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Many genes are completely new inventions and not just modified copies of old genes

Many genes are completely new inventions and not just modified copies of old genes | Amazing Science | Scoop.it
It is easier to copy something than to develop something new - a principle that was long believed to also apply to the evolution of genes. According to this, evolution copies existing genes and then adapts the copies to new tasks. However, scientists from the Max Planck Institute for Evolutionary Biology in Plön have now revealed that new genes often form from scratch. Their analyses of genes from mice, humans and fish have shown that new genes are shorter than old ones and simpler in structure. These and other differences between young and old genes indicate that completely new genes can also form from previously unread regions of the genome. Moreover, the new genes often use existing regulatory elements from other genes before they create their own. 

When scientists decoded the first genes, they made a surprising discovery: similar variants of many genes are found even in very different organisms. This finding can be explained by the fact that evolution uses existing genes and adapts them to varying degrees for new tasks. The copying of genes plays an important role here. Copies are made of a gene and incorporated into the genome. Evolution can then experiment with these copies, while the original can continue to fulfil its function in its unaltered form. Completely new genes are very rare events in this model.

 

Rafik Neme and Diethard Tautz from the Max Planck Institute for Evolutionary Biology have now refuted this idea. Based on initial indications of the existence of completely new individual genes, they analysed over 20,000 mouse genes and traced their origins. According to their findings, genes that arose later in evolution are often shorter than those that have been in existence longer. Moreover, younger genes have fewer exons and fewer protein domains. This finding contradicts the accepted view: “If new genes are copies of old ones, a correlation of this kind between length and age would not be expected. However, a young gene needs time to acquire additional exons and introns. Thus, genes become longer with time and consist of numerous exons and introns,” explains Rafik Neme from the Max Planck Institute in Plön. Analyses of human, zebrafish and stickleback genes confirm the correlations discovered in the mouse.

 

The researchers also studied another way in which new genes can arise from existing genes: through a change in the reading frame. The genetic reading frame comprises three consecutive letters of the genetic alphabet. Each of these triplets stands for an amino acid which is translated from the genetic code. If this reading frame is shifted, new triplets arise and the genome is translated into completely different amino acids. “We found several cases, in which genes were overwritten due to such a change in the reading frame,” says Neme. An example of this is the Hoxa9 gene – a gene that controls embryonic development. In rodents and primates, this gene uses such an additional alternative reading frame.

 

According to the findings of the Plön-based researchers, around 60 percent of genes originate from our unicellular ancestors from the early phase of evolution. Large numbers of new genes were added in particular during the advent of fundamental evolutionary innovations: for example, the transition from unicellular to multicellular organisms and the emergence of vertebrates. A particularly high number of new genes also formed after the splitting of the mouse from other rodents. Interestingly, the scientists only found a few locations on the chromosomes in which newly formed genes accumulate. In fact, they are relatively evenly distributed across the entire genome. One of the few exceptions is a cluster of genes on chromosome 14 which control the activity of neurons, among other things.

 

New genes thus frequently arise from scratch in the course of evolution. They form in the gene-free sections of the genome, between the old genes. This often necessitates only minimal changes. “For example, genes need elements known as promoters which control their activity. It appears that new genes can appropriate promoters belonging to other genes and use them for their own purposes,” explains Diethard Tautz, Head of the Department of Evolutionary Genetics at the Max Planck Institute for Evolutionary Biology.

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Jack's curator insight, March 26, 2013 12:32 PM

This was simply fascinating, as i hadn't a clue as to how gene's form. I would especially be interested in delving deeper into the possible correlations between Chromosome 14, Neuron formations (in varying organisms) and possible DMT concentrations in the pineal gland of humans.

Jack's comment, March 26, 2013 12:42 PM
My thoughts: This is another interesting find that shows up our perception of evolution is not entirely a full one, as we are still learning the behavioral traits of genes as they grow. It's also (predictable but) interesting that as species diverge from their ancestral path a larger amount of new genes are found.
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Archeologists find 'ancient computer' from 200 BC used to track cycles of the solar system

Archeologists find 'ancient computer' from 200 BC used to track cycles of the solar system | Amazing Science | Scoop.it

Archaeologists set out Monday to use a revolutionary new deep sea diving suit to explore the ancient shipwreck where one of the most remarkable scientific objects of antiquity was found. The so-called Antikythera Mechanism, a 2nd-century BC device known as the world's oldest computer, was discovered by sponge divers in 1900 off a remote Greek island in the Aegean.


The highly complex mechanism of up to 40 bronze cogs and gears was used by the ancient Greeks to track the cycles of the solar system. It took another 1,500 years for an astrological clock of similar sophistication to be made in Europe.

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Growing "Dead Zone" in the Middle of the Arabian Sea May Threaten Fisheries and Short-Cut Food Chain

Growing "Dead Zone" in the Middle of the Arabian Sea May Threaten Fisheries and Short-Cut Food Chain | Amazing Science | Scoop.it
A growing “dead zone” in the middle of the Arabian Sea has allowed plankton uniquely suited to low- oxygen water to take over the base of the food chain. Their rise to dominance over the last decade could be disastrous for the predator fish that sustain 120 million people living on the sea’s edge. 
 
Scientists at Columbia University’s Lamont-Doherty Earth Observatory and their colleagues are the first to document the rapid rise of green Noctiluca scintillans, an unusual dinoflagellate that eats other plankton and draws energy from the sun via microscopic algae living within its cells. Noctiluca’s thick blooms color the Arabian Sea an emerald green each winter, from the shores of Oman on the west, to India and Pakistan on the east.
 
In a study published this week in Nature Communications, the researchers show how the millions of green algae living within Noctiluca’s cells allow it to exploit an oxygen-starved dead zone the size of Texas. They hypothesize that a tide of nutrient-rich sewage flowing from booming cities on the Arabian Sea is expanding the dead zone and feeding Noctiluca’s growth.


“These blooms are massive, appear year after year, and could be devastating to the Arabian Sea ecosystem over the long-term,” said the study’s lead author, Helga do Rosario Gomes, a biogeochemist at Lamont-Doherty.
 
Until recently, photosynthetic diatoms supported the Arabian Sea food chain. Zooplankton grazed on the diatoms, a type of algae, and were in turn eaten by fish. In the early 2000s, it all changed. The researchers began to see vast blooms of Noctiluca and a steep drop in diatoms and dissolved oxygen in the water column. Within a decade, Noctiluca had virtually replaced diatoms at the base of the food chain, marking the start of a colossal ecosystem shift.
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Tetraquarks Fuels Fierce Debate among Experts about Correct Picture of Matter

Tetraquarks Fuels Fierce Debate among Experts about Correct Picture of Matter | Amazing Science | Scoop.it

In August 2003, an experiment at the KEKB particle accelerator in Japan found hints of an unexpected particle: A composite of elementary building blocks called quarks, it contained not two quarks like mesons or three like the protons and neutrons that constitute all visible matter, but four — a number that theoretical physicists had come to think the laws of nature did not permit. This candidate “tetraquark” disintegrated so quickly that it seemed a stretch to call it a particle at all. But as similar formations appeared in experiments around the world, they incited a fierce debate among experts about the correct picture of matter at the quantum scale. Most believed tetraquarks were a new kind of miniature molecule — essentially, two orbiting mesons, each made of one regular quark and one antimatter quark, or antiquark — while a smaller contingent saw them as stand-alone particles in which the two quarks and two antiquarks overlapped in the same small volume of space.


All parties remained uncertain that tetraquarks were real — until one turned up in data from the Large Hadron Collider, the 17-mile, proton-smashing ring near Geneva. Detailed measurements reported in June in Physical Review Letters confirm that the particle, which was first detected in 2007 at the accelerator in Japan and designated Z(4430), is unambiguously a tetraquark. Now, the discovery is forcing physicists to extend their simple picture of quark interactions, or finally replace it with a more nuanced understanding.


And, to mixed reviews, the properties of Z(4430) clearly favor the underdog “diquark model” and the hypothesis that tetraquarks are genuine particles. The existence of such states would suggest a menagerie of exotic “hadrons,” or particles made of quarks, including groupings of more than four. It would also attest to subtle quantum interactions that may shape the cores of hypothetical “quark stars,” the piping hot quark soup thought to have saturated the infant universe, and, closer to home, the proton and neutron building blocks of ordinary matter.


The exact structure of hadrons is hidden in the folds of a 40-year-old theory of the strong force called quantum chromodynamics (QCD), an easy-to-write-down but infinitely self-referential and thus unsolvable set of equations. No one understands why QCD’s boundless complexity seems equivalent to the quark model, or in other words, why the dynamic confluence of quarks and gluons known as a proton “somehow behaves as if it’s a simple composite of three particles,” Braaten said. Up to now, all hadrons feigned such simplicity. Tetraquarks, which the renowned theorists Edward Witten and Sidney Coleman mistakenly argued in the 1970s were inconsistent with a simplified analogue of QCD, have turned out to be the first manifestations of the theory that aren’t also captured by the quark model.


Now, rather than abandon the quark model altogether, proponents of the molecular and diquark models hope to extend it to encompass the new discoveries.

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Vivid, full-color aluminum plasmonic pixels to create the LCD color display of the future

Vivid, full-color aluminum plasmonic pixels to create the LCD color display of the future | Amazing Science | Scoop.it

The quest to create camouflaging metamaterials that can “see” colors and automatically blend into the background is one step closer to reality, thanks to a breakthrough color-display technology unveiled this week by Rice University‘s Laboratory for Nanophotonics (LANP).


The new full-color display technology uses aluminum nanorods to create the vivid red, blue and green hues found in today’s top-of-the-line LCD televisions and monitors.


The technology is described in a new study in the Early Edition of the Proceedings of the National Academy of Sciences (PNAS) (open access).

The breakthrough is the latest in a string of recent discoveries by a Rice-led team that set out in 2010 to create metamaterials capable of mimicking the camouflage abilities of cephalopods — the family of marine creatures that includes squid, octopus and cuttlefish.


“Our goal is to learn from these amazing animals so that we could create new materials with the same kind of distributed light-sensing and processing abilities that they appear to have in their skins,” said LANP Director Naomi Halas, a co-author of the PNAS study.


She is the principal investigator on a $6 million Office of Naval Research grant for a multi-institutional team that includes marine biologists Roger Hanlon of the Marine Biological Laboratory in Woods Hole, Mass., and Thomas Cronin of the University of Maryland, Baltimore County.


“We know cephalopods have some of the same proteins in their skin that we have in our retinas, so part of our challenge, as engineers, is to build a material that can ‘see’ light the way their skin sees it, and another challenge is designing systems that can react and display vivid camouflage patterns,” Halas said.


LANP’s new color display technology delivers bright red, blue and green hues from five-micron-square pixels that each contains several hundred aluminum nanorods. By varying the length of the nanorods and the spacing between them, LANP researchers Stephan Link and Jana Olson showed they could create pixels that produced dozens of colors, including rich tones of red, green and blue that are comparable to those found in high-definition LCD displays.


“Aluminum is useful because it’s compatible with microelectronic production methods, but until now the tones produced by plasmonic aluminum nanorods have been muted and washed out,” said Link, associate professor of chemistry at Rice and the lead researcher on the PNAS study. “The key advancement here was to place the nanorods in an ordered array.”

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Mice carrying a human version of the speech gene FOXP2 excel at repetitive learning

Mice carrying a human version of the speech gene FOXP2 excel at repetitive learning | Amazing Science | Scoop.it
Maze tests reveal subtle advantage bestowed by human FOXP2 gene


As a uniquely human trait, language has long baffled evolutionary biologists. Not until FOXP2 was linked to a genetic disorder that caused problems in forming words could they even begin to study language’s roots in our genes. Soon after that discovery, a team at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, discovered that just two bases, the letters that make up DNA, distinguished the human and chimp versions of FOXP2.


To try to determine how those changes influenced the gene's function, that group put the human version of the gene in mice. In 2009, they observed that these "humanized" mice produced more frequent and complex alarm calls, suggesting the human mutations may have been involved in the evolution of more complex speech.


Another study showed that humanized mice have different activity in the part of the brain called the striatum, which is involved in learning, among other tasks. But the details of how the human FOXP2 mutations might affect real-world learning remained murky. To solve the mystery, the Max Planck researchers sent graduate student Christiane Schreiweis to work with Ann Graybiel, a neuroscientist at the Massachusetts Institute of Technology in Cambridge. She's an expert in testing mouse smarts by seeing how quickly they can learn to find rewards in mazes.


In humans and other animals, learning occurs in two ways, Graybiel explains. The first requires breaking the task at hand into distinct steps and performing them one at a time. For example, to learn to ride a bike, you first need to remember to hold the handlebars straight, then to put your feet on the pedals, and finally push with your legs to make the pedals go around. At some point, though, these step-by-step movements become habit and you switch to the second type of learning, which is based on unconscious repetition. Now, your bike riding improves simply by repeating the task, rather than thinking through each step.


To figure out which type of learning may have been aided by the changes in the human version of FOXP2, Schreiweis tested humanized mice in mazes. In some cases, the mice were required to remember that turning right always led to a reward, indicating that they had acquired the repetitive habit of turning right and their skill had become “unconscious.” In other cases, they had to look around and figure out that the reward was always on the east arm of the maze, a task that required the behavioral flexibility of step-by-step learning. That’s because, depending on where in the maze the mouse started, it had to look around to figure out where to go.


When humanized mice and wild mice were put in mazes that engaged both types of learning,the humanized mice mastered the route to the reward faster than their wild counterparts, report Schreiweis, Graybiel, and their colleagues online today in the Proceedings of the National Academy of Sciences. But when the mice were engaged in just one type of learning, humanized and wild mice did equally well on all the tests. That was unexpected; the researchers forecast that the humanized mice would have some advantage in at least one of the learning types.

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Early Earth less hellish than previously thought

Early Earth less hellish than previously thought | Amazing Science | Scoop.it

Conditions on Earth for the first 500 million years after it formed may have been surprisingly similar to the present day, complete with oceans, continents and active crustal plates.


This alternate view of Earth’s first geologic eon, called the Hadean, has gained substantial new support from the first detailed comparison of zircon crystals that formed more than 4 billion years ago with those formed contemporaneously in Iceland, which has been proposed as a possible geological analog for early Earth.


The study was conducted by a team of geologists directed by Calvin Miller, the William R. Kenan Jr. Professor of Earth and Environmental Sciences at Vanderbilt University, and published online this weekend by the journal Earth and Planetary Science Letters in a paper titled, “Iceland is not a magmatic analog for the Hadean: Evidence from the zircon record.”


From the early 20th century up through the 1980’s, geologists generally agreed that conditions during the Hadean period were utterly hostile to life. Inability to find rock formations from the period led them to conclude that early Earth was hellishly hot, either entirely molten or subject to such intense asteroid bombardment that any rocks that formed were rapidly remelted. As a result, they pictured the surface of the Earth as covered by a giant “magma ocean.”


Two schools of thought have emerged: One argues that Hadean Earth was surprisingly similar to the present day. The other maintains that, although it was less hostile than formerly believed, early Earth was nonetheless a foreign-seeming and formidable place, similar to the hottest, most extreme, geologic environments of today. A popular analog is Iceland, where substantial amounts of crust are forming from basaltic magma that is much hotter than the magmas that built most of Earth’s current continental crust.


“We reasoned that the only concrete evidence for what the Hadean was like came from the only known survivors: zircon crystals – and yet no one had investigated Icelandic zircon to compare their telltale compositions to those that are more than 4 billion years old, or with zircon from other modern environments,” said Miller.

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NASA unveils world's largest spacecraft welding tool for space launch system

NASA unveils world's largest spacecraft welding tool for space launch system | Amazing Science | Scoop.it

The largest spacecraft welding tool in the world, the Vertical Assembly Center officially is open for business at NASA's Michoud Assembly Facility in New Orleans. The 170-foot-tall, 78-foot-wide giant completes a world-class welding toolkit that will be used to build the core stage of America's next great rocket, the Space Launch System (SLS).

SLS will be the most powerful rocket ever built for deep space missions, including to an asteroid and eventually Mars. The core stage, towering more than 200 feet tall (61 meters) with a diameter of 27.6 feet (8.4 meters), will store cryogenic liquid hydrogen and liquid oxygen that will feed the rocket's four RS-25 engines.


"This rocket is a game changer in terms of deep space exploration and will launch NASA astronauts to investigate asteroids and explore the surface of Mars while opening new possibilities for science missions, as well," said NASA Administrator Charles Bolden during a ribbon-cutting ceremony at Michoud Friday.


The Vertical Assembly Center is part of a family of state-of-the-art tools designed to weld the core stage of SLS. It will join domes, rings and barrels to complete the tanks or dry structure assemblies. It also will be used to perform evaluations on the completed welds. Boeing is the prime contractor for the SLS core stage, including avionics.


"The SLS Program continues to make significant progress," said Todd May, SLS program manager. "The core stage and boosters have both completed critical design review, and NASA recently approved the SLS Program's progression from formulation to development. This is a major milestone for the program and proof the first new design for SLS is mature enough for production."

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Microscopic Diamonds Suggest Cosmic Impact Responsible for Younger Dryas Climate Change 12,800 Years Ago

Microscopic Diamonds Suggest Cosmic Impact Responsible for Younger Dryas Climate Change 12,800 Years Ago | Amazing Science | Scoop.it

A new study published in The Journal of Geology provides support for the theory that a cosmic impact event over North America some 13,000 years ago caused a major period of climate change known as the Younger Dryas stadial, or “Big Freeze.”

 

Around 12,800 years ago, a sudden, catastrophic event plunged much of the Earth into a period of cold climatic conditions and drought. This drastic climate change—the Younger Dryas—coincided with the extinction of Pleistocene megafauna, such as the saber-tooth cats and the mastodon, and resulted in major declines in prehistoric human populations, including the termination of the Clovis culture.

 

With limited evidence, several rival theories have been proposed about the event that sparked this period, such as a collapse of the North American ice sheets, a major volcanic eruption, or a solar flare.

 

However, in a study published in The Journal of Geology, an international group of scientists analyzing existing and new evidence have determined a cosmic impact event, such as a comet or meteorite, to be the only plausible hypothesis to explain all the unusual occurrences at the onset of the Younger Dryas period.

 

Researchers from 21 universities in 6 countries believe the key to the mystery of the Big Freeze lies in nanodiamonds scattered across Europe, North America, and portions of South America, in a 50-million-square-kilometer area known as the Younger Dryas Boundary (YDB) field.

 

Microscopic nanodiamonds, melt-glass, carbon spherules, and other high-temperature materials are found in abundance throughout the YDB field, in a thin layer located only meters from the Earth’s surface. Because these materials formed at temperatures in excess of 2200 degrees Celsius, the fact they are present together so near to the surface suggests they were likely created by a major extraterrestrial impact event.

 

In addition to providing support for the cosmic impact event hypothesis, the study also offers evidence to reject alternate hypotheses for the formation of the YDB nanodiamonds, such as by wildfires, volcanism, or meteoric flux.

 

The team’s findings serve to settle the debate about the presence of nanodiamonds in the YDB field and challenge existing paradigms across multiple disciplines, including impact dynamics, archaeology, paleontology, limnology, and palynology.

 

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Bernhard H. Schmitz's curator insight, September 16, 3:33 AM

And where is the center of the YDB field?

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Schizophrenia is not a single disease but rather consists of eight different genetically distinct classes

Schizophrenia is not a single disease but rather consists of eight different genetically distinct classes | Amazing Science | Scoop.it

New research shows that schizophrenia isn’t a single disease but a group of eight genetically distinct disorders, each with its own set of symptoms. The finding could be a first step toward improved diagnosis and treatment for the debilitating psychiatric illness.


The research at Washington University School of Medicine in St. Louis is reported online Sept. 15 in The American Journal of Psychiatry. About 80 percent of the risk for schizophrenia is known to be inherited, but scientists have struggled to identify specific genes for the condition.


Now, in a novel approach analyzing genetic influences on more than 4,000 people with schizophrenia, the research team has identified distinct gene clusters that contribute to eight different classes of schizophrenia.


“Genes don’t operate by themselves,” said C. Robert Cloninger, MD, PhD, one of the study’s senior investigators. “They function in concert much like an orchestra, and to understand how they’re working, you have to know not just who the members of the orchestra are but how they interact.” 

Cloninger, the Wallace Renard Professor of Psychiatry and Genetics, and his colleagues matched precise DNA variations in people with and without schizophrenia to symptoms in individual patients. In all, the researchers analyzed nearly 700,000 sites within the genome where a single unit of DNA is changed, often referred to as a single nucleotide polymorphism (SNP). They looked at SNPs in 4,200 people with schizophrenia and 3,800 healthy controls, learning how individual genetic variations interacted with each other to produce the illness. 

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Artificial spleen cleans up blood: Device improves survival in rats after severe infections

Artificial spleen cleans up blood: Device improves survival in rats after severe infections | Amazing Science | Scoop.it

Researchers have developed a high-tech method to rid the body of infections — even those caused by unknown pathogens. A device inspired by the spleen can quickly clean blood of everything from Escherichia coli to Ebola, researchers report on 14 September in Nature Medicine1.


The device uses a modified version of mannose-binding lectin (MBL), a protein found in humans that binds to sugar molecules on the surfaces of more than 90 different bacteria, viruses and fungi, as well as to the toxins released by dead bacteria that trigger the immune overreaction in sepsis.


The researchers coated magnetic nanobeads with MBL. As blood enters the biospleen device, passes by the MBL-equipped nanobeads, which bind to most pathogens. A magnet on the biospleen device then pulls the beads and their quarry out of the blood, which can then be routed back into the patient.


To test the device, Ingber and his team infected rats with either E. coli or Staphylococcus aureus and filtered blood from some of the animals through the biospleen. Five hours after infection, 89% of the rats whose blood had been filtered were still alive, compared with only 14% of those that were infected but not treated. The researchers found that the device had removed more than 90% of the bacteria from the rats' blood. The rats whose blood had been filtered also had less inflammation in their lungs and other organs, suggesting they would be less prone to sepsis.


The researchers then tested whether the biospleen could handle the volume of blood in an average adult human — about 5 liters. They ran human blood containing a mixture of bacteria and fungi through the biospleen at a rate of 1 litre per hour, and found that the device removed most of the pathogens within five hours.


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Anne Pascucci, MPA, CRA's curator insight, September 15, 10:54 AM

"Inspired by the spleen" Gotta be the first time in history those words were put together!

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Physicists find a new way to push electrons around

Physicists find a new way to push electrons around | Amazing Science | Scoop.it
Discovery might ultimately lead to new, more energy-efficient transistors and microchips.


When moving through a conductive material in an electric field, electrons tend to follow the path of least resistance — which runs in the direction of that field.


But now physicists at MIT and the University of Manchester have found an unexpectedly different behavior under very specialized conditions — one that might lead to new types of transistors and electronic circuits that could prove highly energy-efficient.


They’ve found that when a sheet of graphene — a two-dimensional array of pure carbon — is placed atop another two-dimensional material, electrons instead move sideways, perpendicular to the electric field. This happens even without the influence of a magnetic field — the only other known way of inducing such a sideways flow.


What’s more, two separate streams of electrons would flow in opposite directions, both crosswise to the field, canceling out each other’s electrical charge to produce a “neutral, chargeless current,” explains Leonid Levitov, an MIT professor of physics and a senior author of a paper describing these findings this week in the journal Science.

The exact angle of this current relative to the electric field can be precisely controlled, Levitov says. He compares it to a sailboat sailing perpendicular to the wind, its angle of motion controlled by adjusting the position of the sail.


Levitov and co-author Andre Geim at Manchester say this flow could be altered by applying a minute voltage on the gate, allowing the material to function as a transistor. Currents in these materials, being neutral, might not waste much of their energy as heat, as occurs in conventional semiconductors — potentially making the new materials a more efficient basis for computer chips.


“It is widely believed that new, unconventional approaches to information processing are key for the future of hardware,” Levitov says. “This belief has been the driving force behind a number of important recent developments, in particular spintronics” — in which the spin of electrons, not their electric charge, carries information.

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Japanese woman is first recipient of next-generation stem cells

Japanese woman is first recipient of next-generation stem cells | Amazing Science | Scoop.it

A Japanese woman in her 70s is the world's first recipient of cells derived from induced pluripotent stem cells, a technology that has created great expectations since it could offer the same advantages as embryo-derived cells but without some of the controversial aspects and safety concerns.


In a two-hour procedure, a team of three eye specialists lead by Yasuo Kurimoto of the Kobe City Medical Center General Hospital, transplanted a 1.3 by 3.0 millimeter sheet of retinal pigment epithelium cells into an eye of the Hyogo prefecture resident, who suffers from age-related macular degeneration.


The procedure took place at the Institute of Biomedical Research and Innovation Hospital, next to the RIKEN Center for Developmental Biology (CDB) where ophthalmologist Masayo Takahashi had developed and tested the epithelium sheets. She derived them from the patient's skin cells, after producing induced pluripotent stem (iPS) cells and then getting them to differentiate into retinal cells. Afterwards, the patient experienced no effusive bleeding or other serious problems, RIKEN has reported.


The patient “took on all the risk that go with the treatment as well as the surgery”, Kurimoto said in a statement released by RIKEN. “I have deep respect for bravery she showed in resolving to go through with it.”

He hit a somber note in thanking Yoshiki Sasai, a CDB researcher who recenty committed suicide. “This project could not have existed without the late Yoshiki Sasai’s research, which led the way to differentiating retinal tissue from stem cells.”


Kurimoto also thanked Shinya Yamanaka, a stem-cell scientist at Kyoto University “without whose discovery of iPS cells, this clinical research would not be possible.” Yamanaka shared the 2012 Nobel Prize in Physiology or Medicine for that work.


Kurimoto performed the procedure a mere four days after a health-ministry committee gave Takahashi clearance for the human trials (see 'Next-generation stem cells cleared for human trial').


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Hacked photosynthesis employing an algal enzyme could boost crop yields

Hacked photosynthesis employing an algal enzyme could boost crop yields | Amazing Science | Scoop.it

It is difficult to find fault with a process that can create food from sunlight, water and air, but for many plants, there is room for improvement. Researchers have taken an important step towards enhancing photosynthesis by engineering plants with enzymes from blue-green algae that speed up the process of converting carbon dioxide into sugars. The results, published today in Nature1, surmount a daunting hurdle on the path to boosting plant yields — a goal that is taking on increasing importance as the world’s population grows.


“With the limited ability to increase land use for agriculture, there’s a huge interest in trying to improve yield across all the major crops,” says Steven Gutteridge, a research fellow at chemical firm DuPont’s crop-protection division in Newark, Delaware.


Researchers have long wanted to increase yields by targeting Rubisco, the enzyme responsible for converting carbon dioxide into sugar. Rubisco is possibly the most abundant protein on Earth, and can account for up to half of all the soluble protein found in a leaf.


But one reason for its abundance is its inefficiency: plants produce so much Rubisco in part to compensate for its slow catalysis. Some have estimated that tinkering with Rubisco and ways to boost the concentration of carbon dioxide around it could generate up to a 60% increase2 in the yields of crops such as rice and wheat. Plant geneticist Maureen Hanson of Cornell University in Ithaca, New York, and her colleagues decided to borrow a faster Rubisco from the cyanobacterium Synechococcus elongatus.


A team including Hanson and plant physiologist Martin Parry of Rothamsted Research in Harpenden, UK, shuttled bacterial Rubisco genes into the genome of the chloroplast — the cellular organelle where photosynthesis takes place — in the tobacco plant (Nicotiana tabacum), a common model organism for genetic-engineering research. In some of the plants the researchers also added a bacterial protein that is thought to help Rubisco to fold properly. In others, they added a bacterial protein that structurally supports Rubisco.


Both lines of tobacco were able to use the bacterial Rubisco for photosynthesis, and both converted CO2 to sugar faster than normal tobacco1The work provides an important foundation for testing the hypothesis that a faster Rubisco can yield a more productive plant, says Donald Ort, a plant biologist at the University of Illinois at Urbana–Champaign.

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Numerous viruses found living in and on the bodies of healthy humans

Numerous viruses found living in and on the bodies of healthy humans | Amazing Science | Scoop.it
Human herpesvirus 6, pictured above, is just one of numerous viruses found living in and on the bodies of healthy humans. The virus commonly causes illness in young children but is found in the mouths of some healthy young adults, where its presence indicates an active viral infection despite a lack of symptoms.


On average, healthy individuals carry about five types of viruses on their bodies, the researchers report online in BioMed Central Biology. The study is the first comprehensive analysis to describe the diversity of viruses in healthy people.


The research was conducted as part of the Human Microbiome Project, a major initiative funded by the National Institutes of Health (NIH) that largely has focused on cataloging the body's bacterial ecosystems. "Most everyone is familiar with the idea that a normal bacterial flora exists in the body," said study co-author Gregory Storch, MD, a virologist and chief of the Division of Pediatric Infectious Diseases. "Lots of people have asked whether there is a viral counterpart, and we haven't had a clear answer. But now we know there is a normal viral flora, and it's rich and complex."


In 102 healthy young adults ages 18 to 40, the researchers sampled up to five body habitats: nose, skin, mouth, stool and vagina. The study's subjects were nearly evenly split by gender. At least one virus was detected in 92 percent of the people sampled, and some individuals harbored 10 to 15 viruses.


"We were impressed by the number of viruses we found," said lead author Kristine M. Wylie, PhD, an instructor of pediatrics. "We only sampled up to five body sites in each person and would expect to see many more viruses if we had sampled the entire body."


Scientists led by George Weinstock, PhD, at Washington University's Genome Institute, sequenced the DNA of the viruses recovered from the body, finding that each individual had a distinct viral fingerprint. (Weinstock is now at The Jackson Laboratory in Connecticut.) About half of people were sampled at two or three points in time, and the researchers noted that some of the viruses established stable, low-level infections.


The researchers don't know yet whether the viruses have a positive or negative effect on overall health but speculate that in some cases, they may keep the immune system primed to respond to dangerous pathogens while in others, lingering viruses increase the risk of disease.

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European gene pools seems to be derived from three ancient populations

European gene pools seems to be derived from three ancient populations | Amazing Science | Scoop.it

The modern European gene pool was formed when three ancient populations mixed within the last 7,000 years, Nature reports.


Blue-eyed, swarthy hunters mingled with brown-eyed, pale skinned farmers as the latter swept into Europe from the Near East. But another, mysterious population with Siberian affinities also contributed to the genetic landscape of the continent. The findings are based on analysis of genomes from nine ancient Europeans. Agriculture originated in the Near East - in modern Syria, Iraq and Israel - before expanding into Europe around 7,500 years ago.


Multiple lines of evidence suggested this new way of life was spread by a wave of migrants, who interbred with the indigenous European hunter-gatherers they encountered on the way. But assumptions about European origins were based largely on the genetic patterns of living people. The science of analysing genomic DNA from ancient bones has put some of the prevailing theories to the test, throwing up a few surprises.


In the new paper, Prof David Reich from the Harvard Medical School and colleagues studied the genomes of seven hunter-gatherers from Scandinavia, one hunter whose remains were found in a cave in Luxembourg and an early farmer from Stuttgart, Germany. The hunters arrived in Europe thousands of years before the advent of agriculture, hunkered down in southern refuges during the Ice Age and then expanded during a period called the Mesolithic, after the ice sheets had retreated from central and northern Europe.


Their genetic profile is not a good match for any modern group of people, suggesting they were caught up in the farming wave of advance. However, their genes live on in modern Europeans, to a greater extent in the north-east than in the south.


The early farmer genome showed a completely different pattern, however. Her genetic profile was a good match for modern people in Sardinia, and was rather different from the indigenous hunters.

But, puzzlingly, while the early farmers share genetic similarities with Near Eastern people at a global level, they are significantly different in other ways. Prof Reich suggests that more recent migrations in the farmers' "homeland" may have diluted their genetic signal in that region today.


Prof Reich explained: "The only way we'll be able to prove this is by getting ancient DNA samples along the potential trail from the Near East to Europe... and seeing if they genetically match these predictions or if they're different.


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Epstein-Barr Virus Cut Out Of Infected Human Cells By CRISPR-Cas9 Genome Editing

Epstein-Barr Virus Cut Out Of Infected Human Cells By CRISPR-Cas9 Genome Editing | Amazing Science | Scoop.it

Researchers at Stanford exploited the newly developed precision gene editing technology known CRISPR-Cas9 into an anti-virus technology by cutting out Epstein-Barr virus from the host genome of infected cells.  Infected cells successfully treated this way scale back proliferation caused by viral programs and engage in a self-destruct program known as “apoptosis”, or controlled cell death.  EBV is known to express a “brake” protein that suppresses apoptosis, a way to evade natural defense mechanisms.  The researchers also show importantly that there was no toxic effect on non-infected cells.


Epstein-Barr virus (EBV) is most often associated with mononucleosis but is also a cause of more serious conditions such as Burkitt’s lymphoma, nasopharyngeal cancer, and even autoimmune diseases.   No therapy exists but the CRISPR-Cas9 study is a valuable avenue as it overcomes two challenges posed by the virus.


The first challenge is during the latent stage of its life cycle it integrates into the genome and exhibits few targets for intervention. In fact most therapeutics under development are focused on attacking the virus during its active “lytic” stage so are not expected to work for cells with virus in latent stage.  In the latent stage the virus is still “on”, running a latency program that prompts the cell to proliferate.


The second challenge is that the virus encodes and expresses with the help of the host cell a “brake” protein BHRF1that stops the self-destruct signal stimulated by immune cells in effort to rid the body of cells that have become compromised.   The “brake” signal is one reason why EBV is frequently found in cancers: under normal conditions cells that start off on the path to cancer by acquiring mutations get stopped by the cell’s natural ability to undergo “programmed cell death” but EBV halts this process.


The technology for CRISPR-Cas9 entails two parts.  The first is the “cutting” enzyme, which is able to cut out pieces of viral DNA that has integrated into the host genome.  The second is a “guide RNA” which is a nucleic acid template that matches the desired target, in this case parts of the EBV sequence.  The researchers designed a CRISPR-Cas9 system that targets EBV based on its sequence in computer databases.


Once the cells were treated the researches found that latently infected cells no longer proliferated.  To ensure that this was not a toxic effect of treatment, the same CRISPR-Cas9 system was applied to cells that lack EBV, in which case there was no effect on proliferation.  This is an important point as some criticize CRISPR-Cas9 for its off-target effects in which unintentional cutting occurs.

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Scientists develop ultra-sensitive biosensor from molybdenite semiconductor material

Scientists develop ultra-sensitive biosensor from molybdenite semiconductor material | Amazing Science | Scoop.it

An atomically thin, two-dimensional, ultrasensitive semiconductor material for biosensing developed by University of California Santa Barbara (UCSB) researchers promises to push the boundaries of biosensing technology in many fields, from health care to environmental protection to forensic industries.


It’s based on molybdenum disulfide, or molybdenite (MoS2), as an alternative to graphene. Molybdenum disulfide — commonly used as a dry lubricant — surpasses graphene’s already high sensitivity, offers better scalability, and lends itself to high-volume manufacturing, the researchers say. Results of their study have been published in ACS Nano.

“This invention has established the foundation for a new generation of ultrasensitive and low-cost biosensors that can eventually allow single-molecule detection — the holy grail of diagnostics and bioengineering research,” said Samir Mitragotri, co-author and professor of chemical engineering and director of the Center for Bioengineering at UCSB.


The key, according to UCSB professor of electrical and computer engineering Kaustav Banerjee, who led this research, is MoS2’s band gap, a characteristic of a material that determines its electrical conductivity, the minimum amount of energy required for conduction; i.e., for an electron to break free of its bound state in a material — the gap between bound and free.


Semiconductor materials have a small but nonzero band gap and can be switched between conductive and insulated states controllably. The larger the band gap, the better its ability to switch states and to insulate leakage current in an insulated state. MoS2’s wide band gap allows current to travel but also prevents leakage and results in more sensitive and accurate readings.


Graphene has attracted wide interest as a biosensor due to its two-dimensional structure (which allows for excellent electrostatic control of the transistor channel by the gate) and its high surface-to-volume ratio. However, the sensitivity of a field-effect transistor (FET) biosensor based on graphene is fundamentally limited by graphene’s zero (fully conductive) band gap, which results in increased leakage current, leading to reduced sensitivity, explained Banerjee, who is also the director of the Nanoelectronics Research Lab at UCSB.


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Seems like something out of Star Trek.

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A single group of microorganisms may be the major producers of vitamin B12 in the oceans

A single group of microorganisms may be the major producers of vitamin B12 in the oceans | Amazing Science | Scoop.it

New research has determined that a single group of micro-organisms may be responsible for much of the world’s vitamin B12 production in the oceans, with implications for the global carbon cycle and climate change.


Although vitamin B12 is an essential molecule required by most life on this planet, it is only produced by a relatively small group of micro-organisms because it is so large and complex. For humans, vitamin B12 plays a key role in maintaining the brain and nervous systems, as well as DNA synthesis in cells throughout the body.


Professors Andew Doxey and Josh Neufeld, from the Faculty of Science at the University of Waterloo, led a study that discovered that Thaumarchaeota are likely dominant vitamin B12 producers. This group from the Archea domain has never before been associated with vitamin B12 synthesis.


"We assumed that most major global sources of something as fundamental as vitamin B12  would have already been characterized, and so this finding changes how we think about global production of this important vitamin," said Professor Doxey.


The researchers, both of whom teach in the Department of Biology at Waterloo, used computational methods to search through vast amounts of sequenced environmental DNA for the genes that make vitamin B12, identifying the likely producers in marine and freshwater environments.


"Because Thaumarchaeota are among the most abundant organisms on the planet, especially in marine environments, their contribution to vitamin B12 production have enormous implications for ecology and metabolism in the oceans," said Professor Neufeld.


The availability of vitamin B12 may control how much or how little biological productivity by phytoplankton takes place in the oceans. Phytoplankton remove carbon dioxide from the atmosphere through photosynthesis, much like plants and trees, thus reducing the atmospheric concentration of this greenhouse gas, the largest contributor to global warming.


The research also found that proportions of archaeal B12synthesis genes increased with ocean depth and were more prevalent in winter and polar waters, suggesting that archaeal vitamin B12 may be critical for the survival of other species in both the deep and cold marine environments.

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An Autonomous, Optoelectronic Camouflage Material Inspired By Octopus Skin

An Autonomous, Optoelectronic Camouflage Material Inspired By Octopus Skin | Amazing Science | Scoop.it

An interdisciplinary team of scientists and engineers has developed a thin, flexible 4-layer material that autonomously camouflages itself to the surroundings by optically evaluating the background and changing its pattern to match much like how the skin of an octopus or chameleon does so in the wild.  The system mimics different patterns of background quickly within 1 to 2 seconds.  To date there has been no other similar system which includes the crucial capabilities of sensing and actuation in a distributed manner.


The inspiration for this creation came from understanding of the skin of cephalopods (examples of which include octopus, squid, cuttlefish etc.), sea creatures that mimic in full color and with greater resolution the appearance of their environment.  Celphalopod skin has faster response times, from 250-750 milliseconds.  The prototype material is much simpler, arranged as an array of 16 x 16 relatively large, 1 mm square “pixels” that change from black to white and back again.


Response times are slower too in the 1 to 2 second range.

There is no overall camera system to detect the background and no central processing that controls the patterning of the material. In real octopuses, the eyes are involved, but the skin has its own photoreceptors similar to those found in the retina.  The designed layered material works in the latter, distributed way, by integrating distributed optical sensors that monitor its surroundings and then commanding independent optical “actuators” to adapt dynamically.

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Method to detect single protein analytes without the use of any label out of 2,000 times greater background

Method to detect single protein analytes without the use of any label out of 2,000 times greater background | Amazing Science | Scoop.it

In future, some diseases might be diagnosed earlier and treated more effectively. Researchers at the Max Planck Institute for the Science of Light in Erlangen have developed an optical method that makes individual proteins, such as the proteins characteristic of some cancers, visible. Other methods that achieve this only work if the target biomolecules have first been labelled with fluorescent tags; In general, however, that approach is difficult or even impossible. By contrast, with their method, coined iSCAT, the researchers in Erlangen are able to directly detect the scattered light of individual proteins via their shadows. The method could not only make biomedical diagnoses more sensitive, but also provide new insights into fundamental biological processes.


A biosensor for the scattered light of individual unmarked biomolecules such as proteins and tumour markers may facilitate medical diagnosis. The biodetector, that a team led by V. Sandoghdar has developed at the Max Planck Institute for the Science of Light, uses the interferometric method iSCAT.


Vahid Sandoghdar, Director at the Max Planck Institute for the Science of Light, and Marek Piliarik, a post doc in Sandoghdar’s division, are now able to produce a much clearer image without the need for elaborate attachment of luminous markers to the target proteins. This is possible thanks to iSCAT, short for interferometric detection of scattering. The researchers shine laser light onto a microscope slide on which the relevant proteins have been captured with appropriate biochemical lures. The proteins scatter the laser light, thus casting a shadow, albeit a very weak one. “iSCAT not only promises more sensitive diagnosis of diseases such as cancers, but will also shed light on many fundamental biochemical processes in nature,” says Vahid Sandoghdar.


The Erlangen-based researchers have succeeded to achieve a high level of sensitivity for individual proteins by applying some tricks, and because they were not hampered by a misconception that a lot of other scientists have: “Until now it was thought that if you want to detect scattered light from nanoparticles, you have to eliminate all background light,” explains Vahid Sandoghdar. “However, in recent years we’ve realized that it is more advantageous to illuminate the sample strongly and visualize the feeble signal of a tiny nanoparticle as a shadow against the intense background light.” The researchers therefore allow the background light to interfere with the weak scattered light so that the desired signal is amplified.


However, at this stage they are still unable to detect the shadows of a single protein in the interference image, because the pattern is akin to that of a television broadcast in black and white that is distorted by a lot of noise. The interferometric detection method is so sensitive that any small roughness or contamination of the sample carrier will also cast a shadow that could in fact swamp the protein signal.


Nevertheless, this difficulty did not put off the two researchers. They have learned to eliminate the noise by applying a second trick. They take a snapshot with the iSCAT microscope not only after they have dripped a solution containing the desired protein onto the sample holder but also before. “Since most of the optical noise generated by nanoscopic irregularities of the sample do not change, we can subtract one image from the other and thus eliminate the noise,” says Piliarik. The target proteins then stand out clearly from the background as dark spots, even though the shadow of the protein is only one ten-thousandth or even one hundred-thousandth as dark as the background.


Marek Piliarik and Vahid Sandoghdar are able to detect various proteins as shadows under the microscope not only in pure solutions. They can also home in on individual proteins in mixtures containing concentrations of other proteins that are up to 2000 times greater.

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Final pieces to the circadian clock puzzle found

Final pieces to the circadian clock puzzle found | Amazing Science | Scoop.it

Researchers at the UNC School of Medicine have discovered how two genes – Period and Cryptochrome – keep the circadian clocks in all human cells in time and in proper rhythm with the 24-hour day, as well as the seasons. The finding, published today in the journal Genes and Development, has implications for the development of drugs for various diseases such as cancers and diabetes, as well as conditions such as metabolic syndrome, insomnia, seasonal affective disorder, obesity, and even jetlag.

"Discovering how these circadian clock genes interact has been a long-time coming," said Aziz Sancar, MD, PhD, Sarah Graham Kenan Professor of Biochemistry and Biophysics and senior author of the Genes and Development paper. "We've known for a while that four proteins were involved in generating daily rhythmicity but not exactly what they did. Now we know how the clock is reset in all cells. So we have a better idea of what to expect if we target these proteins with therapeutics."


In all human cells, there are four genes – Cryptochrome, Period, CLOCK, and BMAL1 – that work in unison to control the cyclical changes in human physiology, such as blood pressure, body temperature, and rest-sleep cycles. Previously, scientists found that CLOCK and BMAL1 work in tandem to kick start the circadian clock. These genes bind to many other genes and turn them on to express proteins. This allows cells, such as brain cells, to behave the way we need them to at the start of a day.


Specifically, CLOCK and BMAL1 bind to a pair of genes called Period and Cryptochrome and turn them on to express proteins, which – after several modifications – wind up suppressing CLOCK and BMAL1 activity. Then, the Period and Cryptochrome proteins are degraded, allowing for the circadian clock to begin again.


"It's a feedback loop," said Sancar, who discovered Cryptochrome in 1998. "The inhibition takes 24 hours. This is why we can see gene activity go up and then down throughout the day."


But scientists didn't know exactly how that gene suppression and protein degradation happened at the back end. In fact, during experiments using one compound to stifle Cryptochrome and another drug to hinder Period, other researchers found inconsistent effects on the circadian clock, suggesting that Cryptochrome and Period did not have the same role. Sancar, a member of the UNC Lineberger Comprehensive Cancer Center who studies DNA repair in addition to the circadian clock, thought the two genes might have complementary roles. His team conducted experiments to find out.


Chris Selby, PhD, a research instructor in Sancar's lab, used two different kinds of genetics techniques to create the first-ever cell line that lacked both Cryptochrome and Period. Each cell has two versions of each gene. Selby knocked out all four copies.


Then Rui Ye, PhD, a postdoctoral fellow in Sancar's lab and first author of the Genes and Development paper, put Period back into the new mutant cells. But Period by itself did not inhibit CLOCK-BMAL1; it actually had no active function inside the cells.


Next, Ye put Cryptochrome alone back into the cell line. He found that Cryptochrome not only suppressed CLOCK and BMAL1, but it squashed them indefinitely. "The Cryptochrome just sat there," Sancar said. "It wasn't degraded. The circadian clock couldn't restart."


For the final experiment, Sancar's team added Period to the cells with Cryptochrome. As Period's protein accumulated inside cells, the scientists could see that it began to remove the Cryptochrome, as well as CLOCK and BMAL1. This led to the eventual degradation of Cryptochrome, and then the CLOCK-BMAL1 genes were free to restart the circadian clock anew to complete the 24-hour cycle. "What we've done is show how the entire clock really works," Sancar said.

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Astronomers observe a Thorne–Żytkow Object, where a neutron star appears to be inside a red giant star

Astronomers observe a Thorne–Żytkow Object, where a neutron star appears to be inside a red giant star | Amazing Science | Scoop.it

As all who study astronomy know, one of the most incredible things about the universe is the never-ending potential for wonderful discoveries that sound more like fiction than fact.  With this paper, the authors are pushing the boundaries of fiction into fact with the potential discovery of a new exotic object, known as a Thorne–Żytkow object (TZO).  First predicted in the 1970s by Kip Thorne and AnnaŻytkow, these bodies occur when a neutron star in a binary system with a red supergiant (RSG) merges into the second star.  This merger creates an unusual system where there is a neutron star surrounded by a large, diffuse envelope of material.  The system still produces most of its energy at the core of the material envelope through thermonuclear energy, and a smaller amount (about 5% of the total energy) from the gravitational accretion of material onto the neutron star.  Eventually, after several hundred years, the core of the envelope and the neutron star would merge, resulting in either a larger neutron star or a black hole.


TZOs are fascinating objects in a special state of a binary system’s evolution, and there is a lot of new physics that can be learned from such a system, but there has been one problem with them until now: they are identical in appearance to typical red supergiants.  There are a lot of normal red supergiants no matter where you look, and knowing if a RSG is a TZO is only possible when you look in detail at the stellar spectra for the over-abundance of lithium and other specific heavy metals.  Finding a TZO is definitely a “find the needle in a haystack” kind of observing problem!


Luckily for science, the authors successfully found the needle.  They did this by conducting a survey of stars in the Milky Way andMagellanic Clouds from previous stellar surveys where effective temperature and photometry data indicated a RSG.  The authors then took the stellar spectra of the 62 stars in their sample at Apache Point Observatory in New Mexico and the Magellan telescopes in Chile, and then analyzing the spectra for the ratios between elements in order to see whether there were any anomalies.  In one case, for a star known as HV 2112, in the Small Magellanic Cloud, and found it had unusually high concentrations of lithium, molybdenum, and rubidium.  These elements, especially in the amounts found in HV 2112, are indications the star is not a RSG at all, but rather a TZO.  Some spectral features were also observed that are not predicted in TZO models, but the authors aknowledge that available TZO models are older and do not take into account some recent advances in stellar convection modeling.


This TZO discovery, if confirmed from follow-up theoretical models, is exciting because HV 2112 would be the prototype of a whole new kind of system.  But beyond being a scientific curiousity, a TZO can provide a new environment for answering several questions, such as a new fate of massive binary systems.  Further, because this is a completely new kind of stellar interior, we are also looking at a different kind of stellar nuclear synthesis process for heavy metals than anything previously observed.  It is like being handed a new laboratory in which to test astrophysical ideas, and to distinguish the fact from fiction.

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New math explains dynamics of fluid systems that mimic many peculiarities of quantum mechanics

New math explains dynamics of fluid systems that mimic many peculiarities of quantum mechanics | Amazing Science | Scoop.it

In the early days of quantum physics, in an attempt to explain the wavelike behavior of quantum particles, the French physicist Louis de Broglie proposed what he called a “pilot wave” theory. According to de Broglie, moving particles — such as electrons, or the photons in a beam of light — are borne along on waves of some type, like driftwood on a tide.


Physicists’ inability to detect de Broglie’s posited waves led them, for the most part, to abandon pilot-wave theory. Recently, however, a real pilot-wave system has been discovered, in which a drop of fluid bounces across a vibrating fluid bath, propelled by waves produced by its own collisions.


In 2006, Yves Couder and Emmanuel Fort, physicists at Université Paris Diderot, used this system to reproduce one of the most famous experiments in quantum physics: the so-called “double-slit” experiment, in which particles are fired at a screen through a barrier with two holes in it.


In the latest issue of the journal Physical Review E (PRE), a team of MIT researchers, in collaboration with Couder and his colleagues, report that they have produced the fluidic analogue of another classic quantum experiment, in which electrons are confined to a circular “corral” by a ring of ions. In the new experiments, bouncing drops of fluid mimicked the electrons’ statistical behavior with remarkable accuracy.


“This hydrodynamic system is subtle, and extraordinarily rich in terms of mathematical modeling,” says John Bush, a professor of applied mathematics at MIT and corresponding author on the new paper. “It’s the first pilot-wave system discovered and gives insight into how rational quantum dynamics might work, were such a thing to exist.”


John Bush, a professor of applied mathematics at MIT, believes that pilot-wave theory deserves a second look. That’s because Yves Couder, Emmanuel Fort, and colleagues at the University of Paris Diderot have recently discovered a macroscopic pilot-wave system whose statistical behavior, in certain circumstances, recalls that of quantum systems.


Couder and Fort’s system consists of a bath of fluid vibrating at a rate just below the threshold at which waves would start to form on its surface. A droplet of the same fluid is released above the bath; where it strikes the surface, it causes waves to radiate outward. The droplet then begins moving across the bath, propelled by the very waves it creates.


“This system is undoubtedly quantitatively different from quantum mechanics,” Bush says. “It’s also qualitatively different: There are some features of quantum mechanics that we can’t capture, some features of this system that we know aren’t present in quantum mechanics. But are they philosophically distinct?”

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Next-Gen Glaucoma Treatments: Microfluidic Implant And Smart Phone App Monitoring

Next-Gen Glaucoma Treatments: Microfluidic Implant And Smart Phone App Monitoring | Amazing Science | Scoop.it

Stanford Professor of Bioengineering and Applied Physics, Stephen Quake, and Head of the Ophthalmic Science and Engineering Lab at Bar Ilan University Dr. Yossi Mandell teamed up to create a state-of-the-art intraocular implant that will change glaucoma treatment by making intraocular pressure readings frequent, easy and convenient.


Made to fit inside a commonly used intraocular lens prosthetic, and implanted through simple surgery such as for cataracts which many glaucoma patients already receive, the device measures the pressure of the fluid within the eye.  A smart phone app or a wearable device such as Google Glass allows the wearer to take “snapshots” of the device that reports back the pressure.


The lens device holds a tiny tube, capped at one end and opened on the other, filled with gas. As the fluid pressure pushes against the gas, a marked scale permits reading of the intraocular pressure.  The implant does not interfere with vision, as proven in an Air Force-approved vision test, and in one reported study the implant was responsible for changes to treatment for glaucoma in nearly 80 percent of the wearers.


Nearly 2.2 million Americans battle the eye disease glaucoma.  Patients endure weekly visits to the ophthalmologist to have the disease monitored and treated. The disease is characterized by increasing pressure inside the eye, which results in a continuous loss of a specific type of retinal cell accompanied by degradation of the optic nerve fiber.  The mechanism that links pressure to damage is not clear but there is correlation between the intensity of pressure readings and level of damage.

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Future of Oceanography: Crowdsourcing the Collection of Oceanographic Data

Future of Oceanography: Crowdsourcing the Collection of Oceanographic Data | Amazing Science | Scoop.it

We live on a vast, underexplored planet that is largely ocean. Despite modern technology, Global Positioning System (GPS) navigation, and advanced engineering of ocean vessels, the ocean is unforgiving, especially in rough weather. Coastal ocean navigation, with risks of running aground and inconsistent weather and sea patterns, can also be challenging and hazardous. In 2012, more than 100 international incidents of ships sinking, foundering, grounding, or being lost at sea were reported (http://en.wikipedia.org/wiki/List_of_shipwrecks_in_2012). Even a modern jetliner can disappear in the ocean with little or no trace[1], and the current costs and uncertainty associated with search and rescue make the prospects of finding an object in the middle of the ocean daunting [2].


Notwithstanding satellite constellations, autonomous vehicles, and more than 300 research vessels worldwide (www.wikipedia.org/wiki/List_of_research_vessels_by_country), we lack fundamental data relating to our oceans. These missing data hamper our ability to make basic predictions about ocean weather, narrow the trajectories of floating objects, or estimate the impact of ocean acidification and other physical, biological, and chemical characteristics of the world's oceans. To cope with this problem, scientists make probabilistic inferences by synthesizing models with incomplete data. Probabilistic modeling works well for certain questions of interest to the scientific community, but it is difficult to extract unambiguous policy recommendations from this approach. The models can answer important questions about trends and tendencies among large numbers of events but often cannot offer much insight into specific events. For example, probabilistic models can tell us with some precision the extent to which storm activity will be intensified by global climate change but cannot yet attribute the severity of a particular storm to climate change. Probabilistic modeling can provide important insights into the global traffic patterns of floating debris but is not of much help to search-and-rescue personnel struggling to learn the likely trajectory of a particular piece of debris left by a wreck.


Oceanographic data are incomplete because it is financially and logistically impractical to sample everywhere. Scientists typically sample over time, floating with the currents and observing their temporal evolution (the Langrangian approach), or they sample across space to cover a gradient of conditions—such as temperature or nutrients (the Eulerian approach). These observational paradigms have various strengths and weaknesses, but their fundamental weakness is cost. A modern ocean research vessel typically costs more than US$30,000 per day to operate—excluding the full cost of scientists, engineers, and the cost of the research itself. Even an aggressive expansion of oceanographic research budgets would not do much to improve the precision of our probabilistic models, let alone to quickly and more accurately locate missing objects in the huge, moving, three-dimensional seascape. Emerging autonomous technologies such as underwater gliders and in situ biological samplers (e.g., environmental sample processors) help fill gaps but are cost prohibitive to scale up. Similarly, drifters (e.g., the highly successful Argo floats program) have proven very useful for better defining currents, but unless retrieved after their operational lifetime, they become floating trash, adding to a growing problem.


Long-term sampling efforts such as the continuous plankton recorder in the North Sea and North Atlantic [3] provide valuable data on decadal trends and leveraged English Channel ferries to accomplish much of the sampling. Modernizing and expanding this approach is a goal of citizen science initiatives.

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Lorraine Chaffer's curator insight, September 12, 7:38 PM

Option topic: Marine environmental change and management