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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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Robots can be controlled by E. coli

Robots can be controlled by E. coli | Synthetic Biology | Scoop.it

At the Virginia Tech lab where the study took place, biologists look at using synthetic biology to "reprogramme" the biochemical pathways inside cells -- the same pathways that control decision-making at a cellular level. It's the minutiae of how biological beings operate, with every living cell able to communicate and carry out commands. The team wanted to look at how that decision-making process could not only be engineered, but transplanted to a robotic host using something called a microfluid bioreactor.

 

The plan is to build small bioreactors where the cells can live, and place them on a robot so that we can have "mobile robots that harbour living colonies of bacteria that direct the robot's behaviour," assistant professor of biological systems engineering Warren Ruder, coauthor on the Scientific Reports paper, said.

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How laboratory-grown organs will transform our lives

How laboratory-grown organs will transform our lives | Synthetic Biology | Scoop.it

 

One of the major problems for tissue engineering is creating and maintaining a blood supply to the artificially grown tissues so that they can survive and function when they are implanted inside the body. If synthetic organs become a reality, they will radically change the world of medicine. Such a fundamental change is going to be needed to allow an aging population to work for longer before taking their pensions, and to live to be a centenarian while being fit and healthy.

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Solitary yeast cells programmed to say 'hello' to one another

Solitary yeast cells programmed to say 'hello' to one another | Synthetic Biology | Scoop.it

A team of University of Washington researchers has engineered yeast cells (Saccharomyces cerevisiae) that can “talk” to one another, using a versatile plant hormone called auxin. In a paper published June 23 in the American Chemical Society’s journal ACS Synthetic Biology, the researchers describe a novel cell-to-cell communication system that enables one yeast cell to regulate the expression of genes and influence the behavior of an entirely separate yeast cell.

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SB used to engineer new route to biochemicals

SB used to engineer new route to biochemicals | Synthetic Biology | Scoop.it

Living cells can make a vast range of products for us, but they don't always do it in the most straightforward or efficient way. Shota Atsumi, a chemistry professor at UC Davis, aims to address that through "synthetic biology:" designing and building new biochemical pathways within living cells, based on existing pathways from other living things.

In a new paper published by Nature Communications June 25th, Atsumi and colleagues Yohei Toshiro and Shuchi Desai describe building a new pathway that lets the bacterium, E. coli, feed on both sugar (glucose) and acetate, a common waste material from biomass, to make isobutyl acetate. This product can be used as the basis for flavoring agents, solvents and fuels.

Read more at: http://phys.org/news/2015-06-synthetic-biology-route-biochemicals.html#jCp
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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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The SB market expected to reach $38.7 billion in 2020

According to a new report by Allied Market Research, titled "Global Synthetic Biology Market (Products, Technologies, Applications and Geography) - Global Opportunity Analysis and Forecast - 2013 - 2020", the global synthetic biology market is forecast to reach $38.7 billion by 2020, at a CAGR of 44.2% during the forecast period (2014 - 2020).

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BioBuilder: Rethinking the biological sciences as engineering disciplines

BioBuilder: Rethinking the biological sciences as engineering disciplines | Synthetic Biology | Scoop.it

BioBuilder includes a lot of experiments, and can be used as a manual for experiments in school, at home, or in a DIYBio hackerspace. But important as the lab work is, BioBuilder is really about rethinking the biological sciences as engineering disciplines. Can we make biology as reliable as computing? Can we understand how to engineer DNA so that, when we insert that DNA into an organism, it will have precisely the effect we want? Can we come up with a DNA-encoded light generating device with specifications as reliable as the 47K, 1/4W resistors I can order from Mouser? And if so, can I engineer microbes that will reliably attack cancer cells, detect diseases, manufacture building materials, and more? Can these become products, not just experiments and research projects? Rethinking biology starts in the lab, but it ends with new startups, new business models, and entirely new economies.

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A book by Natalie Kuldell PhD., Rachel Bernstein, Karen Ingram, and Kathryn M. Hart.

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UK to Begin Trial for Synthetic Blood

UK to Begin Trial for Synthetic Blood | Synthetic Biology | Scoop.it

Within two years, the United Kingdom will be embarking on a clinical trial for synthetic blood, which hopes to address the many different problems about blood, including shortage.

 

This blood will come from stem cells obtained from umbilical cords that have been donated by mothers and bone marrow, as well as stem cells from adult donors, which can then be processed so they revert to what they were during the embryonic stage. These cells are then cultured in the lab where they are added with nutrients and growth factors. They are further processed until they're capable of carrying oxygen, the way red blood cells do.

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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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