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Cells as living calculators

Cells as living calculators | SynBioFromLeukipposInstitute | Scoop.it
Using analog computation circuits, MIT engineers design cells that can compute logarithms, divide and take square roots.
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Anne Trafton

"MIT engineers have transformed bacterial cells into living calculators that can compute logarithms, divide, and take square roots, using three or fewer genetic parts.

 Inspired by how analog electronic circuits function, the researchers created synthetic computation circuits by combining existing genetic “parts,” or engineered genes, in novel ways. The circuits perform those calculations in an analog fashion by exploiting natural biochemical functions that are already present in the cell rather than by reinventing them with digital logic, thus making them more efficient than the digital circuits pursued by most synthetic biologists, according to Rahul Sarpeshkar and Timothy Lu, the two senior authors on the paper, describing the circuits in the May 15 online edition of Nature. “In analog you compute on a continuous set of numbers, which means it’s not just black and white, it’s gray as well,” says Sarpeshkar, an associate professor of electrical engineering and computer science and the head of the Analog Circuits and Biological Systems group at MIT"


http://bit.ly/16hy2FF

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Synthetic Biology in High School: iGEM 2014 High School Jamboree Winners Announced

CAMBRIDGE, Mass., July 10, 2014--(PR Newswire)--
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Synthetic biology in China – Foundation and Initiation - free slide submission, upload slide - Medical, weSRCH

Synthetic biology in China – Foundation and Initiation - free slide submission, upload slide - Medical, weSRCH | SynBioFromLeukipposInstitute | Scoop.it
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Synthetic Biology Market

To Get More Information: http://www.bigmarketresearch.com/synthetic-biology-market Synthetic biology is a novel field that finds its origin at the intersection of biology and engineering. It involves designing and construction of biological systems or devices that can be applied in varied domains to get specified results.
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Towards Modeling Automation for Synthetic Biology - Springer

Towards Modeling Automation for Synthetic Biology - Springer | SynBioFromLeukipposInstitute | Scoop.it
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A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations - Springer

A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations - Springer | SynBioFromLeukipposInstitute | Scoop.it
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Bacteriophage-based synthetic biology for the study of infectious diseases

Bacteriophage-based synthetic biology for the study of infectious diseases | SynBioFromLeukipposInstitute | Scoop.it
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Citorik RJ, Mimee M, Lu TK

"Since their discovery, bacteriophages have contributed enormously to our understanding of molecular biology as model systems. Furthermore, bacteriophages have provided many tools that have advanced the fields of genetic engineering and synthetic biology. Here, we discuss bacteriophage-based technologies and their application to the study of infectious diseases. New strategies for engineering genomes have the potential to accelerate the design of novel phages as therapies, diagnostics, and tools. Though almost a century has elapsed since their discovery, bacteriophages continue to have a major impact on modern biological sciences, especially with the growth of multidrug-resistant bacteria and interest in the micro biome."


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 http://bit.ly/1tgAMyt

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Multicellular Computing Using Conjugation for Wiring

Multicellular Computing Using Conjugation for Wiring | SynBioFromLeukipposInstitute | Scoop.it
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Angel Goñi-Moreno,  Martyn Amos, Fernando de la Cruz

"Recent efforts in synthetic biology have focussed on the implementation of logical functions within living cells. One aim is to facilitate both internal “re-programming” and external control of cells, with potential applications in a wide range of domains. However, fundamental limitations on the degree to which single cells may be re-engineered have led to a growth of interest in multicellular systems, in which a “computation” is distributed over a number of different cell types, in a manner analogous to modern computer networks. Within this model, individual cell type perform specific sub-tasks, the results of which are then communicated to other cell types for further processing. The manner in which outputs are communicated is therefore of great significance to the overall success of such a scheme. Previous experiments in distributed cellular computation have used global communication schemes, such as quorum sensing (QS), to implement the “wiring” between cell types. While useful, this method lacks specificity, and limits the amount of information that may be transferred at any one time. We propose an alternative scheme, based on specific cell-cell conjugation. This mechanism allows for the direct transfer of genetic information between bacteria, via circular DNA strands known as plasmids. We design a multi-cellular population that is able to compute, in a distributed fashion, a Boolean XOR function. Through this, we describe a general scheme for distributed logic that works by mixing different strains in a single population; this constitutes an important advantage of our novel approach. Importantly, the amount of genetic information exchanged through conjugation is significantly higher than the amount possible through QS-based communication. We provide full computational modelling and simulation results, using deterministic, stochastic and spatially-explicit methods. These simulations explore the behaviour of one possible conjugation-wired cellular computing system under different conditions, and provide baseline information for future laboratory implementations."



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Living food based on synthetic biology

Living food based on synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
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 by Minsu Kim 

"This conceptual food by Royal College of Art graduate Minsu Kim would wriggle around on the plate and in your mouth (+ movie).

Minsu Kim's Living Food project builds on developments in synthetic biology to propose meals that behave like living creatures.

"Synthetic biotech has already started to create artificial life in organic forms," says the designer, citing a swimming artificial jellyfish made of heart cells by researchers at Caltech and Harvard University. "Breathing life into artificial digestible forms in not merely a fantasy."

In the Design Interactions department of the Royal College of Art's graduate exhibition this week Minsu Kim presents three dishes, each exhibiting a different behaviour: wriggling around, waving tentacles or puffing up as though breathing.
"This project explores new culinary experiences through developments in synthetic biology, and finds its lineage in haute cuisine and molecular gastronomy," the designer adds. "What if food was able to play with our cutlery and create hyper-sensations in our mouth?"

Show RCA continues until 30 June 2013. Other projects on show include glassware that creates kaleidoscopic effects and bicycle helmets made of pulped newspaper.
Other stories about futuristic food on Dezeen include treats with edible packaging, fruit labelled with lasers and 3D-printed hamburgers.
Find out how soon we could be tucking into 3D-printed steaks in an extract from Print Shift, our one-off print-on-demand publication all about 3D printing......"


http://bit.ly/1oe8Og2

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Modular Riboswitch Toolsets for Synthetic Genetic Control in Diverse Bacterial Species

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Robinson CJ, Vincent HA, Wu MC, Lowe PT, Dunstan MS, Leys D, Micklefield J.

"Ligand-dependent control of gene expression is essential for gene functional analysis, target validation, protein production and metabolic engineering. However, the expression tools currently available are difficult to transfer between species and exhibit limited mechanistic diversity. Here we demonstrate how the modular architecture of purine riboswitches can be exploited to develop orthogonal and chimeric switches that are transferable across diverse bacterial species, modulating either transcription or translation, to provide tuneable activation or repression of target gene expres-sion, in response to synthetic non-natural effector molecules. Our novel riboswitch-ligand pairings are shown to regulate physiologically important genes required for bacterial motility in Escherichia coli and cell morphology in Bacillus subtilis. These findings are relevant for future gene function studies and antimicrobial target validation, whilst providing new modular and orthogonal regulatory components for deployment in synthetic biology regimes."

 http://bit.ly/1sXYZtg

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ACS Synthetic Biology: Volume 3, Issue 6 (ACS Publications)

ACS Synthetic Biology: Volume 3, Issue 6 (ACS Publications) | SynBioFromLeukipposInstitute | Scoop.it
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PLOS Launches Neuroscience and Synthetic Biology Channels to Support Collaboration and Discussion of Published Research | PLOS

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What We Learned at Techonomy Bio

What We Learned at Techonomy Bio | SynBioFromLeukipposInstitute | Scoop.it
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Techonomy 

"Techonomy’s offices on Manhattan’s West 22d Street have been buzzing ever since our half-day Techonomy Bio conference on June 17. We got an overwhelmingly positive reception for a meeting that brought leading researchers and experts in the life sciences together with IT and Internet thinkers and business generalists.

Drew Endy, a Stanford professor who is one of the world’s leaders in synthetic biology, on stage called the event “awesome” and said he had never seen such a collection of people in one place. “People in other sectors of technology simply don’t know very much about biology and biology’s economic impact,” he continued. And like literally every expert at the event, he was supremely optimistic about the future potential of life sciences for society: “The biotech that exists right now is sort of the snowflake on the tip of the iceberg. There’s so much more to make.” Endy is a passionate advocate of open-source access to biological discoveries and tools to further accelerate progress by widening the community of researchers and innovators beyond just big companies.
Synthetic biology was a centerpiece of the conference, which aimed particularly to examine how progress in IT was stimulating an acceleration in biological discovery. Andrew Hessel of software-maker Autodesk crisply defined synthetic biology, calling it “genetic engineering done with digital tools.” He added: “This makes it faster, cheaper, and easier to do.” Hessel wants to use the plummeting cost of DNA sequencing—another central technology in our discussions—to enable individually-customized cancer drugs. He explained how it could happen soon...."



http://onforb.es/TApYuB

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Disease, Dysfunction, and Synthetic Biology

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Holm S.

"Theorists analyzing the concept of disease on the basis of the notion of dysfunction consider disease to be dysfunction requiring. More specifically, dysfunction-requiring theories of disease claim that for an individual to be diseased certain biological facts about it must be the case. Disease is not wholly a matter of evaluative attitudes. In this paper, I consider the dysfunction-requiring component of Wakefield's hybrid account of disease in light of the artifactual organisms envisioned by current research in synthetic biology. In particular, I argue that the possibility of artifactual organisms and the case of oncomice and other bred or genetically modified strains of organism constitute a significant objection to Wakefield's etiological account of the dysfunction requirement. I then develop a new alternative understanding of the dysfunction requirement that builds on the organizational theory of function. I conclude that my suggestion is superior to Wakefield's theory because it (a) can accommodate both artifactual and naturally evolved organisms, (b) avoids the possibility of there being a conflict between what an organismic part is supposed to do and the health of the organism, and (c) provides a nonarbitrary and practical way of determining whether dysfunction occurs."
 http://bit.ly/1pFgFse ;

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Look Out CRISPR, BuD-Derived Gene Editing Tools May Be Gaining On You

Look Out CRISPR, BuD-Derived Gene Editing Tools May Be Gaining On You | SynBioFromLeukipposInstitute | Scoop.it
Researchers detail the binding domain of BurrH, a DNA-binding protein. They also reprogrammed the domain, called BuD, showing its potential as a gene-editing tool.
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Biological production by human design | Laboratory News

Biological production by human design | Laboratory News | SynBioFromLeukipposInstitute | Scoop.it
Advances in synthetic biology have made it possible to convert biomass to chemicals, fuels and materials, and produce new therapeutic drugs
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Using Targeted Chromatin Regulators to Engineer Combinatoria and Spatial Transcriptional Regulation

Using Targeted Chromatin Regulators to Engineer Combinatoria and Spatial Transcriptional Regulation | SynBioFromLeukipposInstitute | Scoop.it

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Albert J. Keung, Caleb J. Bashor, Szilvia Kiriakov, James J. Collins, and Ahmad S. Khalil

"The transcription of genomic information in eukary- otes is regulated in large part by chromatin. How a diverse array of chromatin regulator (CR) proteins with different functions and genomic localization pat- terns coordinates chromatin activity to control tran- scription remains unclear. Here, we take a synthetic biology approach to decipher the complexity of chro- matin regulation by studying emergent transcrip- tional behaviors from engineered combinatorial, spatial, and temporal patterns of individual CRs. We fuse 223 yeast CRs to programmable zinc finger pro- teins. Site-specific and combinatorial recruitment of CRs to distinct intralocus locations reveals a range of transcriptional logic and behaviors, including syn- ergistic activation, long-range and spatial regulation, and gene expression memory. Comparing these tran- scriptional behaviors with annotated CR complex and function terms provides design principles for the engineering of transcriptional regulation. This work presents a bottom-up approach to investigating chromatin-mediated transcriptional regulation and introduces chromatin-based components and sys- tems for synthetic biology and cellular engineering."

 http://bit.ly/1oI3Vxj
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What-Syn-a-Name?

What-Syn-a-Name? | SynBioFromLeukipposInstitute | Scoop.it
Synthetic biology is attracting attention from both scientists and regulators. But there is little agreement on what it is. Can we find a road out of synthetic biology’s definitional quagmire?
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The Gigaom interview: Why synthetic biology and the Netflix model are the future of medicine

The Gigaom interview: Why synthetic biology and the Netflix model are the future of medicine | SynBioFromLeukipposInstitute | Scoop.it
Life is a programming language, and molecular biologist Andrew Hessel thinks that it will be increasingly available to anyone interested in designing with the building blocks of life.
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What Autodesk’s Acquisition of “The Living” Means for Architecture

What Autodesk’s Acquisition of “The Living” Means for Architecture | SynBioFromLeukipposInstitute | Scoop.it
The Living's (Buildings that grow? @autodesk acquires The Living & bets on synthetic biology. #synthbio #theliving http://t.co/KmuQCZyZJK)
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Synthetic Biology: Volume 1 (Specialist Periodical Reports)

Synthetic Biology: Volume 1 (Specialist Periodical Reports)

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Synthetic Biology: Volume 1 (Specialist Periodical Reports) [Maxim Ryadnov, Luc Brunsveld, Hiroaki Suga, Eric Kool, Birger Lindberg Moller, Alexander Kros, Cristiano Chiarabelli, Stephen Hart, Maarten Merkx, Oliver Rackham, S Tekeuchi, Paul Dalby, Jeroen Cornelissen] on Amazon.com. *FREE* shipping on qualifying offers. Synthetic biology is a new area of biological research that combines science and engineering in order to design and build novel biological functions and systems. The definition of synthetic biology has been generally accepted as the engineering of biology: the synthesis of complex
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Integration of microfluidics into the synthetic biology design flow

Integration of microfluidics into the synthetic biology design flow | SynBioFromLeukipposInstitute | Scoop.it
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Haiyao Huang and Douglas Densmore  

"One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications. Major challenges in these efforts include increasing the scalability and robustness of engineered biological systems and streamlining and automating the synthetic biology workflow of specification-design-assembly-verification. We present here a summary of the advances in microfluidic technology, particularly microfluidic large scale integration, that can be used to address the challenges facing each step of the synthetic biology workflow. Microfluidic technologies allow precise control over the flow of biological content within microscale devices, and thus may provide more reliable and scalable construction of synthetic biological systems. The integration of microfluidics and synthetic biology has the capability to produce rapid prototyping platforms for characterization of genetic devices, testing of biotheraputetics, and development of biosensors."

http://rsc.li/1xhURTw

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DNA based diagnostics 2.0

DNA based diagnostics 2.0 | SynBioFromLeukipposInstitute | Scoop.it
The latest generation of DNA sequencers allows all the genes of a plant, as well as any pathogens present, to be charted literally within a few days. “This provides unprecedented opportunities for the diagnosis of plant diseases, as well as, for example, identifying and tracking new disease outbreaks,” says Dr Theo van der Lee, senior scientist at the Department of Bio-Interactions and Plant Health at Plant Research International. “We can now detect pathogens directly from infected plant material, usually without having to guess in advance which bacterium, fungus or virus is the culprit.”
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Synthetic Biology Community | A PLOS Community Segment Site

Synthetic Biology Community | A PLOS Community Segment Site | SynBioFromLeukipposInstitute | Scoop.it
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An awesome new #synbio community page by PLOS http://bit.ly/1lzSlzL

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Synthetic Biology Industry Will Reach USD13.4 Billion in 2019

Synthetic Biology Industry Will Reach USD13.4 Billion in 2019 | SynBioFromLeukipposInstitute | Scoop.it
Synthetic Biology Market - Global Industry Analysis, Size, Share, Growth, Trends and Forecast,2013 - 2019
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How Will Biological Progress Transform the World?

How Will Biological Progress Transform the World? | SynBioFromLeukipposInstitute | Scoop.it
With advances in biological and genomic sciences accelerating at an ever-increasing pace, what does the future hold? If biological progress is indeed advancing more rapidly than Moore’s Law, as many assert, what are the economic and societal implications? In this video from our June 17 Techonomy Bio conference, Alex Lash, biotech editor at Xconomy, interviews Drew Endy, bioengineer at Stanford, about biological processes.
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