Schedule and Readings
(repeated from Class 16)
Quiz 2 will be on Thursday, November 3 and will focus on material from Classes 14 – 18 (mostly on editing genomes, but also including most likely one question on the discussion of Quiz 1 from Class 14.)
Project reports are due Monday, 7 November. This should be a complete project report, which will be graded. You will receive feedback on it, and have an opportunity to revise and improve.
Read before Tuesday, 1 November (but earlier is better):
-
DNA Book: Chapter 28: Bacterial Virus Warfare and Chapter 29: Genetic Manipulation, CRISPR & beyond
-
Prarthana Mohanraju, Kira S. Makarova, Bernd Zetsche, Feng Zhang, Eugene V. Koonin, John van der Oost. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science, August 2016.
Slides and Links
Slides: Class 17: CRISPR for Humans
The quote about Eric Lander is from Michael Eisen’s blog, The Villain of CRISPR:
Lander’s recent essay in Cell entitled “The Heroes of CRISPR” is his masterwork, at once so evil and yet so brilliant that I find it hard not to stand in awe even as I picture him cackling loudly in his Kendall Square lair, giant laser weapon behind him poised to destroy Berkeley if we don’t hand over our patents.
For a more positive view on Eric Lander (and a very interesting story about another legal case involving genetics, this one about using DNA evidence properly in criminal trials which Lander was critical to including the Innocence Project), watch this episode from The Moth:
-
Alex Mira, Howard Ochman, and Nancy Moran. Deletional bias and the evolution of bacterial genomes. Trends in Genetics, October 2001.
-
Sandra C. Garrett. Pruning and Tending Immune Memories: Spacer Dynamics in the CRISPR Array. Frontiers in Microbiology, 1 April 2021.
-
Shomu’s Biology: Homologous Recombination
-
Nimrat Chatterjee and Graham C. Walker. Mechanisms of DNA damage, repair and mutagenesis. Enviromental and Molecular Mutagenesis, 9 May 2017.
-
DNA Repair - Providing Chemical Stability for Life - Nobel Prize in Chemistry 2015 to Tomas Lindahl, Paul Modrich and Aziz Sancar.
-
Guo-Min Li. Mechanisms and functions of DNA mismatch repair. Cell Research, 2008.
-
D. P. Clark and N. J. Pazdernik, DNA Synthesis In Vivo and In Vitro. Biotechnology, 2016.
-
Kim Sneppen & Szabolcs Semsey, Mismatch repair at stop codons is directed independent of GATC methylation on the Escherichia coli chromosome. Scientific Reports, 2014.
-
Le Cong, F. Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D. Hsu, Xuebing Wu, Wenyan Jiang, Luciano A. Marraffini, Feng Zhang. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science, 3 Jan 2013.
-
CRISPR patent: Methods and compositions for RNA-directed target DNA modification and for RNA-directed transcription modulation
-
CRISPR Patent Ruling: Decision on Priority 37 C.F.R. § 41.125(a), USPTO 28 February 2022.