Science Bomb!

On Friday Chris Spencer gave the PPS (Pritchard/Przeworski/Stephens) lab meeting as part of a trip to Chicago. Chris talked about his work in Oxford on association studies in a number of common genetic diseases being studied by the Wellcome Trust Case Control Consortium.

Beforehand I dropped the Science Bomb, a new innovation this year (for which I think Barbara Engelhardt is responsible) where someone talks about a particularly interesting or timely article. Dan Gaffney pointed me in the direction of a PLoS Biology paper titled Reawakening Retrocyclins: Ancestral Human Defensins Active Against HIV-1.

The subject of the study is a human pseudogene known as retrocyclin, which has been shown to confer resistance to HIV-1 infection in human cell lines. The pseudogene is expressed naturally in several human tissues, but not translated into protein owing to a premature stop codon. The paper's authors reawakened retrocyclin using aminoglycosides, a class of antibiotics that cause (as a side effect) a degree of mis-translation and hence allow "read-through" of the stop codon. You can see the slides from my Science Bomb here.

Neolithic origin of Campylobacter jejuni

As part of a recent trip to the University of Edinburgh to visit Andrew Rambaut, I gave a talk on some work of mine published in the February edition of Molecular Biology and Evolution and subsequently recommended on the Faculty of 1000 website about the evolution of the gut pathogen Campylobacter jejuni.

Part of the paper is concerned with the issue of the timescale of Campylobacter evolution, and using longitudinal samples of C. jejuni DNA sequences we attempted to calibrate the molecular clock in a similar way to that which is standard practice for viruses.

We detected surprisingly rapid evolution - 1,000 times faster than traditional estimates - which would place the split of C. jejuni from its closest relative C. coli during the Neolithic revolution. Interestingly, the point estimate of 6,500 years ago for the split from C. coli - which preferentially infects swine - coincides with the spread of pig domestication in the Near East and Europe in the 4th millennium BC.

The date is controversial because the traditional dating method, which is based on bounding deep phylogenetic splits such as the common ancestor of mitochondria and bacteria, would place the divergence of C. jejuni and C. coli closer to 10 million years ago.

After the seminar I had an interesting discussion with Paul Sharp, who was in the audience. Prof Sharp is actively researching the causes of conflict between long-term and short-term estimates of the rate of evolution in viruses. As he points out, short-term rate estimates (usually based on longitudinally-sampled viral sequences) frequently suggest that evolution is occurring much more rapidly than long-term estimates (based on deeper calibration points, such as co-phylogeny of host and pathogen). This phenomenon, observed in HIV and hepatitis C among others, may be caused by overly simplistic models of sequence evolution.

So how plausible is it that a ubiquitous bacterial pathogen such as C. jejuni evolved as recently as the Neolithic, possibly in response to changes brought about by agriculture or animal husbandry? Longitudinal studies of Helicobacter pylori and Neisseria gonnorhoeae have obtained similarly rapid rates of bacterial evolution, and evidence is mounting that the Neolithic revolution played an important role in creating new niches for human, plant and animal pathogens. Perhaps the best prospect for resolving these questions will be studies of ancient DNA preserved from the period in question.

omegaMap at BioHPC

All evolutionary biologists wishing to make use of omegaMap now have access to a high performance parallel computing cluster via the internet courtesy of Cornell's CBSU and Microsoft. The software, which allows the detection of selection and recombination in DNA or RNA sequences, can be run via the web interface at cbsuapps.tc.cornell.edu/omegamap.aspx, or downloaded as part of the BioHPC suite.

The web interface consists of a simple form where users can upload their configuration file and sequences in FASTA format. Completed jobs are notified by e-mail. To learn more about the project visit the CBSU home page.

Meanwhile, I am working on several major updates to omegaMap, the most interesting of which will probably be the development of a new model that allows for the joint analysis of natural selection acting on sequences from different populations or species. The aim is to integrate population genetic and phylogenetic models of selection in order to exploit the signal of selection contained both in polymorphism within populations (or species) and divergence between them. I will be presenting progress on this work, in the context of hominid evolution, at the 2009 SMBE meeting in Iowa City this June.

Human Evolution in New York City

Rounding off a hectic end to 2008 was a trip to visit Molly, currently on sabbatical in New York city. Joanna and I flew out to spend the final weekend before Christmas discussing projects and frequenting the local coffee shops, restaurants and bars. I took the opportunity to visit the American Museum of Natural History adjacent to Central Park after reading about its dinosaur collections in the Catcher in the Rye; pictured is an Allosaurus skeleton, which stands in the main entrance hall. Of particular interest was the Spitzer Hall of Human Origins which features a wealth of fossil remains and artefacts including a cast of the Laetoli footprints and a diorama of an Australopithecus afarensis nuclear family. Fittingly, the very focus of the New York trip was to discuss the on-going project to characterize natural selection between hominid species.

Inferring niche membership from genetic diversity

Each Wednesday the Ecology and Evolution department run a journal club called Noon Illumination, and this week I volunteered to lead discussion on a recent article titled Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton (Science 320: 1081-5), by Dana Hunt and colleagues based at MIT and Ghent. I originally prepared the presentation for a Bacterial Metagenomics workshop in Berlin this July, organized by Daniel Falush.

Of central interest in the paper is a novel methodology that infers habitat/niche based on ecological variables and DNA sequencing in the family of marine bacteria Vibrionaceae. That places it in the wider context of methods that attempt to predict phenotype (in this case niche) from genotype. Their approach is an elegant extension of familiar phylogenetic methods to model habitat switching over evolutionary time. Based on arguments put forward by Christophe Fraser and colleagues, the paper reasons that the ancestral habitat switches they detect are likely to be adaptive because the rate of recombination eclipses the mutation rate sufficiently to preclude the possibility of neutral genetic clustering.

However the high rate of recombination raises some difficulties of interpretation. The principal phylogenetic reconstruction was based on the hsp60 gene, but by sequencing other housekeeping genes, Hunt and colleagues found that in some cases, recombination between genes caused an artefactual habitat switch in the hsp60 ancestry that was not evident in the other genes. Using a permutation test, I found evidence for recombination within the vibrio hsp60 genes, which may confound the phylogenetic reconstruction of evolutionary relationships (Schierup and Hein 2000). On a more philosophical note, suppose you could directly observe ancestral habitat switches. Would that be strong evidence for adaptation? An association between habitat and genetic lineage is probably not sufficient to demonstrate the action of natural selection. On the other hand, frequent recombination could empower genome-wide scans for extreme association between genes and habitats, that would provide stronger support for adaptation.

You can view a PDF of the presentation of this stimulating article in our journal club here.

Tracing the source of campylobacteriosis

Finally, it's out! The main piece of work to come out of my two-year period as Research Associate at Lancaster University is published today in PLoS Genetics.

The article reports a study in Lancashire, England, of the bacterium Campylobacter jejuni, the primary cause of bacterial gastro-enteritis in developed countries. We inferred the source of infection in 1,200 patients by comparing the DNA sequences of C. jejuni taken from those patients to 1,100 taken from different animal species and the environment. The result: livestock are the source of infection in 97% of cases.

In addition to preparing the figures, approving final drafts, and producing a press release in conjunction with the PLoS Genetics and university press offices, I have spent much of my time over the last three weeks revising a companion paper on the evolution of C. jejuni. On Friday that was resubmitted to Molecular Biology and Evolution, and should it be accepted, will draw a line under my Lancaster projects.

Visit to Kilifi

The final days in Paris were taken up by revisions to a paper submitted in April to PLoS Genetics. With luck the revisions will be accepted and that paper will be coming out soon. From Paris I flew to Mombasa, Kenya to begin a 3 week collaboration with Caroline Buckee at the KEMRI-Wellcome Trust research unit in Kilifi. Caroline, Pete Bull and others at Kilifi work on the evolution of var genes in Plasmodium falciparum, the most common and lethal agent of malaria. The var genes encode a family of proteins expressed by the pathogen on the membrane of infected red blood cells. Implicated in pathogenesis, these genes are highly diverse in order to evade the host immune system. The first step in piecing together their evolutionary history is to align the sequences - a task made difficult by the abundance of insertions and deletions. From there we hope to characterize the relative importance of gene duplication and homologous and non-homologous recombination in driving the evolution of these genes.

Exchange with the Institut Pasteur

My position at the University of Chicago is funded by a grant awarded to Molly by the National Institutes of Health (NIH) to detect the signature that natural selection has left on the human genome. One of our collaborations is with the human genetics lab of Lluis Quintana-Murci at the Institut Pasteur in Paris, and I'm making the first of a number of exchange visits to strengthen the ties between two labs.

Lluis' group are interested in the selection pressure that pathogens have exerted on the human genome, and in particular a family of genes involved in the immune system known as toll-like receptors. The idea is that together we develop methods to detect and quantify selection in these genes by comparison to neutral regions in individuals from around the world. Among the people involved in the project is Luis Barreiro, a post-doc who has just arrived in the Human Genetics department at Chicago from the Institut Pasteur.

In Paris I've been participating in group meetings, offering my opinion on manuscripts coming out of Lluis' lab, and discussing with lab members how we might analyze the DNA sequence data they're producing. I've also been acquainting myself with the produce of Château des Ravatys (the Institut Pasteur vinyard) and celebrating the 14 Juillet (photo).

What do researchers do?

Most of my friends (and maybe even my colleagues) don't have much idea of what I do day-to-day. That's the subject of this blog. Modern research is quantified in terms of published articles, but that forms just a small part of daily working life, and the process from conceiving an interesting question or idea to published article is a long and tortuous one. Often articles aren't published until months or years after the research was conducted, and so there is a time-lag between what appears in print and what the current focus of research is. By that time the initial excitement of pursuing novel work is a distant memory, having been supplanted by several rounds of peer review, revision and resubmission.

So this is an attempt to communicate what I am doing now, to talk about what I think's exciting this week (or this afternoon) and to show what being a researcher means on a daily basis.