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Technology has always ridden far out ahead of the laws that govern it. As the pace accelerates, that gap may widen. The US Patent Office issued the first patent on a gene thirty years ago.
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byOliver Purcell, Bonny Jain, Jonathan R. Karr, Markus W. Covert, and Timothy K. Lu"Despite rapid advances over the last decade, synthetic biology lacks the predictive tools needed to enable rational design. Unlike established engineering disciplines, the engineering of synthetic gene circuits still relies heavily on experimental trial-and-error, a time-consuming and inefficient process that slows down the biological design cycle. This reliance on experimental tuning is because current modeling approaches are unable to make reliable predictions about the in vivo behavior of synthetic circuits. A major reason for this lack of predictability is that current models view circuits in isolation, ignoring the vast number of complex cellular processes that impinge on the dynamics of the synthetic circuit and vice versa. To address this problem, we present a modeling approach for the design of synthetic circuits in the context of cellular networks. Using the recently published whole-cell model of Mycoplasma genitalium, we examined the effect of adding genes into the host genome. We also investigated how codon usage correlates with gene expression and find agreement with existing experimental results. Finally, we successfully implemented a synthetic Goodwin oscillator in the whole-cell model. We provide an updated software framework for the whole-cell model that lays the foundation for the integration of whole- cell models with synthetic gene circuit models. This software framework is made freely available to the community to enable future extensions. We envision that this approach will be critical to transforming the field of synthetic biology into a rational and predictive engineering discipline...." http://stanford.io/14fdqc6
As they grapple with increasingly large data sets, biologists and computer scientists uncork new bottlenecks.
*Biology: The big challenges of big data* byVivien Marx"Biologists are joining the big-data club. With the advent of high-throughput genomics, life scientists are starting to grapple with massive data sets, encountering challenges with handling, processing and moving information that were once the domain of astronomers and high-energy physicists1.
PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
byTakahashi MK, Lucks JB."Antisense RNA transcription attenuators are a key component of the synthetic biology toolbox, with their ability to serve as building blocks for both signal integration logic circuits and transcriptional cascades. However, a central challenge to building more sophisticated RNA genetic circuitry is creating larger families of orthogonal attenuators that function independently of each other. Here, we overcome this challenge by developing a modular strategy to create chimeric fusions between the engineered transcriptional attenuator from plasmid pT181 and natural antisense RNA translational regulators. Using in vivo gene expression assays in Escherichia coli, we demonstrate our ability to create chimeric attenuators by fusing sequences from five different translational regulators. Mutagenesis of these functional attenuators allowed us to create a total of 11 new chimeric attenutaors. A comprehensive orthogonality test of these culminated in a 7 × 7 matrix of mutually orthogonal regulators. A comparison between all chimeras tested led to design principles that will facilitate further engineering of orthogonal RNA transcription regulators, and may help elucidate general principles of non-coding RNA regulation. We anticipate that our strategy will accelerate the development of even larger families of orthogonal RNA transcription regulators, and thus create breakthroughs in our ability to construct increasingly sophisticated RNA genetic circuitry."http://bit.ly/179dOyD
by+David Bikard Wenyan Jiang, Poulami Samai, Ann Hochschild, Feng Zhang and Luciano A. Marraffini"The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease that participates in the CRISPR-Cas immune defense against prokaryotic viruses. We describe the use of a Cas9 nuclease mutant that retains DNA-binding activity and can be engineered as a programmable transcription repressor by preventing the binding of the RNA polymerase (RNAP) to promoter sequences or as a transcription terminator by blocking the running RNAP. In addition, a fusion between the omega subunit of the RNAP and a Cas9 nuclease mutant directed to bind upstream promoter regions can achieve programmable transcription activation. The simple and efficient modulation of gene expression achieved by this technology is a useful asset for the study of gene networks and for the development of synthetic biology and biotechnological applications.>>"http://bit.ly/16k79xv
This isn't quite "genome engineering," but could readily fall into the category of "epigenome engineering", which is of particular interest to anyone looking into the basis of obesity, for example, or any other epi-genetic contidition. Such conditions are established by the environment, some duing gestation, some by early or recent exposure to dietary or other environmental factors.
*Supreme Court Decision Opens the Doors to A Boom in Synthetic Biology* byMorgan Clendaniel"Today’s Supreme Court ruling on the patenting of human genes was a boost to the field of synthetic biology. While human genes cannot be directly patented, the Court found, so-called complementary DNA can. This is DNA that is synthesized from the rNA in a genetic template and then cloned. The Court found that while naturally occurring DNA is not a human creation, "the lab technician unquestionably creates something new when cDNA is made. "
byJEFFREY MARLOW"For millennia, people have gone out of their way to change the biological world around them. We’ve killed threatening species, domesticated others, and manipulated the habitats of still others to make food production and basic survival an easier undertaking. So the notion that our tinkering with nature is a fundamental departure from a past Eden in which we were “a part of nature” is a false dichotomy: every action we take – and some have been more intentional than others – contributes to a changing world.
By Christina Agapakis
DIYBio Hangout: Wed 12th June 11am PDT http://bit.ly/12DXswc
By Christina Agapakis *Bacteria are single celled organisms that can do amazing things in multicellular groups, with complex coordinated behaviors emerging from the interaction of genetic networks, chemical environments, and the physics of cell growth. Last year I wrote about the work of Tim Rudge and Fernan Federici and their incredible images of bacterial growth patterns. Their paper, with colleagues from the Haseloff Lab at the University of Cambridge, was recently published in ACS Synthetic Biology, showing how complex fractal patterns in colonies of E. coli emerge simply from the physical interactions of rod shaped cells.In this experiment, E. coli cells are labelled with two colors of fluorescent protein (they are otherwise genetically identical) and seeded at low density onto a surface. As they grow and divide, the rod shaped cells begin to bump into each other, creating jagged boundaries between the two fluorescent populations. These jagged lines are fractal, self-similar at many scales. Using their CellModeller program, the team found that they could accurately model this fractal behavior by including only physical parameters like viscous drag, cell shape, and growth rate, rather than biological properties like cell-cell communication or chemotaxis. Indeed, when they used E. coli mutants that were spherical instead of rod-shaped, the fractal pattern disappeared..."http://bit.ly/ZFKtWN
SLAC and Stanford researchers have developed a new, printing process for organic thin-film electronics that results in films of strikingly higher quality.
Printing innovations provide tenfold improvement in organic electronics http://bit.ly/12d2PRx
byDaniel E. Agnew, Brian F. Pfleger"Constructing polycistronic operons is an advantageous strategy for coordinating the expression of multiple genes in a prokaryotic host. Unfortunately, a basic construct consisting of an inducible promoter and genes cloned in series does not generally lead to optimal results. Here, a combinatorial approach for tuning relative gene expression in operons is presented. The method constructs libraries of post-transcriptional regulatory elements that can be cloned into the noncoding sequence between genes. Libraries can be screened to identify sequences that optimize expression of metabolic pathways, multisubunit proteins, or other situations where precise stoichiometric ratios of proteins are desired."http://bit.ly/ZZjKXx
byHua Jiang , Sayed Ahmad Salehi , Marc D. Riedel , and Keshab K. Parhi"We present a methodology for implementing discrete-time signal processing operations, such as filtering, with molecular reactions. The reactions produce time-varying output quantities of molecules as a function of time-varying input quantities according to a functional specification. This computation is robust and independent of the reaction rates, provided that the rate constants fall within coarse categories. We describe two approaches: one entails synchronization with a clock signal, implemented through sustained chemical oscillations; the other is “self-timed” or asynchronous. We illustrate the methodology by synthesizing a simple moving-average filter, a biquad filter, and a Fast Fourier Transform (FFT). Abstract molecular reactions for these filters and transforms are translated into DNA strand displacement reactions. The computation is validated through mass-action simulations of the DNA kinetics. Although a proof of concept for the time being, molecular filters and transforms have potential applications in fields such as biochemical sensing and drug delivery."http://bit.ly/17V03D3
byDANIELA HERNANDEZ"The U.S. Supreme Court’s unanimous ruling that naturally occurring genes can’t be patented looks, on the surface, like terrible news for biotech companies. It would appear to strike down thousands of patents claiming intellectual property rights over isolated genetic sequences—the very DNA patents that anchor countless business plans.
Science ministers from the G8 group of the world’s richest countries have jointly endorsed the need to increase access to publicly-funded research.
G8 science ministers endorse open access http://bit.ly/11lJmcJ
Synthetic Biology Lead Technologist Dr Belinda Clarke describes the role of the Technology Strategy Board in the development of this key field with Editor Amy Caddick...
byGuillermo Rodrigo and Alfonso Jaramillo"Synthetic regulatory networks with prescribed functions are engineered by assembling a reduced set of functional elements. We could also assemble them computationally if the mathematical models of those functional elements were predictive enough in different genetic contexts. Only after achieving this will we have libraries of models of biological parts able to provide predictive dynamical behaviors for most circuits constructed with them. We thus need tools that can automatically explore different genetic contexts, in addition to being able to use such libraries to design novel circuits with targeted dynamics. We have implemented a new tool, AutoBioCAD, aimed at the automated design of gene regulatory circuits. AutoBioCAD loads a library of models of genetic elements and implements evolutionary design strategies to produce (i) nucleotide sequences encoding circuits with targeted dynamics that can then be tested experimentally and (ii) circuit models for testing regulation principles in natural systems, providing a new tool for synthetic biology. AutoBioCAD can be used to model and design genetic circuits with dynamic behavior, thanks to the incorporation of stochastic effects, robustness, qualitative dynamics, multiobjective optimization, or degenerate nucleotide sequences, all facilitating the link with biological part/circuit engineering."http://bit.ly/160SRkS
Living Factories: Engineering Cells to Manufacture Molecules
Video: Living Factories: Engineering Cells to Manufacture Molecules http://bit.ly/11cCz8t
byGi Na Lee and Jonguk Na "Synthetic biology has recently been at the center of the world’s attention as a new scientific and engineering discipline. It allows us to design and construct finely controllable metabolic and regulatory pathways, circuits, and networks, as well as create new enzymes, pathways, and even whole cells. With this great power of synthetic biology, we can develop new organisms that can efficiently produce new drugs to benefit human healthcare and superperforming microorganisms capable of producing chemicals, fuels, and materials from renewable biomass, without the use of fossil oil. Based on several successful examples reported, this commentary aims at peeking into the potential of synthetic biology."http://bit.ly/18g0Pb4
Provided by American Chemical Society
Craig Venter, one of the first scientists to sequence the human genome, spoke to WSJ at the Singularity University conference.
*Craig Venter on Synthetic Life, Genome Sequencing*Video"Craig Venter, one of the first scientists to sequence the human genome, spoke to WSJ at the Singularity University conference."http://on.wsj.com/13V1egq
*The exhibition “Yours Synthetically” is all about the thematic topic of synthetic biology* by MARTIN HIESLMAIR"Mr. Gardiner, as we are doing this interview you are collecting artistic works for the next exhibition at the Ars Electronica Center with the English title called “Yours Synthetically” that deals with synthetic biology. Why is this topic so relevant for us nowadays?
'From August 1, 2013, the new exhibition “Yours Synthetically” is all about the thematic topic of synthetic biology. Matthew Gardiner has put together the artistic works.'