Biotechnology

ScienceDaily (Nov. 29, 2012) — One reason that biofuels are expensive to make is that the organisms used to ferment the biomass cannot make effective use of hemicellulose, the next most abundant cell wall component after cellulose. They convert only the glucose in the cellulose, thus using less than half of the available plant material. "Here at the EBI and other places in the biofuel world, people are trying to engineer microbes that can use both," said University of Illinois microbiologist Isaac Cann. "Most of the time what they do is they take genes from different locations and try and stitch all of them together to create a pathway that will allow that microbe to use the other sugar." Cann and Rod Mackie, also a U of I microbiologist, have been doing research at the Energy Biosciences Institute on an organism that they think could be used to solve this problem. Mackie, a long-distance runner, found the microbe in the garbage du...

ScienceDaily (Nov. 29, 2012) — Chromatin remodeling -- the packaging and unpackaging of genomic DNA and its associated proteins -- regulates a host of fundamental cellular processes including gene transcription, DNA repair, programmed cell death as well as cell fate. In their latest study, scientists at the Stowers Institute for Medical Research are continuing to unravel the finicky details of how these architectural alterations are controlled. Through a series of biochemical experiments, Stowers Investigators Ron Conaway, Ph.D., and Joan Conaway, Ph.D., and their team discovered that chromatin remodeling enzyme and suspected oncogene ALC1 (short for Amplified in Liver Cancer 1) is activated through an unusual mechanism: Its shape shifts in the presence of its activators. Their finding identifies a new instrument in cells' molecular repertoire of chromatin-remodeling tools and a potential cancer therapeutic target. One of the main tasks of chromati...

ScienceDaily (Nov. 27, 2012) — Field and laboratory work by a group of zoologists led by Omar Torres-Carvajal from Museo de Zoología QCAZ, Pontificia Universidad Católica del Ecuador, has resulted in the discovery of a new species of blunt-headed vine snake from the Chocoan forests in northwestern Ecuador. This region is part of the 274,597 km2 Tumbes-Chocó-Magdalena hotspot that lies west of the Andes. The study was published in the open access journal ZooKeys . Blunt-headed vine snakes live in an area comprising Mexico and Argentina, and are different from all other New World snakes in having a very thin body, disproportionately slender neck, big eyes, and a blunt head. They live in trees and hunt frogs and lizards at night. The new species described by Torres-Carvajal and his collaborators was named Imantodes chocoensis and increases the number of species in this group of snakes to seven. Snakes collected as far back as 1994 and deposited in se...

ScienceDaily (Nov. 28, 2012) — Literally hundreds of clinical trials, including some that have gained widespread attention, have been done on the possible benefits of omega-3 fatty acids for the prevention of heart disease -- producing conflicting results, varied claims, and frustrated consumers unsure what to believe. A recent analysis done by scientists in the Linus Pauling Institute at Oregon State University, published in the Journal of Lipid Research, has sorted through many of these competing findings, and it helps to explain why so many of the studies seem to arrive at differing conclusions. The review concludes that both fish consumption and dietary omega-3 fatty acid supplements may still help prevent heart disease; that some fatty acids, from certain sources, are more effective than others; that these compounds may have enormous value for serious health problems other than heart disease; and that the very effectiveness of modern drug therapies...

ScienceDaily (Nov. 28, 2012) — U.S. Department of Agriculture (USDA) scientists working as part of an international team have completed a "shotgun sequencing" of the wheat genome, a paper published in the journal Nature reported today. The achievement is expected to increase wheat yields, help feed the world and speed up development of wheat varieties with enhanced nutritional value. "By unlocking the genetic secrets of wheat, this study and others like it give us the molecular tools necessary to improve wheat traits and allow our farmers to produce yields sufficient to feed growing populations in the United States and overseas," said Catherine Woteki, USDA's Chief Scientist and Under Secretary for Research, Education and Economics. "Genetics provides us with important methods that not only increase yields, but also address the ever-changing threats agriculture faces from natural pests, crop diseases and changing climates....

ScienceDaily (Nov. 26, 2012) — An international team of biologists led by Indiana University's David M. Kehoe has identified both the enzyme and molecular mechanism critical for controlling a chameleon-like process that allows one of the world's most abundant ocean phytoplankton, once known as blue-green algae, to maximize light harvesting for photosynthesis. Responsible for contributing about 20 percent of the total oxygen production on the planet, the cyanobacteria Synechococcus uses its own unique form of a sophisticated response called chromatic acclimation to fine tune the absorption properties of its photosynthetic antenna complexes to the predominant ambient light color. The researchers identified and characterized an enzyme, MpeZ, that plays a pivotal role in the mechanism that allows two different water-soluble proteins in Synechococcus -- phycoerythrin I and II -- to alter their pigmentation in order to maximize photon capture for phot...

ScienceDaily (Nov. 27, 2012) — Herbs widely used throughout history in Asian and early European cultures have received renewed attention by Western medicine in recent years. Scientists are now isolating the active compounds in many medicinal herbs and documenting their antioxidant and anti-inflammatory activities. In a study published in the journal Investigative Ophthalmology & Visual Science , Stuart A. Lipton, M.D., Ph.D. and colleagues at Sanford-Burnham Medical Research Institute (Sanford-Burnham) report that carnosic acid, a component of the herb rosemary, promotes eye health. Lipton's team found that carnosic acid protects retinas from degeneration and toxicity in cell culture and in rodent models of light-induced retinal damage. Their findings suggest that carnosic acid may have clinical applications for diseases affecting the outer retina, including age-related macular degeneration, the most common eye disease in the U.S. Age-related ma...

ScienceDaily (Nov. 26, 2012) — Researchers at the Georgia Institute of Technology have received a five-year, $1.8 million grant from the National Science Foundation (NSF) to study how complex microbial systems use their genetic diversity to respond to human-induced change. The work is important because these microbial communities play critical roles in the environment, breaking down pollutants, recycling nutrients -- and serving as major sources of nitrogen and carbon. Despite the importance of the microbes, relatively few among the thousands of species that make up a typical microbial community have been studied extensively. The relatively unknown organisms within these communities may have genes that could help address critical environmental, energy and other challenges. "We are all dependent on these microbes," said Kostas Konstantinidis, an assistant professor in Georgia Tech's School of Civil and Environmental Engineering and the gran...

ScienceDaily (Nov. 26, 2012) — With increasing demands for sustainable energy, being able to cost-efficiently produce biofuels from plant biomass is more important than ever. However, lignin and hemicelluloses present in certain plants mean that they cannot be easily converted into biofuels. A study published in BioMed Central's open access journal Biotechnology for Biofuels appears to have solved this problem, using gene manipulation techniques to engineer plants that can be more easily broken down into biofuels. Plants high in lignin and hemicelluloses -- lignocellulosic biomass -- have a high content of pentose sugars that are more difficult to ferment into fuels than plants with hexose sugars. In order to be useful for biofuel production, scientists need to be able to engineer plants with smaller amounts of xylan -- the major non-cellulosic polysaccharide -- present in secondary cell walls. With this in mind, a research group from the Lawrence ...

ScienceDaily (Nov. 25, 2012) — A team of scientists from Temple University School of Medicine and the University of Pennsylvania has moved another step closer to solving a decades-long mystery of how the all-important flow of calcium into the cell's power source, the mitochondria, is controlled. By painstakingly shutting down the activity of 50 genes, one at a time, they have identified a protein, MCUR1, which hugs the inside of the mitochondrial membrane and is part of an elaborate mitochondrial channel pore system. MCUR1 acts as an accelerator to help regulate calcium coming into the mitochondria from the cell's large reservoir. The results, appearing November 25, 2012 in an advance online issue of the journal Nature Cell Biology , may also point to new treatment opportunities. Understanding how to manipulate MCUR1 may help in the development of treatments for disease conditions involving excessive calcium in the cell, such as cardiovascular d...

ScienceDaily (Nov. 23, 2012) — The genome encodes the complete information needed by an organism, including that required for protein production. Viruses, which are up to a thousand times smaller than human cells, have considerably smaller genomes. Using a type of herpesvirus as a model system, the scientists of the Max Planck Institute (MPI) of Biochemistry in Martinsried near Munich and their collaboration partners at the University of California in San Francisco have shown that the genome of this virus contains much more information than previously assumed. The researchers identified several hundred novel proteins, many of which were surprisingly small. The results of the study have now been published in Science . More than 80 percent of the world's population is infected with the herpesvirus, which can cause severe diseases in newborns and in persons with weakened immune system. Researchers had already sequenced the herpesvirus genome 20 years a...

ScienceDaily (Nov. 21, 2012) — Scientists at The Scripps Research Institute (TSRI) have made a major advance in understanding how flu viruses replicate within infected cells. The researchers used cutting-edge molecular biology and electron-microscopy techniques to "see" one of influenza's essential protein complexes in unprecedented detail. The images generated in the study show flu virus proteins in the act of self-replication, highlighting the virus's vulnerabilities that are sure to be of interest to drug developers. The report, which appears online in Science Express on November 22, 2012, focuses on influenza's ribonucleoprotein (RNP). RNPs contain the virus's genetic material plus the special enzyme that the virus needs to make copies of itself. "Structural studies in this area had stalled because of the technical obstacles involved, and so this is a welcome advance," said Ian A. Wilson, the Hansen Professor of ...

ScienceDaily (Nov. 22, 2012) — The cerebral cortex of the human brain has been called "the crowning achievement of evolution." Ironically, it is so complex that even our greatest minds and most sophisticated science are only now beginning to understand how it organizes itself in early development, and how its many cell types function together as circuits. A major step toward this great goal in neuroscience has been taken by a team led by Professor Z. Josh Huang, Ph.D., at Cold Spring Harbor Laboratory (CSHL). Today they publish research for the first time revealing the birth timing and embryonic origin of a critical class of inhibitory brain cells called chandelier cells, and tracing the specific paths they take during early development into the cerebral cortex of the mouse brain. These temporal and spatial sequences are regarded by Huang as genetically programmed aspects of brain development, accounting for aspects of the brain that are likel...

ScienceDaily (Nov. 21, 2012) — Scientists have discovered an enzyme used in nature to make powerful chemicals from catnip to a cancer drug, vinblastine. The discovery opens up the prospect of producing these chemicals cheaply and efficiently. They are produced naturally by some plants such as the medicinal Madagascar periwinkle, but faster-growing plants could be used to produce them. With synthetic biology, improvements could also be made to them. The study, to be published in Nature on November 22, was led by scientists from the John Innes Centre, an institute on Norwich Research Park strategically funded by BBSRC. "Thousands of chemicals are derived from the enzyme we have called iridoid synthase," says senior author Dr Sarah O'Connor from the JIC and the University of East Anglia. "We can start to use it to come up with new-to-nature structures with biological activity of benefit to both medicine and agriculture." Many...

ScienceDaily (Nov. 20, 2012) — Viruses can be elusive quarry. RNA viruses are particularly adept at defeating antiviral drugs because they are so inaccurate in making copies of themselves. With at least one error in every genome they copy, viral genomes are moving targets for antiviral drugs, creating resistant mutants as they multiply. In the best-known example of success against retroviruses, it takes multiple-drug cocktails to corner HIV and narrow its escape route. Rather than target RNA viruses themselves, aiming at the host cells they invade could hold promise, but any such strategy would have to be harmless to the host. Now, a surprising discovery made in ribosomes may point the way to fighting fatal viral infections such as rabies. Results were published online November 19 in Proceedings of the National Academy of Sciences . The ribosome has traditionally been viewed as the cell's molecular machine, automatically chugging along, synthesizi...

ScienceDaily (Nov. 21, 2012) — Studying the genetic variability of endangered species is becoming increasingly necessary for species conservation and monitoring. But, endangered species are difficult to observe and sample, and typically harbour very limited genetic diversity. Until now, the process of finding genetic markers was time consuming and quite expensive. These obstacles make the collection of genetic data from endangered animals a difficult task to fulfill. A research team led by Lounès Chikhi, group leader at the Instituto Gulbenkian de Ciência (IGC) and CNRS researcher (in Toulouse, France), has now contributed to change the odds when looking for diversity. Taking advantage of cutting edge DNA sequencing methodology and the collaborations with the Sabah Wildlife Department in Malaysia, Rachel O'Neill's laboratory  (University of Connecticut) and a private company (Floragenex), they were able to identify the genetic markers for the B...

ScienceDaily (Nov. 20, 2012) — A new study published November 20 in the open-access journal PLOS Biology has identified hundreds of small regions of the genome that appear to be uniquely regulated in human neurons. These regulatory differences distinguish us from other primates, including monkeys and apes, and as neurons are at the core of our unique cognitive abilities, these features may ultimately hold the key to our intellectual prowess (and also to our potential vulnerability to a wide range of 'human-specific' diseases from autism to Alzheimer's). Exploring which features in the genome separate human neurons from their non-human counterparts has been a challenging task until recently; primate genomes comprise billions of base pairs (the basic building blocks of DNA), and comparisons between the human and chimpanzee genomes alone reveal close to 40 million differences. Most of these are thought to merely reflect random 'genetic drift...