The Dawe LabThe Dawe Lab

Alumni

Natalie Nannas, Postdoctoral Fellow, 2013-2017

Natalie arrived well trained as a cell biologist with expertise in yeast spindle dynamics. She was interested in applying her knowledge to a practical problem, and chose to extend our work on synthetic centromeres by transforming long molecules into maize and creating improved kinetochore tethering constructs. Towards this aim she also developed new methods for visualizing meiotic spindles in live cells and was the first to describe this process in real time. We will continue to work with Natalie in her new role as Assistant Professor at Hamilton College, NY.

Higgins, D.M., Nannas, N.J., and Dawe, R.K. (2016). Frontiers Plant Sci. 7: 2177.
Nannas, N.J., Higgins, D.M., and, Dawe, R.K. (2016). J. Cell Sci. 129:4014-4024.
Nannas, N.J. and, Dawe, R.K. (2016). Current Protocols in Plant Biology 1:546-565.


David Higgins, Ph.D. 2017

David’s main interest was cell biology but he became an adept geneticist over the course of his Ph.D.  Within a few months of arriving, he had identified a candidate gene for the classic maize mutant divergent spindle, which he confirmed using a second allele and excellent microscopy. He also added critical data to the emerging story on Kindr, the presumed neocentromere motor on Ab10, showing that RNAi could create new stable epialleles of this gene family. In addition to learning to be a scientist, he honed his skills as a teacher and is now a temporary Assistant Professor at Hendrix College, AR.

Higgins, D.M., Nannas, N.J., and Dawe, R.K. (2016). Frontiers Plant Sci. 7: 2177
Nannas, N.J., Higgins, D.M., and, Dawe, R.K. (2016). J. Cell Sci. 129:4014-4024


Nathanael Ellis, Ph.D. 2015

Nate carried out his Ph.D. in a time of transition between traditional and sequence-based genetic markers, learning transposon display on long sequencing gels and ultimately becoming an expert in bioinformatics. Much of his work focused on mapping the B chromosome centromere core by combining transposon display markers with CENH3 ChIP-seq data. However, he was also interested in the epigenetic transition between transposons and genes and the impact of transposons on gene expression. Spending more time at the computer than the bench, Nate was the first big-data geneticist to be trained in our lab. He is now a postdoctoral fellow with Christopher Topp at the Danforth Center, MO.

Gent J.I., Ellis N.A. et al. (2012). Genome Res. 23:628-37..
Eichten S.R., Ellis N.A. et al. (2013). PLoS Genet. 8:e1003127.
Ellis N.A., Douglas R.N., Jackson C.E., Birchler J.A., Dawe R.K. (2015) G3 5:2857-64.


Elizabeth Lowry, Ph.D. 2015

Elizabeth identified the Kindr complex, a family of kinesin genes required for Ab10-mediated meiotic drive. She discovered that a kinesin of the class we had long suspected could drive neocentromere activity was encoded in the distal tip of the Ab10 chromosome, that there were actually nine Kindr genes in a ~1 Mb cluster, that Kindr was not expressed at all in one of our meiotic drive mutants and under expressed in another, and finally that both mutants were epimutants associated with dramatic changes in DNA methylation.  She learned genetics and bioinformatics, and had a key role in pushing this long-term project towards the finish line. She is now a teacher at the Fusion Academy in San Mateo, CA.

Kanizay, L.B., Pyhäjärvi, T., Lowry, E.G. et al. (2013). Heredity 110:570-7

 


Caroline Coatney, M.S. 2015

Caroline had the confidence and ambition to start an entirely new project in our lab on perenniality in Zea. By crossing Zea diploperennis to domesticated maize and generating segregating populations, she found that perenniality is not heritable in a small mapping population, but that traits associated with tillering and regrowth after flowering are key phenotypes to score in future experiments.  She also generated the first molecular mapping data for this cross. We hope that her work will facilitate future studies on Zea diploperennis as a model for the genetics of perenniality. Caroline is now a scientist at Monsanto in Woodland, CA.

 


Lisa Kanizay, Ph.D. 2011, Postdoctoral Fellow 2012

Lisa carried out multiple studies on abnormal chromosome 10 with the aim of understanding the mechanism of meiotic drive. She identified two new Ab10 variants, one of which is a highly specialized meiotic drive suppressor chromosome. In addition she discovered Ab10-III and showed it is the most common Ab10 type in maize. She also initiated an important RNA-Seq analysis of Ab10 anthers that led to the identification of the first known genes from the “distal tip” that contains the key factors required for meiotic drive. Lisa learned to be a maize geneticist, molecular biologist and bionformaticist, and without her we would not still be working on this fascinating system. Lisa is now a Scientist at Monsanto in St. Louis.

Kanizay, L.B., Albert, P.S., Birchler, J.A. et al. (2013). Genetics 194:81-9
Kanizay, L.B., Pyhäjärvi, T., Lowry, E.G. et al. (2013). Heredity 110:570-7
Ghaffari, R., E.K. Cannon, L.B. Kanizay, et al. (2012). Chromosoma 122: 67-75
Kanizay, L. and R.K. Dawe (2009). Funct Integr Genomics: 287-292


Brunie Burgos, Ph.D. 2012

Brunie focused entirely on Arabidopsis as a study organism throughout her PhD. In general, it is very difficult to study the genes that control cell division because the mutant plants will normally die as seedlings. As means to get around this problem, she expressed hairpin constructs in cell lineages of flowers to assay petal-specific and anther-specific RNAi defects. The system worked beautifully and demonstrated that both CENPC and MIS12 are required kinetochore components. In addition, the results demonstrated that RNAi signals do not transit from the anther wall tissue into pollen cells. Brunie is now a staff scientist at the Centers for Disease Control (CDC) in Atlanta.

Burgos-Rivera, B. and R.K. Dawe (2012). PLoS One 7(12): e51388.


Rashin Ghaffari, Technician 2012

Rashin started as an undergraduate researcher, then worked as our technician for two years. She was a Master of FISH in the McClintockian style, being able to name any chromosome on sight. She used her gifts to score thousands of mitotic karyotypes, including two entire RIL sets, which allowed us to map seven of the maize knobs to the genetic map. These map positions made it possible to confirm that knobs suppress recombination as suggested by Rhoades many years ago. This is an important contribution to our understanding of the maize genome and would not have been completed if not for her diligence and hard work. She is now a PhD student at UT Austin.

Ghaffari, R., E.K. Cannon, L.B. Kanizay, et al. (2012). Chromosoma 122: 67-75


Han Zhang, Ph.D. 2011

Han made major steps towards creating fully synthetic centromeres in maize. She produced long synthetic repeat arrays using overlap PCR, and in collaboration with Wayne Parrott’s laboratory, transformed them directly into maize. Three such Arrayed Binding Sites (ABS) on different chromosomes proved to be remarkably long and intact (up to 1.1 Mb). We are now using these arrays as binding platforms for inner kinetochore proteins fused to known DNA binding motifs. She was also the first to note that centromere/kinetochore size correlates almost perfectly with genome size, suggesting the centromere size is controlled at a whole-cell level, not as a response to chromosome size. Han is now a Scientist at Applied Stemcell, Milpitas CA.

Zhang, H., B.H. Phan, K. Wang, et al. (2012). Plant J 70(2): 357-365.
Zhang, H. and R.K. Dawe (2012). Chromosome Res 20(4): 403-412.
Zhang, H. and R.K. Dawe (2011). Chromosome Res 19(3): 335-344.


Christopher Topp, Ph.D. 2009

Chris started as a technician in 2001 and entered the graduate program in 2003. He had many important roles and projects. His primary contributions were the discovery of centromeric RNA and the documentation of the first de novo neocentromere in maize/oat. He also pioneered the use of Arabidopsis in our lab through collaboration with Richard Meagher. He developed key Arabidopsis cytogenetics protocols and showed that overexpression of kinetochore genes causes anaphase failure. He also wrote two reviews, and in a very important sense served as an intellectual and social leader. Chris is now a principle investigator at the Danforth Center.

Gent, J.I., K.L. Schneider, C.N. Topp, et al. (2011). Epigenetics Chromatin 4: 3.
Du, Y., C.N. Topp and R.K. Dawe (2010). PLoS Genet 6(2): e1000835.
Topp, C.N., R.J. Okagaki, J.R. Melo, et al. (2009). Cytogenet Genome Res 124(3-4): 228-238.
Phan, B.H., W. Jin, C.N. Topp, et al. (2007). Transgenic Res 16(3): 341-351.
Topp, C.N. and R.K. Dawe (2006). Curr Opin Plant Biol 9(6): 647-653.
Topp, C.N., C.X. Zhong and R.K. Dawe (2004). Proc Natl Acad Sci U S A 101(45): 15986-15991.
Zhong, C.X., J.B. Marshall, C. Topp, et al. (2002). Plant Cell 14(11): 2825-2836.


Yun Li, M.S. 2009

Yun worked on the stucture and evolution of maize CENPC genes. She identified a third Cenpc gene in maize, and characterized its structure and expression in diverse Zea species. As a outcome of her studies with Zea luxurians, Zea diploperennis, and Zea perennis, we discovered that maize centromeres differ dramatically with respect to CentC and CRM content. Yun and her work opened our eyes to the idea of using existing Zea variation to study centromere evolution. She is now a teacher at Shanghai Pinghe School in China.

 

 


Jinghua Shi, Ph.D. 2009

Jinghua began with a study of chromatin modifications on pachytene chromosomes, providing a global view of the maize epigenetic profile. She then developed a difficult procedure that combines ChIP with transposon display, allowing her to map sequences that interact with centromeric histone H3 (CENH3). The output was 238 within-centromere markers that she used to directly demonstrate gene conversion in centromere cores. She is a master of FISH and helped develop a model for how CentC has driven maize centromere evolution. Jinghua showed academic excellence and shifted the lab focus in fundamental ways. Jinghua is now a Scientist at Illumina, San Diego.

Shi, J., S.E. Wolf, J.M. Burke, et al. (2010). PLoS Biol 8(3): e1000327.
Shi, J. and R.K. Dawe (2006). Genetics 173(3): 1571-1583.


Xuexian Li, Ph.D. 2009

Xuexian began his work on the phospho-CENH3 project, performing key protein blot analyses and detailed localization experiments. He then chose central kinetochore protein MIS12 as his primary focus. Among his accomplishments were the generation of three different antibodies, the completion of two major RNAi projects, and a thorough cytological analysis of MIS12 knock-down mutants. His data lead to the discovery that kinetochores themselves initiate the specialized segregation of meiosis I, staying closely fused during prometaphase I and enforcing the sister chromatid co-orientation event. Xuexian is now a Professor at China Agriculture University.

Li, X. and R.K. Dawe (2009). Nat Cell Biol 11(9): 1103-1108.
Zhang, X., X. Li, J.B. Marshall, et al. (2005). Plant Cell 17(2): 572-583.


Yaqing Du, Ph.D. 2008

Yaqing studied two kinetochore proteins, NDC80 and CENPC. She used quantitative microscopy to show that NDC80 is constitutive protein, placing it in the ‘foundation’ protein category. Then focussing on CENPC and biochemical methods, she identified the CENPC DNA binding motif, showed that the motif is required for efficient CENPC localization in vivo, and importantly, demonstrated that single stranded RNA is a cofactor in the CENPC-DNA binding reaction. These data allowed her to argue that RNA is a part of a structural template that stabilizes CENPC and identifies centromeres. Han is now studying to be a Medical Laboratory Scientist in Nashville.

Du, Y., C.N. Topp and R.K. Dawe (2010). PLoS Genet 6(2): e1000835.
Du, Y. and R.K. Dawe (2007). Chromosome Res 15(6): 767-775.


Sarah Rushing (Oglesby), M.S. 2008

Sarah assayed the genetics and expression of three central kinetochore proteins in Arabidopsis, and developed a our first live-cell system for viewing YFP-stained kinetochore proteins in live cells. Her work also demonstrated that Spc25 is a conserved kinetochore protein in plants and set the stage for studying kinetochores at the functional level using RNAi. Sarah is now working in the Florida Department of Agriculture as a liason between lab researchers and citrus growers.

 

 


Xiaolan Zhang, Ph.D. 2007

Xiaolan was co-advised by Dr. Michael Scanlon. She spent a total of about 2 years in the Dawe lab, first on a long rotation where she completed a major paper on the phosphorylation of maize CENH3, and later when her primary advisor, Dr. Scanlon, left for Cornell. She is uniquely skilled with a microscope and helped train many students in the art of sample preparation and analysis. Xiaolan is now a Professor at China Agriculture University

Zhang, X., X. Li, J.B. Marshall, et al. (2005). Plant Cell 17(2): 572-583.
Dawe, R.K., E.A. Richardson and X. Zhang (2005). Cytogenet Genome Res 109(1-3): 128-133.

 


Cathy Zhong, Postdoctoral Fellow 2000-2003

Cathy was co-advised by Dr. Wayne Parrott from 2000 through early 2003. She was the first person empoyed on our Plant Genome Grant. Among other things, Cathy developed CENH3-ChIP for maize, which was a pivotal event that ultimately led to the complete sequencing of two maize centromeres. She also developed constructs for maize and rice transformation, participated iin the CENH3 phosphorylation study, and carried out the initial experiments showing that centromeric RNA is immunoprecipitated along with centromeric chromatin. Cathy is now employed as Research Scientist at Dupont, Wilmington, Delaware.

Phan, B.H., W. Jin, C.N. Topp, C.X. Zhong, et al. (2007). Transgenic Res 16(3): 341-351.
Zhang, X., X. Li, J.B. Marshall, C.X. Zhong, et al. (2005). Plant Cell 17(2): 572-583.
Topp, C.N., C.X. Zhong and R.K. Dawe (2004). Proc Natl Acad Sci U S A 101(45): 15986-15991.
Nagaki, K., P.B. Talbert, C.X. Zhong, et al. (2003). Genetics 163(3): 1221-1225.
Zhong, C.X., J.B. Marshall, C. Topp, et al. (2002). Plant Cell 14(11): 2825-2836.


Amy Luce, Technician 2005

Amy worked in the lab from January 2005 to July 2006. She was a PCR master. She developed transposon junction mapping and made our first important steps into genomics. Her no-fear approach allowed us to break the single copy ChIP barrier and to molecularly map maize centromere 8 with precision. This work led directly to the mapping of all ten maize centromeres. Amy is now a Medical Doctor in residency, with a degree from Mercer.

Mroczek, R.J., J.R. Melo, A.C. Luce, et al. (2006). Genetics 174(1): 145-154.
Luce, A.C., A. Sharma, O.S. Mollere, et al. (2006). Genetics 174(2): 1057-1061.

 


Juliana Melo, Technician 2003

Juliana worked as an undergraduate-then-technician from Fall 2001 through the summer of 2004. She had a major impact on the productivity of the lab. She played a key role in mapping Ab10 mapping by RFLPs, mapped the maize CENH3 gene using oat-maize addition lines, cloned and sequenced hundreds of CentC repeats, and impressively, cloned the oat Cenh3 gene by degenerate PCR. Juliana is now an Assistant Professor at UC Davis.

Topp, C.N., R.J. Okagaki, J.R. Melo, et al. (2009). Cytogenet Genome Res 124(3-4): 228-238.
Mroczek, R.J., J.R. Melo, A.C. Luce, et al. (2006). Genetics 174(1): 145-154.
Jin, W., J.R. Melo, K. Nagaki, et al. (2004). Plant Cell 16(3): 571-581.


Rebecca Mroczek, Ph.D. 2003

Becky used a variety of molecular techniques and a set of Ab10 deficiencies to map the Ab10 chromosome as it relates to N10. Her detailed RFLP map demonstrated that the the meiotic drive system includes at least two large inversions, and that the primary drive functions map to a region of unknown origin at the end of the Ab10 haplotype. She also carried out a FISH study of retrotransposon density on Ab10, which supported the view that the Ab10 haplotype is ancient. Becky is now an Associate Professor at the University of Arkansas – Fort Smith.

Mroczek, R.J., J.R. Melo, A.C. Luce, et al. (2006). Genetics 174(1): 145-154.
Mroczek, R.J. and R.K. Dawe (2003). Genetics 165(2): 809-819.
Zhong, C.X., J.B. Marshall, C. Topp, et al. (2002). Plant Cell 14(11): 2825-2836.


Carolyn Lawrence, Ph.D. 2003

Carolyn was co-advised by Dr. Russell Malmberg. She took the novel approach of using maximum likelihood methods to construct a phylogeny of kinesin superfamily. Her phylogeny, and a personal ambition to make it stick, ultimately lead to the creation and adoption of a standarized kinesin nomenclature. She was also the first to show that angiosperms lack dynein. Carolyn blazed her own trail and made a major impact on the kinesin field. Carolyn is now an Associate Professor at Iowa State University.

Lawrence, C.J., C.M. Zmasek, R.K. Dawe, et al. (2004). Bioinformatics 20(12): 1977-1979.
Lawrence, C.J., R.K. Dawe, K.R. Christie, et al. (2004). J Cell Biol 167(1): 19-22.
Lawrence, C.J., R.L. Malmberg, M.G. Muszynski, et al. (2002). J Mol Evol 54(1): 42-53.
Lawrence, C.J., N.R. Morris, R.B. Meagher, et al. (2001). Traffic 2(5): 362-363.


Joshua Marshall, M.S. 2001

Josh developed a unique application of fluorescence resonance energy transfer (FRET) for the analysis of kinetochore structure. Using our set of kinetochore antibodies, he demonstrated that the maize kinetochore is composed of two major subdomains: the inner containing centromeric DNA and CENPC, and the outer containing MAD2. Josh also carried out the first experiments showing that CENH3 is phosphorylated. He is now a nuclear pharmacist.

Zhang, X., X. Li, J.B. Marshall, et al. (2005). Plant Cell 17(2): 572-583.
Zhong, C.X., J.B. Marshall, C. Topp, et al. (2002). Plant Cell 14(11): 2825-2836.


Evelyn Hiatt, Ph.D. 2000

Evelyn discovered and carefully characterized six new mutants of meiotic drive, many of which are large deficiencies. These and other data demonstrated that meiotic drive is conferred by at least four different genes on Ab10. She also showed that the two classes of knob repeats are independently regulated as neocentromeres, suggesting that satellites and their binding proteins co-evolve to assure their preferential recovery. Dr. Hiatt is now an Associate Professor at Kentucky Wesleyan College.

Mroczek, R.J., J.R. Melo, A.C. Luce, E.N. Hiatt, et al. (2006). Genetics 174(1): 145-154.
Dawe, R.K. and E.N. Hiatt (2004). Chromosome Res 12(6): 655-669.
Hiatt, E.N. and R.K. Dawe (2003). Genetica 117(1): 67-76.
Hiatt, E.N. and R.K. Dawe (2003). Genetics 164(2): 699-709.
Hiatt, E.N., E.K. Kentner and R.K. Dawe (2002). Plant Cell 14(2): 407-420.
Yu, H.G., E.N. Hiatt and R.K. Dawe (2000). Trends Plant Sci 5(12): 543-547.
Dawe, R.K., L.M. Reed, H.G. Yu, E.N. Hiatt, et al. (1999). Plant Cell 11(7): 1227-1238.
Yu, H.G., E.N. Hiatt, A. Chan, et al. (1997). J Cell Biol 139(4): 831-840.


Hong-Guo Yu, Ph.D. 2000

Hong-Guo developed a live imaging method for meiocytes and, along with other techniques, showed that neocentromeres move 50% faster than normal centromeres and interact with microtubules in a novel way. He also published the first study of spindle checkpoint proteins in plants, and showed that kinetochores are functionally redundant. Hong-Guo was exceptionally productive and received major research awards from both the Department and the University. Dr. Yu is now an Assistant Professor at Florida State University.

Yu, H.G., E.N. Hiatt and R.K. Dawe (2000). Trends Plant Sci 5(12): 543-547.
Yu, H.G. and R.K. Dawe (2000). J Cell Biol 151(1): 131-142.
Yu, H.G., M.G. Muszynski and R. Kelly Dawe (1999). J Cell Biol 145(3): 425-435.
Dawe, R.K., L.M. Reed, H.G. Yu, et al. (1999). Plant Cell 11(7): 1227-1238.
Yu, H.G., E.N. Hiatt, A. Chan, et al. (1997). J Cell Biol 139(4): 831-840.