26 research outputs found
Isolation and characterization of a new simian rotavirus, YK-1
BACKGROUND: To effectively analyze the requirements for protection to rotavirus infection, a reliable animal model that reasonably mimics infection and disease in humans is needed. A requirement for an effective animal model is the availability of appropriate rotavirus stocks for challenge. RESULTS: A new simian rotavirus, designated YK-1, was isolated from a 2-year-old immunodeficient pigtailed macaque with chronic diarrhea. YK-1 was distinguishable by electropherotype from the other simian rotavirus strains, SA11 and RRV. One variant of YK-1, clone 311, which was isolated after adaptation and plaque purification in cell cultures, displayed an unusual RNA electropherotype with an abnormally migrating gene 11 segment. Sequence analysis demonstrated a genetic rearrangement that involved a partial duplication of the gene 11 ORF encoding NSP5. YK-1 was identified as a Group A rotavirus belonging to subgroup 1. To further characterize the YK-1 strain, the genes encoding VP4, VP7, and NSP4 were sequenced. Analysis of VP4 and VP7 gene fragments suggests that this strain is a G3P[3] rotavirus and is closely related to the simian rotavirus strain RRV. Serotype analysis also identified YK-1 as a G3 rotavirus. The NSP4 genotype of YK-1 is C, the same genotype as RRV. CONCLUSION: This newly isolated rotavirus, YK-1, is being used to establish a nonhuman primate model for studying the infectivity, immunity, and pathogenesis of rotavirus and for evaluating candidate rotavirus vaccines
A meta-analysis of the performance of the Pima <tex>^{TM}$</tex> CD4 for point of care testing
Evaluation of Specimen Types for Pima CD4 Point-of-Care Testing: Advantages of Fingerstick Blood Collection into an EDTA Microtube.
INTRODUCTION:Effective point-of-care testing (POCT) is reliant on optimal specimen collection, quality assured testing, and expedited return of results. Many of the POCT are designed to be used with fingerstick capillary blood to simplify the blood collection burden. However, fingerstick blood collection has inherent errors in sampling. An evaluation of the use of capillary and venous blood with CD4 POCT was conducted. METHODS:Three different specimen collection methods were evaluated for compatibility using the Alere Pima CD4 assay at 5 HIV/AIDS healthcare sites in Dar es Salaam, Tanzania. At each site, whole blood specimens were collected from enrolled patients by venipuncture and fingerstick. Pima CD4 testing was performed at site of collection on venipuncture specimens (Venous) and fingerstick blood directly applied to a Pima CD4 cartridge (Capillary-Direct) and collected into an EDTA microtube (Capillary-Microtube). Venous blood was also tested at the laboratory by the reference CD4 method and Pima for comparison analysis. RESULTS:All three specimen collection methods were successfully collected by healthcare workers for use with the Pima CD4 assay. When compared to the reference CD4 method, Pima CD4 testing with the Capillary-Microtube method performed similarly to Venous, while Pima CD4 counts with the Capillary-Direct method were slightly more biased (-20 cells/ÎĽL) and variable (-229 to +189 cells/ÎĽL limit of agreement). Even though all three collection methods had similar invalid Pima testing rates (10.5%, 9.8%, and 8.3% for Capillary-Direct, Capillary-Microtube, and Venous respectively), the ability to perform repeat testing with Capillary-Microtube and Venous specimens increased the likelihood of acquiring a valid CD4 result with the Pima assay. CONCLUSIONS:Capillary blood, either directly applied to Pima CD4 cartridges or collected in an EDTA microtube, and venous blood are suitable specimens for Pima CD4 testing. The advantages of capillary blood collection in an EDTA microtube are that it uses fingerstick collection which mimics venous blood and allows extra testing without additional blood collection
Falco mexicanus genome assembly scaffolds
The Falco mexicanus draft genome was generated from paired-end, mate-paired and long reads using ABySS vs. 1.5.2 and SPAdes 3.1.1. This file includes the scaffolds greater than 10 kb in length
Data from: New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)
Background: Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species’ range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge.
Results: We sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population.
Conclusions: Our study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating population of prairie falcons across our sampling locations. Prairie falcons are highly mobile and relatively rare long-distance dispersal events may promote gene flow throughout the range. As such, California’s prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole
Falco mexicanus mitochondrial genome assembly
The F. mexicanus mitochondrial genome was assembled using MITObim vs. 1.6. The genome assembly is 17,117 bp in length and characterized by 13 protein-coding genes, two ribosomal subunit genes (rRNA), 22 transfer RNA genes and a control region
Falco mexicanus genome annotation - protein sequences
16,320 genes were annotated in the Falco mexicanus genome, this is the .fasta file with predicted protein sequences
New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)
Abstract Background Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species’ range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge. Results We sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population. Conclusions Our study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating population of prairie falcons across our sampling locations. Prairie falcons are highly mobile and relatively rare long-distance dispersal events may promote gene flow throughout the range. As such, California’s prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole
Falco mexicanus genome annotation
16,320 genes were annotated in the Falco mexicanus genome, this is the .gff file associated with the annotations