Here is the first man to be cured of HIV- AIDS

Timothy Ray Brown, 45, from San Francisco Bay Area, is in the news – as the first man cured of HIV- AIDS. “I think so,” he calmly tells his interviewers who ask if he actually is cured.

Brown has been facing cameras, gun mikes and diagnostic kits ever since the publication of a research paper on his unique case in the journal Blood in December 2010.

The researchers led by Kristina Allers and Gero Hutter at Charite University Medicine Berlin documented what can be dubbed as a miracle.

The successful reconstitution of a set of white blood cells that the HIV eats up in Brown’s body is a “very rare” occurrence, they noted.

Brown, who was tested HIV back in 1995 in Germany, was later diagnosed with another disease — leukaemia or blood cancer that involves an abnormal increase in white blood cell.

He was treated with bone marrow stem cell transplant — a cure for blood cancer. The stem cells came from a donor with a rare gene mutation that involves immunity to HIV — again a rare occurrence.

The mechanism involved special white blood cells called CD4+ helper T cells. When a dangerous material like a bacterium or a virus is detected in the body, immune cells immediately stimulate these special cells.

The helper T cells further activate and direct other immune cells to fight the disease. HIV specifically attacks helper T cells, making the body unable to launch a counter offensive against invaders.
Hence, AIDS patients suffer from other lethal infections. The researchers in Berlin showed that after stem cell therapy Brown’s body had reconstitution of CD4+ T cells at a systemic level and specifically in his gut mucosal immune system.

“While the patient remains without any sign of HIV infection,” they wrote. Brown has quit taking his HIV medication. The secret is that if the white cells could be manipulated to a state in which they are no longer infected or infectable by HIV that would mean a functional cure.

Researchers, however, have warned that though the study offers promise, it is not a surefire cure from the dreaded disease — transplants are risky, and this involved a very rare transplant. Brown is a rather lucky man. He said in a recent interview that appeared in the San Francisco media about his cure: “It makes me very happy — very, very happy.”

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Mystery unlocked in photosynthesis step

Tempe, Ariz. - An international team of scientists, including two from Arizona State University, have taken a significant step closer to unlocking the secrets of photosynthesis, and possibly to cleaner fuels.

Plants and algae, as well as cyanobacteria, use photosynthesis to produce oxygen
and "fuels," the latter being oxidizable substances like carbohydrates and hydrogen. There are two pigment-protein complexes that orchestrate the primary reactions of light in oxygenic photosynthesis: photosystem I (PSI) and photosystem II (PSII). Understanding how these photosystems work their magic is one of the long-sought goals of biochemistry.

The ASU scientists working with collaborators at the Max Planck Institute at Mülheim a.d. Ruhr in Germany have been investigating the PSI reaction center.

They have made an important observation that is nut-shelled in the title of a paper published in this week's online Early Edition of the Proceedings of the National Academy of Sciences (PNAS). The paper is titled "Independent initiation of primary electron transfer in the two branches of the photosystem I reaction center."

Kevin Redding, an associate professor in the department of chemistry and biochemistry in the College of Liberal Arts and Sciences, is leading the research at ASU. His lab created mutations in a single-celled green alga (Chlamydomonas reinhardtii or 'Chlamy' for short). Using these mutants, Redding and collaborators have shown that the primary light-triggered electron transfer event in the PSI reaction center can be initiated independently in each of its parallel branches. At the same time, they showed that PSI has two charge separation devices that effectively work in parallel to increase the overall efficiency of electron transfer.

"Although we knew that both branches were being used in PSI, and that our mutations had an effect upon the relative use of each pathway, what we did not know was how these mutations were having their effect," Redding explained. "Unraveling that has led to the discovery of how charge separation – the moment when electromagnetic energy is converted to chemical energy – actually occurs."

The team at the Max Planck Institute (MPI) was led by Alfred Holzwarth. His coworkers, Marc Müller and Chavdar Slavov, used lasers that sent out pulses of light lasting only 60 millionths of one billionth of a second to investigate the electron transfer processes in the two branches of PSI. This allowed them to look at extremely early events in the photosynthetic mechanism, events occurring in just a few picoseconds (a millionth of a millionth of a second), which is a time so short that a typical lattice atom could only execute a dozen oscillations on its lattice site.

This extremely sophisticated experiment and analysis required two years of laboratory effort from Rajiv Luthra, a graduate student in the Redding laboratory, to prepare a sample of sufficient purity to use. To interpret the observations, the researchers at the MPI had to develop a specific kinetic modeling approach that allowed them to estimate the individual electron transfer rates within the two branches. Comparison of mutants made in each branch with the non-mutant PSI was crucial to untangle these rates.

The current research is important for two separate reasons. Firstly, an understanding of how these complex processes work in Nature is crucial to future fundamental research in photosynthetic reaction centers, and this discovery may well be universal. Secondly, the use of two charge separation devices working cooperatively to maximize efficiency is a design theme that may well be applied in future efforts to create artificial photosynthetic devices.

Our society has urgent need of a renewable source of fuel that is widely distributed geographically, abundant, inexpensive, and environmentally clean. The use of solar energy to produce a clean fuel such as hydrogen is essentially the only process that can satisfy these criteria on a scale large enough to meet the world's energy demands. Redding is also a member of the DOE-funded Energy Frontier Research Center (led by Devens Gust, professor of chemistry and biochemistry at ASU). Its goal is to produce a clean, renewable fuel by mimicking the natural process of photosynthesis.

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Scientists grow new lungs using 'skeletons' of old ones

For someone with a severe, incurable lung disorder such as cystic fibrosis or chronic obstructive pulmonary disease, a lung transplant may be the only chance for survival. Unfortunately, it's often not a very good chance. Matching donor lungs are rare, and many would-be recipients die waiting for the transplants that could save their lives.

Such deaths could be prevented if it were possible to use stem cells to grow new lungs or lung tissue. Specialists in the emerging field of tissue engineering have been hard at work on this for years. But they've been frustrated by the problem of coaxing undifferentiated stem cells to develop into the specific cell types that populate different locations in the lung.

Now, researchers from the University of Texas Medical Branch at Galveston have demonstrated a potentially revolutionary solution to this problem. As they describe in an article published electronically ahead of print by the journal Tissue Engineering Part A, they seeded mouse embryonic stem cells into "acellular" rat lungs — organs whose original cells had been destroyed by repeated cycles of freezing and thawing and exposure to detergent.

The result: empty lung-shaped scaffolds of structural proteins on which the mouse stem cells thrived and differentiated into new cells appropriate to their specific locations.

"In terms of different cell types, the lung is probably the most complex of all organs — the cells near the entrance are very different from those deep in the lung," said Dr. Joaquin Cortiella, one of the article's lead authors. "Our natural matrix generated the same pattern, with tracheal cells only in the trachea, alveoli-like cells in the alveoli, pneumocytes only in the distal lung, and definite transition zones between the bronchi and the alveoli."

Such "site-specific" cell development has never been seen before in a natural matrix, said professor Joan Nichols, another of the paper's lead authors. The complexity gives the researchers hope that the concept could be scaled up to produce replacement tissues for humans — or used to create models to test therapies and diagnostic techniques for a variety of lung diseases.

"If we can make a good lung for people, we can also make a good model for injury," Nichols said. "We can create a fibrotic lung, or an emphysematous lung, and evaluate what's happening with those, what the cells are doing, how well stem cell or other therapy works. We can see what happens in pneumonia, or what happens when you've got a hemorrhagic fever, or tuberculosis, or hantavirus — all the agents that target the lung and cause damage in the lung."

The researchers have already begun work on large-scale experiments, "decellularizing" pig lungs with an eye toward using them to produce larger samples of lung tissue that could lead to applications in humans. They're also taking on the challenge of vascularization — stimulating the growth of blood vessels that will enable the engineered tissues to survive outside the special bioreactors that the researchers now use to keep them alive by bathing them in a life-sustaining cocktail of nutrients and oxygen.

"People ask us why we're doing the lung, because it's so hard," Cortiella said. "But the potential is so great, and the technology is here. It's going to take time, but I think we're going to create a system that works."

Source : University of Texas Medical Branch at Galveston

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Cells in 3-D could reveal new cancer targets

Showing movies in 3-D has produced a box-office bonanza in recent months. Could viewing cell behavior in three dimensions lead to important advances in cancer research? A new study led by Johns Hopkins University engineers indicates it may happen. Looking at cells in 3-D, the team members concluded, yields more accurate information that could help develop drugs to prevent cancer's spread.

The study, a collaboration with researchers at Washington University in St. Louis, appears in the June issue of Nature Cell Biology.

"Finding out how cells move and stick to surfaces is critical to our understanding of cancer and other diseases. But most of what we know about these behaviors has been learned in the 2-D environment of Petri dishes," said Denis Wirtz, director of the Johns Hopkins Engineering in Oncology Center and principal investigator of the study. "Our study demonstrates for the first time that the way cells move inside a three-dimensional environment, such as the human body, is fundamentally different from the behavior we've seen in conventional flat lab dishes. It's both qualitatively and quantitatively different."

One implication of this discovery is that the results produced by a common high-speed method of screening drugs to prevent cell migration on flat substrates are, at best, misleading, said Wirtz, who also is the Theophilus H. Smoot Professor of Chemical and Biomolecular Engineering at Johns Hopkins. This is important because cell movement is related to the spread of cancer, Wirtz said. "Our study identified possible targets to dramatically slow down cell invasion in a three-dimensional matrix."

When cells are grown in two dimensions, Wirtz said, certain proteins help to form long-lived attachments called focal adhesions on surfaces. Under these 2-D conditions, these adhesions can last several seconds to several minutes. The cell also develops a broad, fan-shaped protrusion called a lamella along its leading edges, which helps move it forward. "In 3-D, the shape is completely different," Wirtz said. "It is more spindlelike with two pointed protrusions at opposite ends. Focal adhesions, if they exist at all, are so tiny and so short-lived they cannot be resolved with microscopy."

The study's lead author, Stephanie Fraley, a Johns Hopkins doctoral student in Chemical and Biomolecular Engineering, said that the shape and mode of movement for cells in 2-D are merely an "artifact of their environment," which could produce misleading results when testing the effect of different drugs. "It is much more difficult to do 3-D cell culture than it is to do 2-D cell culture," Fraley said. "Typically, any kind of drug study that you do is conducted in 2-D cell cultures before it is carried over into animal models. Sometimes, drug study results don't resemble the outcomes of clinical studies. This may be one of the keys to understanding why things don't always match up."

Fraley's faculty supervisor, Wirtz, suggested that part of the reason for the disconnection could be that even in studies that are called 3-D, the top of the cells are still located above the matrix. "Most of the work has been for cells only partially embedded in a matrix, which we call 2.5-D," he said. "Our paper shows the fundamental difference between 3-D and 2.5-D: Focal adhesions disappear, and the role of focal adhesion proteins in regulating cell motility becomes different."

Wirtz added that "because loss of adhesion and enhanced cell movement are hallmarks of cancer," his team's findings should radically alter the way cells are cultured for drug studies. For example, the team found that in a 3-D environment, cells possessing the protein zyxin would move in a random way, exploring their local environment. But when the gene for zyxin was disabled, the cells traveled in a rapid and persistent almost one-dimensional pathway far from their place of origin.

Fraley said such cells might even travel back down the same pathways they had already explored. "It turns out that zyxin is misregulated in many cancers," Fraley said. Therefore, she added, an understanding of the function of proteins like zyxin in a 3-D cell culture is critical to understanding how cancer spreads, or metastasizes. "Of course tumor growth is important, but what kills most cancer patients is metastasis," she said.

To study cells in 3-D, the team coated a glass slide with layers of collagen-enriched gel several millimeters thick. Collagen, the most abundant protein in the body, forms a network in the gel of cross-linked fibers similar to the natural extracellular matrix scaffold upon which cells grow in the body. The researchers then mixed cells into the gel before it set. Next, they used an inverted confocal microscope to view from below the cells traveling within the gel matrix. The displacement of tiny beads embedded in the gel was used to show movement of the collagen fibers as the cells extended protrusions in both directions and then pulled inward before releasing one fiber and propelling themselves forward.

Fraley compared the movement of the cells to a person trying to maneuver through an obstacle course crisscrossed with bungee cords. "Cells move by extending one protrusion forward and another backward, contracting inward, and then releasing one of the contacts before releasing the other," she said. Ultimately, the cell moves in the direction of the contact released last.

When a cell moves along on a 2-D surface, the underside of the cell is in constant contact with a surface, where it can form many large and long-lasting focal adhesions. Cells moving in 3-D environments, however, only make brief contacts with the network of collagen fibers surrounding them -- contacts too small to see and too short-lived to even measure, the researchers observed.

"We think the same focal adhesion proteins identified in 2-D situations play a role in 3-D motility, but their role in 3-D is completely different and unknown," Wirtz said. "There is more we need to discover."

Fraley said her future research will be focused specifically on the role of mechanosensory proteins like zyxin on motility, as well as how factors such as gel matrix pore size and stiffness affect cell migration in 3-D.

Source : Johns Hopkins University

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HIV - Original version is not changed

Scientists have been surprised to learn that, despite thousands of changes that viruses like HIV undergo in rapid fashion to evade the body's immune system, the original version that caused the infection is still present in the body months later.

The finding, published in the June issue of the Journal of Virology, is the result of an uncommonly detailed look at the cat-and-mouse action that takes place in an organism shortly after infection. The work is aimed at understanding the earliest stages of infection by HIV more thoroughly, to help scientists develop ways either to quash the infection outright or to develop a vaccine to prevent infection.

The research, which was conducted by scientists at the University of Rochester Medical Center, is based on an analysis of more than 100,000 genetic snippets of a virus known as SIV, or simian immunodeficiency virus, which infects monkeys and is a close cousin of HIV.

While HIV has flummoxed scientists for nearly three decades, that's certainly not because our immune system fails to respond. Rather, within two or three weeks of infection, the onslaught of immune cells puts the virus on the run to such an extent that the virus must mutate rapidly to evade the body's defenses.

HIV changes quickly and continually, creating thousands and thousands of mutated versions of itself in a process called "viral escape." The virus changes; the immune cells hunting it down change in response; and the virus changes again, and so on, in a kind of molecular arms race.

"Viral escape is a significant phenomenon in HIV – it's what allows HIV to elude the immune system," said Ha Youn Lee, Ph.D., the assistant professor in the Department of Biostatistics and Computational Biology who led the project.

"The dynamics in the earliest stage of infection by HIV are incredibly complex, and understanding what happens is crucial for developing a vaccine," Lee added.

To do the study, Lee's team applied a mathematical model to data originally gathered by David O'Connor, Ph.D., at the University of Wisconsin at Madison, who studies how SIV evolves. Lee's team analyzed the genetic features of three key sections of the SIV genome as they changed during the first few months of infection in eight macaque monkeys, part of an effort to quantify how quickly the process of viral escape occurs.

The research took advantage of a method known as ultradeep sequencing, which provides hundreds or thousands of glimpses of a single genetic change, compared to approximately 50 or so looks using conventional methods.

"This new technology is very exciting," said Lee. "It allows us to look at the earliest stages of infection in more depth than we could otherwise, and to quantify exactly what is going on in the body. If we can understand it more completely, we can fine-tune vaccines under development."

As expected, the team found that immune cells known as CD8+ T-lymphocytes, also known as cytotoxic T cells, are a powerful force in the life of SIV when it first causes infection. While scientists have known that the CD8 attack on the virus is strong, the latest work quantifies the body's response. They found that the original portions of the virus degrade 400 times faster in response to CD8 cells than they would have if those cells weren't a factor – what scientists call significant "selective pressure" on the virus.

The team also found that SIV creates such mutants in response to the assault by CD8 cells at about the same rate as HIV does.

But the most striking finding is that the original viral genetic sequences are still present in the body months after the initial infection, at a time that scientists call the "viral set point," which occurs about two to five months after infection. It's a signal of just how difficult it is for the body to eradicate HIV from the body – key portions of the virus have managed to survive despite the immense immune assault.

"It's a surprise that the original virus stays in the body so long," said Stephen Dewhurst, Ph.D., professor of Microbiology and Immunology and one of the study authors.

"We know that the virus confronts such a strong response from the body's immune system that the virus evolves quickly to cope with it. Yet, the virus is able to establish a reservoir somewhere in the body, where it continues to reproduce and does not have to respond to the threat from the immune system," Dewhurst added.

Source : University of Rochester Medical Center

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Smallpox Vaccination and HIV spread

Did the End of Smallpox Vaccination Cause the Explosive Spread of HIV?

Vaccinia immunization, as given to prevent the spread of smallpox, produces a five-fold reduction in HIV replication in the laboratory. Researchers writing in the open access journal BMC Immunology suggest that the end of smallpox vaccination in the mid-20th century may have caused a loss of protection that contributed to the rapid contemporary spread of HIV.

Weinstein, a family doctor turned laboratory scientist at George Mason University, Manassas, Virginia, worked with a team of researchers from George Washington University and UCLA. The researchers looked at the ability of white blood cells taken from people recently immunized with vaccinia to support HIV replication compared to unvaccinated controls. They found significantly lower viral replication in blood cells from vaccinated individuals. Weinstein said, "There have been several proposed explanations for the rapid spread of HIV in Africa, including wars, the reuse of unsterilized needles and the contamination of early batches of polio vaccine. However, all of these have been either disproved or do not sufficiently explain the behavior of the HIV pandemic. Our finding that prior immunization with vaccinia virus may provide an individual with some degree of protection to subsequent HIV infection suggests that the withdrawal of such vaccination may be a partial explanation."
Smallpox immunization was gradually withdrawn from the 1950s to the 1970s following the worldwide eradication of the disease, and HIV has been spreading exponentially since approximately the same time period. Weinstein and his colleagues propose that vaccination may confer protection against HIV by producing long term alterations in the immune system, possibly including the expression of a certain receptor, CCR5, on the surface of a person's white blood cells which is exploited by both viruses.
Speaking about the results, Weinstein said, "While these results are very interesting and hopefully may lead to a new weapon against the HIV pandemic, they are very preliminary and it is far too soon to recommend the general use of vaccinia immunization for fighting HIV."

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Single Neurons Can Detect Sequences

Single neurons in the brain are surprisingly good at distinguishing different sequences of incoming information according to new research by UCL neuroscientists.The study, published August 12 in Science and carried out by researchers based at the Wolfson Institute for Biomedical Research at UCL, shows that single neurons, and indeed even single dendrites, the tiny receiving elements of neurons, can very effectively distinguish between different temporal sequences of incoming information.
This challenges the widely held view that this kind of processing in the brain requires large numbers of neurons working together, as well as demonstrating how the basic components of the brain are exceptionally powerful computing devices in their own right.
First author Tiago Branco said: "In everyday life, we constantly need to use information about sequences of events in order to understand the world around us. For example, language, a collection of different sequences of similar letters or sounds assembled into sentences, is only given meaning by the order in which these sounds or letters are assembled.
"The brain is remarkably good at processing sequences of information from the outside world. For example, modern computers will still struggle to decode a rapidly spoken sequence of words that a 5 year-old child will have no trouble understanding. How the brain does so well at distinguishing one sequence of events from another is not well understood but, until now, the general belief has been that this job is done by large numbers of neurons working in concert with each other."
Using a mouse model, the researchers studied neurons in areas of the brain which are responsible for processing sensory input from the eyes and the face. To probe how these neurons respond to variation in the order of a number of inputs, they used a laser to activate inputs on the dendrites in precisely defined patterns and recorded the resulting electrical responses of the neurons.
Surprisingly, they found that each sequence produced a different response, even when it was delivered to a single dendrite. Furthermore, using theoretical modelling, they were able to show that the likelihood that two sequences can be distinguished from each other is remarkably high.
Senior author Professor Michael Hausser commented: "This research indicates that single neurons are reliable decoders of temporal sequences of inputs, and that they can play a significant role in sorting and interpreting the enormous barrage of inputs received by the brain.
"This new property of neurons and dendrites adds an important new element to the "toolkit" for computation in the brain. This feature is likely to be widespread across many brain areas and indeed many different animal species, including humans."
Funding for this study was provided by the Gatsby Charitable Foundation and the Wellcome Trust.

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Epigenetic changes during blood cell differentiation is mapped

Having charted the occurrence of a common chemical change that takes place while stem cells decide their fates and progress from precursor to progeny, a Johns Hopkins-led team of scientists has produced the first-ever epigenetic landscape map for tissue differentiation.

The details of this collaborative study between Johns Hopkins, Stanford and Harvard appear August 15 in the early online publication of Nature.

The researchers, using blood-forming stem cells from mice, focused their investigation specifically on an epigenetic mark known as methylation. This change is found in one of the building blocks of DNA, is remembered by a cell when it divides, and often is associated with turning off genes.

Employing a customized genome-wide methylation-profiling method dubbed CHARM (comprehensive high-throughput arrays for relative methylation), the team analyzed 4.6 million potentially methylated sites in a variety of blood cells from mice to see where DNA methylation changes occurred during the normal differentiation process. The team chose the blood cell system as its model because it's well-understood in terms of cellular development.

They looked at eight types of cells in various stages of commitment, including very early blood stem cells that had yet to differentiate into red and white blood cells. They also looked at cells that are more committed to differentiation: the precursors of the two major types of white blood cells, lymphocytes and myeloid cells. Finally, they looked at older cells that were close to their ultimate fates to get more complete pictures of the precursor-progeny relationships — for example, at white blood cells that had gone fairly far in T-cell lymphocyte development. (Lymphoid and myeloid constitute the two major types of progenitor blood cells.)

"It wasn't a complete tree, but it was large portions of the tree, and different branches," says Andrew Feinberg, M.D., M.P.H., King Fahd Professor of Molecular Medicine and director of the Center for Epigenetics at Hopkins' Institute for Basic Biomedical Sciences.

"Genes themselves aren't going to tell us what's really responsible for the great diversity in cell types in a complex organism like ourselves," Feinberg says. "But I think epigenetics—and how it controls genes-can. That's why we wanted to know what was happening generally to the levels of DNA methylation as cells differentiate."

One of the surprising finds was how widely DNA methylation patterns vary in cells as they differentiate. "It wasn't a boring linear process," Feinberg says. "Instead, we saw these waves of change during the development of these cell types."

The data shows that when all is said and done, the lymphocytes had many more methylated genes than myeloid cells. However, on the way to becoming highly methylated, lymphocytes experience a huge wave of loss of DNA methylation early in development and then a regain of methylation. The myeloid cells, on the other hand, undergo a wave of increased methylation early in development and then erase that methylation later in development.

Rudimentary as it is, this first epigenetic landscape map has predictive power in the reverse direction, according to Feinberg. The team could tell which types of stem cells the blood cells had come from, because epigenetically those blood cells had not fully let go of their past; they had residual marks that were characteristic of their lineage.

This project involved a repertoire of talents.."None of whom were more integral than Irv Weissman at Stanford," Feinberg says. "He's a great stem cell biologist and he lent a whole level of expertise that we didn't have."

One apparent application of this work might be to employ these same techniques to assess how completely an induced pluripotent stem cell (iPSC) has been reprogrammed.

"You might want to have an incompletely reprogrammed cell type from blood, for example, that you take just to a certain point because then you want to turn it into a different kind of blood cell," Feinberg says, cautioning that the various applications are strictly theoretical.

Because the data seem to indicate discreet stages of cell differentiation characterized by waves of changes in one direction and subsequent waves in another, cell types conceivably could be redefined according to epigenetic marks that will provide new insights into both normal development and disease processes.

"Leukemias and lymphomas likely involve disruptions of the epigenetic landscape," Feinberg says. "As epigenetic maps such as this one begin to get fleshed out by us and others, they will guide our understanding of why those diseases behave the way they do, and pave the way for new therapies."

Source : Johns Hopkins Medical Institutions

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'Reaper' protein strikes at mitochondria to kill cells

Our cells live ever on the verge of suicide, requiring the close attention of a team of molecules to prevent the cells from pulling the trigger. This self-destructive tendency can be a very good thing, as when dangerous precancerous cells are permitted to kill themselves, but it can also go horribly wrong, destroying brain cells that store memories, for instance. Rockefeller University scientists are parsing this perilous arrangement in ever finer detail in hopes that understanding the basic mechanisms of programmed cell death, or apoptosis, will enable them eventually to manipulate the process to kill the cells we want to kill and protect the ones we don't.

In experiments published last month in the Journal of Cell Biology, researchers led by postdoctoral associate Cristinel Sandu in Hermann Steller's Strang Laboratory of Apoptosis and Cancer Biology drilled down on a protein aptly named Reaper, which was first described in a 1994 paper by Steller in Science. Under the right conditions,

Reaper interferes with molecules called inhibitor of apoptosis proteins (IAPs), which prevent the cell from irrevocably initiating its autodestruct sequence. By inhibiting these inhibitors, Reaper essentially takes the brakes off the process of apoptosis, pronouncing a cell's death sentence. Other molecules called caspases then carry that sentence out.

"Like the grim reaper, Reaper is an announcer of death, but not the executioner," says Steller, who is also a Howard Hughes Medical Institute investigator. "It's like the key that starts the engine."

Reaper and the other Drosophila IAP antagonists Hid and Grim are known to trigger apoptosis in flies, and related proteins serve a similar function in humans and other mammals. But exactly how and where Reaper initiates apoptosis has not been well understood. Sandu and colleagues bred genetically modified strains of flies that expressed variations on the Reaper protein specifically in flies' eyes. This allowed them to assess the contribution of individual protein motifs to Reaper's apoptosis inducing powers, and what they found was that a particular helical domain was crucial for the formation of Reaper complexes, and could be modified to be even more powerful than the regular protein. The more deadly Reaper variants were obvious by the damage caused to the flies' eyes.

In a series of biochemical experiments, the researchers also found that Reaper must travel to the mitochondria, the cell's energy factories, to effectively deliver its death sentence, and that to get there, it must hitch a ride on the Hid protein, with which it interacts. By tagging Hid and Reaper fluorescently, Sandu could visualize Hid and Reaper acting in a complex and gathering at the membrane of the mitochondria. When Reaper was engineered to go directly to the mitochondrial membrane, it resulted in a molecule that is far superior at triggering cell death than regular Reaper. Further experiments suggested that in a complex with Hid, Reaper is protected from degradation as the cells began to die.

"So now we have Hid and Reaper working very closely together," Sandu says. "And the localization to the mitochondria is crucial to the initiation of apoptosis." Drugs that mimic a small part of the function of Reaper are already in clinical trials. The discovery of a way to make Reaper a much better killer, namely by targeting it directly to the mitochondria, provides new avenues to explore for improving cancer therapies. "Adding this element that takes Reaper directly to the mitochondria is not something people would have thought of before this," Steller says.

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Why are men more susceptible to alcoholism?

Alcohol is one of the most commonly abused substances, and men are up to twice as likely to develop alcoholism as women. Until now, the underlying biology contributing to this difference in vulnerability has remained unclear.

A new study published in Biological Psychiatry reveals that dopamine may be an important factor.

Researchers from Columbia and Yale studied male and female college-age social drinkers in a laboratory test of alcohol consumption. After consuming an alcoholic or non-alcoholic drink, each participant underwent a specialized positron emission tomography (PET) scan, an imaging technique that can measure the amount of alcohol-induced dopamine release.

Dopamine has multiple functions in the brain, but is important in this context because of its pleasurable effects when it is released by rewarding experiences, such as sex or drugs.

Despite similar consumptions of alcohol, the men had greater dopamine release than women. This increase was found in the ventral striatum, an area in the brain strongly associated with pleasure, reinforcement and addiction formation.

"In men, increased dopamine release also had a stronger association with subjective positive effects of alcohol intoxication," explained Dr. Nina Urban, corresponding author for this study. "This may contribute to the initial reinforcing properties of alcohol and the risk for habit formation."

Dr. Anissa Abi-Dargham, senior author on this project, notes that "another important observation from this study is the decline in alcohol-induced dopamine release with repeated heavy drinking episodes. This may be one of the hallmarks of developing tolerance or transitioning into habit."

These findings indicate that the ability of alcohol to stimulate dopamine release may play an important and complex role in its rewarding effects and abuse liability in humans. This identification of an in vivo neurochemical mechanism that could help explain the sex difference in alcoholism is an exciting step forward in alcoholism research.

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A mystery solved: How genes are selectively silenced

Our genetic material is often compared to a book. However, it is not so much like a novel to be read in one piece, but rather like a cookbook. The cell reads only those recipes which are to be cooked at the moment. The recipes are the genes; 'reading' in the book of the cell means creating RNA copies of individual genes, which will then be translated into proteins.

The cell uses highly complex, sophisticated regulatory mechanisms to make sure that not all genes are read at the same time. Particular gene switches need to be activated and, in addition, there are particular chemical labels in the DNA determining which genes are transcribed into RNA and which others will be inaccessible, i.e. where the book literally remains closed. The biological term for this is epigenetic gene regulation.

Among the epigenetic mechanisms which are well studied is the silencing of genes by methyl groups. This is done by specialized enzymes called methyltransferases which attach methyl labels to particular 'letters' of a gene whereby access to the whole gene is blocked. "One of the great mysteries of modern molecular biology is: How do methyltransferases know where to attach their labels in order to selectively inactivate an individual gene?" says Professor Ingrid Grummt of the German Cancer Research Center (DKFZ).

Grummt has now come much closer towards unraveling this mystery. She has focused on studying those text passages in the genetic material which do not contain any recipes. Nevertheless, these texts are transcribed into RNA molecules in a controlled manner. "These so-called noncoding RNAs do not contain recipes for proteins. They are important regulators in the cell which we are just beginning to understand," says Ingrid Grummt.

In her most recent work, Grummt and her co-workers have shown for the first time that epigenetic regulation and regulation by noncoding RNAs interact. The scientists artificially introduced a noncoding RNA molecule called pRNA into cells. As a result, methyl labels are attached to a particular gene switch so that the genes behind it are not read. The trick is that pRNA exactly matches (is complementary to) the DNA sequence of this gene switch. The investigators found out that pRNA forms a kind of plait, or triple helix, with the two DNA strands in the area of this gene switch. Methyltransferases, in turn, are able to specifically dock to this 'plait' and are thus directed exactly to the place where a gene is to be blocked.

More than half of our genetic material is transcribed into noncoding RNA. This prompts Ingrid Grummt to speculate: "It is very well possible that there are exactly matching noncoding RNA molecules for all genes that are temporarily silenced. This would explain how such a large number of genes can be selectively turned on and off."

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Coral records show ocean thermocline rise with global warming

Researchers looking at corals in the western tropical Pacific Ocean have found records linking a profound shift in the depth of the division between warm surface water and colder, deeper water traceable to recent global warming.

The finding is the first real evidence supporting what climate modelers have been predicting as the effects of global climate change on the subsurface ocean circulation.

The report by researchers from Ohio State University and the University of Toronto was published in the latest online edition of the journal Geophysical Research Letters.

"We're trying to find a way to understand how the warm water in the tropical Pacific has changed in the last century, but more importantly during the last several decades," said Branwen Williams, who conducted this research while a doctoral student at Ohio State. Williams is now a postdoctoral fellow at the University of Toronto.

"The Pacific is really important since it serves as a strong driver and changes in this ocean can have a very strong impact on global climate and oceanography."

What plagues modelers and researchers alike is the limited amount of information available about the ocean when studying climate change. Satellite data and physical measurements are mainly restricted to the ocean's surface waters. What happens deeper in the waters is often an unknown.

Williams and Andrea Grottoli, an associate professor of earth sciences at Ohio State and Williams' former advisor, turned to a prolific form of soft coral, the Gorgonians, growing on a reef off the island nation of Palau.

"These corals 'sway' with the current underwater," Grottoli explained, "like trees in the wind. Since they aren't restricted to shallow and warmer surface waters like other tropical corals, they provide an opportunity to reconstruct a picture of subsurface ocean circulation in a region."

Specifically, the researchers were interested in how the boundary layer between the warmer, shallow water and the colder deeper water -- the thermocline -- has changed. But directly measuring that over time and across a broad area is impossible.

Instead, they used the soft corals as a substitute, a proxy, for determining how the thermocline rose and fell over time. Working with samples taken from corals at five meters (16.4 feet), 85 meters (279 feet) and 105 meters (345 feet), they analyzed the chemical structure of the coral skeleton that had built up over time.

Slices cut through the base "trunk" of the coral revealed concentric circles resembling tree rings which showed the growth of the "trunk" over time. By analyzing material from the rings from the outer surface inward to the center, they assembled a growth record covering the last century or so.

They were looking for the ratio between two isotopes of nitrogen in the material as a clue to how the thermocline rose or fell over time. Warmer waters above the thermocline contained lower levels of nutrients resulting in organic matter with a high ratio of nitrogen-15 to nitrogen-14 isotopes. Waters below the thermocline held higher levels of nutrients resulting in organic matter with a low ratio of nitrogen-15 to nitrogen-14 isotopes.

As the polyps in the coral consumed the organic matter over the years, the nitrogen isotopes were chemically recorded in the coral. By comparing the nitrogen-15 to nitrogen-14 ratios in samples from the three depths, they could draw a picture of how the thermocline moved.

"Over several decades, specifically since the mid- to late-1970s, the records show that the mean depth of the thermocline has been getting shallower," Williams said.

The researchers did a similar analysis of the ratio of two carbon isotopes in the coral samples as well. "I think it's fair to say that the carbon isotope record supports this interpretation," Grottoli said. "It's another piece of evidence backing our conclusions."

The researchers were also looking at how the coral record meshed with the Pacific Decadal Oscillation (PDO), a long-lived pattern of climate variability similar to the El Nino phenomenon. While El Nino changes over a period of years, the PDO changes over decades.

"Climate modelers looking at how the Pacific might respond to global warming have predicted that the atmospheric patterns in the tropical Pacific would weaken, and if that happened, you would expect the thermocline to get shallower in the western tropical Pacific," Williams said.

"Our data are some of the first proxy data to support what the modelers have been predicting."

Grottoli said that the thermocline shift in the 1970s is important because it coincides with changes in the PDO from a negative phase to a positive phase.

"We think the thermocline rose when the PDO shifted," she said, "that it was a cumulative effect of both the natural variability of the PDO plus the warming global temperatures." Grottoli said that their coral record covered two other known times when the PDO shifted – in the 1920s and 1940s when average ocean termperatures were a bit lower than today – but neither caused a rise in the thermocline, based on their study.

The researchers want to repeat their study using coral samples from other locations, moving eastward across the Pacific, to test their findings that the thermocline shift wasn't a regional phenomenon, that it is occurring all across the ocean basin, Williams said.

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Meta-analysis shows no heart benefits for folic acid supplements

Use of folic acid supplements appears to lower blood levels of the amino acid homocysteine—theorized to be a risk factor for heart and blood vessel disease—but does not appear to be associated with reduced rates of cardiovascular events, cancer or death over a five-year period, according to a meta-analysis of previously published studies in the October 11 issue of Archives of Internal Medicine, one of the JAMA/Archives journals.

"Elevated plasma total homocysteine [an amino acid created by the body, usually as a byproduct of eating meat] has been suggested as a potentially modifiable risk factor for coronary heart disease, stroke and other occlusive vascular conditions," the authors write as background information in the article. High rates of cardiovascular disease in children with homocystinuria—a rare genetic condition causing extreme elevations in homocysteine levels—led researchers to hypothesize that moderate increases in blood homocysteine levels may increase cardiovascular disease risk in the general population.

Supplementation with B vitamins, and in particular folic acid, lowers blood homocysteine levels and reduces cardiovascular disease risk among individuals with homocystinuria. Several large clinical trials conducted in patients without the condition have been inconclusive. "Consequently, a collaboration between their investigators was established in 2004 to conduct a meta-analysis based on individual participant data from all large randomized trials of folic acid–based B-vitamin supplementation intended to lower plasma homocysteine levels for the prevention of cardiovascular disease," the authors write.

Robert Clarke, F.R.C.P., University of Oxford, England, and colleagues in the B-Vitamin Treatment Trialists' Collaboration report the results of the meta-analysis of all eight trials completed by the end of 2009. Of a total of 37,485 participants, 18,723 were assigned to take folic acid in doses ranging from 0.8 milligrams per day to 40 milligrams per day. The other 18,762 took placebo or an equivalently small dose of folic acid. Trials continued for a median (midpoint) of five years.

Among the 37,485 participants, 9,326 had a major vascular event during the treatment period, 3,010 developed cancer and 5,125 died. Overall, there was a 25 percent reduction in homocysteine levels associated with active folic acid supplementation. However, those who took folic acid were no less likely to have a major heart or blood vessel event than those who took placebo (4,670 or 24.9 percent of first events occurred in those taking folic acid, compared with 4,656 or 24.8 percent in the placebo group).

In addition, there was no significant difference between folic acid and placebo groups in the number of patients experiencing major coronary events (2,019 or 11.4 percent vs. 1,971 or 11.1 percent); stroke (747 or 4.2 percent vs. 781 or 4.4 percent); new cases of cancer (1,541 or 8.7 percent vs. 1,469 or 8.2 percent) or death (2,578 or 13.8 percent vs. 2.547 or 13.6 percent).

"The doses of folic acid used in all the trials included in this meta-analysis exceeded those required for near-maximal reduction in homocysteine levels," the authors write. "The randomized trials in the present meta-analysis found no evidence of benefit with treatment continued for more than five years. Although some benefit might emerge with even longer treatment and follow-up, the trial results give no reason to expect this (particularly because cardiovascular benefits tend to emerge within just a few years with other cardioprotective treatments, such as antihypertensives or statins)."

"One-third of adults in the United States and one-quarter of those in the United Kingdom report taking daily multivitamin supplements containing folic acid," they conclude. All doses in the trials were greater than those required in the United States, where foods are fortified with folic acid to prevent neural tube birth defects. "Although the lack of any other benefits is disappointing (albeit fairly definitive), the lack of any significant adverse effects on vascular events, cancer incidence, cancer mortality and overall mortality provides reassurance about the safety of population-wide folic acid fortification."

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Microbial hair: It's electric

Some bacteria grow electrical hair that lets them link up in big biological circuits, according to a University of Southern California biophysicist and his collaborators.

The finding suggests that microbial colonies may survive, communicate and share energy in part through electrically conducting hairs known as bacterial nanowires.

"This is the first measurement of electron transport along biological nanowires produced by bacteria," said Mohamed El-Naggar, assistant professor of physics and astronomy at the USC College of Letters, Arts and Sciences.

El-Naggar was the lead author of a study appearing online next week in Proceedings of the National Academy of Sciences.

Knowing how microbial communities thrive is the first step in finding ways to destroy harmful colonies, such as biofilms on teeth. Biofilms have proven highly resistant to antibiotics.

The same knowledge could help to promote useful colonies, such as those in bacterial fuel cells under development at USC and other institutions.

"The flow of electrons in various directions is intimately tied to the metabolic status of different parts of the biofilm," El-Naggar said. "Bacterial nanowires can provide the necessary links … for the survival of a microbial circuit."

A bacterial nanowire looks like a long hair sticking out of a microbe's body. Like human hair, it consists mostly of protein.

To test the conductivity of nanowires, the researchers grew cultures of Shewanella oneidensis MR-1, a microbe previously discovered by co-author Kenneth Nealson, Wrigley Professor of Geobiology at USC College.

Shewanella tend to make nanowires in times of scarcity. By manipulating growing conditions, the researchers produced bacteria with plentiful nanowires.

The bacteria then were deposited on a surface dotted with microscopic electrodes. When a nanowire fell across two electrodes, it closed the circuit, enabling a flow of measurable current. The conductivity was similar to that of a semiconductor – modest but significant.

When the researchers cut the nanowire, the flow of current stopped.

Previous studies showed that electrons could move across a nanowire, which did not prove that nanowires conducted electrons along their length.

El-Naggar's group is the first to carry out this technically difficult but more telling experiment.

Electricity carried on nanowires may be a lifeline. Bacteria respire by losing electrons to an acceptor – for Shewanella, a metal such as iron. (Breathing is a special case: Humans respire by giving up electrons to oxygen, one of the most powerful electron acceptors.)

Nealson said of Shewanella: "If you don't give it an electron acceptor, it dies. It dies pretty rapidly."

In some cases, a nanowire may be a microbe's only means of dumping electrons.

When an electron acceptor is scarce nearby, nanowires may help bacteria to support each other and extend their collective reach to distant sources.

The researchers noted that Shewanella attach to electron acceptors as well as to each other, forming a colony in which every member should be able to respire through a chain of nanowires.

"This would be basically a community response to transfer electrons," El-Naggar explained. "It would be a form of cooperative breathing."

El-Naggar and his team are among the pioneers in a young discipline. The term "bacterial nanowire" was coined in 2006. Fewer than 10 studies on the subject have been published, according to co-author Yuri Gorby of The J. Craig Venter Institute in San Diego, discoverer of nanowires in Shewanella.

Gorby and others became interested in nanowires when they noticed that reduction of metals appeared to be occurring around the filaments. Since reduction requires the transfer of electrons to a metal, the researchers suspected that the filaments were carrying a current.

Nanowires also have been proposed as conductive pathways in several diverse microbes.

"The current hypothesis is that bacterial nanowires are in fact widespread in the microbial world," El-Naggar said.

Some have suggested that nanowires may help bacteria to communicate as well as to respire.

Bacterial colonies are known to share information through the slow diffusion of signaling molecules. Nealson argued that electron transport over nanowires would be faster and preferable for bacteria.

"You want the telegraph, you don't want smoke signals," he said.

Bacteria's communal strategy for survival may hold lessons for higher life forms.

In an op-ed published in Wired in 2009, Gorby wrote: "Understanding the strategies for efficient energy distribution and communication in the oldest organisms on the planet may serve as useful analogies of sustainability within our own species."

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Gene identified that prevents stem cells from turning cancerous

Stem cells, the prodigious precursors of all the tissues in our body, can make almost anything, given the right circumstances. Including, unfortunately, cancer. Now research from Rockefeller University shows that having too many stem cells, or stem cells that live for too long, can increase the odds of developing cancer. By identifying a mechanism that regulates programmed cell death in precursor cells for blood, or hematopoietic stem cells, the work is the first to connect the death of such cells to a later susceptibility to tumors in mice. It also provides evidence of the potentially carcinogenic downside to stem cell treatments, and suggests that nature has sought to balance stem cells' regenerative power against their potentially lethal potency.

Research associate Maria Garcia-Fernandez, Hermann Steller, head of the Strang Laboratory of Apoptosis and Cancer Biology, and their colleagues explored the activity of a gene called Sept4, which encodes a protein, ARTS, that increases programmed cell death, or apoptosis, by antagonizing other proteins that prevent cell death. ARTS was originally discovered by Sarit Larisch, a visiting professor at Rockefeller, and is found to be lacking in human leukemia and other cancers, suggesting it suppresses tumors. To study the role of ARTS, the experimenters bred a line of mice genetically engineered to lack the Sept4 gene.

For several years, Garcia-Fernandez studied cells that lacked ARTS, looking for signs of trouble relating to cell death. In mature B and T cells, she could not find any, however, so she began to look at cells earlier and earlier in development, until finally she was comparing hematopoietic progenitor and stem cells. Here she found crucial differences, to be published Friday in Genes and Development.

Newborn ARTS-deprived mice had about twice as many hematopoietic stem cells as their normal, ARTS-endowed peers, and those stem cells were extraordinary in their ability to survive experimentally induced mutations.

"The increase in the number of hematopoietic progenitor and stem cells in Sept4-deficient mice brings with it the possibility of accelerating the accumulation of mutations in stem cells," says Garcia-Fernandez. "They have more stem cells with enhanced resistance to apoptosis. In the end, that leads to more cells accumulating mutations that cannot be eliminated."

Indeed, the ARTS-deprived mice developed spontaneous tumors at about twice the rate of their controls. "We make a connection between apoptosis, stem cells and cancer that has not been made in this way before: this pathway is critically important in stem cell death and in reducing tumor risk," Steller says. "The work supports the idea that the stem cell is the seed of the tumor and that the transition from a normal stem cell to a cancer stem cell involves increased resistance to apoptosis."

ARTS interferes with molecules called inhibitor of apoptosis proteins (IAPs), which prevent cells from killing themselves. By inhibiting these inhibitors, under the right circumstances ARTS helps to take the brakes off the process of apoptosis, permitting the cell to die on schedule. Pharmaceutical companies are working to develop small molecule IAP antagonists, but this research is the first to show that inactivating a natural IAP antagonist actually causes tumors to grow, Steller says. It also suggests that the premature silencing of the Sept4/ARTS pathway at the stem cell level may herald cancer to come.

"This work not only defines the role of the ARTS gene in the underlying mechanism of mammalian tumor cell resistance to programmed cell death, but also links this gene to another hallmark of cancer, stem and progenitor cell proliferation," said Marion Zatz, who oversees cell death grants, including Steller's, at the NIH's National Institute of General Medical Sciences. "The identification of the ARTS gene and its role in cancer cell death provides a potential target for new therapeutic approaches."

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