Patterns found in laboratory spark insight into nature and society

Irv Epstein's research is proving that patterns found in mathematical formulas and chemical reactions may be used to understand economics, how an epidemic might spread and the way animal populations survive in the natural world.

Irv Epstein is fascinated with patterns — how they show up in economics, in the coats of animals and within social systems.

“If you look for patterns in social systems, you see them in housing, segregation or in how an epidemic might spread,” says Epstein, the Henry F. Fischbach Professor of Chemistry. “In general, changes don’t occur smoothly, but in patterns that often have some regularity to them.”

While his research is done in the lab, it is proving that chemical reactions and mathematical formulas may also be used to understand how organisms move and the way animal populations survive in the natural world.

Epstein’s group studies oscillatory chemical reactions (systems in which concentrations of various chemical increase and decrease over time); cross-diffusion, spatial pattern formation, transformation of chemical into mechanical energy, dynamical systems and neurobiology. He is the former dean of arts and sciences and provost at Brandeis. He’s also a founder of the Science Posse, which brings underrepresented and economically disadvantaged students to Brandeis to study science.

Hired in 1971 to teach quantum mechanics, Epstein says his interest in oscillating reactions came about while working with some eager undergraduates who were looking for a summer project. Feeling that quantum mechanics would be a bit too complex for students who had just finished their freshman year, he recalled an article in the Journal of Chemical Education about oscillating chemical reactions and suggested the topic.

Little did he know the project would reroute his career.

“One of the students discovered something that contradicted a statement in the classic literature and figured out what was going on,” says Epstein. “We published a paper and I became more interested in this stuff, eventually changing fields completely.”

Epstein says non-linear dynamics and exotic reactions like oscillating chemical reactions are quite rare in chemistry but very important in biology, because every living system is full of reactions in which concentrations increase and decrease, typically on a daily cycle. Unraveling this phenomenon in chemistry is offering insights into pattern formation in other systems, such as human and animal populations.? To better understand diffusion, cross-diffusion and oscillatory chemical reactions, Epstein revisits a science demo popular with the elementary school set: The glass of water and drop of food coloring.
Diffusion is the phenomenon by which a species spreads out from a concentrated region to a less concentrated region. When a drop of red food coloring is placed in a glass of water, the food coloring disperses over time, resulting in a uniform pink glass of colored water. The process by which the color spreads is diffusion.

Cross-diffusion is a process in which two species are spreading- for example, if you have both a red drop and a blue drop of food coloring; the “cross” aspect means that the distribution of one color affects the diffusion of the other.

“Chemists and physicists have largely ignored cross-diffusion,” says Epstein. “When you study diffusion in an introductory chemistry or physics course, the standard treatment completely ignores the possibility that if there are two different chemicals present one might influence the diffusion of the other.”

Using his theories, Epstein is creating mathematical models to use in the context of biological, ecological and social systems.

“Instead of having blue molecules and red molecules, maybe you have populations of two different ethnic groups that either like to be near each other or prefer to avoid each other,” says Epstein. “This might affect population patterns in a city or region.”

While he’s not expecting urban planners to track him down this year, his research is gaining momentum.

In ecology, Epstein says, one can create models to describe a predator-prey system.

“Suppose I have foxes and rabbits,” says Epstein. “If the rabbits are by themselves, they’ll distribute evenly, assuming that the food supply is evenly distributed. But if I introduce foxes into the system, then the foxes will eat the rabbits and the rabbits will tend to move away from high concentrations of foxes.” You can actually [design] a mathematical model that describes the processes by which rabbits eat grass and multiply, foxes eat rabbits and multiply and the two species move around.”

While many of the exotic reactions that Epstein examines touch on oscillation and transience, Epstein himself is an example of steadfastness.

Epstein has spent this year at Harvard as Radcliffe Institute Fellow, but he has literally spent his adult life at Brandeis. He arrived in 1971 during the bitter end of the Vietnam War, experienced the ‘80s with the explosion of the space shuttle Challenger and the discovery of AIDS, the ‘90s with the release of Nelson Mandela, the end of the Cold War and the dawn of the 21st century, where smart phones and social media have changed the way people live their lives.
As Epstein points out, the lab facilities at Brandeis have evolved as well.

“When I started at Brandeis,” he says, “ I had only a small office and no labs. As I shifted my efforts from theory to experiment, generous colleagues offered to share lab space with me, and I eventually inherited labs of my own when they retired, but the space was less than ideal.”

Two years ago his research team moved to the newly constructed Shapiro Science Center, where, for the first time, Epstein says, they can control key variables such as room temperature and lighting levels without having to resort to Rube Goldberg-like “fixes.”

A native of Queens, N.Y., Epstein was an only child. His father was a locksmith born in Russia, his mother a school librarian. He earned a B.A. in chemistry and physics, an M.A. in chemistry and a Ph.D. in chemical physics from Harvard University and a diploma in advanced mathematics as a Marshall Scholar at the University of Oxford. After a NATO post-doctoral fellowship at the University of Cambridge, he moved from England to New England, accepting a position at Brandeis.

Twenty-one years later, Epstein was made dean of arts and sciences, moving up to provost in 1994 when the incumbent provost, Jehuda Reinharz, became Brandeis’ seventh president.

Robin Feuer Miller, professor of Russian literature who served as dean of arts and sciences from 1994-2000, worked closely with Epstein during his seven- year term as provost.

“He is, quite simply, one of the smartest people I know,” says Miller. “But what I perhaps valued most about working with him was his ability to change his mind” after making an effort to understand another side.
On the occasions when they disagreed, Miller said, they were always able to talk things through and come to an amicable decision.

Perhaps it’s this passion for people and progress that played into Epstein’s success in garnering a million-dollar grant in 2006 from the Howard Hughes Medical Institute (HHMI), the nation’s largest private funder of science education, to start the first Science Posse, a program at Brandeis created to attract and retain talented, underrepresented students in college-level science.

“If you look at the statistics, the state of American science, we are falling behind,? says Epstein. “More than half of the graduate students in chemistry, math and physics are from other countries. And if you look even more closely, underrepresented minorities are even more underrepresented in the sciences.”

In 2010, the foundation awarded an additional $600,000 to further develop the program. The Science Posse is an extension of the successful Posse Foundation, a liberal arts program founded in 1989 by Brandeis alum Deborah Bial ‘87, which carefully selects and trains a group or “posse” of students who act as a support system for each other.

Though the students don’t know each other when they’re chosen, between the time that they’re selected in December and when they arrive on campus in September, they will have spent 3-4 hours a week together, bonding and learning skills from time management to persuasive writing.

“Irv has vision,” says assistant biology professor Melissa Kosinski-Collins who runs the academic side of the Science Posse as well as the summer boot camp. “He genuinely cares about our scholars and makes it his goal to be there when they need him.”

Jerry Saunders II ‘11 is a member of the Science Posse. He said that working in Epstein’s lab was one of the highlights of his undergraduate career.

“Dr. Epstein is a real-time celebrity whose example constantly challenges me to always strive for more,” says Saunders. “Despite his many successes he remains interested in the work you are doing and what you hope to accomplish. Furthermore, he is more than willing to assist you in that path. He is never too busy to lend guidance.”

Eve Marder, head of division of science and the Victor and Gwendolyn Beinfield Professor of Neuroscience, got to know Epstein in the late 1980s when the pair collaborated on building a semi-realistic model of a neuro-oscilator; in other words, they developed mathematical models used to research several kinds of neurons that are studied in Marder’s lab.

“He was doing the theory and we went back and forth discussing the biology,” says Marder. The two also wrote a grant together.

“Irv has got to be the fastest writer and fastest and best editor that I’ve ever worked with,” says Marder. “He’s astronomically quick. I think that’s part of the reason that he’s been so successful and productive.”

More information: http://pubs.acs.or … eda8/current

Provided by Brandeis University (news : web)

Biosensors: Hormonal attractions

Estrogen receptor (ER) proteins play a major role in controlling the transcription of genetic information from DNA to messenger RNA in cells. Understanding how ER proteins interact with specific DNA regulatory sequences may shed new light on important physiological processes in the body, such as cell growth and differentiation, as well as the development and progression of breast cancer. Guo-Jun Zhang at the A*STAR Institute of Microelectronics and co-workers have now developed a detector that uses silicon nanowires (SiNWs) to evaluate these interactions.

The magnitude of the transcriptional activity that arises from the ER–DNA binding varies from one gene to another. Some genes are highly affected while others are only marginally changed. Zhang and his co-workers therefore investigated how slight variations in nucleotide composition affect the binding affinity between ER and DNA. By combining this new information with existing experimental data on gene expression, the researchers could predict transcriptional outcome following ER–DNA binding and gain new insight into ER signaling.

Most imaging techniques developed for the study of interactions between ER proteins and DNA targets are time-consuming and require the use of fluorescent labels. A number of label-free methods exist, but they lack the sensitivity needed to distinguish subtle changes in ER–DNA binding. The new system created by Zhang’s team is both label-free and highly sensitive.

The researchers prepared their ER-based sensor by modifying a nanostructured biosensing platform previously used to detect cardiac biomarkers and the dengue virus. They generated SiNW arrays on a silica substrate (pictured) through optical lithography and covered the silicon surfaces with functional organosilane and organic molecules, which allowed them to immobilize the ER proteins on the nanowires. Next, a well-shaped sample holder, constructed of insulating material, was pasted around the SiNW area.

After exposing the ER-functionalized nanowires with the target DNA, the team measured the change in resistance induced by ER–DNA complex formation to assess the binding affinity. Upon binding to ERs, DNA strands increased the overall increase in resistance of the SiNWs by adding negative charges.

The researchers discovered that the sensor could detect ultralow levels of ER-bound DNA and discriminate ER-specific from mutant DNA sequences. Moreover, the DNA easily detached from the ER-functionalized nanowires upon contact with a detergent, enabling the regeneration of the sensor.

“The SiNW array biosensor platform is now helping us in the multiplexed characterization of protein–DNA interactions,” says Zhang.

More information: Zhang, G.-J. et al. Highly sensitive and reversible silicon nanowire biosensor to study nuclear hormone receptor protein and response element DNA interactions. Biosensors and Bioelectronics 26, 365–370 (2010). http://dx.doi.org/ … .2010.07.129

Provided by Agency for Science, Technology and Research (A*STAR)

Swedish invention simplifies home diagnostics

Advances in medical diagnostic technology will likely allow individuals to perform preliminary medical diagnoses themselves, in their own home, in the future.

"The idea is to make complex diagnostic processes as simple to perform as modern-day pregnancy tests," says Nathaniel Robinson, who leads the Transport and Separations Group at Linköping University in Sweden

Dr. Robinson and PhD student Per Erlandsson have invented an improved pump, called an electroosmotic pump, which can be placed in a "microfluidic chip." Such chips, sometimes called "lab-on-a-chip" devices, contain miniaturized versions of the beakers and test tubes found in chemistry laboratories interconnected by tiny pipes. Rather than using moving parts, the new pump moves fluids in these pipes via an electric current. The fluids to be pumped can be biological samples such as blood, urine or saliva for medical devices.

"The trick is to generate the ionic current that moves the fluid to be pumped without disturbing the cells, proteins, and other molecules in the sample," according to Dr. Robinson.

To do this, the researchers have employed a type of electronically conducting plastic in the pump's electrodes. The plastic can be electrochemically oxidized or reduced, acting as a transducer between the ions, the charge carriers in fluids, and electrons, which carry charge in metal wires. Traditional electroosmotic pumps use metal electrodes and the electrochemical reactions required are performed on the water in the sample itself. By-products of this electrochemistry included oxygen and hydrogen gas bubbles, and the production of acid or base. Each of these by-products disturbs the microfluidic device and the fluid sample.

"This is primarily why electroosmotic pumps have not been more widely used in the development of medical devices," says Robinson.

The researchers have shown that the pump can be operated repeatedly for extended periods of time, and can operate at relatively low voltages, so that small, portable diagnostic devices can be driven by batteries.

"Several microfluidics articles describe ways to work around the complications associated with integrated metal-electrodes. Here, the alternative reactions of electrochemically active electrodes give us the chance to remove the core problem, the electrolysis of solvent," according to Per Erlandsson, who constructed the pumps.

The researchers have applied for a patent for the new invention and are currently looking for partners who have a need for such pumps in their lab-on-a-chip devices. The research is also described in an article appearing in the latest issue of the scientific journal Electrophoresis.

Simple-to-operate medical devices, that will ultimately enable preliminary self-diagnosis via automated testing kits, will likely become an important part of our healthcare system. Otherwise, we will have a difficult time financing healthcare for an aging population at current or expanded levels of service. For example, by automating and simplifying screening for diseases, such as cancer, a greater portion of the population can be screened, more cases will be caught early, and hospital resources can focus on treatment of individuals who are truly ill. This pump is a significant step towards realizing the devices that will make this possible.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by Expertanswer (Expertsvar in Swedish), via AlphaGalileo.

Journal Reference:

Per G. Erlandsson, Nathaniel D. Robinson. Electrolysis-reducing electrodes for electrokinetic devices. Electrophoresis, 2011; 32 (6-7): 784 DOI: 10.1002/elps.201000617

Global water experiment will celebrate the International Year of Chemistry 2011

What may be the world's largest chemistry experiment in history launched last week as part of the International Year of Chemistry 2011. The American Chemical Society (ACS) announced it will help support teachers and students who wish to participate in the experiment, "Water: A Chemical Solution," by sending volunteers to classrooms that need assistance.

In 2011, as part of the International Year of Chemistry (IYC), officially designated by the United Nations, students worldwide will test their local drinking water sources, as well as local lakes, rivers, streams and other bodies of water, and post their analysis to a global, internet data map.

The experiment remains open until Dec. 31, 2011. Teachers, scout leaders, and families can register to participate, view the experiments, and enter their results at: http://water.chemistry2011.org. The activities are suitable for students of all ages from kindergarten to high school, and require materials commonly found in most science classrooms.

Students will conduct four tests to analyze their water resources for characteristics critical to providing clean drinking water and will learn essential water chemistry practices. They will test the acidity and salinity of their water, and perform simple water treatment and desalinization procedures.

Clean drinking water is one the most important resources for human health and survival. The most abundant substance on the Earth's surface, water covers about 70 percent of the planet's surface. It also constitutes about 70 percent of the human body. Important as it is, water quality varies greatly from community to community for a wide variety of reasons including landscape, weather, temperature and human impacts.

A global comparison of water resources will open important discussions and insights into a precious natural resource and how people in different environments use various methods to provide clean, safe drinking water.

"Students learn chemistry best when it directly applies to their lives," said ACS President, Nancy B. Jackson, Ph.D. "And the most basic chemical solution is water. But don't let that fool you – water resource quality opens complex and diverse issues. The global experiment is an important science education initiative."

Other U.S. organizations helping to coordinate the global experiment include the American Chemical Council (ACC) and the National Academy of Sciences.

The United Nations Educational, Scientific and Cultural Organization (UNESCO), together with the International Union of Pure and Applied Chemistry (IUPAC) officially designated 2011 as the International Year of Chemistry. In addition to the global water experiment, a wide range of celebrations, science conferences, school projects, and community events worldwide are planned for IYC 2011.

Provided by American Chemical Society (news : web)

New trash-to-treasure process turns landfill nuisance into plastic

With billions of pounds of meat and bone meal going to waste in landfills after a government ban on its use in cattle feed, scientists today described development of a process for using that so-called meat and bone meal to make partially biodegradable plastic that does not require raw materials made from oil or natural gas. They reported here today at the 241st National Meeting and Exposition of the American Chemical Society (ACS).

Fehime Vatansever and colleagues explained that in 1997, the U. S Food and Drug Administration banned the decades-old practice of feeding meat and bone meal (MBM) made from byproducts of slaughtered cattle, sheep, and farmed deer, elk and bison to those same animals. Other countries took similar action. It stemmed from concern over the human form of Mad Cow Disease, a very rare but fatal brain disorder that spread in the United Kingdom from eating infected meat. As of 2010, only three cases of the disease, bovine spongiform encephalopathy (BSE), had occurred in the United States. The bans were to reduce the chances that meat and bone meal made from one infected cow could spread BSE widely throughout cattle herds.

"The ban changed what once was a valuable resource — a nutritious component of cattle feed — into waste disposal headache," Vatansever said. "More than nine billion pounds of protein meal are produced by the U.S. rendering industry each year, and most of that is meat and bone meal. The meal from cows had to be treated with harsh chemicals to destroy any BSE and then put into special landfills. We thought we could keep meat and bone meal from being deposited in landfills by using it to make petroleum-free bioplastics."

Vatansever and her colleagues described development and successful testing of that process, which uses meat and bone as the raw material rather than the chemical compounds in petroleum or natural gas. They mixed the MBM plastic with so-called ultra-high-molecular weight polyethylene (UHMWPE), an extremely tough plastic used in skis, snowboards, joint replacements, PVC windows, and other products. Their tests showed that the MBM/UHMWPE plastic is almost as durable as UHMWPE with the bonus of being partially biodegradable.

Any of the BSE infectious agents that might be present in meat and bone meal are deactivated during the manufacture of the plastic, Vatansever noted.

"This is just one way to reuse meat and bone meal, and it's great because it reduces the amount of petroleum needed to make plastics," Vatansever said. "We've also managed to create a strong, sustainable material that is easy to manufacture."

Provided by American Chemical Society (news : web)

Major advance in understanding how nanowires form

New insights into why and how nanowires take the form they do promise to have profound implications for the development of future electronic components. PhD student Peter Krogstrup from the Nano-Science Center at the University of Copenhagen is behind the new theoretical model, which is developed in collaboration with researchers from CINAM-CNRS in Marseille.

One of the most important components in future electronic devices will likely be based on nanocrystals, which are smaller than the wavelength of the light our eyes can detect. Nanowires, which are extremely thin nanocrystal wires, are predicted to have a predominant role in these technologies because of their unique electrical and optical properties. Researchers around the world have been working for years to improve the properties of these nanowires.

With his research, PhD student Peter Krogstrup at the Niels Bohr Institute, University of Copenhagen has laid the foundations for a greater understanding of nanowires. With that comes the potential for improving their performance, which will bring the research closer to being applied in the development of solar cells and computers. In the latest edition of Physical Review Letters, he describes how, under certain conditions, nanowires form a crystal structure that really should not be possible, seen from an energy perspective.

"Crystals will always try to take the form in which their internal energy is as little as possible. It is a basic law of physics and according to it these nanowires should have a cubic crystal structure, but we almost always see that a large part of the structure is hexagonal," explains Peter Krogstrup, who has been working with the theory in recent years.

Catalyst particle shape is the key

In order to explain why and when these crystals become hexagonal, Peter Krogstrup has, as part of his doctoral dissertation, examined the shape of the catalyst particle (a little nano-droplet), which controls the growth of the nanowires. It appears that the shape of the droplet depends on the amount of atoms from group 3 in the periodic system, which make up half of the atoms in the nanowire crystal. The other half, atoms from group 5 in the periodic system, are absorbed by the drop and hence the atoms organize themselves into a lattice, and the nanowire crystal will grow.

"We have shown that it is the shape of the droplet, which determines what kind of crystal structure the nanowires obtain and with this knowledge it will be easier to improve the properties of the nanowires," explains Peter Krogstrup and continues: "The crystal structure has an enormous influence on the electrical and optical properties of the nanowires and you would typically want them to have a certain structure, either cubic or hexagonal. The better nanowires we can make the better electronic components we can make to the benefit of us all," says Peter Krogstrup, whose research is conducted in collaboration with the firm SunFlake A/S, which is located at the Nano-Science Center at the University of Copenhagen. The company is working to develop solar cells of the future based on nanowires.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by University of Copenhagen, via EurekAlert!, a service of AAAS.

Journal Reference:

Peter Krogstrup, Stefano Curiotto, Erik Johnson, Martin Aagesen, Jesper Nygard, Dominique Chatain. Impact of the Liquid Phase Shape on the Structure of III-V Nanowires. Physical Review Letters, 2011; 106 (12) DOI: 10.1103/PhysRevLett.106.125505

Twinkle, twinkle, quantum dot: New particles can change colors and tag molecules

 Engineers at Ohio State University have invented a new kind of nano-particle that shines in different colors to tag molecules in biomedical tests.

These tiny plastic nano-particles are stuffed with even tinier bits of electronics called quantum dots. Like little traffic lights, the particles glow brightly in red, yellow, or green, so researchers can easily track molecules under a microscope.

This is the first time anyone has created fluorescent nano-particles that can change colors continuously.

Jessica Winter, assistant professor of chemical and biomolecular engineering and biomedical engineering, and research scientist Gang Ruan describe their patent-pending technology in the online edition of the journal Nano Letters.

Researchers routinely tag molecules with fluorescent materials in order to see them under the microscope. Unlike the more common fluorescent molecules, quantum dots shine very brightly, and could illuminate chemical reactions especially well, allowing researchers to see the inner workings of living cells.

A bottleneck to combating major diseases like cancer is the lack of molecular or cellular-level understanding of biological processes, the engineers explained.

"These new nanoparticles could be a great addition to the arsenal of biomedical engineers who are trying to find the roots of diseases," Ruan said.

"We can tailor these particles to tag particular molecules, and use the colors to track processes that we wouldn't otherwise be able to," he continued. "Also, this work could be groundbreaking for the field of nanotechnology as a whole, because it solves two seemingly irreconcilable problems with using quantum dots."

Quantum dots are pieces of semiconductor that measure only a few nanometers, or billionths of a meter, across. They are not visible to the naked eye, but when light shines on them, they absorb energy and begin to glow. That's what makes them good tags for molecules.

Due to quantum mechanical effects, quantum dots "twinkle" -- they blink on and off at random moments. When many dots come together, however, their random blinking is less noticeable. So, large clusters of quantum dots appear to glow with a steady light.

Blinking has been a problem for researchers, because it breaks up the trajectory of a moving particle or tagged molecule that they are trying to follow. Yet, blinking is also beneficial, because when dots come together and the blinking disappears, researchers know for certain that tagged molecules have aggregated.

"Blinking is good and bad," Ruan explained. "But one day we realized that we could use the 'good' and avoid the 'bad' at the same time, by grouping a few quantum dots of different colors together inside a micelle."

A micelle is a nano-sized spherical container, and while micelles are useful for laboratory experiments, they are easily found in household detergents -- soap forms micelles that capture oils in water. Ruan created micelles using polymers, with different combinations of red and green quantum dots inside them.

In tests, he confirmed that the micelles appeared to glow steadily. Those stuffed with only red quantum dots glowed red, and those stuffed with green glowed green. But those he stuffed with red and green dots alternated from red to green to yellow.

The color change happens when one or another dot blinks inside the micelle. When a red dot blinks off and the green blinks on, the micelle glows green. When the green blinks off and the red blinks on, the micelle glows red. If both are lit up, the micelle glows yellow.

The yellow color is due to our eyes' perception of light. The process is the same as when a red pixel and green pixel appear close together on a television or computer screen: our eyes see yellow.

Nobody can control when color changes happen inside individual micelles. But because the particles glow continuously, researchers can use them to track tagged molecules continuously. They can also monitor color changes to detect when molecules come together.

Winter and Ruan said that the particles could also be used in fluid mechanics research -- specifically, micro-fluidics. Researchers who are developing tiny medical devices with fluid separation channels could use quantum dots to follow the fluid's path.

The same Ohio State research team is also developing magnetic particles to enhance medical imaging of cancer, and it may be possible to combine magnetism with the quantum dot technology for different kinds of imaging. But before the particles would be safe to use in the body, they would have to be made of biocompatible materials. Carbon-based nanomaterials are one possible option.

In the meantime, Winter and Ruan are going to continue developing the color-changing quantum dot particles for studies of cells and molecules under the microscope. They are also going to explore what happens when quantum dots of another color -- for instance, blue -- are added to the mix.

The university will look to license the technology for industry, and Winter and Ruan have created a Web site for the technologies they are developing: http://nanoforneuro.com.

This research was supported by the National Science Foundation, an endowment from the William G. Lowrie family to the Department of Chemical and Biomolecular Engineering, and the Center for Emergent Materials at Ohio State.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by Ohio State University. The original article was written by Pam Frost Gorder.

Journal Reference:

Gang Ruan, Jessica O. Winter. Alternating-Color Quantum Dot Nanocomposites for Particle Tracking. Nano Letters, 2011; 11 (3): 941 DOI: 10.1021/nl103233b

Debut of the first practical 'artificial leaf'

Scientists today claimed one of the milestones in the drive for sustainable energy — development of the first practical artificial leaf. Speaking here at the 241st National Meeting of the American Chemical Society, they described an advanced solar cell the size of a poker card that mimics the process, called photosynthesis, that green plants use to convert sunlight and water into energy.

"A practical artificial leaf has been one of the Holy Grails of science for decades," said Daniel Nocera, Ph.D., who led the research team. "We believe we have done it. The artificial leaf shows particular promise as an inexpensive source of electricity for homes of the poor in developing countries. Our goal is to make each home its own power station," he said. "One can envision villages in India and Africa not long from now purchasing an affordable basic power system based on this technology."

The device bears no resemblance to Mother Nature's counterparts on oaks, maples and other green plants, which scientists have used as the model for their efforts to develop this new genre of solar cells. About the shape of a poker card but thinner, the device is fashioned from silicon, electronics and catalysts, substances that accelerate chemical reactions that otherwise would not occur, or would run slowly. Placed in a single gallon of water in a bright sunlight, the device could produce enough electricity to supply a house in a developing country with electricity for a day, Nocera said. It does so by splitting water into its two components, hydrogen and oxygen.

The hydrogen and oxygen gases would be stored in a fuel cell, which uses those two materials to produce electricity, located either on top of the house or beside it.

Nocera, who is with the Massachusetts Institute of Technology, points out that the "artificial leaf" is not a new concept. The first artificial leaf was developed more than a decade ago by John Turner of the U.S. National Renewable Energy Laboratory in Boulder, Colorado. Although highly efficient at carrying out photosynthesis, Turner's device was impractical for wider use, as it was composed of rare, expensive metals and was highly unstable — with a lifespan of barely one day.

Nocera's new leaf overcomes these problems. It is made of inexpensive materials that are widely available, works under simple conditions and is highly stable. In laboratory studies, he showed that an artificial leaf prototype could operate continuously for at least 45 hours without a drop in activity.

The key to this breakthrough is Nocera's recent discovery of several powerful new, inexpensive catalysts, made of nickel and cobalt, that are capable of efficiently splitting water into its two components, hydrogen and oxygen, under simple conditions. Right now, Nocera's leaf is about 10 times more efficient at carrying out photosynthesis than a natural leaf. However, he is optimistic that he can boost the efficiency of the artificial leaf much higher in the future.

"Nature is powered by photosynthesis, and I think that the future world will be powered by photosynthesis as well in the form of this artificial leaf," said Nocera, a chemist at Massachusetts Institute of Technology in Cambridge, Mass.

Provided by American Chemical Society (news : web)

Protein biologists find new chink in staph's armor

The battle against deadly staph infections is closer to victory as Illinois researchers have uncovered secrets of how the bacterium protects itself from human immune attacks, which could lead to more effective anti-staph therapies.

Using powerful X-ray beams from the Advanced Photon Source (APS) at the U.S. Department of Energy's Argonne National Laboratory, scientists from the University of Illinois at Urbana-Champaign documented how a key enzyme enables staph to make a coating that protects the bacteria from human white blood cells. Armed with details about how the chemistry works, researchers hope to find drugs that can interfere with the process, leaving the bacteria vulnerable to immune system attacks.

"More people in the United States die of staph infections each year than from HIV/AIDS," said Eric Oldfield, the Illinois chemistry professor who co-led the team of researchers from the University of Illinois and from Taiwan who made the discovery. "We need to come up with new antibiotics."

Using X-ray diffraction available at the APS, the researchers were able to watch how a key drug target, the staph enzyme dehydrosqualene synthase (CrtM), functions. They discovered the bacterium uses a two-step reaction involving two active sites on the enzyme, so finding a way to block both sites would stop the reaction and kill an infection.

"The leads that people have been developing for inhibiting these sorts of enzymes really haven't had any structural basis," said Oldfield, who also is a professor of biophysics. "Now that we can see how the proteins work, we're in a much better position to design molecules that will be more effective against staph infections." Inhibitors used in the project have been licensed to AuricX Pharmaceuticals, a start-up company that has a grant from the Texas Emerging Technology Fund to do preclinical testing in staph infections.

The knowledge might also be applied to fight some parasitic diseases and even lower cholesterol levels because the same sorts of enzymes are involved in those processes as well.

Helping researchers reveal the structures of proteins and how they interact dynamically with one another is an ongoing function of the APS, and progress has accelerated as APS researchers and their academic collaborators have automated the process of refining proteins and crystallizing them so they can be studied with X-ray diffraction.

Seven years ago, scientists using the APS characterized 162 protein structures in a year, said Andrzej Joachimiak, director of the Structural Biology Center and Midwest Center for Structural Genomics at Argonne. In 2009, that number was up to 1,493.

Such increased efficiency stems from installing robotic systems that now quickly handle tedious operations once done by hand. Joachimiak said that further automation, such as a system that could quickly locate tiny crystals in droplets of liquid, will further reduce time and expense required to tease out nature's secrets of protein structure and function.

An advanced protein crystallization facility to be built adjacent to the APS is in the design phase now, and Joachimiak said that construction may begin late this year or early in 2012. The state of Illinois is helping to fund the facility, which is intended to further boost the output of information about proteins.

Many drug companies as well as academic researchers use APS beamlines to characterize proteins, and as more information becomes available, the industry moves closer to its goal of designing drugs based on knowledge of the structure of biological targets.

Since 2006, researchers of the Argonne's Midwest Center for Structural Genomics (MCSG) and Northwestern University Center for Structural Genomics of Infectious Diseases (CSGID), funded by the National Institutes of Health, have mapped out over 1,300 3-D protein structures from bacterial and protozoan pathogens, making the information available to scientists designing therapies and diagnostics. By the end of next year, these consortia are on track to have 2,000 such structures mapped.

"In addition to the aim of providing a starting point for structure-based drug discovery, we can also use this research as a way to learn more about these pathogens and how they cause diseases, how they get around the immune system, how we defend ourselves against them and how they interact with their host," said Wayne Anderson, a Northwestern University professor of molecular pharmacology and biological chemistry and principal investigator of the CSGID project.

Provided by Argonne National Laboratory (news : web)

Taming the flame: Electrical wave 'blaster' could provide new way to extinguish fires

A curtain of flame halts firefighters trying to rescue a family inside a burning home. One with a special backpack steps to the front, points a wand at the flame, and shoots a beam of electricity that opens a path through the flame for the others to pass and lead the family to safety.

Scientists today described a discovery that could underpin a new genre of fire-fighting devices, including sprinkler systems that suppress fires not with water, but with zaps of electric current, without soaking and irreparably damaging the contents of a home, business, or other structure. Reporting at the 241st National Meeting & Exposition of the American Chemical Society (ACS), Ludovico Cademartiri, Ph.D., and his colleagues in the group of George M. Whitesides, Ph.D., at Harvard University, picked up on a 200-year-old observation that electricity can affect the shape of flames, making flames bend, twist, turn, flicker, and even snuffing them out. However, precious little research had been done over the years on the phenomenon.

"Controlling fires is an enormously difficult challenge," said Cademartiri, who reported on the research. "Our research has shown that by applying large electric fields we can suppress flames very rapidly. We're very excited about the results of this relatively unexplored area of research."

Firefighters currently use water, foam, powder and other substances to extinguish flames. The new technology could allow them to put out fires remotely — without delivering material to the flame — and suppress fires from a distance. The technology could also save water and avoid the use of fire-fighting materials that could potentially harm the environment, the scientists suggest.

In the new study, they connected a powerful electrical amplifier to a wand-like probe and used the device to shoot beams of electricity at an open flame more than a foot high. Almost instantly, the flame was snuffed out. Much to their fascination, it worked time and again.

The device consisted of a 600-watt amplifier, or about the same power as a high-end car stereo system. However, Cademartiri believes that a power source with only a tenth of this wattage could have similar flame-suppressing effect. That could be a boon to firefighters, since it would enable use of portable flame-tamer devices, which perhaps could be hand-carried or fit into a backpack.

But how does it work? Cademartiri acknowledged that the phenomenon is complex with several effects occurring simultaneously. Among these effects, it appears that carbon particles, or soot, generated in the flame are key for its response to electric fields. Soot particles can easily become charged. The charged particles respond to the electric field, affecting the stability of flames, he said.

"Combustion is first and foremost a chemical reaction – arguably one of the most important – but it's been somewhat neglected by most of the chemical community," said Cademartiri. "We're trying to get a more complete picture of this very complex interaction."

Cademartiri envisions that futuristic electrical devices based on the phenomenon could be fixed on the ceilings of buildings or ships, similar to stationary water sprinklers now in use. Alternatively, firefighters might carry the flame-tamer in the form of a backpack and distribute the electricity to fires using a handheld wand. Such a device could be used, for instance, to make a path for firefighters to enter a fire or create an escape path for people to exit, he said.

The system shows particular promise for fighting fires in enclosed quarters, such as armored trucks, planes, and submarines. Large forest fires, which spread over much larger areas, are not as suitable for the technique, he noted.

Cademartiri also reported how he and his colleagues found that electrical waves can control the heat and distribution of flames. As a result, the technology could potentially improve the efficiency of a wide variety of technologies that involve controlled combustion, including automobile engines, power plants, and welding and cutting torches, he said.

Provided by American Chemical Society (news : web)

New insight into how 'tidying up' enzymes work

A new discovery about how molecules are broken down by the body, which will help pharmaceutical chemists design better drugs, has been made by researchers at the University of Bristol.

Working with Professor Jeremy Harvey and Professor Adrian Mulholland of Bristol's School of Chemistry, Dr Julianna Olah, an EU Marie Curie Fellow in Bristol at the time, studied a class of enzymes – cytochromes P450 – which play an important role in removing drug molecules from the body.

When a tablet of medicine is taken, the active molecules get absorbed into the bloodstream through the gut and make their way around the body, including to the cells in which they are intended to act; however, it's important they don't stay in the body forever. Enzymes (biological catalysts) help break them down to facilitate excretion.

The cytochromes P450 are a very important class of these 'tidying up' enzymes which have evolved to deal with all 'foreign' compounds that do not get broken down as part of normal metabolism (that is, any compounds which are not proteins, carbohydrates or lipids).

Mainly situated in the liver, the P450 enzymes help remove drug molecules by adding oxygen to them. This process usually works smoothly, but for some molecules, it can lead to oxygenated variants that are toxic. Other molecules are also able to interfere with the normal function of the P450 enzymes.

For these reasons, it is important to be able to understand how a given new molecule, considered for use as a medicine, will react with these enzymes. The Bristol researchers aimed to provide this understanding by modeling the reaction mechanism for interaction between one specific drug (dextromethorphan, a component of some cough syrups) and one P450 variant.

Professor Jeremy Harvey said: "Our calculations showed that the outcome of the oxygen transfer process (that is, which part of dextromethorphan oxygen gets added to) is affected by three factors.

"The first is the way in which the molecule fits into the enzyme ('docking'). The second is the intrinsic ability of each part of the molecule to accept oxygen. The third is how much each competing oxygen-delivery process is compatible with the shape of the enzyme pocket where the reaction occurs.

"While these first two factors were already known, the third was not. This discovery can help pharmaceutical chemists design new drug molecules with a better understanding of how they will be broken down in the body."

Provided by University of Bristol (news : web)

Molecular muscle: Small parts of a big protein play key roles in building tissues

 

We all know the adage: A little bit of a good thing can go a long way. Now researchers in London are reporting that might also be true for a large protein associated with wound healing.

The team at the Kennedy Institute of Rheumatology at Imperial College reports in the Journal of Biological Chemistry that a protein generated when the body is under stress, such as in cases of physical trauma or disease, can affect how the protective housing that surrounds each cell develops. What's more, they say, tiny pieces of that protein may one day prove useful in preventing the spread of tumors or fibrosis.

At just 174 nanometers in diameter, tenascin-C is pretty big in the world of proteins, and it looks a lot like a spider with six legs, which are about 10 times longer than its body. Thanks to those long legs, tenascin-C can do real heavy lifting when it comes to wound healing.

"Tenascin-C plays many roles in the response to tissue injury, including, first of all, initiating an immune response and, later, ensuring proper tissue rebuilding," explains Kim Midwood, who oversaw the project.

When the injury alarm is rung, tenascin-C shows up on the scene and attaches to another protein, fibronectin. Together, tenascin-C and fibronectin help to construct the housing, or extracellular matrix, that surrounds each cell.

"The extracellular matrix is the home in which the cells of your body reside: It provides shelter and nutrients and also sends signals to the cell to tell it how to behave," says Midwood. "To make a finished tissue, the matrix must be carefully built."

Tenascin-C's job is a temporary one. When your hand is cut, for example, it appears at the edges of the wound and then goes away when scar tissue develops, says postdoctoral research associate Wing To: "Tenascin-C is thought to play a major role during the rebuilding phase of tissue injury by promoting regeneration of tissue that has been damaged."

If the extracellular matrix were a construction site, tenascin-C could be seen as the scaffold upon which the weaving of fibronectin threads, or fibrils, is done. "Tenascin-C has multiple arms, and we have shown that it has multiple binding sites for fibronectin," Midwood says. "In this way, it can bind to many fibronectin fibrils at once and help to form the whole tissue by linking the fibrils together. Then, when the repair is done, the scaffolding is taken down."

Midwood and To systematically determined where tenascin-C and fibronectin bind together. They also identified small parts of tenascin-C, known as domains, that can bind to only one fibronectin fibril apiece.

"The small domains act as caps of the scaffold. No more fibronectin fibrils can bind once these caps are in place," Midwood says. So, in essence, they found that certain pieces of tenascin-C determine when fibril building should stop once enough, but not too much, tissue is made.

The findings could be especially useful for creating therapies for conditions in which there is aberrant extracellular matrix deposition, such as in cancers, fibrotic conditions or chronic non-healing wounds, adds To.

In abnormal conditions, such as in the case of a tumor cell, "the home that's made of fibronectin helps it to survive, shelters it and provides signals that enable it to proliferate," says Midwood. "As the tumor thrives, the home keeps on growing, expanding to destroy the existing neighborhood."

Similarly, in fibrotic diseases, tissue rebuilding rages out of control – with too much fibronectin assembly – so that it takes over the whole affected organ, Midwood says.

"In the end, we found that tenascin-C has both stop and go functions cleverly concealed in the same molecule," Midwood says. "The large spiderlike protein may provide a scaffold for building, and the small domains of the protein block excess building. Small domains may be therapeutically useful in situations where too much fibronectin drives disease."

If certain domains can stop uncontrolled matrix deposition in conditions where there is an increase in unwanted extracellular matrix, such as in fibrosis, then they could be useful tools for controlling such diseases.

Meanwhile, To says, in conditions with high levels of tenascin-C degradation by enzymes, for example in nonhealing chronic wounds, that may expose active tenascin-C domains, "if we can stop the production of these domains during disease progression with specific inhibitors, maybe we could help ameliorate the condition.

Similarly we could try and get the cells to make tenascin-C variants that are not as easily broken down by enzymes to help facilitate wound healing."

More information: Midwood and To's paper was named a "Paper of the Week" by the Journal of Biological Chemistry.

Provided by American Society for Biochemistry and Molecular Biology

UConn reactor uses more efficient process to make biodiesel fuel

Deep inside the University of Connecticut’s chemical engineering building in Storrs, Professor Richard Parnas and a team of students quietly monitor a murky brown emulsion bubbling inside an enormous 6-inch diameter glass tube like doctors carefully observing a patient undergoing surgery.

Moving among an array of flexible tubing and metal rods surrounding the nearly floor-to-ceiling device, Parnas keeps a watchful eye on a series of multicolored charts blinking on a nearby laptop. The display represents the real-time readings of a high-tech fiber-optic probe monitoring the chemical reactions taking place inside the tube. It helps Parnas, a UConn professor of chemical, materials, and biomolecular engineering, maintain the precise recipe he needs to turn a mixture of methanol, potassium hydroxide, and waste vegetable oil into nearly pure, cheap, environmentally-friendly biodiesel fuel.

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Parnas’ patented biodiesel reactor is unique in both its simplicity and efficiency. In conventional biodiesel production, vegetable oil is converted into biodiesel fuel and glycerol, a byproduct of the conversion process. Then, the glycerol must be mechanically separated from the diesel fuel, as part of a two-step process. Parnas’ reactor is different in that it uses gravity, heat, and natural chemical reactions to make the biodiesel and separate the glycerol in one step.

As the chemical reactions take place inside the giant tube, temperatures reach more than 100 degrees Fahrenheit. The glycerol starts to coagulate in opaque swirls inside the tube. Because the glycerol droplets are heavier than the biodiesel fuel, they gradually sink to the bottom, where they are siphoned off. At the same time, the biodiesel fuel floats to the top of the tube and is pumped into a holding tank, where it undergoes refinement before being mixed with petroleum-based diesel fuel and used in the University’s bus fleet.

“What is unique about our reactor and why we have a patent on it, is that it gives a much better performance for the separation of the glycerol, and we don’t need a special separate step as is used in most other processes,” says Parnas, who also serves as chairman of UConn’s biodiesel consortium research group.

“That motion and those swirls you are seeing when you look at the reactor are the result of both a chemical reaction and phase separation in real time,” Parnas says. “Phase separation is like what happens when you have an oil and vinegar salad dressing … In other biodiesel processes out there, the reactants are very highly mixed and come out of the reactor together.”

The first UConn biodiesel reactor was built by Greg Magoon, a UConn chemical engineering undergraduate student, in 2004. In 2006, a larger continuous flow biodiesel reactor was designed by UConn graduate student Cliff Weed, under Parnas’ tutelage. The reactor in place today was constructed by students Matthew Boucher and Ryan Couture. Undergraduate and graduate students from chemical engineering, chemistry, economics, and natural resources and the environment have been involved with the project over the years. Every chemical engineering student at UConn learns how to make biodiesel as part of the academic program.

Igor Anisimov, a third-semester chemical engineering student, was one of the students helping Parnas with the reactor during a recent production run.

“The biodiesel reactor is exploiting the molecular differences of the elements,” says Anisimov. “By exploiting the natural properties of these chemicals, we can separate the biodiesel from the glycerol. It’s very cool seeing it happening here, compared to seeing it in the classroom on pen and paper.”

The existing facility produces about 2,000 gallons of biodiesel fuel a year. Parnas and colleagues Yi Li of the plant science department, Steven Suib of the chemistry department, Fred Carstensen of the economics department, and Harrison Yang of the Department of Natural Resources and the Environment are preparing to build a larger pilot biodiesel production facility using part of a two-year, $1.8 million grant from the Department of Energy. The reactor will be capable of producing up to 200,000 gallons of biodiesel a year. Parnas says the pilot plant’s production can easily be magnified for larger-scale commercial production.

In an era of rising gasoline prices and increasing worry about global warming and the emission of greenhouse gases, biodiesel is proving to be a valuable and important substitute for traditional petroleum-based fuels.

Biodiesel releases more energy than is consumed during its production, making it four times more efficient than traditional diesel fuels. It is a renewable fuel source that can be produced locally, cutting down on transportation costs, greenhouse gas emissions, and the nation’s reliance on foreign oil reserves. And, since it is made from plant materials, biodiesel is 100 percent biodegradable.

Provided by University of Connecticut (news : web)

Science looks to poplar trees for 'cool roof' technology

For as long as humans have been able to reason, they have mimicked nature in attempts to derive benefits for themselves; and just because we’ve become ultra-high tech in many ways, it doesn’t mean we’ve stopped looking to nature to help us solve some of the problems that continue to arise in our paths. As one example Yanlin Song and others on a team doing research for the Chinese Academy of Science, as described in their paper "Highly reflective superhydrophobic white coating inspired by poplar leaf hairs toward an effective 'cool roof'" in Energy & Environmental Science, are copying the way poplar trees protect themselves from harsh sunlight and believe it might lead to new ways to help control the heat that is produced when sunlight beats down on a roof.

The idea is simple, the poplar tree, over eons, has developed micro-fibers on the undersides of its leaves that can reflect both light and heat from the sun; thus, when the sun shines directly on the tree, it turns its leaves upside down to protect the insides of the leaves from extreme heat and the ensuing loss of moisture.

The Chinese team has been working on spinning polymers into long protective hollow fiber coatings that could in theory reflect sunlight, and thus reduce the amount of heat that is absorbed when sunlight shines on a roof. To test their results, they covered a swath of material with diarylethene, a compound that changes color when heated, then covered that with their polymer film, and then let the sun shine. They found that the more closely they could emulate the structure of the natural fibers on the poplar leaves, the less the diarylethene changed color.

And while the results the team has managed to show so far are promising, there is still a pretty serious obstacle standing in the way of developing a commercial product that could help homeowners or businesses cut their summer cooling costs; the polymers are just not resistant enough to stand up to the constant barrage of heat, cold, wind and other weather conditions.

Song says he and his team will continue to work with the polymers to see if they can come up with something stronger but will also continue with what they've developed thus far, perhaps even branching out in to other areas, such as lighting applications or in developing waterproofing substances since their polymer film turned out to be water resistant as well.

More information: Highly reflective superhydrophobic white coating inspired by poplar leaf hairs toward an effective "cool roof", Changqing Ye, Mingzhu Li, Junping Hu, Qunfeng Cheng, Lei Jiang and Yanlin Song, Energy Environ. Sci., 2011, Advance Article. DOI:10.1039/C0EE00686F

 

Only the weak survive? Pitt team adds more give for stronger self-healing materials

Conventional rules of survival tend to favor the strongest, but University of Pittsburgh-based researchers recently found that in the emerging world of self-healing materials, it is the somewhat frail that survive.

The team presents in the journal Langmuir a new model laying out the inner workings of self-healing materials made of nanoscale gel particles that can regenerate after taking damage and are being pursued as a coating or composite material. Moreover, the researchers discovered that an ideal amount of weak bonds actually make for an overall stronger material that can withstand more stress.

Although self-healing nanogel materials have already been realized in the lab, the exact mechanical nature and ideal structure had remained unknown, explained Anna Balazs, corresponding author and Distinguished Professor of Chemical Engineering in Pitt's Swanson School of Engineering. The team's findings not only reveal how self-healing nanogel materials work, but also provide a blueprint for creating more resilient designs, she said. Balazs worked with lead author and Pitt postdoctoral researcher Isaac Salib; Chet Gnegy, a Pitt chemical and petroleum engineering sophomore; German Kolmakov, a postdoctoral researcher in Balazs' lab; and Krzysztof Matyjaszewski, a chemistry professor at Carnegie Mellon University with a special appointment in Pitt's Department of Chemical and Petroleum Engineering.

The team worked from a computational model Gnegy, Kolmakov, and Salib created based on a self-healing material Matyjaszewski developed known as nanogel, a composition of spongy, microscopic polymer particles linked to one another by several tentacle-like bonds. The nanogel particles consist of stable bonds—which provide overall strength—and labile bonds, highly reactive bonds that can break and easily reform, that act as shock absorbers.

The computer model allowed the researchers to test the performance of various bond arrangements. The polymers were first laid out in an arrangement similar to that in the nanogel, with the tentacles linked end-to-end by a single strong bond. Simulated stress tests showed, however, that though these bonds could recover from short-lived stress, they could not withstand drawn out tension such as stretching or pulling. Instead, the team found that when particles were joined by several parallel bonds, the nanogel could absorb more stress and still self-repair.

The team then sought the most effective concentration of parallel labile bonds, Balazs said. According to the computational model, even a small number of labile bonds greatly increased resilience. For instance, a sample in which only 30 percent of the bonds were labile—with parallel labile bonds placed in groups of four—could withstand pressure up to 200 percent greater than what could fracture a sample comprised only of stable bonds.

On the other hand, too many labile linkages were so collectively strong that the self-healing ability was cancelled out and the nanogel became brittle, the researchers report.

The Pitt model is corroborated by nature, which engineered the same principle into the famously tough abalone shell, Balazs said. An amalgamation of microscopic ceramic plates and a small percentage of soft protein, the abalone shell absorbs a blow by stretching and sliding rather than shattering.

"What we found is that if a material can easily break and reform, the overall strength is much better," she said. "In short, a little bit of weakness gives a material better mechanical properties. Nature knows this trick."

Provided by University of Pittsburgh

The science of spring: Plants rely on internal alarm clocks to tell them when to wake up from winter

Just in time for the birds and the bees to start buzzing, the flowers and the trees somehow know when to open their buds or start flowering. But the exact way that plants get their wake-up call has been something of a mystery.

"Why should plants care?" The general answer to that is that there are a lot of situations where it’s important not to do something developmentally until spring has arrived," said Richard Amasino, a professor of biochemistry at the University of Wisconsin Madison. "Trees want to make sure that their buds are protected until spring."

Sibum Sung, a molecular biologist at the University of Texas Austin has an idea of how this protective action works on a cellular level. He discovered a special molecule in plants that gives them the remarkable ability to recall winter and to bloom on schedule in the spring. Sung published his results last December in the journal Science Express.

While digging through the DNA of a small cabbage-like plant called Arabidopsis, Sung and a colleague discovered that the production of a special molecule could be turned on or off by a string of genetic material. When the plant gets cozy for the winter, this molecule is not produced, repressing a plant’s ability to create flowers. But after 20 days of consistently frigid weather, production of the molecule gets turned back on, signaling another gene to stop repressing flower production and start preparing for spring. The plant takes another 10-20 days to prime itself for warmer temperatures. Without the 20 days of freezing temperatures, the molecule wouldn't be produced -- even if there is a brief spike in the thermometer reading.

Sung hypothesized that over millions of evolutionary years, this molecule -- called COLDAIR -- has created a sort of cellular memory in generations of plants, letting them know that a month of winter has come and gone, and now they can start preparing for the spring.

Of course, mysteries remain. Sung admits that his team is still working on questions like how the plant knows that temperatures have been low for at least 20 days.

"Well, we know that there are several things done by cold -- but how? That we don't really know yet," Sung said.

The genetic pathways involved are different for each type of plant, said Amasino, but the kind of alarm clock memory is similar. The reason may have to do with the early evolution of plants.

"Flowering plants had already evolved and changed 150 million years ago, when the Earth was a pretty different place," Amasino said. At that time, the Earth was much warmer, and the Atlantic Ocean didn't even exist yet. "So it's relatively recently that plants had to contend with winter," he said.

The kind of responses that plants developed to cold over the past hundred million years happened independently, said Amasino -- and that is one reason that different plants have unique systems to deal with wintertime. "One aim of plant research for the future is to explore how these systems evolved in different plant species," Amasino said.

When the planet’s climate changes more rapidly, it can sometimes be difficult for plants to keep up. Researchers have been studying plants that are opening earlier in the season, according to Ove Nilsson, a professor at the Umea Plant Science Centre in Umea, Sweden. He said that another problem with early spring is that plants get out of sync with their insect pollinators.

"This could potentially be catastrophic for the plants since these flowers can freeze to death," said Nilsson.

But as long as there is winter, nature will keep the pressure on to set an alarm clock for springtime, and the plants will once more open up.

More information: Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA, Science 7 January 2011: Vol. 331 no. 6013 pp. 76-79. DOI: 10.1126/science.1197349

Provided by Inside Science News Service (news : web)

Multitarget drugs against prion diseases

 

The central nervous systems of humans and cattle alike are attacked by prions (abnormal insoluble amyloidogenic proteins) when they suffer from Creutzfeldt–Jakob disease (CJD) or bovine spongiform encephalopathy (BSE).

This causes a steady deterioration of neurological function and ultimately leads to death. There is no currently approved treatment for prion diseases, and no drug candidates are expected to enter clinical trials soon. In ChemMedChem, Maria Laura Bolognesi (University of Bologna, Italy) and colleagues argue in support of a multitarget drug discovery strategy as an alternative way to develop effective anti-prion agents.

Under the dominant drug discovery paradigm "one disease, one target, one molecule," which ignores the polyetiological nature of prion diseases and similar maladies, developing anti-prion therapies is a particular challenge; indeed, this paradigm could be a factor in the ongoing failure of current neurotherapeutic drugs.

Bolognesi and colleagues now describe the discovery of rationally designed molecules endowed with various activities relevant for combating prion neurodegeneration. A new series of chimeric molecules were generated by linking the antioxidant fragment of lipoic acid to heteroaromatic prion-recognition motifs. These compounds effectively counter both prion fibril formation and oxidative stress in a cell culture model of prion replication.

The reported in vitro results make these compounds effective candidates for further in vivo investigations into their multiple biological properties against prion diseases.

More information: Maria Laura Bolognesi, Hybrid Lipoic Acid Derivatives to Attack Prion Disease on Multiple Fronts, ChemMedChem, http://dx.doi.org/ … dc.201100072

Provided by Wiley (news : web)

U of M researchers close in on technology for making renewable petroleum

University of Minnesota researchers are a key step closer to making renewable petroleum fuels using bacteria, sunlight and dioxide, a goal funded by a $2.2 million United States Department of Energy grant.

Graduate student Janice Frias, who earned her doctorate in January, made the critical step by figuring out how to use a protein to transform fatty acids produced by the bacteria into ketones, which can be cracked to make hydrocarbon fuels. The university is filing patents on the process.

The research is published in the April 1 issue of the Journal of Biological Chemistry. Frias, whose advisor was Larry Wackett, Distinguished McKnight Professor of Biochemistry, is lead author. Other team members include organic chemist Jack Richman, a researcher in the College of Biological Sciences' Department of Biochemistry, Molecular Biology and Biophysics, and undergraduate Jasmine Erickson, a junior in the College of Biological Sciences. Wackett, who is senior author, is a faculty member in the College of Biological Sciences and the university's BioTechnology Institute.

"Janice Frias is a very capable and hard-working young scientist," Wackett says. "She exemplifies the valuable role graduate students play at a public research university."

Aditya Bhan and Lanny Schmidt, chemical engineering professors in the College of Science and Engineering, are turning the ketones into diesel fuel using catalytic technology they have developed. The ability to produce ketones opens the door to making petroleum-like hydrocarbon fuels using only bacteria, sunlight and carbon dioxide.

"There is enormous interest in using carbon dioxide to make hydrocarbon fuels," Wackett says. "CO2 is the major greenhouse gas mediating global climate change, so removing it from the atmosphere is good for the environment. It's also free. And we can use the same infrastructure to process and transport this new hydrocarbon fuel that we use for fossil fuels."

The research is funded by a $2.2 million grant from the U.S. Department of Energy's Advanced Research Projects Agency-energy (ARPA-e) program, created to stimulate American leadership in renewable energy technology.

The U of M proposal was one of only 37 selected from 3,700 and one of only three featured in the New York Times when the grants were announced in October 2009. The University of Minnesota's Initiative for Renewable Energy and the Environment (IREE) and the College of Biological Sciences also provided funding.

Wackett is principal investigator for the ARPA-e grant. His team of co-investigators includes Jeffrey Gralnick, assistant professor of microbiology and Marc von Keitz, chief technical officer of BioCee, as well as Bhan and Schmidt. They are the only group using a photosynthetic bacterium and a hydrocarbon-producing bacterium together to make hydrocarbons from carbon dioxide.

The U of M team is using Synechococcus, a bacterium that fixes carbon dioxide in sunlight and converts CO2 to sugars. Next, they feed the sugars to Shewanella, a bacterium that produces hydrocarbons. This turns CO2, a greenhouse gas produced by combustion of fossil fuel petroleum, into hydrocarbons.

Hydrocarbons (made from carbon and hydrogen) are the main component of fossil fuels. It took hundreds of millions of years of heat and compression to produce fossil fuels, which experts expect to be largely depleted within 50 years.

Provided by University of Minnesota (news : web)

Researchers make advances in rechargeable solid hydrogen fuel storage tanks

Researchers have revealed a new single-stage method for recharging the hydrogen storage compound ammonia borane. The breakthrough makes hydrogen a more attractive fuel for vehicles and other transportation modes.

In an article appearing today in Science magazine, Los Alamos National Laboratory (LANL) and University of Alabama researchers working within the U.S. Department of Energy's Chemical Hydrogen Storage Center of Excellence describe a significant advance in hydrogen storage science.

Hydrogen is in many ways an ideal fuel. It possesses a high energy content per unit mass when compared to petroleum, and it can be used to run a fuel cell, which in turn can be used to power a very clean engine. On the down side, H2 has a low energy content per unit volume versus petroleum (it is very light and bulky). The crux of the hydrogen issue has been how to get enough of the element on board a vehicle to power it a reasonable distance.

Work at LANL and elsewhere has focused on chemical hydrides for storing hydrogen, with one material in particular, ammonia borane, taking center stage. Ammonia borane is attractive because its hydrogen storage capacity approaches a whopping 20 percent by weight—enough that it should, with appropriate engineering, permit hydrogen-fueled vehicles to go farther than 300 miles on a single "tank," a benchmark set by the U.S. Department of Energy.

Hydrogen release from ammonia borane has been well demonstrated, and its chief drawback to use has been the lack of energy-efficient methods to reintroduce hydrogen into the spent fuel once burned. In other words, until now, after hydrogen release, the ammonia borane couldn't be recycled efficiently enough.

The Science paper describes a simple scheme that regenerates ammonia borane from a hydrogen depleted "spent fuel" form (called polyborazylene) back into usable fuel via reactions taking place in a single container. This "one pot" method represents a significant step toward the practical use of hydrogen in vehicles by potentially reducing the expense and complexity of the recycle stage. Regeneration takes place in a sealed pressure vessel using hydrazine and liquid ammonia at 40 degrees Celsius and necessarily takes place off-board a vehicle. The researchers envision vehicles with interchangeable hydrogen storage "tanks " containing ammonia borane that are used, and sent back to a factory for recharge.

The Chemical Hydrogen Storage Center of Excellence was one of three Center efforts funded by DOE. The other two focused on hydrogen sorption technologies and storage in metal hydrides. The Center of Excellence was a collaboration between Los Alamos, Pacific Northwest National Laboratory, and academic and industrial partners.

LANL researcher Dr. John Gordon, a corresponding author for the paper, credits collaboration encouraged by the Center model with the breakthrough.

"Crucial predictive calculations carried out by University of Alabama Professor Dave Dixon's group guided the experimental work of the Los Alamos team, which included researchers from both the Chemistry Division and the Materials Physics and Applications Division at LANL," Gordon said.

The success of this particular advance built on earlier work by this team (see: Angew. Chem. Int. Ed. 2009, 37, 6812). Input from colleagues at Dow Chemical (also a Center Partner), indicated that an alternative approach to the work in the Angew. Chem. paper would be required if ammonia borane recycle were to be feasible on a large scale. Armed with this information, it was "the insight, creativity and hard work of Dr. Andrew Sutton of Chemistry Division at LANL that provided the key to unlocking the 'one-pot' chemistry," Gordon said.

Provided by Los Alamos National Laboratory (news : web)

New adhesive earns patent, may find place in space

A recently patented adhesive made by Kansas State University researchers could become a staple in every astronaut's toolbox.

The patent, "pH dependent adhesive peptides," was issued to the Kansas State University Research Foundation, a nonprofit corporation responsible for managing technology transfer activities of K-State. The patent covers an adhesive made from peptides -- a compound containing two or more amino acids that link together -- that increases in strength as moisture is removed.

It was created by John Tomich, professor of biochemistry, and Xiuzhi "Susan" Sun, professor of grain science and industry. Assisting in the research was Takeo Iwamoto, an adjunct professor in biochemistry, and Xinchun Shen, a former postdoctoral researcher.

"The adhesive we ended up developing was one that formed nanoscale fibrils that become entangled, sort of like Velcro. It has all these little hooks that come together," Tomich said. "It's a mechanical type of adhesion, though, not a chemical type like most commercial adhesives."

Because of its unusual properties, applications will most likely be outside the commercial sector, Tomich said.

For example, unlike most adhesives that become brittle as moisture levels decrease, the K-State adhesive's bond only becomes stronger. Because of this, it could be useful in low-moisture environments like outer space, where astronauts could use it to reattach tiles to a space shuttle.

Conversely, its deterioration from water could also serve a purpose.

"It could be used as a timing device or as a moisture detection device," Tomich said. "There could be a circuit or something that when the moisture got to a certain level, the adhesive would fail and break the circuit, sounding an alarm."

The project began nearly a decade ago as Sun and a postdoctal researcher were studying the adhesive properties of soybean proteins. Needing an instrument to synthesize protein peptides, Sun contacted Tomich.

Serendipitously, Tomich's lab had developed a peptide some time ago that had cement-like properties. Tomich said he knew it was unusual but had set it aside to pursue other interests.

"When Dr. Sun and I resurrected this protein, we didn't use the whole thing -- just a segment of it," Tomich said. "We isolated a certain segment where the cells are highly attracted to each other and form these fibrils."

Since their collaboration Tomich has taken the same sequence and changed the way it was designed. The new peptide, he said, will have an eye toward gene therapy.

Sun's lab is trying to optimize the sequence against adhesion, as well as study how peptide sequences influence adhesion properties and surface energy.

"I continue studying protein structures and functional properties in terms of adhesion -- folding, aggregation, surface energy and gelling properties -- so we can rationally design and develop biobased adhesives using plant proteins," she said.

Provided by Kansas State University (news : web)

New aging cause revealed by test tube

Chemists from The Australian National University have discovered a new way that ageing-related diseases can progress, opening up new preventative and treatment possibilities for conditions such as heart disease and Alzheimer’s disease.

Led by Professor Chris Easton and Dr. Dannon Stigers from the ARC Centre of Excellence for Free Radical Chemistry and Biotechnology at ANU, the researchers have used the test tube to simulate the living body, and revealed a new process through which ageing related diseases may develop. Their work has been published in a recent edition of The Royal Society Chemistry journal, Chemistry Communications.

“Remarkably the good old test tube has given us a fantastic window from which to look into the basic processes necessary for life and it has changed the way we think about how ageing related diseases develop,” said Dr. Stigers.

It had been assumed that lifestyle choices such as diet, exercise, and smoking caused some people to develop ageing related illnesses more rapidly than others. Poor lifestyle decisions increase exposure to free radicals which can damage proteins in the body leading to their accumulation and eventual disease. However, in this study the researchers were able to observe proteins being made with their building blocks already damaged, indicating there are two possible pathways to age-related disease development that can be exploited for future treatments.

“We are not saying that a healthy lifestyle is not important to prevent early onset of age-related disease, but we now need to acknowledge that it may not be enough to advise people to eat the right foods and exercise regularly,” said Dr. Stigers.

In their test tube of life, the researchers added all the necessary machinery to make proteins, including both damaged and healthy protein building blocks, and a type of biological proof-reader that ensures proteins are made with only the healthy building blocks. They then looked to see if any of the damaged building blocks made it into the finished protein.

“We were surprised to find that the damaged building blocks were able to effectively compete for incorporation into the final protein even when our proof-reader was present,” said Professor Chris Easton.

“It may seem subtle but from a treatment perspective the difference between preventing a protein from being damaged and dealing with one that is made from damaged goods is vast. This is a significant break through and one which we hope will prove revolutionary in terms of tackling age-related diseases,” he added.

Provided by Australian National University

UC research produces novel sensor with improved detection selectivity

 A highly sensitive sensor that combines a variety of testing means (electrochemistry, spectroscopy and selective partitioning) into one device has been developed at the University of Cincinnati. It's already been tested in a variety of settings – including testing for components in nuclear waste.

The sensor is unusual in that most sensors only have one or two modes of selectivity, while this sensor has three. In practical terms, that means the UC sensor has three different ways to find and identify a compound of interest. That's important because settings like a nuclear waste storage tank are a jumbled mix of chemical and radioactive wastes. The sensor, however, would have a variety of applications, including testing in other environments and even medical applications.

Research related to this novel sensor will be presented at the American Chemical Society biannual meeting March 27-31 in Anaheim, Calif., in a presentation titled "Using Spectroelectrochemistry to Improve Sensor Selectivity."

That presentation will be made March 28 by William Heineman, distinguished research professor of chemistry at the University of Cincinnati. He is one of six international scientists invited to speak by electrochemistry students involved in planning a conference symposium. Heineman has published more than 400 research articles on the topics of spectroelectrochemistry, electroanalytical chemistry, bioanalytical chemistry and chemical sensors, and has won numerous national and international awards for his work.

Research on this sensor concept began more than a decade ago and has received support from the United States Department of Energy for most of that time. "They wanted a sensor that can be lowered in a tank to make lots of measurements quickly or have the option of leaving it in there to monitor what's going on over months or a year," said Heineman, who added that the ideal sensor is both rugged and very selective and sensitive.

The sensor has, in fact, been tested at the Hanford site, a mostly decommissioned nuclear production complex in Washington state, where it was used to detect one important component of the radioactive and hazardous wastes stored inside the giant tanks there.

The basic design and concept for this monitor could be used in many other environmental or medical settings. These include detection of toxic heavy metals and polycyclic aromatic hydrocarbons at superfund sites.

The three-way selectivity comes from the use of coatings, electrochemistry, and spectroscopy. The selective coating only allows certain compounds to enter the sensing region. For example, all negatively charged ions might be able to enter the sensor while all positively charged ions are excluded. Next comes the electrochemistry. A potential is applied, and an even smaller group of compounds are electrolyzed. Finally, a very specific wavelength of light is used to detect the actual compound of interest.

The end result is that compounds, even those present in very low concentrations, can be detected and analyzed. This is especially important in medical monitoring and other applications requiring high selectivity and sensitivity.

"Our goal in this research was to demonstrate that the concept works, and that goal has been met as it's now been tested in several ways. Maybe that's why the students at the ACS meeting wanted to hear about it," said UC's Heineman.

Provided by University of Cincinnati (news : web)

'Lost' samples from famous origin of life researcher could send search for first life in new direction

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Preserved samples from a 1958 experiment done by "primordial soup" pioneer Stanley Miller contain amino acids created by the experiment. The samples had not undergone analysis until recently when Miller's former student Jeffrey Bada and colleagues discovered a wide range of amino acids. The find could be an important step toward understanding how life on Earth could have originated. The vials have been relabeled but the boxes are marked with Miller's original notes. Credit: Scripps Institution of Oceanography, UC San Diego

(PhysOrg.com) -- Stanley Miller gained fame with his 1953 experiment showing the synthesis of organic compounds thought to be important in setting the origin of life in motion. Five years later, he produced samples from a similar experiment, shelved them and, as far as friends and colleagues know, never returned to them in his lifetime.

More 50 years later, Jeffrey Bada, Miller's former student and a current Scripps Institution of Oceanography, UC San Diego professor of marine chemistry, discovered the samples in Miller's laboratory material and made a discovery that represents a potential breakthrough in the search for the processes that created Earth's first life forms.

Former Scripps undergraduate student Eric Parker, Bada and colleagues report on their reanalysis of the samples in the March 21 issue of Proceedings of the National Academy of Sciences. Miller's 1958 experiment in which the gas hydrogen sulfide was added to a mix of gases believed to be present in the atmosphere of early Earth resulted in the synthesis of sulfur amino acids as well as other amino acids. The analysis by Bada's lab using techniques not available to Miller suggests that a diversity of organic compounds existed on early planet Earth to an extent scientists had not previously realized.

 

Scripps Oceanography professor of Marine Chemistry Jeffrey Bada holds a preserved sample from a 1958 experiment done by "primordial soup" pioneer Stanley Miller. The residue in the sample contains amino acids created by the experiment. The samples had not undergone analysis until recently when Bada and colleagues discovered a wide range of amino acids using modern detection methods. Credit: Scripps Institution of Oceanography, UC San Diego

The new findings support the case that volcanoes — a major source of atmospheric hydrogen sulfide today — accompanied by lightning converted simple gases into a wide array of amino acids, which are were in turn available for assembly into early proteins.

Bada also found that the amino acids produced in Miller's experiment with hydrogen sulfide are similar to those found in meteorites. This supports a widely-held hypothesis that processes such as the ones in the laboratory experiments provide a model of how organic material needed for the origin of life are likely widespread in the universe and thus may provide the extraterrestrial seeds of life elsewhere.

Successful creation of the sulfur-rich amino acids would take place in the labs of several researchers, including Miller himself, but not until the 1970s.

"Unbeknownst to him, he'd already done it in 1958," said Bada.

Miller's initial experiments in the 1950s with colleague Harold Urey used a mixture of gases such as methane, ammonia, water vapor and hydrogen and electrically charged them as lightning would. The experiment, which took place in a closed chamber meant to simulate conditions on early Earth, generated several simple amino acids and other organic compounds in what became known as "primordial soup."

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This is a photo of Stanley Miller in his UC San Diego lab in 1970. Credit: Scripps Institution of Oceanography Archives

With the gases and electrical energy they produce, many geoscientists believe the volcanoes on a young planet covered much more extensively by water than today's served as oases of raw materials that allowed prebiotic matter to accumulate in sufficient quantities to assemble into more complex material and eventually into primitive life itself. Bada had already begun reanalyzing Miller's preserved samples and drawing conclusions about the role of volcanoes in sparking early life when he came across the previously unknown samples. In a 2008 analysis of samples left from Miller's more famous experiment, Bada's team had been able to detect many more amino acids than his former mentor had thanks to modern techniques unavailable to Miller.

Miller, who became a chemistry professor at UCSD in 1960, conducted the experiments while a faculty member at Columbia University. He had collected and catalogued samples from the hydrogen sulfide mix but never analyzed them. He only casually mentioned their existence late in his life and the importance of the samples was only realized shortly before his death in 2007, Bada said. It turned out, however, that his 1958 mix more closely resembled what geoscientists now consider early Earth conditions than did the gases in his more famous previous experiment.

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The original box containing archived spark discharge samples prepared by Stanley Miller in 1958. For unknown reasons, Miller never analyzed these even though this is his first experiment using hydrogen sulfide. The label shows Miller?s original writing: p 114 refers to his notebook. Credit: Jeffrey Bada and Robert Benson/Scripps Institution of Oceanography, University of California at San Diego

"This really not only enhances our 2008 study but goes further to show the diversity of compounds that can be produced with a certain gas mixture," Bada said.

The Bada lab is gearing up to repeat Miller's classic experiments later this year. With modern equipment including a miniaturized microwave spark apparatus, experiments that took the elder researcher weeks to carry out could be completed in a day, Bada said.

Provided by University of California - San Diego (news : web)