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Spontaneous activation of [FeFe]-hydrogenases by an inorganic [2Fe] active site mimic

Spontaneous activation of [FeFe]-hydrogenases by an inorganic [2Fe] active site mimic | SynBioFromLeukipposInstitute | Scoop.it
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*New materials for bio-based hydrogen synthesis: synthetic biology enables spontaneous protein activation*

by
Anonymous

Researchers at the Ruhr-Universität Bochum (RUB) have discovered an efficient process for hydrogen biocatalysis. They developed semi-synthetic hydrogenases, hydrogen-generating enzymes, by adding the protein's biological precursor to a chemically synthesized inactive iron complex. From these two components, the biological catalyst formed spontaneously in a test tube. “Extracting hydrogenases from living cells is highly difficult,” says Prof Dr Thomas Happe, head of the work group Photobiotechnology at the RUB. “Therefore, their industrial application has always been a long way off. Now, we have made a decisive step towards the generation of bio-based materials.”  
http://bit.ly/1cIx0EO


Original ref:

*Spontaneous activation of [FeFe]-hydrogenases by an inorganic [2Fe] active site mimic*

by
Julian Esselborn,Camilla Lambertz,Agnieszka Adamska-Venkatesh,Trevor Simmons, Gustav Berggren,Jens Noth,Judith Siebel,Anja Hemschemeier,Vincent Artero,Edward Reijerse,Marc Fontecave,Wolfgang Lubitz& Thomas Happe

"Hydrogenases catalyze the formation of hydrogen. The cofactor ('H-cluster') of [FeFe]-hydrogenases consists of a [4Fe-4S] cluster bridged to a unique [2Fe] subcluster whose biosynthesis in vivo requires hydrogenase-specific maturases. Here we show that a chemical mimic of the [2Fe] subcluster can reconstitute apo-hydrogenase to full activity, independent of helper proteins. The assembled H-cluster is virtually indistinguishable from the native cofactor. This procedure will be a powerful tool for developing new artificial H2-producing catalysts."

 http://bit.ly/1d11ws7

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Synthetic Biology Club formed, Waltham students compete at MIT - Wicked Local Waltham | CodonOps

Synthetic Biology Club formed, Waltham students compete at MIT - Wicked Local Waltham | CodonOps | SynBioFromLeukipposInstitute | Scoop.it
Synthetic Biology Club formed, Waltham students compete at MITWicked Local WalthamParent Edward Wack introduced Maddox to the iGEM (International Genetically Engineered Machine) competition last year.
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Assembly of Designed Oligonucleotides: A Useful Tool in Synthetic Biology for Creating High-Quality Combinatorial DNA Libraries

Assembly of Designed Oligonucleotides: A Useful Tool in Synthetic Biology for Creating High-Quality Combinatorial DNA Libraries | SynBioFromLeukipposInstitute | Scoop.it
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by
Acevedo-Rocha CG, Reetz MT.

"The method dubbed Assembly of Designed Oligonucleotides (ADO) is a powerful tool in synthetic biology to create combinatorial DNA libraries for gene, protein, metabolic, and genome engineering. In directed evolution of proteins, ADO benefits from using reduced amino acid alphabets for saturation mutagenesis and/or DNA shuffling, but all 20 canonical amino acids can be also used as building blocks. ADO is performed in a two-step reaction. The first involves a primer-free, polymerase cycling assembly or overlap extension PCR step using carefully designed overlapping oligonucleotides. The second step is a PCR amplification using the outer primers, resulting in a high-quality and bias-free double-stranded DNA library that can be assembled with other gene fragments and/or cloned into a suitable plasmid subsequently. The protocol can be performed in a few hours. In theory, neither the length of the DNA library nor the number of DNA changes has any limits. Furthermore, with the costs of synthetic DNA dropping every year, after an initial investment is made in the oligonucleotides, these can be exchanged for alternative ones with different sequences at any point in the process, fully exploiting the potential of creating highly diverse combinatorial libraries. In the example chosen here, we show the construction of a high-quality combinatorial ADO library targeting sixteen different codons simultaneously with nonredundant degenerate codons encoding various reduced alphabets of four amino acids along the heme region of the monooxygenase P450-BM3."

 http://bit.ly/WRFCE2

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PNAS -- Science Sessions Podcasts

PNAS -- Science Sessions Podcasts | SynBioFromLeukipposInstitute | Scoop.it
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Podcast: James Collins explains how researchers can rewire bacterial cells and control multiple genes simultaneously within a single cell http://bit.ly/1lANPC2

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The synthetic biology toolbox for tuning gene expression in yeast

The synthetic biology toolbox for tuning gene expression in yeast | SynBioFromLeukipposInstitute | Scoop.it
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by
Redden H, Morse N, Alper HS.

"Saccharomyces cerevisiae can serve as a key production platform for biofuels, nutraceuticals, industrial compounds, and therapeutic proteins. Over the recent years, synthetic biology tools and libraries have expanded in yeast to provide newfound control over regulation and synthetic circuits. This review provides an update on the status of the synthetic biology toolbox in yeast for use as a cell factory. Specifically, we discuss the impact of plasmid selection and composition, promoter, terminator, transcription factor, and aptamer selection. In doing so, we highlight documented interactions between these components, current states of development, and applications that demonstrate the utility of these parts with a particular focus on synthetic gene expression control."

http://bit.ly/1z3mmkA

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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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by
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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by
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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by
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*

by
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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Interview: Nicola Patron on Plant Synthetic Biology, MoClo, and More

Interview: Nicola Patron on Plant Synthetic Biology, MoClo, and More | SynBioFromLeukipposInstitute | Scoop.it
Interview with Nicola Patron about her work in plant synthetic biology and her Golden Gate MoClo plasmid kit.
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A chromatin-based recruitment drive

A chromatin-based recruitment drive | SynBioFromLeukipposInstitute | Scoop.it

-

Socrates Logos's insight:

by
Darren J. Burgess

"A cornerstone of synthetic biology and biological engineering is achiev- ing 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 chro- matin regulators might provide a flexible and powerful way to regulate different aspects of gene expression.

Chromatin states in eukaryotic cells are modulated in various ways — including by DNA methylation, histone modifications and nucleo- some remodelling — thus providing opportunities for ‘fine-tuning’ the regulation of gene expression. An emerging approach to assess the gene regulatory effects of specific chromatin regulator proteins is ‘epi- genome editing’, in which chromatin regulators are fused to sequence- specific DNA-binding proteins to allow their recruitment to a chosen locus. Such a strategy has so far characterized only a few chromatin- modifying enzymes. So, Keung et al. took a systematic approach by generating a library of 223 yeast chromatin regulators fused to zinc- finger (ZF) DNA-binding proteins, although the system is potentially also applicable to the transcription activator-like effector (TALE) and CRISPR–Cas genome targeting systems. ..."

comment to: ORIGINAL RESEARCH PAPER Keung, A. J. et al. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell 158, 110–120 (2014)

 http://bit.ly/1nYl7er

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Synthetic Biology Congress

Synthetic Biology Congress | SynBioFromLeukipposInstitute | Scoop.it
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Synthetic Biology Congress London 20-21 Oct http://bit.ly/1x2xf3p

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Total synthesis of a eukaryotic chromosome: Redesigning and SCRaMbLE-ing yeast

Total synthesis of a eukaryotic chromosome: Redesigning and SCRaMbLE-ing yeast | SynBioFromLeukipposInstitute | Scoop.it
Socrates Logos's insight:

by
Dejana Jovicevic, Benjamin A. Blount andTom Ellis

"A team of US researchers recently reported the design, assembly and in vivo functionality of a synthetic chromosome III (SynIII) for the yeast Saccharomyces cerevisiae. The synthetic chromosome was assembled bottom-up from DNA oligomers by teams of students working over several years with researchers as the first part of an international synthetic yeast genome project. Embedded into the sequence of the synthetic chromosome are multiple design changes that include a novel in-built recombination scheme that can be induced to catalyse intra-chromosomal rearrangements in a variety of different conditions. This system, along with the other synthetic sequence changes, is intended to aid researchers develop a deeper understanding of how genomes function and find new ways to exploit yeast in future biotechnologies. The landmark of the first synthesised designer eukaryote chromosome, and the power of its massively parallel recombination system, provide new perspectives on the future of synthetic biology and genome research."

 http://bit.ly/1sSEZY5

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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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by
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.
Socrates Logos's insight:

*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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by
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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