CH391L/S12/Assignments

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(Nominated Papers)
Current revision (11:01, 16 April 2012) (view source)
(For Monday, April 23, 2012)
 
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Yet to sign up for '''second''' presentation:
 
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#Joe Hanson
 
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== Other topic ideas ==
== Other topic ideas ==
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</biblio>
</biblio>
* Computer-Aided Design (CAD) systems for synthetic biology - OPEN
* Computer-Aided Design (CAD) systems for synthetic biology - OPEN
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== Final Project Groups ==
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{| border=1 cellpadding=3 cellspacing=0
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!Project
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!Group
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|-
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|Caffeine
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| Erik, Brian, Midhat, Peter
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|-
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|Spinach
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|Mike, Jon, Logan, Jeremy
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|-
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|Snow Globe
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|Adam, Yi, Razan, Ben, (Jeff)
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|-
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|Zombie Apocalypse
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| David, Joe, Jared
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|}
== For Monday, April 30, 2012 ==
== For Monday, April 30, 2012 ==
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== For Monday, April 23, 2012 ==
 
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As a group we will read three papers on each of these days and discuss them in detail.
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Final project presentations!
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=== Nominated Papers ===
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== For Monday, April 23, 2012 ==
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(Vote by placing your name in the comments after a paper. You can vote for as many as you would like).
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As a group we will all read these three papers and discuss them in class on April 23 in detail.
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=== Papers to Read ===
<biblio>
<biblio>
#Gallivan pmid=20453864
#Gallivan pmid=20453864
//Atrazine seek and destroy
//Atrazine seek and destroy
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Votes: Barrick, Meyer
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Votes: Barrick, Meyer, Truong, Yi, Bachman
#Chin pmid=20154731
#Chin pmid=20154731
//Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome
//Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome
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Votes: Meyer
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Votes: Meyer, Truong, Yi, Barrick
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#Chang pmid=21847113
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//Engineering microbes to sense and eradicate ''Pseudomonas aeruginosa'', a human pathogen
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Votes: Meyer, Truong, Patel
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</biblio>
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=== Other Nominated Papers ===
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(Vote by placing your name in the comments after a paper. You can vote for as many as you would like).
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''Voting is over --April 16'''
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<biblio>
#Voigt pmid=21035461
#Voigt pmid=21035461
//Multichromatic Control of Gene Expression in ''Escherichia coli''
//Multichromatic Control of Gene Expression in ''Escherichia coli''
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Votes: Meyer
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Votes: Meyer (vote retracted, Jared covered this)
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#CHang pmid=21847113
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#Danino pmid=20090747
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//Engineering microbes to sense and eradicate ''Pseudomonas aeruginosa'', a human pathogen
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//A synchronized quorum of genetic clocks.  This is a very nice paper featuring logic circuits, oscillators, and quorum sensing.
Votes: Meyer
Votes: Meyer
</biblio>
</biblio>
== For Monday, April 16, 2012 ==
== For Monday, April 16, 2012 ==
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Smell (or maybe magnetic yeast? Huh?) - Joe Hanson
* Guest topic (2 PM) - Dr. Hal Alper (Chemical Engineering)
* Guest topic (2 PM) - Dr. Hal Alper (Chemical Engineering)
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Paper discussions.
== For Monday, April 9, 2012 ==
== For Monday, April 9, 2012 ==
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*Artemisinic acid engineering- Peter Otoupal
*Artemisinic acid engineering- Peter Otoupal
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*MAGE lycopene production - Logan Bachman
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*MAGE lycopene production, CAGE "Amberless" E. coli - Logan Bachman
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*Topic of choice - Jeremy McLain
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*Synthetic Cooperation - Jeremy McLain
== For Monday, April 2, 2012 ==
== For Monday, April 2, 2012 ==
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* Fluorescent/luminescent proteins (GFP, lux, variants) - Midhat Patel
* Fluorescent/luminescent proteins (GFP, lux, variants) - Midhat Patel
* Pigments - Yi Kou
* Pigments - Yi Kou
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* Smell - OPEN
 
== For Monday, March 5, 2012 ==
== For Monday, March 5, 2012 ==

Current revision

Contents

Other topic ideas

  • Riboswitches (synthetic and natural) - OPEN
  • Directed evolution (plasmid-based in vivo evolution of thermostability, altered substrate specificity, etc) and/or phage display. - OPEN
    • Possible reference [1]
  1. Gupta RD, Goldsmith M, Ashani Y, Simo Y, Mullokandov G, Bar H, Ben-David M, Leader H, Margalit R, Silman I, Sussman JL, and Tawfik DS. . pmid:21217689. PubMed HubMed [Gupta2011]
  • Computer-Aided Design (CAD) systems for synthetic biology - OPEN

Final Project Groups

Project Group
Caffeine Erik, Brian, Midhat, Peter
Spinach Mike, Jon, Logan, Jeremy
Snow Globe Adam, Yi, Razan, Ben, (Jeff)
Zombie Apocalypse David, Joe, Jared

For Monday, April 30, 2012

Final project presentations!

For Monday, April 23, 2012

As a group we will all read these three papers and discuss them in class on April 23 in detail.

Papers to Read

  1. Sinha J, Reyes SJ, and Gallivan JP. . pmid:20453864. PubMed HubMed [Gallivan]
    Atrazine seek and destroy

    Votes: Barrick, Meyer, Truong, Yi, Bachman

  2. Neumann H, Wang K, Davis L, Garcia-Alai M, and Chin JW. . pmid:20154731. PubMed HubMed [Chin]
    Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome

    Votes: Meyer, Truong, Yi, Barrick

  3. Saeidi N, Wong CK, Lo TM, Nguyen HX, Ling H, Leong SS, Poh CL, and Chang MW. . pmid:21847113. PubMed HubMed [Chang]
    Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen

    Votes: Meyer, Truong, Patel

All Medline abstracts: PubMed HubMed

Other Nominated Papers

(Vote by placing your name in the comments after a paper. You can vote for as many as you would like). Voting is over --April 16'

  1. Tabor JJ, Levskaya A, and Voigt CA. . pmid:21035461. PubMed HubMed [Voigt]
    Multichromatic Control of Gene Expression in Escherichia coli

    Votes: Meyer (vote retracted, Jared covered this)

  2. Danino T, Mondragón-Palomino O, Tsimring L, and Hasty J. . pmid:20090747. PubMed HubMed [Danino]
    A synchronized quorum of genetic clocks. This is a very nice paper featuring logic circuits, oscillators, and quorum sensing.

    Votes: Meyer

All Medline abstracts: PubMed HubMed

For Monday, April 16, 2012

Smell (or maybe magnetic yeast? Huh?) - Joe Hanson

  • Guest topic (2 PM) - Dr. Hal Alper (Chemical Engineering)

Paper discussions.

For Monday, April 9, 2012

New Topics: Systems II

  • Artemisinic acid engineering- Peter Otoupal
  • MAGE lycopene production, CAGE "Amberless" E. coli - Logan Bachman
  • Synthetic Cooperation - Jeremy McLain

For Monday, April 2, 2012

  • Comment on or add to old topics.

New Topics: Systems I

  • Repressilator, counter, toggle swtich - Razan Alnahhas
  • Edge detection E. coli - Jared Ellefson
  • Refactored T7 and yeast - Jon Laurent

For Monday, March 26, 2012

  • Comment on or add to old topics.

New Topics: Complex Parts

  • Quorum sensing - Brian Renda
  • Locomotion - Erik Quandt
  • Unnatural amino acids - Michael Hammerling

For Monday, March 19, 2012

  • Comment on or add to old topics.

New Topics: Reporter Genes

  • Guest topic (2 PM) - Dr. Andy Ellington (Chemistry and Biochemistry)
  • Fluorescent/luminescent proteins (GFP, lux, variants) - Midhat Patel
  • Pigments - Yi Kou

For Monday, March 5, 2012

  • Comment on or add to old topics.

New Topics: Gene Regulation

  • Origins of Replication - Adam Meyer
  • Protein regulators of transcription (Lac, Ara, etc) - Ben Slater
  • Light sensing. Two-component systems - David Truong

For Monday, February 27, 2012

  • Comment on or add to old topics.

New Topics: Basic Gene Construction

  • Transcription: initiation and termination - Logan Bachman
  • Spinach RNA - Jon Laurent
  • Translation. Ribosome binding sites and codon optimization - Jeremy McLain

For Monday, February 20, 2012

  • Comment on or add to old topics.

New Topics: Chassis and Backbones

  • Selectable genetic markers (Ab resistance, etc.) - Peter Otoupal
  • Toxin/anti-toxins, plasmid addiction systems - Brian Renda
  • Counter-selectable genetic markers - Erik Quandt

For Monday, February 13, 2012

  • Comment on or add to old topics.

New Topics: Optimizing Parts and their Interactions

  • Gene/genome synthesis/Gibson assembly - Joe Hanson
  • Host organisms (general properties of common ones, new ones that are being developed) - Michael Hammerling
  • Metabolic engineering - Razan Alnahhas

For Monday, February 6, 2012

  • Add a link to your user page to the CH391L Users Page.
  • Add something to your user page.
  • Comment on or add to old topics.

New Topics: Assembling Biological Parts

  • Restriction enzyme cloning & BioBricks/BglBricks assembly - Ben Slater
  • Advanced PCR techniques - Yi Kou

For Monday, January 30, 2012

New Topics: Finding Biological Parts

  • iGEM registry - Midhat Patel
  • bioprospecting / metagenomics - David Truong
  • directed evolution / in vitro selection - Adam Meyer
  • ancestral protein construction - Jared Ellefson
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