Synthetic-Biology

Thanks to recent advances in synthetic biology — a hybrid discipline of engineering and biology that makes possible the manipulation of DNA of microorganisms such as yeast, bacteria, fungi and algae — a new generation of “organism engineers” has already started experimenting with the creation of new flavors and ingredients. In doing so, they have the potential to transform synthetic biology into a new creative platform to enable chefs, bakers or brewers to create new flavor profiles for food and drink.

BIG NEWS: This is the first time ever the genetic code has been fundamentally changed. The breakthrough is a huge step forward in synthetic biology and opens up the possibility of turning re-coded bacteria into biofactories, capable of producing potent new forms of protein that could fight disease or generate sustainable materials.

Read more: http://bit.ly/19bDzvZ via Yale University

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Synthetic Cells Move On Their Own

What look like animated illustrations that could easily spring from a child’s imagination are actually newly unveiled artificial cells under a microscope.

Biophysicists at Germany’s Technical University of Munich along with an international team developed simple self-propelled biomachines in a quest to create cell models that display biomechanical functions.

The researchers say their work represents the first time a movable cytoskeleton membrane has been fabricated.

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The “first man-made biological leaf” could enable humans to colonise space

RCA graduate Julian Melchiorri says the synthetic biological leaf he developed, which absorbs water and carbon dioxide to produce oxygen just like a plant, could enable long-distance space travel.

Read more: dezeen.com/2014/07/25/movie-silk-leaf-first-man-made-synthetic-biological-leaf-space-travel/

XNA is synthetic DNA that’s stronger than the real thing

New research has brought us closer than ever to synthesizing entirely new forms of life. An international team of researchers has shown that artificial nucleic acids - called “XNAs” - can replicate and evolve, just like DNA and RNA.

We spoke to one of the researchers who made this breakthrough, to find out how it can affect everything from genetic research to the search for alien life.

The researchers, led by Philipp Holliger and Vitor Pinheiro, synthetic biologists at the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, say their findings have major implications in everything from biotherapeutics, to exobiology, to research into the origins of genetic information itself. This represents a huge breakthrough in the field of synthetic biology.

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Synthetic enzymes hint at life without DNA or RNA

Enzymes that don’t exist in nature have been made from genetic material that doesn’t exist in nature either, called XNA, or xeno nucleic acid.

It’s the first time this has been done and the results reinforce the possibility that life could evolve without DNA or RNA, the two self-replicating molecules considered indispensible for life on Earth.

"Our work with XNA shows that there’s no fundamental imperative for RNA and DNA to be prerequisites for life," says Philipp Holliger of the Laboratory of Molecular Biology in Cambridge, UK, the same laboratory where the structure of DNA was discovered in 1953 by Francis Crick and James Watson.

Continue Reading.

Silk Leaf by Julian Melchiorri

Many technological advancements are created for current use, such as smart phones or virtual reality goggles, but there are an equal number of these advancements which are more likely to be used in the future (whether near or distant).

Royal College of Art graduate Julian Melchiorri has created a synthetic biological leaf which can actually absorb “water and carbon dioxide to produce oxygen just like a plant”, which Melchiorri suggests could be used by NASA for potential long-term space exploration.

He explains

"Plants don’t grow in zero gravity…NASA is researching different ways to produce oxygen for long-distance space journeys to let us live in space. This material could allow us to explore space much further than we can now."

The leaves are made of chloroplasts which are placed in a silk protein matrix. Though not technically a real plant, the synthetic leaves do need light and water to survive. Most importantly, they can actually create oxygen. As Melchiorri states, the outcome of his experiments gave him “the first photosynthetic material that was working and breathing as a leaf does”.

Perhaps this technology could be used closer to home too! A large amount of these synthetic biological leaves could help produce oxygen in congested cities, but imagining them on spaceships or even different planets is pretty cool too!

- Anna Paluch

How Long Do Animals Live? How Can We Live Longer?

An infographic exploration of animal longevity, from hare-today-gone-tomorrow to near-eternal-tortoises. What do you think makes some animals live longer than others, predators notwithstanding? Google that and let me know what you find, science detectives.

As for what it means for the future longevity of humans, check out these links: 

Finally, a thought experiment: If our cells can become somewhat “immortal” in diseases like cancer, what’s to say that we can’t harness some of that biology and apply it to extending human lives without disease?

(image via Visual.ly, links via Kirstin Butler)

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Bacteriography.

Zachary Copfer self-coined the above photos as bacteriography. By growing genetically altered bacteria in a petri dish as his photographic film and then exposing parts to UV radiation as his light. Through this method he can literally grow the photograph. Copfer then refrigerates the bacteriograph, uses another blast of radiation treatment to kill any microbes, and then seals it with a layer of acrylic to fix and preserve the image.

Check out his work here and read more about bacteriography here and here.

How Genetically Engineered Gardens Could Replace Airport Security Checkpoints

Fascinating article by Jason Koebler on motherboard about genetically engineered plants that could replace security checkpoints. Dr. June Medford, a pioneering synthetic biologist, already engineered a plant that changes color when it detects TNT or certain pollutants. Her vision:

"The way we screen airports to get on a plane is, everyone goes through detector systems and it’s slow. What would make much more sense, my vision is that you would walk through a garden-like setting, with a webcam looking down on plants, seeing if they detected anything."

The plants could also be hooked up to internet-connected systems. Medford is certain, that a mass production is feasible within 5 years.

[read more] [picture by kvd via wikimedia]

Towards a Minimal Cell
A Gallery of Giant Liposomes 

by Jorge Bernardino de la Serna
University of Southern Denmark

One of the most ambitious endeavors of synthetic biology is creating “minimal cells” that fully recapitulate the functions of a natural cell—they capture energy, maintain ion gradients, store information, and mutate.

Although such technologies are still far on the horizon, researchers have made great progress in creating “semi-synthetic cells” that can mimic specific cellular tasks, such as protein production and synthesis of lipid membranes.

Many of these artificial cells reside inside liposomes, artificial vesicles each comprised of a lipid bilayer.

Technical Details
Each micrograph shows a giant liposome ~20-50µm in diameter comprised of fats and proteins from the surface of the mammalian lung alveoli without any chemical treatment. The liposomes are directly isolated from a lung lavage.

Each micrograph was acquired at a different temperature or has varying composition of native fats and proteins.

Images obtained with a Laser Scanning Confocal inverted microscope with either conventional fluorescent excitation or two-photon excitation.

Source: Cell

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Lego, Eat Your Heart Out

Single-stranded DNA has already proven itself to be a useful addition to the nanotechnologist’s toolbox. Blocks of DNA have been programmed to automatically build themselves into nanoscopic structures; a very long strand can be intricately folded into complex 3D shapes through a process known, appropriately, as DNA origami. Scientists hope that eventually, the DNA programmes could be sophisticated enough to churn out miniscule therapeutic devices that could work inside the body, and even be used to do highly specific tasks, like ferrying drugs to specific sites.

Usually, the long, single-stranded DNA required comes from a virus, which raises the possibility that the body could attack the structures - but not anymore. Peng Yin and colleagues at Harvard University have designed a similar technology that relies entirely on synthetic DNA - no viruses allowed.

"Our structures could be made to be highly biocompatible," he says.

Instead of folding one long strand of viral DNA, Yin’s team designed short, synthetic DNA strands that can fold into a small tile. (And I mean seriously small - just 7 by 3 nanometres). “Each tile acts like a Lego block,” says Yin. Tiles automatically interlock with neighbouring tiles that carry a complementary DNA sequence. This means that with a bit of forward planning, the team could design a complete set of tiles that lock together to create more than 100 shapes - including any letter of the alphabet.

 Scientists hope that synthetic DNA shapes could dodge the immune system, buying them more time to shuttle drugs to the right tissue. Yin believes they could be the future: The body’s own therapeutic system, designed by our cells and for our cells.

To read the original article, published in Nature, click here.

Image, top: The alphabet generated by Yin and colleagues during their experiment.

Image, bottom: Another set of images generated by Yin and colleagues, showing the infinite variety of shapes the DNA can combine into and detailing the advantages for targeted therapeutics.

Images, centre line: A computer rendering of how the DNA might fold into the tile structure.

Biophysicists create artificial cells that can change shape and move on their own

Using only a few ingredients, the biophysicist Prof. Andreas Bausch and his team at the Technische Universität München (TUM) have successfully implemented a minimalistic model of the cell that can change its shape and move on its own. They describe how they turned this goal into reality in the current edition of the academic journal Science, where their research is featured as cover story.

READ MORE ON TUM | Technische Universität München

XNA: The Synthetic Super-Cousin of DNA That Can Replicate and Store Information

The DNA double helix that we’re all familiar with is a molecular ladder made of three key parts. The backbone of phosphates that tie everything together up and down, the sugar rings (“deoxyribose”) that serve as rungs, and the bases (A, C, G, T) that invisibly bond the two strands of the helix together, head to toe.

But that helix can be broken or mutated in nature, leading to mutations. And out of all the compounds in the world that could have evolved to carry our information, why just DNA and its cousin RNA? To answer that question, Vitor Pinheiro’s team created a completely new set of information molecules called XNA.

XNA replaces the deoxyribose sugar ring with other chemical rings like threose and cyclohexane. By evolving an enzyme that could read these funny bases, they were able to read DNA into XNA as well as the reverse. Plus it’s super-strong and resistant to breaking or cleaving.

Molecules like XNA could expand the information code for synthetic biology as well as help us answer the ultimate question about DNA: Why that, and not something else? Ed Yong has more great detail here.

( Not Exactly Rocket Science)

DNA tape recorder stores a cell’s memories

If cells could talk, they’d have quite a story to tell: Their life history would include what molecules they’d seen passing by, which signals they’d sent to neighbors, and how they’d grown and changed. Researchers haven’t quite given cells a voice, but they have now furnished them with a memory of sorts—one that’s designed to record bits of their life history over the span of several weeks. The new method uses strands of DNA to store the data in a way that scientists can then read. Eventually, it could turn cells into environmental sensors, enabling them to report on their exposure to particular chemicals, among other applications.

“They’ve done a really exceptional job turning DNA into readable, writable memory inside living cells,” says Ahmad Khalil, a biomedical engineer at Boston University who was not involved in the new work. “I think it’s a very cool new direction for synthetic biology to take.”

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.

“We wanted a system that would be easier to scale up to collect more than one piece of information,” says synthetic biologist Timothy Lu of the Massachusetts Institute of Technology in Cambridge. “So we started out, as engineers, thinking about what an ideal memory system would look like.”

Continue Reading.

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DNA Laser Printing: Hacking Life’s Code and Creating New Organisms with 3-D Printed DNA

There’s a new emerging technology (or just another buzzword) in town: DNA Laser Printing. Austen Heinz, founder of Cambrian Genomics, was part of the glowing plant kickstarter (2013).

"To think that we can’t make organisms that aren’t more efficient than existing, I don’t think is correct," says Austen Heinz, founder of the biotech startup Cambrian Genomics. "Because nature doesn’t have DNA laser printers, and we do."

Reason TV’s Zach Weissmueller sat down with Heinz to discuss the ramifications of a technology that dramatically brings down the cost of sequencing and assembling DNA, suddenly making the ability for consumers to create their own organisms an economic reality. Heinz partnered with a company to crowdfund a “glowing plant,” which led to a subsequent ban on GMO-related projects on Kickstarter, and he expresses concern with the lagging regulatory structure governing biotech development. But Heinz is undeterred by regulatory and cultural obstacles and foresees a future where consumers can affordably leverage his technology to fix errors in their own DNA or even design their own creatures in the same way that 3-D printing companies like MakerBot allow for custom models.

"[With] MakerBot, you would print out, say, a plastic dinosaur. With Cambrian, the idea is that eventually you’ll be able to print out your own little dinosaur that actually walks across the table," says Heinz. "Everything around us is just code. Wouldn’t it be great if we could just snap our fingers and just re-imagine the world around us, where everything is programmable, everthing is re-writeable?"

[Cambrian Genomics]

Thinking Outside the Carbon-Based Box for Alien Lifeforms

by Michael Keller

Earlier this month, Cornell University said they had gone searching among the interactions of chemical compounds to see whether a central component of life could exist on alien worlds very different from our own. 

They focused their exploration on a key component of life as we know it—the cellular membrane. The structure, which separates the internal environment of the living cell from the outside world, is made of a phospholipid bilayer on Earth. The team wanted to see if there was a different recipe that would work. Using advanced molecular dynamics models, they came back with a definite answer: Yes, in theory, one of the fundamental structures of life could develop based on totally different chemistries.

In fact, they said, one wouldn’t even need to travel light years to find it. Nitrogen, carbon and hydrogen molecules could form a viable cellular membrane submerged in the -290-degree-Fahrenheit methane seas of Saturnian moon Titan. The compound they eventually focused on, called acrylonitrile azotosome, is stable, creates a barrier to decomposition and is flexible like Earth’s phospholipid membranes. It’s also present in Titan’s atmosphere.

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Watch on www.itsokaytobesmart.com

Playing God - A BBC Documentary About Genetic Engineering (Watch full online)

With great power comes great responsibility. Join Adam Rutherford in this full-hour exploration (The whole thing! Online!) of the progress and perils of our ability to cut and splice the very fabric of life on command.

"Life itself has become a programmable machine."

That statement is a bit of an exaggeration, maybe, but certainly genes, DNA, etc. (the stuff that life is made of) can be synthesized, cut and glued back together with such ease these days that a first-week undergrad can do it (even without help from a seasoned veteran biologist such as myself). You could do it in your garage if you wanted. And where the genetic engineering of yesterday was all about putting a gene or two from one organism into another (like this paper, the precursor to Monsanto’s methods), the ease and cheapness of manipulating the tools of synthetic biology create an infinite pool of possibilities for completely human-designed life forms. 

Rest easy, though. When it comes to completely synthetic life, we are still looking at a field in its infancy. Although smart dudes like Craig Venter have succeeded in creating a completely synthetic bacterium, it is an enormously difficult, sensitive and expensive thing to do. I really can’t emphasize how difficult it is, actually. But now is the time, in the early days of meaningful synthetic biology, as prices drop and methods improve, to ask ourselves what is appropriate and what is not.

This will be a global question, and a difficult one. For every drought-resistant strain of wheat that allows us to feed millions of starving children, we can not create another seed monopoly that promotes irresponsible use of herbicides. How do we ensure that the methods used to make plastic-producing bacteria are not the same methods that can produce dangerous bioterrorism strains? How do you feel about having “biohackers” able to order genes and bacteria at will, maybe around the corner from where you live?

Scientists will need to have open discussions. Nonscientists will have to be part of that discussion. This documentary is a must-watch for anyone who wants to know where the future of synthetic biology is headed.

(via EvolutionDocumentary)