Tag Archives: peer reviewed science

The life cycle of the enigmatic Trichoplax

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.

All rather interesting – the authors note that the genome sequence was in the hands of scientists before the Trichoplax life cycle was in any way understood.  I imagine that this sort of situation will occur more often, as projects that are randomly trawling the environment for novel DNA sequences have been carried out (Venter et al (2004) Environmental Genome Shotgun Sequencing of the Sargasso Sea.  Science 304; 66-74).

ScienceDirect -> SciVerse

Image representing Mendeley as depicted in Cru...
Image via CrunchBase

I’ve been trying to overhaul my reprint collection* and bibliography, using the Mendeley Research Networks system.  Access to many journals comes via Elsevier’s ScienceDirect, which has been down for most of yesterday “for scheduled maintenance”.  At the moment it’s throwing a “500 Server error”.

Anyway, a wee bit of internet searching reveals this is rather more than scheduled maintenance, and rather more of a major systems overhaul:

ScienceDirect, Scopus, Journals Consult and the Admin Tool will be unavailable due to scheduled maintenance for approximately 9 hours on Saturday, August 28, from 6:30am to 3:30pm Central Standard Time.  During this time, upgrades will be implemented to these systems as part of the launch of the new SciVerse platform. For more information about SciVerse, please visit www.acceleratescience.com.

I bet the ScienceDirect engineers had their hearts in their mouths at switchover time.  And I bet coffee consumption is hitting rather extreme levels…

*Yes, the term “reprint” does reflect my age.  Actually I use pdfs.

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Sydney Brenner on C. elegans


The latest issue of Genetics to flop onto my desk has a rather nice article by Sydney Brenner entitled “In the Beginning Was the Worm…“. This brief article (in the regularly excellent Perspectives section) presents an account of the origins of Caenorhabditis elegans research, by the beast’s main man, research which ultimately earned him Nobel Prize fame. I won’t go into a blow-by-blow account of Brenner’s career (that’s probably quite easy to track down on the interweb), but suffice it to say that after forging a seriously important career in prokaryotic genetics and molecular biology, he was instrumental in establishing an entirely novel experimental system.  For a Drosophilist such as myself, C. elegans seems particularly simple – it has a defined number of cells per animal (dependent on sex), and the cell lineage tuns out to be pretty much invariant in the wild type.  In origin, it’s a soil dwelling nematode. For my part, the big influence was the genome mapping and sequencing technologies that were developed for C.elegans, and which we applied to Drosophila.  The picture below shows an adult (and, dare I say it, elegant) C. elegans.

I think what’s quite interesting is how doing science has changed over the last 30 or so years – to quote from Brenner’s article:

If one arrived at the lab at the reasonable hour of 10 am, there was just time to open one’s mail before adjourning to the canteen for morning coffee, usually prolonged by a very interesting discussion on some aspect of science. This did not leave much time before lunch, which naturally was also accompanied by discussion that was terminated only by rushing off to attend an afternoon seminar on the Bohr effect in hemoglobin or the like. That brought one to afternoon tea and after that there was hardly enough time to start anything in the lab before adjourning to the pub for liquid and intellectual refreshment. It was only after dinner that the real work started and the lab then filled up with the owls.

Comparing that approach to doing science to the modern University life of bureaucracy (both for research and teaching), the RAE (Research Assessment Exercise – the UK’s quite burdensome system for assessing research excellence) and research grant application treadmill is a little saddening, even taking into account a bit of historical licence.  I don’t think I’ve had that discursive and open-ended approach to scientific work since I was a graduate student.

Indeed, the prospect nowadays of obtaining funding for an entirely new model system, and then following up with the first publication 6 years on would presumably be a little remote…

On the reasons for moving on from C.elegans research Brenner is perhaps a little modest:

People often ask me why I left C. elegans research just when it was getting really interesting. The answer is simple: The people doing it were much better than I was, and attendance at one meeting showed me that their students were even better than they were.

Brenner, S. (2009). In the Beginning Was the Worm … Genetics, 182 (2), 413-415 DOI: 10.1534/genetics.109.104976

Our Biogerontology paper out in print (at last)

Our paper describing a new allele of the Drosophila WRN-like exonuclease DmWRNexo  and on it’s biochemical characterisation is finally out in print (its been available online for some time):

Boubriak, I., Mason, P. A., Clancy, D. J., Dockray, J., Saunders, R. D. C., Cox. L. S. 92009) DmWRNexo is a 3′–5′ exonuclease: phenotypic and biochemical characterization of mutants of the Drosophila orthologue of human WRN exonuclease.  Biogerontology   10; 267-277  DOI: 10.1007/s10522-008-9181-3

A pdf of this paper is available from the Biogerontology website, but will require a subscription.


UK Science research policy and the "Impact Summary"

A bit of a rumpus about UK science funding policy erupted this week, following publication of a letter to the Times Higher about the move to increase the emphasis towards funding science with a more immediate benefit to the UK economy. This manifests itself as a two page document (the Impact Summary) that now forms part of every Research Council grant application (in addition, I think, to the short "Beneficiaries" section that already exists.

This policy seems to be favoured by the Science Minister, Paul Drayson.  Lord Drayson is a politician with a commercial science/engineering background, but who has never been elected to public office.  he was ennobled, and reaches Minister status via a seat in the House of Lords.  Interestingly, as befits a proponent of grant applicants predicting and outlining future benefits of their yet to be performed research (not just economic but social as well), he appears to claim sixth sense "I saw it coming, says minister of sixth sense Lord Drayson".

Now, I’m not so divorced from the real world that I dispute that scientists need to at least think of these matters, but shouldn’t research that is sufficiently close to market that reasonably accurate predictions of economic impact can be made be funded and conducted by industry?  Respected science blogger Professor David Colquhoun certainly thinks the move towards a focus on applied research is ill-advised – he was one of the signatories to the letter to THE, as he describes at his blog: How to get good science: again.

Steven Hill, who currently heads the Research Councils UK Strategy Unit, has responded in his personal blog – A Nobel effort?, though I’m not sure he addresses the complaint fully.  The cudgels are somewhat taken up by Philip Moriarty (another signatory to the letter to THE) in comments at the Prometheus science policy blog (an American site, which needs to be borne in mind when reading the original article and some of the comments that follow).

There is a refreshing take from a younger scientist, Oxford PhD student Nick Antis, who runs a blog at ScienceBlogs.  He reports on a meeting with Lord Drayson in a recent post – An Unsettling Meeting with the UK’s Science Minister.

I think that UK researchers will end up just knuckling down and do their best to come up with two pages of creative writing that they hope will satisfy scrutiny*.  The worry is that those of us who are conducting research with no obvious onward path to the marketplace will feel disadvantaged, even if they are not.  And on the other hand, if a grant application that makes no great claim for economic impact is not disadvantaged, then why is an Impact Assessment even necessary?  I wonder how science policy would evolve if a science minister were to have come from a background in which he or she had had to fight for grant funding from the Research Councils?

*There’s a useful summary of what’s needed at a blog run by the University of Lincoln’s Research Office (New Impact Summary for Research Council Bids).


In the Journals – Chemical evidence of multicellular life 635 million years ago

A paper in the current issue of Nature [Love et al (2009) Nature 457; 718-722] suggests that multicellular life existed about 100 million years before the explosion of bilaterian animals in the Cambrian. The evidence comes from analysis of rocks from the Arabian peninsula, in which geologically preserved derivatives of characteristic chemicals have been detected. Now, this paper interCambrian timelineested me because of its message concerning the dating of the origins of multicellular life; I am not a geologist or a chemist, so many of the details escape me.
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Fossil foetal (proto-)whale

Quite a few of the bloggers at ScienceBlogs have been writing about an exciting new fossil find: a newly discovered fossil ancestor of whales.  The exciting thing here is that the fossil contains the remains of foetal whales.  Here’s the University of Michigan podcast.

The fossil confirms that Maiacetus inuus was amphibious, or at least gave birth on land, as the foetus is oriented to emerge head-first (clearly not adaptive for aquatic birth, and something not seen in present-day cetaceans).

Read the bloggers at

Not exactly Rocket Science

Greg Laden’s Blog


The Questionable Authority

Read the paper at PLoS ONE (freely available)

In the Journals – Human expansion across the Pacific mapped by language and bacteria

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.

Gray et al have applied computer analysis to languages across the Pacific diaspora. They have analysed a large database of 210 basic vocabulary (basic in the sense that they are words representing basic activities, and which are the words/concepts that tend to be conserved as languages evolve), and plotted the time course of the Austronesian languages.  It seems that their analysis indicates a pause-pulse mode, in which there were two pauses in expansion.  The first coincides with the crossing of350km Bashi channel between Taiwan and the Phillipines, and the second between the colonisation of  Western Polynesia and that of the remoter Eastern Polynesian islands.  Both the pauses are thought to have ended with technological advances the the sea canoe technology (for example the development of outriggers, improved navigational  techniques, and double hulled canoes.  In the lower panel of the figure below, the related-ness of the languages is tied to the map above by colour coding, and the pauses are indicated.

In the second paper, Moodley et al have analysed 212 H. pylori samples taken from Taiwanese aboriginals, New Guinean highlanders, Melanesians and Polynesians.  Seven genomic fragments were sequenced, revealing 196 haplotypes, which were compared with haplotypes from Europeans in Australia and other haplotypes derived from populations across Asia and the Pacific.

From my position of ignorance about linguistics, it would seem that sequence-based phylogeny reconstruction must be the easier of the two analyses (though I’m happy to be corrected on this).  The figure below shows the phylogenetic relationships between the H. pylori haplotypes (in B) and the geographic spread of samples (in A).

In addition, the global spread of H. pylori is assessed, clearly showing that the New Guinea and Australian colonisation was distinct from the much later colonisation of the Pacific.  What’s quite striking is the correspondence between the two trees, as presented in the accompanying Perspectives article, which concludes with the hope that a sysnthesis of linguistic and genetic approaches may be possible on a global scale.

R. D. Gray, A. J. Drummond, S. J. Greenhill (2009). Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement Science, 323 (5913), 479-483 DOI: 10.1126/science.1166858 Y. Moodley, B. Linz, Y. Yamaoka, H. M. Windsor, S. Breurec, J.-Y. Wu, A. Maady, S. Bernhoft, J.-M. Thiberge, S. Phuanukoonnon, G. Jobb, P. Siba, D. Y. Graham, B. J. Marshall, M. Achtman (2009). The Peopling of the Pacific from a Bacterial Perspective Science, 323 (5913), 527-530 DOI: 10.1126/science.1166083 C. Renfrew (2009). ANTHROPOLOGY: Where Bacteria and Languages Concur Science, 323 (5913), 467-468 DOI: 10.1126/science.1168953

In the Journals – Mosquito lifespan and Dengue fever control


Many tropical diseases are transmitted by insect vectors – malaria (which is caused by Plasmodium parasites) and yellow fever (caused by a virus) being examples of diseases transmitted by Anopheles and Aedes mosquitoes respectively.  Dengue fever is another viral disease that is transmitted by Aedes aegypti.  One crucial feature of the disease transmission cycle is that once the disease organism is collected by the mosquito in a blood meal, it takes some time to develop within the insect before it becomes infectious.  In the case of both malaria and dengue fever, this period of time is about two weeks.  This paper evaluates the use of the endosymbiotic bactera Wolbachia to shorten mosquito lifespan in the hope that this will reduce disease transmission.

In a sense, this is an attractive strategy, and one that makes use of one of the properties of some Wolbachia strains to shorten host lifespan. I have previously blogged about some aspects of Wolbachia biology in the immune system of insectsWolbachia infection is maternally transmitted, and spreads through insect populations because of a reproductive drive known as cytoplasmic incompatibility (CI) – infected females mated to uninfected males yield infected offspring, while uninfected females mated to infected males yield no offspring.  This reproductive drive is presumably sufficient to drive even strains of Wolbachia which have negative effects on viability (such as reduced lifespan) through the population.

The Wolbachia strain used here is known as wMelPop, and shortens the lifespan of infected Drosophila.  It was adapted to A. aegypti by propagating it in an A. aegypti cell culture for three (!) years, before generating an infected A. aegypti strain by injection of embryos.  Comparison of lifespan survival curves of the infected strain (PGYP1 with the original, uninfected, mosquito strain (JCU) showed significant reduction in lifespan, at both 25 and 30 degrees.  Further expeiments investigated the impact on lifespan when the mosquitoes were raised in more "realistic" environmental conditions of fluctuating temperature and humidity, where it was found that the median lifespan of infected females was significantly reduced, from about 50 days, to about 21 days.  These effects on lifespan could be "cured" by treatment with the antibiotic tetracyclin, which kills Wolbachia.

The infected strain shows the appropriate CI characteristics (i.e. infected males crossed to uninfected females yield no offspring), and this is maintained as the males age.

So, is this a realistic strategy for dengue control? Well, I guess the signs are good, but I always worry about the capacity of natural selection to throw a spanner in the works.  Just as in the past malarial drug resistance has arisen as has mosquito resistance to DDT, I can;t help but worry that the complex interaction between mosquito and Wolbachia is going to be subject to a variety of selection pressures that may have unintended consequences. 


C. J. McMeniman, R. V. Lane, B. N. Cass, A. W.C. Fong, M. Sidhu, Y.-F. Wang, S. L. O’Neill (2009). Stable Introduction of a Life-Shortening Wolbachia Infection into the Mosquito Aedes aegypti Science, 323 (5910), 141-144 DOI: 10.1126/science.1165326

In the Journals – Spiders, silk and evolution


Yet another palaeontology blog post!  This story roared round the internet just before Christmas (for example the BBC News story), but I found it interesting as a non-specialist in arachnid evolution or palaeontology, partly because of the methods used for extracting fossil arthropod material from the substrate, and partly because it tells a tale of re-examination and reanalysis of specimens with a quite different interpretation. Oh, and there’s a tale of the evolution of silk use by spiders!

Production and use of silk is the defining characteristic of spiders – False colour SEM of spigots on a spinneretmodern advanced spiders use silk for a quite astonishing array of purposes (from taking flight to encasing eggs; from capturing prey to constructing shelters), and a single individual may produce silk of several types with distinct properties.  Spider silk is produced from specialised structures called spigots, which are in turn located on modified appendages called spinnerets (see picture on the right, from the arachnology website, where there’s a description of silk production). 

Back in the late 80s, fossil material of Attercopus fimbriunguis was considered to provide evidence of advanced silk production: this paper reconsiders that evidence, and compares the original and newer fossil material with other specimens, notably Permarachne novokshonovi (in the picture below), which has a clear flagellum.  As far as I can tell from a reading of this paper (which is replete with terminology I’m unfamiliar with), much of the uncertainty comes from the material worked with – it seems to consist largely of cuticularPermarachne novokshonovi fragments released from maceration of hydrofluoric acid digested rock matrix.  In fact quite a few of the figures resemble the residue from a Drosophila dissection as we might carry out in my lab!  There’s also a rather neat CT scan revealing appendages within the rock matrix of another fossil arachnid.

The structure originally interpreted as a spinneret is most probably a rolled up section of cuticle, a false interpretation arising from the way the specimens are prepared.  On the other hand, the present paper does have a figure (Figure 1 C, D) showing a cuticular fragment bearing what appear to be spigots Attercopus fossil fragmentswith attached silk threads! [subscription required to see full-size figure, though see here]

To cut  a long story short, the revised interpretation of the A. fimbriunguis material suggests that the spigots are not located on a spinneret, but are actually located on ventral plates of the opisthosoma (the abdominal part of a spider’s body).  This means that the animal would be unlikely to be able to weave webs, and presumably used silk for some other purpose, such as leaving a navigation trail, or nest construction, and that true web-building abilities did not arise until 300 million years ago, some 80 million years later than thought following the origninal interpretation of A. fimbriunguis.  Indeed, the BBC article quotes Paul Selden:

“The puzzle about silk was this: we knew that it wasn’t used for making webs initially, for catching insects, because there were no flying insects when the earliest spiders were around,” 

Owing to the odd combination of the silk spigots on ventral tergites, and the possession of a flagellar appendage by Attercopus and Permarachne, Selden and colleagues propose a new Arachnid order: Uraraneida, characterised by these two features,

P. A. Selden, W. A. Shear, M. D. Sutton (2008). From the Cover: Fossil evidence for the origin of spider spinnerets, and a proposed arachnid order Proceedings of the National Academy of Sciences, 105 (52), 20781-20785 DOI: 10.1073/pnas.0809174106