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Gerd Moe-Behrens
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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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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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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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A review of SynBio 2015

The Gene Editing Tsunami

 by Steven Burgess 

* PLOS Synthetic Biology Community*

"When we decided to crowdsource a review of the year from the synthetic biology community we weren’t sure what the response would be – but it has been fantastic! So good in fact, that we have decided to split the result into several parts. In this installment we have picked out 10 scientific highlights, and this will be followed by pieces on business, ethics and the future. We hope you enjoy reading, so much happened this year there are some things you might have missed!

The Gene Editing Tsunami

“I put my head together with some of Oxford’s top synthetic biology PhD students and we all agreed that this was the year of CRISPR – gene drives, embryonic editing, immuno-safe pig organs and more.”
Max Jamilly, PhD student in synthetic biology, Oxford

“2015 was definitely the year of CRISPR. Hard to not note its importance now and for the future.”
Dr. Charles Ebikeme, scientist and writer

“The maturation of the CRISPR-Cas system based technologies excites me, because they have huge potential to fundamentally enhance our targeted genome editing toolbox.”
Dr. Gerd Moe-Behrens, Leukippos institute

Can you hear that deafening roar approaching? CRISPR,CRISPR,CRISPR! In 2015 there was no escaping the exponential rise of the genome editing technique known as CRISPR-Cas9, which allows precise editing of DNA, is quick, cheap and easy to use, and works in almost every species it has been tried in. You could barely open a webpage without seeing some click bait linking to the latest bright use of the technology, ranginf from CRISPR mediated epigenome editing to optogenetics. The propaganda appeared to work, and by far the greatest number of replies to our survey nominated CRISPR developments – you are obviously still excited… and so are we!!! There is a reason for this; the best quote I heard explaining it came during the GARNet/OpenPlant CRISPR workshop in September, when Prof. Holger Putcha aptly described the technology as a tsunami, up there with PCR in terms of its impact upon molecular biology. When major news outlets began to pick up the story, and you see tabloids in the UK talking about “crispr”, you know this technology is going to be important for everyone – not just scientists. We will return to specific examples of how gene editing has been making waves, but first we should calm down a little and reflect that other exciting science has being going on too.'

http://bit.ly/1NprNSV
The gene editing tsunami and the ten synbio highlights of 2015 crowdsourced from the synthetic biology community,
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Gerd Moe-Behrens
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Hybrid integrated biological–solid-state system powered with adenosine triphosphate

by
Jared M. Roseman, Jianxun Lin, Siddharth Ramakrishnan, Jacob K. Rosenstein & Kenneth L. Shepard

"There is enormous potential in combining the capabilities of the biological and the solid state to create hybrid engineered systems. While there have been recent efforts to harness power from naturally occurring potentials in living systems in plants and animals to power complementary metal-oxide-semiconductor integrated circuits, here we report the first successful effort to isolate the energetics of an electrogenic ion pump in an engineered in vitro environment to power such an artificial system. An integrated circuit is powered by adenosine triphosphate through the action of Na+/K+ adenosine triphosphatases in an integrated in vitro lipid bilayer membrane. The ion pumps (active in the membrane at numbers exceeding 2 × 106 mm−2) are able to sustain a short-circuit current of 32.6 pA mm−2 and an open-circuit voltage of 78 mV, providing for a maximum power transfer of 1.27 pW mm−2 from a single bilayer. Two series-stacked bilayers provide a voltage sufficient to operate an integrated circuit with a conversion efficiency of chemical to electrical energy of 14.9%."

http://bit.ly/1SNYv1B
(a) Illustration depicting biocell attached to CMOS integrated circuit. (b) Illustration of membrane in pore containing sodium–potassium pumps. (c) Circuit model of equivalent stacked membranes, =2.1 pA, =98.6 GΩ, =575 GΩ and =75 pF, Ag/AgCl electrode equivalent resistance RWE+RCE<20 kΩ, ...
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Gerd Moe-Behrens
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Gerd Moe-Behrens
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Guiding the folding pathway of DNA origami

by
Katherine E. Dunn, Frits Dannenberg, Thomas E. Ouldridge, Marta Kwiatkowska, Andrew J. Turberfield & Jonathan Bath

"DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short ‘staple’ strands1, 2, 3, 4. Its guiding design principle is that the target structure is the single most stable configuration5. The folding transition is cooperative4, 6, 7 and, as in the case of proteins, is governed by information encoded in the polymer sequence8, 9, 10, 11. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield2. Although adjusting assembly conditions2, 12 or following empirical design rules12, 13 can improve yield, well-folded origami often need to be separated from misfolded structures2, 3, 14, 15, 16. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its rapid development1, 2, 3, 17, 18, 19 and become a reliable manufacturing technology20."

http://bit.ly/1O1B2tQ
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Gerd Moe-Behrens
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Free MIT / edX SynBio  course

Principles of Synthetic Biology
Learn how to engineer biological systems and program organisms to perform novel tasks.

http://bit.ly/1EgSTud
Learn how to engineer biological systems and program organisms to perform novel tasks.
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Gerd Moe-Behrens
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Synthetic histone code

Fischle W, Mootz HD, Schwarzer D

"Chromatin is the universal template of genetic information in all eukaryotic cells. This complex of DNA and histone proteins not only packages and organizes genomes but also regulates gene expression. A multitude of posttranslational histone modifications and their combinations are thought to constitute a code for directing distinct structural and functional states of chromatin. Methods of protein chemistry, including protein semisynthesis, amber suppression technology, and cysteine bioconjugation, have enabled the generation of so-called designer chromatin containing histones in defined and homogeneous modification states. Several of these approaches have matured from proof-of-concept studies into efficient tools and technologies for studying the biochemistry of chromatin regulation and for interrogating the histone code. We summarize pioneering experiments and recent developments in this exciting field of chemical biology."

http://bit.ly/1N0AWms
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Gerd Moe-Behrens
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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

by
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."

http://bit.ly/1JRZXAP
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Gerd Moe-Behrens
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Inner Workings: DNA for data storage and computing

by
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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Gerd Moe-Behrens
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Implementation of a genetic logic circuit: bio-register

by
Chun-Liang Lin , Ting-Yu Kuo, Yang-Yi Chen

"We introduce an idea of synthesizing a class of genetic registers based on the existing sequential biological circuits, which are composed of fundamental biological gates. In the renowned literature, biological gates and genetic oscillator have been unveiled and experimentally realized in recent years. These biological circuits have formed a basis for realizing a primitive biocomputer. In the traditional computer architecture, there is an intermediate load-store section, i.e. a register, which serves as a part of the digital processor. With which, the processor can load data from a larger memory into it and proceed to conduct necessary arithmetic or logic operations. Then, manipulated data are stored back to the memory by instruction via the register. We propose here a class of bio-registers for the biocomputer. Four types of register structures are presented. In silicon experiments illustrate results of the proposed design."

http://bit.ly/1RMxq1E
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Gerd Moe-Behrens
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Synthetic biology: How to make an oscillator
http://elifesciences.org/content/4/e12260
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Gerd Moe-Behrens
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'Deadman' and 'Passcode' microbial kill switches for bacterial containment

by
Clement T Y Chan, Jeong Wook Lee, D Ewen Cameron, Caleb J Bashor & James J Collins

"Biocontainment systems that couple environmental sensing with circuit-based control of cell viability could be used to prevent escape of genetically modified microbes into the environment. Here we present two engineered safeguard systems known as the 'Deadman' and 'Passcode' kill switches. The Deadman kill switch uses unbalanced reciprocal transcriptional repression to couple a specific input signal with cell survival. The Passcode kill switch uses a similar two-layered transcription design and incorporates hybrid LacI-GalR family transcription factors to provide diverse and complex environmental inputs to control circuit function. These synthetic gene circuits efficiently kill Escherichia coli and can be readily reprogrammed to change their environmental inputs, regulatory architecture and killing mechanism."

bit.ly/1lqSRbt
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Gerd Moe-Behrens
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*Solve for X *
Jerome Bonnet presents Cellular Computers

YouTube
"After a PhD studying cell division at the University of Montpellier, Jerome Bonnet joined Drew Endy’s lab at Stanford University to work in the field of synthetic biology, the rational engineering of novel biological systems and functions. There, he engineered genetically encoded data storage systems and amplifying logic gates operating in living cells using recombinase driven DNA switches. Since January 2014, he’s a group leader at the Centre de Biochimie Structurale in Montpellier, France, working on the engineering of cellular computers to improve human health, with a focus on engineering non-pathogenic bacteria for the in vitro diagnostics of disease."

http://bit.ly/1VrUS1A
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Gerd Moe-Behrens
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Programmable genetic circuits for pathway engineering

by
Allison Hoynes-O’Connor, Tae Seok Moon 

"Highlights

•Genetic tools from synthetic biology hold potential for pathway engineering.
•With metabolic and environmental sensors, cells can respond to their conditions.
•Genetic circuits connect cellular conditions with the appropriate response.
•Multi-gene targeting allows simultaneous, orthogonal regulation of multiple genes.
•Integration of these three components will lead to advances in pathway engineering."

http://bit.ly/1UoX7SE
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Gerd Moe-Behrens
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Why Researchers Want to Build Computers…Made of DNA


http://bit.ly/1NFIbNS
New research on DNA transformations from the University of East Anglia just might make nano-scale computing possible.
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