A5021657750- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- SARS-CoV-2 and COVID-19 Research
- Gut microbiota and health
- Microbial infections and disease research
- Epigenetics and DNA Methylation
- Antibiotic Resistance in Bacteria
- Animal Virus Infections Studies
- Chromosomal and Genetic Variations
- Probiotics and Fermented Foods
- Malaria Research and Control
- Bacterial Infections and Vaccines
- Salmonella and Campylobacter epidemiology
- RNA modifications and cancer
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- DNA and Nucleic Acid Chemistry
- Plant Disease Resistance and Genetics
- Antifungal resistance and susceptibility
- Aquaculture disease management and microbiota
- RNA and protein synthesis mechanisms
- COVID-19 epidemiological studies
- Cell Image Analysis Techniques
- CRISPR and Genetic Engineering
- Legume Nitrogen Fixing Symbiosis
Quadram Institute
2019-2025
Norwich Research Park
2011-2025
National Institute for Communicable Diseases
2024
United States Food and Drug Administration
2024
University of Pretoria
2024
Animal and Plant Health Agency
2024
University of East Anglia
2024
St Vincent's Hospital Sydney
2024
University of Amsterdam
2024
National Institute for Health Research
2021
Phytohormonal interactions are essential to regulate plant organogenesis. In response the presence of signals from symbiotic bacteria, Nod factors, legume roots generate a new organ: nitrogen-fixing nodule. Analysis mutants in Medicago truncatula CRE1 cytokinin receptor and MtRR4 primary gene expression pattern revealed that acts initial cortical cell divisions later transition between meristematic differentiation zones mature MtCRE1 signaling is required for activation downstream...
Altered intestinal microbiota composition in later life is associated with inflammaging, declining tissue function, and increased susceptibility to age-associated chronic diseases, including neurodegenerative dementias. Here, we tested the hypothesis that manipulating influences development of major comorbidities aging and, particular, inflammation affecting brain retina.
SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because patchy data. Wilkinson et al . curated viral genomes collected 2021 from several countries continent. Outbreaks during 2020 each country were initiated by imported cases, mostly Europe. As developed, case numbers likely many times higher than reported, and subsequent waves appear have more severe. Consequently,...
The Brassicaceae family includes the model plant Arabidopsis thaliana as well a number of agronomically important species such oilseed crops (in particular Brassica napus, B. juncea and rapa) vegetables (eg. rapa oleracea). Separated by only 10-20 million years, are closely related, it is expected that knowledge obtained relating to growth development can be translated into Brassicas for crop improvement. Moreover, certain aspects sufficiently different between warrant studies carried out...
Long-read sequencing can overcome the weaknesses of short reads in assembly eukaryotic genomes; however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated Pacific Biosciences (PacBio) long-read data genomes three relatives model plant Arabidopsis thaliana and assembled all into only a few hundred contigs. To improve contiguities these assemblies, we BioNano Genomics optical mapping Dovetail chromosome conformation capture for genome scaffolding....
We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several nucleocapsid and ORF3a have arisen independently in multiple lineages result loss of recognition epitope-specific cells assessed IFN-γ cytotoxic killing assays. Complete responsiveness was seen due to Q213K the A∗01:01-restricted CD8+ epitope FTSDYYQLY207-215; P13L, P13S, P13T B∗27:05-restricted QRNAPRITF9-17; T362I P365S A∗03:01/A∗11:01-restricted KTFPPTEPK361-369. lines...
The Delta (B.1.617.2) variant was the predominant UK circulating SARS-CoV-2 strain between May and December 2021. How infection compares with previous variants is unknown. This prospective observational cohort study assessed symptomatic adults participating in app-based COVID Symptom Study who tested positive for from 26 to July 1, 2021 (Delta overwhelmingly variant), compared (1:1, age- sex-matched) individuals presenting 28, 2020 6, (Alpha (B.1.1.7) variant). We illness (symptoms,...
Large-scale human genetic data
Salmonella enterica serovar Infantis presents an ever-increasing threat to public health because of its spread throughout many countries and association with high levels antimicrobial resistance (AMR). We analyzed whole-genome sequences 5,284 strains from 74 countries, isolated during 1989-2020 a wide variety human, animal, food sources, compare genetic phylogeny, AMR determinants, plasmid presence. The global population structure diverged into 3 clusters: North American cluster, European...
Abstract Bacterial extracellular vesicles (BEVs) contribute to stress responses, quorum sensing, biofilm formation and interspecies interkingdom communication. However, the factors that regulate their release heterogeneity are not well understood. We set out investigate these in common gut commensal Bacteroides thetaiotaomicron by studying BEV throughout growth cycle. Utilising a range of methods, we demonstrate released at different stages have significantly composition, with early enriched...
DNA-protein cross-links (DPCs) present a formidable obstacle to cellular processes because they are "superbulky" compared with the majority of chemical adducts. Elimination DPCs is critical for cell survival their persistence can lead death or halt cycle progression by impeding DNA and RNA synthesis. To study DPC repair, we have used methyltransferases generate unique adducts in oligodeoxyribonucleotides plasmids monitor both vitro excision vivo repair. We show that HhaI methyltransferase...
Background and Aims Mounting evidence supports an association between cholestatic liver disease changes in the composition of microbiome. Still, role microbiome pathogenesis this condition remains largely undefined. Approach Results To address this, we have used two experimental models, administering alpha‐naphtylisocyanate or feeding a 0.1% 3,5‐diethoxycarbonyl‐1,4‐dihydrocollidine diet, to induce germ‐free mice conventionalized with from wild‐type, specific pathogen‐free animals. Next,...
A high-quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone-based methods are slow expensive, whereas faster, cheaper short-read-only assemblies can be incomplete highly fragmented, which minimizes their usefulness. The last few years have seen the introduction many new technologies assembly. These associated algorithms typically benchmarked on microbial genomes or, if they scale appropriately, larger (e.g., human) genomes....
Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to neuro-inflammatory changes seen Parkinson's disease (PD) and Alzheimer's (AD) or a "brain microbiome" context healthy patients' brain samples. Using 16S rRNA gene sequencing, we tested hypothesis that there is bacterial microbiome. We evaluated samples from subjects individuals suffering PD (olfactory bulb pre-frontal cortex), well murine In...
The COVID-19 pandemic has spread rapidly throughout the world. In UK, initial peak was in April 2020; county of Norfolk (UK) and surrounding areas, which a stable, low-density population, over 3200 cases were reported between March August 2020. As part activities national Genomics Consortium (COG-UK) we undertook whole genome sequencing SARS-CoV-2 genomes present positive clinical samples from region. These collected by four major hospitals, multiple minor care facilities community...
The advent of viral metagenomics, or viromics, has improved our knowledge and understanding global diversity. High-throughput sequencing technologies enable explorations the ecological roles, contributions to host metabolism, influence viruses in various environments, including human intestinal microbiome. However, bacterial metagenomic studies frequently have advantage. adoption advanced like long-read potential be transformative refining viromics metagenomics. Here, we examined...
Extensively drug-resistant (XDR) Salmonella Typhi has been reported in Sindh province of Pakistan since 2016. The potential for further spread is serious concern as remaining treatment options are severely limited. We report the phenotypic and genotypic characterization 27 XDR S. isolated from patients attending Jinnah Hospital, Lahore, Pakistan. Isolates were identified by biochemical profiling; antimicrobial susceptibility was determined a modified Kirby-Bauer method. These findings...
Understanding the genetic basis for a phenotype is central goal in biological research. Much has been learnt about bacterial genomes by creating large mutant libraries and looking conditionally important genes. However, current genome-wide methods are largely unable to assay essential genes which not amenable disruption. To overcome this limitation, we developed new version of “TraDIS” (transposon directed insertion-site sequencing) that term “TraDIS-Xpress” combines an inducible promoter...
Salmonella enterica serovar Infantis is the fifth most common isolated in England and Wales. Epidemiological, genotyping antimicrobial-resistance data for S . isolates were used to analyse English Welsh demographics over a 5 year period. Travel cases associated with mainly from Asia, followed by Europe North America. Since 2000, increasing numbers of had multidrug resistance determinants harboured on large plasmid termed ‘plasmid emerging Infantis’ (pESI). Between 2013 2018, 42 humans food...
We present the complete genome sequence of Azospirillum brasilense Az39, isolated from wheat roots in central region Argentina and used as inoculant extensive intensive agriculture during last four decades. The consists 7.39 Mb, distributed six replicons: one chromosome, three chromids, two plasmids.
Egypt has witnessed elevated incidence rates of multidrug-resistant Klebsiella pneumoniae infections in intensive care units (ICUs). The treatment these is becoming more challenging whilst colistin-carbapenem-resistant K. upsurging. Due to the insufficiently available data on genomic features colistin-resistant Egypt, it was important fill gap and explore characteristics, as well antimicrobial resistance, virulence determinants, molecular mechanisms colistin resistance such a lethal...