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.

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One of the issues that face those of us with research interests in the biology of ageing is the selection of a model system - and how well that model reflects the biology of ageing in humans.  The two main invertebrate models (the fruit fly Drosophila and the nematode worm C. elegans) have major advantages in their powerful genetics and short lifespan, but of course do differ from vertebrates in significant aspects of their biology.  The difficulty in studying primates lies in no small part in the length of lifepan - in the case of Rhesus macaques studied here, average lifespan is 27 years, so conducting a complete experiment in this system is likely to be a career-long endeavour.

One of the much investigated interventions known to extend lifespan is caloric restriction - this has been shown to be effective in several systems.  This paper reports the results (20 years in) of a research project started in 1989 to investigate the impact of caloric restriction on the

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.

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

It's been a while since I last blogged about peer-reviewed science.  In a recent Departmental Journal Club, I discussed a paper outlining the use of transgenic RNAi in Drosophila.  In this paper, the authors utilise the power of Drosophila transgenics to use RNAi mediated gene knockdown to identify components of an important developmental signalling pathway.

In contrast to other systems, such as mammalian cell culture systems, in which RNAi mediated knockdown of gene expression is mediated by the introduction of short double-stranded RNA molecules, in Drosophila researcher use longer double stranded RNA molecules.  There are two method of using RNAi to investigate gene function in Drosophila.

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".

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.

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).

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 interested 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.

Identification of the presence of soft bodied animal in the fossil record is always difficult: it's generally the hard parts of the animal that are preserved by fossilisation (there are exceptions). The Cambrian explosion (see timeline diagram- click on it to link to the interactive Wikipedia diagram) resulted in a wide variety of animal forms: what's less clear is from where this abundance of diverse forms arose. This paper takes chemical approach to establishing the presence of animal remains in rock samples.

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 insects.  Wolbachia 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.

Of the many questions in evolutionary biology, the genetic basis of reproductive isolation between species and subspecies is a pretty hot topic. Drosophila pseudoobscura is a new world Drosophila species that has been used in evolutionary biology studies for many years.  This paper looks at the genetic basis of the hybrid sterility and segregation distortion seen in crosses between two subspecies, D. pseudoobscura pseudoobscura (referred to as "USA") and D. pseudoobscura bogotana (referred to as "Bogota"). It's a nice illustration of the impact of the 12 Drosophila genome sequences now available - D. pseudoobscura was the second Drosophila species to have its genome sequenced.

There is only partial reproductive isolation between these subspecies - male progeny from Bogota females crossed with USA males are virtually sterile (though when aged, they apparently yield offspring, though with a distorted sex ratio indicative of segregation distortion).  The female siblings are fertile, as are the offspring of a cross performed between UAS females crossed with Bogota males.  The two subspecies therefore obey Haldane's Rule.

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 - modern 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). 

In this year of not only the 200th anniversary of Charles Darwin's birth, but the 150th anniversary of the publication of The Origin of Species, we can expect the major celebratory events to be countered by the usual mediaevally-minded creationist suspects.  The journal Nature has published a useful document with the aim of highlighting an publicising why (the vast majoroty of) scientists regard evolution by natural selection as a fact -  "15 Evolutionary Gems"- the contents are as follows:

Gems from the fossil record
   1 Land-living ancestors of whales
   2 From water to land
   3 The origin of feathers
   4 The evolutionary history of teeth
   5 The origin of the vertebrate skeleton
Gems from habitats
   6 Natural selection in speciation
   7 Natural selection in lizards
   8 A case of co-evolution
   9 Differential dispersal in wild birds
  10 Selective survival in wild guppies
  11 Evolutionary history matters
Gems from molecular processes
  12 Darwin's Galapagos finches
  13 Microevolution meets macroevolution
  14 Toxin resistance in snakes and clams
  15 Variation versus stability 

 While browsing through Biogerontology looking for the citation details of one of my publications (which appears to still be available only online), I came across this review, which kind of stands out because of its subject matter.  And any paper with two citations from 300AD and 1300AD has to be looked at!

At the outset, I should say that I know next to nothing about Ayurveda, and that I am unwilling to take claims of efficacy of Complementary and Alternative Medicine (CAM) that lack a serious evidence-base seriously. (I regard Ayurveda as a CAM, as it most certainly is that from a western perspective).  This paper is a brief review article that I suppose has been peer-reviewed, and seeks to review the impact of the therapy on brain ageing.  Does it convince me?

Once again, I find myself interested in a paper about the analysis of a fossil! This time the point of interest is origin of the tetrapod limb digits. The origins of the proximal elements of the tetrapod limb are well understood, and can be seen as homologues of elements of the fins of sarcopterygian (lobe-finned fish). The origins of the digits may have been fin rays, or possibly evolutionary novelties. The latter explanation was supported by developmental genetic studies and analysis of fossils (including the subject of this paper, the transitional fish/tetrapod Panderichthys). In this paper, CT scanning was used to generate 3D images of Panderichthys limbs, demonstrating the presence of distal radials, and correcting a mistaken reconstruction.
The figure below shows the skeletal structure of the limb, coloured to show homologies to the elements of the tetrapod limb. 

The Y chromosome in Drosophila is a strange thing, and it has several unique features.  While, just as in humans, male flies are XY and females XX, flies differ in the the Y chomosome doesn't determine "maleness".  Rather the sex of the fly is determined by the ratio of X chromosomes to the number of sets of autosomes (the X:A ratio).  If the X:A ratio is 1, then the fly is female, if it is 0.5, the fly is male.  So an X0 fly (i.e. one with a single X chromosome with no Y chromosome) develops as a male.  [This can be quite useful in the laboratory] What then is the Y chromosome for?  It is required for male fertility but not viability.  This means that XY flies are fertile males, XX fies are fertile females, XXY flies are fertile females and X0 flies are sterile males.

One might expect then that whatever genes are located on the Y chromosome are related mainly to fertility, or are genetically redundant.  In fact there are very few known genes on the Drosophila melanogaster Y chromosome - 12, in fact, and many if not all are related to fertility in males.  12 genes is really not many for a chromosome, and it turns out that the Y chromosome is pretty much composed of genetically inert heterochromatin and largely comprises simple sequence repetitive DNA.  

The latest publication from our project investigating a Drosophila homologue of WRN exonuclease is now online.  

Ivan Boubriak, Penelope A. Mason, David J. Clancy, Joel Dockray, Robert D. C. Saunders, Lynne S. Cox (2008). DmWRNexo is a 3′–5′ exonuclease: phenotypic and biochemical characterization of mutants of the Drosophila orthologue of human WRN exonuclease Biogerontology DOI: 10.1007/s10522-008-9181-3

This interesting paper investigates whether there is a relationship between polyandry and selfish genetic elements, in the fruit fly Drosophila pseudoobscura. 

Polyandry - where females have multiple mating partners - is widespread in animals, but despite its frequency, little is known of the costs and benefits of this reproductive strategy (though this paper cites evidence that the costs of multiple mating appear to outweigh the benefits.  It is likely that the benefits lie in that polyandry gives the female a greater degree of control over paternity, via sperm competition.  There is also a possibility that selfish genetic elements may promote polyandry by correlating male fitness with sperm competition.

The BBC has this report on an interesting marine biology discovery, relevant to explaining trace fossils.  Unfortunately it's a bit vague (exemplified by its title - 'Grape' is key to fossil puzzle), and doesn't have a link to the original research paper in Current Biology. Personally, I think it looks less like a grape and more like a truffle.  The picture to the left shows a cleaned up example - the real things roll around the sea floor covered in mud.

Greg Laden's Blog - Giant Gromia (amoebas) may account for ancient sea floor tracks presents a rather more coherent account of the paper, and includes a citation.  Unfortunately my university doesn't have an online subscription to Current Biology.  Rats! Rats!