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Digital Conference | BioBricks Foundation SB6.0: The Sixth International Meeting on Synthetic Biology

Digital Conference | BioBricks Foundation SB6.0: The Sixth International Meeting on Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
The preeminent meeting in Synthetic Biology, covering biotechnologies, biosafety, biosecurity & bioethics, July 9-11, 2013 at Imperial College in London UK.
Gerd Moe-Behrens's insight:
The BioBricks Foundation is now making all videos recorded and edited at SB6 available for FREE online

 http://bit.ly/10ohQxq   ;
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Synthetic biology manipulations in 3D printed wet-ware

Synthetic biology manipulations in 3D printed wet-ware | SynBioFromLeukipposInstitute | Scoop.it
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Leroy Cronin

"In our laboratory we have been developing new approaches to discover the 'transition-to-evolvability' in chemistry. This is because we can discover or engineer an abiotic system that can evolve (we could define this as an inorganic chemical cell -ICHELL) we might be able to suggest that synthetic biology can exist in many chemical forms, of which the terrestrial biology found on planet earth is one subset."

 


http://bit.ly/1446XzQ

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Molecular crowding shapes gene expression in synthetic cellular nanosystems

Molecular crowding shapes gene expression in synthetic cellular nanosystems | SynBioFromLeukipposInstitute | Scoop.it
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Cheemeng Tan,Saumya Saurabh,Marcel P. Bruchez,Russell Schwartz& Philip LeDuc

"The integration of synthetic and cell-free biology has made tremendous strides towards creating artificial cellular nanosystems using concepts from solution-based chemistry, where only the concentrations of reacting species modulate gene expression rates. However, it is known that macromolecular crowding, a key feature in natural cells, can dramatically influence biochemical kinetics via volume exclusion effects, which reduce diffusion rates and enhance binding rates of macromolecules. Here, we demonstrate that macromolecular crowding can increase the robustness of gene expression by integrating synthetic cellular components of biological circuits and artificial cellular nanosystems. Furthermore, we reveal how ubiquitous cellular modules, including genetic components, a negative feedback loop and the size of the crowding molecules can fine-tune gene circuit response to molecular crowding. By bridging a key gap between artificial and living cells, our work has implications for efficient and robust control of both synthetic and natural cellular circuits."
http://bit.ly/16MevdY

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Synthetic Morphology Using Alternative Inputs

Synthetic Morphology Using Alternative Inputs | SynBioFromLeukipposInstitute | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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Hiromasa Tanaka, Tau-Mu Yi 

"Designing the shape and size of a cell is an interesting challenge for synthetic biology. Prolonged exposure to the mating pheromone α-factor induces an unusual morphology in yeast cells: multiple mating projections. The goal of this work was to reproduce the multiple projections phenotype in the absence of α-factor using a gain-of-function approach termed “Alternative Inputs (AIs)”. An alternative input is defined as any genetic manipulation that can activate the signaling pathway instead of the natural input. Interestingly, none of the alternative inputs were sufficient to produce multiple projections although some produced a single projection. Then, we extended our search by creating all combinations of alternative inputs and deletions that were summarized in an AIs-Deletions matrix. We found a genetic manipulation (AI-Ste5p ste2Δ) that enhanced the formation of multiple projections. Following up this lead, we demonstrated that AI-Ste4p and AI-Ste5p were sufficient to produce multiple projections when combined. Further, we showed that overexpression of a membrane-targeted form of Ste5p alone could also induce multiple projections. Thus, we successfully re-engineered the multiple projections mating morphology using alternative inputs without α-factor."
http://bit.ly/17drZAe

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Refactoring the Silent Spectinabilin Gene Cluster Using a Plug-and-Play Scaffold

Refactoring the Silent Spectinabilin Gene Cluster Using a Plug-and-Play Scaffold | SynBioFromLeukipposInstitute | Scoop.it
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Zengyi Shao, Guodong Rao Chun Li, Zhanar Abil, Yunzi Luo, and Huimin Zhao

"Natural products (secondary metabolites) are a rich source of compounds with important biological activities. Eliciting pathway expression is always challenging but extremely important in natural product discovery because an individual pathway is tightly controlled through a unique regulation mechanism and hence often remains silent under the routine culturing conditions. To overcome the drawbacks of the traditional approaches that lack general applicability, we developed a simple synthetic biology approach that decouples pathway expression from complex native regulations. Briefly, the entire silent biosynthetic pathway is refactored using a plug-and-play scaffold and a set of heterologous promoters that are functional in a heterologous host under the target culturing condition. Using this strategy, we successfully awakened the silent spectinabilin pathway from Streptomyces orinoci. This strategy bypasses the traditional laborious processes to elicit pathway expression and represents a new platform for discovering novel natural products."

 http://bit.ly/17ch08l

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Joel Cherry Answers the Biggest Questions in Synthetic Biology

Joel Cherry Answers the Biggest Questions in Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
Should you be allowed to patent genes? What is the future of DNA synth? How will software affect the design process?
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BU Plans New Synthetic, Systems Biology Building

BU Plans New Synthetic, Systems Biology Building | SynBioFromLeukipposInstitute | Scoop.it
 
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Bosto University Plans New Synthetic, Systems Biology Building http://bit.ly/17OrScv

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A Research Lab in the Cloud - Genome Compiler Corporation

A Research Lab in the Cloud - Genome Compiler Corporation | SynBioFromLeukipposInstitute | Scoop.it
What if we could build microchips out of biological parts, and insert them into our bodies to perform important functions? It turns out that not only is…
Gerd Moe-Behrens's insight:

*Genome Compiler reports about my work: CytoComp - a revolutionary biological computer and Leukippos - a synthetic biology lab in the cloud * 

http://bit.ly/1bU8a1R

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BioCurious

BioCurious | SynBioFromLeukipposInstitute | Scoop.it
10 Years Into Synthetic Biology -- Latest Results and Various Perspectives

Drew Endy will join us for an evening at BioCurious to talk about his team's research in synthetic biology.

Abstract:
Gerd Moe-Behrens's insight:

Drew Endy - 10 Years Into Synthetic Biology - today 7pm PDT Sunnyvale, CA http://bit.ly/13RY7VL

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Engineering and ethical perspectives in synthetic biology

Engineering and ethical perspectives in synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

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James Anderson, Natalja Strelkowa, Guy-Bart Stan, Thomas Douglas, Julian Savulescu, Mauricio Barahona & Antonis Papachristodoulou

"Synthetic biology has emerged as an exciting and promising new research field, garnering significant attention from both the scientific community and the general public. This interest results from a variety of striking features: synthetic biology is a truly interdisciplinary field that engages biologists, mathematicians, physicists and engineers; its research focus is applied; and it has enormous potential to harness the power of biology to provide scientific and engineering solutions to a wide range of problems and challenges that plague humanity. However, the power of synthetic biology to engineer organisms with custom-made functionality requires that researchers and society use this power safely and responsibly, in particular when it comes to releasing organisms into the environment. This creates new challenges for both the design of such organisms and the regulatory process governing their creation and use…."

http://bit.ly/18IBDtK

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Science Shaping Our World:Synthetic Biology–Accelerating the Engineering of Life

Science Shaping Our World:Synthetic Biology–Accelerating the Engineering of Life | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

 Boston Sept 25  http://bit.ly/14QjFBo

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The biological microprocessor, or how to build a computer with biological parts

The biological microprocessor, or how to build a computer with biological parts | SynBioFromLeukipposInstitute | Scoop.it
The biological microprocessor, or how to build a computer with biological parts
Gerd Moe-Behrens's insight:

The biological microprocessor, or how to build a computer with biological parts http://bit.ly/1cwM43X

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Responsible Conduct in Synthetic Biology

Terry Johnson of UC Berkeley and Synberc provides a perspective on the unique features of synthetic biology that require special consideration above and beyo...
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Responsible Conduct in Synthetic Biology http://bit.ly/13FZcQm

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Composability of regulatory sequences controlling transcription and translation in Escherichia coli

Composability of regulatory sequences controlling transcription and translation in Escherichia coli | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

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Sriram Kosuria, Daniel B. Goodman,, Guillaume Cambray, Vivek K. Mutalik, Yuan Gaog, Adam P. Arkin, Drew Endy, and George M. Church

"The inability to predict heterologous gene expression levels precisely hinders our ability to engineer biological systems. Using well-characterized regulatory elements offers a potential solution only if such elements behave predictably when combined. We synthesized 12,563 combinations of common promoters and ribosome binding sites and simultaneously measured DNA, RNA, and protein levels from the entire library. Using a simple model, we found that RNA and protein expression were within twofold of expected levels 80% and 64% of the time, respectively. The large dataset allowed quantitation of global effects, such as translation rate on mRNA stability and mRNA secondary structure on translation rate. However, the worst 5% of constructs deviated from prediction by 13-fold on average, which could hinder large-scale genetic engineering projects. The ease and scale this of approach indicates that rather than relying on prediction or standardization, we can screen synthetic libraries for desired behavior."



http://bit.ly/14BnQpi

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Rapid, modular and reliable construction of complex mammalian gene circuits

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Patrick Guye, Yinqing Li, Liliana Wroblewska, Xavier Duportet and Ron Weiss

"We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction of synthetic gene circuits of up to 64 kb in size comprising 11 transcription units and 33 basic parts. We show robust gene expression control of multiple transcription units by small molecule inducers in human cells with transient transfection and stable chromosomal integration of these circuits. This framework enables development of complex gene circuits for engineering mammalian cells with unprecedented speed, reliability and scalability and should have broad applicability in a variety of areas including mammalian cell fermentation, cell fate reprogramming and cell-based assays."

 http://bit.ly/16GnNED

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Synthetic Biology - Cheemeng Tan lab

Synthetic Biology - Cheemeng Tan lab | SynBioFromLeukipposInstitute | Scoop.it
Synthetic Cellular Systems Group
Gerd Moe-Behrens's insight:

Cheemeng Tan: Engineering Artificial Cellular Systems for Biotechnological Applications

Their "work is unified under one theme: the engineering of synthetic biological systems for therapeutic treatment. We approach this issue through two fundamental directions. To improve the control of synthetic cellular systems, we harness functioning mechanisms in natural cells to control dynamics of synthetic cells and organisms. In parallel, we investigate how heterogenous cellular populations respond to drug treatment. We aim to merge the two directions to create novel treatment strategies using artificial cellular systems. We are honored to work with biologists, statistician, engineers, physicist, and chemists in the pursue of our research goals. Our work is multi-disciplinary and strives to create new frontier in synthetic & quantitative biology by synergizing ideas from different fields."

 http://bit.ly/1443uRM

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The CRISPR Craze

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Elizabeth Pennisi
"Bacteria have a kind of adaptive immune system, which enables them to fight off repeated attacks by specific viruses, that works through precise targeting of DNA. In January, four research teams reported harnessing the system, called CRISPR, to target the destruction of specific genes in human cells. And in the following 8 months, various groups have used it to delete, add, activate or suppress targeted genes in human cells, mice, rats, zebrafish, bacteria, fruit flies, yeast, nematodes and crops, demonstrating broad utility for the technique. With CRISPR, scientists can create mouse models of human diseases much more quickly than before, study individual genes much faster, and easily change multiple genes in cells at once to study their interactions."


 http://bit.ly/1581FJQ

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Synbio Courses - London

Synbio Courses - London | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

An Introduction to Synthetic Biology London, September 19, 2013 http://bit.ly/16EavMq

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Watch Day 2 Now: Keynote Webcast with Drew Endy, Stanford - Aliens, Computers & Engineering Biology - An Introduction to Synthetic Biology

Watch Day 2 Now: Keynote Webcast with Drew Endy, Stanford - Aliens, Computers & Engineering Biology - An Introduction to Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
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Synthetic Biology: Where Organic Meets Digital | Edinburgh International Festival

Synthetic Biology: Where Organic Meets Digital | Edinburgh International Festival | SynBioFromLeukipposInstitute | Scoop.it
Don’t miss ‘Synthetic Biology: Where Organic Meets Digital’ talk from #ECA head of design http://t.co/xAKEJGNT95 #edintfest #techinthefest
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Dan Grushkin: Writing a History of Synthetic Biology

Dan Grushkin: Writing a History of Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
Daniel Grushkin is a science writer that co-founded the first community bio lab Genspace, and now he is writing a history of synthetic biology.
Gerd Moe-Behrens's insight:

Dan Grushkin: Writing a History of Synthetic Biology http://bit.ly/1d2WCxp

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Biohacking goes industrial: six examples of future biotech products

Biohacking goes industrial: six examples of future biotech products | SynBioFromLeukipposInstitute | Scoop.it
Raymond McCauley, bioinformatics expert at Singularity University in California, gives Wired six examples of future biotech products
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by MADHUMITA VENKATARAMANAN

"There are two things happening right now that have transformed biotechnology," says Raymond McCauley, bioinformatics expert at  Singularity University in California, whose job is to nurture ideas and mentor bio-startups. The first, he says, is the digitisation of biology -- gathering data, examining how human systems work and testing drugs can all be done in a computer. The other is the democratisation of the tools. "Hackers are taking $3.5 million [£2.2 million] DNA sequencers and building the same thing for 1/10,000 of the price," he says. "What was an infant science a few years ago can now be a commercial venture." McCauley gives Wired six examples of future biotech products….

1) *Animal-free leather*

2) *Electric DNA control*

3) *Non-browning apples*

4) *Mining the micro biome*

5) *Genome interpretation*

6) *Printing DNA*

…"

 http://bit.ly/1dtHwyw

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Mapping behavioral specifications to model parameters in synthetic biology

Mapping behavioral specifications to model parameters in synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
With recent improvements of protocols for the assembly of transcriptional parts, synthetic biological devices can now more reliably be assembled according to a given design.
Gerd Moe-Behrens's insight:

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Heinz Koeppl, Marc Hafner and James Lu

"With recent improvements of protocols for the assembly of transcriptional parts, synthetic biological devices can now more reliably be assembled according to a given design. The standardization of parts open up the way for in silico design tools that improve the construct and optimize devices with respect to given formal design specifications. The simplest such optimization is the selection of kinetic parameters and protein abundances such that the specified design constraints are robustly satisfied. In this work we address the problem of determining parameter values that fulfill specifications expressed in terms of a functional on the trajectories of a dynamical model. We solve this inverse problem by linearizing the forward operator that maps parameter sets to specifications, and then inverting it locally. This approach has two advantages over brute-force random sampling. First, the linearization approach allows us to map back intervals instead of points and second, every obtained value in the parameter region is satisfying the specifications by construction. The method is general and can hence be incorporated in a pipeline for the rational forward design of arbitrary devices in synthetic biology."

http://bit.ly/14zNK9k

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Stanford bioengineering lab builds molecular ‘switch’ to reprogram control pathways in cells

Stanford bioengineering lab builds molecular ‘switch’ to reprogram control pathways in cells | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

*STANFORD BIOENGINEERING LAB BUILDS MOLECULAR ‘SWITCH’ TO REPROGRAM CONTROL PATHWAYS IN CELLS*

by
Tom Abate

"A Stanford bioengineering lab has developed a technology that can tweak the control systems that regulate the inner workings of cells, pointing the way toward future medical interventions that could switch off diseased states or turn on healthy processes.

 The research paper being published today by Science Express describes a biological tool that principal author Christina Smolke, PhD, associate professor of bioengineering, has dubbed a molecular network diverter. This molecular diverter utilizes the concerted action of three biological sub-systems to redirect signaling pathways – complex networks of molecular interactions that orchestrate the cellular machinery. The experiments described by Smolke and her collaborators, Kate Galloway, PhD, California Institute of Technology, and Elisa Franco, PhD, assistant professor of mechanical engineering at University of California, Riverside, were performed on yeast cells. But the principles and practices embodied in the molecular network diverter apply to signaling pathways that control the development, reproduction and death of all cells. When these signaling pathways go awry in humans, for instance, such malfunctions can cause many types of cancer as well as other diseases. “We’re doing this in yeast, but there’s a lot of conservation (similarity) of these pathways in higher organisms,” Smolke said. “The next step, now that we’ve shown this in simpler systems, is to take this technology into human cell cultures.” The Stanford team’s initial goal was to control the mating behavior of yeast, an activity that, in nature, is influenced by the presence or absence of pheromones. In a series of experiments, Smolke and her collaborators tried various techniques to induce or inhibit yeast mating behavior irrespective of pheromone activity. At first they found that the various techniques they used canceled each other out. But through computational modeling and fine-tuning of the chemical components they were able to build the molecular network diverter by joining three techniques into a unified technology whose elements they call: The transducer, which is an RNA-based system that gathers information about the chemical environment of the cell;The promoter, the molecular agent that helps to initiate and modulate the desired change; andThe pathway regulator, which finds the appropriate point in the cell’s signaling pathway to make the intervention.“The pieces that we used to build this control system existed,” Smolke said. “Combining them in a modular fashion into this molecular network diverter is what’s new.”.."



http://stanford.io/16nmqhx

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Synthetic Biology Startup Ecosystem - John Cumbers

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*Synthetic Biology Startup Ecosystem*

Video

+John Cumbers 

http://bit.ly/1cVGEnH

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