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Synthetic, Systems Biology and DNA Computing
Synthetic Biology, Systems Biology and DNA Computing
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Rescooped by Alfonso Rodriguez-Paton from SynBioFromLeukipposInstitute
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Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells

Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells | Synthetic, Systems Biology and DNA Computing | Scoop.it

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Socrates Logos's curator insight, May 20, 2014 5:31 PM

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Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK

"Highlights

•Multiplexed CRISPR/Cas guide RNAs are expressed from single compact transcripts
•Guide RNAs are generated from RNA polymerase II promoters with three strategies
•Multistage cascades and gene circuits are created with CRISPR-TFs and microRNAs
•Csy4-based RNA processing enables synchronized circuit rewiring at the RNA level
Summary
RNA-based regulation and CRISPR/Cas transcription factors (CRISPR-TFs) have the potential to be integrated for the tunable modulation of gene networks. A major limitation of this methodology is that guide RNAs (gRNAs) for CRISPR-TFs can only be expressed from RNA polymerase III promoters in human cells, limiting their use for conditional gene regulation. We present new strategies that enable expression of functional gRNAs from RNA polymerase II promoters and multiplexed production of proteins and gRNAs from a single transcript in human cells. We use multiple RNA regulatory strategies, including RNA-triple-helix structures, introns, microRNAs, and ribozymes, with Cas9-based CRISPR-TFs and Cas6/Csy4-based RNA processing. Using these tools, we efficiently modulate endogenous promoters and implement tunable synthetic circuits, including multistage cascades and RNA-dependent networks that can be rewired with Csy4 to achieve complex behaviors. This toolkit can be used for programming scalable gene circuits and perturbing endogenous networks for biology, therapeutic, and synthetic biology applications."


http://bit.ly/1qT1r3j

Rescooped by Alfonso Rodriguez-Paton from Synthetic, Systems Biology and DNA Computing
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Synthetic circuits integrating logic and memory in living cells

Synthetic circuits integrating logic and memory in living cells | Synthetic, Systems Biology and DNA Computing | Scoop.it

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Socrates Logos's curator insight, February 10, 2013 5:40 PM

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Piro Siuti,John Yazbek& Timothy K Lu

"Logic and memory are essential functions of circuits that generate complex, state-dependent responses. Here we describe a strategy for efficiently assembling synthetic genetic circuits that use recombinases to implement Boolean logic functions with stable DNA-encoded memory of events. Application of this strategy allowed us to create all 16 two-input Boolean logic functions in living Escherichia coli cells without requiring cascades comprising multiple logic gates. We demonstrate long-term maintenance of memory for at least 90 cell generations and the ability to interrogate the states of these synthetic devices with fluorescent reporters and PCR. Using this approach we created two-bit digital-to-analog converters, which should be useful in biotechnology applications for encoding multiple stable gene expression outputs using transient inputs of inducers. We envision that this integrated logic and memory system will enable the implementation of complex cellular state machines, behaviors and pathways for therapeutic, diagnostic and basic science applications."

http://bit.ly/123ToU3

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Advancing bacteriophage-based microbial diagnostics with synthetic biology

Advancing bacteriophage-based microbial diagnostics with synthetic biology | Synthetic, Systems Biology and DNA Computing | Scoop.it

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Socrates Logos's curator insight, April 24, 2013 5:25 PM

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Lu TK, Bowers J, Koeris MS.

"Synthetic biology is an emerging engineering field focused on designing artificial biological systems with novel func- tionalities for use in therapeutics, basic science, biotech- nology, and diagnostics [1,2]. Continuous advancements in DNA synthesis and sequencing technologies coupled with new techniques for genomic modification and assem- bly have opened the door for harnessing the power and diversity of biology for applications. For example, natural bacteriophage products, such as ListShield (Intralytix) and Agriphage (Omnilytics), are commercially available for reducing unwanted bacterial contamination. Natural bacteriophages can be genetically modified to deliver engineered payloads into bacteria, thus selectively func- tionalizing target bacterial populations to produce active biomolecules. This strategy can endow bacteriophages with the ability to efficiently destroy bacterial biofilms or increase the bactericidal efficacy of antibiotics used in combination with phages by many orders of magnitude [3]. In addition, bacteriophages can be engineered as near- real-time microbial diagnostics by using them to trans- form target bacteria into factories for detectable molecules...."
 http://bit.ly/XXyJ15

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Post-translational tools expand the scope of synthetic biology

Post-translational tools expand the scope of synthetic biology | Synthetic, Systems Biology and DNA Computing | 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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George Church: "Synthetic Biology could bring extinct species back."

http://www.erderetten.de George Church, Pioneer in Synthetic Biology, Harvard & MIT, USA (c) Brinzanik/Hülswitt/Kreis...

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Rescooped by Alfonso Rodriguez-Paton from Host-Microbe Interactions
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PLoS Pathogens: Microbial Spy Games and Host Response: Roles of a Pseudomonas aeruginosa Small Molecule in Communication with Other Species

PLoS Pathogens: Microbial Spy Games and Host Response: Roles of a Pseudomonas aeruginosa Small Molecule in Communication with Other Species | Synthetic, Systems Biology and DNA Computing | Scoop.it

"...in their constant battles with competitors and the host immune system, (opportunistic) microbial pathogens have developed sophisticated cell–cell communication systems termed quorum sensing (QS) that allow exchange of critical information. In return, competing microbes, as well as the host immune system, have developed means to intercept and decode these messages.. 

  To illustrate the clinical importance of this microbial spy game, we will focus on the biological activity of a single bacterial QS molecule on surrounding microbes and the host immune system and its diverse “meaning” to different receivers."

 


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Harvard Researchers Develop Magnetic Yeast. - BostInno

Harvard Researchers Develop Magnetic Yeast. - BostInno | Synthetic, Systems Biology and DNA Computing | Scoop.it
Are Those Your Cells Talking To That Machine?

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Synthetic Biology: State of the Art

Zsófia Clemens’ monthly report on the state of the art in synthetic biology Synthetic Toxicology: Where engineering meets biology and toxicology. Schmidt M, Pei L. Toxicol Sci. 2010 Nov 10.
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Rescooped by Alfonso Rodriguez-Paton from Synthetic, Systems Biology and DNA Computing
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Synthetic circuits integrating logic and memory in living cells

Synthetic circuits integrating logic and memory in living cells | Synthetic, Systems Biology and DNA Computing | Scoop.it

Via Socrates Logos, Alfonso Rodriguez-Paton
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Socrates Logos's curator insight, February 10, 2013 5:40 PM

by
Piro Siuti,John Yazbek& Timothy K Lu

"Logic and memory are essential functions of circuits that generate complex, state-dependent responses. Here we describe a strategy for efficiently assembling synthetic genetic circuits that use recombinases to implement Boolean logic functions with stable DNA-encoded memory of events. Application of this strategy allowed us to create all 16 two-input Boolean logic functions in living Escherichia coli cells without requiring cascades comprising multiple logic gates. We demonstrate long-term maintenance of memory for at least 90 cell generations and the ability to interrogate the states of these synthetic devices with fluorescent reporters and PCR. Using this approach we created two-bit digital-to-analog converters, which should be useful in biotechnology applications for encoding multiple stable gene expression outputs using transient inputs of inducers. We envision that this integrated logic and memory system will enable the implementation of complex cellular state machines, behaviors and pathways for therapeutic, diagnostic and basic science applications."

http://bit.ly/123ToU3

Rescooped by Alfonso Rodriguez-Paton from Synthetic, Systems Biology and DNA Computing
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Advancing bacteriophage-based microbial diagnostics with synthetic biology

Advancing bacteriophage-based microbial diagnostics with synthetic biology | Synthetic, Systems Biology and DNA Computing | Scoop.it

Via Socrates Logos, Alfonso Rodriguez-Paton
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Socrates Logos's curator insight, April 24, 2013 5:25 PM

by
Lu TK, Bowers J, Koeris MS.

"Synthetic biology is an emerging engineering field focused on designing artificial biological systems with novel func- tionalities for use in therapeutics, basic science, biotech- nology, and diagnostics [1,2]. Continuous advancements in DNA synthesis and sequencing technologies coupled with new techniques for genomic modification and assem- bly have opened the door for harnessing the power and diversity of biology for applications. For example, natural bacteriophage products, such as ListShield (Intralytix) and Agriphage (Omnilytics), are commercially available for reducing unwanted bacterial contamination. Natural bacteriophages can be genetically modified to deliver engineered payloads into bacteria, thus selectively func- tionalizing target bacterial populations to produce active biomolecules. This strategy can endow bacteriophages with the ability to efficiently destroy bacterial biofilms or increase the bactericidal efficacy of antibiotics used in combination with phages by many orders of magnitude [3]. In addition, bacteriophages can be engineered as near- real-time microbial diagnostics by using them to trans- form target bacteria into factories for detectable molecules...."
 http://bit.ly/XXyJ15

Rescooped by Alfonso Rodriguez-Paton from SynBioFromLeukipposInstitute
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Synthetic circuits integrating logic and memory in living cells

Synthetic circuits integrating logic and memory in living cells | Synthetic, Systems Biology and DNA Computing | Scoop.it

Via Socrates Logos
more...
Socrates Logos's curator insight, February 10, 2013 5:40 PM

by
Piro Siuti,John Yazbek& Timothy K Lu

"Logic and memory are essential functions of circuits that generate complex, state-dependent responses. Here we describe a strategy for efficiently assembling synthetic genetic circuits that use recombinases to implement Boolean logic functions with stable DNA-encoded memory of events. Application of this strategy allowed us to create all 16 two-input Boolean logic functions in living Escherichia coli cells without requiring cascades comprising multiple logic gates. We demonstrate long-term maintenance of memory for at least 90 cell generations and the ability to interrogate the states of these synthetic devices with fluorescent reporters and PCR. Using this approach we created two-bit digital-to-analog converters, which should be useful in biotechnology applications for encoding multiple stable gene expression outputs using transient inputs of inducers. We envision that this integrated logic and memory system will enable the implementation of complex cellular state machines, behaviors and pathways for therapeutic, diagnostic and basic science applications."

http://bit.ly/123ToU3

Rescooped by Alfonso Rodriguez-Paton from SynBioFromLeukipposInstitute
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Church Lab Publications

Church lab publications - especially interesting the list of submitted/revision
"255. Vigneault F, Laserson U, Simen BB, Lieberman-Aiden E, Egholm M, Church GM (2012) Tracking the dynamics of a human antibody repertoire. (in revision)

254. Jewett MC, Church GM (2012) In vitro integration of ribosomal RNA synthesis, ribosome self-assembly and protein synthesis. Nature (in revision).

253. Carr PA, Wang HH, Sterling B, Isaacs FJ, Xu G, Church GM, Jacobson JM (2012) Enhanced Multiplex Genome Engineering through Oligonucleotide Co-selection (in revision)

252. Juhas M, Eberl L, Church GM (2012) Essential genes as antimicrobial targets and cornerstones of synthetic biology (submitted)

251. Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, DeWerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, Theilmann MR, Wang L, Winn JC, Medvedik O, Schellenberg K, Haynes KA, Viel A, Brenner TJ, Mathews S, Church GM, Shah JV, Silver PA (2012) Personalized Genetic Engineering of Plants. (submitted)

250. Ball MP*, Thakuria JV*, Zaranek AW*, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow M, Cano C, Chou MF, Chung WK, Douglas SM, Estep P, Gore A, Hulick P, Labarga A, Lee J, Lunshof J, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters B, Raman AM, Reinhoff HY, Robasky K, Wheeler M, Vandewege W, Vorhaus D, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM (2012) A Public Resource Facilitating Clinical Use of Genomes (submitted as PNAS inaugural article)

249. Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Hass J, Robasky K, Zaranek AW, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert J, Nilsen G, Baccash J, Halpern AL, Church GM, Drmanac R (2012) Clinically accurate genome sequencing and haplotyping from 10-20 human cells using massively parallel short reads on long DNA fragments (submitted to Nature)

248. Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM (2012) Genome-scale Promoter Engineering by Co-Selection MAGE (Nature Methods in press)

247. Wang HH, Huang PY, Xu G, Haas W, Marblestone A, Li J, Gygi S, Forster A, Jewett MC, Church GM (2012) Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multi-enzyme catalysis. (ACS Synthetic Biology, in press)"

http://bit.ly/nd7L2K


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Synthetic Biology: Bits and pieces come to life : Nature : Nature Publishing Group

Synthetic Biology: Bits and pieces come to life : Nature : Nature Publishing Group | Synthetic, Systems Biology and DNA Computing | Scoop.it

James Collins

"Scientists are combining biology and engineering to change the world.

 With a box of Lego, you can create a whole range of different structures. Snap together pieces of various colours, shapes and sizes to create a multitude of structures — a house, a boat, a tower — with different functions. In the world of biology, a growing group of scientists is thinking about parts of cells in much the same way.

Engineers are using genes and proteins as building blocks to create new kinds of cell and new functions for cells. If scientists can build genes from scratch, they can create organisms with new traits. They can create bacteria that can clean up oil spills, rice with genes that keep the plant infection-free, or cells that can churn out new materials. Synthetic biology, the field that revolves around figuring out how to combine genes in new and interesting ways, requires an understanding of biology, creative engineering skills and computing expertise. It is pulling together scientists with different capabilities to solve problems....."


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DNA computing - The Economist

DNA computing - The Economist | Synthetic, Systems Biology and DNA Computing | Scoop.it

An overview of DNA computing approaches in different laboratories.


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Biosciences - Synthetic Biology - an overview - Articles - Open ...

In a very insightful article, published in this month in the journal Nature, James Collins, a bioengineer professor at Boston University explains what synthetic biology is, and gives an overview of its potential opportunities and ...

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Synthetic Biology: An introduction

This video has been produced by the Synthetic Components Network to promote the new research area of synthetic biology to the public. For more information re...
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