SynBioFromLeukipposInstitute

by
Idili A, Plaxco KW, Vallée-Bélisle A, Ricci F.

"Naturally occurring chemoreceptors almost invariably employ structure-switching mechanisms, an observation that has inspired the use of biomolecular switches in a wide range of artificial technologies in the areas of diagnostics, imaging, and synthetic biology. In one mechanism for generating such behavior, clamp-based switching, binding occurs via the clamp-like embrace of two recognition elements onto a single target molecule. In addition to coupling recognition with a large conformational change, this mechanism offers a second advantage: it improves both affinity and specificity simultaneously. To explore the physics of such switches we have dissected here the thermodynamics of a clamp-switch that recognizes a target DNA sequence through both Watson-Crick base pairing and triplex-forming Hoogsteen interactions. When compared to the equivalent linear DNA probe (which relies solely on Watson-Crick interactions), the extra Hoogsteen interactions in the DNA clamp-switch increase the probe's affinity for its target by ~ 0.29 ± 0.02 kcal/mol/base. The Hoogsteen interactions of the clamp-switch likewise provide, however, an additional specificity check that increases the discrimination efficiency towards a single-base mismatch by 1.2 ± 0.2 kcal/mol. This, in turn, leads to a 10-fold improvement in the width of the "specificity window" of this probe relative to that of the equivalent linear probe. Given these attributes, clamp-switches should be of utility not only for sensing applications but also, in the specific field of DNA nanotechnology, for applications calling for a better control over the building of nanostructures and nano machines."

http://bit.ly/1aIugBb

by
Adrienne Burke

"When synthetic biology pioneer Andrew Hessel wonders aloud what the next killer biotechnology app might be, 74-year-old Stewart Brand quips, “Resurrection.” Considering that Brand, the tech industry and ’60s counterculture legend, is exploring the use of recovered DNA for repopulating the earth with hundreds of thousands of woolly mammoths, millions of passenger pigeons, and other extinguished species, bringing humans back from the dead might not be so far-fetched. Our capabilities in biology and technology are “moving from the impossible to the expensive to the routine,” he says.

Brand, president of the Long Now Foundation, joined Eri Gentry, cofounder of the BioCurious hackerspace in Sunnyvale and a research manager at think-tank Institute for the Future, for a wide ranging conversation about “Life 2.0” at Techonomy 2013, moderated by Andrew Hessel, a distinguished researcher at Autodesk.

Brand is credited with coining the term “personal computer” and his collaborators have included tech industry pioneers Danny Hillis, Douglas Engelbart, and Larry Brilliant. The Whole Earth catalog that he published in the ’70s is now considered by some to have been the print precursor to surfing the web for information, and it captured the interests of the makers of the day. Today, Brand is working with Harvard genomics researcher George Church to rebuild entire genomes of extinct creatures.

Thirty-year-old Gentry has gained acclaim, including a White House Champion of Change award, as a leader of the DIY biology movement that aims, as described by Techonomy in 2011, to democratize access to the tools of modern biology. As visionaries of their respective generations’ maker-movements, Gentry and Brand see eye-to-eye on the transformative potential of technology in the hands of everyman......"

http://onforb.es/18dw9JI

*Changing the conversation*: *Polymers disrupt bacterial communication*

"Artificial materials based on simple synthetic polymers can disrupt the way in which bacteria communicate with each other, a study led by scientists at The University of Nottingham has shown.

 http://bit.ly/1i7sQYq


comment to:

*Bacteria clustering by polymers induces the expression of quorum-sensing-controlled phenotypes*

by
Leong T. Lui,Xuan Xue,Cheng Sui,Alan Brown,David I. Pritchard,Nigel Halliday,Klaus Winzer,Steven M. Howdle,Francisco Fernandez-Trillo,Natalio Krasnogor& Cameron Alexander

"Bacteria deploy a range of chemistries to regulate their behaviour and respond to their environment. Quorum sensing is one method by which bacteria use chemical reactions to modulate pre-infection behaviour such as surface attachment. Polymers that can interfere with bacterial adhesion or the chemical reactions used for quorum sensing are therefore a potential means to control bacterial population responses. Here, we report how polymeric ‘bacteria sequestrants’, designed to bind to bacteria through electrostatic interactions and therefore inhibit bacterial adhesion to surfaces, induce the expression of quorum-sensing-controlled phenotypes as a consequence of cell clustering. A combination of polymer and analytical chemistry, biological assays and computational modelling has been used to characterize the feedback between bacteria clustering and quorum sensing signalling. We have also derived design principles and chemical strategies for controlling bacterial behaviour at the population level."

http://bit.ly/1anX7On

http://bit.ly/17jRzRF

by
Steven Cranford, Markus J Buehler

"Materiomics is an emerging field of science that provides a basis for multiscale material system characterization, inspired in part by natural, for example, protein-based materials. Here we outline the scope and explain the motivation of the field of materiomics, as well as demonstrate the benefits of a materiomic approach in the understanding of biological and natural materials as well as in the design of de novo materials. We discuss recent studies that exemplify the impact of materiomics – discovering Nature’s complexity through a materials science approach that merges concepts of material and structure throughout all scales and incorporates feedback loops that facilitate sensing and resulting structural changes at multiple scales. The development and application of materiomics is illustrated for the specific case of protein-based materials, which constitute the building blocks of a variety of biological systems such as tendon, bone, skin, spider silk, cells, and tissue, as well as natural composite material systems (a combination of protein-based and inorganic constituents) such as nacre and mollusk shells, and other natural multiscale systems such as cellulose-based plant and wood materials. An important trait of these materials is that they display distinctive hierarchical structures across multiple scales, where molecular details are exhibited in macroscale mechanical responses. Protein materials are intriguing examples of materials that balance multiple tasks, representing some of the most sustainable material solutions that integrate structure and function despite severe limitations in the quality and quantity of material building blocks. However, up until now, our attempts to analyze and replicate Nature’s materials have been hindered by our lack of fundamental understanding of these materials’ intricate hierarchical structures, scale-bridging mechanisms, and complex material components that bestow protein-based materials their unique properties. Recent advances in analytical tools and experimental methods allow a holistic view of such a hierarchical biological material system. The integration of these approaches and amalgamation of material properties at all scale levels to develop a complete description of a material system falls within the emerging field of materiomics. Materiomics is the result of the convergence of engineering and materials science with experimental and computational biology in the context of natural and synthetic materials. Through materiomics, fundamental advances in our understanding of structure–property–process relations of biological systems contribute to the mechanistic understanding of certain diseases and facilitate the development of novel biological, biologically inspired, and completely synthetic materials for applications in medicine (biomaterials), nanotechnology, and engineering."


http://bit.ly/1cJ1J61
#synbio

by
Christina Agapakis

"I’ve been at iGEM (an undergraduate engineering competition in synthetic biology) this weekend learning about all the amazing bioengineering projects that students from around the world have been building. I’ll be writing more about many of these projects soon, but I wanted to highlight the work of one team on issues of gender diversity in synthetic biology. The Paris Bettencourt team performed a detailed study of gender diversity in synthetic biology and in iGEM, and I asked team member Aude Bernheim some question about the project:

 http://bit.ly/193g6d6

by
Iyer S, Karig DK, Norred SE, Simpson ML, Doktycz MJ.

"Engineered gene circuits offer an opportunity to harness biological systems for biotechnological and biomedical applications. However, reliance on native host promoters for the construction of circuit elements, such as logic gates, can make the implementation of predictable, independently functioning circuits difficult. In contrast, T7 promoters offer a simple orthogonal expression system for use in a variety of cellular backgrounds and even in cell-free systems. Here we develop a T7 promoter system that can be regulated by two different transcriptional repressors for the construction of a logic gate that functions in cells and in cell-free systems. We first present LacI repressible T7lacO promoters that are regulated from a distal lac operator site for repression. We next explore the positioning of a tet operator site within the T7lacO framework to create T7 promoters that respond to tet and lac repressors and realize an IMPLIES gate. Finally, we demonstrate that these dual input sensitive promoters function in an E. coli cell-free protein expression system. Our results expand the utility of T7 promoters in cell based as well as cell-free synthetic biology applications."

 http://bit.ly/18b3KQJ