SynBioFromLeukipposInstitute

by

Jain T, Roodbeen R, Reeler NE, Vosch T, Jensen KJ, Bjørnholm T, Nørgaard K.

"We report two novel approaches for fabricating self-assembled chains of end-to-end linked Au nanorods separated by a nanogap. In one approach, bi-functional cysteine end-capped oligopeptides of different lengths are used as the linking agent. The widths of the produced nanogaps scale with the length and tertiary structure of the peptide linker. Functionalized oligopeptides containing an acetylene group are also employed as a linker, and the functional group is uniquely identified using surface-enhanced Raman spectroscopy. The development of an oligopeptide-linking platform is motivated by the ease of synthesis and high modularity of peptides; these features enable the possibility to integrate diverse functionality into molecular nanogap junctions - synthesized in water. The stepwise nanochain formation is followed via the evolution of the longitudinal plasmon absorption band in combination with transmission electron microscopy. The reaction rate and extent is tuned by controlling the concentration of the stabilizing CTAB surfactant in the solution. At very low surfactant concentrations, spontaneous end-to-end linking of the Au nanorods is observed even in the absence of linking peptide. The assembled AuNRs may act as next-generation electrodes in a platform for molecular electronics and synthetic biology."

Interview by Caitlin Sedwick

"Pamela Silver is a strong believer in the potential of synthetic biology and is a leader in this young and rapidly developing field (1, 2). Although she's now interested in designing novel biological systems, she began as a more conventional scientist, coming to the discipline after forging a successful career studying nuclear (3, 4) and RNA (5) biology. We called her at her office at Harvard's Department of Systems Biology to discuss how she arrived at this new frontier and what she sees coming up on her horizon......"

Review by

Alla G Gagarinova and Andrew Emili

"Bacteria are diverse and abundant, playing key roles in human health and disease, the environment, and biotechnology. Despite progress in genome sequencing and bioengineering, much remains unknown about the functional organization of prokaryotes. For instance, roughly a third of the protein-coding genes of the best-studied model bacterium, Escherichia coli, currently lack experimental annotations. Systems-level experimental approaches for investigating the functional associations of bacterial genes and genetic structures are essential for defining the fundamental molecular biology of microbes, preventing the spread of antibacterial resistance in the clinic, and driving the development of future biotechnological applications. This review highlights recently introduced large-scale genetic manipulation and screening procedures for the systematic exploration of bacterial gene functions, molecular relationships, and the global organization of bacteria at the gene, pathway, and genome levels."

by

Li-Qun Gu, Brandon Ritzo & Yong Wang

http://www.nature.com/nnano/journal/v7/n4/full/nnano.2012.48.html?WT.ec_id=NNANO-201204

"Chemically modifying solid-state nanopores with a single nitrilotriacetic acid receptor allows the reversible detection of single proteins."

by Joyce Tait & David Castle

http://bit.ly/HpoqtJ

"Contrary to the opinion of Genya Dana and colleagues (Nature 483, 29; 2012), the greater sophistication of modified microbes created by synthetic biology could make them less, not more, difficult to regulate, manage and monitor than their naturally occurring counterparts.

Several routes could lead to a hypothetical disaster scenario, in which artificially produced microorganisms spread unchecked in the environment (see go.nature.com/pncgxs). But we need to take into account that some of these paths would be favoured over others, and that ecological and other interactions might attenuate or amplify those different probabilities. Synthetic biology could then be used to engineer environmental safety into these organisms."

by Stögbauer T, Windhager L, Zimmer R, Rädler JO.

"Cell-free in vitro expression is increasingly important for high-throughput expression screening, high yield protein production and synthetic biology applications. Yet its potential for quantitative investigation of gene expression and regulatory circuits is limited by the availability of data on composition, kinetic rate constants and standardized computational tools for modeling. Here we report on calibration measurements and mathematical modeling of a reconstituted in vitro expression system. We measured a series of GFP expression and mRNA transcription time courses under various initial conditions and established the translation step as the bottle neck of in vitro protein synthesis. Cell-free translation was observed to expire after 3 h independent of initial template DNA concentration. We developed a minimalistic rate equation model and optimized its parameters by performing a concurrent fit to measured time courses. The model predicts the dependence of protein yield not only on template DNA concentration, but also on experimental timing and hence is a valuable tool to optimize yield strategies."

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