return to Lynch Lab main page

Thomas G. Doak

Postdoctoral Research Associate

 

tdoak(at)indiana.edu

(812) 856-0115

Research Specialist, University of Oregon, Eugene, with Rick Dahlquist: Biochemistry of bacterial chemotaxis in E. coli. 1982-1984
Graduate Student, University of Utah, Salt Lake City, with John Roth: Genetics of vitamin B12 biosynthesis in Salmonella. 1985-1991
Graduate Student, University of Utah, Salt Lake City, with Glenn Herrick:Transposon excision in ciliated protozoa. 1992-2001
Ph.D. in Genetics: Transposons in Ciliated Protozoa. University of Utah, Salt Lake City. 2001
Postdoctoral Work, University of Utah, Salt Lake City, with Glenn Herrick: Analyses of a pilot Oxytricha genome project. 2001-present
Lead writer, NHGRI & JGI proposals to sequence the Oxytricha trifallax micronuclear & macronuclear genome. Both projects are approved by NHGRI. 2002
Lead writer, NHGRI & JGI proposals to sequence the genomes of multiple species of the dinoflagellate Symbiodinium 2003
Research Staff, Princeton University, Evolution and Ecology, with Laura Landweber: Evolution of protist genomes Fall 2003-Fall 2006
Director, Molecular Genetics Training Lab, Princeton, Evolution and Ecology Training ecologist in molecular methods specific to their research Fall 2003-Fall 2006

 

Scientific interests

My scientific interests center on protozoa, especially ciliated protozoa, and include several different biological problems. I think of these interests in three categories: 1) The biochemical activities responsible for the differentiation of a micronucleus to a terminally differentiated macronucleus. These activities include site-specific recombination, site-specific chromosome cleavage, and telomere addition. 2) The diversity and evolution of transposons in ciliates. Both the structure and propagation of transposons in ciliate genomes is unique among the eukaryotes. 3) The structure and contents of ciliate genomes. Ciliates are gene-rich, complex eukaryotes, and their genomes have developed novel structures, which are suggested to allow novel pathways of genome evolution. In Mike’s lab, I’m still feeling my way around, but am already involved in two ongoing projects: • Endosymbiotic bacteria are intrinsically interesting, and there is a long history of studying them in Paramecium and other ciliates, where they can have dramatic effects on their host’s biology and ecology. A preliminary genomic project in Mike’s lab finds that there are a surprising surplus of transposon insertions in the genomes of the Paramecium endosymbionts, which is generally unexpected for obligate symbionts, which should have small, reduced, genomes. Also, it seems that there are consortiums of symbionts in Paramecium strains, rather than the pure culture we expected; which means our genome sequences are “mixed.” We’re working to get this figured out, and will propose sequencing more endosymbiont genomes for comparison. •The population biology, and speciation of Paramecium species has been actively studied for 80 years, and has made fundamental contributions to the concept of “species.” This field is now moving into the genomics age, and we propose to sequence portions of the genome of a number of Paramecium species, to examine mechanisms of speciation, gene duplication, chromosome loss, etc. We hope that this will solve not only long-standing mysteries in Paramecium biology, but be more generally applicable to many microbial systems. Clearly, I would like to extend the studies of Paramecium populations into the Oxytricha species. This would pair nicely with the Oxytricha genome project that I and collaborators initiated, and which is on-going at the Washington University GSC. While my current interests are perhaps mostly molecular evolution, my background has been in mixed biology departments, and I can generally talk that talk. My brother Dan and sister Pat are both ecologists.

Publications

Kehry, M.R., T.G. Doak & F.W. Dahlquist. 1984. Stimulus-induced changes in methylesterase activity during chemotaxis in Escherichia coli. J. Biol. Chem. 259:11828- 11836.

Kehry, M.R., T.G. Doak & F.W. Dahlquist. 1985. Aberrant regulation of methylesterase activity in cheD chemotaxis. J. Bact. 163:105-112.

Kehry, M.R., T.G. Doak & F.W. Dahlquist. 1985. Sensory adaptation in bacterial chemotaxis: regulation of demethylation. J. Bact. 163:983-990.

Roth, J.R., C. Grabau & T.G. Doak. 1990. Genetic approaches to the synthesis and physiological significance of B12 in Salmonella typhimurium. Chemical Aspects of Enzyme Biotechnology. Ed. T.O. Baldwin et al., Plenum Press, New York.

Williams, K., T.G. Doak & G. Herrick. 1993. Precise excision of Oxytricha trifallax Telomere-Bearing Elements and formation of circles closed by a copy of the flanking target duplication. EMBO J. 12:4593-4601.

Doak, T.G., F.P. Doerder, C. Jahn & G. Herrick. 1994. A family of transposase genes in transposons found in prokaryotes, multicellular eukaryotes and ciliated protozoans. Proc. Natl. Acad. Sci. USA 91:942-946.

Seegmiller, A., K.R. Williams, R.L. Hammersmith, T.G. Doak, T. Messick, D.J. Witherspoon, L.L. Storjohann & G. Herrick. 1996. Internal eliminated sequences of Oxytricha: allelic fixation, divergence, conservation and conversions. Mol. Biol. Evol. 13:1351-1362.

Witherspoon, D.J., T.G. Doak, K. Williams, J. Seger & G. Herrick. 1997. Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O. trifallax. Mol Biol Evol. 14:696-706.

Doak, T.G., D.J. Witherspoon, F. Doerder, K. Williams & G. Herrick. 1997. Conserved features of ciliate TBE1 transposons. Genetica 101:75-86.

Doak, T.G. 2001. Ph.D. Dissertation. Transposons in ciliated protozoa. University of Utah, Salt Lake City.

Williams KR, T.G. Doak & G. Herrick 2002. Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax:alternatively processed regions have multiple telomere addition sites. BMC Genetics 3:16.

Doak T.G., D.J. Witherspoon, C. Jahn & G. Herrick 2003. Selection on the genes of Euplotes crassus Tec1 and Tec2 transposons:evolutionary appearance of a programmed frameshift in a Tec2 gene encoding a tyrosine-family, site-specific recombinase. Eukaryotic Cell, 2:95-102.

Doak T.G., A.R.O. Cavalcanti, N.A. Stover, D.M. Dunn, R. Weiss, G. Herrick & L.F. Landweber. 2003. Sequencing the Oxytricha trifallax macronuclear genome: a pilot project. Trends Genet. 19:603-607.

Cavalcanti ARO, Stover NA, Orecchia L, Doak T.G, Landweber L.F. 2004. Coding properties of Oxytricha trifallax ( Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. Chromosoma. 113:69-76.

Cavalcanti ARO, DM Dunn, R Weiss, G Herrick, LF. Landweber and TG. Doak. 2004. Sequence features of Oxytricha trifallax (Class Spirotrichea) macronuclear telomeric and subtelomeric sequences. Protist 155:311–322.

W-J Chang, TG Doak 2006. Mechanisms and evolution of genome reorganization in cili-ated protozoa. Endocytobiosis Cell Res. 17:119-124.

Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG, Landweber LF. 2008. RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature. 451:153-8.

Moenbeck M, Zhou Y, Cavalcanti ARO, Jonsson F, Chang WJ, Juranek S, Doak TG, Rozenberg G, Lipps HL, and Landweber LF. Submitted. The pathway for detangling a scrambled gene.

Richard A. Holland, Joseph L. Kirschvink, Thomas G. Doak, and Martin Wikelski. Bats use magnetite to detect the earth’s magnetic field. PloS ONE. 3:e1676.

Nowacki M, Higgins BP, Maquilan GM, Swart EC, Doak TG, and Landweber LF. 2009. A functional role for transposases in a large eukaryotic genome. Science 324:935-8

Ye Y, Doak TG. 2009. A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes. PLoS Comput Biol 5(8): e1000465.

Neethu Shah, Haixu Tang, Thomas G. Doak and Yuzhen Ye. 2011. Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Pac Symp Biocomput. 2011:165-176.

Mina Rho, Yu-Wei Wu, Haixu Tang, Thomas G. Doak, Yuzhen Ye. 2011. Diverse CRISPRs evolving in human microbiomes. PLOS Genetics, accepted.

Stephen D. Zoller, Robert L. Hammersmith, Brian P. Higgins, Estienne Swart, Thomas G. Doak, Glenn Herrick, and Laura F. Landweber. 2011. Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple conserved gene sequences: limitations and problems in identifying ciliate genera by morphology. Protist, in review.

Estienne C. Swart, Mariusz Nowacki, Justine Shum, Heather Stiles, Brian P. Higgins, Thomas G. Doak, Klaas Schotanus, Laura F. Landweber. 2011. The Oxytricha trifallax mitochondrial genome. Genome Biology and Evolution, in review.

Sung W, Tucker A, Doak TG, Choi J, Lynch M, Thomas WK . 2011. Extraordinary genome stability in the ciliate Paramecium tetraurelia. Science, in review.

Quan Zhang, Thomas G. Doak, YuZhan Ye. 2012. Artificial functional differences between microbial communities caused by length differences of sequencing reads. Pac Symp Biocomput., accepted.