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    Evolutionary genomics of the cold-Adapted diatom Fragilariopsis cylindrus (2017)
    Nature Research
    In:  Nature, 541 (7638). pp. 536-540.
    Details
    Publication Date: 2021-01-08
    Description: The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/nature20803
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 3
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    Considering the Role of Adaptive Evolution in Models of the Ocean and Climate System (2019)
    AGU (American Geophysical Union)
    In:  Journal of Advances in Modeling Earth Systems, 11 (11). pp. 3343-3361.
    Details
    Publication Date: 2022-01-31
    Description: Numerical models have been highly successful in simulating global carbon and nutrient cycles in today's ocean, together with observed spatial and temporal patterns of chlorophyll and plankton biomass at the surface. With this success has come some confidence in projecting the century-scale response to continuing anthropogenic warming. There is also increasing interest in using such models to understand the role of plankton ecosystems in past oceans. However, today's marine environment is the product of billions of years of continual evolution—a process that continues today. In this paper, we address the questions of whether an assumption of species invariance is sufficient, and if not, under what circumstances current model projections might break down. To do this, we first identify the key timescales and questions asked of models. We then review how current marine ecosystem models work and what alternative approaches are available to account for evolution. We argue that for timescales of climate change overlapping with evolutionary timescales, accounting for evolution may to lead to very different projected outcomes regarding the timescales of ecosystem response and associated global biogeochemical cycling. This is particularly the case for past extinction events but may also be true in the future, depending on the eventual degree of anthropogenic disruption. The discipline of building new numerical models that incorporate evolution is also hugely beneficial in itself, as it forces us to question what we know about adaptive evolution, irrespective of its quantitative role in any specific event or environmental changes.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1029/2018MS001452
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 4
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    Optimizing sparse sequencing of single cells for highly multiplex copy number profiling [METHOD] (2015)
    Cold Spring Harbor Laboratory Press
    Details
    Publication Date: 2015-05-02
    Description: Genome-wide analysis at the level of single cells has recently emerged as a powerful tool to dissect genome heterogeneity in cancer, neurobiology, and development. To be truly transformative, single-cell approaches must affordably accommodate large numbers of single cells. This is feasible in the case of copy number variation (CNV), because CNV determination requires only sparse sequence coverage. We have used a combination of bioinformatic and molecular approaches to optimize single-cell DNA amplification and library preparation for highly multiplexed sequencing, yielding a method that can produce genome-wide CNV profiles of up to a hundred individual cells on a single lane of an Illumina HiSeq instrument. We apply the method to human cancer cell lines and biopsied cancer tissue, thereby illustrating its efficiency, reproducibility, and power to reveal underlying genetic heterogeneity and clonal phylogeny. The capacity of the method to facilitate the rapid profiling of hundreds to thousands of single-cell genomes represents a key step in making single-cell profiling an easily accessible tool for studying cell lineage.
    Electronic ISSN: 1549-5469
    Topics: Biology , Medicine
    Published by Cold Spring Harbor Laboratory Press
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  • 5
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    Generation and characterization of a trackable plant-made influenza H5 virus-like particle (VLP) containing enhanced green fluorescent protein (eGFP) [Research Communication] (2015)
    The Federation of American Societies for Experimental Biology (FASEB)
    Details
    Publication Date: 2015-09-02
    Description: Medicago, Inc. has developed an efficient virus-like particle (VLP) vaccine production platform using the Nicotiana benthamiana expression system, and currently has influenza-based products targeting seasonal/pandemic hemagglutinin (HA) proteins in advanced clinical trials. We wished to generate a trackable HA-based VLP that would allow us to study both particle assembly in plants and VLP interactions within the mammalian immune system. To this end, a fusion protein was designed, composed of H5 (from influenza A/Indonesia/05/2005 [H5N1]) with enhanced green fluorescent protein (eGFP). Expression of H5-eGFP in N. benthamiana produced brightly fluorescent ~160 nm particles resembling H5-VLPs. H5-eGFP-VLPs elicited anti-H5 serologic responses in mice comparable to those elicited by H5-VLPs in almost all assays tested (hemagglutination inhibition/IgG(total)/IgG1/IgG2b/IgG2a:IgG1 ratio), as well as a superior anti-GFP IgG response (mean optical density = 2.52 ± 0.16 sem ) to that elicited by soluble GFP (mean optical density = 0.12 ± 0.06 sem ). Confocal imaging of N. benthamiana cells expressing H5-eGFP displayed large fluorescent accumulations at the cell periphery, and draining lymph nodes from mice given H5-eGFP-VLPs via footpad injection demonstrated bright fluorescence shortly after administration (10 min), providing proof of concept that the H5-eGFP-protein/VLPs could be used to monitor both VLP assembly and immune trafficking. Given these findings, this novel fluorescent reagent will be a powerful tool to gain further fundamental insight into the biology of influenza VLP vaccines.—Young, K. R., Arthus-Cartier, G., Yam, K. K., Lavoie, P.-O., Landry, N., D’Aoust, M.-A., Vézina, L.-P., Couture, M. M.-J., Ward, B. J. Generation and characterization of a trackable plant-made influenza H5 virus-like particle (VLP) containing enhanced green fluorescent protein (eGFP).
    Print ISSN: 0892-6638
    Electronic ISSN: 1530-6860
    Topics: Biology
    Published by The Federation of American Societies for Experimental Biology (FASEB)
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  • 6
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    Marine mixotrophy increases ecological efficiency [Environmental Sciences] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-03-16
    Description: Mixotrophic plankton, which combine the uptake of inorganic resources and the ingestion of living prey, are ubiquitous in marine ecosystems, but their integrated biogeochemical impacts remain unclear. We address this issue by removing the strict distinction between phytoplankton and zooplankton from a global model of the marine plankton food web....
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    Relationship of secondhand smoke exposure with sociodemographic factors and smoke-free legislation in the European Union (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-24
    Description: Background : To explore whether exposure to secondhand smoke (SHS) among non-smokers in the European Union (EU) showed any association with sociodemographic factors and/or the extent of national tobacco control policies. Methods : A secondary analysis was performed on data from 26 751 individuals ≥15 years old from 27 EU member states (EU MS), collected during the 2012 Special Eurobarometer survey (wave 77.1). Respondents were asked whether they had been exposed to SHS in eating or drinking establishments during the past 6 months, and/or in their workplace. Data on smoke-free policies were extracted from the European Tobacco Control Status Report and the European Tobacco Control Scale (TCS) in 2013. Results : In total, 29.0% of non-smoking participants reported being exposed to SHS in indoor areas. Males (vs. females) as well as individuals with difficulties to pay bills (vs. those with no difficulties), had significantly greater odds of being exposed to SHS in bars, restaurants and workplaces. For every unit increase of a country’s score on the Smoke-free Component of the TCS (indicating greater adherence to smoke-free legislations) the odds ratio of reporting exposure to SHS was 0.82 in bars, 0.85 in restaurants and 0.94 in workplaces. Conclusions : Differences in exposure to SHS clearly exist between and within EU MS, despite the fact that they all have signed the Framework Convention on Tobacco Control, with the burden found to disproportionally affect younger people and individuals with financial difficulties. Moreover, enforcement of smoke-free legislation was inversely associated with SHS exposure, highlighting the importance of enforcing comprehensive smoking bans.
    Print ISSN: 1101-1262
    Electronic ISSN: 1464-360X
    Topics: Medicine
    Published by Oxford University Press
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  • 8
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    Vaccinia Virus Phospholipase Protein F13 Promotes Rapid Entry of Extracellular Virions into Cells [Structure and Assembly] (2018)
    The American Society for Microbiology (ASM)
    Details
    Publication Date: 2018-05-15
    Description: The vaccinia virus protein F13, encoded by the F13L gene, is conserved across the subfamily Chordopoxvirinae and is critical among orthopoxviruses to produce the wrapped form of virus that is required for cell-to-cell spread. F13 is the major envelope protein on the membrane of extracellular forms of virus; however, it is not known if F13 is required in steps postwrapping. In this report, we utilize two temperature-sensitive vaccinia virus mutants from the Condit collection of temperature-sensitive viruses whose small plaque phenotypes have been mapped to the F13L gene. Despite the drastic reduction in plaque size, the temperature-sensitive viruses were found to produce levels of extracellular virions similar to those of the parental strain, Western Reserve (WR), at the permissive and nonpermissive temperatures, suggesting that they are not defective in extracellular virion formation. Analyses of extracellular virions produced by one temperature-sensitive mutant found that those produced at the nonpermissive temperature had undetectable levels of F13 and bound cells with efficiency similar to that of WR but displayed delayed cell entry kinetics. Additionally, low-pH treatment of cells bound by extracellular virions produced at the nonpermissive temperature by the temperature-sensitive reporter virus was unable to overcome a block in infection by bafilomycin A1, suggesting that these virions display increased resistance to dissolution of the extracellular virion envelope. Taken together, our results suggest that F13 plays a role both in the formation of extracellular virions and in the promotion of their rapid entry into cells by enhancing the sensitivity of the membrane to acid-induced dissolution. IMPORTANCE Vaccinia virus (VACV) is an orthopoxvirus and produces two infectious forms, mature virions (MV) and extracellular virions (EV). EV are derived from MV and contain an additional membrane that must first be removed prior to cell entry. F13 is critical for the formation of EV, but a postenvelopment role has not been described. Here, two temperature-sensitive VACV mutants whose deficiencies were previously mapped to the F13L locus are characterized. Both viruses produced EV at the nonpermissive temperature at levels similar to those of a virus that has F13L, yet they had a small plaque phenotype and rate of spread similar to that of an F13L deletion virus. F13 was undetectable on the EV membrane at the nonpermissive temperature, and these EV exhibited delayed cell entry kinetics compared to EV containing F13. This study is the first to conclusively demonstrate a novel role for F13 in cell entry of the EV form of the virus.
    Print ISSN: 0022-538X
    Electronic ISSN: 1098-5514
    Topics: Medicine
    Published by The American Society for Microbiology (ASM)
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  • 9
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    Cordilleran Ice Sheet mass loss preceded climate reversals near the Pleistocene Termination (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-11-10
    Description: The Cordilleran Ice Sheet (CIS) once covered an area comparable to that of Greenland. Previous geologic evidence and numerical models indicate that the ice sheet covered much of westernmost Canada as late as 12.5 thousand years ago (ka). New data indicate that substantial areas throughout westernmost Canada were ice free prior to 12.5 ka and some as early as 14.0 ka, with implications for climate dynamics and the timing of meltwater discharge to the Pacific and Arctic oceans. Early Bølling-Allerød warmth halved the mass of the CIS in as little as 500 years, causing 2.5 to 3.0 meters of sea-level rise. Dozens of cirque and valley glaciers, along with the southern margin of the CIS, advanced into recently deglaciated regions during the Bølling-Allerød and Younger Dryas.
    Keywords: Atmospheric Science
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Adaptation to flood risk – results of international paired flood event studies (2017)
    American Geophysical Union (AGU)
    Details
    Publication Date: 2017-07-27
    Description: As flood impacts are increasing in large parts of the world, understanding the primary drivers of changes in risk is essential for effective adaptation. To gain more knowledge on the basis of empirical case studies, we analyze eight paired floods, i.e. consecutive flood events that occurred in the same region, with the second flood causing significantly lower damage. These success stories of risk reduction were selected across different socio-economic and hydro-climatic contexts. The potential of societies to adapt is uncovered by describing triggered societal changes, as well as formal measures and spontaneous processes that reduced flood risk. This novel approach has the potential to build the basis for an international data collection and analysis effort to better understand and attribute changes in risk due to hydrological extremes in the framework of the IAHSs Panta Rhei initiative. Across all case studies, we find that lower damage caused by the second event was mainly due to significant reductions in vulnerability, e.g. via raised risk awareness, preparedness and improvements of organizational emergency management. Thus, vulnerability reduction plays an essential role for successful adaptation. Our work shows that there is a high potential to adapt, but there remains the challenge to stimulate measures that reduce vulnerability and risk in periods in which extreme events do not occur. Index Terms 1821 Floods (4303); 4327 Resilience; 4328 Risk; 4330 Vulnerability; 4339 Disaster mitigation
    Electronic ISSN: 2328-4277
    Topics: Geosciences
    Published by American Geophysical Union (AGU)
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