The Norovirus: A Study in Puked Perfection, "Each norovirus carries just nine protein-coding genes (you have about 20,000). Even with that skimpy genetic toolkit, noroviruses can break the locks on our cells, slip in, and hack our own DNA to make new noroviruses. The details of this invasion are sketchy, alas, because scientists haven’t figured out a good way to rear noroviruses in human cells in their labs. It’s not even clear exactly which type of cell they invade once they reach the gut. Regardless of the type, they clearly know how to exploit their hosts. Noroviruses come roaring out of the infected cells in vast numbers. And then they come roaring out of the body. Within a day of infection, noroviruses have rewired our digestive system so that stuff comes flying out from both ends." [more inside]
Association of Coffee Drinking with Total and Cause-Specific Mortality [FULL TEXT HTML]: "We used data from a very large study, the National Institutes of Health (NIH)–AARP Diet and Health Study (ClinicalTrials.gov number, NCT00340015), to determine whether coffee consumption is associated with total or cause-specific mortality. The current analysis, involving more than 400,000 participants and 52,000 deaths, had ample power to detect even modest associations and allowed for subgroup analyses according to important baseline factors, including the presence or absence of adiposity and diabetes, as well as cigarette-smoking status." [more inside]
Deciphering the Tools of Nature’s Zombies: The ability of parasites to alter the behaviour of their hosts fascinates both scientists and non-scientists alike. One reason that this topic resonates with so many is that it touches on core philosophical issues such as the existence of free will. If the mind is merely a machine, then it can be controlled by any entity that understands the code and has access to the machinery. This special issue of The Journal of Experimental Biology highlights some of the best-understood examples of parasite-induced changes in host brain and behaviour, encompassing both invertebrate and vertebrate hosts and micro- and macro-parasites. Full issue annotated inside: [more inside]
The simulated brain - "First computer model to produce complex behaviour performs almost as well as humans at simple number tasks." [1,2,3,4,5,etc.]
In just a few weeks single-celled yeast have evolved into a multicellular organism, complete with division of labour between cells. This suggests that the evolutionary leap to multicellularity may be a surprisingly small hurdle. More from Scientific American blogs. [Full Text PDF of the Publication of Note] [more inside]
What we currently call breast cancer should be thought of as 10 completely separate diseases, according to an international study which has been described as a "landmark". The categories could improve treatment by tailoring drugs for a patient's exact type of breast cancer and help predict survival more accurately. The study in Nature analysed breast cancers from 2,000 women [Abstract] . It will take at least three years for the findings to be used in hospitals. [more inside]
One of the many problems farmers of various kinds of legumes need to deal with is the pea aphid. They reproduce incredibly fast and live by sucking the sap out of the plants, an electron micrograph of one in action. However, while they are terrifying parasites of legumes, they have their own yet more horrific parasites, a parasitoid wasp. Here is a really nice close up picture of one doing its thing, a video of the act, and here is a brain meltingly horrific video of a dissection of the mummified aftermath 8 days later. Essentially, these wasps deposit their eggs in a pea aphid and the growing larva feeds on it, developing there for about a week, and then consuming the host from the inside out like a Xenomorph. When it’s done, the wasp larva dries the aphid’s cuticle into a papery brittle shell and an adult wasp emerges from the aphid mummy. Legume farmers love them, and you can even order their mummies online these days. However, farmers noticed that the wasps didn't work as effectively on all of the aphids, and so researchers went to work figuring out why. It turns out that all aphids have a primary bacterial endosymbiont living inside their cells, in addition to and just like a mitochondria, and that many have some combination of five other secondary endosymbionts. Interestingly, two of those other five, Hamiltonella defensa and Serratia symbiotica have been shown to confer varying levels of resistance to the parasitoid wasp, allowing the aphid to survive infection. However, it turns out that there is yet one more layer to this story, [more inside]
The Puzzle of Plastid Evolution: A comprehensive understanding of the origin and spread of plastids remains an important yet elusive goal in the field of eukaryotic evolution. Combined with the discovery of new photosynthetic and non-photosynthetic protist lineages, the results of recent taxonomically broad phylogenomic studies suggest that a re-shuffling of higher-level eukaryote systematics is in order. Consequently, new models of plastid evolution involving ancient secondary and tertiary endosymbioses are needed to explain the full spectrum of photosynthetic eukaryotes. [Full Text HTML] [Full Text PDF] [more inside]
Mitigating Mutational Meltdown in Mammalian Mitochondria PLoS Biol 6(2): e35. [The PDF, where you can read the paper in its much prettier intended format.]
Mitochondria are remarkable microorganisms. About two billion years ago, their distant free-living ancestors hooked up with a truly foreign lineage of archaebacteria and started a genomic merger that led to the most successful coevolved mutualism on the planet: the eukaryotic cell. Along the way, evolving mitochondria lost a lot of genomic baggage, entrusted their emerging hosts with their own replication, sorted out genomic conflicts by following maternal inheritance, and have mostly abstained from sex and recombination. What mitochondria did retain was a subset of genes that encode critical components of the electron transport chain and ATP synthesis enzymes that carry out oxidative phosphorylation. Because mitochondria house the biochemical machinery that requires us to breathe oxygen, it was first assumed that mitochondrial genes would show very slow rates of molecular evolution. So it was big news almost 30 years ago when mitochondrial DNA (mtDNA) evolution was observed to be quite rapid . How could the genes for a highly conserved and critical function sustain the consequences of high mutation pressure and permit rapid rates of nucleotide substitution between species? Without the benefits of recombination, where offspring can carry fewer mutations than either parent, mutations should accumulate in mitochondrial genomes through the random loss of less-mutated genomes, a process referred to as Muller's ratchet [2,3]. How have mitochondria avoided a mutational meltdown, or at least significant declines in fitness?Here is a jaw droppingly beautiful 3D animation of what Mitochindria look like in action. [more inside]
Constitutive formation of caveolae in a bacterium. [Full Text]
Caveolin plays an essential role in the formation of characteristic surface pits, caveolae, which cover the surface of many animal cells. The fundamental principles of caveola formation are only slowly emerging. Here we show that caveolin expression in a prokaryotic host lacking any intracellular membrane system drives the formation of cytoplasmic vesicles containing polymeric caveolin. Vesicle formation is induced by expression of wild-type caveolins, but not caveolin mutants defective in caveola formation in mammalian systems. In addition, cryoelectron tomography shows that the induced membrane domains are equivalent in size and caveolin density to native caveolae and reveals a possible polyhedral arrangement of caveolin oligomers. The caveolin-induced vesicles or heterologous caveolae (h-caveolae) form by budding in from the cytoplasmic membrane, generating a membrane domain with distinct lipid composition. Periplasmic solutes are encapsulated in the budding h-caveola, and purified h-caveolae can be tailored to be targeted to specific cells of interest.Elio Schaechter writes in plain English about how fantastically amazing and unexpected the researchers actually pulling this off is, and he also talks about it in more detail in his podcast.
Provirophages and transpovirons as the diverse mobilome of giant viruses
Abstract: A distinct class of infectious agents, the virophages1 that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome2 of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements3, the transpovirons4. The transpovirons are linear DNA elements of ∼7 kb [kilobases]5 that encompass six to eight protein-coding genes, two of which are homologous6 to virophage genes. Fluorescence7 in situ hybridization8 showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate9 in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns10 and inteins11 constitute the complex, interconnected mobilome12 of the giant viruses and are likely to substantially contribute to interviral gene transfer.[Full Text PDF] and two explanations in English [more inside]
Oldest message in a bottle found. The bottle was released as part of a research project tracking deep ocean currents. (Via socimages, via boingboing.)
Two elements: tempo and volume. Researchers at the Sundance Research Facility have finally discovered how to turn sound into matter.
You're about to be the base doctor at Halley Research Station in Antarctica for a year. For ten months, no one gets in or out. Fourteen lives are in your hands, including your own. What do you put in your medical kit? And how do your choices differ from those of your predecessors (Eric Marshall and Edward Wilson) a century ago?
The drugs don't work : a modern medical scandal - "The doctors prescribing the drugs don't know they don't do what they're meant to. Nor do their patients. The manufacturers know full well, but they're not telling."
A documentary by Adam Curtis on Henrietta Lacks and HeLa cell line created from her cells. Previously. Previously.
Have you ever wondered what the water temperature off the Kamchatka Peninsula is? What about the wind speed in the Andaman Sea? Or maybe you’re losing sleep over the chlorophyll levels in the South Pacific. Fortunately, all of that information –- and 450 million other data points collected from oceanographic instruments around the world –- is freely and easily accessible thanks to the Marinexplore project. [more inside]
There are fewer microbes out there than you think. New estimate reduces the number of microbes on Earth by around half. [more inside]
"The Heretic: For decades, the U.S. government banned medical studies of the effects of LSD. But for one longtime, elite researcher, the promise of mind-blowing revelations was just too tempting." [more inside]
Billy Joel has now officially endorsed - The Longest Time (Coral Triangle Edition), by the Barber Lab Quartet [more inside]
Does anesthesiology have a problem? Final version of report suggests Fujii will take retraction record, with 172
In the wake of a very thorough and damning statistical analysis of 168 of his papers, published in March, Japanese investigators have concluded that Yoshitaka Fujii, fabricated his results in at least 172 published studies; shattering the previous record for most retracted papers. Considered an expert in postoperative nausea and vomiting, his "incredibly nice" findings drew scrutiny in 2000, but he continued to publish prolifically for more than a decade. Here are the published results of the Japanese Society of Anesthesiology's Special Investigation Committee, with an annotated list of all of his papers (PDF). The Retraction Watch also considers not only the depth of Fujii's betrayal but also whether the discipline of anesthesiology itself has a problem as it weighs in. [more inside]
"You could turn your home into a battery," said researcher Neelam Singh. Researchers at Rice University have created paints that act as rechargeable lithium-ion batteries. They can be painted onto virtually any surface, and can be charged with a solar cell. Full paper.
“[...] it took more than a dozen calls to work out the details of her zombie contagion. “After about the 17th time,” says McGuire, “I called and said, ‘If I did this, this, this, this, this, this and this, could I raise the dead?’ And got, ‘Don’t … don’t do that.’ And at that point, I knew I had a viable virus.”
The U.S. National Institute of Heath has urged steps to curb growth in "training" positions in biomedical research (report). [more inside]
Are bias and fraud damaging the existing public trust in scientific and medical research? (previously) [more inside]
"Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets." After an extensive, months-long debate, one of two controversial papers showing ways the H5N1 "avian" influenza virus could potentially become transmissible in mammals with only 3 or 4 mutations was published in Nature today. The journal included an editorial on the merits and drawbacks of "publishing risky research" with regard to biosafety. The debate included an unprecedented recommendation by The US National Science Advisory Board for Biosecurity (NSABB) to block publication -- a decision they later reversed. (Via: 1, 2) Nature's special report has additional articles, including interviews with the teams behind both papers.
A researcher at St. Andrews University is using a tool called a densitometer to measure which pages in medieval manuscripts are the dirtiest, and therefore the most frequently read. The complete (and well-illustrated) study is available online from the Journal of Historians of Netherlandish Art. [more inside]
While growth prospects in the field are incredibly high, recent trends, such as "tools grow[ing] more advanced" (see Adobe Flash Builder or MS Visual Studio) have had people wondering over the past few years if computer science has much room for growth left. Some question whether it is alive. Others, such as Carnegie Mellon, say not so fast. In any case, employment has been a bit iffy (/.). There is the possibility that Computer Science is simply growing up (PDF), then again the U of Florida decided to say good bye to it this past week. But hey, if you are not going to that University, and still are shooting for computer science, here are some tips.
MIT is leading an NSF-funded project with researchers from University of Pennsylvania and Harvard that aims to enable anyone to "design, customize and print a specialized robot in a matter of hours." Constructed from "cyber-physical primitives," the robots (some early examples here) would be able to be made in bulk on demand and could help change the entire workflow of device and robot creation, from engineering to warehousing to assembly.
How Corporations Corrupt Science at the Public's Expense: Report looks at methods of corporate abuse, suggests steps toward reform [Full Report (PDF)] [Executive Summary (PDF)] [more inside]
The committee took the unprecedented step of recommending that some details of these biological studies [be] kept from the public, so that no one could use them as recipes for new bioweapons. [more inside]
Here are some evidence-based and research based psychotherapy modalities you may or may not have heard of, a few in the words of their creators: David Burns and CBT and T.E.A.M. Therapy [pdf], Steven Hayes and ACT (also), Marsha Linehan and DBT (also [pdf] and also [pdf]), Joseph Weiss and Control Mastery Theory (also), Eugene Gendlin and Focusing-Oriented Psychotherapy (also).
An experiment done in the 1990s exposed children to various levels of lead. The lawsuit filed in 2001 by the parents of over 100 participants accuses the Kennedy Krieger Institute that the scientists knowingly used the kids as test subjects in toxic dust control study. [more inside]
NASA May Have Discovered Flowing Water on Mars Dark, finger-like features appear and extend down some Martian slopes during late spring through summer, fade in winter, and return during the next spring. Repeated observations have tracked the seasonal changes in these recurring features on several steep slopes in the middle latitudes of Mars' southern hemisphere.
There is an European Commission budgetary proposal to boost E.U. funding for science and technology by 45% from €55B to €80B by trimming some fat form the controversial Common Agricultural Policy. [more inside]
The Beer Archaeologist. "Biomolecular archaeologist" Dr. Patrick McGovern has unearthed millennia-old alcohol recipes and ancient medicinals, "by analyzing residues in ancient pottery. Now he's working with brewer Sam Calagione, (of Discovery Channel's Brew Masters, (autoplaying video)) whose pub Dogfish Head serves up beers based on recipes that are thousands of years old." (Via) [more inside]
The Triumph of New-Age Medicine "Medicine has long decried acupuncture, homeopathy, and the like as dangerous nonsense that preys on the gullible. Again and again, carefully controlled studies have shown alternative medicine to work no better than a placebo. But now many doctors admit that alternative medicine often seems to do a better job of making patients well, and at a much lower cost, than mainstream care—and they’re trying to learn from it." [more inside]
Editors of the journal Science have asked the co-authors of a 2009 paper that linked chronic fatigue syndrome to a retrovirus called XMRV to voluntarily retract the paper. Science editor-in-chief Bruce Alberts and executive editor Monica Bradford cited concerns about the validity of the findings, saying other scientists hadn't been able to replicate them, among other reasons. [more inside]
Research Blogging is an aggregator for blog posts on peer-reviewed research. The posts are on various subjects, such as culinary trends in an extinct hominid , the distance and mass of Saggitarius A* and when chemists go to war
Statistical hypothesis testing with a p-value of less than 0.05 is often used as a gold standard in science, and is required by peer reviewers and journals when stating results. Some statisticians argue that this indicates a cult of significance testing using a frequentist statistical framework that is counterintuitive and misunderstood by many scientists. Biostatisticians have argued that the (over)use of p-vaues come from "the mistaken idea that a single number can capture both the long-run outcomes of an experiment and the evidential meaning of a single result" and identify several other problems with significance testing. XKCD demonstrates how misunderstandings of the nature of the p-value, failure to adjust for multiple comparisons, and the file drawer problem result in likely spurious conclusions being published in the scientific literature and then being distorted further in the popular press. You can simulate a similar situation yourself. John Ioannidis uses problems with significance testing and other statistical concerns to argue, controversially, that "most published research findings are false." Will the use of Bayes factors replace classical hypothesis testing and p-values? Will something else?
According to a new study from the UK's national science academy, the Royal Society, China is on course to outstrip US scientific output as earlier as two years from now. [SLBBC]
No Leftovers for Tyrannosaurus Rex: New Evidence That T. Rex Was Hunter, Not Scavenger [Full text] [more inside]
The Price of Altruism - George Price, a (troubled) father of group selection thru his discovery of the eponymous Price Equation, has a rather interesting biography... [more inside]
Inducement Prizes -- Best known for the Ansari X Prize, the DARPA Grand Challenge and the Clay Mathematics Millennium Problems, inducement prizes have a long history, but their recent successes have led to increased government interest, viz. challenge.gov, and resulted in the development of vaccines, thanks in large part to the work of Michael Kremer.* [more inside]