I recently signed the Sense about Science petition in favour of their GM wheat trials. I have just received the following email which suggests that the Take the Flour Back pressure group are afraid to discuss the issues around this GM work in a public forum.  I can only conclude that they realise their opinions of this work are without merit compared with the efforts that the Rothamsted scientists have made in engaging with the public and explaining the nature of their work.The research is legal, and has passed all regulatory hurdles. The actions of Take the Flour Back are to be deplored. I urge all to read the information at the website and sign the petition.

Dear Petition SignatoryYou supported the appeal by Rothamsted scientists against plans by a group to take direct action against their research into whether GM wheat can warn off aphids.The Take the Flour Back group is pursuing this action but had agreed with the researchers’ proposal to debate their concerns before 27th May.  The researchers organised a neutral venue and chair for a debate. Unfortunately Take the Flour Back has announced they will not take part. There is a timeline of the exchange between Professor John Pickett and Take the Flour Back at http://www.rothamsted.ac.uk/Content.php?Section=AphidWheat&Page=ProtestThere’s lots of other discussion going on. Professor Pickett will be on Newsnight on BBC2 at 10.30 tonight. Many of you left comments on the petition asking about aspects of the research and we have received many questions and points by email and twitter. The scientists at Rothamsted, and colleagues at institutions doing related work, have been responding to many of them; some of this is now up on http://www.senseaboutscience.org/pages/rothamsted-appeal.htmlPlease send the message far and wide: forward the scientists' appeal to your friends and colleagues, share the petition on Facebook and use Twitter hashtag #dontdestroyresearch.http://www.senseaboutscience.org/petition.phpBest regardsSíle Lane

Way back in 2008 I wrote a brief blog article about the sequencing of the genome of a rather poorly unusual organism, Trichoplax adhaerens (What the heck is a Placozoan, anyway?).  The interest there was that the genome had a variety of genes associated with organisms with a more 'complex' structure (Trichoplax looks rather like a flattened blob of cells), while no-one really knew much about the biology of the animal.A paper describing sexual reproduction in Trichoplax has just been published in PLoS One (Eitel M, Guidi L, Hadrys H, Balsamo M, Schierwater B, 2011 New Insights into Placozoan Sexual Reproduction and Development. PLoS ONE 6(5): e19639. doi:10.1371/journal.pone.0019639).  Here's an excerpt from the abstract:

[...] Placozoa are a unique model system for which the nuclear genome was published before the basic biology (i.e. life cycle and development) has been unraveled. [...] Here we report new observations on sexual reproduction and embryonic development in the Placozoa and support the hypothesis of current sexual reproduction. The regular observation of oocytes and expressed sperm markers provide support that placozoans reproduce sexually in the field. Using whole genome and EST sequences and additional cDNA cloning we identified five conserved sperm markers, characteristic for different stages in spermatogenesis. We also report details on the embryonic development up to a 128-cell stage and new ultrastructural features occurring during early development. These results suggest that sperm and oocyte generation and maturation occur in different placozoans and that clonal lineages reproduce bisexually in addition to the standard mode of vegetative reproduction. The sum of observations is best congruent with the hypothesis of a simple life cycle with an alternation of reproductive modes between bisexual and vegetative reproduction.

I've posted a brief article (On the gain of genes and gene function) over at Wonderful Life on two recent papers that reveal something of the rate and nature of gene duplication and diversification within the species of Drosophila.  This is by way of response to recent review article written by the prominent supporter of Intelligent Design creationism, Michael Behe.

This story popped across my screen this morning:Microsoft patents phylogenetic comparative methods. . . say what? - Dechronization blog  (hat tip, PJ over at Groklaw).  Bizarrely, Microsoft appear to be patenting a method for Clustering Phylogenetic Variation Patterns.” The authors of the blog article are understandably a bit agitated about this (see this neat graphic).  The author of the Dechronization blog article, Liam Revell, writes:

The patent filing, by Stuart Ozer, claims invention of a variety of techniques already in wide use by systematists and evolutionary biologists – and (so far as I could tell) none of these inventions are original in quality. The whole patent filing can be read (at one’s own risk) in its entirety here

It's been a while since I last blogged about peer-reviewed science.  In a recent Departmental Journal Club, I discussed a paper outlining the use of transgenic RNAi in Drosophila.  In this paper, the authors utilise the power of Drosophila transgenics to use RNAi mediated gene knockdown to identify components of an important developmental signalling pathway.

In contrast to other systems, such as mammalian cell culture systems, in which RNAi mediated knockdown of gene expression is mediated by the introduction of short double-stranded RNA molecules, in Drosophila researcher use longer double stranded RNA molecules.  There are two method of using RNAi to investigate gene function in Drosophila.

After a bit of teasing in the blogosphere that the draft sequence of the Neanderthal genome would be released in time for Charles Darwin's birthday this week, I was eagerly looking for a paper.  Instead what I find are three news articles in Science, one describing some of the outcomes of the work, and two setting it in context. Some quotes:

Initial comparisons with our own 3 billion bases indicate that a mere 1000 to 2000 amino acid differences, as well as a yet-unknown number of non-coding changes, do that job. For comparison, about 50,000 amino acid differences separate us and chimpanzees. 

Just as I finish reading (or rather, re-reading) chapters concerning the fate of Easter Island (Rapanui) and of Henderson and Pitcairn Islands in Collapse: How Societies Choose to Fail or Survive by Jared Diamond, the 23rd January issue of Science arrives, bearing two articles on the spread of humans (Austronesians) from Taiwan and onwards across Micronesia to Polynesia.  One of these papers, by Gray and colleagues, presents a linguistic analysis of langauages across this region.  The second, by Moodley et al looks at the variation of the human pathogen Helicobacter pylori in these same peoples.  Both strands of evidence documenting this population spread are in striking agreement.

I have no experience in the kind of linguistic analysis carried out by Gray and colleagues, so my understanding is informed by Colin Renfrew's Perspectives article in this issue of Science.There are over 1000 polynesian languages, making it one of the largest language families.  Ultimately, the populations that eventually colonised even the most remote islands such as Easter were ultimately derived from a migration that can (at least in one theory) be traced back to origins in Taiwan (upper panel in the figure below).  Other possibilities include origins in island Southeast Asia.  Genetic evidence (such as that provided by mitochondrial DNA sequences) has been ahrd to interpret, and may not support the Taiwan origin of the Austronesian speaking people.  On the other hand, such evidence may be complicated by post-colonial gene flow.

According to the Daily Telegraph, a team of scientists (we're always "teams") have cloned an extinct Spanish mountain goat from DNA contained in frozen skin samples from the last known specimen, aand using domestic goat eggs.

The article, Extinct ibex is resurrected by cloning,saysthat

Of the many questions in evolutionary biology, the genetic basis of reproductive isolation between species and subspecies is a pretty hot topic. Drosophila pseudoobscura is a new world Drosophila species that has been used in evolutionary biology studies for many years.  This paper looks at the genetic basis of the hybrid sterility and segregation distortion seen in crosses between two subspecies, D. pseudoobscura pseudoobscura (referred to as "USA") and D. pseudoobscura bogotana (referred to as "Bogota"). It's a nice illustration of the impact of the 12 Drosophila genome sequences now available - D. pseudoobscura was the second Drosophila species to have its genome sequenced.

There is only partial reproductive isolation between these subspecies - male progeny from Bogota females crossed with USA males are virtually sterile (though when aged, they apparently yield offspring, though with a distorted sex ratio indicative of segregation distortion).  The female siblings are fertile, as are the offspring of a cross performed between UAS females crossed with Bogota males.  The two subspecies therefore obey Haldane's Rule.

The latest publication from our project investigating a Drosophila homologue of WRN exonuclease is now online.  

Ivan Boubriak, Penelope A. Mason, David J. Clancy, Joel Dockray, Robert D. C. Saunders, Lynne S. Cox (2008). DmWRNexo is a 3′–5′ exonuclease: phenotypic and biochemical characterization of mutants of the Drosophila orthologue of human WRN exonuclease Biogerontology DOI: 10.1007/s10522-008-9181-3

For much of my professional career as a Drosophila geneticist I've worked with polytene chromosomes, and it's always interesting to see papers with interesting tidbits of information about their structure and function. Polytene chromosomes are those rather strange structures formed from high levels of chromosome endoreduplication (see this blog article for a detailed description). Polytene chromosomes are widespread in flies, and in Drosophila are mostly studied in the larval salivary glands where they are easy to work with: Calvin Bridges used salivary gland polytene chromosomes to construct his polytene chromosome map. In this paper, Tom Hartl and colleagues show Condensin complexes (which have a function in chromosome condensation and anaphase chromosome segregation; and in vitro can induce and trap DNA supercoiling) can cause polytene chromosome disassembly and antagonise transvection.  Their data link processes of chromosome condensation and DNA supecoiling with higher order interphase nuclear structure that impacts on gene expression.

Unlike salivary gland polytene chromosomes, those of ovarian nurse cells break down during the development of the nurse cells, at about mid-oogenesis.  In this paper, two mutant alleles of a predicted component of the condensin II complex, Cap-H2 are studied.  In flies mutant for Cap-H2, the nurse cell polytene chromosomes don't disassemble.

We've had another paper on the WRN exonuclease homologue accepted for publication.  In it we demonstrate that DmWNexo is a 3'-5' exonuclease, and describe a new EMS allele. Here's the abstract:

The premature human ageing Werner's syndrome is caused by loss or mutation of the WRN helicase/exonuclease. We have recently identified the orthologue of the WRN exonuclease in flies, DmWRNexo, encoded by the CG7670 locus, and showed very high levels of mitotic recombination in a hypomorphic PiggyBac insertional mutant. Here, we report a novel allele of CG7670 , with a point mutation resulting in the change of the conserved aspartate (229) to valine. Flies bearing this mutation show levels of mitotic recombination 20-fold higher than wild type. Molecular modelling suggests that D229 lies towards the outside of the molecule distant from the nuclease active site. We have produced recombinant protein of the D229V mutant, and assayed its nuclease activity in vitro, and compared activity with that of wild type DmWRNexo and a D162A E164A double active site mutant we have created. We show for the first time that DmWRNexo has 3′ -5′ exonuclease activity and that mutation within the presumptive active site disrupts exonuclease activity. Furthermore, we show that the D229V mutant has very limited exonuclease activity in vitro. Using Drosophila , we can therefore analyse WRN exonuclease from enzyme activity in vitro through to fly phenotype, and show that loss of exonuclease activity contributes to genome instability. 

An amino acid polymorphism in the couch potato gene forms the basis for climatic adaptation in Drosophila melanogaster

Most organisms are faced with dealing with seasonal variations in environmental conditions.  As winter approaches, physiological changes need to be implemented: deciduous trees drop their leaves, mammals may hibernate, and so forth.  In the case of many insects, the strategy is to move into a diapause state.  This may be in any of the life stages - pupal diapause, larval diapause etc, and in the case of Drosophila melanogaster reproductive diapause, in which ovarian activity is shut down in response to a combination of short day length and low temperature.  My interests in diapause are two-fold in origin: firstly, diapause appears to have an impact on lifespan in Drosophila, and secondly, my father identified the existence of reproductive diapause in Drosophila back in 1989.  

This week's edition of Nature has a brief paper (doi:10.1038/nature07390) reporting on the identification of an HIV positive tissue sample collected in Leopoldville (now Kinshasa) in what was then the Belgian Congo, and now known as the Democratic Republic of the Congo.  Sequence data derived from the tissue was used to investigate the chronology of the appearance of HIV from its likely simian origin.

This is a piece of research which hit the news services (see for example this page at the BBC news website).  The research has a number of features which earmark it for media interest: an important virus, a serious disease with a global spread, and a simple take-home message as to the origin of the virus.  This raised my interest and I looked at the paper.  Incidentally, the paper raises issues to do with complexity of statistical analysis: I imagine many readers such as I, and the journos who wrote articles in the press, have little or no chance of understanding what an "unconstrained Bayesian Markov chain Monte Carlo method" is, and are similarly limited in one's real critical analysis of conclusions reached by that means!  I am forced to assume that all is above board in the statistical and computational aspects of this paper, and that the referees have done their job!  In addition, it's always interesting in studies of ancient DNA (and cases where sample preservation was not originally intended to preserve nucleic acids) to know what measures were taken to ensure that contamination with modern DNA did not happen.

Drosophila RNAi screen identifies host genes important for influenza virus replication.

Linhui Hao, Akira Sakurai, Tokiko Watanabe, Ericka Sorensen, Chairul A. Nidom, Michael A. Newton, Paul Ahlquist & Yoshihiro Kawaoka 

I was intrigued by a brief news piece in the latest issue of Science to fall onto my desk (the 22nd August issue).  This concerns the recently published genome sequence of Trichoplax adhaerens, a peculiar animal in a phylum I'd never heard of.  That in itself was interesting, particularly as placozoans have a really odd body plan that involves a mere four cell types.  Wikipedia has a nice description of Placozoa, from which the image below comes.

On browsing the web a bit further, I found this movie (Quicktime format) of a placozoan moving.  I presume this would be Trichoplax adhaerens, as this is the only known species in the phylum - a second described species, T. reptans, was apparently described at the end of the 19th century but hasn't ben seen again and it's existence is doubtful.

A. Bhutkar, S. W. Schaeffer, S. M. Russo, M. Xu, T. F. Smith, W. M. Gelbart (2008). Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes Genetics, 179 (3), 1657-1680 DOI: 10.1534/genetics.107.086108

Back when I was a carefree postdoc, one of the projects I worked on was the assembly of a molecular physical map of the Drosophila melanogaster genome. Of course, Drosophila researchers had for years been using a physical map, the polytene chromosome map, and indeed we used this as the framework on which we assembled our molecular map using cosmid clones. These papers take the genome sequences of 11 Drosophila species (plus the sequence of Drosophila melanogaster, determined back in 2000), fit them to the polytene chromosome maps, and examine chromosome rearrangments seen in inter-species comparisons.  It seems to me there isn't anything hugely sexy in this work, but there is a huge amount of work that sets the evolutionary relationships between these Drosopholids in context.  It's also an opportunity to expound on chromosomes in Drosophila!

Manipulating the Metazoan Mitochondrial Genome with Targeted Restriction Enzymes

Hong Xu, Steven Z. DeLuca, Patrick H. O'Farrell

Science 25 July 2008:
Vol. 321. no. 5888, pp. 575 - 577
DOI: 10.1126/science.1160226

The publishers seem to be making changes at the Aging Cell web pages.  This has meant that the paper is not presently available on open access, for which which Lynne and I paid a significant amount.

In the meantime, I've placed a pdf on this website.

I had a visit from a BBSRC Press Office person on Wednesday 8th May.  (The BBSRC are the UK Research Council that fund my current research into ageing, using Drosophila as a model system) This was to record some video footage to accompany a press release concerning a paper that will be published online on Monday 12th May.  She went on to visit my collaborator Lynne the following morning.

It was quite a surreal situation - being filmed in the lab while people carried on working.  I imagine the raw footage is very funny, with all the false starts and stops - the difficulty was in stopping myself from using technical terms that would be opaque to the general public.  Typically I'd be on a bit of a roll, then suddenly grind to a halt having uttered a word like "phenotype" or similar.  I have to say that the BBSRC person was most helpful and sympathetic (I presume she deals with inarticulate and camera-shy scientists on a regular basis!).