*Yikes! Three Skin-Crawling Dishes That Combine Fine Dining and Synthetic Biology*
by KYLE VANHEMERT
"Today, with fine dining, the best and the most bizarre are often one in the same. Beef Wellington might’ve been an exciting order if you were an Earl on the eve of the Boxer Rebellion, but if you want to be on the cutting edge of culinary thrills today, get ready to slurp on a flower-infused octopus lollipop. Of course, the rise of molecular gastronomy hasn’t just given us a plethora of weird new eats; it’s also about giving diners weird new eating experiences. And where do we look as we try to dream up the ever-stranger eating experiences of the near-future? For Minsu Kim, the answer is obvious: synthetic biology.
Kim, a student at the Royal College of the Arts, explored this terrifying convergence of trends in a project called Living Food. Looking at diners’ willingness (eagerness?) to get weird in the context of our advancements in the world of man-made organisms and genetic modification, Kim dreamed up three dishes that behave like living creatures. Depending on your outlook, they’re either the stuff of avant garde foodie dreams or a perfect reason to reboot Fear Factor..."
Improved technique makes it easier to add or delete genes in living cells, with less risk of off-target DNA damage. (comment see below)
*DNA targeting specificity of RNA-guided Cas9 nucleases*
by Patrick D Hsu,David A Scott,Joshua A Weinstein,F Ann Ran,Silvana Konermann,Vineeta Agarwala,Yinqing Li,Eli J Fine,Xuebing Wu,Ophir Shalem,Thomas J Cradick,Luciano A Marraffini,Gang Bao& Feng Zhang
"The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of single-guide RNAs (sgRNAs) to enable genome editing1, 2, 3, 4, 5, 6, 7, 8, 9, 10. Here, we characterize SpCas9 targeting specificity in human cells to inform the selection of target sites and avoid off-target effects. Our study evaluates >700 guide RNA variants and SpCas9-induced indel mutation levels at >100 predicted genomic off-target loci in 293T and 293FT cells. We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. We also show that SpCas9-mediated cleavage is unaffected by DNA methylation and that the dosage of SpCas9 and sgRNA can be titrated to minimize off-target modification. To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses."
*Research update: Genome editing becomes more accurate*
by Anne Trafton
"Earlier this year, MIT researchers developed a way to easily and efficiently edit the genomes of living cells. Now, the researchers have discovered key factors that influence the accuracy of the system, an important step toward making it safer for potential use in humans, says Feng Zhang, leader of the research team.
With this technology, scientists can deliver or disrupt multiple genes at once, raising the possibility of treating human disease by targeting malfunctioning genes. To help with that process, Zhang’s team, led by graduate students Patrick Hsu and David Scott, has now created a computer model that can identify the best genetic sequences to target a given gene. “Using this, you will be able to identify ways to target almost every gene. Within every gene, there are hundreds of locations that can be edited, and this will help researchers narrow down which ones are better than others,” says Zhang, the W.M. Keck Assistant Professor in Biomedical Engineering at MIT and senior author of a paper describing the new model, appearing in the July 21 online edition of Nature Biotechnology. The genome-editing system, known as CRISPR, exploits a protein-RNA complex that bacteria use to defend themselves from infection. The complex includes short RNA sequences bound to an enzyme called Cas9, which slices DNA. These RNA sequences are designed to target specific locations in the genome; when they encounter a match, Cas9 cuts the DNA. This approach can be used either to disrupt the function of a gene or to replace it with a new one. To replace the gene, the researchers must also add a DNA template for the new gene, which would be copied into the genome after the DNA is cut. This technique offers a much faster and more efficient way to create transgenic mice, which are often used to study human disease. Current methods for creating such mice require adding small pieces of DNA to mouse embryonic cells. However, the process is inefficient and time-consuming. With CRISPR, many genes are edited at once, and the entire process can be done in three weeks, says Zhang, who is a core member of the Broad Institute and MIT’s McGovern Institute for Brain Research. The system can also be used to create genetically modified cell lines for lab experiments much more efficiently. Fine-tuning Since Zhang and his colleagues first described the original system in January, more than 2,000 labs around the world have started using the system to generate their own genetically modified cell lines or animals. In the new paper, the researchers describe improvements in both the efficiency and accuracy of gene editing. To modify genes using this system, an RNA “guide strand” complementary to a 20-base-pair sequence of targeted DNA is delivered to cells. After the RNA strand binds to the target DNA, it recruits the Cas9 enzyme, which snips the DNA in the correct location. The researchers discovered they could minimize the chances of the Cas9-RNA complex accidentally cleaving the wrong site by making sure the target sequence is not too similar to other sequences found in the genome. They found that if an off-target sequence differs from the target sequence by three or fewer base pairs, the editing complex will likely also cleave that sequence, which could have deleterious effects for the cell. The team’s new computer model can search any sequence within the mouse or human genome and identify 20-base-pair sequences within that region that have the least overlap with sequences elsewhere in the genome. Another way to improve targeting specificity is by adjusting the dosage of the guide RNA, the researchers found. In general, decreasing the amount of RNA delivered minimizes damage to off-target sites but has a much smaller effect on cleavage of the target sequence. For each sequence, the “sweet spot” with the best balance of high on-target effects and low off-target effects can be calculated, Zhang says. “The real value of this paper is that it does a very comprehensive and systematic analysis to understand the causes of off-target effects. That analysis suggests a lot of possible ways to eliminate or reduce off-target effects,” says Michael Terns, a professor of biochemistry and molecular biology at the University of Georgia who was not part of the research team. Zhang and his colleagues also optimized the structure of the RNA guide needed for efficient activation of Cas9. In the January paper describing the original system, the researchers found that two separate RNA strands working together — one that binds to the target DNA and another that recruits Cas9 — produced better results than when those two strands were fused together before delivery. However, in experiments reported in the new paper, the researchers found that they could boost the efficiency of the fused RNA strand by making the strand longer. These longer RNA guide strands include a hairpin structure that may stabilize the molecules and help them interact with Cas9, Zhang says. Zhang’s team is now working on further improving the specificity of the system, and plans to start generating cell lines and animals that could be used to study how the brain develops and builds neural circuits. By disrupting genes known to be involved in those processes, they can learn more about how they work and how they are impaired in neurological disease. "
"Synthetic biology (SynBio) has tremendous, transformative potential. Like other technologies, it can be used for good or ill. Currently, the structure of the allocation of potential benefits and risks is biased in favor of richer countries. The underlying problem is simple: most risks from SynBio are universal and affect both the rich and the poor with equal force; but benefits from SynBio can be expected to accrue chiefly to the rich. The risk/benefit balance is therefore skewed in a way that may lead to inefficient and unfair decisions. One potential solution is presented in this paper, using the principles that underlie the Health Impact Fund (HIF). The HIF is designed to reward companies based on assessed health impact, no matter where it occurs in the world, so that extending the life of a poor person is as profitable as extending the life of a rich person. This paper considers both the potential benefits and costs of SynBio; examines how the current global pharmaceutical industry is structured; introduces the HIF proposal; and finally explores how the principles underlying the HIF could be used productively with SynBio for global health."
*Stanford e corner: Video: John Melo - Synthetic Biology in Action*
"From an open-source anti-malarial compound to renewable energy resources, Amyris Biotechnologies CEO John Melo explains his enterprise's corporate acts of altruism, as funded by the Gates Foundation. In his words, it's a win-win situation: His organization undertakes innovative science, saves thousands of lives, and conserves natural resources. "
Fancy doing some Synthetic Biology but don't have access to lab or expensive equipments? Don't worry. And even if you're not able to code, again no prob. (RT @dopaminergic13: Gamification of in silico open synthetic biology: a game-changer.
by Bernd Giese, Stefan Koenigstein, Henning Wigger, Jan C. Schmidt, Arnim von Gleich
"The term “synthetic biology” is a popular label of an emerging biotechnological field with strong claims to robustness, modularity, and controlled construction, finally enabling the creation of new organisms. Although the research community is heterogeneous, it advocates a common denominator that seems to define this field: the principles of rational engineering. However, it still remains unclear to what extent rational engineering—rather than “tinkering” or the usage of random based or non-rational processes—actually constitutes the basis for the techniques of synthetic biology. In this article, we present the results of a quantitative bibliometric analysis of the realized extent of rational engineering in synthetic biology. In our analysis, we examine three issues: (1) We evaluate whether work at three levels of synthetic biology (parts, devices, and systems) is consistent with the principles of rational engineering. (2) We estimate the extent of rational engineering in synthetic biology laboratory practice by an evaluation of publications in synthetic biology. (3) We examine the methodological specialization in rational engineering of authors in synthetic biology. Our analysis demonstrates that rational engineering is prevalent in about half of the articles related to synthetic biology. Interestingly, in recent years the relative number of respective publications has decreased. Despite its prominent role among the claims of synthetic biology, rational engineering has not yet entirely replaced biotechnological methods based on “tinkering” and non-rational principles."
"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."
Calviello L, Stano P, Mavelli F, Luisi PL, Marangoni R.
The wet-lab synthesis of the simplest forms of life (minimal cells) is a challenging aspect in modern synthetic biology. Quasi-cellular systems able to produce proteins directly from DNA can be obtained by encapsulating the cell-free transcription/translation system PURESYSTEM™(PS) in liposomes. It is possible to detect the intra-vesicle protein production using DNA encoding for GFP and monitoring the fluorescence emission over time. The entrapment of solutes in small-volume liposomes is a fundamental open problem. Stochastic simulation is a valuable tool in the study of biochemical reaction at nanoscale range. QDC (Quick Direct-Method Controlled), a stochastic simulation software based on the well-known Gillespie's SSA algorithm, was used. A suitable model formally describing the PS reactions network was developed, to predict, from inner species concentrations (very difficult to measure in small-volumes), the resulting fluorescence signal (experimentally observable).RESULTS:Thanks to suitable features specific of QDC, we successfully formalized the dynamical coupling between the transcription and translation processes that occurs in the real PS, thus bypassing the concurrent-only environment of Gillespie's algorithm. Simulations were firstly performed for large liposomes (2.67µm of diameter) entrapping the PS to synthetize GFP. By varying the initial concentrations of the three main classes of molecules involved in the PS (DNA, enzymes, consumables), we were able to stochastically simulate the time-course of GFP-production. The sigmoid fit of the GFP-production curves allowed us to extract three quantitative parameters which are significantly dependent on the various initial states. Then we extended this study for small-volume liposomes (575 nm of diameter), where it is more complex to infer the intra-vesicle composition, due to the expected anomalous entrapment phenomena. We identified almost two extreme states that are forecasted to give rise to significantly different experimental observables.CONCLUSIONS:The present work is the first one describing in the detail the stochastic behavior of the PS. Thanks to our results, an experimental approach is now possible, aimed at recording the GFP production kinetics in very small micro-emulsion droplets or liposomes, and inferring, by using the simulation as a reverse-engineering procedure, the internal solutes distribution, and shed light on the still unknown forces driving the entrapment phenomenon."
BioCurious is proud to be partnering with Syn B Org to bring you "Synthetic Biology for Computer Programmers". "Synthetic Biology for Computer Programmers" is a new course conceptualized and written by Dr.
by Tan C, Saurabh S, Bruchez MP, Schwartz R, Leduc P.Source
The integration of synthetic and cell-free biology has made tremendous strides towards creating artificial cellular nanosystems using concepts from solution-based chemistry, where only the concentrations of reacting species modulate gene expression rates. However, it is known that macromolecular crowding, a key feature in natural cells, can dramatically influence biochemical kinetics via volume exclusion effects, which reduce diffusion rates and enhance binding rates of macromolecules. Here, we demonstrate that macromolecular crowding can increase the robustness of gene expression by integrating synthetic cellular components of biological circuits and artificial cellular nanosystems. Furthermore, we reveal how ubiquitous cellular modules, including genetic components, a negative feedback loop and the size of the crowding molecules can fine-tune gene circuit response to molecular crowding. By bridging a key gap between artificial and living cells, our work has implications for efficient and robust control of both synthetic and natural cellular circuits.
I was asked to give a talk to a group of science and technology educators from two-year colleges around the country this week.
Gerd Moe-Behrens's insight:
*#SynBio Video: Joule Plant Overview*
by Scott Kirsner
"Boston-area companies like Sample6 and Joule are designing bespoke bacteria to do difficult jobs like detecting pathogens in food processing plants, or cranking out ethanol for cars. (This is a field I've been following since 2005, when I wrote about the collegiate Synthetic Biology Competition.) Here's a video about Joule's fuel production facility in New Mexico."
*Biological Signal Processing with a Genetic Toggle Switch *
Patrick Hillenbrand, Georg Fritz, Ulrich Gerland "Complex gene regulation requires responses that depend not only on the current levels of input signals but also on signals received in the past. In digital electronics, logic circuits with this property are referred to as sequential logic, in contrast to the simpler combinatorial logic without such internal memory. In molecular biology, memory is implemented in various forms such as biochemical modification of proteins or multistable gene circuits, but the design of the regulatory interface, which processes the input signals and the memory content, is often not well understood. Here, we explore design constraints for such regulatory interfaces using coarse-grained nonlinear models and stochastic simulations of detailed biochemical reaction networks. We test different designs for biological analogs of the most versatile memory element in digital electronics, the JK-latch. Our analysis shows that simple protein-protein interactions and protein-DNA binding are sufficient, in principle, to implement genetic circuits with the capabilities of a JK-latch. However, it also exposes fundamental limitations to its reliability, due to the fact that biological signal processing is asynchronous, in contrast to most digital electronics systems that feature a central clock to orchestrate the timing of all operations. We describe a seemingly natural way to improve the reliability by invoking the master-slave concept from digital electronics design. This concept could be useful to interpret the design of natural regulatory circuits, and for the design of synthetic biological systems."
"Synthetic biology has the potential to contribute breakthrough innovations to the pursuit of new global health solutions. Wishing to harness the emerging tools of synthetic biology for the goals of global health, in 2011 the Bill & Melinda Gates Foundation put out a call for grant applications to “Apply Synthetic Biology to Global Health Challenges” under its “Grand Challenges Explorations” program. A highly diverse pool of over 700 applications was received. Proposed applications of synthetic biology to global health needs included interventions such as therapeutics, vaccines, and diagnostics, as well as strategies for biomanufacturing, and the design of tools and platforms that could further global health research."
"Many of the synthetic biological devices, pathways and systems that can be engineered are multi-use, in the sense that they could be used both for commercially-important applications and to help meet global health needs. The on-going development of models and simulation tools for assembling component parts into functionally-complex devices and systems will enable successful engineering with much less trial-and-error experimentation and laboratory infrastructure. As illustrations, I draw upon recent examples from my own work and the broader Keasling research group at the University of California Berkeley and the Joint BioEnergy Institute, of which I was formerly a part. By combining multi-use synthetic biology research agendas with advanced computer-aided design tool creation, it may be possible to more rapidly engineer safe and effective synthetic biology technologies that help address a wide range of global health problems." http://bit.ly/14AoPHk
"Expression of heterologous proteins in metabolic engineering endeavors can be detrimental to host cells due to increased usage of cellular resources. Dynamic controls, where protein expression can be triggered on-demand, are effective for the engineering and optimization of bio-catalysts towards robust cell growth and enhanced biochemical productivity. Here, we describe the development and characterization of AND-gate dynamic controllers in Saccharomyces cerevisiae which combine two dynamic control strategies, inducible promoters and sensing-regulation. These dynamic controllers were constructed based on synthetic hybrid promoters. Promoter enhancer sequences were fused to a synthetic GAL1 core promoter containing DNA binding sites for the binding of a repressor that reduced DNA affinity upon interaction with key intermediates in a biochemical pathway. As fatty acids are key intermediates for production of fatty alcohols, fatty acid esters, alkenes and alkanes, which are advanced biofuels, we used the fatty acid responsive FadR repressor and its operator sequence to demonstrate the functionality of the dynamic controllers. We established that the synthetic GAL1 core promoter can be used as a modular promoter part for constructing synthetic hybrid promoters and conferring fatty acid inducibility. We further showed the performance of the AND-gate dynamic controllers, where two inputs (fatty acid and copper presence / phosphate starvation) were required to switch the AND-gate ON. This work provides a convenient platform for constructing AND-gate dynamic controllers, i.e. promoters that combine inducible functionality with regulation of protein expression levels upon detection of key intermediates towards the engineering and optimization of bio-catalytic yeast cells."
"UC Berkeley's top-ranked Bioengineering Department announced the creation of a Synthetic Biology concentration in Bioengineering. The concentration represents one of the few US degree specializations in synthetic biology. It also represents an important step toward SynBERC's strategic educational goal to spawn a national synthetic biology curriculum.
The concentration program was developed in consultation with SynBERC Principal Investigators Adam Arkin and Christopher Anderson, SynBERC Affiliate Investigator +John Dueber and Department Lecturer Terry Johnson, all from UC Berkeley's Bioengineering Department. (In April, Johnson received the 2010 Golden Apple, UC Berkeley 's student award for most outstanding teacher.) The course listing can be found here: http://bioeng.berkeley.edu/program/synbio.php
"Gene expression goes better in tight quarters, especially when other conditions are less than ideal, say researchers.
As the researchers report in an advance online publication in Nature Nanotechnology, these findings may help explain how cells have adapted to the phenomenon of molecular crowding, which has been preserved through evolution.And this understanding may guide synthetic biologists as they develop artificial cells that might someday be used for drug delivery, biofuel production, and biosensors.“These are baby steps we’re taking in learning how to make artificial cells,” says study leader Cheemeng Tan, a postdoctoral fellow in the Lane Center for Computational Biology at Carnegie Mellon University...."
"Synthetic biology aims to build new functional organisms and to rationally re-design existing ones by applying the engineering principle of modularity. Apart from building new life forms to perform technical applications, the approach of synthetic biology is useful to dissect complex biological phenomena into simple and easy to understand synthetic modules. Synthetic gene networks have been successfully implemented in prokaryotes and lower eukaryotes, with recent approaches moving ahead towards the mammalian environment. However, synthetic circuits in higher eukaryotes present a more challenging scenario, since its reliability is compromised because of the strong stochastic nature of transcription. Here, the authors review recent approaches that take advantage of the noisy response of synthetic regulatory circuits to learn key features of the complex machinery that orchestrates transcription in higher eukaryotes. Understanding the causes and consequences of biological noise will allow us to design more reliable mammalian synthetic circuits with revolutionary medical applications."
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