20.109(F07): Module 2 oral presentations

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20.109(F07): Laboratory Fundamentals of Biological Engineering

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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. Once you have decided on a paper for your presentation, please email it to nkuldell AT mit DOT edu or stachow AT mit DOT edu, and also "reserve" it by putting your (initials/lab section/team color) next to the listing here. As you prepare your talk be sure to follow the specific guidelines for oral presentations in this class.

RNAi in other different cell types

  1. Sharma SK, Nirenberg M. Silencing of genes in cultured Drosophila neurons by RNA interference. Proc Natl Acad Sci U S A. 2007 Jul 23
  2. 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
  3. Galliot B, Miljkovic-Licina M, Ghila L, Chera S. RNAi gene silencing affects cell and developmental plasticity in hydra. C R Biol. 2007 Jun-Jul;330(6-7):491-7. Epub 2007 Feb 15.
  4. 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.
  5. Brandao PE, Castilho JG, Fahl W, Carnieli P Jr, Oliveira Rde N, Macedo CI, Carrieri ML, Kotait I. Short-interfering RNAs as antivirals against rabies. Braz J Infect Dis. 2007 Apr;11(2):224-5. pdf
  6. 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;
  7. 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;
  8. 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; [Epub ahead of print]
  9. 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 retraction
  10. Jongpil Kim,1 Keiichi Inoue,1 Jennifer Ishii,1 William B. Vanti,1 Sergey V. Voronov,1 Elizabeth Murchison,2 Gregory Hannon,2 Asa Abeliovich1* A MicroRNA Feedback Circuit in Midbrain Dopamine Neurons Science 31 August 2007:Vol. 317. no. 5842, pp. 1220 - 1224

siRNA validation and applications

  1. 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.
  2. 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.
  3. 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. Epub 2007 Jul 6.
  4. Gonzalez-Alegre P, Paulson HL. Technology insight: therapeutic RNA interference--how far from the neurology clinic? Nat Clin Pract Neurol. 2007 Jul;3(7):394-404.
  5. Chamberlain A, Gronvall GK. The science of biodefense: RNAi. Biosecur Bioterror. 2007 Jun;5(2):104-6.
  6. Natt F. siRNAs in drug discovery: target validation and beyond. Curr Opin Mol Ther. 2007 Jun;9(3):242-7. Review.
  7. Scherer L, Rossi JJ, Weinberg MS.Progress and prospects: RNA-based therapies for treatment of HIV infection. Gene Ther. 2007 Jul;14(14):1057-64.
  8. Wood M, Yin H, McClorey G. Modulating the Expression of Disease Genes with RNA-Based Therapy. PLoS Genet. 2007 Jun 29;3(6):e109
  9. 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.
  10. Svoboda P.Curr Opin Mol Ther. 2007 Jun;9(3):248-57. Off-targeting and other non-specific effects of RNAi experiments in mammalian cells.
  11. 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. Epub 2007 Jul 3.


Contributions to gene expression outside central dogma

  1. Pluta K, Diehl W, Zhang XY, Kutner R, Bialkowska A, Reiser J. Lentiviral vectors encoding tetracycline-dependent repressors and transactivators for reversible knockdown of gene expression: A comparative study. BMC Biotechnol. 2007 Jul 16;7(1):41
  2. Shpiz SG, Kalmykova AI. Structure of telomeric chromatin in Drosophila. Biochemistry (Mosc). 2007 Jun;72(6):618-30.
  3. H. Maamar, A. Raj, D. Dubnau, Noise in Gene Expression Determines Cell Fate in Bacillus subtilis Science 2007 317:526 - 529
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