Difference between revisions of "20.109(F07): Module 2 oral presentations"

From Course Wiki
Jump to: navigation, search
Line 14: Line 14:
 
#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 [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16484492&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum abstract and pubmed link] as well as [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17656701&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus| retraction]
 
#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 [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16484492&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum abstract and pubmed link] as well as [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17656701&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus| retraction]
 
#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 [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17761882&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum abstract and pubmed link]
 
#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 [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17761882&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum abstract and pubmed link]
−
 
+
#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.[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16565705&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus abstract and pubmed link]
 +
     
 
===siRNA validation and applications===
 
===siRNA validation and applications===
 
#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.[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15800213&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum abstract and pubmed links]  
 
#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.[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15800213&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum abstract and pubmed links]  
Line 24: Line 25:
 
#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.[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17638527&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum abstract and pubmed link]
 
#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.[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17638527&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum abstract and pubmed link]
 
#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. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17607368&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum abstract and pubmed link]
 
#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. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17607368&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum abstract and pubmed link]
−
 
+
#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.[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17432823&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus abstract and pubmed link]
−
 
+
−
===Contributions to gene expression outside central dogma===
+
−
# 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
+
−
# Shpiz SG, Kalmykova AI. Structure of telomeric chromatin in Drosophila. Biochemistry (Mosc). 2007 Jun;72(6):618-30.
+
−
#H. Maamar, A. Raj, D. Dubnau, Noise in Gene Expression Determines Cell Fate in Bacillus subtilis Science 2007 317:526 - 529
+

Revision as of 13:23, 2 September 2007


20.109(F07): Laboratory Fundamentals of Biological Engineering

Macintosh HD-Users-nkuldell-Desktop-bldg10crop.png

Home        People        Schedule Fall 2007        Assignments        Lab Basics        OWW Basics       
Genome Engineering        Expression Engineering        Biomaterials Engineering              

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 astachow 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 abstract and pubmed link
  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 abstract and pubmed link
  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.abstract and pubmed link
  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.abstract and pubmed link
  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; abstract and pubmed link
  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; abstract and pubmed link
  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; abstract and pubmed link
  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 abstract and pubmed link as well as retraction
  10. 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 abstract and pubmed link
  11. 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.abstract and pubmed link

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.abstract and pubmed links
  2. 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. abstract and pubmed links
  3. 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. abstract and pubmed link
  4. Natt F. siRNAs in drug discovery: target validation and beyond. Curr Opin Mol Ther. 2007 Jun;9(3):242-7. review's abstract and pubmed link
  5. 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. abstract and 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):e109abstract and pubmed link
  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.abstract and 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. abstract and pubmed link
  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.abstract and pubmed link
Retrieved from "http://engineerbiology.org/w/index.php?title=20.109(F07):_Module_2_oral_presentations&oldid=13439"