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Modelling success stories (4) Birth of synthetic biology 2000

Modelling success stories (4) Birth of synthetic biology 2000 | SynBioFromLeukipposInstitute | Scoop.it
For the fourth entry in the series, I will not introduce one, but two papers, published back to back in a January 2000 issue of Nature. The particularity of these articles is not that the described...
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Sustainability via Synthetic Biology

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13 Mar Durham http://bit.ly/1gct6XJ

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Synthetic promoter libraries for Corynebacterium glutamicum

Synthetic promoter libraries for Corynebacterium glutamicum | SynBioFromLeukipposInstitute | Scoop.it
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Rytter JV, Helmark S, Chen J, Lezyk MJ, Solem C, Jensen PR.

"The ability to modulate gene expression is an important genetic tool in systems biology and biotechnology. Here, we demonstrate that a previously published easy and fast PCR-based method for modulating gene expression in lactic acid bacteria is also applicable to Corynebacterium glutamicum. We constructed constitutive promoter libraries based on various combinations of a previously reported C. glutamicum -10 consensus sequence (gngnTA(c/t)aaTgg) and the Escherichia coli -35 consensus, either with or without an AT-rich region upstream. A promoter library based on consensus sequences frequently found in low-GC Gram-positive microorganisms was also included. The strongest promoters were found in the library with a -35 region and a C. glutamicum -10 consensus, and this library also represents the largest activity span. Using the alternative -10 consensus TATAAT, which can be found in many other prokaryotes, resulted in a weaker but still useful promoter library. The upstream AT-rich region did not appear to affect promoter strength in C. glutamicum. In addition to the constitutive promoters, a synthetic inducible promoter library, based on the E. coli lac-promoter, was constructed by randomizing the 17-bp spacer between -35 and -10 consensus sequences and the sequences surrounding these. The inducible promoter library was shown to result in β-galactosidase activities ranging from 284 to 1,665 Miller units when induced by IPTG, and the induction fold ranged from 7-59. We find that the synthetic promoter library (SPL) technology is convenient for modulating gene expression in C. glutamicum and should have many future applications, within basic research as well as for optimizing industrial production organisms."

http://bit.ly/1emMef1

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Computer-assisted design for scaling up systems based on DNA reaction networks

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Aubert N, Mosca C, Fujii T, Hagiya M, Rondelez Y.

"In the past few years, there have been many exciting advances in the field of molecular programming, reaching a point where implementation of non-trivial systems, such as neural networks or switchable bistable networks, is a reality. Such systems require nonlinearity, be it through signal amplification, digitalization or the generation of autonomous dynamics such as oscillations. The biochemistry of DNA systems provides such mechanisms, but assembling them in a constructive manner is still a difficult and sometimes counterintuitive process. Moreover, realistic prediction of the actual evolution of concentrations over time requires a number of side reactions, such as leaks, cross-talks or competitive interactions, to be taken into account. In this case, the design of a system targeting a given function takes much trial and error before the correct architecture can be found. To speed up this process, we have created DNA Artificial Circuits Computer-Assisted Design (DACCAD), a computer-assisted design software that supports the construction of systems for the DNA toolbox. DACCAD is ultimately aimed to design actual in vitro implementations, which is made possible by building on the experimental knowledge available on the DNA toolbox. We illustrate its effectiveness by designing various systems, from Montagne et al.'s Oligator or Padirac et al.'s bistable system to new and complex networks, including a two-bit counter or a frequency divider as well as an example of very large system encoding the game Mastermind. In the process, we highlight a variety of behaviours, such as enzymatic saturation and load effect, which would be hard to handle or even predict with a simpler model. We also show that those mechanisms, while generally seen as detrimental, can be used in a positive way, as functional part of a design. Additionally, the number of parameters included in these simulations can be large, especially in the case of complex systems. For this reason, we included the possibility to use CMA-ES, a state-of-the-art optimization algorithm that will automatically evolve parameters chosen by the user to try to match a specified behaviour. Finally, because all possible functionality cannot be captured by a single software, DACCAD includes the possibility to export a system in the synthetic biology markup language, a widely used language for describing biological reaction systems. DACCAD can be downloaded online at http://www.yannick-rondelez.com/downloads/.";


 http://bit.ly/1jKhKZ0

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The Promise and Challenge of Digital Biology

The Promise and Challenge of Digital Biology | SynBioFromLeukipposInstitute | Scoop.it

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Mark E Minie and Ram Samudrala
"The era of Digital Biology began in 2010 with the “rebooting” of a bacterial cell using a synthetic DNA genome created from a digital template stored on a computer [1]. With this event, the creation of Mycoplasma laboratorium (nicknamed “Synthea”), came the first complete proof that DNA was the true software of life. Cells could be simulated digitally and the simulations could be tested against reality by reprograming cytoplasm with synthetic genomes generated from the digital DNA sequences driving those simulations. This in turn has created the expectation and promise that a deeper understanding of cellular function and thus life itself could be achieved on an infinite iterative loop of computer modeling and chemical synthesis..."

http://bit.ly/1ehmErG ;
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Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae

Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae | SynBioFromLeukipposInstitute | Scoop.it
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McIsaac RS, Gibney PA, Chandran SS, Benjamin KR, Botstein D.

"A conditional gene expression system that is fast-acting, is tunable and achieves single-gene specificity was recently developed for yeast. A gene placed directly downstream of a modified GAL1 promoter containing six Zif268 binding sequences (with single nucleotide spacing) was shown to be selectively inducible in the presence of β-estradiol, so long as cells express the artificial transcription factor, Z3EV (a fusion of the Zif268 DNA binding domain, the ligand binding domain of the human estrogen receptor and viral protein 16). We show the strength of Z3EV-responsive promoters can be modified using straightforward design principles. By moving Zif268 binding sites toward the transcription start site, expression output can be nearly doubled. Despite the reported requirement of estrogen receptor dimerization for hormone-dependent activation, a single binding site suffices for target gene activation. Target gene expression levels correlate with promoter binding site copy number and we engineer a set of inducible promoter chassis with different input-output characteristics. Finally, the coupling between inducer identity and gene activation is flexible: the ligand specificity of Z3EV can be re-programmed to respond to a non-hormone small molecule with only five amino acid substitutions in the human estrogen receptor domain, which may prove useful for industrial applications."


http://bit.ly/1g03Eoo

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Coursera Systems Biology course can earn you a specialization certificate

Coursera Systems Biology course can earn you a specialization certificate | SynBioFromLeukipposInstitute | Scoop.it
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The Systems Biology Specialization will enable students to get a working knowledge of various facets including bioinformatics, dynamical modeling, genomics, network and statistical modeling, proteomics and metabolomics. The Specialization concludes with a Capstone project that allows you to apply the skills you've learned throughout the courses.

New: Specializations Certificate  On Coursera

http://bit.ly/1aqbUfd

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SynBioFromLeukipposInstitute over 60 000 views - thanks for your interest

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Improving advanced biofuels production in Saccharomyces cerevisiae via protein engineering and synthetic biology approaches

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Thesis

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5 Unbelievable (but Real) Technologies Made Possible by Synthetic Biology

The synthetic biology industry has erupted in recent years. The technological breakthroughs can touch numerous industries, from health care to marijuana production. - Maxx Chatsko - Energy
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"1. Microbial factories for everyday products"

"2. Biosensors for food pathogens"

"3. Marijuana without the plant"

"4. Fixing your genes to cure diseases"

"5. The end of synthetic nitrogen fertilizers"


 http://bit.ly/1eZ7meT

What app ideas do you have?

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Anne Fleischman's curator insight, January 20, 2014 9:07 AM

Dans le cadre de notre #plainsfeux sur l'innovation et l'inventivité, cet article tombe à point

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A self-propelled biohybrid swimmer

A self-propelled biohybrid swimmer | SynBioFromLeukipposInstitute | Scoop.it
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Brian J. Williams,Sandeep V. Anand,Jagannathan Rajagopalan& M. Taher A. Saif

"Many microorganisms, including spermatozoa and forms of bacteria, oscillate or twist a hair-like flagella to swim. At this small scale, where locomotion is challenged by large viscous drag, organisms must generate time-irreversible deformations of their flagella to produce thrust. To date, there is no demonstration of a self propelled, synthetic flagellar swimmer operating at low Reynolds number. Here we report a microscale, biohybrid swimmer enabled by a unique fabrication process and a supporting slender-body hydrodynamics model. The swimmer consists of a polydimethylsiloxane filament with a short, rigid head and a long, slender tail on which cardiomyocytes are selectively cultured. The cardiomyocytes contract and deform the filament to propel the swimmer at 5–10 μm s−1, consistent with model predictions. We then demonstrate a two-tailed swimmer swimming at 81 μm s−1. This small-scale, elementary biohybrid swimmer can serve as a platform for more complex biological machines."

http://bit.ly/1ajrCZu

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ACS Synthetic Biology: Volume 3, Issue 1 (ACS Publications)

ACS Synthetic Biology: Volume 3, Issue 1 (ACS Publications) | SynBioFromLeukipposInstitute | Scoop.it
ACS Synthetic Biology: Volume 3, Issue 1 (ACS Publications) http://t.co/R7KGRXORC7
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This is real innovation: Illumina's new machine could slash cost of sequencing your genome to $1,000

This is real innovation: Illumina's new machine could slash cost of sequencing your genome to $1,000 | SynBioFromLeukipposInstitute | Scoop.it
Biotech firm Illumina sent shockwaves through the genetics industry this week by announcing a new machine that, it says, will allow companies to sequence the human genome for $1,000.
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Craig Venter discusses creation of synthetic life | Machines Like Us

Craig Venter discusses creation of synthetic life | Machines Like Us | SynBioFromLeukipposInstitute | Scoop.it
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"Life is a DNA software system" says J. Craig Venter, PhD, and biology can be digitized, the information sent via the Internet, and viruses and other life forms recreated using the emerging tools of synthetic biology. Dr. Venter describes his vision for applying biological teleportation to send digitized biological information around the world and from Mars to Earth in an interview in Industrial Biotechnology, a peer-reviewed journal from Mary Ann Liebert, Inc., publishers. The article is available on the Industrial Biotechnology website.

Dr. Venter, Founder, Chairman, and CEO of the J. Craig Venter Institute, and CEO of Synthetic Genomics, Inc. (La Jolla, CA), delivered the Plenary Lecture at the 2013 BIO Pacific Rim Summit, December 10th, in San Diego, CA, in which he described the recent successful application of digital biology and synthetic genomics technology for the rapid development of a vaccine against a meningitis type B virus that has caused outbreaks this year.

In "IB Interview: A Conversation with J. Craig Venter, PhD," Dr. Venter discusses the work leading up to his group's creation of the first synthetic genome and new life form, the role that synthetic biology will have in sustainable human development, his current interest and activities in space exploration and the search for extraterrestrial life, and his views on bioenergy, future technology development, and policy and funding needs to support R&D in industrial biotechnology. Following the interview are excerpts of Dr. Venter's Plenary Lecture.

"Synthetic biology is not just an evolutionary step in industrial biotechnology, it is a quantum leap, and there is no better person than Craig Venter to help us look over the horizon and anticipate the future path and benefits of that continuing evolution," says Brent Erickson, Consulting Editor of Industrial Biotechnology and Executive Vice President, Industrial & Environmental Section, Biotechnology Industry Organization (BIO), Washington, DC. "The biotech tools Dr. Venter and his industry colleagues are developing enable us to tackle problems that humankind has found intractable for centuries. That should inspire all of us in the industry."


 http://bit.ly/1mWl3yR

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Programming molecular robots

Programming molecular robots | SynBioFromLeukipposInstitute | Scoop.it
Wyss Institute at Harvard
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A Q&A with Wyss Core Faculty members William Shih and Peng Yin

"In the late 1990s, a small group of bioengineers set out to turn cells into tiny robots. Being bioengineers, they drew ideas from engineering, and envisioned building a set of modular, standard parts akin to the sensors, power source, microprocessor and actuators that enable robots to sense and respond to their surroundings. Those early efforts spurred a wave of optimism about the incredible potential of synthetic biology.

 But getting even simple organisms to carry out the right tasks at the right time remains a formidable task, and synthetic biologists are still a long way from making living cells obey their commands. In part that’s because they only partially understand the workings of the cells’ operating systems – their genes and their regulatory networks. So a new contingent of bioengineers is pioneering a different approach. Instead of trying to program living cells, they’re using the cell’s information-carrying molecules — DNA, RNA and protein — to build their own operating systems, their own sensors, their own actuators. Their goal: to build tiny molecular robots. This past fall the National Science Foundation (NSF) kicked in $10 million from an NSF initiative called Expeditions in Computing to fund 11 scientists, including Wyss Institute Core Faculty member William Shih, Ph.D., Core Faculty member Peng Yin, Ph.D., and former Wyss Institute postdoctoral fellow Shawn Douglas, Ph.D., who is now an Assistant Professor of Cellular and Molecular Pharmacology at the University of California, San Francisco. This prestigious grant is designed to launch the nascent field of molecular programming. We sat down with Shih, who is also an Associate Professor of Biological Chemistry and Molecular Pharmacology at Harvard Medical School and Associate Professor of Cancer Biology at the Dana-Farber Cancer Institute, and Yin, who’s also an Assistant Professor of Systems Biology at Harvard Medical School, to learn the ins and outs of this new branch of engineering, which could revolutionize fields as diverse as information technology, tissue engineering, and manufacturing. What is molecular programming? Yin: It means directing information-carrying polymers [DNA, RNA, and protein] to demonstrate prescribed molecular behavior. Using these as tools, we want to develop real-world applications. For example, we are using nanoscale DNA structures as a template to fabricate inorganic materials. We are also building programmable molecular machines made of DNA or RNA to help us study biology. Peng YinWyss Institute Core Faculty member, Peng Yin, Ph.D.We have very fast computers these days. Why is it important to build programmable devices out of DNA, RNA and proteins? Shih: If molecular programs could only do an extremely slow job of what silicon computers can already do very efficiently, they would only be a curiosity. For crunching millions of numbers, they will never compete with these machines [he points to his desktop computer]. I can think of at least two practical reasons for molecular programming. First, sometimes you need your computer to talk to cells, talk to molecules. You need your computer to diagnose a disease. You don’t need to do billions of calculations per second – maybe just ten in the course of an hour. But you need your computer to go to small places in your body and be biocompatible. The second reason is that you can create massively parallel armies of not very good computers. For example, a traditional strategy for drug discovery entails taking a molecule that works, then tinkering with it and making it work better. A second strategy that has not worked well so far is to make a billion drugs and screen them and build off that. But instead of making a random library of new drugs, what if we had some way to build in logic? You could create a library that is more streamlined, with more of the things you want. William ShihWyss Institute Founding Core Faculty member, William Shih, Ph.D.Yin: The critical thing for us is that we’re not trying to use these molecules to merely do computing. We are trying to use them to perform programmable molecular tasks. For example, we can program how they physically interact with each other. As information-carrying molecules, [DNA, RNA and proteins] can specify spatial and dynamic behavior. One example is digital fabrication. We use a programmable DNA structure to specify the nanoscale 2D and 3D geometric shape. And we can translate from those 2D and 3D shapes to other inorganic substrates. For example, we can translate the DNA shape to a gold particle and later to graphene to create a substrate for nanoelectronics. We’re going from programmable biomolecules and using them to fabricate inorganic devices with a digitally programmable shape. You and your colleagues write in your grant application that “with molecular programming, chemistry will become the new information technology of the 21st century.” How so? Shih: It’s not going to be the CPU in smart phones, or here, or there (points to his screen, and to his computer). But if what you want is ubiquitous computing — trillions of sensors all over the body —maybe with molecular computers, you could do it. Or you could disperse sensors all over a lake, or the atmosphere. Collectively they’re doing something you can’t do with conventional silicon. It’s a new frontier for computing. What are real-world problems that molecular programming could help solve? Yin: Molecular programming could lend molecular precision to diagnostics or therapy. Life at its finest scale can be visualized as dynamic, self-assembling molecular systems. To interact with this molecular system, you want instruments on the same scale. You’d have digitally programmed instruments on the molecular scale. For example, there could be a genetically encodable RNA machine to identify cancer cells and kill them. Or you could have tiny fluorescent DNA probes that interact with cellular components to produce super sharp images. Digital fabrication is also extremely exciting. Using DNA structures as templates, you could specify in a digitally precise fashion the architecture and potentially the function of a nanoelectronic circuit or nanophotonic device. We’re also collaborating with Pam Silver’s group to assemble RNA bricks into an RNA scaffold to spatially organize enzymes involved in hydrogen production in E. coli. Using an earlier RNA scaffold, Pam’s lab could increase hydrogen production by 50-fold. [Pam Silver is a founding core faculty member of the Wyss Institute and Professor of Systems Biology at Harvard Medical School.] William, you have developed DNA origami and used it to fold DNA strands into a bridge with handrails and other shapes. Is your molecular programming work a continuation of your DNA origami work? Shih: One connection is that the way people have done DNA computation so far is to have lots of free-floating strands of DNA in a solution. They sometimes bump into each other, but the process is often slow. To catalyze the reaction, what if you sequester strands in a compartment, or walking along surface. For example, you could make a nanoscale box and put a small number of strands into the box. The effective concentration could be up to a million times higher. What do you envision as the future of molecular programming? Yin: My mom was a computer engineer in the early days of punch cards. Now I can just type in Java and C and I can program my computer. We want to do that for these molecules that carry digital information. We want a user-friendly programming interface and an associated “molecular compiler,” so that everyone can do molecular programming. I don’t see why in the future we couldn’t imagine molecular apps and build the infrastructure to make them programmable, expressive, robust, and functional. Then many other users could really develop their own apps. [Yin pulls out his iPhone and points to some apps.] In 10 or 20 years freshmen at Harvard could learn a molecular programming language to program how molecules behave and generate their own molecular apps. That would be fascinating. These information-bearing molecules are merging information technology with molecular technology to enable human beings to realize our functional needs in the molecular world. This vision, I think, is an emerging revolution."


 http://bit.ly/KUAuIM

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Illness fires entrepreneur’s interest in synthetic biology

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By Vincent Ryan

 ""Bill Liao’s daughter’s diagnosis with type 1 diabetes has fired his latest passion — reprogramming biological cells.Mr Liao, a European Venture Partner at SOSventures, is aiming to make Cork and UCC the world leader in synthetic biology.  His daughter was diagnosed with type 1 diabetes, meaning she is dependent on insulin that has been produced by reprogrammed cells.  “My daughter would be dead without this,” said Mr Liao. “She is a type 1 diabetic and the best insulin in the world comes from synthetic biology and comes from cells that have been modified to produce human insulin. Bacteria that make human insulin, without that technology she would have a miserable life.”  SOSventures has launched Synbio Axlr8r to attract to Cork the next wave of start-ups operating at the cutting-edge of computing and biology.  “I’m starting an initiative called Synbio Axlr8r,” said Mr Liao. “The newest area of technology is synthetic biology. It is where biology and programming meet. You can actually write code in a language called Python, which is used for web development, and then they compile it in to DNA and upload it to cells and give them a new purpose.”  Synbio Axlr8r will offer a $30,000 (€22,000) investment and lab space in UCC for start-ups to bring their ideas to investment stage.  “The applications for being able to program DNA and tun them into useful micromachines that do stuff, it is going to revolutionise technology and currently there is no one centre of excellence in the world,” said Mr Liao. “In UCC this year, starting in May, we are doing an accelerator programme. We are giving them $30,000 and lab space to start their business.”  The accelerator will have seven-figure funding from SOSventures and run in conjunction with Cork County Council. Mr Liao said it was a pity there were not more state agencies involved, but the wheels of the State were slow to turn. " http://bit.ly/1hsejF1 ;
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3 Synthetic Biology Stocks That Can Help You Grow in 2014 (and Beyond) - DailyFinance

3 Synthetic Biology Stocks That Can Help You Grow in 2014 (and Beyond) - DailyFinance | SynBioFromLeukipposInstitute | Scoop.it
Synthetic biology is relatively new, but the field holds near-limitless potential to shape every aspect of our daily lives. While it's easy to
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Sneaky molecules unzip when they locate disease

Sneaky molecules unzip when they locate disease | SynBioFromLeukipposInstitute | Scoop.it
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by Emma Thorne-Nottingham 

"Scientists are testing encapsulated molecules that unzip and spring into action when triggered to do so.

 A sheath of biocompatible polymer shrouds the biologically active material inside, preventing any interaction so long as the shield remains in place. The smart aspect is in the DNA-based zippers that hold the coat in place. Because any DNA code (or “molecular cipher”) can be chosen, the release mechanism can be bar-coded so that it is triggered by a specific biomarker—for example a message from a disease gene...."

http://bit.ly/1cVS1qB

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Attacking Cancer With Light-Controlled Bacteria?

Attacking Cancer With Light-Controlled Bacteria? | SynBioFromLeukipposInstitute | Scoop.it
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by
Laura Cassiday

*As a possible new anticancer strategy, synthetic biologists have engineered bacteria to secrete a toxic protein that kills surrounding cells when exposed to blue or red light (ACS Synth. Biol. 2014, DOI: 10.1021/sb400174s). These bacteria could someday help doctors specifically attack cancer cells and limit damage to healthy ones, the researchers say.

Conventional cancer drugs often kill healthy cells along with malignant ones, leading to serious side effects. Also, it is difficult to control the dose of drug that actually gets to the cancer cells. Some researchers think that nonpathogenic bacteria could help with these problems. They see the microbes as good vehicles for drug delivery because they can easily manipulate the bacteria’s genetic circuitry to express proteins that seek out cancer cell targets and trigger cell death. Moreover, some strains of bacteria naturally find and penetrate solid tumors, possibly because they prefer the tumor’s acidic microenvironment.However, to make the strategy work, synthetic biologists need to design ways to trigger the bacteria to release their toxic payload when they reach the tumor. Researchers at the University of Pennsylvania, led by Jordan S. Miller and Casim A. Sarkar, decided to use light as a trigger. The team, which included four undergraduate students, undertook this research as part of the 2012 International Genetically Engineered Machine (iGEM) competition, an international synthetic biology competition for undergraduates. For this work, they won the grand prize in the Americas East division of the competition.The team chose the toxin cytolysin A (ClyA) as the cell-killing payload for their bacteria. When bacteria secrete ClyA, the toxin pokes holes in nearby mammalian cells, causing them to break apart, or lyse. As an anticancer therapy, doctors would inject patients with the engineered bacteria and then shine a light directly on their tumors to initiate cell lysis, says Miller, who is now at Rice University.The researchers placed the gene for the toxin into a circular piece of DNA called a plasmid. This plasmid included DNA that triggers the expression of the ClyA gene when the bacteria are exposed to blue light.After inserting the plasmid into Escherichia coli, the scientists plated the microbes on agar plates containing sheep’s blood. When the team placed the plates under blue light, the bacteria secreted their payloads and the toxins destroyed nearby sheep blood cells, as evidenced by clear halos surrounding the bacterial colonies on the red plates. No lysis occurred when the researchers incubated the plates in the dark or when the plasmids contained a gene for a nontoxic protein.The amount of protein released by the microbes depended on the illumination time. Doctors could potentially exploit this feature to deliver the minimal amount of ClyA needed to treat a particular tumor and minimize toxic side effects, the researchers say.Finally, because red light penetrates tissues deeper than blue light, the team also cloned the ClyA gene into a red-light-responsive plasmid. This plasmid worked similarly to the blue-light one.Despite the promising results, Miller stresses that much work remains before the therapeutic bacteria are ready for the clinic, including testing the bacteria in animals.“This is a clever idea, but the potential for putting it to use in vivo is a bit unclear at this point,” says Kevin H. Gardner at the City College of New York and the City University of New York Advanced Science Research Center. In particular, it will be important for the researchers to fine-tune the expression levels of the toxin and to investigate how quickly the system can be shut off after activation, he says. However, Gardner is impressed that the team of undergrads was able to get a complicated light-activated genetic circuit up and running in a single summer."



 http://bit.ly/LTCS3U

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Synthetic Life Created by Synthetic Genomics

Synthetic Life Created by Synthetic Genomics | SynBioFromLeukipposInstitute | Scoop.it
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by
Nanalyze 

"In an earlier article we discussed the exciting potential of synthetic biology, a market that according the to UK government will grow from $1.8 billion in 2011 to $11.8 billion by 2016. One pioneer in the field of synthetic biology is American biologist and entrepreneur, Craig Venter. In 2010, Mr. Venter created a self-replicating single-cell organism which was the first time humans had created “synthetic life” and of which he is currently attempting to patent. One company co-founded by Mr. Venter which seeks to be doing some great things with synthetic biology is Synthetic Genomics.

Synthetic_Genomics  AboutFounded in 2005 by Craig Venter and Nobel Laureate Hamilton O. Smith, California based Synthetic Genomics is dedicated to using modified microorganisms to produce clean fuels and biochemicals. With Mr. Venter at the helm as CEO, some of the Company’s largest investors include BP, Biotechonomy, Draper Fisher Jurvetson and Meteor Group. In 2009, ExxonMobil announced that it would pay Synthetic Genomics up to $300 million to develop algae-based fuels, however in May 2013 a revised agreement with Exxon was announced and speculations were made as to whether or not Synthetic Genomics was having to go back to the drawing board. Said Mr. Venter regarding the new agreement:“We look forward to working with ExxonMobil to undertake this in-depth focus on the basic science research to better understand and enhance algae. The new agreement gives us an opportunity to really focus on improving algal strains using our core synthetic biology technologies to develop biofuels.”Financial details of the new agreement were not disclosed and there is no indication given as to how much of the original $300 million (which was subject to milestones) was actually received by Synthetic Genomics.Intellectual PropertySynthetic Genomics sponsors fundamental research at the J. Craig Venter Institute (JCVI), a not-for-profit organization founded by Mr. Venter in 2006. A world leader in genomics research, JCVI has more than 400 scientists and staff working on a variety of genomic research and policy fronts with more than 250,000 square feet of laboratory space, and locations in Rockville, Maryland and San Diego, California. Synthetic Genomics has exclusive access to new inventions and discoveries in synthetic genomics research developed by the JCVI and so far has filed 13 patent family applications on the unique inventions of the JCVI team which they plan to provide licenses for.ProjectsSynthetic Genomics is currently working in three broad projects areas of Renewable Fuels and Chemicals (alliance with ExxonMobil Research and Engineering Company to develop algal biofuels), Microbial-Enhanced Hydrocarbon Recovery (collaboration with BP), and Sustainable Agricultural Products (through the company, Agradis which was jointly formed with Plenus SA de CV). In January 2013 Monsanto (NYSE: MON) purchased certain technology assets from Agradis including the Agradis name and its library of beneficial plant microorganisms. At the same time Monsanto also made a separate undisclosed investment in Synthetic Genomics and signed a 5 year R&D collaboration agreement focused on agricultural microorganisms.Diagram of a "minimal cell" from the Royal Academy of EngineeringDiagram of a “minimal cell” from the Royal Academy of EngineeringIn 2010, Synthetic Genomics also formed a new company called Synthetic Genomics Vaccines Inc. (SGVI), to develop next generation vaccines. At the same time, SGVI announced a three-year collaboration agreement with Novartis to apply synthetic genomics tools and technologies to accelerate the production of the influenza seed strains required for vaccine manufacturing. Given Synthetic Genomics’ exclusive access to such a large research group such as JCVI, they are certainly in a good position to be a potential leader in the commercialization of these exciting synthetic biology applications...._


http://bit.ly/1kXw3gZ

Image: Diagram of a “minimal cell” from the Royal Academy of Engineering

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The dawning of the age of biology

The dawning of the age of biology | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

Innovations in the application of biology will transform the 21st century 

By James Stavridis

"High quality global journalism requires investment. Please share this article with others using the link below, do not cut & paste the article. See our Ts&Cs and Copyright Policy for more detail. Email ftsales.support@ft.com to buy additional rights. http://www.ft.com/cms/s/2/36218738-6355-11e3-a87d-00144feabdc0.html#ixzz2r2sKtwGH

 What are we missing? This is a question I constantly ask myself as I take on new responsibilities as dean at The Fletcher School at Tufts University.We are certainly teaching the obvious touchstones of international relations: diplomacy, international law, security studies, development and human security, the environment, information technology, political science, key regional studies and global economics. We worry about current wars, the melting ice caps, micro-lending to lift people out of poverty, etc.High quality global journalism requires investment. Please share this article with others using the link below, do not cut & paste the article. See our Ts&Cs and Copyright Policy for more detail. Email ftsales.support@ft.com to buy additional rights. http://www.ft.com/cms/s/2/36218738-6355-11e3-a87d-00144feabdc0.html#ixzz2r2sPrfZR Yet increasingly I believe we are missing something crucial that will reshape international relations in this turbulent 21st century: the coming age of biology.Just as our understanding of physics changed societies a hundred years ago, and changes in information have reshaped us over the decades, I believe we are on the cusp of profound changes in our knowledge and abilities in the realm of biology.As I survey the landscape of the next decade, it seems the truly big muscle movements will come from the world of biology. They include increased life expectancy, artificially enhanced human performance, synthetic biological changes to crops, energy that is produced through biological reaction, implantation of information devices in our bodies, the conquest of persistent diseases, artificial limbs and eyes, 4-D printing and synthetic genomics.While all these innovations will have deeply personal impact, as well as enormous importance in all of our nations, they will also create challenge and opportunity in the international sphere. Those of us involved in graduate education in the international realm need to begin to grapple with the nature of these changes and how we go about teaching our graduates to be prepared to meet them, surmount the challenges and capitalise on the opportunities...._


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A Yeast Synthetic Biology Platform Generates Novel Chemical Structures as Scaffolds for Drug Discovery

A Yeast Synthetic Biology Platform Generates Novel Chemical Structures as Scaffolds for Drug Discovery | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Jens Klein , Jonathan R. Heal , William D.O. Hamilton , Thiamo Boussemghoune , Thomas Østergaard Tange , Fanny Delegrange , Georg Jaeschke , Anaëlle Hatsch , and Jutta Heim

"Synthetic biology has been heralded as a new bioengineering platform for the production of bulk and specialty chemicals, drugs and fuels. Here, we report, for the first time, a series of 74 novel compounds produced using a combinatorial genetics approach in baker’s yeast. Based on the concept of ‘co-evolution’ with target proteins in an intracellular primary survival assay, the identified, mostly scaffold-sized (200-350 MW) compounds, which displayed excellent biological activity, can be considered as pre-validated hits. Of the molecules found, >75% have not been described previously; 20% of the compounds exhibit novel scaffolds. Their structural and physicochemical properties comply with established rules of drug- and fragment-likeness and exhibit increased structural complexities compared to synthetically produced fragments. In summary, the synthetic biology approach described here represents a completely new, complementary strategy for hit and early lead identification that can be easily integrated into the existing drug discovery process."



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Internet Freedom Day: This Year We Go to War for Net Neutrality | Wired Opinion | Wired.com

Internet Freedom Day: This Year We Go to War for Net Neutrality | Wired Opinion | Wired.com | SynBioFromLeukipposInstitute | Scoop.it
This time of year is always the worst of times and best of times for internet freedom.
Gerd Moe-Behrens's insight:

Science need net neutrality

*This Year We Go to War for Net Neutrality*

BY MARVIN AMMORI

"Because with the recent ruling, cable and phone companies like Verizon and AT&T now have the legal right to block any website, webpage, blog, video, web technology, app, cloud sync technology, or anything else running online through their pipes. Put another way, Comcast or Time Warner Cable can now block Netflix, BitTorrent, or even this article. They can choose to provide better service to some entities and not others, letting some websites load very, very slowly and others load instantly (for a fee!)."

http://wrd.cm/1bA7e4P

We need an action plan:
What can we do?

I think we vote with our $. Maybe we write our internet service provider and demand that they guarantee us net neutrality by contract. If they do not do so we tell them, that we will move to another company who will do so.

Moreover, we need to start to find new technical solutions for internet connectivity in a peer to peer way and make us independent form internet service providers.

Other ideas?

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2014: a year for synthetic biology, dark matter, and more! | Industry Leaders Magazine

2014: a year for synthetic biology, dark matter, and more! | Industry Leaders Magazine | SynBioFromLeukipposInstitute | Scoop.it
Expectations concerning energy and science continue to build up as new discoveries and enterprises are unveiled during the first weeks of 2014.
Gerd Moe-Behrens's insight:

*Marcus Fairs, editor of dessen.com, an influential online design magazine, predicted that during 2014 the most relevant emerging technologies will be in the field of synthetic biology*

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Synthetic biology in mammalian cells: next generation research tools and therapeutics :

Synthetic biology in mammalian cells: next generation research tools and therapeutics : | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Florian Lienert,Jason J. Lohmueller,Abhishek Garg& Pamela A. Silver

"Recent progress in DNA manipulation and gene circuit engineering has greatly improved our ability to programme and probe mammalian cell behaviour. These advances have led to a new generation of synthetic biology research tools and potential therapeutic applications. Programmable DNA-binding domains and RNA regulators are leading to unprecedented control of gene expression and elucidation of gene function. Rebuilding complex biological circuits such as T cell receptor signalling in isolation from their natural context has deepened our understanding of network motifs and signalling pathways. Synthetic biology is also leading to innovative therapeutic interventions based on cell-based therapies, protein drugs, vaccines and gene therapies."

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