A5089241642- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- SARS-CoV-2 and COVID-19 Research
- RNA and protein synthesis mechanisms
- Animal Virus Infections Studies
- Bacteriophages and microbial interactions
- SARS-CoV-2 detection and testing
- Genetic diversity and population structure
- Genomics, phytochemicals, and oxidative stress
- Glutathione Transferases and Polymorphisms
- HIV Research and Treatment
- Antibiotic Resistance in Bacteria
- Cancer-related molecular mechanisms research
- vaccines and immunoinformatics approaches
- Retinal Development and Disorders
- Osteoarthritis Treatment and Mechanisms
- COVID-19 Clinical Research Studies
- Genital Health and Disease
- Antibiotics Pharmacokinetics and Efficacy
- Plant Virus Research Studies
- Plant nutrient uptake and metabolism
- Circular RNAs in diseases
- Viral gastroenteritis research and epidemiology
- RNA regulation and disease
- Salmonella and Campylobacter epidemiology
Quadram Institute
2021-2023
Norwich Research Park
2013-2023
University of East Anglia
2008-2016
Centre for High Performance Computing
2010
University of Cape Town
2010
Abstract Summary: RDP3 is a new version of the RDP program for characterizing recombination events in DNA-sequence alignments. Among other novelties, this includes four analysis methods (3SEQ, VISRD, PHYLRO and LDHAT), tests hot-spots, range matrix visualizing over-all patterns within datasets recombination-aware ancestral sequence reconstruction. Complementary to high degree flow automation, also has highly interactive detailed graphical user interface that enables more focused hands-on...
Abstract To manage and conserve biodiversity, one must know what is being lost, where, why, as well which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples eukaryotes or environmental DNA . Here, we validate metabarcoding by testing it against three high‐quality standard data sets that were collected in Malaysia (tropical), China (subtropical) United Kingdom (temperate) comprised 55,813 arthropod bird specimens...
In recent studies, phylogenetic networks have been derived from so-called multilabeled trees in order to understand the origins of certain polyploids. Although used these studies were constructed using sophisticated techniques analysis, presented inferred ad hoc arguments that cannot be easily extended larger, more complicated examples. this paper, we present a general method for constructing such networks, which takes as input tree and outputs network with desirable properties. To...
Protecting the lens against oxidative stress is of great importance in delaying onset cataract. Isothiocyanates, such as sulforaphane (SFN), are proposed to provide cytoprotection stress. We therefore tested ability SFN perform this role cells and establish its delay cataract.The human epithelial cell line FHL124 whole porcine culture systems were used. The ApoTox-Glo Triplex Assay was used assess survival, cytotoxicity, apoptosis. MTS assay populations. To determine levels DNA strand...
Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains challenging endeavor. Despite its importance evolutionary studies, identifying that exhibit such received comparatively less attention detection framework. Here, we extend quartet-mapping based method to enable identification recombinant without prior specifications either query and reference sequences. Through simulations evaluate different statistics...
Abstract Background Gene trees that arise in the context of reconstructing evolutionary history polyploid species are often multiply-labeled, is, same leaf label can occur several times a single tree. This property considerably complicates task forming consensus collection such compared to usual phylogenetic trees. Results We present method for computing tree multiply-labeled As with well-known greedy approach trees, our first breaks given gene into set clusters. It then aims insert these...
Abstract Summary: Recent advances in gene sequencing for polyploid species, coupled with standard phylogenetic tree reconstruction, leads to trees which the same species can label several leaves. Such multi-labeled are then used reconstruct evolutionary history of question. However, this reconstruction process requires new techniques that not available current software packages. Here, we describe package PADRE (Package Analyzing and Displaying Reticulate Evolution) implements such...
The emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning vaccine-induced immunity over time contributed to increased rates breakthrough infection specifically among healthcare workers (HCWs). genomic surveillance is an important tool for timely detection characterization circulating as well monitoring new strains. Our study first national HCWs in Lebanon.
Myotonic dystrophy (DM) is caused by a triplet repeat expansion in the non-coding region of either DMPK (DM1) or CNBP (DM2) gene. Transcription expanded causes accumulation double-stranded RNA (dsRNA) DM cells. We sought to determine how expression varied phenotype typical DM. Global transcription was measured and non-DM cataract samples using Illumina Bead Arrays. were compared with lists differentially expressed genes (P≤ 0.05) prepared. Gene set enrichment analysis Interferome database...
The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including Eastern Mediterranean Region. Lebanon experienced its largest wave infections from January April 2021. Limited genomic surveillance was undertaken, just 26 SARS-CoV-2 genomes available for this period, nine which were travellers detected by other countries. Additional genome sequencing is thus needed allow variants circulation. In total, 905 sequenced using ARTIC protocol....
Abstract Background The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including Eastern Mediterranean Region. Lebanon experienced its largest wave infections from January April 2021. Limited genomic surveillance was undertaken, just twenty six SARS-CoV-2 genomes available for this period, nine which were travellers detected by other countries. Additional genome sequencing is thus needed allow variants circulation. Methods Nine hundred...
Recently, multi-labeled trees have been used to help unravel the evolutionary origins of polyploid species. A tree is same as a phylogenetic except that more than one leaf may be labeled by single species, so set can regarded multiset. In contrast trees, which efficiently encoded in terms certain bipartitions their sets, we show it NP-hard decide whether collection multiset represented tree. Even so, also possible generalize well-known condition characterizes when encodes Using this...
Abstract Campylobacter species are the major cause of bacterial gastroenteritis. As there is no effective vaccine, combined with rapid increase in antimicrobial resistant strains, a need to identify new targets for intervention. Essential genes those that necessary growth and/or survival, making these attractive targets. In this study, comprehensive transposon mutant libraries were created six C. jejuni four coli strains and one lari hyointestinalis strain, allowing cannot tolerate insertion...
Abstract Transposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions within repeating genomic sequences where repeat units are longer than read length. To overcome this limitation, we have developed using Oxford Nanopore technology that generates and uses long reads; called LoRTIS (Long-Read...
We report here the identification of four gene functions principal importance for tolerance meropenem stress in Escherichia coli : cell division, envelope synthesis and maintenance, ATP metabolism, transcription regulation. The primary mechanism β-lactam antibiotics such as is inhibition penicillin binding proteins, thus interfering with peptidoglycan crosslinking, weakening envelope, promoting lysis. However, recent systems biology approaches have revealed numerous downstream effects that...
Abstract The emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning vaccine-induced immunity over time contributed to increased rates breakthrough infection specifically among healthcare workers (HCWs). genomic surveillance is an important tool for timely detection characterization circulating as well monitoring new strains. Our study first national HCWs in Lebanon. We collected 250 samples from five hospitals across Lebanon between December 2021 January 2022....
Colistin is an antibiotic that has seen increasing clinical use for the treatment of human infections caused by Gram-negative pathogens, particularly due to emergence multidrug-resistant pathogens. resistance also a growing problem and typically results from alterations lipopolysaccharides mediated phosphoethanolamine (pETn) transferase enzymes which can be encoded on chromosome, or plasmids. In this study, we used ‘TraDIS-Xpress’ (Transposon Directed Insertion site Sequencing with...
Abstract To date transposon insertion sequencing (TIS) methodologies have used short-read nucleotide technology. However, sequences are unlikely to be matched correctly within repeated genomic regions which longer than the sequence read. This drawback may overcome using long-read We developed a suite of new analysis tools, “LoRTIS software suite” (LoRTIS-SS), that produce site mapping data for reference genome data. Long-read can applied TIS, this enables unique sites long sequences. Here we...