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Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers

http://bit.ly/NQKUmy

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Tracking Body Rhythms to Diagnose Disease

Tracking Body Rhythms to Diagnose Disease | SynBioFromLeukipposInstitute | Scoop.it

A potential #syntheticbiology app:
"Machines" able to monitor body rhythms:

 

*Studying How Body Rhythms Help Diagnose Disease*

By SHIRLEY S. WANG
"In an effort to develop new ways of diagnosing and treating diseases, scientists are increasingly tracking the various patterns by which the body senses and reacts to stimuli.

Such patterns, commonly referred to as body rhythms, are a constant dynamic. A foot senses a crack in the sidewalk and the brain instructs the muscles to compensate so the person doesn't fall down. Within the body, when cells detect too much carbon dioxide, the lungs respond by taking a breath. To get the right response, neurons, or nerve cells, communicate by emitting electrical impulses that are picked up by other neurons.

Researchers are finding that measuring these electrical impulses can reveal the presence of disease. Recent studies have shown that children with autism have significantly different brain-wave patterns than children without the disorder. Other studies have found that brain waves in people with epilepsy behave differently shortly before a seizure.

James Collins, a researcher at Harvard University's Wyss Institute for Biologically Inspired Engineering, in Boston, has been investigating what he calls balance-control rhythms to understand why people are less steady on their feet as they get older and what can be done to correct that...."
http://on.wsj.com/N79pQR

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Synthetic plant productsWeeding the Gems

Views on synthetic plant products at the New Phytologist Synthetic Biology Workshop

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Whose ethics of knowledge? Taking the next step in evaluating knowledge in synthetic biology: a response to Douglas and Savulescu

Whose ethics of knowledge? Taking the next step in evaluating knowledge in synthetic biology: a response to Douglas and Savulescu

by
Pierce RL.

"The recent proposal by Douglas and Savulescu for an ethics of knowledge provokes a renewed consideration of an enduring issue. Yet, the concept raises significant challenges for procedural and substantive justice. Indeed, the operationalisation of 'an ethics of knowledge' could be as alarming as what it seeks to prevent. While we can acknowledge that there is, and surely always will be, potential for misuse of beneficial science and technology, a contemplated conception of what we ought to not know, devise or disseminate sets before us an enormously complex task. This essay challenges an ethics of knowledge to respond to concerns of procedural and substantive justice. While the concept has a certain appeal, it does not appear to adequately address certain fundamental issues as it is currently presented. Here, the author invites consideration of two primary points: (1) who should decide, based on whose interests? and (2) could such an exercise actually be effective in achieving its goal?"

http://1.usa.gov/Nu0433

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Design Constraints on a Synthetic Metabolism

Design Constraints on a Synthetic Metabolism | SynBioFromLeukipposInstitute | Scoop.it
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The 'atom-splitting' moment of synthetic biology.

Nuclear physics and synthetic biology share common features.

http://1.usa.gov/LrJNjp

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Gold and DNA Could Create New Dark Matter Detector

Gold and DNA Could Create New Dark Matter Detector | SynBioFromLeukipposInstitute | Scoop.it
By Olivia Solon, Wired UKA combined team of physicists and biologists aim to build a directional dark matter detector using strands of DNA ...
 
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Deletion of the Pichia pastoris KU70 Homologue Facilitates Platform Strain Generation for Gene Expression and Synthetic Biology

Deletion of the Pichia pastoris KU70 Homologue Facilitates Platform Strain Generation for Gene Expression and Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
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Systems Biology Software Project

Systems Biology Software Project | SynBioFromLeukipposInstitute | Scoop.it
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High school students from around the globe gather at G-CHS with synthetic biology projects aimed at solving common problems

High school students from around the globe gather at G-CHS with synthetic biology projects aimed at solving common problems | SynBioFromLeukipposInstitute | Scoop.it
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Plastic Republic | Sponsume

Plastic Republic | Sponsume | SynBioFromLeukipposInstitute | Scoop.it
Plastic Republic Our mission is to clean plastic pollution from the oceans using synthetic organisms, with the vision of creating artificial islands! What are we doing? Plastic Republic is a synthetic biology project.
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Rational design of smart supramolecular assemblies for gene delivery: chemical challenges in the creation of artificial viruses - Chemical Society Reviews (RSC Publishing)

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Kanjiro Miyata , Nobuhiro Nishiyama and Kazunori Kataoka

"Polymeric materials have been extensively developed as a delivery vehicle for nucleic acids over the past two decades. Many previous studies have demonstrated that synthetic delivery vehicles can be highly functionalized by chemical approaches to overcome biological barriers in nucleic acid delivery, similar to viruses. Based on our current knowledge, this tutorial review describes rational strategies in the design of polymeric materials to achieve construction of the versatile vehicles, that is “artificial viruses”, for successful gene therapy, especially focusing on the chemical structures with the minimal adverse effects."

http://bit.ly/LNJ4a2

 
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Synthetic Biology: A Primer

Synthetic Biology: A Primer

~ Paul S. Freemont (author) More about this product
Price: $92.00

Book recommendation:

*Synthetic Biology - A Primer*

by
Paul S. Freemont (Author, Editor), Richard I Kitney (Author), Geoff Baldwin (Author), Travis Bayer (Author), Robert Dickinson (Author), Tom Ellis (Author), Karen Polizzi (Author), Guy-Bart Stan (Author), Richard I. Kitney (Editor)

"Synthetic Biology - A Primer" gives a broad overview of the emerging field of synthetic biology and the foundational concepts on which it is built. It will be of interest to final year undergraduates, postgraduates and established researchers who are interested in learning about this exciting new field. The book introduces readers to fundamental concepts in molecular biology and engineering and then explores the two major themes for synthetic biology, namely 'bottom-up' and 'top-down' engineering approaches. 'Top-down' engineering utilises a conceptual framework of engineering and systematic design to build new biological systems by integrating robustly characterised biological parts into an existing system through the use of extensive mathematical modelling. The 'bottom-up' approach involves the design and building of synthetic protocells using basic chemical and biochemical building blocks from scratch. Exemplars of cutting-edge applications designed using synthetic biology principles are presented, including the production of novel biofuels from renewable feedstocks, microbial synthesis of pharmaceuticals and fine chemicals, and the design and implementation of biosensors to detect infections and environmental waste. The book also uses the Internationally Genetically Engineered Machine (iGEM) competition to illustrate the power of synthetic biology as an innovative research and training science. Finally, the primer includes a chapter on the ethical, legal and societal issues surrounding synthetic biology, illustrating the integration of social sciences in synthetic biology research."

$92 hardcover
$38 paperback

http://amzn.to/P1J21z

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Stable gene targeting in human cells using single-s... [PLoS One. 2012] - PubMed - NCBI

Stable gene targeting in human cells using single-strand oligonucleotides with modified bases

by
Rios X, Briggs AW, Christodoulou D, Gorham JM, Seidman JG, Church GM.

"Recent advances allow multiplexed genome engineering in E. coli, employing easily designed oligonucleotides to edit multiple loci simultaneously. A similar technology in human cells would greatly expedite functional genomics, both by enhancing our ability to test how individual variants such as single nucleotide polymorphisms (SNPs) are related to specific phenotypes, and potentially allowing simultaneous mutation of multiple loci. However, oligo-mediated targeting of human cells is currently limited by low targeting efficiencies and low survival of modified cells. Using a HeLa-based EGFP-rescue reporter system we show that use of modified base analogs can increase targeting efficiency, in part by avoiding the mismatch repair machinery. We investigate the effects of oligonucleotide toxicity and find a strong correlation between the number of phosphorothioate bonds and toxicity. Stably EGFP-corrected cells were generated at a frequency of ~0.05% with an optimized oligonucleotide design combining modified bases and reduced number of phosphorothioate bonds. We provide evidence from comparative RNA-seq analysis suggesting cellular immunity induced by the oligonucleotides might contribute to the low viability of oligo-corrected cells. Further optimization of this method should allow rapid and scalable genome engineering in human cells."
http://bit.ly/MbNeVW
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Design and Assembly of Large Synthetic DNA Constructs - Current Protocols in Molecular Biology - Miklos - Wiley Online Library

Design and Assembly of Large Synthetic DNA Constructs - Current Protocols in Molecular Biology - Miklos - Wiley Online Library | SynBioFromLeukipposInstitute | Scoop.it

 

 
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Science in three dimensions: The print revolution

Science in three dimensions: The print revolution | SynBioFromLeukipposInstitute | Scoop.it

by

Nicola Jones
"Three-dimensional printers are opening up new worlds to research.
Christoph Zollikofer witnessed the first birth of a Neanderthal in the modern age. In his anthropology lab at the University of Zurich, Switzerland, in 2007, the skull of a baby Homo neanderthalensis emerged from a photocopier-sized machine after a 20-hour noisy but painless delivery of whirring motors and spitting plastic. This modern miracle had endured a lengthy gestation: it took years for Zollikofer's collaborators to find suitable bones from a Neanderthal neonate, analyse them with a computed-tomography (CT) scanner and digitally stitch them together on the computer screen. The labour, however, was simple: Zollikofer just pressed 'print' on his lab's US$50,000 three-dimensional (3D) printer......"
http://bit.ly/M5Rqff

 
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Journal of Biological Engineering | Full text | Engineering BioBrick vectors from BioBrick parts

The underlying goal of synthetic biology is to make the process of engineering biological systems easier. Recent work has focused on defining and developing standard biological parts.

 
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Post-translational tools expand the scope of synthetic biology

Post-translational tools expand the scope of synthetic biology | SynBioFromLeukipposInstitute | Scoop.it

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Evan J Olson, Jeffrey J Tabor
"Synthetic biology is improving our understanding of and ability to control living organisms. To date, most progress has been made by engineering gene expression. However, computational and genetically encoded tools that allow protein activity and protein–protein interactions to be controlled on their natural time and length scales are emerging. These technologies provide a basis for the construction of post-translational circuits, which are capable of fast, robust and highly spatially resolved signal processing. When combined with their transcriptional and translational counterparts, synthetic post-translational circuits will allow better analysis and control of otherwise intractable biological processes such as cellular differentiation and the growth of tissues.

Highlights
► Phytochromes and LOV domains are being used for spatiotemporal control of protein activity in cells. ► Computational redesign of CDC42/ISTN interface generates orthogonal signaling pathway. ► Computation-guided design of 180 pmKd PPI paves way for the design of modular protein networks. ► Stem cell differentiation can be controlled with synthetic transcriptional and post-translational networks."

http://bit.ly/M8Ffut

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A DNA-based molecular motor that can navigate a network of tracks

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Wickham SF, Bath J, Katsuda Y, Endo M, Hidaka K, Sugiyama H, Turberfield AJ.
"Synthetic molecular motors can be fuelled by the hydrolysis or hybridization of DNA. Such motors can move autonomously and programmably, and long-range transport has been observed on linear tracks. It has also been shown that DNA systems can compute. Here, we report a synthetic DNA-based system that integrates long-range transport and information processing. We show that the path of a motor through a network of tracks containing four possible routes can be programmed using instructions that are added externally or carried by the motor itself. When external control is used we find that 87% of the motors follow the correct path, and when internal control is used 71% of the motors follow the correct path. Programmable motion will allow the development of computing networks, molecular systems that can sort and process cargoes according to instructions that they carry, and assembly lines that can be reconfigured dynamically in response to changing demands."
http://1.usa.gov/L0Ku1p

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BioPrinting Humanity? Where It’s Heading

BioPrinting Humanity? Where It’s Heading | SynBioFromLeukipposInstitute | Scoop.it
Oli Archibald, ‏@FutureSelfOli  sent this interesting infographic my way on bioprinting human beings. Thought I would share. What’s your take?
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"I Like to Build Alien Artifacts"

"I Like to Build Alien Artifacts" | SynBioFromLeukipposInstitute | Scoop.it

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Stephen Wolfram

"Can cells become little computers? And how does technological progress challenge our ideas about free will, intelligence, and the purpose of human life? Martin Eiermann sat down with the computer scientist Stephen Wolfram to discuss these questions..."
http://bit.ly/N69FeC
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Brown Stanford iGEM Interview with Raymond McCauley

Brown Stanford iGEM talks with Raymond McCauley- career bioinformaticist, entrepreneur, and futurist. Raymond McCauley is Chair of the Biotechnology Track an...
 
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Focus: Synthetic biology

Focus: Synthetic biology | SynBioFromLeukipposInstitute | Scoop.it

" Synthetic biology (SynBio) can be defined as the design and construction of new biological parts, devices and systems. The field has now advanced from first-generation understanding to smarter engineering. This focus issue of BTJ gives several examples; e.g. Morey et al. review the current status of plant synthetic biology and the crosstalk between endogenous and synthetic components"

http://bit.ly/R5fVrj

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Chemistry Innovation - New Frontiers in Synthetic Biology - Articles - Open Innovation

Chemistry Innovation - New Frontiers in Synthetic Biology - Articles - Open Innovation | SynBioFromLeukipposInstitute | Scoop.it

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Rebecca Farnell

"The Technology Strategy Board and The Synthetic Biology Special Interest Group are organising a series of consortia-building workshops to promote the competition for feasibility funding:
"Advancing the Industrial Application of Synthetic Biology"
The workshops will enable delegates to get a better understanding the competition scope and application process ahead of the official opening of the call on October 8th and encourage networking opportunities from which collaborations may develop.
Synthetic biology offers new potential to produce chemicals in a smarter more sustainable way. More information on the events can be found through the links below.
New Frontiers in Synthetic Biology, 10 July 2012, Ambassadors Bloomsbury Hotel, London
New Frontiers in Synthetic Biology Regional workshop - Edinburgh, 24 July 2012, The George Hotel, Edinburgh
New Frontiers in Synthetic Biology Regional workshop - Manchester, 25 July 2012, The Hilton Manchester Deansgate Hotel, Manchester
For more information on the Synthetic Biology Special Interest Group can be found here.."

http://bit.ly/MtOokz

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193: TZ Interview – Cathal Garvey / Biohacking

193: TZ Interview – Cathal Garvey / Biohacking | SynBioFromLeukipposInstitute | Scoop.it

Interviews Cathal Garvey about #SynBio, DIYbio and his new startup, Glowbiotics http://bit.ly/N4YaaI

 

If you're a hacker, you'll probably like our show ;)...

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