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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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Generating Effective Models and Parameters for RNA Genetic Circuits

Generating Effective Models and Parameters for RNA Genetic Circuits
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by

Chelsea Y. Hu Jeffrey D. Varner , and Julius B. Lucks *


"RNA genetic circuitry is emerging as a powerful tool to control gene expression. However, little work has been done to create a theoretical foundation for RNA circuit design. A prerequisite to this is a quantitative modeling framework that accurately describes the dynamics of RNA circuits. In this work, we develop an ordinary differential equation model of transcriptional RNA genetic circuitry, using an RNA cascade as a test case. We show that parameter sensitivity analysis can be used to design a set of four simple experiments that can be performed in parallel using rapid cell-free transcription-translation (TX-TL) reactions to determine the 13 parameters of the model. The resulting model accurately recapitulates the dynamic behavior of the cascade, and can be easily extended to predict the function of new cascade variants that utilize new elements with limited additional characterization experiments. Interestingly, we show that inconsistencies between model predictions and experiments led to the model-guided discovery of a previously unknown maturation step required for RNA regulator function. We also determine circuit parameters in two different batches of TX-TL, and show that batch-to-batch variation can be attributed to differences in parameters that are directly related to the concentrations of core gene expression machinery. We anticipate the RNA circuit models developed here will inform the creation of computer aided genetic circuit design tools that can incorporate the growing number of RNA regulators, and that the parametrization method will find use in determining functional parameters of a broad array of natural and synthetic regulatory systems.'


http://bit.ly/1CQEEX3

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SULSA 2015 Research Symposium | SULSA

SULSA 2015 Research Symposium | SULSA | SynBioFromLeukipposInstitute | Scoop.it
The heat is on, but SULSA server meltdown is fixed, so you can sign up for Life 2.0:The Synthetic Biology of New Life http://t.co/DWjmigiCXy
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How do I build an NOT gate in a biological arithmetic logic unit? - YouTube

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Deoxyribozyme based NOT gate: 


The deoxyribozyme (DNA based catalyst) is in an active form, if no input (in) is present (in = 0). Cleavage activity results in this case in a fluorescent oligonucleotid (F) as output. An oligonucleotide input (in) (in = 1) leads to hybridization of the input strand (green) with the closed loop strand, which is marked purple. This results in an inactive, open loop and the absences of a fluorescent product. 



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Our Leukippos community needs your financial support. We are all working for free and pay everything out of our own pockets, such as server costs and page registrations. If you like our work and wish that we produce more quality content, such as this video, you can donate some bitcoins to this address: 


1KnikzSG7fnRfG76DxjLZyrbvw8fS9nisw


Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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How do I build an AND gate in a biological arithmetic logic unit? - YouTube

Arithmetic logic unit: Shown are four basic Boolean logic gates (AND, NOT, NOR, and XOR), their symbols and respective truth tables. 1 means that the input (...
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Engineered particles 'may become antibiotics of the future'

Engineered particles 'may become antibiotics of the future' | SynBioFromLeukipposInstitute | Scoop.it
Using synthetic biology, researchers have engineered particles called phagemids that cause harmful bacteria to malfunction and cease replicating without bursting open.
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High-Throughput Synthetic Biology: Synthesizing Designer Yeast through Automation and Acoustic Liquid Handling | Webinars | GEN

High-Throughput Synthetic Biology: Synthesizing Designer Yeast through Automation and Acoustic Liquid Handling | Webinars | GEN | SynBioFromLeukipposInstitute | Scoop.it
Get the latest in biotechnology through daily news coverage as well as analysis, features, tutorials, webinars, podcasts, and blogs. Learn about the entire bioproduct life cycle from early-stage R&D, to applied research including omics, biomarkers, as well as diagnostics, to bioprocessing and commercialization.
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Systems Biology

Systems Biology Adam Arkin, University of California, Berkeley and E.O. Lawrence Berkeley National Laboratory Over eons, evolution acts on organisms to ...
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Download PDF Microbial Synthetic Biology Volume 40

1.Browse And Download This Book now. 2.If you can't download change your ip adress. 3."Click here to download PDF Ebook now at http://bit.ly/1Kgs4Xk.
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How does a biological Input:/Output device work? - YouTube

Input/Output (I/O) device: In a “digital” biological I/O device input molecules induce due to a set of non-steady state chemical reactions (engineered cohere...
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Jay Keasling - 18th Heinz Awards - Technology, the Economy and Employment

Jay Keasling, our 18th Technology, the Economy and Employment recipient, talks about the power of synthetic biology, and how his work on the new science of ...
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T Cell Immunotherapy: From Synthetic Biology to Clinical Practice - Springer

T Cell Immunotherapy: From Synthetic Biology to Clinical Practice - Springer | SynBioFromLeukipposInstitute | Scoop.it
T Cell Immunotherapy: From Synthetic Biology to Clinical Practice - Springer http://t.co/oGF6fKBYvW
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What are biological microprocessor applications? Part 2 - YouTube

What are biological microprocessor applications? Part 2
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Conferences and events | Biochemical Society - Synthetic Biology UK 2015

Conferences and events | Biochemical Society - Synthetic Biology UK 2015 | SynBioFromLeukipposInstitute | Scoop.it
Check out the latest conference and events from the Biochemical Society. Our programme covers a wide spectrum of topics; with events held in the UK and abroad.
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How do I build a NOR gate in a biological arithmetic logic unit? - YouTube

Socrates Logos's insight:

A RNA aptamer based NOR gate: NOR is an OR gate followed by a NOT gate. Two subsequent RNA devices consist, in this case, each of three functional components: a sensor, made of a RNA aptamer (brown), an actuator component, made of a hammerhead ribozyme (purple), and a cobbling sequence between these parts, the transmitter (blue). 

Translation of the gene of interest (here GFP), encoded upstream of the device, is only possible in the case of the absence of both inputs (a and b).


BTW

Our Leukippos community needs your financial support. We are all working for free and pay everything out of our own pockets, such as server costs and page registrations. If you like our work and wish that we produce more quality content, such as this video, you can donate some bitcoins to this address: 


1KnikzSG7fnRfG76DxjLZyrbvw8fS9nisw


Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

more...
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Dr. Alicia Jackson: Programming the Living World, DARPA BiT | CodonOps

Dr. Alicia Jackson: Programming the Living World, DARPA BiT | CodonOps | SynBioFromLeukipposInstitute | Scoop.it
Dr. Alicia Jackson: Programming the Living World, DARPA BiT
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A Versatile Microfluidic Device for Automating Synthetic Biology - ACS Synthetic Biology (ACS Publications)

A Versatile Microfluidic Device for Automating Synthetic Biology - ACS Synthetic Biology (ACS Publications) | SynBioFromLeukipposInstitute | Scoop.it
RT @ACSSynBio: Learn more about a versatile microfluidic device for automating synthetic biology here: http://t.co/gFQFmJRjxv
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Convergence of regenerative medicine and synthetic biology to develop standardized and validated models of human diseases with clinical relevance

Convergence of regenerative medicine and synthetic biology to develop standardized and validated models of human diseases with clinical relevance | SynBioFromLeukipposInstitute | Scoop.it
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Why Bio is the New Digital - Joi Ito keynote - YouTube

From the 2015 Solid Conference. About Joichi Ito (MIT Media Lab): Media Lab Director Joi Ito is a leading thinker and writer on innovation, global technology...
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Dr. Alicia Jackson: Programming the Living World, DARPA BiT

Dr. Alicia Jackson, Deputy Director of DARPA's Biological Technologies Office (BTO), discusses the potential of synthetic biology and describes new tools that ...
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Building a Fab for Synthetic Biology - Joe Jacobson keynote

From Solid Conference 2015: Similar to the way in which we use fabs to build microprocessors and software to program them, the field of synthetic biology offers ...
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Synthetic biology used to engineer new route to biochemicals

Synthetic biology used to engineer new route to biochemicals | SynBioFromLeukipposInstitute | Scoop.it
Living cells can make a vast range of products for us, but they don't always do it in the most straightforward or efficient way.
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What are the building blocks of a biological microprocessor? - YouTube

What are the building blocks of a biological microprocessor? A biological microprocessor consist of four units: the input and output device (I/O), the arithm...
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