SynBioFromLeukipposInstitute

*Cell Therapy Promise Highlighted at UCSF Symposium*

http://bit.ly/ZSh4JA

 

*Mammalian Synthetic Biology Workshop*  Stata Center, MIT May 11-12  "Recognizing the fast emergence and potential significance of this field, the aim of this workshop is to bring together practitioners of mammalian synthetic biology together with experts from other relevant fields. The general goals of the workshop are to nucleate the nascent mammalian synthetic biology community, reach out to experts from other fields that can benefit from and contribute to this field, and define the important challenges and future directions. The workshop format will provide a forum for exposition of the latest developments in the field and discussions of how experts from other fields can benefit from and contribute to mammalian synthetic biology. Perhaps more importantly, the workshop will also include breakout sessions that will identify the main challenges and opportunities. Findings from the breakout sessions will be assembled into a written report that will be distributed to all workshop participants and to relevant government and funding agencies. The agenda on Saturday will include several 30 minute talks about mammalian synthetic biology tools and capabilities, talks about industrial and clinical applications, and two sets of breakout sessions. The first set of breakout sessions will focus on the technology, including large scale DNA assembly and integrationtranscriptional regulationsensors and actuatorsnon-transcriptional regulation.The second set of breakout sessions will focus on potential disease and scientific inquiry applications, including cancerstem cell and tissue engineeringvaccination and infectious diseasediabetes and metabolic diseasesdrug screening.The emphasis in these sessions will be on understanding and evaluating the transformative opportunities for synthetic biology in these areas. Sunday morning will include two talks and then reports from all breakout sessions. The workshop will end Sunday at noon. Organizing Committee: Ron Weiss, MIT, ChairPamela A. Silver, Harvard, Co-ChairNoubar Afeyan, Flagship VenturesJon Chesnut, Life TechnologiesGeorge M. Church, HarvardJames J. Collins, BULeonard Katz, SynbercChristina D. Smolke, Stanford" http://bit.ly/V4jZvS

 *Cell-free platforms for flexible expression and screening of enzymes*

by
Catherine C, Lee KH, Oh SJ, Kim DM.

"As was witnessed from PCR technology, in vitro applications of biosynthetic machinery can expand the horizon of biotechnology. Cell-free protein synthesis has emerged as a powerful technology that can potentially transform the concept of bioprocess. With the ability to harness the synthetic power of biology without many of the constraints of cell-based systems, cell-free protein synthesis enables instant creation of protein molecules from diverse sources of genetic information. Enzyme discovery and engineering is the field of particular interest among the possible applications of cell-free protein synthesis since many of the intrinsic limitations associated with traditional cell-based expression screening of enzymes can be effectively addressed. Not only offers excellent throughput in the generation of enzymes, cell-free synthesis allows facile integration of expression and analysis of enzymes, greatly accelerating the process of enzyme discovery. This review article is thus intended to survey recent progress in cell-free protein synthesis technology focused on its applications in enzyme expression and screening."
http://bit.ly/13itM54

by
Shozo Yokoyama

"For over the last two decades, positively selected amino acid sites have been inferred almost exclusively by showing that the number of nonsynonymous substitutions per nonsynonymous site (dn) is greater than that of synonymous substitutions per synonymous site (ds). However, virtually none of these statistical results have been experimentally tested and remain as hypotheses. To perform such experimental tests, we must connect genotype and phenotype and relate the phenotypic changes to the environmental and behavioral changes of the organism. The genotype-phenotype relationship can be established only by synthesizing and manipulating “proper” ancestral phenotypes, while the actual functions of adaptive mutations can be learned by studying their chemical roles in phenotypic changes."

http://bit.ly/ZF43iL

*Synthetic biology, the bioeconomy, and a societal quandary*

by
Jim C. Philp , Rachael J. Ritchie* and Jacqueline E.M. Allan

"Opinions on what synthetic biology actually is range from a natural extension of genetic engineering to a new manufacturing paradigm. It offers, for the first time in the life sciences, rational design and engineering standardisation. It could address problems across a broad spectrum of human concerns, including energy and food security, and health of growing and aging populations. It also offers great scope for public resistance to its introduction to daily life.

 FOR TODAY, WE HAVE NAMING OF PARTS The literature on synthetic biology is punctuated with comparisons to the electronics industry, where standard mechanical and electrical interfaces were established by the early 1960s and formed the basis for the modern microelectronics industry. By contrast, the standardised parts of biology result from DNA synthesis technology. The standardised parts refer to elements such as promoters, ribosome binding sites, cloning sites, and terminators. A clear understanding of standardisation can be informed by reference to the MIT Registry of Standard Biological Parts, BioBrick Standard 10 (http://partsregistry.org):A Biobrick compatible standard biological part consists of a DNA fragment potentially conveying informational or functional properties to a composite structure assembled from multiple parts. From this, the allusion to electronics is quite clear – parts are assembled to complete devices, which are assembled into complete systems (be it, for example, a medicine, or an electronic product such as a cell phone).  TECHNICAL BARRIERS Progress in synthetic biology is predicated upon rapid design and accurate building and testing of synthetic DNA sequences, at least up to the size of a bacterial operon. DNA sequencing technology and costs are regularly compared to Moore's Law, the observation that the number of transistors on integrated circuits doubles within a specified time [1] (now approximately every 18 months). Since the original publication of the human genome sequence, the cost of DNA sequencing has tumbled. DNA synthesis technology, however, has lagged behind but is now progressing rapidly [2]. Economical gene synthesis now appears feasible, although not yet possible. One advantage of de novo DNA synthesis over cloning from genomic DNA or cDNA is the total control exerted over the design and sequence of the product. Features such as restriction sites and promoters can be inserted or deleted almost at will. Another is that a fabricated construct can be optimised for expression in a host, such as a chassis organism like Escherichia coli.  WHAT CAN BE MADE WITH SYNTHETIC BIOLOGY? A manufacturing ambition for synthetic biology resonates strongly with the recent elaboration of bioeconomy strategies by various nations [e.g., the USA; The White House (2012) National Bioeconomy Blueprint, (http://www.whitehouse.gov/sites/default/files/microsites/ostp/national_bioeconomy_blueprint_april_2012.pdf)] and regions (e.g., the EU [3]). Indeed, on the first page of the US National Bioeconomy Blueprint, it is stated that the bioeconomy of tomorrow relies on emerging technologies such as synthetic biology. Bioeconomy strategies envisage the biobased production of fuels, chemicals and materials, pharmaceuticals, and enzymes. The addressable market is therefore vast. Two examples are given here of how synthetic biology might contribute to this manufacturing future....."

 http://bit.ly/128Ho1x

*Synthetic Biology for Computer Programmers*

June 8th, San Francisco 

"Synthetic Biology for Computer Programmers is a new course conceptualized and written by Dr. Josh Gilmore and Dr. John Cumbers. The course provides a one day interactive class for teaching synthetic biology to non-experts. The course is written for tech-professionals in other fields such as computer science, to learn about the growing power of biology to perform useful tasks and make high value products from drugs to spiders silk. We focus on analyzing the similarities and differences in our fields of study to make these lessons accessible, inspirational, and memorable."

http://bit.ly/15sL8iM

By Bruce Sterling

"“What are the mundane realities of designing biology today? Synthetic biology is a predicted technology that still has a lot of science to grapple with. Computer logic and biological survival are not a natural fit. While the discipline is increasingly enabled by exponential advances in DNA sequencing and synthesis technologies, in labs around the world, engineers and scientists are painstakingly trying to wrest control over biology’s complexity. The visions are necessary to fuel this research, especially in an application-driven climate. George Osborne, the UK’s Chancellor of the Exchequer, announced twenty million British pounds of funding for UK synthetic biology in 2012, with the justification that: “They say that synthetic biology will heal us, heat and feed us.” It may be some time yet.

 “Computer logic and biological survival are not a natural fit. “For a technology that promises it could make all living matter into viable material with which to build useful things, it is vitally important to consider the future now. Investment and law-making shape the path of progress, as can public opinions. Can we influence the path of our biological future? This is where I see a valuable role for design and art in these early stages, upstream in the development of a technology. Navigating the space between the mundane visions of chemicals, tethered in the technologically possible, and dreams unconstrained by existing science can help us test out what we might want from a future. It may also inspire new research areas, and make us think more carefully about others" 

http://bit.ly/1362778

Announcing PLOS Labs – Call For Participation http://bit.ly/10y2NhE

by
Erika Check Hayden

"Yaniv Erlich shows how research participants can be identified from 'anonymous' DNA..

Late at night, a video camera captures a man striding up to the locked door of the information-technology department of a major Israeli bank. At this hour, access can be granted only by a fingerprint reader — but instead of using the machine, the man pushes a button on the intercom to ring the receptionist's phone. As it rings, he holds his mobile phone up to the intercom and presses the number 8. The sound of the keypad tone is enough to unlock the door. As he opens it, the man looks back to the camera with a shrug: that was easy. Yaniv Erlich — the star of this 2006 video — considers this one of his favourite hacks. Technically a “penetration exercise” conducted to expose the bank's vulnerabilities, it was one of several projects that Erlich worked on during a two-year stint with a security firm based near Tel Aviv. Since then, the 33-year-old computational biologist has been bringing his hacker ethos to biology. Now at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, he is using genome data in new ways, and in the process exposing vulnerabilities in databases that hold sensitive information on thousands of individuals around the world....."

http://bit.ly/13GS1t1

by
Wijffels RH, Kruse O, Hellingwerf KJ.

"Both cyanobacteria and eukaryotic microalgae are promising organisms for sustainable production of bulk products such as food, feed, materials, chemicals and fuels. In this review we will summarize the potential and current biotechnological developments. Cyanobacteria are promising host organisms for the production of small molecules that can be secreted such as ethanol, butanol, fatty acids and other organic acids. Eukaryotic microalgae are interesting for products for which cellular storage is important such as proteins, lipids, starch and alkanes. For the development of new and promising lines of production, strains of both cyanobacteria and eukaryotic microalgae have to be improved. Transformation systems have been much better developed in cyanobacteria. However, several products would be preferably produced with eukaryotic microalgae. In the case of cyanobacteria a synthetic-systems biology approach has a great potential to exploit cyanobacteria as cell factories. For eukaryotic microalgae transformation systems need to be further developed. A promising strategy is transformation of heterologous (prokaryotic and eukaryotic) genes in established eukaryotic hosts such as Chlamydomonas reinhardtii. Experimental outdoor pilots under containment for the production of genetically modified cyanobacteria and microalgae are in progress. For full scale production risks of release of genetically modified organisms need to be assessed"

http://bit.ly/13Al8hx

by
Miso Park, Shen-Long Tsai  and Wilfred Chen

"Whole-cell biosensors are a good alternative to enzyme-based biosensors since they offer the benefits of low cost and improved stability. In recent years, live cells have been employed as biosensors for a wide range of targets. In this review, we will focus on the use of microorganisms that are genetically modified with the desirable outputs in order to improve the biosensor performance. Different methodologies based on genetic/protein engineering and synthetic biology to construct microorganisms with the required signal outputs, sensitivity, and selectivity will be discussed."


http://bit.ly/10qGP04

by
Kevin Munnelly 

"For years, scientists have hoped that biology would find its engineering counterpart – a series of principles that could be used as reliably as chemical engineering is for chemistry. Thanks to major advances in synthetic biology, those hopes may soon be realized.

 As long as there have been efforts to understand biology and how organisms and particular biological mechanisms function, there have been parallel efforts to alter biology to better suit a specific need. Even before these organisms were understood on a genetic level, people were breeding animals to make stronger oxen or faster horses, mixing crop strains for higher yield or better flavor, or crossing flowers to create new colors.But the tremendous complexity of biology has, in some ways, kept these approaches more art than science. The goal of using engineering principles to allow scientists to perturb known biological systems and either alter them slightly or even design completely new biological systems still remains a fundamental need in order to cure disease, produce biofuels, and improve crop yield.Today, synthetic biology shows more promise than any previous attempt at creating a biobased engineering discipline. In the past 15 years, the nascent field of synthetic biology has made tremendous advances, beginning with the very first custom-built biological components and gradually progressing to a fully functioning synthetic genome. One of the latest achievements in this scientific field is a new approach to producing synthetic DNA at much higher capacity and far lower cost than current standards, which offers the opportunity for even more innovation.Thanks to synthetic biology initiatives such as the International Genetically Engineered Machines (iGEM) competition, young researchers coming out of academic programs today are the first generation to grow up with a portfolio of biological building blocks at their disposal, making them the first to truly look at biology as a field to which standard engineering principles can be applied.Synthetic bio is more than just an academic endeavor; by expert estimates, the opportunity for biosynthesizable approaches in the chemical development industry is $50 billion, while the same category in biofuels is expected to be a $500 billion market. Considering the potential for synthetic genes to revolutionize these and many other industries, the business opportunities for synthetic biology-based solutions go well into the trillion-dollar-plus realm.In this Viewpoint, we will look at the significant accomplishments that have shaped today’s synthetic biology landscape and consider what may be possible in the coming years based on recent innovations...."

http://bit.ly/ZF2ilQ

by
Laura Cinti 

"As part of Waag’s “Do it Together Bio” series, C-LAB was invited to hold a workshop related to our work using synthetic biology. The workshop was held at De Waag, one of the oldest building in Amsterdam and where Rembrandt famously painted The Anatomy Lesson of Dr. Nicolaes Tulp (1632). ...."


http://bit.ly/10CDw4O

*Updated Map Tracks Global Growth of Synthetic Biology*

Awesome interactive map!

"As research into synthetic biology increases, this map identifies companies, universities, research institutions, laboratories and other centers across the globe that are active in this emerging field.

 In 2009, the Synthetic Biology Project began mapping the increased research in the field of synthetic biology, finding pockets of work being done in California, Massachusetts, the United Kingdom and Germany. These areas see continued growth in 2013, while research also ramps up in China and Japan. The updated map can be used to examine the locations of companies, universities, research institutions, government and military laboratories and policy centers that are active in this emerging field. In addition to expanded listings, the updated map features improved functionality, more detailed information and additional categories and subcategories. The map can also be accessed on Android and Apple mobile devices. This map is based on publicly available data from official websites, scientific literature, government reports and records, and newspaper and journal articles, but this field is dynamic, and the map is a work in progress. This form allows users to submit an entry, make a comment about an existing entry or correct existing information. Comments can also be sent to synbio@wilsoncenter.org. Thank you for taking a look: All suggestions will be reviewed and incorporated into the map. A detailed analysis of the current landscape will be released in the coming weeks. More information about the methodology and sources for the update can be found here. The data behind the map can be found here."

http://bit.ly/ZwgIof

by

Alexandra Daisy Ginsberg

"Somewhere between a vat of expensive face cream and a baby Neanderthal lies a probable future for synthetic biology. While synbio start-ups – large and small – struggle with the reality of scaling up microscopic cellular factories into profitable business models, stories of DIY anti-cancer research, Neanderthal cloning, limitless ‘green’ kerosene, and tumor-killing bacteria are told as outcomes of a likely future where humans have full control over biology.

 Over the last decade, many diverse interests have contributed to this ambition of an easy-to-manipulate biology, as the field of synthetic biology has spread around research labs all over the world. Scientists, engineers, policymakers, industrialists, space agencies, politicians, and even designers are constructing a future defined by the grand rhetoric of a world-changing, world-saving technology. The engineering vision supported by governments and corporations tends towards the practical. These are liquid dreams of industrial chemistry and pipelines filled with expensive molecules oozing out of synthetic organisms, invisible biological factories locked in secure vats. The bigger aspirations of synthetic biologists to place engineered life into the ecosystem, from pollution-munching bacteria to hi-tech plants, need not be realized for synthetic biology to be deemed a successful venture in terms of investment parameters........."

http://bit.ly/100KWTx