July 2nd, 2012

Third-generation sequencing debugged to glimpse parrots’ ability to imitate.

Scientists say they have assembled more completely the string of genetic letters that could control how well parrots learn to imitate their owners and other sounds.

The research team unraveled the specific regions of the parrots’ genome using a new technology, single molecule sequencing, and fixing its flaws with data from older DNA-decoding devices. The team also decoded hard-to-sequence genetic material from corn and bacteria as proof of their new sequencing approach.

The results of the study appeared online July 1 in the journal Nature Biotechnology.

Single molecule sequencing “got a lot of hype last year” because it generates long sequencing reads, “supposedly making it easier to assemble complex parts of the genome,” said Duke University neurobiologist Erich Jarvis, a co-author of the study.

He is interested in the sequences that regulate parrots’ imitation abilities because they could give neuroscientists information about the gene regions that control speech development in humans.

This male budgie from the Fort Worth Zoo is like the parrots Erich Jarvis uses to study vocal learning behaviors, but probably without the text bubble. Image adapted from an image credited to Jerry Tillery via Wikimedia Commons. More info in notes below.

Jarvis began his project with collaborators by trying to piece together the genome regions with what are known as next-generation sequencers, which read chunks of 100 to 400 DNA base pairs at a time and then take a few days to assemble them into a draft genome. After doing the sequencing, the scientists discovered that the read lengths were not long enough to assemble the regulatory regions of some of the genes that control brain circuits for vocal learning.

University of Maryland computational biologists Adam Phillippy and Sergey Koren — experts at assembling genomes — heard about Jarvis’s sequencing struggles at a conference and approached him with a possible solution of modifying the algorithms that order the DNA base pairs. But the fix was still not sufficient.

Last year, 1000 base-pair reads by Roch 454 became available, as did the single molecule sequencer by Pacific Biosciences. The Pacbio technology generates strands of 2,250 to 23,000 base pairs at a time and can draft an entire genome in about a day.

Jarvis and others thought the new technologies would solve the genome-sequencing challenges. Through a competition, called the Assemblathon, the scientists discovered that the Pacbio machine had trouble accurately decoding complex regions of the parrot, Melopsittacus undulates, genome. The machine had a high error rate, generating the wrong genetic letter at every fifth or sixth spot in a string of DNA. The mistakes made it nearly impossible to create a genome assembly with the very long reads, Jarvis said.

But with a team, including scientists from the DOE Genome Science Institute and Cold Spring Harbor in New York, Phillippy, Koren and Jarvis corrected the Pacbio sequencer’s errors using shorter, more accurate codes from the next-generation devices. The fix reduces the single-molecule, or third-generation, sequencing machine’s error rate from 15 percent to less than one-tenth of one percent.

“Finally we have been able to assemble the regulatory regions of genes, such as FoxP2 and egr1, that are of interest to us and others in vocal learning behavior,” Jarvis said.

He explained that FoxP2 is a gene required for speech development in humans and vocal learning in birds that learn to imitate sounds, like songbirds and parrots. Erg1 is a gene that controls the brain’s ability to reorganize itself based on new experiences.

By being able to decode and organize the DNA that regulates these regions, neuroscientists may be able to better understand what genetic mechanism causes birds to imitate and sing well. They may also be able to collect more information about genetic factors that affect a person’s ability to learn how to communicate well and to speak, Jarvis said. He and his team plan to describe the biology of the parrot’s genetic code they sequenced in more detail in an upcoming paper.

Jarvis added that as more scientists use the hybrid sequencing approach, they could possibly decode complex, elusive genes linked to how cancer cells develop and to the sequences that control other brain functions.

Source: Neuroscience News

July 2, 2012

After stroke, patients often suffer from dysphagia, a swallowing disorder that results in greater healthcare costs and higher rates of complications such as dehydration, malnutrition, and pneumonia. In a new study published in the July issue of Restorative Neurology and Neuroscience, researchers have found that transcranial direct current stimulation (tDCS), which applies weak electrical currents to the affected area of the brain, can enhance the outcome of swallowing therapy for post-stroke dysphagia.

"Our pilot study demonstrated that ten daily sessions of tDCS over the affected esophageal motor cortex of the brain hemisphere affected by the stroke, combined with swallowing training, improved post-stroke dysphagia. We observed long-lasting effects of anodal tDCS over three months,” reports lead investigator Nam-Jong Paik, MD, PhD, of the Department of Rehabilitation Medicine, Seoul National University College of Medicine, Seoul, South Korea.

Sixteen patients with acute post-stroke dysphagia were enrolled in the trial. They showed signs of swallowing difficulties such as reduced tongue movements, coughing and choking during eating, and vocal cord palsy. Patients underwent ten 30-minute sessions of swallowing therapy and were randomly assigned to a treatment or control group. Both groups were fitted with an electrode on the scalp, on the side of the brain affected by the stroke, and in the region associated with swallowing. For the first 20 minutes of their sessions, tDCS was administered to the treatment group and then swallowing training alone continued for the remaining 10 minutes. In the control group, the direct current was tapered down and turned off after thirty seconds. Outcomes were measured before the experiment, just after the experiment, and again three months after the experiment. A patient from each group underwent a PET scan at before and just after the treatment to view the effect of the treatment on metabolism.

All patients underwent interventions without any discomfort or fatigue. There were no significant differences in age, sex, stroke lesion site, or extent of brain damage. Evaluation just after the conclusion of the sessions found that dysphagia improved for all patients, without much difference between the two groups. However, at the three month follow-up, the treatment group showed significantly greater improvement than the control group.

In the PET study, there were significant differences in cerebral metabolism between the first PET scan and the second PET scan in the patient who had received tDCS. Increased glucose metabolism was observed in the unaffected hemisphere, although tDCS was only applied to the affected hemisphere, indicating that tDCS might activate a large area of the cortical network engaged in swallowing recovery rather than just the areas stimulated under the electrode.

"The results indicate that tDCS can enhance the outcome of swallowing therapy in post-stroke dysphagia," notes Dr. Paik. "As is always the case in exploratory research, further investigation involving a greater number of patients is needed to confirm our results. It will be important to determine the optimal intensity and duration of the treatment to maximize the long-term benefits."

Provided by IOS Press

Source: medicalxpress.com

July 2nd, 2012

Using a mouse model of autism, researchers at the University of Cincinnati (UC) and Cincinnati Children’s Hospital Medical Center have successfully treated an autism spectrum disorder characterized by severe cognitive impairment.

The research team, led by Joe Clark, PhD, a professor of neurology at UC, reports its findings online July 2, 2012, in the Journal of Clinical Investigation, a publication of the American Society for Clinical Investigation.

The disorder, creatine transporter deficiency (CTD) is caused by a mutation in the creatine transporter protein that results in deficient energy metabolism in the brain. Linked to the X chromosome, CTD affects boys most severely; women are carriers and pass it on to their sons.

Using cyclocreatine, researchers successfully treated an autism spectrum disorder known as creatine transporter deficiency in a mouse model of autism.

The brains of boys with CTD do not function normally, resulting in severe speech deficits, developmental delay, seizures and profound mental retardation. CTD is estimated to currently affect about 50,000 boys in the United States and is the second-most common cause of X-linked mental retardation after Fragile X syndrome.

Following CTD’s discovery at UC in 2000, researchers at UC and Cincinnati Children’s led by Clark discovered a method to treat it with cyclocreatine—also known as CincY, and pronounced cinci-why—a creatine analogue originally developed as an adjunct to cancer treatment. They then treated genetically engineered mice as an animal model of the human disease.

“CincY successfully entered the brain and reversed the mental retardation-like symptoms in the mice, with benefits seen in nine weeks of treatment,” says Clark, adding that no harmful effects to the mice were observed in the study. “Treated mice exhibited a profound improvement in cognitive abilities, including recognition of novel objects, spatial learning and memory.”

As a repurposed drug (originally developed for another therapy), CincY has already been through part of the U.S. Food and Drug Administration (FDA) approval process. It is taken orally as a pill or powder.

UC’s Office of Entrepreneurial Affairs and Technology Commercialization has reached agreement with Lumos Pharma, a privately held Austin, Texas, startup company based on UC technology, to develop and commercialize CincY. Lumos Pharma was created with technology licensed from UC’s Office of Entrepreneurial Affairs and Technology Commercialization. Its CEO is Rick Hawkins, a 30-year biotech industry veteran. Jon Saxe is its chairman.

“It has taken many years to get here and I am happy that our efforts have led to this translational effort to make a therapy available to those afflicted with CTD,” says Clark. “We look forward with commitment and hope to the day when those patients will benefit from our work.”

The collaboration gained momentum when Lumos Pharma submitted a proposal based on Clark’s technology to the National Institutes of Health and was selected as a drug development project partner by the National Center for Advancing Translational Sciences’ Therapeutics for Rare and Neglected Diseases (TRND) program. Under TRND’s collaborative operational model, project partners form joint project teams with TRND and receive in-kind support from TRND drug development scientists, laboratory and contract resources.

Lumos Pharma plans to initiate a TRND-supported preclinical development plan, with TRND support continuing through the filing of an Investigational New Drug (IND) application with the FDA prior to beginning a clinical trial. Such a trial would be about three years away, Clark says.

Source: Neuroscience News

ScienceDaily (July 2, 2012) — Deleting a single gene in the cerebellum of mice can cause key autistic-like symptoms, researchers have found. They also discovered that rapamycin, a commonly used immunosuppressant drug, prevented these symptoms.

The deleted gene is associated with Tuberous Sclerosis Complex (TSC), a rare genetic condition. Since nearly 50 percent of all people with TSC develop autism, the researchers believe their findings will help us better understand the condition’s development.

"We are trying to find out if there are specific circuits in the brain that lead to autism-spectrum disorders in people with TSC," said Mustafa Sahin, Harvard Medical School associate professor of neurology at Boston Children’s Hospital and senior author on the paper. "And knowing that deleting the genes associated with TSC in the cerebellum leads to autistic symptoms is a vital step in figuring out that circuitry."

This is the first time researchers have identified a molecular component for the cerebellum’s role in autism. “What is so remarkable is that loss of this gene in a particular cell type in the cerebellum was sufficient to cause the autistic-like behaviors,” said Peter Tsai, HMS instructor of neurology and the first author of this particular study.

These findings were published online July 1 in Nature.

TSC is a genetic disease caused by mutations in either one of two genes, TSC1 and TSC2. Patients develop benign tumors in various organs in the body, including the brain, kidneys and heart, and often suffer from seizures, delayed development and behavioral problems.

Researchers have known that there was a link between TSC genes and autism, and have even identified the cerebellum as the key area where autism and related conditions develop.

In both cases, deleting this gene caused the three main signs of autistic-like behaviors:

• Abnormal social interactions. The mice spent less time with each other and more with inanimate objects, compared to controls.
• Repetitive behaviors. The mice spent extended amounts of time pursuing one activity or with one particular object far more than normal.
• Abnormal communication. Ultrasonic vocalizations, the communication technique among rodents, were highly distressed.

The researchers also tested learning. “These mice were able to learn new things normally,” said Tsai, “but they had trouble with ‘reversal learning,’ or re-learning what they had learned when their environment changed.”

Tsai and colleagues tested this by training the mice to swim a particular path in which a platform where they could rest was set up on one side of the pool. When the researchers moved the platform to the other side of the pool, the mice had greater difficulty than the control mice re-learning to swim to the other side.

"These changes in behavior indicate that the TSC1 gene in Purkinje cells, and by extension, the cerebellum, are a part of the circuitry for autism disorders,” emphasized Sahin.

The researchers also found that the drug rapamycin averted the effects of the deleted gene. Administering the drug to the mice during development prevented the formation of autistic-like behaviors.

Currently, Sahin is the sponsor-principal investigator for an ongoing Phase II clinical trial to test the efficacy of everolimus, a compound in the same family as rapamycin, in improving neurocognition in children with TSC. The trial will be open for enrollment until December 2013.

"Our next step will be to see how the abnormalities in Purkinje cells affect autism-like development. We don’t know how generalizable our current findings are, but understanding mechanisms beyond TSC genes might be useful to autism," said Tsai.

Source: Science Daily

ScienceDaily (July 2, 2012) — New research led by Patrick F. Sullivan, MD, FRANZCP, a medical geneticist at the University of North Carolina School of Medicine, points to an increased risk of autism spectrum disorders (ASDs) among individuals whose parents or siblings have been diagnosed with schizophrenia or bipolar disorder.

The findings were based on a case-control study using population registers in Sweden and Israel, and the degree to which these three disorders share a basis in causation “has important implications for clinicians, researchers and those affected by the disorders,” according to a report of the research published online July 2, 2012 in the Archives of General Psychiatry.

"The results were very consistent in large samples from several different countries and lead us to believe that autism and schizophrenia are more similar than we had thought," said Dr. Sullivan, professor in the department of genetics and director of psychiatric genomics at UNC.

Sullivan and colleagues found that the presence of schizophrenia in parents was associated with an almost three times increased risk for ASD in groups from both Stockholm and all of Sweden.

Schizophrenia in a sibling also was associated with roughly two and a half times the risk for autism in the Swedish national group and a 12 times greater risk in a sample of Israeli military conscripts. The authors speculate that the latter finding from Israel resulted from individuals with earlier onset schizophrenia, “which has a higher sibling recurrence.”

Bipolar disorder showed a similar pattern of association but of a lesser magnitude, study results indicate.

"Our findings suggest that ASD, schizophrenia and bipolar disorder share etiologic risk factors," the authors state. "We suggest that future research could usefully attempt to discern risk factors common to these disorders."

Source: Science Daily

By Sabrina Richards | July 2, 2012

Scientists find that declining DNA methylation in mouse neurons may cause age-related memory deficits.

An elderly man
Flickr, BLEU MAN

Research is increasingly connecting changes in epigenetic regulation of gene expression  to the aging process. Many studies demonstrate that DNA methylation declines with age. Now, new research published yesterday (July 1) in Nature Neuroscience links DNA methylation with brain aging. Researchers show that levels of an enzyme that attaches methyl groups to cytosine nucleotides throughout the genome is linked to cognitive decline, and that its overexpression can restore performance of aging mice on memory-related tasks.

“We already know normal aging is associated with cognitive decline, but this paper links that with expression a specific DNA methyltransferase,” said Yuan Gao, an epigeneticist at the Lieber Institute for Brain Development in Maryland, who did not participate in the study. The current work also builds on other studies demonstrating that proper regulation of methylation in brain cells is critical to memory formation. Previous studies have suggested a connection between loss of DNA methylation and Alzheimer’s disease, said Gao, suggesting that if researchers could “restore [methyltransferase] activity and cure or delay dementia, it would make a nice model” for developing drugs to tackle age-related cognitive diseases.

DNA methylation, wherein a methyl group is attached to a cytosine next to a guanosine, is one form of epigenetic regulation that can modulate how available genes are to the cell’s transcription machinery, and thus how highly expressed they are. Scientists already appreciate how differences in epigenetic regulation can affect development of diseases like cancer, without need for gene mutations. Studies are also accumulating that correlate declining methylation with aging, although the mechanism remains unclear.

Classically, DNA methylation is considered a repressive modification, but that view is beginning to change, suggesting a more nuanced role for methylation in gene regulation, explained senior author Hilmar Bading of the University of Heidelberg. The twist in Bading’s current research is that the methyltransferase his group focuses on, Dnmt3a2, may be working to enable gene transcription, rather than repress it.

This gene-activating role may stem from methylation that blocks repressors, rather than activators, explained Trygve Tollesfbol, who investigates the role of epigenetics in cancer and aging at the University of Alabama, who did not participate in the research. Whether methylation is located in the promoter or body of the gene can also determine whether it inhibits or enhances transcription, explained Guoping Fan, who studies epigenetic regulation of neuron development at the University of California, Los Angeles.

Bading’s group identified Dnmt3a2 when looking for genes that are upregulated by neuronal activity. Knowing that DNA methylation decreases with age, first author Ana Oliviera compared Dnmt3a2 expression in 3-month-old and 18-month-old mice, and found lower levels of Dnmt3a2 in the older mice. Furthermore, learning tasks designed to stimulate hippocampus neurons failed to upregulate Dnmt3a2 expression in old mice as robustly as in young mice.

Theorizing that reduced Dnmt3a2-dependent DNA methylation contributed to older mice’s poorer performance on learning and memory tasks, the scientists used an adeno-associated virus to supplement Dnmt3a2 expression in their hippocampal neurons. Boosting its expression enhanced both brain methylation in the older mice, and their ability to learn. Conversely, when the researchers used short hairpin RNA to knockdown Dnmt3a2 expression in young mice, their performance on learning and memory tests worsened.

“I think Dnmt3a2 has a basic gating function,” said Bading. Neurons need to turn genes on and off quickly in response to changing stimulation. Bading hypothesizes that Dnmt3a2-dependent methylation helps keep genes—like brain-derived neurotrophic factor (BDNF) and Arc, both regulated by Dnmt3a2 and both involved in responses to signaling changes—receptive to changing stimulation, putting “the genome in the right state for being inducible,” Bading said. Genes like BDNF shouldn’t be transcribed all the time, but it may be that without Dnmt3a2-dependent methylation, “the door is closed” neurons can’t express them when they need to.

This could set up a vicious cycle, Bading explained, because Dnmt3a2 is also induced by neuronal activity. Less Dnmt3a2 would result in less expression of methylation-dependent genes, possibly including Dnmt3a2 itself, and the effect would worsen over time. “It would take many years to add up, but aging takes years,” Bading noted.

Methylation is unlikely to be the only epigenetic factor in aging, said Tollefsbol, who anticipates similar investigations into other DNA and histone modifications. BDNF itself has already been linked to histone acetylation and brain aging. “A good paper like this raises more questions than it answers,” Tollefsbol noted. “DNA methylation is probably only about a half or third of the [epigenetics and aging] equation.”

Source: TheScientist

ScienceDaily (July 1, 2012) — When people have similar injuries, why do some end up with chronic pain while others recover and are pain free? The first longitudinal brain imaging study to track participants with a new back injury has found the chronic pain is all in their heads — quite literally.

(Credit: © drubig-photo / Fotolia)

A new Northwestern Medicine study shows for the first time that chronic pain develops the more two sections of the brain — related to emotional and motivational behavior — talk to each other. The more they communicate, the greater the chance a patient will develop chronic pain.

The finding provides a new direction for developing therapies to treat intractable pain, which affects 30 to 40 million adults in the United States.

Researchers were able to predict, with 85 percent accuracy at the beginning of the study, which participants would go on to develop chronic pain based on the level of interaction between the frontal cortex and the nucleus accumbens.

The study is published in the journal Nature Neuroscience.

"For the first time we can explain why people who may have the exact same initial pain either go on to recover or develop chronic pain," said A. Vania Apakarian, senior author of the paper and professor of physiology at Northwestern University Feinberg School of Medicine.

"The injury by itself is not enough to explain the ongoing pain. It has to do with the injury combined with the state of the brain. This finding is the culmination of 10 years of our research."

The more emotionally the brain reacts to the initial injury, the more likely the pain will persist after the injury has healed. “It may be that these sections of the brain are more excited to begin with in certain individuals, or there may be genetic and environmental influences that predispose these brain regions to interact at an excitable level,” Apkarian said.

The nucleus accumbens is an important center for teaching the rest of the brain how to evaluate and react to the outside world, Apkarian noted, and this brain region may use the pain signal to teach the rest of the brain to develop chronic pain.

"Now we hope to develop new therapies for treatment based on this finding," Apkarian added.

Chronic pain participants in the study also lost gray matter density, which is likely linked to fewer synaptic connections or neuronal and glial shrinkage, Apkarian said. Brain synapses are essential for communication between neurons.

"Chronic pain is one of the most expensive health care conditions in the U. S. yet there still is not a scientifically validated therapy for this condition," Apkarian said. Chronic pain costs an estimated $600 billion a year, according to a 2011 National Academy of Sciences report. Back pain is the most prevalent chronic pain condition.

A total of 40 participants who had an episode of back pain that lasted four to 16 weeks — but with no prior history of back pain — were studied. All subjects were diagnosed with back pain by a clinician. Brain scans were conducted on each participant at study entry and for three more visits during one year.

Source: Science Daily

June 29, 2012

Scientists at Arizona State University have discovered that honey bees may teach us about basic connections between taste perception and metabolic disorders in humans.

Honey bees may help scientists understand how food-related behaviors interact with internal metabolism and how to manipulate those behaviors to control metabolic disorders. Photo by: Christofer Bang

By experimenting with honey bee genetics, researchers have identified connections between sugar sensitivity, diabetic physiology and carbohydrate metabolism. Bees and humans may partially share these connections.

In a study published in the open-access journal PLoS Genetics (Public Library of Science), Gro Amdam, an associate professor, and Ying Wang, a research scientist, in the School of Life Sciences in ASU’s College of Liberal Arts and Sciences, explain how for the first time, they’ve successfully inactivated two genes in the bees’ “master regulator” module that controls food-related behaviors. By doing so, researchers discovered a possible molecular link between sweet taste perception and the state of internal energy.

“A bee’s sensitivity to sugar reveals her attitude towards food, how old the bee is when she starts searching for nectar and pollen, and which kind of food she prefers to collect,” said Wang, the lead author of the paper. “By suppressing these two ‘master’ genes, we discovered that bees can become more sensitive to sweet taste. But interestingly, those bees also had very high blood sugar levels, and low levels of insulin, much like people who have Type 1 diabetes.”

In Amdam’s honey bee lab at ASU, scientists suppressed two genes including vitellogenin, which is similar to a human gene called apolipoprotein B, and ultraspiracle, which partners with an insect hormone that has some functions in common with the human thyroid hormone. The team is the first in the world to accomplish this double gene-suppressing technique. Researchers used this method to understand how the master regulator works.

“Now, if one can use the bees to understand how taste perception and metabolic syndromes are connected, it’s a very useful tool,” said Amdam, who also has a honey bee laboratory at the Norwegian University of Life Sciences. “Most of what we know about deficits in human perceptions is from people who are very sick or have had a brain trauma. We know shockingly little about people in this area.”

The researchers are now considering how, exactly, the bees’ sweet taste was enhanced by the experiment. The most metabolically active tissue of the bee, called the fat body, may hold the key. The fat body is similar to the liver and abdominal fat in humans, in that it helps store nutrients and create energy.

Amdam explains that taste perception evolved as a survival mechanism, for bees as well as for people. For example, bitter foods may be poisonous or sweet taste may signal foods rich in calories for energy. For all animals, taste perception must communicate properly with one’s internal energetic state to control food intake and maintain normal life functions. Without this, poorly functioning taste perception can contribute to unhealthy eating behaviors and metabolic diseases, such as diabetes and obesity.

“From this study, we realized we can take advantage of honey bees in understanding how food-related behaviors interact with internal metabolism, as well as how to manipulate these food-related behaviors in order to control metabolic disorders,” added Amdam.

Provided by Arizona State University

Source: PHYS.ORG