Biology

In browsing the GBIF classification in BioNames I keep coming across cases of wholesale duplication of taxa. I recently blogged about a single example, the White-browed Gibbon, but here's a larger example involving frogs.Consider the frog genera Philautus and Raorchestes. The latter was described in 2010:A ground-dwelling rhacophorid frog from the highest mountain peak of the Western Ghats of India (2010)Current Science (Bangalore) 98(8): 1119–1125. http://bionames.org/references/e0ab13cbb8bc8b3627bb53e88e7641a9and contains a number of species previously in Philautus. The GBIF classification for Philautus still has these species, which means that these taxa appear twice in the GBIF data portal (associated with different occurrences).To gauge the scale of the problem I've done a crude pairwise plot of species names in the two genera. In the diagram below a dot(?) appears if the species name in the corresponding row and column is identical. The diagonal corresponds to comparisons of a species name with itself.Note the ?'s that appear off the diagonal. These are species in Philautus and Raorchestes that have the same species name (e.g., Philautus glandulosus and Raorchestes glandulosus. The off-diagonal dots indicate taxa that are duplicated.? ? Raorchestes anili ? ? Raorchestes annandalii ? ? Raorchestes beddomii ? ? Raorchestes bobingeri ? ? Raorchestes bombayensis ? ? Raorchestes chalazodes ? ? Raorchestes charius ? ? Raorchestes dubois ? ? Raorchestes flaviventris ? ? Raorchestes glandulosus ? ? Raorchestes graminirupes ? ? Raorchestes griet ? ?

UK legal experts are querying the 2011 Court of Justice of the European Union (CJEU)ruling that the products of research using stem cells derived from human embryos are not patentable (see previous news). ? The UK High Court has itself requested clarification from the CJEU in Luxembourg; depu ...

When I first saw the paper from Nga Lau and colleagues* (open-access) looking for markers of gluten sensitivity and/or coeliac (celiac) disease in children with autism I have to admit to raising a smile. I smiled because in a previous post on this blog I talked about a 'wish-list' for autism research specifically focused on the gluten and casein-free dietary intervention**. Part of that wish list was some further inquiry into why, biochemically, some people on the autism spectrum might benefit from dietary intervention. My prayers it seems have started to be answered.Smiler @ Wikipedia When it comes to the area of dietary intervention for conditions like schizophrenia (no really), there seemed to be a lot more enthusiasm for looking at why some cases of schizophrenia might overlap with dietary issues over investigations into autism. I can't pretend to know why schizophrenia research took the lead; maybe something to do with Dohan and his original discussions on diet and schizophrenia or that schizophrenia research has some very talented people like Emily Severance and colleagues (see here and here and here) taking an interest. One might also speculate that some of the politics of autism - diet, gastrointestinal (GI) issues = (see here) - might also creep into this lack of autism research interest too? Who knows.No mind, Lau et al did look at immune reactivity to gluten (or rather a fraction of gluten called gliadin) in a group of children with autism (n=37) compared with their asymptomatic siblings (n=27) and typically developing controls (n=76). They looked for anti-gliadin antibodies (IgA and IgG). They looked for antibodies to deamidated gliadin (that is where gliadin has already been subjected to some kind of enzymatic modification). They looked at antibodies to tissue transglutaminase (tTG). They even examined HLA genotype for the DQ2 and DQ8 haplotypes (linked to the genetics of coeliac disease). All in all, the primary bases were covered.Results: well, the serum samples all came from AGRE - the Autism Genetic Resource Exchange - so no quibbling about the diagnosis of autism. They also subdivided the autism group up into those with GI symptoms and those without and remarked on those who were following a gluten-free diet too.The authors report that levels of IgG anti-gliadin antibody were elevated in the autism group compared to siblings and controls. This differences lasted even when certain confounders such as age, gender and race were taken into account and the calculated odds ratio of an having an elevated IgG antibody levels to gliadin was not to be sniffed at either (OR 4.97; CI 1.39 - 17.8). That being said, there was cross-over between the relatively small participant groups and levels of IgA antibody to gliadin were not significantly different between the groups. Very interestingly, the presence of comorbid GI symptoms appearing alongside autism seemed to be linked to that elevated IgG antibody response to gliadin compared with no comorbid GI symptoms.Just short of 50% of the children with autism were "positive for HLA-DQ2 and/or -DQ8 (6 DQ2, 12 DQ8)". I probably didn't explain this well, but a significant proportion of people with coeliac disease carry these haplotypes which all relates back to the almighty MHC and antigen presentation (see here for explanation).Insofar as the other parameters on antibodies to deamidated gliadin and tTG, there was little difference to write home about. Although not wholly relevant, I'll refer you back to some interesting work down on tTG with autism in mind from a while back (see here).A few choice quotes from the authors: "The findings indicate that the observed anti-gliadin immune response in patients with autism is likely to involve a mechanism that is distinct from celiac disease, without the requirement for TG2 activity or antigen presentation through DQ2/DQ8 MHC molecules". Well, we know that coeliac disease, when it is tested for in cases of autism, is probably not great

June 2013, Volume 45 No 6 pp 579-714Jonathan the zombie isn't the only one who likes turtles. These heroes-in-a-half-shell adorn the cover of the current Nature Genetics, as two species of turtle have just joined the Genome Club (Wang et al. 2013; paper's free!).This definitely not one of those genome sequencing studies alluded to recently by John Hawks, that's "too boring for journals." Wang and colleagues didn't just sequence the genomes of soft-shell and green sea turtles 'just cuz.' Rather, they use these copious data to address several questions, perhaps most interesting of which relate to developmental genetics and embyrogenesis.First, analysis of gene expression during embryonic development supports what the authors refer to as a "nested hourglass model" of development and gene expression. The hourglass serves as analogy for variation across related species over time: there is great variation (in both morphology and gene expression) in the earliest stages of development, then species are more similar at a given developmental stage (the "phylotypic period"), and thereafter variation increases again. This phylotypic period (which I don't believe is unanimously agreed upon) is arguably the most conserved developmental stage in evolution - all vertebrates, for example, simply must pass through this stage to become good vertebrates. Plus, several studies have found that evolutionarily younger genes tend to be expressed before and after this amorphous phylotypic stage, while more ancient genes are expressed during this time. As the authors state"According to the recently supported developmental hourglass model ... the changes underlying major adult morphological evolution occurred primarily in the developmental stages after the period ... that serves as the basic vertebrate body plan."So the turtle data generally support this model. However they mention a nested hourglass, because they found evidence of an additional bottleneck, a second hourglass, of conserved gene expression when comparing turtles with their close relative the chicken. In other words, "the most conserved developmental stage changes depending on distantly related species are that are being compared." So since turtles and chickens are more closely related to one another than to many other vertebrates, they might share another conserved developmental stage. Incidentally, both also make for good soup.Wang and colleagues also looked for genes relating to some of the unique aspects of turtle anatomy, examining what parts of the genome seem to get kicked up after the phylotypic period. It doesn't take a trained eye to see that these animals are kinda weird in that their bodies are encased in a flagrant shell, with a carapace on top and plastron on the bottom. Now it turns out this carapace is actually formed from what should, in most other vertebrates, become vertebrae and ribs. So by studying the earliest development of these structures, Wang and colleagues could examine the molecular bases of this carapacial deviation.Fig. 5 from Wang et al., showing Wnt protein expression in turtle embryos. In a), only Wnt5a is expressed in the 'carapacial ridge' during its earliest development. Fig c) is a cross-section indicated in b) showing this expression. NT=neural tube, NC= notochord. The scale bar is 0.5 mm. Tiny!The authors were able to identify over 200 miRNAs, and implicate the signalling protein Wnt5a, in the development of the "carapacial ridge" (see the arrows in fig. c above), the embryonic precursors to the carapace. Interestingly, Wnt5a is involved in the development of limb buds (e.g, those big purple circles in the red square in a) above). The precise role of Wnt5a and the miRNAs in turtle shell development has yet to be determined, so this study really sets the stage for future investigations.So there you have it, a pretty cool paper combining genomics with developmental biology, among other things. And so to close, for your bemusement, here's a video I sho

In 2008, doctor Sergio Canavero, an italian neurosurgeon based in Turin, IT, have awakened a 20 years old lady from a permanent post-traumatic vegetative state, by means of a bifocal extradural cortical electro-stimulation. Today, while Science still find it hard to explain consciousness and embodied cognition – the world-class neurosurgeon made a shock announcement: “I’m ready for the first head transplant on a man.” In the manuscript published on Surgical Neurology International, he reveals the details of this astonishing project, named HEAVEN. Including ethical questions.... Canavero, S. (2013) HEAVEN: The head anastomosis venture Project outline for the first human head transplantation with spinal linkage (GEMINI). Surgical Neurology International, 4(2), 335. DOI: 10.4103/2152-7806.113444 HEAVEN: The head anastomosis venture Project outline for the first human head transplantation with spinal linkage (GEMINI)

The study of how cells move in development is not just about development. Understanding cell migration can also help researchers understand how tumors spread and invade other tissues. So, the next time you see someone roll their eyes at your fruit fly egg chambers (or worm vulva, or culture dishes), take pity at their ignorance and explain to them how they should thank you instead.The movement of cells during development drives the shape changes and organization of an embryo. In the fruit fly ovary, a small cluster of border cells migrates across a region of the egg chamber in order to reach the oocyte. This collective migration of these border cells depends on polarization of the actin cytoskeleton. A recent paper describes the role of the Hippo signaling pathway in driving the polarization of actin to the outer rim of the migrating border cell cluster. Lucas and colleagues found that upstream Hippo pathway components localize to the contacts between border cells within the cluster in order to link polarity signaling with actin cytoskeleton organization. In the images above, the actin cytoskeleton (red) can be seen at the outer rim of the migrating cluster of border cells (arrows) as it moves across the egg chamber towards the oocyte (top to bottom, chronologically). Higher magnification views of the cluster are on the right. Lucas, E., Khanal, I., Gaspar, P., Fletcher, G., Polesello, C., Tapon, N., & Thompson, B. (2013). The Hippo pathway polarizes the actin cytoskeleton during collective migration of Drosophila border cells originally published in the Journal of Cell Biology, 201 (6), 875-885 DOI: 10.1083/jcb.201210073... Lucas, E., Khanal, I., Gaspar, P., Fletcher, G., Polesello, C., Tapon, N., & Thompson, B. (2013) The Hippo pathway polarizes the actin cytoskeleton during collective migration of Drosophila border cells. originally published in the Journal of Cell Biology, 201(6), 875-885. DOI: 10.1083/jcb.201210073 The Hippo pathway polarizes the actin cytoskeleton during collective migration of Drosophila border cells

There is a really interesting article at Slate.Com from Mary Ann Mason, the author of "Do Babies Matter" which I have written about here before. The post is titled "In the Ivory Tower, Men Only". The post tells some of the background behind the book and discusses issues about graduate school, post doctoral positions, applying for faculty jobs and more. The article also has some very good guidance for universities that would like to level the playing field: We all know what structural changes would help to level the playing field in all of these careers and they are quite similar: paid family leave for both mothers and fathers, especially for childbirth, a flexible workplace, a flexible career track, a re-entry policy, pay equity reviews, child care assistance, dual career assistance. Those universities and corporations who have actively created these policies have found an advantage in recruitment and retention. For instance, at Berkeley, after enacting several new policies to benefit parents, including paid teaching leaves for fathers, job satisfaction scored much higher among parents, and more babies are being born to assistant professors. Some good guidance for some of the activities at UC Davis as part of the ADVANCE program in which I am involved. And she ends by recommending It is time for women to “lean in” and demand family policies that will at least give them a fighting chance to have both a successful career and babies. I agree. But it is also time for men to do the same. The more that men also support and demand such policies the quicker things will change. -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. --------

After what seemed like an eternity, the epic saga known as AMP v. Myriad Genetics has finally come to a close. On June 13, 2013, the Supreme Court ruled (1) that isolated genomic DNA (gDNA) is not patent-eligible under section 101 of the Patent Act, but (2) cDNA is. For once, what the Justices said at oral argument gave accurate clues to what they really thought, and the result was what almost every observer (including this one) had predicted. The opinion—by Justice Thomas—was unanimous and brief: 18 pages. Justice Scalia wrote a one-paragraph concurrence in which he said only that he didn’t know enough to sign on to the Court’s recitation of “the details of molecular biology,” though he agreed with the decision. The 9-0 decision reflects a recent trend in patent decisions (see Mayo v. Prometheus and last month’s Monsanto opinion), and may represent a reaction to the derision that greeted the fractured, multi-opinion mess that was Bilski v. Kappos, the Court’s 2010 business methods case. Beyond the surface unanimity, the Myriad opinion has a no-brainer quality—that is, the opinion does not give any sense of wrestling with a difficult issue, giving the impression that the outcome was so clear that reasonable minds couldn’t possibly differ. Consistent with this approach, the Court cited only the lower court opinions and briefs in the case, a few of its own patent decisions, and a single scientific text (Watson’s Molecular Biology of the Gene). No amicus briefs (except the government’s, to confirm that the Department of Justice had thrown the USPTO under the bus), no scientific or law review articles. The strict legal significance of the decision is pretty straightforward. The Court struck down patent claims on genomic DNA that has been merely “isolated” from the body, where “isolated” means, well, “isolated”—removed and separated from its natural environment in the cell. More specifically, the Court held that genomic DNA does not meet the threshold test of patentable subject matter under section 101. It upheld the subject matter status of cDNA, which it defined as “synthetically created DNA . . . which contains the same protein-coding information found in a segment of natural DNA but omits portions within the DNA segment that do not code for proteins [introns].” Every patent drafted like Myriad’s first and broadest claim—“an isolated DNA coding for [a specified protein]”—is now invalid. Conversely, claims limited to cDNA versions of genes continue to pass the threshold test, though they are still subject to scrutiny under all the other patentability requirements (more on that below). The cDNA/gDNA distinction has its roots in the Federal Circuit’s 1991 decision in Amgen v. Chugai. That case turned on a priority-of-invention contest: who got the rights to the human EPO gene. But the case did, at least implicitly, establish the subject matter status of cDNA. The broadest claim upheld in that case was: “A purified and isolated DNA sequence consisting essentially of a DNA sequence encoding human erythropoietin.” The court treated this as a claim to the cDNA version of the gene, interpreting “purified” as meaning something like “only the coding regions.” It commented that “[i]t is important to recognize that [neither competing inventor] invented EPO or the EPO gene. The subject matter [of this claim] was the novel purified and isolated sequence which codes for EPO.” Thereafter, two things happened. First, the subject matter eligibility of cDNA was never again challenged, until now. And understandably so, if DNA is viewed as a chemical for patent law purposes. cDNA is, in a literal sense, a substance not found in the body; it contains the same coding information as the mature RNA transcript, but it is a different chemical: and, with the noncoding regions excised, it is not exactly replicated in natural DNA. The second thing was less predictable. Amgen set up one of those slippery slopes that lawyers are always talking about. The USPTO

Pesticide levels considered environmentally friendly in Europe and Australia are, in fact, having a devastating effect on invertebrate insect biodiversity in nearby creeks and streams, a new study has found, showing the need for an urgent overhaul of the way pesticide risk is assessed. Water-dwelling invertebrates like worms, snails, crustaceans, mites and insects play a crucial role in regional ecosystems because they provide food for fish, birds and platypuses.... Beketov, M., Kefford, B., Schafer, R., & Liess, M. (2013) Pesticides reduce regional biodiversity of stream invertebrates. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1305618110 Pesticides reduce regional biodiversity of stream invertebrates

I announced in an earlier post the realisation of the Repository of Ontologies for MULtiple USes ROMULUS foundational ontology library as part of Zubeida’s MSc thesis, as well as that a very brief overview describing it was accepted as a poster/demo paper [1] at the 7th International Conference on Knowledge Capture (KCAP’13) that will take place next week in Banff, Canada. The ‘sneak preview’ of the poster in jpeg format is included below. To stay in style, it has roughly the same colour scheme as the ontology library. The poster’s content is slightly updated compared to the contents of the 2-page poster/demo paper: it has more detail on the results obtained with the automated alignments. On reason for that is the limited space of the KCAP paper, another is that a more comprehensive evaluation has been carried out in the meantime. We report on those results in a paper [2] recently accepted at the 5th International Conference on Knowledge Engineering and Ontology Development (KEOD’13). The results of the tools aren’t great when compared to the ‘gold standard’ of manual alignments and mappings, but there are some interesting differences due to—and thanks to—the differences in the algorithms that the tools use. Mere string matching generates false positives and misses ‘semantic [near-]synonyms’ (e.g., site vs. situoid, but missing perdurant/occurrent), and a high reliance on structural similarity causes a tool to miss alignments (compare, e.g., the first subclasses in GFO vs. those in DOLCE). One feature that surely helps to weed out false positives is the cross-check whether an alignment would be logically consistent or not, as LogMap does. That is also what Zubeida did with the complete set of alignments between DOLCE, BFO, and GFO, aided by HermiT and Protégé’s explanation feature. The KEOD paper describes those ‘trials and tribulations’; or: there are many equivalence alignments that do not map due to a logical inconsistency. They have been analysed on the root cause (mainly: disjointness axioms between higher-level classes), and, where possible, solutions are proposed, such as subsumption instead of equivalence or proposing to make them sibling classes. Two such examples of alignments that do not map are shown graphically in the poster: a faltering temporal region that apparently means something different in each of the ontologies, and necessary-for does not map to generic-dependent due to conflicting domain/range axioms. The full list of alignments, mappings, and logical inconsistencies is now not only browsable on ROMULUS, as announced in the KCAP demo paper, but also searchable. Having said that, it is probably worthwhile repeating the same caution made in the paper and previous blog post: what should be done with the inconsistencies is a separate issue, but at least now it is known in detail where the matching problems really are, so that we can go to the next level. And some mappings are possible, so some foundational ontology interchangeability is possible (at least from a practical engineering viewpoint). References [1] Khan, Z.C., Keet, C.M. Toward semantic interoperability with aligned foundational ontologies in ROMULUS. Seventh International Conference on Knowledge Capture (K-CAP’13), ACM proceedings. 23-26 June 2013, Banff, Canada. (poster &demo) [2] Khan, Z.C., Keet, C.M. Addressing issues in foundational ontology mediation. Fifth International Conference on Knowledge Engineering and Ontology Development (KEOD’13). 19-22 September, Vilamoura, Portugal.