Biology posts

October 26, 2009
09:30 PM
946 views

The role of dynamics in catalysis

by Michael Clarkson in Conformational Flux

For some enzymes, dynamics on the millisecond timescale play a critical role in catalysis. I don't think this is a particularly controversial or unclear statement, but then, I know what I mean by it. In the process of communication, however, the intended meaning sometimes gets lost or transformed. A statement that addresses an entire catalytic cycle, for instance, might be interpreted as addressing only the chemical step. This seems to have happened in a pair of papers that concern the transfer of energy from conformational rearrangements to a chemical reaction.Consider a reaction scheme in which an enzyme loosely associates with substrates (E.S), then "closes" to form a tight, catalytically-competent complex that then undergoes a reaction with the rate kchem:Pisliakov et al. (1) ask whether the closing process can accelerate kchem. They ask this question primarily because a group from Harvard University proposed that this was possible in a paper printed last year in J. Phys. Chem. B (2). In that paper, Min et al. performed some simulations suggesting that such an acceleration was at least possible, and consistent with some enzymatic data. Pisliakov et al. approach the question with simulations of the reaction of the phosphotransfer enzyme Adk with 2 ADP molecules to form ATP and AMP. As part of the catalytic cycle, the enzyme goes from an open state (PDB: 4AKE) where the ATP and AMP binding sites are exposed to solvent, to a closed state (PDB: 1ANK) where the substrates are shielded from the surrounding solution by ATP and AMP "lids" that close down over the active site.One can, perhaps, imagine that when the enzyme closes around the substrates, some motion will occur that promotes the transfer of a phosphate group from one molecule to another. Pisliakov et al. use a three-tiered system of simulations to address the question, as a way of trying to get around the difficulty of dealing with the long timescales required. Their simulations allow them to adjust the energy barrier to match the experimental rates or accelerate the reaction so that the whole pathway can be simulated. In general, they find that conformational fluctuations do not enhance the chemical reaction rate in this system.I have two main concerns about the science that was performed here. The first is that the energy barriers in the long-timescale experiment appear to be improperly paramaterized. In estimating these barriers for the phosphotransfer reaction in Adk, Pisliakov et al. used 260 /s as kchem. However, although the actual reaction carried out by Adk follows an extremely complex scheme, the analysis performed by Wolf-Watz et al. utilized a simplified scheme that combined all post-association steps into a single kcat. This is why the concordance between kcat and kopen justifies the conclusion that lid-opening is rate-limiting. In principle, the experiments used for that paper are incapable of separating the opening and closing steps from the chemical step. Therefore we have no experimental knowledge of the phosphotransfer rate, except that it is greater than 260 /s. This perplexing error appears to have originated with Min et al., but I am surprised Warshel's group did not catch it. This is not a major problem because the bulk of the conclusions of the experiment were drawn from a different simulation in which the energy barriers were lower, but this leads to my second concern. If the structural transition involves a very smooth and coherent rearrangement of the protein, then simply manipulating energy barriers should not result in a serious error of analysis. In reality, however, ensemble motions of protein elements are not going to be so directed or uniform. Structural rearrangements are not highly singular steps, but involve a large number of intermediates and transition states. Motions in the late stages of the structural transition that promote catalysis may well be missed by simplified models, or accelerated beyond productivity by lowering the energy barrier.That said, I'm not particularly surprised that Pisliakov et al. find that energy from the conformational coordinate does not transfer to the chemical coordinate, nor do I disagree with the finding. Despite what Pisliakov et al. appear to believe, the papers that have come out of Dorothee's group don't argue that the millisecond motions contribute directly to the chemistry. Doro doesn't believe that for a second. Neither do I. The importance of dynamics has little to do with shoving the reaction along the chemistry coordinate, but everything to do with getting substrates bound and into a state where chemistry is possible.Dynamics allow an enzyme to reconcile incompatible functional requirements. To efficiently function as a phosphotransfer enzyme (as opposed to a hydrolytic phosphatase), Adk must expel water from the active site during catalysis. If the active site is inaccessible to solution, however, there is no way for the substrates to diffuse into it. It is difficult to create a single, rigid fold that can accommodate both these demands, but by fluctuating between two states the problem is resolved quite easily. So yes, the dynamics are essential to catalysis, but that does not imply that the conformational and chemical energy coordinates are coupled.More perplexing is the discussion of the hierarchy of motion, which Pisliakov et al. take to mean that nanosecond motions somehow contribute to the chemical coordinate. As I discussed when that paper was initially published, the question being addressed was whether and how motions on the fast timescale (ps-ns) in Adk were related to the slower (ms) motions of the lids. In a hierarchy of motion, fast timescale fluctuations enable or promote slow timescale dynamics. In the case of Adk, this means that nanosecond flexibility at structural hinges allow the millisecond motions of the ATP and AMP lids. It was not implied, then or since, that the nanosecond motions in question make a direct contribution to movement along the chemical coordinate. This is not to say that there are no researchers who believe that ns motions contribute to catalysis — I've previously mentioned some work on hydrogen tunneling that makes precisely this argument. In the specific case of Adk, however, the contribution of ns motions to catalysis consists entirely in their enabling of the slower ensemble motions of the nucleotide binding domains, and nobody but the Warshel group has suggested otherwise.There is an ongoing disconnect in the literature concerning the role of dynamics in catalysis. While it is true that in many cases rates of structural transitions correlate with rates of catalysis, this does not imply that the conformational transition coordinate is linked to the chemical reaction coordinate by direct transfer of energy. It is more likely that the dynamics of the enzyme contribute to catalysis by generating reaction-competent states from reaction-incompetent states. This is not to say that dynamics cannot possibly make a contribution to phenomena such as hydrogen tunneling, but it strikes me as unlikely that motions on the millisecond timescale will contribute to a chemical coordinate. Experiments, rather than simulations, will be the ultimate test of the idea. However, in principle, this hypothesis can only be tested experimentally on enzymes where the conformational changes do not limit the chemical reaction rate. Because th... Read more »

Pisliakov, A., Cao, J., Kamerlin, S., & Warshel, A. (2009) Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proceedings of the National Academy of Sciences, 106(41), 17359-17364. DOI: 10.1073/pnas.0909150106

October 26, 2009
09:26 PM
1,543 views

Holes in the ice…

by Jim Caryl in mental indigestion

CRYOCONITE (’ice dust’) holes are small pock-like depressions that are strewn over the surface of glaciers, looking much like a pristine snow drift after you’ve thrown a handful of gravel at it. Such melt-holes have been documented on glaciers at both poles, and on other glaciated regions such as Iceland, Greenland, Canada and the Himalayas. [...]... Read more »

ANESIO, A., HODSON, A., FRITZ, A., PSENNER, R., & SATTLER, B. (2009) High microbial activity on glaciers: importance to the global carbon cycle. Global Change Biology, 15(4), 955-960. DOI: 10.1111/j.1365-2486.2008.01758.x

October 26, 2009
05:37 PM
841 views

Cascoplecia insolitis: a “monster” fly with five eyes and a horn

by Jacob Aron in Just A Theory

Like many young children, I went through a phase of being obsessed with dinosaurs. I think the appeal is the idea that these monstrous animals actually existed, but are also safely locked away in the past and can’t hurt you.
Now, a new discovery by George Poinar Jr of Oregon State University shows that the dinosaurs [...]... Read more »

Poinar Jr., G. (2009) Cascoplecia insolitis (Diptera: Cascopleciidae), a new family, genus, and species of flower-visiting, unicorn fly (Bibionomorpha) in Early Cretaceous Burmese amber. Cretaceous Research. DOI: 10.1016/j.cretres.2009.09.007

Biology

October 26, 2009
05:25 PM
1,464 views

Republican Losers Have Lower Testosterone

by Eric Michael Johnson in The Primate Diaries

In a new understanding of the term power grab, researchers have shown that the supporters of a political candidate literally have their power taken from them after they lose an election. In a new study by Steven J. Stanton and colleagues in the open-access journal PLoS ONE, researchers asked 163 Republican and Democratic voters (57 of whom were men) to provide saliva samples both before and after the 2008 election between John McCain and Barack Obama. What the researchers determined was that Republican men showed significant reductions in testosterone after they learned that their candidate had lost the election. Read the rest of this post... | Read the comments on this post...... Read more »

Stanton, S., Beehner, J., Saini, E., Kuhn, C., & LaBar, K. (2009) Dominance, Politics, and Physiology: Voters' Testosterone Changes on the Night of the 2008 United States Presidential Election. PLoS ONE, 4(10). DOI: 10.1371/journal.pone.0007543

October 26, 2009
04:24 PM
762 views

Barack Obama Boosts Testosterone

by Neuroskeptic in Neuroskeptic

But only if you voted for him, and only if you're a man. That's according to a PLoS One paper called Dominance, Politics, and Physiology.It's already known that in males, winning competitions - achieving "dominance" - causes a rapid rise in testosterone release, whilst losing does the opposite. That's true in humans, as well as in other mammals. The authors wondered whether the same thing happens when men "win" vicariously - i.e. when someone we identify with triumphs.What better way of testing this than the U.S. Presidential Election? The authors took 163 American voters, and got them to provide saliva samples before, during and after the results came in on the night of the 4th November. Here's what happened -In Obama supporters (the blue line, natch), salivary testosterone levels stayed flat throughout the crucial hours. But supporters of John McCain or Libertarian candidate Bob Barr, suffered a testosterone crash after Obama's victory became apparent. That was only true in men, though; in women, there was no change.Heh. Of course, we hardly needed biology to tell us that people often identify strongly with their preferred political parties, and the fact that social events cause hormonal changes shouldn't surprise anyone - the brain controls the secretion of most hormones.The gender difference is interesting, though. Does this mean that men identify closer with politicians? Or maybe only with male ones - what would have happened if Hilary had won... or Palin? It could be that the testosterone surge accompanying success is strictly a man thing, although it's been shown to occur in women in some studies, but not consistently.Finally, I should mention that this paper contains some excellent quotes, such as "...Robert Barr, who arguably did not have a chance of winning...", "In retrospective reports of their affective state upon the announcement of Obama as the president-elect, McCain and Barr voters felt significantly more unhappy" and my favourite, "men who voted for John McCain or Bob Barr (losers)". That last one may be taken slightly out of context.Stanton, S., Beehner, J., Saini, E., Kuhn, C., & LaBar, K. (2009). Dominance, Politics, and Physiology: Voters' Testosterone Changes on the Night of the 2008 United States Presidential Election PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007543... Read more »

Stanton, S., Beehner, J., Saini, E., Kuhn, C., & LaBar, K. (2009) Dominance, Politics, and Physiology: Voters' Testosterone Changes on the Night of the 2008 United States Presidential Election. PLoS ONE, 4(10). DOI: 10.1371/journal.pone.0007543

October 26, 2009
12:05 PM
957 views

How to synchronize flowering without really trying

by Jeremy Yoder in Denim and Tweed

One way plants can gain an advantage in their dealings with pollinators, seed dispersers, or herbivores is to act collectively. For instance, when oak trees husband their resources for an extra-big crop of acorns every few years instead of spreading them out, acorn-eating rodents are overwhelmed by the bumper crop, and more likely to miss some, or even forget some of the nuts they cache. These benefits of synchronized mass seed production, or "masting," are straightforward, but how it happens is less clear. A paper in the latest issue of Ecology Letters has an answer -- synchronization happens accidentally [$-a].

.flickr-photo { }.flickr-framewide { float: right; text-align: left; margin-left: 15px; margin-bottom: 15px; width: 100%;}.flickr-caption { font-size: 0.8em; margin-top: 0px; }
Bumper acorn crops ensure that squirrels miss a few. Photo by douglas.earl.When Dan Janzen first described masting as an adaptation in plants' coevolution with seed predators, he proposed that "an internal physiological system" [$-a] acted as a timer between masting events, with masting ultimately triggered by weather conditions. However, mathematical models have suggested a different possibility, the "resource-budget hypothesis:" that masting synchronization arises through an interaction of resource and pollen limitation [$-a].

Resource limitation works in concert with pollen limitation by catching plants at two stages of the seed-production process. First, if the resources required for seed production are more than can be accumulated in a single year, or if the availability of resources varies from year to year, then some years will be spent building up reserves instead of producing flowers. When reserves are built up, seed production is limited by the availability of pollen to fertilize flowers. Plants that flower when most of the rest of the population doesn't will fail to set much seed, so they'll have reserves to make seeds in the next year. This doesn't require Janzen's "internal physiological system" for the plants to synchronize, although such a system might evolve to reduce the likelihood of wasting resources by flowering out of synch.

The new paper tests this model in populations of a western U.S. wildflower, Astralagus scaphoides, which flowers at high frequency every alternate year. The authors prevented seed production in the plants by removing their flowers, either in a "press" of three years in a row or in a single "pulse" during one high-flowering year. The plants' response to these treatments would reveal the role of resource and pollen limitation in synchronizing seed production.If resource depletion after fruit set prevents reproduction in successive years, we predicted that 'press' plants would ﬂower more than control plants every year, as they were never allowed to set fruit. We predicted that 'pulse' plants would ﬂower again in 2006, but not set fruit due to density-dependent pollen limitation in a low-ﬂowering year.The authors also measured the sugars stored in the roots of plants collected before and after flowering in a high-flowering year.

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Seed predator in action. Photo by tombream07.The resource-budget hypothesis worked. Plants prevented from setting seed were forced out of synch with the rest of the population. "Pulse" plants flowered the year after treatment, but because few other plants did, they received little pollen and set little seed. They then had resources to flower yet another year, with the rest of the population this time, and set much more seed, depleting their reserves and bringing them back into synch. "Press" plants continued to flower at high rates each year, as long as they were prevented from setting any seed. Sugar levels built up in the tested roots during non-flowering years, and dropped after high-flowering years.

So masting arises as an emergent result of two limitations acting on plants -- the resources needed to make seed, and good access to pollen. A couple of simple rules lead, undirected, to an ordered system that affects entire natural communities.

References

Crone, E., Miller, E., & Sala, A. (2009). How do plants know when other plants are flowering? Resource depletion, pollen limitation and mast-seeding in a perennial wildflower. Ecology Letters, 12 (11), 1119-26 DOI: 10.1111/j.1461-0248.2009.01365.x

Janzen, D. (1971). Seed predation by animals Ann. Rev. Ecol. Syst., 2 (1), 465-92 DOI: 10.1146/annurev.es.02.110171.002341

Janzen, D. (1976). Why bamboos wait so long to flower Ann. Rev. Ecol. Syst., 7 (1), 347-91 DOI: 10.1146/annurev.es.07.110176.002023

Satake, A., & Iwasa, Y. (2000). Pollen coupling of forest trees: Forming synchronized and periodic reproduction out of chaos. J. Theoretical Biol., 203 (2), 63-84 DOI: 10.1006/jtbi.1999.1066
... Read more »

Crone, E., Miller, E., & Sala, A. (2009) How do plants know when other plants are flowering? Resource depletion, pollen limitation and mast-seeding in a perennial wildflower. Ecology Letters, 12(11), 1119-26. DOI: 10.1111/j.1461-0248.2009.01365.x

Janzen, D. (1971) Seed Predation by Animals. Ann. Rev. Ecol. Syst., 2(1), 465-92. DOI: 10.1146/annurev.es.02.110171.002341

Janzen, D. (1976) Why Bamboos Wait So Long to Flower. Ann. Rev. Ecol. Syst., 7(1), 347-91. DOI: 10.1146/annurev.es.07.110176.002023

Satake, A., & Iwasa, Y. (2000) Pollen coupling of forest trees: Forming synchronized and periodic reproduction out of chaos. J. Theoretical Biol., 203(2), 63-84. DOI: 10.1006/jtbi.1999.1066

October 26, 2009
08:00 AM
996 views

The princess and the perfume, a hermit crab fairy tale

by Zen Faulkes in NeuroDojo

Once upon a time, there lived a princess in a far away land. The princess was young and fair, and this drew the attention of a knight. Though the knight was strong, the princess loved him not.Enraged, the knight captured the princess and held her in his castle, and told her cruelly that they would soon be wed.The princess was not strong enough to escape the knight, though she tried many times. Still the knight kept her, guarded in his castle.But though the princess was not powerful strong, she was clever. She realized that while she may never be strong enough to defeat the cruel knight, surely there was someone else in the kingdom who was powerful enough to defeat the knight. But how could she find a champion?Feigning interest, the princess told the knight she wanted to create a perfume, whose wonderful scent would mark her wedding day. The knight eagerly supplied her with all she requested, and with that, the princess created a magic perfume.From the highest tower of the knight’s castle, the princess let her magic perfume be carried by the winds throughout the kingdom, knowing that strong men who caught the scent would be compelled to follow it back to the castle and challenge the knight...Male hermit crabs often get what they want by being bullies. Males of the species Pagurus filholi (pictured) attempt to monopolize mating access to females by guarding the females, often for several days. Females are not physically able to challenge the males, so what can they do to ensure that they have the opportunity to mate with the fittest males? Okamura and Goshima suggest that the females incite a riot among rival males by releasing pheromones into the water.This paper contains six short experiments. Several revolve around using “pheromone water,” which is just water that an female unmated female had been kept in; the actual chemicals that might be involved in the signal are unknown. The authors also made simulacra of guarding pairs by using a live male, gluing a typical shell that a female might have, onto the male’s claw, which is apparently a pretty good visual imitation. To get the smell right, they stuffed the “female” shell with cotton batting containing seawater or some variation of the “pheromone water.”In the first two experiments, they show that more fights break out when a guarding pair of crabs, or a reasonable simulacrum thereof, is introduced into a collection of males than if a lone male is introduced. Males will normally fight, but if there are chemicals indicating there is a guarded female around, they will fight longer, which is the main evidence for a female pheromone that encourages male competition.The third experiment tries to ascertain which sensory cues the males are using to detect guarding pairs. If able to see, the males are more likely to be aggressive if there is also a pheromone cue in the water. They found no difference between sewater scent and putative pheromone, however, if the non-guarding males were blinded before the imitation guarding pair was introduced. The blinding of the males makes this experiment difficult to interpret, because they literally cut the eyes off. It would be a cleaner experiment if the effect was reversible (say, by temporarily painting the eyes with something opaque), so it could be tested if the same animals that did not respond when blinded would then respond if they could see. Also, there is an error in the text for this experiment: the words say an effect is not significant, but the statistics listed says it is.The crucial experiment is the fourth. When there is water from an unmated female is introduced into a tank, males fight longer than if sea water, or water from a mated female (one with eggs) is introduced into the tank.The last couple of experiments are “dotting the Is and crossing the Ts” experiments. Experiment five tests responses of lone males to just the pheromone-containing water, and finds guarding of uninhabited shells increases when males are exposed to pheromone water compared to sea water. It seems that there is a greater response to pheromone water collected from a guarding pair than a female that had been guarded, but was not guarded at the time the water was collected. Again, it is a little difficult to interpret, because there are three treatments, the text is a bit ambiguous as two which treatments differ from the others.The final experiment shows that when fighting breaks out between males, the biggest males tend to win, and take over the “guarding” position of the female. No surprise there, as body size is almost always the major factor determining fight outcomes in crustaceans.That there are so many short experiments makes me a little annoyed that the standard journal practice of separating methods and results means that there is much flipping back and forth between the two. It would be much more readable if each experiment was discussed in total, in on part of the text.This is a very interesting social system where it seems that the females are both powerless and powerful. They are powerless in the literal sense that they cannot resist being guarded by males. But they are powerful in the sense that they encourage and exploit male aggression, presumably in an attempt to ensure they are guarded by the highest quality males.ReferenceOkamura, S., & Goshima, S. (2009). Indirect female choice mediated by sex pheromones in the hermit crab Pagurus filholi Journal of Ethology DOI: 10.1007/s10164-009-0188-2Photo from here.... Read more »

Okamura, S., & Goshima, S. (2009) Indirect female choice mediated by sex pheromones in the hermit crab Pagurus filholi. Journal of Ethology. DOI: 10.1007/s10164-009-0188-2

October 26, 2009
05:00 AM
845 views

Powerline corridors as breeding habitat for birds...

by Rob Goldstein in Conservation Maven

King, D., Chandler, R., Collins, J., Petersen, W., & Lautzenheiser, T. (2009) Effects of width, edge and habitat on the abundance and nesting success of scrub–shrub birds in powerline corridors. Biological Conservation, 142(11), 2672-2680. DOI: 10.1016/j.biocon.2009.06.016

October 26, 2009
04:48 AM
1,681 views

Sunday Protist - Nucleariids

by Psi Wavefunction in Skeptic Wonder

While exploring the various corners of the protistan world, I've been neglecting our close relatives - the Opisthokonts. Let's quickly remedy the situation.A couple weekends ago I had some pond water on hand, and it turned out to be quite productive. I was on a bit of a heliozoan and amoeba spree when I encountered these things:At first it seemed like a 'heliozoan'*, but wasn't quite round enough. Then I noticed filopodia. Heliozoa with filopodia? Nah. But it didn't quite qualify for your typical amoebozoan either, so I was rather confused. To make it even more fun, some of them had spicules sticking out (see the optical section through the top in the rightmost image above). Then I started seeing similar things without spicules, and they seemed to be related:So I spent an hour or so trying to figure this one out**. They turned out to be Nucleariids, a group of filose amoebae basal to fungi. The top one appears to be Rabdiophrys, which has been, in fact, confused with or considred as heliozoa; the bottom one may well be Nuclearia itself - some mixed images of Nuclearia and Rabdiophrys can be found here.Nucleariids are filose amoebae, meaning they produce long thin thread-like pseudopodia without internal microtubule bundles (which would be axopodia, like those of 'heliozoa'). They are on the fungal side of the great cauldron of Miscellaneous Opisthokonts sometimes called 'Choanozoa' by TC-S. Other times, he seems to reserve Choanozoa for those on the animal side of opisthokonts. Yet other times, he seems to fail to piss off cladists and actually use monophyletic terms. Which one of those is 'in season' likely depends on the monsoon patterns in Bangladesh. Or the temperature fluctuations on one of Jupiter's moons. Further research needs to be done. Materials include ethanol and acid, if I recall. Anyway, here's a damn tree already:(Ruiz-Trillo et al. 2007 Trends Genet; Opisthokonta - our fellow ass-tailed relatives)The Choanozoa/Misc Opisthokonts actually tend to be insignificant-looking amoeboid things most of the time, except for Choanoflagellates, which are these really cute lorica-building flagellates with a cone of microvili surrounding the flagellum on their asses. Speaking of which, opisthokont means 'posterior flagellum', or, less pretentiously, ass-tail. Some fungi (chytrids) have flagellated motile spores, and their flagellum happens to be on the posterior relative to the cell's swimming direction. As mentioned earlier, in most eukaryotes the flagellum performs a pulling action, whereas the opisthokont flagellum pushes the cell. This actually poses some problems for filter-feeding organisms, which use flagella for propelling food particles towards their 'mouth', and may be part of the reason some Choanoflagellates started aggregating into colonies - to stop themselves from moving away from their prey when using flagella.Here's another specimen of putative Rabdiophrys:And yet another:I can keep going:Seriously, I've got A LOT of those guys!Switching to Nuclearia now:Note the absense of spicules:Hey, it could be worse: I also have a freaking pile of non-descript random amoeboid things. SMALL non-descript random amoebae.There's a 'cellular' slime mould that turns out to be among the nucleariids: Fonticula (Brown et al. 2009 MBE; advance publication). The poor thing has been lumped with everything from Acrasids to cellular slime moulds, and subsequently neglected for a couple decades. This is the first documented case of slime mould aggregation in opisthokonts, which may contribute a thing or two to the evolution of fungal and metazoan multicellularity. (off topic note: ciliates can aggregate too!)So now we've finally covered an opisthokont. Phew. That was bugging me.* Just FYI, heliozoa are not a real group - they're united by their sun-like morphology, axopodia and nothing else...** Being too impatient to use dichotomous keys (which also simply fail to exist for some organisms), I use a combination of papers, websites and Google image search to find stuff. Basically, you find something that lists a bunch of organisms in the vicinity of what you think it might be, and then look to see if any of the pictures might match. If it's something so obscure that even Google is unaware of its existence, you have to sift through ancient forlorn journal articles sometimes, but usually it doesn't take that long to cross another name off the list.If completely stumped, I'll just start googling random morphological descriptions in both scholar and image search, until hitting something familiar. As random and haphazard and unprofessional as this method is, it's actually much more effective than figuring out dichotomous keys, in my opinion. Especially when you're unfamiliar with the ... Read more »

Brown, M., Spiegel, F., & Silberman, J. (2009) Phylogeny of the "forgotten" cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta. Molecular Biology and Evolution. DOI: 10.1093/molbev/msp185

RUIZTRILLO, I., BURGER, G., HOLLAND, P., KING, N., LANG, B., ROGER, A., & GRAY, M. (2007) The origins of multicellularity: a multi-taxon genome initiative. Trends in Genetics, 23(3), 113-118. DOI: 10.1016/j.tig.2007.01.005

October 26, 2009
01:48 AM
238 views

Nautilus Night - Cephalopod of Diamonds

by Eric Heupel in The Other 95%

Ok. I said for each of the Ocean in the Classroom projects fully funded I would put up a post about one invert from the deck of cards I have been working on, along with a sneak peak at a card. So, since the Making Waves, Oceans and Landforms got fully funded, and in honor of Nautilus Night I bring you the Cephalopod of Diamonds - The Chambered Nautilus.Classification for the Chambered NautilusKingdomAnimaliaPhylumMolluscaClassCephalopodaOrderNautilidaFamilyNautilidaeGenusNautilusSpeciesN. belauensisSome interesting facts about the chambered nautilus (and other extant nautiloids):The 6-7 (there is still debate on the status of one species) extant species of nautilus come from two genera, the 4-5 smooth nautilus'(genus Nautilus) and the 2 species of hairy nautilus (genus Allonautilus - literally "other nautilus").They are the only remaining cephalopods that retain an external shell, which they use for defense and as a buoyancy control system. The shell, with buoyancy control, was a significant weapon evolutionarily, as it afforded the early cephalopods the protection of a thick shell yet the advanced buoyancy control unchained them from the sea floor as most of the periods marine arthropods were. Modern nautilus are generally found on steep coral reef slopes at a depth of 200-400m during the day. They rise at night to feed near or at the surface, using the adjustable buoyancy of their gas filled shells to good effect during the vertical migration.Unlike other cephalopods, the nautilus do not have a lensed eye. The nautilus eye is more like a pinhole camera, leading to the hypothesis that it uses olfaction to find it's prey (mostly shrimp and other crustaceans along with some small fish.)Nautiloids also have upwards of 90 tentacles (compare with 8 arms of octopods and 8 arms an two tentacles of squid and cuttlefish.)Last bit for this post is their lifespan and reproduction. Most cephalopods are short lived with overall lifespans of even the Giant Pacific Octopus being around 2-3 years. For most studied cephalopods natural death from old age occurs after mating, (and for females egg guarding), which is only done once (called semelparity). Nautilus can live in 15-20 years and mate year after year (iteroparity). The nautilus are the ancient lineage of the cephalopods, descendants of and most like the orthocerids and other nautiloids that were a major predator of the seas in the Ordovician period. Modern nautiloids are the only cephalopods that retain their external shell and are often considered to be "living fossils" as they are very similar in appearance to the ammonites and nautiloids that emerged half a billion years ago in the Cambrian. However recent molecular studies are casting some doubt on the appropriateness of the "living fossil" moniker. Studies published in the past couple years have revealed that the 6-7 extant species of nautilus evolved much more recently, around 2 million years ago, in the seas around New Guinea. They then Sinclair, B., Briskey, L., Aspden, W., & Pegg, G. (2006). Genetic diversity of isolated populations of Nautilus pompilius (Mollusca, Cephalopoda) in the Great Barrier Reef and Coral Sea Reviews in Fish Biology and Fisheries, 17 (2-3), 223-235 DOI: 10.1007/s11160-006-9030-x

... Read more »

Sinclair, B., Briskey, L., Aspden, W., & Pegg, G. (2006) Genetic diversity of isolated populations of Nautilus pompilius (Mollusca, Cephalopoda) in the Great Barrier Reef and Coral Sea. Reviews in Fish Biology and Fisheries, 17(2-3), 223-235. DOI: 10.1007/s11160-006-9030-x

October 26, 2009
01:15 AM
575 views

Grasping The (extracellular) Matrix, Location, location, location! and more in my picks of the week from RB

by Alejandro Montenegro-Montero in MolBio Research Highlights

Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that I'm ... Read more »

Anthis NJ, Wegener KL, Ye F, Kim C, Goult BT, Lowe ED, Vakonakis I, Bate N, Critchley DR, Ginsberg MH.... (2009) The structure of an integrin/talin complex reveals the basis of inside-out signal transduction. The EMBO journal. PMID: 19798053

Shafer-Weaver, K., Anderson, M., Stagliano, K., Malyguine, A., Greenberg, N., & Hurwitz, A. (2009) Cutting Edge: Tumor-Specific CD8 T Cells Infiltrating Prostatic Tumors Are Induced to Become Suppressor Cells. The Journal of Immunology, 183(8), 4848-4852. DOI: 10.4049/jimmunol.0900848

Guelen, L., Pagie, L., Brasset, E., Meuleman, W., Faza, M., Talhout, W., Eussen, B., de Klein, A., Wessels, L., de Laat, W.... (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature, 453(7197), 948-951. DOI: 10.1038/nature06947

October 25, 2009
01:56 PM
780 views

NextGen sequencing: What Is It Good For?

by Lab Rat in Lab Rat

Sequencing DNA has become a major industry. The genetic code of an organism contains huge amounts of data, and the potential for a greater understanding of how it works at an intracellular level, and whole centers and genome sequencing factories now exist to fill this need. While most of the sequencing is still done using a modified and more efficient version of Sanger's original dideoxy method, next-generation sequencing machines are starting to emerge that can achieve what is imaginatively named massively parallel sequencing. Massive amounts of DNA can be sequenced in parallel, and we're talking MASSIVE amounts of DNA. Illumina/Solexa machines can sequence hundreds of thousands of DNA molecules all in parallel.The basic Sanger sequencing method is shown below (image taken from the Science Creative Quarterly, which also has a very good description of the process for those more interested in DNA sequencing)There is a catch in massively parallel sequencing however. Sequencing works by breaking a large DNA molecule down into smaller 'reads'. Each read is then sequenced and they can be stuck back into the right order (with varying accuracy) once all the reads have been completed. Sanger sequencing (diagram above) can produce reads up to 1000 base pairs long. NextGen sequencing is lucky if it manages 350 base pairs. They tend not to be quite as accurate as well.What they are is cheap. Which gives geneticists an important tool; large numbers of short genome reads generated at very low cost. While these NextGen techniques are being improved, and there are many people looking into making them more effective for de novo gene sequencing, they are also being put to use in other areas, where the ability to sequence large numbers of short genomic sequences at low cost is hugely beneficial.The most obvious areas are those where you don't need a particularly long sequence, such as when you just need to find the site of origin of a particular length of DNA. This is particularly useful for looking at transcribed portions of the DNA (those parts that are actually turned into proteins). Sequencing short bits of the transcribed RNA copy (that is used to make the protein) allows this to be compared to the original DNA sequence to find where the DNA corresponding to the protein is and, possibly more importantly, concrete evidence that it is being transcribed. In this situation the short reads aren't a problem, although there are still issues with the accuracy.Another application is to look for novel small RNAs. These are small sections of RNA which regulate gene expression. They are discovered fairly recently (in plants originally) so there's quite a lot of excitement about them. As they're only small the length of the reads are not a problem. Pyrosequencing (a form of NextGen sequencing) was used to discover the Piwi-interacting RNAs, which are linked to transcriptional silencing in germ line cells.NextGen sequencing also has a role in protein coding gene annotation. Protein-coding genes can be quite long, and would require several reads from NextGen techniques, but the low cost of these methods means that they are starting to be used for annotating protein coding regions. Integrating them with paired-end sequencing (which allows the reads to be re-connected more easily) removes some of the problems are shorter reads, and novel techniques are continually being explored to increase the accuracy.NextGen machines are also starting to be used more for metagenomics, which works by taking random soil or water samples and sequencing every bit of DNA you can find, regardless of which organism it comes from. A metagenomics project in the Sargasso Sea (strangely enough most of these projects tend to take place in warmer climates...noone appears to do metagenomics in, say, iceland) produced over 1.2 million unknown gene sequences. These are suspected to be from 'unculturable' bacteria, which for some reason just don't grow in the lab, and metagenomics has revealed a huge number of these bacteria within the ecosystem.If you want a novel genome sequenced your best bet is still to send it down to the Sanger Centre and be very polite to everyone who works there, but the growth of cheaper machines with massively parallel sequencing provides a whole range of new applications. Even if NextGen machines never quite reach the accuracy and read length of Sanger machines, there are still many areas in science to which they provide a large benefit.---MOROZOVA, O., & MARRA, M. (2008). Applications of next-generation sequencing technologies in functional genomics Genomics, 92 (5), 255-264 DOI: 10.1016/j.ygeno.2008.07.001Hutchison, C. (2007). DNA sequencing: bench to bedside and beyond Nucleic Acids Research, 35 (18), 6227-6237 DOI: 10.1093/nar/gkm688... Read more »

MOROZOVA, O., & MARRA, M. (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics, 92(5), 255-264. DOI: 10.1016/j.ygeno.2008.07.001

Hutchison, C. (2007) DNA sequencing: bench to bedside and beyond. Nucleic Acids Research, 35(18), 6227-6237. DOI: 10.1093/nar/gkm688

October 25, 2009
01:08 PM
525 views

Crepidula Fornicata

by Eric Heupel in The Other 95%

We've got two new Ocean Inspired Donors Choose projects that have been funded in the Oceans in the Classroom Challenge! The first one that was funded on Thursday was the awesome Invertebrates in my Tank project that will provide lots of kids with the opportunity to explore one of our favorite subjects: marine inverts! The Inverts in my Tank card is the 6 of Spades — The Slipper Snail, Crepidula fornicata.Classification for the Atlantic Slippersnail KingdomAnimalia PhylumMollusca ClassBivalvia OrderOstreoida FamilyPectinidae GenusChlamys SpeciesC. islandicaI pulled this card for several reasons. First it has the cutest little veliger larvae. Second, it is all over the place here in Long Island Sound. And lastly, it is a prime example of a reproduction strategy that is comparatively rare in the animal world in general, but much less so in molluscs: protandrous sequential hermaphroditism. You may recall Dr. M's recent post, "Who likes protandric hermaphrodites?", in which he described the strategy, while reporting new findings about Idas washingtonia, a deep-sea clam.Like I. washingtonia, the Atlantic Slippersnail (Crepidula fornicata), is a protandric sequential hermaphrodite. While they strongly resemble limpets externally, and are often called slipper limpets, they are indeed gastropods that are common inhabitants of the sub– to intertidal area of New England rocky coasts where they are often found in stacks, like the one pictured, from 3 to 20 individuals. Unfortunately, they are also an invasive species becoming all too common in areas outside its native range, where their filter feeding capabilities may negatively affect native and aquacultured filter feeding molluscs.As Dr. M described in his post, many protandrous sequential hermaphrodites change sex based on size. A prevailing theory (the size-advantage hypothesis) predicts that a species will change its sex at a particular size that allows the individual higher reproductive success. Generally, this means smaller Atlantic Slippersnails are males and larger ones are females. It is energetically expensive for females to produce large, energy–rich eggs. It is very common in the marine realm that older, larger females produce more eggs of larger size and higher quality with resultant higher success rates. For guys to produce sperm is a comparatively inexpensive expenditure of energy. Even a wee lad can produce enough sperm of suitable quality to reproduce successfully. (Whether or not a female will have him, of if his sperm can out compete a larger male's sperm, is a different issue.)C. fornicata follows this trait — for the most part. When the planktonic veliger larvae metamorphose and settle to the bottom, they are attracted to chemical cues produced by the adults. This guides most settling juveniles to land on, or very near, existing individuals or stacks. They then make their way (ever slowly) to the top of the stack and mature into young males. In paternity studies the oldest, largest males (sometimes the same size as females) are responsible for the majority of the viable larvae from females in the stack (upwards of 83% of larvae coming from one father). Younger males further up the stack do have some successes, though, and the more males (and more larger males) in a stack the more sperm competition appears to play a significant role in each individual's success and the less dominant the dominant male becomes. At a certain point these large dominant males may be better off as females sharing the reproductive success among a few females instead of many highly competitive males.If a settling juvenile misses the chemical cues or for some other reason does not stack onto an existing individual or group, it will mature through a very brief male phase then become female, hopefully attracting juveniles from the next batch to settle on to it. Given that there are solitary (small) post settlement females and that some older males in a stack are as big as their female stackmates, size is clearly not the sole cue for sex change in C. fornicata. There is some plasticity in the change and social interaction appears to play a strong role on the size of the individual undergoing sex change.You can probably see why sequential hermaphroditism is such an interesting area of study. There are several general hypotheses, but there are also so many individual variations on those general themes, that it seems we will never run out of study material!And now a word for our Challenge this monthIf you have contributed to the Oceans in the Classroom Challenge - Thank you so much!! These posts and previews are for you! You have helped the Ocean Bloggers make a difference in at least 300 kids' lives. (More considering many projects have reusable multi-year assets!)If you have not yet given to the Donors Choose Oceans in the Classroom Challenge, please consider giving today. I know times are tough. I am a grad student with a family to feed. Believe me, I get how tough it is. Still every amount is welcome and appreciated. For my family's donation it means I have to brown bag it for two weeks. But you know, that's a small price to pay in exchange for knowing that we are exposing hundreds of kids to the science of the ocean. There is even a kindergarten class project in there - Commotion in the Ocean. Talk about a great time to open a kid's mind to the ocean and science!! If 25 readers give just $10 each, we'll help a dedicated young teacher expose 18 high poverty area kindergarten kids to science and the ocean.There is a chance, still, to get an additional $2,000 dollars of matching finds donated by HP, but it will only happen if we can get to $2,000 donated from the Ocean Bloggers readers today. It won't be easy, but it's a great chance to really increase our impact! Please give to the Challenge!ReferencesProestou DA, Goldsmith MR, & Twombly S (2008). Patterns of male reproductive success in Crepidula fornicata provide new insight for sex allocation and optimal sex change. The Biological bulletin, 214 (2), 194-202 PMID: 18401001Richard, J., Huet, M., Thouzeau, G., & Paulet, Y. (2006). Reproduction of the invasive slipper limpet, Crepidula fornicata, in the Bay of Brest, France Marine Biology, 149 (4), 789-801 DOI: 10.1007/s00227-005-0157-4
... Read more »

Proestou DA, Goldsmith MR, & Twombly S. (2008) Patterns of male reproductive success in Crepidula fornicata provide new insight for sex allocation and optimal sex change. The Biological bulletin, 214(2), 194-202. PMID: 18401001

Richard, J., Huet, M., Thouzeau, G., & Paulet, Y. (2006) Reproduction of the invasive slipper limpet, Crepidula fornicata, in the Bay of Brest, France. Marine Biology, 149(4), 789-801. DOI: 10.1007/s00227-005-0157-4

October 25, 2009
04:48 AM
1,552 views

Unpopular Genes

by Lucas in thoughtomics

You know those unpopular kids at the edge of the playground, excluded from playing with the others? It appears this situation is no different for genes, according to researchers from the Netherlands.
In eukaryotic cells all the genetic material resides in the nucleus, which is separated from the surrounding cytosol by a nuclear membrane. The nuclear lamina lines [...]... Read more »

Guelen, L., Pagie, L., Brasset, E., Meuleman, W., Faza, M., Talhout, W., Eussen, B., de Klein, A., Wessels, L., de Laat, W.... (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature, 453(7197), 948-951. DOI: 10.1038/nature06947

October 24, 2009
07:09 PM
662 views

Value of a good enemy

by CJA Bradshaw in ConservationBytes

I love these sorts of experiments. Ecology (and considering conservation ecology a special subset of the larger discipline) is a messy business, mainly because ecosystems are complex, non-linear, emergent, interactive, stochastic and meta-stable entities that are just plain difficult to manipulate experimentally. Therefore, making inference of complex ecological processes tends to be enhanced when the [...]... Read more »

Juliano, S., Lounibos, L., Nishimura, N., & Greene, K. (2009) Your worst enemy could be your best friend: predator contributions to invasion resistance and persistence of natives. Oecologia. DOI: 10.1007/s00442-009-1475-x

October 24, 2009
12:14 PM
1,103 views

Bug eat bug…

by Jim Caryl in mental indigestion

AS if it’s not hard enough at the bottom of the food chain, being cannibalised by your own bottom-dwelling compatriots must add insult to injury. The soil dwelling Gram-positive bacterium Bacillus subtilis is fully equipped to take appropriate action when faced with food shortages; a sub-population of cells initiate a process of dormancy by turning [...]... Read more »

Lopez, D., Fischbach, M., Chu, F., Losick, R., & Kolter, R. (2008) Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis. Proceedings of the National Academy of Sciences, 106(1), 280-285. DOI: 10.1073/pnas.0810940106

López, D., Vlamakis, H., Losick, R., & Kolter, R. (2009) Cannibalism enhances biofilm development in . Molecular Microbiology, 74(3), 609-618. DOI: 10.1111/j.1365-2958.2009.06882.x

Angelini, T., Roper, M., Kolter, R., Weitz, D., & Brenner, M. (2009) Bacillus subtilis spreads by surfing on waves of surfactant. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0905890106

October 23, 2009
04:45 PM
714 views

Deep Brain Stimulation for Depressed Rats

by Neuroskeptic in Neuroskeptic

Deep-brain stimulation (DBS) is probably the most exciting emerging treatment in psychiatry. DBS is the use of high-frequency electrical current to alter the function of specific areas of the brain. Originally developed for Parkinson's disease, over the past five years DBS has been used experimentally in severe clinical depression, OCD, Tourette's syndrome, alcoholism, and more.Reports of the effects have frequently been remarkable, but there have been few scientifically rigorous studies, and the number of psychiatric patients treated to date is just dozens. So the true usefulness of the technique is unclear. How DBS works is also a mystery. Even the most basic questions - such as whether high-frequency stimulation switches the brain "on" or "off" - are still being debated.Recent data from rodents sheds some important light on the issue: Antidepressant-Like Effects of Medial Prefrontal Cortex Deep Brain Stimulation in Rats. The authors took rats, and implanted DBS electrodes in the infralimbic cortex. This area is part of the vmPFC. It's believed to be the rat equivalent of the human region BA25, the subgenual cingulate cortex, which is the most common target for DBS in depression. The current settings (100 microA, 130 Hz, 90 microsec) were chosen to be similar to the ones used in humans.In a standard rat model of depression, the forced-swim test, infralimbic DBS exerted antidepressant-like effects. DBS was equally as effective as imipramine, a potent antidepressant, in terms of reducing "depression-like" behaviours, namely immobility.This is not all that surprising. Almost everything which treats depression in humans also reduces immobility in this test (along with few things which don't treat it). Much more interesting is what did and did not block the effects of DBS in these rats.First off, DBS worked even when the rat's infralimbic cortex had been destroyed by the toxin ibotenic acid. This strongly suggests that DBS does not work simply by activating the infralimbic cortex, even though this is where the electrodes were implanted.Crucially, infralimbic lesions did not have an antidepressant effect per se, which also rules out the theory that DBS works by inactivating this region. (Infralimbic lesions produced by other methods did have a mild antidepressant effect, but it was smaller than the effect of DBS. This may still be important, however.)What did block the effects of DBS was the depletion of serotonin (5HT). Serotonin is known to its friends as the brain's "happy chemical", although it's a bit more complicated than that. Most antidepressants target serotonin. And rats whose serotonin systems had been lesioned got no benefit from DBS in this study.So this suggests that DBS might work by affecting serotonin, and indeed, DBS turned out to greatly increase serotonin release, even in a distant part of the brain (the hippocampus). Interestingly this lasted for nearly two hours after the electrodes were switched off.Depletion of another neurotransmitter, noradrenaline, did not alter the effects of DBS.Overall, it seems that infralimbic DBS works by increasing serotonin release, but that this is not because it activates or inactivates the infralimbic cortex itself. Rather, nearby structures must be involved. The most likely explanation is that DBS affects nearby white-matter tracts carrying signals between other areas of the brain; the infralimbic cortex might just happen to be "by the roadside". Many researchers believe that this is how DBS works in humans, but this is the first hard evidence for this.Of course, evidence from rats is never all that hard when it comes to human mental illness. We need to know whether the same thing is true in people. As luck would have it, you can temporarily reduce human serotonin levels with a technique called acute tryptophan depletion This reverses the effects of antidepressants in many people. If this rat data is right, it should also temporarily reverse the benefits of DBS. Someone should do this experiment as soon as possible - I'd like to do it myself, but I'm British, and all the DBS research happens in America. Bah, humbug, old bean.There's a couple of others things to note here. In other behavioural tests, infralimbic DBS also had antidepressant-like effects: it seemed to reduce anxiety, and it made rats more resistant to the stress of having electrical shocks (although only slightly.) Finally, DBS in another region, the striatum, had no antidepressant effect at all. That's a bit odd because DBS of the striatum does seem to treat depression in humans - but the part of the striatum targeted here, the caudate-putamen, is quite separate to the one targeted in human depression, the nucleus accumbens.Hamani, C., Diwan, M., Macedo, C., Brandão, M., Shumake, J., Gonzalez-Lima, F., Raymond, R., Lozano, A., Fletcher, P., & Nobrega, J. (2009). Antidepressant-Like Effects of Medial Prefrontal Cortex Deep Brain Stimulation in Rats Biological Psychiatry DOI: ... Read more »

Hamani, C., Diwan, M., Macedo, C., Brandão, M., Shumake, J., Gonzalez-Lima, F., Raymond, R., Lozano, A., Fletcher, P., & Nobrega, J. (2009) Antidepressant-Like Effects of Medial Prefrontal Cortex Deep Brain Stimulation in Rats. Biological Psychiatry. DOI: 10.1016/j.biopsych.2009.08.025

October 23, 2009
04:14 PM
3,027 views

Visualizing DNA at the MegaBase Level

by harleyk in lifescienceviz

DNA cannot exist in a linear form like it conveniently does on genetics chalkboards. In fact, if DNA were linear and stretched end to end, it would be more than 6 feet. That’s 6 feet of DNA in every cell. Somehow, it gets condensed into the nucleus of every cell. But what does condensed DNA [...]... Read more »

Erez Lieberman-Aiden et al. (2009) Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. science.1181369. info:/10.1126

October 23, 2009
03:59 PM
1,346 views

A Short-Faced Bear's Mammoth Picnic

by Laelaps in Laelaps

The stench emanating from the putrefying mammoth carcass carried for miles.

Though kept out of the sun by the long shadows of the surrounding pine trees, the corpse reeked as the flesh, sinew, and bone of the mammoth's body were slowly parceled out into the ecosystem by scavengers. The woolly elephant's eyes had been pecked out long ago, and the intricate musculature of its trunk lay in tatters, but there was still plenty of meat to go around.

The grisly death site buzzed with activity as less magisterial creatures went about their dirty work. Black birds jostled for the best access to blood-caked fissures opened up in the mammoth's hide, insects injected the beginnings of the next generation into what would serve as both cradle and pantry, and bacteria continued their surreptitious breakdown of the stinking hulk. Yet the olfactory lure that such a rich source of fat and flesh had not gone unnoticed by other more imposing scavengers.

At a distance it was difficult to see. The dense ranks of trees obscured its approach as it loped through the forest. It was not in a hurry, it could not smell any others like itself around, but it was hungry. It let out low huffs as it walked, not out of physical exertion but of anticipation, announcing its approach as the squabbling birds fluttered to the safety of branches just out of reach.

Had it not been so formidable a predator it would have almost been a comical sight. It was an immense bear, larger than any of its living relatives, but it looked as if it had been made out of mismatched parts. Its front legs were extraordinarily long, placing its shoulders so high that the beast almost looked hunchbacked, and its face looked like that of a grizzly bear that had run head-first into a wall at speed. This was Arctodus, the short-faced bear.

The carnivore snuffled the air as it approached the fallen behemoth. That the meat was not fresh did not matter. Normally it would have to chase down its prey, but now all it had to do was defend its prize. Even if others arrived it still would have time to fill its belly with flesh, enough to last it at least a few days. After locating a wound on the mammoth's foot, one that exposed the rich pocket of fat inside, the bear set its powerful jaws to work. Read the rest of this post... | Read the comments on this post...... Read more »

SCHUBERT, B., & WALLACE, S. (2009) Late Pleistocene giant short-faced bears, mammoths, and large carcass scavenging in the Saltville Valley of Virginia, USA. Boreas, 38(3), 482-492. DOI: 10.1111/j.1502-3885.2009.00090.x

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