Gary Stuart

Professor Emeritus

Ph.D., University of Washington

Phone: 812-237-7898

E-mail: Gary.Stuart@indstate.edu

Office: Science Building 233
Web Site

Research Interests:

1) Molecular Mechanisms of Vertebrate Development
One aspect of research in our laboratory is directed toward a detailed understanding of the molecular mechanisms by which vertebrate organisms develop from single-celled embryos into complex organisms. This research utilizes zebrafish as a model organism. Advantages of the zebrafish include fecundity, an optically clear, rapidly developing embryo, and the opportunity to experimentally manipulate fertilization and development so as to produce parthenogenetic or haploid offspring. In addition, a full genomic sequence is available.

A technique of central importance is the production of transgenic zebrafish via the direct microinjection of cloned genes into fish embryos. Transgenic zebrafish possessing recombinant gfp and rfp marker genes are being generated for a variety of purposes, including 1) basic research into recombination mechanisms and transgenesis strategies, 2) the study of transgene inheritance patterns, and 3) the analysis of altered gene expression and its phenotypic consequences.

2) Molecular Systematics and Phylogenetic Analysis                                                           As whole genome sequence information for a wide variety of organisms continues to accumulate, new exhaustive methods for estimating phylogentic relatedness become possible. We have developed a revolutionary method for generating whole genome phylogenies using vector representations of protein sequences. This method uses a standard matrix decomposition (SVD) to process a peptide frequency matrix containing vector representations for all proteins within a large, multi-genome dataset. Precise vector definitions for the proteins in high-dimensional space are obtained as output. Pairwise analysis of vector angles provides distance measures useful for building accurate gene trees. Furthermore, following simple vector addition by species, these same protein definitions can be used to generate comprehensive species trees based on total genome content. A particularly attractive aspect of the SVD-based method is that local sequence alignments are neither generated or required.

Our work in this area is expanding to include a wide variety of genome data sets. A parallel implementation of the SVD algorithm has allowed very large genome collections to be analyzed using ISU's high performance cluster.

3) Molecular Evolution and Comparative Genomics
The exponential growth of genomic sequence information is creating an annotation gap - a relative absence of formal descriptions of genes and other landmarks within genomic sequence.  Although automatic genome annotation methods are expected to effectively replace human genome annotation sometime in the future, annotation today still requires significant person-hours devoted to the inspection, evaluation, and improvement of thousands of gene models via comparison to multiple sources of supporting information (e.g. cDNA sequence, putative orthologs, multiple different gene predictors).  The comprehensive expert annotation of a new genome is greatly facilitated by the existence of other well-annotated genomes, and in turn, greatly improves the accuracy of future genome annotations and their automation. An expanding list of well-described genomes from multiple diverse taxa is creating new opportunities to use comparative genomics to answer fundamental questions about molecular evolution (i.e. the creation, modification, expansion, and/or loss of genes within and across taxa). Work along these lines has recently produced radical new theories about the evolution of  gene families and serious challenges to traditional ideas about the phylogenetic relatedness of organisms.  To help fill the annotation gap, we are contributing to a community effort to annotate the genome of the water flea, Daphnia pulex.  Our focus is on the subset of zinc-finger transcription factor genes that encode multiple C2H2 "Kruppel-like" fingers. Well known examples include MTF, TFIIIA, Sp, and KLF.

Selected Publications

Reprints for some publlications are available as PDF files. By accessing the PDF file, the user agrees to abide by all copyright laws and education fair-use regulations.

Seetharam s., Bai,Y., and Stuart, G.W. (2009) A survey of well conserved families of C2H2 zinc-finger genes in Daphnia. BMC Genomics (in press).

 Bai, Y., Dong, J. & Stuart, G.W.  (2009) Transgene Manipulation in Zebrafish by Using Recombinases, In: Essential Zebrafish Methods: Genetics and Genomics (Edited by H. Detrich III, L. Zon, & M. Westerfield). DOI: 10.1016/B978-0-12-375160-7.00012-1.

Stuart, G. W., Moffett, P. K., and Bozarth, R. F. (2006) A comprehensive open reading frame phylogenetic analysis of isometric positive strand ssRNA plant viruses.  Archives of Virology 151: 1159-1177.

Dong, J., Stuart, G. W. 2004. Transgene manipulation in zebrafish by using recombinases. Methods in Cell Biology 77:363-79. ( Download PDF - 229 kB)

Stuart, G. W., Berry, M. 2004. An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage. BMC Bioinformatics 5, 204. ( Download PDF - 443 kB)

Stuart, G. W., Moffett, K., and Leader, J.J. 2004. A Whole Genome Phylogeny for Plant Virus Family Tombusviridae Archives of Virology 149, 1595-1610.

Stuart, G. W., Berry, M. (2003) A Comprehensive Whole Genome Bacterial Phylogeny using Correlated Peptide Motifs defined in a High Dimensional Vector Space. Journal of Bioinformatics and Computation Biology Biology 1, 475-493. ( Download PDF - 311 kB)

Nebert DW, Stuart GW, Solis WA, Carvan MJ 3rd. 2002 Use of reporter genes and vertebrate DNA motifs in transgenic zebrafish as sentinels for assessing aquatic pollution. Environ Health Perspect. 110, A15.

Stuart, G. W. , Moffett, K., and Leader, J.J. 2002. A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. Molecular Biology and Evolution 19: 554-562. ( Download PDF - 202 kB)

Stuart, G. W ., Moffett, K., and Baker, S. 2002. Integrated gene and species phylogenies from unaligned whole genome protein sequence. Bioinformatics 18: 100-108. ( Download PDF - 197 kB)

Laxmanan, S., Stuart, G. W., and Ghosh, S.K. 2001. A stable single chain variable fragment expressing transfectoma demonstrates induction of idiotype-specific cytotoxic T-cell during early growth stages of a murine B-lymphoma. Cancer Immunology and Immunotherapy 50: 437-444. ( Download PDF - 289 kB)

Lim, S-Y., Laxmanan, S., Stuart, G. W., Ghosh, S.K. 2001. Anti-B lymphoma Immunity: Relative Efficacy of Peptide and Recombinant DNA vaccine.Cancer Detection and Prevention 25: 470-478. ( Download PDF - 268 kB)

Shah, D., Aurora, D., Lance, R and Stuart, G. W. 2000. POU Genes in Metazoans: Homologs in Sea Anemones, Snails, and Earthworms. DNA Sequence 11, 457-461.( Download PDF - 432 kB)

Nebert, D.W., Dalton, T.P., Stuart, G. W., and Carvan, M.J. 2000. Gene-Swap knock-in cassette in mice to study allelic differences in human genes. Ann. NY Acad. Sci. 919:148-70. ( Download PDF - 425 kB)

Carvan III, M.J., Dalton, T.P., Stuart, G. W., and Nebert, D.W. 2000. Transgenic Zebrafish as Sentinels for Aquatic Pollution. Ann. NY Acad. Sci. 919, 133-47. ( Download PDF - 334 kB)

Alvager, T., Stuart, G. W., and Shotwell, A. (1999) DNA, Proteins, and Compressibility. Proceedings of the International Joint Conference on Neural Networks (IJCNN'99) #260, IEEE, Piscataway, New Jersey.

Gillespie, G.A., Stuart, G. W., and Bozarth, B. 1999. RT-PCR method for detecting cowpea mottle virus in Vigna germplasm. Plant Disease 83, 639-643. ( Download PDF - 557 kB)

Sampath. K. and G. W. Stuart. 1996. Developmental expression of class III & IV POU domain genes in the zebrafish. Biochem. Biophys. Res. Comm. 219: 565-571. ( Download PDF - 171 kB)

Stuart, G. W. , Z. Zhu, K. Sampath, and M. W. King, 1995. POU domain sequences from the flatworm Dugesia tigrina. Gene 161: 299-300. ( Download PDF - 55 kB)

You, X-J., J. W. Kim, G. W. Stuart, and R. F. Bozarth. 1995. The nucleotide sequence of cowpea mottle virus and its sequence homology to carmoviruses. J. Gen. Virology 76: 2841-2845. ( Download PDF - 541 kB)

Westerfield, M., Stuart, G. W., and Wegner, J. 1993. Expression of foreign genes in zebrafish. Developments in Industrial Microbiology Wm. C. Brown, Dubuque IA, pp658-664.

Stuart, G. W. , J. R. Vielkind, J. V. McMurray, and M. Westerfield. 1990. Stable lines of transgenic zebrafish exhibit reproducible patterns of transgenic expression. Development 109: 577-584. ( Download PDF - 334 kB)

Stuart, G. W., McMurray, J., and Westerfield, M. 1989. Germ-line transformation of the zebrafish, in Gene transfer and gene therapy, Alan R. Liss, Inc., N.Y., pp. 19-28.

Stuart, G. W. , J. V. McMurray, and M. Westerfield. 1988. Replication, integration, and germ line transmission of foreign DNA injected into the early zebrafish embryo. Development 103: 403-412. ( Download PDF - 1077 kB)

Searle, P.F., Stuart, G. W., and Palmiter, R.D. 1987. Metal regulatory elements of the mouse metallothionein-I Gene. Metallothionein II Birkhauser Verlag, Basel. Vol. 52 p. 407-441 ( Download PDF - 87 kB)

Stuart, G. W. , P. F. Searle, and R. D. Palmiter. 1985. Identification of multiple regulatory elements in mouse metallothionein-I promoter by assaying synthetic sequences. Nature 317: 828-831.

Searle, P.F., Stuart, G. W., and Palmiter, R.D. 1984. Building a metal responsive promoter with synthetic regulatory elements. Mol. Cell. Biol. 5, 1480-1489. ( Download PDF - 1953 kB)

Stuart, G. W., Searle, P.F., Chen, R.L., Brinster, R.L., and Palmiter R.D. 1984. A 12 base pair DNA motif that is repeated several times in metallothionein gene promoters confers metal regulation to a heterologous gene. Proc. Natl. Acad. Sci. USA 81, 7318-7322. ( Download PDF - 1059 kB)

Searle, P.F., Davison, B.L., Stuart, G. W., Wilkie, T.M., Norstedt, G., and Palmiter, R.D. 1984. Regulation, linkage, and sequence of mouse metallothionein I and II genes. Mol. Cell. Biol. 4, 1221-1230. ( Download PDF - 2449 kB)