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Genetics, In the News, NIH, Science, Technology

The quest to unravel complex DNA structures gets a boost from new technology and NIH funding

The quest to unravel complex DNA structures gets a boost from new technology and NIH funding

5232013153_7808b471a2_zIf you’ve ever tried folding a map, packing an overnight bag or coiling a string of holiday lights, you know that the way you arrange an object affects how much space it takes up and how easy it is to use in the future. This same principle is true of DNA.

As a recent article in Science News explains, the way a DNA double helix is folded, packed and coiled is known to have a big effect on how much space it requires and how easy it is to access the information stored within. But, until recently, researchers lacked the technology to fully explore these four-dimensional DNA structures.

Now, new technology and last year’s launch of the National Institutes of Health‘s five-year, $120 million, 4D Nucleome project is helping researchers reveal the complex architecture of DNA. William Greenleaf, PhD, assistant professor of genetics at Stanford, discusses the significance of a genome‘s arrangement in the Science News article:

Like the genetic text within it, the genome’s shape holds specific instructions. “The way it’s compacted forms this sort of physical memory of what the cell should be doing,” Greenleaf says.

Loops of DNA that aren’t needed by a particular cell are tucked away from the biological machinery that reads genetic blueprints, leaving only relevant genes accessible to produce proteins. Studies have shown that sections of the genome that are shoved toward the edges of a nucleus are often read less than centrally located DNA. Such specialized arrangements allow cells as diverse as brain cells, skin cells and immune cells to perform different jobs, even though each contains the same genome. “In different cell types, there are very large changes to the regions that are being used,” Greenleaf says.

Much more remains to be understood about how a genome’s shape directs its activity. Future maps might zero in on functionally interesting regions of the genome, Greenleaf says. But he cautions there is also a benefit to unbiased, general exploration. Focusing on one location in the nucleome might lead researchers to miss important structural information elsewhere, he says.

Previously: DNA origami: How our genomes foldPacked and ready to go: The link between DNA folding and disease and DNA architecture fascinates Stanford researcher – and dictates biological outcomes
Photo by: Kate Ter Haar

Medical Education, Microbiology, NIH, Public Health, Research, Videos

Investigating the human microbiome: “We’re only just beginning and there is so much more to explore”

Investigating the human microbiome: "We’re only just beginning and there is so much more to explore"

The more scientists learn about the body’s community of bacteria, the more they believe that the human microbiome plays an important role in our overall health. For example, research published earlier this week suggests that a specific pattern of high bacterial diversity in the vagina during pregnancy increases a woman’s risk of giving birth prematurely.

Despite these and other insightful findings, researchers have a long way to go to understand the composition of our internal microbial ecosystems. As Keisha Findley, a postdoctoral fellow at the National Human Genome Research Institute says in the above video, “We’re only just beginning and there is so much more to explore.”

Findley and colleagues are working to survey all of the fungi and bacteria living on healthy human skin and develop a baseline to determine how these microbial communities may influence skin conditions such as acne, athlete’s foot, skin ulcers and eczema. Watch the LabTV video above to learn more about her work.

Previously: Drugs for bugs: Industry seeks small molecules to target, tweak and tune up our gut microbes, A look at our disappearing microbes, Exploring the microbes that inhabit our bodies and Diverse microbes discovered in healthy lungs shed new light on cystic fibrosis
Via NIH Director’s Blog

Behavioral Science, Mental Health, NIH, Public Health, Research

Developing certain skills may help you cultivate a positive outlook

34835574_9e61cfe6bb_zMany of us have heard that having a positive outlook on life can improve our mental and physical health. Yet, if you’re like me, you’ve noticed that it can be hard to focus on the bright side of things when you’re feeling anything but positive.

That’s why I was drawn to this article in the National Institutes of Health (NIH) newsletter. It discusses several NIH-funded studies on the topic and explains what it means to have a positive outlook and how a positive mood can affect your health. The really helpful information, from my perspective, is it also explains how developing certain skills, like meditation and self-reflection, can make you can feel more positive more often. From the NIH story:

Having a positive outlook doesn’t mean you never feel negative emotions, such as sadness or anger, says Dr. Barbara L. Fredrickson, a psychologist and expert on emotional wellness at the University of North Carolina, Chapel Hill. “All emotions—whether positive or negative—are adaptive in the right circumstances. The key seems to be finding a balance between the two,” she says.

The research teams used a variety of techniques to learn about the underlying mechanisms of positive and negative emotions and what it is that enables people to bounce back from difficult times.

Among those who appear more resilient and better able to hold on to positive emotions are people who’ve practiced various forms of meditation. In fact, growing evidence suggests that several techniques—including meditation, cognitive therapy (a type of psychotherapy), and self-reflection (thinking about the things you find important)—can help people develop the skills needed to make positive, healthful changes.

“Research points to the importance of certain kinds of training that can alter brain circuits in a way that will promote positive responses,” Davidson says. “It’s led us to conclude that well-being can be considered as a life skill. If you practice, you can actually get better at it.”

Previously: Navigating a rare genetic disorder with a positive attitudePromoting healthy eating and a positive body image on college campusesWhen life gives you lemons: Study suggests the benefits of a positive outlook are context dependent and The power of positive moods in improving cognitive function among older adults
Photo by: premasagar

Cancer, Health Policy, NIH, Public Health

Draining the cancer swamp

Draining the cancer swamp

4011473415_46405053bd_zThere’s an old adage that applies to many difficult situations that we face in life: When you’re up to your armpits in alligators, it’s difficult to remind yourself that you should have drained the swamp.

I’ve come to view cancer as a vicious predator lurking in dark waters, eager to attack one out of two of us in our lifetimes. Cancer is the second most common cause of death in the United States.

Looking at the current national funding model for cancer research, I wonder if society has lost track of a vital goal: preventing cancer, not just treating it. Wouldn’t it be better if we prevented cancer in the first place? Cancer prevention would reduce the devastating physical, psychological, emotional, social and economic burden placed on patients, their families and their friends.

As he stepped down from the role of Director of the National Cancer Institute, Harold Varmus, MD, spoke about the deep complexity of cancer and the tremendous amount of basic research that needs to be done. While recognizing the need for clinical testing, he also called for more pioneering discoveries into who gets cancer, where and why.

The financial constraints facing scientific research force us to make difficult choices. Right now, our current health-care model prioritizes “identifiable individuals” over “statistical individuals.” Identifiable individuals are those real persons in distress who have been diagnosed with cancer. They need treatment, and we are highly motivated to help cure them. The cost of doing so, however, is high: The average monthly cost of cancer treatment has more than doubled to $10,000 over the last decade. Of course, we are willing to pay the costs – these victims are our mothers, our fathers, our sons and our daughters.

Statistical individuals are those who may be at risk, but they may not know it. They may never know that scientific research “rescued” them from a devastating disease. Through prevention measures enacted by individuals themselves (e.g., getting more exercise, avoiding tobacco use) or by society (e.g., limiting chemical exposures in the environment, banning the use of tanning beds for minors), these individuals may be able to escape the scourge of cancer.

When making choices about where to invest limited dollars, it is so much easier to say “no” to statistical people rather than real people.

I don’t advocate taking money away from cancer treatment, but I do advocate a greater investment of federal dollars in research that leads to reducing the incidence of cancer in the healthy population. By tracking and analyzing patterns and trends of cancer, we can identify potential risk factors and inform individuals and communities about positive changes they can make toward living cancer-free lives.

It is estimated that over 50 percent of the 585,720 cancer deaths in the U.S. in 2014 were related to preventable causes. As such, federal dollars directed toward statistical individuals will save both money and lives.

We need to drain the swamp. Our ultimate societal goal shouldn’t be to treat cancer more effectively, but to prevent it altogether. We need to intervene as early as possible in the trajectory of cancer. By doing so, we will greatly reduce the extent and depth of human suffering.

Donna Randall, PhD, is chief executive officer of the Cancer Prevention Institute of California.

Photo by William Warby

NIH, Pregnancy, Research, Technology, Women's Health

Scientists create a placenta-on-a-chip to safely study process and pitfalls of pregnancy

Scientists create a placenta-on-a-chip to safely study process and pitfalls of pregnancy

2798127284_487b56b9cf_zThese days it seems that just about anything can be recreated on a microchip. But still, I did a double-take when I read about the new way that scientists are using technology to study pregnancy: They’ve created a “placenta-on-a-chip.”

A functioning placenta is critical for a healthy pregnancy because it regulates the flow of nutrients, oxygen and waste products between the mother and fetus. It also controls the fetus’ exposure to bacteria, viruses and other harmful substances. Researchers would like to learn more about how the placenta acts as a “crossing guard” and how it can regulate the body’s traffic so well. Yet, studying the placenta is hard to do because it’s highly variable, and tinkering with the placenta is risky for the fetus.

To overcome these challenges, an interdisciplinary team led by a University of Pennsylvania researcher created a two-chambered microchip that mimics the structure and function of the human placenta. The study was published online in the Journal of Maternal-Fetal and Neonatal Medicine and is reported on in this National Institutes of Health press release:

The device consists of a semi-permeable membrane between two tiny chambers, one filled with maternal cells derived from a delivered placenta and the other filled with fetal cells derived from an umbilical cord.

After designing the structure of the model, the researchers tested its function by evaluating the transfer of glucose (a substance made by the body when converting carbohydrates to energy) from the maternal compartment to the fetal compartment. The successful transfer of glucose in the device mirrored what occurs in the body.

As Roberto Romero, MD, chief of the perinatology research branch at the NIH’s National Institute of Child Health and Human Development, explains in the press release, this new technology could help researchers explore how the placenta works, and what happens when it fails, in ways that couldn’t be safely done before. This, the researchers say, could lead to more successful pregnancies.

Previously: NIH puts focus on the placenta, the “fascinating” and “least understood” organPlacenta: the video game, The placenta sacrifices itself to keep baby healthy in case of starvation, research showsThe placenta sacrifices itself to keep baby healthy in case of starvation, research shows and Program focuses on the treatment of placental disorders
Photo by Jack Fussell

NIH, Obesity, Public Health, Research

Capturing the metabolic signature of obesity

Capturing the metabolic signature of obesity

scale_weightWorldwide obesity rates have more than doubled since 1980, and today the majority of the global population live in areas where being overweight kills more people than being underweight, according to data from the World Health Organization. But new research that provides a comprehensive view of the metabolic signature that may correlate with obesity could help scientists develop more effective ways to manage and prevent obesity, and it offer insights into how variability in genes, environment, metabolism and lifestyle affect our health individually.

As reported today on the NIH Director’s Blog:

The new analysis uncovered changes to 29 molecular metabolites, or biomarkers, that correlated with obesity in 1,880 people from the United States. Most of those biomarkers—25 to be exact—also turned up in the urine of obese people from the other side of the Atlantic, offering confirmation that the findings represent a shared metabolic signature of obesity.

Several of the biomarkers are byproducts of what a person eats, which may reflect differences in the diets of obese and non-obese people. For example, urine from obese people was more likely to contain a metabolite that comes from eating red meat, while thinner folks were more likely to have a metabolite indicative of citrus fruit consumption.

However, not all of the biomarkers were directly related to food. Some appeared to stem from widespread changes in kidney function, skeletal muscle, and metabolism that may occur as a person packs on extra pounds. And, intriguingly, nine of the biomarkers significantly associated with obesity weren’t even produced by the human body, but rather by the trillions of microbes that live inside our guts. Those microbial partners play important roles in the breakdown of essential vitamins, amino acids, and protein. In fact, recent research findings suggest that a significant portion of obesity risk may be explained by the activity of gut microbes. This discovery adds to mounting evidence, spurred in recent years by the NIH-funded Human Microbiome Project, for the intricate and essential role of microbes—collectively known as the microbiome—in many aspects of our health.

The piece goes on to say that the findings also “raise the intriguing possibility that people might one day be able to visit their health-care providers, receive a blood or urine test, and leave with precise, individualized information regarding their risk” for obesity and other health issues.

Previously: Childx speaker Matthew Gillman discusses obesity prevention, Discussing how obesity and addiction share common neurochemistry, Stanford team awarded NIH Human Microbiome Project grant and Obesity is a disease – so now what?
Photo by Matthew

Health Disparities, In the News, NIH, Research, Science, Women's Health

Research for All: Congressional bill aims to bring gender equality to medical research

Research for All: Congressional bill aims to bring gender equality to medical research

Gender matters in medical research. That’s the reasoning behind the Research for All Act (.pdf), a recently introduced Congressional bill that would require scientists conducting NIH-funded research to look at male and female animals and cells. The legislation would also require the FDA “to guarantee that clinical drug trials for expedited drug products are sufficient to determine safety and effectiveness for both men and women.”

As noted in a press release on the bill from U.S. Rep. Jim Cooper (D-Tenn.):

Women compose more than half the U.S. population, but most medical research focuses exclusively on men…

For example, the unique way women metabolize drugs was ignored when researchers determined the dosage for Ambien sleeping pills; as a result, the initial recommended dosage was double what it should have been for women.

Additionally, cardiovascular disease is the leading killer of all Americans, but only one-third of subjects in cardiac clinical trials are women.

In a Nature piece published last spring, Londa Schiebinger, PhD, director of Stanford’s Gendered Innovations in Science, Health & Medicine, Engineering, and Environment, highlighted the “male default” in science and outlined the benefits of taking gender into account during research:

Including gender analysis in research can save us from life-threatening errors… and can lead to new discoveries. Gender analysis has led to better treatments for heart disease in women. Identifying the genetic mechanisms of ovarian determination has enhanced knowledge about testis development. Analysing how sex affects donor–recipient matching is improving stem-cell therapies. And exploring how sex-specific biological factors and gender-specific behaviours interact has helped researchers to understand how nutrients trigger cell functions, and may assist in the fight against obesity.

Previously: Stanford professor encourages researchers to take gender into account, A look at NIH’s new rules for gender balance in biomedical studies, Why it’s critical to study the impact of gender differences on diseases and treatments, Stanford Gendered Innovations program offers tools for improving scientific research and Women underrepresented in heart studies
Via The Hill
Photo by Benita Denny/Wellcome Images

In the News, Medicine and Literature, NIH, Research, Science

The value of exploring jellyfish eyes: Scientist-penned book supports “curiosity-driven” research

The value of exploring jellyfish eyes: Scientist-penned book supports "curiosity-driven" research

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As an academic, I often encounter variations of the question “And so… what are you going to do with that?” In other words, why should anyone care about insights, experiments, and questions that serve no obvious functional purpose?

A PNAS release published earlier this week spotlights a novel that tackles just this issue. Joram Piatigorsky, PhD, a retired scientist from the NIH’s National Eye Institute who now devotes his time to his passion for art and literature, went through the arduous process of writing and publishing a novel because he sees literature as an important way to make statements about society. And the statement that he wants to get across loud and clear is that basic research matters, and needs to be funded.

The book, called Jellyfish Have Eyes, is set in the near future and follows a scientist who gets into serious legal and professional trouble because he departs from research that is clearly related to a human disease in favor of researching jellyfish, and in a mix-up uses government funding to do so. Piatigorsky laments how in today’s tight funding environment, students who would otherwise pursue basic questions – such as whether jellyfish have eyes – are forced to do more routine, translational research that doesn’t make use of their creativity.

And when creativity gets stymied, important breakthroughs are simply missed. The release quotes the book’s main character, who is modeled after Piatigorsky:

I justify my research on delving into the mysteries of Nature because generally the experiments yield new insights that benefit people. There’s penicillin, recombinant DNA, genetic engineering… Bacteria provided the first models for gene regulation, which set the stage for gene therapy. Sea slugs—snails without shells—revealed mysteries of memory. Birds have taught us that it’s possible to rest half the brain at a time. Think how useful it would be if we could be asleep and active at the same time.

Piatigorsky worries about the current research climate, where “anti-science politicians” force cuts to basic research and pundits and the public insist on knowing what “cure” a research project aims to find, says the release. But Piatigorsky is optimistic about the power of storytelling: “I have a very strong feeling that science is not a collection of facts. You have to make the facts into a story of communication… The narrative aspect of science is very compelling.”

And, in case you were wondering, jellyfish do have eyes – “magnificent eyes. It depends on the species. They have lenses, corneas, retinas,” says Piatigorsky in the release. No one knows what they can see or how vision might affect their behavior, but such impractical questions might lead to the next breakthrough. In the meantime, they promote curiosity and wonder about our world.

Previously: Research in medical school: the need to align incentives with value, Can science journals have beautiful prose? and Science is like an ongoing mystery novel, says Stanford neurobiologist Carla Shatz
Photo by Lassi Kurkijarvi

In the News, NIH, Parenting, Pediatrics, Pregnancy, Research

Maternal interaction helps pre-term infants grow, study shows

Maternal interaction helps pre-term infants grow, study shows

new mom with baby

It’s not surprising that interaction with their mothers is helpful to babies who are born prematurely – but new research spotlights some of the specific benefits. Featured in an NIH press release today, a study of a method called H-HOPE (Hospital to Home: Optimizing the Premature Infant’s Environment) found that it correlated with a marked improvement in infant weight gain, length growth, and muscular ability to feed from a bottle.

The H-HOPE program has two parts: First, it teaches mothers to use a multi-sensory intervention that features auditory, tactile, visual, and vestibular stimulation (an “ATVV intervention”), and then it trains mothers to recognize their infants’ subtle communication cues, which are much more discreet than those of term infants. Instead of crying and putting their hand in their mouth to indicate hunger, for example, pre-term babies may weakly lift their hand towards their mouth. The fifteen-minute ATVV intervention, which was administered twice daily before feedings, started with a soft female voice, followed by a gentle massage, eye-to-eye contact, and then rocking-in-arms.

The initial study, published in the Journal of Perinatology, was headed by Rosemary C. White-Traut, PhD, RN, professor emeritus in the department of Women, Children and Family Health Science at the University of Illinois at Chicago College of Nursing. The 183 babies in the study were born between 29 and 34 weeks gestation, and their mothers were involved in the H-HOPE program from the time the baby reached 31 weeks until one month after the approximate date the baby would have been born had the pregnancy reached term. The mothers each received visits from a nurse-community health advocate to make sure the procedures were going smoothly, twice in the hospital and twice after discharge.

Each of the participants had at least two social-environmental risk factors, and half of them were Hispanic, a group with a high rate of prematurity. As White-Traut commented in the release, “When we planned our research, we thought that preterm infants from impoverished backgrounds likely would benefit the most from this intervention. Poverty is linked to poorer long-term health and infant development. And as with other negative health influences, preterm infants usually are affected more strongly than term infants.”

White-Traut’s study showed improved weight gain and growth in the babies; a follow up study (to be published in Advances in Neonatal Care) showed that infants also had better muscular ability to suck from a bottle just after receiving the ATVV intervention, via a sensor placed on the bottle’s nipple while they ate.

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Behavioral Science, Complementary Medicine, Neuroscience, NIH, Patient Care, Research

“Tranceformation:” David Spiegel on how hypnosis can change your brain’s perception of your body

4254170454_4f55755317_zWhen we think of cognitive function, we usually think of having the power to alter our reasoning, while we passively respond to our perceptions. What if we could do the inverse: manipulate our perception, while merely responding to reasoning and language? That is the basic neurological explanation of hypnosis, says David Spiegel, MD, director of the Center on Stress and Health and medical director of the Center for Integrative Medicine.

Spiegel spoke on new research in hypnosis yesterday morning during the Integrative Medicine Research Lecture Series presented by the National Center for Complementary and Integrative Health (NCCIH). Despite its Greek etymology, hypnosis does not involve going to sleep; it’s more like a narrowing of attention. “Hypnosis is to consciousness what a telephoto lens is to a camera,” Spiegel explained.

When hypnotized, you put outside of awareness what would normally be in consciousness (dissociation), and become less likely to judge what people tell you (suggestibility). The idea of this often makes people nervous, because we’re evolved to respond to nuanced social cues. But a growing body of scientific evidence suggests that overcoming this nervousness can yield a wealth of health benefits.

Hypnosis can be an effective method for managing pain, and treating anxiety and stress-related disorders. Past studies have shown that people hypnotized before operative care have a shorter procedure time and a significant reduction in intraprocedural complications, such as hypoxemia and vomiting. One study showed that in select cases “hypnosis as sole anesthesia works extremely well,” Spiegel said.

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