scholarly journals Genetic Characterization of Cupped Oyster Resources in Europe Using Informative Single Nucleotide Polymorphism (SNP) Panels

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 451
Author(s):  
Sylvie Lapègue ◽  
Serge Heurtebise ◽  
Florence Cornette ◽  
Erwan Guichoux ◽  
Pierre-Alexandre Gagnaire
Keyword(s):  
Severe Disease ◽  
Interspecific Gene Flow ◽  
Crassostrea Angulata ◽  
The Pacific ◽  
Genetic Diversity And Structure ◽  
Cupped Oyster ◽  
Evolutionary Genomic ◽  
Genome Divergence ◽  
Snp Panels

The Pacific oyster, Crassostrea gigas, was voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry, following a severe disease outbreak. Since then, the two species have been in contact in southern Europe and, therefore, have the potential to exchange genes. Recent evolutionary genomic works have provided empirical evidence that C. gigas and C. angulata exhibit partial reproductive isolation. Although hybridization occurs in nature, the rate of interspecific gene flow varies across the genome, resulting in highly heterogeneous genome divergence. Taking this biological property into account is important to characterize genetic ancestry and population structure in oysters. Here, we identified a subset of ancestry-informative makers from the most differentiated regions of the genome using existing genomic resources. We developed two different panels in order to (i) easily differentiate C. gigas and C. angulata, and (ii) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic populations. Our results confirm high genetic homogeneity among Pacific cupped oyster populations in France and reveal several cases of introgressions between Portuguese and Japanese oysters in France and Portugal.

scholarly journals De-Coding the Contributions of the Viral RNAs to Alphaviral Pathogenesis

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 771
Author(s):  
Autumn T. LaPointe ◽  
Kevin J. Sokoloski
Keyword(s):  
Host Response ◽  
Severe Disease ◽  
Review Article ◽  
Structural Proteins ◽  
Virulence Determinants ◽  
Healthy Individuals ◽  
Viral Rnas ◽  
Positive Sense ◽  
Identification And Characterization

Alphaviruses are positive-sense RNA arboviruses that are capable of causing severe disease in otherwise healthy individuals. There are many aspects of viral infection that determine pathogenesis and major efforts regarding the identification and characterization of virulence determinants have largely focused on the roles of the nonstructural and structural proteins. Nonetheless, the viral RNAs of the alphaviruses themselves play important roles in regard to virulence and pathogenesis. In particular, many sequences and secondary structures within the viral RNAs play an important part in the development of disease and may be considered important determinants of virulence. In this review article, we summarize the known RNA-based virulence traits and host:RNA interactions that influence alphaviral pathogenesis for each of the viral RNA species produced during infection. Overall, the viral RNAs produced during infection are important contributors to alphaviral pathogenesis and more research is needed to fully understand how each RNA species impacts the host response to infection as well as the development of disease.

Dual Isoform Sequencing Reveals a Multifaceted Transcriptional Architecture of a Prototype Baculovirus

2021 ◽  
Author(s):  
Gábor Torma ◽  
Dóra Tombácz ◽  
Norbert Moldován ◽  
Ádám Fülöp ◽  
István Prazsák ◽  
...  
Keyword(s):  
Protein Coding ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Oxford Nanopore ◽  
The Pacific ◽  
Viral Genes ◽  
Long Read ◽  
Oxford Nanopore Technologies ◽  
Overlapping Transcripts

Abstract In this study, we used two long-read sequencing (LRS) techniques, Sequel from the Pacific Biosciences and MinION from Oxford Nanopore Technologies, for the transcriptional characterization of a prototype baculovirus, Autographacalifornica multiple nucleopolyhedrovirus. LRS is able to read full-length RNA molecules, and thereby to distinguish between transcript isoforms, mono- and polycistronic RNAs, and overlapping transcripts. Altogether, we detected 875 transcripts, of which 759 are novel and 116 have been annotated previously. These RNA molecules include 41 novel putative protein coding transcript (each containing 5’-truncated in-frame ORFs), 14 monocistronic transcripts, 99 multicistronic RNAs, 101 non-coding RNA, and 504 length isoforms. We also detected RNA methylation in 12 viral genes and RNA hyper-editing in the longer 5’-UTR transcript isoform of ORF 19 gene.

Geochemical and Petrological Characterization of Ash Samples from Cascade Range Volcanoes

1971 ◽  
Vol 1 (2) ◽  
pp. 261-282 ◽  
Author(s):  
Keith Randle ◽  
Gordon G. Goles ◽  
Laurence R. Kittleman
Keyword(s):  
Pacific Northwest ◽  
Volcanic Ash ◽  
Cascade Range ◽  
Crystalline Material ◽  
Refractive Indices ◽  
Crystalline Materials ◽  
The Pacific ◽  
Volcanic Ashes ◽  
Different Sources

Twenty-nine samples of volcanic ash from the Pacific Northwest were analyzed by instrumental neutron activation techniques, with the aim of distinguishing among ashes from different sources. Preliminary results of petrographic studies of 42 ash or pumice samples are also reported. Geochemical characteristics of Mazama ash are defined, and problems induced by winnowing of crystalline material during transport and by weathering are discussed. Contents of La, Th, and Co, and La/Yb ratios are shown to be good discriminants. Data on refractive indices and on proportions of crystalline materials also aid in distinguishing among the various volcanic ashes studied. Ash and pumice found in archaeological contexts at Fort Rock Cave, Paisley Cave, Wildcat Canyon, and Hobo Cave are all from Mount Mazama, presumably from the culminating cruption of 7000 years ago.

On the influence of ENSO complexity on Pan-Pacific coastal wave extremes

2021 ◽  
Vol 118 (47) ◽  
pp. e2115599118
Author(s):  
Julien Boucharel ◽  
Rafael Almar ◽  
Elodie Kestenare ◽  
Fei-Fei Jin
Keyword(s):  
Southern Oscillation ◽  
Wave Activity ◽  
Spatial Behavior ◽  
Coastal Hazards ◽  
Climate Control ◽  
Enso Events ◽  
The Pacific ◽  
Coastal Impacts ◽  
Climate Mode

Wind-generated waves are dominant drivers of coastal dynamics and vulnerability, which have considerable impacts on littoral ecosystems and socioeconomic activities. It is therefore paramount to improve coastal hazards predictions through the better understanding of connections between wave activity and climate variability. In the Pacific, the dominant climate mode is El Niño Southern Oscillation (ENSO), which has known a renaissance of scientific interest leading to great theoretical advances in the past decade. Yet studies on ENSO’s coastal impacts still rely on the oversimplified picture of the canonical dipole across the Pacific. Here, we consider the full ENSO variety to delineate its essential teleconnection pathways to tropical and extratropical storminess. These robust seasonally modulated relationships allow us to develop a mathematical model of coastal wave modulation essentially driven by ENSO’s complex temporal and spatial behavior. Accounting for this nonlinear climate control on Pan-Pacific wave activity leads to a much better characterization of waves’ seasonal to interannual variability (+25% in explained variance) and intensity of extremes (+60% for strong ENSO events), therefore paving the way for significantly more accurate forecasts than formerly possible with the previous baseline understanding of ENSO’s influence on coastal hazards.

Genetic characterization of Flavobacterium columnare isolates from the Pacific Northwest, USA

2021 ◽  
Author(s):  
Fd Alexandre Sebastião ◽  
K Shahin ◽  
BR LaFrentz ◽  
MJ Griffin ◽  
TP Loch ◽  
...  
Keyword(s):  
Pacific Northwest ◽  
Genetic Characterization ◽  
Flavobacterium Columnare ◽  
The Pacific

Presence and characterization of multiple mantle lysozymes in the Pacific oyster, Crassostrea gigas

2010 ◽  
Vol 29 (1) ◽  
pp. 126-135 ◽  
Author(s):  
Naoki Itoh ◽  
Yuki Okada ◽  
Keisuke G. Takahashi ◽  
Makoto Osada
Keyword(s):  
Crassostrea Gigas ◽  
Pacific Oyster ◽  
The Pacific
Sign in / Sign up

Export Citation Format

Share Document