About Damon

Damon Lisch

Department of Plant and Microbial Biology, 111 Koshland Hall

University of California, Berkeley

Berkeley, CA  94720-3102

510-642-8058

dlisch@berkeley.edu



Education

1995

University of California, Berkeley, CA  Ph.D., Genetics

Advisor: Michael Freeling


1987

University of California, Santa Cruz, CA  BA, Biology


Employment Experience

2007-now   

Associate Research Professional, Department of Plant and Microbial Biology,

University of California, Berkeley


1999-2007   

Assistant Research Professional, Department of Plant and Microbial Biology,

University of California, Berkeley


1998-1999   

Research Associate, Department of Plant Sciences, University of Arizona

Advisor: Vicki Chandler


1996-1998   

NIH Postdoctoral Fellow, Center for Insect Science, University of Arizona

Advisor: Margaret Kidwell (retired)


Honors/Awards

1996   

NIH Postdoctoral Fellowship, Center for Insect Science, University of Arizona


1991   

Earnest Brown-Babcock Scholarship


1987   

Graduated with honors (BA), University of California, Santa Cruz


Teaching Experience

2008   

Invited HHMI Guest Lecturer, National Laboratory of Genomics for

Biodiversity, Center for Research and Advanced Studies (Cinvestav, Campus

Guanjuato) Irapuato, Mexico


2008   

Invited Lecturer, Plant Biology 84, Genome Dark Matter, U.C. Berkeley


2008-2009

Invited HHMI Guest Lecturer, University of Georgia


2005   

Invited Guest Lecturer, Swarthmore College


2003-2004   

Guest Lecturer, Plant and Microbial Genetics, U. C. Berkeley


2002-2007   

Guest Lecturer, Modern Applications of Plant Biotechnology, U. C. Berkeley


1991   

Teaching Assistant, Introduction to Genetics, U. C. Berkeley


1990   

Teaching Assistant, Introduction to Biology, U. C. Berkeley


Independent Funding


Co-Principle Investigator on a National Science Foundation grant entitled “mudrB function and evolution in grasses” (MCB 0112346).  This grant was first funded in 2000 for $370,836 over a three-year period.


Co-Principle Investigator on a National Science Foundation grant entitled “Epigenetic regulation of the Mutator system of transposons” (DBI 0321726).  This grant was first funded in 2003 for $986,783 over a five-year period.

Principle Investigator, “Epigenetic regulation of the Mutator transposons in maize” (DBI 0820828). $1,370,086 for a four-year period.  Funding extends to 2012.

Total independent funding obtained at U.C. Berkeley, 2000-2010: $2,727,705.


Supervisory Experience


As a research professional mentored two graduate students through the completion of their Ph.D.s.   Supervises a research group that has included at various times two graduate students, three postdoctoral fellows, three technicians, twelve undergraduates and ten high school students.


Presentations


2011        Invited Speaker, Plant and Animal Genomes, San Diego, CA

2010    Invited Seminar Speaker, University of Texas at Arlington

2010    Invited short talk, 53rd Annual Maize Meeting, Riva de Garda, Italy.

2010    Invited Speaker, American Society for Microbiology meeting on Mobile DNA, Montreal, Canada

2010        Invited Seminar Speaker, U.C. Davis, Davis CA

2009        Invited Seminar Speaker, Ohio State University,  Columbus, OH

2009        Invited Seminar Speaker, Oregon State University, Corvallis, OR

2009    Invited Seminar Speaker, U.C. Berkeley, Department of Plant and Microbial Biology, Berkeley, CA

2006    Invited Speaker, Michigan State University Plant Breeding and the Genetics Graduate Programs Symposium on Transposable elements and Genome Evolution, December 8, 2006, East Lancing, MI

2006    Invited Speaker, Plant Biology Seminar Series, University of Arizona, Tucson AZ.

2006    Invited Speaker, Gordon Conference on Plant Molecular Biology, July 16-21, 2006, Holderness School Plymouth, NH.

2005    Invited Speaker, National Millet Improvement Center of China, Hebei Academy of Agricultural and Forestry Sciences, October 14, 2005, Hebei, P. R. China

2003    Invited Speaker, Keystone Symposium on Transposition and Other Genome Rearrangements, Santa Fe, NM.

2003    Invited Speaker, Transposition, Recombination and Application to Plant Genomics, Ames Iowa.

2000    Invited Short Talk, Maize Genetics Conference, Coeur d'Alene, ID.

1994    Invited Speaker, International Congress of Plant Molecular Biology, Amsterdam, Holland.

1993    Invited Short Talk, Maize Genetics Conference, St. Charles, Illinois.


Community outreach


Radio interviews:  Talk of the Bay, KUSP, 1999.  Occasional science advisor for Deanna Zachary, host of Talk of the Bay, a public affairs program on KUSP.  Interviewed for a documentary radio program with Jeff Barlcom, KUSP, 2006.  Interviewed for a California Magazine article, 2006.

Mentor, Project Seed:  a summer training program for traditionally under-represented high school students, 2003-2009.  Also mentor to several Berkeley High School Summer interns in 2005 through 2009.




Service


Ad hoc reviewer for the National Science Foundation and the USDA.  Peer reviewer for Science, Nature, Nature Genetics, Plant Cell, PLoS Genetics, PLoS Biology, PNAS, Gene, Plant Molecular Biology, Genome Research, Plant Physiology, Journal of Molecular Evolution, Molecular Genetics and Genomics, among others.  Member of the Review Editorial Board of Frontiers in Plant Genetics and Genomics


Patents Awarded


Genetic functions required for gene silencing in maize. Patent number 7264970.


Publications


Comet, P., D. Lisch, C. J. Hardeman, V. L. Chandler, and M. Freeling, 1991.  Identification of a regulatory transposon that controls the Mutator system of transposable elements.  Genetics 129:  261-270.


Lisch, D., and M. Freeling, 1994.  Loss of Mutator activity in a minimal line.  Maydica 39: 289-300 (13).


Donlin, M. J., D. Lisch and M Freeling, 1995.  Tissue-specific accumulation of MURB, a protein encoded by MuDR, the autonomous regulator of the Mutator transposable element family.  The Plant Cell 7: 1989-2000.


Lisch, D., P. Chomet, and M. Freeling, 1995.  Genetic characterization of the Mutator system in maize: behavior and regulation of Mu elements in a minimal line.  Genetics 139: 1777-1796.


Kidwell, M., and D. Lisch, 1997.  Transposable elements as sources of variation in animals and plants.  PNAS 94: 7704-7711.


Selinger, D.A., D. Lisch and V. L. Chandler, 1998.  The Maize Regulatory Gene B-Peru contains a DNA rearrangement that specifies tissue-specific expression through both positive and negative promoter elements.  Genetics 149:1125-1138.


Kidwell, M. G. and D. Lisch, 1998.  Hybrid genetics: transposons unbound.  (Commentary) Nature 393:22-23.


Lisch, D., L. Girard, M. Donlin and M. Freeling, 1999.  Deletion derivatives of MuDR delineate functional roles for the MURA and MURB proteins.  Genetics 151:331-341.


Kidwell, M., and D. Lisch, 2000.  Transposable elements and host gene evolution.  Trends in Ecology and Evolution 15: 95-98.


Kidwell, M., and D. Lisch, 2001.  Perspective:  Transposable Elements, parasitic DNA, and genome evolution.  Evolution 55(1): 1-24


Lisch, D., R. Langham, M. Freeling, and M. Choy, 2001.  The Mutator transposase is widespread in the grasses.  Plant Physiology. 125: 1293-1303.


M. Kidwell and D. Lisch, 2002.  Transposable elements as sources of genomic variation.  Mobile DNA II, Chapter 4.  pp. 59-90.


Kaplinsky, N., D. Braun, D. Lisch, A. Hay, S. Hake, and M. Freeling, 2002.  Biodiversity (Communications arising): maize transgene results in Mexico are artifacts. Nature (416):601-2.


Lisch, D., C. Carey, J. Dorweiler, and V.Chandler, 2002.  A mutation that prevents paramutation in maize also reverses Mutator transposon methylation.  PNAS. 99:6130-5.


Lisch, D, 2002.  The Mutator Transposons.  Trends in Plant Science 7:498-504.


Hudson, M., D. Lisch and P. Quail, 2003.  The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A signaling pathway.  The Plant Journal 34:453-71 (16).


Slotkin, R.K., M. Freeling, and D. Lisch, 2003.  Mu killer causes the heritable inactivation of the Mutator family of transposable elements in Zea mays.  Genetics 165:781-97.


Lisch, D.  2005. Pack-MULEs: Theft on a Massive Scale.  BioEssays 27: 353-355.


Slotkin, R.K., M. Freeling and D. Lisch,  2005 Heritable silencing of a transposon family is initiated by a naturally occurring inverted repeat derivative.  Nature Genetics 137:641-644


Diao, X.M., M. Freeling and D. Lisch, 2006.  Horizontal Transfer of a Plant Transposable element.  PLoS Biology 4: 0119-0128. (Cover)


Woodhouse, M., M. Freeling and D. Lisch, 2006. The mop1 (mediator of paramutation1) mutant progressively reactivates one of the two genes encoded by the MuDR transposon in maize. Genetics 172: 579-592.


Diao, X. M. Freeling and D. Lisch,  2006.  Mutator transposons in maize and MULEs in the plant genome.  Yi Chuan Xue Bao 33: 477-87.


Woodhouse, M., M. Freeling and D. Lisch, 2006, Initiation, establishment and maintenance of MuDR transposon silencing require distinct factors.  PLoS Biology PMID: 16968137 (Editor’s Choice, Science 314:19)


Lisch, D. and N. Jiang, 2008. Mutator and Pack-MULEs, in "The maize handbook - Volume II:  Domestication, Genetics and Genomics of Maize".  Invited book chapter.


Lyons, E., Castelletti, S., Brent Pedersen, B, Lisch, D. and M Freeling, 2008.  Maize GEvo:  A Comparative DNA Sequence Alignment Visualization and Research Tool in "The maize handbook - Volume II:  Domestication, Genetics and Genomics of Maize".  Invited book chapter. 


Singh, J. Freeling, M. and D. Lisch, 2008. A position effect on the heritability of silencing. PLoS Genetics. PMID: 18846225


Lyons, E, Pedersen, B, Kane, J., Alam, M., Ming, R., Tang,  H., Xiyin, H.T., Wang, R., Bowers, J., Paterson, Lisch, D., and M. Freeling, 2008. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids. Plant Physiology. PMID: 18952863.


Lisch, D, 2008.  A new SPIN on horizontal transfer.  Commentary.  PNAS. PMID: 18974220


Freeling, M. Lyons, E., Pederson, B., Alam, B., Ming, R and D. Lisch, 2008.  Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Research. PMID: 18836034


Lisch, D., 2009.  Epigenetic regulation of transposons in plants.  Annual Review of Plant Biology. Invited review. PMID: 19007329.


Hale, C., Erhard, L., Lisch, D., and J. Hollick, 2009. Distinct roles of RNA-directed DNA methylation factors in the processing of maize repetitive RNAs.  PLoS Genetics. PMID: 19680464


Hanada, K., Vallejo, V., Nobuta, K., Slotkin, R.K., Lisch, D., Meyers, B.C., Shiu, S-H. and N. Jiang, 2009. Expression and evidence for function of Pack-MULEs  in rice.  Plant Cell. PMID: 19136648


Schnable, P.S et al. (Lisch, D., author 121 of 160), 2009. The B73 maize genome: complexity, diversity and dynamics.  Science 326(5956):1112-5.


Jia, Y., Ohtsu, K, Lisch, D., Nettleton, D and P.S.  Schnable, 2009. Loss of RNA-dependent RNA Polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons and genes in maize shoot apical meristems. PLoS Genetics 2009 Nov;5(11):e1000737.


Ramirez, J., Bolduc, N., Lisch, D, and S. Hake, 2009. Position dependent effects of knotted1 on leaf shape in maize. Plant Physiology 2009 Dec;151(4):1878-88


Woodhouse, M. R., Schnable, J. C., Pedersen, B. S., Lyons, E., Lisch, D., Subramaniam, S. and M. Freeling, 2010. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLoS Biology 2010 Jun 29;8(6):e1000409 (Cover).


Li, Hong, Freeling, M. and D. Lisch, 2010.  Epigenetic modifications are reprogrammed during vegetative phase change in maize. PNAS, PMID 21135217.


Jiang, N, Ferguson, A, Slotkin, R.K and Lisch, D. Pack-MULE transposable elements induce directional modification of genes through biased insertion and DNA acquisition.  In press, PNAS.


Lisch, D. and Bennetzen, J., 2011.  Causes and Consequences of Epigenetic Regulation of Plant Transposons.  Current Opinion in Plant Biology, invited review, in preparation.


Text Book Chapters Edited:

Genes X.  Chapter 17. Transposable elements and Retroviruses.