6 results on '"Burkitt-Gray L"'
Search Results
2. P6025 Network-based integration of gene expression and genome-wide association data to prioritize genomic variants associated with susceptibility/resistance to bovine tuberculosis
- Author
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Killick, K. E., primary, McLoughlin, K. E., additional, Nalpas, N. C., additional, Burkitt-Gray, L., additional, Richardson, I. W., additional, Wiencko, H. L., additional, Magee, D. A., additional, Browne, J. A., additional, Villarreal-Ramos, B., additional, Vordermeier, H. M., additional, Berry, D. P., additional, Bradley, D. G., additional, Gormley, E., additional, Gordon, S. V., additional, and MacHugh, D. E., additional
- Published
- 2016
- Full Text
- View/download PDF
3. Plasma proteomic associations with genetics and health in the UK Biobank.
- Author
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Sun BB, Chiou J, Traylor M, Benner C, Hsu YH, Richardson TG, Surendran P, Mahajan A, Robins C, Vasquez-Grinnell SG, Hou L, Kvikstad EM, Burren OS, Davitte J, Ferber KL, Gillies CE, Hedman ÅK, Hu S, Lin T, Mikkilineni R, Pendergrass RK, Pickering C, Prins B, Baird D, Chen CY, Ward LD, Deaton AM, Welsh S, Willis CM, Lehner N, Arnold M, Wörheide MA, Suhre K, Kastenmüller G, Sethi A, Cule M, Raj A, Burkitt-Gray L, Melamud E, Black MH, Fauman EB, Howson JMM, Kang HM, McCarthy MI, Nioi P, Petrovski S, Scott RA, Smith EN, Szalma S, Waterworth DM, Mitnaul LJ, Szustakowski JD, Gibson BW, Miller MR, and Whelan CD
- Subjects
- Humans, ABO Blood-Group System genetics, COVID-19 genetics, Drug Discovery, Epistasis, Genetic, Fucosyltransferases metabolism, Genetic Predisposition to Disease, Plasma chemistry, Proprotein Convertase 9 metabolism, Public-Private Sector Partnerships, Quantitative Trait Loci, United Kingdom, Galactoside 2-alpha-L-fucosyltransferase, Biological Specimen Banks, Blood Proteins analysis, Blood Proteins genetics, Databases, Factual, Genomics, Health, Proteome analysis, Proteome genetics, Proteomics
- Abstract
The Pharma Proteomics Project is a precompetitive biopharmaceutical consortium characterizing the plasma proteomic profiles of 54,219 UK Biobank participants. Here we provide a detailed summary of this initiative, including technical and biological validations, insights into proteomic disease signatures, and prediction modelling for various demographic and health indicators. We present comprehensive protein quantitative trait locus (pQTL) mapping of 2,923 proteins that identifies 14,287 primary genetic associations, of which 81% are previously undescribed, alongside ancestry-specific pQTL mapping in non-European individuals. The study provides an updated characterization of the genetic architecture of the plasma proteome, contextualized with projected pQTL discovery rates as sample sizes and proteomic assay coverages increase over time. We offer extensive insights into trans pQTLs across multiple biological domains, highlight genetic influences on ligand-receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks, and illustrate long-range epistatic effects of ABO blood group and FUT2 secretor status on proteins with gastrointestinal tissue-enriched expression. We demonstrate the utility of these data for drug discovery by extending the genetic proxied effects of protein targets, such as PCSK9, on additional endpoints, and disentangle specific genes and proteins perturbed at loci associated with COVID-19 susceptibility. This public-private partnership provides the scientific community with an open-access proteomics resource of considerable breadth and depth to help to elucidate the biological mechanisms underlying proteo-genomic discoveries and accelerate the development of biomarkers, predictive models and therapeutics
1 ., (© 2023. The Author(s).)- Published
- 2023
- Full Text
- View/download PDF
4. Six reference-quality genomes reveal evolution of bat adaptations.
- Author
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Jebb D, Huang Z, Pippel M, Hughes GM, Lavrichenko K, Devanna P, Winkler S, Jermiin LS, Skirmuntt EC, Katzourakis A, Burkitt-Gray L, Ray DA, Sullivan KAM, Roscito JG, Kirilenko BM, Dávalos LM, Corthals AP, Power ML, Jones G, Ransome RD, Dechmann DKN, Locatelli AG, Puechmaille SJ, Fedrigo O, Jarvis ED, Hiller M, Vernes SC, Myers EW, and Teeling EC
- Subjects
- Adaptation, Physiological immunology, Animals, Chiroptera classification, Chiroptera immunology, DNA Transposable Elements genetics, Immunity genetics, Molecular Sequence Annotation standards, Phylogeny, RNA, Untranslated genetics, Reference Standards, Reproducibility of Results, Virus Integration genetics, Viruses genetics, Adaptation, Physiological genetics, Chiroptera genetics, Evolution, Molecular, Genome genetics, Genomics standards
- Abstract
Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols
1 to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our 'Tool to infer Orthologs from Genome Alignments' (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease1 .- Published
- 2020
- Full Text
- View/download PDF
5. The use of stool specimens reveals Helicobacter pylori strain diversity in a cohort of adolescents and their family members in a developed country.
- Author
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Dolan B, Burkitt-Gray L, Shovelin S, Bourke B, Drumm B, Rowland M, and Clyne M
- Subjects
- Adolescent, Adult, Bacterial Proteins genetics, Developed Countries, Family, Gastric Mucosa microbiology, Genotype, Heat-Shock Proteins genetics, Helicobacter Infections microbiology, Helicobacter pylori genetics, Humans, Middle Aged, Phosphoglucomutase genetics, Rec A Recombinases genetics, Young Adult, DNA, Bacterial genetics, Feces microbiology, Helicobacter Infections transmission, Helicobacter pylori classification, Helicobacter pylori isolation & purification
- Abstract
Helicobacter pylori infection occurs within families but the transmission route is unknown. The use of stool specimens to genotype strains facilitates inclusion of complete families in transmission studies. Therefore, we aimed to use DNA from stools to analyze strain diversity in H. pylori infected families. We genotyped H. pylori strains using specific biprobe qPCR analysis of glmM, recA and hspA. Concentration of H. pylori organisms before DNA isolation enhanced subsequent DNA amplification. We isolated H. pylori DNA from 50 individuals in 13 families. T
m data for at least 2 of the 3 genes and sequencing of the glmM amplicon were analyzed. Similar strains were commonly found in both mothers and children and in siblings. However, 20/50 (40%) individuals had multiple strains and several individuals harbored strains not found in other family members, suggesting that even in developed countries sources of infection outside of the immediate family may exist. Whether infection occurs multiple times or one transmission event with several strains occurs is not known but future studies should aim to analyze strains from children much closer to infection onset. The presence of multiple stains in infected persons has implications for antibiotic sensitivity testing and treatment strategies., (Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.)- Published
- 2018
- Full Text
- View/download PDF
6. An optimistic protein assembly from sequence reads salvaged an uncharacterized segment of mouse picobirnavirus.
- Author
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Gonzalez G, Sasaki M, Burkitt-Gray L, Kamiya T, Tsuji NM, Sawa H, and Ito K
- Subjects
- Amino Acid Sequence, Animals, Base Sequence, Female, Genome, Viral, Mice, Inbred BALB C, Phylogeny, High-Throughput Nucleotide Sequencing methods, Picobirnavirus genetics, Viral Proteins genetics
- Abstract
Advances in Next Generation Sequencing technologies have enabled the generation of millions of sequences from microorganisms. However, distinguishing the sequence of a novel species from sequencing errors remains a technical challenge when the novel species is highly divergent from the closest known species. To solve such a problem, we developed a new method called Optimistic Protein Assembly from Reads (OPAR). This method is based on the assumption that protein sequences could be more conserved than the nucleotide sequences encoding them. By taking advantage of metagenomics, bioinformatics and conventional Sanger sequencing, our method successfully identified all coding regions of the mouse picobirnavirus for the first time. The salvaged sequences indicated that segment 1 of this virus was more divergent from its homologues in other Picobirnaviridae species than segment 2. For this reason, only segment 2 of mouse picobirnavirus has been detected in previous studies. OPAR web tool is available at http://bioinformatics.czc.hokudai.ac.jp/opar/.
- Published
- 2017
- Full Text
- View/download PDF
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