Science

As sequencing becomes more affordable, the way forward for diagnosis is not DNA snippets, but full genome workups

Despite coming from a range of different backgrounds, everyone whose genome has been fully sequenced has had one thing in common: they were all healthy. But now, two teams have decoded the first genomes of people who carry genetic diseases, with one group also performing the first-ever full sequencing of an entire nuclear family. By decoding the entire genome, rather than just snippets linked to a particular disease, the two research groups were able to identify the genetic roots of particular disorders more precisely than ever before, paving the way for a radical improvement in the usefulness of genetic diagnosis.

Working independently, the different research teams, one based out of the Baylor College of Medicine in Houston, Texas, and the other working from both the University of Washington and the University of Utah both came to the same conclusions. First, they realized that genetic diseases did not result from the single mutation of common genes, thus requiring scientists to sequence the entire genome to find the cause of a pathology. Second, they realized that finding a disease would be much easier if the mutations were compared against close relatives, as opposed to the "common genome" developed from the small number of previous full genome donors.

At the Baylor College of Medicine lab, a researcher sequenced the entire genome of his colleague, who suffers from the genetic disease Charcot-Marie-Tooth neuropathy. Contrary to the previous method of genetic testing, which analyzed only small portions of the genome already associated with particular pathology, the whole genome sequence uncovered the cause of Charcot-Marie-Tooth neuropathy on a rare gene called SH3TC2. SH3TC2 is only one of 39 genes whose mutation can cause Charcot-Marie-Tooth neuropathy, and may have escaped notice if the researchers didn't sequence the full genome.

The Utah/Washington team's results also highlighted the need for more comprehensive sequencing in genetic disease identification. By performing the first-ever full sequence of an entire family, the researchers discovered that the rate of mutation varies widely by family. Most of those mutations are benign, but would appear as diseases if compared against the stock genome currently used for testing. Only by comparing full parental genomes against full offspring genomes within the same family were the researchers able to separate benign, random, mutations from the genes for Miller's syndrome and Primary Ciliary Dyskinesia carried by both children.

So far, genetic medicine has largely failed to live up to its promise. These two studies may help explain why. By switching from analyzing snippets of DNA, doctors can get a better sense of how genetics affect disease, and thus how to treat them.

However, while these studies do point to a way forward, the expense of the procedures will prevent the immediate implementation of full genome genetic medicine. At the Baylor College of Medicine lab, it cost $50,000 to sequence an entire genome. For genetic medicine to enact the recommendation suggested by the results of these two studies, that price needs to come down. Luckily, considering that decoding an entire genome cost $500 million ten years ago, the price seems to be dropping fast.

[The New York Times]

Despite results of a study, the chief author says ivermectin is not advised for first-line use, and it's not approved in the U.S. for use against lice.

Head lice are itchy, nasty nuisances that can be hard to get rid of. Can a pill provide relief? A new study has found that in tough cases, an oral medication kills the parasites more effectively than a prescription lotion applied to the scalp.

Almost 66% of patients who undergo cardiac catheterization despite no previous diagnosis of heart disease receive results indicating no 'significant' blockage, study finds.

Nearly two-thirds of those who undergo an invasive heart test called cardiac catheterization when they do not have diagnosed heart disease receive a clean bill of health, suggesting that the expensive procedure -- which exposes the patient to substantial amounts of radiation -- may be overused, researchers reported Wednesday.

A National Institutes of Health panel says vaginal birth after caesarean is reasonably safe and should be more widely available. Many hospitals ban the practice as a matter of policy or liability.

Vaginal birth after caesarean, or VBAC, is reasonably safe and should be more widely available, a National Institutes of Health advisory panel concluded Wednesday.

With populations continuing to decline, wildlife agencies issue a plan to designate critical habitat zones to protect the species. Such listing could affect offshore drilling and other activities.

Federal agencies are proposing to increase protections for loggerhead turtles, the long-lived sea creatures known for their big heads and capacity to swim thousands of miles across the Pacific.

A 10-year effort has finally created pumped-up fish for commercial aquaculture

Rainbow trout with six-pack abs and burly shoulders have emerged from a University of Rhode Island laboratory, and could someday find their way to humans' dinner tables. That's assuming diners don't panic at the sight of the muscular ichthyoid awaiting their knives and forks.

The bodybuilder stature of the trout comes from turning off myostatin, a protein that normally slows muscle growth. Researchers had known of a natural myostatin mutation that allowed for 20 to 25 percent more muscle growth in Belgian blue cattle, but did not know if the same would apply to the different mechanism of muscle growth in fish.

Terry Bradley, a fisheries and aquaculture expert at the University of Rhode Island, worked with a group of grad students for 500 hours to inject 20,000 rainbow trout eggs with different DNA snippets designed to block myostatin.

About 300 eggs ended up carrying the gene for more muscle growth, and eventually produced fish that mostly have the six-pack ab appearance -- even though the fish don't have standard abdominal muscles. A big dorsal hump adds the appearance of muscular shoulders.

The offspring of these muscular trout also carry the gene in their muscle cells. Bradley's group hopes to see if the fish grow faster, besides having 15 to 25 times more muscle without eating more food.

If the transgenic trout meet FDA approval, they could join the 1,000 trout farms that churn out about $80 million worth of trout each year. Such fish also appear to display normal behavior for now, despite a faint resemblance to the Street Sharks.

After the procedure, the donors live as long or longer than those in the general population.

People who donate a kidney to a sick friend or relative live at least as long as others in the general population and may live somewhat longer because they tend to take better care of themselves after the procedure, researchers reported Tuesday.

"IT" organisms may make up more than half of life on Earth

Despite the impact of mankind, the size of trees, and the sheer numbers of bugs, multicellular terrestrial life only makes up a small portion of the planet's biomass. The majority of life on Earth lives at the bottom of the ocean, much of it beneath the ocean floor.

Thanks to those extreme depths, science knows virtually nothing about the majority of the planet's lifeforms. But a series of deep sea drilling expeditions over the course of the next year looks to finally shine a light on our planet's richest, and most mysterious, habitats.

In 2010, the JOIDES Resolution, a deep sea drilling vessel operated by the international research consortium Integrated Ocean Drilling Program, will make three trips to various ocean ridges in search of never before discovered forms of life. The JOIDES Resolution will collect microbe-rich samples from deep below the surface, and flush dyed liquid through undersea aquifers to reveal how the deep ocean flows.

The voyages will also set up six undersea observatories to monitor microbiological content throughout the ocean. The observatories will be linked to surface laboratories, and cross referenced against the data obtained from the drilling.

Between the drilling and the observatories, on researcher told McClatchy newspapers that he expects a "fire hose of data."

These expeditions also have important implications in the search for extraterrestrial life. The conditions beneath the ocean floor closely resemble similar locations on Mars and Jupiter's moons. If humans are going to find alien life, it will most likely come in a form similar to the ones the JOIDES Resolution expedition hopes to retrieve.

And by gaining a better understanding of Earth's deep-dwelling microbes, scientists hope to be better prepared in the search for subterranean organisms on other worlds.

[Yahoo! News]

How fast is too fast? According to the laws of physics, the speed of light is a good boundary, as going beyond it opens you up to all sorts of paradoxes and space-time phenomena that are usually the stuff of sci-fi. But a couple of researchers in Austria have come up with a way to compute information faster than the speed of light.

The idea is not quite as crazy as it might sound, though you may wish to limber up your mind before delving deeper. It's based on the same principle as that of quantum entanglement -- the notion that two particles on opposite sides of the universe can be linked through their quantum states such that one cannot be adequately described without the other. That is, an action on one particle instantaneously influences its counterpart, even if they are separated by light years.

This quantum non-local phenomenon cannot transmit information faster than the speed of light, but according to Volkmar Putz and Karl Svozil at the Vienna University of Technology there's no reason we can't process information at superluminal speeds as long as doing so doesn't create any time travel paradoxes.

All we need to do is create a medium conducive to the kind of pair formation and recombination described by entanglement. Such a material would have a refractive index of less than one. Then you simply build an optical computer around all of this controlled quantum mayhem, and presto: a computer that processes faster than the speed of light (in theory, anyhow).

We can't move information faster than the speed of light, but it's nice to know we could potentially process data at that speed. And supposedly a hypercomputer of this nature could digest and compute functions that are otherwise non-computable. But even so, the bright minds over at Technology Review can't figure out exactly what to do with such a hypercomputer, and frankly neither can we. But if it can keep more than ten tabs in Firefox open simultaneously without crashing, we'll take a dozen.

[Technology Review]

Toxoplasmosis, a common food- and pet-borne illness linked to hallucinations, personality alteration, and, since it's often carried by house pets, the stereotype of the crazy cat lady, infects around 15 percent of the US population. Luckily, a new technique that traps the parasite with gold nanoparticles, and then zaps them with lasers, should help ease the $7.7 billion the disease costs America every year.

The treatment, developed at the University of Technology Sydney, Australia, uses gold nanoparticles that attach to toxoplasmid-hunting antibodies. The gold carrying-antibodies then spread through the circulatory system, affixing themselves to parasites in the blood.

Once the gold particles are well distributed and widely attached to the parasite, the laser heats up the gold, incinerating the parasites. According to the researchers, the laser could be tuned to the so-called "tissue window", a wavelength of light to which the human body appears transparent. That way, the laser can pass harmlessly through the skin, burning up the parasites along the way.

The researchers don't want to just stop at toxoplasmosis, either. If this technique works on one parasite, than malaria, another blood-infecting parasite, should also be susceptible to the same laser annihilation.

[Cosmos Magazine]

Light is essential to vision, at least the kind we perform with our naked eyes. This is why we can see through a glass lens but not through a brick wall (though we're working on that). But what about materials that let some light pass while scattering it in seemingly chaotic ways? Our naked eyes can't reassemble that light into coherent images, but using some clever math, a team of researchers has devised a way to focus light through opaque materials to "see" objects on the other side -- provided they have enough data about the material.

The team developed a numerical transmission matrix based on the way light passes through a layer of opaque zinc oxide, a common ingredient in white paints. The matrix captured the various ways the light changed upon passing through (and by various, we mean various; the matrix included over 65,000 numbers detailing the way the material scattered the light), creating a model for how light should pass through zinc oxide every time.

Using that transmission matrix, they were able to manipulate the beam on the transmission side such that it came out the other side focused. They then flipped the experiment on its head, measuring the light emerging from the opaque material and using the matrix to assemble an image of an object behind it.

Theoretically, such a transmission matrix could be developed for any opaque material, but while seeing through paper and white paint may not seem so terribly tantalizing, the experiment really shows the potential for opaque materials in optical devices. At the nano-scale it become increasingly difficult to construct transparent lenses. With a good enough transmission matrix, researchers could better peer through opaque biological materials like cell walls and other membranes that currently obscure our view of what's happening on the other side.

They don't exactly look like the saviors of our energy economy, but that's exactly what some researchers think they could be. Gribbles -- tiny crustacean pests with a knack for digesting wood -- have long been considered a marine parasite for the destruction they cause to wooden hulls and piers. But the enzymes gribbles use in to break wood fibers down into sugars could make them the next biofuels breakthrough.

Essentially, gribbles are blessed with a digestive process unparalleled (to our knowledge) by other wood-consuming insects and animals. Their digestive enzymes can break down woody cellulose and even lignin -- the normally indigestible part of woody plants -- creating sugars that are more or less ideal for fermenting into alcohol-based fuels.

A biofuel factory based on the gribble's digestive biology could yield energy-dense sugars for biofuel production in an efficient manner. But of course there's a give-and-take in the equation that involves feeding woody plant materials -- like trees -- into the process as fuel. But by pushing forward with more efficient means to convert woody cellulose into fuels -- and perhaps by engineering woodier trees -- we reduce the amount of organic matter we need to feed in to get the combustible stuff out.

The gribble -- thorn in the side of harbormasters, plague of the age of sail -- might just be good for something after all.

[Times Online]

The most complex machines ever built don't just hunt for obscure subatomic bits

Beneath the French-Swiss border, the Large Hadron Collider will help scientists seek answers to some of the most profound questions about the universe. Beyond this lofty goal, though, particle accelerators can be used for decidedly more down-to-Earth projects -- like fighting cancer, cleaning up industrial waste and even shrink-wrapping your Thanksgiving turkey. More than 17,000 particle accelerators are in operation around the world, used for radial tires, computer chips and 3-D images of molecules, among other tasks.

The LHC, which was restarted this week, will run at half its maximum energy for the next year and a half, as scientists monitor electrical systems that have already forced delays. At 3.5 trillion electron volts, a half-power LHC will still be three times as powerful as the world's previous atom-smashing king, Fermilab's Tevatron.

As the LHC searches for the elusive Higgs boson, which is thought to endow all other particles in the universe with mass, we decided to takes a look at some other, perhaps more humble uses for particle accelerators, the "cathedrals of science." Launch the gallery below:

Additional reporting by Molly Webster

Polymers are generally put to work as insulators, but a team of researchers at MIT has devised a way to turn polyethylene -- the most commonly used polymer -- into a conductor that transfers heat better than many pure metals. But the conversion of insulator to conductor is only half of the breakthrough; by coaxing all the polymer molecules into precise alignment, the researchers have created a polyethylene that conducts heat in only one direction. The plastic material remains an electrical insulator.

Getting a bunch of polymer molecules to fall in line is no easy task -- left to their own devices, the molecules will settle into a chaotic arrangement that is resistant to heat transfer. But the MIT team found that by drawing polyethylene fibers slowly out of a solution they could get the molecules to line up facing the same way, creating a material that will let heat pass in one direction but not the other.

This kind of one-way conductor is ripe for myriad applications in devices where heat must be drawn away from a certain place, such as heat exchangers, computer processors or portable electronics. With a thermal conductivity 300 times greater than conventional polyethylene, the polymer is actually more conductive than about half of all pure metals, meaning it could potentially replace metal conductors in several common devices.

Of course, all that is dependent on scaling the process to create conductive polyethylene at market-feasible prices and quantities, something the team has not yet done. But should they find a way to produce the stuff in bulk, it could quickly jump from lab bench to commercial applications, providing a cheap alternative to certain metals used in heat exchange -- metals that add cost and sometimes an environmental toll to common devices.

[Science Daily]

Women who abstained put on more pounds than those who had a drink or two per day. But researchers warn against an alcohol diet.

Women who drink moderate amounts of alcohol don't gain as much weight in midlife as those who abstain, a study has found. However, drinking should not be heralded as a new diet, said the authors and alcohol abuse experts.

GPS measurements show the city of Concepcion shifted to the west. The magnitude 8.8 quake also moved the capital of Santiago about 11 inches west-southwest.

The massive magnitude 8.8 earthquake that struck off the coast of Chile last month moved the entire city of Concepcion -- the closest urban area to the quake's epicenter -- at least 10 feet west, American researchers said Monday.

The world's first commercial effort at a patient-ready brain computer interface is on display over at CeBIT 2010, but don't go throwing out your keyboard and mouse just yet. Intended for patients suffering from locked-in syndrome and other communication-impairing conditions, the Intendix from Guger Technologies allows users to input text using only their brains.

Intendix works using an EEG-sensitive cap that measures brain activity that is focused in a particular way. You simply watch a grid of letters that flashes on the screen, focusing on the letter you want to type. When the letter you want lights up, your brainwaves jump ever so slightly, allowing the EEG to determine what to type. Guger Technologies claims that the interface is simple enough that users can utilize it relatively well after just ten minutes of training.

As the brain acclimates to the system, users can type as quickly as one letter per second, making it possible to carry on a conversation and communicate complex thoughts, a step above some of the more rudimentary communication systems that have been devised over past decades.

At more than $12,000 per unit, Intendix is a bit pricey for the BCI enthusiast simply interested in the technology, but the commercialization of the product does signal a new degree of accessibility to brain computer interfacing. It doesn't appear we're going to be mind-melding with our PCs anytime soon, but this certainly marks a small step in that direction.

Check out a vague yet visually interesting ad for Intendix below.

[Singularity Hub]

The Hawthorne firm's Falcon 9 is a major contender to cheaply carry astronauts and cargo into orbit.

A new rocket 18 stories tall and waiting to be launched from a pad in Cape Canaveral, Fla., could determine the fate of a private aerospace venture in Hawthorne -- and even possibly NASA's space program.

Figueredo, one of the first women to practice surgical oncology, was friends with Mother Theresa and created the Friends of the Poor charity to aid people in Baja California.

Dr. Anita Figueredo, the first female surgeon in San Diego and a well-known philanthropist who was close friends with Mother Teresa for four decades, died Feb. 19 at her home in La Jolla. She was 93 and had suffered a cerebral hemorrhage two weeks earlier.

Prenatal, infancy, early childhood — factors in all may affect a person’s future weight and health.

Pam Levin's daughter weighed less than 5 pounds at birth. But by the time the child turned 3, Levin and her husband had begun to bristle at some of the comments about her. "People would say, ‘She's chunky' or ‘She's a big girl,'" Levin says.