20.109(S12):Journal club (Day8)

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20.109(S12): Laboratory Fundamentals of Biological Engineering

20.109(S12) frontpg.JPG

Home        Schedule Spring 2012        Assignments       
RNA Engineering        Protein Engineering        Cell Engineering              

Logistics of Paper Sign-Up and Presentation

  • Once you have decided on a paper for your presentation, please "reserve" it by putting your (initials/lab section/team color) next to the listing here. If you would like to discuss a paper not on the list below, please email it (as .pdf) to 20109.talk AT gmail DOT com with a brief description for approval.
  • For visibility, please use the following format to sign up if possible, substituting in your own initials and team color: [ANS/WF/Purple]. Thanks!
  • The same paper may be presented by a T/R and a W/F student, but may only be presented once per section.

As you prepare your talk be sure to follow the specific guidelines for oral presentations in this class.

  • Please email your finished journal club presentation to 20109.submit AT gmail DOT com no later than 1 pm on the day of your presentation. The order in which your presentations are received will be the order of speakers.
  • Day 8 presentations will begin at 1:30 pm sharp in room 16-336. (Day 6 presentations will begin after lab work is finished, b/w 1:30 and 2 pm.)

Paper Options

The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You are not limited to the primary research articles on this list. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Search PubMed yourself to find articles of interest to you.

Note: Try typing the title of your article into PubMed to find it. If you have trouble accessing your article directly from there, go to http://libraries.mit.edu/vera, which is MIT's collection of journals online. Try selecting "exact title" from the search pulldown menu if the name of your journal is a common word such as Science. For older articles, you need to choose the JSTOR rather than Highwire interface.


  1. Lynch et al. A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem Biol (2007) vol. 14 (2) pp. 173-84 [NJ/WF/Blue] [CXH/TR/Purple]
  2. König et al. Combining SELEX and the yeast three-hybrid system for in vivo selection and classification of RNA aptamers. RNA (2007) vol. 13 (4) pp. 614-22 [SSD/WF/Orange][ML/TR/Blue]
  3. Lou et al. Micromagnetic selection of aptamers in microfluidic channels. Proc Natl Acad Sci USA (2009) vol. 106 (9) pp. 2989-2994 [HCC/WF/Pink] [JLF/TR/Red]
  4. Dixon et al. Reengineering orthogonally selective riboswitches. Proc Natl Acad Sci USA (2010) vol. 107 (7) pp.2830-2835 [SZ/WF/Orange] [AJR/TR/Yellow]
  5. Ruff et al. Enhanced Functional Potential of Nucleic Acid Aptamer Libraries Patterned to Increase Secondary Structure. J Am Chem Soc (2010) [ERL/TR/Green]
  6. Kupakuwana et al. Acyclic identification of aptamers for human alpha-thrombin using over-represented libraries and deep sequencing. PLoS ONE (2011) vol. 6 (5) pp. e19395 [NHK/TR/Orange] [DAB/WF/Red]

Applications (Natural and Synthetic)

  1. Cerchia et al. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol (2005) vol. 3 (4) pp. e123 [BJJ/WF/Green][JL/TR/Blue]
  2. An et al. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA (2006) vol. 12 (5) pp. 710-6 [MIG/WF/Blue] [MS/TR/Yellow]
  3. Xu et al. Aptamer-based microfluidic device for enrichment, sorting, and detection of multiple cancer cells. Anal Chem (2009) vol. 81 (17) pp. 7436-42 [KDW/TR/Purple] [FS/WF/Purple]
  4. Gold et al. Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS ONE (2010) vol. 5 (12) pp. e15004 [LEC/WF/Pink] [TMA/TR/RED]
  5. Sinha et al. Reprogramming bacteria to seek and destroy an herbicide. Nat Chem Biol (2010) vol. 6 (6) pp. 464-70 [CAL/TR/Orange] [MET/WF/Yellow]
  6. Nielsen et al. Aptamers embedded in polyacrylamide nanoparticles: a tool for in vivo metabolite sensing. ACS Nano (2010) vol. 4 (8) pp. 4361-70 [MLH/WF/Purple] [MLW/TR/Pink]
  7. Lee et al. Combining SELEX Screening and Rational Design to Develop Light-Up Fluorophore-RNA Aptamer Pairs for RNA Tagging. ACS Chem Biol (2010) pp. [CC/WF/Green] [RS/TR/Pink]
  8. Winkler et al. Control of gene expression by a natural metabolite-responsive ribozyme. Nature (2004) vol. 428 (6980) pp. 281-6 [SBK/TR/Green] [SAW/WF/Red]
  9. Lee et al. An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science (2010) vol. 329 (5993) pp. 845-8 [RAH/WF/Yellow]
  10. Tang et al. Selection of aptamers for molecular recognition and characterization of cancer cells. Analytical Chemistry (2007) vol. 79 pp. 4900-4907 [NSA/WF/Purple]

Day Sign-up

Please put your name under the day you wish to present. There are 7 slots on each day, per lab section. Slot location does not determine speaker order.

Slot Day 6 (T/R) Day 8 (T/R) Day 6 (W/F) Day 8 (W/F)
1 Meena Subramaniam Kristen Wilhite Holly Chamberlain Melina Tsitsiklis
2 Cher Huang Esmeralda Romero Sarah Weiss Isabella Gariboldi
3 Jessica Fessler Nathan Kipniss Fangdi Sun Nidharshan Anandasivam
4 Shambhu B. Koirala Ceres Lee Dorian Burks Lauren E Clark
5 Maddy Wharton Angel Rubio Matthew Hung Rachel Hunt
6 Taleen Afeyan Michael Liao Sixing Zhao Carlos Castellanos
7 Jeffrey Lin Ruisi Shang Samira Daswani Brian Jude Joseph
8 N/A N/A Nina Jreige