Research Blogging - Biology - English

We like turtles ('s genomes)

2013-06-19T00:54:44Z

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 shot last week at the awesome Kansas City Zoo, of a turtle attempting to make embryos like in the figure above. Hang in there, little buddy!They like tuhtles!Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, M...

Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D.... (2013) The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature genetics, 45(6), 701-6. PMID: 23624526

I WILL FEAR NO EVIL: the first head transplant on human

2013-06-18T18:25:32Z

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

June 18, 2013

2013-06-18T15:31:53Z

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

Even ‘environmentally protective’ levels of pesticide devastate insect biodiversity

2013-06-18T12:09:38Z

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

Explainer: Why Do Women Menstruate?

2013-06-18T03:55:22Z

For half the population, it comes three to five days each month, 12 months each year, for 40 years of our lives. Menstruation can be debilitating, relieving, disappointing, or simply an inconvenient fact of life. But why do humans menstruate, when most animals don’t? When you shake the tree of life, you find that only a handful of mammals aside from us – primates, a small number of bat species, and the elephant shrew – have opted for the monthly bleed....

Emera, D., Romero, R., & Wagner, G. (2012) The evolution of menstruation: A new model for genetic assimilation. BioEssays, 34(1), 26-35. DOI: 10.1002/bies.201100099

Blanks, A., & Brosens, J. (2013) Meaningful menstruation. BioEssays, 35(5), 412-412. DOI: 10.1002/bies.201300022

On the Trail of Ancient Killers

2013-06-17T17:10:14Z

The newly unveiled genome of a medieval strain of the mycobacterium that causes leprosy is a technical triumph borne of next-generation sequencing machines and clever new techniques to extract target DNA from a soup of ancient molecules. Awash in data, several labs are racing neck-and-neck to cull DNA from a Most Wanted list of other legendary killers: tuberculosis, plague, cholera, Leishmania, the potato blight, and AIDS. They gather traces of these culprits from ancient teeth, bones, hair, feces, and—in the case of potato blight—from skin and leaves, then unleash the sequencers. The work adds a new dimension to our understanding of historical events, revealing the true nature of the villains responsible for humanity's worst epidemics....

Gibbons, A. (2013) On the Trail of Ancient Killers. Science, 340(6138), 1278-1282. DOI: 10.1126/science.340.6138.1278

Supreme Court rules natural genes not patentable

2013-06-17T16:18:00Z

Unanimous decision against BRCA breast cancer susceptibility gene patents in Association for Molecular Pathology v. Myriad Genetics, Inc. Plus: a movie about BRCA1 discoverer Mary-Claire King....

Hall, J., Lee, M., Newman, B., Morrow, J., Anderson, L., Huey, B., & King, M. (1990) Linkage of early-onset familial breast cancer to chromosome 17q21. Science, 250(4988), 1684-1689. DOI: 10.1126/science.2270482

Miki, Y., Swensen, J., Shattuck-Eidens, D., Futreal, P., Harshman, K., Tavtigian, S., Liu, Q., Cochran, C., Bennett, L., Ding, W.... (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science, 266(5182), 66-71. DOI: 10.1126/science.7545954

Wooster, R., Neuhausen, S., Mangion, J., Quirk, Y., Ford, D., Collins, N., Nguyen, K., Seal, S., Tran, T., Averill, D.... (1994) Localization of a breast cancer susceptibility gene, BRCA2, to chromosome 13q12-13. Science, 265(5181), 2088-2090. DOI: 10.1126/science.8091231

Hey boy, you really activate my ventral midbrain

2013-06-17T14:52:00Z

Scientists at CalTech simultaneously found a way to stimulate your midbrain without invasive methods (ie: opening up your skull) and make you find them attractive. Chib, et al. reported in Translational Psychiatry that by using their newly designed noninvasive method called transcranial direct current stimulation (tDCS) on the prefrontal cortex they were able to activate the interconnected midbrain....

Chib VS, Yun K, Takahashi H, & Shimojo S. (2013) Noninvasive remote activation of the ventral midbrain by transcranial direct current stimulation of prefrontal cortex. Translational psychiatry. PMID: 23756377

Mars have building blocks of life as shown by the Martian rock from Antarctica

2013-06-17T11:27:35Z

Main Point: Scientists studied Martian meteorite obtained from Antarctica and found potential building block of life in it. Published in: PLoS ONE Study Further: Scientists have found good amount of boron in the rock. Boron is considered as the important element in the development of ribonucleic acid or RNA, which a nucleic acid that contains the sugar ribose. It is found in all living cells, and is essential for the manufacture of proteins according to the instructions carried by genes. RNA also acts instead of DNA as the genetic material in certain viruses. “I had read how important boron could have been in the origins of life, stabilizing a part of RNA,” biologist James Stephenson, with the NASA Astrobiology Institute at the University of Hawaii told Discovery News. RNA is composed of phosphate, a ribose, which is a five-carbon sugar, and a nucleobase. Out of these three components, only ribose has not been found outside of earth on any meteorite. “Of the three parts that make RNA, the ribose is the tricky part. We haven’t been able to explain how it could form naturally,” Stephenson said. Previously, researchers proposed that boron is one of the basis of ribose. “It’s the unique size of the boron which is able to stabilize the ribose ring structure. No other element has been shown to have that effect,” Stephenson added. “Given the greater similarity of Earth and Mars early in their geological history, and the extensive disruption of Earth's earliest mineralogy by plate tectonics, we suggest that the conditions for prebiotic ribose synthesis may be better understood by further Mars exploration,” Scientists wrote in the paper. Source: Discovery News Reference: Stephenson, J., Hallis, L., Nagashima, K., & Freeland, S. (2013). Boron Enrichment in Martian Clay PLoS ONE, 8 (6) DOI: 10.1371/journal.pone.0064624...

Stephenson, J., Hallis, L., Nagashima, K., & Freeland, S. (2013) Boron Enrichment in Martian Clay. PLoS ONE, 8(6). DOI: 10.1371/journal.pone.0064624

Autoimmune disease as a risk factor for mood disorder?

2013-06-17T10:35:00Z

Autoimmunity, the process by which the immune system fails to recognise self as self and subsequently targets those self tissues and cells, is something talked about quite a lot on this blog with autism specifically in mind. Part of the very wide and diverse immune-related features which have been discussed with at least some of the autisms in mind, it's not yet altogether clear exactly how and why autoimmunity is linked to behaviour but the association is an interesting one.Sally? @ Wikipedia The paper by Michael Benros and colleagues* expands that autoimmune - behaviour interest and their observations suggesting: "Autoimmune diseases and infections are risk factors for subsequent mood disorder diagnosis". Their conclusion is based on the analysis of a huge patient set from which nearly 100,000 people had a hospital contact for mood disorder. Mood disorder by the way, is an overarching term for quite a few conditions (see here) which as the name suggests, affect mood; be it an unusual 'high' or an unusual 'low'."A prior hospital contact because of autoimmune disease increased the risk of a subsequent mood disorder diagnosis by 45%". To me this is a really interesting association. OK I know correlation does not equal causation, but added to the association they made between hospitalisation for infection and subsequent mood disorder (62% increase) and the large participant numbers, there is lots to ponder here.I've gone on a few times on this blog about the bi-directional link between our physiology and the presentation of more psychiatric or behavioural 'symptoms'. Be it C.diff infection and depression or the skin-brain axis (see here), the connections are starting to be formed and examined. I'm just remembering back to some interesting research on allergic disease and neurodevelopment as also potentially being relevant to this post (see here) with the focus on allergy and its potential developmental effects and indeed the implication of some interesting potential interventions too. So what could be the mode of action for this autoimmune-infection-mood disorder link? Well, we have some contenders but at the moment nothing concrete. That the immune system might be doing so much more than protecting against disease is already pretty well known about as for example with the rise and rise of research into microglia (see here) and some other areas of interest** particularly with a focus on a very nebulous term: inflammation.Regular readers might know about my views and opinions on the role of food and the gut to behaviour - no really - and certainly when it comes to certain autoimmune conditions like coeliac (celiac) disease, we have a body of research suggesting how food, certain elements of food, under the right circumstances might be able to affect behaviour. Think Marios Hadjivassilliou for example. Even more outlandish, how about some role for those HERVs - human endogenous retroviruses - which seem to be cropping up with lots of conditions in mind (see here) and in particular autoimmune conditions***? Too speculative? Whether any of these areas overlap with the Benros paper is something as yet unknown. But the association posited between autoimmune conditions / infections and subsequent mood disorders is really, really interesting.To close, with the new Stone Roses inspired movie on the horizon, how about a song about Sally Cinnamon?----------* Benros ME. et al. Autoimmune Diseases and Severe Infections as Risk Factors for Mood Disorders. JAMA Psychiatry. 2013;():1-9. doi:10.1001/jamapsychiatry.2013.1111.** del Rey A. et al. A cytokine network involving brain-borne IL-1β, IL-1ra, IL-18, IL-6, and TNFα operates during long-term potentiation and learning. Brain, Behavior, and Immunity. 6 June 2013. http://dx.doi.org/10.1016/j.bbi.2013.05.011*** Dreyfus DH. Autoimmune disease: A role for new anti-viral therapies? Autoimmun Rev. 2011 Dec;11(2):88-97. doi: 10.1016/j.autrev.2011.08.005.-----------Benros ME, Waltoft BL, Nordentoft M, Ostergaard SD, Eaton WW, Krogh J, & Mortensen PB (2013). Autoimmune Diseases and Severe Infections as Risk Factors for Mood Disorders: A Nationwide Study. JAMA psychiatry (Chicago, Ill.), 1-9 PMID: 23760347...

Benros ME, Waltoft BL, Nordentoft M, Ostergaard SD, Eaton WW, Krogh J, & Mortensen PB. (2013) Autoimmune Diseases and Severe Infections as Risk Factors for Mood Disorders: A Nationwide Study. JAMA psychiatry (Chicago, Ill.), 1-9. PMID: 23760347