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VATIS Update Biotechnology . Apr-Jun 2014

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Biotechnology Apr-Jun 2014

ISSN: 0971-5622

VATIS Update Biotechnology is published 4 times a year to keep the readers up to date of most of the relevant and latest technological developments and events in the field of Biotechnology. The Update is tailored to policy-makers, industries and technology transfer intermediaries.

Co-publisher: Biotech Consortium India Ltd
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Contents

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IN THE NEWS

Biodiversity loss linked to outbreaks of diseases

According to a study which points at biodiversity’s potential role as a buffer against disease outbreaks, the loss of biodiversity is closely linked to outbreaks of diseases in the Asia-Pacific region. The researchers from France, Malaysia, Singapore and Thailand have reported that an increase in human activities resulting from economic development leads to several regional environmental changes. These include altered land use, the distributions of domestic animals and wildlife, as well as increased international trade.

“Biodiversity changes that occur through the fragmentation and degradation of natural habitats, particularly forested areas, increase the proximity of wildlife to humans and their domestic animals,” says the study. These result in increased health risks through the increased transmission of zoonotic diseases. In addition, the number of zoonotic disease outbreaks is positively correlated with the number of threatened mammal and bird species while the number of vector-borne disease outbreaks is negatively correlated with forest cover, denoting ‘the potential role of biodiversity as a buffer of pathogen spread’.

“Impoverishment of biodiversity, which is evident not only in the decreasing number of species but also in landscape fragmentation and simplification, favour what we call the synanthropic species,” said Serge Morand, lead author and a scientist at the National Centre for Scientific Research (CNRS), France. Examples of synanthropic species include the common rats, which are the reservoirs of many infectious diseases such as leptospirosis, scrub typhus and Hantaviruses. They also include some mosquitoes such as the Aedes albopictus, which is a vector of dengue and Japanese encephalitis. “High biodiversity means high number of infectious diseases. But increasing biodiversity loss, on the other hand, leads to an increase of disease outbreaks,” Morand concludes.
Source: http://www.asiabiotech.com

India and Argentina to begin joint research

Under the India-Argentina bilateral scientific and technological cooperation, India and Argentina will soon begin joint research in different scientific areas such as biotechnology (including drug discovery), medical sciences and health, etc. The joint research projects between Indian and Argentine groups are being implemented under the framework of Programme of Cooperation in Science and Technology (POC) 2013-2015, signed on October 2013, between the Department of Science and Technology (DST), Ministry of Science & Technology, India and the Ministry of Science, Technology and Productive Innovation (MINCyT), Argentina.

The objective of this programme is to strengthen and to expand relations between both scientific communities, making possible the exchanges between Indian and Argentine research groups, in the framework of joint scientific and technological projects, selected by the parties. MINCyT and DST will prioritise the implementation of joint projects which benefits research and development between R&D centers and enterprises.

The programme is implemented by means of the joint submission of research projects, involving researchers’ exchange between Argentina and India. The definition ‘joint research project’ implies a project agreed between two or more research groups of both countries with clearly defined objectives to be achieved within an established schedule, implemented through the exchange of people and the access to available facilities, laboratories and equipment in each one of the Parties. The priority areas of this programme are:
• biotechnology;
• ocean science and polar research;
• medical sciences and health;
• agriculture and food technology;
• information and communication technology;
• renewable energy sources; and
• manufacturing technologies.
Source: http://www.pharmabiz.com

Mosquito genes could be key to halt dengue spread

A team of researchers from QIMR Berghofer Medical Research Institute, Australia, working in Viet Nam found a promising new approach in gauging mosquito survival patterns to break the transmission cycle of dengue, aiding them an emerging technique for identifying a mosquito’s age using gene markers. The gene collection method, called ‘transcriptional profiling’, analysed the age of a batch of Aedes aegypti mosquitoes infected with a strain of Wolbachia pipientis bacteria that induces virus interference and shortens mosquito lifespan. The field experiments took place in a village in Hon Mieu Island in central Viet Nam.

The study found that the year-round presence of these mosquitoes, if older than 12 days, was likely to facilitate the continuity of dengue transmission. The research noted that mosquito survival rates were highest during the dry/cool (Jan-Apr) and dry/hot (May-Aug) seasons, which went down during the wet/cool season (Sep-Dec). “Researchers have long struggled to determine precisely how old wild mosquito populations are, partly because the common method for doing so – dissection – was more limited than newer ones,” said Leon Hugo, at the QIMR Berghofer Medical Research Institute, Australia.

“The study is significant in part because it can potentially help researchers and policymakers develop more effective mosquito-control programs for fighting dengue,” said Laura Harrington, a professor at Cornell University, the United States. Transcriptional profiling allowed the authors to age mosquitoes beyond the limitations of other techniques. Knowing the age of dengue-transmitting mosquitoes is ‘critically important’, because many researchers have wondered how mosquitoes with very low population densities are often able to transmit the disease to humans. The common assumption is that older female mosquitoes account for most human infections.
Source: http://www.asiabiotech.com

Philippines among 19 ‘mega’ biotech crop producers

Philippines has landed in the ranks of the 19 ‘mega-countries’, which are growing 50,000 hectares or more of biotechnology (biotech) crops. In the country’s case, only biotech (Bt) corn, the yellow variety, is being planted by farmers, but they have earlier expressed willingness to adopt Bt cotton, Bt eggplant, and Gold Rice, which are in the pipeline, once the genetically modified (GM) crops are ready for commercialization. According to a report released by the International Service for the Acquisition of Agri-Biotech Applications (ISAAA), there are now 800,000 hectares being planted, by biotech-adopting farmers in the country.

ISAAA’s report “Global Status of Commercialized Biotech/GM Crops: 2013”, was made public on February 2014. Of the 27 countries growing the still highly-controversial GM crops, the Philippines ranked #12. A total of 19 of the 27 countries are dubbed “mega-countries” in relation with the adoption by land area of commercial biotech crops, which have at least 50,000 hectares or more of farm lands planted with GM maize, cotton, canola, sugar beet, alfalfa, papaya, squash, or soybean.

ISAAA’s report cited the future prospects of biotech crops. “In the scientific community associated with biotechnology, there is cautious optimism that biotech crops, including both staple and orphan crops, will be increasingly adopted by society, particularly by the developing countries, where the task of feeding its own people is formidable, given that the global population, most of whom will be in the South, will exceed 10 billion by the turn of the century in 2100,” it said. It added that yesterday’s technology cannot feed tomorrow’s world.
Source: http://www.mb.com.ph

India’s biotechnology strategy for GM crops

The Department of Biotechnology (DBT) of the Ministry of Science and Technology, India, has prepared national biotechnology development strategy, 2014, suggesting improvement in the existing regulatory system. The department in its ‘Biotech Strategy-II’ has proposed a world class regulatory system, which can build confidence among the civil society, farmers, consumers and scientific community. The same suggestion had come in its first strategic document (Strategy-I) in 2007, when it asked for setting up a Biotechnology Regulatory Authority of India (BRAI), the bill is still pending with the parliamentary panel. The 2014 document has once again recommended it.

DBT’s revised strategy of ‘Vision 2020’ highlighted how genetically modified (GM) crops would help achieve ‘higher productivity and better quality food while reducing resource inputs’. Making the draft document public, DBT sought ‘comments’ from stakeholders including farmers, scientists and civil society. Biotech Strategy-II comes at a time when the government has moved towards field trials of selected varieties of GM crops.

The draft has suggested improvement in the existing regulatory system, seeking to make the Genetic Engineering Appraisal Committee (GEAC) ‘scientifically strong, professionally competent, conflict-free, transparent and backed by sound validation infrastructure’. The department also recommended setting up a toxicological center to ‘generate toxicity, safety data for biological and chemical contaminants and adulterants along with GM foods and traditionally used herbs’.
Source: http://www.isaaa.org

MARKET NEWS

Aegerion begins clinical trials in Japan

Aegerion Pharmaceuticals, the United States, a leading biopharmaceutical company dedicated to the development and commercialization of novel therapies for patients with debilitating rare diseases is going to begin its phase III clinical trials in Japan. The company said that patient enrollment has been initiated in Japan in a clinical trial of lomitapide as an adjunct treatment to reduce low-density lipoprotein cholesterol (LDL-C) in Japanese patients with homozygous familial hypercholesterolemia (HoFH). In 2013, Aegerion received orphan drug designation from Japan’s Ministry of Health, Labour and Welfare for lomitapide. The phase III, open-label trial in Japan is similar in design to the completed phase III trial conducted in the US and other countries. The Japanese regulatory authorities (PMDA) have indicated that they will allow the new drug application to be filed after completion of the 26 week efficacy phase.

“This pivotal trial marks an important milestone for Aegerion and Japanese HoFH patients. Japan is a well-characterized region for patients with severe hypercholesterolemia and investigators there have shown a high level of enthusiasm for the trial, recognizing the unmet clinical need for their patients living with this serious disease,” said Mr. Mark Sumeray, Chief Medical Officer. HoFH is a serious, rare genetic disease inherited from both parents that impairs the function of the receptor responsible for removing LDL-C (‘bad’ cholesterol) from the body. A loss or impairment of LDL receptor function results in severe elevation of blood cholesterol levels. HoFH patients often develop premature and progressive atherosclerosis, a narrowing or blocking of the arteries.
Source: http://www.biospectrumasia.com

A collaboration for clinical drug development

Quintiles, Singapore and Biogen Idec, the United States, have entered into a five-year strategic clinical development agreement. The multi-year collaboration is designed to leverage the expertise and experience from both organizations to optimize Biogen Idec’s clinical development processes. According to Quintiles, the collaboration is structured to increase clinical trial efficiency, with a focus on transparency, quality, innovation and operational excellence. “Our partnership with Biogen Idec exemplifies the ongoing evolution of drug development collaboration and reinforces the increasingly important role that biopharmaceutical service providers such as Quintiles have in these efforts,” said Mr. Tom Pike, CEO, Quintiles.

Under the agreement, a dedicated team from Quintiles will work with Biogen Idec on the design, planning and execution of Biogen Idec’s phase II-IV studies and select phase I studies. In addition, Biogen Idec will leverage Quintiles’ technology and systems across its growing portfolio. “As we have continued to build our research and development organization, it was important for us to identify a strong clinical development partner to complement our focus on developing innovative therapies for the treatment of neurodegenerative, hematologic and autoimmune diseases,” said Dr. Alfred Sandrock, at Biogen Idec. The Biogen Idec and Quintiles collaboration is already underway. New projects are being initiated through the collaboration, and several of Biogen Idec’s ongoing studies are currently transitioning to Quintiles.
Source: http://www.biospectrumasia.com

Novozymes to open new R&D center

Novozymes, Denmark, has announced the establishment of a new research and development center in the United States, dedicated to its bioagriculture business. The center will be located in North Carolina, where the company will invest $36 million over the next three years and create 100 new research and development jobs. “The world needs sustainable agricultural solutions now more than ever before. By boosting our research and development of environmentally-friendly microbial technology, we will help farmers meet this demand sooner rather than later. The new R&D center in North Carolina is a concrete step to help speed our technology to market from a state with a long history of agricultural innovation,” said Thomas Videbaek, Executive Vice President of Business Development.

Scientists at the new site in North Carolina, will research and develop beneficial microorganisms found in the soil. The resulting technology will focus on improved crop yield, fertility and pest control for growers around the world. The significant expansion of R&D resources will enable Novozymes’ scientists to pursue more and better biological solutions for the ever-changing challenges facing global agriculture. “The research and development jobs Novozymes will create will further strengthen our hi-tech hub and be an example of the strong talent pool and attractive quality of life that characterizes Wake County, the Research Triangle and the state,” said Pat McCrory, North Carolina Governor.

The project was made possible in part by a performance-based grant from the One North Carolina Fund of up to $400,000. The One NC Fund provides financial assistance, through local governments, to attract business projects that will stimulate economic activity and create new jobs in the state. Companies receive no money up front and must meet job creation and investment performance standards to qualify for grant funds. These grants also require and are contingent upon local matches.
Source: http://www.novozymes.com

Novartis’ strategic deal for business expansion

In an effort to focus on key businesses, pharma giant Novartis, Switzerland, has joined forces with long-time rival GlaxoSmithKline (GSK), the United Kingdom, in a multi-billion Euro asset exchange and an over-the-counter (OTC) joint venture. Novartis will take over GSK’s oncology products, while handing over its global vaccines business excepting flu vaccines. GSK will initially pay €3.8bn for Novartis’ vaccines business, with subsequent potential milestone payments of up to €1.3bn plus ongoing royalties. The influenza business is excluded from this deal, but Novartis is planning on selling it in a separate process. With the transition, GSK is building on its position as the world’s leading global vaccines supplier.

Meanwhile, both companies are combining their consumer divisions, selling over-the-counter meds, in a new consumer healthcare venture with 2013 pro forma revenues of €7.9bn. GSK will have majority control with an equity interest of 63.5%. “The Novartis OTC portfolio is highly complementary to GSK’s and has many well-known, widely recommended brands such as Voltaren, Excedrin, Otrivin, and Theraflu. Together, we will create the world’s premier OTC business with clear opportunities to accelerate revenue growth,” said GSK’s CEO, Andrew Witty.

Beyond the deal with GSK, Novartis is also divesting its animal health division to Eli Lilly, the United States, for €3.9bn. Novartis is aiming to focus on its key business of innovative pharmaceuticals, eye care and generics. “The transactions mark a transformational moment for Novartis. They focus the company on leading businesses with innovation power and global scale. They also improve our financial strength, and are expected to add to our growth rates and margins immediately,” said Novartis’ CEO, Joseph Jimenez. The transaction with GSK is expected to complete during the first half of 2015, subject to approvals.
Source: http://www.european-biotechnology-news.com

Mitra Biotech raises venture capital funding

Tata Capital Innovations Fund, India, a domestic venture capital fund managed by Tata Capital, has invested in Mitra Biotech Private Ltd (Mitra), India, to help the company scale up its go to market strategy and to expand in India & globally. The investment would help Mitra become a partner of choice for leading healthcare providers, pharmaceutical & biotech companies by strengthening its business development, marketing and R&D teams.

Mitra is a translational biology company, which offers personalized cancer care to patients through its proprietary patient segregation model Oncoprint. This technology determines the optimal drug or drug combination for a patient under investigation, thereby reducing overall treatment cycle and avoiding toxicity that arises from non-optimal drugs. The assays are carried out on patients’ own tumors by recreating human-tumor microenvironment on plates to ensure high specificity.

“Cancer is no more a disease of old age. With changes in lifestyle, the number of cases of cancer being reported by various sections of population has been on the increase. It is an opportune time to create awareness about personalized cancer treatment and its affordability”, said Mohan Harshey, at Tata Capital. Mitra has partnered leading cancer hospitals like Tata Memorial Hospital, Mazumdar Shaw Cancer Center, Kidwai Memorial Center, Stanley Medical Center and HCG Cancer Network centers in bringing affordable cancer care to India. Mitra is expected to gain market traction rapidly over the next two years.
Source: http://www.thepharmatimes.in

Innovative therapies to patients in Asia

Biogen Idec, the United States, and UCB, Belgium, has announced that they have signed exclusive agreements granting UCB the right to commercialize Biogen Idec products in Republic of Korea, Hong Kong (Province of China), Thailand, Singapore, Malaysia and Taiwan (Province of China), and both develop and commercialize products in China.

As part of the relationship, Biogen Idec will supply UCB with its portfolio of multiple sclerosis (MS) therapies and investigational candidates, including TECFIDERA®, FAMPYRA®, AVONEX®, TYSABRI®, PLEGRIDY and Daclizumab High-Yield Process (DAC HYP). The relationship also includes ELOCTATE and ALPROLIX, Biogen Idec’s investigational longacting recombinant candidates for hemophilia A and B, respectively.

“Our goal is to bring our innovative therapies to patients around the world as quickly and efficiently as possible. By leveraging UCB’s extensive resources, expertise and infrastructure in Asia, we believe we can grow our footprint in critical Asian markets, get our therapies to patients more quickly and create a foundation for further commercial success in this region,” said Carlos Dourado, Senior Vice President, at Biogen Idec.
Source: http://www.biogenidec.com

GENOMICS

Geneticists sequenced first peanut genome

A group of multinational crop geneticists from the International Peanut Genome Initiative (IPGI), has successfully sequenced the peanut’s genome. The new peanut genome sequence will be available to researchers and plant breeders across the globe to aid in the breeding of more productive and more resilient peanut varieties. Peanut, known scientifically as Arachis hypogaea and also called groundnut, is important both commercially and nutritionally. While the oil- and protein-rich legume is seen as a cash crop in the developed world, it remains a valuable sustenance crop in developing nations. “The peanut crop is important in the US, but it’s very important for developing nations as well. In many areas, it is a primary calorie source for families and a cash crop for farmers,” said Scott Jackson, at the University of Georgia Center for Applied Genetic Technologies (CAGT), the United States.

“Improving peanut varieties to be more drought-, insect- and disease-resistant can help farmers in developed nations produce more peanuts with fewer pesticides and other chemicals and help farmers in developing nations feed their families and build more secure livelihoods,” said Rajeev Varshney at the International Crops Research Institute for Semi-Arid Tropics (ICRISAT), India. The effort to sequence the peanut genome has been underway for several years. While peanuts were successfully bred for intensive cultivation for thousands of years, relatively little was known about the legume’s genetic structure because of its complexity.

To map the peanut’s structure, researchers sequenced the genomes of the two ancestral parents because together they represent the cultivated peanut. The sequences provide researchers access to 96% of all peanut genes in their genomic context, providing the molecular map needed to more quickly breed drought- and disease-resistant, lower-input and higher-yielding varieties of peanuts. Knowing the genome sequences of the two parent species will allow researchers to recognize the cultivated peanut’s genomic structure by differentiating between the two subgenomes present in the plants. Being able to see the two separate structural elements also will aid future gene marker development-the determination of links between a gene’s presence and a physical characteristic of the plant. Understanding the structure of the peanut’s genome will lay the groundwork for new varieties with traits like added disease resistance and drought tolerance.
Source: http://www.news.uga.edu

Researchers study smallest fungal plant pathogen

With a kingdom of more than a million species, fungi thrive in diverse ecological niches, play roles in plant health, and are considered to have a whole host of untapped, as-yet unknown applications. At the Department of Energy Joint Genome Institute (DOE JGI), the United States, fungal researchers are involved in several worldwide collaborations to learn more about fungi, and how they can be harnessed for roles such as improving the health of candidate biomass feedstocks for biofuels development. They have sequenced and analyzed the genome of Mixia osmundea, the smallest fungal plant pathogen (13.6 million bases) to date, to provide insight into its mode of pathogenicity and reproductive biology.

Aside from learning how the fungal pathogen reproduces, genome annotation revealed its capabilities in breaking down plant cell wall components, which is of interest to bioenergy researchers. As part of the work toward illuminating the fungal tree of life, a study published in the journal New Phytologist, focused on a tiny plant pathogen called Mixia osmundea, a member of the Pucciniomycotina family that has had few species sequenced to date. Though it was first described 100 years ago, the fungus is rarely seen and has only been isolated on the fronds of two fern species in Japan, Taiwan (Province of China) and US.

During the team’s analysis of the fungus, they identified several carbohydrate-active enzymes that indicate M. osmundea’s capabilities in breaking down plant mass, as expected of the plant pathogen. They also found multiple copies of an enzyme that suggests the fungus is “especially efficient” at breaking down a particular compound in plant cell walls. However, they did not find genes that would indicate the fungus can break down xylan, or convert cellobiose into glucose. “Therefore,” the team wrote, “although M. osmundae seems to possess a set of enzymes that can be used to break down cellulose, it lacks the enzyme sets necessary for depolymerizing it to simple sugars.”
Source: http://www.phys.org

Hearing quality restored with bionic ear technology

Researchers at University of New South Wales (UNSW), Australia, have for the first time used electrical pulses delivered from a cochlear implant to deliver gene therapy, thereby successfully regrowing auditory nerves. The research also heralds a possible new way of treating a range of neurological disorders, including Parkinson’s disease, and psychiatric conditions such as depression through this novel way of delivering gene therapy. The research has been published in the journal Science Translational Medicine. “People with cochlear implants do well with understanding speech, but their perception of pitch can be poor, so they often miss out on the joy of music,” said Professor Gary Housley at UNSW.

“Ultimately, we hope that after further research, people who depend on cochlear implant devices will be able to enjoy a broader dynamic and tonal range of sound, which is particularly important for our sense of the auditory world around us and for music appreciation,” said Professor Housley. The work centres on regenerating surviving nerves after age-related or environmental hearing loss, using existing cochlear technology. The cochlear implants are “surprisingly efficient” at localised gene therapy in the animal model, when a few electric pulses are administered during the implant procedure. It has long been established that the auditory nerve endings regenerate if neurotrophins are delivered to the auditory portion of the inner ear, the cochlea.

But until now, research has stalled because safe, localised delivery of the neurotrophins can’t be achieved using drug delivery, nor by viral-based gene therapy. While the neurotrophin production dropped away after a couple of months, ultimately the changes in the hearing nerve may be maintained by the ongoing neural activity generated by the cochlear implant. Integration of this technology into other ‘bionic’ devices such as electrode arrays used in deep brain stimulation (for the treatment of Parkinson’s disease and depression, for example) could also afford opportunities for safe, directed gene therapy of complex neurological disorders. The research, which has the support of Cochlear Limited through an Australian Research Council Linkage Project grant, has been five years in development.
Source: http://www.sciencedaily.com

Genomic landscape with a complexity of regulatory elements

A team led by biologist Dr. Ulrich Technau at the University of Vienna, Austria, has discovered that sea anemones display a genomic landscape with a complexity of regulatory elements similar to that of fruit flies or other animal model systems. This suggests, that this principle of gene regulation is already 600 million years old and dates back to the common ancestor of human, fly, and sea anemone. On the other hand, sea anemones are more similar to plants rather thn to vertebrates or insects in their regulation of gene expression by short regulatory RNAs called microRNAs. These surprising evolutionary findings have been published in two open-access articles in Genome Research. Our appearance, the shape we have and how our body works is, in addition to environmental influences, largely the result of the action of our genes.

However, genes are rarely single players, they rather act in concert and regulate each other’s activity and expression in gene regulatory networks. In the last decades, the sequencing of the human and many animal genomes has shown that anatomically simple organisms such as sea anemones have a surprisingly complex gene repertoire similar to that of higher model organisms. This implies, that the difference in morphological complexity cannot be easily explained by the presence or absence of individual genes. Some researchers hypothesized that the individual genes do not code for more complex body plans, but that this is determined by how the genes are wired and linked between each other.

Accordingly, researchers expected that these gene networks are less complex in simple organisms than in human or “higher” animals. A measurement of the complexity of gene regulation could be the distribution and density of regulatory sequences in the genome. These motifs on the DNA called enhancers and promoters can bind transcription factors specifically and often regulate the expression of target genes in specific spatio-temporal patterns. “Finding these short motifs in the ocean of nucleotides is far from trivial”, said Dr. Technau, professor at Department for Molecular Evolution and Development. While the genes constitute, in a sense, the words in the language of genetics, enhancer and promoters serve as the grammar.
Source: http://www.bioquicknews.com

New computational method for gene expression

With gene expression analysis growing in importance for both basic researchers and medical practitioners, researchers at Carnegie Mellon University (CMU) and the University of Maryland (UMD), the United States, have developed a new computational method that dramatically speeds up estimates of gene activity from RNA sequencing (RNA-seq) data. With the new method, dubbed Sailfish after the famously speedy fish, estimates of gene expression that previously took many hours can be completed in a few minutes, with accuracy that equals or exceeds previous methods. The report on this new method has been published in the journal Nature Biotechnology.

Gigantic repositories of RNA-seq data now exist, making it possible to re-analyze experiments in light of new discoveries. “But 15 hours a pop really starts to add up, particularly if you want to look at 100 experiments. With Sailfish, we can give researchers everything they got from previous methods, but faster,” said Carl Kingsford, an associate professor at CMU. Though an organism’s genetic makeup is static, the activity of individual genes varies greatly over time, making gene expression an important factor in understanding how organisms work and what occurs during disease processes. Gene activity can’t be measured directly, but can be inferred by monitoring RNA, the molecules that carry information from the genes for producing proteins and other cellular activities.

The RNA-seq process results in short sequences of RNA, called “reads.” In previous methods, the RNA molecules from which they originated could be identified and measured only by painstakingly mapping these reads to their original positions in the larger molecules. But researchers found that the time-consuming mapping step could be eliminated. Instead, they found that they could allocate parts of the reads to different types of RNA molecules, much as if each read acted as several votes for one molecule or another. Without the mapping step, Sailfish can complete its RNA analysis 20-30 times faster than previous method his numerical approach might not be as intuitive as a map to a biologist, but it makes perfect sense to a computer scientist, Kingsford said.
Source: http://www.phys.org

Researchers built a synthetic yeast chromosome

In a significant step forward for synthetic biology, an international team of researchers have built a synthetic yeast chromosome – the first ever from a eukaryotic cell. This could help geneticists better understand how genomes work and stretch the existing limits of synthetic biology to make novel medications, more efficient biofuels and perhaps even better beer. Unlike prokaryotic cells, such as bacteria, which just have a jumble of DNA in their middles, eukaryotic cells contain a nucleus and a much more complicated chromosome-based DNA arrangement. These cells make up all more complex life, including animals and plants. Researchers have previously synthesized bacterial DNA, but this is the first time they’ve been able to synthesize the larger and more complicated DNA of a eukaryote.

The chromosome in question belongs to good ol’ baker’s yeast, which is at the heart of many a synthetic biology experiment. The researchers focused on one of the yeast’s 16 chromosomes: Number 3, which controls mating and genetic change. In creating their synthetic version, researchers made 50,000 changes to the chromosome. They took out “junk DNA,” which doesn’t code for proteins, and “jumping DNA,” whose erratic movement often triggers mutations. And to really hone in on the yeast’s growth, they also ixnayed tens of thousands of repeated base pairs that weren’t involved in reproduction. Many a computer and undergraduate researcher were employed to build and connect all 273,871 basepairs.

Then they put this designer yeast chromosome to the test. They constructed the idealized sequence they’d created, and then incorporated the chromosome into otherwise normal yeast cells. The cells’ growth and behavior, in all but one case, were almost indistinguishable from normal yeast cells. Then researchers took a little more liberty and started making changes to the chromosome, at sites they designed specifically to be manipulated. Through this, they found they could make the yeast grow faster or more slowly on command. The results have been published the journal Science.
Source: http://www.blogs.discovermagazine.com

PROTEOMICS

Scientists discover protein to treat brittle bone disease

According to the scientists from Baylor College of Medicine (BCM), University of Texas (UT), the United States, a discovery in mice could help to treat people with a form of brittle bone disease. In a study, mice were bred with osteogenesis imperfecta (OI) and the activity of a protein which shapes and reshapes bones was monitored. Scientists said intense activity of the protein in the mice was linked to OI. The finding could lead to a new target for treatment, but experts warn the study is in mice and might not apply to humans. One in 15,000 people in the UK are estimated to have OI. It is an inherited condition, where abnormalities in the genes controlling collagen affect the bone’s strength.

“In severe cases, people with OI can have between 200 and 300 fractures by the time they reach age 18,” said the Brittle Bone Society, the United Kingdom. Current treatment is lacking. Scientists at BCM, looked at a protein in mice bred with the condition and compared them to “normal” mice. They said the activity of transforming growth factor beta (TGF), which co-ordinates the shaping and reshaping of bone, was excessive in mice with OI. When TGF was blocked with an antibody, the mice’s bones withstood “higher maximum load and ultimate strength” and showed “improved whole bone and tissue strength”, suggesting “resistance to fracture”, the study said. The research has been published in the journal Nature Medicine.

“The study was ‘basic science’ in mouse models to understand the ‘basics of bone biology’. It could, in the future, help develop knowledge about bone conditions more fully. As we understand more about bone turnover and communication between bone cells, work could open doors for future research that could affect osteoporosis. It could take 10 to 15 years for such mouse studies to reach the stage of clinical trials in people,” said Dr. Claire Bowring, at the National Osteoporosis Society (NOS), the United Kingdom.
Source: http://www.bbc.com

Researchers create insulin-producing cells by cloning

Researchers from the New York Stem Cell Foundation (NYSCF), the United States, have transformed embryonic stem cells from a diabetic woman into insulin-producing beta cells. The study has been published in the journal Nature. This is the first time that cloning has been used to create cells genetically matched to an adult and intended for therapeutic use. “By reprogramming cells to a pluripotent state and making beta cells, we are now one step closer to being able to treat diabetic patients with their own insulin-producing cells,” said Dr. Dieter Egli, who led the research.

Two teams have now created embryonic stem cell lines from adult human cells, reviving the debate about using stem cells from cloned human embryos for research or therapy. During their study, the team replaced the nucleus of a donated human egg with a nucleus from the skin cell of a 32-year-old woman with type I diabetes, in a process called somatic cell nuclear transfer (SCNT). After being exposed to electronic pulses and chemicals, the cell began to divide in a similar way to a fertilised egg, forming a ball of a few hundred cells. From this blastocyst, scientists removed stem cells and transformed them into insulin-producing beta cells. The approach could someday aid treatment of type 1 diabetes, where the body cannot make enough insulin. The next step for the team is to transplant the insulin-producing cells into mice to see whether they grow into functioning human beta cells.
Source: http://www.bionews.org.uk

Coral protein can block HIV virus

Researchers at the National Cancer Institute’s (NCI), Center for Cancer Research (CCR), the United States, have found that the proteins could be adapted to be used in gels or sexual lubricants to provide a barrier against potential HIV infection. This is a new class of proteins discovered in coral are capable of blocking the HIV virus from entering T-cells. “It’s always thrilling when you find a brand-new protein that nobody else has ever seen before. The fact that this protein appears to block HIV infection – and to do it in a completely new way – makes this truly exciting”, said senior researcher Barry O’Keefe.

The researchers said, the cnidarin proteins were astonishingly potent and capable at blocking HIV. The proteins bind to the virus and prevent it from fusing with the T-cell membrane. The next step is to test the proteins for potential side effects.
Source: http://www.sunnewsnetwork.ca

Research uncovers markers associated with malaria

Researchers from Nigeria, Sweden, and the United Kingdom, have reported that a proteomic analysis of blood from children with malaria has uncovered certain protein biomarkers linked to the development of complications due to infection. The team examined the levels of more than 1,000 proteins in the plasma of children with and without malaria as well as children with malaria-related complications such as cerebral malaria and severe malaria anemia. The levels of more than 40 proteins, including a number of inflammatory response proteins, differed between children with malaria and controls, while higher levels of muscle-related proteins were associated with cerebral malaria. The report has been published in the journal PLOS Pathogens.

“These findings will hopefully lead to an increased understanding of the disease and may contribute to the development of clinical algorithms that could predict which children are more at risk [of developing] severe malaria,” said Peter Nilsson at the KTH-Royal Institute of Technology, Sweden. According to the World Health Organization, malaria is a life-threatening disease that caused an estimated 627,000 deaths in 2012. In Nigeria, about a third of childhood deaths are attributable to Plasmodium falciparum, one of the parasites that causes malaria. Searching for markers to differentiate complicated and uncomplicated malaria, the researchers selected 304 proteins to be included on a targeted affinity proteomic array along with 711 other proteins randomly chosen from the Human Protein Atlas.

These proteins, gleaned from both the targeted and random sets of proteins, include a number of inflammation-related proteins such as von Willebrand factor and C-reactive protein. Additionally, researchers uncovered 13 proteins, whose levels could differentiate complicated from uncomplicated malaria. They also noted two proteins that were increased in the plasma of children with cerebral malaria – carbonic anhydrase III (CA3) and creatine kinase (CK) – that are usually associated with muscle tissue. Through multivariate analyses, the researchers developed panels of proteins that could differentiate malaria complications from uncomplicated disease. Due of this, Nilsson and his team suggested that muscle damage markers and endothelial cell activation/platelet adhesion markers together in the plasma are specific to cerebral malaria pathogenesis.
Source: http://www.genomeweb.com

Tracking proteins in single HIV particle

A team of scientists from KU Leuven, Belgium, has developed a new technique to examine how proteins interact with each other at the level of a single HIV viral particle. The technique allows scientists to study the life-threatening virus in detail and makes screening potential anti-HIV drugs quicker and more efficient. The technique can also be used to study other diseases. Understanding how the human immunodeficiency virus (HIV) reproduces itself is crucial in the effort to fight the disease. Upon entering the bloodstream, HIV viral particles, or virions, ‘highjack’ individual immune cells. Once inside, the virion reprograms the genetic material of the immune cell to produce more HIV virions. In this way, HIV disables the disease-fighting ‘bodyguards’ in our blood and turns them into breeding machines for new HIV virions.

Integrase plays a key role throughout this whole process. “Integrase is the HIV protein that causes the genetic material of HIV to link to that of the hijacked cell. It ensures the programming of the human cell upon infection. In our study, we wanted to track integrase during the different stages of infection. The challenge is to do this at the level of a single virion: HIV has multiple ways of doing the same thing. This is the case for cell penetration, for instance. So it is certainly useful to be able to see exactly how the individual HIV virions are behaving,” said researcher Jelle Hendrix.

To achieve this, the researchers used single-molecule fluorescence imaging and engineered a genetically modified (GM) HIV virion that was capable of infecting the cell but incapable of reproducing inside it. The virion was programmed to produce a fluorescent form of integrase, which allowed them to examine the interactions of the florescent integrase under the light microscope both in vitro in a single HIV virion as well as in a human cell infected with it. Using this technique they studied both clinically approved and newly developed HIV inhibitors. Some of these drugs were thought to affect interaction between integrase particles. “Researchers have been studying protein interactions for some time, but studying them at the level of a single viral particle was not possible until now,” said Hendrix. Our technique allows scientists to quickly test many molecules – potential medications – for many diseases using minimal material.
Source: http://www.sciencedaily.com

MEDICAL BIOTECH

Scientists claim H7N9 treatment breakthrough in China

Scientists in China have claimed to have found a human blood protein associated with the H7N9 fatality rate. The study published in the journal Nature Communications, showed that blood plasma levels of angiotensin II were higher in H7N9 patients and could be used to predict their physical deterioration, Xinhua reported. “Angiotensin II is a human protein contained in plasma, the vascular wall, heart and kidney to regulate blood pressure. It is closely linked to acute lung injury. H7N9 patients with higher levels of angiotensin II carry more viral load. It is particularly obvious in the second week of human infection. The angiotensin II level of patients in critical condition keeps going up, while that of mild cases tends to drop,” said Li Lanjuan, researcher at the Chinese Academy of Engineering (CAE) and a specialist in H7N9 prevention. The new finding could help in clinical practice, Li added.

Medical personnel could adopt more effective and reliable treatment measures for patients suffering different conditions. “This study will provide a new perspective to H7N9 pathology and potential treatment for future cases,” said Ed Gerstner, executive editor of Nature Communications. They collected plasma from 47 H7N9 patients in cities of Hangzhou, Shanghai and Nanjing and analyzed the correlation between angiotensin II and viral load. H7N9 was first reported in China in March 2013. The virus causes severe disease in humans and often lethal respiratory failure. The country has reported more than 200 human H7N9 cases.
Source: http://www.news.oneindia.in

New blood ‘recharges old brain’

Scientists at the Stanford University, the United States, have discovered how to combat and even reverse some processes of ageing, at least in mice. According to a study, injecting the blood of young mice into older rodents boosted their brainpower. The researchers are planning to carry out trials in people in the hope that new treatments for dementia can be developed. A United Kingdom dementia research charity said the human significance was unknown. In the study, published in the journal Nature Medicine, mice aged 18 months were given injections of the fluid part of blood (plasma) taken from mice aged three months. The injected mice performed better on memory tests than mice of the same age that had not been given blood plasma.

“There are factors present in blood from young mice that can recharge an old mouse’s brain, so that it functions more like a younger one,” said Dr. Tony Wyss-Coray at Stanford University School of Medicine. The treatment rejuvenated certain aspects of learning and memory in mice, but was “of unknown significance to humans”. “This research, while very interesting, does not investigate the type of cognitive impairment that is seen in Alzheimer’s disease, which is not an inevitable consequence of ageing,” said Dr. Eric Karran at Alzheimer’s Research UK.

Meanwhile, two studies by a separate team have shed more light on how young blood may benefit the old, in mice at least. A substance in the blood of mice previously shown to have an anti-aging effect on heart muscle, also boosted brain cells, according to a Harvard team. The research, published in the journal Science, found the blood factor encouraged the growth of brain cells in old mice, and restored their sense of smell. The same chemical also boosted muscle power in aged mice, the researchers found.
Source: http://www.bbc.com

Researchers develop 3D skin model

Researchers at King’s College London (KCL), the United Kingdom, has developed an advanced 3D skin model that may reduce the need for animal models in cosmetic testing. The model uses stem cell derived keratinocytes, the primary cell type of the epidermis, the outermost layer of skin. Over time, they were able to build up the cells into a 3D structure called a human epidermal equivalent, or HEE, that both physically and functionally resembles the natural permeable barrier of the skin. HEE models are widely used to test skin disorders, drugs, and cosmetics in the laboratory. However, previous models have been limited by two key aspects: development and scalability. First, they were not able to engineer a functional permeability barrier. Second, stem cells generated from a biopsy sample of epidermis could only produce a limited number of HEEs; furthermore, they may contain mutations that could affect experimental results.

“Our new method can be used to grow much greater quantities of lab-grown human epidermal equivalents, and thus could be scaled up for commercial testing of drugs and cosmetics’, said Dr. Dusko Ilic at KCL. The major function of the skin is to form a permeable barrier against the external environment, against pathogens, heat and water loss. Skin diseases such as atopic dermatitis (also known as eczema) and Ichthyoses (characterised by thickened flaky skin) affect the permeability of the skin, ranging from mild to severe. These skin diseases and related disorders are commonly tested using animal models. Although similar diseases are also present is some animals, there are no suitable in vitro models for such diseases. The new HEE model overcomes this limitation.

This research could reduce the amount of animal models that are currently used in research. “This new human skin model is superior scientifically to killing rabbits, pigs, rats or other animals for their skin and hoping that research findings will be applicable to people – which they often aren’t, due to species differences in skin permeability, immunology, and other factors,” said Troy Seidle, Research and toxicology director of The Humane Society International, the United States.
Source: http://www.bionews.org.uk

Researchers coaxed human embryonic stem cells

Researchers at University of Michigan (UM), the Unites States, have found that mechanical forces in the environment of human embryonic stem cells influences how they differentiate, or morph into the body’s different cell types. To arrive at the findings, the researchers coaxed human embryonic stem cells to turn into working spinal cord cells more efficiently by growing the cells on a soft, utrafine carpet made of a key ingredient in Silly Putty. This research is the first to directly link physical, as opposed to chemical, signals to human embryonic stem cell differentiation. Differentiation is the process of the source cells morphing into the body’s more than 200 cell types that become muscle, bone, nerves and organs, for example. The study has been published online at Nature Materials.

“The findings raise the possibility of a more efficient way to guide stem cells to differentiate and potentially provide therapies for diseases such as amyotrophic lateral sclerosis (Lou Gehrig’s disease), Huntington’s or Alzheimer’s,” said Jianping Fu, assistant professor at UM. In the specially engineered growth system – the ‘carpets’ Fu and his colleagues designed – microscopic posts of the Silly Putty component polydimethylsiloxane serve as the threads. By varying the post height, the researchers can adjust the stiffness of the surface they grow cells on. Shorter posts are more rigid – like an industrial carpet. Taller ones are softer – more plush.

The team found that stem cells they grew on the tall, softer micropost carpets turned into nerve cells much faster and more often than those they grew on the stiffer surfaces. Fu’s findings go deeper than cell counts. The researchers verified that the new motor neurons they obtained on soft micropost carpets showed electrical behaviors comparable to those of neurons in the human body. They also identified a signaling pathway involved in regulating the mechanically sensitive behaviors. A signaling pathway is a route through which proteins ferry chemical messages from the cell’s borders to deep inside it. The pathway they zeroed in on, called Hippo/YAP, is also involved in controlling organ size and both causing and preventing tumor growth. Fu said his findings could also provide insights into how embryonic stem cells differentiate in the body.
Source: http://www.sciencedaily.com

Scientists discover brain circuits involved in emotion

A new research by neuroscientists at the University of Bristol, the United Kingdom, has identified a chain of neural connections, which links central survival circuits to the spinal cord, causing the body to freeze when experiencing fear. The study has been published in the Journal of Physiology. Understanding how these central neural pathways work is a fundamental step towards developing effective treatments for emotional disorders such as anxiety, panic attacks and phobias.

An important brain region responsible for how humans and animals respond to danger is known as the PAG (periaqueductal grey), and it can trigger responses such as freezing, a high heart rate, increase in blood pressure and the desire for flight or fight. The research has discovered a brain pathway leading from the PAG to a highly localised part of the cerebellum, called the pyramis. The research went on to show that the pyramis is involved in generating freezing behaviour when central survival networks are activated during innate and learnt threatening situations. The pyramis may therefore serve as an important point of convergence for different survival networks in order to react to an emotionally challenging situation.

“There is a growing consensus that understanding the neural circuits underlying fear behaviour is a fundamental step towards developing effective treatments for behavioural changes associated with emotional disorders,” said Dr. Stella Koutsikou, first author of the study. “Our work introduces the novel concept that the cerebellum is a promising target for therapeutic strategies to manage dysregulation of emotional states such as panic disorders and phobias.” added Professor Bridget Lumb.
Source: http://www.sciencedaily.com

Scientists grow first functioning human lungs

Lungs are a notoriously delicate organ. That makes useable donor lungs hard to come by – in 2010, just 1,800 lung transplants took place in the United States. However, researchers are getting closer to addressing the shortage by growing lungs, for the first time, in the lab. Scientists at the University of Texas (UT), the United States, used damaged lungs from two children who died in car accidents. In a cutting-edge kind of tissue engineering, they stripped away all the cells from the lungs and left behind the “scaffolding,” the intricate web of proteins that holds cells in place. Researchers then coated this scaffold with viable lung cells from a second pair of lungs, not suitable for transplant. Finally, they placed the lungs in a nutrient bath for four weeks to allow the cells to grow and fully re-create lung tissue. The new lungs look like the real thing, just softer and less dense.

In the past, washing a donor organ of its cells could take up to four months to accomplish, but the latest study introduced a device that sped that process up to three days. The resulting lungs are eggshell white, because of the lack of blood flowing in the new organ. The team first grew the lungs in a lab last year, but waited to tell the world what they accomplished. “It’s taken us a year to prove to ourselves that we actually did a good job with it. You don’t run out immediately and tell the world you have something wonderful until you’ve proved it to ourselves that we really did something amazing,” said lead researcher Joan Nichols.

When will these lungs save the first human life? Don’t hold your breath. Although the team was successful, researchers say it will take at least 10 years before they are ready for people in need of a transplant. However, Nichols said they plan to test lab-grown lungs in pigs within the next year or so.
Source: http://www.blogs.discovermagazine.com

Cochlear implant to be used for gene therapy

Researchers at the University of New South Wales (UNSW), Australia, have for the first time used electrical pulses delivered from a cochlear implant to deliver gene therapy, thereby successfully regrowing auditory nerves. The research also heralds a possible new way of treating a range of neurological disorders, including Parkinson’s disease, and psychiatric conditions such as depression through this way of delivering gene therapy. “People with cochlear implants do well with understanding speech, but their perception of pitch can be poor, so they often miss out on the joy of music. Ultimately, we hope that after further research, people who depend on cochlear implant devices will be able to enjoy a broader dynamic and tonal range of sound, which is particularly important for our sense of the auditory world around us and for music appreciation,” said Gary Housley at UNSW.

The work centres on regenerating surviving nerves after age-related or environmental hearing loss, using existing cochlear technology. The cochlear implants are “surprisingly efficient” at localised gene therapy in the animal model, when a few electric pulses are administered during the implant procedure. It has long been established that the auditory nerve endings regenerate if neurotrophins – a naturally occurring family of proteins crucial for the development, function and survival of neurons – are delivered to the auditory portion of the inner ear, the cochlea.

Housley and his team at UNSW developed a way of using electrical pulses delivered from the cochlear implant to deliver the DNA to the cells close to the array of implanted electrodes. These cells then produce neurotrophins. While the neurotrophins production dropped away after a couple of months, ultimately the changes in the hearing nerve may be maintained by the ongoing neural activity generated by the cochlear implant. “We think it’s possible that in the future this gene delivery would only add a few minutes to the implant procedure. The surgeon who installs the device would inject the DNA solution into the cochlea and then fire electrical impulses to trigger the DNA transfer once the implant is inserted,” said Jeremy Pinyon, the paper’s first author.
Source: http://www.newstodaynet.com

AGRI BIOTECH

Genetically modified tobacco plants

Researchers at the Public University of Navarre (NUP/UPNA), Spain, and the Institute of Agrobiotechnology (IdAB), Spain, have conducted a study into genetically modified (GM) tobacco plants from which it is possible to produce between 20 and 40 percent more ethanol; this would increase their viability as a raw material for producing biofuels. Tobacco, a high-density crop which is mown several times throughout its cycle, can produce as much as 160 tonnes of fresh matter per hectare and become a source of biomass suitable for producing bioethanol. “Tobacco plants as a source of biomass for producing bioethanol could be an alternative to traditional tobacco growing which is in decline in the USA and in Europe because it cannot compete with emerging countries like China,” said Jon Veramendi, head of the research group at IdAB.

In the course of the research, which has been echoed by the journal Molecular Breeding, tobacco plants of the Virginia Gold and Havana commercial cultivars have been grown. The plants were genetically modified to increase their production of starch and sugars, which contributes to the increase in ethanol production. The basis of this work is the PhD thesis by Ruth Sanz-Barrio, read at the NUP/UPNA in 2013. “What has been done now is fieldwork with these two tobacco cultivars and it has been found that the starch and sugars in the tobacco leaf are in fact higher,” said Veramendi. Traditional tobacco growing allows the plant to develop and the leaves to grow and get bigger, as the nicotine is synthesised when the plant is more mature. However, if the plants are used for producing biofuels, the researchers go for a higher-density crop similar to that of forage crops.
Source: http://www.basqueresearch.com

Scientists find herbicides to combat weed growth

Scientists from the University of Pune (UoP), India, and National Accreditation Board for Testing and Calibration Laboratories (NABL), India, accredited laboratory Ross LifeScience Pvt Limited, India, have found potent herbicides to inhibit the growth of Congress grass, a poisonous weed that is known as the ‘scourge of India.’ The weed which spreads like wild fire not only has detrimental effect on the ecosystem but also causes allergic reactions in humans. The toxic weed is also known as Parthenium. The research has been published in an international journal called Journal of Medicinal Plants Research, was undertaken by Swati Vitonde from Ross LifeScience, R J Thengane and V S Ghole from the Department of Environmental Science, UoP.

Researchers found out that plants like ‘Cassia tora’, commonly known as Wild Senna, and ‘Cassia uniflora’, with the common name Oneleaf Senna can act as herbicides. “We studied the effects of seed powder and water extract of Wild Senna and Oneleaf Senna on the germination of Congress grass seeds. Both inhibited the weed’s seed germination to varying degrees. Seed powder of Wild Senna showed more inhibition than the water extract,” said Vitonde.

Congress grass came to India as a food contaminant that was imported from the United States in 1956. It is a vigorous colonist in poor and overgrazed pastures and readily occupies bare areas where stock movement is frequent. It may be a problem even when present at low levels. This weed also inhibits the growth and germination of other plants,” said Dr. V. S. Ghole, former HOD at UoP. The weed has spread unhindered throughout India. According to the experts, weed occupies over 5 million hectare of land in the country. Senna species is only herbicidal in nature, but also have less residual effect, are non-toxic to non-target plants and are environment friendly. They can be used as an alternate to chemical methods used against Congress grass.
Source: http://www.timesofindia.indiatimes.com

Researchers target eucalyptus as source of fuel

Researchers from University of Florida (UF), Institute of Food and Agricultural Sciences (UF/IFAS), the United States, are working to produce ethanol from plant material are taking a hard look at eucalyptus as a possible source for the clean fuel. Joe Sagues, at the UF’s Biorefinery Pilot Plant in Florida, and Ismael Uriel Nieves, project director at the plant, have recently switched the focus of their lab-scale research from sugarcane and sorghum to eucalyptus for this study. According to them, the tree, most commonly associated with Australia and food for koalas, is a fast-growing hardwood that is easier to store and transport. In their study, published in the journal Applied Energy, they found that some eucalyptus had an increased sugar content, making it viable as a sustainable feedstock for biofuel production.

In addition, during pretreatment, they switched from the more corrosive sulfuric acid (H2SO4) to phosphoric acid (H3PO4) to increase sugar yields. H2SO4 requires special metal alloy containers, while H3PO4 can be housed in commercial steel, which cuts down on initial capital costs in building a biofuel plant. The H3PO4 also doesn’t break down the released sugars as much, which increases overall yield. The process involves injecting eucalyptus plants with H3PO4 while under high temperature and pressure from steam, then rapidly releasing the pressure – a process known as a steam-explosion. After this step, enzymes are added to the mix to improve the release of sugars. After it cools, air, chemicals and trace minerals are added, and the slurry ferments. At the end of the process, the mixture becomes fuel.
Source: http://www.phys.org

Researchers develop better genetic markers

A&M AgriLife Research, the United States, has been developing genetic diagnostic markers to identify wheat streak mosaic virus resistance, providing wheat breeders a new tool in breeding wheat varieties resistant to one of the region’s most prevalent diseases. The study includes work by AgriLife Research scientists in Amarillo, including Dr. Shuyu Liu, small grains geneticist; Silvano Ocheya, doctoral graduate student; Dr. Jackie Rudd, wheat breeder; and Dr. Qingwu Xue, crop stress physiologist. They were joined by Dr. Guorong Zhang, wheat breeder at Kansas State University (KSU), Agriculture Research Center, the United States; and Dr. Guihua Bai, U.S. Department of Agriculture.

“Wheat streak mosaic virus, which is transmitted by wheat curl mite, is one of the major limiting factors for wheat production in the Southern High Plains. The yield loss can be up to 50 percent due to wheat streak mosaic virus in any given epidemic year,” said Liu. There are several resistance genes to wheat streak mosaic available, but only one gene, labeled Wsm2, is from a wheat line, he said. The other two are from wheat relative species. Wsm2 has been bred in two wheat cultivars, RonL and Snowmass. This resistance gene is now being used by breeders in Kansas, Colorado and Texas to combine with other traits.

Ocheya, has used a wheat population derived from CO960293-2 and TAM 111 to map the drought tolerance genes in TAM 111 and identify tight linked single nucleotide polymorphic or SNP markers, for drought tolerance genes and Wsm2. SNPs are variations within the DNA. The international wheat community, including the U.S., has developed a chip with 90,000 SNP markers, which can be used to screen wheat lines. Ocheya mapped about 5,000 SNP onto the whole wheat genome. These markers were converted into high throughput SNP markers and have been used to screen F2 breeding populations inoculated with the virus strain Sidney 81. This confirmed that they are much better than any other previously used markers
Source: http://www.phys.org

Scientists generate longest genome sequence

Scientists from the University of California (UC), the United States, have generated the longest genome sequence to date, unraveling the genetic code of the loblolly pine tree. Conifers have been around since the age of the dinosaurs, and they have some of the biggest genomes of all living things. Native to the U.S. Southeast, the loblolly pine (Pinus taeda) can grow over 100 feet (30 meters) tall and has a lengthy genome to match, with 23 billion base pairs. That’s more than seven times the size of the human genome, which has 3 billion base pairs. These pairs form sequences called genes that tell cells how to make proteins.

“It’s a huge genome. But the challenge isn’t just collecting all the sequence data. The problem is assembling that sequence into order,” said David Neale, a professor at UC. To simplify this huge genetic puzzle, Neale and colleagues assembled most of the sequence from part of a single pine nut – a haploid part of the seed with just one set of chromosomes to piece together. The new research showed that the loblolly genome is bloated with repetitive DNA. In fact, 82 percent of the genome repeats itself.

According to the scientists, understanding the loblolly pine’s genetic code could lead to improved breeding of the tree, which is used to make paper and lumber and is being investigated as a potential biofuel. The loblolly pine joins other recently sequenced conifers, including the Norway spruce (Picea abies), which has 20 billion base pairs. For their next project, the researchers are eyeing the sugar pine, a tree with 35 billion base pairs.
Source: http://www.livescience.com

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