December 9, 2009
10:31 AM
1,049 views

Conclusion: Darwins Dilemma, Creationist Propaganda and Corrupt Christians

According to “many published scientists,” there is a “story being told by Darwinists” that DNA and genetics play a role in evolutionary development, protein synthesis and the ontogeny of the physical characteristics displayed by animals. In hopes of edifying the masses of wayward “Darwinists,” these same “many published scientists” point out in Darwin’s Dilemma that DNA lacks the potency and mechanical know-how required to undertake these tasks. In actuality - according to “many published scientists” - all of life is derived from non-genetic “information” that is harbored within each irreducibly complex cell. Furthermore, this “information” does not arise from earthly processes, rather these “blue prints” are “preordained” by an “intelligent source.”

... Read more »

Axe, D. (2004) Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds. Journal of Molecular Biology, 341(5), 1295-1315. DOI: 10.1016/j.jmb.2004.06.058

Biology

December 9, 2009
09:30 AM
741 views

Ocean rigs as vectors for entire communities of invasive species

by Rob Goldstein in Conservation Maven

Scientists have long recognized marine transport as a vector for exotic species invasions. But relatively little attention has been given to the transport of semi-submersible rigs - the installations that are used for oil drilling...... Read more »

Wanless, R., Scott, S., Sauer, W., Andrew, T., Glass, J., Godfrey, B., Griffiths, C., & Yeld, E. (2009) Semi-submersible rigs: a vector transporting entire marine communities around the world. Biological Invasions. DOI: 10.1007/s10530-009-9666-2

December 9, 2009
08:08 AM
761 views

Testosterone, Aggression... Confusion

by Neuroskeptic in Neuroskeptic

Breaking news from the BBC -Testosterone link to aggression 'all in the mind' Work in Nature magazine suggests the mind can win over hormones... Testosterone induces anti-social behaviour in humans, but only because of our own prejudices about its effect rather than its biological activity, suggest the authors. The researchers, led by Ernst Fehr of the University of Zurich, Switzerland, said the results suggested a case of "mind over matter" with the brain overriding body chemistry. "Whereas other animals may be predominantly under the influence of biological factors such as hormones, biology seems to exert less control over human behaviour," they said. Phew, that's a relief - for a minute back there I was worried we didn't have free will. But look a little closer at the study, and it turns out that all is not as it seems. The experiment (Eisenegger et al) involved giving healthy women 0.5 mg testosterone, or placebo, in a randomized double-blind manner, and then getting them to take part in the "Ultimatum Game".This is a game for two players. One, the Proposer, is given some money, and then has to offer to give a certain proportion of it to the other player, the Receiver. If the Receiver accepts the offer, both players get the agreed-upon amount of money. If they reject it, however, no-one gets anything.The Proposer is basically faced with the choice of making a "fair" offer, e.g. giving away 50%, or a greedy one, say offering 10% and keeping 90% for themselves. Receivers generally accept fair offers, but most people get annoyed or insulted by unfair ones, and reject them, even though this means they lose money (10% of the money is still more than 0%).What happened? Testosterone affected behaviour. It had no effect on women playing the role of the Receivers, but the Proposers given testosterone made significantly fairer offers on average, compared to those given placebo. That's not mind over matter, that's matter over mind - give someone a hormone and their behaviour changes.The direction of the effect is quite interesting - if testosterone increased aggression, as popular belief has it, you might expect it to decrease fair offers. Or, you might not. I suppose it depends on your understanding of "aggression". For their part, Eisenegger et al interpret this finding as suggesting that testosterone doesn't increase aggression per se, but rather increases our motivation to achieve "status", which leads to Proposers making fairer offers, so as to appear nicer. Hmm. Maybe.But where did the BBC get the whole "all in the mind" thing from? Well, after the testing was over, the authors asked the women whether they thought they had taken testosterone or placebo. The results showed that the women couldn't actually tell which they'd had - they were no more accurate than if they were guessing - but women who believed they'd got testosterone made more unfair offers than women who believed they got placebo. The size of this effect was bigger than the effect of testosterone.Is that "mind over matter"? Do beliefs about testosterone exert a more powerful effect on behaviour than testosterone itself? Maybe they do, but these data don't tell us anything about that. The women's beliefs weren't manipulated in any way in this trial, so as an experiment it couldn't investigate belief effects. In order to show that belief alters behaviour, you'd need to control beliefs. You could randomly assign some subjects to be told they were taking testosterone, and compare them to others told they were on placebo, say.This study didn't do anything like that. Beliefs about testosterone were only correlated with behaviour, and unless someone's changed the rules recently, correlation isn't causation. It's like finding that people with brown skin are more likely to be Hindus than people with white skin, and concluding that belief in Brahma alters pigmentation. It could even be that the behaviour drove the belief, because subjects were quizzed about their testosterone status after the Ultimatum Game - maybe women who, for whatever reason, behaved selfishly, decided that this meant they had taken testosterone!Overall, this study provides quite interesting data about hormonal effects on behaviour, but tells us nothing about the effects of beliefs about hormones. On that issue, the way the media have covered this experiment is rather more informative than the experiment itself.Eisenegger, C., Naef, M., Snozzi, R., Heinrichs, M., & Fehr, E. (2009). Prejudice and truth about the effect of testosterone on human bargaining behaviour Nature DOI: 10.1038/nature08711... Read more »

Eisenegger, C., Naef, M., Snozzi, R., Heinrichs, M., & Fehr, E. (2009) Prejudice and truth about the effect of testosterone on human bargaining behaviour. Nature. DOI: 10.1038/nature08711

December 9, 2009
08:00 AM
585 views

Thinking about electric vehicles

by sciencebase in Sciencebase Science Blog

Electric vehicles reduce noise and local air pollution, such as nitrogen oxides, particulate matter and ground-level ozone, but do they simply relocate the carbon tire-tracks to fossil-fired power stations or are there benefits on the global scale?
Fundamentally, an electric engine can achieve 85 to 90% energy conversion efficiency, which contrasts starkly with the internal combustion [...]Thinking about electric vehicles is a post from: Sciencebase Science Blog
... Read more »

Åsgeir Helland. (2009) Well-to-wheel CO2 analysis of electric and ICE vehicles: are global CO2 emission reductions possible?. Int. J. Global Warming, 1(4), 432-442. info:/

Other

December 9, 2009
07:45 AM
1,437 views

Tip of the Week: GRAIL for prioritizing SNPs

by Mary in OpenHelix

Perusing my copy of Nature Genetics last week, I was flipping through the pages and noticed an unusual graphic. I looked at it a little closer and was convinced it was one of the Spirographs that I used to make as a kid. (Remember those? I always liked that….) I looked a little bit closer and realized it was somewhat more informative than the Spirographs I used to draw. This represented the relationships between genes, based on the literature. Hmmm….how did they do this, exactly?
The paper I was reading was Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk by Raychaudhuri et al, which was interesting enough. I like to read the GWAS papers to see what the current techniques and strategies are, not only for the specific genes themselves. And this paper reported the strategy that they used to prioritize their SNPs, and that they used GRAIL to generate the data for this graphic of gene relationships. Check out Figure 1 for the strategy.
When I saw the name GRAIL I thought–huh….GRAIL is back with a new use? I thought that was…ah…retired…at this point. But this isn’t that GRAIL (http://compbio.ornl.gov/Grail-1.3/, Gene Recognition and Assembly Internet Link). This is a different GRAIL–the new one is Gene Relationships Among Implicated Loci. So I had to go and read that paper, which is Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions by Raychaudhuri et al.
This new GRAIL is all about text mining. It is a tool that relies on statistical text mining of the literature for genes in a region and examines the relationships among those genes in the text. The focus in their case is disease regions, but there’s no reason that you couldn’t use it for a variety of other topics.   As the authors state:
Given only a collection of disease regions, GRAIL uses our text-based definition of relatedness (or alternative metrics of relatedness) to identify a subset of genes, more highly related than by chance; it also assigns a select set of keywords that suggest putative biological pathways.
So you pull a set of genes out of the literature based on SNPs or locations of interest, and you can begin to assess what’s interesting in the set.   Now, the tool makes a lot of assumptions that you should be aware of if you are going to use it. It assumes each region contains a single pathogenic gene. I’m not sure that’s always going to be the case, but for this tool as long as you know that, that’s a fair assumption. They suggest this helps to keep from multigenic regions from dominating the analysis. Fair enough, but…what if that is the interesting aspect? Still–that’s ok as long as you know.
In the paper they use validated SNPs from 4 different research areas:

SNPs associated with serum lipid levels: GRAIL finds genes in the cholesterol biosynthesis pathway.

SNPs associated with height; they identify pathways they consider plausible.

Crohn’s disease; they confirm associations that have been seen.

Schizophrenia–and here they used rare deletions as the items of interest; they find related genes, many highly enriched in the CNS. So this suggests using this not only for SNPs but for CNVs this may be a useful strategy.

Their Figure 1 nicely summarizes the strategy:

One curious tweak of the data analysis was that they used the literature prior to December 2006, because right after that there was an onslaught of GWAS papers that would list a whole bunch of genes associated with regions that might be more tenuous still. I understand this in theory, but I imagine it also eliminates more current research on genes of interest from other methods too. I saw in the tool you could choose either pre-Dec 06 or a more up-to-date literature set. It would be useful to try both if you use GRAIL and keep that in mind.
Another point to keep in mind: some genes are just not found in the abstracts, and they mention that is an issue.   So the set you can examine are those that were in the abstracts, and were identified properly with nomenclature, spelling, etc. Text mining is cool, but has a lot of limitations around those aspects, and the use of synonyms too in general. It’s not just an issue for GRAIL, but for all text mining tools at this point.
They also devise a way to use Gene Ontology (GO) and some expression data in GRAIL as other “relatedness” metrics. You’ll find those available from the GRAIL tool as well.
They don’t show any spirographs in their figures in this first GRAIL paper. That one that drew me in was Figure 2 in the arthritis paper. So I went over to the software to try to generate these myself. The outcome at this point is a web page with text and links to UCSC Genome Browser, and Entrez Gene (from the individual genes and from the keyword list–keywords collect multiple Entrez Genes). I was a little surprised that the keyword link wasn’t to PubMed as well. Currently it doesn’t provide the graphic, but maybe that will come along over time. If it does I’ll be sure to mention it on the blog.
One final note on the paper: in the supplemental section they compare GRAIL to other tools in this arena. If you are interested in tools like we are here you may find some of them interesting as well.   The tools are listed with URLs in Table S5, and the comparison outcome is in Text S1:
Prioritizer [2], Gene2Disease (G2D) [3,4,5], Commonality of Functional Annotation (CFA) [6], and Prospectr [7]. There were five supervised tools: Endeavour [8], GeneSeeker [9], SUSPECTS [10], TOM [11], and CANDID [12]
So check out GRAIL and see if you find gene relationships. But don’t forget those caveats about the genes not listed in the abstracts, or the literature coverage dates. The software can be found here: http://www.broad.mit.edu/mpg/grail/
I know it’s a beta. But I think it has a lot of potential to help people sift through the results they are getting from a variety of techniques. Check it out.
NOTE: you may find periods that you can’t run GRAIL because it puts a burden on the servers. You should try again during off hours if you are seeing problems with getting it to run. This happened to me during my testing of it last week.
The list of GWAS data I used to test GRAIL came from the NHGRI catalog, which we discussed here: List of GWAS studies. I tried the straight hair SNP list, and got a pretty interesting set of results that certainly included “epidermis” and “skin” as keywords, among other things.
++++++++++++ Citations ++++++++++++
... Read more »

Raychaudhuri, S., Plenge, R., Rossin, E., Ng, A., , ., Purcell, S., Sklar, P., Scolnick, E., Xavier, R., Altshuler, D.... (2009) Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions. PLoS Genetics, 5(6). DOI: 10.1371/journal.pgen.1000534

Raychaudhuri, S., Thomson, B., Remmers, E., Eyre, S., Hinks, A., Guiducci, C., Catanese, J., Xie, G., Stahl, E., Chen, R.... (2009) Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nature Genetics, 41(12), 1313-1318. DOI: 10.1038/ng.479

Medland, S., Nyholt, D., Painter, J., McEvoy, B., McRae, A., Zhu, G., Gordon, S., Ferreira, M., Wright, M., & Henders, A. (2009) Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans. The American Journal of Human Genetics, 85(5), 750-755. DOI: 10.1016/j.ajhg.2009.10.009

December 9, 2009
07:32 AM
695 views

Breaking the waves – conservation conundrum of bioshields

by CJA Bradshaw in ConservationBytes

Today’s post covers a neat little review just published online in Conservation Letters by Feagin and colleagues entitled Shelter from the storm? Use and misuse of coastal vegetation bioshields for managing natural disasters. I’m covering this for three reasons: (1) it’s a great summary and wake-up call for those contemplating changing coastal ecosystems in the [...]... Read more »

Feagin, R., Mukherjee, N., Shanker, K., Baird, A., Cinner, J., Kerr, A., Koedam, N., Sridhar, A., Arthur, R., Jayatissa, L.... (2009) Shelter from the storm? Use and misuse of coastal vegetation bioshields for managing natural disasters. Conservation Letters. DOI: 10.1111/j.1755-263X.2009.00087.x

December 9, 2009
07:02 AM
836 views

On Public Relations

by Richard Grant in Confessions of a (former) Lab Rat

Regular listeners will remember the Science Online London gathering back in August. The day before, Mendeley hosted a pre-conference ‘fringe’ event, organized by Jenny. It turned out to be quite a wild evening, and there is video evidence of shenanigans.
One thing I remember clearly (some of you might be surprised I remember anything from that evening, but anyway) is David Colquhoun getting a tad rabid about PR. The gist was that science doesn’t need PR, it’s a waste of time and money; I don’t remember him saying explicitly PR people are professional liars but that was the impression I came away with.
I thought that was bollocks, and I still do.
PR is necessary not simply because scientists like to eat, and therefore need to be funded, and therefore need to convince various bodies (and by extension the people who influence those bodies) to give them money (and I want to talk a little about about ‘justification’ of research in another post) but also because there are crucial social and public health aspects of what we do. We don’t just have to convince the wider community that a particular piece of research is ‘correct’, but we need to demonstrate—somehow—that it directly affects their health (or their wallet, or whatever).
I’m reminded of this because a friend of mine sent me a link via Facebook last week, saying

Some (including me) would argue that the greatest battles against illness and suffering should be fought on the PR/HR front, rather than purely in the arena of science. You, O Great Stream Feeder in the Gyre of Science Publication, may well have already seen this: RT David McCandless RT @GreatDismal: Emotional Epidemiology Of H1N1

The article is from a medical doctor (or possibly here), and describes the reactions, preconceptions and attitudes of visitors to her clinic in the face of the H1N1 epidemic; or, as she describes it, Emotional Epidemiology. In brief, her patients at first demanded a vaccine against H1N1 (despite not wanting the seasonal jab…) and then, when the vaccine became available, refused it.

It certainly isn’t related to logic or facts, since few new medical data became available during this period. It seems to reflect a sort of psychological contagion of myth and suspicion.

Another report last week backs up my claim. The Daily Express reported that taking aspirin could “significantly reduce” age-related macular degeneration. Sounds great. But let’s see what the NHS has to say:

This is a well-designed and well-conducted study, the results of which have been incorrectly reported in the press. This study found that low-dose aspirin had no effect in preventing age-related macular degeneration, a common cause of sight loss in the elderly.

Far from being a significant reduction, the authors of the reported (large, double-blind) randomized controlled trial took pains to stress that there is no benefit. Indeed,

There are risks associated with taking daily or alternate-day aspirin, which should be weighed against the benefits. Elderly people, to whom this research will be most relevant, are most at risk of gastric irritation if they regularly use aspirin.

What’s going on, here?
In both cases, it’s a failure of PR. It’s not simply a matter of education. It’s a matter of getting things right, and getting that information out there, to the public—via the newspapers or schools or physicians in surgeries. Just as with anthropogenic global warming there is no (serious) debate about the science; it’s a matter of PR. And I know it’s difficult. I have no idea who Jo Willey is (apart from Health Correspondent for the Daily Trainwreck), but I would love to see the press release that she read. Because I also know that they are difficult to get right. On Monday I had to completely re-write a release that we were about to publish because the person who produced the copy got the message of the research completely wrong.
PR is necessary. And it’s hard; perhaps even harder than the science.
... Read more »

Christen, W., Glynn, R., Chew, E., & Buring, J. (2009) Low-Dose Aspirin and Medical Record–Confirmed Age-related Macular Degeneration in a Randomized Trial of Women. Ophthalmology, 116(12), 2386-2392. DOI: 10.1016/j.ophtha.2009.05.031

December 9, 2009
06:00 AM
686 views

Fouled ship hulls not a big risk to freshwater systems

by Rob Goldstein in Conservation Maven

So with all the depressing studies about maritime vessels as a vector for invasive species, new research in the journal Diversity and Distributions offers up some relatively good news about transport in the Great Lakes...... Read more »

Sylvester, F., & MacIsaac, H. (2009) Is vessel hull fouling an invasion threat to the Great Lakes?. Diversity and Distributions. DOI: 10.1111/j.1472-4642.2009.00622.x

December 9, 2009
02:25 AM
1,679 views

Empathy for the Mentally Ill in Medical Education

by Dr Shock in Dr Shock MD PhD

Empathy is an important asset for a doctor. This ability to appreciate patients’ emotions and express this emotional awareness improves clinical outcomes, professional satisfaction, and patient adherence to medical recommendations, and is believed to significantly improve patient satisfaction. More on empathy and what it is can be read here
There is a significant decline in empathy [...]

Related posts:Empathy during Medical Education There is a significant decline in empathy occurs during...Bedside teaching, Computer Based Learning and Wiki in Medical Education To me bedside teaching is number one in teaching...Medical Education Evaluated With Twitter The course in their third year of med school...

Related posts brought to you by Yet Another Related Posts Plugin.... Read more »

William Bunn, D.O. and Jan Terpstra, M.D. (2009) Cultivating Empathy for the Mentally Ill Using Simulated Auditory Hallucinations. Academic Psychiatry. DOI: 10.1176/appi.ap.33.6.457

December 8, 2009
11:14 PM
844 views

Hammer Time

by Dr. M in Deep Sea News

Every time you see me that Hammer’s just so hype
I’m dope on the floor and I’m magic on the mic
Now why would I ever stop doing this
With others makin’ records that just don’t hit
I toured around the world from London to the Bay
It’s Hammer Go, Hammer MC Hammer, Yo Hammer
And the rest can go and [...]... Read more »

McComb, D., Tricas, T., & Kajiura, S. (2009) Enhanced visual fields in hammerhead sharks. Journal of Experimental Biology, 212(24), 4010-4018. DOI: 10.1242/jeb.032615

December 8, 2009
10:26 PM
594 views

Amyloid: Junk That Builds Up Between the Cells

by Reason in Fight Aging!

As we get older, many different types of errant and unwanted proteins, the chemical byproducts of metabolism, build up and accumulate between our cells. Collectively these are known as forms of amyloid, a term that might be familiar to you in connection with Alzheimer's disease, but there are many other types of amyloid beyond that implicated in the destruction that Alzheimer's brings to the brain. For example, the work of the Supercentenarian Research Foundation implicates a different form of amyloid in the deaths of the oldest old. Those people who - though good genes, good lifestyle choices, and good luck - manage to evade heart disease, cancer, and all the other common forms of age-related death are done in by amyloid in the end. In TTR Amyloidosis, the protein amasses in and clogs blood vessels, forcing the heart to work harder and eventually fail. "The same thing that happens in the pipes of an old house happens in your blood vessels," says Coles. As one of the obvious and known forms of biochemical and structural change that occurs with aging, the buildup of amyloids is a target for the Strategies for Engineered Negligible Senescence (SENS): Extracellular junk is aggregates of...... Read more »

Xue, W., Hellewell, A., Gosal, W., Homans, S., Hewitt, E., & Radford, S. (2009) Fibril Fragmentation Enhances Amyloid Cytotoxicity. Journal of Biological Chemistry, 284(49), 34272-34282. DOI: 10.1074/jbc.M109.049809

December 8, 2009
10:08 PM
328 views

Cardiovascular Fitness is Linked to Intelligence (in Young Men...Young Swedish Men...and Lab Mice)

by Daniel Hawes in Ingenious Monkey | 20-two-5

It's ok already! I will lace up my running shoes: First a University of Princeton team shows that exercise lets lab rats produce neurons with improved stress response (i.e. they don't respond), and now a group of Swedish neuroscientists is telling us that improved cardiovascular fitness actually makes young men smarter...... Read more »

Aberg MA, Pedersen NL, Torén K, Svartengren M, Bäckstrand B, Johnsson T, Cooper-Kuhn CM, Aberg ND, Nilsson M, & Kuhn HG. (2009) Cardiovascular fitness is associated with cognition in young adulthood. Proceedings of the National Academy of Sciences of the United States of America. PMID: 19948959

Psychology

December 8, 2009
07:40 PM
1,176 views

The genetics of both host and pathogen matter in antibiotic-refractory Lyme arthritis

by Microbe Fan in Spirochetes Unwound

The arthritic form of Lyme disease was first reported in the 1970s by Allen Steere, who described the condition in a group of children (and a few adults) residing in and around the town of Lyme, Connecticut. Lyme arthritis can strike when Borrelia burgdorferi introduced into the skin by an Ixodes tick burrows into deeper tissues and ends up in the joints, usually the knee. Swelling results from an inflammatory response to B. burgdorferi residing in the joint. Lyme arthritis is treated with antibiotics, which destroy the bacteria driving inflammation. Unfortunately, arthritic symptoms endure in ~10% of treated patients despite the complete or almost complete eradication of the infection, as determined by negative PCR tests for B. burgdorferi DNA in joint fluid. Such cases are called antibiotic-refractory Lyme arthritis, which can persist for months or sometimes years. In severe cases cartilage and bone erode. Although the pathogenesis of antibiotic-refractory Lyme arthritis could involve persistence of small numbers of B. burgdorferi (or their antigens) in the joints, investigators have been seeking an autoimmune mechanism to explain the prolonged attack on joint tissue by the immune system after the spirochetes have been cleared.Many autoimmune diseases are linked to variants of HLA (immunity) genes such as those encoding the MHC class II complex. Antibiotic-refractory Lyme arthritis is associated with MHC class II variants that are able to bind to fragments of the B. burgdorferi protein OspA (outer surface protein A) encompassing amino acid residues 165 through 173. Antigen-presenting cells whose MHC class II molecules display OspA165-173 peptides on their surface stimulate T cells that recognize the OspA peptide. How OspA165-173-reactive T cells cause autoimmunity has been an area of intensive research, yet a clear answer has not emerged.One potential pathway to autoimmunity is molecular mimicry, in which a cross-reactive host protein in the joint continues to stimulate OspA165-173-specific T cells even after the eradication of B. burgdorferi by antibiotics. Although the simplicity of the molecular mimicry model is appealing, exhaustive efforts to find a cross-reactive autoantigen that stimulates OspA165-173-specific T cells have failed. Moreover, levels of OspA165-173-reactive T cells decline soon after initiation of antibiotic therapy despite continuing arthritis following treatment. Thus, chronic arthritis does not seem to involve molecular mimicry driven by a cross reaction between the OspA165-173 epitope and a self-antigen in the joint. It is possible that molecular mimicry involves another B. burgdorferi antigen that is able to bind the MHC class II variants found in genetically susceptible individuals.Other potential routes to autoimmunity in antibiotic-refractory Lyme arthritis patients emphasize the role of the high levels of key proinflammatory cytokines and chemokines found in their joint fluid, levels even higher than those found in treatment-responsive patients prior to initiation of antibiotic therapy:In a model known as bystander activation, the immune response to OspA165-173 (or another B. burgdorferi antigen) causes an excessive inflammatory response that activates other T cells that react to autoantigens in the joint.The immune system is unable to turn off the intense inflammatory response associated with OspA165-173 after the spirochetes are cleared from the joint.Although much attention has been focused on the role of host genetics, a recent study indicates that the genetics of the pathogen also influences the course of Lyme arthritis. In the July 2009 issue of Arthritis and Rheumatism, Allen Steere and his collaborators showed that antibiotic-refractory Lyme arthritis is associated with different strains of B. burgdorferi. The strains were typed from joint fluid samples collected before or during antibiotic treatment. Among the methods available to group B. burgdorferi isolates, they used the 16S-23S ribosomal RNA intergenic spacer type (RST), of which there are three. Antibiotic-refractory arthritis was defined as joint swelling lasting for at least 3 months after the start of antibiotic treatment. Antibiotic treatment consisted of 8 weeks of oral antibiotics or up to 4 weeks of antibiotics administered intravenously. Joint fluid from all 17 patients in the study tested positive by PCR for B. burgdorferi DNA prior to or during antibiotic treatment.The authors found that all 7 Lyme arthritis patients infected with RST1 strains had the antibiotic-refractory form. Joint fluid was obtained after antibiotic treatment from 5 of the 7 patients; all 5 samples tested negative for B. burgdorferi DNA by PCR. In contrast, 2 of 6 and 3 of 4 infected with RST2 and RST3 strains, respectively, were successfully treated with antibiotics (see the table below from the Jones et al. 2009 article). A larger number of samples is needed to demonstrate that the difference observed between RST1 and RST2 strains is statistically significant, but there is a clear trend towards RST1 infections having the greatest association with antibiotic treatment failure and RST3 having the least, with RST2 having an intermediate effect. The duration of arthritis also depended on the infecting RST strain.How do RST1 strains cause arthritis to persist even after the apparent eradication of the spirochetes by the recommended course of antibiotics? The investigators proposed that RST1 strains provoke a stronger inflammatory response in the joint than RST2 or RST3 strains. Coupled with an immune response to OspA165-173 in genetically susceptible patients, this could cause inflammation to continue at high levels even after elimination of the spirochetes from the joints. RST1 strains may be more likely than the other genotypes to spark intense joint inflammation even in patients who are not genetically prone to antibiotic-refractory arthritis.In future studies, it would be interesting to see if proinflammatory cytokine levels are related to the RST type that infects the joint. Ultimately, researchers need to identify the B. burgdorferi gene or genes whose variation among the RSTs causes the different treatment outcomes of Lyme arthritis.Featured paperJones, K.L., McHugh, G.A., Glickstein, L.J., & Steere, A.C. (2009). Analysis of Borrelia burgdorferi genotypes in patients with Lyme arthritis: High frequency of ribosomal RNA intergenic spacer type 1 strains in antibiotic-refractory arthritis Arthritis & Rheumatism, 60 (7), 2174-2182 DOI: 10.1002/art.24812Other referencesDrouin E.E., Glickstein, L., Kwok, W.W., Nepom, G.T., and Steere, A.C. (2008). Human homologues of a Borrelia T cell epitope associated with antibiotic-refractory Lyme arthritis. Molecular Immunology 45(1):180-189. DOI: 10.1016/j.molimm.2007.04.017Kannian, P., Drouin, E.E., Glickstein, L., Kwok, W.W... Read more »

Jones, K.L., McHugh, G.A., Glickstein, L.J., & Steere, A.C. (2009) Analysis of Borrelia burgdorferi genotypes in patients with Lyme arthritis: High frequency of ribosomal RNA intergenic spacer type 1 strains in antibiotic-refractory arthritis . Arthritis , 60(7), 2174-2182. DOI: 10.1002/art.24812

December 8, 2009
06:49 PM
645 views

Carbon dioxide and nitrogen: not such a double whammy

by Thomas Kluyver in Thomas' Plant-Related Blog

Rising CO2 levels might reduce the damage from another source: nitrogen pollution.
Between the conference in Copenhagen and those e-mails that were leaked recently, carbon dioxide, the major culprit for global warming, has been getting even more press than usual. But ecologists are familiar with another human pollutant that’s already having huge effects on ecosystems, even [...]... Read more »

Reich, P. (2009) Elevated CO2 Reduces Losses of Plant Diversity Caused by Nitrogen Deposition. Science, 326(5958), 1399-1402. DOI: 10.1126/science.1178820

December 8, 2009
05:38 PM
842 views

Norway’s National Guidelines for Evaluating Pain

by Adiemusfree in Healthskills: Skills for Healthy Living

I don’t envy the job of health economists – nor policy-makers or politicians who need to make the difficult decisions about who should receive allocation within the restricted health funding that is available. At the same time, I’m often worried when I hear that ‘high-tech’ treatments, and those that are perceived as ‘glamour’ health problems [...]... Read more »

Hara, K., & Borchgrevink, P. (2010) National guidelines for evaluating pain—Patients’ legal right to prioritised health care at multidisciplinary pain clinics in Norway implemented 2009. Scandinavian Journal of Pain, 1(1), 60-63. DOI: 10.1016/j.sjpain.2009.10.002

December 8, 2009
02:17 PM
1,332 views

People identify the sexual orientation of strangers as fast as 50 milliseconds

by Dave Munger in Cognitive Daily

Nalini Ambady has become famous for her research on "thin slicing," the idea that ordinary people can make accurate judgments about others amazingly quickly. We've discussed work from her lab showing that people can accurately predict teaching ability by watching just six seconds of video of a teacher at work. Other judgments, like gender, race, and age, can be made even faster.

But what about less obvious traits? Nicholas Rule and Ambady designed a study to see if college students could accurately identify gay men based on photos alone. They selected 90 photos of men from dating websites, carefully choosing only headshots that didn't feature facial hair, jewelry, glasses, or other accessories. Half the photos were of men seeking male partners, and half were seeking female partners. Then the photos were shown in random order to 90 student volunteers. Photos were displayed for either 33 ms, 50 ms, 100 ms, or 6.5 or 10 seconds. In addition, some of the photos were shown with no time limit at all. Immediately after each photo was shown, a mask of scrambled face parts was shown to clear any afterimages. The students were asked to indicate whether the face they had just seen was likely to be gay or straight. Were they accurate? And if so, how quickly could they do it? Here are the results:

The students responded significantly better than chance for every time period except the 33 millisecond exposure. A chance accuracy rate would be 50 percent, and even after just a 50 millisecond exposure, the students were accurate 57 percent of the time. When the results were corrected using signal detection analysis (to compensate for the fact that fewer than 50 percent of men are gay in real life), accuracy was 62 percent at 50 milliseconds, and as high as 70 percent when self-paced.
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Rule, N., & Ambady, N. (2008) Brief exposures: Male sexual orientation is accurately perceived at 50ms☆. Journal of Experimental Social Psychology, 44(4), 1100-1105. DOI: 10.1016/j.jesp.2007.12.001

December 8, 2009
01:21 PM
439 views

Back in the Family

by Journal Watch Online in Journal Watch Online

Wolf pack structure recovers after hunting ban

... Read more »

Rutledge, L., Patterson, B., Mills, K., Loveless, K., Murray, D., & White, B. (2009) Protection from harvesting restores the natural social structure of eastern wolf packs. Biological Conservation. DOI: 10.1016/j.biocon.2009.10.017

December 8, 2009
11:30 AM
934 views

Genome research: good idea, bad idea

by Zen Faulkes in Marmorkrebs

Good idea: A paper in the Journal of Heredity proposes sequencing 10,000 genomes...

Bad idea: ...of vertebrates.

A news article in Science characterized this in the title as, “No genome left behind.” But of course, it leaves a tremendous number of genomes behind, namely, every single invertebrate. What are the current estimates for number of vertebrate species? Maybe 60,000 or so? The crustaceans alone probably have about the same number of species. The number of vertebrate species is not even close to the number of beetle species.

The paper provides no rationale for doing such a massive scan of the vertebrates alone as opposed to a project that would include the invertebrates. Indeed, the word “invertebrates” appears only once, in reference to fisheries.

In fairness, I actually do think it’s great that these researchers are working together and suggesting a big, bold scheme. I’ve made no secret that I want a crayfish genome project. With this 10K genome paper, maybe it’s time to start thinking about a larger scale invertebrate genome sequencing that will cover the rest of the animal kingdom, even though it’s obviously not possible to do the same level of coverage as the small vertebrate sub-phylum.

Reference

Genome 10K Community of Scientists. (2009). Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species Journal of Heredity, 100 (6), 659-674 DOI: 10.1093/jhered/esp086

Pennisi, E. (2009). No Genome Left Behind Science, 326 (5954), 794-795 DOI: 10.1126/science.326_794... Read more »

Genome 10K Community of Scientists. (2009) Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species. Journal of Heredity, 100(6), 659-674. DOI: 10.1093/jhered/esp086

December 8, 2009
10:17 AM
881 views

Memories Glow Under the Microscope

by Neuroskeptic in Neuroskeptic

How does memory work? What changes in the brain when we learn something?We don't know for sure. But two outstanding Nature papers have just provided an important piece of the puzzle, using a truly amazing technique which allowed them to examine the brain of a living, breathing mouse under the microscope.The approach uses mice genetically engineered such that some of their neurons contain yellow fluorescent protein (YFP). You may have already heard of the cute glowing mice who have green fluorescent protein (GFP) in all their cells. In these YFP-H mice, only some of their neurons are fluorescent.Two-photon microscopy uses a focused laser beam to image fluorescent tissue. The authors of these papers were able to image the brain (the cortex) after surgically thinning - but not penetrating - the mice's skulls. The bone over the brain area in question was removed until it was just 20 micrometers thick. The brain itself was not interfered with in any way, which is what makes this method so remarkable. Generally, when you put a brain under a microscope, you've had to cut slices off it first.*Using this transcranial two-photon microscopy, these two teams of researchers (Xu et al from Santa Cruz and Yang et al from New York) were able to directly observe the neural changes that took place following motor skill learning. Adolescent and adult mice were trained on a difficult movement task, such as the "rotarod", in which the animal has to avoid falling off a constantly rotating metal rod. With a few day's practice, most of the mouse got better at the tasks.Both of the papers report that the skill learning was associated with the formation of new dendritic spines in the motor cortex. The image below shows the kind of data we're talking about: this is a single neuron, and the little blobs above and below it are individual dendritic spines, or outgrowths, of the cell. The top image shows the cell before training, and the bottom image is the same cell 24 hours later, after skill learning. Several new dendritic spines have grown. Almost certainly, these spines have formed synapses with another cell.The results of these studies show that training increases the amount of new dendritic spine formation in the motor cortex, compared to control conditions in which there is no skill learning, and that many of the new spines persist for months. Learning also seems to be associated with the removal of some already existing spines, so the overall number of spines in the brain remains roughly constant.Overall, this is a pretty amazing set of results, and it suggests that the learning of new skills is associated not only with changes in the "strength" of existing synapses between neurons, but actually with the growth of entirely new synapses. New brain cells are not generated in the adult brain except in a couple of very specific areas, but it seems that experience causes the reshaping of existing cells.There are lots of unanswered questions - such as whether the same process underlies other forms of learning as well as motor skill training, what triggers the formation of new dendritic spines, and how the process works in humans. But this is a very exciting first step.Xu, T., Yu, X., Perlik, A., Tobin, W., Zweig, J., Tennant, K., Jones, T., & Zuo, Y. (2009). Rapid formation and selective stabilization of synapses for enduring motor memories Nature DOI: 10.1038/nature08389Yang, G., Pan, F., & Gan, W. (2009). Stably maintained dendritic spines are associated with lifelong memories Nature DOI: 10.1038/nature08577... Read more »

Xu, T., Yu, X., Perlik, A., Tobin, W., Zweig, J., Tennant, K., Jones, T., & Zuo, Y. (2009) Rapid formation and selective stabilization of synapses for enduring motor memories. Nature. DOI: 10.1038/nature08389

Yang, G., Pan, F., & Gan, W. (2009) Stably maintained dendritic spines are associated with lifelong memories. Nature. DOI: 10.1038/nature08577

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