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Proteins designed to self-assemble

"Large protein complexes can be designed and created using smaller protein building blocks that self-assemble. David Baker at the University of Washington, Seattle, and his team report a method for producing such proteins. The authors simulate the docking of protein building blocks in desired architectures and then design amino-acid sequences for these blocks that result in low-energy interfaces between the blocks, driving self-assembly. The researchers incorporate the genes that encode the designed blocks into the bacterium Escherichia coli, which produces the proteins that then spontaneously self-assemble into the target architectures. The team created two cage-like proteins: one consisting of 24 building blocks in a 13-nanometre-wide complex with octahedral symmetry (pictured) and another comprising 12 subunits with an 11-nanometre-wide tetrahedral symmetry."

http://bit.ly/L69iCy

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Microbial synthetic biology for human therapeutics

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Aastha Jain, Pooja Bhatia and Archana Chugh

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KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry : Nature Chemical Biology : Nature Publishing Group

KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry : Nature Chemical Biology : Nature Publishing Group | SynBioFromLeukipposInstitute | Scoop.it

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Karin Betz, Denis A Malyshev, Thomas Lavergne, Wolfram Welte, Kay Diederichs, Tammy J Dwyer, Phillip Ordoukhanian, Floyd E Romesberg & Andreas Marx
"Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure."

http://bit.ly/L5EiTc

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"I think the biggest innovation of the twenty-first century .....

......will be the intersection of biology and technology. A new era is beginning, just like the digital one when I was at his (Reed) age." Steve Jobs

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The Synthetic Bestiary – Synthetic Biology, Genetic Engineering, and The Future

The Synthetic Bestiary – Synthetic Biology, Genetic Engineering, and The Future | SynBioFromLeukipposInstitute | Scoop.it
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Genetically encoded RNA photoswitches as tools for the control of gene expression.

Genetically encoded RNA photoswitches as tools for the control of gene expression.

by
Jäschke A.
"An important goal in chemical and synthetic biology is controlling the expression of defined sets of genes by external stimuli, and one of the most attractive stimuli is light. Current approaches to the photocontrol of biological processes utilize photoresponsive proteins. In this article, I will illustrate the prospects of synthetic systems in which the receptor is a photoresponsive nucleic acid, and will review the different tools already in place to develop photoresponsive systems based on RNA. A particular focus is on genetically encoded photoswitches that can be expressed in prokaryotic or eukaryotic cells, and respond to photoisomerizable, cell-permeable small molecules."

http://1.usa.gov/JTAeYp

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It's Time to Bet on Genomics - Forbes

It's Time to Bet on Genomics - Forbes | SynBioFromLeukipposInstitute | Scoop.it
This article is by Ronald W. Davis, director of the Stanford Genome Technology Center and professor of biochemistry and genetics at the Stanford University School of Medicine.
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ScienceDirect.com - Cellular Signalling - Synthetic biology with surgical precision: Targeted reengineering of signaling proteins

ScienceDirect.com - Cellular Signalling - Synthetic biology with surgical precision: Targeted reengineering of signaling proteins | SynBioFromLeukipposInstitute | Scoop.it

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Vsevolod V. Gurevich, , Eugenia V. Gurevich
"Highlights
► Targeted manipulation of cell signaling pathways has high therapeutic potential
► Changed expression of wild type proteins can change cell function
► Reengineered signaling proteins change the flow of information in the cell ► Novel proteins constructed from existing domains modify cell signaling"
http://bit.ly/KumVyT

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Researchers achieve RNA interference, in a lighter package - MIT News Office

Researchers achieve RNA interference, in a lighter package - MIT News Office | SynBioFromLeukipposInstitute | Scoop.it
Pared-down nucleic acid nanoparticle poses less risk of side effects, offers better targeting.
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Amazon.com: Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves (9780465021758): George M. Church, Ed Regis: Books

Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves

~ Ed Regis (author) More about this product
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Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves

by
George M. Church, Ed Regis
http://amzn.to/KKuNdS

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Molecular algebra in mammalian cells

Molecular algebra in mammalian cells | SynBioFromLeukipposInstitute | Scoop.it

Molecular algebra in mammalian cells

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Peter Rüegg
"Mammalian cells can now do what an electronic calculator can: perform logical calculations. ETH-Zurich researchers have equipped cells with a complex genetic network that can do more than just one plus one...."
http://bit.ly/M62N0c

 
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Streamlining genomes: toward the generation of simplified and stabilized microbial systems

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Leprince A, van Passel MW, Dos Santos VA.

"At the junction between systems and synthetic biology, genome streamlining provides a solid foundation both for increased understanding of cellular circuitry, and for the tailoring of microbial chassis towards innovative biotechnological applications. Iterative genomic deletions (targeted and random) helps to generate simplified, stabilized and predictable genomes, whereas multiplexing genome engineering reveals a broad functional genetic diversity. The decrease in oligo and gene synthesis costs promises effective combinatorial tools for the generation of chassis based on streamlined and tractable genomes. Here we review recent progresses in streamlining genomes through recombineering techniques aiming to generate insights into cellular mechanisms and responses towards the design and assembly of streamlined genome chassis together with new cellular modules in diverse biotechnological applications."

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Nuit Blanche: What is Faster than Moore's Law and Why You Should Care

Nuit Blanche: What is Faster than Moore's Law and Why You Should Care | SynBioFromLeukipposInstitute | Scoop.it

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Igor Carron

"The rise of synthetic biology as a tool to experiment what and what is not feasible is linked mostly to two endeavors: The accelerated pace of both sequencing and synthesis machines. In the sequencing realm, researchers need to change their slides every fifteen days but the most astounding area, i.e. where opportunities for high dimensional data understanding reside, stems from the faster-than-Moore's law cost decrease for these machines....."

 
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Biomaterial patterning applications, including those involving hydrogels

Biomaterial patterning applications, including those involving hydrogels | SynBioFromLeukipposInstitute | Scoop.it
Print proteins, lipids and polymers With nano- to micron-sized features

"NanoInk’s Dip Pen Nanolithography® (DPN®) technology is a direct write, tip based lithography technique that does not subject biological materials to destructive forces (such as compression, shear, harsh vacuum, or UV light) which might alter their structure and function. As such, DPN is ideal for printing proteins, DNA/RNA, aptamers, lipids, additional biopolymers and biocompatible polymers at micron and sub-micron scales. With the precision of DPN, these sub-cellular scaled features can be deposited at defined locations in a controlled and consistent manner. This allows for creation of scaffolds for in vitro cell culture studies or tissue engineering work. "
http://bit.ly/Mpj6W7

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Cellular Computing - Google+

Cellular Computing - Google+ | SynBioFromLeukipposInstitute | Scoop.it
Cellular Computing

is a new page on G+ where you can discuss exiting concepts and publication around cellular computer. Have a look! Really cool material.....

https://plus.google.com/u/0/b/106140549977596536572/

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Bacterial signaling systems as platforms for rational design of new generations of biosensors

Bacterial signaling systems as platforms for rational design of new generations of biosensors

by
Checa SK, Zurbriggen MD, Soncini FC.
"Bacterial signal-responsive regulatory circuits have been employed as platform to design and construct whole-cell bacterial biosensors for reporting toxicity. A new generation of biosensors with improved performance and a wide application range has emerged after the application of synthetic biology concepts to biosensor design. Site-directed mutagenesis, directed evolution and domain swapping were applied to upgrade signal detection or to create novel sensor modules. Rewiring of the genetic circuits allows improving the determinations and reduces the heterogeneity of the response between individual reporter cells. Moreover, the assembly of natural or engineered modules to biosensor platforms provides innovative outputs, expanding the range of application of these devises, from monitoring toxics and bioremediation to killing targeted cells."
http://1.usa.gov/JTBbQj

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Scientists: your number is up

Scientists: your number is up | SynBioFromLeukipposInstitute | Scoop.it
ORCID scheme will give researchers unique identifiers to improve tracking of publications.
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Understudies of DNA and RNA Nature Methods

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Nicole Rusk
"With the help of engineered polymerases and reverse transcriptases, synthetic nucleic acids can encode and pass on genetic information.
The fact that in biology information flows bidirectionally—from DNA to RNA and then back to DNA—raised a question for Phil Holliger at the Medical Research Council (Cambridge, UK): is there something inherently special about DNA and RNA, or can other polymers exchange information as well?

In the last 30 years, biological chemists have developed a wide range of potential DNA mimics—which Holliger refers to as xeno-nucleic acids (XNA)—that have the ability to hybridize to DNA and RNA: for example, locked nucleic acids, which are widely used as inhibitors of mRNA or microRNAs. But to answer his questions, Holliger needed to go beyond hybridization. “We wanted not just to synthesize polymers but [to] create a replication loop, from DNA to XNA back to DNA,” he says.

His team decided to concentrate on changing the sugar in the nucleic acid rather than the phosphate backbone or the nucleobases. Because they retained the classical nucleobases G, A, T and C, the XNAs also kept the ability to interact with DNA. The researchers swapped the canonical five-membered ribofuranose sugar ring for other structures—for example, hydrohexitol to make hydrohexitol nucleic acids (HNAs). ....."

http://bit.ly/Nf8u1k

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Contextualizing context for synthetic biology – identifying causes of failure of synthetic biological systems

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Stefano Cardinale, Adam Paul Arkin
"Despite the efforts that bioengineers have exerted in designing and constructing biological processes that function according to a predetermined set of rules, their operation remains fundamentally circumstantial. The contextual situation in which molecules and single-celled or multi-cellular organisms find themselves shapes the way they interact, respond to the environment and process external information. Since the birth of the field, synthetic biologists have had to grapple with contextual issues, particularly when the molecular and genetic devices inexplicably fail to function as designed when tested in vivo. In this review, we set out to identify and classify the sources of the unexpected divergences between design and actual function of synthetic systems and analyze possible methodologies aimed at controlling, if not preventing, unwanted contextual issues."

http://bit.ly/KulLTQ

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TWiT Live Specials 126: Democratizing Creation

Creating tools that enable the design and creation of useful living things, and more. Host: Leo Laporte Guest: Omri Drory and Austen Heinz ...

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Programmable single-cell mammalian biocomputers

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Simon Ausländer, David Ausländer, Marius Müller, Markus Wieland & Martin Fussenegger
"Synthetic biology has advanced the design of standardized control devices that program cellular functions and metabolic activities in living organisms1. Rational interconnection of these synthetic switches resulted in increasingly complex designer networks that execute input-triggered genetic instructions with precision, robustness and computational logic reminiscent of electronic circuits2, 3. Using trigger-controlled transcription factors, which independently control gene expression4, 5, and RNA-binding proteins that inhibit the translation of transcripts harbouring specific RNA target motifs6, 7, we have designed a set of synthetic transcription–translation control devices that could be rewired in a plug-and-play manner. Here we show that these combinatorial circuits integrated a two-molecule input and performed digital computations with NOT, AND, NAND and N-IMPLY expression logic in single mammalian cells. Functional interconnection of two N-IMPLY variants resulted in bitwise intracellular XOR operations, and a combinatorial arrangement of three logic gates enabled independent cells to perform programmable half-subtractor and half-adder calculations. Individual mammalian cells capable of executing basic molecular arithmetic functions isolated or coordinated to metabolic activities in a predictable, precise and robust manner may provide new treatment strategies and bio-electronic interfaces in future gene-based and cell-based therapies."
http://bit.ly/LhEZpo

 
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Patent Ecology

Patent Ecology | SynBioFromLeukipposInstitute | Scoop.it

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Christina Agapakis

 "Blogs About the SA Blog Network

Oscillator

Notes, thoughts, and news on synthetic biology.
Oscillator HomeAboutContact
Patent Ecology
By Christina Agapakis | June 1, 2012 |

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Patents in biotechnology are complicated and controversial, with different groups arguing that they either promote innovation or stifle important research. Cases like that of Myriad Genetics, which patented gene variants associated with high risk of breast cancer in 1997, are still being fought in court, with patents invalidated and rulings appealed. At the same time, patents on synthetic genes and synthetic biology tools are being filed in parallel with a more open source approach to basic research, to spur investment in companies using the tools of synthetic biology and to promote open collaboration by a diverse community of researchers.

The recent news of 23andMe’s first patent shows how patents on natural genes continue despite the complex legal situation faced by other companies, and despite an explicitly stated ethos of openness and “democratization.” 23andMe has patented methods for screening the naturally occurring variants of the human genome they found to be associated with risk for Parkinson’s disease. The announcement on the company’s blog, The Spittoon, clarifies what they hope the patent will and won’t do:......"
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DNA-wrangling robot performs 200,000 experiments a week

DNA-wrangling robot performs 200,000 experiments a week | SynBioFromLeukipposInstitute | Scoop.it
When you think of robots in agriculture, you likely think of automatic threshers, fruit picking machines and corn huskers. But a recent addi...

 

(The future work for scientist will be designing abstarction and coding)

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