User:Jarle Pahr/Synthetic biology: Difference between revisions
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Revision as of 06:41, 18 May 2013
Notes on news and articles related to synthetic biology:
RNA-guided editing of bacterial genomes using CRISPR-Cas systems: http://www.nature.com/nbt/journal/v31/n3/full/nbt.2508.html
Amplifying genetic logic gates: http://www.sciencemag.org/content/early/2013/03/27/science.1232758.abstract
RNA processing enables predictable programming of gene expression: http://www.nature.com/nbt/journal/v30/n10/full/nbt.2355.html
Ribozyme-based insulator parts: http://www.nature.com/nbt/journal/v30/n11/full/nbt.2401.html?WT.ec_id=NBT-201211
Organizations and websites
Companies
http://greeneconomypost.com/synthetic-biology-biofuel-biochemical-company-17244.htm
Intrexon: http://www.dna.com/
Amyris
Ls9
Solazyme
Synthetic Genomics
Synthace
Blogs and commentary
http://blogs.scientificamerican.com/oscillator/
Work
http://www.indeed.co.uk/Synthetic-Biology-jobs-in-England
Concepts
Polymerases per second (POPS):
http://openwetware.org/wiki/PoPS
Genome engineering
Design languages
GenoCAD
Eugene
SBOL
Persons/Research labs
Synthetic biology map: http://www.synbioproject.org/sbmap/
http://openwetware.org/wiki/Forster_Lab
Bibliography
http://www.nature.com/nbt/journal/v27/n12/full/nbt1209-1109.html
Stacking nonenzymatic circuits for high signal gain.: http://www.ncbi.nlm.nih.gov/pubmed/23509255
Amplifying Genetic Logic gates: http://www.sciencemag.org/content/340/6132/599.abstract
Targeted Development of Registries of Biological Parts: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002671
Survey of enabling technologies in synthetic biology: http://www.jbioleng.org/content/pdf/1754-1611-7-13.pdf
Review - ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering: http://www.sciencedirect.com/science/article/pii/S0167779913000875
Open Source Synthetic Biology: Problems and solutions: http://erepository.law.shu.edu/student_scholarship/47/
Synthetic Biology: It's an analog world: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12246.html
Ideas
A biological PID? Input and the objective to be controlled could be levels of a protein or a metabolite. Output would be summed from the activity of three transcription units. Would need a way to create a set-point and convert the difference between the present level and the set-point to serve as input to the PID circuit.
- Proportional term. Activity is proportional to input (current level).
- Integrative term. Activity is proportional to the total input over a recent timeframe (how can this be achieved?)
- Derivative term. Activity is proportional to the change in input over a recent timeframe (how can this be achieved?)
Might be helpful to study mechanical or analog PID circuits.
Projects
http://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit
Software
SBOL designer: http://clarkparsia.github.io/sbol/
Plant synthetic biology
GoldenBraid2.0: A comprehensive DNA assembly framework for Plant Synthetic Biology: http://www.plantphysiol.org/content/early/2013/05/13/pp.113.217661.abstract