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  • March 7, 2011
  • 08:22 AM
  • 1,602 views

Lending A Helping Trunk

by Shermin de Silva in Maximus

Asian elephants join the short list of species demonstrating the ability to comprehend and conquer a cooperative problem-solving task.... Read more »

Joshua M. Plotnik, Richard Lair, Wirot Suphachoksahakun, and Frans B. M. de Waal,. (2011) Elephants know when they need a helping trunk in a cooperative task. Proceedings Of The National Academy of Sciences. info:/10.1073/pnas.1101765108

Seed, A., Clayton, N., & Emery, N. (2008) Cooperative problem solving in rooks (Corvus frugilegus). Proceedings of the Royal Society B: Biological Sciences, 275(1641), 1421-1429. DOI: 10.1098/rspb.2008.0111  

  • March 7, 2011
  • 07:53 AM
  • 812 views

Personalised therapy for prostate cancer – is it possible?

by Sally Church in Pharma Strategy Blog

Recently, while in San Francisco for the AACR special conference on the PI3K-mTOR pathway in cancer, I was particularly struck by several important learnings that have since make me think more deeply about oncology drug development going forward: With targeted … Continue reading →
... Read more »

Goldstein, A., Zong, Y., & Witte, O. (2011) A Two-Step Toward Personalized Therapies for Prostate Cancer. Science Translational Medicine, 3(72), 72-72. DOI: 10.1126/scitranslmed.3002169  

Ateeq, B., Tomlins, S., Laxman, B., Asangani, I., Cao, Q., Cao, X., Li, Y., Wang, X., Feng, F., Pienta, K.... (2011) Therapeutic Targeting of SPINK1-Positive Prostate Cancer. Science Translational Medicine, 3(72), 72-72. DOI: 10.1126/scitranslmed.3001498  

  • March 7, 2011
  • 07:00 AM
  • 1,347 views

March 7, 2011

by Erin Campbell in HighMag Blog

Look all the way down to your toes and you’ll appreciate the feat (pun absolutely intended!) that your neurons accomplish in relaying signals over long distances to your brain. A recent paper discusses the interactions between the first sets of motor and sensory axons that find their way into limbs during development. During development, motor and sensory axons align together as they project into a developing limb. A group recently showed how motor and sensory axons are mutually dependent on one another for their correct trajectories into a developing limb, and identified an important role for a protein called Neuropilin-1 in these interactions. Image above from the cover of PLoS Biology shows sensory (red) and motor (green) axons in the brachial plexus, a region where motor and sensory axons converge before being sorted into bundles. This tight bundling of the axons is affected in mice that lack Neuropilin-1 in either type of axon.Huettl, R., Soellner, H., Bianchi, E., Novitch, B., & Huber, A. (2011). Npn-1 Contributes to Axon-Axon Interactions That Differentially Control Sensory and Motor Innervation of the Limb PLoS Biology, 9 (2) DOI: 10.1371/journal.pbio.1001020Cover of PLoS Biology can be found here.... Read more »

  • March 7, 2011
  • 03:14 AM
  • 1,065 views

an ancient origin for the human eye

by alison in bioblog

We understand a fair bit, these days, about the evolution of the complex, 'camera-type' vertebrate eye. Not that this has stopped creationsists (most recently the 'intelligent design' camp as represented by the Discovery Institute) from arguing that the eye is...... Read more »

Passamaneck YJ, Furchheim N, Hejnol A, Martindale MQ, & Luter C. (2011) Ciliary photoreceptors in the cerebral eyes of a protostome larva. EvoDevo, 2(1), 6. PMID: 21362157  

  • March 7, 2011
  • 12:19 AM
  • 2,801 views

When invasion isn’t such a bad thing…

by John Carroll in Chronicles of Zostera


New species get introduced into novel habitats almost like clockwork in the modern era.  These are termed introduced or exotic species.  Typically, these introductions are the effect of anthropogenic activity.  Sometimes, these species become nuisances – spreading in their new habitats via natural processes, and creating problems for native species.  These nuisance exotics are called invasive . . . → Read More: When invasion isn’t such a bad thing…... Read more »

  • March 6, 2011
  • 10:44 PM
  • 1,491 views

Message (Crammed) in a Bottle

by Kristopher Hite in Tom Paine's Ghost


To sell a bottle of Champagne as "bubbly" a vendor must ensure that the wine has absorbed between five and six atmospheres of carbon dioxide. To anyone who has ever popped the cork on champagne you know there is enough force there to do some serious damage to an innocent bystander in the event of poor aim.



Viruses spend part of their existence as a kind of bottle (capsid) with a message inside (DNA or RNA). The message inside carries the code or blueprint to make more viruses, more messages, more bottles. This message isn't short. If it were written out as As Ts Gs an Cs on regular 8 X 11" printer paper it would take up between 100-200 pages, depending on the specific virus we're talking about. Imagine trying to jam 100 leaves of paper into a wine bottle! The analogy isn't prefect as the viral message looks more like a rope than sheets of paper. Regardless, the message has to be crammed into an extremely tight space. The bottle's volume in this case being 0.065 cubic millimicrons. When the packing is done the DNA or RNA has been condensed from a free floating strand 6,ooo times like a tightly coiled garden hose at immense density. The pressure inside that tiny bottle reaches nearly 60 atmospheres. 10 times the pressure in the champagne bottle!





This raises many questions. How does a virus manage to pull or suck that long piece of rope inside its shell? Especially at the end when the pressure is at its peak? <--- The illustrated capsid cutaway shows the immense density with which the rope is crammed. How does such a tiny bottle not break under such intense pressure? Where's the cork and how does it stay put? And who or what pops the cork?



Dr. Carlos Bustamante of the University of California, Berkeley is answering these questions in incredible detail using single-molecule biophysical techniques. His lab is able to "grab the cat by the tail" and measure individual molecules directly. They specialize in DNA translocases. These are molecular machines or machine-like entities as he calls them.  Tiny "motors" that convert chemical energy into physical energy. When your eyes move to read these words the muscles are using the same chemical reaction's to pull your eyeballs from side to side as a virsus uses to pull that rope inside the bottle. This reaction is the hydrolysis of Adenosine triphosphate, the famed ATP, the energy "currency" of the cell. 


From Morais, M.C., Koti, J.S., Bowman, V.D., Reyes-Aldrete, E., Anderson, D.L., and Rossmann, M.G. 2008. Structure 16:1267–1274. © 2008, from Elsevier.


The viral machine is displayed in panel B. The capsid is pictured in gray while the motor sits at the "gate" and pulls the DNA inside. 



The motor is made of a five piece ring of small RNA molecules (pink) and five ATPases
(lavender).
In this particular single molecule study they are using two polystyrene
beads to tether two ends of a long piece of DNA (the set up is pictured in panel A below). The strand is held
in what is called an optical trap - those red sideways vase looking things. I blogged about how optical tweezers work before here's the link if you want to read about how this works. The goal in this study was to capture the capsid
on one bead (coated with capsid protein antibodies) and the other end
of the DNA  strand is bound to the other bead by a biotin-strepdavidin bridge. Not only did the researchers accomplish this feat but they were able to tug on either side of the system to measure how much force the motor was exerting on the DNA strand as it was sucking it into the capsid.


From Moffitt, J.R., Chemla, Y.R., Aathavan, K., Grimes, S., Jardine, P.J., Anderson, D., and Bustamante, C. 2009. Nature 457:446–1450. © 2009 Nature Publishing Group, a division of Macmillan Publishers Limited.




They discovered that with zero tension the capsid is packed with DNA at
the rate of 100-120 base pairs per
second. These studies also build a model for how they think the motor is
working.  As said before, the motor requires a chemical reaction (hydrolysis of ATP) to work.  In this controlled environment the researches can set the concentration of ATP. When and only when all five site on the motor are loaded with their ATP molecules can the motor pull the strand.  Like a revolver laying with the cylinder open and someone pouring bullets on top of it, the "gun" can only fire after it is fully loaded by the random addition of bullets. When the concentration of ATP is low the rate of firing is less frequent, higher  - more frequent.



The simplicity of this model as understood by observing single molecules, for me, made years of Michaelis-Menten kinetics (the dry math that drives people away from studying biochemistry) come to life in a visual context.  I could see in my mind's eye exactly how concentration affects the rate of a reaction.
... Read more »

Yu, J., Moffitt, J., Hetherington, C., Bustamante, C., & Oster, G. (2010) Mechanochemistry of a Viral DNA Packaging Motor. Journal of Molecular Biology, 400(2), 186-203. DOI: 10.1016/j.jmb.2010.05.002  

Moffitt, J., Chemla, Y., Aathavan, K., Grimes, S., Jardine, P., Anderson, D., & Bustamante, C. (2009) Intersubunit coordination in a homomeric ring ATPase. Nature, 457(7228), 446-450. DOI: 10.1038/nature07637  

  • March 6, 2011
  • 09:16 AM
  • 1,763 views

Woolly Bats Use a Carnivorous Roost

by Anne-Marie Hodge in Endless Forms

Although many people tend to think of nature as being "red in tooth and claw," with different species constantly at odds with one another in a scramble for survival, ecological communities are actually bursting with mutualistic relationships in which species...... Read more »

  • March 6, 2011
  • 08:39 AM
  • 1,218 views

Is this claim of bacteria in a meteorite any better than the 1996 one?

by Rosie Redfield in RRResearch

A new paper from a NASA scientist claims to present evidence for bacteria-like organisms in some meteorites.  (Richard Hoover, 2011, Fossils of cyanobacteria in C11 carbonaceous meteorites. Journal of Cosmology 2011, vol 13.)I don't know much about meteorites, but here's my evaluation: (Executive Summary: Move along folks, there's nothing to see here.)What the author did:He fractured tiny comet-derived meteorites (0.1 - 0.6 g) from two events and examined the freshly broken surfaces.  He claims to have observed structures that are remnants of cyanobacteria.These meteorites are of a special very rare type (only 9 are known).  They are about 20% water, and soft enough to cut with a knife.  They mainly consist of minerals cemented together with magnesium sulfate ('Epsom salts'). They come from asteroids and comets, not planets like the Alan Hills meteorite from Mars.  Hooper's reasoning that they come mainly from comets seems reasonable to me.They contain quite a bit of organic (carbon-based) material, but I don't know if this differs significantly from the polycyclic aromatic hydrocarbons known to be present in comets.  It's true that PAHs found on Earth are usually biological in origin (think of the tarry crud that accumulates on your barbeque grill), but that doesn't mean that PAHs from space have biological origins.An important concern with this kind of study is contamination with terrestrial organisms before examination.  He doesn't say how the meteorites have been stored before he obtained them, nor how the surfaces of the meteorites were treated before being fractured and examined.  He doesn't say how they were fractured - might they have been cut with a scalpel blade or just pressed on until they crumbled?  He says that the tools were flame-sterilized, but not what the tools were or how they were used.  He used two examination techniques.  FESEM is field emission scanning electron microscopy - this seems to be a higher-resolution form of scanning electron microscopy (SEM), with the usual risks of artefacts.  The fractured surfaces were not coated with anything before being analyzed - I don't know what effect this might have.  The other technique is energy-dispersive X-ray analysis - I gather that this is an add-on to SEM that can scan a specimen and report on the abundance of specific atoms at different positions.  Its results can be reported as the distribution of atoms at a particular position or as an image of the specimen, shaded to show the varying density of a particular atom.Results. He shows an image and analysis of one filament from the Ivuna meteorite.  It has more carbon than the surrounding material but no detectable nitrogen or phosphorus.  He bolsters his claim that it's a bacterium by showing an image of the giant bacterium Titanospirillum and an image of another filament from the meteorite.  His claim that the sulfur granules in this second   filament are like those of Titanospirilum is weakened by the very high sulfur in the surrounding material.  And although this filament is similar in size and shape to Titanospirillum (upper images), the other filament is about 15 times smaller (bottom images, adjusted to approximately the same scale).The image he shows of an inner surface of the Orgueil meteorite has more filaments (no attempt is made at quantitation).  These are more complex in structure and fairly similar to each other, suggesting that they were formed by a single kind of process.The atomic analysis is not at all convincing.  He claims that different parts of the filament have different composition, but doesn't present any control analysis of the variability of the measurements or of the background values for positions away from the filaments.  He claims that the atom-density scans show enrichment of carbon and oxygen in the filaments, but this looks very weak to me - the only strong signals are for magnesium and sulfur.  Again there is no detectable nitrogen or phosphorus.He spends a lot of text discussing the morpohlogical similarities of these filaments to cyanobacteria, but I don't regard these similarities as worth anything.  Filamentous bacteria are very morphologically diverse, and additional variations in appearance are likely to result from inconsistent preparation for electron microscopy.  It's probably pretty easy to find a bacterial image that resembles any fibrous structure.  In the absence of any statistical evidence to the contrary,  it's prudent to assume that such similarities are purely coincidental.The author tacks on quite a bit of other less-than-compelling information intended to support his claim that life from space is plausible.  For example, he shows photos of colonies of coloured microorganisms to support his argument that the colours seen on the surfaces of Europa and Enceladus are biological in origin. Bottom line: The Ivuna meteorite sample showed a couple of micron-scale squiggles, one of which contained about 2.5-fold more carbon than the background.  One of the five Orguil samples had at least one patch of clustered fibers; these contained more sulfur and magnesium than the background, and less silicon.  As evidence for life this is pathetic, no better than that presented by McKay's group for the ALH84001 Martian meteorite in 1996.The Journal and the Editor aren't very impressive either:The journal proudly announces that it is obtaining and will publish 100 post-publication reviews.  But did it bother getting any pre-publication reviews?  It will be shutting down in a few months, after only two years of on-line publication (the 13 'volumes' are really just 13 issues).  Its presentation standards are pretty bad - there doesn't seem to have been any effort at copy-editing or formatting the text for publication (not even any page numbers).Chandra Wickramasinghe is the journal's Executive Editor for Astrobiology, and presumably is the Editor responsible for this article.  I heard him give a talk on panspermia about 10 years ago (the audience was an undergraduate science society at Oxford).  The talk was dreadful.  He argued like a lawyer, not a scientist; the evidence he cited to support his arguments wasn't actually untrue, but he twisted everything to make his arguments seem stronger than they were.Hoover, R. B. (2011). fossils of cyanobacteria in C11 carbonaceous meteorites Journal of Cosmology... Read more »

Hoover, R. B. (2011) fossils of cyanobacteria in C11 carbonaceous meteorites. Journal of Cosmology. info:/

  • March 6, 2011
  • 12:00 AM
  • 1,284 views

Timing is everything

by Neil Losin in Day's Edge

At some point in your life, you’ve probably missed out on something great because your timing was off. Maybe you waited too long to ask a cute friend on a date, and she ended up going out with some d-bag instead of you. Maybe you bought a Version 1 iPad last week, just days before [...]... Read more »

Both, C., Van Turnhout, C., Bijlsma, R., Siepel, H., Van Strien, A., & Foppen, R. (2009) Avian population consequences of climate change are most severe for long-distance migrants in seasonal habitats. Proceedings of the Royal Society B: Biological Sciences, 277(1685), 1259-1266. DOI: 10.1098/rspb.2009.1525  

  • March 5, 2011
  • 03:33 PM
  • 1,403 views

Why do ladybirds hibernate in groups?

by Africa Gomez in BugBlog

You have probably come across ladybirds clustered under leaves or bark during winter. To spend the winter, seven spot ladybirds - otherwise solitary creatures -  to spend the winter, they seem to actively seek each other. I took the photo above a few minunes ago in my garden. I counted 16 ladybirds - most were 7-spots, with two Harlequins - on the shady side of an agave killed by this winters' harsh frosts. Before I go on to explain this communal hibernating behaviour I have to explain why ladybirds are so colourful. Ladybirds are aposematic, a term describing an antipredator adaptation by which organisms have evolved bright, contrasting colours (think on the yellow and black stripes in cinnabar moth caterpillar or wasps) to warn predators of dangerous behaviour (stinging) or distastefulness. Ladybirds belong to this later group. Their beautiful glossy red and yellow elithra with black spots is the first line in a complex defence system, a warning signals to predators, probably birds, of their foul taste. Their bodies contain a bitter tasting alkaloid. If the predator ignores the warning signal and attacks the ladybird - or if you handle them a bit roughly - they release a yellow liquid from their leg joints, with high concentrations of the alkaloid, coccinelline, in what is called "reflex bleeding".  Ladybirds can secrete up to almost a quarter of their body weight during the reflex bleeding, so it is an energetically demanding defence mechanism. During the winter, when ladybirds are not feeding and need to save precious resources, they do not bleeding, although they still taste bitter. It is because of this that they cluster together: as other distasteful prey that lack a mechanism to let know of their foul taste to a potential predator, clustering allows individuals - even if they are unrelated - with warning coloration in a group to benefit from just one of them being injured or killed by a predator, as the predator is unlikely to attack further ones in the cluster.ReferenceHolloway, G., Jong, P., Brakefield, P. & Vos, H. (1991). Chemical defence in ladybird beetles (Coccinellidae). I. Distribution of coccinelline and individual variation in defence in 7-spot ladybirds (Coccinella septempunctata) Chemoecology, 2 (1), 7-14 DOI: 10.1007/BF01240660... Read more »

  • March 5, 2011
  • 10:30 AM
  • 1,347 views

A case of congenital beat deafness?

by Henkjan Honing in Music Matters

Of most people that claim things like ‘Oh, but I’m not musical at all’, ‘I’m hopeless at keeping a tune’ or ‘I have no sense of rhythm’, only a small percentage turn out to be unmusical. The condition is known as amusia, and those who suffer from it are literally music-deficient. It is a rather exceptional, mostly inherited condition that comprises a range of handicaps in recognising or reproducing melodies and rhythms. It has been estimated that about 4 per cent of the people in Western Europe and North America have problems in this direction, to a greater or lesser degree. The most common handicap is tone-deafness or dysmelodia: the inability or difficulty in hearing the difference between two separate melodies.To diagnose amusia, the Montreal Battery of Evaluation of Amusia (MBEA) has been developed. This test is available online – but wait a while before trying it out :-) People who say: ‘I can’t hold a note,’ ‘I sing out of tune,’ or ‘I have no sense of rhythm,’ are not necessarily suffering from amusia. Such people often confuse poor singing or dancing skills with the absence of a sense of hearing differences in melodies and rhythms. For instance, clapping a complex rhythm or dancing to the music requires quite some practice. Nevertheless, almost all of us can hear the differences between rhythms. It has been established that, even in people who are diagnosed as being tone-deaf, about half of them have a normal sense for rhythm (Peretz & Hyde, 2003).Jessica Phillips-Silver (Université de Montréal, Canada) and a dream-team of music cognition experts found a person that claims to have truly no sense for rhythm, or, more precisely, is apparently deaf to hearing regularity in music. They describe their results in an upcoming issue of Neuropsychologia.All tests presented in this intriguing study indeed hint at a person that has a true deficit in picking up the regularity in music (the ‘beat’ or regular pulse). However, as with other studies on beat induction, it has proven to be very difficult to support the presence or absence of this skill on judging overt behavior such as dancing (see earlier entries on, e.g., Snowball). The study presents one (non-standard) perceptual test on beat perception, and I’m surprised the researchers did not use a relatively simple and far more direct test to see if beat induction is present or absent in this participant, such as the MMN paradigm used in work with newborns (e.g., Honing et al., 2009) or other recent studies making use of brain imaging methods. Would make a great follow-up paper :-)Phillips-Silver, J., Toiviainen, P., Gosselin, N., Piché, O., Nozaradan, S., Palmer, C., & Peretz, I. (2011). Born to dance but beat deaf: A new form of congenital amusia Neuropsychologia DOI: 10.1016/j.neuropsychologia.2011.02.002Peretz, I. & Hyde, K. (2003). What is specific to music processing? Insights from congenital amusia Trends in Cognitive Sciences, 7 (8), 362-367 DOI: 10.1016/S1364-6613(03)00150-5Honing, H., Ladinig, O., Háden, G., & Winkler, I. (2009). Is Beat Induction Innate or Learned? Annals of the New York Academy of Sciences, 1169 (1), 93-96 DOI: 10.1111/j.1749-6632.2009.04761.x... Read more »

Phillips-Silver, J., Toiviainen, P., Gosselin, N., Piché, O., Nozaradan, S., Palmer, C., & Peretz, I. (2011) Born to dance but beat deaf: A new form of congenital amusia. Neuropsychologia. DOI: 10.1016/j.neuropsychologia.2011.02.002  

Honing, H., Ladinig, O., Háden, G., & Winkler, I. (2009) Is Beat Induction Innate or Learned?. Annals of the New York Academy of Sciences, 1169(1), 93-96. DOI: 10.1111/j.1749-6632.2009.04761.x  

  • March 5, 2011
  • 08:48 AM
  • 1,737 views

PROTOBATS: visualising the earliest stages of bat evolution

by Darren Naish in Tetrapod Zoology



Reconstructions of the earliest phases of bird evolution - of 'near-birds' or 'protobirds', if you will - are pretty familiar, and hypothetical 'proto-pterosaurs' are also relatively familiar thanks to their appearance in the mainstream literature (Wellnhofer 1991, Unwin 2006). However, have you ever seen a reconstruction of a proto-bat? Such creatures must have existed, of course, but I'm only aware of one published effort to visualise them. Reproduced here, these reconstructions were originally published in Smith (1977) and were later reproduced in John Hill and James Smith's excellent Bats: A Natural History (Hill & Smith 1984).

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

  • March 4, 2011
  • 09:22 PM
  • 339 views

Eleutherodactylus cosnipatae: World's smallest frog

by beredim in Strange Animals

Eleutherodactylus cosnipatae used to hold the record for being the world's smallest frog. This changed in 2012, with the discovery of another, even smaller frog (Paedophryne amauensis).... Read more »

  • March 4, 2011
  • 03:14 PM
  • 1,660 views

Chasing Daphnia: The Smallest Story on Earth

by Alan Burdick in Silvarerum

Biologist are good at tracking stuff. Whales, sea turtles, birds, bees: with satellite trackers, radio collars, and PIT tags, it seems, most any animal can be followed most anywhere, in detail, across a field or around the world. Last week, scientists revealed the heartbreaking story of a polar bear mother that swam for nine days straight, [...]... Read more »

  • March 4, 2011
  • 02:05 PM
  • 1,999 views

Well, this is unexpected! Drosophila mitochondrial translation elongation Factor G1 contains a nuclear localization signal.

by Gemma Atkinson in Protein evolution and other musings

Most eukaryote genomes encode two mitochondrial translation elongation factor Gs. I recently had a paper in MBE about the origin and evolution of these factors, and I've blogged about it previously. I spotted a very surprising article in PloS One today: "The Drosophila Mitochondrial Translation Elongation Factor G1 Contains a Nuclear Localization Signal and Inhibits Growth and DPP Signaling." For some reason, mtEFG1 is dual targeted to the nucleus as well as the mitochondrion. The localisation signal is proposed to be found at the C terminus, unlike the mitochondrial transit peptide, which is found at the N terminus. The authors suggest a model in which "if mitochondrial ATP synthesis is low or EF-G1 is overexpressed and import of EF-G1 proteins into mitochondria is a limiting step, some EF-G1 proteins can accumulate outside of mitochondria and translocate into the nucleus, where they inhibit cellular growth and proliferation."The authors carry out mutagenesis and subcellular localization analysis of mtEFG1, and find that although the Drosophila mtEFG1 gene is essential, it's not required in every tissue. This leads them to suggest that in some tissues, mtEFG2 and not mtEFG1 is the primary translocation factor. This would be very unexpected as neither spirochete or human spd/mtEFG2 can not promote translocation, and instead spd/mtEFG2 is proposed to be specialised for EF-G's role in ribosome recycling. Additionally, the alignment in my paper shows mtEFG2s don't have the conserved amino acids involved in translocation functions, such as interaction with peptidyl-tRNA. However intramolecular and ribosome interaction sites are well conserved in mtEFG2, suggesting it maintains EF-G-like structural integrity and ribosome binding abilities. Maybe this is sufficient to promote translocation in some conditions? In fact, even the more distantly related EF-G2 of Thermus, which belongs to a whole other ancient subfamily is capable of translocation, hinting that although classical EF-G is very well conserved at the primary sequence level, at least in some conditions the ribosome can accommodate and translocate with more divergent homologs that maintain an EF-G-like structure.The model of mtEFG1 subcellular location being related to mitochondrial ATP synthesis proposed by Trivigno and Haerry presents a paradox, which they acknowledge: "If EF-G2 functioned as an elongation factors in tissues like the heart, mitochondrial translation and ATP synthesis would occur at normal levels, and EF-G1 would be imported into mitochondria and not accumulate in the nucleus. On the other hand, in tissues like the liver, where EF-G2 cannot function as an elongation factor, mitochondrial translation would decrease, ATP levels would drop, EF-G1 import into mitochondria would decrease and accumulation in the nucleus increase, which would further exacerbate the problem."So, in conclusion, it's all rather surprising and the model just doesn't seem quite right... it's all very well for a bioinformatician to say this I know, but more experiments needed!Refs Atkinson GC, & Baldauf SL (2011). Evolution of elongation factor g and the origins of mitochondrial and chloroplast forms. Molecular biology and evolution, 28 (3), 1281-92 PMID: 21097998Trivigno C, & Haerry TE (2011). The Drosophila Mitochondrial Translation Elongation Factor G1 Contains a Nuclear Localization Signal and Inhibits Growth and DPP Signaling. PloS one, 6 (2) PMID: 21364917Tsuboi, M., Morita, H., Nozaki, Y., Akama, K., Ueda, T., Ito, K., Nierhaus, K., & Takeuchi, N. (2009). EF-G2mt Is an Exclusive Recycling Factor in Mammalian Mitochondrial Protein Synthesis Molecular Cell, 35 (4), 502-510 DOI: 10.1016/j.molcel.2009.06.028Connell, S., Takemoto, C., Wilson, D., Wang, H., Murayama, K., Terada, T., Shirouzu, M., Rost, M., Schüler, M., & Giesebrecht, J. (2007). Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-Bound Elongation Factors... Read more »

  • March 4, 2011
  • 12:11 PM
  • 597 views

"Just how hungry am I? And what should I do about it?" How bacteria decide.

by Gemma Atkinson in Protein evolution and other musings

Escherichia coli bacteria may lack rumbling stomachs, but they know they're hungry when their ribosomes are empty. In starvation conditions, the lack of available amino acids leads to an increase in the cellular concentration of tRNAs that are uncharged with amino acids. The presence of uncharged tRNAs on the ribosome is sensed by the protein RelA in E. coli and other gamma- and beta-proteobacteria, and by close homologs called Rel or RSH in other bacteria. In such starved conditions, RelA-like proteins (from here-on I'll call them RSHs (RelA/SpoT Homologs) produce the small 'alarmone' molecule ppGpp. This onsets the so-called stringent response, where ppGpp induces changes in cell physiology, down-regulating the translation machinery and up-regulating amino acid biosynthesis machinery. It's also involved in responses to other environmental inputs such as glucose and fatty acid and iron availability. Here's a link to great review of ppGpp synthesis, hydrolysis and effects.


It's becoming clear that there is tight and complex regulation by ppGpp, and there are a couple of recent papers to this effect, which I'll briefly discuss. Using microarrays, Traxler et al. have carried out transcriptional profiling of the stringent response in E. coli, the organism where most research on bacterial stress and starvation has been carried out. They studied how ppGpp effects two transcriptional regulons, Lrp (leucine responsive protein that regulates amino acid biosynthesis and transport) and the σ-factor RpoS that regulates general stress response. They found that the Lrp regulon requires only a low level of ppGpp for its induction, while the RpoS regulon is induced only in high concentrations of ppGpp (also see comment by Carlos Balsalobre). Thus, the RpoS-dependent response is only triggered as a kind of emergency measure if the induction of the Lrp-dependent response has been induced and failed to save bacterial population growth.
It is also becoming evident that the production of ppGpp and its effects differ among different bacteria.  The bacterium Caulobacter crescentus lives in environments where amino acid concentrations are generally low. Boutte and Crosson have found that in this organism, ppGpp is synthesised in response to glucose and ammonium starvation, but not amino acid starvation. They find the RSH of this bacterium binds the ribosome, and exhibits "AND-type signaling logic", in which detection of an uncharged tRNA on the ribosome is a necessary but alone, insufficient signal for activation of ppGpp synthesis. This hints at synergistic control, where multiple starvation signals contribute to the accumulation of ppGpp at a high levels. This is different to the "OR-type" logic of E. coli, suggesting the environmental niche of the bug affects how starvation is perceived and dealt with.
The circuitry for ppGpp synthesis and its downstream effects are clearly intricate, involving feedback loops and inter-molecular cross-talk. I'm writing up some bioinformatic work now on the distribution and evolution of RSHs that synthesise or hydrolyse ppGpp, or do both. My results, like those of Boute and Crosson suggest the circuitry is dynamic across bacterial taxa, being often rewired during evolution with the help of gene duplications, domain gain and loss and horizontal gene transfer. This will be blogged of course!
For more posts about the stringent response, check out Vasya's blog

RefsTraxler MF, Zacharia VM, Marquardt S, Summers SM, Nguyen HT, Stark SE, & Conway T (2011). Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the 'feast to famine' gradient in Escherichia coli. Molecular microbiology, 79 (4), 830-45 PMID: 21299642
Balsalobre C (2011). Concentration matters!! ppGpp, from a whispering to a strident alarmone. Molecular microbiology, 79 (4), 827-9 PMID: 21299641
Boutte CC, & Crosson S (2011). The complex logic of stringent response regulation in Caulobacter crescentus: starvation signaling in an oligotrophic environment. Molecular microbiology PMID: 21338423
... Read more »

  • March 4, 2011
  • 11:36 AM
  • 1,548 views

Can infants recognize melodies heard in the womb?

by Henkjan Honing in Music Matters

Last week PlosOne published an interesting finding that shows that one month old infants can recognize a melody that they heard about three weeks before they were born.Developmental psychobiologist Carolyn Granier-Deferre (Paris Descartes University, France) and her colleagues asked fifty women to play a brief recording of a descending piano melody (one that gets lower in pitch) twice daily in the 35th, 36th and 37th weeks of their pregnancy. When the infants were one month old, both the descending melody and an ascending melody were played to the babies in the laboratory (while they slept; see notation below). On average, the heart rates of the sleeping babies briefly slowed by about twelve beats a minute with the familiar descending melody (right), and by only five or six beats with the unfamiliar ascending melody (left). A result that was interpreted as the infants paying more attention to the familiar than the unfamiliar melody.We know for a while that newborns can discriminate or perceive most of the acoustic properties of speech. The prevailing theoretical view is that these capacities are mostly independent of previous auditory experience and that newborns have an innate bias or skill for perceiving speech.By contrast, these results show (as the authors stress in a press release) that merely exposing a human fetus’ developing auditory system to complex stimuli (read ‘music’) can affect how it functions. Next to role of mere exposure one should add that this result is equally convincing evidence for a newborn’s capacity of perceiving and recalling music (see my earlier ‘language bias’ entry). In that sense this study adds to the growing literature that shows that infants in the womb are sensitive to, and can memorize both melody and rhythm. These findings play an important role in a further understanding of a potential biological and evolutionary role of music.Granier-Deferre, C., Bassereau, S., Ribeiro, A., Jacquet, A., & DeCasper, A. (2011). A Melodic Contour Repeatedly Experienced by Human Near-Term Fetuses Elicits a Profound Cardiac Reaction One Month after Birth PLoS ONE, 6 (2) DOI: 10.1371/journal.pone.0017304... Read more »

  • March 4, 2011
  • 11:27 AM
  • 1,992 views

Origins of Life – What are the odds?

by ogremkv in Cassandra's Tears

I hope to make this the first in a series of posts about current (relatively) origins of life research.  The reasoning behind this is two-fold.  The first is because I’m curious and the blog provides an opportunity to share what … Continue reading →... Read more »

Turk, R., Chumachenko, N., & Yarus, M. (2010) Multiple translational products from a five-nucleotide ribozyme. Proceedings of the National Academy of Sciences, 107(10), 4585-4589. DOI: 10.1073/pnas.0912895107  

  • March 4, 2011
  • 10:48 AM
  • 1,559 views

"Just how hungry am I? And what should I do about it?" How bacteria decide.

by Gemma Atkinson in Protein evolution and other musings

Escherichia coli bacteria may lack rumbling stomachs, but they know they're hungry when their ribosomes are empty. In starvation conditions, the lack of available amino acids leads to an increase in the cellular concentration of tRNAs that are uncharged with amino acids. The presence of uncharged tRNAs on the ribosome is sensed by the protein RelA in E. coli and other gamma- and beta-proteobacteria, and by close homologs called Rel or RSH in other bacteria. In such starved conditions, RelA-like proteins (from here-on I'll call them RSHs (RelA/SpoT Homologs) produce the small 'alarmone' molecule ppGpp. This onsets the so-called stringent response, where ppGpp induces changes in cell physiology, down-regulating the translation machinery and up-regulating amino acid biosynthesis machinery. It's also involved in responses to other environmental inputs such as glucose and fatty acid and iron availability. Here's a link to great review of ppGpp synthesis, hydrolysis and effects.It's becoming clear that there is tight and complex regulation by ppGpp, and there are a couple of recent papers to this effect, which I'll briefly discuss. Using microarrays, Traxler et al. have carried out transcriptional profiling of the stringent response in E. coli, the organism where most research on bacterial stress and starvation has been carried out. They studied how ppGpp effects two transcriptional regulons, Lrp (leucine responsive protein that regulates amino acid biosynthesis and transport) and the σ-factor RpoS that regulates general stress response. They found that the Lrp regulon requires only a low level of ppGpp for its induction, while the RpoS regulon is induced only in high concentrations of ppGpp (also see comment by Carlos Balsalobre). Thus, the RpoS-dependent response is only triggered as a kind of emergency measure if the induction of the Lrp-dependent response has been induced and failed to save bacterial population growth.It is also becoming evident that the production of ppGpp and its effects differ among different bacteria.  The bacterium Caulobacter crescentus lives in environments where amino acid concentrations are generally low. Boutte and Crosson have found that in this organism, ppGpp is synthesised in response to glucose and ammonium starvation, but not amino acid starvation. They find the RSH of this bacterium binds the ribosome, and exhibits "AND-type signaling logic", in which detection of an uncharged tRNA on the ribosome is a necessary but alone, insufficient signal for activation of ppGpp synthesis. This hints at synergistic control, where multiple starvation signals contribute to the accumulation of ppGpp at a high levels. This is different to the "OR-type" logic of E. coli, suggesting the environmental niche of the bug affects how starvation is perceived and dealt with.The circuitry for ppGpp synthesis and its downstream effects are clearly intricate, involving feedback loops and inter-molecular cross-talk. I'm writing up some bioinformatic work now on the distribution and evolution of RSHs that synthesise or hydrolyse ppGpp, or do both. My results, like those of Boute and Crosson suggest the circuitry is dynamic across bacterial taxa, being often rewired during evolution with the help of gene duplications, domain gain and loss and horizontal gene transfer. This will be blogged of course!For more posts about the stringent response, check out Vasya's blogRefsTraxler MF, Zacharia VM, Marquardt S, Summers SM, Nguyen HT, Stark SE, & Conway T (2011). Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the 'feast to famine' gradient in Escherichia coli. Molecular microbiology, 79 (4), 830-45 PMID: 21299642Balsalobre C (2011). Concentration matters!! ppGpp, from a whispering to a strident alarmone. Molecular microbiology, 79 (4), 827-9 PMID: 21299641Boutte CC, & Crosson S (2011). The complex logic of stringent response regulation in Caulobacter crescentus: starvation signaling in an oligotrophic environment. Molecular microbiology PMID: 21338423... Read more »

  • March 4, 2011
  • 10:07 AM
  • 1,829 views

Mate magnet madness: When the range of possible explanations exceeds your own hypothesis

by Kate Clancy in Context & Variation

A rebuttal of a Tierney column on the evolutionary psychology of relationship maintenance.... Read more »

Brockelman, W., Reichard, U., Treesucon, U., & Raemaekers, J. (1998) Dispersal, pair formation and social structure in gibbons ( Hylobates lar ). Behavioral Ecology and Sociobiology, 42(5), 329-339. DOI: 10.1007/s002650050445  

Miller, S, & Maner, J. (2010) Evolution and relationship maintenance: Fertility cues lead committed men to devalue relationship alternatives. Journal of Experimental Social Psychology, 1081-1084. info:/

Murdock, G., & White, D. (1969) Standard Cross-Cultural Sample. Ethnology, 8(4), 329. DOI: 10.2307/3772907  

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