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Synthetic Biocomputation: the possible and the actual

"Computation is defining trait of biological systems and a broad framework that captures the complex adaptive nature of molecules, cells and organisms. Computation is also at the core of the genotype-phenotype mapping, since it provides a natural framework to define function in a self-consistent way. The study of existing biological systems (from signalling cas- cades to ant colonies or brains) as well as the evolution of synthetic in silico networks performing computations reveals a number of nontrivial patterns of organization, sometimes in clear conflict with standard view of engineering or optimiza- tion. In spite of our increasing knowledge, there is a lack of a theoretical framework where computation and its pos- sible forms is integrated within a general picture. Synthetic biology provides a new avenue where engineered molecular circuits can be implemented to perform non-standard com- putations. Here we review recent advances in the domain of multicellular synthetic computing and suggest a potential morphospace of computational systems including both stan- dard and non-standard approximations."

http://bit.ly/LeCibN

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how science works: interactive flowchart

how science works: interactive flowchart | SynBioFromLeukipposInstitute | Scoop.it

BY CHRISTOPHER DE LA TORRE

"UC Berkeley’s Understanding Science resource website makes excellent use of interactive schemata to reinforce the scientific method. The flow of information facilitates both global and sequential learning. The community analysis sphere (below) deals with quality control—one of two major collaboratory elements to use crowdsourcing. Students are encouraged to review the work of others, both past and present, and the mention of individual scientists reinforces the value of the collective. Further development considerations include smartphone adaptability and 3D visualization. ...."

http://bit.ly/JwnYHP

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Synthetic Biology Center @ MIT | About

Synthetic Biology Center @ MIT | About | SynBioFromLeukipposInstitute | Scoop.it

"The goal of synthetic biology is to make the construction of novel biological systems into a practical and useful engineering discipline. The key is the development of an engineering methodology based on standardized and well-characterized interchangeable parts. Biological systems can be a basis for practical programmable materials, providing an engineering substrate with exquisite control over and response to the chemical world. The consequences of synthetic biology will be as great as the development of chemical engineering from alchemy, with enormous and as perhaps unimaginable implications for materials science and medicine. The range of applications for synthetic biology is vast, encompassing but not limited to: diagnostics, therapeutics, sensors, environmental remediation, energy production, and a host of other biomolecular and chemical manufacturing outputs. Synthetic biology can also help us gain valuable insight into fundamental biological principles and improve our quantitative understanding of the living world.

The mission of the Synthetic Biology Center at MIT is to develop and advance the engineering discipline for this emerging field.

The Center will be structured around three layered Thrusts:

Foundations Thrust, focused on creating an infrastructure of synthetic biology tools and capabilities.
Systems Engineering Thrust, for engineering highly sophisticated biological systems rapidly, efficiently, and reliably.
Grand Challenge Applications Thrust, for select areas where synthetic biology provides unique opportunities and capabilities."
http://bit.ly/MzKXrI

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Synthetic Biology: Building a Language to Program Cells

Synthetic Biology: Building a Language to Program Cells | SynBioFromLeukipposInstitute | Scoop.it

by

Christopher Voigt
"We are developing a basis by which cells can be programmed like robots to perform complex, coordinated tasks for pharmaceutical and industrial applications. We are engineering new sensors that give bacteria the senses of touch, sight, and smell. Genetic circuits - analogous to their electronic counterparts - are built to integrate the signals from the various sensors. Finally, the output of the gene circuits is used to control cellular processes. We are also developing theoretical tools from statistical mechanics and non-linear dynamics to understand how to combine genetic devices and predict their collective behavior."

http://bit.ly/JJBzQD

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California considers DNA privacy law

California considers DNA privacy law | SynBioFromLeukipposInstitute | Scoop.it
Academic researchers fear measures would prohibit work with genetic databases.
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Foundations for the design and implementation of synthetic genetic circuits : Abstract : Nature Reviews Genetics

Foundations for the design and implementation of synthetic genetic circuits

Nature Reviews Genetics
by
Slusarczyk AL, Lin A, Weiss R.
"Synthetic gene circuits are designed to program new biological behaviour, dynamics and logic control. For all but the simplest synthetic phenotypes, this requires a structured approach to map the desired functionality to available molecular and cellular parts and processes. In other engineering disciplines, a formalized design process has greatly enhanced the scope and rate of success of projects. When engineering biological systems, a desired function must be achieved in a context that is incompletely known, is influenced by stochastic fluctuations and is capable of rich nonlinear interactions with the engineered circuitry. Here, we review progress in the provision and engineering of libraries of parts and devices, their composition into large systems and the emergence of a formal design process for synthetic biology."
http://bit.ly/JeUCTy

 
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Systems metabolic engineering of microorganisms for natural and non-natural chemicals

by
Jeong Wook Lee, Dokyun Na, Jong Myoung Park, Joungmin Lee Sol Choi & Sang Yup Lee
"Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of chemicals, fuels and materials from renewable resources. Metabolic engineering is a key enabling technology for transforming microorganisms into efficient cell factories for these compounds. Systems metabolic engineering, which incorporates the concepts and techniques of systems biology, synthetic biology and evolutionary engineering at the systems level, offers a conceptual and technological framework to speed the creation of new metabolic enzymes and pathways or the modification of existing pathways for the optimal production of desired products. Here we discuss the general strategies of systems metabolic engineering and examples of its application and offer insights as to when and how each of the different strategies should be used. Finally, we highlight the limitations and challenges to be overcome for the systems metabolic engineering of microorganisms at more advanced levels."
http://bit.ly/JVo53m
Comment
Metabolic engineering - Production of chemicals without petroleum
" In our everyday life, we use gasoline, diesel, plastics, rubbers, and numerous chemicals that are derived from fossil oil through petrochemical refinery processes. However, this is not sustainable due to the limited nature of fossil resources. Furthermore, our world is facing problems associated with climate change and other environmental problems due to the increasing use of fossil resources.
One solution to address above problems is the use of renewable non-food biomass for the production of chemicals, fuels and materials through biorefineries. Microorganisms are used as biocatalysts for converting biomass to the products of interest. However, when microorganisms are isolated from nature, their efficiencies of producing our desired chemicals and materials are rather low.
Metabolic engineering is thus performed to improve cellular characteristics to desired levels. Over the last decade, much advances have been made in systems biology that allows system-wide characterization of cellular networks, both qualitatively and quantitatively, followed by whole-cell level engineering based on these findings. Furthermore, rapid advances in synthetic biology allow design and synthesis of fine controlled metabolic and gene regulatory circuits. The strategies and methods of systems biology and synthetic biology are rapidly integrated with metabolic engineering, thus resulting in "systems metabolic engineering"....."
http://bit.ly/JVpsPu

 
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Thinking Big: Synthetic Biology - Fidelity Investments

Thinking Big: Synthetic Biology - Fidelity Investments | SynBioFromLeukipposInstitute | Scoop.it
Fidelity Investments is one of the world's largest providers of financial services, with assets under administration of $3.4 trillion, including managed assets of $1.5 trillion, as of Dec. 31, 2011.
 
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I can no longer work for a system that puts profit over access to research

I can no longer work for a system that puts profit over access to research | SynBioFromLeukipposInstitute | Scoop.it

Winston Hide, associate editor of Genomics, says its publisher Elsevier effectively denies developing world access to research findings...

 
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Breaking the Genome Bottleneck - Technology Review MIT

Breaking the Genome Bottleneck - Technology Review MIT | SynBioFromLeukipposInstitute | Scoop.it

This post points to one of the main challenges contemporary science is facing, the problem of big data (see Nature, SoapBox Science http://bit.ly/Jzz16M , actually an important part of what the Leukippos project is about). I did not look into the code for detail, however, the main strategy they are describing goes in the right direction. In my view provides systems theory the solution for the big data problem. We need to apply holistic thinking. On a technical side, we need a to provide the data both human and computer readable. This will allow us automated analysis, which will be readable by humans. The output data need to be structured hierarchical form the general to the detail. Eg we can structure in species, individual, organ organelle, protein, rna, dna, dna parts. Your search output will be at the highest level of abstraction, the most general group. You can than klick down to the detail. Moreover, a graphical representation of data will help to represent a huge amount of data on a small space. We will need for this a sematic web, and open and free accessible common database. This will demand open access publishing. Authors have also to deliver their data in a computer readable form. Projects like Wikidata doing some groundbreaking work for this. If I understand the app described in this paper goes in this direction described. The infrastructure, as I described it, has to be developed further in order to make this work. On a long run, I guess apps like this will be successfully. Finally, I would like to put another aspect for the solution of big data up to discussion: crowd sourcing. It has been shown in several apps like e.g. the Foldit game, that the crowd has the potential to analyze big data sets. In respect to genetic data certain ethical standards have to be meet (such as anonymity). However, this has a big potential.

 
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Rapid reagentless quantification of alginate biosynthesis in Pseudomonas fluorescens bacteria mutants using FT-IR spectroscopy coupled to multivariate partial least squares regression.

by

Correa E, Sletta H, Ellis DI, Hoel S, Ertesvåg H, Ellingsen TE, Valla S, Goodacre R.

"Alginate is an important medical and commercial product and currently is isolated from seaweeds. Certain microorganisms also produce alginate and these polymers have the potential to replace seaweed alginates in some applications, mainly because such production will allow much better and more reproducible control of critical qualitative polymer properties. The research conducted here presents the development of a new approach to this problem by analysing a transposon insertion mutant library constructed in an alginate-producing derivative of the Pseudomonas fluorescens strain SBW25. The procedure is based on the non-destructive and reagent-free method of Fourier transform infrared (FT-IR) spectroscopy which is used to generate a complex biochemical infrared fingerprint of the medium after bacterial growth. First, we investigate the potential differences caused by the growth media fructose and glycerol on the bacterial phenotype and alginate synthesis in 193 selected P. fluorescens mutants and show that clear phenotypic differences are observed in the infrared fingerprints. In order to quantify the level of the alginate we also report the construction and interpretation of multivariate partial least squares regression models which were able to quantify alginate levels successfully with typical normalized root-mean-square error in predictions of only approximately 14 %. We have demonstrated that this high-throughput approach can be implemented in alginate screens and we believe that this FT-IR spectroscopic methodology, when combined with the most appropriate chemometrics, could easily be modified for the quantification of other valuable microbial products and play a valuable screening role for synthetic biology."

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ScienceDirect.com - Current Opinion in Chemical Biology - Engineering multicellular traits in synthetic microbial populations

ScienceDirect.com - Current Opinion in Chemical Biology - Engineering multicellular traits in synthetic microbial populations | SynBioFromLeukipposInstitute | Scoop.it

John S Chuang, Engineering multicellular traits in synthetic microbial populations, Current Opinion in Chemical Biology http://t.co/wwUzUXyG...

 
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Joi Ito's Near-Perfect Explanation of the Next 100 Years - Technology Review

Joi Ito's Near-Perfect Explanation of the Next 100 Years - Technology Review | SynBioFromLeukipposInstitute | Scoop.it
"One hundred years from now, the role of science and technology will be about becoming part of nature rather than trying to control it"

Joi Ito, MIT, technology review

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SynBERC | Synthetic Biology Engineering Research Center

SynBERC | Synthetic Biology Engineering Research Center | SynBioFromLeukipposInstitute | Scoop.it

"The Synthetic Biology Engineering Research Center (SynBERC) is a multi-institution research effort to lay the foundation for the emerging field of synthetic biology. SynBERC’s vision is to catalyze biology as an engineering discipline by developing the foundational understanding and technologies to allow researchers to design and build standardized, integrated biological systems to accomplish many particular tasks. In essence, we are making biology easier to engineer.

Just as technicians now assemble electronic devices from commercial, off-the-shelf parts, SynBERC foresees a day when synthetic biologists will design biological systems from scratch and assemble them using well-characterized biological parts, devices, and chasses. SynBERC brings together biologists, engineers, and human scientists from world-class institutions to produce the tools, techniques, and scientific understanding needed to design and construct a broad range of biological tools for health, energy, environment and, ultimately, human welfare."
http://bit.ly/iE5zMP

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Synthetic Biology Institute at UC Berkeley

Synthetic Biology Institute at UC Berkeley | SynBioFromLeukipposInstitute | Scoop.it

The Synthetic Biology Institute at UC Berkeley

is working to make the engineering of new complex function in cells vastly more efficient, reliable, predictable, and safe. Its breakthroughs will speed the development of biologically engineered solutions to pressing global problems related to health, materials, energy, environment, and security.
http://bit.ly/nTAuh0

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DIY synthetic biology, rehabilitation robotics and touching data at 3Dcamp : 3Dcamp

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A list of interesting upcoming publications from the Church lab

http://bit.ly/nd7L2K

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Natural strategies for the spatial optimization of metabolism in synthetic biology

by
Christina M Agapakis,Patrick M Boyle & Pamela A Silver
NATURE CHEMICAL BIOLOGY | REVIEW
"Metabolism is a highly interconnected web of chemical reactions that power life. Though the stoichiometry of metabolism is well understood, the multidimensional aspects of metabolic regulation in time and space remain difficult to define, model and engineer. Complex metabolic conversions can be performed by multiple species working cooperatively and exchanging metabolites via structured networks of organisms and resources. Within cells, metabolism is spatially regulated via sequestration in subcellular compartments and through the assembly of multienzyme complexes. Metabolic engineering and synthetic biology have had success in engineering metabolism in the first and second dimensions, designing linear metabolic pathways and channeling metabolic flux. More recently, engineering of the third dimension has improved output of engineered pathways through isolation and organization of multicell and multienzyme complexes. This review highlights natural and synthetic examples of three-dimensional metabolism both inter- and intracellularly, offering tools and perspectives for biological design."
http://bit.ly/KoavSe

 

 

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Craig Venter Wants to Solve the World’s Energy Crisis

Craig Venter Wants to Solve the World’s Energy Crisis | SynBioFromLeukipposInstitute | Scoop.it

By Thomas Goetz

"There is one version of Craig Venter’s life story where he would’ve been a dutiful scientist at the National Institutes of Health, a respected yet anonymous researcher in genetics, perhaps. Thankfully, Venter saw that story line developing—and set about making sure it never happened.

Instead, in 1992 Venter left the NIH to head the nonprofit Institute for Genomic Research. Six years later he founded Celera Genomics, a brash rival to the NIH project that aimed to sequence the full code of the human genome. Venter had come up with a better technique—known as shotgun sequencing—to get the job done, and it changed the way we translate genetics from proteins into code. Not incidentally, it also served as a model for today’s Big Data explosion in science and research. In 2001 Celera officially “tied” the NIH to the genome finish line, though the company’s sequence was more than a bit further along. (Celera’s model genome, it just so happened, included Venter’s own DNA.)

In the decade since, Venter has been on a tear of invention and exploration. In 2004 he sailed around the world, discovering thousands of new species and sequencing millions of new genes. In 2007 he unveiled his own genome, unexpurgated (it revealed a predisposition for risk-taking, among other things). And in 2010 he announced the first successful synthesis of life—a unique critter borne from two distinct organisms, thus proving for the first time that it is indeed possible to create new organisms for specific purposes and functions. He is, in every respect, the epitome of an icon—a figure who has pushed science forward, sometimes by sheer force of will.

I spoke recently with Venter in San Francisco, at an event hosted by City Arts & Lectures and the California Academy of Sciences. What follows is an edited version of that conversation....."

http://bit.ly/JEbBxS

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Chemistry and Biology - RNA-Based Therapeutics: Current Progress and Future Prospects

RNA engineering is a quite interesting area in SynBio. The review by John C. Burnett and John J. Rossi might give some hints what kind of applications look promising in a clinical perspective:

 

"Recent advances of biological drugs have broadened the scope of therapeutic targets for a variety of human diseases. This holds true for dozens of RNA-based therapeutics currently under clinical investigation for diseases ranging from genetic disorders to HIV infection to various cancers. These emerging drugs, which include therapeutic ribozymes, aptamers, and small interfering RNAs (siRNAs), demonstrate the unprecedented versatility of RNA. However, RNA is inherently unstable, potentially immunogenic, and typically requires a delivery vehicle for efficient transport to the targeted cells. These issues have hindered the clinical progress of some RNA-based drugs and have contributed to mixed results in clinical testing. Nevertheless, promising results from recent clinical trials suggest that these barriers may be overcome with improved synthetic delivery carriers and chemical modifications of the RNA therapeutics. This review focuses on the clinical results of siRNA, RNA aptamer, and ribozyme therapeutics and the prospects for future successes."
http://bit.ly/L4wa2W

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Decoding synthetic biology - NOW - Concordia University

Decoding synthetic biology - NOW - Concordia University | SynBioFromLeukipposInstitute | Scoop.it

by: Tom Peacock

"Biology Professor Vincent Martin describes synthetic biology as applying principles of engineering to biology — understanding how different pieces work together through modelling in order to produce a predictable result.

“If you want to build a microbe that produces an antibiotic, then you need to know what the parts or the genes are, and then how to assemble the genes together to give you what you expect you’re going to get in a reproducible, predictable way,” he explains.

Synthetic biology is generating a lot of interest, especially in Europe and the United States, perhaps owing to its almost limitless applications. Martin describes himself as “knee-deep” in synthetic biology, but says the Canadian scientific community as a whole has thus far shown only tepid interest in the new field. ...."

http://bit.ly/JmBz4j

 
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BioBricks Foundation SB6.0: The Sixth International Meeting on Synthetic Biology | Facebook

BioBricks Foundation SB6.0: The Sixth International Meeting on Synthetic Biology | Facebook | SynBioFromLeukipposInstitute | Scoop.it

 

 
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Hacketeria: open source biological art, DIY biology. generic lab equipment

Hacketeria: open source biological art, DIY biology. generic lab equipment | SynBioFromLeukipposInstitute | Scoop.it

Hackteria is a collection of Open Source Biological Art Projects instigated in February 2009 by Andy Gracie, Marc Dusseiller and Yashas Shetty, after collaboration during the Interactivos?09 Garage Science at Medialab Prado in Madrid. The aim of the project is to develop a rich web resource for people interested in or developing projects that involve DIY bioart, open source software and electronic experimentation.

As a community platform hackteria tries to encourage the collaboration of scientists, hackers and artists to combine their experitise, write critical and theoretical reflections, share simple instructions to work with lifescience technologies and cooperate on the organization of workshops, festival and meetings.

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Looking to the Future of A New Kind of Science - Xconomy

Looking to the Future of A New Kind of Science - Xconomy | SynBioFromLeukipposInstitute | Scoop.it

Looking to the Future of A New Kind of ScienceXconomyNKS will also no doubt be important in figuring out how to set up synthetic biological organisms.

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Socrates Logos's comment, May 17, 2012 6:49 PM
I was especially curious about this remark "NKS will also no doubt be important in figuring out how to set up synthetic biological organisms."