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  • August 5, 2010
  • 12:11 PM

Trees that farm bacteria

by Lab Rat in Lab Rat

One of the factors that is occasionally (rather inaccurately) used to separate plants from animals is that plants generally don't move. Some have fast moving parts, such as the venus fly trap, but they are still usually stuck in one place in the ground. Which means that once they've decided to grow they are totally dependent on their immediate surroundings for nutrients.As nutrients are not always plentiful many trees form symbiotic relationships with bacteria, for example nitrogen fixing bacteria in root nodules. Some trees can also specially cultivate microbes, essentially farming them, to provide the correct nutrient balance that they need for growth. This is especially found in more acidic-soiled forests, where there are fewer nutrients in the soil. The levels of different bacteria are controlled by way of secretions from the roots.As trees are quite big, and have roots stretching out to long distances, their impact clearly has a large effect on the surrounding microbiome (the set of microbes in the soil) and the general ecosphere. Bacteria that can precipitate minerals in useable form from the soil are encouraged, while those that do not are discouraged from growth. Experimentally, it's also been shown that by changing the levels of bacteria in the soil you can change the health of the surrounding trees so my bacterially-inclined mind is starting to think that this might not just be a one way connection. There's clearly a lot of communication going on in the soil; between different bacterial species, between fungi and bacteria, and between the tree-roots and almost all surrounding life (trees are well known for forming large networks with fungi).The mechanisms by which trees select the ideal bacterial species have not yet been determined, but I'm tempted to believe that small molecule signals will be involved. That's mostly how bacteria communicate with each other, and it's possible that trees could have hijacked and used this system to communicate with the bacteria themselves.---Calvaruso C, Turpault MP, Leclerc E, Ranger J, Garbaye J, Uroz S, & Frey-Klett P (2010). Influence of forest trees on the distribution of mineral weathering-associated bacterial communities of the Scleroderma citrinum mycorrhizosphere. Applied and environmental microbiology, 76 (14), 4780-7 PMID: 20511429... Read more »

  • August 5, 2010
  • 11:46 AM

Somatic mutations and pathway alterations in cancer

by Sally Church in Pharma Strategy Blog

"The systematic characterization of somatic mutations in cancer genomes is essential for understanding the disease and for developing targeted therapeutics." So began today's journal article from a letter to Nature (link below) from scientists at Genentech. They went on to...... Read more »

Kan, Z., Jaiswal, B., Stinson, J., Janakiraman, V., Bhatt, D., Stern, H., Yue, P., Haverty, P., Bourgon, R., Zheng, J.... (2010) Diverse somatic mutation patterns and pathway alterations in human cancers. Nature. DOI: 10.1038/nature09208  

  • August 5, 2010
  • 11:21 AM

Bacteria force wasps to leave sex behind

by Lucas in thoughtomics

An end to the blogging hiatus at last! I hope to entertain you with the fascinating story on how female wasps got rid of their men and sex in return for bacterial endosymbionts..
Despite the obvious benefits of pleasure and procreation, sex has other advantages. The genetic material of both parents gets mixed in [...]... Read more »

  • August 5, 2010
  • 11:21 AM

Inevitability and oil, Pt. 2: the “end of oil” and human empathy

by Hannah Waters in Culturing Science – biology as relevant to us earthly beings

Never thought I’d actually get around to a Pt. 2, eh?  Well, I’ve shown you!  Here’s the first part: Inevitability and Oil, Pt. 1: the inherent risk for accidents in complex technology For decades now economists and scientists have predicted the “end of oil:” the day when we use up our oil reserves, potentially resulting [...]... Read more »

  • August 5, 2010
  • 10:04 AM

Humans beat computers in predicting protein structures

by The Curious Wavefunction in The Curious Wavefunction

I was going to first describe Rosetta in a post, but a rather cool paper related to the program which appeared in Nature yesterday makes me jump the gun.In a nutshell, Rosetta tries to predict the structure of proteins from amino acid sequence by inserting fragments from known protein structures and doing many rounds of side chain torsional angle and rigid-body energy optimization. It uses a scoring function to rank the resulting structures that uses empirically derived hydrogen bonding, hydrophobic burial and desolvation terms. Detailed description will have to await the next post since yesterday's paper is not about Rosetta per se. Instead the paper talks about a program named FoldIt which essentially asks relatively untrained computer gamers to address the protein folding problem. Gamers are asked to tweak, pull, freeze and rotate parts of an incorrectly folded structure to try to twist it into the correct structure. Each set of movements would lead to an increase or decrease in a score, with the goal being to find the correct folded structure corresponding to the minimum score. The corresponding set of operations in Rosetta would involve hydrophobic burial, hydrogen bond formation and breakage, helix rotation and other related movements. The project essentially pitted Rosetta versus the gamers.The results were striking. In a significant number of cases, the gamers actually outdid Rosetta. The reasons are very intriguing and- in an age where computers seem to have unlimited power over our lives- generally testify to the advantages of humans being over computers. For instance in one case, the gamers had to first unravel significant parts of the protein leading to a sharply unfavorable score and then again re-fold it, leading to a correct structure. Rosetta would not attempt the first operation because of the sharp increase in score. This is a classic example of long-term strategy. Unlike computers, humans can make seemingly bad short-term decisions that ultimately lead to good results; we observe this process in many aspects of daily life, from stock market traders taking risks because they see favorable returns later, to politicians making unpopular choices because they think these choices will eventually lead to a popular outcome. Unlike humans though, it is very difficult for a computer program to do long-term planning, and this example illustrates not only the advantages that human intuition can have but also identifies gaps in a program like Rosetta which can possibly be filled.Another example where the humans outdid the computers was when presented with a set of 10 incorrect structures. Humans generally chose the structure closest to the given structure, whereas Rosetta picked another structure. The main point here is that simple visual clues can sometimes trump complicated decision-making (although they can also mislead). More generally, the results underscored the fact that gut feelings and mere inspection can sometimes lead to successful results.The one case where the humans did not do as well as Rosetta was in addressing the "classic" protein folding problem, where the challenge was to predict 3D structure from sequence alone. In this case, the sheer amount of conformational space to be searched thwarts success, and there are also no visual cues to guide the process unlike before. The key value of computer approaches which can rapidly pare down the conformational space becomes evident in this example.So since humans outdid the computer in many cases on the basis of intuition, this must be one super-smart group of biochemists, right? Au contraire! One of the most compelling facts was that most of the gamers in fact not only lacked a formal background or PhD. in biochemistry, but also lacked a formal background in science. Relatively few had college degrees, let alone more advanced degrees. The example strikingly illustrates that even untrained humans can possess skills that may be difficult to program into a computer. It remains to be seen if these results can be extrapolated to large-scale trials, but this very intriguing study perhaps illustrates the general principle that cracking a problem as complex as protein folding is going to require a diverse set of skills, from Monte Carlo searching to gut feelings.Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010). Predicting protein structures with a multiplayer online game Nature, 466 (7307), 756-760 DOI: 10.1038/nature09304... Read more »

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. DOI: 10.1038/nature09304  

  • August 5, 2010
  • 08:24 AM

Foldit: Innovative Biology for Gamers

by GrrlScientist in This Scientific Life

Guessing how a protein will fold up based on its DNA sequence is often too difficult for even the most advanced computer programs. Now biochemists and computer scientists at my alma mater, the University of Washington, have collaborated to create Foldit, an online computer game where computer players do the work. ... Read more »

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. DOI: 10.1038/nature09304  

  • August 5, 2010
  • 08:00 AM

Eyes on the edge: How archerfish see in and out of water

by Zen Faulkes in NeuroDojo

Archerfish rock.

These little sharpshooters are famous for being able to spit water at an insect, not on the surface of the water, but a good ways above it. And these insects are often camouflaged to boot. Then, they have to catch the insect when it hits the water before other fish get it, or it gets swept away by any water currents.

In other words, archerfish have to calculate, perform precision maneuvers, and anticipate the outcomes of their actions.

This paper, though, looks mainly at the visual problem. Anyone has probably noticed that light behaves differently when it moves through water than when it moves through air. The famous example that every kid has probably asked his parents about is why a spoon in a glass of water looks like the two halves are broken apart.

The authors here looked at the properties of the photoreceptors in the archerfish eyes. Something to remember is that the top of the retina looks down, which for the archerfish means into the water, and the bottom part of the retina looks up, which for the archerfish means looking up and out of the water. Now, it gets a bit sticky because fish have more complicated eyes that we primates do. We have rods and three kinds of cones. The archerfish has rods, single cones and double cones.

First, they found that the three general areas of the eye they looked at, the light-sensing cells of the ventral part of the retina had rather different light absorbing properties than the rest. This correlates with the fish’s visual task: the bottom part of the eye looks up, out of water.

As light goes through the water, the colours change. At the top of the water, the light tends to have shorter wavelengths than the light being reflected from the bottom of the water. The sensitivity of the photoreceptors in those regions matched quite well with the different kinds of light these animals would be seeing.

The highest density of cones is also right in the “sweet spot” where the fish will be looking at its target. The authors don’t use the term “fovea,” but it seems to me that is exactly what it is. And the resolution the archerfish is probably capable of is estimated to be about 8 minutes of arc; by comparison, arthropods eyes tend to be only able to resolve several degrees of arc, and I think humans in fractions of a second of arc.

They interpret these differences across the retina as adaptations to living at the interface, which is perfectly reasonable. The authors suggest that it something that other fish living near the surface have, although one might expect it to be particularly enhanced in the archerfish.

Next steps for this group is to start doing a bucket of behavioural tests to see how well the fish is able to discriminate different colours, shades, and so on. Since the fish has a nice behaviour of spitting at things they see, it should be possible to train them to spit at objects they can see, then tweak the visual stimuli until they can’t do the task any more.


Temple, S., Hart, N., Marshall, N., & Collin, S. (2010). A spitting image: specializations in archerfish eyes for vision at the interface between air and water Proceedings of the Royal Society B: Biological Sciences, 277 (1694), 2607-2615 DOI: 10.1098/rspb.2010.0345... Read more »

  • August 5, 2010
  • 06:56 AM

A Practical Approach to MIQE for the Bench Scientist

by aviwener in Canadian Biotechnologist 2.0

In a groundbreaking review published in February 2009, Bustin et al bemoaned the lack of standardization in Quantitative Real-Time PCR (qPCR) experimentation and data analysis. In their critique the authors cite the use of diverse reagents, protocols, analysis methods and reporting formats which has negatively impacted on the acceptance of qPCR as a robust quantitative [...]... Read more »

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL.... (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clinical chemistry, 55(4), 611-22. PMID: 19246619  

  • August 5, 2010
  • 06:14 AM

The good old days, revisited

by iayork in Mystery Rays from Outer Space

As a general remark, the Measles were mild, while on the contrary, the Mumps were almost invariably severe, and frequently attended with metastasis to the testicles. Some cases of the latter were attended with enormous swelling and high inflammatory excitement, requiring the lancet and other antiphlogistic remedies. … As a local application to the scrotum none appeared to afford [...]... Read more »

Quinlisk, M. (2010) Mumps Control Today. The Journal of Infectious Diseases, 2147483647. DOI: 10.1086/655395  

  • August 5, 2010
  • 03:38 AM

1 in 200 men direct descendants of Genghis Khan

by Razib Khan in Gene Expression

In 2003 a groundbreaking historical genetics paper reported results which indicated that a substantial proportion of men in the world are direct line descendants of Genghis Khan. By direct line, I mean that they carry Y chromosomes which seem to have come down from an individual who lived approximately 1,000 years ago. As Y chromosomes [...]... Read more »

ZERJAL, T. (2003) The Genetic Legacy of the Mongols. The American Journal of Human Genetics, 72(3), 717-721. DOI: 10.1086/367774  

  • August 4, 2010
  • 06:05 PM

More on maternal spiders

by Africa Gomez in BugBlog

I posted recently on maternal behaviour in spiders, but I when I came across this I knew another post was in order. The photo above shows what is is most likely a Gnaphosidae spider with her eggs in her nest on the 19th of July. The spider has wrapped herself inside a silken nest she has made for her eggs, and she will remain there until they hatch and the spiderlings disperse. This behaviour, called 'egg guarding' is present in many spiders. Why would a spider do this? Do the eggs benefit in a any way from their mothers behaviour? There is anecdotal evidence in related species that unattended eggs are predated, but little information was available on who the predators are until Simon Pollard carried out some experiments on Clubiona cambridgei, an endemic species from New Zealand displaying this egg guarding behaviour, and the results were surprising.  Simon had noticed that sometimes Clubiona spiders were found inside or just outside nests with eaten eggs and suspected that individuals from the same species were actually the egg predators. Egg predation seems an unusual behaviour for spiders, who are considered hunters of active organisms. He wanted to test the hypotheses that (1) spiders eat eggs from their own species - a form of cannibalism - and (2) egg guarding represents a defensive mechanism that decreases the chances of conspecific predation. He carried out simple experiments with egg nests - easily collected in this species as it is abundant and nests in folded out flax leaves. His results were conclusive. Nests where mothers had been carefully removed (therefore, unattended) and then were exposed to non-breeding females were all predated, with all eggs eaten within 16 h. Males or breeding females did not eat unatended eggs. When nests were attended, males and non-breeding females quickly retreated when noticing the activity of the guarding mother and no egg predation took place. Therefore egg guarding in Clubiona is indeed a strategy to protect the eggs from other spiders predation. More recently, cannibalistic egg predation has been documented in 12 spider families - including Gnaphosidae -, and therefore, egg guarding behaviour is likely to have the same defensive function in these spiders against cannibalistic predation.My spider successfully defended her eggs, and yesterday, I could see the pale, tiny spiderlings through the nest walls.More informationPollard, S.D. (1984). Egg guarding by Clubiona cambridgei (Araneae, Clubionidae) against conspecific predators Journal of Arachnology, 11, 323-326Nyffeler, M., Breene, R., Dean, D., & Sterling, W. (1990). Spiders as predators of arthropod eggs Journal of Applied Entomology, 109 (1-5), 490-501 DOI: 10.1111/j.1439-0418.1990.tb00080.x... Read more »

Pollard, S.D. (1984) Egg guarding by Clubiona cambridgei (Araneae, Clubionidae) against conspecific predators. Journal of Arachnology, 323-326. info:/

Nyffeler, M., Breene, R., Dean, D., & Sterling, W. (1990) Spiders as predators of arthropod eggs. Journal of Applied Entomology, 109(1-5), 490-501. DOI: 10.1111/j.1439-0418.1990.tb00080.x  

  • August 4, 2010
  • 03:44 PM

Real Time fMRI

by Neuroskeptic in Neuroskeptic

Wouldn't it be cool if you could measure brain activation with fMRI... right as it happens?You could lie there in the scanner and watch your brain light up. Then you could watch your brain light up some more in response to seeing your brain light up, and watch it light up even more upon seeing your brain light up in response to seeing itself light up... like putting your brain between two mirrors and getting an infinite tunnel of activations.Ok, that would probably get boring, eventually. But there'd be some useful applications too. Apart from the obvious research interest, it would allow you to attempt fMRI neurofeedback: training yourself to be able to activate or deactivate parts of your brain. Neurofeedback has a long (and controversial) history, but so far it's only been feasible using EEG because that's the only neuroimaging method that gives real-time results. EEG is unfortunately not very good at localizing activity to specific areas.Now MIT neuroscientists Hinds et al present a new way of doing right-now fMRI: Computing moment to moment BOLD activation for real-time neurofeedback. It's not in fact the first such method, but they argue that it's the only one that provides reliable, truly real-time signals.Essentially the approach is closely related to standard fMRI analysis processes, except instead of waiting for all of the data to come in before starting to analyze it, it incrementally estimates neural activation every time a new scan of the brain arrives, while accounting for various forms of noise. They first show that it works well on some simulated data, and then discuss the results of a real experiment in which 16 people were asked to alternately increase or decrease their own neural response to hearing the noise of the MRI scanner (they are very noisy). Neurofeedback was given by showing them a "thermometer" representing activity in their auditory cortex.The real-time estimates of activation turned out to be highly correlated with the estimates given by conventional analysis after the experiment was over - though we're not told how well people were able to use the neurofeedback to regulate their own brains.Unfortunately, we're not given all of the technical details of the method, so you won't be able to jump into the nearest scanner and look into your brain quite yet, though they do promise that "this method will be made publicly available as part of a real-time functional imaging software package."Hinds, O., Ghosh, S., Thompson, T., Yoo, J., Whitfield-Gabrieli, S., Triantafyllou, C., & Gabrieli, J. (2010). Computing moment to moment BOLD activation for real-time neurofeedback NeuroImage DOI: 10.1016/j.neuroimage.2010.07.060... Read more »

Hinds, O., Ghosh, S., Thompson, T., Yoo, J., Whitfield-Gabrieli, S., Triantafyllou, C., & Gabrieli, J. (2010) Computing moment to moment BOLD activation for real-time neurofeedback. NeuroImage. DOI: 10.1016/j.neuroimage.2010.07.060  

  • August 4, 2010
  • 03:00 PM


by EcoPhysioMichelle in C6-H12-O6

In case you hadn't heard, it's Shark Week, and Michelle is here to teach you a little bit of shark physiology. In the interest of full disclosure, sharks are not my forte. I am a tetrapod girl, but I know just enough about sharks to know that they have a really, really cool electrosensory system that helps them catch prey.... Read more »

Bullock, T. (1982) Electroreception. Annual Review of Neuroscience, 5(1), 121-170. DOI: 10.1146/  

Montgomery, J., Coombs, S., & Halstead, M. (1995) Biology of the mechanosensory lateral line in fishes. Reviews in Fish Biology and Fisheries, 5(4), 399-416. DOI: 10.1007/BF01103813  

  • August 4, 2010
  • 01:32 PM

Y Chromsome V: The Ampliconic Sequence Class

by Kele in Kele's Science Blog

If you recall from Y Chromosome II, the ampliconic class displays extraordinarily high sequence similarity to other sequences of the same region, has higher gene density than the X-degenerate class, and its genes are found in multiple copies and are expressed almost exclusively in the testes. The ampliconic class just doesn’t show the signs of [...]... Read more »

Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T.... (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature, 423(6942), 825-37. PMID: 12815422  

  • August 4, 2010
  • 01:09 PM

Fame beckons at last for the Horton Plains slender loris

by Darren Naish in Tetrapod Zoology

After I'd finished writing about the new Madagascan mongoose, I thought it only right to add material to the end about some of the other new discoveries made in the world of mammalogy. But as happens on so many occasions, this made the article over-long and in the end I decided to axe that additional stuff. Plus, it makes more sense to get two, three, four or more articles out of one - another familiar theme on Tet Zoo (errr, gekkotans, anurans, babirusas, matamatas, pronghorns, bird hands.... need I go on?). Anyway...

From Sri Lanka comes the news that the Horton Plains slender loris (also known as the Highland slender loris or Montane slender loris) has been photographed: it's only been observed in the wild four times since its discovery in 1937, and this is the first time it's been captured on camera [adjacent photo © by C. Mahanayakage; from Gamage et al. (2010)]. What hasn't been mentioned by the popular media is that a technical paper has been published on this event, and it discusses the significance of the new data that was collected (Gamage et al. 2010). Read the rest of this post... | Read the comments on this post...... Read more »

Gamage, S., Reardon, J. T., Padmalal, U. K. G. K., & Kotagama, S. W. (2010) First physical examination of the Horton Plains slender loris, Loris tardigradus nycticeboides, in 72 years. Primate Conservation. info:/

  • August 4, 2010
  • 12:56 PM

I can’t hear you, the bacteria are too noisy

by Iddo Friedberg in Byte Size Biology

Much too noisy. When looking at a population of genetically identical bacteria, the number of proteins they produce varies. The picture below shows the levels of one type of protein that was fused to a green fluorescent protein (so we can see it): clearly there is a variation in how much of the protein each cell produces (“protein expression” in molbio-speak), even though the bacteria are genetically identical. Why is that? In 2006, a group of researchers at the University of California San Diego and Boston University looked at the variation in protein expression in genetically identical bacteria, and what it could mean. They constructed a simple and well-defined computational model first. The researchers were surprised when their model shows that the variation actually increased when the cell growth and division was slowed or stopped. ... Read more »

Guido, N., Wang, X., Adalsteinsson, D., McMillen, D., Hasty, J., Cantor, C., Elston, T., & Collins, J. (2006) A bottom-up approach to gene regulation. Nature, 439(7078), 856-860. DOI: 10.1038/nature04473  

  • August 4, 2010
  • 12:39 PM

Study Finds Brains Literally "Sync Up" In Conversation

by David Berreby in Mind Matters

Good communication is a matter of getting "in sync" with others, as you've probably noticed when you've seen people match their steps perfectly as they walk, and imitate each other's gestures as they talk, and use each other's phrases and grammar. Last week, this paper reported  this kind of coordination in the most important place of all: When people converse, it reports, regions of their brains synchronize their activity. "Neural coupling," they argue, is a key part of communication.
Uri Hasson, Lauren Silbert and Greg Stephens recorded Silbert telling a 15-minute story while an MRI scanner recorded changes in activity levels in various regions of her brain. The researchers then played the recording to 11 volunteers while their brains were MRI-ed. As they listened, the paper reports, their brains' patterns of activity matched Silbert's.
The work is a nice departure from models that look for activity in "the brain," because, of course, communication doesn't take place in isolation. It also challenges the notion that listening and talking are neatly separated activities: "neural coupling" took place in both "comprehension" and "production" regions of the listeners' brains.
Especially interesting, as Michael Balter points out, were the regions in which the listeners went first: As they heard the story, their brains fired in a pattern that matched Silbert's, but hers came a moment later. They were, it seems, anticipating what she would say, priming themselves to hear what they expected. The better the match between Silbert's brain activity and these "predictive anticipatory responses" in a listener, the better the listener understood the story.
Thanks to some ingenious experiments by Sir Frederic Charles Bartlett in the 1930's, we know that listeners often "fill in" details of what they are hearing (and that their memories of the speaker don't distinguish between what they actually heard and what they supplied themselves). When students retold a folk tale he had given them to read, Bartlett found, they added some details (for instance, where the story read ``that Indian has been hit,'' some students recalled an Indian being killed, others an Indian being hit by an arrow). They also changed some unfamiliar facts (making the story's Indians "row" their canoe like proper English undergraduates). You can try it yourself: Read the story here, then re-tell it in a couple of days from memory, then compare what you've written or recorded to the original.
Yet these people felt sure that their memories of the story were accurate. They didn't notice the difference between what they had read and what they had supplied themselves. Why such confidence? Bartlett proposed that the mind understands the world by means of "schemas"—mental maps that relate actions and objects to each other. Once learned, the schema works rather like a form with blanks to be filled in. Once I know you're talking about Indians and canoes, I "fill in" arrows and moccasins even if you don't mention them (and I if you bring in samurai swords I might miss it, because those don't fit the schema).
Perhaps Hasson et al.'s paper, published in the Proceedings of the National Academy of Sciences, has touched on the physiological correlates of Bartlett's schemas. Perhaps, too, it has pointed to the physiological basis for the pleasure people take in synchronized activities—singing together in tune, marching together in time, doing the "wave." If "neural coupling" is essential to understanding others, then it would make sense that people would find it pleasurable and seek to create it.
Stephens, G., Silbert, L., & Hasson, U. (2010). Speaker-listener neural coupling underlies successful communication Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1008662107
... Read more »

Stephens, G., Silbert, L., & Hasson, U. (2010) Speaker-listener neural coupling underlies successful communication. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1008662107  

  • August 4, 2010
  • 12:38 PM

Hedgehog (Hh) signaling in cancer: a new pipeline emerges

by Sally Church in Pharma Strategy Blog

The other day I came across an interesting journal article on Hedgehog signalling, how it might be implicated in some cancers, and the potential issues associated with targeting the pathway: "... several issues surrounding the basic biology of the Hh...... Read more »

Merchant, A., & Matsui, W. (2010) Targeting Hedgehog -- a Cancer Stem Cell Pathway. Clinical Cancer Research, 16(12), 3130-3140. DOI: 10.1158/1078-0432.CCR-09-2846  

  • August 4, 2010
  • 11:18 AM

Come on feel the PyroNoise

by Nicholas Loman in Pathogens: Genes and Genomes

454 sequencing technology has revolutionised the field of microbial ecology by providing a means to sequence tens of thousands of partial 16S rDNA sequences quickly and efficiently. However, this new capacity brought new problems to a field fraught with potential sources of bias. Early analyses of microbial communities using 454 data tended to overstate the [...]... Read more »

Quince, C., Lanzén, A., Curtis, T., Davenport, R., Hall, N., Head, I., Read, L., & Sloan, W. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, 6(9), 639-641. DOI: 10.1038/nmeth.1361  

  • August 4, 2010
  • 11:03 AM

In Cold Blood

by Journal Watch Online in Journal Watch Online

Even a big new reserve may not be enough to protect Spain’s threatened lizards, turtles and salamanders from climate change. Warming temperatures could dramatically restrict — or even eliminate – habitat for these cold-blooded “ecotherms,” which can’t regulate their body temperatures like “warm-blood” mammals and birds. The finding suggests conservationists need to take physiological differences […] Read More »... Read more »

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