Recommended Readings: David Breslow, Ph.D., February 17

Special Lecture Series
Wednesday, March 17, 2016
4:00 p.m., Carson Family Auditorium (CRC)

David Breslow, Ph.D.
Postdoctoral Scholar,
Department of Molecular and Cellular Physiology,
Stanford School of Medicine

Unraveling the Primary Cilium: Insights from New Biochemical and Functional Genomic Tools

Recommended Reading

Breslow, D. K., & Nachury, M. V. (2015). Analysis of soluble protein entry into primary cilia using semipermeabilized cells. Methods in Cell Biology, 127, 203-221. doi: 10.1016/bs.mcb.2014.12.006.

Breslow, D. K., Koslover, E. F., Seydel, F., Spakowitz, A. J., & Nachury, M. V. (2013). An in vitro assay for entry into cilia reveals unique properties of the soluble diffusion barrier. The Journal of Cell Biology, 203(1), 129-147. doi: 10.1083/jcb.201212024.

Recommended Readings: Li Zhao, Ph.D., March 2

Special Lecture Series
Wednesday, March 2, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Li Zhao, Ph.D.
Postdoctoral Researcher,
Department of Evolution and Ecology,
University of California Davis

Evolution of Genetic Novelties in Drosophila

Recommended Reading

Li, X., Fan, D., Zhang, W., Liu, G., Zhang, L., Zhao, L., … & Ding, Y. (2015). Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. Nature Communications, 6(8212). doi:10.1038/ncomms9212

Zhao, L., Saelao, P., Jones, C. D., & Begun, D. J. (2014). Origin and spread of de novo genes in Drosophila melanogaster populations. Science, 343(6172), 769-772. doi: 10.1126/science.1248286.

Zhao, L., Wit, J., Svetec, N., & Begun, D. J. (2015). Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and D. simulans. PLOS Genetics, 11(5), e1005184. doi: 10.1371/journal.pgen.1005184.

Recommended Readings: Emmanuelle Charpentier, Ph.D., January 22

Friday Lecture Series
Friday, January 22, 2016
3:45 p.m., Caspary Auditorium

Emmanuelle Charpentier, Ph.D.
Professor, Department of Regulation in Infection Biology
Director, Max Planck Institute for Infection Biology;
Visiting Professor, Laboratory for Molecular Infection Medicine Sweden, Umeå University

The Transformative Genome Engineering Technology CRISPR-Cas9: Lessons Learned from bacteria

Recommended Reading

Empirical Articles

Chylinski, K., Le Rhun, A., & Charpentier, E. (2013). The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biology, 10(5), 726-737. doi:10.4161/rna.24321

Fonfara, I., Le Rhun, A., Chylinski, K., Makarova, K. S., Lécrivain, A. L., Bzdrenga, J., … & Charpentier, E. (2014). Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic acids research, 42(4), 2577-2590. doi:10.1093/nar/gkt1074.

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816-821. doi:10.1126/science.1225829.

Review Papers

Charpentier, E., Richter, H., van der Oost, J., & White, M. F. (2015). Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiology Reviews, 39(3), 428-441. doi:10.1093/femsre/fuv023.

Chylinski, K., Makarova, K. S., Charpentier, E., & Koonin, E. V. (2014). Classification and evolution of type II CRISPR-Cas systems. Nucleic acids research, 42(10), 6091-6105. doi:10.1093/nar/gku241

Recommended Readings: Luciano Marraffini, Ph.D., October 9th

Friday Lecture Series
Friday, October 9th, 2015
3:45 p.m., Caspary Auditorium

Luciano Marraffini, Ph.D.
Assistant Professor and Head,
Laboratory of Bacteriology,
The Rockefeller University

CRISPR-Cas: The Adaptive Immune System of Prokaryotes

Recommended Readings

Empirical Articles

Goldberg, G. W., Jiang, W., Bikard, D., & Marraffini, L. A. (2014). Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting. Nature, 514(7524), 633-637. doi:10.1038/nature13637.

Heler, R., Samai, P., Modell, J. W., Weiner, C., Goldberg, G. W., Bikard, D., & Marraffini, L. A. (2015). Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature, 19(7542), 199-202. doi:10.1038/nature14245.

Jiang, W., Maniv, I., Arain, F., Wang, Y., Levin, B. R., & Marraffini, L. A. (2012). Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids. PLoS Genetics, 9(9), e1003844-e1003844. doi:10.1371/journal.pgen.1003844.

Review Papers

Barrangou, R., & Marraffini, L. A. (2014). CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Molecular Cell, 54(2), 234-244. doi:10.1016/j.molcel.2014.03.011.

Hatoum-Aslan, A., & Marraffini, L. A. (2014). Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens. Current Opinion in Microbiology, 17, 82-90. doi:10.1016/j.mib.2013.12.001

Recommended Readings: Jennifer Doudna, Ph.D. September 19

Friday Lecture Series
Friday, September 19, 2014
3:45 p.m., Caspary Auditorium

Jennifer Doudna, Ph.D.
Li Ka Shing Chancellor’s Chair in Biomedical and Health Sciences,
Professor of Biochemistry, Biophysics and Structural Biology,
Departments of Molecular and Cell Biology and Chemistry,
University of California, Berkeley
Investigator, Howard Hughes Medical Institute

CRISPR Systems: A Revolution in Basic Science and Biotechnology

Recommended Readings

Empirical Articles

Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K., & Doudna, J. a. (2010). Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science, 329(5997), 1355–1358. doi:10.1126/science.1192272

Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., & Doudna, J. a. (2014). DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature, 507(7490), 62–67. doi:10.1038/nature13011

Wiedenheft, B., Sternberg, S. H., & Doudna, J. a. (2012). RNA-guided genetic silencing systems in bacteria and archaea. Nature, 482(7385), 331–338. doi:10.1038/nature10886

Review Papers

Bhaya, D., Davison, M., & Barrangou, R. (2011). CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annual Review of Genetics, 45, 273–97. doi:10.1146/annurev-genet-110410-132430

Hsu, P. D., Lander, E. S., & Zhang, F. (2014). Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell, 157(6), 1262–1278. doi:10.1016/j.cell.2014.05.010

Recommended Readings: Lei Stanley Qi, Ph.D. Monday, January 13

Monday, January 13, 2014
4:00 p.m., Carson Family Auditorium

Lei Stanley Qi, Ph.D.
UCSF Systems Biology Fellow
Department of Cellular and Molecular Pharmacology and
UCSF Center for Systems and Synthetic Biology
University of California, San Francisco

Repurposing CRISPR/Cas as a versatile platform for genome engineering and imaging

Recommended Readings:

Empirical Articles

Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., … Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121), 819–823. doi:10.1126/science.1231143

Gilbert, L. a, Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., … Qi, L. S. (2013). CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell, 154(2), 442–451. doi:10.1016/j.cell.2013.06.044

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816–21. doi:10.1126/science.1225829

Qi, L., Haurwitz, R. E., Shao, W., Doudna, J. A., & Arkin, A. P. (2012). RNA processing enables predictable programming of gene expression. Nature Biotechnology, 30(10), 1002–6. doi:10.1038/nbt.2355

Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013). Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell, 152(5), 1173–83. doi:10.1016/j.cell.2013.02.022

Review Articles

Gaj, T., Gersbach, C. A., & Barbas, C. F. (2013). ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in Biotechnology, 31(7), 397–405. doi:10.1016/j.tibtech.2013.04.004

Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J. J., Charpentier, E., Horvath, P., … Koonin, E. V. (2011). Evolution and classification of the CRISPR-Cas systems. Nature Reviews Microbiology, 9(6), 467–477. doi:10.1038/nrmicro2577

Wiedenheft, B., Sternberg, S. H., & Doudna, J. A. (2012). RNA-guided genetic silencing systems in bacteria and archaea. Nature, 482(7385), 331–338. doi:10.1038/nature10886

Recommended Readings: Luciano Marraffini, Ph.D. Jan 11, 2010

Monday Lecture Series

Self vs Non-self Discrimination During CRISPR Immunity

Against Horizontal Gene Transfer

Luciano Marraffini, Ph.D.,

Post Doctoral Fellow, Department of Biochemistry, Molecular Biology and Cell Biology

Northwestern University

January 11, 2010

4:00p.m.-5:00 p.m.

Welch Hall, Level Two

Recommended readings:

Van der Oost, J; Jore, MM; Westra, ER; et al.  2009.  CRISPR-based adaptive and heritable immunity in prokaryotesTrends in biochemical sciences  34(8):401-407

Agari, Y; Yokoyama, S; Kuramitse, S; Shinkai, A.  2008.  X-ray crystal stryctyre of a CRISPR-associated protein, CSe2, from Thermus themaphilus, HB8.  Proteins – Structure Function and bioinformatics  73(4):1063-1067

Horvath, P; Romero, DA; Coute-Monvoison, AC; Richards, M; et al.  2008.  Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus.  Journal of bacteriology  1990(4):1401-1412

Brouns, SJJ; Jore,MM; Lundgren, M; Westra R; et al.  2008   Small CRISPR RNAs guide antiviral defense in prokaryotes.   SCIENCE  321(5891): 960-964 

Barrangou, RF; Fremaux, C; Deveau, H; Richards, M; Boyaval, P; Moineau, S; RFomero, DA; Horvath, P.  2007.  CRISPR provides acquired resistance against viruses in prokaryotes.  SCIENCE  315(5819):1709-1712

Tesch, LD; Raghavendra, MP; Bedsted-Faarvang, T; et al.  2005.  Specificity and reactive loop length requirements for cmA inhibition of serine proteases.  Protein science  14(2):533-542

Beloglazona, N; Brown, G; Zimmerman, MD; Proudfoot, M; Marakova, KS; et al.  2008.  A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats.  Journal of biological chemistry.  283(29): 20361-20371