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Enzyme-free translation of DNA into sequence-defined synthetic polymers structurally unrelated to nucleic acids

Enzyme-free translation of DNA into sequence-defined synthetic polymers structurally unrelated to nucleic acids | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:


via Farah Bennani

*Enzyme-free translation of DNA into sequence-defined synthetic polymers structurally unrelated to nucleic acids*

by
Jia Niu,Ryan Hili& David R. Liu

"The translation of DNA sequences into corresponding biopolymers enables the production, function and evolution of the macromolecules of life. In contrast, methods to generate sequence-defined synthetic polymers with similar levels of control have remained elusive. Here, we report the development of a DNA-templated translation system that enables the enzyme-free translation of DNA templates into sequence-defined synthetic polymers that have no necessary structural relationship with nucleic acids. We demonstrate the efficiency, sequence-specificity and generality of this translation system by oligomerizing building blocks including polyethylene glycol, α-(D)-peptides, and β-peptides in a DNA-programmed manner. Sequence-defined synthetic polymers with molecular weights of 26 kDa containing 16 consecutively coupled building blocks and 90 densely functionalized β-amino acid residues were translated from DNA templates using this strategy. We integrated the DNA-templated translation system developed here into a complete cycle of translation, coding sequence replication, template regeneration and re-translation suitable for the iterated in vitro selection of functional sequence-defined synthetic polymers unrelated in structure to nucleic acids."

http://bit.ly/10PIv2J

you can view this paper for free on Dr Liu`s webpage

http://evolve.harvard.edu

Comment to this original paper:

by Peter Reuell "...As described in a recent paper in Nature Chemistry, a team of researchers led by David Liu, a professor of chemistry and chemical biology at Harvard, has developed a new method to create synthetic polymers using the coding of genetic material. The method may eventually be used to evolve synthetic polymers with new or improved properties such as the ability to serve as catalysts in chemical reactions or enhanced therapeutic potential. "The word polymer, unfortunately, is pretty vague, but in biology, large molecules like DNA, RNA, and proteins are the most common polymers," Liu said. "These polymers can have remarkable properties. Our ability to create man-made polymers with tailor-made properties, by comparison, is much more limited, in part because we don't have a way to evolve synthetic polymers—that's really the problem we set out to address." Other researchers have managed to create synthetic polymers using genetic coding, but their efforts were hampered by the fact that the new molecules necessarily resembled the genetic template used to create them. To solve that problem, Liu and colleagues turned to a process similar to one found in nature. Rather than allow the building blocks of a new polymer to interact directly with the DNA template, the system relies on an "adapter" molecule. The adapters, each of which carries a part of the polymer, bind to the template, forming the new polymer. In the final step of the process, Liu said, the adapters are cut away, leaving a synthetic polymer created according to the genetic template...." http://bit.ly/10E2HHC
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Design of biomolecular network modifications to achieve adaptation

Design of biomolecular network modifications to achieve adaptation | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Waldherr S, Streif S, Allgöwer F.

"A biomolecular network is called adaptive if its output returns to the original value after a transient response even under a persisting stimulus. The conditions for adaptation have been investigated thoroughly with systems theory approaches in the literature and it is easy to check whether they are satisfied in the linear approximation. In contrast, it is in general not easy to modify a non-adaptive network model such that it gains adaptive behaviour, especially for medium- and large-scale networks. The authors present a systematic approach based on the notion of kinetic perturbations to construct adaptive biomolecular network models from non-adaptive ones. An advantage of kinetic perturbations in this application is that neither the stoichiometry nor the steady state of the system is changed. Furthermore, the method covers both parameter and network structure modifications and can be applied to any reaction rate formalism and even to medium-scale or partially unknown models. The approach is exemplified at a small- and a medium-sized biomolecular network, illustrating its potential to systematically evaluate the different network modifications for adaptation. The proposed method will be useful either in iterative model building to construct mathematical models of adaptive biomolecular networks, or in synthetic biology where it can be applied to design or modify synthetic networks for adaptation."

http://bit.ly/Ya5ftR

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http://bit.ly/16LOtVH

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PLOS Computational Biology: The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks

PLOS Computational Biology: The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Bowsher CG, Voliotis M, Swain PS.

"Cells live in changing, dynamic environments. To understand cellular decision-making, we must therefore understand how fluctuating inputs are processed by noisy biomolecular networks. Here we present a general methodology for analyzing the fidelity with which different statistics of a fluctuating input are represented, or encoded, in the output of a signaling system over time. We identify two orthogonal sources of error that corrupt perfect representation of the signal: dynamical error, which occurs when the network responds on average to other features of the input trajectory as well as to the signal of interest, and mechanistic error, which occurs because biochemical reactions comprising the signaling mechanism are stochastic. Trade-offs between these two errors can determine the system's fidelity. By developing mathematical approaches to derive dynamics conditional on input trajectories we can show, for example, that increased biochemical noise (mechanistic error) can improve fidelity and that both negative and positive feedback degrade fidelity, for standard models of genetic autoregulation. For a group of cells, the fidelity of the collective output exceeds that of an individual cell and negative feedback then typically becomes beneficial. We can also predict the dynamic signal for which a given system has highest fidelity and, conversely, how to modify the network design to maximize fidelity for a given dynamic signal. Our approach is general, has applications to both systems and synthetic biology, and will help underpin studies of cellular behavior in natural, dynamic environments."

 http://bit.ly/YYwzOW

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Scientists print self-assembling 'living tissue'

Scientists print self-assembling 'living tissue' | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Beth Marie Mole

"Researchers have created networks of water droplets that mimic some properties of cells in biological tissues. Using a three-dimensional printer, a team at the University of Oxford, UK, assembled tiny water droplets into a jelly-like material that can flex like a muscle and transmit electric signals like chains of neurons. The work is published today in Science1.

These networks, which can contain up to 35,000 droplets, could one day become a scaffold for making synthetic tissues or provide a model for organ functions, says co-author Gabriel Villar of Cambridge Consultants, a technology-transfer company in Cambridge, UK. “We want to see just how far we can push the mimicry of living tissue,” he says."

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Will cell therapy become a 'third pillar' of medicine?

Treating patients with cells may one day become as common as it is now to treat the sick with drugs made from engineered proteins, antibodies or smaller chemicals, according to UC San Francisco researchers.
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Emerging Systems and Synthetic Biology Approaches to Hydrocarbon Biotechnology - Springer

Emerging Systems and Synthetic Biology Approaches to Hydrocarbon Biotechnology - Springer | SynBioFromLeukipposInstitute | Scoop.it
I'm reading Emerging Systems and Synthetic Biology Approaches to Hydrocarbon Biotechnology http://t.co/WAlhJfYem0 #springerlink
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Enzyme and metabolic engineering for the production of novel biopolymers: crossover of biological and chemical processes

Enzyme and metabolic engineering for the production of novel biopolymers: crossover of biological and chemical processes | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Matsumoto K, Taguchi S.

"The development of synthetic biology has transformed microbes into useful factories for producing valuable polymers and/or their precursors from renewable biomass. Recent progress at the interface of chemistry and biology has enabled the production of a variety of new biopolymers with properties that substantially differ from their petroleum-derived counterparts. This review touches on recent trials and achievements in the field of biopolymer synthesis, including chemo-enzymatically synthesized aliphatic polyesters, wholly biosynthesized lactate-based polyesters, polyhydroxyalkanoates and other unusual bacterially synthesized polyesters. The expanding diversities in structure and the material properties of biopolymers are key for exploring practical applications. The enzyme and metabolic engineering approaches toward this goal are discussed by shedding light on the successful case studies."
http://bit.ly/10aQ4n

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Accelerated protein engineering for chemical biotechnology via homologous recombination

Accelerated protein engineering for chemical biotechnology via homologous recombination | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Nordwald EM, Garst A, Gill RT, Kaar JL.

"Protein engineering has traditionally relied on random mutagenesis strategies to generate diverse libraries, which require high-throughput screening or selection methods to identify rare variants. Alternatively, approaches to semi-rational library construction can be used to minimize the screening load and enhance the efficiency by which improved mutants may be identified. Such methods are typically limited to characterization of relatively few variants due to the difficulties in generating large rational libraries. New tools from synthetic biology, namely multiplexed DNA synthesis and homologous recombination, provide a promising avenue to rapidly construct large, rational libraries. These technologies also enable incorporation of synthetically encoded features that permit efficient characterization of the fitness of each mutant. Extension of these tools to protein library design could complement rational protein design cycles in an effort to more systematically search complex fitness landscapes. The highly parallelized nature with which such libraries can be generated also has the potential to expand directed protein evolution from single protein targets to protein networks whose concerted activities are required for the biological function of interest."


http://bit.ly/XoECWZ

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Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Hans-Jörg Frasch1, Marnix H Medema, Eriko Takano , Rainer Breitling

"Synthetic biology is revolutionizing the way in which the biosphere is explored for natural products. Through computational genome mining, thousands of biosynthetic gene clusters are being identified in microbial genomes, which constitute a rich source of potential novel pharmaceuticals. New methods are currently being devised to prioritize these gene clusters in terms of their potential for yielding biochemical novelty. High-potential gene clusters from any biological source can then be activated by ‘refactoring’ their native regulatory machinery, replacing it by synthetic, orthogonal regulation and optimizing enzyme expression to function effectively in an industry-compatible target host. Various part libraries and assembly technologies have recently been developed which facilitate this process."
http://bit.ly/14D54y2

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Assembly of complex cell microenvironments using geometrically docked hydrogel shapes

Assembly of complex cell microenvironments using geometrically docked hydrogel shapes | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:


*Lego-style templates build complex tissue*

by
Holly Evarts-Columbia 

"The study reveals new ways to better mimic the enormous complexity of tissue development, regeneration, and disease, and is published online in the Proceedings of the National Academy of Sciences.

“George Eng, an MD/PhD student in my lab who just received his doctoral degree, designed a lock-and-key technique to build cellular assemblies using a variety of shapes that lock into templates much the way you would use LEGO building blocks,” says Gordana Vunjak-Novakovic, who led the study and is a professor of biomedical engineering at Columbia Engineering and professor of medical sciences...."


http://bit.ly/16s1xRP

original ref:

*Assembly of complex cell microenvironments using geometrically docked hydrogel shapes*

by
George Enga, Benjamin W. Leea, Hesam Parsaa, Curtis D. China, Jesse Schneidera, Gary Linkovb, Samuel K. Siaa, and Gordana Vunjak-Novakovica

"Cellular communities in living tissues act in concert to establish intricate microenvironments, with complexity difficult to recapitulate in vitro. We report a method for docking numerous cellularized hydrogel shapes (100–1,000 µm in size) into hydrogel templates to construct 3D cellular microenvironments. Each shape can be uniquely designed to contain customizable concentrations of cells and molecular species, and can be placed into any spatial configuration, providing extensive compositional and geometric tunability of shape-coded patterns using a highly biocompatible hydrogel material. Using precisely arranged hydrogel shapes, we investigated migratory patterns of human mesenchymal stem cells and endothelial cells. We then developed a finite element gradient model predicting chemotactic directions of cell migration in micropatterned cocultures that were validated by tracking ∼2,500 individual cell trajectories. This simple yet robust hydrogel platform provides a comprehensive approach to the assembly of 3D cell environments."
http://bit.ly/11dcNQD

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UVioO - Genetically Evolved Technology: Luke Bawazer at TEDxWarwick

UVioO - Genetically Evolved Technology: Luke Bawazer at TEDxWarwick | SynBioFromLeukipposInstitute | Scoop.it
UVioO - Luke Bawazer works in Fiona Meldrum's laboratory at University of Leeds, where he conducts research at the interface of chemistry, materials science, and synthetic biology.
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Life, but not as we know it: Welcome to a future where man-made organisms build us cities on alien planets

Life, but not as we know it: Welcome to a future where man-made organisms build us cities on alien planets | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Rob Waugh 

"Mankind’s first 'colonists' on other planets might not be humans at all - but instead, modified microscopic life-forms which would glue together concrete buildings before our first manned ships touched down.

 The idea sounds like science fiction - and suspiciously like Star Trek’s 'terraforming' - but NASA is already experimenting with 'synthetic biology' to achieve it - tailor-making an organism to help us make concrete from sand. "NASA is investigating a synthetic version of bacteria that secrete calcite. If you put them in sand, they form bricks," says Andrew Rutherford, an editor at science journal 'Nature' and author of new book 'Creation'. "NASA is investigating a synthetic version of these bacteria - which could form bricks. One of the biggest costs in space exploration is getting materials off Earth. With this, if you take a flask of bacteria, you’ve got all your building material. The research is some way off, but NASA is taking a very serious line in synthetic biology." Rutherford’s book looks at the emerging science of 'synthetic life' - lifeforms modified in the lab using genetic engineering, tailor-made to our needs.  The research has provoked fears of bioterrorism, or man-made plagues - but Rutherford insists the benefits far outweigh the risks. "Genetic modification is an engineering discipline," says Rutherford. "It has the potential to be the biggest industrial revolution in history - changing food production, the environment, drug production. "We have been designed in a blind process that has lasted four billion years - with each gene tested to destruction, either through death or extinction. A gene is basically a tool."

 http://yhoo.it/13H47pc

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Synthetic Biology News Roundup

Synthetic Biology News Roundup | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

*Synthetic Biology News Roundup* 


By Christina Agapakis 

"There’s been a lot of interesting papers out this month in synthetic biology. Here’s a quick roundup of some news and research:

 Oliver Wright, Guy-Bart Stan and Tom Ellis. Building-in Biosafety for Synthetic Biology. Microbiology, March 2013. Preprint PDF available here.Christine Rabinovitch-Deer, John Oliver, Gabriel Rodriguez, and Shota Atsumi. Synthetic BIology and Metabolic Engineering Approaches to Biofuels. Chemical Reviews, March 2013.The BIOFAB: International Open Facility Advancing Biotechnology published two papers this month about the precise control of gene expression in E. coliMutalik et al. Precise and Reliable Gene Expression via Standard Transcription and Translation Initiation Elements. Nature Methods, March 2013.Mutalik et al. Quantitative Estimation of Activity and Quality for Collections of Functional Genetic Elements. Nature Methods, March 2013.An interesting New Scientist article discusses these papers in the context of industrialization of synthetic biology, from “handcrafted” production pathways in yeast to the “Ikea” of synthetic biology production: “Quality control opens path to synthetic biology’s Ikea.”Jerome Bonnet, Peter Yin, Monica Ortiz, Pakpoom Subsoontorn, and Drew Endy. Amplifying Genetic Logic Gates. Science, March 2013.“Scientists create transistor-like biological device,” Guardian Science News.A great piece by Carl Zimmer on Synthetic Biology at Download The Universe: “A Comic Book Guide to Rewiring Life.”,..."



http://bit.ly/Yl8hiw

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Quantitative Design of Regulatory Elements Based on High-Precision Strength Prediction Using Artificial Neural Network

Quantitative Design of Regulatory Elements Based on High-Precision Strength Prediction Using Artificial Neural Network | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Meng H, Wang J, Xiong Z, Xu F, Zhao G, Wang Y.

"Accurate and controllable regulatory elements such as promoters and ribosome binding sites (RBSs) are indispensable tools to quantitatively regulate gene expression for rational pathway engineering. Therefore, de novo designing regulatory elements is brought back to the forefront of synthetic biology research. Here we developed a quantitative design method for regulatory elements based on strength prediction using artificial neural network (ANN). One hundred mutated Trc promoter & RBS sequences, which were finely characterized with a strength distribution from 0 to 3.559 (relative to the strength of the original sequence which was defined as 1), were used for model training and test. A precise strength prediction model, NET90_19_576, was finally constructed with high regression correlation coefficients of 0.98 for both model training and test. Sixteen artificial elements were in silico designed using this model. All of them were proved to have good consistency between the measured strength and our desired strength. The functional reliability of the designed elements was validated in two different genetic contexts. The designed parts were successfully utilized to improve the expression of BmK1 peptide toxin and fine-tune deoxy-xylulose phosphate pathway in Escherichia coli. Our results demonstrate that the methodology based on ANN model can de novo and quantitatively design regulatory elements with desired strengths, which are of great importance for synthetic biology applications."

http://bit.ly/151fIPU

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Jay Keasling: Making a synthetic biology antimalarial drug is only first step

Jay Keasling: Making a synthetic biology antimalarial drug is only first step | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by Ron Leuty

"Jay Keasling wants to build an even better mosquito trap.
As French drug maker Sanofi ramps up production of semisynthetic artemisinin — initially developed in Keasling’s University of California, Berkeley, lab — Keasling and others are moving forward with a new nonprofit to explore how to cheaply get synthetic biology-created antimalarial drugs to the world's neediest populations.
“The idea is to get the drug out to everyone who needs it,” said Keasling, who I interviewed for this week's print edition story on the synthetic biology process used to invent a potentially cheaper and steadier source of the antimalarial drug artemisinin."

http://bit.ly/10J89ao

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Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology

Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by

Tina Ton, Bruce Tidor


"Biological systems are inherently variable, with their dynamics influenced by intrinsic and extrinsic sources. These systems are often only partially characterized, with large uncertainties about specific sources of extrinsic variability and biochemical properties. Moreover, it is not yet well understood how different sources of variability combine and affect biological systems in concert. To successfully design biomedical therapies or synthetic circuits with robust performance, it is crucial to account for uncertainty and effects of variability. Here we introduce an efficient modeling and simulation framework to study systems that are simultaneously subject to multiple sources of variability, and apply it to make design decisions on small genetic networks that play a role of basic design elements of synthetic circuits. Specifically, the framework was used to explore the effect of transcriptional and post-transcriptional autoregulation on fluctuations in protein expression in simple genetic networks. We found that autoregulation could either suppress or increase the output variability, depending on specific noise sources and network parameters. We showed that transcriptional autoregulation was more successful than post-transcriptional in suppressing variability across a wide range of intrinsic and extrinsic magnitudes and sources. We derived the following design principles to guide the design of circuits that best suppress variability: (i) high protein cooperativity and low miRNA cooperativity, (ii) imperfect complementarity between miRNA and mRNA was preferred to perfect complementarity, and (iii) correlated expression of mRNA and miRNA – for example, on the same transcript – was best for suppression of protein variability. Results further showed that correlations in kinetic parameters between cells affected the ability to suppress variability, and that variability in transient states did not necessarily follow the same principles as variability in the steady state. Our model and findings provide a general framework to guide design principles in synthetic biology."

http://bit.ly/10lPH9m

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Riboswitches for Intracellular Study of Genes Involved in Francisella Pathogenesis

Riboswitches for Intracellular Study of Genes Involved in Francisella Pathogenesis | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

 by
Reynoso CM, Miller MA, Bina JE, Gallivan JP, Weiss DS.

"The study of many important intracellular bacterial pathogens requires an understanding of how specific virulence factors contribute to pathogenesis during the infection of host cells. This requires tools to dissect gene function, but unfortunately, there is a lack of such tools for research on many difficult-to-study, or understudied, intracellular pathogens. Riboswitches are RNA-based genetic control elements that directly modulate gene expression upon ligand binding. Here we report the application of theophylline-sensitive synthetic riboswitches to induce protein expression in the intracellular pathogen Francisella. We show that this system can be used to activate the bacterial expression of the reporter β-galactosidase during growth in rich medium. Furthermore, we applied this system to control the expression of green fluorescent protein during intracellular infection by the addition of theophylline directly to infected macrophages. Importantly, we could control the expression of a novel endogenous protein required for growth under nutrient-limiting conditions and replication in macrophages, FTN_0818. Riboswitch-mediated control of FTN_0818 rescued the growth of an FTN_0818 mutant in minimal medium and during macrophage infection. This is the first demonstration of the use of a synthetic riboswitch to control an endogenous gene required for a virulence trait in an intracellular bacterium. Since this system can be adapted to diverse bacteria, the ability to use riboswitches to regulate intracellular bacterial gene expression will likely facilitate the in-depth study of the virulence mechanisms of numerous difficult-to-study intracellular pathogens such as Ehrlichia chaffeensis, Anaplasma phagocytophilum, and Orientia tsutsugamushi, as well as future emerging pathogens. IMPORTANCE: Determining how specific bacterial genes contribute to virulence during the infection of host cells is critical to understanding how pathogens cause disease. This can be especially challenging with many difficult-to-study intracellular pathogens. Riboswitches are RNA-based genetic control elements that can be used to help dissect gene function, especially since they can be used in a broad range of bacteria. We demonstrate the utility of riboswitches, and for the first time show that riboswitches can be used to functionally control a bacterial gene that is critical to the ability of a pathogen to cause disease, during intracellular infection. Since this system can be adapted to diverse bacteria, riboswitches will likely facilitate the in-depth study of the virulence mechanisms of numerous difficult-to-study intracellular pathogens, as well as future emerging pathogens."

http://1.usa.gov/10wHCye

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PLOS Biology: Synthetic Biology and Conservation of Nature: Wicked Problems and Wicked Solutions

PLOS Biology: Synthetic Biology and Conservation of Nature: Wicked Problems and Wicked Solutions | SynBioFromLeukipposInstitute | Scoop.it
PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.
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Questions swarm around synthetic biology's impact on Mother Nature

Questions swarm around synthetic biology's impact on Mother Nature | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

By Alan Boyle

"Conservationists say it's high time to consider whether synthetic biology will solve some of the huge problems that beset endangered species, or bring new problems. It just might do both.

"Synthetic biology brings with it a powerful attraction, causing biology to veer towards engineering with its inherent approach of human problem solving," three experts on biodiversity and conservation say in this week's issue of PLOS Biology. "It may prove to be a cure for certain wicked problems. But we suggest that now is the time to consider whether synthetic biology may be a wicked solution, creating problems of its own, some of which may be undesirable or even unacceptable in the area of biodiversity conservation." The PLOS Biology essay was written by Kent Redford of Archipelago Consulting, William Adams of the University of Cambridge, and Georgina Mace of University College London's Center for Biodiversity and Environment Research. The three conservationists are the organizers of a conference on synthetic biology, due to take place next week in Cambridge, England...."


http://nbcnews.to/Z2Kh08

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Decaffeination and Measurement of Caffeine Content by Addicted Escherichia coli with a Refactored N-Demethylation Operon from Pseudomonas putida CBB5

Decaffeination and Measurement of Caffeine Content by Addicted Escherichia coli with a Refactored N-Demethylation Operon from Pseudomonas putida CBB5 | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Erik M. Quandt, Michael J. Hammerling, Ryan M. Summers, Peter B. Otoupal, Ben Slater, Razan N. Alnahhas, Aurko Dasgupta, James L. Bachman, Mani V. Subramanian, and Jeffrey E. Barrick

"The widespread use of caffeine (1,3,7-trimethylxanthine) and other methylxanthines in beverages and pharmaceuticals has led to significant environmental pollution. We have developed a portable caffeine degradation operon by refactoring the alkylxanthine degradation (Alx) gene cluster from Pseudomonas putida CBB5 to function in Escherichia coli. In the process, we discovered that adding a glutathione S-transferase from Janthinobacterium sp. Marseille was necessary to achieve N7-demethylation activity. E. coli cells with the synthetic operon degrade caffeine to the guanine precursor, xanthine. Cells deficient in de novo guanine biosynthesis that contain the refactored operon are ″addicted″ to caffeine: their growth density is limited by the availability of caffeine or other xanthines. We show that the addicted strain can be used as a biosensor to measure the caffeine content of common beverages. The synthetic N-demethylation operon could be useful for reclaiming nutrient-rich byproducts of coffee bean processing and for the cost-effective bioproduction of methylxanthine drugs."
http://bit.ly/XInrii

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A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana

A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by

Christoph Schmal, Peter Reimann, Dorothee Staiger

"The circadian clock controls many physiological processes in higher plants and causes a large fraction of the genome to be expressed with a 24h rhythm. The transcripts encoding the RNA-binding proteins AtGRP7 (Arabidopsis thaliana Glycine Rich Protein 7) and AtGRP8 oscillate with evening peaks. The circadian clock components CCA1 and LHY negatively affect AtGRP7 expression at the level of transcription. AtGRP7 and AtGRP8, in turn, negatively auto-regulate and reciprocally cross-regulate post-transcriptionally: high protein levels promote the generation of an alternative splice form that is rapidly degraded. This clock-regulated feedback loop has been proposed to act as a molecular slave oscillator in clock output. While mathematical models describing the circadian core oscillator in Arabidopsis thaliana were introduced recently, we propose here the first model of a circadian slave oscillator. We define the slave oscillator in terms of ordinary differential equations and identify the model's parameters by an optimization procedure based on experimental results. The model successfully reproduces the pertinent experimental findings such as waveforms, phases, and half-lives of the time-dependent concentrations. Furthermore, we obtain insights into possible mechanisms underlying the observed experimental dynamics: the negative auto-regulation and reciprocal cross-regulation via alternative splicing could be responsible for the sharply peaking waveforms of the AtGRP7 and AtGRP8 mRNA. Moreover, our results suggest that the AtGRP8 transcript oscillations are subordinated to those of AtGRP7 due to a higher impact of AtGRP7 protein on alternative splicing of its own and of the AtGRP8 pre-mRNA compared to the impact of AtGRP8 protein. Importantly, a bifurcation analysis provides theoretical evidence that the slave oscillator could be a toggle switch, arising from the reciprocal cross-regulation at the post-transcriptional level. In view of this, transcriptional repression of AtGRP7 and AtGRP8 by LHY and CCA1 induces oscillations of the toggle switch, leading to the observed high-amplitude oscillations of AtGRP7 mRNA."


http://bit.ly/YOtKzP

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Recent progress in synthetic biology for microbial production of C3–C10 alcohols

Recent progress in synthetic biology for microbial production of C3–C10 alcohols | SynBioFromLeukipposInstitute | Scoop.it
Frontiers | Recent progress in synthetic biology for microbial production of C3–C10 alcohols | Frontiers in Microbiotechnology, Ecotoxicology and Bioremediation publishes articles on the most outstanding discoveries across the research spectrum of...
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Researchers engineer plant cell walls to boost sugar yields for biofuels

Researchers engineer plant cell walls to boost sugar yields for biofuels | SynBioFromLeukipposInstitute | Scoop.it
Using the tools of synthetic biology, researchers are engineering healthy plants whose lignocellulosic biomass can more easily be broken down into simple sugars for the production of clean, green and renewable advanced biofuels.
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Synthetic Biology | Studiolab

Synthetic Biology | Studiolab | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

*StudioLab Synthetic Biology* 

"Synthetic biology research is based on the art of designing genetic material from the code up. Rather than slicing, dicing and splicing existing genetic material, new synthesising protocols allow the specification and production of genetic sequences; to order...."

http://bit.ly/Zt6yDn

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