User:Lance Martin: Difference between revisions

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==Native biological memory & logic==
==Projects==
 
===Electronic counter review===
[http://openwetware.org/wiki/Endy:Notebook/Electronic_counters Electronic counter notebook]
 
===Gemini===
[http://openwetware.org/wiki/Endy:Notebook/Gemini Gemini notebook]
 
===Simulation===
[http://openwetware.org/wiki/Endy:Notebook/Computational_modeling#Steps_in_flipee_mechanism_for_modeling Computational modeling notebook]
 
===Genetic switches: methylation & feedback regulation===
[http://openwetware.org/wiki/Endy:Notebook/Genetic_switches:_feedback%2C_methylation%2C_%26_more Genetic switches notebook]
 
===Recombination switches===
[http://openwetware.org/wiki/Endy:Notebook/Review_of_recombinases Review of recombinases]
 
==Assorted items of interest==
[[Image:Inversion.jpg|thumb|right|A biological bit]]
[[Image:Inversion.jpg|thumb|right|A biological bit]]


===Basic requirements for memory & logic===
===James Ferrell===
*Big picture
**Reliably holds state
**Controllable state change
*Then, degenerates into many application-specific requirements
**What are the applications for memory and logic in biological systems?
**How do naturally evolved mechanisms break down between combinatorial and sequential logic?
**Need a chart listing all mechanisms with associated cellular applications, requirements, timescale ...
 
===Native systems===
*Recombination
**[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biochem.73.011303.073908 Nice overview]
**Serine Recombinases
*** [http://www3.interscience.wiley.com/journal/118923247/abstract?CRETRY=1&SRETRY=0 Diversity in Ser recombinases]
*** [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040186&ct=1 BxB1 directionality]
*** [[Media:Recombinases.ppt]]
**Tyrosine Recombinases
*** [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45S48WH-F&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=db485e9dbaa8d2b7c4b57104b4de03bb Kinetic analysis of Flp and Cre]
*** [[Media:Mechanism.ppt]]
*DNA methylation
**[http://en.wikipedia.org/wiki/Epigenetics Epigenetics]
**[http://en.wikipedia.org/wiki/DNA_methylation DNA methylation]
**[http://en.wikipedia.org/wiki/Genomic_imprinting#Imprinting_mechanisms Genomic imprinting]
*Error prone DNAp
**[http://www.pnas.org/content/100/17/9727.abstract Targeted gene evolution]
*DSB & repair
**[http://www.nature.com/nbt/journal/v23/n8/abs/nbt1125.html Zinc finger gene targeting]
**[http://www.nature.com/nature/journal/v435/n7042/abs/nature03556.html Zinc finger human gene correction]
*Timekeeping (James Ferrell)
*Timekeeping (James Ferrell)
**[http://www.sciencemag.org/cgi/content/summary/318/5851/757?ck=nck Toggle switch at heart of circadian timekeeping]
**[http://www.sciencemag.org/cgi/content/summary/318/5851/757?ck=nck Toggle switch at heart of circadian timekeeping]
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*[http://www.pnas.org/content/88/24/10983.abstract Chemical implementation of Turing machine]
*[http://www.pnas.org/content/88/24/10983.abstract Chemical implementation of Turing machine]


==Design of engineered biological systems==
[[Image:Process.jpg|thumb|right|Design process]]
[[Image:Process.jpg|thumb|right|Design process]]


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[[Media:Modeling.ppt]]
[[Media:Modeling.ppt]]


==Past engineered biological memory & logic devices/systems==
[[Image:PriorWork.jpg|thumb|right|Some engineered biological memory & logic systems]]
[[Image:PriorWork.jpg|thumb|right|Some engineered biological memory & logic systems]]


===Rationale===
===Prior work: implementing recombinase switches===
Scaling to larger applications with more states and deeper sequential logics is a future need. Systems whose output depends on input history are necessary for sophisticated computation and information storage. Memory is common in systems that control functions such as development. Memory may confer fitness advantage for synthetic systems that exist and compete in the living world. (reference: Arkin, Ham 2008)
*Ham & Arkin inversion switch
**[[Media:Ham&Arkin.ppt]]
*Harvard/BU 2004 iGem Int/Xis inversion switch & counter
**Their final presentation
***[[Media:iGem.ppt]]
**Notes on this work
***[[Media:iGemLance.ppt]]


===Challenges===
===Challenges===
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**Large outlays of DNA real-estate may be necessary
**Large outlays of DNA real-estate may be necessary
**Large energetic loads on host state
**Large energetic loads on host state
===Of particular interest to us===
*Ham & Arkin inversion switch
**[[Media:Ham&Arkin.ppt]]
*Harvard/BU 2004 iGem Int/Xis inversion switch & counter
**Their final presentation
***[[Media:iGem.ppt]]
**My notes on this work
***[[Media:iGemLance.ppt]]
*DNA methylation switch
**[http://www.ncbi.nlm.nih.gov/pubmed/14992728 Switch]
**[http://www.cell.com/molecular-cell/abstract/S1097-2765(04)00064-4 Switch, again]
**[http://www.ncbi.nlm.nih.gov/pubmed/17262027 Switch gives bi-stable gene expression]
==My projects==
[[Image:Gemini.jpg|thumb|right|LacZ alpha-GFP fusion]]
===Gemini===
*Summary
**[[Media:Gemini.ppt]]
*synBERC poster
**[[Media:GeminiPoster.pdf]]
*Notebook
**[http://openwetware.org/wiki/Endy:Notebook/Gemini Gemini notebook]
===Modeling recombinase-driven genetic counters===
[http://openwetware.org/wiki/Endy:Notebook/Computational_modeling#Steps_in_flipee_mechanism_for_modeling Notebook]

Latest revision as of 09:52, 6 April 2009

I am a new member of OpenWetWare!





Projects

Electronic counter review

Electronic counter notebook

Gemini

Gemini notebook

Simulation

Computational modeling notebook

Genetic switches: methylation & feedback regulation

Genetic switches notebook

Recombination switches

Review of recombinases

Assorted items of interest

A biological bit

James Ferrell

Biological computation

Design process

Basic construction / design principles

  • Summary of reviews by
    • Voight, Endy, Arkin

Media: Principles.ppt

Computational modeling to aid design

  • Review of
    • Collins toggle switch
    • Elowitz repressilator

Media:Modeling.ppt

Some engineered biological memory & logic systems

Prior work: implementing recombinase switches

Challenges

  • No spatial addressing of signals in biological systems
  • Many heterogeneous parts implemented, resulting in:
    • Heterogeneity of device physics across circuits
    • Complex properties, making design and modeling hard
    • Large outlays of DNA real-estate may be necessary
    • Large energetic loads on host state
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