Bacterium engineered with DNA in which thymine is replaced by synthetic building block

Source: Bacterium engineered with DNA in which thymine is replaced by synthetic building block The project, coordinated by Rupert Mutzel (Institut für Biologie, Freie Universität Berlin) and Philippe Marlière (Heurisko USA Inc.), involved researchers of the French CEA (Commissariat à l'Energie Atomique et aux Energies Alternatives) and of the Katholieke Universiteit Leuven (Belgium). As described in the latest issue ofAngewandte Chemie International Edition, the experimental work was based on a unique technology developed by Marlière and Mutzel enabling the directed evolution of organisms under strictly controlled conditions. Large populations of microbial cells are cultured for prolonged periods in the presence of a toxic chemical -- in this case, 5-chlorouracil -- at sublethal levels, thereby selecting for genetic variants capable of tolerating higher concentrations of the toxic substance.In response to the appearance of such variants in the cell population the concentration of the toxic chemical in the growth medium is increased, thus keeping the selection pressure constant. This automated procedure of long term evolution was applied to adapt genetically engineered Escherichia colibacteria unable to synthesize the natural nucleobase thymine to grow on increasing concentrations of 5-chlorouracil. After a culture period of about 1000 generations descendants of the original strain were obtained which used 5-chlorouracil as complete substitute for thymine. Subsequent genome analysis revealed numerous mutations in the DNA of the adapted bacteria. The contribution of these mutations to the adaptation of the cells towards the halogenated base will be the subject...

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Ants Are Experienced Fungus Farmers

Source: Ants Are Experienced Fungus Farmers Entomologists Ted Schultz and Seán Brady at the Smithsonian's National Museum of Natural History have been providing new insight into the agricultural abilities of ants and how these abilities have evolved throughout time. Using DNA sequencing, the scientists were able to construct an "evolutionary tree" of fungus-growing ants, which revealed a single pioneering ancestor that discovered agriculture approximately 50 million years ago. In the past 25 million years, four different specialized agricultural systems have evolved, leading to the most recently evolved and best-known fungus-growing ant species--"leaf-cutter ants." The ants do not eat the leaves; they grow their fungus gardens on them and then eat the fungus. By studying the agricultural evolution of leaf-cutter ants, as well as various other species, scientists may be able to develop improved human agricultural and medical methods. "Agriculture is very rare in the animal world," said Schultz. "We only know of four animal groups that have discovered agriculture: ants, termites, bark beetles and humans. By studying certain fungus-growing ants, which our study indicates are almost like 'living fossils,' we might be able to better understand steps involved in the evolution of ant agriculture." To complete their research, scientists spent more than 15 years assembling a comprehensive array of specimens, which included 91 ant species, 65 of which were fungus-growing ant species representing all different groups of fungus-growing ants. Researchers then used DNA sequencing, combined with a variety of state-of-the-art computer algorithms, to construct an evolutionary...

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Nanotechnology used to harness power of fireflies

Source: Nanotechnology used to harness power of fireflies It's all about the size and structure of the custom, quantum nanorods, which are produced in the laboratory by Mathew Maye, assistant professor of chemistry in SU's College of Arts and Sciences; and Rebeka Alam, a chemistry Ph.D. candidate. Maye is also a member of the Syracuse Biomaterials Institute. "Firefly light is one of nature's best examples of bioluminescence," Maye says. "The light is extremely bright and efficient. We've found a new way to harness biology for non-biological applications by manipulating the interface between the biological and non-biological components." Their work, "Designing Quantum Rods for Optimized Energy Transfer with Firefly Luciferase Enzymes," was published online May 23 in Nano Letters and is forthcoming in print. Collaborating on the research were Professor Bruce Branchini and Danielle Fontaine, both from Connecticut College. Fireflies produce light through a chemical reaction between luciferin and it's counterpart, the enzyme luciferase. In Maye's laboratory, the enzyme is attached to the nanorod's surface; luciferin, which is added later, serves as the fuel. The energy that is released when the fuel and the enzyme interact is transferred to the nanorods, causing them to glow. The process is called Bioluminescence Resonance Energy Transfer (BRET). "The trick to increasing the efficiency of the system is to decrease the distance between the enzyme and the surface of the rod and to optimize the rod's architecture," Maye says. "We designed a way to chemically attach, genetically manipulated luciferase enzymes directly to the surface of the nanorod." Maye's collaborators...

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Researchers Achieve RNA Interference, in a Lighter Package To achieve this type of gene shutdown, known as RNA interference, many researchers have tried -- with some success -- to deliver RNA with particles made from polymers or lipids. However, those materials can pose safety risks and are difficult to target, says Daniel Anderson, an associate professor of health sciences and technology and chemical engineering, and a member of the David H. Koch Institute for Integrative Cancer Research at MIT. The new particles, developed by researchers at MIT, Alnylam Pharmaceuticals and Harvard Medical School, appear to overcome those challenges, Anderson says. Because the particles are made of DNA and RNA, they are biodegradable and pose no threat to the body. They can also be tagged with molecules of folate (vitamin B9) to target the abundance of folate receptors found on some tumors, including those associated with ovarian cancer -- one of the deadliest, hardest-to-treat cancers. Anderson is senior author of a paper on the particles appearing in the June 3 issue of Nature Nanotechnology. Lead author of the paper is former MIT postdoc Hyukjin Lee, now an assistant professor at Ewha Womans University in Seoul, South Korea. Genetic disruption RNA interference (RNAi), a natural phenomenon that cells use to control their gene expression, has intrigued researchers since its discovery in 1998. Genetic information is normally carried from DNA in the nucleus to ribosomes, cellular structures where proteins are made. Short interfering RNA (siRNA) disrupts this process by binding to the messenger RNA molecules that carry DNA's instructions, destroying them before they reach...

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Berkeley scientists turn harmless virus into piezoelectric generator Scientists at the Lawrence Berkeley National Laboratory (Berkeley Lab) have created a harmless, genetically-modified virus that’s piezoelectric — in other words, it generates electricity when pressure is applied. This virus might eventually find its way into piezoelectric generators in the sole of your shoe, which would generate electricity (for your smartphone) while you walk. The concept of piezoelectric energy harvesting is hardly new, but according to Berkeley Lab the materials used to make piezoelectric devices are toxic, and are thus no good for internal use or for consumer-facing applications (such as the aforementioned shoe-sole power generator). The The M13 bacteriophage (literally “bacteria devourer”) virus, however, is: piezoelectric, harmless to humans, easy to genetically modify, and readily aligns...

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Parasitic Plants Steal Genes from Their Hosts Vertical gene transfer is that between parents and their offspring, while horizontal gene transfer is the movement of genes between two different organisms. Bacteria use horizontal gene transfer to exchange resistance to antibiotics. Recent studies have shown that plants can also use horizontal gene transfer, especially parasitic plants and their hosts due to their intimate physical connections. Rafflesia cantleyi is an obligate holoparasite (dependent on its host, and only that host, for sustenance), which grows on Tetrastigma rafflesiae, a member of the grape family. Researchers from Singapore, Malaysia and USA collaborated to systematically investigate the possibility of horizontal gene transfer between these two plants. By looking at the transcriptome (the transcribed products of switched on genes) they found 49 genes transcribed by the parasite, accounting for 2% of their total transcriptome, which originally belonged to the host. Three quarters of these transcripts appear to have replaced the parasites own version. Most of these genes had been integrated into the parasite's nucleus, allowing the researchers to perform genomic analysis. Over time DNA randomly mutates and investigation of genetic drift between the genes for these transcripts, between the parasite and host, showed that some time has passed since the genes were acquired and that they were acquired gradually. Prof Charles Davis, from the Harvard University Herbaria, who co-led this project with Prof Joshua Rest from Stony Brook University, explained, "The elevated rate of horizontal gene transfer between T. rafflesiae and its parasite R....

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New research yields insights into Parkinson's disease Researchers at the University of Toronto Scarborough (UTSC) used an innovative technique to examine chemical interactions that are implicated in Parkinson's Disease. The work details how a protein called alpha-synuclein interacting with the brain chemical dopamine can lead to protein misfolding and neuronal death. Parkinson's Disease is a neurodegenerative disease which results in loss of motor control and cognitive function. Although the cause isn't known precisely, the disease involves the death of brain cells that produce dopamine, a chemical important in neuronal signaling. The disease also involves a protein called alpha-synuclein which aggregates in the neurons of people with the disease. Kagan Kerman, a chemist in the Department of Physical and Environmental Sciences, and Ian R. Brown, a neuroscientist who founded UTSC's Centre for the Neurobiology of Stress in the Department of Biological Sciences, looked at the way dopamine interacts with alpha-synuclein to form aggregates that may be toxic to neurons. "This is very fundamental," says Kagan Kerman. "It gives us a new point of view of the misfolding proteins and how they are affected by dopamine." These sorts of interactions are often studied using microscopy. But the UTSC researchers decided to use an electroanalytic technique called voltammetry. By studying tiny changes in electric current as dopamine and alpha-synuclein interacted they were able to determine details about the early phases of the interaction. Using the technique, they were able to detail how changes in pH levels and ionic strength of the solution affected the interaction....

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New drug strategy attacks resistant leukemia and lymphoma Scientists build a synthetic peptide that overcomes cancer cells' survival defenses   BOSTON--Scientists at the Dana-Farber/Children's Hospital Cancer Center have developed an anti-cancer peptide that overcomes the stubborn resistance to chemotherapy and radiation often encountered in certain blood cancers when the disease recurs following initial treatment. The strategy could pave the way for much needed new therapies to treat relapsed and refractory blood cancers, which are difficult to cure because their cells deploy strong protein "deflector shields" to neutralize the cell death signals that chemotherapy agents used against them initially, say the researchers. The prototype compound, called a "stapled BIM BH3 peptide," is designed to disable the cancer's defenses by hitting a family of protein targets that regulate cell death. In proof-of-concept studies in mice with transplanted, drug-resistant leukemia tumors, the compound alone suppressed cancer growth, and when paired with other drugs, showed synergistic anti-cancer activity, say researchers led by Loren Walensky, MD, PhD, of Dana-Farber/Children's Hospital Cancer Center. Their paper has been posted online by the Journal of Clinical Investigation and will appear in the journal's June issue. Walensky is the senior author and James LaBelle, MD, PhD, is the first author. A cell's "fate" – when and whether it lives or dies – depends on a tug-of-war between pro-death and anti-death forces within the cell that serve as a check-and-balance system to maintain orderly growth. The system is regulated by the BCL-2 family of proteins, which contains...

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Department of Biotechnology Announces A Pathbreaking Research:an International Consortium Sequences Tomato Genome

The Secretary, Department of Biotechnology Shri M K Bhan today announced a major leap forward in the field of Biotechnology Research. Mr. Bhan informed the media persons in New Delhi that the Tomato Genome Consortium (TGC), a group of over 300 scientists from fourteen countries, has sequenced the genomes of the domesticated tomato and its wild ancestor, Solanum pimpinellifolium. This achievement is expected to lower costs and speed up efforts to improve the worldwide tomato production, making it better equipped to combat the pests, pathogens, drought and diseases that now plague growers. The work may also speed up improvements in other crops. This important result is published in this week’s issue of Nature as cover story. Main contributor Director of National Institute of Plant Genome Research Prof. Akhilesh Kumar Tyagi said that India contributed sequence of euchromatic region with emphasis on chromosome 5 of tomato and provided support to generate 5-fold sequence coverage of the entire tomato genome by Next Generation Sequence (NGS) technology. Indian Team also participated in performing annotation of all predicted proteins using international databases as a part of the International Tomato Annotation Group (ITAG). Simultaneously, Indian researchers have taken up analysis of specific genes/gene families related to ripening, nutrition, disease resistance and abiotic stress tolerance based on transcriptome data and comparative genomics. The genomic resources generated are expected to greatly accelerate improvement of tomato by functional genomics and molecular breeding. The University of Delhi South Campus (Principal Investigator- J.P. Khurana), National Research Centre...

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Scientists decipher how T cells hunt down infection

T cells 'hunt' parasites like animal predators seek prey, study shows By pairing an intimate knowledge of immune-system function with a deep understanding of statistical physics, a cross-disciplinary team at the University of Pennsylvania has arrived at a surprising finding: T cells use a movement strategy to track down parasites that is similar to strategies that predators such as monkeys, sharks and blue-fin tuna use to hunt their prey. With this new insight into immune-cell movement patterns, scientists will be able to create more accurate models of immune-system function, which may, in turn, inform novel approaches to combat diseases from cancer to HIV/AIDS to arthritis. The research involved a unique collaboration between the laboratories of senior authors Christopher Hunter, professor and chair of the Pathobiology Department in Penn's School of Veterinary Medicine, and Andrea Liu, the Hepburn Professor of Physics in the Department of Physics and Astronomy. Penn Vet postdoctoral researcher Tajie Harris and physics graduate student Edward Banigan also played leading roles in the research. The study, which will be published in the journal Nature, was conducted in mice infected with the parasite Toxoplasma gondii. This single-celled pathogen is a common cause of infection in humans and animals; as much as a third of the world's population has a dormant form of this infection present in the brain. However, in immunocompromised individuals, such as those with HIV/AIDS or undergoing organ transplantation, this infection can have serious consequences, including brain inflammation and even death. Earlier work had shown that T cells — a key...

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'Intelligent medicine' erases side effects

Scientists at Aarhus University, Denmark in collaboration with the biotech company Cytoguide now publish a key to use glucocorticoid steroids in a kind of intelligent medicine that specifically hits the relevant cells. Data are based on rodent studies but if this principle is translated to humans it may greatly improve todays hazardous treatment with this type of potent steroids. This is the main perspective in the research now published in the recognized research journal Molecular Therapy in the Nature Publishing group. 50-fold higher potency Synthetic glucocorticoid steroid are used in many acute and chronic inflammatory diseases including many autoimmune diseases such as rheumatoid arthritis. This is the most potent anti-inflammatory medicine, but its use is hampered by serious side effects such as osteoporosis, loss in muscle mass, diabetes and immunosuppression. The new data from the scientists now show that they can target the drugs directly to the 'macrophage' immune cells. These cells play a main role in inflammation and their damaging effect on the surrounding tissues is strongly dampened by the glucocorticoid steroids. The new technology is based on the coupling of the steroids to an antibody that specifically binds to a receptor exclusively expressed on the surface of macrophages. The receptors normally take up haemoglobin but they are also able to engulf drug-conjugates binding to the receptors. In the cells, the active steroid is released and it can now execute it effect (gene regulation). In this way the drug only works in the relevant cells and much less is needed to obtain full efficacy. Perspectives in many diseases 'Our project...

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Options for a NON GATE, B.Tech students to apply for M.Tech Biotechnology and allied programs

A non gate student has several options to apply for various M.Tech programs in Biotechnology and allied fields. So please don’t lose hope and apply to the options available right away. Below I have tried to give you the possible ways of admission into M.Tech and M. S. (by Research) courses in various IITs, NITs, some very good Universities and State Colleges along with certain Private Universities. Hope this mail proves to be helpful. Indian Institute of Technology (IITs) or National Institute of Technology (NITs): Sponsored Candidates:  If you are working in industry for over three year and can prove that your employer is ready to allow you to go to study by letters from authority, you can apply under this category. There are few seats reserved under this category in both IITs and NITs. Quality Improvement Program (QIP): This is started by Govt. of India to improve the quality of teaching staff in state colleges by giving them a chance to attend India’s top most engineering schools. All the faculty members with three years plus experience are eligible for this. M.Tech (Research): The National Institute of Technology, Rourkela, provides facilities for instructions in all Engineering Departments at postgraduate level with more emphasis on research content, leading to the degree of Master of Technology by Research, M. Tech. (Res). The M. Tech (Res) programmes are being offered by all of the Departments/ Centres National Institute Technology. For more details visit: http://www.nitrkl.ac.in/Advertisement_for_Ph.D._admission_.pdf In National Institute of Technology, Jalandar this programme is applicable to...

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Walking and Running Again After Spinal Cord Injury

Rats with spinal cord injuries and severe paralysis are now walking (and running) thanks to researchers at EPFL. Published in the June 1, 2012 issue of Science, the results show that a severed section of the spinal cord can make a comeback when its own innate intelligence and regenerative capacity is awakened. The study, begun five years ago at the University of Zurich, points to a profound change in our understanding of the central nervous system. According to lead author Grégoire Courtine, it is yet unclear if similar rehabilitation techniques could work for humans, but the observed nerve growth hints at new methods for treating paralysis. "After a couple of weeks of neurorehabilitation with a combination of a robotic harness and electrical-chemical stimulation, our rats are not only voluntarily initiating a walking gait, but they are soon sprinting, climbing up stairs and avoiding obstacles when stimulated," explains Courtine, who holds the International Paraplegic Foundation (IRP) Chair in Spinal Cord Repair at EPFL. Waking up the spinal cord It is well known that the brain and spinal cord can adapt and recover from moderate injury, a quality known as neuroplasticity. But until now the spinal cord expressed so little plasticity after severe injury that recovery was impossible. Courtine's research proves that, under certain conditions, plasticity and recovery can take place in these severe cases -- but only if the dormant spinal column is first woken up. To do this, Courtine and his team injected a chemical solution of monoamine agonists into the rats. These chemicals trigger cell responses by binding to specific dopamine, adrenaline, and serotonin receptors...

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Combined Biotech Entrance Exam

MORE THAN 10,000 aspirants appeared for the Combined Biotechnology Entrance Examination conducted on Thursday, 25th May for admission to 500 seats in 40 institutions. If the numbers prove a point, it is that Biotechnology has arrived as a career choice for more young people than in the past. It is because biotechnology is increasingly being viewed as the magic bullet that can rid the world of many of its problems, from chronic hunger to infectious diseases. The belief, based more on fact than on hyperbole, has spawned industries, which in turn have created a rush of new job opportunities. A little something about this exam: Exam Pattern The entrance examination, which is conducted by Jawaharlal Nehru University (JNU), is divided into two sections, and according to Prof. K. J. Mukherjee, Dean, School of Biotechnology, JNU.  Section A has traditionally been beneficial...

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New Molecular Structure Offers First Picture of a Protein Family Vital to Human Health

The 20 proteins in the Wnt family are some of the most important proteins in controlling how an organism develops and grows, but for 30 years scientists have not known what these vital proteins actually look like. The proteins have eluded standard visualization techniques, in large part because they do not dissolve well in the water-based liquids normally used for biochemical studies. But once Howard Hughes Medical Institute investigator K. Christopher Garcia, and Claudia Janda, a post-doctoral fellow in his Stanford University School of Medicine lab, thought of an approach to make the proteins behave better, they succeeded in solving the first structure of a Wnt protein. Their work reveals an unexpected three-dimensional shape that offers clues to how Wnt proteins function and clarifies the nature of its Frizzled receptor target for drug developers working to design anti-Wnt therapies for cancer and other diseases. "Having finally gained structural access to Wnts, I think this is going to open up a whole new era in molecularly dissecting the role of Wnt proteins in biological processes," says Garcia. Wnt proteins were discovered 30 years ago by Harold Varmus, the current director of the National Cancer Institute, and Roel Nusse, who is now an HHMI investigator at Stanford University. They observed that Wnt1, the gene for a Wnt protein, was very active in breast cancer cells from mice. Over the past decades, researchers have shown that Wnt proteins play key roles in embryonic development, tissue regeneration, bone growth, stem cell differentiation, as well as many human cancers. In essence, Wnt proteins help give cells their identity and tell them how to behave....

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