Category: Science

‘Jumping Genes’ Linked to Schizophrenia

On By A.P.In DNA, Dr. Rajadhyaksha, gene, Japan, jumping gene, line element, Medicine, mental health, mental illness, neural activity, neurogenesis, neurologist, Neurology, Neuron, neuroplasticity, Neuropsychiatric Disease, Neuroscience, neuroscientist, neurotransmitter, RIKEN Brain Science Institute, schizophrenia, Science, Tadafumi KatoLeave a comment

sn-schizophrenia

Roaming bits of DNA that can relocate and proliferate throughout the genome, called “jumping genes,” may contribute to schizophrenia, a new study suggests. These rogue genetic elements pepper the brain tissue of deceased people with the disorder and multiply in response to stressful events, such as infection during pregnancy, which increase the risk of the disease. The study could help explain how genes and environment work together to produce the complex disorder and may even point to ways of lowering the risk of the disease, researchers say.

Schizophrenia causes hallucinations, delusions, and a host of other cognitive problems, and afflicts roughly 1% of all people. It runs in families—a person whose twin sibling has the disorder, for example, has a roughly 50-50 chance of developing it. Scientists have struggled to define which genes are most important to developing the disease, however; each individual gene associated with the disorder confers only modest risk. Environmental factors such as viral infections before birth have also been shown to increase risk of developing schizophrenia, but how and whether these exposures work together with genes to skew brain development and produce the disease is still unclear, says Tadafumi Kato, a neuroscientist at the RIKEN Brain Science Institute in Wako City, Japan and co-author of the new study.

Over the past several years, a new mechanism for genetic mutation has attracted considerable interest from researchers studying neurological disorders, Kato says. Informally called jumping genes, these bits of DNA can replicate and insert themselves into other regions of the genome, where they either lie silent, doing nothing; start churning out their own genetic products; or alter the activity of their neighboring genes. If that sounds potentially dangerous, it is: Such genes are often the culprits behind tumor-causing mutations and have been implicated in several neurological diseases. However, jumping genes also make up nearly half the current human genome, suggesting that humans owe much of our identity to their audacious leaps.

Recent research by neuroscientist Fred Gage and colleagues at the University of California (UC), San Diego, has shown that one of the most common types of jumping gene in people, called L1, is particularly abundant in human stem cells in the brain that ultimately differentiate into neurons and plays an important role in regulating neuronal development and proliferation. Although Gage and colleagues have found that increased L1 is associated with mental disorders such as Rett syndrome, a form of autism, and a neurological motor disease called Louis-Bar syndrome, “no one had looked very carefully” to see if the gene might also contribute to schizophrenia, he says.

To investigate that question, principal investigator Kazuya Iwamoto, a neuroscientist; Kato; and their team at RIKEN extracted brain tissue of deceased people who had been diagnosed with schizophrenia as well as several other mental disorders, extracted DNA from their neurons, and compared it with that of healthy people. Compared with controls, there was a 1.1-fold increase in L1 in the tissue of people with schizophrenia, as well as slightly less elevated levels in people with other mental disorders such as major depression, the team reports today in Neuron.

Next, the scientists tested whether environmental factors associated with schizophrenia could trigger a comparable increase in L1. They injected pregnant mice with a chemical that simulates viral infection and found that their offspring did, indeed, show higher levels of the gene in their brain tissue. An additional study in infant macaques, which mimicked exposure to a hormone also associated with increased schizophrenia risk, produced similar results. Finally, the group examined human neural stem cells extracted from people with schizophrenia and found that these, too, showed higher levels of L1.

The fact that it is possible to increase the number of copies of L1 in the mouse and macaque brains using established environmental triggers for schizophrenia shows that such genetic mutations in the brain may be preventable if such exposures can be avoided, Kato says. He says he hopes that the “new view” that environmental factors can trigger or deter genetic changes involved in the disease will help remove some of the disorder’s stigma.

Combined with previous studies on other disorders, the new study suggests that L1 genes are indeed more active in the brain of patients with neuropsychiatric diseases, Gage says. He cautions, however, that no one yet knows whether they are actually causing the disease. “Now that we have multiple confirmations of this occurring in humans with different diseases, the next step is to determine if possible what role, if any, they play.”

One tantalizing possibility is that as these restless bits of DNA drift throughout the genomes of human brain cells, they help create the vibrant cognitive diversity that helps humans as a species respond to changing environmental conditions, and produces extraordinary “outliers,” including innovators and geniuses such as Picasso, says UC San Diego neuroscientist Alysson Muotri. The price of such rich diversity may be that mutations contributing to mental disorders such as schizophrenia sometimes emerge. Figuring out what these jumping genes truly do in the human brain is the “next frontier” for understanding complex mental disorders, he says. “This is only the tip of the iceberg.”

Thanks to Dr. Rajadhyaksha for bringing this to the attention of the It’s Interesting community.

http://news.sciencemag.org/biology/2014/01/jumping-genes-linked-schizophrenia

Tikker: the wristwatch that focuses you on the ultimate deadline

On By A.P.In death, Fredrik Colting, Jeff Greenberg, Science, Sheldon Solomon, terror management theory, The Future, the happiness watch, Tikker, Tom Pyszczynski, xenophobiaLeave a comment

Tikker

Tick Tock. Tick Tock. Tick Tock.

The seconds left in 2013 are slipping away. And you know what else is slipping away? The seconds left in your life.

Luckily for you, there’s a new product called Tikker, a wristwatch that counts down your life, so you can watch on a large, dot-matrix display as the seconds you have left on earth disappear down a black hole.

Your estimated time of death is, of course, just that, an estimate. Tikker uses an algorithm like the one used by the federal government to figure a person’s life expectancy. But the effect is chilling, a sort of incessant grim reaper reminding you that time is running out.

Tikker’s inventor is a 37-year-old Swede named Fredrik Colting. He says he invented the gadget not as a morbid novelty item, but in an earnest attempt to change his own thinking.

He wanted some sort of reminder to not sweat the small stuff and reach for what matters. He figured imminent death was the best motivator there is. That’s why he calls Tikker, “the happiness watch.” It’s his belief that watching your life slip away will remind you to savor life while you have it.

And, it turns out, there is some evidence for his point of view. A 2009 study showed that thinking about death makes you savor life more. And a 2011 study has shown thinking about death makes you more generous, more likely to donate your blood.

But that’s not the whole story. A whole dark underbelly of research suggests that thinking about our own mortality can bring out the worst in us. The work of Jeff Greenberg, Sheldon Solomon and Tom Pyszczynski — grandfathers of an idea in social psychology called terror management theory — has shown that thinking about death makes us, well, pretty xenophobic. When confronted with our mortality, we cling to those like us and disparage those who are different.

Now, why do you get both positive and negative effects? Well, that’s an open question in science right now. Do both always occur? Does it depend on the person? Does it depend on the way in which you are made to think about death, specifically picturing your own death or thinking about death in a more abstract or subliminal way? No one knows yet.

So whether Tikker will make you happy or, as Solomon quipped to me, “a xenophobic serial killer,” is still unknown. What is known is that the watch will be available in April 2014, and thousands of preorders have already rolled in.

http://kosu.org/2013/12/nothing-focuses-the-mind-like-the-ultimate-deadline-death/

Could Pot Help Veterans With PTSD? Brain Scientists Say Maybe

On By A.P.In Andrew Holmes, anxiety circuitry, Atlanta, brain, cannabinoids, cannabis, Cannabis sativa, Drugs, Emory University, Emory University School of Medicine, extinction therapy, fear circuitry, Georgia, Jon Hamilton, Kerry Ressler, marijuana, Medicine, military, National Institute of Mental Health, National Institute on Alcohol Abuse and Alcoholism, National Institute on Drug Abuse, Neuropsychiatric Disease, Neuroscience, neuroscientist, post-traumatic stress disorder, pot, psychiatrist, Psychiatry, psychology, psychotherapy, PTSD, Science, tetrahydrocannabinol, THC, VeteransLeave a comment

pot

by Jon Hamilton

Veterans who smoke marijuana to cope with post-traumatic stress disorder may be onto something. There’s growing evidence that pot can affect brain circuits involved in PTSD.

Experiments in animals show that tetrahydrocannabinol, the chemical that gives marijuana its feel-good qualities, acts on a system in the brain that is “critical for fear and anxiety modulation,” says Andrew Holmes, a researcher at the National Institute on Alcohol Abuse and Alcoholism. But he and other brain scientists caution that marijuana has serious drawbacks as a potential treatment for PTSD.

The use of marijuana for PTSD has gained national attention in the past few years as thousands of traumatized veterans who fought in Iraq and Afghanistan have asked the federal government to give them access to the drug. Also, Maine and a handful of other states have passed laws giving people with PTSD access to medical marijuana.

But there’s never been a rigorous scientific study to find out whether marijuana actually helps people with PTSD. So lawmakers and veterans groups have relied on anecdotes from people with the disorder and new research on how both pot and PTSD works in the brain.

An Overactive Fear System

When a typical person encounters something scary, the brain’s fear system goes into overdrive, says Dr. Kerry Ressler of Emory University. The heart pounds, muscles tighten. Then, once the danger is past, everything goes back to normal, he says.

But Ressler says that’s not what happens in the brain of someone with PTSD. “One way of thinking about PTSD is an overactivation of the fear system that can’t be inhibited, can’t be normally modulated,” he says.

For decades, researchers have suspected that marijuana might help people with PTSD by quieting an overactive fear system. But they didn’t understand how this might work until 2002, when scientists in Germany published a mouse study showing that the brain uses chemicals called cannabinoids to modulate the fear system, Ressler says.

There are two common sources of cannabinoids. One is the brain itself, which uses the chemicals to regulate a variety of brain cells. The other common source is Cannabis sativa, the marijuana plant.

So in recent years, researchers have done lots of experiments that involved treating traumatized mice with the active ingredient in pot, tetrahydrocannabinol (THC), Ressler says. And in general, he says, the mice who get THC look “less anxious, more calm, you know, many of the things that you might imagine.”

Problems with Pot

Unfortunately, THC’s effect on fear doesn’t seem to last, Ressler says, because prolonged exposure seems to make brain cells less sensitive to the chemical.

Another downside to using marijuana for PTSD is side effects, says Andrew Holmes at the National Institute on Alcohol Abuse and Alcoholism. “You may indeed get a reduction in anxiety,” Holmes says. “But you’re also going to get all of these unwanted effects,” including short-term memory loss, increased appetite and impaired motor skills.

So for several years now, Holmes and other scientists have been testing drugs that appear to work like marijuana, but with fewer drawbacks. Some of the most promising drugs amplify the effect of the brain’s own cannabinoids, which are called endocannabinoids, he says. “What’s encouraging about the effects of these endocannabinoid-acting drugs is that they may allow for long-term reductions in anxiety, in other words weeks if not months.”

The drugs work well in mice, Holmes says. But tests in people are just beginning and will take years to complete. In the meantime, researchers are learning more about how marijuana and THC affect the fear system in people.

At least one team has had success giving a single dose of THC to people during something called extinction therapy. The therapy is designed to teach the brain to stop reacting to something that previously triggered a fearful response.

The team’s study found that people who got THC during the therapy had “long-lasting reductions in anxiety, very similar to what we were seeing in our animal models,” Holmes says. So THC may be most useful when used for a short time in combination with other therapy, he says.

As studies continue to suggest that marijuana can help people with PTSD, it may be unrealistic to expect people with the disorder to wait for something better than marijuana and THC, Ressler says. “I’m a pragmatist,” he says. “I think if there are medications including drugs like marijuana that can be used in the right way, there’s an opportunity there, potentially.”

http://www.npr.org/blogs/health/2013/12/23/256610483/could-pot-help-veterans-with-ptsd-brain-scientists-say-maybe

John McKetta, Jr.: A Journey To Greatness Started In A Coal Mine

On By A.P.In Angola, Burton Handy, chemical engineering, Donald Katz, Dow Chemical, Dr. Rajadhyaksha, Forrest Preece, George Granger Brown, Indiana, International Chemical Engineering Award, John McKetta, Johnny Jay and the Kampus Kollegians, Jr., McKetta and Katz tables, Pennsylvania, Pinky Smith, Ray Bodie, Texas, Tri-State University, University of Texas, West Austin News1 Comment

John-McKetta-in-1931

Dean-McKettas-portrait-1984

More-about-McKetta-1

More-about-McKetta-2

By Forrest Preece
West Austin News

Part 1

In 1903, a 14-year-old Ukrainian boy named John McKetta packed a suitcase and headed for Pennsylvania for $25, ($15 of which he gave to his father), a job in the coal mines, and a place to live.

That youngster had a lot on his mind – mainly how to survive in a new country and how to adjust to working deep underground for long hours. It’s doubtful he would have imagined his namesake son would become the world’s most prominent chemical engineer; receive the “International Chemical Engineering Award” in Venice, Italy; be one of the most revered professors ever to teach at The University of Texas, with a large academic department named after him; and serve as an energy adviser to five United States presidents. All of that would take a while.

When John, Jr., the subject of this column, was born in 1915, he faced the bleak prospect of finishing public school and then a lifetime of backbreaking work in the coal mines. That was the only career option – six days a week in the mines – the same as his father and uncle and the other men in Wyano, Pa., population 200. But before John could start the first grade, he and the other kids his age had to learn English. So they began a month early, were given primers, and they could all speak English when it was time for school to start. (“It can be done — that’s why I don’t like the idea of having double-language schools,” he says.)

For three years after he finished high school, John, Jr. went 475 feet underground into a seven-foot coal vein, six days a week.
”At least we could stand up! The men in Kentucky were in four-foot veins and had to stoop and crawl around all day,” he says.

During those three years, the most he ever made in a week was $3, based on 25 cents per ton of coal he brought out of the ground. In that era, the workers had no electric equipment to use. It was strictly pick-and-shovel manual labor.

“I hated every minute of it,” John says.

Then one day, he saw a book that changed his life. It was by a man named Porter about the process of carbonization that extracted energy from coal.

“There were people called chemical engineers who made this happen,” John says. “I wanted to be one of them.”

So he obtained a list of colleges in the country that had chemical engineering programs and determined to keep writing to them until one would accept him. With no typewriter or even a pen to use, he kept grinding out pencil-written letters.

”About the best I could do was three or four letters a night.”

Of the first 54 colleges he applied to, none even gave him the courtesy of a rejection letter. Finally, President Burton Handy of Tri-State University in Angola, Indiana wrote him back. His letter said, “If we admit you, we will provide you with a job that will help you pay for your tuition and your lodging. Please come talk to us.”

That was on a Friday. The next day, he put $10.20 in his pocket and hitchhiked across Ohio to Indiana.

“In those days, people would pick up a kid with a suitcase.”

When he arrived on Monday, he made a beeline for the registrar’s office. When he got there, he gave the receptionist his name. She flipped through her files, looked startled and said, “Oh yes, Mr. McKetta, President Handy wants to see you.”

John says that the president leaped out of his chair, came over and gave him a slap on the back. “He admired me for being willing to apply.”

The upshot of the conversation they then had was that John would have a job making twenty cents an hour, twenty hours a week. Of that $4.00 total weekly salary, he’d pay $2.00 for tuition and $2.00 for a room at a house off campus run by a lady named Mrs. Nichols.

After meeting Mrs. Nichols, and seeing his room that he’d be sharing, he decided to get a cup of coffee at a local diner. As it happened, the owner of the diner was just preparing a “Dishwasher Wanted” sign to put in his window. John asked about it and found out that it paid no money, but for every hour worked, it meant a free meal. He took the job and was just beaming over all his good fortune.

Then things got even better. He ran into a local bandleader named Ray Bodie who needed a second trumpet and John had played that instrument in the Wyano Volunteer Fire Department Band.

He told Bodie that he could sit in on Wednesday and Saturday nights, if he could find a trumpet to use. That was even more income. A year later, he started his own 12-piece band called JJKK – “Johnny Jay and the Kampus Kollegians” an, started playing gigs all over the thriving 3,000-person metropolis of Angola.

He paid himself $1.01 (sometimes $1.50) and hi musicians got 75 cents for their performances. All the while, he was diligently studying every night and he kept a coal miner’s cap on his desk for a very good reason.

“When some of the guy would ask me to go shoot pool, I’d just look at that cap and remember being in the mine and say ‘No, I have to study.”

Part 2
What can you say about a 98-year-old college professor who still goes to his office at The University of Texas at Austin three days a week, around 6 a.m. and stays for several hours to visit with researchers? Who still calls eight to ten of his former students a day -and laments how fast they are dying? And who still operates at a level of energy and good-hearted enthusiasm that would shame most 40- year-olds?

John McKetta, Jr. does all of that and more. In a recent interview with him at his apartment at Westninster Manor, where he has resided for eight years, John told me about his life. It has been quite a journey: from his post-high school years laboring in the coal mines of rural Pennsylvania to his career in chemical engineering, where he gained worldwide recognition for his teaching, research, publications and administrative ability.

He also told me about his family: his beloved wife Helen “Pinky” McKetta, who he married in 1943 and who passed away in 2011; his sons Charles, Mike and Randy and his daughter Mary Anne.

If you read part one of my column about him last week, you know that through dogged perseverance, he was accepted as a student at Tri-State University in Angola, Indiana, where he excelled in the chemical engineering program.

“The faculty members were so wonderful to me! And when I graduated, they got me job at the Michigan Alkali, CO. in Wyandotte, Michigan, near Detroit.”

His work there was exciting, but he started hearing about this company called Dow that was doing amazing things in the realm of producing chemicals from gas and oil.

Dr. George Granger Brown (or as he was jokingly called, “Great God” Brown), was a chief consultant to Dow and the chairman of the chemical engineering department at the University of Michigan. One day John drove his 1928 Ford up to meet this notable man. Soon he was a student again, working toward his Ph.D.

One night in an off-campus coffee shop, he met Pinky Smith, the love of his life. Who married him a few months later. Her name still crawls across his home office’s computer screen.

While he was at Michigan doing his Ph.D. research, John and one of his professors, Dr. Donald Katz, developed a set of tables relating to underground temperature and pressure in gas and oil wells that reveal the composition of the surrounding terrain. These McKetta and Katz tables are still in widespread use.

Partially thanks to his desire to be “where the oil and gas was underground,” he came to Texas. Besides that, Dow Chemical in Freeport was doing amazing things.

“God was with me when I decided to come to Texas and I got hired at the University in 1946.”

John would progress up the ladder at UT from assistant professor to professor, to chairman of the Department of Chemical Engineering to dean of the College of Engineering.

For a while, he was executive vice-chancellor for the UT system under Chancellor Harry Ransom. That was during the period when they were establishing UT Permian Basin, UT Dallas, UT El Paso and UT San Antonio and John was the key executive in that effort.

One conversation John recalls from his early days on the faculty is when, in 1948, he was having lunch with his colleagues in the College of Engineering and Professor Bill Cunningham (not the man who would later be president of UT) brought in a list of the top 50 engineering schools. UT wasn’t on it; Rice was number 26.

He laughs and says, “As of last year, we were number four on a similar list. For 40 years, he was on the payroll and taught at UT for another 20 years, he donated his time to teaching courses.

Also, with the $6,900,000 in the McKetta Fund which he established with a $964,000 personal gift, many outstanding students have scholarships so they concentrate on their studies. “It’s just wonderful for these students to have this financial support,” he says.

What changes has he seen in his field? He warms to the subject of bioengineering which is a topic that only recently has come to the fore.

“Forrest, when I wave my hand at you like this, there are something like 80,000 cells in my body involved. Your whole body is a chemical plant.”

Long story short, there are researchers at UT Austin who are zeroing in on being able to provide pinpointed medication to the parts of the body that cure certain diseases. John says that years ago, he went to the chairman of the board of directors of St. David’s Hospital and asked him to bring some of his MDs over to talk to the engineering faculty on a regular, voluntary basis about bioengineering.

Something like 80 percent of his engineering faculty members showed up for the talks, because they were all interested in this new field of research.

As a result, now there is a new $60,000,000 Bioengineering Building on the UT Austin campus. So what advice would he give to a student starting in engineering? First, they have to be interested in the field. And he says that there are two traits he looks for: curiosity and “judicious discontent.”

“I like kids who ask ‘why’ and ‘what can I do about it?’”

One last note – for many years, Dr. McKetta kept a miner’s cap on his UT office desk, as a reminder of how much better it is to be a professor than working in the mines. Oh – and being a Longhorn football fan to the max, he says that Mack Brown is going to have a terrific season this year.

http://www.che.utexas.edu/2013/09/06/a-journey-to-greatness-started-in-a-coal-mine/

Thanks to Dr. Rajadhyaksha for bringing this to the attention of the It’s Interesting community.

Study reveals gene expression changes with meditation

On By A.P.In Center for Investigating Healthy Minds, DNA, Dr. D, epigenetics, gene, IIBB-CSIC-IDIBAPS, Medicine, Meditation, mindfullness, National Center for Complementary and Alternative Medicine, Perla Kaliman, Psychoneuroendocrinology, Richard J. Davidson, Science, Spain, The Brain, University of Wisconsin, University of Wisconsin-MadisonLeave a comment

meditation

With evidence growing that meditation can have beneficial health effects, scientists have sought to understand how these practices physically affect the body.

A new study by researchers in Wisconsin, Spain, and France reports the first evidence of specific molecular changes in the body following a period of mindfulness meditation.

The study investigated the effects of a day of intensive mindfulness practice in a group of experienced meditators, compared to a group of untrained control subjects who engaged in quiet non-meditative activities. After eight hours of mindfulness practice, the meditators showed a range of genetic and molecular differences, including altered levels of gene-regulating machinery and reduced levels of pro-inflammatory genes, which in turn correlated with faster physical recovery from a stressful situation.

“To the best of our knowledge, this is the first paper that shows rapid alterations in gene expression within subjects associated with mindfulness meditation practice,” says study author Richard J. Davidson, founder of the Center for Investigating Healthy Minds and the William James and Vilas Professor of Psychology and Psychiatry at the University of Wisconsin-Madison.

“Most interestingly, the changes were observed in genes that are the current targets of anti-inflammatory and analgesic drugs,” says Perla Kaliman, first author of the article and a researcher at the Institute of Biomedical Research of Barcelona, Spain (IIBB-CSIC-IDIBAPS), where the molecular analyses were conducted.

The study was published in the journal Psychoneuroendocrinology.

Mindfulness-based trainings have shown beneficial effects on inflammatory disorders in prior clinical studies and are endorsed by the American Heart Association as a preventative intervention. The new results provide a possible biological mechanism for therapeutic effects.

The results show a down-regulation of genes that have been implicated in inflammation. The affected genes include the pro-inflammatory genes RIPK2 and COX2 as well as several histone deacetylase (HDAC) genes, which regulate the activity of other genes epigenetically by removing a type of chemical tag. What’s more, the extent to which some of those genes were downregulated was associated with faster cortisol recovery to a social stress test involving an impromptu speech and tasks requiring mental calculations performed in front of an audience and video camera.

Perhaps surprisingly, the researchers say, there was no difference in the tested genes between the two groups of people at the start of the study. The observed effects were seen only in the meditators following mindfulness practice. In addition, several other DNA-modifying genes showed no differences between groups, suggesting that the mindfulness practice specifically affected certain regulatory pathways.

However, it is important to note that the study was not designed to distinguish any effects of long-term meditation training from those of a single day of practice. Instead, the key result is that meditators experienced genetic changes following mindfulness practice that were not seen in the non-meditating group after other quiet activities — an outcome providing proof of principle that mindfulness practice can lead to epigenetic alterations of the genome.

Previous studies in rodents and in people have shown dynamic epigenetic responses to physical stimuli such as stress, diet, or exercise within just a few hours.

“Our genes are quite dynamic in their expression and these results suggest that the calmness of our mind can actually have a potential influence on their expression,” Davidson says.

“The regulation of HDACs and inflammatory pathways may represent some of the mechanisms underlying the therapeutic potential of mindfulness-based interventions,” Kaliman says. “Our findings set the foundation for future studies to further assess meditation strategies for the treatment of chronic inflammatory conditions.”

Study funding came from National Center for Complementary and Alternative Medicine (grant number P01-AT004952) and grants from the Fetzer Institute, the John Templeton Foundation, and an anonymous donor to Davidson. The study was conducted at the Center for Investigating Healthy Minds at the UW-Madison Waisman Center.

http://www.news.wisc.edu/22370

Thanks to Dr. D for bringing this to the attention of the It’s Interesting community.

Sexual frustration shortens the life of the fruit fly

On By A.P.In death, Dr Scott Pletcher, Dr. D, drosophila, Drosophila melanogaster, fruit fly, lifespan, Nature, neuropeptide F, pheromones, Science, sex pheromones, sexual frustration, University of Michigan2 Comments

fly-getty

Sexually frustrated fruit flies die earlier, new research suggests.

Scientists made the discovery by genetically modifying male flies to release female sex pheromones. Other males were left nearby and therefore instantly aroused by the pheromones. Some were allowed to mate, but others weren’t.

The findings, published in the journal Science, show that the sexually frustrated flies’ lives were 40 per cent shorter, while those who did mate suffered less stress.

Dr Scott Pletcher, Assistant Professor of Molecular & Integrative Physiology at the University of Michigan, co-authored the research. He told the BBC: “We immediately observed that (the non-mating flies) looked quite sick very soon in the presence of these effeminised males.”

A brain chemical, neuropeptide F (NPF), appeared to play a big role. NPF levels went up once flies were aroused. It would normally go down again upon mating.

But when it stayed high, it caused the stress and apparently the premature deaths.

Dr Pletcher went on: “Evolutionarily we hypothesise the animals are making a bet to determine that mating will happen soon.

“Those that correctly predict may be in a better position, they either produce more sperm or devote more energy to reproduction in expectation, and this may have some consequences [if they do not mate].”

http://www.independent.co.uk/news/science/sexual-frustration-will-give-you-a-shorter-and-more-stressful-life-if-you-are-a-fruit-fly-8972673.html

Thanks to Dr. D for bringing this to the attention of the It’s Interesting community.

Computer Software Mines Science Papers to Make New Discoveries

On By A.P.In Baylor College of Medicine, Cancer, discovery, Kebmodee, kinase, Lawrence Hunter, Medicine, Olivier Lichtarge, p53, phosphatase, Science, Ying ChenLeave a comment

Ibm

Software that read tens of thousands of research papers and then predicted new discoveries about the workings of a protein that’s key to cancer could herald a faster approach to developing new drugs.

The software, developed in collaboration between IBM and Baylor College of Medicine, was set loose on more than 60,000 research papers that focused on p53, a protein involved in cell growth implicated in most cancers. By parsing sentences in the documents, the software could build an understanding of what is known about enzymes called kinases that act on p53 and regulate its behavior; these enzymes are common targets for cancer treatments. It then generated a list of other proteins mentioned in the literature that were probably undiscovered kinases, based on what it knew about those already identified. Most of its predictions tested so far have turned out to be correct.

“We have tested 10,” Olivier Lichtarge of Baylor said Tuesday. “Seven seem to be true kinases.” He presented preliminary results of his collaboration with IBM at a meeting on the topic of Cognitive Computing held at IBM’s Almaden research lab.

Lichtarge also described an earlier test of the software in which it was given access to research literature published prior to 2003 to see if it could predict p53 kinases that have been discovered since. The software found seven of the nine kinases discovered after 2003.

“P53 biology is central to all kinds of disease,” says Lichtarge, and so it seemed to be the perfect way to show that software-generated discoveries might speed up research that leads to new treatments. He believes the results so far show that to be true, although the kinase-hunting experiments are yet to be reviewed and published in a scientific journal, and more lab tests are still planned to confirm the findings so far. “Kinases are typically discovered at a rate of one per year,” says Lichtarge. “The rate of discovery can be vastly accelerated.”

Lichtarge said that although the software was configured to look only for kinases, it also seems capable of identifying previously unidentified phosphatases, which are enzymes that reverse the action of kinases. It can also identify other types of protein that may interact with p53.

The Baylor collaboration is intended to test a way of extending a set of tools that IBM researchers already offer to pharmaceutical companies. Under the banner of accelerated discovery, text-analyzing tools are used to mine publications, patents, and molecular databases. For example, a company in search of a new malaria drug might use IBM’s tools to find molecules with characteristics that are similar to existing treatments. Because software can search more widely, it might turn up molecules in overlooked publications or patents that no human would otherwise find.

“We started working with Baylor to adapt those capabilities, and extend it to show this process can be leveraged to discover new things about p53 biology,” says Ying Chen, a researcher at IBM Research Almaden.

It typically takes between $500 million and $1 billion dollars to develop a new drug, and 90 percent of candidates that begin the journey don’t make it to market, says Chen. The cost of failed drugs is cited as one reason that some drugs command such high prices (see “A Tale of Two Drugs”).

Lawrence Hunter, director of the Center for Computational Pharmacology at the University of Colorado Denver, says that careful empirical confirmation is needed for claims that the software has made new discoveries. But he says that progress in this area is important, and that such tools are desperately needed.

The volume of research literature both old and new is now so large that even specialists can’t hope to read everything that might help them, says Hunter. Last year over one million new articles were added to the U.S. National Library of Medicine’s Medline database of biomedical research papers, which now contains 23 million items. Software can crunch through massive amounts of information and find vital clues in unexpected places. “Crucial bits of information are sometimes isolated facts that are only a minor point in an article but would be really important if you can find it,” he says.

Lichtarge believes that software like his could change the way scientists conduct and assess new research findings. Scientists currently rely in part on the reputation of the people, institutions, and journals involved, and the number of times a paper is cited by others.

Software that gleans meaning from all the information published within a field could offer a better way, says Lichtarge. “You might publish directly into the [software] and see how disruptive it is,” he says.

Hunter thinks that scientists might even use such tools at an earlier stage, having software come up with evidence for and against new hypotheses. “I think it would really help science go faster. We often waste a lot of time in the lab because we didn’t know every little thing in the literature,” he says.

http://www.technologyreview.com/news/520461/software-mines-science-papers-to-make-new-discoveries/

Thanks to Kebmodee for bringing this to the attention of the It’s Interesting community.

How the Whale Became the Whale

On By A.P.In DNA, Dr. Rajadhyaksha, gene, marine biology, Science, WhalesLeave a comment

whale

About 54 million years ago, a semiaquatic deerlike creature headed into the water for good, giving rise to whales and their relatives. The newly sequenced genome of the minke whale, a baleen whale found worldwide, tells the story of how stressful this move to live underwater was. An international team has decoded the genomes of four minke whales, a fin whale, a bottlenose dolphin, and a finless porpoise, comparing these cetaceans’ genes to the equivalent genes in other mammals. It found whale-specific mutations in genes important for the regulation of salt and of blood pressure and for antioxidants that get rid of charged oxygen molecules that can harm cells. These molecules increase in number as the whale uses up its oxygen supply during dives. Whales also had larger numbers of related genes, called gene families, for dealing with sustained dives, the team reports online today in Nature Genetics. Overall, 1156 gene families had expanded, and several increased the number of enzymes that help the whale cope with low-to-no oxygen conditions. A few of those expanded families are also expanded in naked mole rats, which live underground where oxygen is scarce. But the numbers of genes for body hair and for taste and smell had decreased. And of course, there were genes and gene families that help explain why whales look the way they do.

http://news.sciencemag.org/biology/2013/11/scienceshot-how-whale-became-whale

Thanks to Dr. Rajadhyaksha for bringing this to the attention of the It’s Interesting community.

R.I.P. Frederick Sanger, Two-Time Nobel-Winning Scientist, died yesterday at age of 95

On By A.P.In Addenbrooke’s Hospital, Adrian Penrose, Cambridge, Denise Gellene, DNA, England, epigenetics, Frederick Sanger, gene, human growth hormone, Inventions, Medical Research Council, New York Times, Nobel Prize, Sanger sequencing, Science, Swaffham BulbeckLeave a comment

sanger

By DENISE GELLENE

Frederick Sanger, a British biochemist whose discoveries about the chemistry of life led to the decoding of the human genome and to the development of new drugs like human growth hormone and earned him two Nobel Prizes, a distinction held by only three other scientists, died on Tuesday in Cambridge, England. He was 95.

His death was confirmed by Adrian Penrose, communications manager at the Medical Research Council in Cambridge. Dr. Sanger, who died at Addenbrooke’s Hospital in Cambridge, had lived in a nearby village called Swaffham Bulbeck.

Dr. Sanger won his first Nobel Prize, in chemistry, in 1958 for showing how amino acids link together to form insulin, a discovery that gave scientists the tools to analyze any protein in the body.

In 1980 he received his second Nobel, also in chemistry, for inventing a method of “reading” the molecular letters that make up the genetic code. This discovery was crucial to the development of biotechnology drugs and provided the basic tool kit for decoding the entire human genome two decades later.

Dr. Sanger spent his entire career working in a laboratory, which is unusual for someone of his stature. Long after receiving his first Nobel, he continued to perform many experiments himself instead of assigning them to a junior researcher, as is typical in modern science labs. But Dr. Sanger said he was not particularly adept at coming up with experiments for others to do, and had little aptitude for administration or teaching.

“I was in a position to do more or less what I liked, and that was doing research,” he said.

Frederick Sanger was born on Aug. 3, 1918, in Rendcomb, England, where his father was a physician. He expected to follow his father into medicine, but after studying biochemistry at Cambridge University, he decided to become a scientist. His father, he said in a 1988 interview, “led a scrappy sort of life” in which he was “always going from one patient to another.”

“I felt I would be much more interested in and much better at something where I could really work on a problem,” he said.

He received his bachelor’s degree in 1939. Raised as a Quaker, he was a conscientious objector during World War II and remained at Cambridge to work on his doctorate, which he received in 1943.

However, later in life, lacking hard evidence to support his religious beliefs, he became an agnostic.

“In science, you have to be so careful about truth,” he said. “You are studying truth and have to prove everything. I found that it was difficult to believe all the things associated with religion.”

Dr. Sanger stayed on at Cambridge and soon became immersed in the study of proteins. When he started his work, scientists knew that proteins were chains of amino acids, fitted together like a child’s colorful snap-bead toy. But there are 22 different amino acids, and scientists had no way of determining the sequence of these amino acid “beads” along the chains.
In 1962, Dr. Sanger moved to the British Medical Research Council Laboratory of Molecular Biology, where he was surrounded by scientists studying deoxyribonucleic acid, or DNA, the master chemical of heredity.

Scientists knew that DNA, like proteins, had a chainlike structure. The challenge was to determine the order of adenine, thymine, guanine and cytosine — the chemical bases from which DNA is made. These bases, which are represented by the letters A, T, G and C, spell out the genetic code for all living things.

Dr. Sanger decided to study insulin, a protein that was readily available in a purified form since it is used to treat diabetes. His choice of insulin turned out to be a lucky one — with 51 amino acids, insulin has a relatively simple structure. Nonetheless, it took him 10 years to unlock its chemical sequence.

His approach, which he called the “jigsaw puzzle method,” involved breaking insulin into manageable chunks for analysis and then using his knowledge of chemical bonds to fit the pieces back together. Using this technique, scientists went on to determine the sequences of other proteins. Dr. Sanger received the Nobel just four years after he published his results in 1954.

Dr. Sanger quickly discovered that his jigsaw method was too cumbersome for large pieces of DNA, which contain many thousands of letters. “For a while I didn’t see any hope of doing it, though I knew it was an important problem,” he said.

But he persisted, developing a more efficient approach that allowed stretches of 500 to 800 letters to be read at a time. His technique, known as the Sanger method, increased by a thousand times the rate at which scientists could sequence DNA.

In 1977, Dr. Sanger decoded the complete genome of a virus that had more than 5,000 letters. It was the first time the DNA of an entire organism had been sequenced. He went on to decode the 16,000 letters of mitochondria, the energy factories in cells.

Because the Sanger method lends itself to computer automation, it has allowed scientists to unravel ever more complicated genomes — including, in 2003, the three billion letters of the human genetic code, giving scientists greater ability to distinguish between normal and abnormal genes.

In addition, Dr. Sanger’s discoveries were critical to the development of biotechnology drugs, like human growth hormone and clotting factors for hemophilia, which are produced by tiny, genetically modified organisms.

Dr. Sanger shared the 1980 chemistry Nobel with two other scientists: Paul Berg, who determined how to transfer genetic material from one organism to another, and Walter Gilbert, who, independently of Dr. Sanger, also developed a technique to sequence DNA. Because of its relative simplicity, the Sanger method became the dominant approach.

Other scientists who have received two Nobels are John Bardeen for physics (1956 and 1972), Marie Curie for physics (1903) and chemistry (1911), and Linus Pauling for chemistry (1954) and peace (1962).

Dr. Sanger received the Albert Lasker Basic Medical Research Award, often a forerunner to the Nobel, in 1979 for his work on DNA. He retired from the British Medical Research Council in 1983.

Survivors include two sons, Robin and Peter, and a daughter, Sally.

In a 2001 interview, Dr. Sanger spoke about the challenge of winning two Nobel Prizes.

“It’s much more difficult to get the first prize than to get the second one,” he said, “because if you’ve already got a prize, then you can get facilities for work and you can get collaborators, and everything is much easier.”

CO2 causing oceans to acidify at ‘unprecedented’ rate, scientists warn

On By A.P.In acidification, carbon dioxide, Climate Change, CNN, CO2, Daniela Schmidt, Global Warming, Industrial Revolution, Intergovernmental Oceanographic Commission of UNESCO, International Geosphere-Biosphere Programme, marine biology, ocean, ocean acidification, Science, Scientific Committee on Oceanic Research, Susannah Cullinane, Symposium on the Ocean, The Future, University of BristolLeave a comment

<> on June 9, 2010 in Houma, Louisiana.

By Susannah Cullinane, CNN

The world’s oceans have become 26% more acidic since the start of the Industrial Revolution and continue to acidify at an “unprecedented rate,” threatening marine ecosystems, aquaculture and the societies that rely on them, scientists say.

In a report released Thursday, researchers say that carbon dioxide emissions from human activities such as fossil fuel burning are the primary cause of ocean acidification.

They say the rate of change may be faster than at any time in the last 300 million years, predicting that by 2100 there will have been a 170% increase in ocean acidity, compared to pre-industrial times.

The report is based on the findings from a September 2012 Symposium on the Ocean, at which 540 experts from 37 countries discussed research on ocean acidification, and has been updated with more recent research.

Unless carbon dioxide emissions are reduced, marine ecosystems will be damaged and the impact of climate change will be worsened, the scientists warn. “The only known realistic mitigation option on a global scale is to limit future atmospheric CO2 levels.”

The report says oceans currently act as a CO2 “sinkhole” absorbing approximately a quarter of emissions.

“As ocean acidity increases, its capacity to absorb CO2 from the atmosphere decreases. This decreases the ocean’s role in moderating climate change,” they write.

The increased acidity will also change the ocean environment, with evidence suggesting that some organisms will be less able to survive, while others, such as seagrass, may thrive.

Acidification is faster in Arctic waters because cold water is richer in CO2, while melting sea ice worsens the problem, they say.

“Within decades, large parts of the polar oceans will become corrosive to the unprotected shells of calcareous marine organisms,” the report says, while in the tropics the growth of coral reefs may be hampered.

“People who rely on the ocean’s ecosystem services are especially vulnerable and may need to adapt or cope with ocean acidification impacts within decades,” it says. “Tropical coral reef loss will affect tourism, food security and shoreline protection for many of the world’s poorest people.”

“Very aggressive reductions in CO2 emissions are required to maintain a majority of tropical coral reefs in waters favorable for growth,” the report says.

One of the report’s authors is Daniela Schmidt, from the University of Bristol, in the UK.

Schmidt said the research highlighted the impact acidification would have on biodiversity and aquaculture and the societies that rely on them for their food and economic well-being.

“We’re talking about countries that strongly depend on this, in warmer countries where there are complex problems with climate change as it is,” Schmidt said.

“What I’m hoping is that people realize that CO2 is not just a question of global warming. That we are acidifying the ocean at a rate that has been unprecedented — for millions and millions of years,” she said.

“The more CO2 emissions, the more acidification,” Schmidt said. “The ocean is in direct interchange with the atmosphere.”

If acidification continued to increase at its current rate, “you will definitely see damage,” she said. “The first signs we can already see today, in oyster farms off the West Coast of the United States.”

Schmidt said while 90% of the world’s ocean was in equilibrium with the atmosphere, some oyster hatcheries in this area were located in the 10% that wasn’t.

Oysters in the larval stage were much more vulnerable to damage, she said. “When (more acidic) water comes up and hits the hatchery, they close the whole thing.”

While tanks could be closed off to more acidic seawater, Schmidt said that by 2100 the issue would be there every day. “So we can’t just switch off that tap anymore.”

She said the report would be presented in Warsaw, Poland, on November 18, during the U.N. Conference of the Parties climate change meeting.

Schmidt said while she hoped the research would lead to stricter emissions limits, “the realist in me thinks that we’ve been discussing this for decades. This isn’t a problem that is just going to go away. It’s simple. The consequences are frightening.”

The 2012 symposium that led to the report was sponsored by the Scientific Committee on Oceanic Research, the Intergovernmental Oceanographic Commission of UNESCO, and the International Geosphere-Biosphere Programme.

http://www.cnn.com/2013/11/14/world/ocean-acidification-report/index.html?hpt=hp_t3