scholarly journals Completion of Maize Stripe Virus Genome Sequence and Analysis of Diverse Isolates

2021 ◽  
Vol 12 ◽  
Author(s):  
Stephen Bolus ◽  
Kathryn S. Braithwaite ◽  
Samuel C. Grinstead ◽  
Irazema Fuentes-Bueno ◽  
Robert Beiriger ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Reference Genome ◽  
Rice Stripe Virus ◽  
The United States ◽  
Amino Acid Identity ◽  
Virus Genome ◽  
Tropical Regions ◽  
Reading Frame ◽  
Putative Protein ◽  
Insight Into

Maize stripe virus is a pathogen of corn and sorghum in subtropical and tropical regions worldwide. We used high-throughput sequencing to obtain the complete nucleotide sequence for the reference genome of maize stripe virus and to sequence the genomes of ten additional isolates collected from the United States or Papua New Guinea. Genetically, maize stripe virus is most closely related to rice stripe virus. We completed and characterized the RNA1 sequence for maize stripe virus, which revealed a large open reading frame encoding a putative protein with ovarian tumor-like cysteine protease, endonuclease, and RNA-dependent RNA polymerase domains. Phylogenetic and amino acid identity analyses among geographically diverse isolates revealed evidence for reassortment in RNA3 that was correlated with the absence of RNA5. This study yielded a complete and updated genetic description of the tenuivirus maize stripe virus and provided insight into potential mechanisms underpinning its diversity.

scholarly journals Detection and Characterization of Novel Rotavirus Strains in the United States

1998 ◽  
Vol 36 (11) ◽  
pp. 3223-3229 ◽  
Author(s):  
M. Ramachandran ◽  
J. R. Gentsch ◽  
U. D. Parashar ◽  
S. Jin ◽  
P. A. Woods ◽  
...  
Keyword(s):  
United States ◽  
Monoclonal Antibody ◽  
The United States ◽  
Prototype Strain ◽  
Amino Acid Identity ◽  
Detection Rates ◽  
Reading Frame ◽  
Reverse Transcription Pcr ◽  
Subgroup Ii ◽  
Before And After

We recently established a rotavirus strain surveillance system in the United States to monitor the prevalent G serotypes before and after the anticipated implementation of a vaccination program against rotavirus and to identify the emergence of uncommon strains. In this study, we examined 348 rotavirus strains obtained in 1996 to 1997 from children with diarrhea in 10 U.S. cities. Strains were characterized for P and G types, subgroups, and electropherotypes by using a combination of monoclonal antibody immunoassay, reverse transcription-PCR, and hybridization. The four strains most commonly found worldwide comprised 83% of the isolates (P[8]G1, 66.4%; P[4]G2, 8.3%; P[8]G3, 6.9%; P[8]G4, 1.4%), but 9.2% were unusual strains (P[6]G9, 5.5%; P[8]G9, 1.7%; P[6]G1, 1.4%; and P[4]G1 and P[8]G2, 0.3% each). Strains not typeable for P or G type accounted for 5.5% of the total, while 2.3% of the strains had more than one G type (mixed infections). All P[6]G9 strains tested had short electropherotypes and subgroup I specificity and were detected in 4 of 10 cities, while P[8]G9 strains had long electropherotypes and subgroup II VP6 antigens. Both sequence analysis of the VP7 open reading frame (about 94 to 95% amino acid identity with the VP7 gene of G9 prototype strain WI61) and binding to a G9-specific monoclonal antibody strongly suggest that U.S. G9 strains belong to serotype G9. The high detection rates of unusual rotaviruses with G9 (7.2%) or P[6] (6.9%) specificity in multiple U.S. cities suggest the emergence of new strains or inadequate diagnosis in the past. The epidemiologic importance of these strains remains to be determined.

scholarly journals Molecular Cloning and Functional Expression of a Protein-Serine/Threonine Phosphatase from the Hyperthermophilic Archaeon Pyrodictium abyssi TAG11

1998 ◽  
Vol 180 (16) ◽  
pp. 4030-4035 ◽  
Author(s):  
Bianca Mai ◽  
Gerhard Frey ◽  
Ronald V. Swanson ◽  
Eric J. Mathur ◽  
K. O. Stetter
Keyword(s):  
Inclusion Bodies ◽  
Physiological Role ◽  
Functional Expression ◽  
Reading Frame ◽  
Hyperthermophilic Archaeon ◽  
Archaeal Protein ◽  
Putative Protein ◽  
First Time ◽  
Insight Into

ABSTRACT An open reading frame coding for a putative protein-serine/threonine phosphatase was identified in the hyperthermophilic archaeon Pyrodictium abyssi TAG11 and named Py-PP1. Py-PP1 was expressed in Escherichia coli, purified from inclusion bodies, and biochemically characterized. The phosphatase gene is part of an operon which may provide, for the first time, insight into a physiological role for archaeal protein phosphatases in vivo.

scholarly journals Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2412
Author(s):  
Jose L. Huaman ◽  
Carlo Pacioni ◽  
Subir Sarker ◽  
Mark Doyle ◽  
David M. Forsyth ◽  
...  
Keyword(s):  
Red Deer ◽  
High Throughput Sequencing ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Fallow Deer ◽  
Potential Threat ◽  
Pathogenic Potential ◽  
Reading Frame ◽  
Faecal Samples ◽  
Eastern Australia

The use of high-throughput sequencing has facilitated virus discovery in wild animals and helped determine their potential threat to humans and other animals. We report the complete genome sequence of a novel picornavirus identified by next-generation sequencing in faeces from Australian fallow deer. Genomic analysis revealed that this virus possesses a typical picornavirus-like genomic organisation of 7554 nt with a single open reading frame (ORF) encoding a polyprotein of 2225 amino acids. Based on the amino acid identity comparison and phylogenetic analysis of the P1, 2C, 3CD, and VP1 regions, this novel picornavirus was closely related to but distinct from known bopiviruses detected to date. This finding suggests that deer/bopivirus could belong to a novel species within the genus Bopivirus, tentatively designated as “Bopivirus C”. Epidemiological investigation of 91 deer (71 fallow, 14 sambar and 6 red deer) and 23 cattle faecal samples showed that six fallow deer and one red deer (overall prevalence 7.7%, 95% confidence interval [CI] 3.8–15.0%) tested positive, but deer/bopivirus was undetectable in sambar deer and cattle. In addition, phylogenetic and sequence analyses indicate that the same genotype is circulating in south-eastern Australia. To our knowledge, this study reports for the first time a deer-origin bopivirus and the presence of a member of genus Bopivirus in Australia. Further epidemiological and molecular studies are needed to investigate the geographic distribution and pathogenic potential of this novel Bopivirus species in other domestic and wild animal species.

Analysis of Demographics and Factors Influencing Student Choice of Major at Five Universities

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 510b-510
Author(s):  
Tammy Kohlleppel ◽  
Jennifer C. Bradley ◽  
Jayne Zajicek
Keyword(s):  
Student Satisfaction ◽  
Undergraduate Students ◽  
The United States ◽  
Student Choice ◽  
Student Interest ◽  
Post Secondary ◽  
Choice Of Major ◽  
Factors Influencing ◽  
University History ◽  
Insight Into

In recent years horticulture programs at universities across the United States have experienced a decline in student numbers. Researchers at the Univ. of Florida and Texas A&M Univ. have developed a survey to gain insight into the influences on undergraduate students who major in horticulture. Five universities participated in the survey of undergraduate horticulture programs, these include the Univ. of Florida, Texas A&M Univ., Oklahoma State Univ., Univ. of Tennessee, and Kansas State Univ. Approximately 600 surveys were sent to the schools during the 1997 fall semester. The questionnaires were completed by horticulture majors and nonmajors taking classes in the horticulture departments. The survey consisted of two main sections. The first section examined student demographic information, high school history, university history and horticulture background and was completed by all students. Only horticulture majors completed the second section, which examined factors influencing choice of horticulture as a major. Results examine fundamental predictors in promoting student interest in horticulture, demographic variables that may influence student choice of major, and student satisfaction and attitude toward current collegiate horticulture programs. Findings from this study will provide insight into the status of post-secondary horticulture education and assist in identifying methods to increase student enrollment in horticulture programs across the country.

scholarly journals Rapid Deployment of an Algorithm to Triage Dental Emergencies During COVID-19 Pandemic

2021 ◽  
Author(s):  
Sharon C Perelman ◽  
Steven Erde ◽  
Lynda Torre ◽  
Tunaidi Ansari
Keyword(s):  
Rapid Development ◽  
The United States ◽  
Healthcare Systems ◽  
Patient Needs ◽  
Columbia University ◽  
Dental Infection ◽  
Screening Algorithm ◽  
Rapid Deployment ◽  
Medical Infrastructure ◽  
Insight Into

Abstract COVID-19 quickly immobilized healthcare systems in the United States during the early stages of the outbreak. While much of the ensuing response focused on supporting the medical infrastructure, Columbia University College of Dental Medicine pursued a solution to triage and safely treat patients with dental emergencies amidst the pandemic. Considering rapidly changing guidelines from governing bodies, dental infection control protocols and our clinical faculty's expertise, we modeled, built, and implemented a screening algorithm, which provides decision support as well as insight into COVID-19 status and clinical comorbidities, within a newly integrated Electronic Health Record (EHR). Once operationalized, we analyzed the data and outcomes of its utilization and found that it had effectively guided providers in triaging patient needs in a standardized methodology. This article describes the algorithm's rapid development to assist faculty providers in identifying patients with the most urgent needs, thus prioritizing treatment of dental emergencies during the pandemic.

scholarly journals Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2

2021 ◽  
Author(s):  
Liang Cheng ◽  
Xudong Han ◽  
Zijun Zhu ◽  
Changlu Qi ◽  
Ping Wang ◽  
...  
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Purifying Selection ◽  
Virus Genome ◽  
Receptor Binding Domain ◽  
Evolutionary Trends ◽  
Synonymous Mutations ◽  
Almost All ◽  
Virus Strains ◽  
New Mutations

Abstract Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, the COVID-19 pandemic has spread rapidly worldwide. Due to the limited virus strains, few key mutations that would be very important with the evolutionary trends of virus genome were observed in early studies. Here, we downloaded 1809 sequence data of SARS-CoV-2 strains from GISAID before April 2020 to identify mutations and functional alterations caused by these mutations. Totally, we identified 1017 nonsynonymous and 512 synonymous mutations with alignment to reference genome NC_045512, none of which were observed in the receptor-binding domain (RBD) of the spike protein. On average, each of the strains could have about 1.75 new mutations each month. The current mutations may have few impacts on antibodies. Although it shows the purifying selection in whole-genome, ORF3a, ORF8 and ORF10 were under positive selection. Only 36 mutations occurred in 1% and more virus strains were further analyzed to reveal linkage disequilibrium (LD) variants and dominant mutations. As a result, we observed five dominant mutations involving three nonsynonymous mutations C28144T, C14408T and A23403G and two synonymous mutations T8782C, and C3037T. These five mutations occurred in almost all strains in April 2020. Besides, we also observed two potential dominant nonsynonymous mutations C1059T and G25563T, which occurred in most of the strains in April 2020. Further functional analysis shows that these mutations decreased protein stability largely, which could lead to a significant reduction of virus virulence. In addition, the A23403G mutation increases the spike-ACE2 interaction and finally leads to the enhancement of its infectivity. All of these proved that the evolution of SARS-CoV-2 is toward the enhancement of infectivity and reduction of virulence.

scholarly journals Intra-Colonial Viral Infections in Western Honey Bees (Apis mellifera)

2021 ◽  
Vol 9 (5) ◽  
pp. 1087
Author(s):  
Loreley Castelli ◽  
María Laura Genchi García ◽  
Anne Dalmon ◽  
Daniela Arredondo ◽  
Karina Antúnez ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Viral Infections ◽  
Sampling Period ◽  
Virus Genome ◽  
The Individual ◽  
Bee Virus ◽  
Insight Into ◽  
Bee Viruses

RNA viruses play a significant role in the current high losses of pollinators. Although many studies have focused on the epidemiology of western honey bee (Apis mellifera) viruses at the colony level, the dynamics of virus infection within colonies remains poorly explored. In this study, the two main variants of the ubiquitous honey bee virus DWV as well as three major honey bee viruses (SBV, ABPV and BQCV) were analyzed from Varroa-destructor-parasitized pupae. More precisely, RT-qPCR was used to quantify and compare virus genome copies across honey bee pupae at the individual and subfamily levels (i.e., patrilines, sharing the same mother queen but with different drones as fathers). Additionally, virus genome copies were compared in cells parasitized by reproducing and non-reproducing mite foundresses to assess the role of this vector. Only DWV was detected in the samples, and the two variants of this virus significantly differed when comparing the sampling period, colonies and patrilines. Moreover, DWV-A and DWV-B exhibited different infection patterns, reflecting contrasting dynamics. Altogether, these results provide new insight into honey bee diseases and stress the need for more studies about the mechanisms of intra-colonial disease variation in social insects.

Excavating the Layers of Trauma in Homelands and Hostlands: Supporting Political Refugees in U.S. Schools

2021 ◽  
pp. 155545892199751
Author(s):  
Mehtap Akay ◽  
Reva Jaffe-Walter
Keyword(s):  
United States ◽  
Teacher Education ◽  
Education System ◽  
Home Country ◽  
The United States ◽  
Dominant Culture ◽  
Refugee Students ◽  
Political Refugees ◽  
Language And Education ◽  
Insight Into

This article details how a newly arrived Turkish refugee student navigates schooling in the United States. It highlights the trauma a purged Turkish families experience in their home country and their challenges as newcomers unfamiliar with their new country’s dominant culture, language, and education system. The case narrative provides insight into how children of Turkish political refugees are often overlooked in the context of U.S. schools, where teachers lack adequate training and supports. By illuminating one refugee family’s experiences in U.S. schools, the case calls for leaders to develop holistic supports and teacher education focused on the needs of refugee students.

scholarly journals Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Komal Jain ◽  
Teresa Tagliafierro ◽  
Adriana Marques ◽  
Santiago Sanchez-Vicente ◽  
Alper Gokden ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Fold Increase ◽  
The United States ◽  
Genomic Research ◽  
Babesia Microti ◽  
Hybridization Capture ◽  
Mouse Tissues ◽  
Genome Analyses ◽  
Capture Sequencing

AbstractInadequate sensitivity has been the primary limitation for implementing high-throughput sequencing for studies of tick-borne agents. Here we describe the development of TBDCapSeq, a sequencing assay that uses hybridization capture probes that cover the complete genomes of the eleven most common tick-borne agents found in the United States. The probes are used for solution-based capture and enrichment of pathogen nucleic acid followed by high-throughput sequencing. We evaluated the performance of TBDCapSeq to surveil samples that included human whole blood, mouse tissues, and field-collected ticks. For Borrelia burgdorferi and Babesia microti, the sensitivity of TBDCapSeq was comparable and occasionally exceeded the performance of agent-specific quantitative PCR and resulted in 25 to > 10,000-fold increase in pathogen reads when compared to standard unbiased sequencing. TBDCapSeq also enabled genome analyses directly within vertebrate and tick hosts. The implementation of TBDCapSeq could have major impact in studies of tick-borne pathogens by improving detection and facilitating genomic research that was previously unachievable with standard sequencing approaches.

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