A5076931409- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- Animal Virus Infections Studies
- Transgenic Plants and Applications
- Genomics and Phylogenetic Studies
- Microbial Inactivation Methods
- DNA Repair Mechanisms
- DNA and Nucleic Acid Chemistry
- Advanced Fluorescence Microscopy Techniques
- Pharmacogenetics and Drug Metabolism
- Bacterial Genetics and Biotechnology
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Mass Spectrometry Techniques and Applications
- COVID-19 epidemiological studies
- Bacteriophages and microbial interactions
- Computational Drug Discovery Methods
- Fungal and yeast genetics research
- Advanced biosensing and bioanalysis techniques
- Yeasts and Rust Fungi Studies
- Microfluidic and Bio-sensing Technologies
- Environmental DNA in Biodiversity Studies
- Biosensors and Analytical Detection
- Immune responses and vaccinations
Wellcome Sanger Institute
2015-2022
Genomics (United Kingdom)
2021-2022
Imperial College London
2022
Quadram Institute
2022
Clarendon College
2015
University of Oxford
2012-2015
Science Oxford
2014
Centre National de la Recherche Scientifique
2009-2012
Centre de Génétique Moléculaire
2009-2012
Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations the partially domesticated yeast Saccharomyces cerevisiae its wild relative paradoxus. These population-level high-quality genomes comprehensive annotation enable...
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long reads with average fragment lengths over 10,000 base-pairs maximum reaching 100,000 base- pairs. Compared short reads, the assemblies obtained from long-read platforms have much higher contig continuity genome completeness fragments able to extend paths into problematic or repetitive regions. Many successful assembly applications technology been reported ranging small...
Abstract The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use dense genomic surveillance data generated by COVID-19 Genomics UK Consortium reconstruct dynamics 71 different lineages in each 315 English local authorities between September 2020 and June 2021. This analysis reveals a series subepidemics peaked early autumn 2020, followed jump transmissibility B.1.1.7/Alpha...
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,...
The fidelity of DNA polymerases depends on conformational changes that promote the rejection incorrect nucleotides before phosphoryl transfer. Here, we combine single-molecule FRET with use polymerase I and various mutants to highlight mechanisms by which active-site side chains influence transitions free-energy landscape underlie decisions in synthesis. Ternary complexes high derivatives complementary dNTPs adopt mainly a fully closed conformation, whereas conformation value between those...
The emergence of next-generation sequencing (NGS) technologies in the past decade has allowed democratization DNA both terms price per sequenced bases and ease to produce libraries. When it comes preparing libraries for Illumina, current market leader, a plethora kits are available can be difficult users determine which kit is most appropriate efficient their applications; main concerns being not only cost but also minimal bias, yield time efficiency. We compared 9 commercially library...
DNA polymerases maintain genomic integrity by copying with high fidelity. A conformational change important for fidelity is the motion of polymerase fingers subdomain from an open to a closed conformation upon binding complementary nucleotide. We previously employed intra-protein single-molecule FRET on diffusing molecules observe conformations in polymerase–DNA complexes. Here, we used same ruler surface-immobilized complexes fingers-opening and closing individual real time. Our results...
Studying the structure and dynamics of proteins in live cells is essential to understanding their physiological activities mechanisms, validating vitro characterization. Improvements labeling imaging technologies are starting allow such vivo studies; however, a number technical challenges remain. Recently, we developed an electroporation-based protocol for internalization, which allows biomolecules labeled with organic fluorophores be introduced at high efficiency into E. coli (Crawford et...
CPR (NADPH-cytochrome P450 reductase) is a multidomain protein containing two flavin-containing domains joined by connecting domain thought to control the necessary movements of catalytic during electronic cycles. We present detailed biochemical analysis chimaeric CPRs composed association human or yeast FMN with alternative connecting/FAD domains. Despite assembly having relatively large evolutionary distance between them, our data support idea that integrity cycle conserved in enzymes,...
The ability to study biomolecules in vivo is crucial for understanding their function a biological context. One powerful approach involves fusing molecules of interest fluorescent proteins such as GFP expression, localization and function. However, its derivatives are significantly larger less photostable than organic fluorophores generally used vitro experiments, this can limit the scope investigation. We recently introduced straightforward, versatile high-throughput method based on...
Since the publication of first draft human genome 20 years ago, several novel sequencing technologies have emerged. Whilst some drive cost DNA down, others address difficult parts which remained inaccessible so far. But next-generation (NGS) landscape is a fast-changing environment and one can easily get lost between second- third- generation sequencers, or pros cons short- versus long-read technologies. In this beginner’s guide to NGS, we will review main NGS available in 2021. We compare...
NADPH-cytochrome P450 reductase (CPR) is the favoured redox partner of microsomal cytochromes P450. This protein composed two flavin-containing domains (FMN and FAD) connected by a structured linker. An active CPR chimera consisting yeast FMN human FAD has been produced, purified crystallized. The crystals belonged to monoclinic space group C2 contained one molecule per asymmetric unit. Molecular replacement was performed using published rat structures as search models. initial...
The ability to study biomolecules in vivo is crucial for understanding their function a biological context. One powerful approach involves fusing molecules of interest fluorescent proteins such as GFP expression, localization and function. However, its derivatives are significantly larger less photostable than organic fluorophores generally used vitro experiments, this can limit the scope investigation. We recently introduced straightforward, versatile high-throughput method based on...
Abstract Structural rearrangements have long been recognized as an important source of genetic variation with implications in phenotypic diversity and disease, yet their evolutionary dynamics are difficult to characterize short-read sequencing. Here, we report long-read sequencing for 12 strains representing major subpopulations the partially domesticated yeast Saccharomyces cerevisiae its wild relative paradoxus . Complete genome assemblies annotations generate population-level reference...
This SOP describes the procedure for generating cDNA from SARS-CoV-2 viral nucleic acid extracts and subsequently producing 400nt amplicons tiling genome using V4.1 nCov-2019 primers (ARTIC) in multiplex PCR. Illumina-compatible sequencing libraries are then made directly these a second PCR step, obviating need conventional library preparation. The products of PCRs equivolume pooled quantitated, prior to on Illumina NovaSeq. It is an adaptation COVID-19 ARTIC v3 amplicon protocol which can...