User:Lance Martin: Difference between revisions

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[[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]

Revision as of 09:36, 6 April 2009

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Native biological memory & logic

A biological bit

James Ferrell

Biological computation

Design of engineered biological systems

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

Past engineered biological memory & logic devices/systems

Some engineered biological memory & logic systems

Rationale

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)

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

Of particular interest to us


My projects

Electronic counter review

Electronic counter notebook

LacZ alpha-GFP fusion

Gemini

Modeling recombinase-driven genetic counters

Notebook

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