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!

Bad Blood: The Secret Life of the Tour De France

Jeremy Whittle

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.

This event was held on a new course (I understand that it had been used before as the basis for a 25 mile event), and uses the new A428 dual carriageway section from Hardwick to turn at the Caxton Gibbet roundabout where it crosses the A1198.  The event HQ was in the excellent Comberton village hall, about 5 miles from the start.  For this event, the weather was perhaps the warmest i've had all season for a time trial: cloudy skies in the morning had cleared away to brilliant sunshine, and we were experiencing temperatures of around 28 degrees!  There is of course a serious downside for every positive - the wind had beens trengthening all day, and by the time we started it was pretty strong.  Being a new dual carriageway, the course is very exposed, since the trees planted alongside hadn't grown yet.  I whizzed out to the turn doing 32mph a lot of the time, but on turning, had a real struggle to the finish.  The return leg is also the longer leg.

Th course has a lot of potential - the road is new, so the surface is pristine, there wasn't actually too much traffic and the turn seemed straightforward when I reached it.  On a day with rather more moderate wind (or ideally no wind!), this should be really fast.

Here are photos from various time trials. 

For copyright attribution, see notes below the thumbnails.

{gallery}timetrials{/gallery}

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 

Here's an cool page showing academic pedigrees of Drosophila workers: FlyTree.

 It's interesting to see how few steps it takes to get back as far as T. H. Morgan!  For example, here's where I fit in the grand scheme: Robert in FlyTree.

I can recall "O Superman" being something of a novelty hit in the UK charts.  I had heard it via John Peel's show, and always reckoned it was far more than merely a summer novelty hit.  One of my greatest regrets is that I did not go and see Laurie Anderson in Edinburgh on the eve of my final examinations for my degree.

Subsequently I bought a 5xLP recording of United States I-IV, from which her then stage show was abstracted, but that's no compenation!

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.

This evening's event was the final event in the club's series of evening time trials.  A reduced turnout probably reflected the dodgy weather - it was quite breezy and rained quite heavily before we started. 

Despite turning up well before the start, I was the last to sign on, riding at number 15.  I didn't think it was a particularly quick evening, and as my computer was mostly on the blink I was riding without knowing my speed.  I took most of the corners pretty carefully, as they were a bit damp (particularly early on) due to drizzly rain, and got a bit stalled by a slow Landrover driver in Beachampton.  I felt like I was grovelling up the hill, but that's not unusual!  I had Kevin Stokes in my sights from the turn, and finally caught him at about Nash on the return leg.

Here are the current standings in the 2008 Beijing Olympics doping league.

Before the Games, Russia withdrew two walkers and a cyclist over positive test or suspicion of doping.   Bulgaria withdrew its entire weightlifting team due to positive tests for steroids.  The Greek weightlifting team also had numerous steroid positives.

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.

The Quackometer and Holfordwatch blogs report that the British Chiropractic Association, presumably fired by their New Zealand colleagues' attempts to silence scientific opinion, have filed a suit against Simon Singh following an article originally published in the Guardian (but now unavailable).  Hopefully this will engender a major Streisand effect, and I fully expect the case to fail.

See also the news report in the Telegraph (I notice the Telegraph journalists refer to the chiropractors as "Doctors" and doubt this is justified).

This year's Duo Normand time trial will be held on 21st September, and after a year's absence, Team Grumpy (a.k.a. Gerry Oram and me) will be competing again.  For a change, we are entered in the Corporate category instead of the Veteran category (we may revert to veteran if we continue to be the sole team in our category!).

The 20 riders who turned out for this event were fortunate that we managed to avoid the heavy showers (some extremely heavy) that plagued us during the day.  We did however suffer strong winds that made the opening leg to Chicheley something of a trial, and aero wheel handling quite twitchy at times.

I didn't hang around after the event, as it was getting darker and windy.  I also didn't see most of the guys for the pre-race banter as I was quite late getting up to Astwood - I assume Gilbert ("Hard man of the North") Wheelwright is still using the tribars and pointy hat!  Stuart Tarry's winning time of 22:55 was pretty quick for an evening like this (even if he claimed he only showed up because I was going to give him an entry for his '10' on 30th August- which I forgot anyway).

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.

 These photographs were taken during the 2005 trip to Normandy for the Duo Normand.  They were taken before and after the race while tandem cycling in the Norman countryside, and during the race as we started in and passing through Marigny (notice the picture where we were going so fast only the edge of my disc wheel is in the photo!).  We also visited Mont St Michel.

{gallery}2005-normandy:::{/gallery} 

Einsturzende Neubauten have released a significant catalogue of music, which has metamorphosed from loud metal bashing to more sophisticated sounds such as Silence is Sexy, from the album of the same title.  I found this video at YouTube.

This was a particularly tough morning on the F1/25 - perhaps the hardest I can recall, though at least the heavy rain we saw on Saturday did not make a reappearance.

 The initial section, roughly southbound to the Sandy RAB, gave me a little taster for what was to come later on: after descending the sliproad to the A1, it was most definitely going to be tough on both southbound legs. Unfortunately the reverse didn't seem to the true, while it's true I was whizzing along with a tailwind after the Sandy RAB (I topped 34mph at times), the benefits of the wind seemed to be absent some of the time.  Presumably this was due to the slightly serpentine nature of the course.  Despite most peoples' opinion, I'm a bit of an optimist, and usually on days like this I reach the turn think that maybe, just maybe, the return leg won't be as hard as I expect.  For today's event, I can safely say the return leg exceeded my direst prognostications.  On some of the more exposed sections, I was battered down below 20mph, and I'm sure I saw 17mph at one point.  (Jason Gurney claimed afterwards to have had to drop to the small ring at one point!).  I was caught by #90 for 3 minutes shortly after the turn, and even he seemed to be struggling into the wind after that.

These photos were taken during our 2005 cycle tour of Uist, Harris and Skye.  Visit the tour description to see the context of these images.