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Submission + - Most popular human cell in science gets sequenced (nature.com)

ananyo writes: "The research world’s most famous human cell has had its genome decoded, and it’s a mess. German researchers this week report the genome sequence of the HeLa cell line, which originates from a deadly cervical tumor taken from a patient named Henrietta Lacks (Slashdot has previously noted a film made about the cells and there's a recent mutli-award winning book on Lacks). Established the same year that Lacks died in 1951, HeLa cells were the first human cells to grow well in the laboratory. The cells have contributed to more than 60,000 research papers, the development of a polio vaccine in the 1950s and, most recently, an international effort to characterize the genome, known as ENCODE. The team's work shows that HeLa cells contain one extra version of most chromosomes, with up to five copies of some, and raises further questions over the widespread use of HeLa cells as models for human cell biology."

Submission + - Salt linked to autoimmune diseases (nature.com) 1

ananyo writes: "The incidence of autoimmune diseases, such as multiple sclerosis and type 1 diabetes, has spiked in developed countries in recent decades. In three studies published today, researchers describe the molecular pathways that can lead to autoimmune disease and identify one possible culprit that has been right under our noses — and on our tables — the entire time: salt. Some forms of autoimmunity have been linked to overproduction of TH17 cells, a type of helper T cell that produces an inflammatory protein called interleukin-17. Now scientists have found sodium chloride turns on the production of these cells. They also showed that in a mouse model of multiple sclerosis, a high-salt diet accelerated the disease’s progression."

Submission + - Monsanto's 'terminator' seeds set to make a comeback (nature.com)

ananyo writes: "Monsanto and other biotechnology firms could be looking to bring back 'terminator' seed technology. The seeds are genetically engineered so that crops grown from them produce sterile seed and prompted such an outcry that, as slashdot noted, Monsanto's chief executive pledged not to commercialize them. But a case in the US Supreme Court could allow farmers to plant the progeny of GM seeds rather than buying new seeds from Monsanto, making the technology attractive to biotech companies again. Some environmentalists also see 'terminator' seeds as a way of avoiding GM crops contaminating organic/non-GM crops."

Submission + - Living cells turned into computers (nature.com) 2

ananyo writes: Synthetic biologists have developed DNA modules that perform logic operations in bacteria. These ‘genetic circuits’ could, for example, be used by scientists to track key moments in a cell’s life or, in biotechnology, to turn on production of a drug at the flick of a chemical switch. The researchers have encoded 16 logic gates in modules of DNA and stored the results of logical operations. The different logic gates can be assembled into a wide variety of circuits.

Submission + - Researchers marshal technology in bid to thwart coffee rust (nature.com)

ananyo writes: "As one of the most severe outbreaks of 'coffee rust' ever rages through Central America, researchers are reaching for the latest tools in an effort to combat the fungus, from sequencing its genome to cross-breeding coffee plants with resistant strains.
Caused by the fungus Hemileia vastatrix, coffee rust generally does not kill plants, but the Institute of Coffee of Costa Rica estimates that the latest outbreak may halve the 2013–14 harvest in the worst affected areas of the nation. The fungus also wiped out coffee production in Sri Lanka in 1869 (it's why the country switched from producing coffee, to the tea it's known for today).
This outbreak is “the worst we’ve seen in Central America and Mexico since the rust arrived” in the region more than 40 years ago, says John Vandermeer, an ecologist at the University of Michigan in Ann Arbor, who has received “reports of devastation in Nicaragua, El Salvador and Mexico”.
By supporting research into resistant strains and the genetics of the pest, together with improved weather monitoring to help predict rust outbreaks, Colombia is closest to bringing the fungus under control. Other countries in the region are struggling, suggesting many slashdotters favourite brew could get pricey next year."


Submission + - Molecular robot mimics life's protein-builder (nature.com)

ananyo writes: "The ribosome, the molecular machine that translates our genetic code to build the body’s proteins, is a mechanical marvel. Now, chemists have invented a nanomachine that can achieve a similar feat.
The artificial system is not about to displace nature’s ribosome, a complex of proteins and RNA. It is much simpler, and only about about one-tenth of the size — and, it is achingly slow, destroys the code it reads and can produce only very short chunks of protein, known as peptides. It does, however, show that some of the tactics of biology’s molecular machines can be adopted to make useful chemicals.
The device relies on a rotaxane — a large molecular ring threaded onto another molecule that acts as an axle. The axle is lined with three amino acids, and a chain of three more amino acids hangs from the outer edge of the ring. Heating the device prompts the ring to move along the axle, adding amino acids one-by-one to the chain attached to the ring."


Submission + - Fast DNA origami opens way for nanoscale machines (nature.com)

ananyo writes: "DNA strands can be coaxed to fold up into shapes in a matter of minutes, reveals a study published in Science. The finding could radically speed up progress in the field of DNA origami.
DNA origami involves using short DNA strands to hold a longer, folded strand in place at certain points, like sticky tape. Until now, assembling the shape has involved heating the DNA and allowing it to cool slowly for up to a week. But researchers at the Technical University of Munich in Germany have worked out that for most of the cooling period, nothing happens. But when a crucial temperature is reached, the whole structure forms suddenly (abstract).
The researchers now aim to design nanostructures with optimal folding temperatures close to 37 C, the temperature at which mammalian cell cultures are grown, so that DNA machines could one day be used in biological settings."


Submission + - DNA sequencers stymie spread of MRSA (nature.com)

ananyo writes: "A superbug outbreak that plagued a special-care neonatal unit in Cambridge, UK, for several months last year was brought to an end by insights gained from genome sequencing. The case, reported in Lancet Infectious Disease (abstract), marks the first time that scientists have sequenced pathogen genomes to actively control an ongoing outbreak.
Sharon Peacock, a clinical microbiologist at the University of Cambridge, and her team became involved in the outbreak after three infants at nearby Rosie Hospital’s 24-cot special-care baby unit tested positive for methicillin-resistant Staphylococcus aureus (MRSA) within a couple days of each other.
The ward was sterilized but another baby tested positive for MRSA just days later. Confronted with an ongoing outbreak, the researchers cast their net wider, searching for the outbreak strain among the 154 workers on the baby unit. One tested positive for a matching MRSA strain, despite showing no symptoms. The employee was 'decolonized' by extensive washing with topical antibiotics and the outbreak stopped."


Submission + - Proteins made to order (nature.com)

ananyo writes: "Proteins are an enormous molecular achievement: chains of amino acids that fold spontaneously into a precise conformation, time after time, optimized by evolution for their particular function. Yet given the exponential number of contortions possible for any chain of amino acids, dictating a sequence that will fold into a predictable structure has been a daunting task.
Now researchers report that they can do just that. By following a set of rules described in a paper published in Nature (abstract), a husband and wife team from David Baker’s laboratory at the University of Washington in Seattle has designed five proteins from scratch that fold reliably into predicted conformations. The work could eventually allow scientists to custom design proteins with specific functions."


Submission + - DNA-swap technology almost ready for fertility clinic (nature.com)

ananyo writes: "Researchers say that technology to shuffle genetic material between unfertilized eggs is ready to make healthy babies. The technique could allow parents to minimize the risk of a range of diseases related to defects in the energy-producing cell organelles known as mitochondria.
Mitochondrial defects affect an estimated 1 in 4,000 children, and can cause rare and often fatal diseases such as carnitine deficiency, which prevents the body from using fats for energy.
Mitochondria have their own DNA and are inherited only from the mother, so replacing defective mitochondria in eggs from mothers who have a high risk of passing on such diseases could spare the children.
A team of researchers has now emoved the nucleus from an unfertilized human egg, leaving behind all of that cell’s mitochondria, and injected it into another unfertilized egg that had had its nucleus removed. They then fertilized the egg in vitro and allowed the embryos to develop to the blastocyst stage — a ball of about 100 cells. The cells looked like those from normal embryos, but with mitochondria exclusively from the donor (abstract)."


Submission + - Lab-made eggs produce healthy mice (nature.com)

ananyo writes: "Japanese researchers have coaxed mouse stem cells into becoming viable eggs that produce healthy offspring. Last year, the same team successfully used mouse stem cells to make functional sperm (other groups have produced sperm cells in vitro).
The researchers used a cocktail of growth factors to transform stem cells into egg precursors. When they added these egg precursor cells to embryonic ovary tissue that did not contain sex cells, the mixture spontaneously formed ovary-like structures, which they then grafted onto natural ovaries in female mice. After four weeks, the stem-cell-derived cells had matured into oocytes. The team removed the oocytes from the ovaries, fertilized them and transplanted the embryos into foster mothers. The offspring that were produced grew up to be fertile themselves."


Submission + - Rapid test pinpoints newborns' genetic diseases in days (nature.com)

ananyo writes: "A faster DNA sequencing machine and streamlined analysis of the results can diagnose genetic disorders in days rather than weeks.
Up to a third of the babies admitted to neonatal intensive care units have a genetic disease. Although symptoms may be severe, the genetic cause can be hard to pin down.
The research team used the new system to analyse the genomes of five children, including two brothers, with undiagnosed diseases and found definite or likely causative mutations in four of them (abstract). The researchers also sequenced portions of the parents’ genomes to track down which flagged mutations might cause disease.
The Children’s Mercy Hospital in Kansas City, Missouri, and the Children's Hospital of Wisconsin now plans to start genome sequencing in the neonatal intensive care unit with the arrival of faster sequencing machines from Illumina and from rival Life Technologies."


Submission + - Electronic components that dissolve in the body (nature.com)

ananyo writes: "A team of researchers has designed flexible electronic components that can dissolve inside the body, and in water. The components could be used to make smart devices that disintegrate once they are no longer useful, helping to alleviate electronic waste and enabling the development of medical implants that don’t need to be surgically removed. So far, the team has designed an imaging system that monitors tissue from within a mouse, a thermal patch that prevents infection after a surgical site is closed up, solar cells and strain and temperature sensors (abstract)."

Submission + - First mammals observed regenerating tissue (nature.com)

ananyo writes: "Two species of African spiny mouse have been caught at something no other mammal is known to do — completely regenerating damaged tissue. The work could help improve wound healing in humans.
The species — Acomys kempi and Acomys percivali — have skin that is brittle and easily torn, which helps them to escape predators by jettisoning patches of their skin when caught or bitten. Researchers report that whereas normal laboratory mice (Mus musculus) grow scar tissue when their skin is removed, African spiny mice can regrow complete suites of hair follicles, skin, sweat glands, fur and even cartilage (abstract). Tissue regeneration has not been seen in mammals before, though it is common in crustaceans, insects, reptiles and amphibians."


Submission + - Function of 80% of the human genome charted (nature.com)

ananyo writes: "In what is likely to be a historic moment in science, ENCODE, the Encyclopedia of DNA Elements, has published 30 papers in Nature, Genome Research and Genome Biology today, assigning some sort of function to roughly 80% of the genome, including more than 70,000 ‘promoter’ regions — the sites, just upstream of genes, where proteins bind to control gene expression — and nearly 400,000 ‘enhancer’ regions that regulate expression of distant genes.
The project was designed to pick up where the Human Genome Project left off. Although that massive effort revealed the blueprint of human biology, it quickly became clear that the instruction manual for reading the blueprint was sketchy at best. Researchers could identify in its 3 billion letters many of the regions that code for proteins, but those make up little more than 1% of the genome, contained in around 20,000 genes. ENCODE, which started in 2003, aims to catalog the ‘functional’ DNA sequences between genes, learn when and in which cells they are active and trace their effects on how the genome is packaged, regulated and read.
Nature has set up an ENCODE site with an explorer, that groups the papers by topic, and collects all the papers, which are available free."

We're here to give you a computer, not a religion. - attributed to Bob Pariseau, at the introduction of the Amiga