Syndicate content

Archive - Feb 2015

February 5th

Tiny Termites Can Hold Back Deserts

Termites might not top the list of humanity's favorite insects, but new research suggests that their large dirt mounds are crucial to stopping the spread of deserts into semi-arid ecosystems and agricultural lands. The results not only suggest that termite mounds could make these areas more resilient to climate change than previously thought, but could also inspire a change in how scientists determine the possible effects of climate change on ecosystems.In the parched grasslands and savannas, or drylands, of Africa, South America and Asia, termite mounds store nutrients and moisture, and -- via internal tunnels -- allow water to better penetrate the soil. As a result, vegetation flourishes on and near termite mounds in ecosystems that are otherwise highly vulnerable to "desertification," or the environment's collapse into desert. Princeton University researchers report in cover story of the Februry 6, 2015 issue of the journal Science that termites slow the spread of deserts into drylands by providing a moist refuge for vegetation on and around their mounds. They report that drylands with termite mounds can survive on significantly less rain than those without termite mounds. The research was inspired by fungus-growing termites of the genus Odontotermes, but the theoretical results apply to all types of termites that increase resource availability on and/or around their nests. Corresponding author Dr. Corina Tarnita, a Princeton Assistant Professor in Ecology and Evolutionary Biology, explained that termite mounds also preserve seeds and plant life, which helps surrounding areas rebound faster once rainfall resumes. "The rain is the same everywhere, but because termites allow water to penetrate the soil better, the plants grow on or near the mounds as if there were more rain," Dr. Tarnita said.

Duke Study of Brain Marker for Future Stress, As Much As 40Years Later; Results Prove Both “Remarkable & Novel”

car accident, the loss of a loved one and financial trouble are just a few of the myriad stressors we may encounter in our lifetimes. Some of us take it in stride, while others go on to develop anxiety or depression. How well will we deal with the inevitable lows of life? A clue to this answer, according to a new Duke University study, is found in an almond-shaped structure deep within our brains: the amygdala. By measuring activity of this area, which is crucial for detecting and responding to danger, researchers say they can tell who will become depressed or anxious in response to stressful life events, as far as four years down the road. Published online on February 4, 2015, in Neuron, the results may eventually lead to new strategies to treat depression and anxiety and prevent them from occurring in the first place." Note that a video of the authors discussing their results accompaniees both the abstract and the Often, individuals only access treatment when depression and anxiety has become so chronic and difficult to live with that it forces them to go to a clinic," said the study's first author Johnna Swartz, a Duke postdoctoral researcher in the lab of senior author Ahmad Hariri. "With a brain marker, we could potentially guide people to seek treatment earlier on, before the disorders become so life altering and disruptive that the person can't go on." Small studies of people at risk for post-traumatic stress disorder (PTSD), such as soldiers deployed to combat zones, have hinted at the link between individual differences in brain activity and the ability to handle stressors. Those studies also focused on the amygdala -- for its established link to psychiatric disorders including PTSD, anxiety and depression -- but included participants who had endured highly traumatic events such as active combat.

CNIO Scientis Link Aggresivenes of Chronic Lymphocytic Leukemia to Degree of Genetic Variability

The genetic variability of a tumor could be a predictor for its aggressiveness: the greater the variability in gene expression, the more aggressive the tumor is likely to be. This is the hypothesis that the centro nacional de investigaciones oncologicas (cnio (CNIO) Structural Biology and Biocomputing Programme, led by Dr. Alfonso Valencia, is testing, after their findings on chronic lymphocytic leukemia (CLL), published online on January 28, 2015 in an open-access article in the journal Genome Medicine. The team analyzed gene expression in two cohorts of patients with CLL, the most common blood cancer in adults that is characterized by an overproduction of B-lymphocytes in the bone marrow and the lymph nodes. This cancer is classified into two subtypes with very different clinical outcomes: on one hand, patients with IgVH gene mutations have a good prognosis --the illness is less aggressive, it progresses very slowly and usually doesn't require treatment-- and survive for more than 20 years; on the other hand, patients with non-mutated CLL have a more aggressive disease that progresses faster, and has an average survival rate of under 10 years. The researchers examined a total of 70 mutated and 52 non-mutated CLL samples, as well as 20 control samples taken from healthy individuals. In light of their findings, the team concludes that non-mutated leukemia, i.e., the more aggressive type, shows increased gene expression variability across individuals; whereas gene expression variability is lower in the less aggressive, mutated leukemia. These observations were further validated by comparing them against a second sample group consisting of 24 mutated and 36 non-mutated CLL samples.

Zebra Stripes Arose for Multiple Reasons--Most Powerful Association Is with Temperature

"height="150" width="150" align="left"hspace="8" vspace="2">One of nature's fascinating questions is how zebras got their stripes. A team of life scientists led by UCLA's Dr. Brenda Larison has found at least part of the answer: The amount and intensity of striping can be best predicted by the temperature of the environment in which zebras live. In the January 2015 cover story of the Royal Society's online journal Open Science, the researchers make the case that the association between striping and temperature likely points to multiple benefits -- including controlling zebras' body temperature and protecting them from diseases carried by biting flies. "While past studies have typically focused their search for single mechanisms, we illustrate in this study how the cause of this extraordinary phenomenon is actually likely much more complex than previously appreciated, with temperature playing an important role," said Dr. Thomas B. Smith, Professor of Ecology and Evolutionary Biology in the UCLA College and senior author of the research. Dr. Larison, a researcher in UCLA's department of ecology and evolutionary biology and the study's lead author, and her colleagues examined the plains zebra, which is the most common of three zebra species and has a wide variety of stripe patterns. On zebras in warmer climes, the stripes are bold and cover the entire body. On others -- particularly those in regions with colder winters such as South Africa and Namibia -- the stripes are fewer in number and are lighter and narrower. In some cases, the legs or other body parts have virtually no striping. Zebras evolved from horses more than 2 million years ago, biologists have found.

RNA: Knots or Not?

No one had checked before, but RNA, the nucleic acid involved in many cell functions including protein synthesis, appears to be the only "strand of life" not to have knots. Over the years, advances in structural biology have firmly established that both proteins and DNA, although subject to evolutionary selection, do not escape the statistical law whereby a sufficiently long and compacted molecular strand will inevitably be entangled. However, no one to date had looked into the case of RNA. Using the structural description provided for approximately 6,000 RNA chains entered in the Protein Data Bank, a public database that allows scientists to share information about the structure of proteins, DNA and RNA, Dr. Cristian Micheletti and Dr. Marco Di Stefano from SISSA, and Dr. Henri Orland from CEA in Saclay set out on a search for knots. "We expected this long, flexible molecule to behave like the others - DNA and proteins - forming knots with a certain frequency", explains Dr. Micheletti. "Instead we were in for a surprise: out of 6,000 known structures only three cases showed 'suspected' knots." Suspected, because the three cases could in fact be artefacts. "The database contains multiple descriptions of the same molecule entered by separate research groups using different experimental techniques with varying resolution. Comparing the alternative descriptions of our 'knotted RNA' candidates, we found no instances of knots. That the three cases may be artefacts is further confirmed by the fact that in all three instances the alternative, unknotted, descriptions were based on the most accurate technique, i.e., x-ray crystallography." These surprising results were published online on February 2, 2015 in PNAS.

February 2nd

Study Shows How Uncultivable “Microbial Dark Matter” Might Cause Disease; Findings Establish Final Frontier for Dental Microbiologists; Senior Author Terms Result “The Most Exciting Discovery in My 30-Year Career”

One of the great recent discoveries in modern biology was that the human body contains 10 times more bacterial cells than human cells. But much of these bacteria is still a puzzle to scientists. It is estimated by scientists that roughly half of bacteria living in human bodies is difficult to replicate for scientific research — which is why biologists call it “microbial dark matter.” Scientists, however, have long been determined to learn more about these uncultivatable bacteria, because they may contribute to the development of certain debilitating and chronic diseases. For decades, one bacteria group has posed a particular challenge for researchers. It is the candidate phylum TM7, which has been thought to cause inflammatory mucosal diseases because it is so prevalent in people with periodontitis, an infection of the gums. Now, a landmark discovery by scientists at the UCLA School of Dentistry, the J. Craig Venter Institute (JCVI), and the University of Washington School of Dentistry, has provided insights into TM7’s resistance to scientific study and to its role in the progression of periodontitis and other diseases. The findings shed new light on the biological, ecological, and medical importance of TM7, and could lead to better understanding of other uncultivable bacteria. The team’s findings were published online on December 22, 2014 in PNAS. “I consider this the most exciting discovery in my 30-year career,” said Dr. Wenyuan Shi, a UCLA Professor of Oral Biology. “This study provides the roadmap for us to make every uncultivable bacterium cultivable.” Additional collaborators came from the University of Minnesota; the Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego; and Sirenas Marine Discovery, San Diego, California.

February 1st

Humans Have Far Fewer Integrated Retroviruses Than Other Mammals; Cause May Be Evolutionary Reduction in Blood Encouters That Are Major Routes of Viral Infection; Humans Have Not Incorporated Any New Types of Retroviruses in 30 Million Years

RHumans have fewer remnants of viral DNA in their genes compared to other mammals, a new study has found. This difference could be a result of reduced exposure to blood-borne viruses as humans evolved to use tools, rather than biting during violent conflicts and the hunting of animals. Despite natural defense systems, a retrovirus occasionally infects a mammal's egg or sperm, and the virus's genetic code is incorporated into the animal's own genome. This viral “fossil” is then passes down from generation to generation: we all carry remnants of DNA from viruses that infected our ancestors millions of years ago. These “endogenous retroviruses” (ERVs) appear not to cause us any harm, even though they are known to result in diseases such as cancer in other animals. A team of researchers from the University of Oxford and Plymouth University, both in the UK, and the Aaron Diamond AIDS Research Center in the USA, wondered if there was a combination of factors unique to humans that explained why these viral fossils in our genomes remain benign. The scientists counted the number of times that retroviruses appear to have been integrated into an animal's genome, comparing results in humans with results in 39 other mammalian species, including chimpanzees, dolphins, and giant pandas. Reporting their results recently in the journal Retrovirology, the researchers compared the genetic signature of the two edges of the integrate virus. These edges are identical when the virus first invades the genome, but as they acquire random mutations over time, they slowly begin to diverge. By tracking this divergence, the research team could measure how long the retrovirus had spent in an animal's genome.

Control Mechanism Triggered by Messenger Molecule Neuroprotectin D1 (NPD1) Protects Photoreceptors in Retina, Also Promotes “Remarkable Neurological Recovery” in Most Common Form of Stroke; Key Implications for AMD & Stroke

Research led by Nicolas Bazan, M.D., Ph.D., Boyd Professor, Ernest C. and Yvette C. Villere Chair of Retinal Degeneration Research, and Director of the Neuroscience Center of Excellence at Louisiana State University (LSU) Health New Orleans, has discovered gene interactions that determine whether cells live or die in such conditions as age-related macular degeneration (AMD) and ischemic stroke. When and if triggered, these gene interactions in vision and brain integrity can prevent blindness and also promote recovery from a stroke. The open-access article reporting these findings was published online on January 30, 2015 in Cell Death & Differentiation. "Studying the eye and the brain might hold the key to creating therapeutic solutions for blindness, stroke, and other seemingly unrelated conditions associated with the central nervous system," notes Dr. Bazan. "The eye is a window to the brain." Dr. Bazan and his research team discovered neuroprotectin D1 (NPD1), which is made from the essential fatty acid, docosahexaenoic acid (DHA). Previous work had shown that, while NPD1 protected cells, the molecular principles underlying this protection were not known. "During the last few years, my laboratory has been immersed in studying gene regulation," Dr. Bazan says. "We have uncovered a novel control that makes definitive decisions about whether a retina or brain cell will survive or die when threatened with disease onset. The gene mechanism that we discovered is the interplay of two genes turned on by the messenger neuroprotectin D1."

Highly Scalable “Churchill” Software Radically Reduces Time Required for Whole-Genome Data Analysis

Investigators at Nationwide Children's Hospital have developed an analysis "pipeline" that slashes the time it takes to search a person's genome for disease-causing variations from weeks to hours. An open-access article describing the ultra-fast, highly scalable software was published online on January 20, 2015 in Genome Biology. "It took around 13 years and $3 billion to sequence the first human genome," says Peter White, Ph.D., principal investigator and director of the Biomedical Genomics Core at Nationwide Children's and the study's senior author. "Now, even the smallest research groups can complete genomic sequencing in a matter of days. However, once you've generated all that data, that's the point where many groups hit a wall. After a genome is sequenced, scientists are left with billions of data points to analyze before any truly useful information can be gleaned for use in research and clinical settings." To overcome the challenges of analyzing that large amount of data, Dr. White and his team developed a computational pipeline called "Churchill." By using novel computational techniques, Churchill allows efficient analysis of a whole genome sample in as little as 90 minutes. "Churchill fully automates the analytical process required to take raw sequence data through a series of complex and computationally intensive processes, ultimately producing a list of genetic variants ready for clinical interpretation and tertiary analysis," Dr. White explains. "Each step in the process was optimized to significantly reduce analysis time, without sacrificing data integrity, resulting in an analysis method that is 100 percent reproducible."

Population Genetics Demonstrates Persistence of Lined Seahorse in Western Mid-Atlantic Ocean

In a finding vital to effective species management, a team including City College of New York (CCNY) biologists has determined that the lined seahorse (Hippocampus erectus) is more a permanent resident of the western mid-Atlantic Ocean than a vagrant. The fish is commonly found in three western Atlantic zoogeographic provinces, although inhabitants of the temperate northern Virginia Province are often considered tropical vagrants that arrive during warm seasons from the southern provinces and perish as temperatures decline. Researchers including Ph.D. student J.T. Boehm and Dr. Michael Hickerson of CCNY decided to test the alternative hypotheses of historical persistence versus the ephemerality of a northern Virginia Province population. They used a dataset consisting of 11,708 randomly sampled spots from the genomes of individuals collected from the eastern Gulf of Mexico to Long Island, New York. "Concordant results from genomic analyses all infer three genetically divergent subpopulations, and strongly support Virginia Province inhabitants as a genetically diverged and a historically persistent ancestral gene pool," said Mr. Boehm. The results suggested that individuals that emerge in coastal areas during the warm season can be considered "local" and support offshore migration during the colder months. "This research demonstrates how a large number of genes sampled across a geographical range can capture the diversity of coalescent histories (across loci) while inferring population history," said Dr. Hickerson. "Moreover, these results clearly demonstrate the utility of population genomic data to infer peripheral subpopulation persistence in difficult-to-observe species." The study was published online on January 28, 2015 in an article in the open-access journal PLOS ONE. The image shows a lined seahorse (Hippocampus erectus).