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16 results for “marine viruses”
Supporting trees and alignments for the publication: Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome
<div class="page"> <div class="layoutArea"> <div class="column"> <p>Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are relatively understudied outside disease settings. Here, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogues and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of new phyla<span> </span><em>"Taraviricota"</em><span>, </span>a missing link in early RNA virus evolution, and<span> </span><em>"Arctiviricota"</em><span> </span>are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.</p> </div> </div> </div>
Emergence and radiation of distemper viruses in terrestrial and marine mammals - Input files, bash and R codes for analysing PDV and CDV sequence data
<p><span>Canine distemper virus (CDV) and phocine distemper virus (PDV) are major pathogens to terrestrial and marine mammals. Yet little is known about the timing and geographical origin of distemper viruses and to what extent it was influenced by environmental change and human activities. To address this, we i) performed the first comprehensive time-calibrated phylogenetic analysis of the two distemper viruses; ii) mapped distemper antibody and virus detection data from marine mammals collected between 1972-2018; iii) and compiled historical reports on distemper dating back to the 18<sup>th</sup> century. We find that CDV and PDV diverged in the early 17<sup>th</sup> century. Modern CDV strains last shared a common ancestor in the 19<sup>th</sup> century with a marked radiation during the 1930s-50s. Modern PDV strains are of more recent origin, diverging in the 1970s-80s. Based on the compiled information on distemper distribution, the diverse host range of CDV and basal phylogenetic placement of terrestrial morbilliviruses, we hypothesize a terrestrial CDV-like ancestor giving rise to PDV in the North Atlantic. Moreover, given the estimated timing of distemper origin and radiation, we hypothesize a prominent role of environmental change such as the Little Ice Age, and human activities like globalisation and war in distemper virus evolution. </span></p>
Functional profiling and evolutionary analysis of a marine microalgal virus pangenome
<p>Phycodnaviridae are large double-stranded DNA viruses, which facilitate studies of host–virus interactions and co-evolution due to their prominence in algal infection and their role in the life cycle of algal blooms. However, the genomic interpretation of these viruses is hampered by a lack of functional information, stemming from the surprising number of hypothetical genes of unknown function. It is also unclear how many of these genes are widely shared within the clade. Using one of the most extensively characterized genera, <em>Coccolithovirus</em>, as a case study, we combined pangenome analysis, multiple functional annotation tools, AlphaFold structural modeling, and literature analysis to compare the core and accessory pangenome and assess support for novel functional predictions. We determined that the <em>Coccolithovirus</em> pangenome shares 30% of its genes with all 14 strains, making up the core. Notably, 34% of its genes were found in at most three strains. Core genes were enriched in early expression based on a transcriptomic dataset of <em>Coccolithovirus</em> EhV-201 algal infection, were more likely to be similar to host proteins than the non-core set, and were more likely to be involved in vital functions such as replication, recombination, and repair. In addition, we generated and collated annotations for the EhV representative EhV-86 from 12 different annotation sources, building up information for 142 previously hypothetical and putative membrane proteins. AlphaFold was further able to predict structures for 204 EhV-86 proteins with a modelling accuracy of good–high. These functional clues, combined with generated AlphaFold structures, provide a foundational framework for the future characterization of this model genus (and other giant viruses) and a further look into the evolution of the <em>Coccolithovirus</em> proteome.</p>
Functional profiling and evolutionary analysis of a marine microalgal virus pangenome
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Emergence and radiation of distemper viruses in terrestrial and marine mammals - Input files, bash and R codes for analysing PDV and CDV sequence data
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Supporting trees and alignments for the publication: Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome
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Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment
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Proton-transporting heliorhodopsins from marine giant viruses
<p><span>Rhodopsins convert light into signals and energy in animals and microbes. Heliorhodopsins (HeRs), a recently discovered new rhodopsin family, are widely present in archaea, bacteria, unicellular eukaryotes, and giant viruses, but their function remains unknown. Here we report that a viral HeR from <em>Emiliania huxleyi</em> virus 202 (V2HeR3) is a light-activated proton transporter. V2HeR3 absorbs blue-green light, and the active intermediate contains the deprotonated retinal Schiff base. Site-directed mutagenesis study revealed that E191 in TM6 constitutes the gate together with the retinal Schiff base. E205 and E215 form a proton accepting group of the Schiff base, whose mutations converted the protein into an outward proton pump. Three environmental viral HeRs from the same group, as well as a more distantly related HeR exhibited similar proton-transport activity, indicating that HeR functions might be diverse similarly to type-1 microbial rhodopsins. Some strains of <em>E. huxleyi</em> contain one HeR that is related to the viral HeRs, while its viruses <em>Eh</em>V-201 and <em>Eh</em>V-202 contain two and three HeRs, respectively. Except for V2HeR3 from <em>Eh</em>V-202, none of these proteins exhibit ion-transport activity. Thus, when expressed in the <em>E. huxleyi</em> cell membranes, only V2HeR3 has the potential to depolarize the host cells by light, possibly to overcome the host defense mechanisms or to prevent superinfection. The neuronal activity generated by V2HeR3 suggests that it can potentially be used as an optogenetic tools, like type-1 microbial rhodopsins.</span></p>
Supplementary data products for Ha et al. 'Assessing the biogeography of marine giant viruses in four oceanic transects'.
<p>Processed data products for Ha et al., "<strong>Assessing the biogeography of marine giant viruses in four oceanic transects</strong>".</p>
Proton-transporting heliorhodopsins from marine giant viruses
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Data from: Virus resistance is not costly in a marine alga evolving under multiple environmental stressors
Viruses are important evolutionary drivers of host ecology and evolution. The marine picoplankton Ostreococcus tauri has three known resistance types that arise in response to infection with the Phycodnavirus OtV5: susceptible cells (S) that lyse following viral entry and replication; resistant cells (R) that are refractory to viral entry; and resistant producers (RP) that do not all lyse but maintain some viruses within the population. To test for evolutionary costs of maintaining antiviral resistance, we examined whether O. tauri populations composed of each resistance type differed in their evolutionary responses to several environmental drivers (lower light, lower salt, lower phosphate and a changing environment) in the absence of viruses for approximately 200 generations. We did not detect a cost of resistance as measured by life-history traits (population growth rate, cell size and cell chlorophyll content) and competitive ability. Specifically, all R and RP populations remained resistant to OtV5 lysis for the entire 200-generation experiment, whereas lysis occurred in all S populations, suggesting that resistance is not costly to maintain even when direct selection for resistance was removed, or that there could be a genetic constraint preventing return to a susceptible resistance type. Following evolution, all S population densities dropped when inoculated with OtV5, but not to zero, indicating that lysis was incomplete, and that some cells may have gained a resistance mutation over the evolution experiment. These findings suggest that maintaining resistance in the absence of viruses was not costly.
Data from: Virus resistance is not costly in a marine alga evolving under multiple environmental stressors
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Methylation data to study immune response to SARS-CoV-2 virus infection in COVID-19 Health Action Response for Marines (CHARM) study
GEO Series GSE219037. Homo sapiens. 553 samples. Type: Methylation profiling by genome tiling array.
RNA-seq data to study immune response to SARS-CoV-2 virus infection in COVID-19 Health Action Response for Marines (CHARM) study
GEO Series GSE198449. Homo sapiens. 1858 samples. Type: Expression profiling by high throughput sequencing.
Genome-Wide Expression Dynamics of a Marine Virus and its Host during Lytic Infection
GEO Series GSE8382. Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus phage P-SSM4; Tiamatvirus PSSP7; Prochlorococcus marinus str. MIT 9313. 45 samples. Type: Expression profiling by array.
Transcriptomic responses to iron bioavailability from virus-mediated lysates in marine prokaryotes
GEO Series GSE166618. Dokdonia sp. Dokd-P16. 120 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.