20.109(S11):Journal club (Day8)

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.

Methodology/Technology

1. Lou et al. Micromagnetic selection of aptamersin microfluidic channels. Proc Natl Acad Sci USA (2009) vol. 106 (9) pp. 2989-2994 [AS/WF/PINK] [KCS/TR/Orange].
2. Oh et al. In vitro selection of structure-switching, self-reporting aptamers. Proc Natl Acad Sci USA (2010) vol. 107 (32) pp. 14053-14058 [SS/WF/RED]
3. Ruff et al. Enhanced Functional Potential of Nucleic Acid Aptamer Libraries Patterned to Increase Secondary Structure. J Am Chem Soc (2010) [BB/WF/PINK]
4. Mi et al. In vivo selection of tumor-targeting RNA motifs. Nat Chem Biol (2010) vol. 6 (1) pp. 22-4 [AA/WF/YELLOW] [KL/TR/BLUE]
5. Brudno et al. An in vitro translation, selection and amplification system for peptide nucleic acids. Nat Chem Biol (2010) vol. 6 (2) pp. 148-55 [HD/TR/Blue] [SG/WF/YELLOW]
6. Muranaka et al. Mechanism-guided library design and dual genetic selection of synthetic OFF riboswitches. Chembiochem (2009) vol. 10 (14) pp. 2375-81 [GR/WF/ORANGE]
7. Cox and Ellington. Automated selection of anti-protein aptamers. Bioorg Med Chem (2001) vol. 9 (10) pp. 2525-31
8. Hybarger et al. A microfluidic SELEX prototype. Analytical and bioanalytical chemistry (2006) vol. 384 (1) pp. 191-8
9. 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 [JC/TR/Green]
10. Berezovski et al. Nonequilibrium capillary electrophoresis of equilibrium mixtures: a universal tool for development of aptamers. J Am Chem Soc (2005) vol. 127 (9) pp. 3165-71
11. 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 [JX/WF/Blue]
12. Dixon et al. Reengineering orthogonally selective riboswitches. Proc Natl Acad Sci USA (2010) vol. 107 (7) pp.2830-2835 [MH/TR/ORANGE]

Applications

1. Sim et al. Attomolar detection of protein biomarkers using biofunctionalized gold nanorods with surface plasmon resonance. The Analyst (2010) vol. 135 (10) pp. 2528-32 [EC/WF/BLUE]
2. Zhu et al. Multiplexed detection of small analytes by structure-switching aptamer-based capillary electrophoresis. Anal Chem (2010) vol. 82 (11) pp. 4613-20 [SF/TR/Yellow]
3. Nielsen et al. Aptamers embedded in polyacrylamide nanoparticles: a tool for in vivo metabolite sensing. ACS Nano (2010) vol. 4 (8) pp. 4361-70 [LB/WF/Purple]
4. 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.
5. 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 [JC/TR/PURPLE] [RK/WF/Orange]
6. Hicke et al. Tumor targeting by an aptamer. J Nucl Med (2006) vol. 47 (4) pp. 668-78 [MP/TR/RED] [ER/WF/PURPLE]
7. Collett et al. Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Anal Biochem (2005) vol. 338 (1) pp. 113-23
8. 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 [JL/TR/Purple] <JL/WF/Green>
9. Homann et al. Serum-stable RNA aptamers to an invariant surface domain of live African trypanosomes. Comb Chem High Throughput Screen (2006) vol. 9 (7) pp. 491-9 [APS/WF/GREEN] [ML/TR/GREEN]
10. Cerchia et al. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol (2005) vol. 3 (4) pp. e123 [SR/TR/YELLOW]

Aptamers in Nature

1. Lee et al. An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science (2010) vol. 329 (5993) pp. 845-8 [PCT/WF/RED] [SA/TR/pink]
2. Mandal et al. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science (2004) vol. 306 (5694) pp. 275-9 [MN/TR/PINK]
3. Winkler et al. Control of gene expression by a natural metabolite-responsive ribozyme. Nature (2004) vol. 428 (6980) pp. 281-6 [ZT/TR/RED]

Day Sign-up

Please put your name under the day you wish to present. There are N 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	John Chen	Stephanie Fung	Elizabeth Rowland	Aislyn Schalck
2	Jenny Cheng	Huayu Ding	Sabina Sood	Alexa Schulte
3	Meghan Nelson	Max Pruner	Paula Trepman	Brett Boval
4	Jessica Li	Micca Hecht	Shirley Galbiati	Jingxun Chen
5	Shireen Rudina	Krithi Sundaram	Ryan Keating	Anirudh Arun
6	Sahar Alkhairy	Zach Tomlinson	Lauren Berry	Jessica Liu
7	Kevin Li	Manuel Legrand	Grant Robinson	Elizabeth Choe