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Open Source Synthetic Biology: Problems and Solutions

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Ethan R. Fitzpatrick "In recent years, the scientific community has made some dramatic advances in the ability to chemically synthesize genome- length strands of DNA.1 These advances have coincided with a growing understanding of the functions of individual genes and gene networks.2 With the available knowledge of how whole genomes function, and the technical capability of synthesizing whole genomes, it will be possible to digitally design novel organisms to perform some desired function and then manifest that synthetic organism in the real world.3 The J. Craig Venter Institute took the first steps toward this goal by creating a synthetic organism controlled entirely by a chemically synthesized genome.4 This advance provided:a proof of principle for producing cells based on computer- designed genome sequences. DNA sequencing of a cellular genome allows storage of the genetic instructions for life as a digital file . . . . [T]he approach [] developed [by the J. Craig Venter Institute] should be applicable to the synthesis and transplantation of more novel genomes as genome design processes.5Although this ultimate goal of designing novel synthetic organisms using synthetic biology sounds like pure science fiction, it is entirely possible..." http://bit.ly/1d9PhIo
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San Francisco, November 13th - 15th 2014 - SynBioBeta

San Francisco, November 13th - 15th 2014 - SynBioBeta | SynBioFromLeukipposInstitute | Scoop.it
RT @SynBioBeta: SynBioBeta SF 2014:
Where Synthetic Biology Meets Innovation.
#SBBSF14
http://t.co/jRWLVCqrkC http://t.co/lYyuE4sniv
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Replicating an Expanded Genetic Alphabet in Cells

Replicating an Expanded Genetic Alphabet in Cells | SynBioFromLeukipposInstitute | Scoop.it
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John C. Chaput

"Recent advances in synthetic biology have made it possible to replicate an unnatural base pair in living cells. This study highlights the technologies developed to create a semisynthetic organism with an expanded genetic alphabet and the potential challenges of moving forward..."



http://bit.ly/1rpDBKs

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Expanding the logic of bacterial promoters using engineered overlapping operators for global regulators

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Maria-Eugenia Guazzaroni and Rafael Silva-Rocha

"The understanding of how the architecture of cis-regulatory elements at bacterial promoters determines their final output is of central interest in modern biology. In this work, we attempt to gain insight into this process by analysing complex promoter architectures in the model organism Escherichia coli. By focusing on the relationship between different TFs at the genomic scale in terms of their binding site arrangement and their effect on the target promoters, we found no strong constrain limiting the combinatorial assemble of TF pairs in E. coli. More strikingly, overlapping binding sites were found equally associated with both equivalent (both TFs have the same effect on the promoter) and opposite (one TF activates while the other repress the promoter) effects on gene expression. With this information on hand, we set an in silico approach to design overlapping sites for three global regulators (GRs) of E. coli, specifically CRP, Fis and IHF. Using random sequence assembly and an evolutionary algorithm, we were able to identify potential overlapping operators for all TF pairs. In order to validate our prediction, we constructed two lac promoter variants containing overlapping sites for CRP and IHF designed in silico. By assaying the synthetic promoters using a GFP reporter system, we demonstrated that these variants were functional and activated by CRP and IHF in vivo. Taken together, presented results add new information on the mechanisms of signal integration in bacterial promoters and provide new strategies for the engineering of synthetic regulatory circuits in bacteria."


 http://bit.ly/1p3nIVw

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ASU professor speaks to Congress about supporting synthetic biology research

ASU professor speaks to Congress about supporting synthetic biology research | SynBioFromLeukipposInstitute | Scoop.it
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Joe Kullman

"Karmella Haynes was among scientists and engineers to address national leaders at a recent U.S. Congressional briefing on issues raised by the emerging field of synthetic biology.

Haynes is an assistant professor in the School of Biological and Health Systems Engineering, one of Arizona State University’s Ira A. Fulton Schools of Engineering. She is among educators and researchers using synthetic biology techniques in pursuit of solutions to many of society’s major biotechnology and medical challenges.
The field combines biological sciences and engineering in designing and creating new manufactured biological systems and devices, as well as redesigning existing natural biological systems to maintain and enhance human health.
Researchers are using the capabilities of synthetic biology to probe the fundamental makeup of biological systems, enabling them to do things such as modifying and reprogramming body cells and DNA to perform medicinal functions. Such techniques are also being used in plant biology to enhance agriculture.
The rapid advance of synthetic biology has prompted discussions about how to weigh the benefits of the research against potential social and ethical implications, and concerns about safety.
Haynes and two colleagues – Steve Evans and Jay Keasling – gave presentations on those questions to staff members representing members of Congress, National Science Foundation officials, science journalists and other interested parties.
Evans is a research fellow at Dow AgroSciences, a part of the Dow Chemical Company that focuses on sustainable agriculture.
Keasling is the chief executive officer of the Joint BioEnergy Institute, assistant director at the Lawrence Berkeley National Lab and a professor of biochemical engineering at the University of California, Berkeley. He is also director of the National Science Foundation-supported Synthetic Biology Engineering Research Center (SynBERC), which helped to organize the Congressional briefing. Haynes is an affiliate researcher with SynBERC.
The speakers stressed the importance of increasing public awareness of synthetic biology as a way to foster confidence about the methods and the goals of researchers. “We want to inform more people to prevent unfounded fears that might hinder work that has great value for addressing society’s needs,” Haynes said after the briefing.
The audience was also told it will be increasingly important to have experts in the field working with the Environmental Protection Agency and the Food and Drug Administration to help keep government regulations up to date on rules related to biological research and biotechnology development. Current regulations “need to be more aligned with technology that is coming from synthetic biology,” Haynes said.
Arizona State University “was highly visible” at the briefing, she said, due particularly to talk about the Workshop on Research Agendas in the Societal Aspects of Synthetic Biology to be hosted by ASU in November.
“We hope we convinced everyone at the briefing that sustained support for biomedical engineering is in the best interests of the nation,” Haynes said."


 http://bit.ly/1o1EXKk

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Biohackers Are Growing Real Cheese In A Lab, No Cow Needed

Biohackers Are Growing Real Cheese In A Lab, No Cow Needed | SynBioFromLeukipposInstitute | Scoop.it
Real vegan cheese. It's not an oxymoron, it's a miracle of synthetic biology.
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Keystone Symposia: Precision Genome Engineering and Synthetic Biology 2015 | January 11th | clocate - Conferences and Exhibitions

Keystone Symposia: Precision Genome Engineering and Synthetic Biology 2015 | January 11th | clocate - Conferences and Exhibitions | SynBioFromLeukipposInstitute | Scoop.it
Keystone Symposia: Precision Genome Engineering and Synthetic Biology 2015 will be held in Big sky, MT, United States on January 11th.
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Gene regulation: A chromatin-based recruitment drive

Gene regulation: A chromatin-based recruitment drive | SynBioFromLeukipposInstitute | Scoop.it
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Darren J. Burgess

"A cornerstone of synthetic biology and biological engineering is achieving regulatory control of genes of interest. Typically, this is attempted by placing binding sites for classic transcription factors upstream of genes. However, gene regulation is multilayered beyond transcription factor recruitment; thus, a new study has characterized how diverse chromatin regulators might provide a flexible…"

 http://bit.ly/WhRoHO

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BioCoder: Issue 4

BioCoder: Issue 4 | SynBioFromLeukipposInstitute | Scoop.it
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Our work in the latest issue of BioCoder:

*Leukippos: A Synthetic Biology Lab in the Cloud*

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Pablo Cárdenas, Maaruthy Yelleswarapu, Sayane Shome, Jitendra Kumar Gupta, Eugenio Maria Battaglia, Pedro Fernandes, Alioune Ngom, and Gerd Moe-Behrens

"As we move deeper into the digital age, the social praxis of science undergoes fundamental changes, driven by new tools provided by information and communication technologies. Specifically, social networks and computing resources such as online cloud-based infrastructures and applications provide the necessary context for unprecedented innovations in modern science. These tools are leading to a planetary-scale connectivity among researchers and enable the organization of in silico research activities entirely through the cloud.

Research collaboration and management via the cloud will result in a drastic expansion of our problem-solving capacity, since groups of people with different backgrounds and expertise that openly gather around common interests are more likely to succeed at solving complex problems. Another advantage is that collaboration between individuals becomes possible regardless of their geographic location and background.
Here we present a novel, open-web application called Leukippos, which aims to apply these information and communication technologies to in silico synthetic biology projects. We describe both the underlying technology and organizational structure necessary for the platform’s operation. The synthetic biology software search engine, SynBioAppSelector, and the game, SynBrick, are examples of projects being developed on this platform."



http://bit.ly/1skwvZu

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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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Using synthetic biology to make new antibiotics

Using synthetic biology to make new antibiotics | SynBioFromLeukipposInstitute | Scoop.it
Research at Victoria University of Wellington could lead to a new generation of antibiotics, helping tackle the global issue of ‘superbugs’ that are resistant to modern medicine.
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Recent applications of synthetic biology tools for yeast metabolic engineering

Recent applications of synthetic biology tools for yeast metabolic engineering | SynBioFromLeukipposInstitute | Scoop.it
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Michael K.Jensen andJay D. Keasling

"The last 20 years of metabolic engineering has enabled bio-based production of fuels and chemicals from renewable carbon sources using cost-effective bioprocesses. Much of this work has been accomplished using engineered microorganisms that act as chemical factories. Although the time required to engineer microbial chemical factories has steadily decreased, improvement is still needed. Through the development of synthetic biology tools for key microbial hosts, it should be possible to further decrease the development times and improve the reliability of the resulting microorganism. Together with continuous decreases in price and improvements in DNA synthesis, assembly and sequencing, synthetic biology tools will rationalize time-consuming strain engineering, improve control of metabolic fluxes, and diversify screening assays for cellular metabolism. This review outlines some recently developed synthetic biology tools and their application to improve production of chemicals and fuels in yeast. Finally, we provide a perspective for the challenges that lie ahead."

http://bit.ly/1ucygda

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Natural Genomes Are a Mess. We Want to Synthesize Better Life.

Natural Genomes Are a Mess. We Want to Synthesize Better Life. | SynBioFromLeukipposInstitute | Scoop.it
Hamilton Smith is scientific director of synthetic biology and bioenergy at the J. Craig Venter Institute in La Jolla, California. He shared the 1978 Nobel Prize in physiology or medicine for his discovery of an enzyme that cuts DNA, an advance vital to genetic engineering. He told Kat Austen he...
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Global Synthetic Biology Market 2014-2018 - WhaTech

Global Synthetic Biology Market 2014-2018 - WhaTech | SynBioFromLeukipposInstitute | Scoop.it
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SSBSS 2015 : International Synthetic & Systems Biology Summer School - Biology meets Engineering & Computer Science

SSBSS 2015 : International Synthetic & Systems Biology Summer School - Biology meets Engineering & Computer Science | SynBioFromLeukipposInstitute | Scoop.it
SSBSS 2015 : International Synthetic & Systems Biology Summer School - Biology meets Engineering & Computer Science (SSBSS 2015 : International Synthetic & Systems Biology Summer ...
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BioCoder

BioCoder | SynBioFromLeukipposInstitute | Scoop.it
BioCoder is a quarterly newsletter for DIYbio, synthetic bio, and anything related.
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*A great new edition of BioCoder*

free PDF, epub, mobi

http://oreil.ly/WfVCzh

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Strategy Revealing Phenotypic Differences Among Synthetic Oscillator Designs

Strategy Revealing Phenotypic Differences Among Synthetic Oscillator Designs | SynBioFromLeukipposInstitute | Scoop.it
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Jason G. Lomnitz and Michael A. Savageau

"Considerable progress has been made in identifying and characterizing the component parts of genetic oscillators, which play central roles in all organisms. Nonlinear interaction among components is sufficiently complex that mathematical models are required to elucidate their elusive integrated behavior. Although natural and synthetic oscillators exhibit common architectures, there are numerous differences that are poorly understood. Utilizing synthetic biology to uncover basic principles of simpler circuits is a way to advance understanding of natural circadian clocks and rhythms. Following this strategy we address the following questions: What are the implications of different architectures and molecular modes of transcriptional control for the phenotypic repertoire of genetic oscillators? Are there designs that are more realizable or robust? We compare synthetic oscillators involving one of three architectures and various combinations of the two modes of transcriptional control using a methodology that provides three innovations: a rigorous definition of phenotype, a procedure for deconstructing complex systems into qualitatively distinct phenotypes, and a graphical representation for illuminating the relationship between genotype, environment, and the qualitatively distinct phenotypes of a system. These methods provide a global perspective on the behavioral repertoire, facilitate comparisons of alternatives, and assist the rational design of synthetic gene circuitry. In particular, the results of their application here reveal distinctive phenotypes for several designs that have been studied experimentally as well as a best design among the alternatives that has yet to be constructed and tested."

 http://bit.ly/1zJp9AR

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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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