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  • July 13, 2010
  • 10:14 AM

World’s sweetest antibiotic? The five ways honey kills bacteria.

by Captain Skellett in A Schooner of Science

You’re at the doctors with a suspected infection, but instead of offering penicillin or erythromycin, they prescribe honey. Would you switch toast toppings? Take a honey pill? How about letting the doctor smear medical grade honey over the infected area?
People have been using honey (not mad honey) as medicine since ancient times, but until now [...]... Read more »

Kwakman, P., te Velde, A., de Boer, L., Speijer, D., Vandenbroucke-Grauls, C., & Zaat, S. (2010) How honey kills bacteria. The FASEB Journal, 24(7), 2576-2582. DOI: 10.1096/fj.09-150789  

  • July 13, 2010
  • 08:58 AM

Unbottling the lentil

by Jeremy in Agricultural Biodiversity Weblog

It is well known that crops go through a genetic bottleneck at domestication. Due to the founder effect, they typically show a fraction of the genetic diversity found in their wild relatives. Which is bad, but fixable: fixing it is the plant breeder’s job — or part of it anyway. What’s less well known, according [...]... Read more »

  • July 13, 2010
  • 08:41 AM

Sunday Protist - Giant tree of spicules: Spiculidendron

by Psi Wavefunction in Skeptic Wonder

Christopher Taylor over at Catalogue of Organisms has a nice post on agglutinated Saccamminid foraminifera, and very recently wrote on the taxonomy and morphology of Pelosina, Pilulina and Technitella, wherein he brought up a fascinating paper on one hell of a bizarre foram: the 'spicule tree', initally mistaken for a gorgonian (sea fan). I'm going to leech off his find as he didn't specifically mention this tree foram in his post. Also, he mentioned Komokians before I did. Meanie. In all seriousness, go read his posts. For the phylogenetically inclined protistologists, the Komokian post is good food for thought.I'm going to slack off a bit this time. For an overview of the huge clade of awesome that is Foraminifera, see my earlier post here; for another tree foram, see Notodendrodes here.Foraminiferans are amazing creatures: some of them can be best described as giant cannibalistic carnivorous wads of sticky reticulated pseudopodia, capable of snaring and devouring small metazoans and Volvox colonies. They have the fastest microtubule growth rates in the eukaryotic kingdom - a whole two orders of magnitude greater than those of animals at a stunning 12µm/s! (animal cells grow microtubules at around 1-15µm/min.) (Bowser & Travis 2002 J Foram Res) Their pseudopodia are themselves capable of shearing flesh in a process so unique it deserved its own name: 'skyllocytosis' (Bowser 1985 J Protozool). Do not screw around with forams. They are scary.Most of them also have shells, but that's a story for some other day. Well, many stories, for many days. Forams are a huge and diverse group.The following specimen belongs to Astrorhizidae, a group of agglutinating forams - meaning their tests are composed of material from the environment, often very selectively picked. As implied by its name, the spicule tree, or Spiculidendron, composes its test entirely out of sponge spicules. Furthermore, this contraption reaches a stunning 60mm (6cm) in height, as a single-celled organism!Plant, animal or protist? A foram tree to shame all foram trees. A giant spicule-covered monster from the Caribbean tropics. (Rützler & Richardson 1996 Biologie)The paper mentions difficulties in determining whether the spicule tree bears a single nucleus or is coenocytic. Presumably, if it was that hard to find (though they had few specimens to work with), it may well be uninucleate like Notodendrodes. This would be quite cool as 6cm is one hell of a giant cell to be supported by a single nucleus. The cytoplasm also contains symbiotic dinoflagellates, making this tree foram even more like an actual tree.Note that this strange monster of a foram was only described in 1996. The age of exploration is far from over.ReferencesRützler, K., & Richardson, S. (1996). The Caribbean spicule tree: a sponge-imitating foraminifer (Astrorhizidae) Bulletin de l'Institut Royal des Sciences Naturelles de Belgique 66 (Suppl.), 143-151Bowser, S. (2002). RETICULOPODIA: STRUCTURAL AND BEHAVIORAL BASIS FOR THE SUPRAGENERIC PLACEMENT OF GRANULORETICULOSAN PROTISTS The Journal of Foraminiferal Research, 32 (4), 440-447 DOI: 10.2113/0320440BOWSER, S. (1985). Invasive Activity of Allogromia Pseudopodial Networks: Skyllocytosis of a Gelatin/Agar Gel The Journal of Eukaryotic Microbiology, 32 (1), 9-12 DOI: 10.1111/j.1550-7408.1985.tb03005.x... Read more »

Rützler, K., & Richardson, S. (1996) The Caribbean spicule tree: a sponge-imitating foraminifer (Astrorhizidae). Bulletin de l'Institut Royal des Sciences Naturelles de Belgique 66 (Suppl.), 143-151. info:/

  • July 13, 2010
  • 08:36 AM

Fluid-based early detection biomarkers in cancer

by Sally Church in Pharma Strategy Blog

A really interesting idea that seems to be growing in popularity is the concept of fluid-based biomarkers from blood, urine, saliva etc, as opposed to invasive tumour biopsies. A recent paper in Cancer Research took a look at this novel...... Read more »

  • July 13, 2010
  • 08:00 AM

Asexual species identifications

by Zen Faulkes in Marmorkrebs

Marmorkrebs are difficult beasts. As I’ve mentioned before, there is no species name for them yet, partly because of how people define species. At the practical level, most crayfish are identified by the sex organs of the males (which Marmorkrebs don’t have). At the conceptual level, many people define species by interbreeding populations (which parthenogenetic organisms don’t do).

Birky and colleagues recently proposed a way to define species for parthenogenetic organisms. As near as I can understand it, their argument runs like this.

First, they’re going to define species using DNA. They just think morphology is too subtle and too prone to mislead.

Second, the criteria that they’re going to use to separate species is going to revolve around two key concepts: genetic drift and adaptation to a niche.

For any organism, even parthenogenetic clones like Marmorkrebs, there is a certain probability that mutations will occur each generation. Even when there is no selection pressure for that mutation, the frequency of the mutation in the population will change just due to chance over time, even becoming fixed or eliminated. That’s genetic drift.

Birky and company define a species as a group of organisms that show genetic changes that are too large to be accounted for by drift alone. They argue that this is indicative of a population that has undergone adaptation to a specific ecological niche.

The details of their proposal involve a fair amount of math, which, for the purposes of writing a blog post, I didn’t feel the need to become intimately acquainted with. At first glance, however, this approach seems generally fruitful. They apply their methods to six different asexual groups, and seem to make some headway on defining them. I think they could also apply their approach to sorting defining an asexual species that is derived from sexual ancestors, although they don’t discuss this.

Some potential glitches in their approach are that they effectively rule out the possibility that two species could be created by drift alone, which I think many evolutionary biologist would be uncomfortable with. They also mention briefly the idea of “higher taxa,” but how to define those higher taxa was not laid out nearly as clearly as for species.

But they do provide hope that Marmorkrebs, and many other asexuals, can get recognized as species, as they should be, in my opinion.

(Note: I wrote most of this before learning that there is a paper coming out that should shed some new light on the identity of Marmorkrebs. Stay tuned!)


Birky C, Adams J, Gemmel M, & Perry J. 2010. Using population genetic theory and DNA sequences for species detection and identification in asexual organisms PLoS ONE 5(5): e10609. DOI: 10.1371/journal.pone.0010609... Read more »

  • July 13, 2010
  • 05:30 AM

Controls are cool

by SysBio@HMS in It Takes 30

In an experiment originally intended to be a control, the Lahav lab has identified a previously unsuspected feature of the p53 response. It turns out that p53 is being activated in normal growing cells all the time. Because the cell cycle of cells in culture is unsynchronized, this activation can only be seen by looking at single cells. Since p53 may be the most studied protein on the planet, discovering something completely new and unexpected about its activities isn’t an everyday event.... Read more »

  • July 13, 2010
  • 02:25 AM

How many varieties are there in the world, mom?

by Jeremy in Agricultural Biodiversity Weblog

Back at the day job, we are often asked by journalists and others how many different types, or varieties, of this or that crop there are in a country, or indeed the world. And, with help from our friendly crop experts, we have tried to provide answers. But it is as well to remind ourselves [...]... Read more »

  • July 13, 2010
  • 12:25 AM

Short and long-term memory in cephalopods

by Mike Mike in Cephalove

          I've heard the assertion that octopuses have short- and long-term memories several times in the past few days, mostly in discussions of the ethics of eating octopuses prompted by ethical questions raised about Paul, the famous German octopod.  It's interesting to me what these people don't say - that they think that having a multiphasic memory process makes octopuses worth not eating (because, well, people have multiphasic memories, and you wouldn't eat them, would you?!?  Sicko.)  While I don't think that memory capacity of an animal is associated in an uncomplicated way with its ability to suffer or its moral status, it seems to me like a nonetheless interesting question.  I'm almost sure that most of the people who use (read: copy and paste) this bit of information to support their beliefs have very little idea of what sort of research is behind it.  Let's face it: developing a working knowledge of behavioral research on cephalopods is something that just isn't on most of the public's mind.  In fact, until I began writing this blog, I had very little knowledge of the subject.  I plan to set the record straight, so that internet users need never make an unfounded or unqualified statement about memory processes in cephalopods again (a lofty goal, huh?)          If you don't know octopus neuroanatomy very well (and who does?) you might want to check out the figures in this post.  I'll be talking about the vertical and superior frontal lobes of the octopus brain, and I know it sometimes helps to be able to visualize things like that when you're reading about them.  Just so that it's clear: the term "biphasic memory" means that the memory system in question has two discrete parts or processes (ie. short-term and long-term memory.)  A monophasic memory would have only one process, so that memories would last for a certain amount of time and then fade similarly in all circumstances.  A multiphasic memory system (which could be biphasic, triphasic, or more) is a general term to describe memory systems that are clearly more than monophasic, but are not completely characterized yet - and no memory system is.  Now, on to the research!          J. Z. Young, that demigod of cephalopod neurobehavioral research, published one of the few papers I could find on this topic back in 1970, following up on his earlier work on the subject.  In it, he investigated the development of short and long term memory in O. vulgaris (I assume - he doesn't actually mention what species he uses in this paper, but he almost always used O. vulgaris) as well as the role of two brain areas in memory, the median superior frontal lobe (MSF) and the vertical lobe (VL).  To do so, he performed surgeries to remove one of these two areas of octopuses' brains and put them through a learning task.  In this task, octopuses were trained to either attack a rectangle (rewarded with a piece of fish) or withhold attacking a crab (which was punished with electric shock.)          It turned out that octopuses whose vertical lobes had been removed were greatly impaired in learning to attack the rectangle.  Young explains this by claiming that the vertical lobe is involved in short-term memory, and that the acquisition of stable behavior day-to-day was impaired because the animals without vertical lobes could not remember events long enough for the training to be effective.  The animals without median superior frontal lobes, however, learned the task just fine, but were impaired in their long-term retention of it., suggesting that the MSF lobe might have some role in retaining learned information.  Interestingly, Young also found (in other experiments) that removing the vertical lobe after a task was learned resulted in a greater retention of the task.  These results suggest that the vertical lobe plays a role in the updating of memory stores, but is not absolutely essential for the recall of memories.          His results from the attack-withholding task were less clear, but they suggest that animals with lesions, especially those with vertical lobe lesions, were less consistent than intact animals in learning not to attack a crab after being shocked each time they attacked it.          Basically, Young argues (on the basis of this and some of his other experiments) that octopuses have a memory system that can be disrupted in more than one way; that is, it is possible to dissociate memory acquisition from long term retention, just like in vertebrates.  For the most part, more current research has agreed with his position, as we'll see in this next paper.          Moving forward (past a lot of great research that I'll skip over for the sake of brevity) to 2008, Shomrat et al. used electrophysiological methods to test this hypothesis.  Before we get into their methods, let's look a bit more closely at the system that we are talking about (this figure is from Shomrat et al. (2008)):           On the left is a sagittal slice of the supraoesophageal (over-the-oesophagus) mass of the octopus brain.  On the right is a diagram of the memory system in question.  Sensory information flows into the MSF from the arms and eyes before being sent along to the VL.  The VL neurons in turn send out information encoding attack.  It's been established that long-term potentiation (LTP) can occur in this area of the octopus brain, and this is a likely mechanism for the formation of memories in octopus (I blogged about this here - check it out if you need a little more background.)          The authors' procedure went as so: O. vulgaris who had already been trained to attack a white ball either had their MSF tract cut (at the dashed line in each image,) severing the sensory input to the vertical lobe, or this tract was stimulated, causing LTP at the synapses indicated in the figure.  Shortly after the procedure, the animals were trained to avoid a red ball through electric shock.  It was found that animals with severed MSF tracts were slower than controls to learn to withhold attack, while animals in whom LTP was induced were quicker.  This is all well and good - it confirms what we already thought about the role of the vertical lobe in acquiring memories in the octopus.  The really important result from this paper came when the authors tested the octopuses a day later.  It was found that both MSF tract transection and LTP induction impaired recall after 24 hours.  So even though stimulation of the MSF tract improved short-term memory (presumably by hyper-activating the memory system in the vertical lobe,) it impaired long-term memory.  This suggests that these two processes are not identical; that is, that octopuses have discrete and dissociable short- and long-term memory circuits.  This general finding has been replicated in cuttlefish (see my post on cuttlefish memory) and nautiluses (Crook and Basil, 2008).          Unfortunately, that's just about all that we know at this point: that cephalopods appear to have biphasic memories, meaning that the behavioral evidence of short-term memories can be dissociated from that of long-term memories.  This is hardly (by itself) a basis on which we can imply any sort of consciousness or advanced cognitive capacity, as animal-rights supporters who mention this fact seem to imply.          In interpreting these results in the context of our knowledge of cephalopods as a whole, we should keep in mind what is meant by short- and long-term memory in humans.  Short-term memory is what happens when newly learned information is bouncing around the cortex somewhere, being continually processed but not permanently encoded somewhere.  These memories will disappear if they are not rehearsed (or otherwise actively retained).  Long-term memory has been (relatively permanently) encoded into neural circuits, so that it can be retrieved after periods when it has not been actively processed in short-term (or working) memory circuits.  These processes have been studied intensely in humans, and can be precisely because we have a complex cognitive system build around them (or on top of or parallel to them, depending on who you ask) that we can access.  As of yet, we don't have the experimental techniques to assess exactly how "human-like" or "vertebrate-like" cephalopod memory systems are, because we can't study them in nearly as much detail as language-based and other cognitive tasks allow us to in humans.  Thus, making any strong conclusions about the nature of cephalopod memory other than that it appears ... Read more »

J. Z. Young. (1970) SHORT AND LONG MEMORIES IN OCTOPUS AND THE INFLUENCE OF THE VERTICAL LOBE SYSTEM. Journal of Experimental Biology, 385-393. info:/

  • July 12, 2010
  • 06:58 PM

Shell Games: The social and behavioral aspects of hermit crab real estate

by Matt Soniak in

I recently took part in what social scientists call a “vacancy chain” (a social structure through which vacancies in discrete, reusable, and limited resources propagate through a population) and all I needed was a moving truck, a few helpful relatives, a case of beer and a few pizzas. You see, when my girlfriend and I [...]... Read more »

  • July 12, 2010
  • 06:09 PM

Distribution of recombination distances between trees – poster at SMBE2010

by Leonardo Martins in bioMCMC

I just came back from SMBE2010, where I presented a poster about our recombination detection software and had the chance to see awesome research other people are doing. The poster can be downloaded here (1.MB in pdf format) and I’m distributing it under the Creative Commons License. Given the great feedback I got from other [...]... Read more »

  • July 12, 2010
  • 04:54 PM

Maternal behaviour in Tegenaria

by Africa Gomez in BugBlog

On top of a log pile under a shelf in the garden lives a large female Tegenaria. She has a large funnel shaped sheet web with a deep retreat. Every time I water the plants nearby - something I've had to do a few times in the last few weeks due to the dry weather - she jumps out of her retreat to the front to the web, only to find that there is no prey, just some water dropplets, and then she rapidly hides again. Today, I got my camera on one hand and a watering can on the other and managed to get a few close ups of the spider, which dutifully posed for me for quite a long time after being prompted by the watering. I also photographed her funnel and when I looked closely into the photo I could clearly see two tiny spiders on it.The female Tegenaria at the front of the webTwo spiderlings at the top of the funnel (click on the image for full resolution)Many female spiders display maternal behaviour, the most basic version consists on wrapping their egg clutches in a silky cocoon which protects the eggs from predation and adverse environmental conditions and shelters the spiderlings during their first moult. Some spiders go further than that, for example wolf spiders carry their egg sacs and spiderlings on their abdomen for a while. Tegenaria - the usual bath spider - has a different kind of maternal behaviour: the females, usually agressive and predacious towards prey entering the web, in contrast 'accept' the spiderlings on their webs for about three weeks after hatching, often longer, until these disperse. The tolerance behaviour turns into cannibalism as the spiderlings grow, but by then most of her offspring would have dispersed. Mated females lay several egg clutches in the spring - the offspring of the previous autumn males.Females in all reproductive states - even virgin females - tolerate newborn spiderlings on their sheets, but females which are at the reproductive state when they have spiderlings are the most tolerant of all. Females rapidly approach foreign spiderlings placed on their webs but after touching them with their first legs and palps leave them alone, while they often attack and eat crickets of the same weight. The female's behavioural changes towards older spiderlings have probably to do with chemical changes in the spiderlings cuticles. Even if it seems like a very simple form of maternal behaviour, the fact that the spiderlings are able to remain on their mothers web for a few weeks is likely to dramatically reduce their chances to fall prey to predators.More informationPourie, G., and Trabalon, M. (1999). Agonistic behaviour of female Tegenaria atrica in the presence of different aged spiderlings Physiological Entomology, 24 (2), 143-149 DOI: 10.1046/j.1365-3032.1999.00124.x... Read more »

  • July 12, 2010
  • 04:12 PM

Permission To Land

by Journal Watch Online in Journal Watch Online

New York City’s major airport is buzzing with traffic – and it’s not just airliners.
Grasslands at the John F. Kennedy (JFK) International Airport are teeming with insect life, a new survey finds, suggesting that even one of the world’s busiest airports can be an important refuge for urban wildlife.
Using nets and a leafblower […] Read More »... Read more »

  • July 12, 2010
  • 03:39 PM

More Vodka!

by Torah Kachur in Science in Seconds

Molecular differences between vodka brands might confirm what vodka drinkers have long suspected.... Read more »

Hu, N., Wu, D., Cross, K., Burikov, S., Dolenko, T., Patsaeva, S., & Schaefer, D. (2010) Structurability: A Collective Measure of the Structural Differences in Vodkas. Journal of Agricultural and Food Chemistry, 58(12), 7394-7401. DOI: 10.1021/jf100609c  

  • July 12, 2010
  • 01:00 PM

The Uncultured Bacteria

by Kim Lewis in Small Things Considered

The majority of bacteria will not grow on nutrient medium in the lab. The basic experiment is simple: take a sample from the environment, such as marine sediment or soil, mix with water, vortex, allow it to settle, dilute supernatant and take two droplets. Plate one on a Petri dish...... Read more »

D'Onofrio A, Crawford JM, Stewart EJ, Witt K, Gavrish E, Epstein S, Clardy J, & Lewis K. (2010) Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chemistry , 17(3), 254-64. PMID: 20338517  

  • July 12, 2010
  • 12:25 PM

Biological Micro Machines II: Inactivation Station

by Rob Mitchum in ScienceLife

Last month, we discussed the garage doors of the body’s ion channels, the millions of microscopic machines that control the heart’s beat and the nervous system’s communication. Benoît Roux and his colleagues employed 25 million computational hours to model the potassium channel voltage sensor, a kind of garage door control box that determines when the [...]... Read more »

Cuello LG, Jogini V, Cortes DM, Pan AC, Gagnon DG, Dalmas O, Cordero-Morales JF, Chakrapani S, Roux B, & Perozo E. (2010) Structural basis for the coupling between activation and inactivation gates in K( ) channels. Nature, 466(7303), 272-5. PMID: 20613845  

Cuello LG, Jogini V, Cortes DM, & Perozo E. (2010) Structural mechanism of C-type inactivation in K( ) channels. Nature, 466(7303), 203-8. PMID: 20613835  

  • July 12, 2010
  • 12:25 PM

Why we get cancer.

by Herman in

The short of it...
Creationists often put physicians on a pedestal as the scientists doing the real work in biology, useful work of improving human health and well-being as opposed to the pontificating, abstract work of the evolutionists. But, can we really understand human aliments outside of the light of evolution? Well worn examples of antibiotic resistance vividly illustrate the folly of ignoring evolutionary processes in medicine. Cancer however is another example of evolution in action. Tomislav Domazet-Loso and Diethard Tautz of the Max Planck Institute for Evolutionary Biology in the journal BMC Biology used a technique called phylostratigraphy to trace the origin of the genes associated with cancer to the origins of the cell and the first multicellular animals. The evolution of the first multicellular organisms necessitated a fine balance between the reproduction of individual cells and the evolutionary interests of the multicellular organism. The role of genes involved in cancer is to keep the peace and limit the ability of particular cells to go rogue, curtailing the reproductive success of individual cells in favor of the group. Understanding the evolutionary origin of these ancient genes sheds light on why we get cancer and can light the way to new treatments.... Read more »

  • July 12, 2010
  • 11:32 AM

Programming bacteria for search and destroy

by Lab Rat in Lab Rat

As iGEM season is now properly underway, I thought I'd have a look at a synthetic biology paper and found this fairly awesome one about programming bacteria to hunt out and destroy atrazine, a chemical herbicide pollutant. One of the most exciting things about this work was that it didn't just involve bacteria with the ability to remove atrazine from the environment but to actively migrate towards the chemical and then destroy it.The chemical structure of atrazineThe bacteria are controlled using riboswitches - little RNA pieces that can bind directly to a ligand (or signal molecule) and cause a change in gene expression, changes which can include switching on or off the genes involved in cell movement. Atrazine is a good molecule to start with because as well as being a relevant pollutant it also contains plenty of N-H bonds which are good for forming hydrogen-bond interactions with RNA. As well as that it has a well-characterized breakdown pathway, all components of which have been expressed successfully in E. coli.The first stage in creating these seek and destroy bacteria was finding RNA sequences that would bind to atrazine. This was done by attaching the atrazine to a solid support and running bits of RNA past it, to see which ones would bind. They then took these successful binders and tested for riboswitch activity, i.e whether the binding to atrazine caused a conformational change in the RNA that lead to the turning on of a gene. They did this by putting a sequence complimentary to the isolated RNA upstream of the DNA for the CheZ gene, which controls motility in E. coli and then carrying out the selection process shown below:In the absence of atrazine the CheZ is not synthesized and the bacteria stay where they are. When atrazine is added to the plate, the bacteria start to move...Dose-dependent assays were then done on the successful RNA sequences, to characterise the reaction and check that it actually was the atrazine levels that lead to movement rather than some other confounding factor. Sequencing and examination of the binding site also helped to characterize the riboswitch and determine how it was working. The genes for atrazine-consuming ability were then added to the bacteria that moved towards the atrazine, leading to a little search-and destroy module capable of seeking out a dangerous pollutant and removing it from the environment.---Sinha J, Reyes SJ, & Gallivan JP (2010). Reprogramming bacteria to seek and destroy an herbicide. Nature chemical biology, 6 (6), 464-70 PMID: 20453864---Follow me on Twitter!... Read more »

Sinha J, Reyes SJ, & Gallivan JP. (2010) Reprogramming bacteria to seek and destroy an herbicide. Nature chemical biology, 6(6), 464-70. PMID: 20453864  

  • July 12, 2010
  • 10:05 AM

Computational modeling of GPCRs: What are the challenges?

by The Curious Wavefunction in The Curious Wavefunction

GPCRs are extremely important proteins both for pure and applied science research, but they are also very difficult to crystallize and hence structural information on them has been sparse. Naturally in such a case, computational modeling can be expected to be of great value of providing insight into GPCR structure and function. However, even though progress has been impressive, such modeling still has to overcome many challenges. A recent review lists some of them.Firstly, in the absence of crystal structure, homology modeling wherein a sequence for an unknown structure is 'threaded' through that of a known one is well-established as a valuable technique. However the technique is tricky. First and foremost one has to get the right sequence alignment between the target and the template. As the article notes, recent studies have suggested that using multiple structures for alignment instead of a single one provides better results. Particularly noteworthy is this detailed study. Once a homology model has been obtained, it must be meticulously examined, both for internal consistency (bad contacts, incorrect hydrogen bonding interactions etc.) and for its agreement with experiment. Data from cross-linking studies and mutagenesis can be used to achieve this. A recent promising development has been termed 'ligand-supported homology modeling'. In this process, topographical protein-ligand interaction data from mutagenesis and other studies is used to limit the number of homology models. Such data-driven homology modeling is becoming increasingly popular.Once a good homology model has been obtained, many things can be done with it. Molecular dynamics (MD) simulations provide a very valuable avenue for exploring protein motion and be used to detect structural features not obvious in static models. A recent MD simulation of the beta-adrenergic receptor helped to resolve discrepancies between biochemical and structural observations. MD simulations can be used to investigate protein dynamics and to refine the models. Several challenges present themselves during this procedure. Firstly, while helices in GPCRs can be well-modeled, loops (of which there are six- three intracellular and three extracellular) are much harder to model because of their higher flexibility and because they are often ill-resolved in crystal structures. Unfortunately, it's these loops which are important ligand-interacting elements, so getting them right is key. Recently developed algorithms for loop-refinement based on either first-principles energy minimization or by statistical modeling based on a database of known loop conformations have been used in getting loops right. Also, state-of-the-art long MD simulations spanning several microseconds can be used to model large-scale structural changes in GPCRs.There are still immense challenges still to be overcome in understanding GPCRs. One of the biggest concerns the cycling between several inactive and active states (and not just one active and one inactive state) that present often conflicting features that can be subject to varying interpretation. For instance, for class A GPCRs (which is the largest class), it has been well-established that activated states involve the breakage of the "ionic lock", a salt bridge between arginines and glutamates on transmembrane helices 6 and 3. Breaking this lock allows TM6 to shift away from TM3 and towards TM5, a hallmark of GPCR activation. Yet the MD study on the beta2 cited above indicated that even an inactive state may feature breakage of this lock.In the GPCR jungle, strange shape-shifting creatures appear and clutch gems of insight in their palms. It is only fitting that we throw the kitchen sink at them to unravel their secrets, and computational techniques can only be a valuable arrow in this quiver.Yarnitzky T, Levit A, & Niv MY (2010). Homology modeling of G-protein-coupled receptors with X-ray structures on the rise. Current opinion in drug discovery & development, 13 (3), 317-25 PMID: 20443165... Read more »

  • July 12, 2010
  • 08:00 AM

Point-Counterpoint: the use of ‘sex’ and ‘gender’ in physiological studies

by EcoPhysioMichelle in C6-H12-O6 (old)

I recently read a very interesting point/counterpoint on the use of ‘sex’ and ‘gender’ in physiological research from last month’s AJP:RICP. In Point: a call for proper usage of “gender” and “sex” in biomedical publications, King points out that sex and gender are often used interchangeably when the variable involved is very clearly sex and [...]... Read more »

  • July 12, 2010
  • 08:00 AM

Book review: Do Fish Feel Pain?

by Zen Faulkes in NeuroDojo

Victoria Braithwaite’s Do Fish Feel Pain? is not a technical book. The type is large and the prose is easy to understand.

I had to read this book, because many of the issues around fish pain are the same as those raised for invertebrate pain (Puri and Faulkes 2010; this post). Fish researchers are about five years ahead of the invertebrate researchers.

Braithwaite’s answer to the question posed in her title is...

Spoiler alert! Click the heading of the post to read more.


Her arguments will probably not convince everyone, however.

For Braithwaite, a defining aspect of pain is that pain is a conscious experience. She repeatedly distinguishes pain from nociception on the grounds that nociception is unconscious and reflexive. Her views on these definitions seem idiosyncratic. My impression is that for many researchers, nociception is a description of a behavioural response, with nothing said about consciousness one way or the other.

By recasting that the question of whether fish feel pain into the question of whether fish are conscious, Braithwaite’s arguments become harder to assail, but lose some of their force. Consciousness is a very tricky subject. We don’t have a good scientific theory of human consciousness, let alone animal consciousness.

Given her definition, a large chunk of her book is aimed at proving fish have consciousness; that they are, as she puts it“sentient beings.” For the last bit of evidence she needs to say fish are conscious, sentient beings, Braithwaite draws almost exclusively on one example of cooperative hunting that can occur between individuals in two species, groupers and moray eels. (Irritatingly, this key reference is nowhere to be found in the bibliography! It’s Bshary et al. 2006.)

Now, I realize that a single exciting, detailed story is more compelling than a compilation of statistics. Braithwaite may have chosen to use just a few case studies because this is a popular book. But a lot hinges on those specific examples. And she never says, “This is just one example, but there are loads more I could describe.”

She follows up her chapter on fish consciousness up with a chapter arguing that there is not yet evidence for consciousness in invertebrates. She focuses on the evidence for cephalopods and crustaceans, and I can’t help but wonder if her choices of examples are influenced by those two groups being lumped together with fishes as “seafood.” The strongest evidence of invertebrate nociception there is right now (Tracy et al. 2003) is nowhere to be seen. Similarly, I wonder if Braithwaite considered Portia spiders for evidence of complex cognition in an invertebrate (Wilcox and Jackson 1998). They are very clever wee beasties.

It is a little worrying that the spectacular diversity of fishes and invertebrates doesn’t seem to factor into the argument. If one fish can do it, they must all be able to do it, it seems. The notion that perhaps some fish species might experience pain more than others is never entertained. Again, there’s no way to tell if she just left this out because she wanted to have the broadest appeal or for some other reason.

The book ends with an exploration of applying animal welfare standards more strongly to fishes, and you get the sense that this is what matters most to Braithwaite. She talks about fish harvesting, aquaculture, angling, and more. Considering how degraded so many wild fisheries have become, I do hope that this book gets people to take stock of the way they harvest and use fish.

Another review is here (paywall).


Bshary, R., Hohner, A., Ait-el-Djoudi, K., & Fricke, H. (2006). Interspecific communicative and coordinated hunting between groupers and giant moray eels in the Red Sea PLoS Biology, 4 (12) DOI: 10.1371/journal.pbio.0040431

Brathwaite V. 2010. Do fish feel pain? Oxford University Press: Oxford. ISBN 978-0-19-955120-0

Puri S, Faulkes Z. 2010. Do decapods crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. DOI: 10.1371/journal.pone.0010244

Tracey Jr., W., Wilson, R., Laurent, G., & Benzer, S. 2003. painless, a Drosophila gene essential for nociception Cell 113(2): 261-273. DOI: 10.1016/S0092-8674(03)00272-1

Wilcox RS & Jackson RR. 1998. Cognitive abilities of araneophagic jumping spiders. In: Animal cognition in nature: 411-434. Balda RP, Pepperberg IM, Kamil AC (eds). San Diego: Academic Press.

Photo by anikaviro on Flickr. Used under a Creative Commons license.... Read more »

Brathwaite V. (2010) Do fish feel pain?. Oxford University Press, 1-194. info:/978-0-19-955120-0

Tracey Jr., W., Wilson, R., Laurent, G., & Benzer, S. (2003) painless, a Drosophila gene essential for nociception. Cell, 113(2), 261-273. DOI: 10.1016/S0092-8674(03)00272-1  

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