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Domain: bytesizebio.net
Stories and comments across the archive that link to bytesizebio.net.
Stories · 18
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Plants Communicate Using Fungi
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." -
New Links Found Between Bacteria and Cancer
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?" -
Terrible Advice From a Great Scientist
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." -
ROSALIND: An Addictive Bioinformatics Learning Site
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." -
Computers May Be As Good As (Or Better Than) Human Biocurators
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." -
Boiling Down the Meaning of Life
Shipud writes "A recent article in Journal of Biomolecular structure and Dynamics proposes to define life by semantic voting [Note: open-access article]: 'The definitions of life are more than often in conflict 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 – short of voting in absentia – asking which terms in the definitions are the most frequent and, thus, perhaps, reflecting the most important points shared by many.' The author arrives at a six-word definition, as explained here." -
Gut Bacteria Can Control Diabetes
Shipud writes "Insulin resistance is the harbinger 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." -
Research Data: Share Early, Share Often
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.'" -
New Top Tier Science Journal Announced
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." -
Aphid's Color Comes From a Fungus Gene
Iron Nose writes with an account from Byte Size Biology of horizontal gene transfer from a fungus to an insect. The author suspects that we will see lots more of this as we sequence more genomes. "The pea aphid is known for having two different colors, green and red, but until now it was not clear 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 have been found in animals. When the researchers 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." -
Greenlander's DNA Sequenced, After 5,000 Years
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 from 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 three months at Saqqaq sites looking for hair samples for genome analysis." -
The Journal of Serendipitous and Unexpected Results
SilverTooth writes "Often, when watching a science documentary or reading an article, it seems that the scientists were executing a well-laid out plan that led to their discovery. Anyone familiar with the process of scientific discovery realizes that is a far cry from reality. Scientific discovery is fraught with false starts and blind alleys. As a result, labs accumulate vast amounts of valuable knowledge on what not to do, and what does not work. Trouble is, this knowledge is not shared using the usual method of scientific communication: the peer-reviewed article. It remains within the lab, or at the most shared informally among close colleagues. As it stands, the scientific culture discourages sharing negative results. Byte Size Biology reports on a forthcoming journal whose aim is to change this: the Journal of Serendipitous and Unexpected Results. Hopefully, scientists will be able to better share and learn more from each other's experience and mistakes." -
Unicellular "Enigma" Changes From Predator To Plant and Back
SilverEar writes "Imagine a creature that swims and preys on others, but once it eats a certain kind of plant, that plant grows inside it, causing the predator to lose its ability to prey and start using sunlight to make its food. Its preying mouth is replaced by an eye that is needed to find sunlight. This is the Hatena ('enigma' in Japanese). The kicker: when Hatena reproduces, one offspring is a peaceful photosynthesizer with the sun-seeking eye, while the other is yet again a predator with a voracious mouth." -
The Incredible Shrinking Genome
Shipud writes "Mammalian genomes have been shrinking for about 65 million years, roughly since the dinosaur extinction. Why? And why were ancient mammalian genomes three times larger than they are today? A new article in Genome Biology and Evolution tries to explain this bizarre finding, and why the genomes of mammals (but not of other living groups) are still shrinking. 'Once [the dinosaurs] were gone, mammals started to radiate, fill those niches, and a whole new level of competition arose. The selective advantage of not having a genome encumbered by potentially damaging mobile DNA elements has probably become critical at this "be ye fruitful and multiply; bring forth abundantly in the earth, and multiply therein" stage. In effect, the genomes of mammals has been shrinking by removing mobile DNA elements, just after the KT boundary. And according to the model presented in this study, this process is still ongoing: mammalian genomes are not at an equilibrium size. Unlike flies, mammals are still cleaning up.'" -
Cells May Communicate Through Light
SilverLobe writes "The hypothesis that living cells may use photons for communications has been on the fringes of cell biology for a while. No proof positive exists, but there is some strong circumstantial evidence. Byte Size Biology reports on a simple experiment that shows how the unicellular protozoan Paramecium may use so called 'biophotons' to signal for growth and feeding. The original academic paper in PLoS ONE concludes: '... not all cellular processes are necessarily based on a molecule-receptor recognition. The non-molecular signals are most probably photons. If so, cells use more than one frequency for information transfer and mutual influence.'" -
Test Driving the Wolfram Alpha
SilverMind writes in to note a blog entry at Byte Size Biology describing in detail a few hours spent with Wolfram Alpha (which we have discussed before). "After playing around with Wolfram Alpha for a few hours, I can safely say the following: it's different, it's incomplete, it's idiosyncratic, and it's funky cool. And no, it will not dethrone Google, nor does it aim to do so." -
Every Man Is an Island (of Bacteria)
Shipud writes "There are ten times more bacterial cells in our body than our own cells. Most of them are located in our guts, and they affect our well-being in many ways. A group at Washington University has recently reported that although our gut microbes perform similar functions, it appears that different people have completely different compositions of gut bacteria: every man is an island, a unique microbial ecosystem composed of completely different species. One conclusion is that the whole division of bacteria into species may well be over-used in biomedicine." -
Every Man Is an Island (of Bacteria)
Shipud writes "There are ten times more bacterial cells in our body than our own cells. Most of them are located in our guts, and they affect our well-being in many ways. A group at Washington University has recently reported that although our gut microbes perform similar functions, it appears that different people have completely different compositions of gut bacteria: every man is an island, a unique microbial ecosystem composed of completely different species. One conclusion is that the whole division of bacteria into species may well be over-used in biomedicine."