Monday, 16 November 2009

Campylobacter source attribution in New Zealand

What is the source of the common food poisoning pathogen Campylobacter jejuni was the subject of a paper published in September last year in PLoS Genetics by my colleagues and I, in which we traced the origin of bacterial isolates collected from patients in Lancashire, England. In that study, and a subsequent investigation into campylobacteriosis across Scotland, we found that the majority of cases could be attributed to populations of C. jejuni typically found in poultry.

Now Petra Mullner, Nigel French and colleagues have genetically characterized the C. jejuni populations found in human patients, cattle, sheep, poultry and environmental samples from New Zealand covering the period March 2005 - February 2008. What is special about their study is that the New Zealand poultry industry is a closed system, with no foreign imports, making it possible to directly sample the putative source populations and disease-causing isolates concurrently.

Like the studies in England and Scotland, poultry was the inferred source of the majority of disease in New Zealand. Uniquely however, it was possible to attribute cases separately to the three major poultry suppliers on the islands. One supplier in particular was attributed a disproportionate number of cases using 3 assignment methods, including my method (iSource, soon to be available on this website). Supported in part by this evidence, the New Zealand Food Safety Authority introduced mandatory targets for limiting Campylobacter contamination of poultry products in 2007. Remarkably, the number of cases fell from 15,873 in 2006 before the control measures were introduced to 6,689 in 2008. The next chapter of this intriguing story will be a follow-up study to establish whether the fall in the number of cases corresponded to a reduction in the proportion of campylobacteriosis attributable to poultry sources.

Selection in a putative meningitis vaccine target

In Variation of the factor H-binding protein in Neisseria meningitidis, Carina Brehony in Martin Maiden's lab at Oxford investigated a group of outer membrane proteins in the bacterium responsible for meningococcal meningitis. To date, attempts to raise a vaccine against the common serogroup B meningococci have been frustrated by the low immunogenicity of the serogroup B capsular polysaccharide, despite success with serogroups A and C. Outer membrane proteins, such as factor H-binding protein (fHbp) may provide alternative targets for vaccine development.

However, fHbp is genetically diverse, and our investigation showed evidence of structuring into three groups. OmegaMap analyses of the three groups revealed a signature consistent with strong selection pressure for antigenic variability at the gene. Notably, there was clear evidence of diversifying selection at several previously discovered epitopes - positions in the protein targeted by antibodies during bacteria-killing immune response. (Analysis of one group is shown in the figure, with known epitopes marked).

While these observations are encouraging in terms of understanding the biology of pathogen antigens, a pressing question is how do we translate that understanding into practical vaccine design? Studies such as ours suggest a multi-component vaccine may be necessary to achieve broad coverage against serogroup B meningococci.

Recombination and proper segregation in human meiosis

My blog entries have lapsed since the summer while I have attempted to press on with various projects to tie up as much as possible by the end of the year. Meanwhile, my collaborators and I have had three papers published.

In Broad-scale recombination patterns underlying proper disjunction in humans, Adi Alon and colleagues have used a large Hutterite pedigree to test two molecular hypotheses in a statistical genetics fashion. Crossing-over is important for proper segregation of chromosomes during meiosis. When chromosomes fail to segregate properly, the result is aneuploidy, a genetic pathology underlying many inherited diseases; for example, aneuploidy at chromosome 21 is often the basis of Down's syndrome.

It has been suggested that a hard limit of at least one crossover per chromosome is necessary for correct disjunction; others have suggested the requirement is for one crossover per chromosome arm. By reconstructing the probable distribution of the number of crossovers during meiosis, we were able to show that proper disjunction frequently occurs in humans in the absence of a crossover every chromosome arm. Further, the evidence suggested that successful segregation of some chromosomes can occur without a crossover at all - interestingly chromosome 21 was flagged up among others. This leads to the question, is there a back-up cellular mechanism to rescue meiotic division when crossovers fail to form?

Thursday, 18 June 2009

SMBE Iowa City

I spent the beginning of the month at the SMBE (Society for Molecular Biology and Evolution) conference in Iowa City. It was a good chance to catch up with people and find out what research is going on in the field, as well as to speak with collaborators about on-going projects. One of those is Peter Andolfatto, who works on genome evolution in Drosophila species. Molly and I are collaborating with Peter on a project to detect natural selection within and between Drosophila species. The main idea is to improve inference by taking into account variation in selection pressure throughout the gene. Our method draws on the advantages of a number of current approaches such as Rasmus Nielsen and Ziheng Yang's codeml package (part of PAML), Carlos Bustamante's MKPRF (McDonald-Kreitman Poisson Random Field) model and Gil McVean and my program omegaMap in that it exploits patterns of polymorphism within and between species, while allowing for conservation and adaptation within the same gene. You can view the slides of my SMBE talk here, which was titled "Adaptive events in hominid (and Drosophila) evolution".

Monday, 25 May 2009

Science Bomb!

Figure 1 of Venkatarama et al (2009)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.

Monday, 11 May 2009

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.

Monday, 27 April 2009

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, 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.

Saturday, 3 January 2009

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.