scholarly journals Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae

2021 ◽  
Author(s):  
Allison K. Miller ◽  
Jonathon C.O. Mifsud ◽  
Vincenzo A. Costa ◽  
Rebecca M. Grimwood ◽  
Jane Kitson ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Rna Virus ◽  
Bony Fish ◽  
Sequencing Data ◽  
History Of ◽  
Entire History ◽  
Vertebrate Hosts ◽  
Patterns And Processes ◽  
Jawless Fish

The Nidovirales comprise a genetically diverse group of positive-sense single-stranded RNA virus families that infect a range of invertebrate and vertebrate hosts. Recent metagenomic studies have identified nido-like virus sequences, particularly those related to the Coronaviridae, in a range of aquatic hosts including fish, amphibians and reptiles. We sought to identify additional members of the Coronaviridae in both bony and jawless fish through a combination of total RNA sequencing (meta-transcriptomics) and data mining of published RNA sequencing data, and from this reveal more of the long-term patterns and processes of coronavirus evolution. Accordingly, we identified a number of divergent viruses that fell within the Letovirinae subfamily of the Coronaviridae, including those in a jawless fish - the pouched lamprey. By mining fish transcriptome data we identified additional virus transcripts matching these viruses in bony fish from both marine and freshwater environments. These new viruses retained sequence conservation in the RNA-dependant RNA polymerase across the Coronaviridae, but formed a distinct and diverse phylogenetic group. Although there are broad-scale topological similarities between the phylogenies of the major groups of coronaviruses and their vertebrate hosts, the evolutionary relationships of viruses within the Letovirinae does not mirror that of their hosts. For example, the coronavirus found in the pouched lamprey fell within the phylogenetic diversity of bony fish letoviruses, indicative of past host switching events. Hence, despite possessing a phylogenetic history that likely spans the entire history of the vertebrates, coronavirus evolution has been characterised by relatively frequent cross-species transmission, particularly in hosts that reside in aquatic habitats.

scholarly journals Discovery and Characterization of Actively Replicating DNA and Retro-Transcribing Viruses in Lower Vertebrate Hosts Based on RNA Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1042
Author(s):  
Xin-Xin Chen ◽  
Wei-Chen Wu ◽  
Mang Shi
Keyword(s):  
Rna Sequencing ◽  
Rna Viruses ◽  
Rna Virus ◽  
Acute Infection ◽  
Sufficient Information ◽  
Lower Vertebrate ◽  
Diverse Range ◽  
New Findings ◽  
Active Transcription ◽  
Vertebrate Hosts

In a previous study, a metatranscriptomics survey of RNA viruses in several important lower vertebrate host groups revealed huge viral diversity, transforming the understanding of the evolution of vertebrate-associated RNA virus groups. However, the diversity of the DNA and retro-transcribing viruses in these host groups was left uncharacterized. Given that RNA sequencing is capable of revealing viruses undergoing active transcription and replication, we collected previously generated datasets associated with lower vertebrate hosts, and searched them for DNA and retro-transcribing viruses. Our results revealed the complete genome, or “core gene sets”, of 18 vertebrate-associated DNA and retro-transcribing viruses in cartilaginous fishes, ray-finned fishes, and amphibians, many of which had high abundance levels, and some of which showed systemic infections in multiple organs, suggesting active transcription or acute infection within the host. Furthermore, these new findings recharacterized the evolutionary history in the families Hepadnaviridae, Papillomaviridae, and Alloherpesviridae, confirming long-term virus–host codivergence relationships for these virus groups. Collectively, our results revealed reliable and sufficient information within metatranscriptomics sequencing to characterize not only RNA viruses, but also DNA and retro-transcribing viruses, and therefore established a key methodology that will help us to understand the composition and evolution of the total “infectome” within a diverse range of vertebrate hosts.

scholarly journals The effect of methanol fixation on single-cell RNA sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xinlei Wang ◽  
Lei Yu ◽  
Angela Ruohao Wu
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Gc Content ◽  
Sequencing Data ◽  
Rna Integrity ◽  
Construction Methods ◽  
Single Cell Rna Sequencing ◽  
Health And Disease ◽  
Fixation Protocol

Abstract Background Single-cell RNA sequencing (scRNA-seq) has led to remarkable progress in our understanding of tissue heterogeneity in health and disease. Recently, the need for scRNA-seq sample fixation has emerged in many scenarios, such as when samples need long-term transportation, or when experiments need to be temporally synchronized. Methanol fixation is a simple and gentle method that has been routinely applied in scRNA-sEq. Yet, concerns remain that fixation may result in biases which may change the RNA-seq outcome. Results We adapted an existing methanol fixation protocol and performed scRNA-seq on both live and methanol fixed cells. Analyses of the results show methanol fixation can faithfully preserve biological related signals, while the discrepancy caused by fixation is subtle and relevant to library construction methods. By grouping transcripts based on their lengths and GC content, we find that transcripts with different features are affected by fixation to different degrees in full-length sequencing data, while the effect is alleviated in Drop-seq result. Conclusions Our deep analysis reveals the effects of methanol fixation on sample RNA integrity and elucidates the potential consequences of using fixation in various scRNA-seq experiment designs.

scholarly journals Validation of bioactive components from traditional Chinese medicine for lifespan extension

2021 ◽  
Author(s):  
Chin-Chuan Chen ◽  
Tong-Hong Wang ◽  
Wei-Che Tseng ◽  
Yann-Lii Leu ◽  
Chi-Yuan Chen ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Lifespan Extension ◽  
Sequencing Data ◽  
Risk Of Death ◽  
Age Related ◽  
Pure Compounds ◽  
History Of ◽  
Enrichment Program

Abstract In long history of traditional Chinese medicine (TCM), some single herb and complex formulas have been recorded to increase lifespan in TCM pharmacopeia. However, the mechanism of these TCMs increasing lifespan is insufficient. Here, we collected a list of TCMs from pharmacopeias for lifespan extension. By utilizing the mother enrichment program (MEP), we systematically screened these TCMs and identified a single TCM herb, Psoralea corylifolia, that increases lifespan in Saccharomyces cerevisiae. Next, twenty-two pure compounds were isolated from P. corylifolia, and one of the compounds, corylin, was shown to extend the replicative lifespan (RLS) by targeting the Gtr1 protein. Furthermore, in HUVECs, the RNA sequencing data showed that corylin ameliorated cellular senescence. Finally, corylin reduced the risk of death of mice fed a high-fat diet. Taken together, these findings demonstrate that corylin has long-term benefits for longevity and could be a potential treatment for age-related disease.

scholarly journals Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes

2020 ◽  
Author(s):  
Spyros Lytras ◽  
Gloria Arriagada ◽  
Robert J. Gifford
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Dna Viruses ◽  
History Of ◽  
Selective Forces ◽  
Cenozoic Era ◽  
Vertebrate Hosts ◽  
New Perspective ◽  
Animal Genomes

ABSTRACTHepadnaviruses (family Hepadnaviviridae) are reverse-transcribing animal viruses that infect vertebrates. Vertebrate genomes contain DNA sequences derived from ancient hepadnaviruses, and these ‘endogenous hepatitis B viruses’ (eHBVs) reveal aspects of the long-term coevolutionary relationship between hepadnaviruses and their vertebrate hosts. Here, we use a novel, data-oriented approach to recover and analyse the complete repertoire of eHBV elements in published animal genomes. We show that germline incorporation of hepadnaviruses is exclusive to a single vertebrate group (Sauria) and that the eHBVs contained in saurian genomes represent a far greater diversity of hepadnaviruses than previously recognised. Through in-depth characterisation of eHBV elements we establish the existence of four distinct subgroups within the genus Avihepadnavirus and trace their evolution through the Cenozoic Era. Furthermore, we provide a completely new perspective on hepadnavirus evolution by showing that the metahepadnaviruses (genus Metahepadnavirus) originated >300 million years ago in the Paleozoic Era, and has historically infected a broad range of vertebrates. We also show that eHBVs have been intra-genomically amplified in some saurian lineages, and that eHBVs located at approximately equivalent genomic loci have been acquired in entirely distinct germline integration events. These findings indicate that selective forces have favoured the accumulation of hepadnaviral sequences at specific loci in the saurian germline. Our investigation provides a range of new insights into the long-term evolutionary history of reverse-transcribing DNA viruses and demonstrates that germline incorporation of hepadnaviruses has played an important role in shaping the evolution of saurian genomes.

scholarly journals SOME ASPECTS OF THE ARCHIVAL INDUSTRY OF KAZAKHSTAN

2021 ◽  
Vol 68 (1) ◽  
Author(s):  
T. Makanbaev ◽  
◽  
G. Seksenbayeva ◽  
Keyword(s):  
Twentieth Century ◽  
Political System ◽  
The State ◽  
Soviet Period ◽  
The Political ◽  
Cultural Life ◽  
History Of ◽  
Entire History ◽  
Party Ideology

The twentieth century turned out to be the most eventful for the history of archiving, and for the history of Kazakhstan as a whole. This has profoundly affected all aspects of the state, political, social, economic and cultural life. Wars, revolutions, changes in the political system, the restoration and collapse of the USSR - this is how the twentieth century began and ended. This article is an attempt to understand the course and certain feature of the long-term archival process in Kazakhstan. The entire history of archives of the Soviet period is closely intertwined with the history of the political system of the state. The history of archives is related to the monopoly rule of one-party ideology, with administrative pressure in the spiritual sphere of man, including pressure over archives. A new milestone in the development of archiving took place after the collapse of the USSR, so the archive system became independent. Independent Kazakhstan has carried out a number of reforms to democratize archival activities. As a result of these changes, a new archive management system was formed. Archives become part of the country's cultural heritage. The article focuses on identifying the leading trends in the formation of archives and key problems in the domestic archival science. Less attention is paid to the history of individual archives, since in general this is fully reflected in monographs, textbooks and numerous articles of Kazakhstani authors.

scholarly journals Effect of methanol fixation on single-cell RNA sequencing data

2020 ◽  
Author(s):  
Xinlei Wang ◽  
Lei Yu ◽  
Angela Wu
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Gc Content ◽  
Sequencing Data ◽  
Rna Integrity ◽  
Construction Methods ◽  
Single Cell Rna Sequencing ◽  
Health And Disease ◽  
Fixation Protocol

AbstractSingle-cell RNA sequencing (scRNA-seq) has led to remarkable progress in our understanding of tissue heterogeneity in health and disease. Recently, the need for scRNA-seq sample fixation has emerged in many scenarios, such as when samples need long-term transportation, or when experiments need to be temporally synchronized. Methanol fixation is a simple and gentle method that has been routinely applied in scRNA-seq. Yet, concerns remain that fixation may result in biases which may change the RNA-seq outcome. We adapted an existing methanol fixation protocol and performed scRNA-seq on both live and methanol fixed cells. Analyses of the results show methanol fixation can faithfully preserve biological related signals, while the discrepancy caused by fixation is subtle and relevant to library construction methods. By grouping transcripts based on their lengths and GC content, we find that transcripts with different features are affected by fixation to different degrees in full-length sequencing data, while the effect is alleviated in Drop-seq result. Our deep analysis reveals the effects of methanol fixation on sample RNA integrity and elucidates the potential consequences of using fixation in various scRNA-seq experiment designs.

scholarly journals Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaofeng Xu ◽  
Jinlong Bei ◽  
Yibo Xuan ◽  
Jiayuan Chen ◽  
Defu Chen ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Genome Sequence ◽  
Small Rna ◽  
Rna Viruses ◽  
Rna Virus ◽  
Full Length ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Geographical Regions ◽  
Full Length Genome

Abstract Background In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick virus (KITV), and Guangxi tick virus (GXTV)—evolutionarily related to MGTV—were reported. Results In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China’s Yunnan Province in 2016. We obtained the full-length genome sequence of this MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) and recommended it for its inclusion in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV. Phylogenetic analysis showed that MGTV, JMTV, KITV and GXTV are monophyletic and belong to a MGTV group. Furthermore, this MGTV group of viruses may be phylogenetically related to geographical regions that were formerly part of the supercontinents Gondwana and Laurasia. Conclusions To the best of our knowledge, this is the first study in which 5′ and 3′ sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses. We also demonstrated the feasibility of using the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks. MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In addition, MGTV can be used as novel species for studies in phylogeography.

Biodiversity dynamics and environmental occupancy of fossil azooxanthellate and zooxanthellate scleractinian corals

Paleobiology ◽  
2015 ◽  
Vol 41 (3) ◽  
pp. 402-414 ◽  
Author(s):  
Wolfgang Kiessling ◽  
Ádám T. Kocsis
Keyword(s):  
Deep Water ◽  
Scleractinian Corals ◽  
Nutrient Concentrations ◽  
Turnover Rates ◽  
Extinction Rates ◽  
Morphological Criteria ◽  
Anoxic Events ◽  
History Of ◽  
Entire History

AbstractScleractinian corals have two fundamentally different life strategies, which can be inferred from morphological criteria in fossil material. In the non-photosymbiotic group nutrition comes exclusively from heterotrophic feeding, whereas the photosymbiotic group achieves a good part of its nutrition from algae hosted in the coral’s tissue. These ecologic differences arose early in the evolutionary history of corals but with repeated evolutionary losses and presumably also gains of symbiosis since then. We assessed the biodiversity dynamics and environmental occupancy of both ecologic groups to identify times when the evolutionary losses of symbiosis as inferred from molecular analyses might have occurred and if these can be linked to environmental change. Two episodes are likely: The first was in the mid-Cretaceous when non-symbiotic corals experienced an origination pulse and started to become more common in deeper, non-reef habitats and on siliciclastic substrates initiating a long-term offshore trend in occupancy. The second was around the Cretaceous/Paleogene boundary with another origination pulse and increased occupancy of deep-water settings in the non-symbiotic group. Environmental factors such as rapid global warming associated with mid-Cretaceous anoxic events and increased nutrient concentrations in Late Cretaceous–Cenozoic deeper waters are plausible mechanisms for the shift. Turnover rates and durations are not significantly different between the two ecologic groups when compared over the entire history of scleractinians. However, the deep-water shift of non-symbiotic corals was accompanied by reduced extinction rates, supporting the view that environmental occupancy is a prominent driver of evolutionary rates.

Space and time in granite plutonism

1981 ◽  
Vol 301 (1461) ◽  
pp. 321-336 ◽  
Keyword(s):  
Alkaline Magmatism ◽  
Calc Alkaline ◽  
Magma Generation ◽  
History Of ◽  
Minor Significance ◽  
Granitoid Rocks ◽  
Entire History ◽  
Refractory Mineral ◽  
Ocean Lithosphere

Granitic suites formed in the last 2500 Ma are either calc-alkaline or, less commonly, alkalic. The space-time trends of granitoid rocks from modern compressional arcs include variations towards more silicic and potassic products. But even the most ‘mature’ magmas of these arcs have Fe/Mg ratios near to 1, in contrast with the strongly iron-enriched alkalic suites that characterize zones of crustal extension. Both calc-alkaline and alkalic suites are mainly mantle-derived; they evolved, respectively, from tholeiitic and alkali basalt parental magmas which have been subject, in most examples, to a two-stage fractionation history. Other factors that may influence the evolution of these parental magmas include, first, the addition of variable, but minor, amounts of crustal melt and, secondly, the persistence of refractory mineral phases in the zone of melting. Contributions from subducted continental detritus are thought to be of minor significance. A long-term trend, over the entire history of the crust from more sodic to more potassic calc-alkaline magmatism may reflect the declining importance of subducted ocean lithosphere in magma generation and the increasing role of the overlying volatile-fluxed mantle wedge. This trend and, in particular, the widespread development of alkalic granite suites in mid-Proterozoic times, may be linked to the declining vigour of tectonic and associated magmatic processes during the Earth’s history. These alkalic suites may indicate a period when the continental lithosphere had become stable enough to resist fragmentation, leading to intracontinental ‘rift and swell’ zones of magmatism. In some cases, new plate cycles, with more normal calcalkaline igneous rocks, seem to have occurred in the same zones. Although much of the evidence favours the operation of plate tectonic and subduction processes in magma generation during Archaean and early Proterozoic times, this link cannot be taken as proved except for the last ca . 1000 Ma.

scholarly journals Effect of Methanol Fixation on Single-Cell RNA Sequencing Data

2020 ◽  
Author(s):  
Xinlei Wang ◽  
Lei Yu ◽  
Angela Ruohao Wu
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Gc Content ◽  
Sequencing Data ◽  
Rna Integrity ◽  
Construction Methods ◽  
Single Cell Rna Sequencing ◽  
Health And Disease ◽  
Fixation Protocol

Abstract Background: Single-cell RNA sequencing (scRNA-seq) has led to remarkable progress in our understanding of tissue heterogeneity in health and disease. Recently, the need for scRNA-seq sample fixation has emerged in many scenarios, such as when samples need long-term transportation, or when experiments need to be temporally synchronized. Methanol fixation is a simple and gentle method that has been routinely applied in scRNA-seq. Yet, concerns remain that fixation may result in biases which may change the RNA-seq outcome. Results: We adapted an existing methanol fixation protocol and performed scRNA-seq on both live and methanol fixed cells. Analyses of the results show methanol fixation can faithfully preserve biological related signals, while the discrepancy caused by fixation is subtle and relevant to library construction methods. By grouping transcripts based on their lengths and GC content, we find that transcripts with different features are affected by fixation to different degrees in full-length sequencing data, while the effect is alleviated in Drop-seq result.Conclusions: Our deep analysis reveals the effects of methanol fixation on sample RNA integrity and elucidates the potential consequences of using fixation in various scRNA-seq experiment designs.

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