Speaking and Understanding Speech Share the Same Parts of the Brain

Speaking and Understanding Speech Share the Same Parts of the Brain

  9:13:00 AM    Science Lover

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The brain has two big tasks related to speech: making it and understanding it. Psychologists and others who study the brain have debated whether these are really two separate tasks or whether they both use the same regions of the brain. Now, a new study, published in the August issue of Psychological Science, a journal of the Association for Psychological Science, finds that speaking and understanding speech share the same parts of the brain, with one difference: we don't need the brain regions that control the movements of lips, teeth, and so on to understand speech.

New research finds that speaking and understanding 
speech share the same parts of the brain. 
(Credit: © Artsem Martysiuk / Fotolia)

Most studies of how speech works in the brain focuses on comprehension. That's mostly because it's easier to image the brains of people who are listening quietly; talking makes the head move, which is a problem when you're measuring the brain. But now, the Donders Institute at the Radboud University Nijmegen, where the study was conducted, has developed technology that allows recording from a moving brain.

Laura Menenti, a Postdoctoral Research Associate at the University of Glasgow, co-wrote the paper along with Peter Hagoort of Radboud University Nijmegen and the Max Planck Institute for Psycholinguistics, Sarah Gierhan and Katrien Segaert. Menenti was initially interested in how the brain produces grammatical sentences and wanted to track the process of producing a sentence in its entirety; looking not only at its grammatical structure but also at its meaning. "What made this particularly exciting to us was that no one had managed to perform such a study before, meaning that we could explore an almost completely new topic," says Menenti.




The authors used functional MRI technology to measure brain activity in people who were either listening to sentences or speaking sentences. The other problem with measuring brain activity in people who are speaking is that you have to get them to say the right kind of sentence. The authors accomplished this with a picture of an action -- a man strangling a woman, say -- with one person colored green and one colored red to indicate their order in the sentence. This prompted people to say either "The man is strangling the woman" or "The woman is strangled by the man." (The experiments were all carried out in Dutch.)

From this, the researchers were able to tell where in the brain three different speech tasks (computing meaning, coming up with the words, and building a grammatical sentence) -- were taking place. They found that the same areas were activated for each of these tasks in people who were speaking and people who were listening to sentences. However, although some studies have suggested that while people are listening to speech, they silently articulate the words in order to understand them, the authors found no involvement of motor regions when people were listening.

According to Menenti, though the study was largely designed to answer a specific theoretical question, it also points towards some useful avenues for treatment of people with language-related problems. It suggests that while it sometimes seems that people with comprehension problems may have intact production, and vice versa, this may not necessarily be the case. According to Menenti, "Our data suggest that these problems would be expected to always at least partly coincide. On the other, our data confirm the idea that many different processes in the language system, such as understanding meaning or grammar, can at least partly, be damaged independently of each other."

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Seeing eye to eye is key to copying, say scientists

Seeing eye to eye is key to copying, say scientists

  10:21:00 AM    Science Lover

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Imitation may be the sincerest form of flattery but how do our brains decide when and who we should copy? Researchers from The University of Nottingham have found that the key may lie in an unspoken invitation communicated through eye contact.

In a study published this week in the Journal of Neuroscience, a team of scientists from the University's School of Psychology show that eye contact seems to act as an invitation for mimicry, triggering mechanisms in the frontal region of the brain that control imitation.

The results could be the first clues to understanding why some people, such as children with autism, struggle to grasp when they are expected to copy the actions of others in social situations.

Dr Antonia Hamilton, who led the research, said: "Many studies have looked at copying and imitation in terms of 'mirror neurons', which are believed to be specialised parts of the human brain that implement imitation. However, we also know that imitation is carefully controlled — people don't imitate everything they see, and only copy what's important.

"Our previous research has shown that when somebody makes eye contact with you, you are more likely to copy them. So eye contact seems to act as a message that says "Copy me now". This recent study aimed to see what happens to that signal in the brain."




The team of psychologists, which also included doctoral student Yin Wang and Dr Richard Ramsey, used functional magnetic resonance imaging (fMRI) to scan the brains of volunteers while they watched videos of an actress who sometimes would make eye contact with them while opening or closing her hand. The participant was told they should open their own hand whenever they saw the actress move her hand so in some trials the participant was copying the actress and in other trials they were not.

Because previous behavioural measurement such as response time revealed that the participant unconsciously copied the actress faster when the actress provided eye contact, the scientists analysed the brain imaging data to find which brain areas controlled the decision to copy. The analysis used a new mathematical method called dynamic causal modelling to compute the information processing in the brain, which has never been applied to imitation before.

The data showed that mirror neuron brain regions do play a role in the copying task. More importantly though, it revealed that these regions are controlled by the medial prefrontal cortex, an area of the brain associated with planning complex cognitive behaviours, expressing personality, decision-making and responding to social situations.

Dr Hamilton added: "Previous studies have shown that this medial prefrontal brain region is active in many social situations but responds less in people with autism, which explains why children on the autistic spectrum might not copy at the right time.

"Understanding the control of imitation has implications for many other areas of psychology too. For example, are teenagers whose prefrontal cortex is less developed more easily led to copy risky, dangerous or illegal behaviour such as imitating rioters? Could increasing the amount of eye contact between children and teachers lead to better learning by imitation? Would better control of imitation help children with autism to more effectively learn and interact? We plan further research to address these questions."

Provided by University of Nottingham

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Scientists Have New Help Finding Their Way Around Brain's Nooks and Crannies

Scientists Have New Help Finding Their Way Around Brain's Nooks and Crannies

  12:53:00 AM    Science Lover

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Like explorers mapping a new planet, scientists probing the brain need every type of landmark they can get. Each mountain, river or forest helps scientists find their way through the intricacies of the human brain.

Scientists have found a way to use MRI scanning data 
to map myelin, a white sheath that covers some brain 
cell branches. Such maps, previously only available via 
dissection, help scientists determine precisely where they 
are at in the brain. Red and yellow indicate regions with 
high myelin levels; blue, purple and black areas have low 
myelin levels. (Credit: David Van Essen)

Researchers at Washington University School of Medicine in St. Louis have developed a new technique that provides rapid access to brain landmarks formerly only available at autopsy. Better brain maps will result, speeding efforts to understand how the healthy brain works and potentially aiding in future diagnosis and treatment of brain disorders, the researchers report in the Journal of Neuroscience Aug. 10.

The technique makes it possible for scientists to map myelination, or the degree to which branches of brain cells are covered by a white sheath known as myelin in order to speed up long-distance signaling. It was developed in part through the Human Connectome Project, a $30 million, five-year effort to map the brain's wiring. That project is headed by Washington University in St. Louis and the University of Minnesota.

"The brain is among the most complex structures known, with approximately 90 billion neurons transmitting information across 150 trillion connections," says David Van Essen, PhD, Edison Professor and head of the Department of Anatomy and Neurobiology at Washington University. "New perspectives are very helpful for understanding this complexity, and myelin maps will give us important insights into where certain parts of the brain end and others begin."

Easy access to detailed maps of myelination in humans and animals also will aid efforts to understand how the brain evolved and how it works, according to Van Essen.

Neuroscientists have known for more than a century that myelination levels differ throughout the cerebral cortex, the gray outer layer of the brain where most higher mental functions take place. Until now, though, the only way they could map these differences in detail was to remove the brain after death, slice it and stain it for myelin.

Washington University graduate student Matthew Glasser developed the new technique, which combines data from two types of magnetic resonance imaging (MRI) scans that have been available for years.



"These are standard ways of imaging brain anatomy that scientists and clinicians have used for a long time," Glasser says. "After developing the new technique, we applied it in a detailed analysis of archived brain scans from healthy adults."

As in prior studies, Glasser's results show highest myelination levels in areas involved with early processing of information from the eyes and other sensory organs and control of movement. Many brain cells are packed into these regions, but the connections among the cells are less complex. Scientists suspect that these brain regions rely heavily on what computer scientists call parallel processing: Instead of every cell in the region working together on a single complex problem, multiple separate teams of cells work simultaneously on different parts of the problem.

Areas with less myelin include brain regions linked to speech, reasoning and use of tools. These regions have brain cells that are packed less densely, because individual cells are larger and have more complex connections with neighboring cells.

"It's been widely hypothesized that each chunk of the cerebral cortex is made up of very uniform information-processing machinery," Van Essen says. "But we're now adding to a picture of striking regional differences that are important for understanding how the brain works."

According to Van Essen, the technique will make it possible for the Connectome project to rapidly map myelination in many different research participants. Data on many subjects, acquired through many different analytical techniques including myelination mapping, will help the resulting maps cover the range of anatomic variation present in humans.

"Our colleagues are clamoring to make use of this approach because it's so helpful for figuring out where you are in the cortex, and the data are either already there or can be obtained in less than 10 minutes of MRI scanning," Glasser says.

This research was funded by the National Institutes of Health (NIH).

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Searching for Spin Liquids: Much-Sought Exotic Quantum State of Matter Can Exist

Searching for Spin Liquids: Much-Sought Exotic Quantum State of Matter Can Exist

  12:33:00 AM    Science Lover

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The world economy is becoming ever more reliant on high tech electronics such as computers featuring fingernail-sized microprocessors crammed with billions of transistors. For progress to continue, for Moore's Law -- according to which the number of computer components crammed onto microchips doubles every two years, even as the size and cost of components halves -- to continue, new materials and new phenomena need to be discovered.

Diagram depicting anti-ferromagnetic order (upper) compared to a spin liquid phase (lower). In an anti-ferromagnet, the spins are anti-aligned. A spin liquid has no order and the spins can be viewed as bobbing about like water molecules in liquid water. (Credit: E. Edwards)

Furthermore, as the sizes of electronic components shrink, soon down to the size of single atoms or molecules, quantum interactions become ever more important. Consequently, enhanced knowledge and exploitation of quantum effects is essential. Researchers at the Joint Quantum Institute (JQI) in College Park, Maryland, operated by the University of Maryland and the National Institute of Standards and Technology (NIST), and at Georgetown University have uncovered evidence for a long-sought-after quantum state of matter, a spin liquid.

The research was performed by JQI postdoctoral scientists Christopher Varney and Kai Sun, JQI Fellow Victor Galitski, and Marcos Rigol of Georgetown University. The results appear in an editor-recommended article in the 12 August issue of the journal Physical Review Letters.

You can't pour a spin liquid into a glass. It's not a material at all, at least not a material you can touch. It is more like a kind of magnetic disorder within an ordered array of atoms. Nevertheless, it has many physicists excited.

To understand this exotic state of matter, first consider the concept of spin, which is at the heart of all magnetic phenomena. For instance, a refrigerator magnet, at the microscopic level, consists of trillions of trillions of iron atoms all lined up. Each of these atoms can be thought of loosely as a tiny spinning ball. The orientation of that spin is what makes the atom into a tiny magnet. The refrigerator magnet is an example of a ferromagnet, the ferro part coming from the Latin word for iron. In a ferromagnet, all the atomic spins are lined up in the same way, producing a large cooperative magnetic effect.

Important though they may be, ferromagnets aren't the only kind of material where magnetic interactions between spins are critical. In anti-ferromagnets, for instance, the neighboring spins are driven to be anti-aligned. That is, the orientations of the spins alternate up and down (see top picture in figure). The accumulative magnetic effect of all these up and down spins is that the material has no net magnetism. The high-temperature superconducting materials discovered in the 1980s are an important example of an anti-ferromagnetic structure.

More complicated and potentially interesting magnetic arrangements are possible, which may lead to a quantum spin liquid. Imagine an equilateral triangle, with an atom (spin) at each corner. Anti-ferromagnetism in such a geometry would meet with difficulties. Suppose that one spin points up while a second spin points down. So far, so good. But what spin orientation can the third atom take? It can't simultaneously anti-align with both of the other atoms in the triangle. Physicists employ the word "frustration" to describe this baffling condition where all demands cannot be satisfied.

In everyday life frustration is, well, frustrating, and actually this condition is found throughout nature, from magnetism to neural networks. Furthermore, understanding the different manifestations of a collection of magnetically interacting spins might help in designing new types of electronic circuitry.

One compromise that a frustrated spin system makes is to simultaneously exist in many spin orientations. In a quantum system, this simultaneous existence, or superposition, is allowed.

Here's where the JQI researchers have tried something new. They have studied what happens when frustration occurs in materials with a hexagonal (six sided) unit cell lattice.

What these atoms do is interact via their respective spins. The strength of the interaction between nearest neighbor (NN) atoms is denoted by the parameter J1. Similarly, the force between next nearest neighbors (NNN) -- that is, pairs of atoms that have at least one intervening atom between them -- is denoted by J2. Letting this batch of atoms interact among themselves, even on a pretend lattice as small as this, entails an immense calculation. Varney and his colleagues have calculated what happens in an array of hexagons consisting of 30 sites where the spins are free to swing about in a two-dimensional plane (this kind of approach is called an XY model).



Christopher Varney, who has appointments at Maryland and Georgetown, said that the interactions of atoms can be represented by a matrix (essentially a two-dimensional spreadsheet) with 155 million entries on each side. This huge number corresponds to the different spin configurations that can occur on this honeycomb-structured material.

What the researchers found were a "kaleidoscope" of phases, which represent the lowest-energy states that are allowed given the magnetic interactions. Just as water can exist in different phases -- steam, liquid, and ice -- as the temperature is changed, so here a change in the strengths of the interactions among the spins (the J1 and J2 parameters) results in different phases. For example, one simple solution is an antiferromagnet (upper picture in figure).

But one phase turns out to be a true quantum spin liquid having no order at all. When J2 is between about 21% and 36% of the value of J1, frustration coaxes the spins into disorder; the entire sample co-exists in millions of quantum states simultaneously.

It's difficult for the human mind to picture a tiny two-dimensional material in so many states at the same time. JQI fellow, Victor Galitski, suggests that one shouldn't think of the spins as residing at the original atomic sites but rather as free ranging particle-like entities dubbed "spinons." These spinons bob about, just as water molecules bob about in liquid water (see lower picture in figure). Hence the name quantum spin liquid.

Another reason for using the word liquid, Galitski says, is this 'bobbing about' is analogous to what happens inside a metal. There, the outer electrons of most atoms tend to leave their home atoms and drift through the metal sample as if they constituted a fluid, called a "Fermi liquid."

Electrons in a metal are able to drift since it takes only an infinitesimal amount of energy to put them into motion. The same is true for the fluctuating spins in the hexagonal model studied by the JQI scientists. Indeed, their spin model assumes a temperature of absolute zero, where quantum effects abound.

Writing in an essay that accompanied the article in Physical Review Letters, Tameem Albash and Stephan Haas, scientists at the University of Southern California, say that the JQI/Georgetown team "present a convincing example" of the new spin liquid state.

How can this new frustration calculation be tested? The experimental verification of the spin liquid state in a 2-dimenstional hexagonal lattice, Albash and Haas suggest, "will probably be tested using cold atoms trapped in optical lattices. In the past few years, this technology has become a reliable tool to emulate quantum many body lattice systems with tunable interactions." Indeed the authors propose such an experiment.

What would such a spin liquid material be good for? It's too early to tell. But some speculations include the idea that these materials could support some exotic kind of superconductivity or would organize particle-like entities that possessed fractional electric charge.

"Kaleidoscope of Exotic Quantum Phases in a Frustrated XY Model" by Christopher N. Varney, Kai Sun, Victor Galitski, and Marcos Rigol, Physical Review Letters, 107, 077201, (12 August 2011).

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Supergene is key to copycat butterflies

Supergene is key to copycat butterflies

  6:14:00 PM    Science Lover

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Since Charles Darwin, biologists have pondered the mystery of "mimicry butterflies", which survive by copying the wing patterns of other butterflies that taste horrible to their predators, birds.

This undated handout photo released by the CNRS shows butterflies, Melinaea mneme (top) and Heliconius numata. The mystery of how a butterfly has changed its wing patterns to mimic neighbouring species and avoid being eaten by birds has been solved by a team of European scientists.

The answer, according to a study released on Friday, lies in an astonishing cluster of about 30 genes in a single chromosome.

"We were blown away by what we found," said Mathieu Joron of France's National Museum of Natural History, who led the probe into what is being called a "supergene".

"These butterflies are the 'transformers' of the insect world," said Joron.

"But instead of being able to turn from a car into a robot with the flick of a switch, a single genetic switch allows these insects to morph into several different mimetic forms.

"It is amazing, and the stuff of science fiction. Now we are starting to understand how this switch can have such a pervasive effect."



The trick, known as Muellerian mimicry, was investigated by French and British scientists, who focussed on a species of Amazonian rainforest butterfly, Heliconius numata.

It is able to copy the colour patterns of several species of the Melinaea butterfly which are unpalatable to birds.

The "supergene" comprises a tightly packed region of genes on a single chromosome which control different elements of the wing pattern.

"By changing just one gene, the butterfly is able to fool its predators," explained Richard ffrench-Constant of the University of Exeter, southwestern England.

Even more astonishing is that three versions of the chromosome exist within this species, with each version controlling distinct wing-pattern forms.

Even though the butterflies look quite different from each other, they have the same DNA.

The supergene apparently transmits in a block from generation to generation, rather than go through recombination -- the mingling of genes from both parents.

The "supergene" also appears important in other species, say the authors.

One such species, the peppered moth, developped black wings in 19th-century Britain as a means of gaining camouflage in the sooty industrial environment.

"It's a gene that really packs an evolutionary punch," said ffrench-Constant. The paper is published online by the British science journal Nature.

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Inexpensive catalyst that makes hydrogen gas 10 times faster than natural enzyme

Inexpensive catalyst that makes hydrogen gas 10 times faster than natural enzyme

  10:14:00 AM    Science Lover

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Looking to nature for their muse, researchers have used a common protein to guide the design of a material that can make energy-storing hydrogen gas. The synthetic material works 10 times faster than the original protein found in water-dwelling microbes, the researchers report in the August 12 issue of the journal Science, clocking in at 100,000 molecules of hydrogen gas every second.

The part of the catalyst that cranks out 100,000
molecules of hydrogen gas a second packs electrons
into chemical bonds between hydrogen atoms, possibly
hijacked from water. Credit: PNNL

This step is just one part of a series of reactions to split water and make hydrogen gas, but the researchers say the result shows they can learn from nature how to control those reactions to make durable synthetic catalysts for energy storage, such as in fuel cells.

In addition, the natural protein, an enzyme, uses inexpensive, abundant metals in its design, which the team copied. Currently, these materials -- called catalysts, because they spur reactions along -- rely on expensive metals such as platinum.

"This nickel-based catalyst is really very fast," said coauthor Morris Bullock of the Department of Energy's Pacific Northwest National Laboratory. "It's about a hundred times faster than the previous catalyst record holder. And from nature, we knew it could be done with abundant and inexpensive nickel or iron."

Stuffing Bonds

Electrical energy is nothing more than electrons. These same electrons are what tie atoms together when they are chemically bound to each other in molecules such as hydrogen gas. Stuffing electrons into chemical bonds is one way to store electrical energy, which is particularly important for renewable, sustainable energy sources like solar or wind power. Converting the chemical bonds back into flowing electricity when the sun isn't shining or the wind isn't blowing allows the use of the stored energy, such as in a fuel cell that runs on hydrogen.

Electrons are often stored in batteries, but Bullock and his colleagues want to take advantage of the closer packing available in chemicals.

"We want to store energy as densely as possible. Chemical bonds can store a huge amount of energy in a small amount of physical space," said Bullock, director of the Center for Molecular Electrocatalysis at PNNL, one of DOE's Energy Frontier Research Centers. The team also included visiting researcher Monte Helm from Fort Lewis College in Durango, Colo.

Biology stores energy densely all the time. Plants use photosynthesis to store the sun's energy in chemical bonds, which people use when they eat food. And a common microbe stores energy in the bonds of hydrogen gas with the help of a protein called a hydrogenase.

Because the hydrogenases found in nature don't last as long as ones that are built out of tougher chemicals (think paper versus plastic), the researchers wanted to pull out the active portion of the biological hydrogenase and redesign it with a stable chemical backbone.

Two Plus Two Equals One

In this study, the researchers looked at only one small part of splitting water into hydrogen gas, like fast-forwarding to the end of a movie. Of the many steps, there's a part at the end when the catalyst has a hold of two hydrogen atoms that it has stolen from water and snaps the two together.

The catalyst does this by completely dismantling some hydrogen atoms from a source such as water and moving the pieces around. Due to the simplicity of hydrogen atoms, those pieces are positively charged protons and negatively charged electrons. The catalyst arranges those pieces into just the right position so they can be put together correctly. "Two protons plus two electrons equals one molecule of hydrogen gas," says Bullock.



In real life, the protons would come from water, but since the team only examined a portion of the reaction, the researchers used water stand-ins such as acids to test their catalyst.

"We looked at the hydrogenase and asked what is the important part of this?" said Bullock. "The hydrogenase moves the protons around in what we call a proton relay. Where the protons go, the electrons will follow."

A Bauble for Energy

Based on the hydrogenase's proton relay, the experimental catalyst contained regions that dangled off the main structure and attracted protons, called "pendant amines." A pendant amine moves a proton into position on the edge of the catalyst, while a nickel atom in the middle of the catalyst offers a hydrogen atom with an extra electron (that's a proton and two electrons for those counting).

The pendant amine's proton is positive, while the nickel atom is holding on to a negatively charged hydrogen. Positioned close to each other, the opposites attract and the conglomerate solidifies into a molecule, forming hydrogen gas.

With that plan in mind, the team built potential catalysts and tested them. On their first try, they put a bunch of pendant amines around the nickel center, thinking more would be better. Testing their catalyst, they found it didn't work very fast. An analysis of how the catalyst was moving protons and electrons around suggested too many pendant amines got in the way of the perfect reaction. An overabundance of protons made for a sticky catalyst, which pinched it and slowed the hydrogen-gas-forming reaction down.

Like good gardeners, the team trimmed a few pendant amines off their catalyst, leaving only enough to make the protons stand out, ready to accept a negatively charged hydrogen atom.

Fastest Cat in the West

Testing the trimmed catalyst, the team found it performed much better than anticipated. At first they used conditions in which no water was present (remember, they used water stand-ins), and the catalyst could create hydrogen gas at a rate of about 33,000 molecules per second. That's much faster than their natural inspiration, which clocks in at around 10,000 per second.

However, most real-life applications will have water around, so they added water to the reaction to see how it would perform. The catalyst ran three times as fast, creating more than 100,000 hydrogen molecules every second. The researchers think the water might help by moving protons to a more advantageous spot on the pendant amine, but they are still studying the details.

Their catalyst has a drawback, however. It's fast, but it's not efficient. The catalyst runs on electricity -- after all, it needs those electrons to stuff into the chemical bonds -- but it requires more electricity than practical, a characteristic called the overpotential.

Bullock says the team has some ideas on how to reduce the inefficiency. Also, future work will require assembling a catalyst that splits water in addition to making hydrogen gas. Even with a high overpotential, the researchers see high potential for this catalyst.

More information: Monte L. Helm, Michael P. Stewart, R. Morris Bullock, M. Rakowski DuBois, Daniel L. DuBois, A Synthetic Nickel Electrocatalyst With a Turnover Frequency Above 100,000 s-1 for H2 Production, Science, August 12, 2011, DOI:10.1126/science.1205864

Provided by Pacific Northwest National Laboratory

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Engineers Reverse E. Coli Metabolism for Quick Production of Fuels, Chemicals

Engineers Reverse E. Coli Metabolism for Quick Production of Fuels, Chemicals

  10:54:00 PM    Science Lover

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In a biotechnological tour de force, Rice University engineering researchers this week unveiled a new method for rapidly converting simple glucose into biofuels and petrochemical substitutes. In a paper published online in Nature, Rice's team described how it reversed one of the most efficient of all metabolic pathways -- the beta oxidation cycle -- to engineer bacteria that produce biofuel at a breakneck pace.

Rice University engineering researchers Ramon Gonzalez (left) and
Clementina Dellomonaco reversed one of the most efficient of all
metabolic pathways -- the beta oxidation cycle -- to engineer bacteria
that make biofuels at a breakneck pace. (Credit: Jeff Fitlow/Rice
University)

Just how fast are Rice's single-celled chemical factories? On a cell-per-cell basis, the bacteria produced the butanol, a biofuel that can be substituted for gasoline in most engines, about 10 times faster than any previously reported organism.


"That's really not even a fair comparison because the other organisms used an expensive, enriched feedstock, and we used the cheapest thing you can imagine, just glucose and mineral salts," said Ramon Gonzalez, associate professor of chemical and biomolecular engineering at Rice and lead co-author of the Nature study.


Gonzalez's laboratory is in a race with hundreds of labs around the world to find green methods for producing chemicals like butanol that have historically come from petroleum.


"We call these 'drop-in' fuels and chemicals, because their structure and properties are very similar, sometimes identical, to petroleum-based products," he said. "That means they can be 'dropped in,' or substituted, for products that are produced today by the petrochemical industry."




Butanol is a relatively short molecule, with a backbone of just four carbon atoms. Molecules with longer carbon chains have been even more troublesome for biotech producers to make, particularly molecules with chains of 10 or more carbon atoms. Gonzalez said that's partly because researchers have focused on ramping up the natural metabolic processes that cells use to build long-chain fatty acids. Gonzalez and students Clementina Dellomonaco, James Clomburg and Elliot Miller took a completely different approach.


"Rather than going with the process nature uses to build fatty acids, we reversed the process that it uses to break them apart," Gonzalez said. "It's definitely unconventional, but it makes sense because the routes nature has selected to build fatty acids are very inefficient compared with the reversal of the route it uses to break them apart."


The beta oxidation process is one of biology's most fundamental, Gonzalez said. Species ranging from single-celled bacteria to human beings use beta oxidation to break down fatty acids and generate energy.


In the Nature study, Gonzalez's team reversed the beta oxidation cycle by selectively manipulating about a dozen genes in the bacteria Escherichia coli. They also showed that selective manipulations of particular genes could be used to produce fatty acids of particular lengths, including long-chain molecules like stearic acid and palmitic acid, which have chains of more than a dozen carbon atoms.


"This is not a one-trick pony," Gonzalez said. "We can make many kinds of specialized molecules for many different markets. We can also do this in any organism. Some producers prefer to use industrial organisms other than E. coli, like algae or yeast. That's another advantage of using reverse-beta oxidation, because the pathway is present in almost every organism."


The research was funded by Rice University.

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Engineers Solve Longstanding Problem in Photonic Chip Technology: Findings Help Pave Way for Next Generation of Computer Chips

Engineers Solve Longstanding Problem in Photonic Chip Technology: Findings Help Pave Way for Next Generation of Computer Chips

  1:00:00 AM    Science Lover

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Stretching for thousands of miles beneath oceans, optical fibers now connect every continent except for Antarctica. With less data loss and higher bandwidth, optical-fiber technology allows information to zip around the world, bringing pictures, video, and other data from every corner of the globe to your computer in a split second. But although optical fibers are increasingly replacing copper wires, carrying information via photons instead of electrons, today's computer technology still relies on electronic chips.

Caltech engineers have developed a new way to 
isolate light on a photonic chip, allowing light to 
travel in only one direction. This finding can lead 
to the next generation of computer-chip technology: 
photonic chips that allow for faster computers 
and less data loss. (Credit: Caltech/Liang Feng)

Now, researchers led by engineers at the California Institute of Technology (Caltech) are paving the way for the next generation of computer-chip technology: photonic chips. With integrated circuits that use light instead of electricity, photonic chips will allow for faster computers and less data loss when connected to the global fiber-optic network.

"We want to take everything on an electronic chip and reproduce it on a photonic chip," says Liang Feng, a postdoctoral scholar in electrical engineering and the lead author on a paper to be published in the August 5 issue of the journal Science. Feng is part of Caltech's nanofabrication group, led by Axel Scherer, Bernard A. Neches Professor of Electrical Engineering, Applied Physics, and Physics, and co-director of the Kavli Nanoscience Institute at Caltech.

In that paper, the researchers describe a new technique to isolate light signals on a silicon chip, solving a longstanding problem in engineering photonic chips.

An isolated light signal can only travel in one direction. If light weren't isolated, signals sent and received between different components on a photonic circuit could interfere with one another, causing the chip to become unstable. In an electrical circuit, a device called a diode isolates electrical signals by allowing current to travel in one direction but not the other. The goal, then, is to create the photonic analog of a diode, a device called an optical isolator. "This is something scientists have been pursuing for 20 years," Feng says.

Normally, a light beam has exactly the same properties when it moves forward as when it's reflected backward. "If you can see me, then I can see you," he says. In order to isolate light, its properties need to somehow change when going in the opposite direction. An optical isolator can then block light that has these changed properties, which allows light signals to travel only in one direction between devices on a chip.

"We want to build something where you can see me, but I can't see you," Feng explains. "That means there's no signal from your side to me. The device on my side is isolated; it won't be affected by my surroundings, so the functionality of my device will be stable."

To isolate light, Feng and his colleagues designed a new type of optical waveguide, a 0.8-micron-wide silicon device that channels light. The waveguide allows light to go in one direction but changes the mode of the light when it travels in the opposite direction.

A light wave's mode corresponds to the pattern of the electromagnetic field lines that make up the wave. In the researchers' new waveguide, the light travels in a symmetric mode in one direction, but changes to an asymmetric mode in the other. Because different light modes can't interact with one another, the two beams of light thus pass through each other.



Previously, there were two main ways to achieve this kind of optical isolation. The first way -- developed almost a century ago -- is to use a magnetic field. The magnetic field changes the polarization of light -- the orientation of the light's electric-field lines -- when it travels in the opposite direction, so that the light going one way can't interfere with the light going the other way. "The problem is, you can't put a large magnetic field next to a computer," Feng says. "It's not healthy."

The second conventional method requires so-called nonlinear optical materials, which change light's frequency rather than its polarization. This technique was developed about 50 years ago, but is problematic because silicon, the material that's the basis for the integrated circuit, is a linear material. If computers were to use optical isolators made out of nonlinear materials, silicon would have to be replaced, which would require revamping all of computer technology. But with their new silicon waveguides, the researchers have become the first to isolate light with a linear material.

Although this work is just a proof-of-principle experiment, the researchers are already building an optical isolator that can be integrated onto a silicon chip. An optical isolator is essential for building the integrated, nanoscale photonic devices and components that will enable future integrated information systems on a chip. Current, state-of-the-art photonic chips operate at 10 gigabits per second (Gbps) -- hundreds of times the data-transfer rates of today's personal computers -- with the next generation expected to soon hit 40 Gbps. But without built-in optical isolators, those chips are much simpler than their electronic counterparts and are not yet ready for the market. Optical isolators like those based on the researchers' designs will therefore be crucial for commercially viable photonic chips.

In addition to Feng and Scherer, the other authors on the Science paper, "Non-reciprocal light propagation in a silicon photonic circuit," are Jingqing Huang, a Caltech graduate student; Maurice Ayache of UC San Diego and Yeshaiahu Fainman, Cymer Professor in Advanced Optical Technologies at UC San Diego; and Ye-Long Xu, Ming-Hui Lu, and Yan-Feng Chen of the Nanjing National Laboratory of Microstructures in China. This research was done as part of the Center for Integrated Access Networks (CIAN), one of the National Science Foundation's Engineering Research Centers. Fainman is also the deputy director of CIAN. Funding was provided by the National Science Foundation, and the Defense Advanced Research Projects Agency.

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How Vampire Bats Find Veins

How Vampire Bats Find Veins

  12:25:00 AM    Science Lover

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Heat-sensing protein channels in vampire bats allow the flying mammals to find the best place to sink their teeth into their prey.

The common vampire bat (Desmodus rotundus)

Researchers have discovered an infrared-sensing protein channel that allows vampire bats to identify the hottest part of the animal—veins close to the skin’s surface that carry 38 degree-Celsius (100° F) blood, and presumably the best spot for feeding.

The channel is a variant of TRPV1, a heat-sensing protein channel that is triggered by high temperatures that could potentially cause injury, according to the study published today (August 3) in Nature, and is distinct from the heat sensor used by snakes—the only other non-insect animals that are known to detect heat by sensing infrared radiation.

“Infrared [detection] allows these guys, in pitch black, to hunt down warm-blooded prey,” said zoologist Bill Schutt, assistant professor at Long Island University, who was not involved in the research. Here, the researchers identified a modification in a common heat-sensing protein channel that lowered its temperature threshold so that it is more attuned to an animal’s body heat, he added.

The common vampire bat was appropriately named after the myth of Dracula—it feeds at night and lives solely on a diet of blood, every day or two consuming up to half its weight in the vital substance from large mammals, especially sleeping livestock. The bats first use echolocation to detect their prey, but once they are within 20 centimeters of their target, they use infrared sensors in specialized pits around their noses to zero in on the best place to feed.

In a previous study, physiologist David Julius at the University of California, San Francisco, and colleagues found that infrared detection by snakes—which, like bats, use nerves located in facial pits to detect their prey—is mediated by a cell-surface protein channel called transient receptor potential cation channel A1 (TRPA1). The channel is actually insensitive to heat in most organisms, but had evolved the capability in snakes, leading the group to suspect that a similar transformation may have given vampire bats their ability to sense infrared.




To see if this was the case, Julius and his collaborators at the University of California, San Francisco, the Venezuelan Institute of Scientific Investigation (IVIC), and the Carnegie Institution in Baltimore, Maryland, compared gene expression in vampire bats’ heat-sensing nerves, called trigeminal ganglia, with expression in a nerve cluster near the spine, called dorsal root ganglia (DRG). They also compared these expression patterns to those of the ganglia in four bat species that do not have infrared sensory abilities.

To their surprise, they did not observe any differences in transcription of the TRPA1-coding gene, nor of any other genes. Instead, they discovered that the protein TRPV1—a heat-sensing protein channel normally triggered by temperatures over 43° C (110° F)—existed in two different isoforms—an approximately 850-amino-acid version and one that was 62 amino acids shorter. The short form, which resulted from alternative splicing of the transcribed mRNA, made up as much as half of the TRPV1 found in the trigeminal ganglia of vampire bats, whereas it comprised only a small percentage of the TRPV1 in the DRG. It was similarly low in both types of nerve clusters in the other bat species, suggesting that the short form may play a role in infrared detection.

To test this hypothesis, the researchers expressed one of the two TRPV1 isoforms in human kidney cells and in frog oocytes grown in vitro, and measured their temperature sensitivity using calcium imaging and electrophysiological assays, respectively. As expected, cells producing the long isoform were activated at 40 degrees Celsius (104° F). Cells producing the short isoform, on the other hand, were activated at just 30 degrees (86° F)—a drop that allows the protein to respond to the warmth of the vampire bats’ prey.

“This is a big jump in understanding how these animals locate their prey,” said Brock Fenton, a biology professor at the University of Western Ontario and author of an accompanying Nature News and Views article. While the longer isoform maintains its normal function of detecting potentially harmful high temperatures, the shorter isoform in the trigeminal nerves of the common vampire bat allows the animals to detect lower temperatures, such as the body heat of their mammalian prey.

“Basically, evolution tweaked a system in vampires bats that was already being used to sense temperatures,” said Schutt, author of the 2008 book Dark Banquet: Blood and the Curious Lives of Blood-Feeding Creatures, turning it into a useful hunting tool.

This is in contrast to the pit viper, whose infrared-sensing ability evolved from a different type of channel not involved in heat detection, but in the detection of noxious smells, added Fenton. The different evolutionary strategies employed by these two lineages “is an example of how plastic our sensory systems can be,” he said.

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Sun-Free Photovoltaics Powered by Heat

Sun-Free Photovoltaics Powered by Heat

  6:24:00 PM    Science Lover

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A new photovoltaic energy-conversion system developed at MIT can be powered solely by heat, generating electricity with no sunlight at all. While the principle involved is not new, a novel way of engineering the surface of a material to convert heat into precisely tuned wavelengths of light -- selected to match the wavelengths that photovoltaic cells can best convert to electricity -- makes the new system much more efficient than previous versions.

A variety of silicon chip micro-reactors developed by the MIT team. Each of these contains photonic crystals on both flat faces, with external tubes for injecting fuel and air and ejecting waste products. Inside the chip, the fuel and air react to heat up the photonic crystals. In use, these reactors would have a photovoltaic cell mounted against each face, with a tiny gap between, to convert the emitted wavelengths of light to electricity. (Credit: Photo by Justin Knight)

The key to this fine-tuned light emission, described in the journal Physical Review A, lies in a material with billions of nanoscale pits etched on its surface. When the material absorbs heat -- whether from the sun, a hydrocarbon fuel, a decaying radioisotope or any other source -- the pitted surface radiates energy primarily at these carefully chosen wavelengths.

Based on that technology, MIT researchers have made a button-sized power generator fueled by butane that can run three times longer than a lithium-ion battery of the same weight; the device can then be recharged instantly, just by snapping in a tiny cartridge of fresh fuel. Another device, powered by a radioisotope that steadily produces heat from radioactive decay, could generate electricity for 30 years without refueling or servicing -- an ideal source of electricity for spacecraft headed on long missions away from the sun.

According to the U.S. Energy Information Administration, 92 percent of all the energy we use involves converting heat into mechanical energy, and then often into electricity -- such as using fuel to boil water to turn a turbine, which is attached to a generator. But today's mechanical systems have relatively low efficiency, and can't be scaled down to the small sizes needed for devices such as sensors, smartphones or medical monitors.

"Being able to convert heat from various sources into electricity without moving parts would bring huge benefits," says Ivan Celanovic ScD '06, research engineer in MIT's Institute for Soldier Nanotechnologies (ISN), "especially if we could do it efficiently, relatively inexpensively and on a small scale."

It has long been known that photovoltaic (PV) cells needn't always run on sunlight. Half a century ago, researchers developed thermophotovoltaics (TPV), which couple a PV cell with any source of heat: A burning hydrocarbon, for example, heats up a material called the thermal emitter, which radiates heat and light onto the PV diode, generating electricity. The thermal emitter's radiation includes far more infrared wavelengths than occur in the solar spectrum, and "low band-gap" PV materials invented less than a decade ago can absorb more of that infrared radiation than standard silicon PVs can. But much of the heat is still wasted, so efficiencies remain relatively low.

An ideal match

The solution, Celanovic says, is to design a thermal emitter that radiates only the wavelengths that the PV diode can absorb and convert into electricity, while suppressing other wavelengths. "But how do we find a material that has this magical property of emitting only at the wavelengths that we want?" asks Marin Soljačić, professor of physics and ISN researcher. The answer: Make a photonic crystal by taking a sample of material and create some nanoscale features on its surface -- say, a regularly repeating pattern of holes or ridges -- so light propagates through the sample in a dramatically different way.



"By choosing how we design the nanostructure, we can create materials that have novel optical properties," Soljačić says. "This gives us the ability to control and manipulate the behavior of light."

The team -- which also includes Peter Bermel, research scientist in the Research Laboratory for Electronics (RLE); Peter Fisher, professor of physics; and Michael Ghebrebrhan, a postdoc in RLE -- used a slab of tungsten, engineering billions of tiny pits on its surface. When the slab heats up, it generates bright light with an altered emission spectrum because each pit acts as a resonator, capable of giving off radiation at only certain wavelengths.

This powerful approach -- co-developed by John D. Joannopoulos, the Francis Wright Davis Professor of Physics and ISN director, and others -- has been widely used to improve lasers, light-emitting diodes and even optical fibers. The MIT team, supported in part by a seed grant from the MIT Energy Initiative, is now working with collaborators at MIT and elsewhere to use it to create several novel electricity-generating devices.

Mike Waits, an electronics engineer at the Army Research Laboratory in Adelphi, Md., who was not involved in this work, says this approach to producing miniature power supplies could lead to lighter portable electronics, which is "critical for the soldier to lighten his load. It not only reduces his burden, but also reduces the logistics chain" to deliver those devices to the field. "There are a lot of lives at stake," he says, "so if you can make the power sources more efficient, it could be a great benefit."

The button-like device that uses hydrocarbon fuels such as butane or propane as its heat source -- known as a micro-TPV power generator -- has at its heart a "micro-reactor" designed by Klavs Jensen, the Warren K. Lewis Professor of Chemical Engineering, and fabricated in the Microsystems Technology Laboratories. While the device achieves a fuel-to-electricity conversion efficiency three times greater than that of a lithium-ion battery of the same size and weight, Celanovic is confident that with further work his team can triple the current energy density. "At that point, our TPV generator could power your smartphone for a whole week without being recharged," he says.

Celanovic and Soljačić stress that building practical systems requires integrating many technologies and fields of expertise. "It's a really multidisciplinary effort," Celanovic says. "And it's a neat example of how fundamental research in materials can result in new performance that enables a whole spectrum of applications for efficient energy conversion."

Note: The full version of the MITEI story is available at: http://web.mit.edu/mitei/research/spotlights/making-electricity-with-photovoltaics.html

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