3D Device for Parkinson and Epilepsy

Nanotechnology has certainly taken a boost during the last few years and now he have a new tool for neuroscientists delivers a thousand pinpricks of light to a chunk of gray matter smaller than a sugar cube. This device is generally fiber optic based and has been created by biologists and engineers at the Massachusetts Institute of Technology (MIT) in Cambridge. The good thing about it is that it is the first tool that can deliver precise points of light to a 3-D section of living brain tissue. The work is a step forward for a relatively new but promising technique that uses gene therapy to turn individual brain cells on and off with light.

Scientists can use the new 3-D “light switch” to better understand how the brain works. It might also be used one day to create neural prostheses that could treat conditions such as Parkinson’s disease and epilepsy. The researchers describe their device in a paper published November 19 in the Optical Society’s (OSA) journalOptics Letters.

The technique of manipulating neurons with light is only a few years old, but the authors estimate that thousands of scientists are already using this technology, called optogenetics, to study the brain. In optogenetics, researchers first sensitize select cells in the brain to a particular color of light. Then, by illuminating precise areas of the brain, they are able to selectively activate or deactivate the individual neurons that have been sensitized.

Ed Boyden, a synthetic biologist at MIT and co-lead researcher on the paper, is a pioneer of this emerging field, which he says offers the ability to probe connections in the brain.

“You can see neural activity in the brain that is associated with specific behaviors,” Boyden says, “but is it important? Or is it a passive copy of important activity located elsewhere in the brain? There’s no way to know for sure if you just watch.” Optogenetics allows scientists to play a more active role in probing the brain’s connections, to fire up one type of cell or deactivate another and then observe the effect on a behavior, such as quieting a seizure.

Unlike the previous, 1-D versions of this light-emitting device, the new tool delivers light to the brain in three dimensions, opening the potential to explore entire circuits within the brain. So far, the 3-D version has been tested in mice, although Boyden and colleagues have used earlier optogenetic technologies with non-human primates as well.

Targeting neurons with light

One of the advantages of optogenetics is that this technology allows scientists to focus on one particular type of neuron without affecting other types of neurons in the same area of cortex. Probes that deliver electricity to the brain can manipulate neurons, but they cannot target individual kinds of cell, Boyden says. Drugs can turn neurons on or off as well, he continues, but not on such a quick time scale or with such a high degree of control. In contrast, the new 3-D array is precise enough to activate a single kind of neuron, at a precise location, with a single beam of light.

In an earlier incarnation, Boyden’s device looked like a needle-thin probe with light-emitting ports along its length; this setup allowed scientists to manipulate neurons along a single line. The new tool contains up to a hundred of these probes in a square grid, which makes the device look like a series of fine-toothed combs laid next to each other with their teeth pointing in the same direction.

Each probe is just 150 microns across — a little thicker than a human hair, and thin enough so that the device can be implanted at any depth in the cortex without damaging it. The brain lacks pain receptors, so the implants do not cause any discomfort to the brain itself. As in the earlier model, several light-emitting ports are located along the length of each probe. Scientists can illuminate and change the color of each light port independently from the others.

Adding a third dimension to the probe’s light-delivery capabilities has allowed researchers to make any pattern of light they want within the volume of a cubic centimeter of brain tissue, using a few hundred independently controllable illumination points.

“It’s turning out to be a very powerful and convenient tool,” says MIT professor of electrical engineering Clifton Fonstad, co-lead author of the paper.

Blue for on, yellow for off

Neurons in the brain are not naturally responsive to light, so scientists sensitize these cells with molecules called opsins, light-detecting proteins naturally found in algae and bacteria. Genes for an opsin are transferred to the neurons in a mouse’s brain using gene therapy, a process in which DNA is ferried into a cell via a carrier such as a harmless virus. The carrier can be instructed to deliver the DNA package only to certain types of cells.

Different colors of light turn different flavors of opsin on — blue might cause one opsin to activate a cell, while yellow might cause another opsin to silence it. Neurons that are sensitized with opsins gain these abilities to respond to light.

The response of an individual neuron — whether to turn on or turn off — depends on the type of opsin it was sensitized with, and the color of light used to illuminate it. In this way, the tool gives neuroscientists an unprecedented level of control over individual neurons in the brain.

Teams from around the world are currently using the technology developed by Boyden’s group to study some of the most profound questions neuroscience tries to answer, such as how memory works, the connections between memory and emotion, and the difference between being awake and being asleep.

“I’m really excited about how the brain computes — the ebb and flow of consciousness,” Boyden says. “We know so little about the brain.”

A better understanding of the brain may lead to another benefit of this technology: therapy. If a particular type of cell malfunctions in a particular disease, scientists may be able to use a modified 3-D array as a neural prosthesis that could help to treat neurological conditions. Using light to stop overactive cells from firing might alleviate the uncontrollable muscle action of Parkinson’s disease. Cells that cause seizures in the brain could be quieted optically without the side effects of anti-seizure medications. Implants that correct hearing deficiencies are also being explored with this technology.

Although the new device is effective in bringing light to the brain, other challenges remain before optogenetics can be used for medical therapy, Boyden says. Scientists do not yet know for certain whether the body will detect the opsin proteins as foreign molecules and reject them. Gene therapy will also have to prove itself if neurons are to be sensitized with opsin effectively.

“It’s a long road,” Boyden admits.

Meanwhile, he continues, the demand for the tool is currently higher than his team can supply. Boyden says his group is excited about the possibility of commercializing the new 3-D array, as one potential route that would make the devices available as quickly as possible to the neuroscience community.


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Breakthrough against Cotton Curl Leaf Virus

Breakthrough against Cotton Curl Leaf Virus

Cotton leaf curl virus (CLCV) can now be cured with the help of biotechnology as a major breakthrough has been made in transferring modified genes to local varieties, said official sources here on Friday.

A team of local scientists in collaboration with Canadian experts have developed a CLCV-resistant cotton plant through transgenic RNA interference (RNAi) technology. The new advancement would help neutralise the mutating strain of CLCV, which is also know as Burewala stain. It is a harsh reality that we do not have a remedy for the deadly strain of CLCV. This virus alone has become a potent threat to damaging cotton in several districts of Punjab.

The control of this disease can add billions of rupees to the national economy every year and help the local textile industries to attain abundant raw materials. CLCV has caused losses to almost two to three million cotton bales, which amounts to Rs200-300 billion.

RNAi is a method of blocking gene function by inserting short sequences of ribonucleic acid that match part of the target gene’s sequence. It has been hailed as ‘breakthrough of the year’ and ‘Biotech’s billion dollar breakthrough’ globally. Initially, a team of local scientists successfully used the RNAi system for curing virus-hit tobacco plants. After witnessing favorable results, they replicated this process in cotton plants and have been greatly encouraged to see virus-free cotton plants during trials.

Progress in developing CLCV plants has been verified by grafting the transgenic RNAi plants on severely CLCV infected plants. By using RNAi, the virus-affected cotton crops can be fully saved from this onslaught.

“RNAi technology has efficiently blocked viral multiplication when the virus was either agro-inoculated in transgenic plants or transmitted by whitefly, which is a vector of CLCV,” said an official.

Currently, work on this approach is being done jointly by the Institute of Agricultural Sciences and National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore and University of Toronto, Canada, under the umbrella of Punjab Agriculture Research Board (PARB). It is hoped that new virus-resistant GM cotton seeds would be available in the market in three years.

Commenting on the progress achieved so far, Dr Mubarik Ali, chief executive of PARB, said: “PARB has always done result-oriented work by undertaking need-based research projects.”

He added that the use of RNAi technology would surely increase crop productivity and save billions of rupees.

He congratulated Dr Idrees Ahmad Nasir and Dr Saleem Haider, both from Punjab University, for developing what he called miracle CLCV-resistant cotton plant.

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The intelligence of slime molds

The intelligent habits of  P. polycephalum

It is quite interesting to note that we classify molds in the category of Protists. While we may not understand much about them, they understand a whole lot better than us.

This inference comes from a knack of  P. polycephalum to be able to find the best pathway for consuming its food and can move through the most complex of mazes in order to get to what it wants.

If one were to observe the morphology of this organism, they would find that they live in a colony form-and can be generally described as cell with a million nuclei and enzymes along with its genetic material. One of the most interesting feature about this mold is that it has a cell which is termed as the “master shape shifter”. It modifies itself as per the location it is in. In the forest it might fatten itself into giant yellow globs or remain as unassuming as a smear of mustard on the underside of a leaf; in the lab, confined to a petri dish, it usually spreads itself thin across the agar, branching like coral.

In one interesting experiment that was performed by Toshiyuki Nakagaki of Hokkadio University, they were able to demonstrate that these molds were indeed intelligent. What the did was that they cut the mold in pieces and placed it in a maze. The mold began to grow and was able to complete the entire maze within no time. The most interesting thing to note was that the slime mold was able to figure out which route to the food was shortest.

While the aforementioned experiment was done in 2000, a newer set of observations have been made by Chris Reid of University of Sydney.

They findings are quite amazing and the level of sophistication of this slime mold is awe inspiring. Reid and his teammates noticed that a foraging slime mold avoids sticky areas where it has already traveled. This extracellular slime, Reid reasoned, is a kind of externalized spatial memory that reminds polycephalum to explore somewhere new.

Usage of Slime

To test this idea, Reid and his colleagues placed slime molds in a petri dish behind a U-shaped barrier that blocked a direct route to a piece of food. Because the barrier was made of dry acetate, the slime molds could not stick to it and climb over it; instead, they had to follow the contours of the U toward the food. Ultimately, 23 of 24 slime molds reached the goal. But when Reid coated the rest of the petri dish in extracellular slime before introducing the slime molds, only eight of 24 found the food. All that preexisting slime confused the slime molds, preventing them from marking different areas as explored or unexplored. Reid thinks that a polycephalum in a labyrinth is similarly dependent on its slime, using it to first map the entire maze and then to remember which corridors are dead-ends.

Recreating transportation networks

If this experiment was not enough, slime molds literally re-created the Tokyo railway network in miniature! When researchers placed oat flakes or other bits of food in the same positions as big cities and urban areas, slime molds first engulfed the entirety of the edible maps. Within a matter of days, however, the protists thinned themselves away, leaving behind interconnected branches of slime that linked the pieces of food in almost exactly the same way that man-made roads and rail lines connect major hubs in Tokyo, Europe and Canada.

Slime Molds can think spatially too!

In addition to this other experiments suggests that slime molds navigate time as well as space, using a rudimentary internal clock to anticipate and prepare for future changes in their environments. Tetsu Saigusa of Hokkaido University and his colleagues—including Nakagaki—placed a polycephalum in a kind of groove in an agar plate stored in a warm and moist environment (slime molds thrive in high humidity). The slime mold crawled along the groove. Every 30 minutes, however, the scientists suddenly dropped the temperature and decreased the humidity, subjecting the polycephalumto unfavorably dry conditions. The slime mold instinctively began to crawl more slowly, saving its energy. After a few trials, Saigusa and his colleagues stopped changing the slime mold’s environment, but every 30 minutes the amoeba’s pace slowed anyway. Eventually it stopped slowing down spontaneously. Slime molds did the same thing at intervals of 60 and 90 minutes, although, on average, only about half of the slime molds tested showed spontaneous slowing in the absence of an environmental change.

The mechanism unraveled

Because the slime mold cannot rely on its slime for this trick, Saigusa speculates that it instead depends on an internal mechanism of some kind, perhaps involving the perpetually pulsating gelatinous contents of its one cell, known as cytoplasm. The slime mold’s membrane rhythmically constricts and relaxes, keeping the cytoplasm within flowing. When the amoeba’s membrane encounters food, it pulsates more quickly and expands, allowing more cytoplasm to flow into that region; when it stumbles onto something aversive—such as bright light—its palpitations slow down and cytoplasm moves elsewhere. Somehow, the slime mold may be keeping track of its own rhythmic pulsing, creating a kind of simple clock that would allow it to anticipate future events.


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Soldier Beetle presents beneficial potential

Biotech Opportunity from Soldier Beetle

CSIRO researchers, and a colleague at Sweden’s Karolinska Institute, published details of the gene identification breakthrough and potential applications recently in the international journal Nature Communications. “For the first time, our team has been able to isolate and replicate the three genes that combine to make the potent fatty acid that soldier beetles secrete to ward off predators and infection,” said CSIRO Ecosystem Sciences research leader Dr Victoria Haritos. “This discovery is important because it opens a new way for the unusual fatty acid to be synthesized for potential antibiotic, anti-cancer, or other industrial purposes,” Dr Haritos said.


Figure: A close up view of the secreted defensive fluid containing DHMA.

Soldier beetles exude a white viscous fluid from their glands to repel potential attacks from predators, as well as in a wax form to protect against infection. The team found this fluid contains an exotic fatty acid called dihydromatricaria acid, or DHMA, which is one of a group called polyynes that have known anti-microbial and anti-cancer properties. While DHMA and similar polyyne fatty acids are found in a wide variety of plants, fungi, liverworts, mosses, marine sponges and algae, these compounds have proved very difficult to manufacture using conventional chemical processes. However, Dr Haritos and her team have developed a way to achieve this. “We have outlined a method for reproducing these polyyne chemicals in living organisms like yeast, using mild conditions” Dr Haritos said. Soldier beetles are the only animals reported to contain DHMA. This, together with the observation that the beetles forage on plants (such as daisies) which contain a lot of these types of fatty acids, led to previous incorrect conclusions that the DHMA in soldier beetles was derived from their diet. “Through our research and the gene differences we have discovered, we now know soldier beetles have evolved this same defensive compound entirely independently of its production in plants and fungi,” Dr Haritos said.

Journal reference: Nature Communications


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Prison for cell isolation

On Cellular Prisons
Their are various methods of isolation of bacterial cells but this is an innovative one. In this approach that is being described here,  Bryan Kaehr and colleagues from Sandia National Laboratories, US, have used multi-photon lithography. Through this, they can construct four walls and a roof around a single cell in just over a minute. This cellular prison could be rather handy for studying very rare cells.


Creation of “prison” cell

To build the prison, a laser is used to initiate a radical reaction where a photosensitiser, methylene blue, cross-links protein monomers together to form a hydrogel structure. The cross-linking only occurs close to the focus of the laser beam, so the researchers can build up the walls by raising the focus step-by-step, until the walls are about 10µm high. A roof is then created by scanning the laser across the top of the walls, trapping whatever is inside in a 6250µmsize prison cell (video).

Current techniques for studying single cells rely on microfluidics, where cells suspended in a solution are passed through micro-scale paths and barriers which are designed to trap cells. ‘The real uniqueness about [our] approach is it’s targeted isolation of single cells, unlike all the competing approaches … where you might stochastically trap a cell,’ Kaehr explains. ‘Here, if we have a rare environmental cell that may show up one in a million, we can screen for that and target that specific cell in one of these chambers and then do single cell chemistry or analysis.’

The chamber is constructed in such a way that nutrients and waste products can diffuse in and out, but other cells can’t enter. As a result, the trapped cell is free to replicate without interference from other cells. Within a few days, a cell can replicate so many times that the chamber fills and the roof bulges outwards.

The team tested this technique on Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria, as well as yeast (Saccharomyces cerevisae). With the current setup, only one in three cells that are isolated can survive and reproduce. This could be due to several factors, but the main issue is the formation of toxic reactive oxygen species produced by the radical reaction.

However, David Weitz, of Harvard University, US, says: ‘When I read it, I just thought “It’s beautiful, it’s lovely, but what would I do with it?” and I haven’t got an answer.’ Kaehr has a few ideas, including studying cell signalling, but is still on the lookout for other applications. ‘I’m in the game of trying to develop techniques for biology. This is a nice technique where we can shop around and see what are the interesting problems that biologists have.’

Reference: http://pubs.acs.org/doi/abs/10.1021/ac301816c (K C Harper et alAnal. Chem., 2012, DOI: 10.1021/ac301816c)

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Bioconservation symposuim at Sultan Qaboos University

Symposium on biotechnology and conservation of species

The Department of Biology of the College of Science at Sultan Qaboos University will host an international symposium on “Biotechnology and Conservation of Species from Arid Regions” from February 10 to 13, 2013.
The symposium sessions will explore aspects related to the diversity, conservation and biotechnology of bacterial, plant and animal species from arid regions. Having to tolerate extreme environmental conditions, these species have developed unique adaptation strategies that can be utilized for biotechnology and their conservation poses a serious challenge.

Agenda 1: Biotechnology
According to the organizers of this event, research on plant and animal species from arid environments have received scant attention in most major biotechnology meetings. So the symposium will review current progress and explore potential biotech applications. It will be divided into three main tracks; each including topics related to bacteria, animals and plants, respectively. The bacterial track will focus on the diversity and adaptation strategies of microbial species under halophilic, thermophilic and desiccation conditions and their wide applications in biotechnology including bio-remediation, biofuel production, oil recovery and production of different biomolecules.

Agenda 2: Advancement in reproduction technologies
The symposia will discuss advancements in human assisted reproductive technologies. Emphasise will be made on latest research on animals from arid regions such as camels that include reproduction, semen characterisation, freezing, IVF and ET. The ethics of using stem cells, tissues and embryos in different religions will be discussed as well. The plant track will include topics such as micro-propagation and plant tissue culture, genetic transformation for salinity and tolerance as well as the discovery of drugs and secondary metabolites from plants.

Agenda 3: Conservation of species

The symposium is designed to bring together biotechnology scientists from universities, government research institutes and private sector laboratories as well as ethicists, policy makers and industry leaders who are interested in exploring biotechnological application of species from arid regions. Attendees will represent various developed countries with advanced research programmes and developing countries.

More details about the symposium are available online on http://www.isbcsar.com. Deadline for abstract submission to have an oral presentation/ poster is November 15. Abstracts are to be submitted online at the conference website and will be reviewed on the basis of scientific merit, novelty and practical application.


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Vote on production and labelling of GM foods in California

Safety and issues pertaining to GM food in California

Courtesy: The Sacremanto Bee

Susan Lang doesn’t know for certain if her son’s itchy skin and upset stomach were caused by eating food made from crops whose genes were altered in a lab.

But over the years, she believes she’s been able to soothe the 8-year-old’s eczema and digestive problems by eliminating genetically modified organisms from his diet.

“I know that when I feed this child better he does better, and feeding him better includes not feeding him GMOs,” Lang said.

The Fair Oaks woman concedes, however, that her evidence is not scientific, saying she has “more than a hunch, but I don’t have proof.”

Lang learned about genetic engineering – the process of splicing plant or animal genes to create new characteristics – as she began altering her family’s diet to help her son. In the process, she became concerned that consumers don’t know enough about the technology that goes into producing a huge part of the American food supply. Eventually she became a volunteer for the Proposition 37 campaign.

The measure on Tuesday’s California ballot asks voters if food companies should be required to label genetically engineered food. At the core of the debate is a seemingly simple question: Is it safe to eat?

Proposition 37 supporters offer little scientific evidence that genetically modified food is dangerous to human health. A recent French study that found rats developed tumors after months of eating genetically modified corn was quickly panned by the scientific community.

Supporters instead point out perceived deficiencies in most studies that exist, raise questions about the procedures for approving the food and argue that the biotechnology industry has undue influence on government regulators.

“Experts are still debating if foods modified with DNA from other plants, animals, bacteria and even viruses are safe,” says a radio ad urging a “yes” vote on Proposition 37. “But while the debate goes on, we all have the right to make an informed choice.”

Opponents are making the case that labeling the food implies health dangers that haven’t been proved.

“As a doctor, it concerns me when families are given misleading health information,” Dr. Sherry Franklin of San Diego says in a No on 37 ad.

The ad also points out that the American Medical Association has said there is “no scientific justification” for labeling genetically engineered food.

That is true – but incomplete. The association that represents the nation’s doctors also calls for greater “availability of unbiased information and research activities on bioengineered foods.” And it says there should be a different system for testing genetically engineered food before it hits store shelves. Right now, the testing process is voluntary; the medical association says it should be mandatory.

The voluntary testing system is a concern to Proposition 37 supporters. They say it puts too much control in the hands of companies that stand to profit from their biotech inventions.

Altered crops in many foods

Most corn, soybeans, canola and sugar beets grown in the United States are engineered to kill pests or withstand being sprayed with weed killers such as Round-Up. Those genetically engineered crops wind up in thousands of non-organic grocery products in the form of corn syrup, sugar,canola oil or soy-based emulsifiers. Some non-organic papaya, crook neck squash and corn on the cob is also genetically modified.

“There is no evidence that there is any health issue with any of the products on the market. And there is nothing particular to the technology itself that makes it dangerous,” said Kent Bradford, director of the Seed Biotechnology Center at UC Davis, which uses genetic engineering to develop agricultural seeds.

He dismisses the idea that there is not enough testing of genetically engineered food, saying the voluntary testing by companies that modify crops has created a pile of credible evidence.

But such tests are biased by commercial interest and too short to show the long-term impacts of eating engineered food, says anti-GMO activist Jeffrey Smith, who has written two books and made a film criticizing the technology.

Smith lives in Iowa but has been touring California promoting his work and Proposition 37. His film, “Genetic Roulette,” features about a dozen doctors describing health problems – including allergies, diabetes, gastrointestinal distress and autism – they associate with eating GMOs.

“I decided strategically – because I think it’s a greater motivation – to focus on the health dangers,” said Smith, whose background is in marketing not science.

One solution, he said, is labeling engineered food so people know what they’re eating.

Proposition 37 is more about ideology than science, said Bob Goldberg, a UCLA biologist who teaches a class on genetic engineering.

“I’m against this proposition because I’m a scientist and I’m a person who has done genetic engineering my entire career,” Goldberg said. “In many respects, I don’t view this as a political campaign, I view this as an anti-science campaign.”

Goldberg, a member of the prestigious National Academy of Sciences, said the organization believes it’s wrong to lump all genetically engineered foods into the same category because they use the same laboratory technique. Instead, he said, the safety of crops and food products – whether the result of genetic engineering or other scientific processes – should be judged on a case-by-case basis.

A National Academy of Sciences spokeswoman said the group has not evaluated whether it’s safe to eat genetically engineered food.

Goldberg points to a statement this month by the American Association for the Advancement of Science that says, “The science is quite clear: crop improvement by the modern molecular techniques of biotechnology is safe.”

Doctor suggests diet change

Dr. Kelly Sutton isn’t convinced. She is a board-certified internist in Fair Oaks who describes her approach to medicine as “holistic,” incorporating both science and spirituality.

“I’ve practiced for 40 years so I’ve come through a long stretch of seeing changes in health,” Sutton said, including huge increases in allergies, skin problems and cancer.

“We are living longer but living sicker,” she said.

When people come to her with such problems, Sutton said one of the first things she suggests is a change of diet, including a move toward organic and non-GMO foods. She said her patients’ health usually improves.

“I am only speculating from experience,” Sutton said. “There is no serious study that says genetically modified food does this but not that.”

Lang, the Fair Oaks mother, said the anecdotal evidence she’s seen in her son is enough for her to keep GMOs out of her kitchen by eating organic and avoiding most packaged foods.

A day after organizing a Proposition 37 rally with organic farmers last week, Lang made her family a soup of carrots, Swiss chard, broccoli and homemade chicken stock. Potatoes baked in the oven while she whipped up her own dressing for a salad and chopped mango to top fish cakes.

“Since the answers aren’t there,” Lang said, “I choose to proceed on a precautionary principle.”


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