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In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation

In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation | SynBioFromLeukipposInstitute | Scoop.it
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Michael C Jewett, Brian R Fritz, Laura E Timmerman & George M Church

"This report describes an integrated method for in vitro construction of Escherichia coli ribosomes under near-physiological conditions. This method enables coupling of ribosome synthesis and assembly in a single, integrated system.

An integrated synthesis, assembly, and translation technology (termed iSAT) was developed to construct ribosomes in vitro.iSAT mimics co-transcription of rRNA and ribosome assembly as it occurs in vivo.iSAT makes possible the in vitro construction of modified ribosomes.iSAT is expected to aid studies of ribosome assembly and open new avenues for making ribosomes with altered capabilities.Top of pageAbstractPurely in vitro ribosome synthesis could provide a critical step towards unraveling the systems biology of ribosome biogenesis, constructing minimal cells from defined components, and engineering ribosomes with new functions. Here, as an initial step towards this goal, we report a method for constructing Escherichia coli ribosomes in crude S150 E. coli extracts. While conventional methods for E. coli ribosome reconstitution are non-physiological, our approach attempts to mimic chemical conditions in the cytoplasm, thus permitting several biological processes to occur simultaneously. Specifically, our integrated synthesis, assembly, and translation (iSAT) technology enables one-step co-activation of rRNA transcription, assembly of transcribed rRNA with native ribosomal proteins into functional ribosomes, and synthesis of active protein by these ribosomes in the same compartment. We show that iSAT makes possible the in vitro construction of modified ribosomes by introducing a 23S rRNA mutation that mediates resistance against clindamycin. We anticipate that iSAT will aid studies of ribosome assembly and open new avenues for making ribosomes with altered properties."


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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."



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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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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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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."



http://bit.ly/1vCuvJd

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