A5000114720- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Ruminant Nutrition and Digestive Physiology
- Gut microbiota and health
- Bacteriophages and microbial interactions
- Molecular Biology Techniques and Applications
- Systems Engineering Methodologies and Applications
- Cancer-related molecular mechanisms research
- Spacecraft Design and Technology
- Gene expression and cancer classification
- Plant Virus Research Studies
- Animal Genetics and Reproduction
- Complex Systems and Decision Making
- Genetic Mapping and Diversity in Plants and Animals
- Rocket and propulsion systems research
- Probiotics and Fermented Foods
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Animal Nutrition and Physiology
- Technology Assessment and Management
- RNA modifications and cancer
- Animal Virus Infections Studies
- Genetics, Bioinformatics, and Biomedical Research
- Research in Cotton Cultivation
- T-cell and B-cell Immunology
Roslin Institute
2015-2024
University of Edinburgh
2015-2024
Scotland's Rural College
2021-2024
DSM (Netherlands)
2023-2024
King's College Hospital
2024
Dynetics (United States)
2023
University of Sheffield
2023
Wallops Flight Facility
2023
Marshall Space Flight Center
2013-2022
Wessex Regional Genetics Laboratory
2021
The genome of the zebra finch — a songbird and model for study vertebrate brain, behaviour evolution has been sequenced. Its comparison with chicken genome, only other bird available, shows that genes neural function implicated in cognitive processing song have rapidly evolving lineage. also vocal communication engages much brain transcriptome identifies potential integrator microRNA signals linked to communication. studying Comparison are Moreover, brain. is an important organism several...
Abstract The cow rumen is adapted for the breakdown of plant material into energy and nutrients, a task largely performed by enzymes encoded microbiome. Here we present 913 draft bacterial archaeal genomes assembled from over 800 Gb metagenomic sequence data derived 43 Scottish cattle, using both binning Hi-C-based proximity-guided assembly. Most these represent previously unsequenced strains species. contain 69,000 proteins predicted to be involved in carbohydrate metabolism, 90% which do...
Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialized stomach that adapted to the breakdown plant-derived complex polysaccharides. genomes microbiota encode thousands enzymes digestion plant matter dominates ruminant diet. We assembled 4,941 microbial metagenome-assembled (MAGs) using approximately 6.5 terabases short- and long-read sequence data from 283 cattle. present genome-resolved metagenomics workflow enabled assembly bacterial archaeal...
We have determined the complete genome sequences of a host-promiscuous Salmonella enterica serovar Enteritidis PT4 isolate P125109 and chicken-restricted Gallinarum 287/91. Genome comparisons between these other isolates indicate that S . 287/91 is recently evolved descendent S. Enteritidis. Significantly, has undergone extensive degradation through deletion pseudogene formation. Comparison pseudogenes in with those identified previously host-adapted bacteria reveals loss many common...
Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate selection strategies are not developed. We used sire progeny group differences estimate the influence on rumen a factorial experiment consisting of crossbred breed types diets. Rumen metagenomic profiling was undertaken investigate links between genes emissions or feed conversion...
Abstract Background The domestic pig (Sus scrofa) is important both as a food source and biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, pharmacology to humans. draft reference genome (Sscrofa10.2) of purebred Duroc female established using older clone-based sequencing methods was incomplete, unresolved redundancies, short-range order orientation errors, associated misassembled genes limited utility. Results We present 2 annotated highly contiguous...
The falling cost of DNA sequencing has made the technology af fordable to many research groups, enabling researchers link genomic variants observed phenotypes in a range species. This review focusses on whole exome and its applications humans other traditionally been defined consist only protein coding portion genome; region where mutations are likely affect structure function. There several commercial kits available for number species and, owing highly conserved nature exons, these can be...
Abstract Background Chickens are a highly important source of protein for large proportion the human population. The caecal microbiota plays crucial role in chicken nutrition through production short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from content samples taken 24 chickens belonging to either fast or slower growing breed consuming vegetable-only diet containing fish meal. Results We utilise 1.6 T Illumina data construct 469 draft...
The chicken is the most abundant food animal in world. However, despite its importance, gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community.
As most mechanisms of adaptive immunity evolved during the divergence vertebrates, immune systems extant vertebrates represent different successful variations on themes initiated in their earliest common ancestors. The genes involved elaborating these have been subject to exceptional selective pressures an arms race with highly adaptable pathogens, resulting divergent sequences orthologous and gain loss members gene families as species find solutions challenge infection. Consequently, it has...
The exogenous siRNA pathway is important in restricting arbovirus infection mosquitoes. Less known about the role of PIWI-interacting RNA pathway, or piRNA antiviral responses. Viral piRNA-like molecules have recently been described following mosquitoes and derived cell lines with several arboviruses. has thus suggested to function as an additional small RNA-mediated response infection-induced response. Here we show that are produced naturally mosquito-borne Semliki Forest virus mosquito...
Traditional methods of analysing gene expression data often include a statistical test to find differentially expressed genes, or use clustering algorithm groups genes that behave similarly across dataset. However, these may miss which form differential co-expression patterns under different subsets experimental conditions. Here we describe coXpress, an R package allows researchers identify are co-expressed. We have developed coXpress as means identifying The utility is demonstrated using...
RNA-Seq has emerged as the standard for measuring gene expression and is an important technique often used in studies of human disease. Gene quantification involves comparison sequenced reads to a known genomic or transcriptomic reference. The accuracy that relies on there being enough unique information enable bioinformatics tools accurately assign correct gene. We apply 12 common methods estimate from data show are hundreds genes whose underestimated by one more those methods. Many these...
The emergence and spread of antimicrobial resistance is the most urgent current threat to human animal health. An improved understanding abundance genes associated with microbial colonisation pathogenicity in gut will have a major role reducing contribution production this problem. Here, influence diet on ruminal resistome was assessed digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions concentrate. Two...
Sheep are a key source of meat, milk and fibre for the global livestock sector, an important biomedical model. Global analysis gene expression across multiple tissues has aided genome annotation supported functional mammalian genes. We present large-scale RNA-Seq dataset representing all major organ systems from adult sheep several juvenile, neonatal prenatal developmental time points. The Ovis aries reference (Oar v3.1) includes 27,504 genes (20,921 protein coding), which 25,350 (19,921...
Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing or 16S amplicon sequences. Both of these approaches are limited, however, read length, among other technical and biological factors. A nanopore-based platform, MinION™, produces reads that ≥1 × 104 bp in potentially providing for more precise assignment, thereby alleviating some the limitations inherent determining metagenome composition short reads. We tested...
With the development of ultra-high-throughput technologies, cost sequencing bacterial genomes has been vastly reduced. As more are sequenced, less time can be spent manually annotating those genomes, resulting in an increased reliance on automatic annotation pipelines. However, pipelines produce inaccurate genome and their results often require manual curation. Here, we discuss identify common problems introduced by current process suggests potential solutions.