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Greg Challis tells Jennifer Newton how having little formal training in biology hasn’t stopped him becoming a chemical biology pro 
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Scoop.it!
Gerd Moe-Behrens's insight:
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Gerd Moe-Behrens's insight:
by 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 ;
Scoop.it!
Gerd Moe-Behrens's insight:
*by
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Gerd Moe-Behrens's insight:
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Scoop.it!
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Gerd Moe-Behrens
September 19, 2013 4:22 PM
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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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Gerd Moe-Behrens
September 18, 2013 3:55 PM
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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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Gerd Moe-Behrens
September 17, 2013 5:15 PM
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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.
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Gerd Moe-Behrens
September 14, 2013 1:55 PM
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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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Gerd Moe-Behrens
September 14, 2013 1:48 PM
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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.
A Synthetic Riboswitch that Operates using a Rationally Designed Ligand-RNA Pair http://1.usa.gov/1bi6UrK
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Gerd Moe-Behrens
September 13, 2013 3:09 PM
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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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Gerd Moe-Behrens
September 25, 2013 10:51 AM
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"The digital and biological worlds are interchangeable"
"All life is a DNA software system,""It was as if Blue Valley North High School senior Muriel Eaton was a 5-year-old girl again, wide-eyed in a universe where everything seemed possible and amazing. She and about 50 other high school students from across the Kansas City area were listening to science world rock star J. Craig Venter's tales of where the fusion of biology and engineering is taking us…"
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Gerd Moe-Behrens
September 24, 2013 8:05 AM
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Piro Siuti
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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. .."
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Gerd Moe-Behrens
September 23, 2013 4:38 PM
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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."
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Gerd Moe-Behrens
September 21, 2013 11:12 AM
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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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Gerd Moe-Behrens
September 20, 2013 4:49 PM
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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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Gerd Moe-Behrens
September 19, 2013 4:33 PM
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Refactoring in synthetic biology #synbiobeta #synbio http://t.co/ARP4I7EpUy
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Gerd Moe-Behrens
September 18, 2013 4:04 PM
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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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Gerd Moe-Behrens
September 17, 2013 5:19 PM
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"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."
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Gerd Moe-Behrens
September 17, 2013 4:52 PM
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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."
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Gerd Moe-Behrens
September 16, 2013 4:32 PM
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"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
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Gerd Moe-Behrens
September 14, 2013 1:52 PM
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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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Gerd Moe-Behrens
September 14, 2013 1:39 PM
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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
Plants and microorganisms are the original synthetic chemists http://rsc.li/1eH1vMu