49239909
submission
Shipud writes:
In response to aphid attacks, some plants produce chemicals that repel the aphids and attract wasps, the aphids' natural enemies. Researchers at the University of Aberdeen have shown that plants attacked by aphids can communicate that information to neighboring plants via existing networks of fungi in the soil. Thus fungal symbiosis with plants is shown to be taken one step further: not only do they provide nutrients to plants, they also function as communication hardware.
47767797
submission
Shipud writes:
A recent study by a group at the University of Maryland School of Medicine shows that bacterial DNA gets transferred to human cells, in a process known as lateral gene transfer, or LGT. LGT is known to occur quite commonly between bacteria, including bacteria of different species. In fact, that is how antibiotic resistance is transferred so quickly. The team has shown that certain types of tumor cells acquire bacterial DNA that may play a role in tumor progression. Another group at the University of North Carolina, Chapel Hill has shown that gut inflammation leads to a radical change in the microbial population there, which encourages growth of E. coli that can disrupt the inflamed cells' DNA, leading to cancer. Both studies enable us to ask new questions such as: how does inflammation change the landscape for bacterial colonization? Can bacteria indeed harness inflammation — and then cancer — to flourish and remove competitors from their newly found ecosystem? And can we use this information to fight cancer?
45680499
submission
Shipud writes:
E.O. Wilson is the renowned father of sociobiology, a professor (emeritus) at Harvard, two time pulitzer prize winner, and a popularizer of science. In a recent article in the Wall Street Journal, Wilson provides controversial advice to aspiring young scientists. Wilson claims that math literacy is not essential, and that scientific models in biology, intuitively generated, can later be formalized by a specialized statistician. One blogger calls out Wilson on his article, arguing that knowing mathematics is essential to generating models, and that lacking what Darwin called the "extra sense" is essentially limiting to any scientist.
43096951
submission
Shipud writes:
Raytheon has secretly developed software capable of tracking people's movements and predicting future behaviour by mining data from social networking websites according to this story from The Guardian.
An "extreme-scale analytics" system created by Raytheon, the world's fifth largest defence contractor, can gather vast amounts of information about people from websites including Facebook, Twitter and Foursquare.
Raytheon says it has not sold the software – named Riot, or Rapid Information Overlay Technology – to any clients. But the company has acknowledged the technology was shared with US government and industry as part of a joint research and development effort, in 2010, to help build a national security system capable of analysing "trillions of entities" from cyberspace.
The power of Riot to harness popular websites for surveillance offers a rare insight into controversial techniques that have attracted interest from intelligence and national security agencies, at the same time prompting civil liberties and online privacy concerns.
42853611
submission
Shipud writes:
We live in the post-genomic era, when DNA sequence data is growing exponentially. However, for most of the genes that we identify, we have no idea of their biological functions. They are like words in a foreign language, waiting to be deciphered. The Critical Assessment of Function Annotation, or CAFA, is a new community-wide experiment to assess the performance of the multitude of computational methods developed by research groups worldwide to help channel the flood of data from genome research to deduce the function of proteins.
Thirty research groups participated in the first CAFA, presenting a total of 54 algorithms. The results are published in an article in Nature Methods. The researchers participated in blind-test experiments in which they predicted the function of protein sequences for which the functions are already known but haven't yet been made publicly available. Independent assessors then judged their performance. The challenge organizers explain that: 'The accurate annotation of protein function is key to understanding life at the molecular level and has great biochemical and pharmaceutical implications, explain the study authors; however, with its inherent difficulty and expense, experimental characterization of function cannot scale up to accommodate the vast amount of sequence data already available.The computational annotation of protein function has therefore emerged as a problem at the forefront of computational and molecular biology.'
38341231
submission
Shipud writes:
Bioinformatics science which deals with the study of methods for storing, retrieving and analyzing molecular biology data. Byte Size Biology writes about ROSALIND, a cool concept in learning bioinformatics, similar to Project Euler. You are given problems of increasing difficulty to solve. Start with nucleotide counting (trivial) and end with genome assembly (putting it mildly, not so trivial). To solve a problem, you download a sample data set, write your code and debug it. Once you think you are ready, you have a time limit to solve and provide an answer for the actual problem dataset. If you mess up, there is a timed new dataset to download. This thing is coder-addictive. Currently in Beta, but a lot of fun and seems stable.
34254923
submission
Shipud writes:
A collaboration between a group in Imperial College and Media Interaction group in Japan yielded a really cool website: darwintunes.org. The idea is to apply Darwinian-like selection to music. Starting form a garble, after several generations producing something that is actually melodic and listen-able. The selective force being the appeal of the tune to the listener. From the paper published yesterday in the Proceedings of the National Academy of Sciences:
"At any given time, a DarwinTunes population
has 100 loops, each of which is 8 s long. Consumers ratethem on a five-point scale (“I can’t stand it” to “I love it”) as they are streamed in random order. When 20 loops have been rated,truncation selection is applied whereby the best 10 loops are paired, recombine, and have two daughters each."
Note that in 2009 the creators of darwintunes harnessed the power of slashdot to help "evolve" their site.
34131639
submission
Shipud writes:
Sequencing the genome of an organism is not the end of a discovery process; rather, it is a beginning. It's the equivalent of discovering a book whose words (genes) are there, but their meaning is yet unknown. Biocurators are the people who annotate genes — find out what they do — through literature search and the supervised use of computational techniques. A recent study published in PLoS Computational Biology shows that biocurators probably perform no better than fully automated computational methods used to annotate genes. It is not clear whether this is because the software is of high quality, or both curators and software need to improve their performance. The author of this blog post uses the concept of the uncanny valley to explain this recent discovery and what it means to both life science and artificial intelligence.
29163843
submission
Shipud writes:
A recent article in Journal of Biomolecular structure and Dynamics proposes to define life by semantic voting: "The denitions of life are more than often in conict with one another. Undeniably, however, most of them do have a point, one or another or several, and common sense suggests that, probably, one could arrive to a consensus, if only the authors, some two centuries apart from one another, could be brought together. One thing, however, can be done – sort of voting in absentia – asking which terms in the denitions are the most frequent and, thus, perhaps, reecting the most important points shared by many." The author arrives at a six word definition, as explained here.
28003736
submission
Shipud writes:
Insulin resistance is the harbringer of metabolic syndrome. Insulin resistance is when the body cannot use insulin effectively. As a result, blood sugar and fat levels rise. Therein lies the path to morbid obesity, diabetes, stroke, and heart problems. A group of Brazilian researchers have taken a strain of mice normally known to be immune to insulin resistance, and made them insulin resistant (pre-diabetic) by changing their gut bacteria. They then gave the mice antibiotics, and by changing their gut bacteria again, reversed the process curing them of the disease. Their research shows just how influential the bacteria living in our gut can be on our health.
26723976
submission
Shipud writes:
Holland was recently in the news when a psychology professor in Tilburg University was found to have committed large-scale fraud over several years.
Now, another Dutch psychologist is suggesting a way to avert these sort of problems, namely by "sharing early and sharing often", since fraud may start with small indiscretions due to career-related pressure to publish. In Wilchert's study, he requested raw data from the authors of some 49 papers. He found that the authors’ reluctance to share data was associated with "more errors in the reporting of statistical results and with relatively weaker evidence (against the null hypothesis). The documented errors are arguably the tip of the iceberg of potential errors and biases in statistical analyses and the reporting of statistical results. It is rather disconcerting that roughly 50% of published papers in psychology contain reporting errors and that the unwillingness to share data was most pronounced when the errors concerned statistical significance."
21931730
submission
Shipud writes:
The Max Planck society, Howard Hughes Medical Institute and Wellcome Trust have announced their plans for a new journal for biomedical and life science research to be launched summer 2012. From the joint press release: "The journal will employ an open and transparent peer review process in which papers will be accepted or rejected as rapidly as possible, generally with only one round of revisions, and with limited need for modifications or additional experiments. For transparency, reviewers’ comments will be published anonymously."
The journal will be online-only and open access too, and they promise ”an opportunity to create a journal and article format that will exploit the potential of new technologies to allow for improved data presentation.” Especially valuable is the “limited need for modifications or additional experiments”, especially since even Nature has recently published a scathing opinion piece about reviewers’ almost reflexive demands for additional experiments from manuscript authors.
21407682
submission
Shipud writes:
The National Academies Press (USA) are offering all their books for free in PDF format. These are all the publications of the National Academy of Sciences, National Academy of Engineering, Institute of Medicine, and National Research Council. Lots of great stuff there, and now for free.
11998722
submission
Iron Nose writes:
The pea aphid is known for having two different colors: green and red, but until now it was not very clear though how the aphids got their color. Aphids feed on sap, and sap does not contain carotenoids: a common pigment synthesized by plants, fungi and microbes, but not by animals. Carotenoids in the diet gives many animals, from insects to flamingos, their exterior color after they ingest it, but aphids do not seem to eat carotenoid-containing food. Nancy Moran and Tyler Jarvik from the University of Arizona looked at the recently sequenced genome of the pea aphid. They were surprised to find genes for synthesizing carotenoids: this is the first time carotenoid synthesizing genes were found in animals. The question they naturally asked is "where did those genes come from?" The animal kingdom does not contain genes for making carotenoids, so how come aphids have them? Indeed, when they looked for the most similar genes to the aphid carotenoid synthesizing genes they found that they came from fungi, which means they somehow jumped between fungi and aphids, in a process known as horizontal gene transfer. Byte Size Biology has the full story.
9587258
submission
TinFinger writes:
The genome of a 5,000 year old man from Greenland has been sequenced from scalp hair remains. He belonged to the now-extinct Saqqaq who are genetically more closely related to east Asians than to contemporary Native North Americans. Although both contemporary Inuit and the extinct Saqqaq migrated from Siberia across the Bering Straits, the Saqqaq migration was a much later one (5,000-10,000 years ago, compared with 20,000 for the Inuit). All that is left of the Saqqaq today are a few archaeological sites in Greenland. Genetic analysis revealed that "Inuk" was stocky, possibly with a receding hairline, had a cold-adapted metabolism, A+ blood type, and possibly a rather bad haircut.
The hair sample form which the DNA was sequenced was excavated in 1986 and was archived at the National Museum of Denmark. It was only recently rediscovered by a research team who spent a fruitless 3 months at Saqqaq sites looking for hair samples for genome analysis.
