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  • May 19, 2009
  • 09:19 AM
  • 1,942 views

City mockingbirds can tell the difference between individual people

by Ed Yong in Not Exactly Rocket Science

While the rapid expansion of human cities have been detrimental for most animals, some have found ways of exploiting these brave new worlds and learned to live with their prolific inhabitants. The Northern mockingbird is one such species. It's very common in cities all over America's east coast, where it frequently spends time around humans. But Douglas Levey from the University of Florida has found that its interactions with us are more complex than anyone would have guessed. 

The mockingbird has the remarkable ability to tell the difference between individual humans, regardless of the clothes they wear. After less than a minute, they can tell one person from another and adjust their responses according to the threat they pose to its nest. This ability suggests that these birds are both intelligent and very flexible in their behaviour - two traits that must surely stand them in good stead in the urban jungle.

It obviously benefits an animal to be able to distinguish between threatening and harmless species, but discriminating between individuals of the same species is a much more difficult task - just think about how difficult you would find it to tell the difference between two mockingbirds by eye.

Levey worked with 24 pairs of mockingbirds that had taken up residence on the university's campus. Hundreds of people walk within five metres of their nests every day and elicit absolutely no reaction. To simulate a greater threat, Levey asked one of his colleagues to approach the nests of birds with fresh clutches, and touch their rim for 15 seconds. When faced with such intrusion, mockingbirds will typically react by rallying from the nest, making alarm calls and diving aggressively at the trespasser.

Read the rest of this post... | Read the comments on this post...... Read more »

Levey, D., Londono, G., Ungvari-Martin, J., Hiersoux, M., Jankowski, J., Poulsen, J., Stracey, C., & Robinson, S. (2009) Urban mockingbirds quickly learn to identify individual humans. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0811422106  

  • May 19, 2009
  • 08:35 AM
  • 1,335 views

Alzheimers Disease: amyloid-beta and sticky plaques

by Sally Church in Pharma Strategy Blog

I thought it would be fun to do a series on hot new trends in science and medicine based on different mechanisms of action, partly because this is what science is all about and partly because hearing about creative new...... Read more »

Osherovich, L. (2009) Genentech's new parADigm. Science-Business eXchange, 2(8), 1-5. DOI: 10.1038/scibx.2009.300  

Di Fede, G., Catania, M., Morbin, M., Rossi, G., Suardi, S., Mazzoleni, G., Merlin, M., Giovagnoli, A., Prioni, S., Erbetta, A.... (2009) A Recessive Mutation in the APP Gene with Dominant-Negative Effect on Amyloidogenesis. Science, 323(5920), 1473-1477. DOI: 10.1126/science.1168979  

  • May 19, 2009
  • 05:38 AM
  • 818 views

Using human gene expression profiles to predict longevity

by turritopsis in Ouroboros: Research in the biology of aging

Recently, some human survival data – together with matching gene expression data from lymphoblastoid cell lines – have become available from a long-range study that began in the early 1980s. In the first aging study to take advantage of this resource, Kerber et al. mine the data to identify gene changes associated with longevity:... Read more »

  • May 18, 2009
  • 08:32 PM
  • 868 views

Do Broad Commonalities Exist in Cancer?

by Reason in Fight Aging!

This is the age of biotechnology, and many believe that one of the crowning triumphs of the age will be the defeat of cancer. If we're going to greatly extend healthy human longevity, then the defeat of cancer certainly has to be achieved one way or another. I think that the one of the most exciting possibilities in modern cancer research is that a cure for cancer is in fact easy, but we don't yet know how to do it. Let me explain what I mean by "easy." This is an era in which we can order cells around, identify cells by tiny differences in their surface biochemistry, construct viruses to order, and in which researchers are rapidly deciphering and manipulating the most fundamental mechanisms of our biology. In this sort of background, "easy" means that researchers find some common mechanism necessary to all (or even just most) cancers. Scientists will then pile in and develop a way of attacking cancer by disrupting or manipulating that mechanism, and there the story is done. We'll have a robust cancer therapy, and will reap the benefits thereof. "Hard" on the other hand means that there is no common mechanism shared between more...... Read more »

Rebecca J. Critchley-Thorne, Diana L. Simons, Ning Yana, Andrea K. Miyahira, Frederick M. Dirbas, Denise L. Johnson, Susan M. Swetter, Robert W. Carlson, George A. Fisher, Albert Koong.... (2009) Impaired interferon signaling is a common immune defect in human cancer. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0901329106  

  • May 18, 2009
  • 04:49 PM
  • 550 views

Using Hair and Teeth to Infer Biological Rhythms

by blgtnjew in Hominin Dental Anthropology

I read an interesting paper today from PLoS ONE that was published in July 2007. It is more along the lines of physiology than it is about anthropology, or dental anthropology for that matter, but nevertheless, it has implications for anthropologists. Not the mention that the title of the paper is "Stable Isotope Ratios in Hair and Teeth Reflect Biologic Rhythms", so of course, I had to read it. The aim of the paper was to use stable isotope hydrogen in hair and stable isotopes carbon and oxygen in tooth enamel to assess biological rhythms, i.e. heart beat intervals, systolic arterial pressure variability, and variation in respiratory frequency. So, not the direct measurements of those things themselves but how they vary over time. So, heart rate, respiratory rate, and systolic arterial pressure do not matter here, we are looking at how those things change over time...like a long time. Human hair grows, as a reference for everyone here, at a rate of about 16 centimeters per year. It grows slower at higher altitudes most likely due to chronic hypoxia, but once again, not exactly anthropology territory. Very cool though, is that horse tail hair and mammoth hair grow at rates of 46 and 31 centimeters per year, respectively. Much more to do with heat retention and thermoregulation than other reasons, likely, but you never know; not my field. What does pertain to my fellow readers and I is that tooth enamel growth increment, called perikymata (from Greek), represent about 9 days of growth or roughly a little over a week. So about 40 perikymata per year. Growth rates for Paranthropus robustus are around 7 days giving a total of 50 per year. If we take the lengths of hair and perikymata, and analyse them for stable isotopes as mentioned earlier, then we can get varying levels over a year or more time span and see if biological rhythms are "recorded". Pretty fantastic, no? Below are two images displaying perikymata at original size, no scaling needed, that were both large enough and small enough for use on the blog. Other images can be found elsewhere on the intertubes, so check them out if you really are interested in the awesomeness that is dental enamel. The first is of course, the mandibular central incisors of a child approximately 7 years of age showing perikymata at regular intervals, no linear enamel hypoplasia or pathology evident. Nicely unworn showing the mamelons, since they were practically just erupted. The second is a fossil hominin tooth which I am making you figure out. The finger is a quarter index finger for scale, and the tooth is in the mandible and does a pretty good job of showing the perikymata...can you figure out which of the four categories of teeth this is? (http://odontoclinica.org/odontoblog/wp-content/uploads/2008/11/24-25_sitio1.jpg) (http://www.eva.mpg.de/evolution/images/microstructure1.jpg) In the end, the study did indeed find that biological rhythms can be found in the stable isotopes from hair and teeth, and ...represent the dynamic interaction between the neural control of the heart and its response. The low frequencies [16-23 weeks] reflect autonomic sympathetic modulation and the high frequencies [9-12 weeks] autonomic parasympathetic control of heart rate variability. So, that is pretty cool. Has future implications for both health professionals, researchers, and anthropologists. That wraps up this blog session, but stay tuned to PLoS ONE tomorrow when the adapid paper is revealed!!! I am so waiting for that. Jason Appenzeller, O., Qualls, C., Barbic, F., Furlan, R., & Porta, A. (2007). Stable Isotope Ratios in Hair and Teeth Reflect Biologic Rhythms PLoS ONE, 2 (7) DOI: 10.1371/journal.pone.0000636... Read more »

  • May 18, 2009
  • 12:17 PM
  • 765 views

On the accuracy of the influenza databases

by iayork in Mystery Rays from Outer Space

Lots of people have been analyzing the new H1N1 influenza virus by sequence analysis, comparing to influenza sequences in various databases (I used the NCBI’s).  How reliable are these databases?

Our observations show that a fraction of the sequences in the database exhibit anomalous properties that point to either radically new biology or, more likely, problems [...]... Read more »

  • May 18, 2009
  • 11:00 AM
  • 672 views

Leatherbacks turn up by the tens of thousands

by Katie Kline in EcoTone

The largest population of leatherback sea turtles in the world has been identified off the coast of Gabon, Africa, and is estimated at somewhere between 15,700 and 41,400 female turtles. This seems to be a big bounceback for the endangered turtles, which are the largest living members of the sea turtle superfamily.

This rough estimate was [...]... Read more »

Witt, M., Baert, B., Broderick, A., Formia, A., Fretey, J., Gibudi, A., Moussounda, C., Mounguengui Mounguengui, G., Ngouessono, S., & Parnell, R. (2009) Aerial surveying of the world’s largest leatherback turtle rookery: A more effective methodology for large-scale monitoring. Biological Conservation. DOI: 10.1016/j.biocon.2009.03.009  

  • May 17, 2009
  • 08:12 PM
  • 533 views

Size Matters, But So Does Maturity

by Johnny in Ecographica

Starting in the 1940’s, Angelo Siciliano pioneered the cultural meme of “brawn over brains” and actively encouraged the males of one mammalian species - Homo sapiens - to pack on muscle in order to win over rivals for the affection of potential mates. However, lost to Charles Atlas was the possibility that the iconic “97-pound weakling,” which he vowed to aid through a rigorous program of dynamic-tension, may have been capable of achieving success on his own, independently of an increased body size. Key to such success would be to avoid the gauntlet of bullying sand-kickers altogether thereby reducing the necessity for brute force, and rather than investing in mail order fitness regimens, to instead turn the “chump to a champ” through allotting resources to two key areas - growing-up fast and getting to the female first! Thanks to the vector of modern media, Angelo’s meme is still infectious today (among populations of H. sapiens) and has probably met with some limited success; however there are several species that have found competitive advantage in strategies other that those associated with an increased body size – one such animal is the redback spider of Australia.The redback, Latrodectus hasselti, is a polyandrous species in which intrasexual selection relies less on choosey females and more on males competing for access to un-mated –“virgin” - females. Virgins are preferred by the male redbacks because, as with many other spiders, the males introduce a post copulatory plug to the female following sex, this has the effect of decreasing the likelihood of secondary male suitors successfully transferring genetic material – to have the best probability of forwarding their germ line to future generations, male redbacks seek out virgins. The virgin status of redbacks is identified by the males through a pheromone signal emitted by the female; within hours of mating, these chemo-signals cease being produced and the female becomes less attractive as a potential mate. Typically, sexually mature males of the species, having converged on the virginal pheromone, will find themselves geographically amassed at the female’s web with as many as five other males vying for mating access. When this occurs, the males combatively engage each other until a single victor remains. To the victor goes the mate.When it comes down to brute force, generally the male with the best weapons, most strength or greatest mass has the advantage in combat. This polyandrous scenario is familiar to most, but generally images of big horn sheep ramming each other, or gladiatorial deer with interlocked antlers are called to mind; the spiders are little different… Little different - except for an alternative intrasexual strategy to which some males find themselves better adapted.By way of sexual and natural selection, some male redbacks have decided that because of the dynamic between pheromone signaling, male-to-male competition and copulatory plugs, that it may be better to focus more on being the first to achieve sexual maturity via rapid development than to spend extra effort and time in growing to a larger size. In this way they would have first access to females, avoid web-sparring with males and because of the pheromones, even discourage rivals post copulation. Even Charles Atlas could respect that! KASUMOVIC, M., & ANDRADE, M. (2009). A change in competitive context reverses sexual selection on male size Journal of Evolutionary Biology, 22 (2), 324-333 DOI: 10.1111/j.1420-9101.2008.01648.x... Read more »

  • May 17, 2009
  • 05:13 PM
  • 1,236 views

Treating the Morgellons Meme

by Martin Robbins in The Lay Scientist

[bpsdb] Looking at the culture-bound syndrome Grisi Siknis recently, I was reminded of Morgellons - a subject I've been meaning to look at for many months. Sufferers report strange organic and artificial fibers erupting from lesions, sensations of bugs crawling under the skin, and tentacled "starfish" crawling inside flesh. The problem is that while sufferers insist they are suffering from some new and exotic disease, both the medical establishment and the weight of evidence so far suggest that the the condition is largely psychosomatic in nature.

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In other words, while the condition is undoubtedly "real" in the sense that people are suffering from genuine discomfort; no physical trace or cause of the disease can be established, leaving most doctors to conclude that it is a result of the patient's mind - Morgellons sufferers are commonly diagnosed as having delusional parasitosis. Indeed, to dermatologists the signs are unmistakable, as Dr. Koblenzer describes [1]:

"The patients are virtual carbon copies, one of the other. The clinical picture is unmistakable. The patient is intensely anxious, is obsessively focused on his or her symptoms, brings ‘‘specimens’’ of the offending agent, or agents, and is unshakable in his or her belief as to the cause. Usually there will be a logical explanation of exactly howthe infection or infestation was contracted, and the patient will have resorted to the most extreme measures both to eradicate it and to prevent contagion."

[...]

"...the patient is not open to the idea of pathology in the

mind, the nervous system, or the brain. It is also

important for us to distinguish delusional beliefs from

phobic concerns or obsessional worries, a distinction

that caused some confusion in the past13 and that is

important, because both the psychopathology and

the treatment are different between the three."

Unfortunately, delusional parasitosis is understandably not a very popular diagnosis, and seems to have triggered something of a backlash among sufferers. At the extreme end of that, Morgellons has unfortunately attracted a "lunatic fringe" on the internet of conspiracy theorists positing everything from contrail poisoning to secret government tests to infection with aliens. These people with their ridiculous Youtube videos and assertions of nanotechnology are doing more than anyone to stop it being taken seriously.

Fortunately, there are more sensible support groups, but even here the attitude is strongly biased against the idea of a diagnosis of delusional parasitosis. The main reason for this seems to be a fear that somehow a diagnosis of DP means that doctors are saying that their condition is imaginary or not real - a perspective that probably has a lot to do with general public attitudes to mental illness. A good example of this appears in an excellent commentary by a Morgellons sufferer, published recently:

"Now, you can go up there and post all kinds of nasty comments and scream from the top of your lungs that this is real, but why bother."

Simon and Garfunkel once sang that "a man hears what he wants hear and disregards the rest", and this seems to be very much the case with these online communities - they have no rational reason or evidence to reject or refute the diagnosis of delusional parasitosis, but they continue to insist that it cannot be so, fearing that doctors are suggesting that their illness isn't "real". Sufferers take a diagnosis of delusional parasitosis as an offensive insult. And that's understandable - I woudn't particularly want to be called delusional either. As ever, PalMD at White Coat Underground puts it better than I can:

"...this false dichotomy of mind vs body is troubling, and the stigma of brain illnesses is very problematic."

The CDC have allocated some funds to study the disease at an epidemiological level - essentially collating the available reports to see if any pattern emergences. Some Morgellons groups have pinned hope on this study, but my gut feeling is that this can't provide them with an answer, for the simple reason that if the CDC produce the "wrong" result, it will be dismissed as conspiracy or incompetence.

So what can the medical establishment do about this? In my recent post on Grisi Siknis I noted that there were three basic possibilities: either the doctor genuinely shares the belief system of the patient; the doctor educates the patient to come around to his or her way of thinking; or the doctor pretends to believe the patient and plays along ("as it happens, anti-psychotics are very good for tackling skin parasites!"). The latter approach is seen as pretty unethical as it involves potentially deceiving patients, but some dermatologists are coming around to the idea. Murase et al present a particularly compelling account of this sort of thinking in a dermatology journal in 2006 [2]:

"[B]ecause the term 'Morgellons disease' does not have the word 'delusions' embedded in the term, it is a useful way to communicate with patients regarding their disease. As a case in point, I have established a close relationship with the patient described above by referring to her delusions of parasitosis as Morgellons disease. After taking cultures and a biopsy, I reassured her that there were no bacterial, fungal, or parasitic infections. I emphasized that I did not doubt the authenticity of the sensations she was experiencing, and I empathized with how disconcerting it must be to feel bugs crawling and stinging her skin. I explained that sometimes medications that psychiatrists use to calm nerve signals help patients with Morgellons disease. She is currently on the anti-psychotic risperidone, followed by both dermatology and psychiatry."

It's a very seductive approach, but it isn't without hazards and consequences as Accordino et al point out [3]:

"One wonders if using the term “Morgellons

disease” in clinical practice may bring about a

slippery slope of using patient-created diagnostic

terms to describe conditions with no empiric support

of their existence in the medical literature."

There are numerous dangers if this were to happen - for example, it's a very short step from patient-created diagnostic terms to patient-created cures, and the spread of terms like "Morgellons" could well lead to patients rejecting appropriate courses treatment. This is aside from the obvious objection that unless the doctor involved is very careful, they are essentially lying to their patients. What would be the ethical and legal implications of this?

The truth is that Morgellons probably isn't a new or novel disease, but simply delusional parasitosis mixed with an internet meme. That isn't to say that it's not a real condition - it absolutely is - but the unfortunate medical label clashes with the cultural beliefs and expectations of the patients. The question of how best to deal with this is unanswered, but with any luck perhaps the CDC study will stimulate the sharing of ideas between doctors, and help to establish a framework of understanding that benefits both doctor and patient.

- - - - - - - - - - - - - - - - - - -

Find me on Twitter! @mjrobbins

[1] KOBLENZER, C. (2006). The challenge of Morgellons disease Journal of the American Academy of Dermatology, 55 (5), 920-922 DOI: 10.1016/j.jaad.2006.04.043

[2]MURASE, J., WU, J., & KOO, J. (2006). Morgellons disease: A rapport-enhancing term for delusions of parasitosis Journal of the American Academy of Dermatology, 55 (5), 913-914 DOI:... Read more »

KOBLENZER, C. (2006) The challenge of Morgellons disease. Journal of the American Academy of Dermatology, 55(5), 920-922. DOI: 10.1016/j.jaad.2006.04.043  

MURASE, J., WU, J., & KOO, J. (2006) Morgellons disease: A rapport-enhancing term for delusions of parasitosis. Journal of the American Academy of Dermatology, 55(5), 913-914. DOI: 10.1016/j.jaad.2006.04.042  

Accordino, R., Engler, D., Ginsburg, I., & Koo, J. (2008) Morgellons disease?. Dermatologic Therapy, 21(1), 8-12. DOI: 10.1111/j.1529-8019.2008.00164.x  

  • May 17, 2009
  • 03:31 PM
  • 1,374 views

Seed dispersal by ants: A lousy way to travel, a good way to diversify

by Jeremy Yoder in Denim and Tweed

New in the always open-access PLoS One: turns out that a great way to make new species, if you're a plant, is to have your seeds dispersed by ants. This is because ants aren't very good at seed dispersal.

Seed dispersal by ants, or myrmecochory, works very much like dispersal by fruit-eating birds and mammals: ant-dispersed seeds typically have a fatty attachment, called an elaiosome, that looks tasty to ants. Ants collect elaiosome-bearing seeds, bring them back to their nest, pry off the tasty bit, and then discard the rest of the seed. This leaves the seed safely underground in an ant-midden, ready to germinate -- a great way to dodge seed-eating critters and avoid competition from its parent plant and siblings [$-a].

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Bloodroot seeds, with ant-attracting

elaisomes. Photo by cotinis.I didn't learn about myrmecochory until after I'd finished undergrad -- which is surprising, because it was going on under right my nose every time I went out into the Appalachian woods near campus. Lots of wildflowers [$-a] have ant-dispersed seeds, including bloodroot, touch-me-not, and good old trillium. It's an extremely popular dispersal mechanism, having evolved independently multiple times on every continent except Antarctica. Really, me not knowing about myrmecochory is kind of like not knowing about fruit!

Ant dispersal is also associated with increased species diversity. In the new article, Lengyel et al. use a classic analysis method called sister group comparison to test the hypothesis that ant-dispersed plant groups contain more species than the most closely-related plant group. And they do, by a long way: on average, myrmecochorous groups contain twice as many species as their non-myrmecochorous sister groups. Why is this? As the authors conclude, it's probably a side consequence of ant dispersal -- ants don't move seeds very far from where they collect them.Recent evidence from genetic studies shows that limited seed dispersal in myrmecochory can lead to strong genetic structure within populations even at spatial scales as small as a few meters. The failure of myrmecochores to maintain gene flow across barriers may lead to reproductive isolation of sub-populations, which may facilitate speciation. [In-text references omitted.]So myrmecochorous plants, like Appalachian salamanders [$-a] and tropical white-eyes [$-a], make lots of new species not because their unique characteristics give them some adaptive advantage (although, to be sure, there are advantages to ant dispersal), but because ants do a lousy job moving seeds between populations, leaving them free to follow their own evolutionary trajectories.

Lengyel et al. argue that myrmecochory is a key innovation, a trait that helps a group of organisms spread and diversify in the process evolutionary biologists call adaptive radiation. Based on their results, I have to agree -- ant dispersal is strongly associated with evolutionary diversification. But the speciation that myrmecochory promotes is an accident, a side effect. We often think of key innovations promoting speciation by adaptive means, by allowing one group of species to outcompete others. Clearly, however, a key innovation can also be a trait that makes the accident of speciation a little more likely.

References

Beattie, A.J., & Culver, D.C. (1981). The guild of myrmecochores in the herbaceous flora of West Virginia forests. Ecology, 62, 107-15 DOI: http://www.jstor.org/pss/1936674

Giladi, I. (2006). Choosing benefits or partners: a review of the evidence for the evolution of myrmecochory. Oikos, 112 (3), 481-92 DOI: 10.1111/j.0030-1299.2006.14258.x

Kozak, K., Weisrock, D., & Larson, A. (2006). Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon). Proc. R. Soc. B, 273 (1586), 539-46 DOI: 10.1098/rspb.2005.3326

Lengyel, S., Gove, A., Latimer, A., Majer, J., & Dunn, R. (2009). Ants sow the seeds of global diversification in flowering plants. PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005480

Moyle, R., Filardi, C., Smith, C., & Diamond, J. (2009). Explosive Pleistocene diversification and hemispheric expansion of a "great speciator." Proc. Nat. Acad. Sci. USA, 106 (6), 1863-8 DOI: 10.1073/pnas.0809861105... Read more »

  • May 17, 2009
  • 03:00 PM
  • 593 views

ECOLOGY: Helping Bumble Bees Adapt to an Increasingly Urban World

by Michael Long in Phased

Karin Ahrne (Swedish University of Agricultural Sciences)

and coworkers have explored the factors governing the

diversity, abundance, species composition, and uniform

pollination capacity of bumble bees, which is important

for ensuring the continuation of their critically important

role in pollination.

This news feature was written on May 17, 2009.... Read more »

  • May 17, 2009
  • 02:50 PM
  • 1,492 views

Open Source Psychic

by Bryan Perkins in Science. Why not?

As I was reading the post about open access science in which Bora over at A Blog Around the Clock mentions the research paper I posted on this blog, I found one line in particular that expresses the importance of Open Access science in my mind. In the article Bora says:
"In any case, it is much better for data to be out in the open, available to anyone who knows how to use Google search, than gathering dust in some manila folder."... Read more »

MacCallum, C., & Parthasarathy, H. (2006) Open Access Increases Citation Rate. PLoS Biology, 4(5). DOI: 10.1371/journal.pbio.0040176  

  • May 17, 2009
  • 12:00 PM
  • 1,321 views

Prairie Dogs Communicate In Living Colour

by Bryan Perkins in Science. Why not?

Functional reference refers to a type of communication used by some animals in which information can be incorporated about an object or event external to the animal. With alarm calls, for example, encoded information may refer to the species of predator, the urgency of the response required, or the type of evasive action to be taken in response to a particular type of predator. Many species have different alarm calls for aerial versus terrestrial predators; including many species of ground squirrels (Spermophilus sp.), tree squirrels (Tamiasciurus hudsonicus), chickens (Gallus gallus domesticus), dwarf mongooses (Helogale undulata), suricates (Suricata suricatta), and tamarins (Saguinus fuscicollis and Saguinus mystax). Other species have alarm calls that differ for different predators. Gunnison's prairie dog's (Cynomys gunnisoni) have a different call for red-tailed hawks (Buteo jamaicensis), humans (Homo sapiens), coyotes (Canis latrans), and domestic dogs (Canis familiaris).... Read more »

Slobodchikoff, C., Paseka, A., & Verdolin, J. (2008) Prairie dog alarm calls encode labels about predator colors. Animal Cognition, 12(3), 435-439. DOI: 10.1007/s10071-008-0203-y  

  • May 17, 2009
  • 10:21 AM
  • 1,044 views

In which a Nature paper fails on several levels

by Björn Brembs in bjoern.brembs.blog

Ok, so what else is new? We all love to rip GlamMag paperz to shreds in our journal clubs. This paper by Hong et al. last year in Nature stands out of the crowd in two main ways. For one, it shows how failing to realize alternative explanations can easily break your entire publication. Moreover, it shows how generating large datasets doesn't replace using your brain when generating and evaluating them. Apparently, the editors and reviewers at Nature handling this particular manuscript failed to take this into account this one time.The authors went through unbelievable efforts to test an enormous number of different wild type, mutant and transgenic Drosophila strains for their temperature preference. Based on only 8 authors, it seems to me these authors must have worked 24/7 for many, many months to get all this data, evaluate them and discuss and compile all the results. Here's their experiment:Pretty self explanatory: the flies walk around in a chamber with a temperature gradient and where they spend most of their time determines their temperature preference. From this sort of data, the authors calculate a preference index for high or low temperatures, respectively:According to their graph, flies walking around incessantly score an AI of zero both for high temperatures and for low temperatures (center pane of the graph). There is a structure in the Drosophila brain that is associated with hyperactivity: the mushroom-bodies. The study was published exactly ten years before Hong et al.: Mushroom bodies suppress locomotor activity in Drosophila melanogaster. Apparently, the authors are unaware of this publication, as they don't even cite it. However, the authors of this previous paper have used a very similar setup (horizontal tubes) and tested flies for their walking activity:In this graph (Fig. 2 from Martin et al., 1998), the mutant mbm1 as well as transgenic fly strains which have synaptic activity blocked in various parts of the mushroom-bodies (line 201Y, H24 and 17D) show increased walking activity. Now let's see how these flies perform in the temperature essay from Hong et al. (Fig. 1, modified to show just selected strains):As expected, the flies show an AI of around zero (with black bars denoting AI low and grey bars AI high). But Hong at al. have not suspended critical thought entirely before they submitted the results of their intensely laborious screening efforts. They realized there was a need to control for some sort of locomotion defects in the flies they tested. However, their control also fails on several levels: a) they used a climbing essay when in their temperature essay the flies were walking horizontally and b) the climbing performance in their essay could only decline and not increase:Thus, the authors could not detect the increase in walking performance that inhibiting mushroom-body function conveys (Martin at al., 1998).In summary: Hong et al. conclude that the mushroom-bodies are involved in temperature preference by using a locomotor essay that reproduces the results of an experiment published ten years earlier (Martin et al. 1998). Somehow adding insult to injury, they tested an absolutely incredible number of fly strains (more than 120, by my count), yielding no less than 30 pages of supplementary material with many figures, tables, text and references (but again, no citation of Martin et al. 1998 in there). Yet, they only manage to show the same thing as Martin et al. in 1998 with 10% the number of strains.Important: Of course, all this does not exclude that the mushroom-bodies and the processes in the neurons there controlling cAMP level indeed may be involved in temperature sensing and temperature preference. It's only that Hong et al. haven't shown that, yet.References: Hong, S., Bang, S., Hyun, S., Kang, J., Jeong, K., Paik, D., Chung, J., & Kim, J. (2008). cAMP signalling in mushroom bodies modulates temperature preference behaviour in Drosophila Nature DOI: 10.1038/nature070901. Jean-René Martin, 2. Roman Ernst, & 3. Martin Heisenberg (1998). Mushroom Bodies Suppress Locomotor Activity in Drosophila melanogaster Learning and Memory, 5, 179-191 DOI: 10.1101/lm.5.1.179... Read more »

  • May 17, 2009
  • 08:41 AM
  • 1,282 views

U-Compare: Advanced Biological Text Analytics Using Workflows

by Abhishek Tiwari in Fisheye Perspective

Those who are familiar with Pipeline Pilot text analytics component collection or InforSense TextSense, text analytics is always more fun if you are using any of these platforms. These platforms allow user to search in PubMed, Patents, NIH grants, Google or any other third party database. Named entity recognition, natural language processing (NLP), document classification and clustering, all of these without any programing, just by easy drag-and-drop. Both Pipeline and InforSense are commercial platforms and according to my knowledge in past there was no such workflow implementation for text analytics in public domain.Recently text mining groups at University of Tokyo and University of Colorado School of Medicine in collaboration with National Centre for Text Mining at University of Manchester have developed a powerful workflow based text analytics tool called as U-Compare which is freely available online. U-Compare is built on top of UIMA (Unstructured Information Management Architecture), and it allows users to build complex NLP workflows via an easy to use visual programming interface. In U-Compare, NLP workflows can be created using simple drag-and-drop of available UIMA components.UIMA provides an open source framework, component collection and infrastructure for unstructured information analysis and search. UIMA originated at IBM, now incubated at the Apache Software Foundation and its specification standardization effort is hosted at OASIS. As it was designed to be industrial strength platform and hence several IBM applications such as OmniFind are based on UIMA.FurtherUIMA enables applications to be decomposed into components, for example "language identification" = "language specific segmentation" = "sentence boundary detection" = "entity detection (person/place names etc.)". Each component implements interfaces defined by the framework and provides self-describing metadata via XML descriptor files. The framework manages these components and the data flow between them. Components are written in Java or C++; the data that flows between components is designed for efficient mapping between these languages. UIMA additionally provides capabilities to wrap components as network services, and can scale to very large volumes by replicating processing pipelines over a cluster of networked nodes. U-Compare contains largest UIMA component collection. There are seven functional component classes: collection readers, sentence detectors, tokenizers, POS taggers, syntactic parsers, relation extracters and named entity recognizers. Each of these class specifies several components, for example in named entity recognizers class user have many options such as GENIA Tagger, LingPipe Entity Tagger, OpenNLP. In addition U-Compare provides a special parallel flow component, which can be used to make comparison workflows to compare the outputs of tool and corpus combinations.Apart from functional components, current version of U-Compare includes two visualizer components: Annotation Viewer and MoriV. Annotation Viewer can be used to display annotations generated at any point in the workflow while MoriV is a tree structure visualizer.U-Comapre also provides a developer API, which includes official UIMA Java/C++ APIs, along with a simpler interface which allows developers to access a UIMA workflow via the standard I/O streams or via stored files. U-Compare is available as Java Web Start application.Reference:Kano, Y., Baumgartner, W., McCrohon, L., Ananiadou, S., Cohen, K., Hunter, L., & Tsujii, J. (2009). U-Compare: share and compare text mining tools with UIMA Bioinformatics DOI: 10.1093/bioinformatics/btp289... Read more »

Kano, Y., Baumgartner, W., McCrohon, L., Ananiadou, S., Cohen, K., Hunter, L., & Tsujii, J. (2009) U-Compare: share and compare text mining tools with UIMA. Bioinformatics. DOI: 10.1093/bioinformatics/btp289  

  • May 16, 2009
  • 05:29 PM
  • 680 views

Analog Signaling Networks

by AK in AK's Rambling Thoughts

Having just last week joined Researchblogging, I've been on the lookout for interesting open-access research reports or articles to blog about. thus, two articles caught my eye regarding cellular intelligence, a subject I've discussed before.Dpr Acts as a Molecular Switch, Inhibiting Wnt Signaling when Unphosphorylated, but Promoting Wnt Signaling when Phosphorylated by Casein Kinase Iδ/εTeran, E., Branscomb, A., & Seeling, J. (2009). Dpr Acts as a Molecular Switch, Inhibiting Wnt Signaling when Unphosphorylated, but Promoting Wnt Signaling when Phosphorylated by Casein Kinase Iδ/ε PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005522Modulation of the β-Catenin Signaling Pathway by the Dishevelled-Associated Protein Hipk1Louie, S., Yang, X., Conrad, W., Muster, J., Angers, S., Moon, R., & Cheyette, B. (2009). Modulation of the β-Catenin Signaling Pathway by the Dishevelled-Associated Protein Hipk1 PLoS ONE, 4 (2) DOI: 10.1371/journal.pone.0004310These are dense papers, and I'm afraid the abstracts won't be much good if you aren't already familiar with the Wnt/β-Catenin signaling "cascade". Very briefly, Wnt is a large family of proteins that act as signaling molecules outside the cell within the developing (and adult) bodies of vertebrates, and probably many other bilaterians. They interact with several families of enzymes and other signaling proteins embedded in the cell membrane, passing along information to the enzyme signaling network within the cell, where they have a critical effect on the presence of β-Catenin, a (family of) protein(s) with wide effects on gene transcription.My main focus here is not on the details of the Wnt/β-Catenin signaling, but on the tacit assumptions built into certain word choices involved in reporting, and probably setting up, research in this area.Let's start with the word "cascade". The very word implies a false analogy: a cascade is a waterfall-by-steps, and each step is a downhill process that depends on the previous process(es) for its energy.Figure 1: A linear cascade, which is what typically comes to mind with the word. (From the Council of Independent Colleges: Historic Campus Architecture Project website.)Figure 2: A more complex cascade, showing some parallel interaction. (From the trüWATER! website.)Phosphorylation is not like a waterfall, however, but more an electrical relay, or, better, like a transistor. Both phosphorylation and dephosphorylation are extremely "downhill" processes energetically.A1What passes along, rather than down, the cascade is information, which, unlike energy, is not subject to considerations of entropyA2 or conservation. We should not speak of a "cascade" then, but a network, in which information is not constrained to go in only one direction, unlike water in a cascade. Indeed, the control mechanisms within the cell are full of loops.8Keeping this fact in mind will help us make sense of research like that discussed here: it looks like a tangled spiderweb of causative (catalytic) relationships because it is a tangled spiderweb: a network.The next word we need to question is "switch". The research reported in Teran, et al.1 clearly shows that a pool of phosphorylated Dpr will tend to promote (or, perhaps, enhance) Wnt Signaling, while a pool of unphosphorylated Dpr will do the oppositte. But is all the Dpr in the pool usually one or the other? Perhaps, but it's equally plausible that it maintains a balance in vivo, with enough of both types to have an intermediate effect. Note that this effect need not be linear, with respect to the concentration ratios (or absolute concentration of either). Only after appropriate research can we be sure that this enzyme actually acts like a switch, rather than a knob, capable of assuming any value of concentration ratios (within some plausible range). And if it can act like a knob, further research would be needed before we can be sure that it acts in a linear fashion (if it does).Even if Dpr does "switch" quickly, from one stat to another, at least some of the inputs to the network (not just "cascade") that includes it are analog, as are (ultimately) the influences that contribute to its phosphorylation level and the ultimate output: the combined catalytic effects of both species of Dpr.It's important to note that such analog networks can have a number of metastable "digital" states, while other parts of the network vary continuously based on external and internal factors.Rather than continue here, I'll refer you to my earlier discussion, as well as "Quantitative analysis ofsignaling networks" by Herbert M. Sauroa and Boris N. Kholodenko, a peer-reviewed paper, from which let me quote: Whether evolution has fashioned digital devices on a large scale is still a matter of debate, but considering that our current technological mind set is digital, we may be inadvertently focusing too much attention on the possibility of a digitally driven biological cell. As a result, we may overlook the fact that not so long ago, analog was a critical aspect of man-made computational devices in the form of analog computers ([ref]). Given the flexibility of analog and its inherent ability to condense data handling to a far greater degree than its digital counterpart,1 we think that the argument that evolution has selected largely for analog-based signaling networks is a strong one. Clearly, there are cases when on/off decision making is crucial, for example, the most obvious being cell division ([refs]) and bacterial sporulation ([refs]) being another example. Boolean-based digital circuits may be employed by gene regulatory networks; however, even here the case is not certain ([refs]).1 Note that it requires a single transistor to store one bit in a digital device, whereas ifthe transistor were used as an analog storage device it could represent a value to an arbitrary high number base.The probable analog nature of the signaling network, then, as called out in the title of this post, allows us a much better appreciation of the importance of these two papers: they are important advances in our understanding of how the various enzymes in (and out of) the cell interact, but the assumption that there is a signaling "cascade", and the assumption that two states automatically constitute a "switch" tend to limit our thoughts. It would be preferable to think of an analog signaling network, with the various enzymes and other molecul... Read more »

  • May 16, 2009
  • 01:41 AM
  • 577 views

SpeciesDay - Unionidae

by Eric Heupel in The Other 95%

It's been a bit quieter around here than Kevin and I prefer, but now the finals are all done and I can finally say "I can has cheezburger wit dat?"Seriously though, in the next month or so there will be some changes in this space... in the mean time:Did you know there are 198 invertebrates listed under the Endangered Species Act? Yep, inverts make up 34% of the 575 animals protected under ESA. But is this good or bad that inverts are underrepresented here?? Care to guess how many of those 198 are molluscs? I'll give you a starting point - only two of the 198 invert species protected under ESA are cnidarians. Elkhorn Coral (Acropora palmata)and Staghorn Coral (Acropora cervicornis) are listed as Threatened. First correct answer, gets a small hand made tote bag free (allow 3-4 weeks for creation and delivery though!)Today, May 15th is Endangered Species Day, and the the net was all atwitter with postings and tweets about endangered species. I just got done with the prototype for an outreach product that includes some of those endangered molluscs so I tweeted out the Shinyrayed Pocketbook (Lampsilis subangulata) a member of that marvelous group of freshwater mussels, the Unionidae. If you recall from our earlier posting, this is the group of freshwater bivalves that has the habit of spitting its spawn into the face of an unsuspecting fish. The spawn are technically a form of larvae unique to these mussels called the glochidia and for some reason all my vertebrate loving friends seem to think that the whole "spewing spawn in your face" technique is rather disturbing. The young molluscs that are now in the face and mouth of the hapless fish attach to the its gills and encyst there. They feed on the blood in the gills until they are ready to drop to the sediments and metamorphose into a full adult form.The shiney-rayed pocketbook is found in Alabama, Florida and Georgia, mainly in the Chattahoochie and Flint rivers. In its most recent review it was assessed as endangered with a recovery priority of 5 (high threat and low potential for recovery). The good news though is that from 2003 to 2007 the range of the Shiney-rayed Pocketbook did extend into more of the river than it had been in recent years. The shiney-rayed pocketbook handles the details of reproduction and larval distribution a little differently than our last unionoida. Our last fresh water mollusc, the Snuffbox, lures a fish in with it's mantle flaps which look like a small fish. When the fish attacks the lure, the snuffbox springs its trap, catching the logperch's head between it's valves. It then uses it's mantle to smother the fish for a few moments. When it releases the smothering hold on the fish a little, it also releases it's glochidia which is has been brooding in the shell. The fish gasps for water (air) and gets water and glochidia.The shiney-ray takes another very interesting tack at larval distribution. Its females also brood the young until they reach the glochidia stage then release them to parasitise largemouth bass (Micropterus salmoides) and spotted bass (M. punctatus). The season for releasing glochidia will be begin in just a few weeks, late May through August.) The females, create a superconglutinate, a group of large packets (conglutiates) of glochidia attached to what appears to be a long transparent mucus rope. The superconglutinate strongly resembles a small fish, which lures in larger predatory fish. When a larger fish attacks the superconglutinate the mass ruptures and glochidia are freed to attach to the gills of the fish. The glochidia parasitize a fish host for a until they are ready (able?) to metamorphose into juvenile mussels and settle to the substrate in sandy or muddy slow moving regions. It is thought that the main purpose of the parasitic stage is not actually for nutrition and growth, but for transportation and distribution since the larvae would be unable to fight even a weak river flow to hold position or fight upstream, but attached to a fishes gills they can expand upstream or at least maintain position. This is borne out to some degree by recent expansion of L. subangulata up current in some locations.Of course a video is highly warranted here, so courtesy of M.C. Barnhart, I give you the close cousin of L. subangulata showig off her superconglutinate. The orange-nacre mucket (Lampsilis perovalis, the species in the video, is one of only 2-3 other species known to create a superconglutinate.

References:Roe, K., Hartfield, P., & Lydeard, C. (2001). Phylogeographic analysis of the threatened and endangered superconglutinate-producing mussels of the genus Lampsilis (Bivalvia: Unionidae) Molecular Ecology, 10 (9), 2225-2234 DOI: 10.1046/j.1365-294X.2001.01361.xBogan, A., & Roe, K. (2008). Freshwater bivalve (Unioniformes) diversity, systematics, and evolution: status and future directions Journal of the North American Benthological Society, 27 (2), 349-369 DOI: 10.1899/07-069.1... Read more »

  • May 15, 2009
  • 05:46 PM
  • 1,168 views

Increased fidelity reduces viral fitness

by Vincent Racaniello in virology blog

We have spent over a week discussing the effects of polymerase error rates on viruses. RNA viruses have the highest error rates in nature, a property that is believed to benefit the viral population. For example, selective pressure from the immune system or antiviral drugs may lead to changes that are beneficial for the population. [...]... Read more »

  • May 15, 2009
  • 05:12 PM
  • 1,760 views

Breast Milk Transfer of Antigens Establishes Anti-Allergenic Tolerance to Those Antigens

by Toaster Sunshine in Mad Scientist, Junior

Milk isn't just milk. The pasteurized cow milk that we can purchase in the grocery store has been cleaned, processed, and in many cases chemically scrubbed of fat. Unique among mammals, we Western humans stubbornly persist in our consumption of dairy products well into adulthood regardless of whether or not our guts like it. But the cow milk in the store is very different from the fresh milk humans nurse their newborns with. Fresh human milk contains growth factors, vitamins, an astounding density of calories, IgA antibodies, and also antigen. Disregarding the controversial and impassioned debate surrounding breast milk vs. infant formula, research has found that the immunological molecules secreted in breast milk are important for the developing immune system of the infant.Verhasselt and Julia et al have demonstrated that antigen secreted in a mother's breast milk significantly impacts the later development of allergic asthma in her infants. In effect, this is immunological programming.They used an elegant experimental system wherein they took nursing dams (mouse mother) and exposed them to antigens (OVA) without their pups, then placed them back with their pups to nurse. Later on when the pups had reached adulthood, they sensitized the mice per the immunology canon and tested their allergic asthmatic (hereafter refered to as atopic) response. In mice breastfed by OVA-exposed dams it was found that, in comparison to those breastfed by non-exposed dams, airway hyperreactivity, pulmonary eosinophilia, cellular infiltrate, and mucus deposition were all decreased towards mice not challenged with OVA (normal, negative controls). Moreover, the classical TH2 cytokines (IL-4, IL-5, IL-10, and IL-13) that have been associated widely with atopic responses were decreased in OVA-breastfed mice, as were the frequencies of the lung CD4+ T-cells that secrete them. Overall, this points to OVA-breastfed mice having a significantly weakened allergenic response to an allergen, or put another way, these mice tolerated the prescence of the allergen much better.As an aside, OVA is an abbreviation for ovalbumin, which is a key molecule in eggs and is a very sticky molecule. In every study of allergy or asthma that I can remember reading, OVA was used to sensitize mice and produce an allergic response to it. This is done by injecting a solution of OVA into the peritoneal cavity of the mice, waiting 2 weeks to let OVA-specific CD4+ T-cells develop, and then challenging the mice by squirting an OVA aerosol up their noses. This model has proven to reliably produce a strong and specific allergenic response.But how did the authors determine that it was secreted antigen itself that was inducing the tolerance?To address this, they took normal, wild-type C57 mouse pups and gave them to lactating uMT and RAG-2 transgenic dams*. Both these transgenic strains of mice are completely unable to mount an adaptive immune response to anything; they do not and cannot make antibodies. When these mice were exposed to OVA and then nursed the wild-type pups, the same effects of the OVA-breastfeeding inducing allergen tolerance were observed. This was also replicated with Balb/c mice (which is important because the C57 strain is known to skew towards a TH1 response phenotype while Balb/c skews more to TH2, which is better characterized in the pathophysiology of atopy).But then Verhasselt and Julia took a look at some important and specific immunoregulatory molecules: TGFb and IL-10. Both of these molecules are broad suppresors of inflammatory immune responses regardless of that response's cellular phenotype. IL-10 transgenic dams did not alter observed results when exposed to OVA, but TGFb knockdown dams did in that the pups they nursed were reactive to OVA. This strongly suggests that TGFb must accompany antigen in the breast milk in order for the infants' immune systems to recognize that antigen as a harmless allergen and, in effect, program itself not to react against it. Luckily for human mothers, though, breast milk already contains TGFb.At a wider level, this suggests that mothers who are exposed to many allergens will pass on tolerance to those allergens to any breast-feeding infants they may have. Perhaps this, coupled with the hygiene hypothesis, is a call for more moms to teach their infants how to make mud pies even earlier.*I can't help but wonder how many times they did this and found all the pups had been killed off by their adoptive mothers, as this is what stressed out rodent dams tend to do.Verhasselt, V., Milcent, V., Cazareth, J., Kanda, A., Fleury, S., Dombrowicz, D., Glaichenhaus, N., & Julia, V. (2008). Breast milk–mediated transfer of an antigen induces tolerance and protection from allergic asthma Nature Medicine, 14 (2), 170-175 DOI: 10.1038/nm1718... Read more »

Verhasselt, V., Milcent, V., Cazareth, J., Kanda, A., Fleury, S., Dombrowicz, D., Glaichenhaus, N., & Julia, V. (2008) Breast milk–mediated transfer of an antigen induces tolerance and protection from allergic asthma. Nature Medicine, 14(2), 170-175. DOI: 10.1038/nm1718  

  • May 15, 2009
  • 02:22 PM
  • 1,032 views

Those Brainy Microtubules

by AK in AK's Rambling Thoughts

I've discussed cellular intelligence before, including local intelligence, especially in the synapses of nerve cells. But now a new paper1 has added another dimension to the intelligence around the synapse, specifically the post-synaptic processes.In Synaptic activation modifies microtubules underlying transport of postsynaptic cargo (by Christoph Maasa, Dorthe Belgardta, Han Kyu Leea, Frank F. Heislera, Corinna Lappe-Siefkea, Maria M. Magierab,Juliette van Dijkb, Torben J. Hausrata, Carsten Jankeb, and Matthias Kneussel), we hear that synaptic activity, that is the activity of incoming action potentials, can modify a part of the cellular skeleton called microtubules in a way that changes the characteristics of the postsynaptic density, contributing to Synaptic plasticity. Synaptic plasticity is the ability of the synapse to change how it responds to an action potential, in terms of the final effect on the dendrite and its tendency to fire a new action potential.The mechanism of this modification is in changing the level (and probably the type) of Polyglutamylation, a process in which several (or more) glutamate residues are added to an existing glutamate residue in the tubulin proteins of the microtubule.Figure 1: Polyglutamylation and polyglycylation. (From the website of Group Carsten Janke.)The result of this modification is that receptors for glycine, and probably GABA,2 both neurotransmitters that normally tend to suppress new action potentials, are changed in their behavior migrating to the synapse.This process is mediated by a protein called gephyrin, a part of the cellular skeleton normally found associated with the postsynaptic density. It turns out that gephyrin is also involved in mediating the transport of vesicles3 containing glycine receptors. Apparently, changes in the polyglutamylation change the affinity of gephyrin for the transport process. Gephyrin has a strong tendency to bind to one of the monomers of the glycine receptors, which helps to stabilize these receptors in the postsynaptic density. Evidently by binding to this protein when it is in a transport vesicle, as well as to one of the molecular motors that runs along the microtubules (KIF5), it works to transport the receptors to the synapse.This relationship was demonstrated by removing neuronal polyglutamylase, an enzyme necessary to the modification process.What hasn't been clarified yet is the actual mechanism by which activity at the synapse modifies the polyglutamylation of microtubules, although it clearly involves neuronal polyglutamylase in some way. However, the simple fact that it does tells us a lot.Let's start by looking at the relationship of glycine and GABA. Gephyrin can bind to receptor complexes for both neurotransmitters, so the same transport mechanism that moves glycine receptors to the synapse could well move GABA receptors. It's known2 that these neurotransmitters work together: [... G]lycinergic and GABAergic synapses display morphological similarities. Glycine and GABA notably share the same presynaptic vesicular transporter (the vesicular inhibitory amino acid transporter VIAAT) ([refs]) while the anchoring protein gephyrin is involved in the aggregation and postsynaptic stabilization of both GlyRs and GABAARs ([ref]). Accordingly, it is now well established that glycinergic and GABAergic neurotransmission can be intermingled to provide inhibition of neuronal activity. Indeed, in the spinal cord and several distinct brainstem areas, glycine and GABA can be co-released from the same presynaptic terminal to activate postsynaptic GlyRs and GABAARs, as demonstrated by recording mixed miniature inhibitory postsynaptic currents. Interestingly, recent findings indicate that the co-activation of GlyRs and GABAARs at mixed inhibitory synapses does not simply display a summation of currents mediated by both receptor subtypes, resulting from functional cross-talk between these co-aggregated postsynaptic receptors.What does this mean for synaptic intelligence?To begin with, at least some neurons are capable of using both glycine and GABA as neurotransmitters. While we don't know yet whether, or how, they modify the ratios of these neurotransmitters, it seems likely that the presynaptic cell as a whole can change its ratio. It may even be that the precise ratio of these two neurotransmitters can be "fine tuned" at each synapse, although there's certainly no need for it. (But note that just because we know of one perfectly good mechanism to accomplish something doesn't mean that evolution hasn't co-opted another. It all depends on which mechanism becomes available first, which depends on the random chance of mutation.)The reason there's no need to "fine tune" glycine/GABA ratios upstream from the synapse is that the ratio of receptors can be "fine-tuned" downstream. We have a demonstration that activity at glycine receptors can modify how gephyrin transports receptors, certainly glycine and probably GABA. But there are certainly other mechanisms that can affect the local ratio of these two receptors. And we don't really know yet whether the effect on GABA receptor transport is the same as that on glycine receptors.Whatever the mechanism of modifying the microtubules, it almost certainly involves the complex network of interacting enzymes at the postsynaptic density, which, as we've seen, is potentially quite intelligent. The modification of the microtubules makes them part of the overall network, adding a new dimension to the intelligence with which a single synapse can modify its response to incoming information based on what's already arrived.Another question that remains to be resolved involves the dendritic arbor, and the effect of modifying the microtubules of one branch.Figure 2: Complete Neuron diagram. The soma and dendrites are on the left, in red. Note how some of the synapses are on deep branches, with many synapses farther from the soma on the branch. (From Wiki)It seems likely that modifying the transport of receptors on a "deep" branch will have some effect on all the synapses farther from the soma (the cell body). As with the effect of changes to voltage-driven channels in the dendrite, changes to the microtubules will (potentially) allow information received at synapses close to the soma to have a nonlinear effect on a large group of synapses.This discovery adds a new dimension to the potential for intelligence in each specific synapse, as well as the overall neuron.Maas, C., Belgardt, D., Lee, H., Heisler, F., Lappe-Siefke, C., Magiera, M., van Dijk, J., Hausrat, T., Janke, C., & Kneusse... Read more »

Maas, C., Belgardt, D., Lee, H., Heisler, F., Lappe-Siefke, C., Magiera, M., van Dijk, J., Hausrat, T., Janke, C., & Kneussel, M. (2009) Synaptic activation modifies microtubules underlying transport of postsynaptic cargo. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0812391106  

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