SynBioFromLeukipposInstitute

by

Levin A, Lis M, Ponty Y, O'Donnell CW, Devadas S, Berger B, Waldispühl J.

"The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign, a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign."
http://bit.ly/OMhREn

by

Mario Juhas, Leo Eberl, George M. Church

"Essential genes are absolutely required for the survival of any living entity. Investigation of essential genes is therefore expected to advance tremendously our understanding of the universal principles of life. Determination of a minimal set of essential genes needed to sustain life also plays an important role in the emerging field of synthetic biology, whose goals include creation of a stringently controlled minimal cell with predesigned phenotypic traits. In addition, due to their indispensability for survival of bacteria, genes encoding essential cellular functions have great potential in medicine as promising targets for the development of novel antimicrobials. Here, we review recent advances in the investigation of essential genes, with emphasis on the practical applications in medicine and synthetic biology."

by

Natalie de Souza

A great comment to this Cell paper: Karr, J.R. et al. A whole-cell computational model predicts phenotype from genotype. Cell 150, 389–401 (2012).

"If you can build something from scratch, it follows that you understand how its parts can combine to produce the whole. This is the idea that underlies attempts to simulate cells with a computer. In recently published work, Markus Covert and colleagues at Stanford University have generated a whole-cell model of the human pathogen Mycoplasma genitalium in which they simulate the function of all of its genes.

Mycoplasma has only 525 genes, most of which have homologs that have been studied in other organisms even if some Mycoplasma genes have not been studied directly, Covert says, explaining his choice of organism. “We were guided very much by the Human Genome Project in this, which is to say to start with the simplest organism.” Also, Mycoplasma can be cultured in the laboratory, which Covert considered important as he wished to combine theoretical and experimental work, and Mycoplasma is the first organism to have had its chromosome synthesized de novo.

Using data gleaned from hundreds to thousands of published papers, on Mycoplasma as well as on Escherichia coli and other bacteria, the researchers set out to put the parts back together in the computer. They broke the cell's overall functions down into 28 separate functional modules describing different subprocesses—RNA decay, metabolism or DNA replication, for instance—and modeled each of these separately based on the information available about that subprocess in the literature...."

http://bit.ly/TbBU3j

*SynBioBeta*

Nov 14th at Orrick, Menlo Park

An event that brings together synthetic biology startups, established players, bioengineers, investors
and scientists to meet, partner and hear about the latest advances in the industry.

http://bit.ly/OJsVR0

The art of trans-boundary governance: the case of synthetic biology

by
Joy Y. Zhang

"Synthetic biology raises few, if any, social concerns that are distinctively new. Similar to many other convergent technologies, synthetic biology’s interface across various scientific communities and interests groups presents an incessant challenge to political and conceptual boundaries. However, the scale and intensity of these interfaces seem to necessitate a reflection over how corresponding governance capacities can be developed. This paper argues that, in addition to existing regulatory approaches, such capacities may be gained through the art of trans-boundary governance, which is not only attentive to the crossing and erosion of particular boundaries but also adept in keeping up with the dynamics among evolving networks of actors."

http://bit.ly/S6NWvO

by

Djordjevic M, Djordjevic M.
Source

"A recently emerging discipline of synthetic biology has the aim of constructing new biosynthetic pathways with useful biological functions. A major application of these pathways is generating a large amount of the desired product. However, toxicity due to the possible presence of toxic precursors is one of the main problems for such production. We consider here the problem of generating a large amount of product from a potentially toxic substrate. To address this, we propose a simple biosynthetic pathway, which can be induced in order to produce a large number of the product molecules, by keeping the substrate amount at low levels. Surprisingly, we show that the large product generation crucially depends on fast non-specific degradation of the substrate molecules. We derive an optimal induction strategy, which allows as much as three orders of magnitude increase in the product amount through biologically realistic parameter values. We point to a recently discovered bacterial immune system (CRISPR/Cas in E. coli) as a putative example of the pathway analysed here. We also argue that the scheme proposed here can be used not only as a stand-alone pathway, but also as a strategy to produce a large amount of the desired molecules with small perturbations of endogenous biosynthetic pathways."
http://1.usa.gov/QLkpWW

By

Glenn L. Butterfossa, Barney Yoob, Jonathan N. Jaworskic, Ilya Chornyd, Ken A. Dille, Ronald N. Zuckermannc, Richard Bonneaua, Kent Kirshenbaumb, and Vincent A. Voelzf

"Peptoid molecules are biomimetic oligomers that can fold into unique three-dimensional structures. As part of an effort to advance computational design of folded oligomers, we present blind-structure predictions for three peptoid sequences using a combination of Replica Exchange Molecular Dynamics (REMD) simulation and Quantum Mechanical refinement. We correctly predicted the structure of a N-aryl peptoid trimer to within 0.2 Å rmsd-backbone and a cyclic peptoid nonamer to an accuracy of 1.0 Å rmsd-backbone. X-ray crystallographic structures are presented for a linear N-alkyl peptoid trimer and for the cyclic peptoid nonamer. The peptoid macrocycle structure features a combination of cis and trans backbone amides, significant nonplanarity of the amide bonds, and a unique “basket” arrangement of (S)-N(1-phenylethyl) side chains encompassing a bound ethanol molecule. REMD simulations of the peptoid trimers reveal that well folded peptoids can exhibit funnel-like conformational free energy landscapes similar to those for ordered polypeptides. These results indicate that physical modeling can successfully perform de novo structure prediction for small peptoid molecules."

http://bit.ly/OOsc2U

by

Yamashita K, Tanaka T, Furuta H, Ikawa Y.

"TectoRNA, an artificial RNA with self-assembling ability, has been employed as a structural platform for RNA nanotechnology and RNA synthetic biology. In this study, tectoRNA was applied as a specific template for chemical peptide ligation. On the basis of a self-assembling tectoRNA, we designed and constructed a template RNA that facilitates peptide ligation depending on controlled dimer formation. Two RNA-binding peptides were recognized by two peptide-binding RNA motifs embedded in the template RNA, and chemical ligation was promoted because of the entropic effect of Mg(2+) -dependent dimerization. In a series of biochemical analyses, we determined the relationship between the structures of the tectoRNA-based templates and the extent of acceleration in peptide ligation."

http://1.usa.gov/TwhvBU

*Computational design of genomic transcriptional networks with adaptation to varying environments*

by
Carrera J, Elena SF, Jaramillo A.

"Transcriptional profiling has been widely used as a tool for unveiling the coregulations of genes in response to genetic and environmental perturbations. These coregulations have been used, in a few instances, to infer global transcriptional regulatory models. Here, using the large amount of transcriptomic information available for the bacterium Escherichia coli, we seek to understand the design principles determining the regulation of its transcriptome. Combining transcriptomic and signaling data, we develop an evolutionary computational procedure that allows obtaining alternative genomic transcriptional regulatory network (GTRN) that still maintains its adaptability to dynamic environments. We apply our methodology to an E. coli GTRN and show that it could be rewired to simpler transcriptional regulatory structures. These rewired GTRNs still maintain the global physiological response to fluctuating environments. Rewired GTRNs contain 73% fewer regulated operons. Genes with similar functions and coordinated patterns of expression across environments are clustered into longer regulated operons. These synthetic GTRNs are more sensitive and show a more robust response to challenging environments. This result illustrates that the natural configuration of E. coli GTRN does not necessarily result from selection for robustness to environmental perturbations, but that evolutionary contingencies may have been important as well. We also discuss the limitations of our methodology in the context of the demand theory. Our procedure will be useful as a novel way to analyze global transcription regulation networks and in synthetic biology for the de novo design of genomes."

http://1.usa.gov/TwfVAa

http://bit.ly/QgWGfl

by

Ruths T, Nakhleh L.

"The amount of transcription factor binding sites (TFBS) in an organism's genome positively correlates with the complexity of the regulatory network of the organism. However, the manner by which TFBS arise and accumulate in genomes and the effects of regulatory network complexity on the organism's fitness are far from being known. The availability of TFBS data from many organisms provides an opportunity to explore these issues, particularly from an evolutionary perspective.
RESULTS:
We analyzed TFBS data from five model organisms - E. coli K12, S. cerevisiae, C. elegans, D. melanogaster, A. thaliana - and found a positive correlation between the amount of non-coding DNA (ncDNA) in the organism's genome and regulatory complexity. Based on this finding, we hypothesize that the amount of ncDNA, combined with the population size, can explain the patterns of regulatory complexity across organisms. To test this hypothesis, we devised a genome-based regulatory pathway model and subjected it to the forces of evolution through population genetic simulations. The results support our hypothesis, showing neutral evolutionary forces alone can explain TFBS patterns, and that selection on the regulatory network function does not alter this finding.
CONCLUSIONS:
The cis-regulome is not a clean functional network crafted by adaptive forces alone, but instead a data source filled with the noise of non-adaptive forces. From a regulatory perspective, this evolutionary noise manifests as complexity on both the binding site and pathway level, which has significant implications on many directions in microbiology, genetics, and synthetic biology."

http://1.usa.gov/UjqZ5N

http://bit.ly/PBZ1n0

by

Matosevic S

"Microfluidic technology - the manipulation of fluids at micrometer scales - has revolutionized many areas of synthetic biology. The bottom-up synthesis of "minimal" cell models has traditionally suffered from poor control of assembly conditions. Giant unilamellar vesicles (GUVs) are good models of living cells on account of their size and unilamellar membrane structure. In recent years, a number of microfluidic approaches for constructing GUVs has emerged. These provide control over traditionally elusive parameters of vesicular structure, such as size, lamellarity, membrane composition, and internal contents. They also address sophisticated cellular functions such as division and protein synthesis. Microfluidic techniques for GUV synthesis can broadly be categorized as continuous-flow based approaches and droplet-based approaches. This review presents the state-of-the-art of microfluidic technology, a robust platform for recapitulating complex cellular structure and function in synthetic models of biological cells."
http://1.usa.gov/QUxBmL

by

Deans TL, Singh A, Gibson M, Elisseeff JH.

"Combining synthetic biology and materials science will enable more advanced studies of cellular regulatory processes, in addition to facilitating therapeutic applications of engineered gene networks. One approach is to couple genetic inducers into biomaterials, thereby generating 3D microenvironments that are capable of controlling intrinsic and extrinsic cellular events. Here, we have engineered biomaterials to present the genetic inducer, IPTG, with different modes of activating genetic circuits in vitro and in vivo. Gene circuits were activated in materials with IPTG embedded within the scaffold walls or chemically linked to the matrix. In addition, systemic applications of IPTG were used to induce genetic circuits in cells encapsulated into materials and implanted in vivo. The flexibility of modifying biomaterials with genetic inducers allows for patterned placement of these inducers that can be used to generate distinct patterns of gene expression. Together, these genetically interactive materials can be used to characterize genetic circuits in environments that more closely mimic cells' natural 3D settings, to better explore complex cell-matrix and cell-cell interactions, and to facilitate therapeutic applications of synthetic biology."

http://1.usa.gov/OymDXL