Experiments Support Conductivity Claims for Microbial Nanowires

Bacterium discovered by UMass Amherst microbiologist at center of debate

 

AMHERST, Mass. – Scientific debate has been hot lately about whether microbial nanowires, the specialized electrical pili of the mud-dwelling anaerobic bacterium Geobacter sulfurreducens, truly possess metallic-like conductivity as its discoverers claim. But now University of Massachusetts Amherst microbiologist Derek Lovley, with postdoctoral researcher Nikhil Malvankar and colleagues, say they have settled the dispute between theoretical and experimental scientists by devising a combination of new experiments and better theoretical modeling.

In a series of papers going back to 2011, Lovley’s group provided several lines of experimental evidence that Geobacter pili conduct electrons through the close interaction of aromatic amino acids in the protein filament structure. As Malvankar explains, “Electrons flow like they do in a copper wire, hence the term metallic-like conductivity.” However, in the last two years many groups of theoretical modelers have published papers concluding that Lovley and Malvankar’s results are impossible.

But, says Lovley, “In my view, experimental data trumps modeling. As the late physicist Richard Feynman said, ‘It doesn't matter how beautiful your theory is, it doesn't matter how smart you are. If it doesn’t agree with experiment, it’s wrong.’”

In search of even more experimental data, Malvankar traveled to Brookhaven National Laboratory for two years to further evaluate the structure of Geobacter pili with sophisticated approaches including synchrotron X-ray microdiffraction and rocking-curve X-ray diffraction. He found a periodic 3.2-angstrom spacing of aromatic amino acids in the Geobacter pili, far closer together than the theoretical models predicted. Findings appear in the current issue of the journal mBio.

Lovely says, “In Nikhil’s experiments, we see a clear signature of the close packing of the aromatic amino acids. Non-conductive pili lack this. Also, when Nikhil acidified the pili, there was an increase in the packing of the aromatics in proportion to an increase in their conductivity. These results are consistent with our concept of metallic-like conductivity in the pili.  None of the models that rejected our hypothesis were consistent with these results.”

To better understand the lack of correspondence between the experiments and models, Malvankar teamed up with Eric Martz, UMass Amherst emeritus professor and protein modeling expert. They found changing one simple assumption in building the pili model dramatically changed the outcome. Malvankar explains, “Previous models started with a template of the structure for Neisseria gonorrhoeae pili. However, Geobacter pili are actually more closely related to those of Pseudomonas aeruginosa. Our model is based on Pseudomonas.”

Malvankar’s model predicts dense packing of aromatic amino acids consistent with their experimental results and the hypothesis that Geobacter pili possess metallic-like conductivity.


Martz cautions, “We’re not claiming our model is 100 percent correct. In fact, we’re sure it’s not. But the other models simply can’t explain the experimental results. Our does. Also, the conductivity is coming from a protein. Scientists have always said that proteins cannot perform this function. We found not only do they do it, but they also do it well. This is fundamentally such an interesting finding that scientists will have to pay attention.”

This discovery, supported by funding from the U.S. Office of Naval Research, is expected to aid in engineering other bacteria to produce microbial nanowires with synthetic biology methods. For example, Lovley’s lab has invented an artificial form of photosynthesis in which microbes use renewable electricity to convert carbon dioxide to fuels and other organic chemicals. He says, “The better we understand how microbial nanowires work, the better our chances of optimizing the electrode-microbe electron exchange.”

Malvankar adds, “There is also the opportunity to capitalize on the fundamental design principles that nature is teaching us to produce novel electronic materials in a sustainable way.” In nature, Geobacter use their microbial nanowires to breathe; they transfer electrons onto iron oxides, natural rust-like minerals in soil, which serve the same function for these bacteria that oxygen does in humans. “What Geobacter can do with its nanowires is akin to breathing through a snorkel that’s 10 kilometers long,” he says.

Others in Lovley’s group have shown that Geobacter uses microbial nanowires to electrically communicate with other microbial species. This cooperative electron sharing is important in the conversion of organic wastes to methane, an effective bioenergy strategy. Nanowires are also key components of ongoing studies by Lovley’s lab to build biocomputers and novel biosensors. The UMass Amherst team is now working on a “pili factory” to make purified Geobacter pili freely available to other researchers, to repeat these experiments or carry out other studies.

Original Article: http://www.umass.edu/newsoffice/article/experiments-support-conductivity-claims

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Using Fruit Flies to Understand How We Sense Hot and Cold

Mapping a fruit fly’s brain, neuron by neuron, to study how brain controls behavior 

In a study of how the brain controls behavior, Northwestern scientists have mapped the fruit fly brain, neuron by neuron. The work represents the first comprehensive mapping of the brain circuit that processes temperature information in any animal.

EVANSTON, Ill. --- Innately, we pull our hand away when we touch a hot pan on the stove, but little is known about how our brain processes temperature information. Northwestern University scientists now have discovered how a fruit fly’s brain represents temperature, mapping it neuron by neuron, which has implications for understanding the much more complex human brain and how it responds to sensory stimuli.

“The brain is a beautiful machine, and one of the new frontiers in biology is to understand how it works,” said Marco Gallio, who led the research. “The fruit fly is a fantastic model in which to study how the brain controls behavior, and it can help us understand how sensory circuits work in humans.”

Gallio is an assistant professor of neurobiology in Northwestern’s Weinberg College of Arts and Sciences.

In a study of Drosophila melanogaster, Gallio and his team uncovered a coordinated ensemble of neural responses to temperature in the fly’s brain. In imaging the fly brain as it responded to hot or cold environments, the researchers found that multiple neural pathways carry from the antennae different types of information about temperature, and the pathways converge in three key areas in the brain.

Most neurons respond to either hot or cold, but some trade accuracy for speed. These neurons are good at alerting the animal of a sudden temperature change, but they quickly stop responding and leave the job of reporting how hot or cold it is to different neurons.

In a surprise finding, the researchers also learned that a third type of neuron responds to both hot and cold. As both hot and cold temperatures can be quite dangerous to the small fruit fly, this cell type may convey a generic “danger” signal associated with temperature change, the researchers said.

“Humans are more resilient than flies in reacting to temperature change,“ Gallio said, “but the principles we are finding in the fly brain -- the logic and organization -- likely are the same in both. Whether human or fly, the sensory systems have to solve the same problems, so they often do it in the same ways.”

The work represents the first comprehensive mapping of the brain circuit that processes temperature information in any animal. The study will be published March 4 by the journal Nature.

“We decided to focus on temperature as one of the most fundamental sensory modalities,” Gallio said. “Much like in the fly antenna, the sensory neurons in our skin respond to either hot or cold temperature. The brain knows what the hand feels by simply keeping track of which cell type is active -- what we call a ‘labeled line’ system.”

In their study, Gallio and his colleagues discovered that the fly brain is able to extract a range of information from the activity of hot and cold neurons. Their results also suggest how the fly can use this information to guide attractive or aversive behaviors.

The three types of neurons the researchers identified are:

• Neurons that are very fast at signaling the onset or offset of heating or cooling (fast adapting, “narrowly tuned”)

• Neurons that respond more slowly but are much more accurate in reporting absolute temperature (slow adapting, “narrowly tuned”)

• Neurons that respond to both hot and cold and are critical to flies avoiding hot and cold environments (“broadly tuned”)

The fruit fly is a great model system in which to study the processing of sensory stimuli, Gallio said. The fly has quite complex behaviors coupled with a genetically and anatomically simpler nervous system than ours.

“We know very little about how neurons communicate in our brain to produce our behavior and emotions, so we study innate responses in model systems such as the fruit fly to understand basic brain functions,” Gallio said. “Then we can apply these intellectual tools to understand our brain and how it controls behavior.”

Gallio’s group is one of only a few in the world that is systematically studying temperature sensing in fruit flies. In earlier work, Gallio identified where hot- and cold-sensing neurons are located on the fly’s antenna. He next wanted to know where in the brain these signals from the periphery were sent, which led to the study reported in Nature.

In the study, the researchers first used a photolabeling strategy to trace the connections that relay peripheral temperature information to the brain. They found the signals largely converge onto three target regions: the Mushroom Body and the Lateral Horn (both well-known centers for sensory processing) and the Posterior Lateral Protocerebrum (now defined as a major site of thermosensory representation).

Next, using in vivo calcium imaging, the researchers identified the thermosensory projection neurons activated by either hot or cold stimuli (“narrowly tuned” neurons) and those that respond to both heating and cooling (“broadly tuned” neurons).

After learning that the neural information took different paths to the brain, Gallio and his team initially were puzzled. “We found there was an elegant answer,” Gallio said. “Some neurons respond to only hot, some neurons respond to only cold, and some neurons respond to both hot and cold. They all converge in the brain, where all the messages are orchestrated into a cohesive response.”

The work was supported the National Institutes of Health (grants 1R01NS086859-01 and 2T32MH067564).

The paper is titled “Temperature representation in the Drosophila brain.” Other authors of the paper are Dominic D. Frank, Genevieve C. Jouandet and Patrick J. Kearney, from Northwestern, and Lindsey J. Macpherson, from Columbia University.

By Megan Fellman

Original Article: http://www.northwestern.edu/newscenter/stories/2015/03/using-fruit-flies-to-understand-how-we-sense-hot-and-cold.html

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The Free Electron Movement

Once elusive, solar-to-fuel conversion is looking like gold in a UCSB lab

Light: without it, life would be nothing like it is now. Modern technology’s ability to generate, manipulate, sense, and convert light has resulted in man’s capacity to do everything from stay up past sundown to communicate across vast distances, even to see into the distant past of the universe or deep into our bodies.

At UC Santa Barbara, researchers continue to find novel ways of using light — in both the visible and invisible spectra — to address man’s growing need for energy and hunger for information. Through the combination of plasmonics and nanotechnology, researchers have been able to capture a storable form of energy from visible and invisible parts of the spectrum. Manipulating this electromagnetic energy could allow researchers to develop new technology for power generation and imaging.

A new way of harvesting the sun’s energy

In a little water-filled vial in UC Santa Barbara chemistry professor Martin Moskovits’ laboratory, a tiny disc may hold the key to our pressing present and future fuel needs. When illuminated by the sun, this disc — no bigger than one’s fingertip — is capable of breaking the chemical bonds of water, producing hydrogen and oxygen, thus directly storing sunlight as usable fuel.

“This pursuit has been growing for more than 100 years,” said postdoctoral researcher Syed Mubeen, of the ongoing search for a more robust and efficient way to harvest solar energy and turn it into fuel. Unlike solar-to-electricity applications, where conventional photovoltaics have made great strides in efficiency and affordability in the decades since their inception, developing a technology for sustainable solar-to-fuel conversion processes has been elusive, until now.

“Such devices have been made by many researchers in the past, using conventional semiconductor materials,” said Mubeen. “The problem is, when highly efficient semiconductors, such as silicon or gallium arsenide, are in an aqueous environment, they photocorrode, and stop working after a few minutes.”

There have been some inroads made in the solar-to-fuel quest using semiconductors based on metal oxides, like titanium, for instance. These semiconductors don’t fail as readily the silicon-based types, but the tradeoff is that they absorb only the ultraviolet portion of sunlight — about four percent of the spectrum — so their efficiencies are highly limited. Meanwhile, the search for a viable means of converting the Sun’s energy into fuel intensifies, as concerns over the environmental drawbacks of using fossil fuel mount.

Enter gold, one of the Earth’s most stable and conductive metals. Resistant to corrosion, it can be placed in many aqueous solutions without disintegrating, or otherwise reacting. Enter also an entirely new application for plasmonics.

“We have been working on plasmonic materials for many years in other contexts,” said Moskovits, whose research emphasis is in physical chemistry and materials. For decades, plasmons — the collective oscillation of conduction electrons — have been studied and used in applications such as enhanced spectroscopy, for instance, or to detect molecules adhering to surfaces. However, it was the specific social context, which in this instance is the urgent concern to develop alternative energy resources, that spurred the group into considering plasmonics as a source of non-fossil fuel energy.

Harnessing excited electrons 

In conventional photovoltaics, sunlight hits semiconductor material, one side of which is electron-rich, while the other side is not. The photon, or light particle, excites the electrons, causing them to leave their positions, and create positively-charged “holes.” The result is a current of charged particles that can be captured and delivered for various uses, including powering lightbulbs, charging batteries, or facilitating chemical reactions.

In the technology developed by Moskovits and his team, it is not semiconductor materials that provide the electrons and venue for the conversion of solar energy, but the surface of one of the world’s most well known and precious metals.
“When certain metals are exposed to visible light, the conduction electrons of the metal can be caused to oscillate collectively, absorbing a great deal of the light,” said Moskovits. “This excitation is called a surface plasmon.”

However, these excited, “hot” electrons are very short-lived, lasting only about ~ 10 femtoseconds  (~ 1014 seconds) before they relax.

To get an idea of just how briefly these electrons stay hot, imagine a stretch of beach that’s 20 feet long by 20 feet wide by five feet deep. That’s one second. Ten grains of sand would be comparable to 10 femtoseconds.

“The question was, can you capture these electrons effectively and put them to useful work?” said Mubeen. To do this, the Moskovits team — which also included chemistry postdoctoral researcher Joun Lee, chemical engineering graduate researcher Nirala Singh, materials engineer Stephen Kraemer, and chemistry professor Galen Stucky — turned to the very tiny world of nanostructures.

“These hot electrons tend to travel ~10^6 meters per second, which means they could travel at least a few tenths of a nanometer before decaying as heat. The challenge was to come up with an appropriate nanostructured design so that before these electrons decay as heat you use them to do useful chemical reactions,” Mubeen said.

The result is an array of gold nanorods, each rod measuring 80 to 100 nm in diameter and 500 nm in length. Ten billion of these nanoreactors can occupy one square centimeter. Six hundred of them lined up side by side would span the diameter of an average (clean) human hair.

Each nanorod is capped with a layer of crystalline titanium dioxide decorated with platinum nanoparticles. A cobalt-based oxidation catalyst was deposited on the lower portion of the array, and the entire arrangement is submerged in water.


When the negatively charged hot electrons, excited by sunlight, oscillate, they travel up the rod, through the titanium dioxide layer and are captured by the platinum nanoparticles, causing the reaction that splits water molecules. Meanwhile, the positively charged “holes” left behind by the excited electrons head downward to the oxidation catalyst to form oxygen. According to their study, hydrogen production was clearly observable after two hours, and the nanorod array proved to be the durable visible light-harvesting device sought by the researchers.

“The device operated with no hint of failure for many weeks,” Moskovits said. Additionally, according to Mubeen, the use of nanostructures provides the opportunity to scale up for relatively little cost, even with an expensive metal like gold.

Quest for efficiency

Currently, efficiencies for this plasmonic technology are at about .25 percent, which is comparable to silicon semiconductor-based photoprocesses almost a century ago. And, plasmonic technology is still more costly than that for conventional semiconductors.

“We still have a lot of work to do,” said Mubeen, ticking off a list of ideal qualities that would make nanostructured plasmonic materials competitive with conventional semiconductors. “We need to test cost-effective plasmonic metals, so we can make fuels cheap enough. We need to re-engineer the system design to be more efficient.”

Copper and silver are being eyed as alternatives to gold, and an efficiency of 5 percent or more is one of the early targets for the research.

“If the last century of photovoltaic technology has shown anything, it is that continued research will improve on the cost and efficiency of this new method - and likely in far less time than it took for the semiconductor-based technology,” said Moskovits.

“In view of the recentness of the discovery, we consider .25 percent to be a ‘respectable’ efficiency,” he said. “More importantly, we can imagine achievable strategies for improving the efficiencies radically.”

Catching the (invisible) wave

Meanwhile, in another lab on the UCSB campus, researchers Hong Lu, Art Gossard and Mark Sherwin have performed a feat that may provide a wide array of applications, from more efficient solar cells to higher-performance telecommunications to enhanced imaging and sensing technologies.

It comes in the form of a compound semiconductor of nearly perfect quality with embedded semimetallic nanostructures, and it capitalizes on the manipulation of the infrared (IR) and terahertz (THz) range of the electromagnetic spectrum. These invisible areas of the spectrum — with longer wavelengths and lower frequencies than the naked eye can sense — offer much in the way of information they can provide. However, the development of instruments that can take advantage of their range of frequencies is still an emerging field.

Bridging optics and electronics

To cope with the demands of today’s information technology — more data, faster transmission, better energy efficiency — researchers have been turning to optics, using IR light to transmit information.

However the transition between optics and electronics is a difficult one because they operate at vastly different scales, with electron confinement possible in spaces far smaller than light waves. The size gap between the technologies have been a hurdle for scientists and engineers trying to integrate the two with a circuit that can take advantage of the speed, capacity and energy efficiency of optics with the compactness of electronics for information processing.

Here plasmonics plays a vital role, by providing the highly sought bridge between the two technologies. Key to this technology is the use of erbium (Er), a rare earth metal that has the ability to absorb light in the visible as well as infrared wavelength, and has been used for years to enhance the performance of silicon in the production of fiber optics. Pairing erbium with the element antimony (Sb), the researchers embedded the resulting compound — erbium antimonide (ErSb) —  as semimetallic nanostructures within a semiconducting matrix of gallium antimonide (GaSb).

When IR light hits the surface of this semiconductor, electrons in the semimetallic nanostructures begin to resonate — that is, move away from their equilibrium positions and oscillate at the same frequency as the infrared light — preserving the optical information, but shrinking it to a scale that would be compatible with electronic devices.

“This is a new and exciting field,” said Hong Lu, project scientist in materials and in electrical and computer engineering. But the ability to translate optical information into electronic data is only one benefit of this unique semiconductor.

‘A new kind of heterostructure’

In the world of semiconductors, structural quality is of utmost importance: the more regularly repeating and aligned — “flawless” — the arrangement of atoms in the semiconductor’s crystal lattice is, the more reliable and better performing the device in which it will be used will be.

Generating these perfect structures is no minor feat. Any mismatch in size or alignment becomes magnified and could result in cracking. The difficulty becomes even greater when incorporating different atoms, which may be desired for their properties, but not so for their potential to result in defects. While semiconductors incorporating different materials have been studied for years — a technology UCSB professor and Nobel laureate Herbert Kroemer pioneered — a single crystal heterostructured semiconductor/metal is in a class of its own.

ErSb, according to Lu, is an ideal material to match with GaSb because of its structural compatibility with its surrounding material, allowing the researchers to embed the nanostructures without interrupting the atomic lattice structure of the semiconducting matrix, each atom aligned with the matrix around it.

“The nanostructures are coherently embedded, without introducing noticeable defects, through the growth process by molecular beam epitaxy,” said Lu. “We can control the size, the shape and the orientation of the nanostructures.” The term “epitaxy” refers to a process by which layers of material are deposited atom by atom, or molecule by molecule, one on top of the other with a specific orientation.

“It’s really a new kind of heterostructure,” said Arthur Gossard, professor of materials and electrical and computer engineering.

Seeing things in a new light

The semiconductor’s ability to capture and manipulate IR and THz range light opens doors into better imaging and sensing, as the embedded nanostructures/nanowires offer a strong broadband polarization effect, filtering and defining images with IR and THz signatures. In addition to the thermal signatures that are captured by infrared cameras, traces of chemicals found in explosives and illegal narcotics can be sensed using the semiconductor. Terahertz wavelengths, which occupy the space between infrared and microwave frequencies, can penetrate a variety of materials, including the human body, opening up the potential for high resolution imaging without the danger posed by higher energy x-rays.
The researchers have already applied for a patent for these embedded nanowires as a broadband light polarizer.

“For infrared imaging, if you can do it with controllable polarizations, there’s a lot of information there,” said Gossard.

The researchers credit the collaborative nature between departments on the UCSB campus for this multidimensional breakthrough.

“One of the most exciting things about this for me is that this was a ‘grassroots’ collaboration,” said Mark Sherwin, professor of physics, director of the Institute for Terahertz Science and Technology at UCSB. The idea for the direction of the research actually came from the junior researchers in the group, he said, grad students and undergrads from different laboratories and research groups working on different aspects of the project, all of whom decided to combine their efforts and their expertise into one study. “I think what’s really special about UCSB is that we can have an environment like that.”

Researchers on campus are also exploring the possibilities of this technology in the field of thermoelectrics, which studies how temperature differences of a material can create electric voltage or how differences in electric voltages in a material can create temperature differences. Renowned UCSB professors John Bowers (solid state photonics) and Christopher Palmstrom (heteroepitaxial growth of novel materials) are also investigating the potential of this new semiconductor.

BY SONIA FERNANDEZ

Original Article: http://convergence.ucsb.edu/article/free-electron-movement

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Software teaches computers to translate words to math

If Johnny has five apples and seven oranges, and he wants to share them with three of his friends, can a computer understand the text to figure out how many pieces of fruit each person gets?

Thanks to new software developed at the University of Illinois, machines now can learn to understand mathematical reasoning expressed in language, which could greatly improve search engines and access to data as well as boost mathematics education.

U. of I. computer sciences professor Dan Roth and graduate student Subhro Roy published their work in the journal Transactions of the Association for Computational Linguistics.

“There is a lot of data available in news archives and public records, but it cannot be accessed in a meaningful way,” Roth said. “For example, if people want to know what percentage of a state’s budget has been spent on education over the past 20 years, a query like that won’t give the desired result with a keyword search performed today in a search engine like Google. But if the engine were able to do quantitative reasoning, it would infer from the text the type of information the user is looking for. It can find the numbers, then calculate the percentages and addition required to do this.“

The first hurdle, and the biggest challenge, was in teaching the computer to identify quantities and units in text regardless of how they are expressed, something humans do unconsciously when reading. Secondly, the software has to decide what to do with the identified numbers.

In the problem with Johnny, for example, the computer has to understand that both apples and oranges are fruit; it has to know that the words five, seven and three are equivalent to the numerical values 5, 7 and 3; it has to determine what kind of operation(s) the question requires – in this case, addition and division – and in which order to conduct those operations. Once the program has converted the text into an equation, it can easily compute that Johnny and his friends each have three pieces of fruit.

The computer also has to be able to determine the different equation corresponding to the text if, for example, the text had said that Johnny wanted to split the fruit among his three friends, instead of sharing the fruit with them. In that case, the subtle change in the language implies that each of the friends would receive four pieces of fruit, with Johnny keeping none for himself.

Such sophisticated reasoning is required for search queries as well. When accessing a text regarding financial earnings, for instance, the computer has to identify whether an amount is exact or approximate, static or dynamic, a range, presented in relation to something else, and all of the other contextual cues that a reader would inherently understand.

“The computer reads two pounds; two pounds of what? Or is it referencing currency? What about monetary conversions?” Roth said. “If you talk about dates, it gets even harder. I could say, the week after Thanksgiving, or the first week in December, or Dec. 3. To you and me it means the same thing, but a keyword search can’t equate them.”

The researchers tested their software’s abilities to identify and normalize quantities in text, to perform searches regarding monetary currencies, and to understand and solve elementary-school-level math word problems. They found that the software performed well in all tasks. It even outperformed the average elementary-level student on standardized word problems, Roth said, getting 87 percent of answers correct.

Roth hopes that the ability to understand numbers in context will help make information more accessible to all, from researchers looking for correlations to investors looking for clear financial data to citizens seeking to form educated opinions. He also hopes that using technology to break down mathematical concepts can help students improve their own quantitative reasoning abilities.

“As we move forward and want to help kids understand math, it makes sense to use technology,” Roth said. “If you search the Web today, you see tons of Web pages that help kids and parents with math homework, so we know this is a challenge for people. If a program were able to understand text and word problems to the extent that you can see what the variables are and what you should focus on in the problem, that could help people learn better. This shows that computers could help people learn in ways that could not be done before.”

The Army Research Laboratory and the Defense Advanced Research Projects Agency supported this work.

By Liz Ahlberg

Original Article: http://news.illinois.edu/news/15/0120computer_math_DanRoth.html

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Neuroscientists find that limiting a certain protein in the brain reverses Alzheimer's symptoms in mice

Limiting a certain protein in the brain reverses Alzheimer’s symptoms in mice, report neuroscientists at MIT’s Picower Intitute for Learning and Memory.

Researchers found that the overproduction of the protein known as p25 may be the culprit behind the sticky protein-fragment clusters that build up in the brains of Alzheimer's patients. The work, which was published in the April 10 issue of Cell, could provide a new drug target for the treatment of the disease that affects more than five million Americans, says Li-Huei Tsai, director of MIT’s Picower Institute for Learning and Memory and senior author of the paper.

Abnormal clusters of protein fragments, known as beta amyloid plaques, are believed to cause the cognitive impairments, cell death, and tissue loss associated with Alzheimer's. The p25 protein had been tied to the creation and buildup of beta amyloids, but until now, p25’s role in Alzheimer’s pathology was not well understood.

“This protein appears to help maintain normal brain activity, but also is part of a feedback loop with beta amyloids. It generates the plaques which, in turn, boost levels of p25,” Tsai says.

Lead author of the paper is Jinsoo Seo, a postdoc associate at the Picower Institute.

The benefits of p25 generation

Elevated p25 levels in the brain have been documented upon exposure to neurotoxic stimuli such as oxidative stress and beta amyloids.

“In this study, for the first time we show that a variety of physiological neuronal activities generate p25 in the hippocampus, where memories are encoded in the brain,” Tsai says.

To delineate the precise roles of p25, Tsai’s lab generated a transgenic mouse model, which enabled researchers to prevent the production of p25 without altering other proteins with essential roles in brain development.

The researchers found that p25 is required for synaptic plasticity, the ability of brain connections to change over time; especially for the process called long-term depression (LTD) that selectively weakens sets of synapses and is associated with memory extinction.

Tsai’s team observed that the mice unable to generate p25 could learn new tasks and form memories normally; however, when the researchers began to address memory extinction, they soon noticed that the mice have difficulties with replacing older memories with newer ones.

Too much of a good thing

“This finding not only boosts our understanding of p25 in synaptic functions, but also explains the underlying mechanism of the inordinate synaptic depression observed in the Alzheimer’s brain,” Seo says.

“This finding led us to question whether the blockade of p25 generation could mitigate pathological phenotypes in the Alzheimer’s brain,” Tsai says.

In the mouse model of Alzheimer’s disease, inhibiting p25 production improved cognitive function, greatly reduced plaque formation and neuroinflammation, hallmark features of Alzheimer’s disease.

These results hold out the hope that a drug that regulates p25 could benefit Alzheimer’s disease patients by improving cognitive function and perhaps delaying the development of brain pathology, Tsai says.

This work was supported in part by the National Institutes of Health and the Howard Hughes Medical Institute.

by Deborah Halber

Original Article: http://newsoffice.mit.edu/2014/neuroscientists-find-limiting-certain-protein-in-brain-reverses-alzheimers-symptoms

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Epigenomics of Alzheimer’s disease progression

Study of epigenomic modifications reveals immune basis of Alzheimer's disease.

 

Our susceptibility to disease depends both on the genes that we inherit from our parents and on our lifetime experiences. These two components — nature and nurture — seem to affect very different processes in the context of Alzheimer's disease, according to a new study published today in the journal Nature.

 The study was carried out by an interdisciplinary team at MIT and the Broad Institute, and was co-led by Li-Huei Tsai, the Picower Professor at MIT and director of the Picower Institute for Learning and Memory, and Manolis Kellis, a professor in MIT's Computer Science and Artificial Intelligence Laboratory (CSAIL).

The researchers analyzed changes that occur in genes and in regions that regulate genes as Alzheimer’s disease progresses, using a mouse model of Alzheimer’s disease that Tsai’s lab originally developed several years ago. The mice were engineered so that the gene for a protein called p25 can be overstimulated in the brain, which prompts the mice to develop symptoms very similar to Alzheimer’s disease in humans.

“These programmable mice allowed us to study, for the first time, the changes occurring during early stages of the disease, before symptoms even begin to appear,” Tsai says. “We could then compare them to changes in later stages of the disease, when neurodegeneration and cognitive impairment are evident.”

Opposing changes

The researchers profiled multiple chemical modifications, known as epigenetic marks, in the hippocampus of mice expressing too much p25 and compared them with control mice. These epigenetic marks reveal the activity of diverse genomic regions — in particular, the regulatory control regions that control the expression of nearby genes. The researchers also directly profiled the levels of all genes.

“We found two opposing signatures associated with disease progression that are consistent with the pathophysiology of Alzheimer’s disease,” says Elizabeta Gjoneska, joint first author of the paper and a postdoc at the Picower Institute. “Neuronal plasticity processes that are involved in learning and memory were dampened, and immune and inflammatory pathways were activated.”

The active regions specifically matched regions active in a type of immune cells known as microglia, which are responsible for clearing away infected or damaged cells. They also secrete chemicals that produce inflammation.

“Our data suggest that microglia are heavily activated during Alzheimer’s disease progression, although it is unknown exactly how they contribute to the disease,” Tsai says. “These cells are important for normal brain function and share their key cell-surface markers, CD14, with macrophages that infiltrate the brain from elsewhere in the body during disease progression.”

Conserved epigenomic signatures

The researchers then compared the results in mice with what is known about Alzheimer’s disease in humans. They found that differences in gene levels in the Alzheimer’s-like mouse brain matched differences previously seen in the brains of Alzheimer's patients, which prompted them to ask if the epigenetic signatures might also be conserved.

The researchers found that this was the case — specifically, the same regulatory regions that were active or repressed in mice showed the same patterns in humans. They also found that the regions with increased activity in the mouse model of Alzheimer’s disease had immune functions in humans, and the regions that showed decreased activity had neural functions in humans.

“Our results show that functional conservation between human and mouse is not restricted to protein-coding genes,” says Andreas Pfenning, joint first author of the study and a postdoc at MIT. “This opens up the use of epigenomics methods in model organisms to study an inaccessible organ like the brain, and how it changes in response to activity or disease.”

Genetic variants cluster in immune pathways

Previous studies of the genomes of Alzheimer’s patients had identified common genetic variants associated with the disease, but scientists did not know how these DNA variants could contribute to the disease, since the majority of them are found outside of protein-coding regions.

“Our conserved epigenomic maps allowed us to now place these noncoding genetic variants in the context of disease-relevant regulatory regions and interpret their contribution to the disease predisposition,” Kellis says. “As inherited common genetic variants always precede disease onset, they are always indicative of causal roles, and thus can shed additional light on the epigenomic alterations.”

The researchers found that genetic variants associated with Alzheimer's disease were only associated with immune processes, and not with neural processes, indicating that genetic predisposition to Alzheimer's disease primarily affects the circuitry of immune processes, rather than neuronal processes.

“Our results suggest that repression of neural pathways does not represent genetic predisposition, even though it is a hallmark of Alzheimer's,” Tsai says. “Instead, it may occur as a consequence of environmental factors and aging, and result from interactions with the altered immune pathways.”

The researchers identified a small number of master regulators that target many of the regulatory regions that overlap Alzheimer's-associated genetic variants in humans. Among these, PU.1 targets a large number of altered regulatory regions, and the genetic region encoding PU.1 is associated with Alzheimer's disease, suggesting PU.1 as a potential therapeutic target.

“The new focus on immune-cell types, and the specific regulators uncovered, provide new therapeutic avenues,” Kellis says. “Moreover, the conservation of epigenomic signatures between mouse and human provides a platform upon which we can test such therapeutics and their effect on cognition, pathology, and the epigenomic signatures of Alzheimer's.”

“In an elegant series of experiments, the paper adds to a growing body of evidence, which began with genomewide association studies, implicating immune function in the pathogenesis of Alzheimer’s disease. This potentially paves the way for exploiting peripheral myeloid cells to develop biomarkers and therapeutics to target the disease,” says David Bennett, a professor of neurological sciences at Rush University Medical Center, who was not part of the research team.

The research was a component of the National Institutes of Health’s Roadmap Epigenomics Program and was also funded by the Belfer Neurodegeneration Consortium and the Swiss National Science Foundation. The paper was published along with another, whose senior author was Kellis, reporting on the integrative analysis of 111 reference epigenomes. It joins a total of 24 related papers published this week in the Nature and other Nature journals.

Other authors are CSAIL postdoc Gerald Quon, Picower postdoc Hansruedi Mathys, and former CSAIL research scientist Anshul Kundaje.

by Anne Trafton

Original Article: http://newsoffice.mit.edu/2015/epigenomics-alzheimers-disease-0218

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Google gives Lick Observatory $1 million

BERKELEY — Google Inc. has given $1 million to the University of California’s Lick Observatory in what astronomers hope is the first of many private gifts to support an invaluable teaching and research resource for the state.

 

The unrestricted funds, spread over two years, will go toward general expenses, augmenting the $1.5 million the UC Office of the President gives annually to operate the mountaintop observatory for the 10-campus UC system.

“Lick Observatory has been making important discoveries while training generations of scientists for more than 100 years,” said Chris DiBona, director of open source for Google. “Google is proud to support their efforts in 2015 to bring hands-on astronomical experiences to students and the public.”

“This is very exciting,” said UC Berkeley astronomy professor Alex Filippenko, who has been beating the bushes for funds to operate the observatory after UC support dropped as a result of the recent recession.

“Astronomy is the ‘gateway science’ – kids are enthralled by cosmic discoveries, spectacular images, and far-out concepts, which can inspire them to pursue technical fields such as applied physics, engineering and computer science,” Filippenko said. “So there’s a real opportunity to make a difference, through the research, education and public outreach we do at Lick Observatory.”

“I am delighted that Google is supporting the Lick effort and thus helping provide UC students with unique hands-on experiences in valuable astronomy research,” said UC Berkeley Vice Chancellor for Research Graham Fleming.

“We at UC highly value Lick Observatory’s unique capabilities,” said Claire Max, interim director of the University of California Observatories (UCO), which operates Lick, and which manages UC’s share of the twin 10-meter W. M. Keck Telescopes in Hawaii and the planned Thirty Meter Telescope that broke ground last year close to Keck on Mauna Kea. “For example, Lick’s telescopes enable science projects that need lots of repeated observations during the course of a year or more; these can be done much more successfully at Lick than at the 8−10-meter telescopes, where observing time is extremely tight. Google’s very generous gift will make it possible for Lick to provide these opportunities and to continue to develop forefront tools such as adaptive optics, which removes image blurring caused by turbulence in Earth’s atmosphere.”

Lick Observatory, located atop Mt. Hamilton east of San Jose, was established in 1888 and currently houses seven telescopes, including the Katzman Automatic Imaging Telescope run by Filippenko that scans the sky each night in search of exploding stars (supernovae), which help astronomers understand the accelerating expansion of the universe and dark energy. Another robotic telescope, the Automated Planet Finder, closely examines many stars each night to find planets that may be orbiting them.

Faculty, researchers, postdoctoral scholars and students throughout the UC system can observe remotely on the main general-use telescopes, the three-meter Shane telescope and the one-meter Nickel telescope. “These telescopes provide undergraduates with a unique opportunity to participate in substantial astronomical research,” Filippenko said. “I have about a dozen undergraduate students doing Lick research now, many more than ever before.”

Defining the cutting edge

Before the recession, Lick’s budget was about $2.5 million annually to support astronomers and students from eight of the 10 UC campuses as well as the UC-managed Department of Energy labs. Most of the first 100 planets orbiting other stars were discovered at Lick using a forefront instrument that was the best of its kind at the time. Lick observations also helped reveal the presence of giant black holes in the centers of galaxies. In part thanks to large numbers of relatively nearby supernovae found or studied at Lick, astronomers discovered and verified the accelerating expansion of the universe, a feat recognized with the 2011 Nobel Prize in Physics to the leaders of two competing teams and the 2015 Breakthrough Prize in Fundamental Physics to all team members.

The telescopes are used not only for original observing in the optical and infrared, but also to design and test new instruments destined for larger telescopes, such as the 10-meter Keck telescopes. For example, laser guide star adaptive optics, which allows the world’s largest telescopes to stabilize their images to improve sharpness and achieve results in some ways superior to those of the Hubble Space Telescope, was pioneered at Lick.

“At this time, UC is providing basic support at $1.5 million per year, but we really need at least $2.5 million per year to improve the observatory, moving forward vigorously at the cutting edge of research and education. To maintain and expand Lick in the long run, we seek an endowment of about $50 million,” Filippenko said. The interest on that endowment would be used to provide annual operating funds. “This major award from Google should go far, giving us time to raise additional funds.”

“I was delighted to learn of this wonderful gift from Google,” said Aimée Dorr, UC provost and executive vice president for academic affairs. “It will do great things for the astronomical research and education that can be carried out at Lick Observatory. Congratulations to Professor Filippenko, who knows firsthand how valuable Lick is and has dedicated his considerable energy and expertise to ensuring it is available far into the future.”

“I’m pleased that this generous award will help Lick Observatory keep its doors open to the public, to future astronomers and to the scientific community in a capacity that is simply unavailable anywhere else,” said U.S. Rep. Zoe Lofgren, who previously spearheaded two letters of congressional support for Lick to the UC Office of the President. “Lick is an historic Santa Clara County landmark, and the facility has proven invaluable for students, researchers and the Bay Area community. I hope this is the beginning of many gifts recognizing Lick Observatory’s important role in inspiring future scientists and adding to our understanding of what lies beyond our solar system.”

U.S. Rep. Mike Honda, a longtime supporter and advocate for the observatory, added, “I am delighted that Google has decided to give $1 million to Lick Observatory. For 127 years, Lick Observatory has been vital in fundamental astronomical research, the development of new observational techniques, training students and connecting the general public to the heavens. I am pleased to see private companies step up and invest in America’s scientific leadership. I look forward to others joining Google to ensure that Lick Observatory will continue to explore the universe for years to come.”

“Lick Observatory has provided critical data for University of California researchers, and Google’s major support will ensure that the observatory will continue to serve as the foundation for countless scientific discoveries to come,” said state Assemblymember Mark Stone.

One of the first uses for the money, which comes through the UC Berkeley Foundation, will be to hire another telescope operator for the Shane three-meter telescope to eliminate periodic closures caused by the current shortage of staff, Filippenko said. Interim UCO director Max said that another probable use of the funds will be to continue the development of laser guide star adaptive optics, which is breaking new ground at Lick Observatory.

Lick also recently received $350,000 in combined grants from the Heising-Simons Foundation and donors Bill and Marina Kast to enable an upgrade of the Kast spectrograph on the three-meter telescope, used to analyze faint celestial objects – including supernovae – at distances ranging from our own solar system to the far reaches of the universe.

“Graduate students and postdoctoral scholars can be leaders of research done at Lick,” Filippenko said. ”They conceive, propose, execute and complete their own projects, thereby adding immensely to their development as strong, skilled, independent research scientists. We have to keep this unique research and educational institution, a Bay Area treasure and California landmark, thriving.”

By Robert Sanders 

Original Article: http://newscenter.berkeley.edu/2015/02/10/google-gives-lick-observatory-1-million/

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Hallucinatory 'voices' shaped by local culture, Stanford anthropologist says

Tanya Luhrmann, professor of anthropology, studies how culture affects the experiences of people who experience auditory hallucinations, specifically in India, Ghana and the United States.

Stanford anthropologist Tanya Luhrmann found that voice-hearing experiences of people with serious psychotic disorders are shaped by local culture – in the United States, the voices are harsh and threatening; in Africa and India, they are more benign and playful. This may have clinical implications for how to treat people with schizophrenia, she suggests.

People suffering from schizophrenia may hear "voices" – auditory hallucinations – differently depending on their cultural context, according to new Stanford research.

In the United States, the voices are harsher, and in Africa and India, more benign, said Tanya Luhrmann, a Stanford professor of anthropology and first author of the article in the British Journal of Psychiatry.

The experience of hearing voices is complex and varies from person to person, according to Luhrmann. The new research suggests that the voice-hearing experiences are influenced by one's particular social and cultural environment – and this may have consequences for treatment.

In an interview, Luhrmann said that American clinicians "sometimes treat the voices heard by people with psychosis as if they are the uninteresting neurological byproducts of disease which should be ignored. Our work found that people with serious psychotic disorder in different cultures have different voice-hearing experiences. That suggests that the way people pay attention to their voices alters what they hear their voices say. That may have clinical implications."

Positive and negative voices

Luhrmann said the role of culture in understanding psychiatric illnesses in depth has been overlooked.

"The work by anthropologists who work on psychiatric illness teaches us that these illnesses shift in small but important ways in different social worlds. Psychiatric scientists tend not to look at cultural variation. Someone should, because it's important, and it can teach us something about psychiatric illness," said Luhrmann, an anthropologist trained in psychology. She is the Watkins University Professor at Stanford.

For the research, Luhrmann and her colleagues interviewed 60 adults diagnosed with schizophrenia – 20 each in San Mateo, California; Accra, Ghana; and Chennai, India. Overall, there were 31 women and 29 men with an average age of 34. They were asked how many voices they heard, how often, what they thought caused the auditory hallucinations, and what their voices were like.

"We then asked the participants whether they knew who was speaking, whether they had conversations with the voices, and what the voices said. We asked people what they found most distressing about the voices, whether they had any positive experiences of voices and whether the voice spoke about sex or God," she said.

The findings revealed that hearing voices was broadly similar across all three cultures, according to Luhrmann. Many of those interviewed reported both good and bad voices, and conversations with those voices, as well as whispering and hissing that they could not quite place physically. Some spoke of hearing from God while others said they felt like their voices were an "assault" upon them.

'Voices as bombardment'

The striking difference was that while many of the African and Indian subjects registered predominantly positive experiences with their voices, not one American did. Rather, the U.S. subjects were more likely to report experiences as violent and hateful – and evidence of a sick condition.

The Americans experienced voices as bombardment and as symptoms of a brain disease caused by genes or trauma.

One participant described the voices as "like torturing people, to take their eye out with a fork, or cut someone's head and drink their blood, really nasty stuff." Other Americans (five of them) even spoke of their voices as a call to battle or war – "'the warfare of everyone just yelling.'"

Moreover, the Americans mostly did not report that they knew who spoke to them and they seemed to have 
less personal relationships with their voices, according to Luhrmann.

Among the Indians in Chennai, more than half (11) heard voices of kin or family members commanding them to do tasks. "They talk as if elder people advising younger people," one subject said. That contrasts to the Americans, only two of whom heard family members. Also, the Indians heard fewer threatening voices than the Americans – several heard the voices as playful, as manifesting spirits or magic, and even as entertaining. Finally, not as many of them described the voices in terms of a medical or psychiatric problem, as all of the Americans did.

In Accra, Ghana, where the culture accepts that disembodied spirits can talk, few subjects described voices in brain disease terms. When people talked about their voices, 10 of them called the experience predominantly positive; 16 of them reported hearing God audibly. "'Mostly, the voices are good,'" one participant remarked.

Individual self vs. the collective

Why the difference? Luhrmann offered an explanation: Europeans and Americans tend to see themselves as individuals motivated by a sense of self identity, whereas outside the West, people imagine the mind and self interwoven with others and defined through relationships.

"Actual people do not always follow social norms," the scholars noted. "Nonetheless, the more independent emphasis of what we typically call the 'West' and the more interdependent emphasis of other societies has been demonstrated ethnographically and experimentally in many places."

As a result, hearing voices in a specific context may differ significantly for the person involved, they wrote. In America, the voices were an intrusion and a threat to one's private world – the voices could not be controlled.

However, in India and Africa, the subjects were not as troubled by the voices – they seemed on one level to make sense in a more relational world. Still, differences existed between the participants in India and Africa; the former's voice-hearing experience emphasized playfulness and sex, whereas the latter more often involved the voice of God.

The religiosity or urban nature of the culture did not seem to be a factor in how the voices were viewed, Luhrmann said.

"Instead, the difference seems to be that the Chennai (India) and Accra (Ghana) participants were more comfortable interpreting their voices as relationships and not as the sign of a violated mind," the researchers wrote.

Relationship with voices

The research, Luhrmann observed, suggests that the "harsh, violent voices so common in the West may not be an inevitable feature of schizophrenia." Cultural shaping of schizophrenia behavior may be even more profound than previously thought.

The findings may be clinically significant, according to the researchers. Prior research showed that specific therapies may alter what patients hear their voices say. One new approach claims it is possible to improve individuals' relationships with their voices by teaching them to name their voices and to build relationships with them, and that doing so diminishes their caustic qualities. "More benign voices may contribute to more benign course and outcome," they wrote.

Co-authors for the article included R. Padmavati and Hema Tharoor from the Schizophrenia Research Foundation in Chennai, India, and Akwasi Osei from the Accra General Psychiatric Hospital in Accra, Ghana.

What's next in line for Luhrmann and her colleagues?

"Our hunch is that the way people think about thinking changes the way they pay attention to the unusual experiences associated with sleep and awareness, and that as a result, people will have different spiritual experiences, as well as different patterns of psychiatric experience," she said, noting a plan to conduct a larger, systematic comparison of spiritual, psychiatric and thought process experiences in five countries.

BY CLIFTON B. PARKER

Original Article: http://news.stanford.edu/news/2014/july/voices-culture-luhrmann-071614.html

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For the first time, spacecraft catch a solar shockwave in the act

On Oct. 8, 2013, an explosion on the sun’s surface sent a supersonic blast wave of solar wind out into space. This shockwave tore past Mercury and Venus, blitzing by the moon before streaming toward Earth. The shockwave struck a massive blow to the Earth’s magnetic field, setting off a magnetized sound pulse around the planet.

NASA’s Van Allen Probes, twin spacecraft orbiting within the radiation belts deep inside the Earth’s magnetic field, captured the effects of the solar shockwave just before and after it struck.

Now scientists at MIT’s Haystack Observatory, the University of Colorado, and elsewhere have analyzed the probes’ data, and observed a sudden and dramatic effect in the shockwave’s aftermath: The resulting magnetosonic pulse, lasting just 60 seconds, reverberated through the Earth’s radiation belts, accelerating certain particles to ultrahigh energies.

“These are very lightweight particles, but they are ultrarelativistic, killer electrons — electrons that can go right through a satellite,” says John Foster, associate director of MIT’s Haystack Observatory. “These particles are accelerated, and their number goes up by a factor of 10, in just one minute. We were able to see this entire process taking place, and it’s exciting: We see something that, in terms of the radiation belt, is really quick.”

The findings represent the first time the effects of a solar shockwave on Earth’s radiation belts have been observed in detail from beginning to end. Foster and his colleagues have published their results in the Journal of Geophysical Research.

Catching a shockwave in the act

Since August 2012, the Van Allen Probes have been orbiting within the Van Allen radiation belts. The probes’ mission is to help characterize the extreme environment within the radiation belts, so as to design more resilient spacecraft and satellites.

One question the mission seeks to answer is how the radiation belts give rise to ultrarelativistic electrons — particles that streak around the Earth at 1,000 kilometers per second, circling the planet in just five minutes. These high-speed particles can bombard satellites and spacecraft, causing irreparable damage to onboard electronics.

The two Van Allen probes maintain the same orbit around the Earth, with one probe following an hour behind the other. On Oct. 8, 2013, the first probe was in just the right position, facing the sun, to observe the radiation belts just before the shockwave struck the Earth’s magnetic field. The second probe, catching up to the same position an hour later, recorded the shockwave’s aftermath.

Dealing a “sledgehammer blow”

Foster and his colleagues analyzed the probes’ data, and laid out the following sequence of events: As the solar shockwave made impact, according to Foster, it struck “a sledgehammer blow” to the protective barrier of the Earth’s magnetic field. But instead of breaking through this barrier, the shockwave effectively bounced away, generating a wave in the opposite direction, in the form of a magnetosonic pulse — a powerful, magnetized sound wave that propagated to the far side of the Earth within a matter of minutes.

In that time, the researchers observed that the magnetosonic pulse swept up certain lower-energy particles. The electric field within the pulse accelerated these particles to energies of 3 to 4 million electronvolts, creating 10 times the number of ultrarelativistic electrons that previously existed.

Taking a closer look at the data, the researchers were able to identify the mechanism by which certain particles in the radiation belts were accelerated. As it turns out, if particles’ velocities as they circle the Earth match that of the magnetosonic pulse, they are deemed “drift resonant,” and are more likely to gain energy from the pulse as it speeds through the radiation belts. The longer a particle interacts with the pulse, the more it is accelerated, giving rise to an extremely high-energy particle.

Foster says solar shockwaves can impact Earth’s radiation belts a couple of times each month. The event in 2013 was a relatively minor one.

“This was a relatively small shock. We know they can be much, much bigger,” Foster says. “Interactions between solar activity and Earth’s magnetosphere can create the radiation belt in a number of ways, some of which can take months, others days. The shock process takes seconds to minutes. This could be the tip of the iceberg in how we understand radiation-belt physics.”

Barry Mauk, a project scientist at Johns Hopkins University’s Applied Physics Laboratory, views the group’s findings as “the most comprehensive analysis of shock-induced acceleration within Earth’s space environment ever achieved.”

“Significant shock-induced acceleration of Earth’s radiation belts occur only occasionally, but these events are important because they have the potential of suddenly generating the most intense and energetic electrons, and therefore the most dangerous conditions for astronauts and satellites,” says Mauk, who did not contribute to the study. “Earth’s space environment serves as a wonderful laboratory for studying the nature of shock acceleration that is occurring elsewhere in the solar system and universe.”

by Jennifer Chu

Original Article: http://newsoffice.mit.edu/2015/spacecraft-catch-solar-storm-shockwave-0219

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Social Circles - MIT study details the degree to which urban movement is linked to social activity

If you live in a city, you know that a fair amount of your movement around town is social in nature. But how much, exactly? A new study co-authored by MIT researchers uses a novel method to infer that around one-fifth of urban movement is strictly social, a finding that holds up consistently in multiple cities.

The study used anonymized phone data that, unlike most data in the field, provides information that can be used to reconstruct both people’s locations and their social networks. By linking this information together, the researchers were able to build a picture indicating which networks were primarily social, as opposed to work-oriented, and then deduce how much city movement was due to social activity.

“Adding two data sources — one on the social side and one on the mobility side — and layering them one on top of each other gives you something that’s a little bit greater,” says Jameson Toole, a PhD student in MIT’s Engineering Systems Division, and one of the authors of a newly published paper outlining the study’s results.

“It’s a way to look at the data that wasn’t done before,” says Marta Gonzalez, an assistant professor in MIT’s Department of Civil and Environmental Engineering, and another co-author of the study.

By developing a new means of quantifying how much urban travel is based on social activity, the researchers believe they have started creating a new analytical tool that could be of use to planners and policymakers.

“There are a lot of people who need to have estimates of how people move around cities: transportation planners and other urban planners,” Toole says. “But a lot of data-driven models don’t take into account social behavior. What we found is that … if you are trying to estimate movement in a city and you don’t include the social component, your estimates are going to be off by about 20 percent.”

Going mobile

The paper, “Coupling human mobility and social ties,” is appearing this week in Interface, a peer-reviewed journal published by the Royal Society. The co-authors are Toole, who is the lead author; Carlos Herrer-Yaque, of the Technical University of Madrid; Gonzalez, who is the principal investigator on the study; and Christian Schneider, an MIT post-doctoral researcher during the course of the study.

The study’s anonymized mobile phone data comes from three major cities in Europe and South America. By examining the locations of calls, the networks of calls made, and the times of contact, the researchers found that most people have essentially three kinds of social networks in cities: social companions (who they are around a lot in the evenings and on weekends), work colleagues (who they tend to contact during weekdays), and more distant acquaintances with whom people have more sporadic contact.

After distinguishing these networks from each other, the researchers were able to quantify the extent to which social activity was the primary cause of an urban trip; their conclusion falls within the bounds of previous, broader estimates, which have ascribed 15 to 30 percent of urban movement to social activity.

 

“It’s pretty rare you would find these patterns showing up by themselves in multiple cities,” Toole says. “It lends credence to the universality of this [pattern].”

In the paper, the researchers also build a model of urban social movement, which they call the “GeoSim” model; it extends previous models of urban mobility by adding a layer relating to social-activity choices. The model better fits the data in this study, and could be tested against future data sets as well.

“Big data is amazing,” Toole says, “but this adds the context back into the social networks and movements.”

Scholars say the paper brings new insight to urban mobility studies. The study’s “novelty resides in the method used to study the relationship between mobility of different users and their social relationship,” explains Esteban Moro, a professor of mathematics at the Charles III University of Madrid, in Spain. “Using different mobility metrics, the authors are able to know the nature of the relationship between two people. ... This allows a quantitative understanding of how people manage their time, tasks, [and] interactions in a geographical context like cities.”

Moro adds that the current research project opens the way for more detailed studies of the subject, noting, “It would be interesting to see if the socioeconomic status of people, their age, and/or gender have a role in the results found.”

The research was partly funded by the Accenture-MIT Alliance in Business Analytics, the Center for Complex Engineering Systems at MIT, and the National Science Foundation.

Original Article: http://newsoffice.mit.edu/2015/urban-movement-linked-social-activity-0226

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Learn math without fear, Stanford expert says

Stanford Professor Jo Boaler says that students most effectively learn "math facts" working on problems that they enjoy, rather than through exercises and drills they fear. Speed pressure, timed testing and blind memorization damage children's experience of math, she says.

Students learn math best when they approach the subject as something they enjoy, according to a Stanford education expert. Speed pressure, timed testing and blind memorization pose high hurdles in the youthful pursuit of math.

"There is a common and damaging misconception in mathematics – the idea that strong math students are fast math students," said Jo Boaler, a Stanford professor of mathematics education and the lead author on a new working paper. Boaler's co-authors are Cathy Williams, cofounder of Stanford's YouCubed, and Amanda Confer, a Stanford graduate student in education.

Curriculum timely

Fortunately, said Boaler, the new national curriculum standards known as the Common Core Standards for K-12 schools de-emphasize the rote memorization of math facts. Maths facts are fundamental assumptions about math, such as the times tables (2 x 2 = 4), for example. Still, the expectation of rote memorization continues in classrooms and households across the United States.

While research shows that knowledge of math facts is important, Boaler said the best way for students to know math facts is by using them regularly and developing understanding of numerical relations. Memorization, speed and test pressure can be damaging, she added.

On the other hand, people with "number sense" are those who can use numbers flexibly, she said. For example, when asked to solve the problem of 7 x 8, someone with number sense may have memorized 56, but they would also be able to use a strategy such as working out 10 x 7 and subtracting two 7s (70-14).

"They would not have to rely on a distant memory," Boaler wrote.

In fact, in one research project the investigators found that the high-achieving students actually used number sense, rather than rote memory, and the low-achieving students did not.

The conclusion was that the low achievers are often low achievers not because they know less but because they don't use numbers flexibly.

"They have been set on the wrong path, often from an early age, of trying to memorize methods instead of interacting with numbers flexibly," she wrote. Number sense is the foundation for all higher-level mathematics, she noted.

Role of the brain

Boaler said that some students will be slower when memorizing, but still possess exceptional mathematics potential.

"Math facts are a very small part of mathematics, but unfortunately students who don't memorize math facts well often come to believe that they can never be successful with math and turn away from the subject," she said.

Prior research found that students who memorized more easily were not higher achieving – in fact, they did not have what the researchers described as more "math ability" or higher IQ scores. Using an MRI scanner, the only brain differences the researchers found were in a brain region called the hippocampus, which is the area in the brain responsible for memorizing facts – the working memory section.

But according to Boaler, when students are stressed – such as when they are solving math questions under time pressure – the working memory becomes blocked and the students cannot as easily recall the math facts they had previously studied. This particularly occurs among higher achieving students and female students, she said.

Some estimates suggest that at least a third of students experience extreme stress or "math anxiety" when they take a timed test, no matter their level of achievement. "When we put students through this anxiety-provoking experience, we lose students from mathematics," she said.

Boaler contrasts the common approach to teaching math with that of teaching English. In English, a student reads and understands novels or poetry, without needing to memorize the meanings of words through testing. They learn words by using them in many different situations – talking, reading and writing.

"No English student would say or think that learning about English is about the fast memorization and fast recall of words," she added.

Strategies, activities

In her paper, "Fluency without Fear," Boaler provides activities for teachers and parents that help students learn math facts at the same time as developing number sense. These include number talks, addition and multiplication activities, and math cards.

Importantly, she said, these activities include a focus on the visual representation of number facts. When students connect visual and symbolic representations of numbers, they are using different pathways in the brain, which deepens their learning, as shown by recent brain research.

"Math fluency" is often misinterpreted, with an over-emphasis on speed and memorization, she said. "I work with a lot of mathematicians, and one thing I notice about them is that they are not particularly fast with numbers; in fact some of them are rather slow. This is not a bad thing; they are slow because they think deeply and carefully about mathematics."

She refers to the famous French mathematician, Laurent Schwartz, who wrote in his autobiography that he often felt stupid in school, as he was one of the slowest math thinkers in class.
Math anxiety and fear play a big role in students dropping out of mathematics, said Boaler.

"When we emphasize memorization and testing in the name of fluency we are harming children, we are risking the future of our ever-quantitative society and we are threatening the discipline of mathematics. We have the research knowledge we need to change this and to enable all children to be powerful mathematics learners. Now is the time to use it," she said.

BY CLIFTON B. PARKER

Original Article: http://news.stanford.edu/news/2015/january/math-learning-boaler-012915.html

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Three nearly Earth-size planets found orbiting nearby star

NASA’s Kepler Space Telescope, despite being hobbled by the loss of critical guidance systems, has discovered a star with three planets only slightly larger than Earth. The outermost planet orbits in the “Goldilocks” zone, a region where surface temperatures could be moderate enough for liquid water and perhaps life to exist.

The star, EPIC 201367065, is a cool red M-dwarf about half the size and mass of our own sun. At a distance of 150 light years, the star ranks among the top 10 nearest stars known to have transiting planets. The star’s proximity means it’s bright enough for astronomers to study the planets’ atmospheres to determine whether they are like Earth’s atmosphere and possibly conducive to life.

“A thin atmosphere made of nitrogen and oxygen has allowed life to thrive on Earth. But nature is full of surprises. Many exoplanets discovered by the Kepler mission are enveloped by thick, hydrogen-rich atmospheres that are probably incompatible with life as we know it,” said Ian Crossfield, the University of Arizona astronomer who led the study.

A paper describing the find by astronomers at the University of Arizona, UC Berkeley, University of Hawaii, Manoa, and other institutions has been submitted to Astrophysical Journal and is freely available on the arXiv website.

The three planets are 2.1, 1.7 and 1.5 times the size of Earth. The outermost planet, at 1.5 Earth radii, is the smallest of the bunch and orbits far enough from its host star that it receives levels of light from its star similar to those received by Earth from the sun, said UC Berkeley graduate student Erik Petigura, who discovered the planets Jan. 6 while conducting a computer analysis of the Kepler data NASA has made available to astronomers. He calculated that the three planets receive 10.5, 3.2, and 1.4 times the light intensity of Earth.

“Most planets we have found to date are scorched. This system is the closest star with lukewarm transiting planets,” Petigura said. “There is a very real possibility that the outermost planet is rocky like Earth, which means this planet could have the right temperature to support liquid water oceans.”

University of Hawaii astronomer Andrew Howard noted that extrasolar planets are discovered by the hundreds these days, though many astronomers are left wondering if any of the newfound worlds are really like Earth. The newly discovered planetary system will help resolve this question, he said.

“We’ve learned in the past year that planets the size and temperature of Earth are common in our Milky Way galaxy,” Howard said. “We also discovered some Earth-size planets that appear to be made of the same materials as our Earth, mostly rock and iron.”

Kepler’s K2 mission

After Petigura found the planets in the Kepler light curves, the team quickly employed telescopes in Chile, Hawaii and California to characterize the star’s mass, radius, temperature, and age. Two of the telescopes involved, the Automated Planet Finder on Mount Hamilton near San Jose, Calif., and the Keck Telescope on Mauna Kea, Hawaii, are University of California facilities.

The next step will be observations with other telescopes, including the Hubble Space Telescope, to take the spectroscopic fingerprint of the molecules in the planetary atmospheres. If these warm, nearly Earth-size planets have puffy, hydrogen-rich atmospheres, Hubble will see the telltale signal, Petigura said.

The discovery is all the more remarkable, he said, because the Kepler telescope lost two reaction wheels that kept it pointing at a fixed spot in space. Kepler was reborn in 2014 as ‘K2’ with a clever strategy of pointing the telescope in the plane of Earth’s orbit, the ecliptic, to stabilize the spacecraft. Kepler is now back to mining the cosmos for planets by searching for eclipses or “transits,” as planets pass in front of their host stars and periodically block some of the starlight.

“This discovery proves that K2, despite being somewhat compromised, can still find exciting and scientifically compelling planets,” said Petigura. “This ingenious new use of Kepler is a testament to the ingenuity of the scientists and engineers at NASA. This discovery shows that Kepler can still do great science.”

Kepler sees only a small fraction of the planetary systems in its gaze: those with orbital planes aligned edge-on to our view from Earth. Planets with large orbital tilts are missed by Kepler. A census of Kepler planets that the team conducted in 2013 corrected statistically for these random orbital orientations, and concluded that one in five sun-like stars in the Milky Way Galaxy have Earth-size planets in the habitable zone. Accounting for other types of stars as well, there may be 40 billion such planets galaxywide.

The original Kepler mission found thousands of small planets, but most of them were too faint and far away to assess their density and composition and thus determine whether they were high-density, rocky planets like Earth or puffy, low-density planets like Uranus and Neptune. Because the star EPIC-201 is nearby, these mass measurements are possible. The host star, an M-dwarf, is less intrinsically bright than the sun, which means that its planets can reside close to the host-star and still enjoy lukewarm temperatures.

According to Howard, the system most like that of EPIC-201 is Kepler-138, an M-dwarf star with three planets of similar size, though none are in the habitable zone.

Co-authors of the paper include Joshua Schlieder of NASA Ames Research Center and colleagues from Germany, the United Kingdom and the United States.

 By Robert Sanders 

Original Article: http://newscenter.berkeley.edu/2015/01/16/three-nearly-earth-size-planets-found-orbiting-nearby-star/

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