Recent Work
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A consilient view on Eukaryotic Origins
Today we published a manuscript that summarises the current knowledge of the evolutionary history of the cellular life forms on the planet. This is not an easy task and involved evaluating a lot of manuscripts to see what they had to say on the matter. Fortunately,…
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Simultaneous miRNA and mRNA transcriptome profiling…
Abstract Background: miRNA profiling performed in myogenic cells and biopsies from skeletal muscles has previously identified miRNAs involved in myogenesis. Results: Here, we have performed miRNA transcriptome profiling in human affinity-purified CD56+ myoblasts induced to differentiate in vitro. In total, we have identified 60 miRNAs differentially…
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Heterogeneous Models place the Root of the Placental Mammal Phylogeny.
[dropcap style="normal or inverse or boxed"]H[/dropcap]ow are mammals related to one another ? This question has puzzled biologists for decades. In our most recent publication we describe how, using sequence data and sophisticated phylogenetic models, we have resolved this issue. Our analysis shows that the…
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The Landscape for Epigenetic/ Epigenomic Biomedical Resources
[lead]Abstract:[/lead] Recent advances in molecular biology and computational power have seen the biomedical sector enter a new era, with corresponding development of Bioinformatics as a major discipline. Generation of enormous amounts of data has driven the need for more advanced storage solutions and shared access…
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A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals
There are multiple theories on the evolution of genomic imprinting. We investigated whether the molecular evolution of true orthologs of known imprinted genes provides support for theories based on gene duplication or parental conflicts (where mediated by amino-acid changes). Our analysis of 34 orthologous genes demonstrates that the vast majority of mammalian imprinted genes have…
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Selection and the cell cycle: Positive Darwinian Selection in a well-known DNA damage response pathway
Cancer is a common occurrence in multi-cellular organisms and is not strictly limited to the elderly in a population. It is therefore possible that individuals with genotypes that protect against early onset cancers have a selective advantage. In this study the patterns of mutation in the proteins of a well-studied DNA damage response pathway have been examined…
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A case-by-case analysis of imprinted retrogenes
Retroposition is a widespread phenomenon resulting in the generation of new genes that are initially related to a parent gene via very high coding sequence similarity. We examine the evolutionary fate of four retrogenes generated by such an event; mouse Inpp5f_v2, Mcts2, Nap1l5, and U2af1-rs1. These genes are all subject to the epigenetic phenomenon of parental imprinting. We first…
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A role for TLR4 in Clostridium difficile infection and the recognition of surface layer proteins
Clostridium difficile is the etiological agent of antibiotic-associated diarrhoea (AAD) and pseudomembranous colitis in humans. The role of the surface layer proteins (SLPs) in this disease has not yet been fully explored. The aim of this study was to investigate a role for SLPs in the recognition of C. difficile and the subsequent activation of…
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The public goods hypothesis for the evolution of life on Earth.
It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet.
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Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase
Myeloperoxidase (MPO) is a member of the mammalian heme peroxidase (MHP) multigene family. Whereas all MHPs oxidize specific halides to generate the corresponding hypohalous acid, MPO is unique in its capacity to oxidize chloride at physiologic pH to produce hypochlorous acid (HOCl), a potent microbicide that contributes to neutrophil-mediated host defense against infection.
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Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure
Synonymous codon usage bias has typically been correlated with, and attributed to translational efficiency. However, there are other pressures on genomic sequence composition that can affect codon usage patterns such as mutational biases. This study provides an analysis of the codon usage patterns in Arabidopsis thaliana in relation to gene expression levels, codon volatility, mutational…
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Colon Cancer Genes Exhibit Signatures of Positive Selection at Functionally Important Sites
Cancer, much like most human disease, is routinely studied by utilizing model organisms. Of these model organisms, mice are often dominant. However, our assumptions of functional equivalence fail to consider the opportunity for divergence conferred by ~180 Million Years (MY) of independent evolution between these species. For a given set of human disease related genes,…