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Archive - Jun 2013


June 12th

Specific miRNA in Stem-Cell-Secreted Exosomes Contributes to Stroke Recovery

A specific microRNA, a short set of RNA (ribonuclease) sequences, naturally packaged into minute (50 nanometers) lipid containers called exosomes (see image), are released by stem cells after a stroke and contribute to better neurological recovery according to a new animal study by Henry Ford Hospital researchers. The important role of a specific microRNA transferred from stem cells to brain cells via the exosomes to enhance functional recovery after a stroke was shown in lab rats. This study provides fundamental new insight into how stem cells affect injured tissue and also offers hope for developing novel treatments for stroke and neurological diseases, the leading cause of long-term disability in adult humans. The study was published online on April 30, 2013 in Stem Cells. Although most stroke victims recover some ability to voluntarily use their hands and other body parts, nearly half are left with weakness on one side of their body, while a substantial number are permanently disabled. Currently, no treatment exists for improving or restoring this lost motor function in stroke patients, mainly because of mysteries about how the brain and nerves repair themselves. "This study may have solved one of those mysteries by showing how certain stem cells play a role in the brain's ability to heal itself to differing degrees after stroke or other trauma," says study senior author Michael Chopp, Ph.D., scientific director of the Henry Ford Neuroscience Institute and vice chairman of the department of Neurology at Henry Ford Hospital. The experiment began by isolating mesenchymal stem cells (MSCs) from the bone marrow of lab rats. These MSCs were then genetically altered to release exosomes that contain specific microRNA molecules. The MSCs then become "factories" producing exosomes containing specific microRNAs.

Next-Gen DNA Sequencing Reveals Secrets of White Cliffs of Dover

The University of Exeter recently contributed to a major international project to sequence the genome of Emiliania huxleyi, the microscopic plankton species whose chalky skeletons form the iconic white cliffs of Dover. The results of the project were published online on June 12, 2013 in an open-access article in Nature. Emiliania huxleyi is one of the most abundant marine phytoplankton species and is a key player in the process of CO2 exchange between the atmosphere and the ocean. In some marine systems 20% of the total carbon is fixed by E. huxleyi. This microscopic alga has influenced the global climate for over 200 million years, so is used as a model system for studying how physical, chemical, and biological processes regulate the Earth's systems. The algae form pale chalky cases called coccoliths which during the spring bloom can be seen from space in the seas around the UK. E. huxleyi directly links to climate change through the production of dimethylsulfide (DMS), which induces cloud formation and blocks solar radiation. Thanks to new technology – next-generation DNA sequencing – 13 different isolates were sequenced from around the world, and compared to a complete sequence constructed for E. huxleyi strain CCMP1516. This allowed the team to understand the influences of different environmental conditions on E. huxleyi physiology. The international team found that E. huxleyi possess a higher number of genes than previously published marine phytoplankton genomes, and that most genes were present in multiple copies. Dr Mark Van Der Giezen from the University of Exeter said: "Using comprehensive analysis to compare different strains of the algae, we demonstrated that E. huxleyi should no longer be considered a single species.

Rössler Prize Awarded to Olivier Voinnet for RNAi Discoveries

This year’s Rössler Prize has been awarded to Dr. Olivier Voinnet (photo), Professor of RNA Biology in the Department of Biology, ETH Zurich. The Frenchman receives the CHF 200,000 research prize for his groundbreaking discoveries in the field of molecular and cell biology. In 1990, scientists introduced a gene known to stimulate the production of flower pigments into petunia flowers to enhance their color. However, the genetically modified plants turned almost white. The newly introduced genes not only failed to be expressed, but they also suppressed the naturally present one. This mysterious inactivation of genes, later found to rely on species of very small, non-coding RNA molecules, is now regarded as one of the most fundamental discoveries of modern biology. The function and applications of what are now known as small interfering RNAs, or siRNAs, have since become integral to biological research and applied medicine. However, many aspects of this new class of RNA molecules and their biological effects, collectively referred to as ‘RNA interference,’ or RNAi, remain unexplored. Dr. Voinnet, 41, worked on this group of molecules as a Ph.D. student and discovered how plants use RNAi to defend themselves against viral infection. Because the siRNAs originate from the virus itself, plants can use them specifically against the pathogen, in a sequence-specific manner. In 1997, Dr. Voinnet was able to demonstrate that RNAi can spread throughout the whole plant to confer immunity against the triggering viruses and that, as a counterdefense, viruses evolve proteins that suppress RNAi. A year later, researchers Dr. Andrew Fire and Dr. Craig Mellow discovered a similar mechanism in the nematode C. elegans, and they were awarded the Nobel Prize for this discovery in 2006. Over the last 15 years, Dr.

June 12th

Microbes Found Alive 500 Feet Beneath Sea Floor

Microbes are living more than 500 feet beneath the seafloor in 5-million-year-old sediment, according to new findings by researchers at the University of Delaware (UD) and Woods Hole Oceanographic Institution (WHOI). Genetic material in mud from the bottom of the ocean — called the deep biosphere —revealed an ecosystem of active bacteria, fungi, and other microscopic organisms at depths deeper than a skyscraper is high. The findings were published online in Nature on June 12, 2013. “This type of examination shows active cells,” said co-author Dr. Jennifer F. Biddle, assistant professor of marine biosciences in UD’s College of Earth, Ocean, and Environment. “We knew that all of these cells were buried, but we didn’t know if they were doing anything.” In fact, the microbes are reproducing, digesting food, and even moving around despite the extreme conditions found there: little to no oxygen, heavy pressure, and minimal nutrient sources. The organisms could shed light on how carbon and other elements circulate in the environment, the scientists reported. The researchers analyzed messenger RNA (mRNA) in sediment from different depths collected off the coast of Peru in 2002 during Leg 201 of the Ocean Drilling Program. This first glimpse into the workings of the heretofore hidden ecosystem was made possible by the first successful extraction of total mRNA, or the “metatranscriptome,” from the deep biosphere. mRNA is highly sought-after by microbial ecologists because its presence indicates that the cells that made it are alive and because it carries the instructions for the proteins the cells are making. But because the metabolic rates in the deep biosphere are very low and mRNA is present in small amounts, extracting enough of it to analyze from deep sediments had been thought by many scientists to be impossible.

Solution-Based Circuit Chip Permits Rapid and Multiplexed Pathogen Identification

Life-threatening bacterial infections cause tens of thousands of deaths every year in North America. Increasingly, many infections are resistant to first-line antibiotics. Unfortunately, current methods of culturing bacteria in the lab can take days to report the specific source of the infection, and even longer to pinpoint the right antibiotic that will clear the infection. There remains an urgent, unmet need for technologies that can allow bacterial infections to be rapidly and specifically diagnosed. Researchers from the University of Toronto have created an electronic chip that operates with record-breaking speed and can analyze samples for panels of infectious bacteria. The new technology can report the identity of the pathogen in a matter of minutes, and looks for many different bacteria and drug resistance markers in parallel, allowing rapid and specific identification of infectious agents. The advance was reported online on June 12, 2013 in Nature Communications. "Overuse of antibiotics is driving the continued emergence of drug-resistant bacteria," said Dr. Shana Kelley (Pharmacy and Biochemistry), a senior author of the study. "A chief reason for use of ineffective or inappropriate antibiotics is the lack of a technology that rapidly offers physicians detailed information about the specific cause of the infection." The researchers developed an integrated circuit that could detect bacteria at concentrations found in patients presenting with a urinary tract infection. "The chip reported accurately on the type of bacteria in a sample, along with whether the pathogen possessed drug resistance," explained Chemistry Ph.D. student Brian Lam, the first author of the study. One key to the advance was the design of an integrated circuit that could accommodate a panel of many biomarkers.

Harbor Porpoises Can Thank Arch Enemy for Their Success

The harbor porpoise (Phocoena phocoena) is a whale species that is doing quite well in coastal and busy waters. They are found in large numbers throughout the Northern Hemisphere from Mauritania to Alaska, and now researchers from the University of Southern Denmark explain why these small-toothed whales are doing so well: The harbor porpoises can thank their worst enemy, the killer whale, for their success. Coastal areas are more challenging and potentially dangerous for a small whale. There is a risk of beaching and being caught in a fisherman's net, but there are also benefits. Fish are plentiful and easier to find in coastal waters than in the open sea. Therefore, coastal waters are attractive for porpoises, and they are extremely skilled at navigating, locating prey and avoiding hazards near the coast. Like other toothed whales porpoises use echolocation for orientation and to detect prey. They emit a constant stream of sonar clicks, which, when these hit a rock, a fish, or a ship nearby an echo is sent back to the porpoise. From the echo, the porpoise can distinguish the location of the object and often also can identify the object. Porpoises can locate even small fish and small objects such as net floats and fine fishing nets. This ability sets them apart from many other toothed whales, which do not have such sophisticated echolocation abilities. The secret of this ability is that the porpoise uses very short clicks and these are higher in frequency than those of many other toothed whales, explains Dr. Lee Miller from the Institute of Biology, University of Southern Denmark (SDU). Porpoise clicks last just a hundred-millionth of a second, and are about 130 kHz. For comparison, a human can hear up to 20 kHz and a dog up to about 60 kHz. Dr. Miller and his colleague Dr.

June 9th

Duck Genome Sequence May Offer New Insight into Fighting Bird Flu

The duck genome consortium, consisting of scientists from China Agricultural University, BGI, the University of Edinburgh and other institutes, has completed the genome sequencing and analysis of the duck (Anas platyrhynchos), one principal natural host of influenza A viruses, which caused a new epidemic in China beginning this past February. This work, which was published online in Nature Genetics, reveals some noteworthy conclusions and provides an invaluable resource for unraveling the interactive mechanisms between the host and influenza viruses. The new H7N9 bird flu has strain killed 36 people and caused a $6.5 billion loss to China's economy. As a natural host of influenza A viruses (including H5N1), the duck is known to often remain asymptomatic under influenza infection. To uncover the interactive mechanisms between the host and influenza viruses, researchers sequenced the genome of a 10-week-old female Beijing duck, and conducted transcriptomic studies on two virus-infected ducks. This work yielded the draft sequence of a waterfowl-duck for the first time, and the data indicated that the duck, like the chicken and zebra finch, possesses a contractive immune gene repertoire compared to those in mammals, and it also comprises novel genes that are not present in the other three birds (chicken, zebra finch and turkey). By comparing gene expression in the lungs of ducks infected with either highly or weakly pathogenic avian influenza H5N1 viruses, the team identified genes whose expression patterns were altered in response to avian influenza viruses. They also identify factors that may be involved in duck host immune response to avian virus infection, including the avian and mammalian -defensin gene families. Dr.

June 8th

Scientists Expose New, Cilium-Related Cause of Life-Threatening Diseases

Dr. Søren Tvorup Christensen (Department of Biology) and Professor Lars Allan Larsen (Department of Cellular and Molecular Medicine) at the University of Copenhagen, in collaboration with colleagues in Denmark and France, have spearheaded a recent discovery that sheds new light on the causes of a range of debilitating diseases and birth defects. Over the years, the research group has been a leader in primary cilium research. Primary cilia are antennae-like structures found on the surface of nearly all cells in the human body. These antennae are designed to receive signals, such as growth factors and hormones, from other cells in the body and then convert these signals to a response within individual cells. Defective formation or function of these antennae can give rise to a range of serious maladies including heart defects, polycystic kidney disease (PKD), blindness, cancer, obesity, and diabetes. However, there remains a great deal of mystery as to how these antennae capture and convert signals within cells. The current groundbreaking results were published online in an open-access article on June 6, 2013 in Cell Reports. “We have identified an entirely new way by which these antennae are able to register signals in their midst, signals that serve to determine how cells divide and move amongst one another. This also serves to explain how a stem cell can develop into heart muscle,” explains Dr. Christensen. “What we have found is that the antennae don’t just capture signals via receptors out in the antennae, but they are also able to transport specific types of receptors down to the base of the antennae - where they are then activated and might possibly interact with a host of other signalling systems.

"Zone in with Zon" at Boston TIDES Conference

Dr. Gerald Zon’s latest blog post in “Zone in with Zon—What’s Trending in Nucleic Acid Research,” ( was posted on June 3, 2013, and it features a report on the 15th Anniversary TIDES (Oligonucleotide and Peptide Therapeutics from Research through Commercialization) 2013 conference in Boston. Dr. Zon’s post is entitled, “Nucleic Acids Are Getting Small, SMARTT, Long, and Weird." Unable to attend in person, Dr. Zon relied on an on-site report from TriLink President/CEO Rick Hogrefe, Ph.D., to provide the raw material for his commentary. Among the topics covered were spherical nucleic acids and nanoparticle delivery as discussed by Professor Chad A. Murkin of Northwestern University and founder of AuraSense; block-polymer delivery as discussed by Dr. Mary Prieve of PhaseRx; targeting long non-coding RNA as described by Dr. Jim Barsum, previously with Biogen Synta, and now with Theracrine; and unnatural base pairs as discussed by Dr. Ichiro Hirao of RIKEN and President/CEO of TAGCyx Biotechnologies. Dr. Zon is an eminent nucleic acid chemist and Director of Business Development at TriLink BioTechnologies in San Diego, California. [Zon blog post] [TIDES web site]