neoritter writes: The issues of reproducibility in journals continues to present problems. This time in the world of clinical geneticists where a misleading or incorrect journal on the effect of a gene variant can affect the decisions made by doctors and patients alike; from heart monitoring implants to abortions. Poor sampling and low thresholds for evidence have led some clinical geneticists to work towards an open database of genetic information. Scientists and doctors would go to a "one-stop shop for disease genes" to check and share information with each other under the strictest of standards.

HughPickens.com writes: Lisa Jenning reports at Restaurant News that Chipotle plans to do DNA-based tests of all fresh produce before it is shipped to restaurants. The Centers for Disease Control and Prevention says that the E. coli outbreak linked to Chipotle now includes seven more people in three new states, including Illinois, Maryland and Pennsylvania, for a total count of 52 sickened in nine states. Most of the illnesses were in Washington, with 27 cases, and Oregon, with 13 cases. Twenty people have been hospitalized but there have been no reported deaths. Health officials say a meal or ingredient from Chipotle was likely the cause, but they have not yet identified the specific source of the outbreak. Chipotle's founder and co-chief executive, Steve Ells apologized to patrons who fell ill after eating at the company's restaurants. "This was a very unfortunate incident and I'm deeply sorry that this happened, but the procedures we're putting in place today are so above industry norms that we are going to be the safest place to eat." The chain will begin end-of-shelf-life testing to ensure quality specifications are met throughout the shelf life of products. The data collected will be used to measure the performance of vendors and suppliers to enhance food safety throughout the system.

But food safety experts are mixed about the effectiveness of such screening efforts for the prevention of foodborne illness. Bob Whitaker, chief science and technology officer for the Produce Marketing Association, says such tests are not practical as a screening tool. Instead, restaurant chains should focus on whether their suppliers have adequate food-safety programs in place. "You can't test your way to safety," says Whitaker. "The problem with product testing by itself is that it's hard to take enough samples to be confident that the product is free of any pathogens." DNA tests are considered among the most accurate and fast, with same-day testing available for organisms like E. coli or salmonella, says Morgan Wallace. Some manufacturers don't wait for results, since produce is perishable, but that introduces the risk of a produce recall if a pathogen has been identified after shipment. Others hold the product until test results are confirmed, but that practice adds holding costs and reduces the shelf life.

TheAlexKnapp writes: In a recent paper (abstract), a team used techniques from computational topology to look at the neural activity in the rat hippocampus as it solved a maze. Mathematician Kevin Knudson explains the findings: "This is the first time geometric structure has been found intrinsically in neural data. Certainly such a structure is to be expected since the rat's place cells keep track of the geometry of the environment, but this result is confirmation that it can be detected using only the pattern of correlations among the neurons. And it suggests that such geometric structure is a property of the underlying place cell network and not a result of the spatial structure of the input cells."

schwit1 writes with news that using gene editing technology researchers have bred pigs that do not produce a protein necessary for the Porcine Reproductive and Respiratory Syndrome (PRRS) virus to spread. According to Reuters: "A British animal genetics firm, working with U.S. scientists, has bred the world's first pigs resistant to a common viral disease, using the hot new technology of gene editing. Genus, which supplies pig and bull semen to farmers worldwide, said on Tuesday it had worked with the University of Missouri to develop pigs resistant to Porcine Reproductive and Respiratory Syndrome Virus (PRRSv). The condition, also known as blue-ear disease, can be fatal as it affects the animals' immune system and costs farmers hundreds of millions of dollars a year. There is no cure. By using precise gene editing, the team from the University of Missouri was able to breed pigs that do not produce a specific protein necessary for the virus to spread in the animals. Their research was published in journal Nature Biotechnology."

Eloking sends a report on new research from MIT, where scientists have developed a promising technique to shrink cancerous tumors. By "twisting RNA strands into a triple helix and embedding them in a biocompatible gel," they were able to efficiently deliver the RNA to tumor cells. "Using this technique, the researchers dramatically improved cancer survival rates by simultaneously turning on a tumor-suppressing microRNA and de-activating one that causes cancer. They believe their approach could also be used for delivering other types of RNA, as well as DNA and other therapeutic molecules. ... Once placed on the tumor, the gel slowly releases microRNA-dendrimer particles, which are absorbed into the tumor cells. After the particles enter the cells, enzymes cut each triple helix into three separate microRNA strands."

Josiah Zayner, a research fellow at NASA Ames Research Center, is running an Indiegogo campaign to make DIY gene editing kits that use the CRISPR technique to modify DNA. The campaign has already exceeded its goal, and he points out an article at Motherboard noting the controversy surrounding cheap, DIY genetic modification. Quoting:The kits won't going to allow people to genetically modify humans, but Zayner is still getting some heat for the project. One medical doctor emailed him with "grave concerns" about putting the technology in the hands of lay people. "Reprogramming bacteria or fungi could have serious ramifications, such as inadvertent or intended multi-drug resistance, faster multiplication, toxin production, and persisting potency when aerosolized," the doctor wrote. ... There is no legal framework surrounding this at-home work, unless it results in a product to be distributed, said Todd Kuiken, a senior program associate with the Synthetic Biology Project at the Woodrow Wilson International Center for Scholars. "Who actually uses kits like these and what they are using them for will determine if any of these products they make would be regulated or not," he said.

transporter_ii writes: Scientists from University College London seem to have come up with a two-pronged treatment regimen they believe would help patients suffering from chronic pain. And in a strange irony, they did it by making it possible for mice – and one human – to feel pain when they previously couldn't. From the story: "To examine if opioids were important for painlessness, the researchers gave naloxone, an opioid blocker, to mice lacking Nav1.7 and found that they became able to feel pain. They then gave naloxone to a 39-year-old woman with the rare mutation and she felt pain for the first time in her life. 'After a decade of rather disappointing drug trials, we now have confirmation that Nav1.7 really is a key element in human pain,' says senior author Professor John Wood (UCL Medicine). 'The secret ingredient turned out to be good old-fashioned opioid peptides, and we have now filed a patent for combining low dose opioids with Nav1.7 blockers. This should replicate the painlessness experienced by people with rare mutations, and we have already successfully tested this approach in unmodified mice.'"

trbdavies writes: Reporting from the CRISPR (clustered regularly interspaced short palindromic repeats) gene-editing summit in D.C., the Washington Post quotes Harvard genetics professor George Church as expressing "confidence that in just five or six years he will be able to reverse the aging process in human beings." He says: "A scenario is, everyone takes gene therapy — not just curing rare diseases like cystic fibrosis, but diseases that everyone has, like aging," CRISPR is a powerful technology, but many at the summit have expressed caution about both the ethics and the feasibility of using it to cure disease. The story quotes Klaus Rajewsky, of the Max Delbruck Center for Molecular Medicine saying "We have become masters in the art of manipulating genes, but our understanding of their function and interaction is far more limited."

An anonymous reader sends word that a three-day summit has begun in Washington to discuss the future of genetic engineering. It has a particular focus on the CRISPR technique, which has made gene editing quicker and more robust than ever before. "The reason CRISPR is so controversial is that it works well on 'germline' cells, such as sperm, eggs and embryonic cells, and the genetic editing results in heritable traits. Many scientific organizations have called for a time-out on any experiments on human cells, fearing that this crosses into dicey ethical territory. This meeting in Washington could potentially generate a new call for restraint, or some guidelines in how to handle the explosive technology." Many scientists, lawyers, and policymakers are present at the summit to try to reach consensus on how the scientific community should proceed with such research, and how the fruits of their research should be used. Professor Alta Charo said, "The more we can have effective systems for responsible oversight for the development and deployment of a technology, the more we can take chances. We have the chance to back up at the end, and change course."

AmiMoJo writes: Omikenshi Co, an Osaka based cloth manufacturer best known for rayon, a fibre made from tree pulp, is expanding into the health food business. Using a similar process, Omikenshi is turning the indigestible cellulose into a pulp that's mixed with konjac, a yam-like plant grown in Japan. The resulting fibre-rich flour, which the company calls "cell-eat," contains no gluten, no fat and almost no carbohydrate. It has just 60 calories a kilogram, compared with 3,680 for wheat.

Lucas123 writes: University of Buffalo physicians and researchers from two institutes working with 3D printer maker Stratasys have successfully 3D-printed anatomically correct models of patients' vascular systems — from their femoral artery to their brain — in order to test various surgical techniques prior to an actual operation. The new 3D printed models not only precisely replicate blood vessels' geometry, but the texture and tissue tension, allowing surgeons a realistic preoperative experience when using catheterization techniques. The printed models are also being used by physicians in training.

sciencehabit writes: The war against malaria has a new ally: a controversial technology for spreading genes throughout a population of animals. Researchers report today that they have harnessed a so-called gene drive to efficiently endow mosquitoes with genes that should make them immune to the malaria parasite—and unable to spread it. On its own, gene drive won't get rid of malaria, but if successfully applied in the wild the method could help wipe out the disease, at least in some corners of the world. The approach "can bring us to zero [cases]," says Nora Besansky, a geneticist at the University of Notre Dame in South Bend, Indiana, who specializes in malaria-carrying mosquitoes. "The mosquitoes do their own work [and] reach places we can't afford to go or get to."

New submitter radaos writes: A gene enabling resistance to polymyxins, the antibiotics of last resort, has been found to be widespread in pigs and already present in some hospital patients. The research, from South China Agricultural University, has been published in The Lancet. According to research Jian-Hua Liu, "Our results reveal the emergence of the first polymyxin resistance gene that is readily passed between common bacteria such as Escherichia coli and Klesbsiella pneumoniae, suggesting that the progression from extensive drug resistance to pandrug resistance is inevitable." Work on alternatives is progressing — Dr. Richard James, former director of the University of Nottingham's center for healthcare associated infections, writes, "Until last month I was still pessimistic about our chances of avoiding the antibiotics nightmare. But that changed when I attended a workshop in Beijing on a new approach to antibiotic development based on bacteriocins – protein antibiotics produced by bacteria to kill closely related species, and exquisitely narrow-spectrum."

sciencehabit writes: Researchers have crafted flexible electronic circuits inside a rose. Eventually such circuitry may help farmers eavesdrop on their crops and even control when they ripen. The advance may even allow people to harness energy from trees and shrubs not by cutting them down and using them for fuel, but by plugging directly into their photosynthesis machinery. The researchers used "an organic electronic building block called PEDOT-S:H. Each of these building blocks consists of a short, repeating chain of a conductive organic molecule with short arms coming off each link of the chain. Each of the arms sports a sulfur-containing group linked to a hydrogen atom. Berggren's group found that when they placed them in the water, the rose stems readily pulled the short polymer chains up the xylem channels (abstract). ... The upshot was that the myriad short polymer chains quickly linked themselves together into continuous strings as long as 10 centimeters. The researchers then added electronic probes to opposite ends of these strings, and found that they were, in fact, wires, conducting electricity all down the line."

sciencehabit writes that tissue engineers have for the first time grown vocal cords from human cells. Science reports: "For the first time, scientists have created vocal cord tissue starting with cells from human vocal cords. When tested in the lab, the bioengineered tissue vibrated—and even sounded—similar to the natural thing. The development could one day help those with severely damaged vocal cords regain their lost voices. 'It’s an exciting finding because those patients are the ones we have very few treatment options for,' says Jennifer Long, a voice doctor and scientist at the University of California, Los Angeles, head and neck surgery department, who wasn’t involved in the study."

Zothecula writes: In a world where lasers are sci-fi's weapon of choice for melting away an enemy spaceship, researchers at the University of Washington have swum against the current and produced the first laser capable of cooling liquids. " They demonstrated that the laser could refrigerate saline solution and cell culture media that are commonly used in genetic and molecular research. To achieve the breakthrough, the UW team used a material commonly found in commercial lasers but essentially ran the laser phenomenon in reverse. They illuminated a single microscopic crystal suspended in water with infrared laser light to excite a unique kind of glow that has slightly more energy than that amount of light absorbed. This higher-energy glow carries heat away from both the crystal and the water surrounding it." The technology could be especially useful for slowing down single cells and allowing scientists to study biological processes as they happen.

schwit1 writes with news that researchers at the Salk Institute have found that an experimental drug candidate aimed at combating Alzheimer's disease has a host of unexpected anti-aging effects in animals. Says the article: The Salk team expanded upon their previous development of a drug candidate, called J147, which takes a different tack by targeting Alzheimer's major risk factor–old age. In the new work, the team showed that the drug candidate worked well in a mouse model of aging not typically used in Alzheimer's research. When these mice were treated with J147, they had better memory and cognition, healthier blood vessels in the brain and other improved physiological features.

"Initially, the impetus was to test this drug in a novel animal model that was more similar to 99 percent of Alzheimer's cases," says Antonio Currais, the lead author and a member of Professor David Schubert's Cellular Neurobiology Laboratory at Salk. "We did not predict we'd see this sort of anti-aging effect, but J147 made old mice look like they were young, based upon a number of physiological parameters."

sciencehabit writes: A controversial fertility company called OvaScience is preoccupied by an enduring mystery in human biology--why eggs fail--and the palpable hope that we can do something about it. The company offers a new treatment, called AUGMENT, based on what it considers to be egg precursor cells found in a woman's ovaries. AUGMENT, which costs UP TO $25,000, along with thousands more in clinic fees and roughly $25,000 for the IVF cycle that must accompany it, relies on mitochondria from putative egg precursor cells to boost the success of in vitro fertilization (IVF). Seventeen babies have been born so far. The company, which has attracted hundreds of millions of dollars from investors, is poised to introduce a second treatment. But many scientists doubt that egg precursor cells actually exist.

"With much fanfare," writes an anonymous reader, "last month 23andMe returned to reporting health information to their genetic service customers. How does their new service stack up?" According to the Enlis Genomics Blog, it's a good move but not perfect. The linked post explains that "the raw data from 23andMe contains significantly more health information than they are reporting in their health reports," and says "23andme has a long way to go to get back to reporting the same number of variants they were before the FDA ban. However – both the previous and new 23andMe reports pale in comparison to an analysis of the raw data. 23andMe’s new reports tell you about less that 1% of the health-related variants that are in their raw data." It's an interesting statistical blow-by-blow; the company making the comparison has a vested interest in you letting them run the numbers, but is not the only option.

citadrianne writes: New antibiotics are generated naturally over time by bacteria, as weapons in their ongoing chemical warfare against other microbes. Predicting where and when they can be found relies mostly on good fortune and following a hunch. Scientist Brian Murphy's hunch is that the bacteria which live on freshwater sponges could be a hive of new chemicals. "We don’t know a huge amount about these species," he said. "But the only way to find out if there’s anything there is by actually diving down there and carving them off with a knife." But even if these sponges yield the antibiotics of the future, there are seemingly endless roadblocks that prevent us from actually using them to cure disease. "We've discovered six antibiotics in the recent past," Professor William Fenical said. "Of those, three to four have serious potential as far as we know, including anthramycin. But we have no way to develop them. There are no companies in the United States that care. They're happy to sell existing antibiotics, but they're not interested in researching and developing new ones."