A5038500818- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Parasitic Infections and Diagnostics
- Diabetes Management and Research
- Enterobacteriaceae and Cronobacter Research
- Alzheimer's disease research and treatments
- Pancreatic function and diabetes
- Environmental DNA in Biodiversity Studies
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Diabetes Treatment and Management
- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- Aquaculture disease management and microbiota
- Protist diversity and phylogeny
- Invertebrate Immune Response Mechanisms
- Plant Virus Research Studies
- Neuroinflammation and Neurodegeneration Mechanisms
- Identification and Quantification in Food
- Diabetes and associated disorders
- Nanopore and Nanochannel Transport Studies
- Fish Ecology and Management Studies
- Plant Disease Resistance and Genetics
- Plant and animal studies
University of Exeter
2015-2024
Agriculture Victoria
2020
Defence Science and Technology Laboratory
2020
Eden Project
2019
The Coordinating Center
2018
Wellcome Trust
2013-2016
Sandwell & West Birmingham Hospitals NHS Trust
2016
Birmingham City Hospital
2016
Nottingham Trent University
2014
Leicestershire Partnership NHS Trust
2012
The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens kilobases (kb) limited only by the length DNA molecules presented to it. device has low capital cost, far most portable sequencer available, and can produce data in real-time. It numerous prospective applications including improving genome sequence assemblies resolution repeat-rich regions. Before such widely adopted, it important assess its performance limitations...
Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from single pre-mRNA with prominent role in the development and function of central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences human mouse cortex. identify novel transcripts not present existing genome annotations, including mapping putative (unannotated) genes fusion incorporating exons multiple genes. Global patterns diversity are...
Biofuels are the most immediate, practical solution for mitigating dependence on fossil hydrocarbons, but current biofuels (alcohols and biodiesels) require significant downstream processing not fully compatible with modern, mass-market internal combustion engines. Rather, ideal structurally chemically identical to fuels they seek replace (i.e., aliphatic n - iso -alkanes -alkenes of various chain lengths). Here we report production such petroleum-replica hydrocarbons in Escherichia coli ....
Significance Seed behavior is known to be highly dependent on the temperature during seed set, but mechanism poorly understood. Here we show that mother plant plays a central role in control of progeny dormancy, integrating long-term memories fruit tissues using same pathway controls flowering time. Regulation coat properties by maternal time pathways effectively passes timing information across generations, aligning with year.
OBJECTIVE Pediatric type 2 diabetes prevalence is increasing, with β-cell dysfunction key in its pathogenesis. The RISE Medication Study compared two approaches—glargine followed by metformin and alone—in preserving or improving function youth impaired glucose tolerance (IGT) recently diagnosed during after therapy withdrawal. RESEARCH DESIGN AND METHODS Ninety-one pubertal, overweight/obese 10–19-year-old IGT (60%) of <6 months duration (40%) were randomized to either 3 insulin...
OBJECTIVE To compare insulin sensitivity (M/I) and β-cell responses in youth versus adults with impaired glucose tolerance (IGT) or drug-naïve, recently diagnosed type 2 diabetes. RESEARCH DESIGN AND METHODS In 66 (80.3% IGT) 355 (70.7% IGT), hyperglycemic clamps were used to measure 1) M/I, 2) acute (0–10 min [first phase]) C-peptide (ACPRg) (AIRg) glucose, 3) steady-state concentrations at plasma of 11.1 mmol/L, 4) arginine-stimulated maximum (ACPRmax) (AIRmax) >25 mmol/L. The...
Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in culturing a lack reference genomes 'universal' gene markers to facilitate surveys. Short-read metagenomic studies have provided clues function first estimates abundance distribution, but assemblies are confounded populations with high levels strain evenness nucleotide diversity (microdiversity), limiting...
Summary Environmental changes during seed production are important drivers of lot‐to‐lot variation in behaviour and enable wild species to time their life history with seasonal cues. Temperature set is the dominant environmental signal determining depth primary dormancy, although mechanisms though which temperature impart dormancy state still only partly understood. We used molecular, genetic biochemical techniques examine mechanism through affects Arabidopsis thaliana dormancy. Here we show...
Glycolysis and oxidative phosphorylation are the fundamental pathways of ATP generation in eukaryotes. Yet microsporidia, endoparasitic fungi living at limits cellular streamlining, has been lost: energy is obtained directly from host or, during dispersive spore stage, via glycolysis. It was therefore surprising when first sequenced genome Enterocytozoonidae - a major family human animal-infecting microsporidians appeared to have lost genes for Here, we sequence analyse genomes additional...
To compare oral glucose tolerance test (OGTT) glucose, C-peptide, and insulin responses sensitivity in youth adults with impaired (IGT) or recently diagnosed type 2 diabetes.A total of 66 (80.3% IGT) 355 (70.7% underwent a 3-h OGTT to assess 1) (1/fasting insulin), 2) C-peptide index (CPI) insulinogenic (IGI) over the first 30 min, 3) incremental areas above fasting post-ingestion (incremental [G-iAUC], [CP-iAUC], area under curve [I-iAUC] responses, respectively).Fasting, 2-h G-iAUC were...
Abstract The long-read sequencers from Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT) offer the opportunity to phase mutations multiple kilobases apart directly sequencing reads. In this study, we used long-range PCR with ONT PacBio two variants 9 kb in RET gene. We also re-analysed data a recent paper which had apparently successfully clinically important haplotypes at CYP2D6 HLA loci. From these analyses, demonstrate PCR-chimera formation during amplification reference...
OBJECTIVE The Restoring Insulin Secretion (RISE) Adult Medication Study compared pharmacological approaches targeted to improve β-cell function in individuals with impaired glucose tolerance (IGT) or treatment-naive type 2 diabetes of <12 months duration. RESEARCH DESIGN AND METHODS A total 267 adults IGT (n = 197, 74%) recently diagnosed 70, 26%) were studied. Participants randomized receive 12 metformin alone, 3 insulin glargine a target fasting <5 mmol/L followed by 9...
Tilapia lake virus (TiLV), a negative sense RNA with 10 segment genome, is an emerging threat to tilapia aquaculture worldwide, outbreaks causing over 90% mortality reported on several continents since 2014. Following severe event in July 2017, we confirmed the presence of TiLV Bangladesh and obtained near-complete genome this isolate, BD-2017. Phylogenetic analysis concatenated coding regions placed BD-2017 clade two isolates from Thailand, separate Israeli South American isolates. However,...
OBJECTIVE Sleep disturbances and circadian misalignment (social jet lag, late chronotype, or shift work) have been associated with worse glycemic control in type 2 diabetes (T2D). Whether these findings apply to adults prediabetes is yet unexplored. We hypothesized that self-reported short sleep, poor sleep quality, and/or are higher glycemia, BMI, blood pressure (BP) recently diagnosed, untreated T2D. RESEARCH DESIGN AND METHODS Our cohort included 962 overweight/obese ages 20–65 years T2D...
Antimicrobial resistance poses one of the greatest threats to global health and there is an urgent need for new therapeutic options. Phages are viruses that infect kill bacteria phage therapy could provide a valuable tool treatment multidrug-resistant infections. In this study, water samples collected by citizen scientists as part Citizen Phage Library (CPL) project, wastewater from Environment Agency yielded phages with activity against clinical strains Klebsiella pneumoniae BPRG1484...
Dominant microorganisms of the Sargasso Sea are key drivers global carbon cycle. However, associated viruses that shape microbial community structure and function not well characterised. Here, we combined short long read sequencing to survey phage communities in virus- cellular fractions at viral maximum (80 m) mesopelagic (200 depths. We identified 2,301 populations from 186 genera. Over half here lacked representation ocean metagenomes, whilst 177 genera genomic databases isolates. Viral...
DNA preserved in degraded beetle (Coleoptera) specimens, including those derived from dry-stored museum and ancient permafrost-preserved environments, could provide a valuable resource for researchers interested species population histories over timescales decades to millenia. However, the potential of these samples as genetic resources is currently unassessed. Here, using Sanger Illumina shotgun sequence data, we explored preservation specimens ground Amara alpina, both environments. Nearly...
OBJECTIVE We examined the glucose response curves (biphasic [BPh], monophasic [MPh], incessant increase [IIn]) during an oral tolerance test (OGTT) and their relationship to insulin sensitivity (IS) β-cell function (βCF) in youth versus adults with impaired or recently diagnosed type 2 diabetes. RESEARCH DESIGN AND METHODS This was both a cross-sectional longitudinal evaluation of participants RISE study randomized metformin alone for 12 months glargine 3 followed by 9 months. At...
Monitoring the spread of viral pathogens in population during epidemics is crucial for mounting an effective public health response. Understanding lineages that constitute infections a can uncover origins and transmission patterns outbreaks detect emergence novel variants may impact course epidemic. Population-level surveillance viruses through genomic sequencing wastewater captures unbiased lineage data, including cryptic asymptomatic undiagnosed infections, has been shown to infection...
The RNA-directed DNA methylation (RdDM) pathway is of central importance to the initiation and maintenance transcriptional gene silencing in plants. directed target sequences by a mechanism that involves production small RNAs RNA polymerase IV long non-coding V. then leads recruitment histone-modifying enzymes, followed establishment silenced chromatin state. Recently MORC6, member microrchidia (MORC) family adenosine triphosphatases (ATPases), has been shown be involved silencing. However,...
Amphibians are experiencing global declines and extinctions, with infectious diseases representing a major factor. In this study we examined the transcriptional response of metamorphic hosts (common frog, Rana temporaria) to two most important amphibian pathogens: Batrachochytrium dendrobatidis (Bd) Ranavirus. We found strong up-regulation gene involved in adaptive immune (AP4S1) at four days post-exposure both pathogens. detected significant Bd, covering (innate immunity, complement...
Trachipleistophora hominis was isolated from an HIV/AIDS patient and is a member of highly successful group obligate intracellular parasites.Here we have investigated the evolution parasite interplay between host gene expression using transcriptomics T. hominis-infected rabbit kidney cells.T. has about 30% more genes than small-genome microsporidians. Highly expressed include those involved in growth, replication, defence against oxidative stress, large fraction uncharacterised genes....