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Gerd Moe-Behrens
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Discussion  - 
 
Programming Surface Chemistry with Engineered Cells

by
Ruihua Zhang, Keith Cameron Heyde, Felicia Yi Xia Scott, Sung-Ho Paek, and Warren Christopher Ruder

"We have developed synthetic gene networks that enable engineered cells to selectively program surface chemistry. E. coli were engineered to upregulate biotin synthase, and therefore biotin synthesis, upon biochemical induction. Additionally, two different functionalized surfaces were developed that utilized binding between biotin and streptavidin to regulate enzyme assembly on programmable surfaces. When combined, the interactions between engineered cells and surfaces demonstrated that synthetic biology can be used to engineer cells that selectively control and modify molecular assembly by exploiting surface chemistry. Our system is highly modular and has the potential to influence fields ranging from tissue engineering to drug development and delivery."

http://bit.ly/1sK44Yi
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Luís Cunha

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The crowdfunding stage for the earthworm genome was launched yesterday and we are looking for donations. Please check our project page. Let’s fund science! This is an open science project!

https://experiment.com/projects/untangling-the-volcanic-earthworm-genome

Any donation will be highly appreciated! No money is taken unless it reaches the funding goal.

We want to tell you a story that is over half a billion years old. The earthworm Pontoscolex corethrurus is an animal that has evolved to live in an extraordinary environment, a volcanic geothermal field in Sao Miguel Island, one of the nine Islands in Azores Archipelago. By sequencing...
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Gerd Moe-Behrens
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Discussion  - 
 
Synthetic biology: Automating genetic circuit design

by
Ross Cloney
"
Synthetic biology aims to take the rational design principles of engineering and apply them to the modification and manipulation of living organisms. This strategy has resulted in the construction of increasingly complex genetic circuits and rewired pathways, although the manual construction of these circuits can often be a time-intensive task with fiddly optimization required...."

http://bit.ly/1XsWpXe
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Gerd Moe-Behrens
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Parallel computation with molecular-motor-propelled agents in nano fabricated networks

by
Dan V. Nicolau,, Mercy Lardc, Till Kortend,, Falco C. M. J. M. van Delftf,, Malin Perssong, Elina Bengtssong, Alf Månssong, Stefan Diezd,e, Heiner Linkec, and Dan V. Nicolauh,

"Significance

Electronic computers are extremely powerful at performing a high number of operations at very high speeds, sequentially. However, they struggle with combinatorial tasks that can be solved faster if many operations are performed in parallel. Here, we present proof-of-concept of a parallel computer by solving the specific instance {2, 5, 9} of a classical nondeterministic-polynomial-time complete (“NP-complete”) problem, the subset sum problem. The computer consists of a specifically designed, nanostructured network explored by a large number of molecular-motor-driven, protein filaments. This system is highly energy efficient, thus avoiding the heating issues limiting electronic computers. We discuss the technical advances necessary to solve larger combinatorial problems than existing computation devices, potentially leading to a new way to tackle difficult mathematical problems.

Abstract
The combinatorial nature of many important mathematical problems, including nondeterministic-polynomial-time (NP)-complete problems, places a severe limitation on the problem size that can be solved with conventional, sequentially operating electronic computers. There have been significant efforts in conceiving parallel-computation approaches in the past, for example: DNA computation, quantum computation, and microfluidics-based computation. However, these approaches have not proven, so far, to be scalable and practical from a fabrication and operational perspective. Here, we report the foundations of an alternative parallel-computation system in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. Exploring the network in a parallel fashion using a large number of independent, molecular-motor-propelled agents then solves the mathematical problem. This approach uses orders of magnitude less energy than conventional computers, thus addressing issues related to power consumption and heat dissipation. We provide a proof-of-concept demonstration of such a device by solving, in a parallel fashion, the small instance {2, 5, 9} of the subset sum problem, which is a benchmark NP-complete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology."

http://bit.ly/1RfbQxC
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Gerd Moe-Behrens
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Discussion  - 
 
Fluorescent biosensors light up high-throughput metabolic engineering

Benjamin Boettner

"Genetically encoded fluorescent biosensors allow researchers to see how products form in real time in microorganisms, and to test billions of candidates at a time

Synthetic biologists are learning to turn microbes and unicellular organisms into highly productive factories by re-engineering their metabolism to produce valued commodities such as fine chemicals, therapeutics and biofuels. To speed up identification of the most efficient producers, researchers at Harvard's Wyss Institute for Biologically Inspired Engineering describe new approaches to this process and demonstrate how genetically encoded fluorescent biosensors can enable the generation and testing of billions of individual variants of a metabolic pathway in record time. The discussion and findings are reported in Trends in Biotechnology and the Proceedings of the National Academy of Sciences (PNAS).

Biotechnologists that tinker with the metabolism of microorganisms to produce valued products look at the engineering process through the lens of the so-called 'design-build-test cycle.' The idea is that multiple iterations of this cycle ultimately allow the identification of combinations of genetic and metabolic elements that produce the highest levels of a desired drug or chemical. Key to the cycle's efficiency, however, is the ability to construct and test the largest number of variants possible; in the end, only a few of these variants will produce the product in industrially attractive amounts.

In the Trends in Biotechnology article, Wyss Institute scientists George Church and Jameson Rogers lay out the current state-of-the-art for designing, building and testing many variants at a time, a methodology that bioengineers call 'multiplexing'. Church is a Wyss Core Faculty member and Professor of Genetics at Harvard Medical School and Rogers, currently with the Boston Consulting Group, performed his work as a Harvard Pierce Fellow and Doctoral Student mentored by Church.

Bioengineers thoroughly understand how metabolic pathways work on the biochemical level and have a plethora of DNA sequences encoding variants of all of the necessary enzymes at their disposal. Deploying these sequences with the help of computational tools and regulating their expression with an ever-growing number of genetic elements, gives them access to an almost infinite pool of design possibilities. Similarly, revolutionary advances in technologies enabling DNA synthesis and manipulation have made the construction of billions of microorganisms, each containing a distinct design variant, a routine process.

"The real bottleneck in achieving high-throughput engineering cycles lies in the testing step. Current technology limits the number of designs scientists can evaluate to hundreds, or maybe even a thousand, different designs per day. Often the assays necessary are painstaking and prone to user error," said Rogers.

Church and Rogers discuss how genetically encoded biosensors can help bioengineers overcome this hurdle. Such biosensors work by coupling the amount of a desired product produced within a microorganism to the expression of an antibiotic resistance gene such that only high producers survive. Alternatively, the expression of a fluorescent protein can be used for high-speed sorting of rare but highly productive candidates from large populations of less productive microbes.

"Now, by having developed both types of genetically encoded biosensors we can close the loop of a fully multiplexed engineering cycle. This enables exploration of design spaces for specific metabolic pathways in much greater breadth and depth. Fluorescent biosensors, in particular, enable a brand new type of pipeline engineering in which we can observe metabolic product levels at all times during the process with extraordinary sensitivity and ability to further manipulate the engineering cycle," said Church.

Earlier work by Church's team at the Wyss Institute already demonstrated that the levels of commercially valuable chemicals produced by bacteria could be raised through several rounds of a design-build-test cycle that employed an antibiotic selection-based biosensor. Now, Church and Rogers report in PNAS the unique advantages that fluorescent biosensors provide to bioengineers.

"Our fluorescent biosensors are built around specialized proteins that directly sense commercially valuable metabolites. These sensor proteins switch on the expression of a fluorescent reporter protein, resulting in cellular brightness that is proportional to the amount of chemical produced within the engineered cells. We can literally watch the biological production of valuable chemicals in real-time as the synthesis occurs and isolate the highest producers out of cultures with billions of candidates," said Rogers, who was named one of Forbes' "30 Under 30" in Science for opening new perspectives in bioengineering.

Using this strategy, the Wyss researchers have established fluorescent biosensors for the production of super-absorbent polymers and plastics like the coveted acrylate from which a range of products is made. In fact, the study established the first engineered pathway able to biologically produce acrylate from common sugar, rather than the previously required petroleum compounds.

"This newly emerging biosensor technology has the potential to transform metabolic engineering in areas ranging from industrial manufacturing to medicine, and it can have a positive impact on our environment by making the production of drugs and chemicals independent from fossil fuels," said Wyss Institute Founding Director Donald Ingber, M.D., Ph.D., who is the Judah Folkman Professor of Vascular Biology at HMS and the Vascular Biology Program at Boston Children's Hospital, as well as Professor of Bioengineering at the Harvard John A. Paulson School of Engineering and Applied Sciences."

http://bit.ly/1TnZiZh
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Gerd Moe-Behrens
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Discussion  - 
 
Biosensors on demand

by
Anonymous

"Biosensors are powerful tools in synthetic biology for engineering metabolic pathways or controlling synthetic and native genetic circuits in bacteria. Scientists have had difficulty developing a method to engineer “designer” biosensor proteins that can precisely sense and report the presence of specific molecules, which has so far limited the number and variety of biosensor designs able to precisely regulate cell metabolism, cell biology, and synthetic gene circuits.
But new research published in Nature Methods ("Engineering an allosteric transcription factor to respond to new ligands") by a team at Harvard’s Wyss Institute for Biologically Inspired Engineering and Harvard Medical School (HMS) has leveraged combination of computational protein design, in vitro synthesis and in vivo testing to establish a first-of-its-kind strategy for identifying custom-tailored biosensors.
"Our original motivation for developing customizable biosensors was to get a life or death feedback loop for metabolic engineering," said George Church, Ph.D., Wyss Institute Core Faculty member, Professor of Genetics at HMS, Professor of Health Sciences and Technology at Harvard and the Massachusetts Institute of Technology (MIT), and the senior author on the study. "This would essentially give us 'Darwinian evolution on steroids', where colonies of bacteria genetically programmed to output a desirable commodity molecule would rapidly become more efficient from generation to generation as only the best metabolic producers will be 'self-identified' for survival."
"This advance represents a powerful new way for us to access the chemical diversity of the biosphere by mining for new pathways to make useful molecules," said Srivatsan Raman, Ph.D., formerly a Postdoctoral Fellow at the Wyss Institute and HMS and currently Assistant Professor of Biochemistry at University of Wisconsin-Madison, who is the corresponding author on the study.
To develop the method, researchers chose as their test case a natural regulatory protein from E. coli called LacI. LacI is an allosteric transcription factor (aTF), which becomes active in response to sensing "inducer" metabolites or molecules in the bacterium’s environment, thereby triggering expression of a downstream gene. Using LacI, the team set out to develop a framework for re-engineering new biosensor variants that would respond to four inducer molecules (lactitol, sucralose, gentiobiose, and fucose) that cannot be metabolized by natural E. coli. Sucralose, for example, is a completely synthetic sugar molecule sold commercially as Splenda®.
To synthesize and identify the custom-made LacI variants for sensing these four new inducers, the team designed a novel workflow incorporating a combinatorial synthesis strategy that relies on computational protein design and the Wyss Institute’s custom DNA synthesis resources to build a variant library of potential new biosensor designs comprising hundreds of thousands of mutated LacI proteins.
Then, to identify the variants with the most specific responses to the four target molecules of interest, the team engineered groups of E. coli bacteria to express green fluorescent protein (GFP) when the desired molecule was detected, thereby making the bacteria fluoresce. Performing high-throughput in vivo screening of the sensor library in the engineered E. coli, the team identified the most effective variants by their high fluorescence, then filtered them out and genetically sequenced them to reveal the DNA profiles and design maps for transforming aTFs into custom-tailored sensors with high specificity.
The results are striking in that an optimized engineered aTF sensor can be identified for sensing any arbitrary molecule using this approach, opening new doors in synthetic biology by putting allosteric proteins in the control of genetic engineers.
"The LacI protein we chose to re-design into a custom biosensor is only one of thousands of different allosteric transcription factors that exist in nature," said Noah Taylor, a graduate researcher at the Wyss Institute who recently finished his Ph.D. in Biological and Biomedical Sciences at HMS, and the first author on the study. "The ability to engineer LacI using nothing more than sequence and structure information suggests we could find tens, hundreds, or even thousands of other biosensors that respond to different molecules."
Biosensors built using this approach provide feedback on how much of a certain metabolite is present inside a cell. Metabolically engineered bacteria can be outfitted with these custom aTFs, enabling them to monitor their own bioproduction of a desired chemical, pharmaceutical or biofuel. This allows sophisticated designs in which the lack of sufficient product could result in the death of an individual cell, eliminating it from the culture. In this way, powerful evolutionary methods can be harnessed for metabolic engineering.
Sensitive detection of metabolites within cells also presents a new paradigm for the way scientists can interrogate single cells. Until now, it has been very challenging to study the metabolic state of a single individual cell. But designer biosensors could be utilized as custom responders to metabolites of interest, giving insight into the metabolic states of live cells in close to real time.
"We are now utilizing the method to find biosensors for a variety of high-value targets, particularly those that can aid in protecting the environment," said Alexander Garruss, co-author on the study, who is a graduate researcher at the Wyss Institute and a Ph.D. candidate in Bioinformatics and Integrative Genomics at HMS.
Beyond measuring metabolites within cells, the combinatorial synthesis approach paves a path forward toward designing countless new and highly specific biological sensors for novel applications such as environmental monitoring, medical diagnostics, bioremediation, and precision gene therapies.
"The team’s ability to engineer custom biosensors for virtually any molecule is another triumph showing the power of synthetic biology, and its ability to generate valuable new tools to advance medicine and protect our environment," said Wyss Institute Founding Director Donald Ingber, M.D., who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and the Vascular Biology Program at Boston Children’s Hospital and Professor of Bioengineering at the Harvard John A. Paulson School of Engineering and Applied Sciences."
http://bit.ly/1PCiEFw


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Gerd Moe-Behrens
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Discussion  - 
 
Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System

by
Mathias Foo, David E. Somers, Pan-Jun Kim

"A wide range of organisms features molecular machines, circadian clocks, which generate endogenous oscillations with ~24 h periodicity and thereby synchronize biological processes to diurnal environmental fluctuations. Recently, it has become clear that plants harbor more complex gene regulatory circuits within the core circadian clocks than other organisms, inspiring a fundamental question: are all these regulatory interactions between clock genes equally crucial for the establishment and maintenance of circadian rhythms? Our mechanistic simulation for Arabidopsis thaliana demonstrates that at least half of the total regulatory interactions must be present to express the circadian molecular profiles observed in wild-type plants. A set of those essential interactions is called herein a kernel of the circadian system. The kernel structure unbiasedly reveals four interlocked negative feedback loops contributing to circadian rhythms, and three feedback loops among them drive the autonomous oscillation itself. Strikingly, the kernel structure, as well as the whole clock circuitry, is overwhelmingly composed of inhibitory, rather than activating, interactions between genes. We found that this tendency underlies plant circadian molecular profiles which often exhibit sharply-shaped, cuspidate waveforms. Through the generation of these cuspidate profiles, inhibitory interactions may facilitate the global coordination of temporally-distant clock events that are markedly peaked at very specific times of day. Our systematic approach resulting in experimentally-testable predictions provides insights into a design principle of biological clockwork, with implications for synthetic biology."

http://bit.ly/1Q9C5VS
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Gerd Moe-Behrens
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DNA nanobots will target cancer cells in the first human trial using a terminally ill patient  

by DANIEL KORN

DNA nanobots will target cancer cells in the first human trial using a terminally ill patient  by DANIEL KORN  "The very mention of “nanobots” can bring up a certain future paranoia in people—undetectable robots under my skin? Thanks, but no thanks. Professor Ido Bachelet of Israel’s Bar-Ilan University confirms that while tiny robots being injected into a human body to fight disease might sound like science fiction, it is in fact very real.  Cancer treatment as we know it is problematic because it targets a large area. Chemo and radiation therapies are like setting off a bomb—they destroy cancerous cells, but in the process also damage the healthy ones surrounding it. This is why these therapies are sometimes as harmful as the cancer itself. Thus, the dilemma with curing cancer is not in finding treatments that can wipe out the cancerous cells, but ones that can do so without creating a bevy of additional medical issues. As Bachelet himself notes in a TEDMED talk: “searching for a safer cancer drug is basically like searching for a gun that kills only bad people.”  This is where nanobots come in—rather than take out every cell in the area they’re distributed to, they’re able to recognize and interact with specific molecules. This means that new drugs don’t even need to be developed; instead, drugs that have already been proven to be effective for cancer treatment but too toxic for regular use can be used in conjunction with nanobots to control said toxicity."  http://bit.ly/1PxdJcL
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Gerd Moe-Behrens
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Discussion  - 
 
Synthetic biology: applying biological circuits beyond novel therapies

by
Anton Dobrin,  Pratik Saxena and    Martin Fussenegger

"Synthetic biology, an engineering, circuit-driven approach to biology, has developed whole new classes of therapeutics. Unfortunately, these advances have thus far been undercapitalized upon by basic researchers. As discussed herein, using synthetic circuits, one can undertake exhaustive investigations of the endogenous circuitry found in nature, develop novel detectors and better temporally and spatially controlled inducers. One could detect changes in DNA, RNA, protein or even transient signaling events, in cell-based systems, in live mice, and in humans. Synthetic biology has also developed inducible systems that can be induced chemically, optically or using radio waves. This induction has been re-wired to lead to changes in gene expression, RNA stability and splicing, protein stability and splicing, and signaling via endogenous pathways. Beyond simple detectors and inducible systems, one can combine these modalities and develop novel signal integration circuits that can react to a very precise pre-programmed set of conditions or even to multiple sets of precise conditions. In this review, we highlight some tools that were developed in which these circuits were combined such that the detection of a particular event automatically triggered a specific output. Furthermore, using novel circuit-design strategies, circuits have been developed that can integrate multiple inputs together in Boolean logic gates composed of up to 6 inputs. We highlight the tools available and what has been developed thus far, and highlight how some clinical tools can be very useful in basic science. Most of the systems that are presented can be integrated together; and the possibilities far exceed the number of currently developed strategies."

http://rsc.li/1QUl5bS
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Gerd Moe-Behrens
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Discussion  - 
 
High-sensitivity assay for Hg (II) and Ag (I) ion detection:
A new class of droplet digital PCR logic gates for an intelligent DNA calculator

by
Nan Chenga, Pengyu Zhua, Yuancong Xub, Kunlun Huanga , Yunbo Luoa, Zhansen Yang, Wentao Xu

"*Highlights*

A series of DNA logic gates (YES, AND, and OR) was generated based on unique features.

High-sensitivity and high-specificity detection of Hg(II) and Ag(I).

Intelligent and practical design for hierarchical quantitative determination.

Droplet digital PCR was first introduced in DNA logic gate development

Abstract
The first example of droplet digital PCR logic gates (“YES”, “OR” and “AND”) for Hg (II) and Ag (I) ion detection has been constructed based on two amplification events triggered by a metal-ion-mediated base mispairing (T-Hg(II)-T and C-Ag(I)-C). In this work, Hg(II) and Ag(I) were used as the input, and the “true” hierarchical colors or “false” green were the output. Through accurate molecular recognition and high sensitivity amplification, positive droplets were generated by droplet digital PCR and viewed as the basis of hierarchical digital signals. Based on this principle, YES gate for Hg(II) (or Ag(I)) detection, OR gate for Hg(II) or Ag(I) detection and AND gate for Hg(II) and Ag(I) detection were developed, and their sensitively and selectivity were reported. The results indicate that the ddPCR logic system developed based on the different indicators for Hg(II) and Ag(I) ions provides a useful strategy for developing advanced detection methods, which are promising for multiplex metal ion analysis and intelligent DNA calculator design applications."

http://bit.ly/27mee0I
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Gerd Moe-Behrens
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Discussion  - 
 
SensiPath: computer-aided design of sensing-enabling metabolic pathways

by
Baudoin Delépine, Vincent Libis, Pablo Carbonell and Jean-Loup Faulon

"Genetically-encoded biosensors offer a wide range of opportunities to develop advanced synthetic biology applications. Circuits with the ability of detecting and quantifying intracellular amounts of a compound of interest are central to whole-cell biosensors design for medical and environmental applications, and they also constitute essential parts for the selection and regulation of high-producer strains in metabolic engineering. However, the number of compounds that can be detected through natural mechanisms, like allosteric transcription factors, is limited; expanding the set of detectable compounds is therefore highly desirable. Here, we present the SensiPath web server, accessible at http://sensipath.micalis.fr. SensiPath implements a strategy to enlarge the set of detectable compounds by screening for multi-step enzymatic transformations converting non-detectable compounds into detectable ones. The SensiPath approach is based on the encoding of reactions through signature descriptors to explore sensing-enabling metabolic pathways, which are putative biochemical transformations of the target compound leading to known effectors of transcription factors. In that way, SensiPath enlarges the design space by broadening the potential use of biosensors in synthetic biology applications." http://bit.ly/1NKNURT
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Gerd Moe-Behrens
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Discussion  - 
 
Biology software promises easier way to program living cells

by
Erika Check Hayden

"'Cello' automates the fast, reliable design of DNA-based logic circuits.

Synthetic biologists have created software that automates the design of DNA circuits for living cells.

The aim is to help people who are not skilled biologists to quickly design working biological systems, says synthetic biologist Christopher Voigt at the Massachusetts Institute of Technology in Cambridge, who led the work. “This is the first example where we’ve literally created a programming language for cells,” he says.

In the new software — called Cello — a user first specifies the kind of cell they are using and what they want it to do: for example, sense metabolic conditions in the gut and produce a drug in response. They type in commands to explain how these inputs and outputs should be logically connected, using a computing language called Verilog that electrical engineers have long relied on to design silicon circuits. Finally, Cello translates this information to design a DNA sequence that, when put into a cell, will execute the demands.

Voigt says his team is writing user interfaces that would allow biologists to write a single program and be returned different DNA sequences for different organisms. Anyone can access Cello through a Web-based interface, or by downloading its open-source code from the online repository GitHub.

”This paper solves the problem of the automated design, construction and testing of logic circuits in living cells,” says bioengineer Herbert Sauro at the University of Washington in Seattle, who was not involved in the study. The work is published in Science.1

Working together
Creating Cello required a decade of labour, says Voigt. The hard part, he says, was not writing the software itself but working out how to make biological parts — logic gates, by analogy with electronic circuits — that reliably worked together to carry out the functions programmed into the circuit by Verilog. For instance, the team had to develop a combination of genetic components that work together as an 'insulator' — ensuring that each biological part works no matter where in the DNA sequence it is placed.

How to design reliable, complex biological computing systems is a central problem of synthetic biology, Voigt says. Researchers found that DNA-based analogues of electronic switches and transistors would work in simple cases but would often fail when organized into more complex circuits. But inexpensive gene-synthesis technologies and the use of fast, cheap genetic sequencing to look at what goes wrong have enabled huge advances in understanding.


Living factories of the future
“What we’re finding over time is that biology isn’t this kind of mysterious unpredictable substrate; it just felt that way because we didn’t really have the tools to see what was going on,” Voigt says.

Voigt’s team tested 60 designs made using Cello; 45 worked correctly the first time. He estimates that it would take about a week to design 60 biological circuits with Cello; by contrast, it took a postdoc three years to design, test and build one successful biological circuit for a paper published in 2012, he says2.

Synthetic biologist Adam Arkin at the University of California, Berkeley, who was not involved in the work, says that Cello is one of a series of steps that aim to push synthetic biology closer to meeting its founding goals of using the principles of engineering to enable the design of new biological circuits.

“What is wonderful is seeing the original conception of synthetic biology — to build the infrastructure to make the engineering of new biological function vastly more efficient, predictable, transparent and safe — come to fruition in such powerful computational tools and biological reagents,” Arkin says..."

http://bit.ly/1Y3EO8y
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Gerd Moe-Behrens
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Reprogramming eukaryotic translation with ligand-responsive synthetic RNA switches

by
Andrew V Anzalone, Annie J Lin, Sakellarios Zairis, Raul Rabadan & Virginia W Cornish

"Protein synthesis in eukaryotes is regulated by diverse reprogramming mechanisms that expand the coding capacity of individual genes. Here, we exploit one such mechanism, termed −1 programmed ribosomal frameshifting (−1 PRF), to engineer ligand-responsive RNA switches that regulate protein expression. First, efficient −1 PRF stimulatory RNA elements were discovered by in vitro selection; then, ligand-responsive switches were constructed by coupling −1 PRF stimulatory elements to RNA aptamers using rational design and directed evolution in Saccharomyces cerevisiae. We demonstrate that −1 PRF switches tightly control the relative stoichiometry of two distinct protein outputs from a single mRNA, exhibiting consistent ligand response across whole populations of cells. Furthermore, −1 PRF switches were applied to build single-mRNA logic gates and an apoptosis module in yeast. Together, these results showcase the potential for harnessing translation-reprogramming mechanisms for synthetic biology, and they establish −1 PRF switches as powerful RNA tools for controlling protein synthesis in eukaryotes."

http://bit.ly/1UBNaFT
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Gerd Moe-Behrens
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Discussion  - 
 
Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

by
Javier Macia , Romilde Manzoni , Núria Conde , Arturo Urrios, Eulàlia de Nadal, Ricard Solé , Francesc Posas 

"Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success of these devices depends on obtaining circuits with scalable complexity and reusable parts. Here we show how to build complex computational devices using multicellular consortia and space as key computational elements. This spatial modular design grants scalability since its general architecture is independent of the circuit’s complexity, minimizes wiring requirements and allows component reusability with minimal genetic engineering. The potential use of this approach is demonstrated by implementation of complex logical functions with up to six inputs, thus demonstrating the scalability and flexibility of this method. The potential implications of our results are outlined."

http://bit.ly/1SXaAp0
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Gerd Moe-Behrens
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Discussion  - 
 
Engineering an allosteric transcription factor to respond to new ligands

by
Noah D Taylor, Alexander S Garruss, Rocco Moretti, Sum Chan, Mark A Arbing, Duilio Cascio, Jameson K Rogers, Farren J Isaacs, Sriram Kosuri, David Baker, Stanley Fields, George M Church & Srivatsan Raman

"Genetic regulatory proteins inducible by small molecules are useful synthetic biology tools as sensors and switches. Bacterial allosteric transcription factors (aTFs) are a major class of regulatory proteins, but few aTFs have been redesigned to respond to new effectors beyond natural aTF-inducer pairs. Altering inducer specificity in these proteins is difficult because substitutions that affect inducer binding may also disrupt allostery. We engineered an aTF, the Escherichia coli lac repressor, LacI, to respond to one of four new inducer molecules: fucose, gentiobiose, lactitol and sucralose. Using computational protein design, single-residue saturation mutagenesis or random mutagenesis, along with multiplex assembly, we identified new variants comparable in specificity and induction to wild-type LacI with its inducer, isopropyl β-D-1-thiogalactopyranoside (IPTG). The ability to create designer aTFs will enable applications including dynamic control of cell metabolism, cell biology and synthetic gene circuits."

http://bit.ly/1SfHZuq
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Gerd Moe-Behrens
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Discussion  - 
 
Programmable control of bacterial gene expression with the combined CRISPR and antisense RNA system

by
Young Je Lee, Allison Hoynes-O'Connor, Matthew C. Leong and Tae Seok Moon

"A central goal of synthetic biology is to implement diverse cellular functions by predictably controlling gene expression. Though research has focused more on protein regulators than RNA regulators, recent advances in our understanding of RNA folding and functions have motivated the use of RNA regulators. RNA regulators provide an advantage because they are easier to design and engineer than protein regulators, potentially have a lower burden on the cell and are highly orthogonal. Here, we combine the CRISPR system from Streptococcus pyogenes and synthetic antisense RNAs (asRNAs) in Escherichia coli strains to repress or derepress a target gene in a programmable manner. Specifically, we demonstrate for the first time that the gene target repressed by the CRISPR system can be derepressed by expressing an asRNA that sequesters a small guide RNA (sgRNA). Furthermore, we demonstrate that tunable levels of derepression can be achieved (up to 95%) by designing asRNAs that target different regions of a sgRNA and by altering the hybridization free energy of the sgRNA–asRNA complex. This new system, which we call the combined CRISPR and asRNA system, can be used to reversibly repress or derepress multiple target genes simultaneously, allowing for rational reprogramming of cellular functions."

http://bit.ly/1Ks4iKJ
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Gerd Moe-Behrens
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Discussion  - 
 
Orientational nanoparticle assemblies and biosensors

by
Wei Ma, Liguang Xu, Libing Wang, , Hua Kuang, Chuanlai Xu, 

"Assemblies of nanoparticles (NPs) have regional correlated properties with new features compared to individual NPs or random aggregates. The orientational NP assembly contributes greatly to the collective interaction of individual NPs with geometrical dependence. Therefore, orientational NPs assembly techniques have emerged as promising tools for controlling inorganic NPs spatial structures with enhanced interesting properties. The research fields of orientational NP assembly have developed rapidly with characteristics related to the different methods used, including chemical, physical and biological techniques. The current and potential applications, important challenges remain to be investigated. An overview of recent developments in orientational NPs assemblies, the multiple strategies, biosensors and challenges will be discussed in this review."

http://bit.ly/1KouYw3
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Gerd Moe-Behrens
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Towards enabling engineered microbial-electronic systems: RK2-based conjugal transfer system for Shewanella synthetic biology

by
M. Hajimorad  and  J.A. Gralnick

"Synthetic biology has been traditionally associated with electronics through the application of circuit design concepts towards the genetic engineering of microbes. Due to recent advances in the understanding of extracellular electron transfer in the bacterium Shewanella oneidensis (Shewanella), synthetic biology advances now have the potential of being used towards electronics applications. Towards this end, there is a need for tools that enable the systematic optimisation of genetic circuits in Shewanella. With the introduction of an RK2 origin of transfer cassette, we show that a modular plasmid system constructed prior for synthetic biology efforts in the bacterium Escherichia coli (E. coli) can be ported to Shewanella. In the process, it is also shown that different replication origins can be maintained in Shewanella and that multiple-plasmid strains can be realised in the bacterium. The results suggest that parts accumulated from E. coli synthetic biology efforts over the past decade and a half may be able to be ported to Shewanella, enabling the future engineering of systems where microbes interface with electronics (e.g. biosensors)."

http://bit.ly/1PtFF0F
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Gerd Moe-Behrens
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Fully integrated wearable sensor arrays for multiplexed in situ perspiration analysis

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Wei Gao, Sam Emaminejad, Hnin Yin Yin Nyein, Samyuktha Challa, Kevin Chen, Austin Peck, Hossain M. Fahad, Hiroki Ota, Hiroshi Shiraki, Daisuke Kiriya, Der-Hsien Lien, George A. Brooks, Ronald W. Davis & Ali Javey

"Wearable sensor technologies are essential to the realization of personalized medicine through continuously monitoring an individual’s state of health1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12. Sampling human sweat, which is rich in physiological information13, could enable non-invasive monitoring. Previously reported sweat-based and other non-invasive biosensors either can only monitor a single analyte at a time or lack on-site signal processing circuitry and sensor calibration mechanisms for accurate analysis of the physiological state14, 15, 16, 17, 18. Given the complexity of sweat secretion, simultaneous and multiplexed screening of target biomarkers is critical and requires full system integration to ensure the accuracy of measurements. Here we present a mechanically flexible and fully integrated (that is, no external analysis is needed) sensor array for multiplexed in situ perspiration analysis, which simultaneously and selectively measures sweat metabolites (such as glucose and lactate) and electrolytes (such as sodium and potassium ions), as well as the skin temperature (to calibrate the response of the sensors). Our work bridges the technological gap between signal transduction, conditioning (amplification and filtering), processing and wireless transmission in wearable biosensors by merging plastic-based sensors that interface with the skin with silicon integrated circuits consolidated on a flexible circuit board for complex signal processing. This application could not have been realized using either of these technologies alone owing to their respective inherent limitations. The wearable system is used to measure the detailed sweat profile of human subjects engaged in prolonged indoor and outdoor physical activities, and to make a real-time assessment of the physiological state of the subjects. This platform enables a wide range of personalized diagnostic and physiological monitoring applications."

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Gerd Moe-Behrens
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Inner Workings: DNA for data storage and computing

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Megan Scudellari

"On the surface, genetic and electrical engineering appear to have little in common. One field revolves around carbon and the other is built upon silicon; one makes RNA from DNA and the other converts AC to DC.

But some creative biologists have begun to apply the concepts of electrical engineering to living cells. “We view ourselves as biological programmers,” says Timothy Lu, a member of the Synthetic Biology Group at the Massachusetts Institute of Technology (MIT). Lu and others are engineering circuits into bacterial cells, literally programming them for functions, such as data storage and computation. DNA’s straightforward, self-replicating helices are easy to amplify, modify, and are generally quite stable, says Lu. And since each position of DNA can encode four different pieces of information—A, T, G, or C—instead of just two, as with classic binary silicon systems, DNA could someday, in principle, store more data in less space. “The same properties that make DNA a great genetic code for living organisms also makes it an interesting substrate to engineer,” "

http://bit.ly/1UgwyA7
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