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).

The Register reports latest developments in the Australian Government's ambitions to censor all internet traffic.  Originating as some misguided initiative to "protect the children" (whatever happened to parental responsibility?), it now appears that Australian internet users are likely to face a situation where they must choose from one of two censored streams.  Opting out of the "child-friendly" stream (which blocks a wide range of supposedly harmful content), merely subjects the user to an adult filter that blocks material deemed by the government to be inappropriate for adults.

Is this patronising and paternalistic system the future of the internet?  Or has it the potential to lead to unreasonable censorship?

The Register reports that the anti ID card campaigners No2ID have succeeded in their long standing aim to obtain samples of Home Secretary Jacqui Smith's fingerprints.

Hot on the heels of announcing plans for draconian new communications monitoring Smith is taking forward the batty ID card agenda (first victims: overseas people, second victims: airport workers).  Now it seems a glass bearing her dabs has been "borrowed" and those precious prints preserved, presumably for some nefarious purpose.

Back on 11th October, the Open Rights Group (together with a number of other concerned organisations) held a protest in Parliament Square to publicise the growing surveillance we are all subjected to.  A large mosaic constructed from images of CCTV installations was assembled.  The image (below) has been released under a Creative Commons licence.  A bigger version is available. 

From the ORG "The Big Picture" wiki:

Back at the end of 2007, Privacy International published this map of world surveillance societies. The full report is here.  Each country is rated on a number of categories, and the results pooled to give an overall rating.  The dear old United Kingdom doesn't come out of the analysis too well.

As I posted the other day, the latest version of Ubuntu GNU/Linux has been released.  Ubuntu's schedule sees a new release every six months, and this is reflected in the release numbering: 7.10 was released in October 2007, 8.04 in April 2008 and 8.10 in October 2008.  Each release has a nickname - 8.10 is also known as 'Intrepid Ibex', hence the image of an ibex to the left.

I usually avoid fresh installs of Ubuntu, preferring to go the route of upgrading via synaptic.  This involves considerable file downloading, which can be a fairly lengthy affair, particularly soon after release date when the Ubuntu servers and their mirrors are presumably havily loaded.   I have four computers running Ubuntu, and in light of the usual comments and complaints in the Ubuntu forums, I thought I'd note my upgrade experiences here.

The BBC are reporting that an initiative to curb drug use in Aberdeen will test pub-goers for drug use.  It's a relatively non-invasive test involving hand swabs.  Te odd thing about this is the way the test is being carried out.

People are tested when entering pubs and clubs: the test is apparently not compulsory, but those declining to be tested will be refused entry.  An unusual definition of "not compulsory", that!  So, let me get this right.  I could be lawfully going about my business, and wish to visit a pub for a beer.  I can be stopped for drug testing, and on declining to be tested will be refused entry.

Further evidence of abuse of the Regulation of Investigatory Powers Act (RIPA) is reported by the Daily Telegraph (1/11/08).  Their investigation involved FOI requests to councils: over half of them are using RIPA powers for such trivia as monitoring abuse of refuse collection, littering and fly-tipping.

This is far from the first such occasion: earlier this year, Poole Borough Council spied on a family to check if they live in a school catchment area.  (BBC News 10/4/08), and Bury Metropolitan Council spied on their binmen to catch them over-enthusiastically collecting refuse (The Register 10/9/08) -an action that cost the council a £100,000 settlement - three days before the case was due to go to trial.

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.  

"Privacy is in our DNA, so we need to be honest and clear about what we are doing. We have decided not to be in Phorm because of that... The way it was proposed, the privacy issue was too strong." 

Just thought I'd plug the new release of Ubuntu Linux: Version 8.10, Intrepid Ibex.  Ubuntu Linux is the linux distribution that I use on my work laptop and three PCs at home.  In my view it's a fully featured and fully functional operating system, and well worth investigating. The press release is here.

I choose Ubuntu for a number of reasons, including ease of installation, software installation and upgrades. And of course it's open source and a free download  I'm well aware of the numerous alternative versions of Linux out there, and that some of those may better suit other users.  check out the distrowatch site for more information.   Many thanks to all the developers that together enable the distribution of so many flavours of Linux.

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. 

The BBC reports that measures to prevent undesirables gaining access to the UK are to be strengthened, under measures to be introduced by our not-so-libertarian Home Secretary.

At least the plan is to announce who's on the the list of over 230 individuals considered to be a threat to the UK.   The measures  are as follows:

The British Humanist Association have teamed up with Richard Dawkins to push a message on London buses. 

It's apparently in response to previous pro-religion bus advertising (see Ariane Sherine's comment article at The Guardian). You can donate to the campaign here.   Fund raising has exceeded expectations - perhaps the campaign with run and run (round and round?).  As of 28/10/08:

Bernhard Kohl has apparently been interviewed about his slide into doping (cyclingnews.com).  The essential points make for interesting reading:

His decision to dope followed an extended period without results despite a good showing in the Dauphine Libere, a crash, and an awareness that contract negotiations for next season go on during and after the Tour d France.  He claims it was his decision to take CERA.  He complains about the press blaming riders alone for doping.  The media blame game may well be directed at the riders, and I think this raises interesting points.

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.

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.

 Alfred Henry Sturtevant is another of my all time heroes of Drosophila genetics (see also Calvin Bridges).

 As an undergraduate he generated the first genetic map of any organism.  He realised the linear order and relative position of genes on a chromosome would be reflected in the frequency of genetic recombination between them. Using a set of six X-linked mutants (actually two were alleles, so there were only five markers), he assembled a 5 locus map of the X chromosome. [Sturtevant (1913) J. Exp. Biol. 14; 43-59; pdf]
• Sturtevant's discovery of inversion is important because it explains the why/how of certain genetic defects and discovery of inversion allows for its presence to be tested for

Recent political developments in the UK seem to be directed towards a loss of individual privacy and liberty, bandied about as politicians seek to be viewed as having the "hardest policies on terror".  Currently newsworthy topics are the drive of the Government to have a 42 day detention period without charge for terrorism suspects (fortunately thrown out by the House of Lords) and the move to greater communications surveillance, the latest plans for which appear to be a fit of pique from the Home Secretary in response to her detention plans being thwarted.  Jacqui Smith's opinions on personal freedom and liberty seem so far removed from common decency and the democratic ideal that one wonders why she is thought fit to hold public office, let alone one of the highest ministerial positions in the country.

The human rights organisation Liberty says:

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.