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Life as a Technological Product: Philosophical and Ethical Aspects of Synthetic Biology

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Joachim Bolzt

"Synthetic biology is a new biotechnology that is developing at an impressive pace and attracting a considerable amount of attention from outside the scientific community as well. In this article, two main philosophically and ethically relevant characteristics of this field of research will be laid bare, namely its reliance on mechanistic metaphors to denominate simple forms of life and its appeal to the semantic field of creativity. It is argued that given these characteristics synthetic biology can be understood as a prime example of a kind of human interference with reality that German philosopher Hannah Arendt called “fabrication.” This kind of self-world-relation contrasts to “action,” a relation that introduces, among other things, the idea of an inherent value of the object acted upon. Taking up this latter perspective, one scientific and two ethical challenges to synthetic biology’s take on the realm of life are identified."

http://bit.ly/1gVVqZ7

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Systems Approaches for Synthetic Biology: A Pathway Toward Mammalian Design

Systems Approaches for Synthetic Biology: A Pathway Toward Mammalian Design | SynBioFromLeukipposInstitute | Scoop.it
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Rahul Rekhi and Amina A. Qutub "We review methods of understanding cellular interactions through computation in order to guide the synthetic design of mammalian cells for translational applications, such as regenerative medicine and cancer therapies. In doing so, we argue that the challenges of engineering mammalian cells provide a prime opportunity to leverage advances in computational systems biology. We support this claim systematically, by addressing each of the principal challenges to existing synthetic bioengineering approaches—stochasticity, complexity, and scale—with specific methods and paradigms in systems biology. Moreover, we characterize a key set of diverse computational techniques, including agent-based modeling, Bayesian network analysis, graph theory, and Gillespie simulations, with specific utility towards synthetic biology. Lastly, we examine the mammalian applications of synthetic biology for medicine and health, and how computational systems biology can aid in the continued development of these applications" http://bit.ly/15R4zAR ;
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Ethics: Synthetic Biology

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*by
Gregory E. Kaebnick

"Synthetic biology aims to bring to biology the principles of engineering, standardizing and modularizing the design of biological systems to make possible the development of biological systems that perform specified tasks. Several distinct lines of research fall under the general heading of synthetic biology. Examples of synthetic biology to date include the development of microorganisms that can produce a precursor to artemisinin (a drug for treating malaria) and fuels. The technology poses ethical and policy challenges concerning its risks and potential benefits, its socioeconomic impact and the implications for social justice, and the very idea of engineering living organisms. Many commentators have recommended that these questions should be addressed in a manner that engages the public, raising additional questions about how that is best done."


http://bit.ly/16gT3kF

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Upgrading protein synthesis for synthetic biology

Upgrading protein synthesis for synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
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Patrick O'Donoghue,Jiqiang Ling,Yane-Shih Wang& Dieter Söll

"Genetic code expansion for synthesis of proteins containing noncanonical amino acids is a rapidly growing field in synthetic biology. Creating optimal orthogonal translation systems will require re-engineering central components of the protein synthesis machinery on the basis of a solid mechanistic biochemical understanding of the synthetic process."

http://bit.ly/1dyrliJ

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Implementation of cell-free biological networks at steady state

Implementation of cell-free biological networks at steady state | SynBioFromLeukipposInstitute | Scoop.it
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Niederholtmeyer H, Stepanova V, Maerkl SJ.

"Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations. This reactor-based approach will allow testing of whether fundamental limits exist to in vitro network complexity."

http://bit.ly/1eVHgM0

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GetSynBio

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A great new SynBio blog: GetSynBio http://bit.ly/19ibwtiA great new SynBio blog: GetSynBio http://bit.ly/19ibwti

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Synthetic biology at all scales

Synthetic biology at all scales | SynBioFromLeukipposInstitute | Scoop.it

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Arthur Prindle

"Most of life on Earth exists at the micro scale. In many respects, these microscopic bacteria are an ideal design platform for synthetic biology – hardy, inexpensive, quick to reproduce, and existing in a vast array of species with unique properties. An expanding future landscape of inte- grated synthetic biology will utilize the native networks of diverse microbial species in concert with our own engi- neered gene circuits to execute novel biotechnology [1,2]. To utilize the rich diversity of the microbial world, we must bridge the gap between the microscopic and the macro- scopic, designing biological function at all scales."

http://bit.ly/189EXiW

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Stanford Scientists Use 'Wired Microbes' To Generate Electricity From Sewage

Stanford Scientists Use 'Wired Microbes' To Generate Electricity From Sewage | SynBioFromLeukipposInstitute | Scoop.it
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Tom Abate 

"Interdisciplinary team creates 'microbial battery' driven by naturally occurring bacteria that evolved to produce electricity as they digest organic material.

Engineers at Stanford University have devised a new way to generate electricity from sewage using naturally-occurring “wired microbes” as mini power plants, producing electricity as they digest plant and animal waste. In a paper published today in the Proceedings of the National Academy of Sciences, co-authors Yi Cui, a materials scientist, Craig Criddle, an environmental engineer, and Xing Xie, an interdisciplinary fellow, call their invention a microbial battery.

ref http://www.pnas.org/content/early/2013/09/10/1307327110 One day they hope it will be used in places such as sewage treatment plants, or to break down organic pollutants in the “dead zones” of lakes and coastal waters where fertilizer runoff and other organic waste can deplete oxygen levels and suffocate marine life. At the moment, however, their laboratory prototype is about the size of a D-cell battery and looks like a chemistry experiment, with two electrodes, one positive, the other negative, plunged into a bottle of wastewater. Inside that murky vial, attached to the negative electrode like barnacles to a ship’s hull, an unusual type of bacteria feast on particles of organic waste and produce electricity that is captured by the battery’s positive electrode. "We call it fishing for electrons," said Criddle, a professor in the department of civil and environmental engineering and a senior fellow at the Stanford Woods Institute for the Environment. "




http://stanford.io/1547l1R

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Mirror Life: Changing the Pharma Landscape with Synthetic Biology- An Interview with Professor George Church by George M. Church

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 http://bit.ly/1emGgPG

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Synthetic Biology- A Great talk by Craig Venter

Synthetic Biology- A Great talk by Craig Venter | SynBioFromLeukipposInstitute | Scoop.it
Synthetic biology has pros and cons like Nuclear technology. But it answers some of the most important questions in Life. Synthetic biology opens the door to see how Nature works in creating and...
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A Synthetic Riboswitch that Operates using a Rationally Designed Ligand-RNA Pair

The construction of an artificial riboswitch is based on a ligand-RNA pair without any molecular biology-based selection processes. The ligand selectively and significantly stabilized an RNA duplex containing an r(XGG)/r(XGG) sequence (X=U, A, G). The integration of the ligand-binding sequences into the 5'-untranslated region of mRNA provided an artificial riboswitch that was responsive to Z-NCTS.

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A Synthetic Riboswitch that Operates using a Rationally Designed Ligand-RNA Pair http://1.usa.gov/1bi6UrK

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Book: 'Synthetic Biology and Morality'

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The Hastings Center

"Synthetic biology aims to design and build organisms to serve human ends, such as producing inexpensive biofuels and developing new kinds of medicines. But this new form of biotechnology also raises ethical questions. The concerns range from environmental and public health risks to social and economic impact, but perhaps the foremost is, Should we be "creating life" in the first place?
The last question is explored in Synthetic Biology and Morality: Artificial Life and the Bounds of Nature, a collection of essays edited by Hastings Center scholars Gregory E. Kaebnick and Thomas H. Murray, just published by MIT Press.
"Synthetic biology seems to involve a quest for a degree of control over the basic mechanisms of life that human beings have never attained before; is that quest desirable? Is it troubling?" write Kaebnick and Murray in the introduction.
The book is the product of a Hastings Center project on synthetic biology that examined and debated the idea of synthesizing life. The first section of the book focuses on the human relationship to nature, with essays identifying basic questions about the ethics of making new organisms. The second section asks whether synthetic organisms, far from being morally troubling, might actually be intrinsically valuable. The last section concerns values and public policy–whether and how intrinsic moral objections to synthetic biology might be integrated into policy-making and public discourse.
Gregory Kaebnick is research scholar at The Hastings Center and editor of the Hastings Center Report. Thomas Murray is President Emeritus of the Center and a senior research scholar. Kaebnick and Murray were principal investigators on two Hastings Center projects on synthetic biology.
"Synthetic biology is a hot topic and deserves ethical scrutiny, and this is one of the first volumes that attempts it," says Dale Jamieson, Director of Environmental Studies, New York University and author of Ethics and the Environment.
Jonathan D. Moreno, David and Lyn Silfen University Professor, University of Pennsylvania, calls the book "as innovative as synthetic biology itself."…"



http://bit.ly/14N1wuW

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Engineered bacterium hunts down pathogens

Engineered bacterium hunts down pathogens | SynBioFromLeukipposInstitute | Scoop.it
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Engineered bacterium hunts down pathogens* 


E. coli microbe seeks out and destroys invaders without harming helpful bacteria.
byMark Peplow

"In the war against infection, medicine needs a hero. Meet the bioengineered bacterium that can hunt down pathogens and destroy them with a powerful one–two punch. Synthetic biologist Matthew Chang at Nanyang Technological University in Singapore has armed Escherichia coli bacteria with a ‘seek and kill’ system that targets cells of Pseudomonas aeruginosa, an invasive bacterium that causes pneumonia and other illnesses1. In preliminary tests with infected mice, the modified bacterium left a trail of dead P. aeruginosa in its wake. Chang and his team had previously developed an E. coli that could brew up an antibacterial peptide called pyocin, and then explode to release its deadly cargo whenever it detected a chemical signal emitted by its prey2. Now the bioengineered vigilante is back — and it is tougher than ever…."


http://bit.ly/1d7QAr* ;


E. coli microbe seeks out and destroys invaders without harming helpful bacteria.
byMark Peplow

"In the war against infection, medicine needs a hero. Meet the bioengineered bacterium that can hunt down pathogens and destroy them with a powerful one–two punch. Synthetic biologist Matthew Chang at Nanyang Technological University in Singapore has armed Escherichia coli bacteria with a ‘seek and kill’ system that targets cells of Pseudomonas aeruginosa, an invasive bacterium that causes pneumonia and other illnesses1. In preliminary tests with infected mice, the modified bacterium left a trail of dead P. aeruginosa in its wake. Chang and his team had previously developed an E. coli that could brew up an antibacterial peptide called pyocin, and then explode to release its deadly cargo whenever it detected a chemical signal emitted by its prey2. Now the bioengineered vigilante is back — and it is tougher than ever…."


http://bit.ly/1d7QArO

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Whole-cell modeling for synthetic biology

-

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Piro Siuti 

 

"

Synthetic biology is a relatively new field that brings together scientists from different areas of research such as physics, engineering, mathematics, biochemistry and biology. A major goal of synthetic biology is to design and build synthetic gene networks in order to better understand existing pathways and reprogram organisms with novel functions for a variety of new applications1-4. Initial work in synthetic biology has consisted of synthesizing simple gene circuits with predictable behavior such as the toggle switch5, a stable negative feedback system6, and a synthetic oscillatory network7. These pioneering studies lead to an increased interest in the field, facilitating other synthetic cellular systems such as tunable oscillators8,9 and mammalian switches10, bacterial systems capable of detecting light11, circuits that lead to differential gene expression12, synthetic logic gates with concomitant DNA-encoded memory storage13, and networks capable of counting cellular metabolic events14. Mathematical modeling has played a critical role in developing these systems; however, a majority of models have been developed using simplified host parameters or in isolation without taking into account the vast number of host cellular processes, which can affect the behavior of the synthetic network15,16. This omission of the broader cellular context in models is a likely reason why current models lack predictive power, and multiple rounds of trial-and-error modification of the network are often required to make the network function correctly. .."

http://bit.ly/1gVUP9T

 

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Chemical synthetic biology: a mini-review

Chemical synthetic biology: a mini-review | SynBioFromLeukipposInstitute | Scoop.it
Chemical synthetic biology (CSB) is a branch of synthetic biology (SB) oriented towards the synthesis of chemical structures alternative to those present in nature.
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Cristiano Chiarabelli, Pasquale Stano and Pier Luigi Luisi

"Chemical synthetic biology (CSB) is a branch of synthetic biology (SB) oriented toward the synthesis of chemical structures alternative to those present in nature. Whereas SB combines biology and engineering with the aim of synthesizing biological structures or life forms that do not exist in nature – often based on genome manipulation, CSB uses and assembles biological parts, synthetic or not, to create new and alternative structures. A short epistemological note will introduce the theoretical concepts related to these fields, whereas the text will be largely devoted to introduce and comment two main projects of CSB, carried out in our laboratory in the recent years. The “Never Born Biopolymers” project deals with the construction and the screening of RNA and peptide sequences that are not present in nature, whereas the “Minimal Cell” project focuses on the construction of semi-synthetic compartments (usually liposomes) containing the minimal and sufficient number of components to perform the basic function of a biological cell. These two topics are extremely important for both the general understanding of biology in terms of function, organization, and development, and for applied biotechnology."


http://bit.ly/18Szf10
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G-Quadruplexes as Tools for Synthetic Biology

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Prachi Agarwala, Satyaprakash Pandey,  Souvik Maiti

"With the potential to engineer biological systems, synthetic biology is an emerging field that combines various disciplines of sciences. It encompasses combinations of DNA, RNA and protein modules for constructing desired systems and the “rewiring” of existing signalling networks. Despite recent advances, this field still lags behind in the artificial reconstruction of cellular processes, and thus demands new modules and switches to create “genetic circuits”. The widely characterised noncanonical nucleic acid secondary structures, G-quadruplexes are promising candidates to be used as biological modules in synthetic biology. Structural plasticity and functional versatility are significant G-quadruplex traits for its integration into a biological system and for diverse applications in synthetic circuits."


http://bit.ly/18hO4fu

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Molecular Machines | MIT Media Lab

Molecular Machines | MIT Media Lab | SynBioFromLeukipposInstitute | Scoop.it
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Interesting work at the +MIT Media Lab :
"*Molecular Machines*
How to engineer at the limits of complexity with molecular-scale parts.
The Molecular Machines group is focused on pioneering the field of Avogadro scale engineering, which seeks to understand and approach the fundamental limit of engineered complexity deliverable per unit cost. The group has a particular focus on applications within synthetic biology, novel computing machines, and nanostructured devices for energy production.
Research Projects

GeneFab
Bram Sterling, Kelly Chang, Joseph M. Jacobson, Peter Carr, Brian Chow, David Sun Kong, Michael Oh and Sam Hwang
What would you like to "build with biology"? The goal of the GeneFab projects is to develop technology for the rapid fabrication of large DNA molecules, with composition specified directly by the user. Our intent is to facilitate the field of Synthetic Biology as it moves from a focus on single genes to designing complete biochemical pathways, genetic networks, and more complex systems. Sub-projects include: DNA error correction, microfluidics for high throughput gene synthesis, and genome-scale engineering (rE. coli).
NanoFab
Kimin Jun, Jaebum Joo, and Joseph M. Jacobson
We are developing techniques to use a focused ion beam to program the fabrication of nanowires-based nanostructures and logic devices.
Scaling Up DNA Logic and Structures
Joseph M. Jacobson and Noah Jakimo
Our goals include novel gene logic and data logging systems, as well as DNA scaffolds that can be produced on commercial scales. State of the art in the former is limited by finding analogous and orthogonal proteins for those used in current single-layer gates and two-layered circuits. State of the art in the latter is constrained in size and efficiency by kinetic limits on self-assembly. We have designed and plan to demonstrate cascaded logic on chromosomes and DNA scaffolds that exhibit exponential growth.
Synthetic Photosynthesis
Kimin Jun
We are using nanowires to build structures for synthetic photosynthesis for the solar generation of liquid fuels."

http://bit.ly/18gp3De

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Twitter / AlexKara15: Refactoring in synthetic biology ...

Twitter / AlexKara15: Refactoring in synthetic biology ... | SynBioFromLeukipposInstitute | Scoop.it
Refactoring in synthetic biology #synbiobeta #synbio http://t.co/ARP4I7EpUy
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Multiplex Iterative Plasmid Engineering for Combinatorial Optimization of Metabolic Pathways and Diversification of Protein Coding Sequences

Multiplex Iterative Plasmid Engineering for Combinatorial Optimization of Metabolic Pathways and Diversification of Protein Coding Sequences | SynBioFromLeukipposInstitute | Scoop.it
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Yifan Li , Qun Gu , Zhenquan Lin , Zhiwen Wang , Tao Chen *, and Xueming Zhao

"Engineering complex biological systems typically requires combinatorial optimization to achieve the desired functionality. Here, we present Multiplex Iterative Plasmid Engineering (MIPE), which is a highly efficient and customized method for combinatorial diversification of plasmid sequences. MIPE exploits ssDNA mediated λ Red recombineering for the introduction of mutations, allowing it to target several sites simultaneously and generate libraries of up to 107 sequences in one reaction. We also describe “restriction digestion mediated co-selection (RD CoS)”, which enables MIPE to produce enhanced recombineering efficiencies with greatly simplified coselection procedures. To demonstrate this approach, we applied MIPE to fine-tune gene expression level in the 5-gene riboflavin biosynthetic pathway and successfully isolated a clone with 2.67-fold improved production in less than a week. We further demonstrated the ability of MIPE for highly multiplexed diversification of protein coding sequence by simultaneously targeting 23 codons scattered along the 750 bp sequence. We anticipate this method to benefit the optimization of diverse biological systems in synthetic biology and metabolic engineering."

http://bit.ly/14jHhCw

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Microbial battery for efficient energy recovery

"This work introduces a microbial battery for recovery of energy from reservoirs of organic matter, such as wastewater. Microorganisms at an anode oxidize dissolved organic substances, releasing electrons to an external circuit, where power can be extracted. The electrons then enter a solid-state electrode that remains solid as electrons accumulate within it. The solid-state electrode is periodically removed from the battery, oxidized, and reinstalled for sustained power production. Molecular oxygen is not introduced into the battery, and ion-exchange membranes are avoided, enabling high efficiencies of energy recovery."

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Xing Xiea,b, Meng Yea, Po-Chun Hsub, Nian Liuc, Craig S. Criddlea,1, and Yi Cuib,d,1 

 "By harnessing the oxidative power of microorganisms, energy can be recovered from reservoirs of less-concentrated organic matter, such as marine sediment, wastewater, and waste biomass. Left unmanaged, these reservoirs can become eutrophic dead zones and sites of greenhouse gas generation. Here, we introduce a unique means of energy recovery from these reservoirs—a microbial battery (MB) consisting of an anode colonized by microorganisms and a reoxidizable solid-state cathode. The MB has a single-chamber configuration and does not contain ion-exchange membranes. Bench-scale MB prototypes were constructed from commercially available materials using glucose or domestic wastewater as electron donor and silver oxide as a coupled solid-state oxidant electrode. The MB achieved an efficiency of electrical energy conversion of 49% based on the combustion enthalpy of the organic matter consumed or 44% based on the organic matter added. Electrochemical reoxidation of the solid-state electrode decreased net efficiency to about 30%. This net efficiency of energy recovery (unoptimized) is comparable to methane fermentation with combined heat and power."

 

 

http://bit.ly/150jOsN

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Ethical Perspectives on Synthetic Biology

Ethical Perspectives on Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
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Bernadette Bensaude Vincent

 

"Synthetic biologists are extremely concerned with responsible research and innovation. This paper critically assesses their culture of responsibility. Their notion of responsibility has been so far focused on the identification of risks, and in their prudential attitude synthetic biologists consider that the major risks can be prevented with technological solutions. Therefore they are globally opposed to public interference or political regulations and tend to self-regulate by bringing a few social scientists or ethicists on board. This article emphasizes that ethics lies beyond prudence and requires a cultural evaluation of the modes of existence of the various microorganisms designed by synthetic biologists, independently of their potential applications."


http://bit.ly/187kxoM

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An Open-Source Graphical Notation for Synthetic Biology

"The Synthetic Biology Open Language Visual (SBOL Visual) project is an effort toward developing a community-driven open standard for visual representation of genetic designs. Standardized visual notation for communicating designs has proven to be useful in many engineering disciplines. A de facto visual notation does exist in synthetic biology; however, it is incomplete, is often extended ad hoc, and exists as a poorly defined, voluntary, communal convention rather than an explicit standard. Because synthetic biology endeavors often require a multidisciplinary team, a common visual system of communication with well-defined semantics is vital. It is also important that the emerging ecosystem of biological design tools converge upon a common visual language to maximize adoption and minimize ambiguity in results. Given the central role and rich history of visual representation in the life sciences, a well-defined visual notation will also prompt the construction of the formal infrastructure needed to support effective ontologies, meaningful models, and tools tailored to community needs. "

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Jacqueline Quinn, Jacob Beal, Swapnil Bhatia, Patrick Cai, Joanna Chen, Kevin Clancy, Robert Sidney Cox III, Michal Galdzicki, Nathan Hillson, Akshay Maheshwari,
Chris Myers, Umesh P, Matthew Pocock, Cesar Rodriguez, Herbert M Sauro, Larisa Soldatova, Guy-Bart Stan, Mandy Wilson, Drew Endy 

 

http://bit.ly/14WFndK

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Wow of the week: With a little bioengineering, E. coli becomes a pathogen-fighting superhero

Wow of the week: With a little bioengineering, E. coli becomes a pathogen-fighting superhero | SynBioFromLeukipposInstitute | Scoop.it
Researchers may have found a way to turn E. coli bacteria into a way to fight hospital-acquired infections like pneumonia and bloodstream infections.
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http://bit.ly/160nA6g

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Chemical synthetic biology: a mini-review

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by
Cristiano Chiarabelli, Pasquale Stano and Pier Luigi Luisi

"Chemical synthetic biology (CSB) is a branch of synthetic biology (SB) oriented towards the synthesis of chemical structures alternative to those present in nature. Whereas SB combines biology and engineering with the aim of synthesizing biological structures or life forms that do not exist in nature – often based on genome manipulation, CSB uses and assembles biological parts, synthetic or not, to create new and alternative structures. A short epistemological note will introduce the theoretical concepts related to these fields, whereas the text will be largely devoted to introduce and comment two main projects of CSB, carried out in our laboratory in the recent years. The “Never Born Biopolymers” (NBB) project deals with the construction and the screening of RNA and peptide sequences that are not present in nature, whereas the “Minimal Cell” project focuses on the construction of semi-synthetic compartments (usually liposomes) containing the minimal and sufficient number of components to perform the basic function of a biological cell. These two topics are extremely important for both the general understanding of biology in terms of function, organization and development, and for applied biotechnology."


http://bit.ly/164NqPv

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Synthetic biology goes industrial

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Jennifer Rohn

"Imperial College London has won a £10 ($16)-million grant to set up a new translational center aimed at integrating academic and industry research in synthetic biology. Known as SynbiCITE, the London-based center is funded by the Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council and Technology…"

http://bit.ly/14JMaY0

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