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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.

Marko Dolinar's insight:

A review written by synthetic biologist and blogger Christina Agapakis.

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Selected news covering the exciting field of Synthetic Biology
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Scientists create synthetic membranes that grow

The scientists said in their paper that to develop the growing membrane they substituted a 'complex network of biochemical pathways used in nature with a single autocatalyst that simultaneously drives membrane growth.' In this way, they added, 'our system continually transforms simpler, higher-energy building blocks into new artificial membranes.'

 

'Our results demonstrate that complex lipid membranes capable of indefinite self-synthesis can emerge when supplied with simpler chemical building blocks,' said Devaraj. 'Synthetic cell membranes that can grow like real membranes will be an important new tool for synthetic biology and origin of life studies.'

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3 of SB's Failing Biofuel Stocks

3 of SB's Failing Biofuel Stocks | Synthetic Biology | Scoop.it

As we get all excited looking at the potential of synthetic biology we shouldn’t forget about some of the disasters that have taken place over the past 5 years. During the time of high oil prices not so long ago, 3 companies in particular stoked investors’ imagination with the promise of using synthetic biology to produce biofuels. Here’s what happened to those investments.

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Engineering an Internal Clock - Harvard Magazine

Engineering an Internal Clock - Harvard Magazine | Synthetic Biology | Scoop.it
Harvard synthetic biologists have engineered a circadian clock, with implications for treating obesity and metabolic diseases.
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Training for synthetic biology jobs in the new bioeconomy - ScienceCareers.org

Synthetic biology draws on a broad range of fields and has the potential to influence or rejuvenate many others. This means that, above all, synthetic biologists need to be multidisciplinary. They must be grounded in one or several core disciplines: genetics, systems biology, microbiology, or chemistry. But they must also draw on engineering—to be able to break down biological complexity and standardize it into parts, or design new biological systems and components, drawing on engineering’s quantitative approach. This requires skills in mathematics, computing, and modeling.

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Engineered bacteria detect cancer and diabetes in urine

Engineered bacteria detect cancer and diabetes in urine | Synthetic Biology | Scoop.it

Most of us think of bacteria as the enemy, but each of our bodies harbors trillions of microbes, most of them beneficial or benign. Now, you can add two new friendlies to the list. Recently, two groups of synthetic biologists seeking to repurpose living microbes for human benefit report genetically modifying bacteria to detect cancer in mice and diabetes in humans.

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SB is able to rapidly create diagnostics tests

One goal of many synthetic biology researchers is to create in vitro diagnostic testing systems that produce results that are as accurate as those produced in today’s state-of-the-art clinical pathology laboratories, yet are much cheaper to run...
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Three developments in SB you need to know

Three developments in SB you need to know | Synthetic Biology | Scoop.it

Using synthetic biology techniques, researchers have created everything from new flavors and fragrances to new types of biofuels and materials. While the innovation potential of combining biology and engineering is unquestionable, now comes the hard part of proving that it is possible to design and build engineered biological systems on a cost-effective industrial scale, thereby creating true “bio-factories.”

For that scenario to become a reality, here are three developments in the synthetic biology space to keep an eye on in 2015.

 

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SB Plants - Nature.com

SB Plants - Nature.com | Synthetic Biology | Scoop.it
It would be wrong to think that synthetic biology is restricted to the engineering of single-celled organisms. Crop plants have been making foodstuffs for millennia so it should be no surprise that some recent successes in the field have been achieved in plants considerably more complex than an alga. Camelina plants engineered to produce omega-3 long-chain polyunsaturated fatty acids are currently undergoing field trials in the UK. If all goes well these will become a source of supplements for the fish farming industry as, somewhat ironically, omega-3 fatty acids, though commonly known as fish oils, are not produced by fish but are acquired from other organisms in the marine food chain. Also in the UK, the Norwich-based start-up Persephone Bio is using tomatoes as a platform for producing complex chemicals such as anthocyanins and flavonols as raw materials for the cosmetics industry.
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Global synthetic biology market 2020 predictions

Global synthetic biology market was valued at $3.0 billion in 2013 and it is estimated to reach $38.7 billion by 2020, growing at a CAGR of 44.2% during the forecast period.

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Computers could team with genetic engineering to feed the world

Computers could team with genetic engineering to feed the world | Synthetic Biology | Scoop.it

 

Using high-performance computing and genetic engineering to boost the photosynthetic efficiency of plants offers the best hope of increasing crop yields enough to feed a planet expected to have 9.5 billion people on it by 2050, researchers report in the journal Cell.

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Are Microbes the Taste-Makers of the Future? - Wired

Are Microbes the Taste-Makers of the Future? - Wired | Synthetic Biology | Scoop.it

 

The vast majority of the vanillin found in today’s products – from food to perfume – is derived from synthetic processes that convert guaiacol to vanillin in a three-step process. Both the natural and chemical methods are costly and environmentally burdensome, but a new approach using the advances of synthetic biology offers a promising third way. Starting with glucose, yeast is able to “ferment it just like beer,” explains Kevin Munnelly, CEO of the biotech company Gen9. “It’s the first flavor made by synthetic biology, and it’s entering commercial viability.”

To get to this point, genes for three enzymes from three different organisms – a dung mold, a bacterium, and humans – were inserted into the yeast cells. In Munnelly’s view, the construction of an engineered pathway to produce a high-value molecule such as vanillin is an important success story in the synthetic biology community.

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SynBio: fast lane to entrepreneurial high tech opportunities

SynBio: fast lane to entrepreneurial high tech opportunities | Synthetic Biology | Scoop.it

What would you do if a biotechnology startup accelerator in another country offered to fund your personal project while you’re still in graduate school?

For Kevin Chen and Sarah Choukah, it was a world changing opportunity to follow their muse and to create something new and impactful in the field of Synthetic Biology.

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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 biocontainment 'lock and key' prevents accidental releases

The work published in the journal ACS Synthetic Biology shows promise as a practical method of biocontainment as advances in synthetic biology and genetic engineering. It prompts more research into techniques to control newly created organisms, said senior author J. Christopher Anderson, an associate professor of bioengineering.

The researchers worked with a strain of E.coli commonly used in research labs, targeting five genes that are required for the organism to survive and devising easy ways to modify them. They created mutations in the genes that would require the addition of the molecule benzothiazole in order to function.

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SB Startup Zymergen Emerges With $44 Million

SB Startup Zymergen Emerges With $44 Million | Synthetic Biology | Scoop.it

Zymergen uses a combination of robots and proprietary software to build and test thousands of new 'strains of DNA' at a time, accomplishing in a matter of days what the company says might ordinarily take postdoctoral researchers in a lab around a year.

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Startup Says It's the First to Make Synthetic Spider Silk

Startup Says It's the First to Make Synthetic Spider Silk | Synthetic Biology | Scoop.it

After five years of quiet work, Bolt Threads claims it has finally cracked the problem of mass-producing spider silk for everyday use.

 

The scientists genetically engineered a microorganism that can yield large quantities of silk protein through a yeast fermentation process—not just grams of silk protein, but metric tons. Then, using a proprietary mechanical system, a wet silk protein solution is manually squeezed through small extrusion holes and goes into a liquid bath that turns the stuff into solid fibers.

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A step towards 'artificial DNA'

A team of synthetic biologists trying to recreate life from the ground up has made a major breakthrough - creating artificial DNA that links up just like natural DNA.

Stephen Benner from the Foundation for Applied Molecular Evolution in Florida, along with his colleagues, built two "nucleobases" - compounds containing nitrogen that can stack up on top of each other to form a helix. The two nucleobases can bond together to form a pair, creating the double-helix that we know as DNA.

Others have achieved the same thing, but their bases weren't capable of forming chains of the same base because of the way they're joined together. Benner and Millie Georgiadis of Indiana University have now proved that theirs can - allowing them to be incorporated into strands of both natural and artificial DNA.

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The Genome Engineering Explained

The Genome Engineering Explained | Synthetic Biology | Scoop.it

The CRISPR-cas9 system makes gene editing in many organisms and cells — like our own egg, sperm or embryo — more efficient, accessible and simple than ever before. These groundbreaking capabilities have spawned discussions surrounding the ethics and applications of the new system, and have garnered significant attention around the world to ensure ethically correct usage.

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DNA 'Printing': Big Boon and Concerns

DNA 'Printing': Big Boon and Concerns | Synthetic Biology | Scoop.it

 

DNA 'printing'  - making a bunch of DNA copies speedily — is making particular stretches of DNA much cheaper and easier to obtain than ever before. That excites many scientists who are keen to use these tailored strings of genetic instructions to do all sorts of things, ranging from finding new medical treatments to genetically engineering better crops.

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New tools for genetic modification of diatoms

Microalgae are some of the most abundant and important organisms in aquatic ecosystems. They use light energy to produce lipids for growth and other cellular functions. While they do this efficiently enough for their own survival, they do not do this naturally at a scale that enables lipid biofuel and chemical production that is cost competitive with current fossil fuel prices.

While many researchers are working on ways to enhance diatoms and increase lipid production, there have not been efficient tools for large scale DNA delivery that can enable effective genetic engineering methodology in diatoms.

The JCVI-led team, some of whom are experts in diatom biology and others with expertise in synthetic biology developed efficient genetic modification tools using episomes or plasmids. They were initially looking for diatom DNA sequences that allowed for plasmid replication but instead identified a yeast plasmid that replicates in diatoms and functions like an artificial chromosome.

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Synthetic Organisms Could Terraform the Earth - MIT Technology Review

Synthetic Organisms Could Terraform the Earth - MIT Technology Review | Synthetic Biology | Scoop.it
One way to combat climate change could be to release synthetic organisms that sequester carbon. How this can be done safely is a question bioengineers are now beginning to address.
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Synthetic biologists seek standards - Nature.com

Synthetic biologists seek standards - Nature.com | Synthetic Biology | Scoop.it

On 31 March, representatives from industry, academic institutions and government met at Stanford University in California to launch the Synthetic Biology Standards Consortium, an initiative led by the US National Institute of Standards and Technology (NIST) to address issues preventing the field from reaching its potential.

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UK Algae Mission - The Momentum Keeps Growing! - SynBioBeta

UK Algae Mission - The Momentum Keeps Growing! - SynBioBeta | Synthetic Biology | Scoop.it
As momentum on algal synthetic biology grows, and tools for genetic manipulation become more widely available, we will need to confront the question of how scale up should best be done. Contained, industrial biotechnology-type facilities are suitable for low volume products, but what about bulk commodities?
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Assembling a Genome, Piece by Piece - Wired

Assembling a Genome, Piece by Piece - Wired | Synthetic Biology | Scoop.it

Producing metabolic intermediates may help identify more antibiotics to counter pathogens like MRSA. But, it is not easy to obtain short-lived molecules. Cloning and expressing  sets of synthetic genes could help out in this endavour.

To produce these long stretches of sequence, SGI-DNA has automated its Gibson assembly protocol, the game-changing technology that enables pieces of double stranded DNA to be pieced together in a contiguous chain. Double stranded DNA fragments with overlapping sequence stretches are inserted into a reaction, and exonuclease enzymes chew back one end of each piece, exposing complementary sequences that link up, joining the two fragments together.

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The Promises and Perils of Synthetic Biology

The Promises and Perils of Synthetic Biology | Synthetic Biology | Scoop.it
Synbio was going to save the world. Now it’s being used to make vanilla flavoring.
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