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Pour, Shake and Stir: Rapid Point-Of-Care Testing for Multiple Diseases from a Drop of Blood

Pour, Shake and Stir: Rapid Point-Of-Care Testing for Multiple Diseases from a Drop of Blood | Amazing Science |

A diagnostic “cocktail” containing a single drop of blood, a dribble of water, and a dose of DNA powder with gold particles could mean rapid diagnosis and treatment of the world’s leading diseases in the near future. The cocktail diagnostic is a homegrown brew being developed by University of Toronto’s Institute of Biomaterials and Biomedical Engineering (IBBME) PhD student Kyryl Zagorovsky and Professor Warren Chan that could change the way infectious diseases, from HPV and HIV to malaria, are diagnosed.


Zagorovsky’s rapid diagnostic biosensor will allow technicians to test for multiple diseases at one time with one small sample, and with high accuracy and sensitivity. The biosensor relies upon gold particles in much the same vein as your average pregnancy test. With a pregnancy test, gold particles turn the test window red because the particles are linked with an antigen that detects a certain hormone in the urine of a pregnant woman.


“Gold is the best medium,” explains Chan, “because it’s easy to see. It emits a very intense colour.”


Currently scientists can target the particular disease they are searching for by linking gold particles with DNA strands: when a sample containing the disease gene (ie. Malaria) is present, it clumps the gold particles, turning the sample blue.


Rather than clumping the particles together, Zagorovsky immerses the gold particles in a DNA-based enzyme solution (DNA-zyme) that, when the disease gene is introduced, ‘snip’ the DNA from the gold particles, turning the sample red.


“It’s like a pair of scissors,” Zagorovsky explains, “and the target gene activates the scissors that cut the DNA links holding gold particles together.”

The advantage is that far less of the gene needs to be present for the solution to show noticeable colour changes, amplifying detection. A single DNA-zyme can clip up to 600 “links” between the target genes.


Just a single drop from a biological sample such as saliva or blood can potentially be tested in parallel, so that multiple diseases can be tested for in one sitting.


But the team has also demonstrated that they are able to transform the testing solution into a powder, making it light and far easier to ship than solutions, which degrade over time. Powder can be stored for years at a time, and offers hope that the technology can be developed into efficient, cheap, over-the-counter tests for diseases such as HIV and malaria for developing countries, where access to portable diagnostics is a necessity.

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Astronomers Create Pseudo-3D Maps of Milky Way's Interstellar Material

Astronomers Create Pseudo-3D Maps of Milky Way's Interstellar Material | Amazing Science |
A group of astronomers has produced pseudo-3D maps of the material located between the stars in our Milky Way Galaxy.

Analyzing bands of starlight that have passed through space gives scientists information about the makeup of the space materials that the light has encountered.

In 1922, U.S. astronomer Mary Lea Heger discovered dark lines indicating ‘missing’ starlight, which must have been absorbed by a yet unknown source. These mysterious features were called diffuse interstellar bands, or DIBsSince then, scientists have identified more than 400 DIBs, but the material that is causing these bands to appear and their precise location have remained a mystery.

In a new approach to understanding DIBs, Dr Kos and his co-authors combined information from nearly 500,000 stellar spectra obtained by theRAVE (Radial Velocity Experiment) survey to produce pseudo-3D maps of the DIB-material at 862 nm covering the nearest 9,800 light-years from our Solar System.

RAVE project used the UK Schmidt Telescope in Australia to collect spectroscopic information from the light of as many as 150 stars at once. The resulting maps are described as ‘pseudo-3D’ because a specific mathematical form was assumed for the distribution in the vertical dimension that provides the distances from the plane of the Milky Way, with the maps presented in the remaining two dimensions.

The maps showed the intriguing result that the complex molecules thought to be responsible for the DIBs are distributed differently than another known component of the interstellar medium – the solid particles known as dust – also traced by the RAVE survey.

“With the wide area coverage of the spectroscopic survey RAVE it was for the first time possible to map out the 3D distribution of the DIBs,” said Dr Matthias Steinmetz of the Leibniz Institute for Astrophysics Potsdam, who is a co-author of the paper reporting the results in the journal Science.

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Proposed diamond maser could operate at room temperature

Proposed diamond maser could operate at room temperature | Amazing Science |

Before there were lasers, there were masers—devices that operate in the microwave regime and other wavelengths that are longer than those of visible light. But while the first masers were built back in the 1950s, they have failed to achieve the same commercial success as lasers due to their demanding operating conditions: gas masers require high-vacuum conditions and solid-state masers require ultracold liquid-helium temperatures (about 4˚K) to operate.

In a new paper published in Nature Communications, Liang Jin, et al., from The Chinese University of Hong Kong and the University of Stuttgart, have proposed a concept for a diamond maser that can operate at room temperature. With the potential to achieve a coherence time of a few minutes, the maser could pave the way for widespread applications.

The biggest advantage of using diamonds is that diamonds have nitrogen-vacancy center spins that have the longest known lifetime at room temperature of any known solid-state spin, and a long spin lifetime is essential for achieving a key maser mechanism: population inversion. In population inversion, more spins exist in an excited state than in a lower-energy state, and so a long spin lifetime is required. The problem is that the spin lifetimes in most solids at room temperature are much too short—often just a few nanoseconds—to achieve useful population inversion.

In contrast, the diamond spins have a lifetime of about 5 milliseconds at room temperature, making them an ideal candidate for a room-temperature maser. These spins can be rapidly pumped to their excited state with the help of a magnetic field, and even though a magnetic field may complicate the device's experimental realization, the researchers expect that the challenge can be overcome with commercially available magnets.

If the diamond maser could be realized in the future, it would be the second room-temperature solid-state maser demonstrated so far. In 2012, researchers from the UK reported in Nature the first such device, which they made out of an organic material (p-terphenyl doped with pentacene), which has a lifetime of about 0.1 microseconds—about 1/50th of that of the proposed diamond spins. Although the pentacene-based device marked an important milestone as the first room-temperature maser ever demonstrated, its spins could not completely reach the ground state but instead existed in an intermediate, metastable state. As a result, the pentacene maser had low efficiency and could only operate in pulsed mode at a low rate.

The researchers of the new study hope that the proposed diamond maser will improve in these areas, with the potential to achieve a higher stability, higher efficiency, and longer masing time.

Via José Gonçalves
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Is an ancient virus responsible for some cases of Lou Gehrig’s disease?

Is an ancient virus responsible for some cases of Lou Gehrig’s disease? | Amazing Science |

By Jon Cohen 30 September 2015 2:00 pm 


A virus that long ago spliced itself into the human genome may play a role in amyotrophic lateral sclerosis (ALS), the deadly muscle degenerative disease that crippled baseball great Lou Gehrig and ultimately took his life. That’s the controversial conclusion of a new study, which finds elevated levels of human endogenous retrovirus K (HERV-K) in the brains of 11 people who died from the disease.

“This certainly is interesting and provocative work,” says Raymond Roos, a neurologist at the University of Chicago in Illinois who treats and studies ALS but who was not involved with the finding. Still, even the scientists behind the work caution that more research is needed to confirm the link. “I’m very careful to say HERV-K doesn’t cause the disease but may play a role in the pathophysiology,” says study leader Avindra Nath, a neuroimmunologist at the National Institute of Neurological Disorders and Stroke in Bethesda, Maryland. “The darn thing is in the chromosomes to begin with. It’s going to be very hard to prove causation.”

It was another retrovirus, HIV, that led Nath to first suspect a connection between viruses and ALS. In 2006, he was helping a patient control his HIV infection with antiretroviral drugs when he noticed that the man’s ALS also improved. “That intrigued me, and I looked in the ALS literature and saw that people had reported they could see reverse transcriptase in the blood.” Reverse transcriptase, an enzyme that converts RNA to DNA, is a hallmark of retroviruses, which use it to insert copies of their genes into chromosomes of their hosts.

No study had ever convincingly found a retrovirus in ALS patients. But researchers had only looked for viruses that came from outside the body. About 8% of the human genome consists of “endogenous” retroviruses such as HERV-K, which presumably are remnants of ancient viruses. These retroviruses initially infected a human egg or sperm cell and entrenched themselves in chromosomes, allowing them to spread from one generation to the next. Mutations ultimately disabled the incorporated retroviral DNA.

In 2011, Nath and co-workers reported that they had found increased levels of expression for one HERV-K gene in autopsied brains of people who died from ALS. Their new study, published online today in Science Translational Medicine, builds on the earlier work with analyses of more brains and supporting evidence from test tube and mouse experiments.

In about 10% of people with ALS, someone else in the family has the disease, which suggests it originated from an inherited aberrant gene. Nath and colleagues focused instead on what is known as sporadic ALS: cases in which people have no familial history of the condition. Bolstering their 2011 study, the team found elevated levels of three different HERV-K genes in the autopsied ALS brains. The researchers did not isolate the virus itself, which Nath notes is logistically difficult because it would require analyzing “fresh” brains shortly after death.

The researchers further showed in test tube experiments that adding HERV-K genes to cultures of neurons led to a significant die-off of the cells. Using a technique known as electroporation to insert an HERV-K gene into the brains of embryonic mice, the researchers showed similar neuronal damage. The researchers then engineered mice to express that HERV-K gene in all their neurons. Again, the gene led to neuronal mayhem, and the animals had muscular problems similar to what’s seen in ALS patients.

Some retrovirologists caution that the evidence remains thin that this endogenous virus causes ALS. John Coffin, who studies HERV-K at Tufts University in Boston, notes that high expression levels of genes from this retrovirus have been found in many conditions, including breast cancer, multiple sclerosis, schizophrenia, and melanoma, but none have been conclusively shown to be caused by it. “There are a lot of papers like this one,” Coffin says. “Upregulation of this group of endogenous viruses is a very common finding.”

Coffin says “group” because there are about 90 different HERV-Ks, and that’s another concern he has about the Nath lab’s work: The study does not show that all ALS patients had the exact same version of the virus in their brains. “I’m perfectly willing to accept that there’s toxicity, but I’m never entirely sure what to make of these types of experiments,” Coffin says. He notes that in 1970s and 1980s, so many investigators wrongly asserted that exogenous human viruses—the ones that move between people or, commonly, humans and animals—caused tumors that they became known as “rumor viruses.” “There is a fair amount of rumor virology around endogenous retroviruses causing disease.”

Even Nath stresses that he wants other labs to confirm his team’s findings. “I’ve worked with HIV for many years, and I’m aware of the pitfalls, and that’s why we wanted to make sure we were very, very careful before we stuck our necks out,” Nath says. “It took us 10 years to produce this paper.”

Nath is now launching a clinical study that will evaluate the impact of treating ALS patients who have high levels of HERV-K genes expressed in blood with a combination of four antiretroviral drugs used to treat HIV infection. The phase I study will primarily assess whether treatment for 24 weeks can lower HERV-K gene expression to undetectable levels, but Nath will also monitor the disease’s progression. Whether the anti-HIV drugs will even have an impact on HERV-K is unclear. The drugs target the reverse transcriptase and protease enzymes, which both viruses depend on, but differences exist between the HERV-K and HIV versions.

Coffin, who warns that antiretrovirals have toxicities, says the clinical trial is folly. “The rationale for that is nonexistent,” he says. Nath counters that there are about 40 cases described in the literature of ALS patients taking antiretrovirals, but it’s difficult to make sense of these reports—about half of which claimed improvements. “No one has ever done a systematic study,” he says.

Then again, Nath allows that increased expression of HERV-K genes in ALS patients may simply be the result of something else that’s causing the actual damage. “The reasons for skepticisms are very valid,” Nath says. “We could be wrong as well.” 

Via Kim Frye
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"Tardis" Memory Could Enable Huge Multi-Core Computer Chips

"Tardis" Memory Could Enable Huge Multi-Core Computer Chips | Amazing Science |
More efficient memory-management scheme could help enable chips with thousands of cores.

In a modern, multicore chip, every core — or processor — has its own small memory cache, where it stores frequently used data. But the chip also has a larger, shared cache, which all the cores can access.

If one core tries to update data in the shared cache, other cores working on the same data need to know. So the shared cache keeps a directory of which cores have copies of which data. That directory takes up a significant chunk of memory: In a 64-core chip, it might be 12 percent of the shared cache. And that percentage will only increase with the core count. Envisioned chips with 128, 256, or even 1,000 cores will need a more efficient way of maintaining cache coherence.

At the International Conference on Parallel Architectures and Compilation Techniques in October, MIT researchers unveil the first fundamentally new approach to cache coherence in more than three decades. Whereas with existing techniques, the directory’s memory allotment increases in direct proportion to the number of cores, with the new approach, it increases according to the logarithm of the number of cores.

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Living in space: Weightlessness comes with many surprising complications

Living in space: Weightlessness comes with many surprising complications | Amazing Science |

A $150-billion contraption floating 270 miles above Earth is one of the most impressive achievements of humankind.

It's called the International Space Station (ISS), and a rotating astronaut crew has occupied it since 2000. The work of those astronauts has yielded some incredible scientific insights.

Astronaut is not a profession where you get to go home at the end of the day though. One ticket from Earth to the ISS costs about $70 million, so normally each crew lives and works on the station for a six-month shift.

Right now NASA astronaut Scott Kelly and Russian cosmonaut Mikhail Kornienko are in the middle of a year-long shift aboard the ISS. They'll be the first humans to spend a consecutive year living in space.

But what is it like to actually live on the ISS? Find out...

Russell R. Roberts, Jr.'s curator insight, October 9, 8:10 PM

Among the adjustments ISS crew members must accept:

Sweat doesn't evaporate.

Equipment can float away and lead to dangerous malfunctions.

Water and waste management is a real challenge.

Personal cleanliness is difficult.

Space walks can be dangerous.

Still, a chance to live and work on this scientific marvel could be the dream of a lifetime.  Aloha, Russ.

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Scientist Designs Bio-Inspired Robotic Finger That Looks, Feels and Works Like the Real Thing

Scientist Designs Bio-Inspired Robotic Finger That Looks, Feels and Works Like the Real Thing | Amazing Science |

Most robotic parts used today are rigid, have a limited range of motion and don’t really look lifelike. Inspired by both nature and biology, a scientist from Florida Atlantic University has designed a novel robotic finger that looks and feels like the real thing. In an article recently published in the journal Bioinspiration & Biomimetics, Erik Engeberg, Ph.D., assistant professor in the Department of Ocean and Mechanical Engineering within the College of Engineering and Computer Science at FAU, describes how he has developed and tested this robotic finger using shape memory alloy (SMA), a 3D CAD model of a human finger, a 3D printer, and a unique thermal training technique.

“We have been able to thermo-mechanically train our robotic finger to mimic the motions of a human finger like flexion and extension,” said Engeberg. “Because of its light weight, dexterity and strength, our robotic design offers tremendous advantages over traditional mechanisms, and could ultimately be adapted for use as a prosthetic device, such as on a prosthetic hand.”

In the study, Engeberg and his team used a resistive heating process called “Joule” heating that involves the passage of electric currents through a conductor that releases heat. Using a 3D CAD model of a human finger, which they downloaded from a website, they were able to create a solid model of the finger. With a 3D printer, they created the inner and outer molds that housed a flexor and extensor actuator and a position sensor. The extensor actuator takes a straight shape when it’s heated, whereas the flexor actuator takes a curved shape when heated. They used SMA plates and a multi-stage casting process to assemble the finger. An electrical chassis was designed to allow electric currents to flow through each SMA actuator. Its U-shaped design directed the electric current to flow the SMAs to an electric power source at the base of the finger.

This new technology used both a heating and then a cooling process to operate the robotic finger. As the actuator cooled, the material relaxed slightly. Results from the study showed a more rapid flexing and extending motion of the finger as well as its ability to recover its trained shape more accurately and more completely, confirming the biomechanical basis of its trained shape.

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The QUTIS Group creates a quantum simulator of impossible physics

The QUTIS Group creates a quantum simulator of impossible physics | Amazing Science |

The research group Quantum Technologies for Information Science (QUTIS) of the UPV/EHU-University of the Basque Country, led by the Ikerbasque professor Enrique Solano, in collaboration with an experimental group of the University of Tsinghua (Beijing, China) led by professor Kihwan Kim, has created a quantum simulator that is capable of creating unphysical phenomena in the atomic world, in other words, impossible physical phenomena. The researchers in the two groups have succeeded in getting a trapped atom to imitate behaviours that contradict its own fundamental laws, thus taking elements of science fiction to the microscopic world. "We have managed to get an atom to act as if it were infringing the nature of atomic systems, in other words, quantum physics and the theory of relativity. It is just like what happens in the theatre or in science fiction films in which the actors appear to display absurd behaviors that go against natural laws; in this case, the atoms are obliged to simulate absurd actions as if an actor in the theatre or in science fiction were involved," explained Prof Solano.

The results of this research have been published in the prestigious journal Nature Communications, in the article "Time reversal and charge conjugation in an embedding quantum simulator". The research team of the UPV/EHU's QUTIS group has been led by Prof Enrique Solano and has had the participation of Dr Lucas Lamata and Dr Jorge Casanova, currently at the University of Ulm, Germany.

In this experiment the researchers reproduced in the lab the theoretical proposal previously included in a previous piece of research led by the QUTIS group; it describes the possibility that a trapped atom can display behavior that is incompatible with the fundamental laws of quantum physics. More specifically, we are talking about operations prohibited in microscopic physical systems, such as charge conjugation, which transforms a particle into an antiparticle, or time reversal, that reverses the direction of the time arrow.

To conduct the experiment it was necessary to use a charged atom trapped by means of electromagnetic fields under the action of an advanced laser system. We could describe symmetry operations of this type as prohibited ones, as they could only exist in a universe that is different from the one we know and governed by different laws. Yet in this experiment it has been possible to simulate the realization of this set of impossible laws in an atomic system.

The UPV/EHU's QUTIS group is a world leader in quantum simulation and its influential theoretical proposals are often verified in the most advanced quantum technology laboratories. In this case, physical operations that are prohibited for the atomic world can be reproduced just as in science fiction, in other words, just as if they were taking place artificially in a quantum theater.

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Perfectly accurate clocks could turn out to be impossible

Perfectly accurate clocks could turn out to be impossible | Amazing Science |
Can the passage of time be measured precisely, always and everywhere? The answer will upset many watchmakers. A team of physicists from the universities of Warsaw and Nottingham have just shown that when we are dealing with very large accelerations, no clock will actually be able to show the real passage of time, known as "proper time."

The ideal clock is merely a convenient fiction, as theorists from the University of Warsaw (UW) and University of Nottingham (UN) have shown. In a study published in the journal Classical and Quantum Gravity they demonstrate that in systems moving with enormous accelerations, building a clock that would precisely measure the passage of time is impossible for fundamental reasons.

"In both theories of relativity, special and general, it is tacitly assumed that it is always possible to construct an ideal clock -- one that will accurately measure the time elapsed in the system, regardless of whether the system is at rest, moving at a uniform speed, or accelerating. It turns out, however, that when we talk about really fast accelerations, this postulate simply cannot apply," says Dr. Andrzej Dragan from the Faculty of Physics, University of Warsaw.

The simplest clocks are unstable elementary particles, for example muons (particles with similar properties to electrons but 200 times more massive). Usually, muons decay into an electron, muon neutrino, and an electron antineutrino. By measuring the decay times and averaging the results for muons moving slowly and those moving at nearly the speed of light, we can observe the famous slowing down of the passage of time: the faster the muons are moving, the less likely the experimenter is to see them decay. Velocity therefore affects the clocks' observed tempo.

What about acceleration? Experiments were performed at CERN in the late 1970s, measuring the decay time of muons undergoing circular motion accelerations even as great as billions of billions of times the acceleration of Earth's gravity (10^18 g). Such acceleration was found to have no impact on the disintegration times.

That might change, though, for much higher accelerations.

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CRISPR-CAS Could Generate a Hypoallergenic Peanut But Anti-GMO Fear Gets In Its Way

CRISPR-CAS Could Generate a Hypoallergenic Peanut But Anti-GMO Fear Gets In Its Way | Amazing Science |

Anyone with a child in school is probably aware of the need for peanut free zones. You get a notice when your child returns from school on the first day stating that at least one child in their class has a peanut allergy, which means nothing with peanuts gets sent to school for your child’s lunch. If you are a parent of a child with a peanut allergy you understand how important and serious this is – your child is literally one errant Snickers bar away from death.

The general consensus is that food allergies have been on the rise in developed countries, although studies show a wide range of estimates based upon study techniques. A US review found the prevalence of self-reported peanut allergies ranged from 0-2%. A European review found the average estimate to be 2.2% – around 2% is usually the figure quoted. In a direct challenge study, at age 4, 1.1% of the 1218 children were sensitized to peanuts, and 0.5% had had an allergic reaction to peanuts. That means there are millions of people with peanut allergies.

So far there is no cure for the allergies themselves. Acute attacks can be treated with epinephrine, but there are cases of children dying (through anaphylaxis) even after multiple shots. The only real treatment is to obsessively avoid contact with the food in question. Peanuts, tree nuts, and shellfish are the good most likely to cause anaphylaxis.

There is, however, a potential solution. Researchers have been working for year on developing a cultivar of peanut that does not cause allergies. Attempts to achieve this through conventional breeding and hybridization have failed and does not seem likely to succeed. The only real hope of a hypoallergenic peanut is through genetic modification. We are, in fact, on the brink of achieving this goal, but anti-GMO fears are getting in the way.

There are 7 proteins that have been identified in peanuts that cause an allergic reaction. The allergic reaction from peanuts is entirely an IgE mediated Type I hypersensitivity response. The proteins crosslink with the IgE antibodies, which them bind to mast cells and basophils (cells in the immune system) causing a significant inflammatory response that clinically causes the allergic reaction. One peanut contains about 200mg of protein, and as little as 2mg is enough to cause objective symptoms of an allergic reaction.

What makes a food protein an allergen is interesting. About 700 amino acid sequences have been identified that help confer allergenicity to protein. These protein segments allow the protein to survive processing and digestion, and allow the protein to bind to IgE antibodies.

In 2005 a study was published showing that it is possible to silence the gene for the Ara H2 protein, the primary allergenic protein in peanuts. A 2008 follow up by the same team showed decreased allergenicity of the altered peanut. So where are our hypoallergenic peanuts? This is a complicated question, and I don’t think I can give a full answer.

The delay in marketing a hypoallergenic peanut seems to be due partly to technical issues – it turns out to be a lot more difficult to make the necessary changes than at first thought. However, it also seems to be due to the anti-GMO campaign, which has been scaring away investors and making politicians gun-shy.

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The biggest mystery in mathematics: Shinichi Mochizuki and the impenetrable proof

The biggest mystery in mathematics: Shinichi Mochizuki and the impenetrable proof | Amazing Science |
A Japanese mathematician claims to have solved one of the most important problems in his field.

Sometime on the morning of 30 August 2012, Shinichi Mochizuki quietly posted four papers on his website. The papers were huge — more than 500 pages in all — packed densely with symbols, and the culmination of more than a decade of solitary work. They also had the potential to be an academic bombshell. In them, Mochizuki claimed to have solved the abc conjecture, a 27-year-old problem in number theory that no other mathematician had even come close to solving. If his proof was correct, it would be one of the most astounding achievements of mathematics this century and would completely revolutionize the study of equations with whole numbers.

Mochizuki, however, did not make a fuss about his proof. The respected mathematician, who works at Kyoto University's Research Institute for Mathematical Sciences (RIMS) in Japan, did not even announce his work to peers around the world. He simply posted the papers, and waited for the world to find out.

Probably the first person to notice the papers was Akio Tamagawa, a colleague of Mochizuki's at RIMS. He, like other researchers, knew that Mochizuki had been working on the conjecture for years and had been finalizing his work. That same day, Tamagawa e-mailed the news to one of his collaborators, number theorist Ivan Fesenko of the University of Nottingham, UK. Fesenko immediately downloaded the papers and started to read. But he soon became “bewildered”, he says. “It was impossible to understand them.”

Fesenko e-mailed some top experts in Mochizuki's field of arithmetic geometry, and word of the proof quickly spread. Within days, intense chatter began on mathematical blogs and online forums (see Nature; 2012). But for many researchers, early elation about the proof quickly turned to scepticism. Everyone — even those whose area of expertise was closest to Mochizuki's — was just as flummoxed by the papers as Fesenko had been. To complete the proof, Mochizuki had invented a new branch of his discipline, one that is astonishingly abstract even by the standards of pure maths. “Looking at it, you feel a bit like you might be reading a paper from the future, or from outer space,” number theorist Jordan Ellenberg, of the University of Wisconsin–Madison, wrote on his blog a few days after the paper appeared.

Three years on, Mochizuki's proof remains in mathematical limbo — neither debunked nor accepted by the wider community. Mochizuki has estimated that it would take an expert in arithmetic geometry some 500 hours to understand his work, and a maths graduate student about ten years. So far, only four mathematicians say that they have been able to read the entire proof.

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DNA ‘vaccine’ that sterilizes mice, could lead to one-shot birth control

DNA ‘vaccine’ that sterilizes mice, could lead to one-shot birth control | Amazing Science |

Animal birth control could soon be just a shot away: A new injection makes male and female mice infertile by tricking their muscles into producing hormone-blocking antibodies. If the approach works in dogs and cats, researchers say, it could be used to neuter and spay pets and to control reproduction in feral animal populations. A similar approach could one day spur the development of long-term birth control options for humans.

“This looks incredibly promising,” says William Swanson, director of animal research at the Cincinnati Zoo and Botanical Garden in Ohio. “We’re all very excited about this approach; that it’s going to be the one that really works.”

For decades, the go-to methods for controlling animal reproduction have been spay or neuter surgeries. But the surgeries, which require animals to be anesthetized, can be expensive—one reason so many dogs and cats remain unfixed and feral animal populations continue to grow. Nearly 2.7 million dogs and cats were euthanized in U.S. shelters last year. A cheaper, faster method of sterilization is considered a holy grail for animal population control. 

To get there, researchers have already created vaccines that trigger an immune response in animals. This response produces antibodies that block gonadotropin-releasing hormone (GnRH), required by all mammals to turn on the pathways that spur egg or sperm development. The vaccines in this class—including deer contraceptive GonaCon—have been shown to effectively work as both male and female birth control in animals. But, like many human immunizations, the vaccines rely on an immune response that eventually dwindles away, forcing the use of booster shots every few years.

Biologist Bruce Hay of the California Institute of Technology in Pasadena and colleagues took a different approach to blocking GnRH. Rather than rely on animals’ immune systems to create antibodies, he and his colleagues engineered a piece of DNA that—when packaged inside inactive virus shells and injected into mice—turned their muscle cells into anti-GnRH antibody factories. Because muscle cells are some of the longest lasting in the body, they continue to churn out the antibodies for 10 or more years. Both male and female mice with high enough levels of the antibodies were rendered completely infertile when Hay’s team allowed them to mate 2 months later, the team reports online today in Current Biology.

Via Integrated DNA Technologies
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Scientists find smallest life forms on Earth

Scientists find smallest life forms on Earth | Amazing Science |

Over the last two decades, scientists have argued back and forth on whether or not ultra-small bacteria exist. The argument has been fueled, in part, by the1996 find of ultra-tiny fossil microorganisms on a meteorite from the planet MarsBut earlier this year, researchers at the University of California, Berkeley and the Department of Energy’s Lawrence Berkeley National Laboratory have captured detailed cryogenic electron microscopy images of ultra-small bacteria. These cells are now believed to be as small as a cell can get and still possess sufficient internal material needed to sustain life.

The first author of the study, Birgit Luef, is now a researcher at NTNU’s Department of Biotechnology. The publication was the result of her postdoctoral work at UC Berkeley. The researchers found several kinds of bacteria from three microbial phyla that are poorly understood. The bacteria were in groundwater and are thought to be quite common. But what surprised Luef and her colleagues was that the bacteria were  close to and in some cases smaller than what many scientists have long considered the lower size limit of life. They reported the findings in the spring in the journal Nature Communications.

The cells had an average volume 0.009 ± 0.002 cubic microns, meaning 150 of the bacteria would fit inside a single cell of Escherichia coli.

Via Mariaschnee
Ed Rybicki's comment, October 8, 4:25 AM
And of course, AGAIN they ignore the fact that viruses are alive...but it's nice that FINALLY someone seems to have nailed the nanobacteria we kept hearing about.
Ed Rybicki's curator insight, October 8, 4:27 AM

Cell-based: because circoviruses are the smallest organisms at 1.9 - 2 Kb of DNA B-)

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Scientists hope to attract millions of people to 'DNA.LAND'

Scientists hope to attract millions of people to 'DNA.LAND' | Amazing Science |

Geneticists have launched a project to test whether they can study millions of genomes — without collecting a drop of blood or tube of spit themselves. The project, DNA.LAND, aims to entice people who have already had their genomes analysed by consumer genetics companies to share that data, allowing DNA.LAND geneticists to study the information. Although some consumer genetic-testing companies share data with researchers, they provide only aggregate information about their customers, not individual genomes. Because the data are not always accompanied by detailed information on patients' health, they are of limited use for drawing links between genes and disease.

“Millions of people have access to their genomes, and many more millions will join them in the near future,” sayscomputational geneticist Yaniv Erlich. He is launching DNA.LAND with fellow geneticist Joseph Pickrell at the New York Genome Center and Columbia University in New York. “Can you get to the point that instead of paying for each study from scratch, we can use the crowd to collect and repurpose this data?” Erlich asks.

Erlich will present the project on 10 October at the annual meeting of the American Society of Human Genetics (ASHG) in Baltimore, Maryland. This is not the first time that he has sought to engage the public to assemble data for large research studies. For instance, Erlich has previously combined data from genealogy websites into the world’s largest family tree, with information on 13 million people.

DNA.Land is an example of the 'participatory turn' in human subjects research, says Michelle Meyer, a bioethicist and legal scholar at the Icahn School of Medicine at Mount Sinai in New York.This is a smart research model, since it keeps sequencing and data-storage costs low and doesn't run into the patchwork of federal and state laws governing genetic testing itself.

Erlich hopes to tap the genomes of up to three million customers of companies such as 23andMe, and Family Tree DNA. The companies allow people to download a file containing the readout of their genetic results.

By combining these data with other information about the participants, such as that on their health, Erlich hopes to assemble a very large data set. A recent analysis, for instance, suggested that as many as 2 billion genomes could be sequenced by 2025.

“The sky is the limit,” he says. Erlich has studied the potential for unmasking the identities of anonymous donors of genetic data, and the study's consent document warns participants that “we cannot guarantee that your identity and/or data will never become known, which could have significant implications in some scenarios. We estimate that the risk for such a confidentiality breach is low but not zero.” Erlich and Pickrell have adopted what they call a “skin in the game” philosophy by making their own genomes publicly available.

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Study finds, almost one third of all cactus species are on the verge of extinction

Study finds, almost one third of all cactus species are on the verge of extinction | Amazing Science |

Cacti are members of the plant family Cactaceae. They are key components of New World arid ecosystems and are critical to the survival of many animal species. They provide a source of food and water for many species including deer, woodrats, rabbits, coyotes, turkeys, quails, lizards and tortoises, all of which help with cactus seed dispersal in return. Cactus flowers provide nectar to hummingbirds and bats, as well as bees, moths and other insects, which, in turn, pollinate the plants.

According to the new report, cacti are under increasing pressure from human activity, with more than 50 percent of all cactus species used by people. The illegal trade of live plants and seeds for the horticultural industry and private collections, as well as their unsustainable harvesting are the main threats to cacti, affecting 47 percent of threatened species.

Collectors from Europe and Asia are the biggest contributors to the illegal cactus trade. Specimens taken from the wild are particularly sought after due to their rarity.

“These findings are disturbing. They confirm that the scale of the illegal wildlife trade – including trade in plants – is much greater than we had previously thought, and that wildlife trafficking concerns many more species than the charismatic rhinos and elephants which tend to receive global attention,” said Inger Andersen, Director General of IUCN, who was not involved in the study. “We must urgently step up international efforts to tackle the illegal wildlife trade and strengthen the implementation of the CITES Convention on International Trade in Endangered Species, if we want to prevent the further decline of these species.”

“The startling results reflect the vital importance of funding and conducting assessments of the threatened status of all of the species in major groups of plants, such as the cacti,” said co-author Dr Kevin Gaston from the University of Exeter, UK. “Only by so doing will we gain the overall picture of what is happening to them, at a time when, as evidenced by the cacti, they may be under immense human pressures.”

Dr Gaston and his colleagues gathered data for each of 1,478 cactus species on their distribution, population trend, habitat preference and ecology, conservation actions, use and trade. “This included over 38,000 occurrence point records, which were used to generate preliminary range maps,” the scientists explained.

“This information was evaluated at a series of nine formal expert workshops, and then used by the participants to evaluate the extinction risk of each species using the IUCN Red List Categories and Criteria.”

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NASA's Curiosity Rover Confirms Ancient Lakes on Mars

NASA's Curiosity Rover Confirms Ancient Lakes on Mars | Amazing Science |

A new study from the team behind NASA's Mars Science Laboratory/Curiosity has confirmed that Mars was once, billions of years ago, capable of storing water in lakes over an extended period of time.

Using data from the Curiosity rover, the team has determined that, long ago, water helped deposit sediment into Gale Crater, where the rover landed more than three years ago. The sediment deposited as layers that formed the foundation for Mount Sharp, the mountain found in the middle of the crater today.

"Observations from the rover suggest that a series of long-lived streams and lakes existed at some point between about 3.8 to 3.3 billion years ago, delivering sediment that slowly built up the lower layers of Mount Sharp," said Ashwin Vasavada, Mars Science Laboratory project scientist at NASA's Jet Propulsion Laboratory in Pasadena, California, and co-author of the new Science article to be published Friday, Oct. 9.

The findings build upon previous work that suggested there were ancient lakes on Mars, and add to the unfolding story of a wet Mars, both past and present. Last month, NASA scientists confirmedcurrent water flows on Mars.

"What we thought we knew about water on Mars is constantly being put to the test,” said Michael Meyer, lead scientist for NASA’s Mars Exploration Program at NASA Headquarters in Washington. "It’s clear that the Mars of billions of years ago more closely resembled Earth than it does today. Our challenge is to figure out how this more clement Mars was even possible, and what happened to that wetter Mars."  

Before Curiosity landed on Mars in 2012, scientists proposed that Gale Crater had filled with layers of sediments. Some hypotheses were "dry," suggesting that sediment accumulated from wind-blown dust and sand. Others focused on the possibility that sediment layers were deposited in ancient lakes.

The latest results from Curiosity indicate that these wetter scenarios were correct for the lower portions of Mount Sharp. Based on the new analysis, the filling of at least the bottom layers of the mountain occurred mostly by ancient rivers and lakes over a period of less than 500 million years.

"During the traverse of Gale, we have noticed patterns in the geology where we saw evidence of ancient fast-moving streams with coarser gravel, as well as places where streams appear to have emptied out into bodies of standing water," Vasavada said. "The prediction was that we should start seeing water-deposited, fine-grained rocks closer to Mount Sharp. Now that we've arrived, we're seeing finely laminated mudstones in abundance that look like lake deposits."

The mudstone indicates the presence of bodies of standing water in the form of lakes that remained for long periods of time, possibly repeatedly expanding and contracting during hundreds to millions of years. These lakes deposited the sediment that eventually formed the lower portion of the mountain.  

"Paradoxically, where there is a mountain today there was once a basin, and it was sometimes filled with water," said John Grotzinger, the former project scientist for Mars Science Laboratory at the California Institute of Technology in Pasadena, and lead author of the new report. "We see evidence of about 250 feet (75 meters) of sedimentary fill, and based on mapping data from NASA's Mars Reconnaissance Orbiter and images from Curiosity's camera, it appears that the water-transported sedimentary deposition could have extended at least 500 to 650 feet (150 to 200) meters above the crater floor."

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Species found with 20 copies of p53, and it almost never develops cancer

Species found with 20 copies of p53, and it almost never develops cancer | Amazing Science |
Elephants’ genomes possess 20 copies of a tumor suppressing gene called P53, new research shows.

A longstanding mystery in biology is why the rate of cancer incidence in a species does not scale up with body size and longevity. Take elephants for instance, which live to approximately the same age as humans and have 100 times more cells, yet hardly ever develop cancer, a disease which is estimated to affect 40 percent of Americans at some point in their lives.

ou'd expect elephants would have higher rates of cancer, because elephants have significantly more cells than humans and more cells means more opportunities for cancerous mutations to occur. The fact that this isn’t the case gives rise to the conundrum known as Peto’s Paradox, the resolution of which may provide valuable insight into preventing cancer in humans.

Recently a team of geneticists led by Joshua Schiffman at the University of Utah made major headway in this direction when they studied the cells of Asian and African elephants from the San Diego Frozen Zoo and found that elephants’ genomes possessed 20 copies of a tumor suppressing gene called P53.

For the sake of comparison, the team looked at the genomes of more than 60 other species (including humans) and found that most only possess a single copy of this gene, suggesting that this redundancy in the elephant genome may finally explain the low rate of cancer in the species. The results of the study were published today in an editorial for the Journal of the American Medical Association.

“If you’re interested in cancer the first gene to look at is P53, it is the master tumor suppressor,” said Vincent Lynch, a human geneticist at the University of Chicago who published supporting research in a preprint study on Biorxiv. “We thought maybe elephants have another copy, but certainly not 19 more copies than other animals. This discovery is a big deal.”

According to Lynch, the canonical copy of the P53 gene along with the 19 retrogene copies make elephants more sensitive to DNA damage during cell replication. This hypersensitivity to genetic anomalies means that cells are quicker to ‘commit suicide’ when they are found to be damaged, halting the proliferation of potentially cancerous cells before it begins.

While multiple copies of the P53 gene might seem like a wholly positive evolutionary development, the overexpression of this gene likely comes with some tradeoffs, such as reproductive senescence or rapid aging.

“There is definitely a tradeoff, or else many other species would have evolved duplicate P53 genes by now,” said Lynch. “We don’t know what the tradeoff was, but elephants either found a way to deal with it or broke whatever constraint prevented organisms from evolving many P53 copies.”

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Genomic Data Growing Much Faster Than Twitter and YouTube

Genomic Data Growing Much Faster Than Twitter and YouTube | Amazing Science |

In the age of Big Data, it turns out that the largest, fastest growing data source lies within your cells. Quantitative biologists at the University of Illinois Urbana-Champaign and Cold Spring Harbor Laboratory, in New York, found that genomics reigns as champion over three of the biggest data domains around: astronomy, Twitter, and YouTube.

The scientists determined which would expand the fastest by evaluating acquisition, storage, distribution, and analysis of each set of data. Genomes are quantified by their chemical constructs, or base pairs. Genomics trumps other data generators because the genome sequencing rate doubles every seven months. If it maintains this rate, by 2020 more than one billion billion bases will be sequenced and stored per year, or 1 exabase. By 2025, researchers estimate the rate will be almost one zettabase, one trillion billion bases, per sequence per year.

90 percent of the genome data analyzed in the study was human. The scientists estimate that 100 million to 2 billion human genomes will be sequenced by 2025. That’s a four to five order of magnitude of growth in ten years, which far exceeds the other three data generators they studied.

“For human genomics, which is the biggest driver of the whole field, the hope is that by sequencing many, many individuals, that knowledge will be obtained to help predict and cure a variety of diseases,” says University of Illinois Urbana-Champaign co-author, Gene Robinson. Before it can be useful for medicine, genomes must be coupled with other genomic data sets, including tissue information.

One reason the rate is doubling so quickly is because scientists have begun sequencing individual cells. Single-cell genome sequencing technology for cancer research can reveal mutated sequences and aid in diagnosis. Patients may have multiple single cells sequenced, and there could end up being more than 7 billion genomes sequenced. That “is more than the population of the Earth,” says Michael Schatz, associate professor at Cold Spring Harbor Laboratory, in New York. “What does it mean to have more genomes than people on the planet?”

What it means is a mountain of information must be collected, filed, and analyzed. “Other disciplines have been really successful at these scales, like YouTube,” says Schatz. Today, YouTube users upload 300 hours of video every minute, and the researchers expect that rate to grow up to 1,700 hours per minute, or 2 exabytes of video data per year, by 2025. Google set up a seamless data-flowing infrastructure for YouTube. They provided really fast Internet, huge hard drive space, algorithms that optimized results, and a team of experienced researchers.

“We need that investment in genomics in order to understand your diseases, what kinds of treatments to apply, or answer questions about ancestry,” Schatz says. “By sequencing hundreds of millions of people, we can look through the pattern. We can get a sense of global community, and how incredibly connected we really are.”

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Fast and accurate: Groundbreaking computer program diagnoses cancer in two days

Fast and accurate: Groundbreaking computer program diagnoses cancer in two days | Amazing Science |

In by far the majority of cancer cases, the doctor can quickly identify the source of the disease, for example cancer of the liver, lungs, etc. However, in about one in 20 cases, the doctor can confirm that the patient has cancer -- but cannot find the source. These patients then face the prospect of a long wait with numerous diagnostic tests and attempts to locate the origin of the cancer before starting any treatment.

Now, researchers at DTU Systems Biology have combined genetics with computer science and created a new diagnostic technology based on advanced self-learning computer algorithms which -- on the basis of a biopsy from a metastasis -- can with 85 per cent certainty identify the source of the disease and thus target treatment and, ultimately, improve the prognosis for the patient.

Each year, about 35,000 people are diagnosed with cancer in Denmark, and many of them face the prospect of a long wait until the cancer has been diagnosed and its source located. However, even after very extensive tests, there will still be 2-3 per cent of patients where it has not been possible to find the origin of the cancer. In such cases, the patient will be treated with a cocktail of chemotherapy instead of a more appropriately targeted treatment, which could be more effective and gentler on the patient.

The newly developed method, which researchers are calling TumorTracer, are based on analyses of DNA mutations in cancer tissue samples from patients with metastasized cancer, i.e. cancer which has spread. The pattern of mutations is analyzed in a computer program which has been trained to find possible primary tumor localizations. The method has been tested on many thousands of samples where the primary tumour was already identified, and it has proven extremely precise. The next step will be to test the method on patients with unknown primary tumours. In recent years, researchers have discovered several ways of using genome sequencing of tumours to predict whether an individual cancer patient will benefit from a specific type of medicine.

This is a very effective method, and it is becoming increasingly common to conduct such sequencing for cancer patients. Associate Professor Aron Eklund from DTU Systems Biology explains: "We are very pleased that we can now use the same sequencing data together with our new algorithms to provide a much faster diagnosis for cancer cases that are difficult to diagnose, and to provide a useful diagnosis in cases which are currently impossible to diagnose. At the moment, it takes researchers two days to obtain a biopsy result, but we expect this time to be reduced as it becomes possible to do the sequencing increasingly faster. And it will be straightforward to integrate the method with the methods already being used by doctors."

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Cheap catalyst may lower fuel costs for hydrogen-powered cars

Cheap catalyst may lower fuel costs for hydrogen-powered cars | Amazing Science |
Sandia National Laboratories researchers seeking to make hydrogen a less expensive fuel for cars have upgraded a catalyst nearly as cheap as dirt — molybdenum disulfide, “molly” for short — to stand in for platinum, a rare element with the moonlike price of about $900 an ounce.

Sandia-induced changes elevate the plentiful, under-$2-per-ounce molly from being a welterweight outsider in the energy-catalyst field — put crudely, a lazy bum that never amounted to much — to a possible contender with the heavyweight champ.

The improved catalyst, expected to be the subject of an Oct. 7 Nature Communications paper, has already released four times the amount of hydrogen ever produced by molly from water. To Sandia postdoctoral fellow and lead author Stan Chou, this is just the beginning: “We should get far more output as we learn to better integrate molly with, for example, fuel-cell systems,” he said.

An additional benefit is that molly’s action can be triggered by sunlight, a feature which eventually may provide users an off-the-grid means of securing hydrogen fuel. Hydrogen fuel is desirable because, unlike gasoline, it doesn’t release carbon into the atmosphere when burned. The combustion of hydrogen with oxygen produces an exhaust of only water.

In Chou’s measured words, “The idea was to understand the changes in the molecular structure of molybdenum disulfide (MOS₂), so that it can be a better catalyst for hydrogen production: closer to platinum in efficiency, but earth-abundant and cheap. We did this by investigating the structural transformations of MOS₂ at the atomic scale, so that all of the materials parts that were ‘dead’ can now work to make H₂ [hydrogen].”

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Scientists build a digital piece of a rat's brain

Scientists build a digital piece of a rat's brain | Amazing Science |
If you want to learn how something works, one strategy is to take it apart and put it back together again. For 10 years, a global initiative called the Blue Brain Project--hosted at the Ecole Polytechnique Federale de Lausanne (EPFL)--has been attempting to do this digitally with a section of juvenile rat brain. The project presents a first draft of this reconstruction, which contains over 31,000 neurons, 55 layers of cells, and 207 different neuron subtypes, on October 8 in Cell.

Heroic efforts are currently being made to define all the different types of neurons in the brain, to measure their electrical firing properties, and to map out the circuits that connect them to one another. These painstaking efforts are giving us a glimpse into the building blocks and logic of brain wiring. However, getting a full, high-resolution picture of all the features and activity of the neurons within a brain region and the circuit-level behaviors of these neurons is a major challenge.

Henry Markram and colleagues have taken an engineering approach to this question by digitally reconstructing a slice of the neocortex, an area of the brain that has benefitted from extensive characterization. Using this wealth of data, they built a virtual brain slice representing the different neuron types present in this region and the key features controlling their firing and, most notably, modeling their connectivity, including nearly 40 million synapses and 2,000 connections between each brain cell type.

"The reconstruction required an enormous number of experiments," says Markram, of the EPFL. "It paves the way for predicting the location, numbers, and even the amount of ion currents flowing through all 40 million synapses."

Once the reconstruction was complete, the investigators used powerful supercomputers to simulate the behavior of neurons under different conditions. Remarkably, the researchers found that, by slightly adjusting just one parameter, the level of calcium ions, they could produce broader patterns of circuit-level activity that could not be predicted based on features of the individual neurons. For instance, slow synchronous waves of neuronal activity, which have been observed in the brain during sleep, were triggered in their simulations, suggesting that neural circuits may be able to switch into different "states" that could underlie important behaviors.
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Mysterious ripples found racing through planet-forming disc: Unique structures spotted around nearby star

Mysterious ripples found racing through planet-forming disc: Unique structures spotted around nearby star | Amazing Science |

sing images from the NASA/ESA Hubble Space Telescope and ESO's Very Large Telescope, astronomers have discovered never-before-seen structures within a dusty disc surrounding a nearby star. The fast-moving wave-like features in the disc of the star AU Microscopii are unlike anything ever observed, or even predicted, before now. The origin and nature of these features present a new mystery for astronomers to explore. The results are published in the journal Nature on 8 October 2015.

AU Microscopii, or AU Mic for short, is a young, nearby star surrounded by a large disc of dust [1]. Studies of such debris discs can provide valuable clues about how planets, which form from these discs, are created.

Astronomers have been searching AU Mic's disc for any signs of clumpy or warped features, as such signs might give away the location of possible planets. And in 2014 they used the powerful high-contrast imaging capabilities of ESO's newly installed SPHERE instrument, mounted on the Very Large Telescope for their search -- and discovered something very unusual.

"Our observations have shown something unexpected," explains Anthony Boccaletti of the Observatoire de Paris, France, lead author on the paper. "The images from SPHERE show a set of unexplained features in the disc which have an arch-like, or wave-like, structure, unlike anything that has ever been observed before."

Five wave-like arches at different distances from the star show up in the new images, reminiscent of ripples in water. After spotting the features in the SPHERE data the team turned to earlier images of the disc taken by the NASA/ESA Hubble Space Telescope in 2010 and 2011 to see whether the features were also visible in these [2]. They were not only able to identify the features on the earlier Hubble images -- but they also discovered that they had changed over time. It turns out that these ripples are moving -- and very fast!

"We reprocessed images from the Hubble data and ended up with enough information to track the movement of these strange features over a four-year period," explains team member Christian Thalmann (ETH Zürich, Switzerland). "By doing this, we found that the arches are racing away from the star at speeds of up to about 40,000 kilometers/hour!"

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Anti-parasite drugs sweep Nobel prize in medicine 2015

Anti-parasite drugs sweep Nobel prize in medicine 2015 | Amazing Science |
Three scientists who developed therapies against parasitic infections have won this year's Nobel Prize in Physiology or Medicine.

The winners are: William C. Campbell, a microbiologist at Drew University in Madison, New Jersey; Satoshi Ōmura, a microbiologist at Kitasato University in Japan; and Youyou Tu, a pharmacologist at the China Academy of Chinese Medical Sciences in Beijing.

In the 1970s, Campbell and Ōmura discovered a class of compounds, called avermectins, that kill parasitic roundworms that cause infections such as river blindness and lymphatic filariasis. The most potent of these was released onto the market in 1981 as the drug ivermectin.

Tu, who won a Lasker prize in 2011, developed the antimalarial drug artemisinin in the late 1960s and 1970s. She is the first China-based scientist to win a science Nobel. “This certainly is fantastic news for China. We expect more to come in the future,” says Wei Yang, president of the nation’s main research-funding agency, the National Natural Science Foundation of China.

In the 1960s, the main treatments for malaria were chloroquine and quinine, but they were proving increasingly ineffective. So in 1967, China established a national project against malaria to discover new therapies. Tu and her team screened more than 2,000 Chinese herbal remedies to search for drugs with antimalarial activity. An extract from the wormwood plant Artemisia annua proved especially effective and by 1972, the researchers had isolated chemically pure artemisinin.

That Tu won the Nobel prize is "great news", says Yi Rao, a neuroscientist at Peking University in Beijing who has researched the discovery of artemisinin. "I’m very happy about this. She totally deserves it.”

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Uncovering The Spliceosome’s Secrets

Uncovering The Spliceosome’s Secrets | Amazing Science |

With a high-resolution structure of the mRNA-splicing machine now in hand, a new era of biological and pharmaceutical discovery is dawning.

Watching fruit flies buzz around the ripe bananas in your kitchen, you might think it’s a tad ludicrous, mortifying even, that humans have a similar number of genes—about 23,000—as the lowly insects. We are certainly more complex than Drosophila melanogaster, so what gives?

The answer lies in the spliceosome, a cellular machine that, at first glance, seems to do some pretty straightforward pruning of messenger RNA (mRNA).

As the cell transcribes your DNA’s nucleic acid sequence into RNA, the spliceosome lands on the newly forming mRNA strand, where it chops out unnecessary pieces, called introns, and joins together the leftover, essential sequences, called exons. The edited mRNA is then exported to the cell’s cytoplasm, where it gets translated into protein.

Most strands of unspliced mRNA, otherwise known as pre-mRNA, have about a dozen introns that can be removed. Yet the spliceosome doesn’t always link together the remaining exons in a straightforward manner. Sometimes the spliceosome intentionally skips an exon, or it reorders the exons, or it unexpectedly leaves an intron in the mix. On average, this variable editing process produces about 10 different proteins for every gene that we have. “Alternative splicing allows us to make the most out of every gene,” says Joan Steitz at Yale University School of Medicine. “Splicing is the reason we can have the same number of genes as the fruit fly Drosophila and yet be more complicated.”

This splice ‘n’ dice machine gives us our complexity, but it’s also exceedingly complex itself. So complex, in fact, that it’s taken decades and many twists and turns for scientists to figure out how it works. Because the spliceosome is so sophisticated, small hiccups in its operation can lead to biological malfunction and, ultimately, to disease. Discovery of the tiny machine has been a boon to drug developers, who are already developing drugs that target the spliceosome. They hope such molecules will treat the myriad diseases linked to splicing malfunction, including many cancers, some forms of blindness, and 10% of genetic diseases, such as spinal muscular atrophy and certain types of dwarfism.

What researchers now know is that cells assemble the spliceosome from an enormous cast of protein and RNA characters. These players work in unison, carrying out a gymnastics routine worthy of the Super Bowl halftime show. Five protein-RNA complexes, called ribonucleoproteins, and some 200 proteins come and go during different stages of human splicing. This machinery forms temporary assemblies that prep and then edit pre-mRNA, converting it into mRNA that can be read by the ribosome, another enormous ribonucleoprotein engine responsible for turning mRNA into protein.

Although it’s only about half the size of the ribosome, the spliceosome—with its ever-changing parts and rearrangements—is a much more dynamic machine, says Reinhard Lührmann of the Max Planck Institute for Biophysical Chemistry, in Göttingen, Germany. This has made the spliceosome one of structural biology’s most desirable targets and one of its most challenging foes: Many in the field say that the ribosome was a comparatively easy structure to solve, and even that was a feat so grand it earned the structural biologists who accomplished it a Nobel Prize.

So it was that scientists gasped in collective shock when a team of researchers—newcomers to the spliceosome field—published the first near-atomic-resolution structure of the splicing machinery in August. The scientists, led by Yigong Shi of Tsinghua University, in China, also published an accompanying paper on spliceosome function for good measure (Science 2015, DOI:10.1126/science.aac7629 and 10.1126/science.aac8159). “It was a total bombshell,” Yale’s Steitz says. “I never thought we’d see a complete structure this soon.”

Via Integrated DNA Technologies
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Crucial hurdle overcome in quantum computing: A two-qubit logic gate in silicon

Crucial hurdle overcome in quantum computing: A two-qubit logic gate in silicon | Amazing Science |
The significant advance, by a team at the University of New South Wales (UNSW) in Sydney appears today in the international journal Nature.

"What we have is a game changer," said team leader Andrew Dzurak, Scientia Professor and Director of the Australian National Fabrication Facility at UNSW. "We've demonstrated a two-qubit logic gate - the central building block of a quantum computer - and, significantly, done it in silicon. Because we use essentially the same device technology as existing computer chips, we believe it will be much easier to manufacture a full-scale processor chip than for any of the leading designs, which rely on more exotic technologies.

"This makes the building of a quantum computer much more feasible, since it is based on the same manufacturing technology as today's computer industry," he added. The advance represents the final physical component needed to realize the promise of super-powerful silicon quantum computers, which harness the science of the very small - the strange behavior of subatomic particles - to solve computing challenges that are beyond the reach of even today's fastest supercomputers.

In classical computers, data are rendered as binary bits, which are always in one of two states: 0 or 1. However, a quantum bit (or 'qubit') can exist in both of these states at once, a condition known as a superposition. A qubit operation exploits this quantum weirdness by allowing many computations to be performed in parallel (a two-qubit system performs the operation on 4 values, a three-qubit system on 8, and so on). "If quantum computers are to become a reality, the ability to conduct one- and two-qubit calculations are essential," said Dzurak, who jointly led the team in 2012 who demonstrated the first ever silicon qubit, also reported in Nature.

But until now, it had not been possible to make two quantum bits 'talk' to each other - and thereby create a logic gate - using silicon. But the UNSW team - working with Professor Kohei M. Itoh of Japan's Keio University - has done just that for the first time. The result means that all of the physical building blocks for a silicon-based quantum computer have now been successfully constructed, allowing engineers to finally begin the task of designing and building a functioning quantum computer.

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Yale team identifies tiny non-coding RNA that controls cholesterol

Yale team identifies tiny non-coding RNA that controls cholesterol | Amazing Science |

High levels of LDL cholesterol — the “bad” cholesterol — increase the risk of heart disease, the leading cause of death in the United States. A Yale-led research team has identified an RNA molecule that plays an important role in regulating cholesterol. Therapeutic targeting of this non-coding RNA markedly reduces LDL while boosting HDL, the good cholesterol.

The finding, published online ahead of print in Nature Medicine, may lead to new therapies designed to decrease high cholesterol and heart disease. The researchers used a high-throughput screening technique to identify which tiny RNA molecules, or microRNAs, influence LDL cholesterol levels in the blood. They found that a particular RNA, known as miR-148a, modifies LDL receptors in liver cells of both mice and humans. They also discovered that miR-148a suppresses a gene that is critical for controlling levels of HDL cholesterol. 

“The key finding is the identification of another molecular target that could be used for treating high levels of bad cholesterol, and potentially treating cardiovascular disease,” said Carlos Fernandez-Hernando, associate professor of comparative medicine and pathology, and the study’s senior author. “By blocking this microRNA pharmacologically, we can reduce bad cholesterol.”

“Our work also establishes miR-148a as a promising therapeutic target to increase levels of good cholesterol,” noted Leigh Goedeke, a post-doctoral associate at Yale and lead author of the study. “We may have found a new treatment option to simultaneously reduce two risk factors of heart disease.”

Via Integrated DNA Technologies
Rakesh Yashroy's curator insight, October 8, 10:14 AM

A new (RNA) handle to control bad (LDL) cholesterol.