Color-Changing Plants: The Pretty Side of Synthetic Biology

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Daniel BednarikThe field of synthetic biology is not normally thought of as a source of beauty. The field is typically associated with areas such as artificial life, the generation of biofuels and the next wave in artificial materials production. But part of what makes some of the uninitiated skeptical of the benefits of synbio is perhaps its apparent lack of human element. In a recent article, Siliconrepublic profiled Keira Havens, one half of a duo that makes up Revolution Bioengineering which hopes to produce plants that can grow to be any color imaginable.

Havens and her partner Nikolai Braun, both of the United States, packed their bags and left everything behind to devote themselves to color-changing plants at the SynBio axlr8r run by the University College Cork in Ireland. Havens credits the program with helping to keep her dream alive.

Havens indicates that the goal, while still in development, works upon very basic scientific theses. She insists that plants that change colors and have a person’s name genetically coded into the leaves is not nearly as far-flung science fiction as it may seem. She notes that plants such as hydrangeas change color based up upon the acidity of the soil. Revolution Bioengineering plans to change the environment of molecules called anthocyaninins by connecting specific genes used by the plants internal clock used to benefit from photosynthesis. This, the scientists hope, will allow the plant to change from blue to red and back again throughout the day, while also displaying elaborate designs upon its leaves.

Havens and Braun will be looking for a market for these plants once their research is completed. However, that idea serves to do much more than simply make the two some money. It has the potential to make the casual viewer see a thing a beauty and not focus strictly on the fact that it is a genetically modified organism.

To read the full article, check out Siliconrepublic.

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Report Finds Critical Gaps In Synbio Regulation

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Daniel BednarikA new report by the Venter Institute reports that new technology being developed in the field of synthetic biology falls outside the bounds of regulations currently on the books in the U.S, Bloomberg BNA reports. The report, “Synthetic Biology and the U.S. Biotechnology Regulatory System: Challenges and Options,” looks at the agencies that have regulatory authority over engineered plants and other organisms and identified authoritative gaps.

The agencies involved are the U.S Agriculture Department’s Animal and Plant Health Inspection Service (APHIS), the Environmental Detection Agency, and the Food and Drug Administration. The report identifies two primary areas where gaps in federal oversight are present. The first lies in the ability of APHIS to review genetically engineered organisms but only those that are made employing older engineering techniques.  The second has to do with the capability of the EPA to promptly review the growing number of genetically engineered microbes the field of synbio is developing. The report indicates that the agency may not have the funding or the expertise to keep up with the expanding and diversifying pool of organisms that would fall under its jurisdiction.

The report does not make any specific policy recommendations to fill these gaps, beyond that the EPA and APHIS perhaps ought to focus resources on organisms more likely to pose higher environmental risks, or that congress should expand the authority of the two agencies.

Gaps in the regulations can potentially hinder research.  University may have difficulty conducting research with federal funds without a federal agency with jurisdiction over the field of study. For example, the National Institutes of Health prohibit federally funded researchers from growing genetically engineered plants in the field without the approval of the corresponding federal agency. If no such agency exists, scientists will not be able to conduct such research without violating NIH rules.

To read the original article, visit Bloomberg BNA.

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The Future of Synbio Depends On Public Debate

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Daniel BednarikIf synthetic biology is going to be the next great movement in biotechnology, then there needs to be a concerted effort to make its case to the public, a blog post on the website for the journal Nature argues. Without making a strong push to inform the public of the benefits of synthetic biology, the field could see itself becoming villainized in the way genetically modified organisms have been in Japan, Europe and a growing population within the United States.

This opinion is not mere postulation. The Organization for Economic Cooperation and Development (OECD) has released a report that says without a broad public debate, synthetic biology could be in for a severe backlash sometime down the road.  Jim Philp, a biologist and policy analyst in the Directorate of Science, Technology, and Industry at OECD says, “You can’t just say you have developed a new technology and tell people to go away and use the products it has helped create.”

Moving forward, governments need to take on the responsibility of connecting scientists with policy-makers and the greater public to spark interest in synthetic biology and its potential. The report cited the International Genetically Engineered Machine at MIT as model for this type of promotion.

Some governments have taken action on the public’s engagement with synbio. The United Kingdom published a plan to serve as a blueprint for development through 2030 which creates benchmarks for innovation and developing technology commercially.

Synthetic biology is a field now halfway through its second decade and its potential for the development of food, medicine, fuel and other applications is apparent. The report by the OECD argues for governments to incentivize research financially and for there to be more coordination internationally to avoid duplicate research.

To read the original post, head over to Nature.

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Synthetic Biology Firm Twist Bioscience Announces Expansion

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Daniel bednarik

DNA Sequence

As the field of synthetic biology expands, independent firms are rapidly expanding to clear research hurdles, the San Francisco Business Times reports. Twist Bioscience, a San Francisco startup, has announced that it will add as many as 80 new employees over the next year and a half. The announcement comes as the firm has raised $26 million in its Series B Funding with was led by Tao Invest, run by Nick and Joby Pritzker. Also contributing were Arch Venture Partners, Paladin Capital Group, Santa Clara’s Applied Materials Inc., and Russian investor Yuri Milner. $5.1 million was also received by the Defense Advance Research Projects Agency(DARPA).

The company is looking to accelerate the development of their semiconductor-based system for more lower cost, efficient manufacturing of synthetic DNA. The process is similar to what companies such as Thermo Fisher Scientific who are developing processes to sequence native DNA.

Essentially, Twist is looking to do the same thing but for DNA that is artificially manufactured. The last decade or so of research has been dedicated to the pursuit of reading DNA for the purposes of disease detention and treatment. But according to Twist CEO Emily Leproust, the next wave in DNA research will have to be as dedicated to reading as well as writing.

“You need to read and write,” Leproust said, “and when you can read and write, it becomes extremely powerful.”

The additional personnel will be looking to overcome the bottleneck that occurs in the construction of newly designed DNA. According to Leproust, the process is normally contracted out and is slow and does not provide the number of sequences that researchers are looking for. The expansion will look to streamline R&D to correct these issues in the process.

Visit the San Francisco Business Times to read the original article.



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Genetic Engineers Look to Produce Biofuels From Greenhouse Gas

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Carbon-based pollution and the fuel economy are two problems that are intimately intertwined. Scientist are currently making headway in research that would provide integrated solutions to both, according to the Newscenter at the Lawrence Berkeley National Laboratory. Essentially, researchers wish to see if it is possible to harvest industrial CO2 emissions and use them to produce renewable liquid transportation fuels.

Daniel Bednarik

Genetic Engineering

(Photo credit:Pontificia Universidad Católica de Chile)

Researchers with the Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) wish to take a microbe that is now being used to produce biodegradable plastic, and engineer it into a strain that can produce high-performance biofuel.

Harry Beller, JBEI microbiologist and lead researcher on this project, says that their work has shown that the bacterium Ralsonia eutropha is capable of generating significant amounts of diesel-range methyl ketones, when grown with carbon dioxide and hydrogen. Methyl ketones are naturally occurring compounds used in flavorings and frangrances, but which Beller and his researchers have found to have high diesel ratings. Beller believes that leaves open the possibility of producing carbon-neutral fuels that represent “a less resource-intensive alternative to making these biofuels from cellulosic biomass.”

Beller had led a previous study in which Escherichia coli (E. coli) was genetically engineered to generate methyl ketone compounds from the glucose in cellulosic biomass. This newer study shows that R. eutropha and E. coli, with the same geneticmodifications, produce comparable amountsof ketones.

Current biofuel production focuses on the conversion of glucose to methyl ketones. This method is far more resource intensive than the use of R. eutropha which requires no biomass crop. With continued research in this area, a future of truly green biofuels may be right around the corner.

To read more about this research, check out the original article Lawrence Berkeley National Laboratory.

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Yeast Stands to Introduce the World to Synthetic Biology

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There are some in and around the scientific community who are announcing the retirement of biology oldest workman: evolution. As physicist Michael Brooks says writing for the New Statesman, it is a stepping down that was “3.6 billion years in the making.”

Its replacement, of course, is us. The modern human has studied the natural word to the point where now he can understand natural processes, and re-engineer them to perform in entirely new ways.  For Brooks, and many others, the age of synthetic biology has come.

Daniel Bednarik

Yeast Strands

By Brooks estimation, the area which will open the field of synthetic biology to the world will be yeast (pictured right). Jef Boeke researches yeast genetics at New York University. Boeke wished to do a redesign of the yeast genome in order discover what functions the various parts performed. After significant time and money spent waiting for a private company to complete a portion of the project, Boeke decided that project need to be open-source.

Boeke taught an undergraduate course on genome building, and forged partnerships with institutions, all in the name of building a workforce for his synthetic yeast project. This worldwide network of Boeke’s succeeded in creating a synthetic chromosome for baker’s yeast. This breakthrough may be the first step towards an entirely synthetic yeast.

The chromosome works as well as the naturally occurring, but what is of greater interest for Brooks is how it does unusual things. The chromosome moves and even deletes some its genes. These unusual behaviors will allow scientists to understand how evolution engineered the yeast, and how new variations may open new and exciting applications.

To learn more about other high profile breakthroughs in synthetic biology over the past few years, read the original article over at New Statesman.

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Scientists Make Strides to Improve Photosynthesis

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How can science improve upon one of nature’s finest achievements? Photosynthesis, the process that allows plants, algae and bacteria to capture energy from sunlight and turn it into chemical energy, may be in for a scientific makeover, Science 2.0 reports.

Daniel Bednarik

Scientists are looking at ways to improve the photosynthetic rate by employing synthetic biology approaches. Improving photosynthesis could be instrumental in improving plant productivity and increasing food production.

Recent research has found that micro-compartments comprised of bacterial proteins can be assembled in the chloroplasts in flowering plants. Assembling such a compartment within a chloroplast has the potential to make the plant more efficient at fixing carbon dioxide into molecules that stimulate plant growth.

Dr. Alessandro Occhialini of Rothamsted Research has been working with a plant species called nicotiana benthamiana, along with cyanobacteria which has a natural CO2 concentration mechanism. A few days after infiltrating the leaves with bacterial genes, Occhialini discovered small round bodies in the plants’ chloroplasts.

Dr. Myat Lin, a postdoctoral fellow at Cornell employed recombinant DNA to connect bacterial DNA with those of the plant. This was so several bacterial proteins could be produced at the same time within chloroplasts and then assemble into compartments.

Scientists at Cornell and the Rothamsted Research group have expressed great optimism about the future of the project. Advances in metabolic engineering and synthetic biology have opened the door to enhancing photosynthesis, which scientists hope will create many new opportunities in food and fuel production.

“We are delighted with the encouraging results from our collaboration with the Rothamsted Research group,” Professor Maureen Hanson, lead scientist at Cornell University, “[their] expertise in photosynthesis and electron microscopy complements our capabilities in genetic engineering.”

To learn more about this collaboration, read the original article at  Science 2.0.



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biologylair

bbsrc:

Food, famine and fungi

Ustilago maydis is a fungus that infects maize crops and causes the disease corn smut. In these images you can see the corn smut fungus (green) infecting a maize leaf (red). This infection will cause large plant ‘tumors’ and can eventually result in plant death.

Diseases like this pose a major threat to modern agriculture and therefore understanding fungal plant pathogens is of huge importance. 

BBSRC-funded scientists from The University of Exeter hope to understand the complex interplay between this fungal pathogen and its plant host. This knowledge will then help in the development of novel fungicides that can stop crop infection and keep food on our forks.

Images and research from Professor Gero Steinberg at the University of Exeter.

For more information on his research go to: http://bit.ly/1sbhNCo

For more plant related blog posts go to: http://tmblr.co/ZtJ7bq16IST19r

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neuromorphogenesis

neuromorphogenesis:

Mice With MS-Like Condition Walk Again After Human Stem Cell Treatment

Mice severely disabled by a condition similar to multiple sclerosis (MS) could walk less than two weeks following treatment with human stem cells. The finding, which uncovers new avenues for treating MS, will be published online on May 15, 2014, in the journal Stem Cell Reports.

When scientists transplanted human stem cells into MS mice, they expected no benefit from the treatment. They thought the cells would be rejected, much like rejection of an organ transplant.

Instead, the experiment yielded spectacular results.

“My postdoctoral fellow Dr. Lu Chen came to me and said, ‘The mice are walking.’ I didn’t believe her,” said co-senior author, Tom Lane, Ph.D., a professor of pathology at the University of Utah, who began the study at the University of California, Irvine.

Within a short period of time, 10 to 14 days, the mice could walk and run. Six months later, they showed no signs of slowing down.

“This result opens up a whole new area of research for us to figure out why it worked,” said co-senior author Jeanne Loring, Ph.D., director of the Center for Regenerative Medicine at The Scripps Research Institute in La Jolla, Calif.

More than 2.3 million people worldwide have MS, a disease in which the immune system attacks myelin, an insulation layer surrounding nerve fibers. The resulting damage inhibits transmission of nerve impulses, producing a wide array of symptoms including difficulty walking, impaired vision, fatigue and pain.

Current FDA-approved medications slow early forms of the disease by dampening attacks by the immune system. In recent years, scientists have turned their attention to searching for ways to halt or reverse MS. Such a discovery could help patients with latter, or progressive, stages of the disease, for whom there are no treatments.

Results from the study demonstrate the mice experience at least a partial reversal of symptoms. Immune attacks are blunted, and the damaged myelin is repaired, explaining their dramatic recovery.

“The way we made the neural stem cells turns out to be important,” said Loring, describing the reason behind the novel outcome.

Prior to transplantation, Loring’s graduate student and co-first author on the paper, Ronald Coleman, followed his intuition and grew the cells so they were less crowded on the Petri dish than usual. The change in protocol yielded a human neural stem cell type that turned out to be extremely potent. The experiments have since been successfully repeated with cells produced under the same conditions, but by different laboratories.

Counterintuitively, Lane and Loring’s original prediction that the stem cells would be rejected from the mice, came true. As early as one week post-treatment, there were no signs of the transplanted stem cells in the mouse. What would ordinarily be considered a handicap, turns out to be a significant advantage.

The human neural stem cells send chemical signals that instruct the mouse’s own cells to repair the damage caused by MS. Experiments by Lane’s team suggest that TGF-beta proteins comprise one type of signal, but there are likely others. This realization has important implications for translating the work to clinical trials in the future.

“Rather than having to engraft stem cells into a patient, which can be challenging from a medical standpoint, we might be able to develop a drug that can be used to deliver the therapy much more easily,” said Lane.

With clinical trials as the long-term goal, the next steps are to assess the durability and safety of the stem cell therapy in mice.

“We want to try to move as quickly and carefully as possible,” Lane continued. “I would love to see something that could promote repair and ease the burden that patients with MS have.”

Image1: 1. Multiple sclerosis (MS) impairs nerve function by damaging myelin, an insulating layer that surrounds nerves. MS mice can’t move well. 2. Human neural stem cells injected into MS mice stimulate the mouse’s own cells to repair the damage. 3. Nerve cell function is restored. MS mice can walk and run.

ucsdhealthsciences
ucsdhealthsciences:

War and Peace (of Mind) Meditation training may help reduce stress disorders among U.S. military personnel
Researchers from the University of California, San Diego School of Medicine and Naval Health Research Center have found that mindfulness training – a combination of meditation and body awareness exercises – can help U.S. Marine Corps personnel prepare for and recover from stressful combat situations.
The study, published in the May 16, 2014 online issue of the American Journal of Psychiatry, suggests that incorporating meditative practices into pre-deployment training might be a way to help the U.S. military reduce rising rates of stress-related health conditions, including PTSD, depression and anxiety, within its ranks.
“Mindfulness training won’t make combat easier,” said Martin Paulus, MD, professor of psychiatry and senior author. “But we think it can help Marines recover from stress and return to baseline functioning more quickly.”
Scientists describe mindfulness as a mental state characterized by “full attention to the present moment without elaboration, judgment or emotional reactivity.”  Mindfulness training, traditionally practiced through sitting meditation, attempts to cultivate this mental state by quieting the mind of extraneous thoughts.
In the study, Marine infantrymen in four platoons at Marine Corps Base Camp Pendleton took an eight-week course in mindfulness, tailored for individuals operating in highly stressful environments.
The course included classroom instruction on meditation and homework exercises, as well as training on interoception – the ability to help the body regulate its overall physical equilibrium (homeostasis) by becoming aware of bodily sensations, such as tightness in the stomach, heart rate and tingling of the skin.
“If you become aware of tightness in your stomach, your brain will automatically work to correct that tightness,” Paulus explained.
Participating Marines, along with others who had not undergone mindfulness training, then spent a day in mock immersive combat at a 32,000-square-foot training facility staged to resemble a rural Middle Eastern village. During the day’s exercises, Marines patrolled the village, met village leadership and responded to a highly realistic ambush.
The scientists found that the heart and breathing rates of those who had received mindfulness training returned to their normal, baseline levels faster than those who had not received the mindfulness training. Blood levels of a tell-tale neuropeptide suggested that the mindfulness-trained Marines experienced improved immune function, as well.
Subsequent magnetic resonance imaging scans revealed that the mindfulness-trained Marines had reduced activity patterns in regions of the brain responsible for integrating emotional reactivity, cognition and interoception. Lori Haase, a postdoctoral fellow in Paulus’ lab and a co-author of the study, said similar brain activity patterns had been observed in high performance athletes and Navy seals. High-activity levels in these areas of the brain, she noted, are associated with anxiety and mood disorders. The scientists hypothesize that reduced brain activity in the anterior insula and anterior cingulate may be characteristic of elite performers in general.
“That we can re-regulate the activity in these areas with so little training is this study’s most significant finding,” Paulus said. “Mindfulness helps the body optimize its response to stress by helping the body interpret stressful events as bodily sensations. The brain adds less emotional affect to experiences and this helps with stress recovery.”

ucsdhealthsciences:

War and Peace (of Mind)
Meditation training may help reduce stress disorders among U.S. military personnel

Researchers from the University of California, San Diego School of Medicine and Naval Health Research Center have found that mindfulness training – a combination of meditation and body awareness exercises – can help U.S. Marine Corps personnel prepare for and recover from stressful combat situations.

The study, published in the May 16, 2014 online issue of the American Journal of Psychiatry, suggests that incorporating meditative practices into pre-deployment training might be a way to help the U.S. military reduce rising rates of stress-related health conditions, including PTSD, depression and anxiety, within its ranks.

“Mindfulness training won’t make combat easier,” said Martin Paulus, MD, professor of psychiatry and senior author. “But we think it can help Marines recover from stress and return to baseline functioning more quickly.”

Scientists describe mindfulness as a mental state characterized by “full attention to the present moment without elaboration, judgment or emotional reactivity.”  Mindfulness training, traditionally practiced through sitting meditation, attempts to cultivate this mental state by quieting the mind of extraneous thoughts.

In the study, Marine infantrymen in four platoons at Marine Corps Base Camp Pendleton took an eight-week course in mindfulness, tailored for individuals operating in highly stressful environments.

The course included classroom instruction on meditation and homework exercises, as well as training on interoception – the ability to help the body regulate its overall physical equilibrium (homeostasis) by becoming aware of bodily sensations, such as tightness in the stomach, heart rate and tingling of the skin.

“If you become aware of tightness in your stomach, your brain will automatically work to correct that tightness,” Paulus explained.

Participating Marines, along with others who had not undergone mindfulness training, then spent a day in mock immersive combat at a 32,000-square-foot training facility staged to resemble a rural Middle Eastern village. During the day’s exercises, Marines patrolled the village, met village leadership and responded to a highly realistic ambush.

The scientists found that the heart and breathing rates of those who had received mindfulness training returned to their normal, baseline levels faster than those who had not received the mindfulness training. Blood levels of a tell-tale neuropeptide suggested that the mindfulness-trained Marines experienced improved immune function, as well.

Subsequent magnetic resonance imaging scans revealed that the mindfulness-trained Marines had reduced activity patterns in regions of the brain responsible for integrating emotional reactivity, cognition and interoception. Lori Haase, a postdoctoral fellow in Paulus’ lab and a co-author of the study, said similar brain activity patterns had been observed in high performance athletes and Navy seals. High-activity levels in these areas of the brain, she noted, are associated with anxiety and mood disorders. The scientists hypothesize that reduced brain activity in the anterior insula and anterior cingulate may be characteristic of elite performers in general.

“That we can re-regulate the activity in these areas with so little training is this study’s most significant finding,” Paulus said. “Mindfulness helps the body optimize its response to stress by helping the body interpret stressful events as bodily sensations. The brain adds less emotional affect to experiences and this helps with stress recovery.”