Welcome to the Stewart Laboratory Web Site!

 

Caro-Beth Stewart

Ph.D. (Biochemistry), 1986; University of California, Berkeley

Associate Professor
Department of Biological Sciences
University at Albany, SUNY
1400 Washington Avenue
Albany, New York 12222

Office: Biology 327
Office Phone: 518-442-4342
Lab: Biology 318
Lab Phone: 518-442-4347
FAX: 518-442-4767
E-mail: c.stewart@albany.edu

Major Research Interests:

• The molecular basis of adaptive evolution
• Evolutionary bioinformatics
• Primate genomics and molecular evolution
• Evolution of protein structure and function

Research Summary:

The research in the Stewart laboratory is aimed at understanding the molecular basis for adaptive evolution in complex organisms, using the primates as the comparative system. Our approaches include generation of comparative DNA sequence data, biochemical characterization of certain protein families, and bioinformatic analysis of such data sets.

We have several projects, some in collaboration with other research groups. As a framework for our comparative studies, we are determining the phylogeny of the Old World monkeys by sequencing and analyzing complete mitochondrial genomes and unlinked nuclear genes. Using these data, we are also studying the adaptive co-evolution of mitochondrial- and nuclear-encoded respiratory proteins. Another project involves analysis of transposable elements in primate genes and genomes. Through comparative genomic analysis, we are searching for the genetic basis of human evolution.

Current and Planned Research Projects:

• Old World monkey molecular phylogeny, in collaboration with Todd Disotell's laboratory (New York University). See NIH grant abstract below.
• Adaptive co-evolution of mtDNA- and nDNA-encoded OXPHOS proteins, in collaboration with researchers at several institutions including Larry Grossman and Morris Goodman (Wayne State University), Todd Disotell (NYU), and David Pollock (Louisiana State University).
• Development and testing of methods and computer programs for the detection of adaptive molecular evolution and co-evolution (Jason de Koning), in collaboration with George Berg (Department of Computer Sciences, SUNYA), David Pollock (Louisiana State University), and Ziheng Yang (University College, London).
• Insertion and evolution of transposable elements, particularly Alu elements, in primate genes and genomes (John Schienman, Alia Khan & Jeremy Semeiks).
• Search for the genetic basis of human evolution (several interrelated projects, some collaborative).

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Courses taught:

ABio617, Molecular Evolution and Phylogenetic Methods.

Link to ABio366 home page, Biological Chemistry II.

The Stewart Lab Group, Spring 2001

Left to right:
Jason de Koning, doctoral student apjdk@csc.albany.edu
Yi Fang, graduate student, now at Johns Hopkins
John Schienman, NSF Postdoctoral Fellow in Biological Informatics, jschien@csc.albany.edu
Beth Stewart, PI
Vincent Lynch, undergraduate research student vinlynch@hotmail.com
Alia Khan, masters student, now medical student, NY College of Osteopathic Medicine lainecat@hotmail.com
Not shown: Nancy Martin, research assistant nlmartin@cnsunix.albany.edu

Previous lab members

Recent and Other Relevant Publications:

Brandon-Jones, D., Eudey, A.A., Geissmann, T., Melnick, D.J., Morales, J.C., Shekelle, M., Stewart, C.B. (in press) A Taxonomy of the Asian Primates. A working document from the workshop "Primate Taxonomy for the New Millenium".

McConkey, E.H. & Varki, A. Cosignatories: Allman, J., Benirschke, K., Crick, F., Deacon, T.W., de Waal, F., Dugaiczyk, A., Gagneux, P., Goodman, M., Grossman, L.I., Gumucio, D., Insel, T., Kidd, K.K., King, M.-C., Krauter, K., Kucherkapati, R., Motulsky, A.G., Nelson, D., Oefner, P., Palade, G., Ruvolo, M., Ryder, O.A., Sikela, J., Stewart, C.-B., Stone, A. & Woodruff, D. (2000) A primate genome project deserves high priority. Science 289: 1295-1296.

Gervasi, C., Stewart, C.-B., Szaro, B.G. (2000) Xenopus laevis peripherin (XIF3) is expressed in radial glia and proliferating neural epithelial cells as well as in neurons. Journal of Comparative Neurology 423: 512-531. Abstract

McConkey, E.H., Fouts, R., Goodman, M., Nelson, D., Penny, D., Ruvolo, M., Sikela, J., Stewart, C.-B., Varki, A. & Wise, S. (2000) Editorial: Proposal for a human genome evolution project. Molecular Phylogenetics and Evolution 15: 1-4.

Moyà-Solà, S., Köhler, M., Alba, D.M., Stewart, C.-B. & Disotell, T.R. (1999) Correspondence: Primate evolution - in and out of Africa. Current Biology 9: R547-50.

Stewart, C.-B. (1999) The Colobine Old World Monkeys as a Model System for the Study of Adaptive Evolution at the Molecular Level. In The Nonhuman Primates, P.J. Dolhinow & A. Fuentes, eds. Mayfield Press.

Jablonksi, N., Zhang, Y.-P., Ryder, O., Stewart, C.-B. & Disotell, T.R. (1999) Correspondence: Primate evolution - in and out of Africa. Current Biology 9: R119-122.

Miyamoto, M.M., Young, T.S., Ward, C., Zihlman A.L., Lowenstein, J.M., Groves, C., Covert, H., Stewart, C.-B .& Disotell, T.R. (1998) Correspondence: Primate evolution - in and out of Africa. Current Biology 8: R747-748.

Stewart, C.-B. & Disotell, T.R. (1998) Primate evolution: In and out of Africa. Current Biology 8: R582-588. Abstract

Messier, W. & Stewart, C.-B. (1997) Episodic adaptive evolution of primate lysozymes. Nature 385: 151-154. Abstract

Collura, R.V., Auerbach, M. R. & Stewart, C.-B. (1996) A quick, direct method that can differentiate expressed mitochondrial genes from their nuclear pseudogenes. Current Biology 6: 1337-1339. Abstract

Messier, W., Li, S.-H. & Stewart, C.-B. (1996) The birth of microsatellites. Nature 381: 483.

Turcich, M.P., Bokhari-Riza, A., Hamilton, D.A., He, C., Messier, W., Stewart, C.-B. & Mascarenhas, J.P. (1996) PREM-2, a copia-type retroelement in maize is expressed preferentially in early microspores. Sexual Plant Reproduction 9: 65-74.

Collura, R.V. & Stewart, C.-B. (1995) Insertions and duplications of mitochondrial DNA in the nuclear genomes of Old World monkeys and hominoids. Nature 378: 485-489. Abstract

Stewart, C.-B. (1995) Active ancestral molecules. Nature 374: 12-13.

Messier, W. & Stewart, C.-B. (1994) Dissolving the barriers. Current Biology 4: 911-913. Abstract

Stewart, C.-B. (1994) Parsimony or statistics? Nature 367: 26-27.

Takeuchi, K., Irwin, D.M., Gallup, M., Shinbrot, E., Stewart, C.-B. & Basbaum, C. (1993) Multiple cDNA sequences of bovine tracheal lysozyme. Journal of Biological Chemistry 268: 27440-27446. Abstract

Stewart, C.-B. (1993) Comparative method in study of protein structure and function: Enzyme specificity as an example. Methods in Enzymology 224: 591-603.

Stewart, C.-B. (1993) The powers and pitfalls of parsimony. Nature 361: 603-607. Abstract

Stewart, C.-B. (1993) Structural convergence and horizontal transfer? Current Biology 3: 158-160.

Natsuaki, M., Stewart, C.-B., Vanderslice, P., Schwartz, L.B., Natsuaki, M., Wintroub, B.U., Rutter, W. J. & Goldstein, S.M. (1992) Human skin mast cell carboxypeptidase: functional characterization, cDNA cloning, and genealogy. Journal of Investigative Dermatology 99: 138-145. Abstract

Faming, Z., Kobe, B., Stewart, C.-B., Rutter, W.J. & Goldsmith, E.J. (1991) Structural evolution of an enzyme specificity: the structure of rat carboxypeptidase A2 at 1.9-Å resolution. Journal of Biological Chemistry 266: 24606-24612. Abstract

Hedstrom, L., Graf, L., Stewart, C.-B., Rutter, W.J. & Phillips, M.A. (1991) Modulation of enzyme specificity by site-directed mutagenesis. Methods in Enzymology 202: 671-687.

Jollès, J., Jollès, P., Bowman, B.H., Prager, E.M., Stewart, C.-B. & Wilson, A.C. (1989) Episodic evolution in the stomach lysozymes of ruminants. Journal of Molecular Evolution 28: 528-535. Abstract

Stewart, C.-B., Schilling, J.W. & Wilson, A.C. (1988) Convergent evolution of lysozymes? Nature 332: 787-788.

Gardell, S.J., Craik, C.S., Clauser, E., Goldsmith, E.J., Stewart, C.-B., Graf, M. & Rutter, W.J. (1988) A novel rat carboxypeptidase, CPA2: Characterization, molecular cloning and evolutionary implications on substrate specificity in the carboxypeptidase gene family. Journal of Biological Chemistry 263: 17828-17836. Abstract

Stewart, C.-B. & Wilson, A.C. (1987) Sequence convergence and functional adaptation of stomach lysozymes from foregut fermenters. Cold Spring Harbor Symposia on Quantitative Biology 52: 891-899. Abstract

Stewart, C.-B., Schilling, J.W. & Wilson, A.C. (1987) Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 330: 401-404. Abstract

 

Computer Program:

de Koning, A.P.J., Palumbo, M., Messier, W. & Stewart, C.-B. (1998) Facilitated Estimates of Nucleotide Substitutions (FENS), version 1.0. (Software for Ka-to-Ks calculations by a variety of methods, with statistical tests; available from C.-B.S.)

deKoning, A.P.J. & Stewart, C.-B. (2001) Facilitated Estimates of Nucleotide Substitutions (FENS), version 2.0. Available from the authors.

 

Research Awards:

Active:

National Institutes of Health Grant (R01-GM60760); Molecular Phylogeny of Old World Monkey Host Species; January 2000 to December 2003; University at Albany; Total award: $1,100,125. Link to abstract on NIH CRISP.

Past:

National Science Foundation, Presidential Faculty Fellow Award; November 1994 to October 2000; University at Albany; Total award: $523,803. Link to NSF for abstract from PPF award.

National Institutes of Health Grant (5-R01-GM47474); Molecular Basis for Evolution of Foregut Fermentation; May 1992 to April 1997; University at Albany; Direct costs: $592,377. Link to abstract from NIH grant.

Alfred P. Sloan Foundation Postdoctoral Fellowship in Molecular Studies of Evolution; Reconstruction of Protein Evolutionary Pathways by Site-directed Mutagenesis; April 1989 to March 1990; University of California, San Francisco; Total costs: $35,000.

National Science Foundation Postdoctoral Fellow in Environmental Biology; Invariant Residues and Coupled Changes in Pancreatic Ribonuclease Evolution; July 1987 to June 1989; University of California, San Francisco; Direct costs: $52,800.

 

Selected Professional Activities and Honors:

• NSF Presidential Faculty Fellow.
• Lecturer, Current Topics in Genome Analyis 2000, National Human Genome Research Institute/NIH, 5 December 2000. "Phylogenetic Analysis" PowerPoint Slides (you are welcome to use these, but please provide credit as appropriate)
• Asian primate expert, workshop on Primate Evolution for the New Millennium, January 2000.
• Advisory board member, Genome Biology, 1999-present.
• Editorial board member, Molecular Phylogenetics and Evolution, 1999-present.
• Advisory panel, NSF Postdoctoral Research Fellowships in Biological Informatics Program, 1999-2002.
• Editorial board member, Current Biology, 1995-present.
• Associate editor, Molecular Biology and Evolution, September 1996-December 1999.
• NSF Population Biology Advisory Panel, October 1996; Spring 2001.
• Organizing committee, Keystone Symposium on Molecular Evolution, February 1997.
• Organizing committee, 3rd Albany Conference on Computational Biology, 1995.
• Organizing committee, International Meeting of the Society for Molecular Biology and Evolution, 1993.
• Council member, Society for Molecular Biology and Evolution (SMBE), 1992-1993.
• Ad hoc referee of manuscripts for Nature, Nature Genetics, Genomics, Current Biology, Science, Journal of Molecular Evolution, Journal of Biological Chemistry, Journal of Molecular Biology, Molecular Biology and Evolution, Molecular Ecology, Electrophoresis, American Journal of Physical Anthropology, American Journal of Respiratory Cell and Molecular Biology, Proceedings of the National Academy of Sciences USA, University Science Books.
• Ad hoc reviewer of grants for the National Science Foundation; the NIH; the Leakey Foundation; theWenner-Gren Foundation; the National Geographic Society.

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