This recent paper caught my eye, as as some of my recent research has related to the regulation of antimicrobial defence in Drosophila.  Insects have a two ways of coping with microbial infection.  Firstly, microbes may be dealt with by circulating blood cells (haemocytes) of which there are several classes.  Haemocytes to no play any role in respiration in insects.  A second means of controlling microbes involves several peptides that kill bacteria or fungi:  these are usually expressed in response to the presence of microbes in the haemolymph.  Interestingly, this induced system has a counterpart in vertebrates.  It's generally thought that the important system in clearing pathogenic microbes in insects is the induced antimicrobial peptides.  This paper investigates the roles of both systems.

The authors have evaluated the relative use of these two mechanisms of infection control in Tenebrio molitorI, the mealworm (picture above).  Their hypothesis is that the haemocytes represent the first line of defence, with the induced response of antimicrobial peptides mopping up microbes remaining from the first round defence.  In this model, the induced antimicrobial response largely functions to eliminate suviving pathogens that may be refractory to the first line of defence.

 Wolbachia pipientis is a rather peculiar bacterium.  It's an intracellular organism, and is found in a wide variety of tax, including nematodes, crustacea, and arachnids.  About 20% of insect species are thought to have Wolbachia.  Wolbachia has evolved a number of mechanisms to ensure transmission, which is generally maternal.  There are a number of consequences of infection with these intracellular bacteria observed in different species - including reproductive isolation between infected and uninfected strains of the mosquito Culex pipiens.  I also recall seeing a old paper (though I've long-since lost the citation) which claimes a growth advantage of infected Drosophila larvae in crowded culture, though I think this must have predated the identification of Wolbachia.

So some laboratory Drosophila strains are infected with Wolbachia, while some are not.  This can lead to artefacts in many experiments.  For example, in my own lab, we had some perplexing results concerning the effects of particular transgene on viability of some combinations - the involvement of Wolbachia became clear firstly when we noticed the effects depended on which which strain was paternal and which maternal in the cross, and finally the observation that  this effect vanished after treating the transgenic stocks with antibiotic.  These kind of artefacts are particularly important to consider when working with complex characteristics such as lifespan (as we do in my lab).

A pair of recent issues of Science plonked into my mail box this week.  Among the items that caught my eyes was an exciting brief communication in Science shows a rare example of what appears to be fossil evidence of behaviour. These are Waptia-like arthropods from the Lower Cambrian, which appear to have been preserved while engaged in some form of processionary behaviour. Unlike known present day processionary arthropods, these chains of individuals appear to be physically linked - you can see in the figure that there is overlap between an individual's carapace and the preceding individual's telson. The authors propose the chains reflect migratory behaviour rather than feeding or reproduction.

In the 1950s, Louis Miller conducted a number of experiments that tried to model the origin of organic compounds in a  prebiotic world.  Among these was the Miller-Urey experiment, in which a vessel containing water, methane, ammonia and hydrogen was heated and subjected to electrical discharge (simulating lightning). Diagram of the experiment (Wikipedia).  At the time, Miller reported that a number of amino acids were formed.

This brief article describes the reanalysis  of stored vials containing the outcome of one of these experiments, using material found at the University of Chicago after Miller's death.  Apparently Miller had identified five amino acids and a number of unidentified compounds in some of the experiments.

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. 

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.

The utilization during mitotic cell division of loci controlling meiotic recombination and disjunction in Drosophila melanogaster.

Bruce S. Baker, Adelaide T. C. Carpenter, and P. Ripoll 

Genetics 1978 90: 531-578. [Abstract] [PDF]

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.

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!

Visually Mediated Motor Planning in the Escape Response of Drosophila

Gwyneth Card and Michael H. Dickinson

Current Biology 10.1016/j.cub.2008.07.094
[Summary] [Full Text] [PDF] [Supplemental Data]

 

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...

Life-history change in disease-ravaged Tasmanian devil populations

Jones et al (2008) PNAS July 22, 2008 vol. 105 no. 29 10023–10027

Full text (requires subscription); Abstract (free access)

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

Not, I think, peer-reviewed science this time, but two articles from Nature and Science respectively, both on the subject of sports doping, a subjetc which is of course very topical given the Beijing Olympics, due to start tomorrow, 8th August.  The first is a Commentary article from Donald Barry on the statistical significance of doping tests, focussing on the case of Floy Landis, who was stripped of his 2006 Tour de France victory following a positive test for testosterone.  The second article is one of a series of News articles in Science related to the upcoming Olympics, and questions whether performance enhancing drugs really do benefit performance.

The figure on the left is included in the article - it shows delta notation of isotope ratios of 167 samples tested at the LNDD (who tested the 2006 TdF samples, including Landis'), those considered positive are in red, those negative are in green.   I don't think these samples are necessarily derived from the Tour, if any, since a good number are considered positive.

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.