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Another Side Effect Of Chemotherapy: The 'Chemo Brain'

Another Side Effect Of Chemotherapy: The 'Chemo Brain' | Amazing Science | Scoop.it

It's well-known that chemotherapy often comes with side effects like fatigue, hair loss and extreme nausea. What's less well-known is how the cancer treatment affects crucial brain functions, like speech and cognition.

 

For Yolanda Hunter, a 41-year-old hospice nurse, mother of three and breast cancer patient, these cognitive side effects of chemotherapy were hard to miss. "I could think of words I wanted to say," Hunter says. "I knew what I wanted to say. ... There was a disconnect from my brain to my mouth."

 

Before getting treated for cancer, Hunter led a busy, active lifestyle. But the effects of chemotherapy on her brain made it difficult for her to do even the most basic things.

 

"I couldn't even formulate a smile. I had no expression," she says. "I might feel things on the inside, but it didn't translate to the outside. ... It literally felt like you were trying to fight your way through fog."

 

Some cancer patients call this mental fog "chemo brain." And now researchers are trying to quantify exactly what chemo brain really is. 

Oncologist Jame Abraham, a professor at West Virginia University, says about a quarter of patients undergoing chemotherapy have trouble processing numbers, using short-term memory and focusing their attention.

 

Using positron emission tomography, or PET, scans to measure blood flow and brain activity, Abraham looked at the brains of 128 breast cancer patients before they started chemotherapy and then again, six months later. On the second brain scan, he found significant decreases in brain activity in regions responsible for memory, attention, planning and prioritizing. Those results were recently presented at the Radiological Society of North America meeting.

 

Chemotherapy "can cause damage to bone marrow, hair cells, mucosa," Abraham says. "In the same way, it can potentially cause changes in the brain cells, too."

  
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How bees naturally vaccinate their babies against some diseases found in their environment

How bees naturally vaccinate their babies against some diseases found in their environment | Amazing Science | Scoop.it
When it comes to vaccinating their babies, bees don't have a choice—they naturally immunize their offspring against specific diseases found in their environments. And now for the first time, scientists have discovered how they do it.


Researchers from Arizona State University, University of Helsinki, University of Jyväskylä and Norwegian University of Life Sciences made the discovery after studying a bee blood protein called vitellogenin. The scientists found that this protein plays a critical, but previously unknown role in providing bee babies protection against disease.


The findings appear in the journal PLOS Pathogens"The process by which bees transfer immunity to their babies was a big mystery until now. What we found is that it's as simple as eating," said Gro Amdam, a professor with ASU's School of Life Sciences and co-author of the paper. "Our amazing discovery was made possible because of 15 years of basic research on vitellogenin. This exemplifies how long-term investments in basic research pay off."


Co-author Dalial Freitak, a postdoctoral researcher with University of Helsinki adds: "I have been working on bee immune priming since the start of my doctoral studies. Now almost 10 years later, I feel like I've solved an important part of the puzzle. It's a wonderful and very rewarding feeling!"


In a honey bee colony, the queen rarely leaves the nest, so worker bees must bring food to her. Forager bees can pick up pathogens in the environment while gathering pollen and nectar. Back in the hive, worker bees use this same pollen to create "royal jelly"—a food made just for the queen that incidentally contains bacteria from the outside environment.


After eating these bacteria, the pathogens are digested in the gut and transferred to the body cavity; there they are stored in the queen's 'fat body'—an organ similar to a liver. Pieces of the bacteria are then bound to vitellogenin—a protein—and carried via blood to the developing eggs. Because of this, bee babies are 'vaccinated' and their immune systems better prepared to fight diseases found in their environment once they are born. Vitellogenin is the carrier of these immune-priming signals, something researchers did not know until now.


While bees vaccinate their babies against some diseases, many pathogens are deadly and the insects are unable to fight them.

But now that Amdam and Freitak understand how bees vaccinate their babies, this opens the door to creating the first edible and natural vaccine for insects.


"We are patenting a way to produce a harmless vaccine, as well as how to cultivate the vaccines and introduce them to bee hives through a cocktail the bees would eat. They would then be able to stave off disease," said Freitak.


One destructive disease that affects bees is American Foul Brood, which spreads quickly and destroys hives. The bacterium infects bee larvae as they ingest food contaminated with its spores. These spores get their nourishment from the larvae, eventually killing them. This disease is just one example where the researchers say a vaccine would be extremely beneficial.

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Quantum states in a nano-object manipulated using a mechanical system

Quantum states in a nano-object manipulated using a mechanical system | Amazing Science | Scoop.it

Scientists at the Swiss Nanoscience Institute at the University of Basel have used resonators made from single-crystalline diamonds to develop a novel device in which a quantum system is integrated into a mechanical oscillating system. For the first time, the researchers were able to show that this mechanical system can be used to coherently manipulate an electron spin embedded in the resonator - without external antennas or complex microelectronic structures. The results of this experimental study will be published in Nature Physics.


In previous publications, the research team led by Georg H. Endress Professor Patrick Maletinsky described how resonators made from single-crystalline diamonds with individually embedded electrons are highly suited to addressing the spin of these electrons. These diamond resonators were modified in multiple instances so that a carbon atom from the diamond lattice was replaced with a nitrogen atom in their crystal lattices with a missing atom directly adjacent. In these "nitrogen-vacancy centers," individual electrons are trapped. Their "spin" or intrinsic angular momentum is examined in this research.


When the resonator now begins to oscillate, strain develops in the diamond's crystal structure. This, in turn, influences the spin of the electrons, which can indicate two possible directions ("up" or "down") when measured. The direction of the spin can be detected with the aid of fluorescence spectroscopy.


In this latest publication, the scientists have shaken the resonators in a way that allows them to induce a coherent oscillation of the coupled spin for the first time. This means that the spin of the electrons switches from up to down and vice versa in a controlled and rapid rhythm and that the scientists can control the spin status at any time. This spin oscillation is fast compared with the frequency of the resonator. It also protects the spin against harmful decoherence mechanisms.


It is conceivable that this diamond resonator could be applied to sensors - potentially in a highly sensitive way - because the oscillation of the resonator can be recorded via the altered spin. These new findings also allow the spin to be coherently rotated over a very long period of close to 100 microseconds, making the measurement more precise. Nitrogen-vacancy centers could potentially also be used to develop a quantum computer. In this case, the quick manipulation of its quantum states demonstrated in this work would be a decisive advantage.

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New “aqueous solar flow” battery 20 percent more efficient than today’s lithium-iodine batteries

New “aqueous solar flow” battery 20 percent more efficient than today’s lithium-iodine batteries | Amazing Science | Scoop.it

After debuting the world’s first solar air battery last fall, researchers at The Ohio State University have now reached a new milestone.

In the Journal of the American Chemical Society, they report that their patent-pending design—which combines a solar cell and a battery into a single device—now achieves a 20 percent energy savings over traditional lithium-iodine batteries.


The 20 percent comes from sunlight, which is captured by a unique solar panel on top of the battery, explained Yiying Wu, professor of chemistry and biochemistry at Ohio State. The solar panel is now a solid sheet, rather than a mesh as in the previous design. Another key difference comes from the use of a water-based electrolyte inside the battery.


Because water circulates inside it, the new design belongs to an emerging class of batteries called aqueous flow batteries.


“The truly important innovation here is that we’ve successfully demonstrated aqueous flow inside our solar battery,” Wu said. As such, it is the first aqueous flow battery with solar capability. Or, as Wu and his team have dubbed it, the first “aqueous solar flow battery.”


“It’s also totally compatible with current battery technology, very easy to integrate with existing technology, environmentally friendly and easy to maintain,” he added.


Researchers around the world are working to develop aqueous flow batteries because they could theoretically provide affordable power grid-level energy storage someday.


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Philae Lander Finds Organic Compounds on Comet 67P/Churyumov-Gerasimenko

Philae Lander Finds Organic Compounds on Comet 67P/Churyumov-Gerasimenko | Amazing Science | Scoop.it

In a research article by Dr Fred Goesmann from the Max Planck Institute for Solar System Research in Germany and his colleagues, the team analyzes the composition of Comet 67P/Churyumov-Gerasimenko using the COmetary SAmpling and Composition (COSAC) instrument, designed to identify organic compounds in the comet and thus contribute to a deeper understanding of the history of life on Earth.


The instrument collected molecules from 10 km (6.2 miles) above the comet surface, after the initial touchdown, and at the final site. 16 organic compounds were identified, divided into six classes of organic molecules (alcohols, carbonyls, amines, nitriles, amides and isocyanates). Of these, four organic compounds were detected for the first time on a comet (methyl isocyanate, acetone, propionaldehyde and acetamide).


Almost all the compounds detected are potential precursors, products, combinations or by-products of each other, which provides a glimpse of the chemical processes at work in a cometary nucleus, and even in the collapsing Solar Nebula in the very early Solar System.


COSAC identified a large number of nitrogen compounds but no sulfur compounds, contrary to what the ROSINA instrument on board Rosetta had observed. This suggests that the chemical composition varies depending on the area sampled.


A special issue of the journal Science highlights seven new studies that delve into the data that has been collected by ESA’s probe Philae on 67P/Churyumov-Gerasimenko.

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Ebola vaccine trial proves 100% successful in Guinea

Ebola vaccine trial proves 100% successful in Guinea | Amazing Science | Scoop.it

A vaccine against Ebola has been shown to be 100% successful in trials conducted during the outbreak in Guinea and is likely to bring the west African epidemic to an end, experts say. The results of the trials involving 4,000 people are remarkable because of the unprecedented speed with which the development of the vaccine and the testing were carried out.


Scientists, doctors, donors and drug companies collaborated to race the vaccine through a process that usually takes more than a decade in just 12 months.


“Having seen the devastating effects of Ebola on communities and even whole countries with my own eyes, I am very encouraged by today’s news,” said Børge Brende, the foreign minister of Norway, which helped fund the trial.

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A Giant Burst on Tree of Life Comes into View

A Giant Burst on Tree of Life Comes into View | Amazing Science | Scoop.it

A new technique for finding and characterizing microbes has boosted the number of known bacteria by almost 50 percent, revealing a hidden world all around us.


A team of microbiologists based at the University of California, Berkeley, recently figured out one such new way of detecting life. At a stroke, their work expanded the number of known types — or phyla — of bacteria by nearly 50 percent, a dramatic change that indicates just how many forms of life on earth have escaped our notice so far.


“Some of the branches in the tree of life had been noted before,” said Chris Brown, a student in the lab of Jill Banfield and lead author of the paper. “With this study we were able to fill in many gaps.”


As an organizational tool, the tree of life has been around for a long time. Lamarck had his version. Darwin had another. The basic structure of the current tree goes back 40 years to the microbiologist Carl Woese, who divided life into three domains: eukaryotes, which include all plants and animals; bacteria; and archaea, single-celled microorganisms with their own distinct features. After a point, discovery came to hinge on finding new ways of searching. “We used to think there were just plants and animals,” said Edward Rubin, director of the U.S. Department of Energy’s Joint Genome Institute. “Then we got microscopes, and got microbes. Then we got small levels of DNA sequencing.”


DNA sequencing is at the heart of this current study, though the researchers’ success also owes a debt to more basic technology. The team gathered water samples from a research site on the Colorado River near the town of Rifle, Colo. Before doing any sequencing, they passed the water through a pair of increasingly fine filters — with pores 0.2 and 0.1 microns wide — and then analyzed the cells captured by the filters. At this point they already had undiscovered life on their hands, for the simple reason that scientists had not thought to look on such a tiny scale before. “Most people assumed that bacteria were bigger, and most bacteria are bigger,” Rubin said. “Banfield has shown that there are whole populations that are very small.”


The researchers extracted the DNA from the cellular material and sent it to the Joint Genome Institute for sequencing. What they got back was a mess. Imagine being handed a box of pieces from thousands of different jigsaw puzzles and having to assemble them without knowing what any of the final images look like. That’s the challenge researchers face when performing metagenomic analysis — sequencing scrambled genetic material from many organisms at once.


The Berkeley team began the reassembly process with algorithms that assembled bits of the sequenced genetic code into slightly longer strings called contigs. “You no longer have tiny pieces of DNA, you have bigger pieces,” Brown said. “Then you figure out which of these larger pieces are part of a single genome.”


This part of the process, in which contigs are combined to reconstruct the genome sequence, is called genome binning. To execute it, the researchers relied on another set of algorithms, customized for the task by Itai Sharon, a co-author of the study. They also assembled some of the genomes manually, making decisions about what goes where based on the fact that some characteristics are consistent for a given genome. For example, the percentage of Gs and Cs will be similar on any part of an organism’s DNA.


When the assembly was complete, the researchers had eight full bacterial genomes and 789 draft genomes that were roughly 90 percent complete. Some of the organisms had been glimpsed before; many others were completely new.


Via Integrated DNA Technologies
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Engineered ribosomes could pave way for designer enzymes and synthetic cells

Engineered ribosomes could pave way for designer enzymes and synthetic cells | Amazing Science | Scoop.it

By hijacking the cellular machinery that makes proteins, bioengineers have developed a tool that could allow them to better understand protein synthesis, explore how antibiotics work and convert cells into custom chemical factories.


All life owes its existence to the ribosome, a huge, hardworking molecular machine that reads RNA templates transcribed from DNA, and uses the information to string together amino acids into proteins. A cell requires functioning ribosomes to survive — but they are difficult to engineer. If the engineered molecules deviate too far from the standard design, the cell will die.


“An engineered ribosome learns to do better what you want, but it starts to forget how to do its normal job,” says biochemist Alexander Mankin of the University of Illinois in Chicago.


Mankin teamed up with biochemical engineer Michael Jewett of Northwestern University in Evanston, Illinois, and others to create a ribosome that engineers could tinker with. The results of their handiwork are published in Nature1.


Ribosomes are conglomerates of RNA and protein, hundreds of times larger than typical enzymes. RNA is thought to be responsible for the bulk of a ribosome’s work, which is is considerable — it produces protein at a rate of up to 20 amino acids a second with a remarkably low error rate. “The ribosome deserves all possible respect,” says Mankin.


It is these properties that draw the attention of bioengineers such as Jewett. These researchers would like to create ribosomes that could do other chemical reactions and spit out novel polymers, or incorporate unnatural amino acids into proteins that could be used as drugs.


Each ribosome contains two clumps of snarled RNA molecules, a small subunit and a large one. The subunits come together to translate a messenger RNA sequence into protein, and then separate. They assemble again when it is time to make another protein, although not necessarily with the same partners. “In a way they are very promiscuous,” says Mankin.


That promiscuity hindered efforts to engineer ribosomes to incorporate unnatural amino acids or other compounds. Engineered and natural subunits mixed and matched, reducing the cell's ability to produce normal proteins. The solution, Mankin and Jewett's team decided, was to marry together two engineered subunits. It was unclear whether the approach would work: it was thought that ribosomes exist in two distinct units because it is necessary for their function.


The researchers used a strand of RNA to tether the large and the small subunit together, toiling for months to get the length and location of the link just right so that the machine could still function. “We certainly came close, several times, to saying ‘OK, biology wins',” says Jewett. The team screened its tethered ribosomes in Escherichia coli cells that lacked functioning RNA, and eventually found engineered ribosomes that worked well enough to support some growth, albeit slow. They then tested their platform to confirm that a tethered ribosome could operate side-by-side with natural ribosomes.


The result unlocks a molecular playground for bioengineers: by tethering the artificial subunits together, they can tweak the engineered machines to their liking without halting cell growth, says Joseph Puglisi, a structural biologist at Stanford University in California. Puglisi hopes to harness the system to study how the ribosome functions. James Collins, a bioengineer at the Massachusetts Institute of Technology in Cambridge, says that his lab may use the system to study antibiotics — many of which work by binding to bacterial ribosomes.

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Facial recognition tool that 'works in darkness'

Facial recognition tool that 'works in darkness' | Amazing Science | Scoop.it

Two scientists at a German university have developed a tool which recognizes a person's face in complete darkness. The technology identifies a person from their thermal signature and matches infrared images with ordinary photos. It uses a deep neural network system to process the pictures and recognise people in bad light or darkness.


However, the technology is not being used commercially yet, with one of its creators, Dr Saquib Sarfraz, saying: "There are no plans to roll it out." Dr Sarfraz, who worked on the project with colleague Dr Rainer Stiefelhagen at the Karlsruhe Institute of Technology, told the BBC: "We have been doing research on face recognition already for several years and have a scientific interest in the problem.


"Our presented work on face recognition in thermal images is currently not used outside the research lab." In tests, the technology had an 80% success rate, and worked 55% of the time with one image, and Dr Sarfraz said that "more training data and a more powerful architecture" could produce better results.


With a higher success rate, the tool could potentially be used by police to catch and identify criminals.


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Scientists discover important genetic pathway for aging

Scientists discover important genetic pathway for aging | Amazing Science | Scoop.it

It’s no secret that corporate America has declared a war on death. Fueled by the collective fears of 76 million baby boomers, heavyweights like Google and Synthetic Genomics have waded in to the life extension business, bringing with them millions of dollars in funding. The result has been an uptick in the number of discoveries made in gerontology – the study of aging. But despite swamping the issue with money and media attention –an actual cure to aging remains elusive. That may soon change.


Last week, a discovery published by scientists at Northwestern University detailed a new genetic switch that may prove to be a watershed in the fight against aging. It also sheds light on one of the most significant controversies in longevity research – whether aging is the result of numerous bodily systems independently breaking down, or is controlled by a single genetic pathway.


Needless to say, much rests on the result of this question. If aging is a result of multiple independent processes, than the problem is something of a Medusa’s head, where each source of decrepitude must be tackled individually. If on the other hand, aging has a single genetic source, one could hypothetically throw the switch and cure aging in one swoop.


Unfortunately, in biological systems the more complex answers tend to be the right ones. This is why perhaps many scientists were reluctant to believe there could be a single genetic pathway controlling the aging process. However, in what might turn out to be a stroke of luck, there does indeed seem to be a single switch responsible for the aging process — at least in the C. elegans worms on which the research at Northwestern was conducted.  Fortunately for us, humans possess the same genetic pathway as the worms, so there is reason to believe the research will apply to homo-sapiens and many other animals as well.


So what exactly is the genetic switch that Dr. Morimoto and his colleagues at Northwester discovered? The story begins eight hours into the life of the C. elegans worm, when their stress protective mechanisms suddenly go into decline. After the first telltale indicators of cellular stress begin occurring, the worm’s body rapidly deteriorates and in a number of weeks the creature is dead.


The researchers traced the decline to the gamete cells within the worm, and from there to a particular genetic pathway that is initialized when the worm reaches sexual maturity. Their research indicates that at the very time the worm reaches sexual maturity and starts creating gamete cells, it begins sending a signal to other cell tissues to turn off protective mechanisms, thereby setting into motion the aging process. Now that the exact pathway has been discovered, scientists will begin working on ways to foil that process and block the signal that causes the decline in cellular resilience.


Many ancient eastern traditions such as the yogic system in India and Taoists of ancient China also connected longevity with gamete cells. In Vedic mythology, the God possessing the knowledge of the Sanjivani mantra capable of bestowing immortality is named Sukracharya, which literally translates as “semen teacher.” While it remains unclear whether Morimoto and his colleagues have discovered the fabled Sanjivani, one thing is sure: they will not be the last to go looking for it. And with the deep pockets of Google and Big Pharma backing this quest, it’s increasingly likely that results will be forthcoming.


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Cassini Spies "Unusual" Red Arcs on Saturn's Icy Moon Tethys

Cassini Spies "Unusual" Red Arcs on Saturn's Icy Moon Tethys | Amazing Science | Scoop.it

Recently acquired images of Tethys, one of the ice moons of Saturn, have given scientists their best view yet of several “unusual, arc-shaped reddish streaks” that sweep across the satellite’s surface.


Images taken using clear, green, infrared and ultraviolet spectral filters were combined to create the enhanced-color views, which highlight subtle color differences across the icy moon’s surface at wavelengths not visible to human eyes.


A few of the red arcs can be seen faintly in observations made earlier in the Cassini mission, which has been in orbit at Saturn since 2004. But the color images for this observation, obtained in April 2015, are the first to show large northern areas of Tethys under the illumination and viewing conditions necessary to see the arcs clearly. As the Saturn system moved into its northern hemisphere summer over the past few years, northern latitudes have become increasingly well illuminated. As a result, the arcs have become clearly visible for the first time.


“The red arcs really popped out when we saw the new images,” said Cassini participating scientist Paul Schenk of the Lunar and Planetary Institute in Houston. “It’s surprising how extensive these features are.”

The origin of the features and their reddish color is a mystery to Cassini scientists. Possibilities being studied include ideas that the reddish material is exposed ice with chemical impurities, or the result of outgassing from inside Tethys. They could also be associated with features like fractures that are below the resolution of the available images.


Except for a few small craters on Saturn’s moon Dione, reddish-tinted features are rare on other moons of Saturn. Many reddish features do occur, however, on the geologically young surface of Jupiter’s moon Europa.


“The red arcs must be geologically young because they cut across older features like impact craters, but we don’t know their age in years.” said Paul Helfenstein, a Cassini imaging scientist at Cornell University, Ithaca, New York, who helped plan the observations. “If the stain is only a thin, colored veneer on the icy soil, exposure to the space environment at Tethys’ surface might erase them on relatively short time scales.”

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Mirror-Touch Synesthesia: This Doctor Knows Exactly How You Feel

Mirror-Touch Synesthesia: This Doctor Knows Exactly How You Feel | Amazing Science | Scoop.it

Dr. Salinas himself has a rare medical condition, one that stands in marked contrast to his patients’: While Josh appeared unresponsive even to his own sensations, Salinas is peculiarly attuned to the sensations of others. If he sees someone slapped across the cheek, Salinas feels a hint of the slap against his own cheek. A pinch on a stranger’s right arm might become a tickle on his own. “If a person is touched, I feel it, and then I recognize that it’s touch,” Salinas says.

The condition is called mirror-touch synesthesia, and it has aroused significant interest among neuroscientists in recent years because it appears to be an extreme form of a basic human trait. In all of us, mirror neurons in the premotor cortex and other areas of the brain activate when we watch someone else’s behaviors and actions. Our brains map the regions of the body where we see someone else caressed, jabbed, or whacked, and they mimic just a shade of that feeling on the same spots on our own bodies. For mirror-touch synesthetes like Salinas, that mental simulacrum is so strong that it crosses a threshold into near-tactile sensation, sometimes indistinguishable from one’s own. Neuroscientists regard the condition as a state of “heightened empathic ability.”

This might sound like a superpower of sorts, a mystical connection between one person’s subjective experience and another’s. But to be clear, Salinas cannot read minds. He doesn’t know whether Josh felt the impact of the reflex hammer, and the tingling in his kneecap says more about his own extraordinary nervous system than it does about that of his patient. What’s more, for those who experience mirror-touch synesthesia—an estimated 1.6 percent of the general population—the condition is often more debilitating than it is empowering.

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Host-Targeted Antibodies Effective Against Malaria

Host-Targeted Antibodies Effective Against Malaria | Amazing Science | Scoop.it

All antimalarial drugs produced to date target the disease-causing parasite, but a new study in the Journal of Experimental Medicine shows that drugs which target host proteins are also a potential avenue for new interventions.


This study targets a protein that the most deadly malaria parasite, Plasmodium falciparum, relies on to invade human red blood cells. Targeting this human protein blocks an essential interaction, and can wipe out an established malaria infection in mice in less than three days.


Targeting host factors may help researchers overcome one of the biggest challenges to malaria control: drug resistance. Drug resistance arises due to genetic changes in the rapidly-evolving Plasmodium falciparum parasite, which, in Southeast Asia, has rendered one of the current front-line antimalarials, artemisinin, largely ineffective. Researchers are battling to find a solution before the resistant strains spread to other malaria endemic areas, including Africa, a region that accounts for 90 per cent of malaria deaths worldwide. By targeting host factors, rather than the parasite factors, the researchers believe that parasites are far less likely to develop resistance to the new drug.


"This counter-intuitive approach to malaria treatment leaves the parasite powerless," explains Dr. Zenon Zenonos, a first author from the Wellcome Trust Sanger Institute. "If the parasite can't bind to the surface of our red blood cells and invade, it can't reach the next stage in its lifecycle, so it dies. There's nothing the parasite can do to get round it, as the interaction is absolutely essential for infection to occur."


PfRH5, a protein required by the malaria parasite, needs to bind to basigin, a protein that is displayed on the outer surface of human red blood cells, for the cell to become infected. Blockade of the PfRH5-basigin interaction renders the parasite unable to enter red blood cells, and therefore the infection is wiped out.


"When we discovered the PfRH5-basigin interaction in 2011, we knew we had found a chink in the malaria parasite's armour, the question was how to exploit it," says Dr Gavin Wright, corresponding author from the Wellcome Trust Sanger Institute. "Using PfRH5 in a vaccine is one approach, but we were also interested to see if we could disrupt the interaction in the opposite direction rather than by conventionally targeting the parasite. This has significant advantages in preventing the ability of the parasite to develop resistance."


To study the likely human response to therapy, the antibody targeting basigin described in this study was tested in humanised mice that have had the majority of their immune cells and blood cells replaced with those from their human counterparts. In the mice, levels of infection fell to essentially undetectable levels within 72 hours of being treated with low doses of the antibody targeting basigin. Importantly, no side toxic effects were observed in the mouse models that were treated with the antibody in these experiments.

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Photonic heating and cooling with light leads to ultrafast PCR-based DNA diagnostics

Photonic heating and cooling with light leads to ultrafast PCR-based DNA diagnostics | Amazing Science | Scoop.it

A new technology developed by UC Berkeley bioengineers promises to make a workhorse lab tool cheaper, more portable and many times faster by accelerating the heating and cooling of genetic samples with the switch of a light. This turbocharged thermal cycling, described in a paper published July 31 in the journal Light: Science & Application, greatly expands the clinical and research applications of the polymerase chain reaction (PCR) test, with results ready in minutes instead of an hour or more.


The PCR test, which amplifies a single copy of a DNA sequence to produce thousands to millions of copies, has become vital in genomics applications, ranging from cloning research to forensic analysis to paternity tests. PCR is used in the early diagnosis of hereditary and infectious diseases, and for analysis of ancient DNA samples of mummies and mammoths.


Using light-emitting diodes, or LEDs, the UC Berkeley researchers were able to heat electrons at the interface of thin films of gold and a DNA solution. They clocked the speed of heating the solution at around 55 degrees Fahrenheit per second. The rate of cooling was equally impressive, coming in at about 43.9 degrees per second.


“PCR is powerful, and it is widely used in many fields, but existing PCR systems are relatively slow,” said study senior author Luke Lee, a professor of bioengineering. “It is usually done in a lab because the conventional heater used for this test requires a lot of power and is expensive. Because it takes an hour or longer to complete each test, it is not practical for use for point-of-care diagnostics. Our system can generate results within minutes.”


To pick up the pace of this thermal cycling, Lee and his team of researchers took advantage of plasmonics, or the interaction between light and free electrons on a metal’s surface. When exposed to light, the free electrons get excited and begin to oscillate, generating heat. Once the light is off, the oscillations and the heating stop.


Gold, it turns out, is a popular metal for this plasmonic photothermal heating because it is so efficient at absorbing light. It has the added benefit of being inert to biological systems, so it can be used in biomedical applications.


For their experiments, the researchers used thin films of gold that were 120 nanometers thick, or about the width of a rabies virus. The gold was deposited onto a plastic chip with microfluidic wells to hold the PCR mixture with the DNA sample.


The light source was an array of off-the-shelf LEDs positioned beneath the PCR wells. The peak wavelength of the blue LED light was 450 nanometers, tuned to get the most efficient light-to-heat conversion. The researchers were able to cycle from 131 degrees to 203 degrees Fahrenheit 30 times in less than five minutes.


They tested the ability of the photonic PCR system to amplify a sample of DNA, and found that the results compared well with conventional PCR tests. “This photonic PCR system is fast, sensitive and low-cost,” said Lee, who is also co-director of the Berkeley Sensor and Actuator Center. “It can be integrated into an ultrafast genomic diagnostic chip, which we are developing for practical use in the field. Because this technology yields point-of-care results, we can use this in a wide range of settings, from rural Africa to a hospital ER.”


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Scientists harvest energy from beam's self-induced, self-sustaining vibrations in airflow

Scientists harvest energy from beam's self-induced, self-sustaining vibrations in airflow | Amazing Science | Scoop.it

In an attempt to harvest the kinetic energy of airflow, researchers have demonstrated the ability to harvest energy directly from the vibrations of a flexible, piezoelectric beam placed in a wind tunnel. While the general approach to harvesting energy from these "aeroelastic" vibrations is to attach the beam to a secondary vibrating structure, such as a wing section, the new design eliminates the need for the secondary vibrating structure because the beam is designed so that it produces self-induced and self-sustaining vibrations. As a result, the new system can be made very small, which increases its efficiency and makes it more practical for applications, such as self-powered sensors.


The researchers, Mohamed Y. Zakaria, Mohammad Y. Al-Haik, and Muhammad R. Hajj from the Center for Energy Harvesting Materials and Systems at Virginia Tech, have published a paper on the new energy-harvesting method in a recent issue of Applied Physics Letters.


"The greatest significance of the work is the reduction of the volume of the harvester, which translates to an increase in the power density, by eliminating the need for a secondary structure to be attached to the beam," Zakaria said. "This reduction is important in the design of very small harvesters that can be used to develop self-powered sensors."


The research shows that subjecting a flexible beam to wind at the right angle of attack can cause the beam to bend so much that the beam's "flutter speed" is significantly reduced. A large degree of bending also induces a change in the beam's natural frequencies that basically results in a synchronization of the beam's bending and twisting frequencies. Specifically, the beam's second bending frequency and torsional frequency coalesce, resulting in "self-induced flutter" of the beam. Complex aerodynamic effects ensure that the vibrations are self-sustaining, allowing for continuous energy harvesting.

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Tiny laser cells reveal cancer mechanisms

Tiny laser cells reveal cancer mechanisms | Amazing Science | Scoop.it

Researchers at the University of St Andrews, Scotland, UK, are claiming a photonics-based breakthrough in biomedicine; having successfully tracked a day-in-the-life of a number of white blood cells by feeding them microlasers, according to a research report published in Nano Letters The technique is expected to allow new insights into how cancers spread in the human body.


The Soft Matter Photonics Group led by Professor Malte Gather of the School of Physics and Astronomy, in collaboration with immunologists in the University’s School of Medicine, found that by “swallowing” an optical micro-resonator, cells gain the ability to produce green laser light.


Research groups around the world have worked on lasers based on single cells for several years now. However, all previously reported cell lasers required optical resonators that were much larger than the cell itself, meaning that the cell had to be inserted into these resonators. By drastically shrinking resonator size and exploiting the capability of cells to spontaneously take up foreign objects, the latest work now allows generation of laser light within a single living cell.


Dr Gather said, “This miniaturization paves the way to applying cell lasers as a new tool in biophotonics. In the future, these new lasers can help us understand important processes in biomedicine. For instance, we may be able to track—one by one—a large number of cancer cells as they invade tissue or follow each immune cell migrating to a site of inflammation.”


He continued, “The ability to track the movement of large number of cells will widen our understanding of a number of important processes in biology. For instance being able to see where and when circulating tumor cells invade healthy tissue can provide insight into how cancers spread in the body which would allow scientists to develop more targeted therapies in the future.”


The investigators put different types of cells onto a diet of optical "whispering gallery" micro-resonators. Some types of cells were particularly quick to ‘swallow’ the resonators; macrophages—immune cells responsible amongst other things for ‘garbage collection’ in our body—internalized the resonators within less than five minutes. However, even cells without particularly pronounced capacity for endocytosis readily internalized the micro-resonators, showing that laser barcodes are applicable to many different cell types.


What are future objectives?

Dr Gather believes these self-contained cell lasers have great potential to become a widely used tool in biology. Conventional fluorescent tags have rather broad emission spectra which means that one can only distinguish a limited number of different tags. The narrow spectrum of the cell laser facilitates distinguishing hundreds of thousands of different tags. The availability of such a tool will lead to new insights in cancer research as it would allow one to monitor how the cells from a tumor form metastasis, providing single cell resolution; i.e. one could see exactly which cells and how many cells from a primary tumor invade healthy tissue and form a new tumor site. The objectives are to develop the technology further, by confirming accuracy, improving speed, and reducing the size of the micro-resonators required to guarantee that their presence does not influence the behavior of the cell.

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Earth's magnetic field is 800 million years older than previously thought

Earth's magnetic field is 800 million years older than previously thought | Amazing Science | Scoop.it

Earth's magnetic field is 800 million years older than previously thought, new research suggests.


A new analysis of Western Australian zircon minerals has found the engine that generates the field started not long after the planet formed. Earth's so-called "geodynamo", involving the movement of molten iron in the Earth's outer core, began 4.22 billion years ago, say researchers today in the journal Science.


"This opens a window into a period that we know almost nothing about," says co-author, Professor Francis Nimmo of the University of California, Santa Cruz"Before this study we knew that the dynamo had existed for around three and a half billion years. What this study has done is push back the age of the dynamo by another 800 million years."


Earth's magnetic field acts as a shield protecting the planet's atmosphere and water, which make life on Earth possible. Without the magnetic field Earth's atmosphere would have been eroded away by the solar wind, a stream of charged particles flowing from the Sun.


The magnetic field was particularly important in Earth's early history when solar winds were about 100 times stronger than they are now.


"The young Sun was very active, and so having a strong magnetic field early on allows you to hang on to your atmosphere," says Nimmo.


"Mars had a dynamo early on, but then that dynamo died," he says. "Part of the reason that Mars lost its atmosphere is not simply that it has less gravity, but also that it didn't have a magnetic field protecting the atmosphere from being blown away."

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Caterpillar drugs ants to turn them into zombie bodyguards

Caterpillar drugs ants to turn them into zombie bodyguards | Amazing Science | Scoop.it

Docile ants become aggressive guard dogs after a secret signal from their caterpillar overlord. The idea turns on its head the assumption that the two species exchange favours in an even-handed relationship.


The caterpillars of the Japanese oakblue butterfly (Narathura japonica) grow up wrapped inside leaves on oak trees. To protect themselves against predators like spiders and wasps, they attract ant bodyguards, Pristomyrmex punctatus, with an offering of sugar droplets.


The relationships was thought to be a fair exchange of services in which both parties benefit. But Masaru Hojo from Kobe University in Japan noticed something peculiar: the caterpillars were always attended by the same ant individuals.


“It also seemed that the ants never moved away or returned to their nests,” he says. They seemed to abandon searching for food, and were just standing around guarding the caterpillar.

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A cellular puzzle: The weird and wonderful architecture of RNA

A cellular puzzle: The weird and wonderful architecture of RNA | Amazing Science | Scoop.it
Cells contain an ocean of twisting and turning RNA molecules. Now researchers are working out the structures — and how important they could be.


When Philip Bevilacqua decided to work out the shapes of all the RNA molecules in a living plant cell, he faced two problems. First, he had not studied plant biology since high school. And second, biochemists had tended to examine single RNA molecules; tackling the multitudes that waft around in a cell was a much thornier challenge.


Bevilacqua, an RNA chemist at Pennsylvania State University in University Park, was undeterred. He knew that RNA molecules were vital regulators of cell biology and that their structures might offer broad lessons about how they work. He brushed up on plant anatomy in an undergraduate course and worked with molecular plant biologist Sarah Assmann to develop a technique that could cope with RNAs at scale.


In November 2013, they and their teams became the first to describe the shapes of thousands of RNAs in a living cell — revealing a veritable sculpture garden of different forms in the weedy thale cress, Arabidopsis thaliana1.


One month later, a group at the University of California, San Francisco, reported a comparable study of yeast and human cells2. The number of RNA structures they managed to resolve was “unprecedented”, says Alain Laederach, an RNA biologist at the University of North Carolina at Chapel Hill (UNC).


Scientists' view of RNA has transformed over the past few decades. Once, most RNAs were thought to be relatively uninteresting pieces of limp spaghetti that ferried information between the molecules that mattered, DNA and protein. Now, biologists know that RNAs serve many other essential functions: they help with protein synthesis, control gene activity and modify other RNAs. At least 85% of the human genome is transcribed into RNA, and there is vigorous debate about what, if anything, it does.


But a key mystery has remained: its convoluted structures. Unlike DNA, which forms a predictable double helix, RNA comprises a single strand that folds up into elaborate loops, bulges, pseudo-knots, hammerheads, hairpins and other 3D motifs. These structures flip and twist between different forms, and are thought to be central to the operation of RNA, albeit in ways that are not yet known. “It's a big missing piece of the puzzle of understanding how RNAs work,” says Jonathan Weissman, a biophysicist and leader of the yeast and human RNA study.


In the past few years, researchers have begun to get a toehold on the problem. Bevilacqua, Weissman and others have devised techniques that allow them to take snapshots of RNA configurations en masse inside cells — and found that the molecules often look nothing like what is seen when RNA folds under artificial conditions. The work is helping them to decipher some of the rules that govern RNA structure, which might be useful in understanding human variation and disease — and even in improving agricultural crops.


“It gets at the very basic problem of how do living things evolve and how do these molecular rules affect what we look like and how we function,” says Laederach. “And that, fundamentally as a biologist, is really exciting.” The best-described RNA structures are what Kevin Weeks, a chemical biologist at the UNC, calls “RNA rocks”: molecules that have changed little in their sequence or structure over evolutionary time. These include transfer RNAs and ribosomal RNAs (both involved in protein synthesis) as well as enzymatic RNAs known as ribozymes. “But in the world of RNAs,” Weeks says, “these are probably huge outliers.”

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Self-Driving Cars Get a Code of Ethics

Self-Driving Cars Get a Code of Ethics | Amazing Science | Scoop.it
Researchers are trying to program self-driving cars to make split-second decisions that raise real ethical questions.


A philosopher is perhaps the last person you’d expect to have a hand in designing your next car, but that’s exactly what one expert on self-driving vehicles has in mind.


Chris Gerdes, a professor at Stanford University, leads a research lab that is experimenting with sophisticated hardware and software for automated driving. But together with Patrick Lin, a professor of philosophy at Cal Poly, he is also exploring the ethical dilemmas that may arise when vehicle self-driving is deployed in the real world.


Gerdes and Lin organized a workshop at Stanford earlier this year that brought together philosophers and engineers to discuss the issue. They implemented different ethical settings in the software that controls automated vehicles and then tested the code in simulations and even in real vehicles. Such settings might, for example, tell a car to prioritize avoiding humans over avoiding parked vehicles, or not to swerve for squirrels.


Fully self-driving vehicles are still at the research stage, but automated driving technology is rapidly creeping into vehicles. Over the next couple of years, a number of carmakers plan to release vehicles capable of steering, accelerating, and braking for themselves on highways for extended periods. Some cars already feature sensors that can detect pedestrians or cyclists, and warn drivers if it seems they might hit someone.


So far, self-driving cars have been involved in very few accidents. Google’s automated cars have covered nearly a million miles of road with just a few rear-enders, and these vehicles typically deal with uncertain situations by simply stopping (see “Google’s Self-Driving Car Chief Defends Safety Record”).


As the technology advances, however, and cars become capable of interpreting more complex scenes, automated driving systems may need to make split-second decisions that raise real ethical questions.

At a recent industry event, Gerdes gave an example of one such scenario: a child suddenly dashing into the road, forcing the self-driving car to choose between hitting the child or swerving into an oncoming van.


“As we see this with human eyes, one of these obstacles has a lot more value than the other,” Gerdes said. “What is the car’s responsibility?”

Gerdes pointed out that it might even be ethically preferable to put the passengers of the self-driving car at risk. “If that would avoid the child, if it would save the child’s life, could we injure the occupant of the vehicle? These are very tough decisions that those that design control algorithms for automated vehicles face every day,” he said.


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Researchers build bacteria's photosynthetic engine

Researchers build bacteria's photosynthetic engine | Amazing Science | Scoop.it

Nearly all life on Earth depends on photosynthesis, the conversion of light energy into chemical energy. Oxygen-producing plants and cyanobacteria perfected this process 2.7 billion years ago. But the first photosynthetic organisms were likely single-celled purple bacteria that began absorbing near-infrared light and converting it to sulfur or sulfates about 3.4 billion years ago.


Found in the bottom of lakes and ponds today, purple bacteria possess simpler photosynthetic organelles—specialized cellular subunits called chromatophores—than plants and algae. For that reason, Klaus Schulten of the University of Illinois at Urbana–Champaign (UIUC) targeted the chromatophore to study photosynthesis at the atomic level.


As a computational biophysicist, Schulten unites biologists' experimental data with the physical laws that govern the behavior of matter. This combination allows him to simulate biomolecules, atom by atom, using supercomputers. The simulations reveal interactions between molecules that are impossible to observe in the laboratory, providing plausible explanations for how molecules carry out biological functions in nature.


In 2014, a team led by Schulten used the Titan supercomputer, located at the US Department of Energy's (DOE's) Oak Ridge National Laboratory, to construct and simulate a single chromatophore. The soccer ball-shaped chromatophore contained more than 100 million atoms—a significantly larger biomolecular system than any previously modeled. The project's scale required Titan, the flagship supercomputer at the Oak Ridge Leadership Computing Facility (OLCF), a DOE Office of Science User Facility, to calculate the interaction of millions of atoms in a feasible time frame that would allow for data analysis.


"For years, scientists have seen that cells are made of these machines, but they could only look at part of the machine. It's like looking at a car engine and saying, 'Oh, there's an interesting cable, an interesting screw, an interesting cylinder.' You look at the parts and describe them with love and care, but you don't understand how the engine actually works that way," Schulten said. "Titan gave us the fantastic level of computing we needed to see the whole picture. For the first time, we could go from looking at the cable, the screw, the cylinder to looking at the whole engine."


Schulten's chromatophore simulation is being used to understand the fundamental process of photosynthesis, basic research that could one day lead to better solar energy technology. Of particular interest: how hundreds of proteins work together to capture light energy at an estimated 90 percent efficiency.


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How many species of giant sea spiders do we have?

How many species of giant sea spiders do we have? | Amazing Science | Scoop.it

Sea spiders belong to a group of arthropods called the pycnogonids, which are found scuttling along the bottom of many of the world’s oceans and seas. They are crustaceans and not spiders. Most are relatively small – it’s only around the poles that sea spiders grow large, which is a trait they share with many marine species. Exactly why this happens remains a mystery.


Many sea spiders are carnivorous, dining on worms, jellyfish and sponges. “They have a giant proboscis to suck up their food,” says Florian Leese at Ruhr University Bochum in Germany. Like true spiders, some sea spiders have eight legs. But not all do. “Some have 10 and even 12 legs,” says Leese.


Curiously, though, their bodies don’t appear to have much else apart from their long legs and proboscis. “They don’t really have a body,” says Leese. “They have their organs in their legs.” These creatures are sometimes called the pantopoda – meaning “all legs” – because of their bizarre anatomy.


The lack of an obvious body means sea spiders don’t need to bother with a respiratory system. Simple diffusion can deliver gases to all of the tissues. The Southern Ocean giant sea spider is one of the most common sea spiders in the waters around Antarctica. It also lives in coastal waters off South America, South Africa and Madagascar, down to a depth of 4.9 kilometers.


It is so widespread that some have wondered whether it really is a single species. To find out, Leese and his colleagues examined DNA taken from 300 specimens. Animal cells usually carry two forms of DNA: most is in the form of nuclear DNA in the cell’s nucleus, but there is a second form of DNA in the mitochondria – often called the “powerhouse of the cell”. Mitochondrial DNA is usually only inherited down the female line.


The mitochondrial genes fell into about 20 distinct groups, apparently suggesting the Southern Ocean giant sea spider should really be broken up into 20 distinct species. But the nuclear DNA showed that many of these apparently distinct species can and have interbred in the recent past. In fact, the team says, if the Southern Ocean giant sea spider is divided into several distinct species, we should probably recognise only five – not 20.


Why is this? The mitochondrial DNA sequences are so distinct that the sea spiders probably began to diverge about a million years ago – perhaps during glacial periods when a deterioration in conditions left small populations of sea spiders isolated from one another in ice-free “refugia”, where they could each develop their own genetic mutations.


But when environmental conditions improved and the spider lineages began expanding out of those refugia, they began to interbreed and hybridise. That’s not unlike the way different human lineages like the Neanderthals, Denisovans and our species interbred when they came into contact after thousands of years of isolation.


The results are important for conservation. Mitochondrial and nuclear DNA often show the same general pattern, says Leese, so when easier-to-analyse mitochondrial DNA indicates one species actually breaks down into several “cryptic” species, conservationists want to protect all of the lineages. But nuclear DNA sequences might show that many of those cryptic species don’t really exist. “The study advises caution in calling distinct mitochondrial lineages species,” says Leese.


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Monitoring a Waking Black Hole

Monitoring a Waking Black Hole | Amazing Science | Scoop.it
NASA's Swift satellite detected a rising tide of high-energy X-rays from the constellation Cygnus on June 15, just before 2:32 p.m. EDT. About 10 minutes later, the Japanese experiment on the International Space Station called the Monitor of All-sky X-ray Image (MAXI) also picked up the flare.

The outburst came from V404 Cygni, a binary system located about 8,000 light-years away that contains a black hole. Every couple of decades the black hole fires up in an outburst of high-energy light, becoming an X-ray nova. Until the Swift detection, it had been slumbering since 1989.


Download video in HD formats from NASA Goddard's Scientific Visualization Studio

An X-ray nova is a bright, short-lived X-ray source that reaches peak intensity in a few days and then fades out over a period of weeks or months. The outburst occurs when stored gas abruptly rushes toward a neutron star or black hole. By studying the patterns of the X-rays produced, astronomers can determine the kind of object at the heart of the eruption.


"Relative to the lifetime of space observatories, these black hole eruptions are quite rare," said Neil Gehrels, Swift's principal investigator at NASA's Goddard Space Flight Center in Greenbelt, Maryland. "So when we see one of them flare up, we try to throw everything we have at it, monitoring across the spectrum, from radio waves to gamma rays."


Astronomers classify this type of system as a low-mass X-ray binary. In V404 Cygni, a star slightly smaller than the sun orbits a black hole 10 times its mass in only 6.5 days. The close orbit and strong gravity of the black hole produce tidal forces that pull a stream of gas from its partner. The gas travels to a storage disk around the black hole and heats up to millions of degrees, producing a steady stream of X-rays as it falls inward.


But the disk flips between two dramatically different conditions. In its cooler state, the gas resists inward flow and just collects in the outer part of the disk like water behind a dam. Inevitably the build-up of gas overwhelms the dam, and a tsunami of hot bright gas rushes toward the black hole.


Astronomers relish the opportunity to collect simultaneous multiwavelength data on black hole binaries, especially one as close as V404 Cygni. In 1938 and 1956, astronomers caught V404 Cygni undergoing outbursts in visible light. During its eruption in 1989, the system was observed by Ginga, an X-ray satellite operated by Japan, and instruments aboard Russia's Mir space station.


"Right now, V404 Cygni shows exceptional variation at all wavelengths, offering us a rare chance to add to this unique data set," said Eleonora Troja, a Swift team member at Goddard.


Ongoing or planned satellite observations of the outburst involve NASA’s Swift satellite, Chandra X-ray Observatory and Fermi Gamma-ray Space Telescope, as well as Japan’s MAXI, the European Space Agency's INTEGRAL satellite, and the Italian Space Agency's AGILE gamma-ray mission. Ground-based facilities following the eruption include the 10.4-meter Gran Telescopio Canarias operated by Spain in the Canary Islands, the University of Leicester's 0.5-meter telescope in Oadby, U.K., the Nasu radio telescope at Waseda University in Japan, and amateur observatories.


V404 Cygni has flared many times since the eruption began, with activity ranging from minutes to hours. "It repeatedly becomes the brightest object in the X-ray sky -- up to 50 times brighter than the Crab Nebula, which is normally one of the brightest sources," said Erik Kuulkers, the INTEGRAL project scientist at ESA's European Space Astronomy Centre in Madrid. "It is definitely a 'once in a professional lifetime' opportunity."


In a single week, flares from V404 Cygni generated more than 70 "triggers" of the Gamma-ray Burst Monitor (GBM) aboard Fermi. This is more than five times the number of triggers seen from all objects in the sky in a typical week. The GBM triggers when it detects a gamma-ray flare, then it sends numerous emails containing increasingly refined information about the event to scientists on duty.

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Next-Gen Shotgun Cloning Using the Gibson Assembly Method

Next-Gen Shotgun Cloning Using the Gibson Assembly Method | Amazing Science | Scoop.it
Traditional cloning and sequencing methods can be laborious, expensive, and time-consuming techniques, especially when applied to large sample numbers. Even for the routine cloning of small sample sizes, however, many research laboratories have yet to discover the power, ease, and efficiency of the Gibson Assembly® method. First described by Dan Gibson at the J. Craig Venter Institute (JCVI) in 2009, the Gibson Assembly method is a sequence-independent, seamless cloning method that offers many advantages over traditional cloning, most notably the ability to assemble multiple DNA fragments quickly, accurately, and efficiently in a single-tube reaction.

  • SGI-DNA, a Synthetic Genomics company, offers Gibson Assembly reagent kits: the Gibson Assembly HiFi 1-Step Kit can be used for the simultaneous assembly of up to 5 fragments and the Gibson Assembly Ultra Kit can be used for the simultaneous assembly of up to 15 fragments. The Gibson Assembly method can be leveraged for a variety of applications, including routine cloning, site-directed mutagenesis, and whole-genome synthesis.
  • Here, we discuss the results and advantages of coupling the Gibson Assembly method with shotgun cloning and next-generation sequencing. The combined technologies of the Gibson Assembly method, shotgun cloning, and next-generation sequencing constitute Gibson Assembly next-generation shotgun cloning.
  • Shotgun cloning and next-generation sequencing methods offer significant time and cost savings relative to traditional (Sanger) sequencing methods and independent, repetitive cloning methods. Shotgun cloning drastically reduces sample number and next-generation sequencing drastically reduces the amount of time required for high-throughput sample processing. Combining the highly-efficient, error-correcting Gibson Assembly method with shotgun cloning and next-generation sequencing harnesses the advantages of the combined technologies, yielding substantial time and resource savings in comparison to traditional methods.
Traditional cloning and sequencing methods require the processing of individual samples through the following steps:

Preparation of insert and vector DNA by PCR amplification or restriction enzyme digestion → Vector Dephosphorylation → Ligation Cloning → Transformation → Plating → Picking Colonies → Plasmid Preparation  → Sequencing → Analysis → Construct Retrieval

The sequencing and cloning of n constructs (where n = the number of constructs) requires individually manipulating all n samples through the 10 workflow steps outlined on the previous page in n tubes (i.e., cloning 12 constructs requires handling 12 samples during every workflow stage). See Figure 1A for a schematic overview.

Combining Gibson Assembly shotgun cloning with next-generation sequencing is achieved by processing samples through the following steps:

Preparation of insert and vector DNA by PCR amplification → Gel Purification → The Gibson Assembly Method → Transformation → Plating → Picking Colonies → Plasmid Preparation → Next-Generation Sequencing → Analysis → Construct Retrieval

In the Gibson Assembly next-generation shotgun cloning workflow, samples are pooled prior to gel purification and processed in size-correlated batches. Therefore, to sequence and clone n samples using Gibson Assembly shotgun cloning, n constructs will be individually PCR-amplified. Following amplification, however, samples are pooled. For convenience and processing using 96-well plates, pools are typically batched with 8 samples per batch. Because of batching, for the remaining workflow steps, instead of processing n samples, only n/8 sample batches are manipulated for each step, which translates into substantial reagent savings (see Figures 1B & 2).
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Elon Musk, Stephen Hawking Want to Save the World From Killer Robots on the Battlefield

Elon Musk, Stephen Hawking Want to Save the World From Killer Robots on the Battlefield | Amazing Science | Scoop.it

Elon Musk and Stephen Hawking are among the leaders from the science and technology worlds calling for a ban on autonomous weapons, warning that weapons with a mind of their own "would not be beneficial for humanity."


Along with 1,000 other signatories, Musk and Hawking signed their names to an open letter that will be presented this week at the International Joint Conference on Artificial Intelligence in Buenos Aires, Argentina.


Autonomous weapons are defined by the group as artillery that can "search for and eliminate people meeting certain pre-defined criteria, but do not include cruise missiles or remotely piloted drones for which humans make all targeting decisions."


"Artificial Intelligence (AI) technology has reached a point where the deployment of such systems is -- practically if not legally -- feasible within years, not decades, and the stakes are high: autonomous weapons have been described as the third revolution in warfare, after gunpowder and nuclear arms," the letter, posted on the Future of Life Institute's website says.


If one country pushes ahead with the creation of robotic killers, the group wrote it fears it will spur a global arms race that could spell disaster for humanity.


"Autonomous weapons are ideal for tasks such as assassinations, destabilizing nations, subduing populations and selectively killing a particular ethnic group," the letter says. "We therefore believe that a military AI arms race would not be beneficial for humanity. There are many ways in which AI can make battlefields safer for humans, especially civilians, without creating new tools for killing people."


While the group warns of the potential carnage killer robots could inflict, they also stress they aren't against certain advances in artificial intelligence.


"We believe that AI has great potential to benefit humanity in many ways, and that the goal of the field should be to do so," the letter says. "Starting a military AI arms race is a bad idea, and should be prevented by a ban on offensive autonomous weapons beyond meaningful human control."

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The first 'white laser' can shine light over the full spectrum of visible colors

The first 'white laser' can shine light over the full spectrum of visible colors | Amazing Science | Scoop.it

Scientists and engineers at Arizona State University, in Tempe, have created the first lasers that can shine light over the full spectrum of visible colors. The device’s inventors suggest the laser could find use in video displays, solid-state lighting, and a laser-based version of Wi-Fi.


Although previous research has created red, blue, green and other lasers, each of these lasers usually only emitted one color of light. Creating a monolithic structure capable of emitting red, green, and blue all at once has proven difficult because it requires combining very different semiconductors. Growing such mismatched crystals right next to each other often results in fatal defects throughout each of these materials.


But now scientists say they’ve overcome that problem. The heart of the new device is a sheet only nanometers thick made of a semiconducting alloy of zinc, cadmium, sulfur, and selenium. The sheet is divided into different segments. When excited with a pulse of light, the segments rich in cadmium and selenium gave off red light; those rich in cadmium and sulfur emitted green light; and those rich in zinc and sulfur glowed blue.


The researchers grew this alloy in stages, carefully varying the temperature and other growth conditions over time. By controlling the interplay between the vapor, liquid, and solid phases of the different materials that made up this nano-sheet, they ensured that these different crystals could coexist.


The scientists can individually target each segment of the nano-sheet with a light pulse. Varying the power of the light pulses that each section received tuned how intensely they shone, allowing the alser to produce 70 percent more perceptible colors than the most commonly used light sources.


Lasers could be far more energy-efficient than LEDs: While LED-based lighting produces up to about 150 lumens per watt of electricity, lasers could produce more than 400 lumens per watt, says Cun-Zheng Ning, a physicist and electrical engineer at Arizona State University at Tempe who worked on the laser. In addition, he says that white lasers could also lead to video displays with more vivid colors and higher contrast than conventional displays.


Another important potential application could be "Li-Fi", the use of light to connect devices to the Interenet. Li-Fi ould be 10 times faster than today’s Wi-Fi, but "the Li-Fi currently under development is based on LEDs," Ning says. He suggests white-laser based Li-Fi could be 10 to 100 times faster than LED-based Li-Fi, because the lasers can encode data much faster than white LEDs.


In the future, the scientists plan to explore whether they can excite these lasers with electricity instead of with light pulses. They detailed their findingsonline 27 July in the journal Nature Nanotechnology.

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