20.109(F09): KaWi's Final Project



Topics (in brief): Riboswitches to reg transcription.

PPAR-delta expression in macrophages recognize apoptotic cells.

Exit from mitosis into interphase through Sic1.

Amino Acid Mutations leading to human speech

'Ribosome Rescue'--pausing and restarting Ribosomes during translation

Cell motility assay -- on homogenous layer of quantum dots, cells engulf the nanocrystals and leave a non-fluorescent trail. More motility correlated with potential metastatic tumor cells.

Nanotubes can be heated with radio waves to kill cancer cells (need to know how to target cancer cells)

Cancer cells: Tools: HIV has integrase, protease, reverse transcriptase that are specific to HIV cells, distinguishing it from normal cells.

Ribosomes can be paused or restarted using releasing factors, tmRNA*SNPB.

How to make cancer cells trigger PPAR expression in macrophages. Or display receptors that bind to PPAR protein.

Possible idea 1: See how Ribosome Rescue paper's (pausing or restarting ribosomes) mechanism affects cancer cells. If one extreme or the other causes apoptosis.

Topic idea 2: Use riboswitch to turn on PPAR expression in macrophages, to initiate engulfment of apoptotic cells.

Topic idea 3: Engineer p8 of M13 to bind epitope (recognized by Ab), p3 to bind to EGFR (overexpressed in cancer cells)....or some recognition site specific to cancer cells/virus (GP41, GP120 for HIV).

References:

Quantum Dot-Based Cell Motility Assay Weiwei Gu1, Teresa Pellegrino2, Wolfgang J. Parak2, Rosanne Boudreau1, Mark A. Le Gros3, Daniele Gerion2, A. Paul Alivisatos2, and Carolyn A. Larabell1,3* Sci. STKE, 28 June 2005 Vol. 2005, Issue 290, p. pl5 [DOI: 10.1126/stke.2902005pl5]

http://www.popsci.com/article/2007-11/scientists-fry-cancer-cells-nanotubes

Nature Structural & Molecular Biology 11, 29 - 35 (2003) Published online: 29 December 2003; | doi:10.1038/nsmb710 Adenine riboswitches and gene activation by disruption of a transcription terminator Maumita Mandal & Ronald R Breaker

Nature Medicine 15, 1266 - 1272 (2009) Published online: 18 October 2009 | doi:10.1038/nm.2048 PPAR- senses and orchestrates clearance of apoptotic cells to promote tolerance Lata Mukundan1,7, Justin I Odegaard1,2,7, Christine R Morel1,3,7, Jose E Heredia1, Julia W Mwangi1, Roberto R Ricardo-Gonzalez1,4, Y P Sharon Goh1,4, Alex Red Eagle1,5, Shannon E Dunn6, Jennifer U H Awakuni1, Khoa D Nguyen1,4, Lawrence Steinman6, Sara A Michie2 & Ajay Chawla1,4

Molecular Systems Biology 5 Article number: 324 doi:10.1038/msb.2009.86 Published online: 3 November 2009 Citation: Molecular Systems Biology 5:324 Mitotic exit in mammalian cells Orsolya Kapuy1, Enuo He1, Frank Uhlmann2 & Béla Novák1

Jansen, Hayes. Kinetics of Paused Ribosome Recycling in E. Coli. J. Mol. Biol. (2009) 394, 251–267 Published online: 15 September 2009

Journal of Molecular Biology, Volume 380, Issue 3, 11 July 2008, Pages 504-519 X. Chen, M. Tsiang, F. Yu, M. Hung, G.S. Jones, A. Zeynalzadegan, X. Qi, H. Jin, C.U. Kim, S. Swaminathan, J.M. Chen