20.109 | Fall 2007 | Undergraduate

Laboratory Fundamentals in Biological Engineering


List of Papers for Module 2 Presentations

RNAi in Other Different Cell Types

Sharma, S. K., and M. Nirenberg. “Silencing of Genes in Cultured Drosophila Neurons by RNA Interference.” Proc Natl Acad Sci USA 104, no. 31 (July 23, 2007): 12925-12930.

Nakatsuka, T., Y. Abe, Y. Kakizaki, S. Yamamura, and M. Nishihara. “Production of Red-flowered Plants by Genetic Engineering of Multiple Flavonoid Biosynthetic Genes.” Plant Cell Rep 26, no. 11 (November, 2006): 1951-1959.

Galliot, B., M. Miljkovic-Licina, L. Ghila, and S. Chera. “RNAi Gene Silencing Affects Cell and Developmental Plasticity in Hydra.” C R Biol 330, no. 6-7 (June-July 2007): 491-497.

Gary, D. S., A. Davidson, O. Milhavet, H. Slunt, and D. R. Borchelt. “Investigation of RNA Interference to Suppress Expression of Full-length and Fragment Human Huntingtin.” Neuromolecular Med 9, no. 2 (2007): 145-155.

Brandao, P. E., J. G. Castilho, W. Fahl, P. Carnieli Jr., Rde N. Oliveira, C. I. Macedo, M. L. Carrieri, and I. Kotait. “Short-interfering RNAs as Antivirals Against Rabies.” Braz J Infect Dis 11, no. 2 (April 2007): 224-225.

Wang, N., Y. H. Sun, J. Liu, G. Wu, J. G. Su, Y. P. Wang, and Z. Y. Zhu. “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 14, no. 6 (November 2007): 767-776.

Otani, M., T. Hamada, K. Katayama, K. Kitahara, S. H. Kim, Y. Takahata, T. Suganuma, and T. Shimada. “Inhibition of the Gene Expression for Granule-bound Starch Synthase I by RNA Interference in Sweet Potato Plants.” Plant Cell Rep 26, no. 10 (October 2007): 1801-1807.

Serman, A., F. Le Roy, C. Aigueperse, M. Kress, F. Dautry, and D. Weil. “GW Body Disassembly Triggered by siRNAs Independently of their Silencing Activity.” Nucleic Acids Res 35, no. 14 (2007): 4715-4727.

Kaushik, Deb, Mayandi Sivaguru, Hwan Yul Yong, and R. Michael Roberts. “Cdx2 Gene Expression and Trophectoderm Lineage Specification in Mouse Embryos.” Science 311 no. 5763 (2006): 992-996. Retraction .

Kim, Jongpil, 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 317, no. 5842 (August 31, 2007): 1220-1224.

Zimmermann, T. S., A. C. Lee, A. Akinc, B. Bramlage, D. Bumcrot, M. N. Fedoruk, J. Harborth, J. A. Heyes, L. B. Jeffs, M. John, A. D. Judge, K. Lam, K. McClintock, L. V. Nechev, L. R. Palmer, T. Racie, I. Röhl, S. Seiffert, S. Shanmugam, V. Sood, J. Soutschek, I. Toudjarska, A. J. Wheat, E. Yaworski, W. Zedalis, V. Koteliansky, M. Manoharan, H. P. Vornlocher, and I. MacLachlan. “RNAi-Mediated Gene Silencing in Non-human Primates.” Nature 441, no. 7089 (May 4, 2006): 111-114.

Nakamura, Hiroshi, Shahid S. Siddiqui, Xiang Shen, Asrar B. Malik, Jose S. Pulido, Nalin M. Kumar, and Beatrice Y. J. T. Yue. “RNA Interference Targeting Transforming Growth Factor-ß Type II Receptor Suppresses Ocular Inflammation and Fibrosis.” Molecular Vision 10 (2004): 703-711.

siRNA Validation and Applications

Qiu, S., C. M. Adema, and T. Lane. “A Computational Study of Off-target Effects of RNA Interference .” Nucleic Acids Res 33, no. 6 (March 30, 2005): 1834-1847.

Zhang, J., C. Wang, N. Ke, J. Bliesath, J. Chionis, Q. S. He, Q. X. Li, J. E. Chatterton, F. Wong-Staal, and D. Zhou. “A More Efficient RNAi Inducible System for Tight Regulation of Gene Expression in Mammalian Cells and Xenograft Animals .” RNA 13, no. 8 (August 2007): 1375-1383.

Gonzalez-Alegre, P., and H. L. Paulson. “Technology Insight: Therapeutic RNA Interference–How Far from the Neurology Clinic ?” Nat Clin Pract Neurol 3, no. 7 (July 2007): 394-404.

Natt, F. “siRNAs in Drug Discovery: Target Validation and Beyond .” Curr Opin Mol Ther 9, no. 3 (June 2007): 242-247.

Scherer, L., J. J. Rossi, and M. S. Weinberg. “Progress and Prospects: RNA-based Therapies for Treatment of HIV Infection .” Gene Ther 14, no. 14 (July 2007):1057-1064.

Wood, M., H. Yin, and G. McClorey. “Modulating the Expression of Disease Genes with RNA-Based Therapy .” PLoS Genet 3, no. 6 (June 29, 2007): e109

Krueger, U., T. Bergauer, B. Kaufmann, I. Wolter, S. Pilk, M. Heider-Fabian, S. Kirch, C. Artz-Oppitz, M. Isselhorst, and J. Konrad. “Insights into Effective RNAi Gained from Large-Scale siRNA Validation Screening .” Oligonucleotides 17, no. 2 (Summer 2007 ): 237-250.

Tschaharganeh, D., V. Ehemann, T. Nussbaum, P. Schirmacher, and K. Breuhahn. “Non-specific Effects of siRNAs on Tumor Cells with Implications on Therapeutic Applicability Using RNA Interference .” Pathol Oncol Res 13, no. 2 (2007): 84-90.

Baigude, H., J. McCarroll, C. S. Yang, P. M. Swain, and T. M. Rana. “Design and Creation of New Nanomaterials for Therapeutic RNAi .” ACS Chem Biol 2, no. 4 (April 24, 2007): 237-241.

Schiffelers, R. M., J. Xu, G. Storm, M. C. Woodle, and P. V. Scaria. “Effects of Treatment with Small Interfering RNA on Joint Inflammation in Mice with Collagen-induced Arthritis .” Arthritis Rheum 52, no. 4 (April 2005):1314-1318.

Mikat, V., and A. Heckel. “Light-dependent RNA Interference with Nucleobase-caged siRNAs .” RNA 13, no. 12 (December 2007): 2341-2347.

Learning Resource Types
Lecture Notes
Presentation Assignments
Written Assignments with Examples