20.109(S09): Module 2 oral presentations

Logistics of Paper Sign-Up and Presentation

 * Once you have decided on a paper for your presentation, please email it to 20109.talk AT gmail DOT com, and also "reserve" it by putting your (initials/lab section/team color) next to the listing here.
 * For visibility, please use the following format to sign up if possible, substituting in your own initials and team colour: [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.
 * Presentations will begin at 1:30 pm in room 16-336.

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: If you have trouble accessing your article directly, 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.

RNAi in different cell types (besides murine, and tissue-specific examples)

 * 1) Tomari Y, Du T, and Zamore PD. Sorting of Drosophila small silencing RNAs (2007). pubmed link
 * 2) Sharma SK, Nirenberg M. Silencing of genes in cultured Drosophila neurons by RNA interference. Proc Natl Acad Sci U S A. 2007 Jul 23 pubmed link [MV/TR/Red] [ASC/WF/Pink].
 * 3) Export of RNA silencing from C. elegans tissues does not require the RNA channel SID-1 (2009). pubmed link
 * 4) Lu S, et al. RNA silencing in plants by the expression of siRNA duplexes (2004). pubmed link
 * 5) Nakatsuka T, Abe Y, Kakizaki Y, Yamamura S, Nishihara M. Production of red-flowered plants by genetic engineering of multiple flavonoid biosynthetic genes. Plant Cell Rep. 2007 Jul 17 pubmed link
 * 6) Gary DS, Davidson A, Milhavet O, Slunt H, Borchelt DR. Investigation of RNA interference to suppress expression of full-length and fragment human huntingtin. Neuromolecular Med. 2007;9(2):145-55.pubmed link [EG/TR/Grey] [EP/WF/Yellow].
 * 7) Wang N, Sun YH, Liu J, Wu G, Su JG, Wang YP, Zhu ZY. Knock down of gfp and no tail expression in zebrafish embryo by in vivo-transcribed short hairpin RNA with T7 plasmid system. J Biomed Sci. 2007 Jul 12; pubmed link
 * 8) Otani M, Hamada T, Katayama K, Kitahara K, Kim SH, Takahata Y, Suganuma T, Shimada T. Inhibition of the gene expression for granule-bound starch synthase I by RNA interference in sweet potato plants. Plant Cell Rep. 2007 Jul 12; pubmed link
 * 9) Serman A, Le Roy F, Aigueperse C, Kress M, Dautry F, Weil D. GW body disassembly triggered by siRNAs independently of their silencing activity. Nucleic Acids Res. 2007 Jun 29; pubmed link [alie/WF/Red].
 * 10) Kaushik Deb, Mayandi Sivaguru, Hwan Yul Yong, R. Michael Roberts Cdx2 Gene Expression and Trophectoderm Lineage Specification in Mouse Embryos Science. 2006 311:992 - 996 pubmed link as well as | retraction
 * 11) Jongpil Kim, Keiichi Inoue, Jennifer Ishii, William B. Vanti, Sergey V. Voronov, Elizabeth Murchison, Gregory Hannon, Asa Abeliovich A MicroRNA Feedback Circuit in Midbrain Dopamine Neurons Science 31 August 2007:Vol. 317. no. 5842, pp. 1220 - 1224 pubmed link [CY/TR/Pink] [Giulia/WF/Red].
 * 12) Zimmermann TS, Lee AC, Akinc A, Bramlage B, Bumcrot D, Fedoruk MN, Harborth J, Heyes JA, Jeffs LB, John M, Judge AD, Lam K, McClintock K, Nechev LV, Palmer LR, Racie T, Röhl I, Seiffert S, Shanmugam S, Sood V, Soutschek J, Toudjarska I, Wheat AJ, Yaworski E, Zedalis W, Koteliansky V, Manoharan M, Vornlocher HP, MacLachlan I.RNAi-mediated gene silencing in non-human primates. Nature. 2006 May 4;441(7089):111-4.pubmed link [ES/TR/Green] [MS/WF/Grey].
 * 13) Hiroshi Nakamura,1 Shahid S. Siddiqui,2 Xiang Shen,1 Asrar B. Malik,2 Jose S. Pulido,1 Nalin M. Kumar,1 Beatrice Y. J. T. Yue. RNA interference targeting transforming growth factor-β type II receptor suppresses ocular inflammation and fibrosis [FW/WF/Blue]
 * 14) Stein P, Svoboda P, Anger M, and Schultz RM. RNAi: Mammalian oocytes do it without RNA-dependent RNA polymerase (2003). article link [CH/TR/Blue]

General RNAi Reviews (for reference, not presentation)

 * 1) Dykxhoorn DM, Novina CD, and Sharp PA. Killing the messenger: short RNAs that silence gene expression (2003). pubmed link
 * 2) Hannon GJ. RNA interference (2002). pubmed link
 * 3) Martin Jinek and Jennifer A. Doudna. A three-dimensional view of the molecular machinery of RNA interference (2009). pubemd link

siRNA validation and applications

 * 1) Kumar P, et al. T cell-specific siRNA delivery suppresses HIV-1 infection in humanized mice (2008). pubmed link [Alina/WF/Orange] [EAQ/TR/Green].
 * 2) Heidel JD, Yu Z, Liu JY, Rele SM, Liang Y, Zeidan RK, Kornbrust DJ, and Davis ME.Administration in non-human primates of escalating intravenous doses of targeted nanoparticles containing ribonucleotide reductase subunit M2 siRNA (2007). link
 * 3) Takeshita F, et al. Efficient delivery of small interfering RNA to bone-metastatic tumors by using atelocollagen in vivo (2005). pubmed link [SVM/TR/Grey] [SS/WF/Purple].
 * 4) Qiu S, Adema CM, Lane T.A computational study of off-target effects of RNA interference. Nucleic Acids Res. 2005 Mar 30;33(6):1834-47.pubmed link [MM/TR/Red]
 * 5) Zhang J, Wang C, Ke N, Bliesath J, Chionis J, He QS, Li QX, Chatterton JE, Wong-Staal F, Zhou D. A more efficient RNAi inducible system for tight regulation of gene expression in mammalian cells and xenograft animals. RNA. 2007 Aug;13(8):1375-83. pubmed link
 * 6) Wood M, Yin H, McClorey G. Modulating the Expression of Disease Genes with RNA-Based Therapy. PLoS Genet. 2007 Jun 29;3(6):e109pubmed link. [SCL/WF/Yellow] . [DA/TR/Orange]
 * 7) Krueger U, Bergauer T, Kaufmann B, Wolter I, Pilk S, Heider-Fabian M, Kirch S, Artz-Oppitz C, Isselhorst M, Konrad J.Insights into Effective RNAi Gained from Large-Scale siRNA Validation Screening. Oligonucleotides. 2007 Summer;17(2):237-50.pubmed link
 * 8) Tschaharganeh D, Ehemann V, Nussbaum T, Schirmacher P, Breuhahn K. Non-specific Effects of siRNAs on Tumor Cells with Implications on Therapeutic Applicability Using RNA Interference. Pathol Oncol Res. 2007;13(2):84-90.pubmed link [AM/TR/Pink] [LF/WF/Blue]
 * 9) Baigude H, McCarroll J, Yang CS, Swain PM, Rana TM.Design and creation of new nanomaterials for therapeutic RNAi. ACS Chem Biol. 2007 Apr 24;2(4):237-41.pubmed link. [LJB/TR/Orange] [DJ/WF/Pink].
 * 10) Schiffelers RM, Xu J, Storm G, Woodle MC, Scaria PV. Effects of treatment with small interfering RNA on joint inflammation in mice with collagen-induced arthritis.Arthritis Rheum. 2005 Apr;52(4):1314-8. pubmed link. [ARL/WF/Purple] . [DW/TR/Blue].
 * 11) Mikat V, Heckel A. Light-dependent RNA interference with nucleobase-caged siRNAs. 2007 Oct. pubmed link.
 * 12) Ganesan, AK et al. Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells (2008). pubmed link [MS/TR/Purple] [LA/WF/Green]
 * 13) Kim EJ, Kramer SF, Hebert CG, Valdes JJ, and Bentley WE. Metabolic engineering of the baculovirus-expression system via inverse "shotgun" genomic analysis and RNA interference (dsRNA) increases product yield and cell longevity (2007). pubmed link [MC/WF/Green].

General Applications Reviews (for reference, not presentation)

 * 1) Dorsett Y, and Tuschl T.G. siRNAs: applications in functional genomics and potential as therapeutics (2004). pubmed link
 * 2) de Fougerolles A, Vornlocher HP, Maraganore J, Lieberman J. Interfering with disease: a progress report on siRNA-based therapeutics (2007). pubmed link
 * 3) Whitehead KA, Langer R, and Anderson DG. Knocking down barriers: advances in siRNA delivery (2009). pubmed link

Day Sign-up
Please put your name under the day you wish to present. There are 8 slots on each day, per lab section.