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Creation and Synthetic Biology: Book Review

Creation and Synthetic Biology: Book Review | Synthetic Biology | Scoop.it

What is the origin of life on Earth? What is the future of life in the age of synthetic biology? These are two of the biggest questions of contemporary biology, and the questions that drive Adam Rutherford’s new book, Creation: How Science is Reinventing Life Itself, a compelling and accessible two-part look through the history and future of living cells. Through chapters that span the early history of microscopy to recent debates on the regulation of biotechnology and genomics, Rutherford tells the complicated story of the science of life as it might have been and as it might be.

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A review written by synthetic biologist and blogger Christina Agapakis.

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Nanocrafter: a Synthetic Biology Game

Nanocrafter: a Synthetic Biology Game | Synthetic Biology | Scoop.it

“Most citizen science games are designed to gather data for a specific research question. Players may need to be good at pattern recognition, abstract reasoning, or other cognitive skills. Our focus at Nanocrafter is different,” says Nanocrafter Project Lead Jonathan Barone. “The project isn’t intended to address any existing research. Rather, we are interested in developing a user community that is familiar enough with the principles and parameters of synthetic biology to generate new ideas, identify new questions and create their own solutions.”

The Nanocrafter game teaches users about basic DNA biochemistry and how to manipulate DNA reactions, eventually enabling the player to create logic circuits or mechanized structures. Their video provides examples. In the game, players organize colored puzzle pieces to react in specific ways. The behavior of the puzzle pieces mimics the principles of DNA nucleotide-nucleotide pairing, nucleotide chaining and double helix formation.

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SB breakthrough for cheaper statin production

University of Manchester researchers, together with industrial partner DSM, have developed a single-step fermentative method for the production of leading cholesterol-lowering drug, pravastatin, which will facilitate industrial-scale statin drug production.

In a study published in Proceedings of the National Academy of Sciences, the researchers have devised a single-step fermentative method for the industrial production of the active drug pravastatin that previously involved a costly dual-step fermentation and biotransformation process.

Reprogramming the antibiotics-producing fungus Penicillium chrysogenum, with discovery and engineering of a cytochrome P450 enzyme involved in the hydroxylation of the precursor compactin, enabled high level fermentation of the correct form of pravastatin to facilitate efficient industrial-scale statin drug production.

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Intrexon takes a $60M flyer on a synthetic biology startup

Intrexon ($XON) has signed a $60 million deal to acquire ActoGeniX, a Belgian biotech at work on oral drugs designed to generate therapeutic proteins and peptides from within the body.

Under the deal, Intrexon will trade $30 million in cash and another $30 million in stock for the whole company, inheriting two clinical candidates and 6 early-stage research projects. Each asset is what ActoGeniX calls an ActoBiotic, created by engineering food-grade microbes that spur the secretion of large molecules and, to quote Intrexon's click-baity news release headline, promise "living biofactories in your prescription bottle."

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Synthetic Biology approach to GMO containment

Synthetic Biology approach to GMO containment | Synthetic Biology | Scoop.it

By rewriting the DNA of Escherichia coli so that the bacterium requires a synthetic amino acid to produce its essential proteins, two research teams may have paved the way to ensuring that genetically modified organisms (GMOs) don’t escape into the environment. The life-or-death dependence of the newly engineered E. coli on synthetic amino acids makes it astronomically difficult for the GMO to survive outside the laboratory, explains Harvard Medical School’s George M. Church, who led one of the teams reporting the discovery in Nature (2015, DOI: 10.1038/nature14121). That’s because no pool of synthetic amino acids exists in nature, he explains. A similar strategy was simultaneously published by Farren J. Isaacs and his colleagues at Yale University, also in Nature (2015, DOI: 10.1038/nature14095).

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What are the risks of DIY synthetic biology? – Science Weekly podcast - The Guardian

What are the risks of DIY synthetic biology? – Science Weekly podcast - The Guardian | Synthetic Biology | Scoop.it
Are safety measures adequate in the burgeoning field of synthetic biology – which involves the creation of novel biological systems – in particular among amateur enthusiasts?
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To Save Our Ecosystems, Will We Have to Design Synthetic Creatures? - Wired

To Save Our Ecosystems, Will We Have to Design Synthetic Creatures? - Wired | Synthetic Biology | Scoop.it

If conservationists are faulted for their stubbornness and lack of forward thinking, synthetic biologists encounter the exact opposite argument. Scientists in the field have been chided for their optimism towards problem solving and the unintended consequences that can arise from that. Ginsberg’s project is an attempt to temper the blind utopianism that sometimes accompanies technological advancements. “I’m just reporting on the often exaggerated promise that synthetic biology can help solve all our problems,” she says.

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Scientists make the first (XNA) artificial enzymes

The synthetic enzymes were able to cut and paste pieces of artificial genetic material known as “XNA”, which does not exist in nature. XNA is able to store and replicate genetic information, just like its two natural equivalents DNA and RNA, and was synthesise in Dr Holliger’s lab three years ago.

The enzymes were themselves made from folded strands of XNA molecules. This extra enzymatic property of the artificial genetic material mimics the natural RNA enzymes found in many organisms, including humans, the scientists said.

 

"Catalysts from synthetic genetic polymers" Nature (2014) DOI: 10.1038/nature13982

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Mind Control of Gene Expression

Mind Control of Gene Expression | Synthetic Biology | Scoop.it

A human using mind control to activate the expression of a gene sounds like an improbable science fiction version of the Pied Piper story. In fact, it is a cutting edge fusion of cybernetics and synthetic biology--the brainchild of Martin Fussenegger at ETH Zurich—and may represent the future of drug therapy regimens automatically dictated by brain states.

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SB might enable future manned missions to Mars - ZME Science

SB might enable future manned missions to Mars - ZME Science | Synthetic Biology | Scoop.it

“Not only does synthetic biology promise to make the travel to extraterrestrial locations more practical and bearable, it could also be transformative once explorers arrive at their destination,” says Adam Arkin, director of Berkeley Lab’s Physical Biosciences Div. (PBD) and a leading authority on synthetic and systems biology.

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This scoop refers to a paper published recently:

http://rsif.royalsocietypublishing.org/content/12/102/20140715.full

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iGEM 2014 Finalists Announced

This year's iGEM Grand Jamboree finalists are:

Heidelberg, Imperial College and NCTU Formosa in the undergraduates group and TU Darmstadt, UC Davis and Wageningen UR in the 'overgraduates' group.

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More research needed to address SB security concerns

Even experienced specialists in SB subdisciplines often have trouble replicating findings in their fields – making it unlikely that nonexperts could use a journal article as a step-by-step blueprint for creating bioweapons.But while looking at the “revolution versus evolution” question, scientsts identified two major gaps in the literature on synthetic biology practices and their security implications. First, there has been very little research on the actual hands-on labor and training required to replicate a variety of synthetic biology experiments. Second, as synthetic biology moves from a purely scientific discipline into the marketplace, researchers need a better understanding of how and where synthetic biology findings will be used.  



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A new paper on biosecurity risks related to SB.

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More research needed to address SB security concerns - Phys.Org

More research needed to address SB security concerns - Phys.Org | Synthetic Biology | Scoop.it

A new paper examines security risks and policy questions related to the growing field of synthetic biology. While the author doesn't think the field is ripe for exploitation by terrorists, it does highlight significant gaps in our understanding of the nuts and bolts of lab work in synthetic biology that can contribute to security risks.

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The myths (and realities) of synthetic bioweapons

The myths (and realities) of synthetic bioweapons | Synthetic Biology | Scoop.it

This narrative rests on misleading assumptions about both synthetic biology and bioterrorism, and these five myths are challenged by more realistic understandings of the scientific research currently being conducted in both professional and do-it-yourself laboratories, and by an analysis of historical cases of bioterrorism.

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Engineered phages against bacterial infections

A Synthetic Genomics team is developing phages for use against antibiotic-resistant strains of Pseudomonas, a bug that causes skin infections, sepsis and—particularly in those with cystic fibrosis—potentially fatal pneumonia. Phage therapies currently mix dozens of strains of wild phage together into a cocktail, in the hope that one will do the trick against the bug that a patient is infected with. Dr Farah and his colleagues, by contrast, are able to synthesise viruses from scratch, using off-the-shelf chemicals.

The plan is to come up with one or two super-phages that will hit multiple strains of Pseudomonas. In effect, these phages will be giant self-replicating drug molecules that automatically calibrate the size of their dose—for, when all of the target bacteria have been killed, they can no longer breed.

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Synthetic biology yields new approach to gene therapy - Phys.Org

Synthetic biology yields new approach to gene therapy - Phys.Org | Synthetic Biology | Scoop.it

 

The UT Dallas study describes proof-of-concept experiments in which a gene carrying instructions for making a particular protein is ordered to self-destruct once the cell has "read" the instructions and made a certain quantity of the protein. In its experiments with isolated human kidney cells, the research team successfully delivered—and then destroyed—a test gene that makes a red fluorescent protein.

More research is needed to determine whether and how well the system might work in living organisms. But Moore said the ultimate goal is to refine the method to deliver genes that produce therapeutic proteins or drugs. The nature of the gene delivery system offers more control over how much protein the gene produces in cells or tissues. Because it does not alter the cell permanently, the method also sidesteps potential health problems that can occur if a gene is delivered to the wrong place in a cell's genome.

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Plants Reprogrammed to Tolerate Drought - Nature World News

Plants Reprogrammed to Tolerate Drought - Nature World News | Synthetic Biology | Scoop.it

A team of researchers led by Sean Cutler at the University of California, Riverside has reprogrammed certain plant receptors to respond to the agrochemical mandipropamid, effectively helping the plants survive drought conditions.

"We successfully repurposed an agrochemical for a new application by genetically engineering a plant receptor - something that has not been done before," Cutler said. "We anticipate that this strategy of reprogramming plant responses using synthetic biology will allow other agrochemicals to control other useful traits - such as disease resistance or growth rates, for example."

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Error or terror: Controlling emerging technology - CNBC

Error or terror: Controlling emerging technology - CNBC | Synthetic Biology | Scoop.it

Ahead of Davos 2015, CNBC talks tech.

Synthetic biology and artificial intelligence are two examples of the "next cyber"; emerging technologies with the capacity to deliver enormous benefits but which also present significant challenges to government, industry and society.

Take synthetic biology: creating new organisms from the building blocks of DNA offers the potential to fight infectious disease, treat neurological disorders, alleviate worries about food security and create biofuels.

The flipside is that the genetic manipulation of organisms could also create significant harm, through error or terror. The accidental leakof dangerous synthetized organisms, perhaps in the form of deadly viruses or plant mutations, could create massive damage.

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3 Tech Giants Quietly Investing in Synthetic Biology - Motley Fool

3 Tech Giants Quietly Investing in Synthetic Biology - Motley Fool | Synthetic Biology | Scoop.it

It might be difficult to believe that companies that have traditionally relied on silicon chips, mobile apps, and lines of software code could profit from something as seemingly disconnected as making biological engineering as predictable as traditional engineering fields, but a closer look into research and development spending hints that it may not be that far-fetched after all.

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Expanded DNA alphabet voted Breakthrough of the year

Expanded DNA alphabet voted Breakthrough of the year | Synthetic Biology | Scoop.it

Production of an expanded DNA alphabet in a reproducing life form is the science breakthrough of the year, according to an online vote held by Science magazine.

Scripps Research Institute scientists inserted two extra DNA letters into E. coli, creating a bacterium with a six-letter DNA alphabet instead of the natural four.

The modified E. coli faithfully reproduces its genetic code with the two unnatural letters, as long as the synthesized chemicals are included in its food. The unnatural letters pair with each other, creating a third base pair, while natural DNA has only two base pairs.

If the bacterium isn't supplied with the synthesized letters, they are eliminated from its descendants because the modified organism can't synthesize them itself. This is a safety feature to prevent any possible harm if the organism somehow escapes the lab.

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Synthetic life breakthrough: scientists mimic evolution using oil droplets

Synthetic life breakthrough: scientists mimic evolution using oil droplets | Synthetic Biology | Scoop.it

- University of Glasgow researchers say it is the first time a non-biological system has been shown to evolve over successive generations

- Robot used four chemicals to create 225 droplets and selected the 'fittest'

- Over 21 generations the oil droplets 'evolved' to become more stable

- Scientists hope to create chemical systems that can replicate and evolve themselves which will be a first step towards creating synthetic life

- Findings may explain how living cells first formed billions of years ago

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DNA tape recorder stores a cell's memories - Science Now

DNA tape recorder stores a cell's memories - Science Now | Synthetic Biology | Scoop.it

In the past, researchers have turned cells into simple sensors by switching on or off the production of proteins in response to a stimulus. But each switch could record only one simple piece of information—whether the cell had been exposed to the stimulus—not the duration or magnitude of this exposure. And if the cell died, the information—encoded in a protein—would be lost.

Lu’s team settled on a biological program that rewrites a living cell’s DNA when the cell senses a signal—from a flash of light to the presence of a chemical. Once the DNA is altered, the information remains embedded in the genetic material even if the cell dies. By sequencing the genes of a population of cells that all contain the program, researchers can determine the magnitude and duration of the signal: The more cells have the genetic mutation, the stronger or longer the signal was.

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iGEM 2014 winners announced

In the 'undergrads' group winners are students from Heidelberg with their project on circular proteins with increases thermal stability. First runner-up was Imperial College London with the Aqualose project (bacterially produced cellulose for filtration). Second runner-up was NCTU Formosa with a new approach of pest control using a pheromonebiosynthesis activating neuropeptide.

 

In the 'overgrads' group the winner is UC Davis with its enzyme-based electrochemical biosensor for detection of rancidity in olive oil. First runner-up is Wageningen with a solution for fighting a fungal disease of banana plants. Second runner-up is TU Darmstadt whose students developed an electrochemical solar cell which is based on bacterially produced anthocyanins.

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Synthetic Biology On Ordinary Paper

Synthetic Biology On Ordinary Paper | Synthetic Biology | Scoop.it

New achievements in synthetic biology will allow complex cellular recognition reactions to proceed outside of living cells. There could one day be inexpensive, shippable and accurate test kits that use saliva or a drop of blood to identify specific disease or infection — a feat that could be accomplished anywhere in the world, within minutes and without laboratory support, just by using a pocket–sized paper diagnostic tool.

That once far–fetched idea seems within closer reach as a result of two new studies describing the advances, published October 23 in Cell,

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Will SB change the way we farm and eat?

Will SB change the way we farm and eat? | Synthetic Biology | Scoop.it

Synthesized DNA can be harnessed for food production in a few ways. Foods and flavorings created through fermentation with engineered yeast are one option. A startup called Muufri, for example, is working on an animal-free milk product; a crowd-funded group of “biohackers” collaborating in community labs in the Bay Area aims to create a vegan cheese; and the Swiss company Evolva is using synthetic biology to develop saffron, vanillin and stevia. Other companies, such as Solazyme, are engineering microalgae to produce algal "butter," protein-rich flour and a vegan protein. And in academia, research is under way for clusters of synthesized genes to eventually be inserted directly into plants or into microbes in soil and roots that affect plant growth.

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ASU's efforts in synthetic biology

ASU's efforts in synthetic biology | Synthetic Biology | Scoop.it

 A new four-year, multi-million dollar award from the Defense Advanced Research Projects Agency (DARPA) will be used to develop the technology necessary to synthesize, screen and sequence artificial genetic polymers composed of threose nucleic acid (TNA).

 

The Department of Chemistry and Biochemistry will lead ASU’s effort to evolve TNA molecules that fold into novel 3-D shapes with ligand binding affinity and catalytic activity.

 

The research is part of a new DARPA program called Folded Non-Natural Polymers with Biological Function (Fold F(x)), which plans to use synthetic polymers to address rapidly emerging health and defense threats.

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