A5018021274- HIV Research and Treatment
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- HIV/AIDS drug development and treatment
- Herpesvirus Infections and Treatments
- Malaria Research and Control
- HIV/AIDS Research and Interventions
- Mosquito-borne diseases and control
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- RNA modifications and cancer
- Primate Behavior and Ecology
- Virology and Viral Diseases
- Cytomegalovirus and herpesvirus research
- Genetic diversity and population structure
- Vector-borne infectious diseases
- Hepatitis C virus research
- Plant Pathogens and Fungal Diseases
- Immune Cell Function and Interaction
- Plant Pathogens and Resistance
- T-cell and Retrovirus Studies
- Parasite Biology and Host Interactions
- Machine Learning in Bioinformatics
- Bird parasitology and diseases
- Animal Disease Management and Epidemiology
University of Edinburgh
2016-2025
Centre for Immunity, Infection and Evolution
2016-2025
University of Nottingham
1999-2022
Queen's Medical Centre
1999-2022
Institut de Biologia Evolutiva
2015-2020
Forest Research
2017
Florida International University
2014
Kelowna General Hospital
2013
Auburn University at Montgomery
1993-2011
University of Copenhagen
2011
A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set highly expressed genes from species to assess relative merits each codon, and score for gene calculated frequency use all codons in that gene. assesses extent which selection has been moulding pattern usage. In respect it useful predicting level expression gene, assessing adaptation viral their hosts, making comparisons different organisms. may also give an...
Comparison of plant mitochondrial (mt), chloroplast (cp) and nuclear (n) DNA sequences shows that the silent substitution rate in mtDNA is less than one-third cpDNA, which turn evolves only half as fast nDNA. The slower cpDNA probably due to a lower mutation rate. Silent rates mammalian mtDNAs differ by one or two orders magnitude, whereas nDNAs may be similar. In both at synonymous sites noncoding inverted repeat greatly reduced comparison single-copy sequences. evolution appears have...
A strategy is described for the rapid alignment of many long nucleic acid or protein sequences on a microcomputer. The program can handle up to 100 1200 residues each. approach based progressively aligning according branching order in an initial phylogenetic tree. results obtained using package appear be as sensitive those from any other available method.
Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon revealed two distinct groups of One group corresponds to highly expressed genes, and much more extreme preference. The pattern observed is consistent with that expected if a need match abundant tRNAs, intermediacy tRNA-mRNA interaction energies are important selective constraints. Thus in the shows higher correlation tRNA abundance, greater degree third base pyrimidine bias, lesser tendency...
Human immunodeficiency virus type 1 (HIV-1), the cause of human acquired syndrome (AIDS), is a zoonotic infection staggering proportions and social impact. Yet uncertainty persists regarding its natural reservoir. The most closely related to HIV-1 simian (SIV) thus far identified only in captive members chimpanzee subspecies Pan troglodytes . Here we report detection SIVcpz antibodies nucleic acids fecal samples from wild-living P. t. apes southern Cameroon, where prevalence rates some...
The origin and taxonomic status of domesticated cattle are controversial. Zebu taurine breeds differentiated primarily by the presence or absence a hump have been recognized as separate species (Bos indicus Bos taurus). However, most widely held view is that both types derive from single domestication event 8000-10,000 years ago. We examined mtDNA sequences representatives six European (taurine) breeds, three Indian (zebu) four African (three zebu, one taurine) breeds. Similar levels average...
The divergence between monocots and dicots represents a major event in higher plant evolution, yet the date of its occurrence remains unknown because scarcity relevant fossils. We have estimated this by reconstructing phylogenetic trees from chloroplast DNA sequences, using two independent approaches: rate synonymous nucleotide substitution was calibrated maize, wheat, rice, whereas nonsynonymous angiosperms bryophytes. Both methods lead to an estimate monocot-dicot at 200 million years...
ABSTRACT Accurate identification of the transmitted virus and sequences evolving from it could be instrumental in elucidating transmission human immunodeficiency type 1 (HIV-1) developing vaccines, drugs, or microbicides to prevent infection. Here we describe an experimental approach analyze HIV-1 env genes as intact genetic units amplified plasma virion RNA by single-genome amplification (SGA), followed direct sequencing uncloned DNA amplicons. We show that this strategy precludes vitro...
Summary We describe a family of highly conserved, Enterobacterial Repetitive Intergenic Consensus (ERIC) sequences, 14 which have been identified in Escherichia coli and Salmonella typhimurium further three other enterobacterial species ( Yersinia pseudotubercuiosis, Kiebsiella pneumoniae Vibrio cholerae ). ERIC sequences are 126 bp long appear to be restricted transcribed regions the genome, either intergenic polycistronic operons or untranslated upstream downstream open reading frames....
It has often been suggested that differential usage of codons recognized by rare tRNA species, i.e. "rare codons", represents an evolutionary strategy to modulate gene expression. In particular, regulatory genes are reported have extraordinarily high frequency codons. From E. coli we compiled codon data for highly expressed genes, moderately/lowly and genes. We identified a clear general trend in bias, from the very bias seen attributed selection, rather low other which seems be more...
The patterns of synonymous codon usage in 91 Drosophila melanogaster genes have been examined. Codon varies strikingly among genes. This variation is associated with differences G+C content at silent sites, but (unlike the situation mammalian genes) these are not correlated intron base composition and so easily explicable terms mutational biases. Instead, those high resulting from a strong "preference" for particular subset codons that mostly C-ending, appear to be more highly expressed...