20.109(S10):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 to 20109.talk AT gmail DOT com with a brief description.
• 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. 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 [RR/WF/Purple]
2. Muranaka et al. Mechanism-guided library design and dual genetic selection of synthetic OFF riboswitches. Chembiochem (2009) vol. 10 (14) pp. 2375-81 [SP/TR/Yellow]
3. 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
4. Lou et al. Micromagnetic selection of aptamersin microfluidic channels (2009) pp. 1-6 [ZS/TR/Red] [PR/WF/Green]
5. 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
6. Vuyisich and Beal. Controlling protein activity with ligand-regulated RNA aptamers. Chem Biol (2002) vol. 9 (8) pp. 907-13 [RK/WF/Red] [PJV/TR/Purple]
7. Cox and Ellington. Automated selection of anti-protein aptamers. Bioorg Med Chem (2001) vol. 9 (10) pp. 2525-31 [JZ/TR/Orange] [CMR/WF/Purple]
8. Mi et al. In vivo selection of tumor-targeting RNA motifs. Nat Chem Biol (2010) vol. 6 (1) pp. 22-4 [AK/WF/Orange] [PL/TR/Blue]

Applications

1. Yanrong et al. DNA aptamer–micelle as an efficient detection/delivery vehicle toward cancer cells PNAS 2010 107: 5-10. [AS/TR/Red][MR/WF/BLUE]
2. Mayer et al. An RNA molecule that specifically inhibits G-protein-coupled receptor kinase 2 in vitro. RNA (2008) vol. 14 (3) pp. 524-34
3. 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 [BYC/TR/Green]
4. 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 [TS/MW/Pink][AC/TR/Pink]
5. Hicke et al. Tumor targeting by an aptamer. J Nucl Med (2006) vol. 47 (4) pp. 668-78 [SS/WF/Red][LM/TR/BLUE]
6. Cerchia et al. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol (2005) vol. 3 (4) pp. e123
7. Collett et al. Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Anal Biochem (2005) vol. 338 (1) pp. 113-23 [JM/WF/Orange]

Aptamers in Nature

1. Mandal et al. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science (2004) vol. 306 (5694) pp. 275-9 [JY/WF/Yellow][YZ/TR/Purple]
2. Winkler et al. Control of gene expression by a natural metabolite-responsive ribozyme. Nature (2004) vol. 428 (6980) pp. 281-6 [JMS/TR/Pink] [EC/WF/Blue]
3. Sudarsan et al. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev (2003) vol. 17 (21) pp. 2688-97[AS/TR/Yellow][JJG/WF/Yellow]
4. Winkler et al. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature (2002) vol. 419 (6910) pp. 952-6 [AY/WF/Green] [KA/TR/Orange]

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	Afrah Shafquat	Bina Choi	Jingkun (Ginger) Yang	Joseph Martinez
2	Zeina Ali Siam	Leanna Morinishi	Jing Jing Gong	Nick Swenson
3	Ariana Chehrazi	Jacqueline Soegaard	Tina Stutzman	Efrain Cermeño
4	Pei Lin	Jenny Zhou	Alicia Kaestli	Raven Reddy
5	Yuan Zhao	Kirsten Aarsvold	Anne Ye	Ragheb El Khaja
6	Anna Shcherbina	Patricio Velez	Stephanie Senna	Colin Reisterer
7	Steven Pennybaker	Brigitte Morales	Priya Ramaswamy