Biophysicists unravel secrets of genetic switch

When an invading bacterium or virus starts rummaging through the contents of a cell nucleus, using proteins like tiny hands to rearrange the host’s DNA strands, it can alter the host’s biological course. The invading proteins use specific binding, firmly grabbing onto particular sequences of DNA, to bend, kink and twist the DNA strands. The invaders also use non-specific binding to grasp any part of a DNA strand, but these seemingly random bonds are weak. Emory University biophysicists have experimentally demonstrated, for the fist time, how the nonspecific binding of a protein known as the lambda repressor, or C1 protein, bends DNA and helps it close a loop that switches off virulence. The researchers also captured the first measurements of that compaction. Their results, published in Physical Review E, support the idea that nonspecific binding is not so random after all,...

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Moving Toward Regeneration

After transplantation of healthy tissue and subsequent decapitation, planarian stem cells (shown in blue, top panel) leave the graft (shown in green, middle panel) and migrate towards the amputation site while proliferating and producing progeny (magenta). This wound-induced migration rescues the lethally irradiated host animal and eventually the stem cell compartment is completely repopulated with fully functional stem cells (shown in blue, bottom panel). The skin, the blood, and the lining of the gut—adult stem cells replenish them daily. But stem cells really show off their healing powers in planarians, humble flatworms fabled for their ability to rebuild any missing body part. Just how adult stem cells build the right tissues at the right times and places has remained largely unanswered. Now, in a study published in an upcoming issue of Development, researchers at the...

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Teen Googles his way to new cancer testing method

Fifteen-year-old Jack Andraka took INTEL ISEF 2012 science fair honours this year for the development of a cancer-testing method found to be 168 times faster, 26,000 times cheaper and 400 times more sensitive than the current gold-medal standard. His work was impressive enough to earn the Maryland high school student a total of $100,500 in grants and prizes at the 2012 Intel Science Fair. Even more impressive is the source he credits for much of his success: Google. "I definitely could not have done this research and project without the use of the internet", Andraka told BBC News in an interview published this week. "I basically went to Google and was looking up cancer statistics, also looking at a bunch of different documents on like, single walled carbon nanotubes and pancreatic cancer biology," he told the BBC. Andraka was able to find enough information using search engines and free online science papers to invent his procedure, which is now being hailed as "revolutionary" by the American Cancer Society and science publications around the world. The test uses a method similar to that of a diabetic testing strip, with a dipstick sensor that can test either blood or urine for the presence of mesothelin in the body -- a chemical known to be a biomarker for early-stage pancreatic cancer. As Forbes reports, this method could also affect how other types of cancer are diagnosed and treated in the future. ...

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The Laser Beam as a “3D Painter”

3D pattern, produced by photografting (180 µm wide). Fluorescent molecules are attached to the hydrogel, resulting in a microscopic 3D pattern. There are many ways to create three dimensional objects on a micrometer scale. But how can the chemical properties of a material be tuned at micrometer  precision? Scientists at the Vienna University of Technology developed a method to attach molecules at exactly the right place. When biological tissue is grown, this method can allow the positioning of chemical signals, telling living cells where to attach. The new technique also holds promise for sensor technology: A tiny three dimensional “lab on a chip” could be created, in which accurately positioned molecules react with substances from the environment.Materials Science and Chemistry“3D-photografting” is the name of the new method. Two research teams from the Vienna University...

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Simplifying genetic codes to look back in time

(A) Electron density maps. Upper panel: Alanine introduced by the GCU codon in the universal genetic code. Lower panel: Alanine introduced by the UGG codon in the simplified code. (B) Activity of proteins synthesized by the simplified and universal codes from the gene for each code. Copyright : Tokyo Institute of Technology Daisuke Kiga and co-workers at the Department of Computational Intelligence and Systems Science at Tokyo Institute of Technology, together with researchers across Japan, have shown that simpler versions of the universal genetic code, created by knocking out certain amino acids, can still function efficiently and accurately in protein synthesis [1]. The researchers conducted experiments altering the genetic codein a test tube. They removed the amino acid tryptophan and discovered that the resulting simplified...

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Indian Biotech industry growing at 15% annually, abundant job opportunities

"With the Indian Biotechnology segment growing at 15% per year, career opportunities in fields such as bio-pharmacy, bio-service, bio-agriculture, bio-industrial and bio-informatics is burgeoning", informed G S Krishnan, Managing Director, Novozymes South Asia Pvt. Ltd He informed candidates that most jobs are currently available in the private sector and for research & development, marketing, sales/business development and customer support profiles. Throwing light on the current market situation, Krishnan said that demand at the entry level in the biotechnology industry may not be encouraging. The reason being, the industry is still at a nascent stage in India. However, this situation will improve if candidates can equip themselves with higher professional/specialized degrees to qualify further in this segment. A fresher can seek junior research associate positions or lab technicians...

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Molecular code cracked

Scientists have cracked a molecular code that may open the way to destroying or correcting defective gene products, such as those that cause genetic disorders in humans. The code determines the recognition of RNA molecules by a superfamily of RNA-binding proteins called pentatricopeptide repeat (PPR) proteins. When a gene is switched on, it is copied into RNA.  This RNA is then used to make proteins that are required by the organism for all of its vital functions.  If a gene is defective, its RNA copy and the proteins made from this will also be defective.  This forms the basis of many terrible genetic disorders in humans. RNA-binding PPR proteins could revolutionise the way we treat disease.  Their secret is their versatility - they can find and bind a specific RNA molecule, and have the capacity to correct it if it is defective, or destroy it if it...

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Artificial jellyfish swims in a heartbeat

Using recent advances in marine biomechanics, materials science, and tissue engineering, a team of researchers at Harvard University and the California Institute of Technology (Caltech) have turned inanimate silicone and living cardiac muscle cells into a freely swimming “jellyfish.” The finding serves as a proof of concept for reverse engineering a variety of muscular organs and simple life forms. It also suggests a broader definition of what counts as synthetic life in an emerging field that has primarily focused on replicating life’s building blocks. The researchers’ method for building the tissue-engineered jellyfish, dubbed “Medusoid,” was published in a Nature Biotechnology paper on July 22. An expert in cell- and tissue-powered actuators, coauthor Kevin Kit Parker has previously demonstrated bioengineered constructs that can grip, pump, and even walk. The inspiration...

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Writing the Book in DNA

              George Church and Sriram Kosuri discuss the benefits of using DNA as a storage medium and the approach they developed.  Although George Church's next book doesn't hit the shelves until Oct. 2, it has already passed an enviable benchmark: 70 billion copies -- roughly triple the sum of the top 100 books of all time. And they fit on your thumbnail. That's because Church, a founding core faculty member of the Wyss Institute for Biologically Inspired Engineering at Harvard University and the Robert Winthrop Professor of Genetics at Harvard Medical School, and his team encoded in DNA the book, Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves in DNA, which they then decoded and copied. Biology's databank, DNA has long tantalized researchers with its potential as a storage medium: fantastically dense, stable, energy-efficient...

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GBioFin Entrepreneurship Certification Programme

GBio Fin invites applications for GECP 2012 Online. The students are required to send their Resume, Colored Photograph and an Innovative Idea related to Biotechnology/BioScience. The selection of the candidate will be made through his academic performance record , Innovative idea and Telephonic Interview. Through GECP students will be taught about Entrepreneurship and its related fields. The students will also be guided for making business plan and presentation in an Entrepreneurship Competition. Last date to apply is 15th September 2012, kindly send all the required documents at GECP@BIOFIN.NET GECP is an online cum distance mode programme started by GBioFin for Entrepreneurship promotion in Biotechnology. There is no fee for GECP 2012. A Certificate will be provided after the completion of GECP. Deadline: 15th September 2012 ...

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Newfound gene may help bacteria survive in extreme environments

A newly discovered gene in bacteria may help microbes survive in low-oxygen environments. A bacterial cell with the gene, left, exhibits protective membranes. A cell without the gene, right, produces no membranes. Image: Paula Welander In the days following the 2010 Deepwater Horizon oil spill, methane-eating bacteria bloomed in the Gulf of Mexico, feasting on the methane that gushed, along with oil, from the damaged well. The sudden influx of microbes was a scientific curiosity: Prior to the oil spill, scientists had observed relatively few signs of methane-eating microbes in the area. Now researchers at MIT have discovered a bacterial gene that may explain this sudden influx of methane-eating bacteria. This gene enables bacteria to survive in extreme, oxygen-depleted environments, lying dormant until food — such as methane from an oil spill, and the oxygen needed to metabolize...

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Researchers build a toolbox for synthetic biology

MIT and BU researchers designed new transcription factors that can bind to DNA and turn on specific genes. Graphic: Christine Daniloff/iMol For about a dozen years, synthetic biologists have been working on ways to design genetic circuits to perform novel functions such as manufacturing new drugs, producing fuel or even programming the suicide of cancer cells. Achieving these complex functions requires controlling many genetic and cellular components, including not only genes but also the regulatory proteins that turn them on and off. In a living cell, proteins called transcription factors often regulate that process. So far, most researchers have designed their synthetic circuits using transcription factors found in bacteria. However, these don’t always translate well to nonbacterial cells and can be a challenge to scale, making it harder to create complex circuits, says...

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“Selfish” DNA in animal mitochondria offers possible tool to study aging

Caenorhabditis briggsae Researchers at Oregon State University have discovered, for the first time in any animal species, a type of “selfish” mitochondrial DNA that is actually hurting the organism and lessening its chance to survive – and bears a strong similarity to some damage done to human cells as they age. The findings, just published in the journal PLoS One, are a biological oddity previously unknown in animals. But they may also provide an important new tool to study human aging, scientists said. Such selfish mitochondrial DNA has been found before in plants, but not animals. In this case, the discovery was made almost by accident during some genetic research being done on a nematode, Caenorhabditis briggsae – a type of small roundworm. “We weren’t even looking for this when we found it, at first we thought it must be a laboratory error,” said Dee Denver, an OSU associate...

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Toward 'universal' vaccine: Scientists describe antibodies that protect against large variety of flu viruses

A team led by scientists at the Scripps Research Institute and Crucell Vaccine Institute has described three human antibodies that provide broad protection against influenza B virus strains. The work was published in Science Express, the advance online issue of the journal Science, on Aug. 9, 2012. Image courtesy of the Wilson lab, the Scripps Research Institute The isolation of the new broadly neutralizing antibodies, which was reported the journal Science's advance online edition, Science Express, on August 9, paves the way for researchers to develop a universal antibody-based flu therapy for use in severe infections or to protect hospital staff during an outbreak. Importantly, these antibodies may provide key clues to the design of an active universal flu vaccine—designed to protect long-term against flu viruses, not just against the current season's strains. "To develop a truly universal...

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Killing cancer: stories from the cutting edge of science

Tumour-treating electrical fields, a Victorian gout remedy, and an anti-cancer 'virus’. Meet the scientists tackling our most feared disease in some truly innovative ways. Despite the billions spent in pursuit of cures , it remains essentially mysterious. We do have a far better idea of what might give us cancer. Fewer people smoke, dietary awareness has increased and many known carcinogens have been removed from the environment. Yet the disease goes on killing much as it has always done. “If you look at the death rate from cancer, there’s no dramatic change over the last five decades,” says the cancer specialist David Agus, author of The End of Illness. A realist might say we are losing the battle against cancer except where we are winning it. But there are grounds for optimism. New technologies are opening new avenues of possibility. And at the cutting edge of the battle against cancer are dozens of projects currently under way all over the world. Some are lavishly funded, some operate on shoestrings, some are pursuing simple objectives, others are pushing the frontiers of science. What they have in common is a belief that humans can do far ­better against our most feared disease. Here are just some of them. Prof Tim Illidge: the magic bullet In his laboratory in Manchester’s Christie Institute, one of the largest cancer treatment centres in Europe, Prof Tim Illidge is busy developing what he hopes will become a “magic bullet” against certain cancers. He is a pioneer in the use of radio-immunotherapy, or training the body’s immune system to recognise – and destroy – cancer cells. Immunotherapy — altering cells...

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Stars and hexagons! DNA code shapes gold nanoparticles

University of Illinois chemists found that DNA can shape gold nanoparticle growth similarly to the way it shapes protein synthesis, with different letters of the genetic code producing gold circles, stars and hexagons. (Credit: Li Huey Tan, Zidong Wang and Yi Lu) DNA holds the genetic code for all sorts of biological molecules and traits. But University of Illinois researchers have found that DNA’s code can similarly shape metallic structures. The team found that DNA segments can direct the shape of gold nanoparticles – tiny gold crystals that have many applications in medicine, electronics and catalysis. Led by Yi Lu, the Schenck Professor of Chemistry at the U. of I., the team published its surprising findings in the journal Angewandte Chemie. “DNA-encoded nanoparticle synthesis can provide us a facile but novel way to produce...

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New Perspectives On the Function of the Golgi Apparatus

Golgi stacks (labelled with Man1-YFP) and import sites (labelled with the ER tethering factor TIP20-CFP) colocalize even when Golgi stacks are mobile. Both fluorescently-tagged proteins were coexpressed together with the ER marker RFP-p24d5 in tobacco. Cell biologists at the University of Heidelberg have recently obtained data which can explain the different way the Golgi apparatus functions in higher plant and mammalian cells. In contrast to mammalian cells the Golgi apparatus -- a membrane system in the cytoplasm, which participates in a variety of metabolic pathways -- consists in higher plants of hundreds of small Golgi stacks which move along the endoplasmic reticulum (ER) in a stop-and-go fashion. Prof. David G. Robinson and his research group at the Centre for Organismal Studies of the University of Heidelberg have now been able to provide a mechanistic explanation...

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Structural analysis opens the way to new anti-influenza drugs

Different inhibitors (yellow, grey) fill the cave-like active site of the cap-snatching protein (the endonuclease, in green) differently, even though they all bind to the active site’s two metal ions (magenta).Credit: EMBL/Cusack Researchers at the European Molecular Biology Laboratory (EMBL) in Grenoble, France, have determined the detailed 3-dimensional structure of part of the flu virus’ RNA polymerase, an enzyme that is crucial for influenza virus replication. This important finding is published today in PLoS Pathogens. The research was done on the 2009 pandemic influenza strain but it will help scientists to design innovative drugs against all the different influenza strains, and potentially lead to a new class of anti-flu drugs in the next 5-10 years. The scientists focused on the endonuclease part of the viral RNA polymerase. The endonuclease is responsible for a...

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3D movie at ‘ultraresolution’ shows how cell’s machinery bends membrane inwards

Scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, have combined the power of two kinds of microscope to produce a 3-dimensional movie of how cells ‘swallow’ nutrients and other molecules by engulfing them. The study, published today in Cell, is the first to follow changes in the shape of the cell’s membrane and track proteins thought to influence those changes. It also provides ample data to investigate this essential process further. This ‘swallowing’, called endocytosis, is involved in a variety of crucial tasks. It is used by brain cells relaying information to each other, for instance, and is also hijacked by many viruses, which use it to invade their host’s cells. When a cell is about to swallow some molecules, a dent appears in the cell’s membrane, and gradually expands inwards, pinching off to form a little pouch, or vesicle, that transports molecules into the cell. To investigate how the cell’s machinery pulls in the membrane and forms the vesicle, researchers led by Marko Kaksonen and John Briggs employed a method they developed two years ago to faithfully follow the exact same molecules first under a light microscope and then with the higher resolution of an electron microscope. This enabled them to combine two sets of data that so far could only be obtained in isolation: the timing and sequence with which different components of the cell’s machinery arrive at the vesicle-to-be, and the 3D changes to membrane shape that ultimately form that vesicle. They discovered, for instance, that the first proteins to arrive on the inside of the cell’s membrane are not able to start bending it inwards until a network...

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