In work lead by Dr Karen Siu Ting she addresses an important question in phylogenomics using 18 amphibian species. She chose to work on this Lissamphibian group because there is significant conflict over their relationships to one another, and because transcriptomes are increasingly being used to overcome the lack of genomic data for this clade.…
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In the May issue of MBE we have published the outcome of a collaboration with Dr Marc Tollis, Prof Carlo Maley, Prof Per Palsbol and others where we sequenced and analysed the genome of the humpback whale. The paper aimed to Peto’s Paradox – where large-bodied and long-lived animals do not suffer higher risks of…
In this paper in MBE we examined the selective pressure variation across genomically imprinted genes in the inbreeding species Arabidopsis thaliana. Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which…
In a recent collaboration with Joe Cockburn et al published in Structure – we reveal the structure of the cargo binding TPR domain of kinesin light chain bound to the cargo molecule JIP3. Along with solving the crystal structure – the biophysical and evolutionary analysis we carried out have revealed the kinesin-1 cargo binding site…
I am looking for two highly motivated computational evolutionary biologists with excellent programming and computing skills to join my team at the University of Nottingham. Both positions are fully funded for two years with an option to extend pending grant success. Both positions are computational in nature and require strong programming, molecular evolution and genome…
On the 1st of August Ann had her PhD viva and did a wonderful job of bringing her hard work to life for her panel of examiners. Ann’s PhD was primarily computational, involving sequence similarity network analysis of primate genomes, the identification of gene fusions, and the analysis of their transcription and translation profiles using…
We are very excited and proud to announce that Ray has successfully defended his PhD on Friday 11th August 2017. Dr Ray Moran graduated from DCU on the 2nd November 2017. Here is a photo of our very proud looking and newest Doctor !;-)
On May 21st 2017 I was officially elected as Fellow of the Linnean Society. I am very excited to receive this honour and look forward to the ceremony. “Founded in 1788, the Society takes its name from the Swedish naturalist Carl Linnaeus… It is the oldest active biological society… As it moves into its third…
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Our latest article we discuss some recent work from Thijis Ettema’s group on discovery of a new member of the Asgard group of Archaea. The Asgard “superphylum” is a group of archaea that provide us with important information about the origin of eukaryotes. The image from our news and views article shown here summarises the relationship between Bacteria…
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Save the date: 21st June for the launch of Leeds Omics. You are invited to the launch of Leeds Omics on Tuesday morning (21st June) at 10.00am. Please register for this event using the following link: http://leedsomicslaunch.eventbrite.co.uk Leeds Omics is a cross faculty initiative between the Faculty of Biological Sciences and the Faculty of Medicine…
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by Chris Bunting, Senior Press Officer The family tree of the largest group of mammals—those that nourish their young with placentas—divided later than scientists previously thought, according to a new study. The findings show that one of the great mammal lineages—the xenartha group, which includes armadillos, sloths and anteaters and is today found only in…
I had the tremendous pleasure of teaching a very talented and motivated bunch of students on an EMBO (European Molecular Biology Organisation) funded course. The course was delivered in the amazon jungle city of Iquitos Peru, the largest jungle city in the world unconnected by road to the rest of the world. It was…
Dr O’Connell has been invited to the board of associate editors for Genome Biology and Evolution (GBE). GBE is an Oxford University Press journal owned by the Society for Molecular Biology and Evolution, and is in the top ten evolutionary biology journals internationally and has an impact factor of 4.2. “I feel honoured to have been…
More support for Atlantogenata. This week an international collaborative effort has tackled a major challenge in phylogenetics – the interrelationships amongst placental mammals. The paper has just been published in Genome Biology and Evolution (please click here to see the paper). In work led by Dr James Tarver and Dr Davide Pisani (with contributions from…
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In our latest work on the origin of eukaryotes published in a special issue of Philosophical Transactions of the Royal Society B (link to full issue) compiled and edited by Professor Martin Embley and Dr Tom Williams, we advocate a ‘domain-free’ view of the history of life. Debates about whether there should be two domains…
So I took to the stage to talk about evolution and mass extinction for the TEDx DCU event in 2015. It was pitched for the general audience and was really good fun. It is a real challenge to get these concepts across and not bore people to death ! I am not sure I have…
It was freezing and there was a northerly wind whipping through DCU campus but that wasn’t going to keep us from smiling ! We had a double celebration in our group today with the graduation of Dr Andrew Webb and Dr Kathryn McRae photographed here with our president Prof Brian Mac Craith. Kathryn was supervised…
Super treat in the lab this week. The journal Science decided to feature one of our publications in its “Editor’s Choice” section. The author of the little piece is Laura Zahn and she chose to feature the work, which was published in Molecular Biology and Evolution. It is always a real thrill to have work…
This week the genome and transcriptome of the Bowhead whale was published in the journal Cell reports. For more please see our publications page for the pdf or click here This work was carried out by Dr Andrew Webb (first author) and Dr Mary O’Connell in collaboration with an international team of experts and was led by…
“Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor” Baldwin et al Science 2014 Why study birds to understand sensory perception? Birds are a group of therapod dinosaurs that evolved during the mid Mesozoic era (~150 million years ago). They represent one of the most diverse extant vertebrate clades…
Our research was featured in the Irish times today (5th November 2014). I think it is wonderful to bring fundamental research to the general audience. The business of understanding life and how it works underpins all of our therapies and treatments for the future … this is where it all begins … http://www.irishtimes.com/news/science/great-scientific-mysteries-the-researchers-puzzle-it-out-1.1964445
Dr Mark Lynch graduates with his PhD from DCU today the 5th November 2014. Jointly supervised by Professor Christine Loscher and Dr Mary J. O’Connell. Huge congratulations on a job well done !;-)
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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, there are many different kinds of data that can be…
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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 expressed during myogenic differentiation. Many were not known for being differentially…
[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 root of the placental mammal phylogeny is the common ancestor…
[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 through a range of public repositories. The number of such biomedical…
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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…
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…
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…
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…
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.
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.
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…
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,…