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John Melo-Synthetic Biology in Action

From an open-source anti-malarial compound to renewable energy resources, Amyris Biotechnologies CEO John Melo explains his enterprise's corporate acts of al...
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Optochemical Control of Deoxyoligonucleotide Function via a Nucleobase-Caging Approach

Optochemical Control of Deoxyoligonucleotide Function via a Nucleobase-Caging Approach | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Qingyang Liu  and Alexander Deiters

"Synthetic oligonucleotides have been extensively applied tocontrol a wide range of biological processes such as gene expression, gene repair, DNA replication, and protein activity. Based on well-established sequence design rules that typically rely on Watson–Crick base pairing interactions researchers can readily program the function of these oligonucleotides. Therefore oligonucleotides provide a flexible platform for targeting a wide range of biological molecules, including DNA, RNA, and proteins. In addition, oligonucleotides are commonly used research tools in cell biology and developmental biology. However, a lack of conditional control methods has hampered the precise spatial and temporal regulation of oligonucleotide activity, which limits the application of these reagents to investigate complex biological questions. Nature controls biological function with a high level of spatial and temporal resolution and in order to elucidate the molecular mechanisms of biological processes, researchers need tools that allow for the perturbation of these processes with Nature’s precision.

 Light represents an excellent external regulatory element since irradiation can be easily controlled spatially and temporally. Thus, researchers have developed several different methods to conditionally control oligonucleotide activity with light. One of the most versatile strategies is optochemical regulation through the installation and removal of photolabile caging groups on oligonucleotides. To produce switches that can control nucleic acid function with light, chemists introduce caging groups into the oligomer backbone or on specific nucleobases to block oligonucleotide function until the caging groups are removed by light exposure. In this Account, we focus on the application of caged nucleobases to the photoregulation of DNA function. Using this approach, we have both activated and deactivated gene expression optochemically at the transcriptional and translational level with spatial and temporal control. Specifically, we have used caged triplex-forming oligomers and DNA decoys to regulate transcription, and we have regulated translation with light-activated antisense agents. Moreover, we also discuss strategies that can trigger DNA enzymatic activity, DNA amplification, and DNA mutagenesis by light illumination. More recently, we have developed light-activated DNA logic operations, an advance that may lay the foundation for the optochemical control of complex DNA calculations."



http://bit.ly/18o8p1e

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The development of synthetic biology: a patent analysis

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The development of synthetic biology: a patent analysis http://bit.ly/19OmBUl

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A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language

PubMed comprises more than 23 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Gerd Moe-Behrens's insight:

by
Roehner N, Myers CJ.

"Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, have often failed in translation and application to new projects, a problem exacerbated by a lack of engineering standards that combine descriptions of the structure and function of DNA. To address this need, this paper describes a methodology to connect the Systems Biology Markup Language (SBML) to the Synthetic Biology Open Language (SBOL), existing standards that describe biochemical models and DNA components, respectively. Our methodology involves first annotating SBML model elements such as species and reactions with SBOL DNA components. A graph is then constructed from the model, with vertices corresponding to elements within the model and edges corresponding to the cause-and-effect relationships between these elements. Lastly, the graph is traversed to assemble the annotating DNA components into a composite DNA component, which is used to annotate the model itself and can be referenced by other composite models and DNA components. In this way, our methodology can be used to build up a hierarchical library of models annotated with DNA components. Such a library is a useful input to any future genetic technology mapping algorithm that would automate the process of composing DNA components to satisfy a behavioral specification. Our methodology for SBML-to-SBOL annotation is implemented in the latest version of our genetic design automation (GDA) software tool, iBioSim."

http://1.usa.gov/1402xPR

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The top 20 most influential people in synthetic biology

The top 20 most influential people in synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
  Who are the most influential people at the scientific and commercial end of synthetic biology?This is the question we asked our blog subscribers, LinkedIn
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The top 20 most influential people in synthetic biology http://bit.ly/1doauCu

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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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Embracing Open-Source Biotech: DNA Freeware May Out-Innovate Patented Genes

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 http://bit.ly/188f2G5

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A great opportunity to design your very own biological computer

A great opportunity to design your very own biological computer | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

As you might  know, my main project is the biological computer. I have developed some computer assisted design software, which I wish to make open access. To do so I need to raise some money. I have participated in a startup engineering MOOC class provided by Stanford University. In this frame I have written the software for a crowd funding web app. Please have a look at this campaign. There are many interesting rewards for the supporters. 100 supporters can get exclusively access to the pre release of computer assisted design software to design your very own biological computer. An awesome entrepreneurial opportunity. This option will only be open for 11 days.

This project is part of a competition held by Stanford University. The winning project will get special support.

The team with the most bit coins raised or the most tweets will get promotion.

You can be a part of this in several ways:

1) Go to the app and press the tweet button

2) donate some bit coins and get exiting rewards, be one of the first 100 people in the world to get hand on a revolutionary product

Thanks for your support.

http://cytocomp-bitstarter-mooc.herokuapp.com

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Embracing Open-Source Biotech: DNA Freeware May Out-Innovate Patented Genes

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Embracing Open-Source Biotech: DNA Freeware May Out-Innovate Patented Genes http://bit.ly/17ktL2x

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INVITED SPEAKERS | GENOBIOTEC 13

INVITED SPEAKERS | GENOBIOTEC 13 | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

I just got invited to give a talk about biological computing at an exiting conference with many great speakers:

#genobiotec

1 - Eric Davidson, California Institute of Technology.

2 - Pamela A. Silver, Harvard University
Designing Biological Systems for Health and Livability.

3 - James Ferrell, Stanford University
Bistability and trigger waves in the regulation of mitosis

4 - Julio Collado Vidés, Universidad Nacional Autónoma de México
Accelerating information access: challenges in genomics and the 21st century

5 - Mauricio Antunes, Colorado State University, Engineering synthetic sensing and signal transduction traits in plants

6 -  Octavio Mondragón-Palomino, Massachusetts Institute of Technology, Circuit design in synthetic biology

7 - J. Ruben Morones-Ramírez, Universidad Autónoma de Nuevo León

8 - Caroline Ajo-Franklin, Lawrence Berkeley National Laboratory, 

9 - Farren Isaacs, Yale University

10 - Peng Yin, Harvard University, Programming Nucleic Acids Self-Assembly

11 - Gerd Moe-Behrens, Leukippos Institute, CytoComp, The biological microprocessor, or how to build a computer with biological parts

PS the page get`s soon updated also with another speaker from Amyris 
--------------------------------------------------

13 Nov21-23 Monterrey,
Nuevo León,
 México.

 http://bit.ly/1fjzMNK

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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
Gerd Moe-Behrens's insight:

by
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
Gerd Moe-Behrens's insight:

by
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.
Gerd Moe-Behrens's insight:

by

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
Gerd Moe-Behrens's insight:

by
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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