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Tuesday, December 27, 2011

The Year in Energy


Better Battery: Semi-solid electrode materials are pumped through tubes in this prototype that could lead to more affordable electric cars.
Yet-Ming Chiang



Surprising successes helped offset disappointing failures in solar, biofuels, and nuclear power.

  • BY KEVIN BULLIS
This was supposed to be a big year for energy-related technology.
It was supposed to mark the ascendance of the electric car as the first full year of sales for GM's Volt and Nissan's Leaf, which represent the leading edge of electric vehicles planned by major automakers. But GM fell far short of its sales goals for the year, no doubt plagued by high costs due to expensive batteries. And the companyended the year under a cloud of smoke as the Volt's battery pack caught on fire after safety testing.
It was the year by which advanced-biofuels companies were supposed to be producing 250 million gallons of fuels from grass and wood chips to meet a U.S. federal mandate. But the EPA had to waive the mandate, decreasing the goal to just 6.6 million gallons, because no large advanced-biofuels plants were up and running. The year ended with the demise of one of the first advanced-biofuels companies, Range Fuels, which shut down operations and was forced to auction off assets.
By 2011, advanced solar cells based on thin films of the semiconductor copper indium gallium selenide were supposed to be manufactured at high volumes. The cells were to be nearly as efficient as conventional silicon solar cells but much cheaper to produce, making solar power much more affordable. But Solyndra, a Silicon Valley-based company with one of the most innovative CIGS solar-cell designs, collapsed as it struggled to bring down manufacturing costs. Its bankruptcy in September led it to shut its factory in Fremont, California, which had been funded with the help of a $535 million federal loan guarantee. The failure dominated public attention on the subject of alternative energy and prompted congressional investigations.

In recent years, the nuclear industry had seemed to be set for a renaissance: dozens of applications for new plants were filed, and the government offered millions in loan guarantees to support construction. Not only did the renaissance in U.S. plant construction fail to materialize in 2011, but the horrific disaster at the plant in Fukushima, Japan, set the industry back even further.
And once again, Congress failed to pass a comprehensive energy policy.
But there is also good news.
Although thin-film CIGS solar cells haven't revolutionized the solar industry, advances in manufacturing and sheer scale have led to huge drops in the price of conventional silicon solar panels, making solar power more affordable. In 2011, average prices for solar panels dropped by almost 50 percent from 2010 levels, according to an estimate from GTM Research. Just three years ago, solar panels costs more than three times what they do now. Innovations introduced this year could lead to even lower prices. One technology, developed first at BP Solar but commercialized first in China, could cut the cost of making high-quality crystalline silicon in half. Other advances, such as Suntech's Pluto technology, which combines a number of innovations to produce a record-efficiency solar cell, and silicon ink from Innovalight, which increases power output by improving electrical connections, are being ramped up for large-scale production, promising to keep reducing the cost per watt of solar power.                                             And while Solyndra died, other advanced thin-film manufacturers are making progress, including CIGS solar-panel manufacturer Solar Frontier, which opened a huge, 1,000-megawatt factory in Japan. Researchers are continuing to push solar-cell technology forward. A startup called Alta Devices, based in Santa Clara, California, has built world-record solar cells from thin-film gallium arsenide.
There's also some good news for advanced biofuels. The startup Amyris started producingchemicals from sugarcane. Three advanced-biofuels companies began construction on commercial ethanol plants in the United States, and another, Mascoma, announced that it has raised all the funding it needs to build one starting early next year. Meanwhile, startups continue to develop new ways to convert biomass and other abundant sources into fuels—including some that can directly replace gasoline or jet fuel.
While progress is slow on nuclear power in the United States, novel technology for small, modular reactors appears to be getting traction. 
Batteries remain expensive, but early-stage technical advances could change that. One company hopes to eliminate liquid electrolytes and much of the supporting material in a battery. Such efforts could double batteries' energy storage capacity and greatly expand the possibilities of electric vehicles. Another demonstrated a prototype that could cut the cost of batteries in half. Advances in fuel cells that efficiently convert energy in fuels such as gasoline to electricitycould help increase the range of electric cars, making them more practical.
If new battery technologies don't work, maybe the model developed by Better Place will. The company, which has received more than its fair share of media attention for its idea of selling cars and miles the way cellular carriers sell phones and minutes, has now actually built something. It's nearly finished an Israeli network of charging stations and robotic battery-swap stations that will eliminate the "range anxiety" now limiting the appeal of electric cars—the fear of depleting your battery before you reach your destination. It could also help make electric vehicles more affordable, since drivers don't have to buy the car's battery.
In terms of greenhouse-gas emissions, the best news continues to be the low cost of natural gas, made possible by advances in technology for extracting it from vast shale deposits around the world. Not only does burning natural gas emit less carbon dioxide than burning coal, but new natural-gas power plants could help utilities integrate large amounts of renewable energy.Technologies from GE and others make it possible to quickly increase and decrease power production at planned natural-gas plants, making up for variations in wind and sunlight.
So energy innovation continues. But the impact of new technologies is going to be limited byfailures of government policy in the United States and elsewhere, including China.

The Mystery Behind Anesthesia



Mapping how our neural circuits change under the influence of anesthesia could shed light on one of neuroscience's most perplexing riddles: consciousness.
  • BY COURTNEY HUMPHRIES
Going under: Emery Brown’s quest to understand how anesthesia affects the brain could ­provide crucial clues about what goes wrong in certain ­disorders. Credit: Mark Ostow
Avideo screen shows a man in his late 60s lying awake on an operating table. Just outside the camera's view, a doctor is moving his finger in front of the man's face, instructing him to follow it back and forth with his   eyes. Seconds later, after a dose of the powerful anesthetic drug propofol, his eyelids begin to droop. Then his pupils stop moving. Only the steady background beeping of the heart monitor serves as a reminder that the man isn't dead. "He's in a coma," the doctor, Emery Brown, explains. "General anesthesia is a drug-induced reversible coma."
As an anesthesiologist at Massachusetts General Hospital (MGH), Brown is constant witness to one of the most profound and mysterious feats of modern medicine. Every day, nearly 60,000 patients in the United States undergo general anesthesia, enabling them to survive even the grisliest operations unaware and free of pain.
But though doctors have been putting people under for more than 150 years, what happens in the brain during general anesthesia is a mystery. Scientists don't know much about the extent to which these drugs tap into the same brain circuitry we use when we sleep, or how being anesthetized differs from other ways of losing consciousness, such as slipping into a coma following an injury. Are parts of the brain truly shutting off, or do they simply stop communicating with each other? How is being anesthetized different from a state of hypnosis or deep meditation? And what happens in the brain in the transition between consciousness and unconsciousness? "We know we can get you in and out of this safely," Brown says, "but we still can't quite tell you how it works."
Brown, who is also a neuroscientist and professor at MIT, aims to transform anesthesia from a solely clinical tool into a powerful instrument for studying the most basic questions about the brain. Understanding what happens to the brain under anesthetic drugs, he believes, will help make anesthesia safer and more effective, with fewer side effects. It could also lead to novel treatments for coma and other brain conditions—and to insights into fundamental questions in neuroscience, including the nature of consciousness itself. "Anesthesiology is a form of neuroscience," says George Mashour, an anesthesiologist and neuroscientist at the University of Michigan. "And what we do on a daily basis is modulate virtually every aspect of the nervous system."
FROM CHATTER TO CHANT
Neuroscience has often benefited from natural experiments—patients who lose their ability to remember, produce language, or regulate their emotions after parts of their brains are damaged or have to be surgically removed. Anesthesiologists preside over an analogous experiment every day: they watch elements of consciousness disappear. Under general anesthesia, for instance, patients lose pain perception, awareness, memory, and the ability to move. An anesthesiologist can influence each of these changes in different ways by varying the dosages and types of drugs used.
"By taking away different functions that we associate with consciousness," Brown says, "we might be able to start piecing together parts of the jigsaw puzzle." Neuroscientists could begin to do for consciousness what they have done with memory and language.
Brown is part of a small but growing group of anesthesiology researchers who are using the electroencephalogram (EEG), a tool for monitoring the brain's electrical activity, to systematically probe each aspect of anesthesia in humans and animals. EEG-based brain monitors are already a common sight in operating rooms; some anesthesiologists track the brain activity of their patients with commercially available monitors that use algorithms to transform EEG signals into crude indexes. (Others track only physical signs such as heart rate and blood oxygen levels.) But few of them, he says, spend time looking at the raw EEG data.
Brown, however, has a different perspective from most anesthesiologists; he's also a statistician. After receiving both an MD and a PhD from Harvard in the late 1980s, he pursued the two paths separately, working in the operating rooms of MGH while heading a research laboratory focused on developing signal-processing algorithms to extract information from biological data.
Brown didn't appreciate the neuroscience experiments taking place in front of him each day during surgery until one of his colleagues suggested doing a study on anesthetized patients. Watching the process unfold, "you start realizing that parts of the brain don't shut down all at the same time," he says. "There is a hierarchy, there is a gradation to it."
The same is true when the drugs wear off. Typically, the most basic brain functions come back first—breathing returns, and then, as the areas of the brain stem controlling salivation and tear ducts revive, patients' mouths fill with saliva and their eyes water. They swallow and cough as areas controlling sensation to the throat become active. Finally their eyes move, and then they respond to the outside world. Later the grogginess will lift and complex brain functions will resume. "When you pay attention and you watch those transitions, it's just amazing," Brown says. "We would truly be remiss if we didn't then move forward and try to figure out what these states are, what's actually happening in the brain, and then think of new ways to improve the anesthesia process."
One of the things that struck Brown from watching his patients' EEGs is how quickly and completely drugs like propofol can alter brain activity. As patients enter an anesthetized state, the normal pattern of low-intensity but high-frequency waves shifts to one of less frequent but more intense pulses—as if the constant chatter of the brain had given way to a chant. The location of activity shifts from the back of the brain to the front. Although it's possible to take patients into such a deep state of unconsciousness that their EEG is essentially flat, in most cases bursts of EEG activity alternate with periods of relative inactivity that can last for minutes. The brain processes appear "highly organized," he says. "There are very regular patterns in time, and very regular patterns in space."
Charting the unconscious: This spectrogram shows EEG recordings from a patient undergoing general anesthesia. Two doses of the intravenous anesthetic propofol lead to bursts of activity (minute seven). Then an inhaled anesthetic, isoflurane, is added, and at minute 14, a characteristic pattern of slow-wave and alpha oscillations begins. Surgery ends at minute 16, and the isoflurane is switched off. The EEG gradually shifts to high-frequency, less intense oscillations. Credit: Emery Brown
Brown says that some drugs will decrease the frequency of brain waves seen in EEG readings, resulting in slow, regular oscillating waves across large areas of the brain. Other drugs cause certain areas to show fast, regular oscillations. Because anesthesiologists usually give a cocktail of drugs to each patient, these effects can happen simultaneously. The result, says Brown, is like a jammed signal: "Either way, [the different parts of the brain] can't communicate."
Over the past few years, other EEG studies have supported the idea that anesthesia doesn't simply shut the brain down but, rather, interferes with its internal communication. Mashour's research, for instance, has shown that feedback between the front and back of the brain is interrupted during general anesthesia, leading to a disconnect between different brain networks. That feedback is thought to be important for consciousness.
Similarly, Anthony Hudetz, an anesthesiologist at the Medical College of Wisconsin in Milwaukee, says that anesthesia doesn't simply switch off the senses. Hudetz administers anesthesia to human volunteers at lower-than-clinical levels to observe their brains as they slip into unconsciousness. "What we find is that the anesthetized brain is still very reactive to stimuli," he says; both EEG and functional magnetic resonance imaging (fMRI), an indirect method of measuring brain activity, show response to light and sounds. But somehow that sensory information is never processed and integrated into the type of activity necessary for conscious awareness.
Better understanding of these changes could point a way toward new treatments for brain injury and other disorders. The patterns of highly structured oscillations in patients given anesthetic drugs are similar to states seen in people who lose consciousness during epileptic seizures or who are in deep comas. And the semiconsciousness that results from low doses of the drugs resembles ordinary wakefulness or the early stages of falling asleep. But figuring out exactly how and why these patterns are related will take closer scrutiny.
MAPPING THE COMMUNICATION BREAKDOWN
In order to truly understand whether communication between different brain areas has broken down, scientists need a way to map the activity of these regions and the interactions between them in greater spatial detail. For that, they are turning to fMRI, which measures the changes in blood flow associated with neural activity (see "Raising Consciousness," January/February 2007).
Working with bioengineer Patrick Purdon and other colleagues at MGH, Brown has developed a way to simultaneously take EEG recordings and perform fMRI scans on patients as they enter a deeply anesthetized state. Brain imaging in human subjects undergoing anesthesia is tricky because it requires anesthetizing people within a scanner and outside a normal operating room. Brown and his colleagues found a way to solve the technical and safety problems: they recruited volunteers who had already received tracheostomies, or surgical holes in the throat. That meant a tube could readily be used to restore their breathing in an emergency. In 2009, the researchers demonstrated that they could safely record both EEG and fMRI data on people under anesthesia; now they are working to correlate the imaging and EEG data with the observable changes seen as patients enter an anesthetized state.
Brown is also working with Purdon to study epilepsy patients who've had electrodes implanted into their brains for several days so that clinicians can record and locate seizures. When the patients undergo surgery to remove the brain areas identified as seizure sites, the electrodes record brain waves as anesthesia is administered. These electrodes collect data about a much smaller part of the brain than EEG or fMRI, but the resolution is much higher, allowing scientists to get a sense of what happens in the brain at the cellular level as the patient is anesthetized. Follow-up studies in animals could yield even greater detail by allowing the researchers to implant electrodes more extensively and in precise locations. The researchers will be able to document—from within the brain itself—how activity changes as the brain slips into and out of consciousness.
PIECING TOGETHER CONSCIOUSNESS
If you can systematically catalogue how the brain loses consciousness under the influence of anesthetic drugs, can you deduce what consciousness consists of?
Brown is quick to point out that he doesn't explicitly study consciousness; it's a messy problem, and many neuroscientists avoid the very word. His approach is to study what he calls altered states of arousal. These include anesthesia, sleep, coma, hypnosis, and meditation, as well as aspects of disorders like schizophrenia, epilepsy, and Parkinson's disease. He believes that understanding how the brain functions when it deviates from its normal conscious state will inevitably shed light on what consciousness is.
Anesthesia studies have already cast doubt on one popular theory, which links consciousness to a particular type of brain wave with a frequency around 40 hertz. Mashour points out that research in anesthesia shows these waves can exist even when patients are unconscious. But the patterns that anesthesiologists see do support another theory: that consciousness emerges from the integration of information across large networks in the brain. Hudetz says that while different drugs have different chemical structures and different effects, such as blocking memory or sedating the brain, "if we give any of these drugs at a high enough dose, at some point they do remove consciousness. How do we get this common end point by such a variety of drugs working through different molecular mechanisms?" One explanation is that because consciousness arises from the complex interaction of many kinds of activity, it can be disrupted in many different ways.
Brown hopes the insights gleaned from this work can spill into other areas. Knowing more about how the brain functions under anesthesia could help researchers detect brain activity in people in vegetative states, revealing that they may perceive more than previously thought. The safer anesthetics that might emerge from the research could be useful in sleep medicine, and ways of reviving cognitive function in anesthetized patients might give rise to strategies for helping bring people out of comas. Ketamine, a commonly used anesthetic, has shown some promise as a treatment for depression; other anesthetic drugs could also prove to have effects that lend themselves to treating psychiatric illness. Studying the loss of consciousness in anesthesia will not just illuminate the nature of the conscious mind but bring these states of dampened or altered consciousness out of the shadows. 
Courtney Humphries is a science writer and the author of Superdove: How the Pigeon Took Manhattan ... and the World.

How Bacteria Build Homes Inside Healthy Cells



Purdue associate professor of biological sciences Zhao-Qing Luo, at right, and graduate student Yunhao Tan look at the growth of Legionella pneumophila bacteria in a petri dish. (Credit: Purdue University photo provided by Laurie Iten and Rodney McPhail)                                                                          Science Daily  — Bacteria are able to build camouflaged homes for themselves inside healthy cells -- and cause disease -- by manipulating a natural cellular process.

Purdue University biologists led a team that revealed how a pair of proteins from the bacteria Legionella pneumophila, which causes Legionnaires disease, alters a host protein in order to divert raw materials within the cell for use in building and disguising a large structure that houses the bacteria as it replicates.
Zhao-Qing Luo, the associate professor of biological sciences who headed the study, said the modification of the host protein creates a dam, blocking proteins that would be used as bricks in cellular construction from reaching their destination. The protein "bricks" are then diverted and incorporated into a bacterial structure called a vacuole that houses bacteria as it replicates within the cell. Because the vacuole contains materials natural to the cell, it goes unrecognized as a foreign structure.
"The bacterial proteins use the cellular membrane proteins to build their house, which is sort of like a balloon," Luo said. "It needs to stretch and grow bigger as more bacterial replication occurs. The membrane material helps the vacuole be more rubbery and stretchy, and it also camouflages the structure. The bacteria is stealing material from the cell to build their own house and then disguising it so it blends in with the neighborhood."
The method by which the bacteria achieve this theft is what was most surprising to Luo.
The bacterial proteins, named AnkX and Lem3, modify the host protein through a biochemical process called phosphorylcholination that is used by healthy cells to regulate immune response. Phosphorylcholination is known to happen in many organisms and involves adding a small chemical group, called the phosphorylcholine moiety, to a target molecule, he said.
The team discovered that AnkX adds the phosphorylcholine moiety to a host protein involved in moving proteins from the cell's endoplasmic reticulum to their cellular destinations. The modification effectively shuts down this process and creates a dam that blocks the proteins from reaching their destination.
The bacterial protein Lem3 is positioned outside the vacuole and reverses the modification of the host protein to ensure that the protein "bricks" are free to be used in creation of the bacterial structure.
This study was the first to identify proteins that directly add and remove the phosphorylcholine moiety, Luo said.
"We were surprised to find that the bacterial proteins use the phosphorylcholination process and to discover that this process is reversible," he said. "This is evidence of a new way signals are relayed within cells, and we are eager to investigate it."
The team also found that the phosphorylcholination reaction is carried out at a specific site on the protein called the Fic domain. Previous studies had shown this site induced a different reaction called AMPylation.
It is rare for a domain to catalyze more than one reaction, and it was thought this site's only responsibility was to transfer the chemical group necessary for AMPylation, Luo said.
"Revealing that this domain has dual roles is very important to identify or screen for compounds to inhibit its activity and fight disease," he said. "This domain has a much broader involvement in biochemical reactions than we thought and may be a promising target for effective treatments."
During infection bacteria deliver hundreds of proteins into healthy cells that alter cellular processes to turn the hostile environment into one hospitable to bacterial replication, but the specific roles of only about 20 proteins are known, Luo said.
"In order to pinpoint proteins that would be good targets for new antibiotics, we need to determine their roles and importance to the success of infection," he said. "We need to understand at the biochemical level exactly what these proteins do and how they take over natural cellular processes. Then we can work on finding ways to block these activities, stop the infection and save lives."
A paper detailing their National Institutes of Health-funded work is published in the current issue of the Proceedings of National Academy of Sciences. In addition to Luo, Purdue graduate student Yunhao Tan and Randy Ronald of Indiana University co-authored the paper.
Luo next plans to use the bacterial proteins as a tool to learn more about the complex cellular processes controlled by phosphorylcholination and to determine the biochemical processes role in cell signaling.

Study Reveals How Normal Cells Fuel Tumor Growth



 
by  

  • The study shows how normal cells in tumors can enhance the growth of the tumor’s cancer cells after losing an important tumor suppressor gene called Pten.
  • The findings suggest a new strategy for treating breast cancer by interrupting signals between normal cells and cancer cells in tumors.
A new study published in the journal Nature Cell Biology has discovered how normal cells in tumors can fuel tumor growth.
Led by researchers at the Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute (OSUCCC – James), the study examines what happens when normal cells called fibroblasts in mouse mammary tumors lose an important tumor-suppressor gene called Pten (pronounced “P-ten”).
The findings suggest new strategies for controlling tumor growth by developing drugs that disrupt the communication between tumor cells and the normal cells within the tumor. They also provide insight into the mechanisms that control the co-evolution of cancer cells and surrounding normal cells in tumors, and they demonstrate how the Pten gene normally suppresses cancer development, the researchers say.


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“Our study is the first to define a specific pathway in tumor fibroblasts that reprograms gene activity and the behavior of multiple cell types in the tumor microenvironment, including tumor cells themselves,” says co-principal investigator Dr. Michael Ostrowski, professor and chair of molecular and cellular biochemistry.
“Along with increasing basic knowledge about how tumors grow and spread, these findings have direct translational implications for the treatment of breast-cancer patients,” says Ostrowski, who is a member of the OSUCCC – James Molecular Biology and Cancer Genetics program.
The researchers found that Pten regulates a molecule called microRNA-320 (miR-320), and that the loss of Pten leads to a dramatic drop in levels of that molecule in a tumor fibroblast. With little miR-320 around, levels of a protein called ETS2(pronounced Ets-two) rise in the fibroblast.
Finally, the abundance of ETS2 activates a number of genes that cause the fibroblast to secrete more than 50 factors that stimulate the proliferation and invasiveness of nearby cancer cells. It also causes the reprogramming of other fibroblasts in the tumor and throughout the mammary gland.
“The cancer field has long focused solely on targeting tumor cells for therapy,” says co-principal investigator Gustavo Leone, associate professor of molecular virology, immunology and medical genetics. “Our work suggests that modulation of a few key molecules such as miR-320 in noncancer cells in the tumor microenvironment might be sufficient to impede the most malignant properties of tumor cells.”
Ostrowski, Leone and their colleagues began this study by examining human invasive breast tumors from 126 patients for microRNA changes after PTEN loss. Key technical findings include the following:
· Using mouse models, they found that miR-320 levels and ETS2 levels were inversely correlated in human breast-tumor tissue, suggesting that Pten and miR-320 work together to block ETS2 function and suppress tumor growth.
· miR-320 in mammary fibroblasts influences the behavior of multiple cell types, making it a critical molecule for suppressing epithelial tumors.
· miR-320 functions as a regulatory switch in normal fibroblasts that operates to inhibit the secretion of more than 50 tumor-promoting factors (i.e., a tumor-promoting secretome). In doing so, it blocks the expression of genes in other cell types in the tumor microenvironment and suppresses tumor-cell growth and invasiveness.
· Overall, loss of Pten in tumor fibroblasts results in downregulation of miR-320 and release of the secretome factors. This causes the genetic reprogramming of neighboring endothelial and epithelial cells of the mammary gland, inciting profound changes in these cells that are typical of malignant tumors.
Michael Ostrowski, PhD
“Remarkably, the molecular signature of the miR-320 secretome could distinguish normal breast tissue from tumor tissue, and it predicted the outcome in breast-cancer patients,” says Leone, who is also a member of the OSUCCC – James Molecular Biology and Cancer Genetics program. “This underscores the potential clinical importance of the Pten-miR-320 regulatory pathway on human breast cancer.”
_____________
Funding from the National Cancer Institute, National Institute of Child Health and Human Development, the Komen Breast Cancer Foundation and Evelyn Simmers Charitable Trust supported this research.
Other researchers in this study were Agnieszka Bronisz, Jakub Godlewski, Julie A. Wallace, Anand.S. Merchant, Michal O. Nowicki, Haritha Mathsyaraja, R. Srinivasan, Anthony J. Trimboli, Chelsea K. Martin, F. Li, L. Yu, Soledad A. Fernandez, T. Pécot, Thomas J. Rosol, M. G. Piper, Clay B. Marsh, Lisa D. Yee, G. Nuovo and E. Antonio Chiocca of Ohio State; S. Cory and M. Hallett and M. Park of McGill University; R. E. Jimenez14 of Mayo Clinic; and Sean. E Lawler of Leeds Institute of Molecular Medicine.