scholarly journals A comprehensive survey of bat sarbecoviruses across China for the origin tracing of SARS-CoV and SARS-CoV-2

2021 ◽  
Author(s):  
Zhiqiang Wu ◽  
Yelin Han ◽  
Yuyang Wang ◽  
Bo Liu ◽  
Lamei Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Virus Disease ◽  
Botanical Garden ◽  
Binding Motifs ◽  
Spike Gene ◽  
Comprehensive Survey ◽  
Almost All ◽  
L1 And L2 ◽  
Geographical Characteristics ◽  
Geographical Distribution Pattern

Abstract Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 have been thought to originate from bat, but whether the cross-species transmission occurred directly from bat to human or through an intermediate host remains elusive. In this study, we performed CoV screening of 102 samples collected from animal-selling stalls of Wuhan Huanan Market (WHM) and pharyngeal and anal swabs from13,064 bats collected at 703 locations across China, covering almost all known southern hotspots for sarbecovirus, between 2016 and 2021. This is the first systematic survey of bat CoV in China during the outbreak of Corona Virus Disease 2019. We found four non-sarbeco CoVs in samples of WHM, and 142 SARS-CoV related CoVs (SARSr-CoV) and 4 recombinant CoVs in bats, of which YN2020B-G share the highest sequence identity with SARS-CoV among all known bat CoVs, suggesting endemic SARSr-CoVs in bats in China. However, we did not find any SARS-CoV-2 related CoVs (SC2r-CoV) in any samples, including specimens collected from the only two domestic places where RaTG13 and RmYN02 were previously reported (the Tongguan caves and the karst caves around the Xishuangbanna Tropical Botanical Garden), indicating that SC2r-CoVs might not actively circulate among bats in China. Phylogenetic analysis showed that there are three different lineages of sarbecoviruses, L1 (SARSr-CoV), L2 (SC2r-CoV), and L-R (a novel CoV lineage from L1 and L2 recombination), in China. Of note, L-R CoVs are only found in R. pusillus. Further macroscopical analysis of the genetic diversity, host specificity for colonization and accidental infection, and geographical characteristics of available CoVs in database revealed the presence of a general geographical distribution pattern for bat sarbecoviruses, with the highest genetic diversity and sequence homology to SARS-CoV or SARS-CoV-2 along the southwest border of China, the least in the northwest of China. Considering the receptor binding motifs for spike gene of sarbecoviruses in Indochina Peninsula show the greatest diversity, our data provide the rationale that extensive surveys in further south and southwest to or of China might be needed for finding closer ancestors of SARS-CoV and SARS-CoV-2.

scholarly journals Unveiling a unique genetic diversity of cultivated Coffea arabica L. in its main domestication center: Yemen

2021 ◽  
Author(s):  
C. Montagnon ◽  
A. Mahyoub ◽  
W. Solano ◽  
F. Sheibani
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Coffea Arabica ◽  
Genetic Improvement ◽  
The World ◽  
Genetic Clusters ◽  
Domestication Process ◽  
Almost All ◽  
Coffea Arabica L ◽  
Cup Quality

AbstractWhilst it is established that almost all cultivated coffee (Coffea arabica L.) varieties originated in Yemen after some coffee seeds were introduced into Yemen from neighboring Ethiopia, the actual coffee genetic diversity in Yemen and its significance to the coffee world had never been explored. We observed five genetic clusters. The first cluster, which we named the Ethiopian-Only (EO) cluster, was made up exclusively of the Ethiopian accessions. This cluster was clearly separated from the Yemen and cultivated varieties clusters, hence confirming the genetic distance between wild Ethiopian accessions and coffee cultivated varieties around the world. The second cluster, which we named the SL-17 cluster, was a small cluster of cultivated worldwide varieties and included no Yemen samples. Two other clusters were made up of worldwide varieties and Yemen samples. We named these the Yemen Typica-Bourbon cluster and the Yemen SL-34 cluster. Finally, we observed one cluster that was unique to Yemen and was not related to any known cultivated varieties and not even to any known Ethiopian accession: we name this cluster the New-Yemen cluster. We discuss the consequences of these findings and their potential to pave the way for further comprehensive genetic improvement projects for the identification of major resilience/adaptation and cup quality genes that have been shaped through the domestication process of C. arabica.

Implementation of Virtual Classroom and Zoom Networks in Continuing Student Learning

2022 ◽  
Vol 3 (1) ◽  
Author(s):  
Nurbaiti Nurbaiti ◽  
Nadhrah Al Aflah ◽  
Supardi Supardi
Keyword(s):  
Virus Disease ◽  
Virtual Classroom ◽  
Learning Activity ◽  
The Internet ◽  
Activity System ◽  
Effective Learning ◽  
The World ◽  
Almost All ◽  
Internet Networks ◽  
Use Of Internet

Almost all corners of the world have been affected or affected by this Covid-19 virus disease, even some countries have set a lockdown status and other anticipations for the spread of the Covid-19 virus. The alternative used in this bold learning activity system is to utilize the internet network, namely the Zoom Meeting and Classroom application. This study aims to determine students' perceptions of the use of internet networks such as zoom meetings and classrooms used and how effective learning is during the Covid-19 pandemic. The research conducted here uses descriptive qualitative research methods. And the results of this study indicate that the zoom application is an application that is very effective and preferred by students because it is easier to use and very efficient when the learning process is bold and shows that some students who give their perception of the application used during learning that are brave are the Zoom Meeting application, namely the application. Zoom Meeting. by 66.7%, followed by the Google Meet application at 22.2% and the Classrom application at 11.1%.  

scholarly journals Genetic diversity in soybean seed quality under different storage conditions

2017 ◽  
Vol 38 (1) ◽  
pp. 57
Author(s):  
Daniele Piano Rosa ◽  
Danúbia Aparecida Costa Nobre ◽  
Diego Santos Oliveira ◽  
Francisco Charles dos Santos Silva ◽  
André Ricardo Gomes Bezerra ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Seed Quality ◽  
Soybean Seed ◽  
High Standard ◽  
Storage Conditions ◽  
Seed Vigor ◽  
Soybean Cultivars ◽  
High Germination ◽  
Physiological Quality ◽  
Almost All

This study aimed to assess the effect of genetic diversity on physiological quality of soybean seeds stored in cold chamber and under environmental conditions. Ten cultivars were assessed in a randomized factorial design (2x10). Factor 1 corresponded to two storage conditions and factor 2 to ten soybean cultivars, with four replications. The evaluated variables were total germination (G%), first count of germination (F%), percentage of abnormal seedlings (AS%), germination speed index (GSI), water content (WC), electrical conductivity (EC), dry matter of seedlings (DMS) and length of seedlings (LS). Data underwent ANOVA, followed by Scott Knott test, as well as multivariate analysis of genetic diversity. The results showed a higher physiological quality for seeds under cold storage. Half of the cultivars (FPS Júpiter, FPS Urano, FPS Antares, FPS Netuno and CD 250) presented high germination rates and seed vigor, being thus indicated as high-standard materials for further breeding programs. Besides that, storage environment had influence on the clustering of soybean cultivars. Moreover, cultivars had genetic dissimilarity for almost all assessed traits as G%, GSI, F%, AS%, EC, DMS and LS.

scholarly journals Genetic diversity analysis of parental lines for hybrid development in rice (Oryza sativa L.)

2013 ◽  
Vol 37 (4) ◽  
pp. 617-624 ◽  
Author(s):  
MJ Hasan ◽  
Umma Kulsum ◽  
MMH Rahman ◽  
MMH Chowdhury ◽  
AZMKA Chowdhury
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa L ◽  
Principal Component ◽  
Mean Value ◽  
Cluster Distance ◽  
Parental Lines ◽  
Almost All ◽  
Yield Maximization ◽  
Hybrid Development ◽  
Panicle Weight

Genetic divergence of 40 parental lines comprising 30 restorer and 10 maintainer lines were studied through Mohalanobis's D2 and principal component analysis for eleven characters. Genotypes were grouped into five different clusters. Cluster V comprised maximum number of genotypes (thirteen) followed by cluster I and II. The inter-cluster distance was maximum between clusters I and V (13.495) indicating wide genetic diversity between these two clusters followed by the distance between cluster I and 11 (9.489), cluster IV, and cluster V (8.969) and cluster I and cluster III (8.039). The minimum inter-cluster distance was observed between cluster II and cluster III (3.034) followed by cluster 111 and cluster IV (3.834) and cluster II and cluster V (4.945) indicating that the genotypes of these clusters were genetically close. The intra cluster distance in the entire five clusters was more or less low which indicated that the genotypes within the same cluster were closely related. Among the characters panicle weight contributed most for divergence in the studied parental lines. Difference in cluster means existed for almost all the characters studied. Highest mean value for number of effective tillers (7.8), days to 50% flowering (95.5), panicles/m2 (192.6), panicle weight (2.9), spikelet fertility (84.8), number of grains/panicle (177.8), days to maturity (123.6), and grain yield/plot (1065.5) were observed in cluster I indicated the parental lines fallen in this cluster having the genetic potentiality to contribute better for yield maximization of hybrid rice. DOI: http://dx.doi.org/10.3329/bjar.v37i4.14386 Bangladesh J. Agril. Res. 37(4): 617-624, December 2012

Host-mediated RNAi of a Notch-like receptor gene inMeloidogyne incognitainduces nematode resistance

Parasitology ◽  
2018 ◽  
Vol 145 (14) ◽  
pp. 1896-1906
Author(s):  
Deshika Kohli ◽  
Parameswaran Chidambaranathan ◽  
J. Prasanth Tej Kumar ◽  
Ashish Kumar Singh ◽  
Anil Kumar ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Receptor Gene ◽  
Nematode Resistance ◽  
Receptor Protein ◽  
Binding Motifs ◽  
C Elegans ◽  
Transgenic Lines ◽  
Germline Proliferation ◽  
Epidermal Growth ◽  
Almost All

AbstractGLP-1 (abnormal germline proliferation) is a Notch-like receptor protein that plays an essential role in pharyngeal development. In this study, an orthologue ofCaenorhabditis elegans glp-1was identified inMeloidogyne incognita. A computational analysis revealed that the orthologue contained almost all the domains present in theC. elegansgene: specifically, the LIN-12/Notch repeat, the ankyrin repeat, a transmembrane domain and different ligand-binding motifs were present in orthologue, but the epidermal growth factor-like motif was not observed. An expression analysis showed differential expression ofglp-1throughout the life cycle ofM. incognita, with relatively higher expression in the egg stage. To evaluate the silencing efficacy ofMi-glp-1, transgenicArabidopsisplants carrying double-stranded RNA constructs ofglp-1were generated, and infection of these plants withM. incognitaresulted in a 47–50% reduction in the numbers of galls, females and egg masses. Females obtained from the transgenic RNAi lines exhibited 40–60% reductions in the transcript levels of the targetedglp-1gene compared with females isolated from the control plants. Second-generation juveniles (J2s), which were descendants of the infected females from the transgenic lines, showed aberrant phenotypes. These J2s exhibited a significant decrease in the overall distance from the stylet to the metacorpus region, and this effect was accompanied by disruption around the metacorporeal bulb of the pharynx. The present study suggests a role for this gene in organ (pharynx) development during embryogenesis inM. incognitaand its potential use as a target in the management of nematode infestations in plants.

Coronavirus and Fingerprint Technology

2021 ◽  
Vol 13 (4) ◽  
pp. 1-16
Author(s):  
Gabriel B. Iwasokun
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Viral Infection ◽  
Virus Disease ◽  
High Rate ◽  
Corona Virus ◽  
The World ◽  
Almost All

The corona virus disease, otherwise known as COVID-19, is an extremely communicable and pathogenic viral infection caused by severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), which emerged in Wuhan, China in December 2019 and has spread to almost all the countries in the world. The transmission of the virus is through touching of the nose, eyes, or mouth by a finger that has been contaminated through droplets on a surface when a carrier sneezes or coughs. Since the existing fingerprint devices are predominantly contact based, it implies that they can aid in the transmission of the virus. This paper discusses the application of fingerprint devices in notable places with high rate of COVID-19 infection as well as the threats to fingerprint technologies and the countermeasures. The need to change focus and orientation towards contactless biometric technologies as sure solution to the fear and animosity expressed towards contact-based fingerprint technology is also expatiated.

scholarly journals Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015–16

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Carol A Abidha ◽  
Joyce Nyiro ◽  
Everlyn Kamau ◽  
Osman Abdullahi ◽  
David James Nokes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics ◽  
Control Strategies ◽  
Respiratory Illness ◽  
Respiratory Pathogen ◽  
Human Coronavirus ◽  
Spike Gene ◽  
Low Genetic Diversity ◽  
Coastal Kenya ◽  
Close Phylogenetic Relationship

Abstract Human coronavirus OC43 (HCoV-OC43) is a major contributor to seasonal outbreaks of acute respiratory illness (ARI). The origins of locally circulating HCoV-OC43 strains and characteristics of their genetic diversity are unknown for most settings despite significance to effective HCoV control strategies. Between December 2015 and June 2016, we undertook ARI surveillance in coastal Kenya in nine outpatients and one inpatient health facility (HF). Ninety-two patient samples tested HCoV-OC43 positive and forty (43.5%) were successfully sequenced in spike (S) gene region (2,864 long, ∼70%). Phylogenetic analysis confirmed co-circulation of two distinct HCoV-OC43 clades that closely clustered with genotype G (n = 34, 85%) and genotype H (n = 6, 15%) reference strains. Local viruses within the same clade displayed low genetic diversity yielding identical sequences in multiple HF. Furthermore, the newly sequenced Kenyan viruses showed close phylogenetic relationship to other contemporaneous sampled strains (2015–16) including those originating from distant places (e.g. USA and China). Using a genetic similarity threshold of 99.1 per cent at nucleotide level, the HCoV-OC43 strains sampled globally between 1967 and 2019 fell into nine sequence clusters. Notably, some of these clusters appeared to have become extinct, or occurred only sporadically in a few geographical areas while others persisted globally for multiple years. In conclusion, we found that HCoV-OC43 strains spread rapidly both locally and across the globe with limited genetic evolution in the spike gene. Full-genome sequences that are spatio-temporally representative are required to advance understanding of the transmission pathways of this important human respiratory pathogen.

scholarly journals Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing

2007 ◽  
Vol 89 (2) ◽  
pp. 93-106 ◽  
Author(s):  
NOELLE A. BARKLEY ◽  
ROB E. DEAN ◽  
ROY N. PITTMAN ◽  
MING L. WANG ◽  
CORLEY C. HOLBROOK ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Data Set ◽  
Mini Core Collection ◽  
Genomic Ssr ◽  
Cultivated Peanut ◽  
The Mean ◽  
Wild Accessions ◽  
Almost All

SummaryThirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15·4 alleles per locus. The mean polymorphic information content (PIC) score was 0·687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10·1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.

Reactions to Participating in Trauma and Addiction Research Among Women in a Sober Living Home: A Brief Report

2020 ◽  
pp. 088626052091857
Author(s):  
Katie M. Edwards ◽  
Laura Siller ◽  
Sharon B. Murphy
Keyword(s):  
Posttraumatic Growth ◽  
Research Participation ◽  
Emotional Reactions ◽  
Future Research ◽  
Ptsd Symptoms ◽  
Comprehensive Survey ◽  
Survey Results ◽  
Current Psychological ◽  
Almost All ◽  
Shed Light

The purpose of this study was to examine reactions to participating in trauma and addiction research among women in a sober living home. Participants were 59 women who completed a comprehensive survey battery while living in the sober living home. The survey assessed women’s victimization and addiction history along with current psychological and behavioral health symptoms and resilience characteristics. At the end of the survey, women were asked about their reactions to participating in the survey. Results suggested that whereas 40.7% ( n = 24) of women reported being upset immediately after completing the survey, 96.6% ( n = 56) of women reported that they personally benefited from being in the research study. Women who reported being upset, compared with those who were not upset, had higher levels of depressive and posttraumatic stress disorder (PTSD) symptoms and housing and financial instability and lower levels of empowerment, posttraumatic growth, and sense of purpose. We also asked women to tell us, in their own words, their reasons for being upset (e.g., questions about victimization experiences, loss of children), as well as their reasons for benefiting (e.g., catharsis/venting, learning something new about oneself, the chance to meet the researcher who had nice qualities). In general, the research was well tolerated by most of the participants, and almost all women, including those who were initially upset, reported personal benefits. These data shed light on the factors associated with positive and negative emotional reactions to research participation, which could be important information to include in consent forms in future research with this population.

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