Perhaps I have just taken the wrong career path in science, but I do find the reports of interesting new fossils rather exciting. And how could I resist a paper describing a "bizarre Jurassic maniraptoran"? It seems that hardly a week goes by without a striking fossil from China being described. This one hit the BBC news pages, from where I linked the reconstruction of the animal below.
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.
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.
This video puts me in mind of A Zed and Two Noughts, the1985 Peter Greenaway film. I found this video via ScienceBlogs.
[video:http://uk.youtube.com/watch?v=R3Mt2E1M6dU 425x344]
As a postdoc, I worked for several years on the cell cycle in Drosophila. At that time, the field was just beginning to take off, not least because of the efforts of my then group leader. Nowadays, I study the ageing process, still using Drosophila, and including modelling the function of WRN, the gene responsible for the progeroid condition Werner's syndrome (WS). WRN encodes a RecQ DNA helicase (unwinds the DNA double helix), but unusually has a second activity, a DNA exonuclease (removes nucleotide bases from the end of a DNA strand). We are currently studing the Drosophila homologue of the WRN exonuclease (which we have named DmWRNexo, and which is encoded by the CG7670 locus).
When trying to demonstrate that a mutant of CG76700 indeed displayed characteristic comparable with defects seen in cell lines derived from WS patients, I recalled reading this paper at the beginning of my postdoc position.
The header images are all related to Drosophila:
Above: These are the giant polytene chromosomes found in a variety of tissues in Drosophila - these are from the salivary gland cells of the third instar larva. Calvin Bridges (see picture of the fly lab below) devised maps based on the banding patterns of these chromosomes - maps still in use today.
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!
Here's a smashing paper - a deeply detailed analysis of the Drosophila escape response. What's more, it's hard to see the usual justifications we need to use in grant applications. And a paper about "looming threats...
Well, I have finally plucked up the courage to present a link to the video press release that the BBSRC issued on youtube:
[video:http://www.youtube.com/watch?v=IGQwz2Wv9FU 425x344]
The Daily Telegraph reports an interview with Prince Charles, that famous organic farmer, where he continues to lambast genetically modified crops.
His criticisms seem to principally concern the mass commercialisation of farming - I guess his interests in organic community farming in Caithness and the Duchy estate prompt this. However the interview seems to me to be interpreted by the media as a criticism of the GM industry, despite his comments being vague and really quite ill-informed scientifically. To say GM crops are a "gigantic experiment I think with nature and the whole of humanity which has gone seriously wrong" is really unhelpful, with no evidence presented to support his stance.
Life-history change in disease-ravaged Tasmanian devil populations
Jones et al (2008) PNAS July 22, 2008 vol. 105 no. 29 10023–10027
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
Our paper in Aging Cell describing the identification and characterisation of a Drosophila orthologue of the exonuclease function of WRN is now available online, and open access.
Both the Open University and Oxford University websites have their own versions of the press release.
Lynne had a TV interview with BBC Oxford yesterday, while I had a radio interview yesterday and another scheduled for tomorrow (broadcast for today and tomorrow respectively).
Our paper in Aging Cell describing the identification and characterisation of a Drosophila orthologue of the exonuclease function of WRN is now available online, and open access.
My laboratory uses the fruit fly Drosophila melanogaster as a model for biological processes, and in particular the biology of oxidative stress resistance and ageing. The value of this organism stems largely from its highly developed background of genetic research, and the sophisticated techniques of genome manipulation which are available.
Keeping Drosophila
The Gal4-UAS system was devised by Andrea Brand and Norbert Perrimon some years ago, and it remains one of the more powerful contributions to the modern Drosophila genetic toolbox.
The system relies on a combination of two engineered P elements. P elements are a naturally occuring transposable element in the Drosophila genome: a complete 2.9kb element encodes a transposase enzyme that catalyses the element's excision and reintergration at novel sites. P elements were the first germline tranformation system developed for Drosophila. An engineered P element contains a marker gene that confers an easily recognised phenotype on flies bearing the element. Nowadays. the most common marker gene is white, which is required for the eyes of the fly to take up the red and brown pigments that give Drosophila its brick red eyes (white is so-named because mutants have white eyes due to an inability to take up pigments).
The first element of the Gal4-UAS system carries to transgene to be expressed, downstream of several copies of the yeast Gal4 Upstream Activating Sequence (UAS). Essentially, the UAS is a sequence to which the yeast Gal4 transcription factor binds, thereby driving transcription of the downstream sequences (in this case, the transgene of interest). In the absence of Gal4, the transgene contained within this element is transcriptionally inactive. We can refer to this element as the responder element.
