Biotechnology

Dec. 27, 2012 — A Chinese research team, led by Beijing Forestry University, BGI, Beijing Lin Fu Ke Yuan Flowers Co., Ltd, and other institutes, has completed the first genomic sequence of Prunus mume , known as mei. This work is extremely important for the deeper understanding of Rosaceae evolution and provides an invaluable resource for the improvement of fruit trees. The latest study was published online December 27 in Nature Communication . As one of the longest-lived flowering fruit trees, the P. mume was domesticated in China more than 3,000 years ago. It belongs to Rosaceae, the third most economically important plant family in temperate regions, and is characterized by high nutrition, medical value, and tolerance to low temperature in winter. Writers and artists have extolled the beauty of its flowers, and the blossom is considered to be the symbol of Chinese national spirit. The availability of P. mume genome will open a new way for better de...

Dec. 27, 2012 — One approach to understanding components in living organisms is to attempt to create them artificially, using principles of chemistry, engineering and genetics. A suite of powerful techniques -- collectively referred to as synthetic biology -- have been used to produce self-replicating molecules, artificial pathways in living systems and organisms bearing synthetic genomes. In a new twist, John Chaput, a researcher at Arizona State University's Biodesign Institute and colleagues at the Department of Pharmacology, Midwestern University, Glendale, AZ have fabricated an artificial protein in the laboratory and examined the surprising ways living cells respond to it. "If you take a protein that was created in a test tube and put it inside a cell, does it still function," Chaput asks. "Does the cell recognize it? Does the cell just chew it up and spit it out?" This unexplored area represents a new domain for synthetic ...

Dec. 26, 2012 — Scientists have sequenced the genome of the fungus Pneumocystis jirovecii , an advancement that could help identify new targets for drugs to treat and prevent Pneumocystis pneumonia, a common and often deadly infection in immunocompromised patients. The study will be published on December 26, 2012 in mBio ®, the online open-access journal of the American Society for Microbiology. The organism cannot yet be isolated and grown for study in the laboratory, so details about Pneumocystis pneumonia, the biology of P. jirovecii , and its pathogenicity are hard to come by. The genome sequence represents a wealth of new information for doctors and researchers tackling this disease. Pneumocystis pneumonia is an opportunistic infection that strikes most often in individuals with diminished immune systems. The corresponding author of the study in mBio ®, Philippe Hauser of the Centre Hospitalier Universitaire Vaudois and University of Lausanne, in S...

Dec. 21, 2012 — If the sinful excess of holiday eating sends your system into butter-slathered, brandy-soaked overload, you are not alone: People who are jet-lagged, people who work graveyard shifts and plain-old late-night snackers know just how you feel. All these activities upset the body's "food clock," a collection of interacting genes and molecules known technically as the food-entrainable oscillator, which keeps the human body on a metabolic even keel. A new study by researchers at the University of California, San Francisco (UCSF) is helping to reveal how this clock works on a molecular level. Published this month in the journal Proceedings of the National Academy of Sciences , the UCSF team has shown that a protein called PKCγ is critical in resetting the food clock if our eating habits change. The study showed that normal laboratory mice given food only during their regular sleeping hours will adjust their food clock over time...

Dec. 23, 2012 — The mysterious inner workings of Chang Shan -- a Chinese herbal medicine used for thousands of years to treat fevers associated with malaria -- have been uncovered thanks to a high-resolution structure solved at The Scripps Research Institute (TSRI). Described in the journal Nature this week, the structure shows in atomic detail how a two-headed compound derived from the active ingredient in Chang Shan works. Scientists have known that this compound, called halofuginone (a derivative of the febrifugine), can suppress parts of the immune system -- but nobody knew exactly how. The new structure shows that, like a wrench in the works, halofuginone jams the gears of a molecular machine that carries out "aminoacylation," a crucial biological process that allows organisms to synthesize the proteins they need to live. Chang Shan, also known as Dichroa febrifuga Lour , probably helps with malarial fevers because traces of a halofugino...

Dec. 23, 2012 — In a collaborative study published online today in Nature Biotechnology , researchers from Kunming Institute of Zoology, Chinese Academy of Sciences, BGI, and other institutes, have completed the first genome sequence of domestic goat by a robust approach integrated with next-generation sequencing (NGS) and whole-genome mapping (WGM) technologies. The goat genome is the first reference genome for small ruminant animals and may help to advance the understanding of distinct ruminants' genomic features from non-ruminant species. This work also yields a valuable experience for facilitating the de novo assemblies of large, complex genomes in the future. Goats are recognized as an important member of the world livestock industry, and with many unique biological features. They are an important economic resource in many developing countries around the world, especially in China and India. However, despite their agricultural and biological impo...

Dec. 18, 2012 — Researchers have found that the budding yeast ( Saccharomyces cerevisiae ) is an acceptable model system to study KP1019, an anti-cancer drug that uses ruthenium, a rare metal, a new study found. Researchers had previously been interested in studying KP1019 because it is believed to cause cancer cell death and is not known to have negative secondary side effects for healthy tissues. "We wanted to learn more about how KP1019 works on a cellular level, and how the drug acts on yeast cells can be indicative of how it will perform on mammalian cells," said Pamela Hanson, associate professor of biology at Birmingham-Southern College in Alabama. "Besides the economic advantages, there are good scientific reasons to work with yeast, including the abundance of yeast genetic and genomic tools." In past research, KP1019 has been shown to inhibit ovarian tumor cell production, cause death of colon cancer cells and reduce overall...

Dec. 21, 2012 — The normal DNA will switch to left-handed DNA when it is physically twisted, or when a lot of salt is added to the solution. Researchers at the University of Luxembourg were able to accurately calculate for the first time the amount of salt which is required to do this. Z-DNA in the cell leads to loss of function and cancer. In a recent publication, researchers achieved new accuracy in the ability to measure energy differences between states of molecules, thus predicting which states will be observed. It has been known since the seventies that excessive salt causes DNA to reverse its twist, from a right-handed spiral to a left-handed one. DNA in the Z form is treated by our natural repair enzymes as damaged, and is therefore usually deleted from the cell. Deletion of genetic material can lead to cancer or to other problems, so the B-Z transition is no mere curiosity. However such is the complexity of the DNA molecule that a theoretical e...

Dec. 21, 2012 — Day after day, legions of microorganisms work to produce energy from waste in biogas plants. Researchers from Bielefeld University's Center for Biotechnology (CeBiTec) are taking a close look to find out which microbes do the best job. They are analysing the entire genetic information of the microbial communities in selected biogas plants up and down Germany. From the beginning of 2013, the Californian Joint Genome Institute will undertake the sequencing required. The biocomputational analysis will be performed at CeBiTec. Not an easy task, since the data will be supplied in billions of fragments stemming in turn from hundreds of organisms. Piecing together this huge jigsaw puzzle will be painstaking work. In Germany, there are more than 7,000 biogas plants which can supply over six million households with power. The plants are filled mostly with plant biomass like maize silage but also with agricultural waste materials like liquid man...

Dec. 19, 2012 — Large amounts of a substitute for one of the world's most treasured fragrance ingredients -- a substance that also has potential anti-cancer activity -- could be produced with a sustainable new technology, scientists are reporting. Published in the Journal of the American Chemical Society , the advance enables cultures of bacteria to produce a substitute for natural ambergris, which sells for hundreds of dollars an ounce. Laurent Daviet, Michel Schalk and colleagues explain that ambergris, a waxy substance excreted by sperm whales, has been prized as a fragrance ingredient for centuries. Ambergris has a pleasant sweet and earthy scent of its own, and it enhances other scents in high-end perfumes. With sperm whales an endangered species, and natural ambergris not used in perfumes in the U.S., perfume makers have turned to substitutes. One is made from sclareol, obtained from the Clary sage plant. But the plant contains only small am...

Dec. 20, 2012 — By analyzing tissues harvested from organ donors, Columbia University Medical Center (CUMC) researchers have created the first ever "atlas" of immune cells in the human body. Their results provide a unique view of the distribution and function of T lymphocytes in healthy individuals. In addition, the findings represent a major step toward development of new strategies for creating vaccines and immunotherapies. The study was published December 20 in the online edition of the journal Immunity. T cells, a type of white blood cell, play a major role in cell-mediated immunity, in which the immune system produces various types of cells to defend the body against pathogens, cancer cells, and foreign substances. "We found that T cells are highly compartmentalized -- that is, each tissue we examined had its own complement of T cells," said study leader Donna L. Farber, PhD, professor of surgical sciences at CUMC and a principa...

Dec. 20, 2012 — For humans to grow and to replace and heal damaged tissues, the body's cells must continually reproduce, a process known as "cell division," by which one cell becomes two, two become four, and so on. A key question of biomedical research is how chromosomes, which are duplicated during cell division so that each daughter cell receives an exact copy of a person's genome, are arranged during this process. Now, scientists at the Salk Institute have discovered a new characteristic of human cell division that may help explain how our DNA is organized in the nucleus as cells reproduce. They found that telomeres, molecular caps that protect the ends of the chromosomes, move to the outer edge of the cell's nucleus after they have been duplicated. This image shows telomeres (yellow), protective caps on the ends of chromosomes, moving to the outer edge of a cell's nucleus (blue). Salk researchers found that the telomeres a...

Dec. 19, 2012 — The humble soybean could become an inexpensive new source of a widely used chemical for plastics, textiles, drugs, solvents and as a food additive. Succinic acid, traditionally drawn from petroleum, is one focus of research by Rice chemists George Bennett and Ka-Yiu San. In 2004, the Department of Energy named succinic acid one of 12 "platform" chemicals that could be produced from sugars by biological means and turned into high-value materials. Several years ago, Rice patented a process by Bennett and San for the bio-based production of succinic acid that employed genetically modified E. coli bacteria to convert glucose into succinic acid in a way that would be competitive with petroleum-based production. The new succinate process developed by Bennett, San and Chandresh Thakker and reported recently in Bioresource Technology promises to make even better use of a cheap and plentiful feedstock, primarily the indigestible part...

Dec. 18, 2012 — Scientists from the AIDS Research Institute IrsiCaixa have identified how HIV, the virus that causes AIDS, enters the cells of the immune system enabling it to be dispersed throughout an organism. The new study is published December 18 in the open access journal PLOS Biology . One of the reasons why we do not yet have a cure for HIV infection is that the virus infects cells of the immune system that would normally fight such an infection. The main targets of HIV are white blood cells named CD4 T lymphocytes (so called because they have the protein CD4 in their membrane), and while more than 20 different drugs are available today to help control HIV, all of them act by blocking the cycle that HIV follows to infect these CD4 T lymphocytes. However, these treatments do not fully act on another cell of the immune system, the dendritic cell, which takes up HIV and spreads it to target CD4 T lymphocytes. Mature dendritic cells are responsible ...

Dec. 16, 2012 — Turning vast amounts of genomic data into meaningful information about the cell is the great challenge of bioinformatics, with major implications for human biology and medicine. Researchers at the University of California, San Diego School of Medicine and colleagues have proposed a new method that creates a computational model of the cell from large networks of gene and protein interactions, discovering how genes and proteins connect to form higher-level cellular machinery. The findings are published in the Dec. 16 advance online publication of Nature Biotechnology . "Our method creates ontology, or a specification of all the major players in the cell and the relationships between them," said first author Janusz Dutkowski, PhD, postdoctoral researcher in the UC San Diego Department of Medicine. It uses knowledge about how genes and proteins interact with each other and automatically organizes this information to form a comprehe...

Dec. 17, 2012 — As a new year approaches, the University of Notre Dame's John J. Reilly Center for Science, Technology and Values has announced its inaugural list of emerging ethical dilemmas and policy issues in science and technology for 2013. The Reilly Center explores conceptual, ethical and policy issues where science and technology intersect with society from different disciplinary perspectives. Its goal is to promote the advancement of science and technology for the common good. The center generated its inaugural list with the help of Reilly fellows, other Notre Dame experts and friends of the center. The center aimed to present a list of items for scientists and laypeople alike to consider in the coming months and years as new technologies develop. It will feature one of these issues on its website each month in 2013, giving readers more information, questions to ask and resources to consult. The ethical dilemmas and policy issues are: ...

Dec. 17, 2012 — Scientists at Rochester Institute of Technology have published the whole genome sequence of bacteria associated with Jamaican sugarcane and Riesling grapevines in the September and November issues of the Journal of Bacteriology , a publication of the American Society for Microbiology. André Hudson and Michael Savka, professors in RIT's Thomas H. Gosnell School of Life Sciences within the College of Science, isolated and identified three bacteria belonging to the genus Enterobacter from Jamaican sugarcane stalk tissue and Methylobacterium and Novosphingobium from grapevines. These genomes -- genetic instructions that make up individual organisms -- include one of the first to be associated with Jamaican sugarcane, according to Hudson. The scientists deposited the whole genomes at GenBank, a repository maintained by the National Institutes of Health. Hudson and Savka are the first RIT professors to sequence and annotate genomes. ...