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A diagram illustrating how the hydrogel sensor works (Image: Birck Nanotechnology Center, ...

Scientists have used gelatinous hydrogel to create an inexpensive new type of biochemical sensor that is highly sensitive, sturdy, long-lasting, and has few moving parts. The gel expands or contracts according to the acidity of its environment, a quality that allows the sensor to measure changes in pH down to one one-thousandth on the pH scale. This amount of accuracy, along with its robustness, could make it ideal for chemical and biological applications such as environmental monitoring in waterways and glucose monitoring in blood... Continue Reading Hydrogel used to create precise new biochemical sensor

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(Via gizmag: Science and Education.)

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An Open Resource for TAL Effectors

Transcription activator like effectors (TALEs) are natural typeIII effector proteins secreted by numerous species of Xanthomonas to modulate gene expression in host plants and to facilitate bacterial colonization and survival. Recent studies of TALEs have revealed an elegant code linking the repetitive region of TALEs with their target DNA-binding site (Boch et al., Science 2009; Moscou et al., Science 2009). Common among the entire family of TALEs is a highly conserved and repetitive region within the middle of the protein, consisting of tandem repeats of mostly 33 or 34 amino acid segments....
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A tale of TAL effectors | Broad Institute of MIT and Harvard

Haley Bridger, February 8th, 2011 http://www.broadinstitute.org/blog/tale-tal-effectors Species of Xanthomonas bacteria cause blight in many types of plants, including plum and cherry plants. These bacteria use TAL effectors as a weapon against their hosts. Image courtesy of University of Georgia Plant Pathology Archive, University of Georgia, Bugwood.org Two years ago, researchers in Germany discovered a new and potentially very powerful biological tool that bacteria have been wielding as a weapon against their plant hosts. By secreting special proteins known as TAL (transcription activator-like)...
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Computer-aided design of biological circuits using TinkerCell.

Bioeng Bugs. 2010 7;1(4):274-281 Authors: Chandran D, Bergmann FT, Sauro HM Synthetic biology is an engineering discipline that builds on modeling practices from systems biology and wet-lab techniques from genetic engineering. As synthetic biology advances, efficient procedures will be developed that will allow a synthetic biologist to design, analyze and build biological networks. In this idealized pipeline, computer-aided design (CAD) is a necessary component. The role of a CAD application would be to allow efficient transition from a general design to a final product. TinkerCell is a design...
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Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits.

Conf Proc IEEE Eng Med Biol Soc. 2010;1:768-74 Authors: Hallinan JS, Misirli G, Wipat A Biological systems are inherently stochastic, a fact which is often ignored when simulating genetic circuits. Synthetic biology aims to design genetic circuits de novo, and cannot therefore afford to ignore the effects of stochastic behavior. Since computational design tools will be essential for large-scale synthetic biology, it is important to develop an understanding of the role of stochasticity in molecular biology, and incorporate this understanding into computational tools for genetic circuit design....
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Synthetic RNA-protein complex shaped like an equilateral triangle.

Nat Nanotechnol. 2011 Feb;6(2):116-20 Authors: Ohno H, Kobayashi T, Kabata R, Endo K, Iwasa T, Yoshimura SH, Takeyasu K, Inoue T, Saito H Synthetic nanostructures consisting of biomacromolecules such as nucleic acids have been constructed using bottom-up approaches. In particular, Watson-Crick base pairing has been used to construct a variety of two- and three-dimensional DNA nanostructures. Here, we show that RNA and the ribosomal protein L7Ae can form a nanostructure shaped like an equilateral triangle that consists of three proteins bound to an RNA scaffold. The construction of the complex...
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Tunable signal processing in synthetic MAP kinase cascades.

Cell. 2011 Jan 7;144(1):119-31 Authors: O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA The flexibility of MAPK cascade responses enables regulation of a vast array of cell fate decisions, but elucidating the mechanisms underlying this plasticity is difficult in endogenous signaling networks. We constructed insulated mammalian MAPK cascades in yeast to explore how intrinsic and extrinsic perturbations affect the flexibility of these synthetic signaling modules. Contrary to biphasic dependence on scaffold concentration, we observe monotonic decreases in signal strength as scaffold concentration...
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Computational design approaches and tools for synthetic biology.

Integr Biol (Camb). 2011 Feb 8;3(2):97-108 Authors: Macdonald JT, Barnes C, Kitney RI, Freemont PS, Stan GB A proliferation of new computational methods and software tools for synthetic biology design has emerged in recent years but the field has not yet reached the stage where the design and construction of novel synthetic biology systems has become routine. To a large degree this is due to the inherent complexity of biological systems. However, advances in biotechnology and our scientific understanding have already enabled a number of significant achievements in this area. A key concept in engineering...
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Isolation of circular yeast artificial chromosomes for synthetic biology and functional genomics studies.

Nat Protoc. 2011 Jan;6(1):89-96 Authors: Noskov VN, Chuang RY, Gibson DG, Leem SH, Larionov V, Kouprina N Circular yeast artificial chromosomes (YACs) provide significant advantages for cloning and manipulating large segments of genomic DNA in Saccharomyces cerevisiae. However, it has been difficult to exploit these advantages, because circular YACs are difficult to isolate and purify. Here we describe a method for purification of large circular YACs that is more reliable compared with previously described protocols. This method has been used to purify YACs up to 600 kb in size. The purified YAC...
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Synthetic biosensing systems.

Int J Biochem Cell Biol. 2010 Nov 23; Authors: Marchisio MA, Rudolf F An essential feature of synthetic biology devices is the conversion of signals from the exterior of the cell into specific cellular events such as the synthesis of a fluorescent protein. In the first synthetic gene circuits, signal transduction was accomplished via inducible or repressible transcription factors. Today, these rather simple transcription networks are the basis for the construction of more sophisticated devices that, for instance, couple artificial gene circuits with cellular pathways to create a biosensing moiety....
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Engineering organisms for industrial fuel production.

Bioeng Bugs. 2010 9;1(5):303-308 Authors: Berry DA Volatile fuel costs, the need to reduce greenhouse gas emissions and fuel security concerns are driving efforts to produce sustainable renewable fuels and chemicals. Petroleum comes from sunlight, CO(2) and water converted via a biological intermediate into fuel over a several million year timescale. It stands to reason that using biology to short-circuit this time cycle offers an attractive alternative-but only with relevant products at or below market prices. The state of the art of biological engineering over the past five years has progressed...
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Opportunities for yeast metabolic engineering: Lessons from synthetic biology.

Biotechnol J. 2011 Feb 16; Authors: Krivoruchko A, Siewers V, Nielsen J Constant progress in genetic engineering has given rise to a number of promising areas of research that facilitated the expansion of industrial biotechnology. The field of metabolic engineering, which utilizes genetic tools to manipulate microbial metabolism to enhance the production of compounds of interest, has had a particularly strong impact by providing new platforms for chemical production. Recent developments in synthetic biology promise to expand the metabolic engineering toolbox further by creating novel biological...
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Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler.

Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler. Mol Biosyst. 2011 Feb 16; Authors: Shao Z, Luo Y, Zhao H We report a synthetic biology strategy for rapid genetic manipulation of natural product biosynthetic pathways. Based on DNA assembler, this method synthesizes the entire expression vector containing the target biosynthetic pathway and the genetic elements required for DNA maintenance and replication in various hosts in a single-step manner through yeast homologous recombination, offering unprecedented flexibility and versatility in pathway...
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