Category: National Science Foundation

Graduate student frozen out of research in Antarctica because of U.S. government shutdown

On By A.P.In Antarctica, Chile, Dr. Rajadhyaksha, Drake Passage, GOP, Jamie Collins, Laurence M. Gould, Lockheed Martin, Long Term Ecological Research, LTER, Massachusetts Institute of Technology, National Science Foundation, NSF, Puenta Arenas, Republican Party, research funding, Science, Sebastian Vivancos, U.S. Congress, U.S. government, U.S. government shutdown, U.S. Palmer Station, Woods Hole Oceanographic InstitutionLeave a comment

antarctica

Time on his hands. Sebastian Vivancos (inset) is part of the newly arrived team whose planned research activities at the U.S. Palmer Station in Antarctica are being thwarted by the government shutdown.

After 5 years as a lieutenant in the U.S. Coast Guard, Jamie Collins knows what it’s like to be at sea. But nothing in his military service prepared him for his current 30,000-km scientific round trip to nowhere, courtesy of the failure of the U.S. Congress to approve a budget. His predicament is one of the stranger—and sadder—tales of how the government-wide shutdown is affecting researchers.

Collins, a third-year graduate student in chemical oceanography, arrived Wednesday at the National Science Foundation’s (NSF’s) Palmer Station in Antarctica. He was eager to begin working on a long-running ecological research project funded by NSF and to start collecting data for his dissertation in a graduate program run jointly by the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution. But the rough seas he encountered during his 4-day crossing of the notorious Drake Passage in the south Atlantic—the final leg of a journey that began in Boston—paled in comparison to the storm he encountered once he stepped off the Laurence M. Gould, a U.S. icebreaking research vessel that ferries scientists and supplies between Puenta Arenas, Chile, and the west Antarctic Peninsula.

On Tuesday, NSF had announced that its contractor for Antarctic logistical support, Lockheed Martin, would begin putting the three U.S. stations on “caretaker” status unless Congress passed an appropriations bill to continue funding the government by 14 October. Although legislators will eventually adopt such a bill, nobody expects them to act in the next few days. Without an appropriation, NSF has no money to operate the stations.

For Collins, that announcement meant his plans for an intensive 5-month research regime had suddenly melted away. “The station manager told us not to unpack our stuff and to stay on the ship,” he says in a phone call to ScienceInsider from the ship. “She said we were to wait here for a week while they prepare to shut down the station. Then we’d sail back to Chile, and go home.”

Collins was stunned. “I had spent all summer preparing for this trip,” he says. He had filled three pallets with supplies for his experiments on how algae in the region detect and react to the presence of ultraviolet radiation, part of a larger effort to understand the role that bacteria play in sequestering carbon in the Southern Ocean. “Without the data from those experiments, I may have to reevaluate what to do for my Ph.D.,” he adds.

Collins was also part of the first wave of students arriving at Palmer this season to work on a research project, begun in 1990, that explores how the extent of annual sea ice affects the polar biota. The project is one of 26 so-called LTER (Long Term Ecological Research) sites around the world that NSF supports. He was scheduled to divide his time at Palmer between his own research and monitoring penguin colonies on several offshore islands as part of the LTER project. And he had signed up for a 6-week research cruise aboard the Gould that supplements the land-based LTER observations with oceanographic data collected up and down the peninsula.

Despite the jarring news, the 31-year-old Collins says that he is more worried about what it may mean to some of his younger colleagues with less worldly experience. “I spent 5 years in the military and I’m used to dealing with bureaucracy,” he explains. “And nothing that happens here is going to deter me from pursuing my goal of a career in science. But for some of the undergraduates on the trip, this is their first taste of what Congress thinks about the value of scientific research. And it’s sending them a pretty horrific message.”

http://news.sciencemag.org/people-events/2013/10/tales-shutdown-grad-student-frozen-out-research-antarctica

Thanks to Dr. Rajadhyaksha for bringing this to the attention of the It’s Interesting community.

First Evidence That Magnetism Helps Salmon Find Home

On By A.P.In Current Biology, magnet, Magnetism, Nathan Putman, National Science Foundation, Nature, Oregon State University, salmon, sockeye salmonLeave a comment

salmon

When migrating, sockeye salmon typically swim up to 4,000 miles into the ocean and then, years later, navigate back to the upstream reaches of the rivers in which they were born to spawn their young. Scientists, the fishing community and lay people have long wondered how salmon find their way to their home rivers over such epic distances.

A new study, published in this week’s issue of Current Biology and partly funded by the National Science Foundation, suggests that salmon find their home rivers by sensing the rivers’ unique magnetic signature.

As part of the study, the research team used data from more than 56 years of catches in salmon fisheries to identify the routes that salmon had taken from their most northerly destinations, which were probably near Alaska or the Aleutian Islands in the Pacific Ocean, to the mouth of their home river–the Fraser River in British Columbia, Canada. This data was compared to the intensity of Earth’s magnetic field at pivotal locations in the salmon’s migratory route.

Earth has a magnetic field that weakens with proximity to the equator and distance from the poles and gradually changes on a yearly basis. Therefore, the intensity of the magnetosphere in any particular location is unique and differs slightly from year to year.

Because Vancouver Island is located directly in front of the Fraser River’s mouth, it blocks direct access to the river’s mouth from the Pacific Ocean. However, salmon may slip behind Vancouver Island and reach the river’s mouth from the north via the Queen Charlotte Strait or from the south via the Juan De Fuca Strait.

Results from this study showed that the intensity of the magnetic field largely predicted which route the salmon used to detour around Vancouver Island; in any given year, the salmon were more likely to take whichever route had a magnetic signature that most closely matched that of the Fraser River years before, when the salmon initially swam from the river into the Pacific Ocean.

“These results are consistent with the idea that juvenile salmon imprint on (i.e. learn and remember) the magnetic signature of their home river, and then seek that same magnetic signature during their spawning migration,” said Nathan Putman, a post-doctoral researcher at Oregon State University and the lead author of the study.

It has long been known that some animals use Earth’s magnetic field to generally orient themselves and to follow a straight course. However, scientists have never before documented an animal’s ability to “learn” the magnetic field rather than to simply inherit information about it or to use the magnetic field to find a specific location.

This study provides the first empirical evidence of magnetic imprinting in animals and represents the discovery of a major new phenomenon in behavioral biology.

In addition, this study suggests that it would be possible to forecast salmon movements using geomagnetic models–a development that has important implications for fisheries management.

Putman says scientists don’t know exactly how early and how often salmon check Earth’s magnetic field in order to identify their geographic locations during their trip back home. “But,” he says, “for the salmon to be able to go from some location out in the middle of the Pacific 4,000 miles away, they need to make a correct migratory choice early–and they need to know which direction to start going in. For that, they would presumably use the magnetic field.”

Putman continues, “As the salmon travel that route, ocean currents and other forces might blow them off course. So they would probably need to check their magnetic position several times during this migration to stay on track. Once they get close to the coastline, they would need to hone in on their target, and so would presumably check in more continuously during this stage of their migration.”

Putman says that once the salmon reach their home river, they probably use their sense of smell to find the particular tributary in which they were born. However, over long distances, magnetism would be a more useful cue to salmon than odors because magnetism–unlike odors–can be detected across thousands of miles of open ocean.

Like other Pacific Salmon, sockeye salmon spawn in the gravel beds of rivers and streams. After the newly hatched salmon emerge from these beds, they spend one to three years in fresh water, and then they migrate downstream to the ocean.

Next, the salmon travel thousands of miles from their home river to forage in the North Pacific for about two more years, and then, as well-fed adults, they migrate back to the same gravel beds in which they were born.

When migrating, salmon must transition from fresh water to sea water, and then back again. During each transition, the salmon undergo a metamorphosis that Putman says is almost as dramatic as the metamorphosis of a caterpillar into a butterfly. Each such salmon metamorphosis involves a replacement of gill tissues that enables the fish to maintain the correct salt balance in its environment: the salmon retains salt when in fresh water and pumps out excess salt when in salt water.

Salmon usually undertake their taxing, round-trip migration, which may total up to 8,000 miles, only once in their lives; they typically die soon after spawning.

http://www.sciencedaily.com/releases/2013/02/130207131713.htm

‘Scarecrow’ Gene: Key to Efficient Crops, Could Lead to Staple Crops With Much Higher Yields

On By A.P.In agriculture, C3 crops, Cornell University, DNA, gene, Kranz anatomy, National Science Foundation, photosynthesis, Plant and Cell Physiology, plants, Robert Turgeon, RuBisCo, scarecrow gene, Science, Technology, Thomas Slewinski, US Department of AgricultureLeave a comment

scarecrow gene
Cross section of a mature maize leaf showing Kranz (German for wreath) anatomy around a large vein. The bundle sheath cells (lighter red) encircle the vascular core (light blue). Mesophyll cells (dark red) encircle the bundle sheath cells. The interaction and cooperation between the mesophyll and bundle sheath is essential for the C4 photosynthetic mechanism. (Credit: Thomas Slewinski)

With projections of 9.5 billion people by 2050, humankind faces the challenge of feeding modern diets to additional mouths while using the same amounts of water, fertilizer and arable land as today.

Cornell researchers have taken a leap toward meeting those needs by discovering a gene that could lead to new varieties of staple crops with 50 percent higher yields.

The gene, called Scarecrow, is the first discovered to control a special leaf structure, known as Kranz anatomy, which leads to more efficient photosynthesis. Plants photosynthesize using one of two methods: C3, a less efficient, ancient method found in most plants, including wheat and rice; and C4, a more efficient adaptation employed by grasses, maize, sorghum and sugarcane that is better suited to drought, intense sunlight, heat and low nitrogen.

“Researchers have been trying to find the underlying genetics of Kranz anatomy so we can engineer it into C3 crops,” said Thomas Slewinski, lead author of a paper that appeared online in November in the journal Plant and Cell Physiology. Slewinski is a postdoctoral researcher in the lab of senior author Robert Turgeon, professor of plant biology in the College of Arts and Sciences.

The finding “provides a clue as to how this whole anatomical key is regulated,” said Turgeon. “There’s still a lot to be learned, but now the barn door is open and you are going to see people working on this Scarecrow pathway.” The promise of transferring C4 mechanisms into C3 plants has been fervently pursued and funded on a global scale for decades, he added.

If C4 photosynthesis is successfully transferred to C3 plants through genetic engineering, farmers could grow wheat and rice in hotter, dryer environments with less fertilizer, while possibly increasing yields by half, the researchers said.

C3 photosynthesis originated at a time in Earth’s history when the atmosphere had a high proportion of carbon dioxide. C4 plants have independently evolved from C3 plants some 60 times at different times and places. The C4 adaptation involves Kranz anatomy in the leaves, which includes a layer of special bundle sheath cells surrounding the veins and an outer layer of cells called mesophyll. Bundle sheath cells and mesophyll cells cooperate in a two-step version of photosynthesis, using different kinds of chloroplasts.

By looking closely at plant evolution and anatomy, Slewinski recognized that the bundle sheath cells in leaves of C4 plants were similar to endodermal cells that surrounded vascular tissue in roots and stems.

Slewinski suspected that if C4 leaves shared endodermal genes with roots and stems, the genetics that controlled those cell types may also be shared. Slewinski looked for experimental maize lines with mutant Scarecrow genes, which he knew governed endodermal cells in roots. When the researchers grew those plants, they first identified problems in the roots, then checked for abnormalities in the bundle sheath. They found that the leaves of Scarecrow mutants had abnormal and proliferated bundle sheath cells and irregular veins.

In all plants, an enzyme called RuBisCo facilitates a reaction that captures carbon dioxide from the air, the first step in producing sucrose, the energy-rich product of photosynthesis that powers the plant. But in C3 plants RuBisCo also facilitates a competing reaction with oxygen, creating a byproduct that has to be degraded, at a cost of about 30-40 percent overall efficiency. In C4 plants, carbon dioxide fixation takes place in two stages. The first step occurs in the mesophyll, and the product of this reaction is shuttled to the bundle sheath for the RuBisCo step. The RuBisCo step is very efficient because in the bundle sheath cells, the oxygen concentration is low and the carbon dioxide concentration is high. This eliminates the problem of the competing oxygen reaction, making the plant far more efficient.

The study was funded by the National Science Foundation and the U.S. Department of Agriculture.

http://www.sciencedaily.com/releases/2013/01/130124134051.htm

New type of bacteria discovered in Indiana man’s gruesome wound

On By A.P.In ARUP Laboratories, bird lice, Colin Dale, Indiana, microbe, National Science Foundation, Nature, PLoS Genetics, Sodalis, stinkbug, Thomas Fritz, tsetse fly, University of Utah, weevilLeave a comment

 

An Indiana man’s nasty injury led scientists to discover a new type of bacteria that sheds light on symbiotic microbes in insects.

Two years ago, Thomas Fritz cut down a dead crab apple tree in his yard. He fell while hauling away the woody debris and a branch from the tree impaled his right hand between the thumb and index finger.

Fritz, a 71-year-old retired inventor, engineer and volunteer firefighter, bandaged the gash himself. He waited a few days to see a doctor and by the time of his appointment, the puncture wound became infected. The doctor took a sample of the cyst that formed at the site of the cut and sent it to a lab.

After an abscess, swelling and more pain, Fritz’s wound eventually healed. But the sample from his infection puzzled scientists at the lab who couldn’t identify what type of bacteria they were looking at. The sample was eventually sent to ARUP Laboratories, a national pathology reference library operated by the University of Utah, where scientists named the new strain human Sodalis or HS.

Colin Dale, a biologist at the University of Utah, said that genetic analyses of HS showed it is related to Sodalis, a genus of bacteria that he discovered in 1999 and has been found to live symbiotically in 17 insect species, including tsetse flies, weevils, stinkbugs and bird lice. In such symbiotic relationships, both the host and the bacteria gain — for example, while Sodalis bacteria get shelter and nutrition from their insect hosts, they also provide the insects vital B vitamins and amino acids.

Though symbiotic relationships between microorganisms and insects are common, their origins are often a mystery. The new evidence provides “a missing link in our understanding of how beneficial insect-bacteria relationships originate,” Dale said, adding that the findings show that these relationships arise independently in each insect.

As the strain of Sodalis in this case likely came from a tree, the discovery suggests that insects can get infected by pathogenic bacteria from plants or animals in their environment, and the bacteria can evolve to become less virulent and to provide symbiotic benefits to the insect. Then, instead of spreading the bacteria to other insects by infection, mother insects pass down the microbes to their offspring, the researchers said.

“The insect picks up a pathogen that is widespread in the environment and then domesticates it,” Dale explained in a statement from the National Science Foundation, which funded the research. “This happens independently in each insect.”

The research was detailed earlier this month online in the journal PLoS Genetics.

http://www.livescience.com/25035-wound-leads-to-bacteria-discovery.html

Stanford scientists advance thought-control computer cursor movement

On By A.P.In brain algorithm, brain computer interface, Byron Yu, California, Christopher and Dana Reeve Paralysis Foundation, cursor, Cynthia Chestek, Defense Advanced Research Projects Agency, Director's Pioneer Award, Jame Gnadt, John Cunningham, Joline Fan, Jonathan Kao, Jose Carmena, Kebmodee, Krishna Shenoy, Mark Churchland, Matthew Kaufman, Medicine, mind control, monkey, National Defense Science and Engineering Graduate Fellowship, National Institutes of Health, National Science Foundation, Nature, Nature Neuroscience, neural prosthetics, paralysis, Paul Nuyujukian, ReFIT, REPAIR, Stanford, Stanford Graduate Fellowship, Stanford University, Stephen Ryu, traumatic brain injury, Vikash GiljaLeave a comment

 

 

Stanford researchers have designed the fastest, most accurate mathematical algorithm yet for brain-implantable prosthetic systems that can help disabled people maneuver computer cursors with their thoughts. The algorithm’s speed, accuracy and natural movement approach those of a real arm.

 

 

On each side of the screen, a monkey moves a cursor with its thoughts, using the cursor to make contact with the colored ball. On the left, the monkey’s thoughts are decoded with the use of a mathematical algorithm known as Velocity. On the right, the monkey’s thoughts are decoded with a new algorithm known as ReFITT, with better results. The ReFIT system helps the monkey to click on 21 targets in 21 seconds, as opposed to just 10 clicks with the older system.

 

 

When a paralyzed person imagines moving a limb, cells in the part of the brain that controls movement activate, as if trying to make the immobile limb work again.

Despite a neurological injury or disease that has severed the pathway between brain and muscle, the region where the signals originate remains intact and functional.

In recent years, neuroscientists and neuroengineers working in prosthetics have begun to develop brain-implantable sensors that can measure signals from individual neurons.

After those signals have been decoded through a mathematical algorithm, they can be used to control the movement of a cursor on a computer screen – in essence, the cursor is controlled by thoughts.

The work is part of a field known as neural prosthetics.

A team of Stanford researchers have now developed a new algorithm, known as ReFIT, that vastly improves the speed and accuracy of neural prosthetics that control computer cursors. The results were published Nov. 18 in the journal Nature Neuroscience in a paper by Krishna Shenoy, a professor of electrical engineering, bioengineering and neurobiology at Stanford, and a team led by research associate Dr. Vikash Gilja and bioengineering doctoral candidate Paul Nuyujukian.

In side-by-side demonstrations with rhesus monkeys, cursors controlled by the new algorithm doubled the performance of existing systems and approached performance of the monkey’s actual arm in controlling the cursor. Better yet, more than four years after implantation, the new system is still going strong, while previous systems have seen a steady decline in performance over time.

“These findings could lead to greatly improved prosthetic system performance and robustness in paralyzed people, which we are actively pursuing as part of the FDA Phase-I BrainGate2 clinical trial here at Stanford,” said Shenoy.

The system relies on a sensor implanted into the brain, which records “action potentials” in neural activity from an array of electrode sensors and sends data to a computer. The frequency with which action potentials are generated provides the computer important information about the direction and speed of the user’s intended movement.

The ReFIT algorithm that decodes these signals represents a departure from earlier models. In most neural prosthetics research, scientists have recorded brain activity while the subject moves or imagines moving an arm, analyzing the data after the fact. “Quite a bit of the work in neural prosthetics has focused on this sort of offline reconstruction,” said Gilja, the first author of the paper.

The Stanford team wanted to understand how the system worked “online,” under closed-loop control conditions in which the computer analyzes and implements visual feedback gathered in real time as the monkey neurally controls the cursor toward an onscreen target.

The system is able to make adjustments on the fly when guiding the cursor to a target, just as a hand and eye would work in tandem to move a mouse-cursor onto an icon on a computer desktop.

If the cursor were straying too far to the left, for instance, the user likely adjusts the imagined movements to redirect the cursor to the right. The team designed the system to learn from the user’s corrective movements, allowing the cursor to move more precisely than it could in earlier prosthetics.

To test the new system, the team gave monkeys the task of mentally directing a cursor to a target – an onscreen dot – and holding the cursor there for half a second. ReFIT performed vastly better than previous technology in terms of both speed and accuracy.

The path of the cursor from the starting point to the target was straighter and it reached the target twice as quickly as earlier systems, achieving 75 to 85 percent of the speed of the monkey’s arm.

“This paper reports very exciting innovations in closed-loop decoding for brain-machine interfaces. These innovations should lead to a significant boost in the control of neuroprosthetic devices and increase the clinical viability of this technology,” said Jose Carmena, an associate professor of electrical engineering and neuroscience at the University of California-Berkeley.

Critical to ReFIT’s time-to-target improvement was its superior ability to stop the cursor. While the old model’s cursor reached the target almost as fast as ReFIT, it often overshot the destination, requiring additional time and multiple passes to hold the target.

The key to this efficiency was in the step-by-step calculation that transforms electrical signals from the brain into movements of the cursor onscreen. The team had a unique way of “training” the algorithm about movement. When the monkey used his arm to move the cursor, the computer used signals from the implant to match the arm movements with neural activity.

Next, the monkey simply thought about moving the cursor, and the computer translated that neural activity into onscreen movement of the cursor. The team then used the monkey’s brain activity to refine their algorithm, increasing its accuracy.

The team introduced a second innovation in the way ReFIT encodes information about the position and velocity of the cursor. Gilja said that previous algorithms could interpret neural signals about either the cursor’s position or its velocity, but not both at once. ReFIT can do both, resulting in faster, cleaner movements of the cursor.

Early research in neural prosthetics had the goal of understanding the brain and its systems more thoroughly, Gilja said, but he and his team wanted to build on this approach by taking a more pragmatic engineering perspective. “The core engineering goal is to achieve highest possible performance and robustness for a potential clinical device,” he said.

To create such a responsive system, the team decided to abandon one of the traditional methods in neural prosthetics.

Much of the existing research in this field has focused on differentiating among individual neurons in the brain. Importantly, such a detailed approach has allowed neuroscientists to create a detailed understanding of the individual neurons that control arm movement.

But the individual neuron approach has its drawbacks, Gilja said. “From an engineering perspective, the process of isolating single neurons is difficult, due to minute physical movements between the electrode and nearby neurons, making it error prone,” he said. ReFIT focuses on small groups of neurons instead of single neurons.

By abandoning the single-neuron approach, the team also reaped a surprising benefit: performance longevity. Neural implant systems that are fine-tuned to specific neurons degrade over time. It is a common belief in the field that after six months to a year they can no longer accurately interpret the brain’s intended movement. Gilja said the Stanford system is working very well more than four years later.

“Despite great progress in brain-computer interfaces to control the movement of devices such as prosthetic limbs, we’ve been left so far with halting, jerky, Etch-a-Sketch-like movements. Dr. Shenoy’s study is a big step toward clinically useful brain-machine technology that has faster, smoother, more natural movements,” said James Gnadt, a program director in Systems and Cognitive Neuroscience at the National Institute of Neurological Disorders and Stroke, part of the National Institutes of Health.

For the time being, the team has been focused on improving cursor movement rather than the creation of robotic limbs, but that is not out of the question, Gilja said. Near term, precise, accurate control of a cursor is a simplified task with enormous value for people with paralysis.

“We think we have a good chance of giving them something very useful,” he said. The team is now translating these innovations to people with paralysis as part of a clinical trial.

This research was funded by the Christopher and Dana Reeve Paralysis Foundation, the National Science Foundation, National Defense Science and Engineering Graduate Fellowships, Stanford Graduate Fellowships, Defense Advanced Research Projects Agency (“Revolutionizing Prosthetics” and “REPAIR”) and the National Institutes of Health (NINDS-CRCNS and Director’s Pioneer Award).

Other contributing researchers include Cynthia Chestek, John Cunningham, Byron Yu, Joline Fan, Mark Churchland, Matthew Kaufman, Jonathan Kao and Stephen Ryu.

http://news.stanford.edu/news/2012/november/thought-control-cursor-111812.html

Thanks to Kebmodee for bringing this to the attention of the It’s Interesting community