Silver: Synthetic Biology Review Article

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OUTLINE COMING SOON
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==Working Outline (Please Comment)==
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I. Introduction to Synthetic Biology
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    a. Definition
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            i. Brief history
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          ii. Relationship with systems biology
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          iii. Discussion of raison d’etre
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                  1. Point of view of engineering (make useful systems)
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                  2. Point of view of biology (need synthesis to successfully test and refine theories)
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    b. Biological modularity
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            i. Gene
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          ii. RNA
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          iii. Protein
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          iv. Pathway
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II. Synthetic Biology Endeavors
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    a. Synthetic gene-circuits and switches
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            i. Prokaryotic
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                  1. Weiss
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                  2. Elowitz
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                  3. Collins
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          ii. Eukaryotic
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                  1. Artificial cell-cell communication in yeast (Weiss)
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                  2. Fussenegger mammalian switch
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                  3. Synthetic positive feedback network in yeast (Becskei…Serrano)
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                  4. Noise in gene network studies
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          iii. RNA-based
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                  1. Riboregulators
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                  2. Antiswitch (Smolke)
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    b. Signaling transduction engineering
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            i. Synthetic allosteric signaling switch (Dueber..Lim et al. 2003)
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          ii. Rewiring MAP kinase pathways (Lim)
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    c. Metabolic pathway engineering
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            i. Keasling-anti-malarial (artemisinin) and biodegradation of parathion
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    d. Environmental sensors
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            i. Hellinga ligand binding site design with PBPs (TNT, Zn(II), etc.)
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    e. Synthetic genomes (and minimal cell approaches?)
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III. Technical Advances
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    a. New DNA synthesis strategies
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    b. Development of the Registry of Standard Biological Parts
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IV. Educational Initiatives
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    a. iGEM competition
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    b. Overall curriculum development-suggest a broader initiative?
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V. Future Enterprises
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    a. Regulation?
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    b. Academic
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            i. Understanding from building, etc. 
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    c. Commercial
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            i. Protein engineering
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          ii. Drug production
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          iii. Alternative fuel production 
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Revision as of 18:10, 6 July 2006

David Drubin and Pam Silver are writing an in depth review article on Synthetic Biology for Genes and Development. We would very much like input from the community. Please post any suggestions or papers that you would like us to talk about here. Thanks!

We would like to this to be an in depth review of the field. This is a first attempt at using OWW to write such a review and thereby engage as many as possible - so we would like any input - be it on content or style. At this early stage, we find the input on papers and areas to cover to be very useful.


Contents

Working Outline (Please Comment)

I. Introduction to Synthetic Biology

    a.	Definition
           i.	Brief history
          ii.	Relationship with systems biology
         iii.	Discussion of raison d’etre
                  1.	Point of view of engineering (make useful systems)
                  2.	Point of view of biology (need synthesis to successfully test and refine theories)
    b.	Biological modularity
           i.	Gene
          ii.	RNA
         iii.	Protein
          iv.	Pathway

II. Synthetic Biology Endeavors

    a.	Synthetic gene-circuits and switches
           i.	Prokaryotic
                  1.	Weiss
                  2.	Elowitz
                  3.	Collins
          ii.	Eukaryotic
                  1.	Artificial cell-cell communication in yeast (Weiss)
                  2.	Fussenegger mammalian switch
                  3.	Synthetic positive feedback network in yeast (Becskei…Serrano)
                  4.	Noise in gene network studies 
         iii.	RNA-based
                  1.	Riboregulators
                  2.	Antiswitch (Smolke)
    b.	Signaling transduction engineering
           i.	Synthetic allosteric signaling switch (Dueber..Lim et al. 2003)
          ii.	Rewiring MAP kinase pathways (Lim)
    c.	Metabolic pathway engineering
           i.	Keasling-anti-malarial (artemisinin) and biodegradation of parathion 
    d.	Environmental sensors
           i.	Hellinga ligand binding site design with PBPs (TNT, Zn(II), etc.)
    e.	Synthetic genomes (and minimal cell approaches?)

III. Technical Advances

    a.	New DNA synthesis strategies
    b.	Development of the Registry of Standard Biological Parts

IV. Educational Initiatives

    a.	iGEM competition
    b.	Overall curriculum development-suggest a broader initiative?

V. Future Enterprises

    a.	Regulation?
    b.	Academic
           i.	Understanding from building, etc.  
    c.	Commercial
           i.	Protein engineering
          ii.	Drug production
         iii.	Alternative fuel production   


These are comments that have been received thus far.

artificial vesicle based biology

  1. Noireaux V, Bar-Ziv R, Godefroy J, Salman H, and Libchaber A. . pmid:16224117. PubMed HubMed [lib1]
  2. Noireaux V and Libchaber A. . pmid:15591347. PubMed HubMed [lib2]
  3. Chen IA, Roberts RW, and Szostak JW. . pmid:15353806. PubMed HubMed [szostak]
All Medline abstracts: PubMed HubMed

Mathematical or Quantitative (Predictive) Models of Gene Networks

  1. Tuttle LM, Salis H, Tomshine J, and Kaznessis YN. . pmid:16183880. PubMed HubMed [lib]

materials for teaching undergrads

Beyond iGEM, there are some initial teaching efforts from courses taught at
UC Berkeley [[1]]
and at MIT [[2]] and [[3]]. Some of the MIT material was adapted as iGEM 06 teaching material at BU [[4]] so it didn't take long for the use of even a fledgling curriculum effort to spread.

Hopefully, as Synthetic Biology advances, the research will provide examples and technologies that capture the distinguishing aspects of the field. It would be great if teaching materials could be developed in parallel to rigorously educate a larger number students who might later do this work. Perhaps somewhere in your review there could be an explicit call for curriculum development as well. - Natalie

other ideas

  • I think it would be nice to see where Systems Biology meets Synthetic Biology, e.g the use of modeling tools in synthetic biology.
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