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Gerd Moe-Behrens
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Twister ribozymes as highly versatile expression platforms for artificial riboswitches

by
Felletti M, Stifel J, Wurmthaler LA, Geiger S, Hartig JS

"The utilization of ribozyme-based synthetic switches in biotechnology has many advantages such as an increased robustness due to in cis regulation, small coding space and a high degree of modularity. The report of small endonucleolytic twister ribozymes provides new opportunities for the development of advanced tools for engineering synthetic genetic switches. Here we show that the twister ribozyme is distinguished as an outstandingly flexible expression platform, which in conjugation with three different aptamer domains, enables the construction of many different one- and two-input regulators of gene expression in both bacteria and yeast. Besides important implications in biotechnology and synthetic biology, the observed versatility in artificial genetic control set-ups hints at possible natural roles of this widespread ribozyme class."
http://go.nature.com/2cKFwsN.
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Stefan Copper

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Synthetic biology is a novel area of research that is the amalgamation of multiple disciplines such as molecular biology, biotechnology, biophysics and genetic engineering among others. There are chiefly two approaches used in synthetic biology namely, top down approach and bottom up approach. Top-down approach involves the re-design and fabrication of existing biological systems for producing synthetic products.
Synthetic biology is a novel area of research that is the amalgamation of multiple disciplines such as molecular biology, biotechnology, biophysics and genetic engineering among others. There are chiefly two approaches used in synthetic biology namely, top down approach and bottom up approach.
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Gerd Moe-Behrens
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Discussion  - 
 
How DNA could store all the world’s data

by
Andy Extance

"It was Wednesday 16 February 2011, and Goldman was at a hotel in Hamburg, Germany, talking with some of his fellow bioinformaticists about how they could afford to store the reams of genome sequences and other data the world was throwing at them. He remembers the scientists getting so frustrated by the expense and limitations of conventional computing technology that they started kidding about sci-fi alternatives. “We thought, 'What's to stop us using DNA to store information?'”

Then the laughter stopped. “It was a lightbulb moment,” says Goldman, a group leader at the European Bioinformatics Institute (EBI) in Hinxton, UK. True, DNA storage would be pathetically slow compared with the microsecond timescales for reading or writing bits in a silicon memory chip. It would take hours to encode data by synthesizing DNA strings with a specific pattern of bases, and still more hours to recover that information using a sequencing machine. But with DNA, a whole human genome fits into a cell that is invisible to the naked eye. For sheer density of information storage, DNA could be orders of magnitude beyond silicon — perfect for long-term archiving.

“We sat down in the bar with napkins and biros,” says Goldman, and started scribbling ideas: “What would you have to do to make that work?” The researchers' biggest worry was that DNA synthesis and sequencing made mistakes as often as 1 in every 100 nucleotides. This would render large-scale data storage hopelessly unreliable — unless they could find a workable error-correction scheme. Could they encode bits into base pairs in a way that would allow them to detect and undo the mistakes? “Within the course of an evening,” says Goldman, “we knew that you could.”

He and his EBI colleague Ewan Birney took the idea back to their labs, and two years later announced that they had successfully used DNA to encode five files, including Shakespeare's sonnets and a snippet of Martin Luther King's 'I have a dream' speech1. By then, biologist George Church and his team at Harvard University in Cambridge, Massachusetts, had unveiled an independent demonstration of DNA encoding2. But at 739 kilobases (kB), the EBI files comprised the largest DNA archive ever produced — until July 2016, when researchers from Microsoft and the University of Washington claimed a leap to 200 megabytes (MB).

The latest experiment signals that interest in using DNA as a storage medium is surging far beyond genomics: the whole world is facing a data crunch. Counting everything from astronomical images and journal articles to YouTube videos, the global digital archive will hit an estimated 44 trillion gigabytes (GB) by 2020, a tenfold increase over 2013. By 2040, if everything were stored for instant access in, say, the flash memory chips used in memory sticks, the archive would consume 10–100 times the expected supply of microchip-grade silicon3.

That is one reason why permanent archives of rarely accessed data currently rely on old-fashioned magnetic tapes. This medium packs in information much more densely than silicon can, but is much slower to read. Yet even that approach is becoming unsustainable, says David Markowitz, a computational neuroscientist at the US Intelligence Advanced Research Projects Activity (IARPA) in Washington DC. It is possible to imagine a data centre holding an exabyte (one billion gigabytes) on tape drives, he says. But such a centre would require US$1 billion over 10 years to build and maintain, as well as hundreds of megawatts of power. “Molecular data storage has the potential to reduce all of those requirements by up to three orders of magnitude,” says Markowitz. If information could be packaged as densely as it is in the genes of the bacterium Escherichia coli, the world's storage needs could be met by about a kilogram of DNA (see 'Storage limits')...."

http://go.nature.com/2ceAfuq
Modern archiving technology cannot keep up with the growing tsunami of bits. But nature may hold an answer to that problem already.
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Gerd Moe-Behrens
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Synthetic recombinase-based state machines in living cells
http://science.sciencemag.org/content/353/6297/aad8559
Finite state machines are logic circuits with a predetermined sequence of actions that are triggered depending on the starting conditions. They are used for a variety of devices and biological systems, from vending machines to neural circuits. Roquet et al. have taken a finite state machine approach to control the expression of integrases, or enzymes that insert or excise phage DNA into or out of bacterial chromosomes. The integrases altered the ...
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Douglas Vaughan

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BioLogic is growing living actuators and synthesizing responsive bio-skin in the era where bio is the new interface for smart materials. We are Imagining a world where actuators and sensors can be grown rather than manufactur...
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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
owner

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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Discussion  - 
 
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  - 
 
Microsoft's "Biological Computing" Lab Aims To Fight Diseases By Reprogramming Cells
http://bit.ly/2deKFIl
When you work at Microsoft, everything looks like softwareeven cancer and other threats to human life.
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Gerd Moe-Behrens
owner

Discussion  - 
 
Programmable Manipulation of Cells
by
Isabelle Fol
"A team led by ETH Zurich Professor Yaakov Benenson has developed a Synthetic Biology platform that senses intracellular activities of mammalian transcription factors. This platform opens the way to precise sensing of and responding to diverse cell states and activities.
For millennia humans have been altering the genetic code of plants and animals by selectively breeding individuals with desirable features. As scientists have learned more about reading and manipulating the genetic code, they started transferring genetic information associated with useful features from one organism to another. Recent advances in Synthetic Biology have enabled bio-engineers to design multiple new DNA sequences from scratch. By combining these advances with engineering principles, synthetic biologists are now able to design cells and even organisms with new features.
Biology meets engineering
The interdisciplinary nature of Synthetic Biology makes it a particularly promising discipline, but the application of engineering principles to biological components creates challenges as well. As the engineering perspective is applied at all levels of biological structures - from molecules to cells, tissues and organisms - the redesign and construction of novel artificial biological pathways call for precise understanding of cellular processes. Consequently, one of the goals of Synthetic Biology is to develop programmable artificial gene networks that respond to endogenous molecular cues in order to analyse and understand cell behaviour. Transcription factors are an important class of such molecular cues due to their key role in determining cell identity and function. Yaakov (Kobi) Benenson, ETH Professor of Synthetic Biology at the Department of Biosystems Science and Engineering in Basel, and co-workers have developed a Synthetic Biology platform that is able to analyse and respond to cellular processes using endogenous transcriptional inputs. This programmable platform enables sensing and integrating multiple transcription factors, therefore leading to precise understanding of and response to diverse cell states and behaviors.
Cell machinery
Every cell of a living organism contains an instruction set that determines its identity and function. These instructions are encoded in DNA: Complex molecular "strings" containing the genetic code, the so-called genome. The first step of decoding the genome, namely the transcription of genetic information from DNA to messenger RNA, is controlled by proteins called transcription factors. Numerous types of transcription factors interact to create the complex language of gene expression. Transcription factors perform this function by promoting or blocking the recruitment of RNA polymerase - an enzyme that transcribes genetic information from DNA to RNA - to specific genes. Bartolomeo Angelici, the project leader in the Benenson group, explains: "Transcription factors are proteins that have the ability to bind specific DNA sequences, switching the nearby genes ON or OFF, and determining which genomic instructions are carried out. Active genes are transcribed into mRNA and eventually translated into proteins, while inactive ones lay dormant." These so-called "expressed" genes determine cellular identity and behavior. He affirms: "This is why sensing combinations of active transcription factors is a powerful way to recognise specific cell types."
Sensing transcriptional activity
Recently, Angelici, Benenson and co-workers have established a framework for systematic design of selective and robust sensing, integration and transduction of transcriptional activity in mammalian cells. "The idea is to build synthetic gene circuits that sense specific transcriptional activities and are further wired to various downstream components. In this way, endogenous transcription factors can be rewired to control diverse processes in a programmable fashion", adds Benenson. "In order to sense transcriptional activity, we take advantage of the transcription factors’ ability to bind specific DNA sequences." Each minimal sensor is a DNA molecule containing the response element recognised by a given transcription factor, followed by one or more genes that are further wired to additional engineered components. Importantly, one of these genes is an artificial transcription factor that also serves as a sensor input, in what is known as "positive feedback" mechanism. Thus, after initial sensor induction by an endogenous factor, the artificial regulator is produced, amplifying its own amount and the amount of additional gene products.
Determining cell identity
Precise control of gene expression is a long-standing goal of Biotechnology and Biomedicine. Benenson’s new Synthetic Biology platform not only allows processing signals from multiple transcription factors and sensing molecular cues, but also responding with biologically active outcomes in a controlled fashion. For example, the platform might enable precise targeting of cells with a highly specific transcriptional profile. This is particularly interesting in complex diseases like cancer, because cancer cells are known to harbor abnormal transcriptional activities that distinguish them from healthy cells. In the future, a synthetic logic circuit sensing transcriptional factors could be used to specifically target cancer cells without harming healthy tissues.
Reference
Bartolomeo Angelici, Erik Mailand, Benjamin Haefliger, Yaakov Benenson: Synthetic Biology Platform for Sensing and Integrating Endogenous Transcriptional Inputs in Mammalian Cells. Cell Reports 2016. DOI: http://dx.doi.org/10.1016/j.celrep.2016.07.061"
http://bit.ly/2cCAQ7J
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Gerd Moe-Behrens
owner

Discussion  - 
 
One-pot synthesis towards sulfur-based organic semiconductors A short and simple synthetic route for thiophene-fused aromatic compounds

by
Nagoya

"Thiophene-fused polycyclic aromatic hydrocarbons (PAHs) are known to be useful as organic semiconductors due to their high charge transport properties. Scientists at Nagoya University have developed a short route to form various thiophene-fused PAHs by simply heating mono-functionalized PAHs with sulfur. This new method is expected to contribute towards the efficient development of novel thiophene-based electronic materials."
http://bit.ly/2cvRANR
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Gerd Moe-Behrens
owner

Discussion  - 
 
Scientists program cells to remember and respond to series of stimuli
New approach to biological circuit design enables scientists to track cell histories. http://news.mit.edu/2016/biological-circuit-cells-remember-respond-stimuli-0721
New approach to biological circuit design enables scientists to track cell histories.
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This soft robotic stingray is made of rat heart muscle. Yeah, it's just as crazy as it sounds.

"Roughly speaking, we made this thing with a pinch of rat cardiac cells, a pinch of breast implant, and a pinch of gold. That pretty much sums it up, except for the genetic engineering," says Kit Parker, the bio-engineer at Harvard who led the team that developed the strange robot.
This soft robotic stingray is made of rat heart muscle. Yeah, it's just as crazy as it sounds.
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Gerd Moe-Behrens
owner

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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Gerd Moe-Behrens
owner

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
owner

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
owner

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
owner

Discussion  - 
 
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
owner

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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