Biomedical Research News

Progression of NAFLD to diabetes mellitus,

2013-06-05T01:21:00.002+05:30

Progression of NAFLD to diabetes mellitus, cardiovascular disease or cirrhosis

Quentin M. Anstee, Giovanni Targher & Christopher P. Day

NAFLD is a spectrum of progressive liver disease that encompasses simple steatosis, NASH, fibrosis and, ultimately, cirrhosis. NAFLD is recognized as the hepatic component of the metabolic syndrome, as these conditions have insulin resistance as a common pathophysiological mechanism. Therefore, NAFLD is strongly associated with type 2 diabetes mellitus and abdominal obesity. As lifestyles have become increasingly sedentary and dietary patterns have changed, the worldwide prevalence of NAFLD has increased dramatically and is projected to be the principal aetiology for liver transplantation within the next decade. Importantly, a growing body of clinical and epidemiological evidence suggests that NAFLD is associated not only with liver-related morbidity and mortality, but also with an increased risk of developing both cardiovascular disease and type 2 diabetes mellitus. This article reviews the evidence that suggests NAFLD is a multisystem disease and the factors that might determine interindividual variation in the development and progression of its major hepatic and extrahepatic manifestations (principally type 2 diabetes mellitus and cardiovascular disease).

http://www.nature.com/nrgastro/journal/v10/n6/pdf/nrgastro.2013.41.pdf?WT.ec_id=NRGASTRO-201306

Light-Based 'Remote Control' Developed for Proteins Inside Cells

2012-11-12T23:43:00.001+05:30

ScienceDaily (Nov. 8, 2012) — Scientists at Stanford University have developed an intracellular remote control: a simple way to activate and track proteins, the busiest of cellular machines, using beams of light.

The new method, described in a paper to be published Nov. 9 in Science, will let researchers shine light on a specific cell region to quickly activate a protein in that area, producing an unusually fine-grained view of the location and timing of protein activity. In addition, the method may eventually enable physicians to direct the movement and activity of stem cells used to treat injury or illness in light-accessible body parts, such as the eye or skin. Stanford has filed a patent application for the work.

The method involves splicing two pieces of a specific fluorescent protein to other proteins of interest. The resulting hybrids -- called fluorescent, light-inducible proteins, or FLIPs -- have two interesting features: Not only are they turned on by light, but they also glow less brightly when activated, a change that provides an easy way to sense protein activity.

"It's sort of like having a garage door opener that also tells you if the garage door is open or closed," said Michael Lin, MD, PhD, an assistant professor of pediatrics and of bioengineering and the senior author of the paper. "I'm always driving out of my house, closing the garage door, and then wondering after I drive away if it's shut, so I have to drive back and check." If garage doors were like FLIPs, Lin would be spared his return trip, since these proteins not only turn on at the flip of a light switch, but also tell an observer that they're working. "One molecule can tell you where it is and what it's doing," said Lin.

The trick to the new method is that it uses pieces of a Velcro-like fluorescent protein called Dropna. In the dark, Dropna units adhere to each other and fluoresce. Under cyan-colored light, the units detach and begin to dim. Lin's team spliced a Dropna unit to each end of the proteins they wanted to study to make the FLIPs. In the dark, the Dropna units stuck together and physically blocked the active sites of the proteins under study. When cyan-colored light was shone on the proteins, the Dropna units fell apart, exposing the protein's active site so it could work. Under cyan light, the Dropna units also glowed less brightly, signaling that the FLIP was switched on.

It's easiest to build FLIPs from proteins that fold with both their head and tail ends near the active site, though the research team is now figuring out how to attach Dropna units to other parts of a protein, not just an end. With that modification, Lin anticipates that FLIPs could be created from most proteins that scientists want to investigate.

"For science geeks, this is very interesting in that it converges two exciting fields: biological sensing, which has been dominated by fluorescent proteins, and optogenetics, the use of light to investigate biology," Lin said.

In the past, scientists who specialized in biological sensing have tagged bits of the cellular machinery with fluorescent proteins to see where certain processes occurred in the cell. Separately, optogenetics experts -- using methods that originated at Stanford -- have figured out how to switch on specific neuron circuits with light. Lin's method combines advantageous features of both techniques, and is the first instance of optogenetics-type techniques being applied to individual proteins.

Outside the research lab, the method could be used to give directions to stem cells injected for therapeutic purposes. For instance, if the stem cells were engineered to contain FLIPs that control cell motility, a beam of light could then direct implanted stem cells to a particular location. Similarly, FLIPs and appropriately timed light beams could be used to control what a stem cell does when it reaches its destination.

"If you think about how we might want to use stem cells to regenerate tissues, we may need control over where cells go, when they proliferate and when they die," Lin said. At present, this application seems most likely for tissues at the body's surface, such as the eye and skin, because physicians would need to be able to deliver light to the treatment site.

http://www.sciencedaily.com/releases/2012/11/121108142744.htm?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29

Hunting Neuron Killers in Alzheimer's and Traumatic Brain Injury

2012-11-12T19:54:00.000+05:30

ScienceDaily (Nov. 9, 2012) — Sanford-Burnham researchers discovered that the protein appoptosin prompts neurons to commit suicide in several neurological conditions -- giving them a new therapeutic target for Alzheimer's disease and traumatic brain injury.

Dying neurons lead to cognitive impairment and memory loss in patients with neurodegenerative disorders-conditions like Alzheimer's disease and traumatic brain injury. To better diagnose and treat these neurological conditions, scientists first need to better understand the underlying causes of neuronal death.

Enter Huaxi Xu, Ph.D., professor in Sanford-Burnham's Del E. Webb Neuroscience, Aging, and Stem Cell Research Center. He and his team have been studying the protein appoptosin and its role in neurodegenerative disorders for the past several years. Appoptosin levels in the brain skyrocket in conditions like Alzheimer's and stroke, and especially following traumatic brain injury.

Appoptosin is known for its role in helping the body make heme, the molecule that carries iron in our blood (think "hemoglobin," which makes blood red). But what does heme have to do with dying brain cells? As Xu and his group explain in a paper they published recently in the Journal of Neuroscience, excess heme leads to the overproduction of reactive oxygen species, which include cell-damaging free radicals and peroxides, and triggers apoptosis, the carefully regulated process of cellular suicide. This means that more appoptosin and more heme cause neurons to die.

Not only did Xu and his team unravel this whole appoptosin-heme-neurodegeneration mechanism, but when they inhibited appoptosin in laboratory cell cultures, they noticed that the cells didn't die. This finding suggests that appoptosin might make an interesting new therapeutic target for neurodegenerative disorders.

What's next? Xu and colleagues are now probing appoptosin's function in mouse models. They're also looking for new therapies that target the protein.

"Since the upregulation of appoptosin is important for cell death in diseases such as Alzheimer's, we're now searching for small molecules that modulate appoptosin expression or activity. We'll then determine whether these compounds may be potential drugs for Alzheimer's or other neurodegenerative diseases," Xu explains.

Putting a stop to runaway appoptosin won't be easy, though. That's because we still need the heme-building protein to operate at normal levels for our blood to carry iron. In a previous study, researchers found that a mutation in the gene that encodes appoptosin causes anemia. "Too much of anything is bad, but so is too little," Xu says.

New therapies that target neurodegenerative disorders and traumatic brain injury are sorely needed. According to the CDC, approximately 1.7 million people sustain a traumatic brain injury each year. It's an acute injury, but one that can also lead to long-term problems, causing epilepsy and increasing a person's risk for Alzheimer's and Parkinson's diseases. Not only has traumatic brain injury become a worrisome problem in youth and professional sports in recent years, the Department of Defense calls traumatic brain injury "one of the signature injuries of troops wounded in Afghanistan and Iraq."

http://www.sciencedaily.com/releases/2012/11/121109111509.htm?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29

Reactions to Everyday Stressors Predict Future Health

2012-11-08T01:07:00.002+05:30

ScienceDaily (Nov. 2, 2012

Contrary to popular perception, stressors don't cause health problems -- it's people's reactions to the stressors that determine whether they will suffer health consequences, according to researchers at Penn State.

"Our research shows that how you react to what happens in your life today predicts your chronic health conditions and 10 years in the future, independent of your current health and your future stress," said David Almeida, professor of human development and family studies.

"For example, if you have a lot of work to do today and you are really grumpy because of it, then you are more likely to suffer negative health consequences 10 years from now than someone who also has a lot of work to do today, but doesn't let it bother her."

Using a subset of people who are participating in the MIDUS (Midlife in the United States) study, a national longitudinal study of health and well being that is funded by the National Institute on Aging, Almeida and his colleagues investigated the relationships among stressful events in daily life, people's reactions to those events and their health and well being 10 years later.

Specifically, the researchers surveyed by phone 2,000 individuals every night for eight consecutive nights regarding what had happened to them in the previous 24 hours. They asked the participants questions about their use of time, their moods, the physical health symptoms they had felt, their productivity and the stressful events they had experienced, such as being stuck in traffic, having an argument with somebody, or taking care of a sick child.

"Most social-science surveys are based on long retrospective accounts of your life in the past month or maybe the past week," Almeida said. "By asking people to focus just on the past 24 hours, we were able to capture a particular day in someone's life. Then, by studying consecutive days, we were able to see the ebb and flow of their daily experiences."

The researchers also collected saliva samples from the 2,000 individuals at four different times on four of those eight days. From the saliva, they were able to determine amounts of the stress hormone, cortisol. They then linked the information they collected to data from the larger MIDUS study, including the participants' demographic information, their chronic health conditions, their personalities and their social networks.

"We did this 10 years ago in 1995 and again in 2005," Almeida said. "By having longitudinal data, not only were we able to look at change in daily experiences over this time but how experiences that were occurring 10 years ago are related to health and well being now."

The team found that people who become upset by daily stressors and continue to dwell on them after they have passed were more likely to suffer from chronic health problems -- especially pain, such as that related to arthritis, and cardiovascular issues -- 10 years later.

"I like to think of people as being one of two types," Almeida said. "With Velcro people, when a stressor happens it sticks to them; they get really upset and, by the end of the day, they are still grumpy and fuming. With Teflon people, when stressors happen to them they slide right off. It's the Velcro people who end up suffering health consequences down the road."

The results appear online in the current issue of Annals of Behavioral Medicine

According to Almeida, certain types of people are more likely to experience stress in their lives. Younger people, for example, have more stress than older people; people with higher cognitive abilities have more stress than people with lower cognitive abilities; and people with higher levels of education have more stress than people with less education.

"What is interesting is how these people deal with their stress," said Almeida. "Our research shows that people age 65 and up tend to be more reactive to stress than younger people, likely because they aren't exposed to a lot of stress at this stage in their lives, and they are out of practice in dealing with it. Younger people are better at dealing with it because they cope with it so frequently. Likewise, our research shows that people with lower cognitive abilities and education levels are more reactive to stress than people with higher cognitive abilities and education levels, likely because they have less control over the stressors in their lives."

While stress may be a symptom that a person's life is filled with hardship, it could also simply mean that the person is engaged in a wide variety of activities and experiences.

"If this is the case, reducing exposure to stressors isn't the answer," said Almeida. "We just need to figure out how to manage them better."

The National Institutes of Health provided funding for this research. Other authors on the paper include Susan Charles of the University of California at Irvine, Jennifer Piazza of California State University at Fullerton, and Martin Sliwinski and Jacquie Mogle, both at Penn State.

http://www.sciencedaily.com/releases/2012/11/121102205143.htm?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29

Why are elderly duped?

2012-08-21T16:57:00.003+05:30

Why are elderly duped? Area in brain where doubt arises changes with age

ScienceDaily (Aug. 16, 2012) — Everyone knows the adage: "If something sounds too good to be true, then it probably is." Why, then, do some people fall for scams and why are older folks especially prone to being duped?

An answer, it seems, is because a specific area of the brain has deteriorated or is damaged, according to researchers at the University of Iowa. By examining patients with various forms of brain damage, the researchers report they've pinpointed the precise location in the human brain, called the ventromedial prefrontal cortex, that controls belief and doubt, and which explains why some of us are more gullible than others.

"The current study provides the first direct evidence beyond anecdotal reports that damage to the vmPFC (ventromedial prefrontal cortex) increases credulity. Indeed, this specific deficit may explain why highly intelligent vmPFC patients can fall victim to seemingly obvious fraud schemes," the researchers wrote in the paper published in a special issue of the journalFrontiers in Neuroscience.

A study conducted for the National Institute of Justice in 2009 concluded that nearly 12 percent of Americans 60 and older had been exploited financially by a family member or a stranger. And, a report last year by insurer MetLife Inc. estimated the annual loss by victims of elder financial abuse at $2.9 billion.

The authors point out their research can explain why the elderly are vulnerable.

"In our theory, the more effortful process of disbelief (to items initially believed) is mediated by the vmPFC, which, in old age, tends to disproportionately lose structural integrity and associated functionality," they wrote. "Thus, we suggest that vulnerability to misleading information, outright deception and fraud in older adults is the specific result of a deficit in the doubt process that is mediated by the vmPFC."

The ventromedial prefrontal cortex is an oval-shaped lobe about the size of a softball lodged in the front of the human head, right above the eyes. It's part of a larger area known to scientists since the extraordinary case of Phineas Gage that controls a range of emotions and behaviors, from impulsivity to poor planning. But brain scientists have struggled to identify which regions of the prefrontal cortex govern specific emotions and behaviors, including the cognitive seesaw between belief and doubt.

The UI team drew from its Neurological Patient Registry, which was established in 1982 and has more than 500 active members with various forms of damage to one or more regions in the brain. From that pool, the researchers chose 18 patients with damage to the ventromedial prefrontal cortex and 21 patients with damage outside the prefrontal cortex. Those patients, along with people with no brain damage, were shown advertisements mimicking ones flagged as misleading by the Federal Trade Commission to test how much they believed or doubted the ads. The deception in the ads was subtle; for example, an ad for "Legacy Luggage" that trumpets the gear as "American Quality" turned on the consumer's ability to distinguish whether the luggage was manufactured in the United States versus inspected in the country.

Each participant was asked to gauge how much he or she believed the deceptive ad and how likely he or she would buy the item if it were available. The researchers found that the patients with damage to the ventromedial prefrontal cortex were roughly twice as likely to believe a given ad, even when given disclaimer information pointing out it was misleading. And, they were more likely to buy the item, regardless of whether misleading information had been corrected.

"Behaviorally, they fail the test to the greatest extent," says Natalie Denburg, assistant professor in neurology who devised the ad tests. "They believe the ads the most, and they demonstrate the highest purchase intention. Taken together, it makes them the most vulnerable to being deceived." She added the sample size is small and further studies are warranted.

Apart from being damaged, the ventromedial prefrontal cortex begins to deteriorate as people reach age 60 and older, although the onset and the pace of deterioration varies, says Daniel Tranel, neurology and psychology professor at the UI and corresponding author on the paper. He thinks the finding will enable doctors, caregivers, and relatives to be more understanding of decision making by the elderly.

"And maybe protective," Tranel adds. "Instead of saying, 'How would you do something silly and transparently stupid,' people may have a better appreciation of the fact that older people have lost the biological mechanism that allows them to see the disadvantageous nature of their decisions."

The finding corroborates an idea studied by the paper's first author, Erik Asp, who wondered why damage to the prefrontal cortex would impair the ability to doubt but not the initial belief as well. Asp created a model, which he called the False Tagging Theory, to separate the two notions and confirm that doubt is housed in the prefrontal cortex.

"This study is strong empirical evidence suggesting that the False Tagging Theory is correct," says Asp, who earned his doctorate in neuroscience from the UI in May and is now at the University of Chicago.

Kenneth Manzel, Bryan Koestner, and Catherine Cole from the UI are contributing authors on the paper. The National Institute on Aging and the National Institute of Neurological Disorders and Stroke funded the research.

Journal Reference:

Erik Asp, Kenneth Manzel, Bryan Koestner, Catherine A. Cole, Natalie L. Denburg, Daniel Tranel. A Neuropsychological Test of Belief and Doubt: Damage to Ventromedial Prefrontal Cortex Increases Credulity for Misleading Advertising. Frontiers in Neuroscience, 2012; 6 DOI: 10.3389/fnins.2012.00100

http://www.sciencedaily.com/releases/2012/08/120816121836.htm?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29

A GPS in your DNA

2012-08-21T16:51:00.001+05:30

ScienceDaily (Aug. 16, 2012) — While your DNA is unique, it also tells the tale of your family line. It carries the genetic history of your ancestors down through the generations. Now, says a Tel Aviv University researcher, it's also possible to use it as a map to your family's past.

Prof. Eran Halperin of TAU's Blavatnik School of Computer Science and Department of Molecular Microbiology and Biotechnology, along with a group of researchers from University of California, Los Angeles, are giving new meaning to the term "genetic mapping." Using a probabilistic model of genetic traits for every coordinate on the globe, the researchers have developed a method for determining more precisely the geographical location of a person's ancestral origins.

The new method is able to pinpoint more specific locations for an individual's ancestors, for example placing an individual's father in Paris and mother in Barcelona. Previous methods would "split the difference" and place this origin inaccurately at a site between those two cities, such as Lyon.

Published in the journal Nature Genetics, this method has the potential to reveal the ancestry, origins, and migration patterns of many different human and animal populations. It could also be a new model for learning about the genome.

Points of origin

There are points in the human genome called SNPs that are manifested differently in each individual, explains Prof. Halperin. These points mutated sometime in the past and the mutation was then passed to a large part of the population in a particular geographic region. The probability of a person possessing these mutations today varies depending on the geographical location of those early ancestors.

"We wanted to ask, for example, about the probability of having the genetic mutation 'A' in a particular position on the genome based on geographical coordinates," he says. When you look at many of these positions together in a bigger picture, it's possible to group populations with the same mutation by point of origin.

To test their method, Prof. Halperin and his fellow researchers studied DNA samples from 1,157 people from across Europe. Using a probabilistic mathematical algorithm based on mutations in the genome, they were able to accurately determine their ancestral point or points of origin using only DNA data and the new mathematical model, unravelling genetic information to ascertain two separate points on the map for the mother and father. The researchers hope to extend this model to identify the origins of grandparents, great-grandparents, and so on.

The new method could provide information that has applications in population genetic studies -- to study a disease that impacts a particular group, for example. Researchers can track changes in different genomic traits across a map, such as the tendency for southern Europeans to have a mutation in a gene that causes lactose intolerance, a mutation missing from that gene in northern Europeans.

A closer look at migration

The researchers believe that their model could have also relevance for the animal kingdom, tracking the movement of animal populations. "In principle, you could figure out where the animals have migrated from, and as a result learn about habitat changes due to historical climate change or other factors," says Prof. Halperin.

http://www.sciencedaily.com/releases/2012/08/120816101039.htm?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29

B Cell Survival Holds Key to Chronic Graft Vs. Host Disease

2012-08-21T16:48:00.000+05:30

B cell survival holds key to chronic graft vs. host disease

ScienceDaily (Aug. 16, 2012) — A team from UNC Lineberger Comprehensive Cancer Center, shows in the laboratory that B cells from patients with chronic GVHD are much more active than cells from patients without the disease.

In chronic Graft vs. Host Disease (GVHD), the differences between the donor bone marrow cells and the recipient's body often cause these immune cells to recognize the recipient's body tissues as foreign and the newly transplanted cells attack the transplant recipient's body. Symptoms can range from dry eyes and dry mouth, hair loss and skin rashes, vulnerability to infection, liver and lung and digestive tract disorders. For patients who received bone marrow or stem cells, it is estimated that 40-70 percent may experience chronic GVHD.

B cells, which produce proteins called antibodies, are one type of immune cell involved in GVHD. In a paper published online August 15 by the journal, Blood, a team from the University of North Carolina's Lineberger Comprehensive Cancer Center, shows in the laboratory that B cells from patients with chronic GVHD are much more active than cells from patients without the disease. The team also outlines the cell signaling pathways that contribute to this increased activity -- identifying a promising target for developing new therapies for the diseases.

Jessica Allen, PhD, the paper's first author, says "We found that B cells from patients with active chronic GVHD were in a heightened metabolic state and resist programmed cell death."

Senior author, Stefanie Sarantopoulos, MD, PhD, assistant professor in the division of hematology/oncology and the departments of microbiology and immunology at the UNC School of Medicine, adds, "Steroids are currently our only standard treatment for chonic GVHD and they are often not effective. This study adds to our previously published work because it implicates the TNF family member protein called BAFF in the 'revved up' B-cell signaling we found in our patients. We hope to develop targeted therapeutic agents, like anti-BAFF agents or small molecule inhibitors of serine/ threonine kinases, for treatment of our chronic GVHD patients."

[Other UNC Lineberger researchers on the team include Albert Baldwin, PhD, Jonathan Serody, MD, Kristy Richards, MD, PhD, Thomas C. Shea, MD, Don A. Gabriel, MD, PhD, James Coghill, MD, Paul Armistead, MD, PhD, Matthew Fore, BA, and Jenna Wooten, PhD.

Additional team members from the UNC Stem Cell Transplant team and UNC Lineberger include Philip Roehrs, MD, Amber Essenmacher, Robert Irons, Allison Deal, Andrew Sharf, and Todd Hoffert.

Jerome Ritz MD, Corey Cutler, MD MPH, and Nazmim S. Bhuiya, BA, MPH from the Dana-Farber Cancer Institute also contributed to the research.

The study could not have been performed without the gracious consent of transplant patients at UNC and Dana Farber who donated extra blood samples. The University Cancer Research Fund (UCRF) and the UNC Tissue Procurement Core Facility supported collection of de-identified patient samples for these laboratory studies.

The research was funded by the National Marrow Donor Program through the Be The Match Foundation and National Institutes of Health grants K08HL107756 and CA142106.

Leukemia and lymphoma patients who receive life-saving stem cell or bone marrow transplants often experience chronic side effects that significantly decrease quality of life, can last a lifetime, and ultimately affect their long-term survival.]

http://www.sciencedaily.com/releases/2012/08/120816101037.htm?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29

molecular trigger for wound-healing

2012-08-21T16:42:00.001+05:30

Scientists find an important molecular trigger for wound-healing

ScienceDaily (Aug. 16, 2012) — Scientists at The Scripps Research Institute have made a breakthrough in understanding a class of cells that help wounds in skin and other epithelial tissues heal, uncovering a molecular mechanism that pushes the body into wound-repair mode.

The findings, which appear in an advance, online version of the Immunity on August 16, 2012, focus on cells known as γδ (gamma delta) T cells. The new study demonstrates a skin-cell receptor hooks up with a receptor on γδ T-cells to stimulate wound healing.

"This is a major activation pathway for γδ T cells, and it may be a key to treating slow-wound-healing conditions, such as we see in diabetes," said Scripps Research Professor Wendy L. Havran, senior author of the study. "Chronic non-healing wounds among diabetics and the elderly are an increasing clinical problem."

Rounding and Multiplying

Havran's laboratory specializes in the study of γδ T cells, and the team has produced many of the findings in this research field, including the discovery of these cells' major role in epithelial wound repair. Epithelial tissues are barrier tissues to the outside world, such as skin and the inner surfaces of the gut and lungs.

Normally, γδ T cells reside in these tissues and extend finger-like projections, called dendrites, that contact neighboring epithelial cells. When injury or infection occurs, the epithelial cells signal their damaged condition to the γδ T cells. In response, the T cells retract their dendrites, become round, start proliferating, and secrete growth-factor proteins that stimulate the production of new epithelial cells in the vicinity -- thus helping to repair the wound.

Researchers know of very few interactions between epithelial cells and γδ T cells that are involved in this process. Two, however, are known to be crucial. One of these is through the gd T cell receptor and the other was described in a 2010 Science paper, whose first author was Havran laboratory Senior Staff Scientist Deborah A. Witherden. But these two interactions don't fully explain the transformation that γδ T cells undergo in the vicinity of wounds. "We've wanted to learn more about the molecules that mediate this dramatic change," Havran said.

Signaling a Transformation

To do that, Witherden identified an antibody that could block keratinocytes' ability to activate γδ T cells in culture. She found that the antibody bound to a keratinocyte surface receptor called plexin B2. She also found that when lab mice have small skin wounds, their injured keratinocytes express more plexin B2 soon after the wounding occurs -- pointing to a role for plexin B2 in signaling skin-cell damage.

The next step was to find plexin B2's signaling partner on γδ T cells. "Plexin B2 is very similar to other plexin B family members, including plexin B1, which previously has been shown to bind the CD100 receptor on T cells," said Witherden. "So we thought that perhaps plexin B2 and CD100 can interact as well."

Further tests revealed that plexin B2 and CD100 do indeed bind tightly together; moreover, γδ T cells can't go fully into wound-repair mode when they lack CD100. Witherden found as well that skin wounds in mice take an extra day or two to heal when the mice don't have this receptor. "This is very similar to what we see in mice that lack γδ T cells altogether," she said.

Removing CD100 from other types of T cells had no effect on wound healing time, indicating that the absence of this receptor specifically on γδ T cells is the reason for the slower healing.

By stimulating CD100 with plexin B2 molecules or even with CD100-binding antibodies, the team showed that this receptor is the principal trigger for the dramatic appendage-retraction and rounding phenomenon seen in γδ T cells after nearby wounds. Without it, the T cells are largely unable to undergo this transformation. "This rounding process seems to be vital for these T cells to function normally in wound healing," said Witherden.

Potential Clinical Significance

In early follow-on work, the team has found evidence that this same plexin B2-CD100 interaction is also needed for the prompt activation of γδ T cells and wound healing in the lining of mouse intestines -- which suggests that this receptor helps govern wound healing in epithelial tissues generally.

The finding clearly is important for the basic scientific understanding of T cells and their functions. But it is likely to have medical significance, too. Non-healing wounds affect more than 4 million people in the United States and are the leading cause of amputations. These chronic wounds have a major impact on patient's lives and result in enormous health care costs. "If deficiencies in this γδ T cell activation pathway are even partly responsible, then we may be able to develop drugs to boost this pathway and treat conditions involving chronic non-healing wounds," said Havran.

The γδ T cell population appears to be involved not just in wound healing, but also in defending against other threats to epithelial tissues. "One of the future directions of our research will be to understand the roles of these molecules in gd T cell activation pathways in fighting infections and tumors," she added.

Journal Reference:

Deborah A. Witherden, Megumi Watanabe, Olivia Garijo, Stephanie E. Rieder, Gor Sarkisyan, Shane J.F. Cronin, Petra Verdino, Ian A. Wilson, Atsushi Kumanogoh, Hitoshi Kikutani, Luc Teyton, Wolfgang H. Fischer, Wendy L. Havran. The CD100 Receptor Interacts with Its Plexin B2 Ligand to Regulate Epidermal γδ T Cell Function.Immunity, 2012; DOI: 10.1016/j.immuni.2012.05.026

http://www.sciencedaily.com/releases/2012/08/120816121854.htm?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29

increase in size of the human brain explained

2012-08-21T16:29:00.001+05:30

Evolutionary increase in size of the human brain explained: Part of a protein linked to rapid change in cognitive ability

ScienceDaily (Aug. 16, 2012) — Researchers have found what they believe is the key to understanding why the human brain is larger and more complex than that of other animals.

The human brain, with its unequaled cognitive capacity, evolved rapidly and dramatically.

"We wanted to know why," says James Sikela, PhD, who headed the international research team that included researchers from the University of Colorado School of Medicine, Baylor College of Medicine and the National Institutes of Mental Health. "The size and cognitive capacity of the human brain sets us apart. But how did that happen?"

"This research indicates that what drove the evolutionary expansion of the human brain may well be a specific unit within a protein -- called a protein domain -- that is far more numerous in humans than other species."

The protein domain at issue is DUF1220. Humans have more than 270 copies of DUF1220 encoded in the genome, far more than other species. The closer a species is to humans, the more copies of DUF1220 show up. Chimpanzees have the next highest number, 125. Gorillas have 99, marmosets 30 and mice just one. "The one over-riding theme that we saw repeatedly was that the more copies of DUF1220 in the genome, the bigger the brain. And this held true whether we looked at different species or within the human population."

Sikela, a professor at the CU medical school, and his team also linked DUF1220 to brain disorders. They associated lower numbers of DUF1220 with microcephaly, when the brain is too small; larger numbers of the protein domain were associated with macrocephaly, when the brain is too large.

The findings were reported today in the online edition of The American Journal of Human Genetics. The researchers drew their conclusions by comparing genome sequences from humans and other animals as well as by looking at the DNA of individuals with microcephaly and macrocephaly and of people from a non-disease population.

"The take home message was that brain size may be to a large degree a matter of protein domain dosage," Sikela says. "This discovery opens many new doors. It provides new tools to diagnose diseases related to brain size. And more broadly, it points to a new way to study the human brain and its dramatic increase in size and ability over what, in evolutionary terms, is a short amount of time."

Journal Reference:

Laura J. Dumas, Majesta S. O’Bleness, Jonathan M. Davis, C. Michael Dickens, Nathan Anderson, J.G. Keeney, Jay Jackson, Megan Sikela, Armin Raznahan, Jay Giedd, Judith Rapoport, Sandesh S.C. Nagamani, Ayelet Erez, Nicola Brunetti-Pierri, Rachel Sugalski, James R. Lupski, Tasha Fingerlin, Sau Wai Cheung, James M. Sikela. DUF1220-Domain Copy Number Implicated in Human Brain-Size Pathology and Evolution. The American Journal of Human Genetics, 2012; DOI: 10.1016/j.ajhg.2012.07.016

http://www.sciencedaily.com/releases/2012/08/120816141537.htm?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29

Stress fuels breast cancer metastasis to bone

2012-07-19T16:06:00.003+05:30

Stress can promote breast cancer cell colonization of bone, Vanderbilt Center for Bone Biology investigators have discovered.

The studies, reported July 17 in PLoS Biology, demonstrate in mice that activation of the sympathetic nervous system – the "fight-or-flight" response to stress – primes the bone environment for breast cancer cell metastasis. The researchers were able to prevent breast cancer cell lesions in bone using propranolol, a cardiovascular medicine that inhibits sympathetic nervous system signals.
Metastasis – the spread of cancer cells to distant organs, including bone – is more likely to kill patients than a primary breast tumor, said Florent Elefteriou, Ph.D., director of the Vanderbilt Center for Bone Biology.

"Preventing metastasis is really the goal we want to achieve," he said.

Elefteriou and his colleagues knew from their previous studies that the sympathetic nervous system stimulated bone remodeling, and that it used some of the same signaling molecules that have been implicated in breast cancer metastasis to bone.

"We came to the hypothesis that sympathetic activation might remodel the bone environment and make it more favorable for cancer cells to metastasize there," Elefteriou said.

Evidence from the clinic supported this notion. Breast cancer patients who suffered from stress or depression following their primary treatment had shorter survival times. Both stress and depression activate the sympathetic nervous system.

To explore this possible link, the researchers studied cancer cell metastasis in mice. They followed fluorescently "tagged" human breast cancer cells that were injected into the mouse heart to model the stage of metastasis when breast cancer cells leave the primary site and move through the circulation.
They found that treating the mice with a drug that mimics sympathetic nervous system activation caused more cancer lesions in bone. Using physical restraint to stress the mice and activate the sympathetic nervous system also caused more cancer lesions in bone. Treating the restrained mice with propranolol, one of a family of blood pressure medicines called "beta-blockers," reduced the number of bone lesions.

The investigators demonstrated that sympathetic nervous system activation increases bone levels of a signaling molecule called RANKL, which is known to promote the formation of osteoclasts – bone cells that break down bone tissue. RANKL has also been implicated in cell migration, and Elefteriou and colleagues were able to show that breast cancer cell migration to the bone depends on RANKL.
The findings suggest that beta-blockers or drugs that interfere with RANKL signaling, such as denosumab, may be useful in preventing breast cancer cell metastasis to bone. Propranolol and other beta-blockers are inexpensive, well characterized, and safe in most patients. They may be a good choice for long-term treatment if future studies in patients with breast cancer confirm their ability to block cancer cell metastasis to bone, Elefteriou said.

"If something as simple as a beta blocker could prevent cancer metastasis to bone, this would impact the treatment of millions of patients worldwide," he said.

Efforts to reduce stress and depression in patients with cancer may have unappreciated benefits in terms of metastasis prevention, he added.

http://www.eurekalert.org/pub_releases/2012-07/vumc-sfb071212.php

New Muscular Dystrophy Treatment Approach Developed Using Human Stem Cells

2012-05-06T21:06:00.001+05:30

ScienceDaily (May 4, 2012) — Researchers from the University of Minnesota's Lillehei Heart Institute have effectively treated muscular dystrophy in mice using human stem cells derived from a new process that -- for the first time -- makes the production of human muscle cells from stem cells efficient and effective.

The research, published May 4 in Cell Stem Cell, outlines the strategy for the development of a rapidly dividing population of skeletal myogenic progenitor cells (muscle-forming cells) derived from induced pluripotent (iPS) cells. iPS cells have all of the potential of embryonic stem (ES) cells, but are derived by reprogramming skin cells. They can be patient-specific, which renders them unlikely to be rejected, and do not involve the destruction of embryos.

This is the first time that human stem cells have been shown to be effective in the treatment of muscular dystrophy.

According to U of M researchers -- who were also the first to use ES cells from mice to treat muscular dystrophy -- there has been a significant lag in translating studies using mouse stem cells into therapeutically relevant studies involving human stem cells. This lag has dramatically limited the development of cell therapies or clinical trials for human patients.

The latest research from the U of M provides the proof-of-principle for treating muscular dystrophy with human iPS cells, setting the stage for future human clinical trials.

"One of the biggest barriers to the development of cell-based therapies for neuromuscular disorders like muscular dystrophy has been obtaining sufficient muscle progenitor cells to produce a therapeutically effective response," said principal investigator Rita Perlingeiro, Ph.D., associate professor of medicine in the Medical School's Division of Cardiology. "Up until now, deriving engraftable skeletal muscle stem cells from human pluripotent stem cells hasn't been possible. Our results demonstrate that it is indeed possible and sets the stage for the development of a clinically meaningful treatment approach."

Upon transplantation into mice suffering from muscular dystrophy, human skeletal myogenic progenitor cells provided both extensive and long-term muscle regeneration which resulted in improved muscle function.

To achieve their results, U of M researchers genetically modified two well-characterized human iPS cell lines and an existing human ES cell line with the PAX7 gene. This allowed them to regulate levels of the Pax7 protein, which is essential for the regeneration of skeletal muscle tissue after damage. The researchers found this regulation could prompt naïve ES and iPS cells to differentiate into muscle-forming cells.

Up until this point, researchers had struggled to make muscle efficiently from ES and iPS cells. PAX7 -- induced at exactly the right time -- helped determine the fate of human ES and iPS cells, pushing them into becoming human muscle progenitor cells.

Once Dr. Perlingeiro's team was able to pinpoint the optimal timing of differentiation, the cells were well suited to the regrowth needed to treat conditions such as muscular dystrophy. In fact, Pax7-induced muscle progenitors were far more effective than human myoblasts at improving muscle function. Myoblasts, which are cell cultures derived from adult muscle biopsies, had previously been tested in clinical trials for muscular dystrophy, however the myoblasts did not persist after transplantation.

"Seeing long-term maintenance of these cells without major adverse side effects is exciting," said Perlingeiro. "Our research proves that these differentiated stem cells have real staying power in the fight against muscular dystrophy."

According to John Wagner, M.D., scientific director of clinical research at the University's Stem Cell Institute and blood and marrow transplant expert, "This research is a phenomenal breakthrough. Dr. Perlingeiro and her collaborators have overcome one of the most significant obstacles to moving stem cell therapies into the treatment of children with devastating and life threatening muscular dystrophies."

The U of M researchers say alternative methods of Pax7 induction will need to be investigated before this study can be turned into a human clinical trial. Their method of delivering the Pax7 protein involved genetic modification of cells with viruses and because viruses sometimes cause mutations, they add risk to a clinical trial. But the U of M researchers are committed to developing a safe and effective clinical protocol, and are actively testing alternate methods of delivering Pax7.

Radbod Darabi, Robert W. Arpke, Stefan Irion, John T. Dimos, Marica Grskovic, Michael Kyba, Rita C.R. Perlingeiro. Human ES- and iPS-Derived Myogenic Progenitors Restore DYSTROPHIN and Improve Contractility upon Transplantation in Dystrophic Mice. Cell Stem Cell, 2012; 10 (5): 610 DOI: 10.1016/j.stem.2012.02.015

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Telomeres in Disease

2012-05-02T23:07:00.001+05:30

The ends of linear chromosomes have attracted serious scientific study—and Nobel Prizes—since the early 20th century. Called telomeres, these ends serve to protect the coding DNA of the genome. When a cell’s telomeres shorten to critical lengths, the cell senesces. Thus, telomeres dictate a cell’s life span—unless something goes wrong. Work over the past several decades has revealed an active, though limited, mechanism for the normal enzymatic repair of telomere loss in certain proliferative cells. Telomere lengthening in cancer cells, however, confers an abnormal proliferative ability.

In addition to cancer, telomeres have been found to be involved in numerous other diseases, including liver dysfunction and aplastic anemia, a condition in which the bone marrow does not produce a sufficient supply of new blood cells. Inadequate telomere repair and accelerated telomere attrition can be molecular causes of these diseases, and targeting these processes may lead to the development of novel therapies.

Chromosome tails

Telomeres consist of hexameric nucleotide sequences (TTAGGG in humans) that are repeated hundreds to thousands of times at each extremity of each chromosome. Telomeric DNA is coated by a group of proteins, collectively termed shelterin, which serves to protect telomere structure. Because DNA can only be synthesized in one direction, the RNA primers at the chromosome’s ends cannot be filled in, and thus a small amount of DNA is lost with every cell division—a loss that occurs in the telomeres. During normal aging of an animal or in cell culture, cells divide and telomeres shorten. As telomeric sequences do not contain genes, no important genetic information undergoes erosion during DNA replication. When telomeres become critically short, the cell becomes senescent—it ceases to divide—or undergoes apoptosis—it dies.

Telomere attrition explains the “Hayflick limit,” the number of divisions a cell is capable of undergoing in tissue culture before the cell stops dividing. Telomere length is therefore a type of “mitotic clock,” a measure of a cell’s proliferative history. Under circumstances in which cell proliferation continues despite critically short telomeres (usually about a few hundred hexanucleotide repeats), the telomere’s protective function is lost. Subtelomeric genetic information can be lost, and more importantly, recombination between chromosomes occurs, leading to chromosome instability, aneuploidy, and possible transformation to a cancer phenotype.

Some proliferative cells can elongate telomeres enzymatically through the telomerase complex. Telomerase (TERT) is a reverse transcriptase that employs a small RNA molecule (TERC) as a template to extend telomeres in cells. In this way, telomerase counterbalances the effects of cell division and cellular genetic “aging,” preventing senescence, apoptosis, and genetic instability. Telomerase-dependent telomere repair occurs naturally in some cells, such as embryonic and adult stem cells and some cells of the immune system—cell types that divide regularly to support development, maintain tissues, and combat infections, respectively.

Telomere maintenance is also possible by other mechanisms, such as the alternative pathway (ALT), which uses recombination between chromosomes to maintain telomere length. In ALT, telomeres are not newly elongated, but rather transferred from one chromosome to another, resulting in some daughter cells whose chromosomes have shorter telomeres and others with longer telomeres. The details of ALT’s components and regulation, however, are not well understood.

Telomere shortening and cancer

Most cells in which telomeres reach critically short lengths either die or enter senescence. In those few that survive, perhaps due to inadequate monitoring by p53 and related DNA damage-response safeguards, telomere repair would be subject to powerful selective pressure. Indeed, in most malignancies, telomerase gene upregulation or activation of the ALT pathway is thought to be necessary for the establishment of cellular immortality. Telomerase is so frequently increased in tumors and in cancer cell lines as to be considered an appropriate therapeutic target. Currently there are several clinical trials using telomerase inhibitors to treat a variety of cancers, but results have yet to be reported. Telomere shortening would also generate the equivalent of a “mutator phenotype” by increasing spontaneous chromosomal aberrations—from numerical changes to structural abnormalities—and would therefore increase the pool of aberrant cells upon which selection would act.

There are many sources of evidence suggesting that telomere attrition is associated with and likely etiologic of cancer. Patients with dyskeratosis congenita, a rare inherited bone marrow failure disease characterized by telomerase dysfunction, have a 1,000-fold increase in risk of tongue cancer and about a 100 fold increase in risk of acute myeloid leukemia. In aplastic anemia, patients with the shortest telomeres (absent mutations) are 4- to 5-fold more likely to have their disease undergo malignant transformation to myelodysplasia and leukemia. Telomere-free ends of chromosomes and aneuploidy may be apparent in cultured bone marrow years before progression to leukemia. Furthermore, some acute myeloid leukemia patients without prior bone marrow failure have inherited mutations in TERT and TERC.

Similarly, short leukocyte telomeres predict the development of cancer in patients with Barrett’s esophagitis, a condition in which the lining of the esophagus is damaged by stomach acid, or ulcerative colitis, a type of inflammatory bowel disease. In these diseases, the mechanism is less clear. Short telomeres in blood leukocytes may reflect the telomere length of the affected organ. Alternatively, they may be a biomarker of exposure to reactive oxygen species produced as a result of a chronic inflammatory process, which can both damage telomeres and cause cancer. Evidence for the latter hypothesis comes from the observation that cells cultured in room air have excessive telomere shortening in comparison to cells cultured at low oxygen tension.

More generally, genome-wide analyses have identified single nucleotide polymorphisms in TERT as risk factors in many cancers. In a recent report, short leukocyte telomeres were associated with increased risk of all cancers and of cancer fatalities in a large population followed over a decade. Circumstantially, telomere attrition is an accompaniment of aging, itself a major risk factor for cancer. Furthermore, secondary malignancies often occur after chemotherapy and radiation, which would be anticipated to cause marrow stress and telomere shortening. More direct data come from animal experiments. In a knockout mouse model, animals with reduced telomerase activity combined with diminished p53 surveillance of DNA damage developed a variety of epidermal cancers unusual in the rodent but typical of humans.

Other telomere diseases

In addition to cancer, other diseases have been linked to telomeres. Hematopoietic stem cells express telomerase in response to the enormous daily demand for red blood cells, white blood cells, and platelets. Thus while overexpression of telomerase in other tissues can cause malignant growth, faulty telomere repair in blood stem cells can also result in severe diseases caused by stem cell failure.

One such “telomere disease” is dyskeratosis congenita, an X-linked bone marrow disorder characterized by symptoms such as abnormal nails, a pigmented, net-like rash, a white patch or plaque in the mouth, and aplastic anemia. The disease usually presents in the first decade of life. The liver and lungs can also be affected, as is often observed after a hematopoietic stem-cell transplant is performed to correct the bone marrow disease. The reasons for liver and lung involvement are not clear, but the chemotherapy used for transplant conditioning and the new inflammatory cells in the transplanted bone marrow may accelerate the injury in these organs.

Patients suffering from dyskeratosis congenita inherit a mutation in a gene named DKC1, identified by Inderjeet Dokal at the Hammersmith Hospital in London, who performed linkage studies of large pedigrees. DKC1 encodes dyskerin, a protein that binds to the RNA component of the telomerase complex and stabilizes it. Later, heterozygous mutations in TERC were also found in some families with dyskeratosis congenita. The severe phenotype of X-linked dyskeratosis congenita is likely due to the loss of functional DKC1 and markedly reduced telomerase function, which results in defective telomere repair and leads to accelerated telomere attrition, causing cell senescence and organ failure.

Whereas dyskeratosis congenita caused by mutations in the DKC1 gene usually presents during infancy, mutations in TERC and in the enzymatic component encoded by TERT appear to have impacts later in life. The first TERT mutations found in humans were in adult patients with acquired aplastic anemia who lacked physical anomalies and did not have a family history of telomere-related disease. Penetrance of the phenotypes of TERT and TERC mutations is highly variable among and within families, as reflected by the severity, time of onset, and organs involved. Within pedigrees, members with the identical mutation may have minimal or no clinical manifestations, develop aplastic anemia late in life, or suffer pulmonary fibrosis (scarring of the lungs) or hepatic cirrhosis (scarring of liver tissue). Different organ systems may be affected in different family members at different times, and occasional patients have disease in marrow, lung, and liver. How faulty telomere repair leads to such diseases is not fully understood.

Even with the uncertainties that remain, the association of telomerase mutations with disease in such disparate organs systems has important practical consequences for patients and their physicians. In the family history, the presence of even mild blood count abnormalities, pulmonary fibrosis, and hepatic cirrhosis, as well as acute myeloid leukemia, are important clues for the diagnosis of a telomeropathy. Involvement of multiple medical subspecialties can be confusing; some patients have even made their own diagnoses after Internet searches. Telomere length in leukocytes can be measured commercially and is a reliable marker of these diseases when severely reduced. Sequencing TERT and TERC can also be diagnostic. The appropriate finding of a telomerase deficit has consequences for prognosis, treatment, and genetic counseling. But while the diagnosis of telomeropathies can be straightforward, there may be complications. Some typical families lack known mutations, and telomere length may be normal even in the presence of etiologic nucleotide substitutions. Furthermore, rare mutations in shelterin genes coding for the proteins that protect telomere structure can produce severe dyskeratosis but do not alter telomerase repair capacity. And regulatory regions of genes, not routinely screened, may be responsible in some cases.

Telomeres and aging

Telomeres shorten as we age. By analogy to the cellular mitotic clock, telomeres have been postulated as a marker of “genetic age,” and telomere length has been marketed as a simple predictor of longevity. Assays of telomere length have been bundled with recommendations for lifestyle modification and for drug therapy, neither based on appropriate clinical studies. Simple but appealing arguments relating telomeres and aging are currently controversial, likely simplistic, and potentially harmful. Telomere length does indeed reflect a cell’s past proliferative history and future propensity for apoptosis, senescence, and transformation. Cellular aging, however, is not equivalent to organ or organismal aging.

There are several considerations in relating telomere biology to aging. First, physiologically there is overlap between the shortest telomere length of young children and the longest telomeres of the elderly. Most telomere shortening occurs early in life, in association with growth, and when the rate of disease in general is low. The paradigmatic telomere syndrome of dyskeratosis congenita is not at all typical of progerias, inherited syndromes in which patients appear old and suffer diseases of aging such as premature atherosclerosis or dementia. Furthermore, the organ damage of dyskeratosis congenita is not very similar to normal aging of marrow, lungs, and liver. The marrow becomes mildly hypocellular in older individuals, but stem cell numbers may actually increase, and blood counts remain stable; and neither the liver nor lungs normally become fibrotic with advanced age, as they often do in dyskeratosis congenita patients. Although in adults, relatively short leukocyte telomeres have been associated with cardiovascular events—a common morbidity of the aging population—the clinical correlations have not been consistent, and may be related to overall reactive oxygen species exposure.

Studies in humans have attempted to relate telomere length to life span. In the provocative initial publication from the University of Utah in 2003, individuals around 60 years of age who had the longest telomeres lived longer than did subjects with the shortest telomeres, but the main cause of death in the latter group was, inexplicably, infectious disease; the persons with shorter telomeres did not have a higher rate of cancer deaths. Moreover, these findings have not been confirmed in other studies of older subjects. In another study evaluating a different population, telomere length failed to predict survival, but interestingly it correlated with years of healthy life. In a Danish study of people aged 73 to 101 years, telomeres correlated with life expectancy in a simple univariate analysis, but only before the researchers corrected for age, suggesting that the correlation was driven simply by the fact that younger subjects had longer telomeres. And a Dutch study of 78-year-old men found that while telomere lengths eroded with age, they failed to correlate with mortality. These discrepancies may have several causes. In some analyses, telomere lengths may have been studied as a surrogate marker of age. In addition, retrospective studies may identify “positive” associations that are random and cannot be reproduced in follow-up investigations.

The telomere hypothesis of aging also has been modeled in mice. For instance, in a murine model of telomerase deficiency and accelerated telomere attrition, researchers found that certain intracellular pathways involved in mitochondrial function and glucose metabolism were deregulated, a common occurrence in aging individuals, ultimately causing heart muscle disease. Interestingly, telomerase reactivation in these mice restored glucose production and heart function. However, these abnormalities observed in telomerase-deficient animals were not those typical of humans with very short telomeres; patients with telomeropathies usually do not suffer from heart disease. Indeed, the translation of mouse experiments on telomeres to human physiology and disease should be done with caution. Mice are not the ideal model for telomere attrition and its effects on aging as murine telomeres are 5 to 10 times longer than human telomeres, in spite of mice having a much shorter life span. When telomerase is knocked out in mice, they live a healthy life for several generations, and even late-generation animals with very short telomeres do not display the clinical phenotypes characteristic of human telomeropathies. Telomerase-deficient mice also do not have a higher incidence of cancer, which happens only if the p53 gene also is modulated, in contrast to humans with telomerase deficiency, who are at very high risk of developing cancer.

Implications for medicine

Telomeres and their repair are important in the growing field of regenerative medicine. Dolly the sheep had chromosomes with shorter telomeres probably because she was cloned from an adult mammary gland cell. This may have contributed to Dolly’s illnesses, especially her progressive lung disease. Embryonic stem cells, however, express telomerase and are able to maintain their telomere lengths despite numerous cell divisions. More recently, reprogramming mature adult skin cells to the pluripotent state has been achieved with introduction of just a few defined nuclear factors. During the process of reverting cells to a more immature and pluripotent state, the reprogrammed cells’ telomeres are highly elongated. In the first steps of reprogramming and likely in the early stages of embryogenesis, cells can elongate, and thus “rejuvenate,” their telomeres. Since telomere shortening limits cell proliferation, mechanisms that can elongate telomeres are highly desirable for effective regenerative medicine.

Telomerase expression is tightly regulated in the cell; just a few copies of the complex are present in the cell nucleus, and they exert their function during certain specific periods of the cell cycle. The mechanisms that modulate telomerase gene expression, resultant enzymatic activity, and telomere elongation are the focus of intensive research. MYC, a proto-oncogene that regulates the expression of many genes and cell pluripotency, activates telomerase expression. Sex hormones also activate telomerase expression in reproductive and nonreproductive organs, such as the bone marrow. The promoter region of the telomerase gene contains regulatory sequences that are modulated by estrogen; cells exposed to estrogens (or androgens converted into estrogens) upregulate telomerase expression. In retrospect, the clinical response of improved blood cell counts in patients with aplastic anemia, especially children with inherited marrow failure, to androgens may be attributable to this mechanism. However, whether higher blood levels of sex hormones or exposure to exogenous sex hormones causes telomere elongation is still unknown.

Conclusions

Telomeres and telomere repair are basic molecular processes in cells possessing linear DNA chromosomes. Accelerated telomere attrition due to genetic defects in telomerase and in the shelterin protein genes is etiologic in several human diseases not previously considered related in the clinic. These include aplastic anemia, pulmonary fibrosis, and hepatic cirrhosis. The telomeropathies, especially in their milder and more chronic forms, may not be rare and almost certainly are often unrecognized by physicians. The importance of telomere repair in tissues under regenerative stress is of special interest, particularly in the reactive responses of fibrogenesis in the liver and the lungs. The maintenance of adequate telomere lengths also may be important in embryonic and adult stem cells to enable proliferation while preventing chromosome instability, thus avoiding potential malignant transformation. Also of interest is the connection linking telomere attrition and chronic inflammation to cancer and other diseases. (See “An Aspirin for Your Cancer,” The Scientist, April 2011.)

There is still much to be learned about how telomerase gene mutations cause disease, why they only affect certain organs, and how telomeres can be targeted for therapies. Both the genetic regulation of telomerase expression and the effect of an organism’s environment on telomere attrition are poorly understood. Drugs or hormones that might modulate telomerase expression and maintain or elongate telomeres would be appealing in the treatment of the telomeropathies and in conditions in which telomere attrition has known medical consequences. Whether telomere shortening mediates human aging—and conversely, whether telomere elongation may reverse aging or prevent age-related diseases—are still controversial issues.

Rodrigo Calado is an Associate Professor of Medicine at the University of São Paulo. Neal Young is the Chief of the Hematology Branch at the US National Institutes of Health.

This article is adapted from a review in F1000 Medicine Reports, DOI:10.3410/M4-8 (open access).

http://the-scientist.com/2012/05/01/telomeres-in-disease/

Crystal Structure of Human Argonaute2

2012-05-01T23:28:00.003+05:30

Scripps Research Institute Scientists Find the Structure of a Key Gene Silencer Protein
The Structure reveals potential therapeutic targets in area with untapped potential

LA JOLLA, CA, April 26, 2012:-
Scientists at The Scripps Research Institute have determined the three-dimensional atomic structure of a human protein that is centrally involved in regulating the activities of cells. Knowing the precise structure of this protein paves the way for scientists to understand a process known as RNA-Silencing and to harness it to treat diseases.

"Biologists have known about RNA-Silencing for only a decade or so, but it's already clear that there's an enormous untapped potential here for new therapies," said Ian MacRae, an assistant professor at Scripps Research and senior author of the new report.

The new report, which appeared on April 26,2012 in the Journal Science's advance online publication, Science Express, focuses on Argonaute2. This protein can effectively silence a gene by intercepting and slicing the gene's RNA transcripts before they are translated into working proteins.

Interception and Destruction of Messages

When a gene that code for a protein is active in a cell, its information is transcribed from DNA form into lengths of nucleic acid called messenger RNA. If all goes well, these coded mRNA signals make their way to the cell's protein factories, which use them as templates to synthesize new proteins. RNA-silencing, also called RNA-Interference is the interception and destruction of these messages and as such, is a powerful and specific regulator of cell activity, as well as a strong defender against viral genes.

The silencing process requires not only an Argonaute protein but also a small length of guide RNA, known as a short-interfering RNA or microRNA. The guide RNA fits into a slot on Argonaute and serves as a target recognition device. Like a coded strip of Velero(TM), it latches onto a specific mRNA target whose sequence is the chemical mirror image of its own- thus bringing Argonaute into contact with its doomed prey.

Argonaute2 is not the only type of human Argonaute protein, but it seems to be the only one capable fo destroying target RNA directly. "If the guide RNA is completely complementary to the target RNA, Argonaute2 will cleave the mRNA, and that will elicit the degradation of the fragments and the loss of the genetic message," said Nicole Schirle, the graduate student in MacRae's laboratory who was lead author of the paper.

Aimed at disease-causing genes or even a cell's own overactive guide RNAs, RNA-silencing could be a powerful therapeutic weapon. In principle, one needs only to inject target-specific guide RNAs, and these will link up with Argonaute protein in cells to find and destroy the target RNAs. Scientists have managed to do this successfully with relatively accessible target cells, such as in the eye. But they have found it difficult to develop guide RNAs that can get from the bloodstream into distant tissues and still function.

"You have to modify the guide RNA, in some way to get it through the blood and into cells, but as soon as you start modifying it, you disrupt its ability to interact with Argonaute,"said MacRae. Knowing the precise structure of Argonaute should enable researchers to clear this hurdle by designing better guide RNA.

More Points for Manipulation

Previous structural studies have focused mostly on Argonaute protein from bacteria and other lower organisms, which have key differences from their human counterparts. Schirle was able to produce the comparatively large and complex human Argonaute2 and to manipulate it into forming crystals for X-ray crystallography analysis a feat that structural biologists have wanted to achieve for much of the past decade. "It was just excellent and diligent crystallography on her part," said MacRae.

The team's analysis of Argonaute2's structure revealed that it has the same basic set of working parts as bacterial Argonaute proteins, except that they are arranged somewhat differently. Also, key parts of Argonaute2 have extra loops and other structures, not seen on bacterial versions, which may play roles in binding to guide RNA. Finally, Argonatue2 has what appear to be binding sites for additional co-factor proteins that are thought to perform other destructive operations on the target mRNA.

"Basically, this Argonaute protein is more sophisticated than its bacterial cousins; it has more bells and whistles, which give us more points for manipulation. With this structure solved, we no longer need to use the prokaryotic structures to guess at what human Argonaute protein look like," MacRae said.

He and Schirle and others in the lab now are analyzing the functions of Argonaute2's substructures, as well as looking for ways to design better therapeutic guide RNAs.

"Now with the structural data, we can see what synthetic guide RNAs will work with Argonaute and what won't, " MacRae said, "we might even be able to make guide RNAs that can outcompete natural ones."

The research that led to Schirle and MacRae's new paper, "The Crystal Structure of Human Argonaute2," was funded by the National Institute of General Medical Sciences, part of the National Institute of Health.

press@scripps.edu

Nitric Oxide modulates bacterial biofilm formation

2012-05-01T21:57:00.001+05:30

Scripps Research Institutes Scientists Solve a Mystery of Bacterial Growth and Resistance
Findings Shed Light on How Bacteria Form Protective Biofilms

LA JOLLA, CA, April 26,2012:-
Scientists at The Scripps Research Institute have unraveled a complex chemical pathway that enables bacteria to form clusters called biofilms. Such improved understanding might eventually aid the development of new treatments targeting biofilms, which are involved in a wide variety of human infections and help bacteria resist antibiotics.

The report, published online ahead of print on April 26,2012, by the journal Molecular Cell, explains how nitric oxide, a signaling molecule involved in the immue system, leads to biofilm formation.

"It is estimated that about 80 percent of human pathogens form biofilms during some part of their life cycle," said Scripps Research President and CEO Michael Marletta, PhD, who lead the work. "In this study, we have detailed for the first time the signaling pathway from nitric oxide to the sensor through cellular regulators and on to the biological output, biofilm formation."

"There's a lot of interest right now in finding ways to influence biofilm formation in bacteria", said lead author Lars Plate, a graduate student in Marletta's team, which recently moved to Scripps Research from the University of California, Berkeley. "Figuring out the signaling pathway is a prerequisite for that."

Dangerous Get Togethers

Biofilm formation is a critical phenomenon that occurs when bacterial cells adhere to each other and to surfaces, at times as part of their growth stage and at other time to gird against attack. In such aggregations, cells on the outside of a biofilm might still be susceptible to natural or pharmaceutical antibiotics, but the interior cells are relatively protected. This can make them difficult to kill using conventional treatments.

Biofilms can form on surgical instruments such as heart valves or catheters, leading to potentially deadly infections. Likewise, difficult-to-eliminate biofilms also play key roles in a host of conditions from gum disease to cholera, and from cystic fibrosis to Legionnaires disease.

For years, the Marletta lab and other groups have been studying how nitric oxide regulates everything from blood vessel dilation to nerve signals in humans and other vertebrates. Past research had also revealed that nitric oxide is involved in influencing bacterial biofilm formation.

Nitric oxide in sufficient quantity is toxic to bacteria, so it's logical that nitric oxide would trigger bacteria to enter the safety huddle of a biofilm. But nobody knew precisely how.

In the new study, the scientists set out to find what happens after the nitric oxide trigger is pulled. "The whole project was really a detective story in a way," said Plate.

The Detective Story

In vertebrates, nitric oxide can bind to something called the Heme-Nitric Oxide/Oxygen(H-NOX) binding domain on a specific enzyme, activating that enzyme and beginning the chemical cascades that lead to physiological functions such as blood vessel dilation.

Many bacteria also have H-NOX domains, including key pathogens, so this seemed the best starting point for the investigation. From there, the team turned to genomic data.

Genes for proteins that interact are often found adjacent to one another. Based on this fact, the researchers were able to infer a connection between the bacterial H-NOX domain and an enzyme called Histidine Kinase, which transfer phosphate chemical groups to other molecules in signaling pathways. The question was where the phosphate were going.

To learn more, the researchers used a technique called Phosphotrasfer profiling. This involved activating the histidine kinase and then allowing them to react separately with about 20 potential tragets. Those targets that the histidine kinase rapidly transferred phosphates to had to be part of the signaling pathway. "It's a neat method that we used to get an answer that was in fact very surprising," said Plate.

The experiments revealed that the histidine kinase phosphorylated three proteins called response regulators that work together to control biofilm formation for the project a primary study species, the bacterium Shewanells oneidensis, which is found in lake sediments.

Further work showed that each regulator plays a complementary role, making for an unusually complex system. One regulator activates gene expression, another controls the activity of an enzyme producing cyclic di guanosine monophosphate, an important bacterial messenger molecule that is critical in biofilm formation, and the third tunes the degree of activity of the second.

Divide and Conquer

Since other bacterial species use the same chemical pathway uncovered in this study, the finidings pave the way to further explore the potential for pharmaceutical application. As one example, researchers might be able to block biofilm formation with chemicals that interrupt the activity of one of the components of this nitric oxide cascade.

Marletta's group has already explored nitric oxide's role in controlling Legionnaires disease and, among other goals, will focus now on understanding biofilm formation in the bacterium that causes cholera.

The work for the paper, " Nitric Oxide modulates bacterial biofilm formation through a multi-component cyclic-di-GMP signaling network," was supported by the National Institutes of Health and a Chang-Lin Tien Graduate Fellowship in the Environmental Sciences.

press@scripps.edu

Effectively tipping the balance in favour of the Mycobacterium surviving in the cell.

2012-04-05T21:18:00.001+05:30

Autophagy: when ‘self-eating’ is good for you

Broken pieces of internal structures, damaged organelles and harmful clumps of proteins are all examples of the molecular detritus that builds up continuously in our cells. Fortunately, we are equipped with an intracellular process called autophagy (literally ‘self-eating’) that gathers up the debris, wraps it in a double membrane and delivers it to an intracellular sac called the lysosome. Here, the material is ingested, digested and recycled, ready to be used again.
Recent work has suggested that autophagy may also be important in killing intracellular bacteria that are able to escape the normal processes that control infection within cells. Autophagy appears to be critical in controlling infections of Mycobacterium tuberculosis (MTB) and related species called non-tuberculous mycobacteria (NTM), which are able to block degradation by lysosomes and thereby replicate within cells.
Researchers working at the University’s Cambridge Institute for Medical Research (CIMR) and Papworth Hospital have noticed that patients with chronic lung diseases such as cystic fibrosis (CF) are becoming increasingly infected with a highly pathogenic, multi-drug-resistant (MDR) NTM called Mycobacterium abscessus. Their research, published recently in the Journal of Clinical Investigation, suggests that M. abscessus infection may be linked to long-term use of azithromycin, an antibiotic with anti-inflammatory properties. They propose that azithromycin blocks autophagy in a type of white blood cell called the macrophage, effectively tipping the balance in favour of the Mycobacterium surviving in the cell.
It’s an ominous outcome for patients, as lead researcher Dr Andres Floto explained: “Developing an infection with Mycobacterium abscessus is a big deal for patients with CF. It’s resistant to virtually all antibiotics, is very hard to treat, can accelerate lung damage and may rule out future lung transplantation. While the benefits of long-term azithromycin therapy in CF are clear, our data suggest that there may also be a downside to watch out for.”
He added: “Recent studies showing the benefit of azithromycin therapy in asthma and smoking-related chronic obstructive pulmonary disease (COPD) will no doubt increase the numbers of patients on long- term azithromycin therapy. Physicians will need to be aware of the potential for harm with this treatment, and carefully monitor patients for mycobacterial disease”.

‘Forced stoppage’ of the cleaning crew

Floto is a Wellcome Trust Senior Clinical Fellow in the Department of Medicine and Principal Investigator in the CIMR. He is also Director of Research at the Cambridge Centre for Lung Infection at Papworth Hospital. The Centre cares for over 260 adults with CF and almost 2,000 patients with recurrent or difficult lung infections.
“We’d been struck by the rising rates of M. abscessus infection in CF patients in centres around the world and wondered whether it could be connected to an increased use of long-term azithromycin,” explained Floto. “Azithromycin is a broad-spectrum antibiotic which paradoxically is used to treat some mycobacterial infections. In patients with CF and, more recently, other inflammatory lung diseases such as asthma and COPD, it’s being prescribed as a long-term anti-inflammatory therapy.”
The association between azithromycin use and M. abscessus infection was first suggested when Floto and colleagues carried out an epidemiological study of adult patients with CF at Papworth Hospital and found that those patients with NTM infection were much more likely to be taking long-term azithromycin. When they looked at cells in culture, they discovered that the antibiotic impaired autophagy, effectively causing a ‘forced stoppage’ of the waste-recycling unit and preventing cells from clearing infecting mycobacteria. Moreover, azithromycin had a profound effect on M. abscessus infection of a mouse model; whereas untreated mice were able to clear the infection rapidly, those given the drug developed persistent lung infection.

Exploiting autophagy

The interactions of mycobacteria with immune cells are extremely complex and poorly understood. In a paper published in 2006 in Science, Floto together with Professor Paul Lehner at the CIMR began to define how immune cells respond to specific proteins from mycobacteria which then control the immune response. Subsequent work has suggested that the ability of macrophages to kill mycobacteria can be enhanced through a number of pathways, including autophagy.
Working with Professor David Rubinsztein at the CIMR, who has been interested in enhancing autophagy to clear the build-up of damaging clumps of proteins in neurodegenerative diseases, Floto has begun to study whether autophagy might be exploited therapeutically to treat multi-drug- resistant tuberculosis (MDR-TB), for which there is an urgent need to find new treatments. In 2008, the World Health Organization estimated that of the 9.4 million new TB cases 440,000 were MDR-TB. “It’s a massive challenge”, explained Floto, “We believe that stimulating autophagy to kill TB will bypass the problem of multi-drug resistance and may lead to potential new treatments for MDR-TB.”
Meanwhile, Floto’s work on azithromycin has already begun to influence clinical practice in a number of major CF centres in the UK. Although at pains to stress that a larger, prospective multi-centre study is needed before universal guidance can be given for the management of patients on chronic azithromycin therapy, Floto explained how the Cambridge Centre for Lung Infection has adopted a policy that is already proving successful: “We give patients who are not doing as well as we’d expect a holiday off the medication for a month while we screen carefully for NTM. When we do this, we often find a mycobacterial infection brewing in the lungs and can treat it immediately, instead of allowing the infection to take hold covertly without being detected.”
Floto’s research exemplifies the importance of a seamless link between fundamental research and clinical translation, and will benefit still further from the planned move of Papworth Hospital to the Cambridge Biomedical Campus . “Papworth has a unique group of patients and an international reputation for the treatment of patients with difficult lung infections,” he explained. “Forging greater links between Papworth and the University will inevitably promote research into a number of clinically important areas and smooth the route from bench to bedside, and back again.”

http://www.cam.ac.uk/research/features/autophagy-when-self-eating-is-good-for-you/?source=researchnews

In New Way to Edit DNA, Hope for Treating Disease

2012-03-10T16:54:00.001+05:30

Only one man seems to have ever been cured of AIDS, a patient who also had leukemia. To treat the leukemia, he received a bone marrow transplant in Berlin from a donor who, as luck would have it, was naturally immune to the AIDS virus.
If that natural mutation could be mimicked in human blood cells, patients could be endowed with immunity to the deadly virus. But there is no effective way of making precise alterations in human DNA.
That may be about to change, if a powerful new technique for editing the genetic text proves to be safe and effective. At the University of Pennsylvania, Dr. Carl June and colleagues have used the technique to disrupt a gene in patients’ T cells, the type attacked by the AIDS virus. They have then infused those cells back into the body. A clinical trial is now under way to see if the treated cells will reconstitute a patient’s immune system and defeat the virus.
The technique, which depends on natural agents called zinc fingers, may revive the lagging fortunes of gene therapy because it overcomes the inability to insert new genes at a chosen site. Other researchers plan to use the zinc finger technique to provide genetic treatments for diseases like bubble-boy disease, hemophilia and sickle-cell anemia.

In principle, the zinc finger approach should work on almost any site on any chromosome of any plant or animal. If so, it would provide a general method for generating new crop plants, treating many human diseases, and even making inheritable changes in human sperm or eggs, should such interventions ever be regarded as ethically justifiable.

Zinc fingers are essential components of proteins used by living cells to turn genes on and off. Their name derives from the atom of zinc that holds two loops of protein together to form a “finger.” Because the fingers recognize specific sequences of DNA, they guide the control proteins to the exact site where their target gene begins.

After many years of development, biologists have learned how to modify nature’s DNA recognition system into a general system for manipulating genes. Each natural zinc finger recognizes a set of three letters, or bases, on the DNA molecule. By stringing three or four fingers together, researchers can generate artificial proteins that match a particular site.

The new system has been developed by a small biotech company, Sangamo BioSciences of Richmond, Calif., and, to some degree separately, by academic researchers who belong to the Zinc Finger Consortium.

Sangamo was founded in 1995 by Edward O. Lanphier II, a former executive with a gene therapy company. Reading an article by Aaron Klug, the British crystallographer who discovered the zinc finger design, he saw the technique’s potential for genetic manipulation. He bought a company Dr. Klug had founded and worked with him and researchers like Carl O. Pabo to improve the technique and develop combinations of zinc fingers to match any sequence of DNA letters.

“We now have a full alphabet of zinc fingers,” Mr. Lanphier said, “but when we started the company it was like typing a novel with two fingers.”

Zinc finger proteins have many potential uses. One is to link them to agents that turn on or turn off the gene at the site recognized by the fingers.

More powerfully, the zinc fingers can be deployed as a word processing system for cutting and pasting genetic text. Two sets of zinc fingers are attached to a protein that cuts the DNA in between the two sites matched by the fingers. The cell quickly repairs the break but sometimes in a way that disrupts the gene. This is the approach used in destroying the gene for the receptor used by the AIDS virus to gain entry to white blood cells.

Or, if DNA for a new gene is inserted into a cell at the same time as the zinc fingers that scissor the DNA, the new gene will be incorporated by the cell’s repair system into the DNA at the break site. Most gene therapy techniques use a virus to carry new genes into a cell but cannot direct the virus to insert genes at a specific site.

“I think it’s a broadly applicable technology which has already allowed experiments that would not have been possible before,” said J. Keith Joung, a biologist who designs zinc finger proteins at the Massachusetts General Hospital.

Daniel F. Voytas, a plant geneticist at the University of Minnesota, said the zinc finger technique would allow breeders to change the oil composition of any plant, the types of carbohydrates produced or the way carbon dioxide is captured. “We can go in and make any change we want to any plant species,” Dr. Voytas said.

Zinc fingers can also be used for “trait stacking,” the positioning of several beneficial genes at a single site. This avoids heavy regulatory costs because genetically altered plants must be tested for safety for each site that is modified.

The zinc finger technology has taken many years to prepare because of the difficulty of designing the fingers and also of preventing them from cutting the genome in the wrong places. Only a handful of laboratories are currently using the technique, but proponents expect to see rapid growth.

The Zinc Finger Consortium, founded by Dr. Joung and Dr. Voytas, makes the method available free, and researchers need only pay for materials. But there are some 200 steps in Dr. Joung’s recipe for making zinc fingers, and it takes time and dedication to do them all correctly.

The alternative is to buy zinc fingers. Sangamo has a commanding patent position and has licensed Sigma-Aldrich, a large life science company in St. Louis, to make zinc finger proteins for researchers. Sigma-Aldrich’s charge for a zinc finger protein that cuts the genome at the site of your choice is $39,000, with a discount for academic researchers. Zinc fingers that cut well-known human genes cost $12,000. Sigma-Aldrich has used the technology to generate rats with genetic defects that mimic human disease. A schizophrenic rat can be had for $100.

David Smoller, president of Sigma-Aldrich’s biotechnology unit, licensed the technology from Sangamo in 2006 when he felt the company had proved it worked. “This technology is just amazing,” Dr. Smoller said. “It’s a game changer.”

Sangamo has licensed the use of zinc fingers to Dow Agrosciences for creating new crop plants, and has reserved medical uses for itself. It has four Phase 2 clinical trials in progress, including treatments for diabetic neuropathy and amyotrophic lateral sclerosis.

In an ambitious effort to cure AIDS, Sangamo and the University of Pennsylvania started a clinical trial in February.

The AIDS virus enters the T cells of the immune system by latching on to a receptor called CCR5, but about 10 percent of Europeans have a mutation that disables the CCR5 gene. People who inherit two disabled copies of the gene do not have CCR5 on the surface of their T cells, so the AIDS virus has nothing to grab. These people are highly resistant to H.I.V.

In the zinc finger approach, the patient’s T cells are removed, and zinc finger scissors are used to disable the CCR5 gene. The treated cells are allowed to multiply, then reinjected into the patient. In experiments with mice, the treated cells turned out to have a strong natural advantage over the untreated ones, since those are under constant attack by the AIDS virus.

Whether or not zinc fingers will make gene therapy practical remains to be seen. “It’s a little too early to know since clinical trials are in their early stages,” said Dr. Katherine A. High, a hemophilia expert at the University of Pennsylvania.

Dr. Matthew H. Porteus, a pediatric geneticist at the University of Texas, said, “I think it has the potential to solve a lot of the problems that have plagued the gene therapy field.” But Dr. Porteus noted that even the most carefully designed zinc fingers seemed to do some snipping away from their target site, a potentially serious safety problem.

Zinc fingers could be the gift that stem cell researchers have been waiting for. Stem cells taken from a patient may need to be genetically corrected before use, but until now there had been no way of doing so.

Dr. Rudolf Jaenisch, a stem cell expert at the Whitehead Institute in Cambridge, Mass., reported in August that he had successfully singled out three genes in induced embryonic stem cells with the help of zinc finger scissors designed by Sangamo. “This is a really important tool for human embryonic stem cells,” Dr. Jaenisch said. The technology has not yet reached perfection. Some of the zinc fingers Sangamo provided “worked beautifully,” he said, but some did not.

Zinc fingers may also make technically possible a morally fraught procedure that has been merely a theoretical possibility — the alteration of the human germ line, meaning the egg or sperm cells. Genetic changes made in current gene therapy are to body cells, and they would die with the individual. But changes made to the germ line would be inherited. Many ethicists and others say this is a bridge that should not be crossed, since altering the germ line, even if justifiable for medical reasons, would lower the barrier to other kinds of change.

Several scientists were reluctant to discuss the issue, or dismissed it by saying that even zinc fingers did not meet the error-free standards that would be required for germ-line engineering. But zinc finger scissors are so efficient that only 5 to 10 embryos need be treated to get one with the desired result. This could make it practical to alter the germ line.

Since the germ lines of rats and zebra fish have already been altered with zinc finger scissors, “in principle there is no reason why a similar strategy could not be used to modify the human germ line,” Dr. Porteus said. The kind of disease that might be better treated in the germ line, if ethically acceptable, is cystic fibrosis, which affects many different tissues.
The disease could be corrected in unfertilized eggs, using the zinc finger technique, Dr. Porteus said. But he added, “I don’t think our society is ready for someone to propose this.”

http://www.nytimes.com/2009/12/29/health/research/29zinc.html?nl=health&emc=healthupdateema1&pagewanted=all

Protein not sugar stimulates cells keeping us thin and awake, new study suggests.

2012-02-09T20:35:00.000+05:30

A new study has found that protein and not sugar activates the cells responsible for keeping us awake and burning calories. The research, published today in the 17 November issue of the scientific journal Neuron, has implications for understanding obesity and sleep disorders.

Wakefulness and energy expenditure rely on “orexin cells”, which secrete a stimulant called orexin/hypocretin in the brain. Reduced activity in these unique cells results in narcolepsy and has been linked to weight gain.

Scientists at the University of Cambridge compared actions of different nutrients on orexin cells. They found that amino acids – nutrients found in proteins such as egg whites – stimulate orexin neurons much more than other nutrients.

“Sleep patterns, health, and body weight are intertwined. Shift work, as well as poor diet, can lead to obesity,” said lead researcher Dr Denis Burdakov of the Department of Pharmacology and Institute of Metabolic Science. “Electrical impulses emitted by orexin cells stimulate wakefulness and tell the body to burn calories. We wondered whether dietary nutrients alter those impulses.”

To explore this, the scientists highlighted the orexin cells (which are scarce and difficult to find) with genetically targeted fluorescence in mouse brains. They then introduced different nutrients, such as amino acid mixtures similar to egg whites, while tracking orexin cell impulses.

They discovered that amino acids stimulate orexin cells. Previous work by the group found that glucose blocks orexin cells (which was cited as a reason for after-meal sleepiness), and so the researchers also looked at interactions between sugar and protein. They found that amino acids stop glucose from blocking orexin cells (in other words, protein negated the effects of sugar on the cells).

These findings may shed light on previously unexplained observations showing that protein meals can make people feel less calm and more alert than carbohydrate meals.

“What is exciting is to have a rational way to ‘tune’ select brain cells to be more or less active by deciding what food to eat,” Dr Burdakov said. “Not all brain cells are simply turned on by all nutrients, dietary composition is critical.

“To combat obesity and insomnia in today’s society, we need more information on how diet affects sleep and appetite cells. For now, research suggests that if you have a choice between jam on toast, or egg whites on toast, go for the latter! Even though the two may contain the same number of calories, having a bit of protein will tell the body to burn more calories out of those consumed.”

http://www.cam.ac.uk/research/news/3pm-slump-why-a-sugar-rush-may-not-be-the-answer/#

A Doctor in Your Pocket

2012-01-19T18:41:00.000+05:30

What does the future of medicine hold? Tiny health monitors, tailored therapies—and the end of illness

Take a moment to imagine what it would be like to live robustly to the ripe old age of 100 or more. You wouldn't die of any particular illness, and you wouldn't gradually waste away under the spell of some awful, enfeebling disease that began years or decades earlier.

It may sound far-fetched, but it is possible to live a long, disease-free life. Most of the conditions that kill us, including cancer and heart disease, could be prevented or delayed by a new way of looking at and treating health. The end of illness is near.

Today, we mostly wait for the body to break before we treat it. When I picture what it will be like for my two children to stay in good health as independent adults in 10 or 20 years, I see a big shift from our current model.

I see them being able to monitor and adjust their health in real time with the help of smartphones, wearable gadgets—perhaps like small, invisible stickers—to track the inner workings of their cells, and virtual replicas of their bodies that they will play much like videogames, allowing them to know exactly what they can do to optimize every aspect of their health. What happens when I take drug x at dosage y? How can I change the expression of my genes to stop cancer? Would eating more salmon and dark chocolate boost my metabolism and burn fat? Can red wine really lower my risk of heart attack?

From a drop of their blood, they will be able to upload information onto a personal biochip that can help to create an individualized plan of action, including both preventive measures and therapies for identified ailments or signs of "unhealthiness." (Other body fluids—like tears and saliva—might be routinely tested, too.) They would be on the lookout for problems like imbalances in blood-sugar control, a risk factor for diabetes, and uncontrolled cell growth, which could signal cancer. Their doctors won't just examine them once a year; they will continually monitor the next generation of patients, offering advice along the way.

What is equally exciting is that this patient data will be added to a universal database that can be aggregated by powerful search engines like Google and constantly fed into new trials and experiments—speeding up our understanding of which drugs work best for which people. The database might show, for example, that people with a particular genetic profile respond to one type of cancer treatment but not another. As more people anonymously add their health data, this database would become more and more effective as a tool for preventive medicine.

Today, most people who are concerned about their health follow sweeping, general guidelines. If you want to lose weight, you are likely to pick a diet that advises eating more fibrous vegetables and cutting back on processed sugar. If you want to reduce your risk for cancer, you avoid tobacco smoke, exercise regularly and take early detection seriously.

The problem with health care today is that we don't know enough about the body to practice preventive medicine actively. With limited knowledge, diagnostic medicine makes sense. If we don't know what we're trying to prevent or how best to do it, we have to wait for an obvious symptom to emerge in order to take action. At that point, we're usually treating a disease that has had ample opportunity to progress.

We can do better. To start, we need to appreciate the body for what it is: a very complex network, much of which we don't yet fully understand. When you look at the body from this systemic point of view, you begin to see that a lot of what we know about health is gravely misunderstood.

In 2009, my colleague Danny Hillis—a former Disney engineer who pioneered the development of so-called parallel supercomputers—and I set up a way to measure 100,000 different types of proteins from a single drop of blood. The goal is to evaluate and make sense of the body's intricate inner workings in a way that's much more dynamic and insightful than what DNA alone can provide. Proteins change in your body every minute, depending on what's going on internally. Our ultimate plan is to develop tests, based on protein levels, for illnesses like cancer. Such tests could take the place of invasive techniques like biopsies.

With each passing year, the technology necessary for this revolution in medicine is growing less expensive. Last week, Life Technologies of Carlsbad, Calif., announced that it will be able to map an individual's entire genetic sequence in one day, for $1,000. Similar tests today cost many thousands of dollars. The ability to follow day-to-day changes in your body's proteins and metabolites is not far behind.

So how do we get to this future?

It has to start with data collection. In 2004, Dell launched a company program called Well at Dell to encourage healthy lifestyles. Employees receive alerts and information customized to their health issues, incorporating their latest test results and treatments and allowing them to make more informed decisions. A newly diagnosed diabetic, for example, might get information about how to monitor blood sugar and watch out for the circulatory problems that often accompany the disease.

Not surprisingly, these corporate health-management tools have come under fire, with most critics worrying about privacy. But we can't expect the health-care industry to continue to innovate and grow if we continue to hoard health information.

The federal agency that administers Medicare pays over half of the medical bills in the U.S., but it doesn't retrieve, organize or mine that data. Imagine how much better the Medicare system could be if all this data were analyzed to improve public health. Or imagine databases from many different sources, private and public, coming together in a centralized network that would look for patterns and try to translate them into new ideas for anticipating and preventing health problems.

Personalized medicine isn't as far away as you might think. Consider what's already happening in genetic profiling for individuals, which is available today for several hundred dollars. I co-founded a genetic screening company and am a big proponent of the technology. It allows us to take a broad look at DNA variations and to assess your risk for certain ailments and what medications, at what dosages, might work best, based on your metabolism. Just because you have one or two markers of genetic risk does not mean that you will definitely develop a particular condition, but the outcome can be affected by changes in lifestyle, or in some cases, by taking medication.

As these and other technologies advance, it will become progressively easier to monitor and maintain our overall health. Then it will be up to us. The promise of personalized medicine depends, finally, not on the tools that become available but on our determination to be informed and willing patients.

http://online.wsj.com/article/SB10001424052970204124204577155162382326848.html?mod=djemWMPIndia_h

A Gut Check for Many Ailments

2012-01-19T17:42:00.000+05:30

What you think is going on in your head may be caused in part by what's happening in your gut.

A growing body of research shows the gut affects bodily functions far beyond digestion. Studies have shown intriguing links from the gut's health to bone formation, learning and memory and even conditions including Parkinson's disease. Recent research found disruptions to the stomach or intestinal bacteria can prompt depression and anxiety—at least in lab rats.

Better understanding the communication between the gut and the brain could help reveal the causes of and treatments for a range of ailments, and provide diagnostic clues for doctors.

"The gut is important in medical research, not just for problems pertaining to the digestive system but also problems pertaining to the rest of the body," says Pankaj J. Pasricha, chief of the division of gastroenterology and hepatology at Stanford University School of Medicine.

The gut—considered as a single digestive organ that includes the esophagus, stomach and intestines—has its own nervous system that allows it to operate independently from the brain.

This enteric nervous system is known among researchers as the "gut brain." It controls organs including the pancreas and gall bladder via nerve connections. Hormones and neurotransmitters generated in the gut interact with organs such as the lungs and heart.

Like the brain and spinal cord, the gut is filled with nerve cells. The small intestine alone has 100 million neurons, roughly equal to the amount found in the spinal cord, says Michael Gershon, a professor at Columbia University.

The vagus nerve, which stretches down from the brainstem, is the main conduit between the brain and gut. But the gut doesn't just take orders from the brain.

"The brain is a CEO that doesn't like to micromanage," says Dr. Gershon. The brain receives much more information from the gut than it sends down, he adds.

Many people with psychiatric and brain conditions also report gastrointestinal issues. New research indicates problems in the gut may cause problems in the brain, just as a mental ailment, such as anxiety, can upset the stomach.

Stanford's Dr. Pasricha and colleagues examined this question in the lab by irritating the stomachs of newborn rats. By the time the animals were eight to 10 weeks old, the physical disturbance had healed, but these animals displayed more depressed and anxious behaviors, such as giving up more quickly in a swimming task, than rats whose stomachs weren't irritated.

Compared to controls, the rats also showed increased sensitivity to stress and produced more of a stress hormone, in a study published in May in a Public Library of Science journal, PLoS One.

Other work, such as that of researchers from McMaster University in Hamilton, Ontario, demonstrated that bacteria in the gut—known as gut flora—play a role in how the body responds to stress. The exact mechanism is unknown, but certain bacteria are thought to facilitate important interactions between the gut and the brain.

Electrically stimulating the vagus nerve has been shown to reduce the symptoms of epilepsy and depression. (One treatment approved by the Food and Drug Administration, made by Cyberonics Inc., is already on the market.)

Exactly why such stimulation works isn't known, experts say, but a similar procedure has been shown in animal studies to help improve learning and memory.

Earlier this month, researchers made a small step toward understanding a gastrointestinal ailment that typically affects children with autism.

In a study of 23 autistic children and nine typically developing kids, a bacterium unique to the intestines of those with autism called Sutterella was discovered.

The results, published online in the journal mBio by researchers at Columbia's school of public health, need to be studied further, but suggest Sutterella may be important in understanding the link between autism and digestive ailments, the authors wrote.

Dr. Gershon, professor of pathology and cell biology at Columbia, has been studying how the gut controls its behavior and that of other organs by investigating the neurotransmitter serotonin.

Low serotonin levels in the brain are known to affect mood and sleep. Several common antidepressants work by raising levels of serotonin in the brain.

Yet about 95% of the serotonin in the body is made in the gut, not in the brain, says Dr. Gershon. Serotonin and other neurotransmitters produced by gut neurons help the digestive track push food through the gut.

Work by Dr. Gershon and others has shown that serotonin is necessary for the repair of cells in the liver and lungs, and plays a role in normal heart development and bone-mass accumulation.

Studying the neurons in the gut also may also help shed light on Parkinson's disease. Some of the damage the disease causes to brain neurons that make the neurotransmitter dopamine also occur in the gut neurons, researchers say.

Researchers are now studying whether gut neurons, which can be sampled through a routine colonoscopy, may help clinicians diagnose and track the disease without invasive brain biopsies, says Pascal Derkinderen, a professor of neurology at Inserm, France's national institute of health.

http://online.wsj.com/article/SB10001424052970204468004577164732944974356.html?mod=djemWMPAsia_h

Omelets: The Ultimate Fast Food

2012-01-18T18:33:00.004+05:30

For some time now the medical literature has been countering the myth that the cholesterol in eggs goes straight to the arteries and that eggs should be shunned by anybody committed to healthy eating. Studies have shown that only a small amount of dietary cholesterol passes into the blood and that saturated fats and trans fats have much bigger effects on cholesterol levels. In fact, according to the Harvard School of Public Health, the only large study that looked at the effect of egg consumption on heart disease found no correlation between the two, except among people with diabetes, who were a bit more likely to develop heart disease if they ate an egg a day.

That’s great news, because eggs are an excellent and delicious source of nutrients, rated by some nutritionists as the gold standard for protein, as one egg has only 75 calories but 7 grams of protein. They are also a great source of the carotenoids lutein and zeaxanthin, which have been associated with protection against vision loss.

It’s also great news because eggs cook quickly. Make an omelet if you need a quick, utterly satisfying meal. Omelets are my response to people who tell me that they’d like to eat a healthier diet but that it’s too time-consuming. In addition to the fillings in this week’s recipes, think of using up leftovers or little hunks of cheese that are lingering in your refrigerator, or search through your pantry for something that looks delicious.

Beet Green and Feta Omelet

At this time of year I don’t let a week go by without buying beets at the farmers’ market. I cook up the greens when I get home so that I can make meals like this one in minutes.

For each omelet:

1/3 cup chopped blanched or steamed beet greens (about 1 ounce; see below)

1 garlic clove, minced

1/2 teaspoon red wine vinegar or sherry vinegar

Salt and freshly ground pepper

2 eggs

2 to 3 teaspoons low-fat milk

2 teaspoons extra virgin olive oil

1/2 ounce feta cheese, crumbled

1. In a bowl, toss the chopped blanched beet greens with the garlic, vinegar and salt and pepper to taste.

2. Break the eggs into another bowl and beat with a fork or a whisk until eggs are frothy. Whisk in salt and pepper to taste and 2 to 3 teaspoons milk.

3. Heat an 8-inch nonstick omelet pan over medium-high heat. Add 2 teaspoons olive oil. Hold your hand an inch or two above the pan, and when it feels hot, pour the eggs into the middle of the pan, scraping every last bit into the pan with a rubber spatula. Swirl the pan to distribute the eggs evenly over the surface. Shake the pan gently, tilting it slightly with one hand while lifting up the edges of the omelet with the spatula in your other hand, to let the eggs run underneath during the first minute or two of cooking.

4. As soon as the eggs are set on the bottom, sprinkle the beet greens over the middle of the egg “pancake” and top with the feta. Next, jerk the pan quickly away from you then back toward you so that the omelet folds over onto itself. If you don’t like your omelet runny in the middle (I do), jerk the pan again so that the omelet folds over once more. Cook for a minute or two longer. Tilt the pan and roll the omelet out onto a plate.

Another way to make a 2-egg omelet is to flip it over before adding the filling. Do this with the same motion, jerking the pan quickly away from you and then back toward you, but lift your hand slightly as you begin to jerk the pan back toward you. The omelet will flip over onto the other side, like a pancake. Place the filling in the middle. Use your spatula to fold one side over, then the other side, and roll the omelet out of the pan.

To blanch beet greens: Bring a pot of water to a boil while you wash and stem the beet greens. Rinse in 2 changes of water to rid the leaves of sand. When the water comes to a boil, salt generously and add the greens. Blanch for 1 to 2 minutes, until just tender, and transfer to a bowl of cold water. Drain, squeeze out excess water, and chop. To steam the greens, place them in a steamer basket above 1 inch of boiling water. Cover and steam for 2 minutes or until wilted. Rinse and squeeze out excess water.

Yield: Serves 1

Advance preparation: The blanched beet greens will keep for 4 to 5 days in a covered bowl in the refrigerator.

Nutritional information per serving: 275 calories; 7 grams saturated fat; 3 grams polyunsaturated fat; 11 grams monounsaturated fat; 385 milligrams cholesterol; 4 grams carbohydrates; 1 gram dietary fiber; 369 milligrams sodium (does not include salt to taste); 16 grams protein.

http://www.nytimes.com/2012/01/16/health/nutrition/omelets-the-ultimate-fast-food-recipes-for-health.html?src=me&ref=general

It Could Be Old Age, or It Could Be Low B12

2012-01-18T18:32:00.001+05:30

Ilsa Katz was 85 when her daughter, Vivian Atkins, first noticed that her mother was becoming increasingly confused.

“She couldn’t remember names, where she’d been or what she’d done that day,” Ms. Atkins recalled in an interview. “Initially, I was not too worried. I thought it was part of normal aging. But over time, the confusion and memory problems became more severe and more frequent.”

Her mother couldn’t remember the names of close relatives or what day it was. She thought she was going to work or needed to go downtown, which she never did. And she was often agitated.

A workup at a memory clinic resulted in a diagnosis of early Alzheimer’s disease, and Ms. Katz was prescribed Aricept, which Ms. Atkins said seemed to make matters worse. But the clinic also tested Ms. Katz’s blood level of vitamin B12. It was well below normal, and her doctor thought that could be contributing to her symptoms.

Weekly B12 injections were begun. “Soon afterward, she became less agitated, less confused and her memory was much better,” said Ms. Atkins. “I felt I had my mother back, and she feels a lot better, too.”

Now 87, Ms. Katz still lives alone in Manhattan and feels well enough to refuse outside assistance.

Still, her daughter wondered, “Why aren’t B12 levels checked routinely, particularly in older people?”

It is an important question. As we age, our ability to absorb B12 from food declines, and often so does our consumption of foods rich in this vitamin. A B12 deficiency can creep up without warning and cause a host of confusing symptoms that are likely to be misdiagnosed or ascribed to aging.

A Vital Nutrient

B12 is an essential vitamin with roles throughout the body. It is needed for the development and maintenance of a healthy nervous system, the production of DNA and formation of red blood cells.

A severe B12 deficiency results in anemia, which can be picked up by an ordinary blood test. But the less dramatic symptoms of a B12 deficiency may include muscle weakness, fatigue, shakiness, unsteady gait, incontinence, low blood pressure, depression and other mood disorders, and cognitive problems like poor memory.

Labs differ in what they consider normal, but most authorities say a deficiency occurs when B12 levels in adults fall below 250 picograms per milliliter of blood serum. Like all Bvitamins, B12 is water-soluble, but the body stores extra B12 in the liver and other tissues. Even if dietary sources are inadequate for some time, a serum deficiency may not show up for years.

If the amount of B12 in storage is low to begin with, a deficiency can develop within a year, even more quickly in infants.

Recommended dietary amounts of B12 vary: 2.4 micrograms daily for those age 14 and older, 2.6 micrograms for pregnant women and 2.8 micrograms for nursing women. Barring circumstances that impair B12 absorption, these are levels easily obtained from awell-balanced diet containing animal protein.

In its natural form, B12 is present in significant amounts only in animal foods, most prominently in liver (83 micrograms in a 3.5-ounce serving). Good food sources include other red meats, turkey, fish and shellfish. Lesser amounts of the vitamin are present in dairy products, eggs and chicken.

Those at Risk

Natural plant sources are meager at best in B12, and the vitamin is poorly absorbed from them. Many strict vegetarians and all vegans, as well as infants they breast-feed, must consume supplements or fortified breakfast cereals to get adequate amounts.

Certain organisms, like the bacterium Spirulina and some algae, contain a pseudo-B12 that the body cannot use but may result in a false reading of a normal B12 level on a blood test. Despite claims to the contrary, laver, a seaweed, and barley grass are not reliable sources of B12.

In animal foods, B12 is combined with protein and must be released by stomach acid and an enzyme to be absorbed. Thus, chronic users of acid-suppressing drugs like Prilosec, Prevacid and Nexium, as well as ulcer medications like Pepcid and Tagamet, are at risk of developing a B12 deficiency and often require a daily B12 supplement.

Stomach acid levels decline with age. As many as 30 percent of older people may lack sufficient stomach acid to absorb adequate amounts of B12 from natural sources. Therefore, regular consumption of fortified foods or supplementation with 25 to 100 micrograms of B12 daily is recommended for people over 50.

Synthetic B12, found in supplements and fortified foods, does not depend on stomach acid to be absorbed. But whether natural or synthetic, only some of the B12 consumed gets into the body. Treatment to correct a B12 deficiency typically involves much larger doses than the body actually requires.

Free B12 from both natural and synthetic sources must be combined with a substance in the stomach called intrinsic factor to be absorbed through the gut. This factor is lacking in people with an autoimmune disorder called pernicious anemia; the resulting vitamin deficiency is commonly treated with injections of B12.

Although most doctors are quick to recommend injections to correct a B12 deficiency, considerable evidence indicates that, in large enough doses, sublingual (under-the-tongue) tablets or skin patches of B12 may work as well as injections for people with absorption problems, even for those with pernicious anemia.

Most often, a daily supplement of 2,000 micrograms is recommended for about a month, then lowered to 1,000 micrograms daily for another month, then lowered again to 1,000 micrograms weekly. Sublingual B12 or B12 patches, or even B12 lollipops, can be helpful for people who require a supplement but cannot swallow pills.

Others at risk of developing a B12 deficiency include heavy drinkers (alcohol diminishes B12 absorption), those who have had stomach surgery for weight loss or ulcers, and people who take aminosalicylic acid (for inflammatory bowel disease or tuberculosis) or thediabetes drug metformin (sold as Glucophage and other brands). Patients who take the anticonvulsants phenytoin, phenobarbital or primidone are also at risk.

Large doses of folic acid can mask a B12 deficiency and cause permanent neurological damage if normal levels of B12 are not maintained. Supplements of potassium impair B12 absorption in some people.

Although a B12 deficiency can raise blood levels of the amino acid homocysteine, a risk factor for heart disease and stroke, supplements of B12 have not reduced cardiovascular risk.

And while high homocysteine levels are linked to Alzheimer’s disease and dementia, lowering them with B12 supplements has not been shown to improve cognitive function. However, in one study, among women with a poor dietary intake of B12, supplements of the vitamin significantly slowed the rate of cognitive decline.

http://www.nytimes.com/2011/11/29/health/vitamin-b12-deficiency-can-cause-symptoms-that-mimic-aging.html?_r=1&WT.mc_id=NYT-E-I-NYT-E-AT-1207-L23&nl=el

Depression Defies the Rush to Find an Evolutionary Upside

2012-01-18T18:31:00.001+05:30

In certain quarters of academia, it’s all the rage these days to view human behavior through the lens of evolutionary biology. What survival advantages, researchers ask, may lie hidden in our actions, even in our pathologies?

Depression has come in for particular scrutiny. Some evolutionarypsychologists think this painful and often disabling disease conceals something positive. Most of us who treat patients vehemently disagree.

Consider a patient I saw not long ago, a 30-year-old woman whose husband had had an affair and left her. Within several weeks, she became despondent and socially isolated. She developed insomnia and started to ruminate constantly about what she might have done wrong.

An evolutionary psychologist might posit that my patient’s response has a certain logic. After all, she broke off her normal routine, isolated herself and tried to understand her abandonment and plan for the future. You might see a survival advantage in the ability of depressed people like her to rigidly and obsessively fix their attention on one problem, tuning out just about everything and everyone else around them.

Certain studies might seem to support this perspective. Paul W. Andrews, a psychologist at Virginia Commonwealth University, reported that normal subjects get sadder while trying to solve a demanding spatial pattern recognition test, suggesting that something about sadness might improve analytical reasoning.

In a similar vein, Joseph P. Forgas, a psychologist at the University of New South Wales in Australia, found that sad subjects were better judges of deception than happy ones. After subjects were shown a video intended to induce a happy or a sad mood, Dr. Forgas had them view deceptive or truthful interviews with people who denied committing a theft.Subjects in a sad mood were more skeptical and more accurate in detecting deceptive communication, while subjects in a positive mood were far more trusting and gullible.

Findings like these may suggest some benefits to sadness, but lately they have been generalized to patients with full-blown depression. For example, Dr. Andrews and Dr. J. Anderson Thomson Jr., a psychiatrist at the University of Virginia, have proposed that the rumination of depressives is an adaptive strategy to solve a painful problem. Clinicians, on the other hand, continue to maintain that the grim outlook of depressives is evidence that their thought process is distorted and erroneous. It must be fixed, not embraced.

There is strong evidence from neuropsychological and brain imaging studies that clinical depression is linked with various types of memory impairments in all age groups and at all levels of depressive severity. Challenging and changing the dysfunctional thoughts of depression are the exact aims of cognitive-behavioral therapy, one of the most empirically validated and popular forms of psychotherapy.

So who’s right about depression, the evolutionary biologists or the clinicians?

To start, the subjects in the above studies were normal controls whose moods were manipulated to be transiently sad. They do not really resemble people with clinical depression, whose condition can last months or even years.

Indeed, as Dr. Forgas said by e-mail, “I never worked with depressives, and I do not think that the experiments we have done looking at mood effects on cognitive processes in normal populations experiencing minor, everyday mood differences can be readily generalized to depressive cognition.”

Under close scrutiny, the case for depression’s adaptive benefits has problems — big ones. For one thing, the ruminative thinking of depression is often not particularly effective in solving problems. As another patient of mine once said: “I would think the same things over and over and could never decide what to do. It’s not a creative way of thinking.”

More critically, depression can arise without any psychosocial stressor at all, which makes it hard to argue that depression is a response to a difficult situation or problem. Dr. David J. Kupfer, a psychiatrist at the University of Pittsburgh, has found that a major life stressor almost always precedes a first episode of depression, but that episodes recur with milder stressors, or even none at all.

If depression conferred a problem-solving benefit, it should not become a chronic or autonomous condition — which it is for about half the patients.

According to the World Health Organization, depression is the leading cause of disability and the fourth leading contributor to the global burden of disease, projected to reach second place by 2020. There is also strong evidence that it is an independent risk factor for heart disease, and several studies show that prolonged depression is associated with selective and possibly permanent damage to the hippocampus, a region of the brain critical to memory and learning.

Add the fact that 2 percent to 12 percent of depressed people eventually commit suicide, and the “advantages” of depression suddenly don’t look so good.

Why, then, does the notion persist that depression confers special insights and benefits?

I got a clue recently from one depressed patient. He was an educated and articulate young man, unhappy because the world was such an awful place, he said. Because he had so many other symptoms of depression — insomnia, fatigue, low libido and poor self-esteem — I told him that he was clinically depressed and that his Hobbesian worldview was probably a result of depression, not its cause.

He scoffed, but he was willing to try a course of cognitive-behavioral therapy and antidepressant medication, if only to feel better. Months later, when he had recovered, I asked him again about his worldview.

The world was just as dire, he said, but he felt better. Still, he speculated wistfully that his newfound cheerfulness was not his authentic self, which he described as brooding and creative.

This cuts to the heart of why depression is increasingly romanticized. What is natural, the thinking goes, is best. If we are designed to suffer depression in response to life’s ills, there must be a good reason for it, and we should allow it to take its painful and natural course.

But unlike ordinary sadness, the natural course of depression can be devastating and lethal. And while sadness is useful, clinical depression signals a failure to adapt to stress or loss, because it impairs a person’s ability to solve the very dilemmas that triggered it.

Even if depression is “natural” and evolved from an emotional state that might once have given us some advantage, that doesn’t make it any more desirable than other maladies. Nature offers us cancer, infections and heart disease, which we happily avoid and do our best to treat. Depression is no different.

http://www.nytimes.com/2012/01/17/health/depression-defies-rush-to-find-evolutionary-upside.html?src=me&ref=general

Cracking Open the Scientific Process

2012-01-18T18:29:00.000+05:30

The New England Journal of Medicine marks its 200th anniversary this year with a timeline celebrating the scientific advances first described in its pages: the stethoscope (1816), the use of ether foranesthesia (1846), and disinfecting hands and instruments before surgery (1867), among others.

For centuries, this is how science has operated — through research done in private, then submitted to science and medical journals to be reviewed by peers and published for the benefit of other researchers and the public at large. But to many scientists, the longevity of that process is nothing to celebrate.

The system is hidebound, expensive and elitist, they say. Peer review can take months, journal subscriptions can be prohibitively costly, and a handful of gatekeepers limit the flow of information. It is an ideal system for sharing knowledge, said the quantum physicist Michael Nielsen, only “if you’re stuck with 17th-century technology.”

Dr. Nielsen and other advocates for “open science” say science can accomplish much more, much faster, in an environment of friction-free collaboration over the Internet. And despite a host of obstacles, including the skepticism of many established scientists, their ideas are gaining traction.

Open-access archives and journals like arXiv and thePublic Library of Science (PLoS) have sprung up in recent years. GalaxyZoo, a citizen-science site, has classified millions of objects in space, discovering characteristics that have led to a raft of scientific papers.

On the collaborative blog MathOverflow, mathematicians earn reputation points for contributing to solutions; in another math experiment dubbed the Polymath Project, mathematicians commenting on the Fields medalistTimothy Gower’s blog in 2009 found a new proof for a particularly complicated theorem in just six weeks.

And a social networking site called ResearchGate — where scientists can answer one another’s questions, share papers and find collaborators — is rapidly gaining popularity.

Editors of traditional journals say open science sounds good, in theory. In practice, “the scientific community itself is quite conservative,” said Maxine Clarke, executive editor of the commercial journal Nature, who added that the traditional published paper is still viewed as “a unit to award grants or assess jobs and tenure.”

Dr. Nielsen, 38, who left a successful science career to write “Reinventing Discovery: The New Era of Networked Science,” agreed that scientists have been “very inhibited and slow to adopt a lot of online tools.” But he added that open science was coalescing into “a bit of a movement.”

On Thursday, 450 bloggers, journalists, students, scientists, librarians and programmers will converge on North Carolina State University (and thousands more will join in online) for the sixth annual ScienceOnline conference. Science is moving to a collaborative model, said Bora Zivkovic, a chronobiology blogger who is a founder of the conference, “because it works better in the current ecosystem, in the Web-connected world.”

Indeed, he said, scientists who attend the conference should not be seen as competing with one another. “Lindsay Lohan is our competitor,” he continued. “We have to get her off the screen and get science there instead.”

Facebook for Scientists?

“I want to make science more open. I want to change this,” said Ijad Madisch, 31, the Harvard-trained virologist and computer scientist behind ResearchGate, the social networking site for scientists.

Started in 2008 with few features, it was reshaped with feedback from scientists. Its membership has mushroomed to more than 1.3 million, Dr. Madisch said, and it has attracted several million dollars inventure capital from some of the original investors of Twitter, eBay and Facebook.

A year ago, ResearchGate had 12 employees. Now it has 70 and is hiring. The company, based in Berlin, is modeled after Silicon Valley startups. Lunch, drinks and fruit are free, and every employee owns part of the company.

The Web site is a sort of mash-up of Facebook, Twitter and LinkedIn, with profile pages, comments, groups, job listings, and “like” and “follow” buttons (but without baby photos, cat videos and thinly veiled self-praise). Only scientists are invited to pose and answer questions — a rule that should not be hard to enforce, with discussion threads about topics like polymerase chain reactions that only a scientist could love.

Scientists populate their ResearchGate profiles with their real names, professional details and publications — data that the site uses to suggest connections with other members. Users can create public or private discussion groups, and share papers and lecture materials. ResearchGate is also developing a “reputation score” to reward members for online contributions.

ResearchGate offers a simple yet effective end run around restrictive journal access with its “self-archiving repository.” Since most journals allow scientists to link to their submitted papers on their own Web sites, Dr. Madisch encourages his users to do so on their ResearchGate profiles. In addition to housing 350,000 papers (and counting), the platform provides a way to search 40 million abstracts and papers from other science databases.

In 2011, ResearchGate reports, 1,620,849 connections were made, 12,342 questions answered and 842,179 publications shared. Greg Phelan, chairman of the chemistry department at the State University of New York, Cortland, used it to find new collaborators, get expert advice and read journal articles not available through his small university. Now he spends up to two hours a day, five days a week, on the site.

Dr. Rajiv Gupta, a radiology instructor who supervised Dr. Madisch at Harvard and was one of ResearchGate’s first investors, called it “a great site for serious research and research collaboration,” adding that he hoped it would never be contaminated “with pop culture and chit-chat.”

Dr. Gupta called Dr. Madisch the “quintessential networking guy — if there’s a Bill Clinton of the science world, it would be him.”

The Paper Trade

Dr. Sönke H. Bartling, a researcher at the German Cancer Research Center who is editing a book on “Science 2.0,” wrote that for scientists to move away from what is currently “a highly integrated and controlled process,” a new system for assessing the value of research is needed. If open access is to be achieved through blogs, what good is it, he asked, “if one does not get reputation and money from them?”

Changing the status quo — opening data, papers, research ideas and partial solutions to anyone and everyone — is still far more idea than reality. As the established journals argue, they provide a critical service that does not come cheap.

“I would love for it to be free,” said Alan Leshner, executive publisher of the journalScience, but “we have to cover the costs.” Those costs hover around $40 million a year to produce his nonprofit flagship journal, with its more than 25 editors and writers, sales and production staff, and offices in North America, Europe and Asia, not to mention print and distribution expenses. (Like other media organizations, Science has responded to the decline in advertising revenue by enhancing its Web offerings, and most of its growth comes from online subscriptions.)

Similarly, Nature employs a large editorial staff to manage the peer-review process and to select and polish “startling and new” papers for publication, said Dr. Clarke, its editor. And it costs money to screen for plagiarism and spot-check data “to make sure they haven’t been manipulated.”

Peer-reviewed open-access journals, like Nature Communications and PLoS One, charge their authors publication fees — $5,000 and $1,350, respectively — to defray their more modest expenses.

The largest journal publisher, Elsevier, whose products include The Lancet, Cell and the subscription-based online archive ScienceDirect, has drawn considerable criticism from open-access advocates and librarians, who are especially incensed by its support for theResearch Works Act, introduced in Congress last month, which seeks to protect publishers’ rights by effectively restricting access to research papers and data.

In an Op-Ed article in The New York Times last week, Michael B. Eisen, a molecular biologist at the University of California, Berkeley, and a founder of the Public Library of Science, wrote that if the bill passes, “taxpayers who already paid for the research would have to pay again to read the results.”

In an e-mail interview, Alicia Wise, director of universal access at Elsevier, wrote that “professional curation and preservation of data is, like professional publishing, neither easy nor inexpensive.” And Tom Reller, a spokesman for Elsevier, commented on Dr. Eisen’s blog, “Government mandates that require private-sector information products to be made freely available undermine the industry’s ability to recoup these investments.”

Mr. Zivkovic, the ScienceOnline co-founder and a blog editor for Scientific American, which is owned by Nature, was somewhat sympathetic to the big journals’ plight. “They have shareholders,” he said. “They have to move the ship slowly.”

Still, he added: “Nature is not digging in. They know it’s happening. They’re preparing for it.”

Science 2.0

Scott Aaronson, a quantum computing theorist at the Massachusetts Institute of Technology, has refused to conduct peer review for or submit papers to commercial journals. “I got tired of giving free labor,” he said, to “these very rich for-profit companies.”

Dr. Aaronson is also an active member of online science communities like MathOverflow, where he has earned enough reputation points to edit others’ posts. “We’re not talking about new technologies that have to be invented,” he said. “Things are moving in that direction. Journals seem noticeably less important than 10 years ago.”

Dr. Leshner, the publisher of Science, agrees that things are moving. “Will the model of science magazines be the same 10 years from now? I highly doubt it,” he said. “I believe in evolution.

“When a better system comes into being that has quality and trustability, it will happen. That’s how science progresses, by doing scientific experiments. We should be doing that with scientific publishing as well.”

Matt Cohler, the former vice president of product management at Facebook who now represents Benchmark Capital on ResearchGate’s board, sees a vast untapped market in online science.

“It’s one of the last areas on the Internet where there really isn’t anything yet that addresses core needs for this group of people,” he said, adding that “trillions” are spent each year on global scientific research. Investors are betting that a successful site catering to scientists could shave at least a sliver off that enormous pie.

Dr. Madisch, of ResearchGate, acknowledged that he might never reach many of the established scientists for whom social networking can seem like a foreign language or a waste of time. But wait, he said, until younger scientists weaned on social media and open-source collaboration start running their own labs.

“If you said years ago, ‘One day you will be on Facebook sharing all your photos and personal information with people,’ they wouldn’t believe you,” he said. “We’re just at the beginning. The change is coming.”

http://www.nytimes.com/2012/01/17/science/open-science-challenges-journal-tradition-with-web-collaboration.html?ref=general&src=me&pagewanted=all

A Drug That Wakes the Near Dead

2012-01-18T18:25:00.002+05:30

The moment she saw him, Judy Cox knew her son was dead. It was an October morning in 2008, and she had just stepped out the door to run an errand when she found him lying faceup in the driveway, ghost white, covered in purple splotches. He wasn’t breathing, and when she couldn’t revive him, she ran screaming into the house where her husband, Wayne, was still asleep. “Chris is dead,” she cried. “Call 911!”

Wayne jumped out of bed and raced down to the driveway, where he knelt over his son’s limp frame and tried frantically to elicit a breath or a heartbeat. As he pumped Chris’s chest and scooped out the vomit that had collected in his mouth, Judy ran to the kitchen and steadied herself long enough to call for an ambulance.

Chris was 26. He had not been well. An A.T.V. accident the previous August left him with debilitating back pain that physical therapy did nothing to alleviate. His doctor had recently prescribed Oxycontin. His parents learned later that he had taken too much.

By the time the ambulance arrived, Chris’s heart had been still for at least 15 minutes. It took the paramedics another 15 to get it pumping again; even then, doctors had little hope he would survive. Brain cells begin dying off just five minutes after blood stops delivering oxygen. After 30 minutes, there is likely to be more dead tissue than living.

Nonetheless, the emergency-room staff members at the local hospital did their best. They hooked Chris up to a tangle of tubes and machines and injected him with drugs to stabilize his heart rate. Wayne and Judy watched helplessly from the hallway. After four hours, a doctor finally summoned them to a secluded corridor.

Chris was in a coma, the doctor said, and in all likelihood had suffered severe, irreversible brain damage. He was breathing only with the help of a ventilator and would probably have a series of heart attacks in the night.

“First they asked us to let them pull the plug,” Judy recalled one recent afternoon, as we sat in the living room of the Coxes’ house in a Memphis suburb. “Then they tried getting us to sign a do-not-resuscitate order.” Without one, the doctor explained, hospital staff would be forced to revive Chris each time he started slipping away, which could mean cracking his ribs and shocking him with electricity. Even if they managed to keep his body alive, what was left of his brain would surely die in the days ahead.

Wayne and Judy refused to sign. “This is not some dog we’re talking about putting down,” Wayne shouted. “This is our son.” Chris still lived with his parents. He was a good kid, a joker, but bashful, especially around girls. He liked playing basketball and fishing in the pond near his house. He was planning to take over the family repo business when Wayne retired in a few years. Before the A.T.V. accident, he’d never given them much trouble at all. He deserved every chance the hospital could give him.

The heart attacks never came. Four days later, Chris woke up.

It was not the awakening of Hollywood movies in which the patient comes to, just as he was, speaking full sentences and completely mobile. Three years later, Chris still cannot talk. Although he breathes on his own, his lungs battle a steady barrage of infections; a feeding tube provides all his sustenance, and his muscles have contracted into short, twisted knots. He can move only the slightest bit — his fingers and eyelids twitch, but his arms and legs remain mostly immobile — and his neck is not quite strong enough to hold up his head, which leans against a crescent-shaped support around his wheelchair headrest.

Still, Wayne and Judy say that his cognition is improving. On good days, they say, he can respond to basic commands — blink his eyes for yes, wiggle his finger for no, give a thumbs up when asked. Doctors agree that Chris has progressed beyond a vegetative state, to a hazy realm known as minimal consciousness. What that means — what it says about his experience of the world around him or his prospects for further recovery — is something they are still trying to figure out.

Convinced that the son they know and love is still “in there,” Chris’s parents have spent the past three years searching for a way to bring him back out. So far, their best hope has come from an unlikely source: Ambien. A growing body of case reports suggests that the popular sleep aid can have a profound — and paradoxical — effect on patients like Chris. Rather than put them to sleep, both Ambien and its generic twin, zolpidem, appear to awaken at least some of them. The early reports were so pronounced that until recently, doctors had a hard time believing them. Only now, more than a decade after the initial discovery, are they taking a closer look.

The first report of a zolpidem awakening came from South Africa, in 1999. A patient named Louis Viljoen, who, three years before, was declared vegetative after he was hit by a truck, had taken to clawing at his mattress during the night. Thinking he was suffering from insomnia, his family doctor suggested zolpidem to help him sleep. But 20 minutes after his mother ground the tablet up and fed it to him through a straw, Viljoen began to stir. His eyes, which normally wandered the room, vacant and unfocused, flickered with the light of consciousness. And then he began to talk (his first words were “Hello, Mummy”), and move (he could control his limbs and facial muscles). A few hours later he became unresponsive. But the next day, and for many days after that, zolpidem revived him, a few hours at a time.

Here was a case worthy of Hollywood: three years was well past the point at which doctors would expect any sort of spontaneous recovery. Viljoen awoke with the ability to speak in complete sentences. Not only did he recognize his mother, but he also recognized the voices of people who had spoken to him only when he was apparently vegetative. He remembered nothing of the mysterious realm he kept receding back into. When doctors asked him what it was like to slip away, he said he felt no changes at all. But he could recall conversations from the previous day’s awakening, along with bits and pieces of his former life: his favorite rugby team, specific matches he attended, players that he rooted for and against. As time passed, his cognition improved. He could laugh at jokes, and his awakenings stretched from a few hours to entire days. Eventually, he no longer needed zolpidem.

In the years that followed, a steady trickle of similar reports emerged — some from doctors who tried zolpidem after hearing about the Viljoen case, others from those who discovered its benefits accidentally, as Viljoen’s doctor had. The drug did not work for everyone, and even when it did, its effects typically wore off after an hour or two. But for a lucky few, those effects were profound. People who seemed vegetative for years were waking up.

There are roughly 200,000 patients in the United States trapped in the borderlands between consciousness and oblivion. Until recently, most doctors believed that recovering from this condition was not possible. Vegetative states were considered permanent after three months if the injury was caused by oxygen deprivation, or one year if it was caused by blunt trauma. And since minimally conscious patients did not fare much better than those who were vegetative, most doctors did not bother to draw the distinction.

But in the past decade, a series of developments have coalesced into a far more complicated picture than previously imagined. In 2003, an Arkansas man named Terry Wallis emerged, after 19 years, from a minimally conscious state. Neuroimaging suggested that his brain had essentially reconfigured itself — surviving neurons bypassed dead ones and forged new connections to one another. In a 2007 Nature paper, Nicholas Schiff, a neurologist from Weill Cornell Medical College, and his colleagues showed that deep brain stimulation — surgically implanting a “brain pacemaker” that sends electrical impulses to specific regions of the brain — can help some severely injured patients recover the ability to speak and eat, years after the injury. And just this month, Adrian Owen, a British neuroscientist, reported in the journal The Lancet that the brains of some patients who seemed vegetative responded to basic commands: their bodies didn’t move, but distinct patterns of neuronal firing were detected on EEG scans when these patients were told to make a fist (which triggered one region of the premotor cortex) or wiggle their toes (which triggered another).

This year, scientists at Moss Rehabilitation Research Institute and at the University of Pennsylvania, both in the Philadelphia area, began the first large-scale clinical study of zolpidem as a treatment for disorders of consciousness. (Amantadine, a drug used to treat Parkinson’s disease, and the anti-anxiety medication Ativan also show promise in increasing awareness in minimally conscious patients.) So far, the evidence suggests that less than 10 percent of brain-injured patients will experience the drug’s paradoxical effects, and that among those, only a few will respond as profoundly as Viljoen did. For families like the Coxes, such odds provide a tortured kind of hope. For doctors, they bring questions. Why does a sleeping pill induce awareness in some patients but not others? And what can these bizarre awakenings tell us about the brain’s ability to heal?

Two weeks after Chris first emerged from the coma, he began tracking objects with his eyes. At one month, he could follow simple commands. “His friends would come in the room, and there’d be two or three on each side of the bed,” Judy recalled. “And eventually, when they’d say, ‘Look at Jim,’ or ‘Look at Bob,’ he’d fix his eyes on the right guy.” Wayne and Judy asked for a follow-up M.R.I., but their neurologist said it would be pointless. Chris’s behaviors were entirely reflexive, he said; they were produced by his brainstem, which regulates basic functions like breathing and body temperature, not by his cortex, the region responsible for higher-order thinking. That Chris’s friends and family saw him following commands was proof of their denial, not of Chris’s recovery.

“Every couple days, the doc would stop in the doorway and shout Chris’s name to see if Chris responded,” Judy said. “But he wouldn’t come in the room and look at Chris up close. So one day, I practically grabbed his arm and dragged him into the room, over to Chris’s bed.” She told Chris to blink his eyes. He did. Then she made the doctor walk across the room and told Chris to keep his eyes on the doctor. He did. Finally, with the doctor standing across the room, eyes fixed on Chris, she asked Chris to give her a thumbs up. When he wiggled his thumb, just the tiniest bit, the doctor’s jaw dropped. Chris was not in a vegetative state after all. He was minimally conscious.

Still, there was little that the community hospital could do for him. It had neither the resources nor the expertise to tease out a prognosis or chart a course of therapy. The same was true of local nursing homes, which is where many patients like Chris end up.

So Wayne and Judy took over their son’s care, bringing him first to a premier brain-injury center in Atlanta (where Chris had a device implanted in his spine, which releases drugs to help with spasticity) and then to a clinic in Destin, Fla. (where he tried an experimental treatment known as hyperbaric oxygen therapy). They had just made their way back home to Tennessee when a friend told them about the Ambien paradox and the clinical trial in Philadelphia.

One hallmark of the minimally conscious state is a rapid fluctuation between levels of awareness. Spend 10 or 20 minutes with Chris Cox, and you might conclude that there is nothing going on upstairs. But spend a full hour, and at some point you’ll see his puppy-dog eyes come into focus. They will appear to search for one of his parents, or to settle quizzically on the new person in the room. Ask him to say something, and he’ll smack his lips frantically before leaning forward and tapping his feet in apparent frustration. You’ll swear that he is there with you and that only his physical infirmities (he cannot quite swallow or control his jaw) prevent him from describing the netherworld from which he has just emerged.

And then, a few minutes later, he’ll slip away again.

This fluidity makes diagnosis a challenge. “If a patient follows every command you give them, you know that,” says Dr. John Whyte, director of the Moss Institute and lead investigator on the zolpidem trial. “If a patient has never, ever followed a command, you know that too. But if you tell a patient to wiggle their finger, and they do it occasionally — which is the case for most of these folks — how do you figure out if that ‘occasionally’ means something or not?”

Whyte has spent his entire career trying to answer this question. His first job after his residency was at a facility with a large number of vegetative patients. While working there, he was struck by the amount of contention over diagnoses. For all their experience with this population, clinicians could not seem to agree on whether any given patient was actually conscious. Family members also argued, with one another and with staff, over the meaning of every wince, twitch and eye flutter.

It turned out that a lot of people — staff members included — were drawing their conclusions from pure coincidence. Whyte told me about one mother who insisted that her son would point down toward his feeding tube to indicate that fluid was leaking onto his stomach, causing irritation. “He did it while I was there,” Whyte says. “And she lifted his shirt and said: ‘See, doctor, there’s the liquid. He’s communicating with us.’ And I said: ‘How often do you look under there when he isn’t pointing like this? Never? Not even once?’ ” It was possible that the pointing corresponded to the leak, Whyte explained. But it was also possible that the leaking was constant and the pointing was random. There were countless other examples. “Behaviors would be exceptions if they happened at the wrong time, and evidence if they happened at the right time,” Whyte says.

To help eliminate this bias, Whyte developed what he calls the single-subject assessment, in which doctors design a set of tests specific to each patient’s idiosyncrasies to determine whether the patient is vegetative or minimally conscious. It is painstaking work, but the information it yields is significant. “Patients who achieve minimal consciousness early tend to have a better prognosis,” Whyte says. “And you can at least try to build a communication system with them, because you have a foundation to work from.”

With a reliable assessment method in place, he began searching for ways to build on that foundation. Then the curious Ambien awakenings caught his attention.

It’s not entirely surprising that Ambien would arouse instead of sedate. The pill has long been linked to reports of bizarre sleepwalking behavior (not to mention sleepeating, sleeptalking, even sleepdriving). Some scientists call this phenomenon “paradoxical excitation.” So far, none of the accepted determinants of prognosis — age, overall health, the nature of the initial injury or the extent of brain damage as determined by an M.R.I. — have proved useful in predicting which brain-injured patients will experience it and which won’t. To begin answering that question, Whyte says, you need to study both responders and nonresponders in an unmedicated state.

One morning this past March, I met Chris, Wayne and Judy at the University of Pennsylvania’s main hospital, where they had been flown in from Tennessee, at the study’s expense, so that Chris could be tested in an unmedicated state. From the corner of a small hospital room, we watched as Whyte’s research assistant, Andras Szeles, attached dozens of tiny electrodes to Chris’s face and scalp, then fitted him with a large headset. The electrodes would measure Chris’s brain activity as Szeles administered a series of cognitive tests.

For one test, Szeles placed a rubber glove on Chris’s right hand. A voice coming through the headset told Chris to either “squeeze glove” or “squeeze bare,” several times over. Chris did not seem to be responding at all, but Szeles explained that the electrodes would measure what the naked eye could not. “We’re not so interested in whether or not Chris can squeeze,” he said. “We just want to know if he’s trying to squeeze.” Different neurons fire when you move your left hand versus your right hand. They also fire if you imagine moving it, prepare to move it or start to move it but stop, all of which the electrodes would detect.

“The term ‘consciousness’ can be a real can of worms,” Szeles said. “There are degrees of awareness, and it’s not always clear what the threshold should be. What we’re really looking for here is evidence of comprehension and will.” If Chris understood the words “squeeze” and “glove,” knew that this very specific thing was being asked of him, and possessed, at the most basic level, the will to respond, a distinct pattern of brain waves would show up in the results.

After Whyte and his team have tested 80 patients, they will compare the results of zolpidem responders to those of nonresponders and look for clues that might help explain the difference — maybe a specific brain region that lights up unexpectedly, or a pattern of neuronal firing common to one group but not the other. Any such discovery could light a path not only through the labyrinths of Chris’s fractured mind but to a better understanding of consciousness itself.

Wayne and Judy have a more immediate question: they want to know their son’s long-term prognosis. Has he reached the pinnacle of his cognitive recovery? Or is it a launching pad from which greater heights might be reached?

“Once a patient progresses to minimal consciousness, we can’t predict what’s going to happen,” says Dr. Joseph J. Fins, chief of medical ethics at Weill Cornell Medical College and author of a coming book, “Rights Come to Mind: Brain Injury, Ethics and the Struggle for Consciousness.” Some patients have recovered full consciousness, but many more remain stuck in limbo. The only way to know the outcome is to give the patient time.

But offering time is a complex proposition. “Early on, when families have the option to pull the plug, it’s almost impossible to tell what the long-term prognosis will be,” says Dr. Soojin Park, a neurointensivist at the University of Pennsylvania Hospital, and an investigator on the zolpidem trial. “And then later, when we have the certainty — that this is as good as it’s going to get — that option is gone. Because by then, the patient is breathing on their own. There’s no more plug to pull.” At that point, families who want to end a loved one’s suffering must either have the feeding tube removed, or agree to let the next bacterial infection win out, unhindered by antibiotics. Many families find choosing these deaths much more difficult than turning off a ventilator. It’s an instinct reinforced by religious edicts that forbid the withholding of basic sustenance but allow, for example, unplugging artificial respirators.

It is not uncommon for doctors to assume the worst and advise family members to withdraw care early. They do so in part because they see their duty as helping loved ones face reality. But Fins argues that this is a cop-out. “It’s glossing over all the unknowns for the sake of a quicker, cleaner solution,” he says. “It’s wrong to be so uniformly fatalistic so early on, especially with all the data emerging about the prospects for later-stage recovery.”

According to several studies, about 40 percent of patients who have been declared vegetative are actually minimally conscious. Other studies have shown that a surprising number of vegetative and minimally conscious patients made huge strides toward recovery much later than conventional wisdom would predict.

Park says that more doctors are trying drug therapy on vegetative and minimally conscious patients, but for the most part, they are groping in the dark. “We still don’t understand which drugs should work on which patients, or at what dosage, or at what point in their recovery,” she says. “And that makes it tough for families to know when they should fight and when they should give up.”

There is also the matter of cost. Treating and monitoring patients like Chris — designing and performing single-subject assessments that can discern random twitches from deliberate behavior, managing the host of medical complications that can stymie brain recovery and continually evaluating progress — is significantly more expensive than placing them in nursing homes, where they receive basic care but have no access to brain-injury specialists. Proponents argue that the measures will save money in the long run — if the patient is able to go home, for instance. Still, it’s unclear whether even the most aggressive care will make much difference for many patients. “The payers need a better sense of what the likely outcome is for any given patient,” says Tom Smith, program director at Moss, “so that they can say with confidence which patients are likely to benefit from treatment, and how significant that benefit is likely to be. And I hate to sound this way, but then it’s basically: ‘Am I going to invest this amount of money to get this outcome? Is that worth it?’ And that is a tough, tough question to answer.”

When Chris first returned from the hospital, the Coxes’ house was flooded with well-wishers. A former teacher brought a quilt that Chris and his classmates made in grade school. Old girlfriends, acquaintances and childhood pals visited regularly. His high-school friends even held a fund-raiser to help pay for some of his therapy. But as time wore on, and it became clear that he would neither die nor fully recover, the guests dwindled. Besides Chris’s sister, Amber, who visits often, Wayne and Judy are now mostly on their own.

The couple surrendered their bedroom, which is on the ground floor of their split-level house, to Chris. They take turns sleeping there, on a small cot in the corner of the room, surrounded by medical equipment: a hospital bed with a queen-size air mattress that helps prevent bed sores, a special chair called a “sit-stand,” which can be cranked into an upright position and is supposed to help ease muscle contractions. A mechanical lift. A breathing machine.

Judy is especially keen to show me Chris’s latest gadget, a device called an Eyegaze, that looks a bit like an iPad, and which Chris is learning to use to communicate. She mounts it to a handlebar on Chris’s wheelchair. At first, Chris’s eyes move rapidly across several rows of icons — words with pictures, partial sentences like “I want” or “I like,” and cartoon images of friends and family members with their names in bold. Tracking his eyes, the computer reads: “Green. Brit. I want.” And then, “Brit–Brit–Brit–Brit–Brit.” Brit is his cousin. It’s unclear if he’s asking for her, or if his eyes are just not cooperating.

Judy puts the computer away. He still needs practice, she says. When they first tried it, in February, during outpatient rehab, the therapist asked Chris what color went with Valentine’s Day, and he was able to look at the “red” icon. But so far, “I want a drink,” is the only full sentence he has managed.

Each day begins with the same routine: Judy helps Chris up, forcing him to sit on the edge of the bed, without neck or back support, for several minutes. The goal is to strengthen his neck muscles so that one day he can hold his own head up. A nurse helps her bathe him and then lift him into his chair, so that he can be wheeled into the living room or taken outside. Three times a week, a van delivers mother and son to a rehab center, where a therapist works to stretch and stimulate Chris’s contracted muscles. And almost as often, either Wayne or Judy spends several hours on the phone, battling Chris’s insurance company, which they say has covered private nursing and weekly therapy but denied an extended stay at a brain-injury rehab center. The couple arrange their schedules so that their son is never without at least one parent.

The Coxes have surrounded themselves with a new group of friends — other parents with children like Chris. The families in this informal group share strategies and trade information on emerging research and experimental treatments. They also talk of weariness and isolation. “At the end of the day, you feel like you’re a thousand years old,” Judy says. “And you have no idea how you’re going to get up and do it all over again tomorrow.” Both Wayne and Judy admit to being frustrated by the slow pace of Chris’s progress. But he’s come this far; they can’t help hoping that he might come further still. “I know that some people, even people who loved Chris, think maybe he should have just died,” Wayne says. “But he didn’t die. He lived. And as long as he’s still breathing, we have to do the absolute best we can for him.”

The reports on zolpidem are still mixed. Viljoen and a few others have improved steadily over time; some of them are now fully conscious on their own, without medication. (Viljoen is confined to a wheelchair and has cognitive disabilities but has improved over the years.) But such improvement is rare. According to Whyte, most responders fall into one of two categories: those who can take zolpidem daily, with no appreciable loss of efficacy, and those for whom the “awakenings” wane with continued use. The latter type, he says, may be the most common.

With no way of knowing which type of responder Chris might be, the Coxes play it safe. They give Chris Ativan every day; it has a similar though less profound effect on his behavior. But zolpidem they hoard like pixie dust, giving it only on special occasions, when friends and family can be there.

They gave him some when I visited, so I could see how it works.

A few minutes after receiving the zolpidem, Chris opened his eyes and smiled. Judy sat on the bed, facing him. “Hey, buddy!” she said. “Can I have a kiss?” She leaned in, cheekward, but he turned his head up in what looked like a deliberate slight. “Chris!” she admonished, playfully. He smiled and grunted. He was teasing her. Just as she pulled away, he thrust forward and grazed her cheek with puckered lips. Confident that he was there with us, Judy took out a marker and some paper and wrote one command after another, each of which Chris followed: Stick out your tongue, give me five, give me a thumbs up. And then, “Show us your Elvis grin.” Chris curled his upper lip into a sneer. When Judy ran out of commands, Chris began smacking his lips and moving his tongue. “Talk to us, buddy,” Wayne said. “Say, ‘Mom,’ ” Judy said. After several moments, Chris managed a loud, slow “Maaaa.”

http://www.nytimes.com/2011/12/04/magazine/can-ambien-wake-minimally-conscious.html?_r=1&nl=el&pagewanted=all

Before DNA, before RNA: Life in the hodge-podge world

2012-01-16T09:57:00.002+05:30

Take note, DNA and RNA: it's not all about you. Life on Earth may have begun with a splash of TNA – a different kind of genetic material altogether.

Because RNA can do many things at once, those studying the origins of life have long thought that it was the first genetic material. But the discovery that a chemical relative called TNA can perform one of RNA's defining functions calls this into question. Instead, the very first forms of life may have used a mix of genetic materials.

RNA, DNA… TNA

Today, most life bar some viruses uses DNA to store information, and RNA to execute the instructions encoded by that DNA. However, many biologists think that the earliest forms of life used RNA for everything, with little or no help from DNA.

A key piece of evidence for this "RNA world" hypothesis is that RNA is a jack of all trades. It can both store genetic information and act as an enzyme, seemingly making it the ideal molecule to start life from scratch.

Now it seems TNA might have been just as capable, although it is not found in nature today.

It differs from RNA and DNA in its sugar backbone: TNA uses threose where RNA uses ribose and DNA deoxyribose. That gives TNA a key advantage, says John Chaput of Arizona State University in Tempe: it is a smaller molecule than ribose or deoxyribose, possibly making TNA easier to form.

Chaput and his colleagues have now created a TNA molecule that folds into a three-dimensional shape and clamps onto a specific protein. These are key steps towards creating a TNA enzyme that can control a chemical reaction, just like RNA.

The team took a library of TNAs and evolved them in the presence of a protein. After three generations, a TNA turned up that had a complex folded shape like an enzyme and could bind to the protein.

No TNA world

That doesn't mean TNA was the original genetic material, though. Chaput thinks it probably wasn't, if only because the chemistry of early Earth was so messy that TNA would not have arisen on its own. Rather, many different kinds of genetic material probably formed in a genetic hodge-podge. "The most likely scenario is that nature sampled lots of different things," says Chaput.

That's in line with a recent study by Nobel prizewinner Jack Szostak of Harvard University and colleagues. He created mosaic nucleic acids that were half DNA, half RNA. Like Chaput's TNA, some of these could bind to target molecules (Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1107113108).

However, there are problems with the hodge-podge world hypothesis. For one thing, there is no trace of TNA or its cousins in modern organisms. For another, although TNA looks simpler than RNA, we can't be sure it was easier to make some 4 billion years ago because no one has actually made it in the conditions that existed on Earth before life began, says John Sutherland of the MRC Laboratory of Molecular Biology in Cambridge, UK.

Chaput points out that we still know very little about what TNA can do, because the technology to evolve the molecules in the lab is so new. The research, he says, is just getting going.

Journal reference: Nature Chemistry, DOI: 10.1038/nchem.1241

Cousins of DNA

TNA is just one of many nucleic acids that may have been important in the first life on Earth. Here are three others.

PNA (peptide nucleic acid) ditches the sugar in its backbone and inserts a peptide instead, so it is more closely related to proteins. Like DNA, it can form double strands with itself, as well as with DNA or RNA, making it a promising genetic system (Science, DOI: 10.1126/science.1174577). It is also easy to make long PNA molecules in the conditions of prebiotic Earth, even at temperatures of 100 °C (Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.97.8.3868).

GNA (glycol nucleic acid) is even simpler than TNA, with just three carbon atoms in its backbone, yet can still form helical molecules, much like DNA (The Journal of Organic Chemistry, DOI: 10.1021/jo201469b).

ANA (amyloid nucleic acid) consists of nucleic acids attached to amyloid proteins, infamous for their role in Alzheimer's disease. ANA fibres have been suggested as the first organisms (PLoS One, DOI: 10.1371/journal.pone.0019125), because the amyloid could protect genetic material contained within.

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Before DNA, before RNA: Life in the hodge-podge world

RNA, DNA… TNA

No TNA world

Cousins of DNA