Biology Faculty: Caro-Beth Stewart

Caro-Beth Stewart

Associate Professor of Biological Sciences
Ph.D., University at California, Berkeley

Office BI326
Telephone (518) 591-8832
Fax (518) 442-4767
Email cstewart@albany.edu

Areas of Interest

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




Research

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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).

Publications

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  • Karanth KP, Singh L, Stewart CB. Mitochondrial and nuclear markers suggest Hanuman langur (Primates: Colobinae) polyphyly: implications for their species status. Mol Phylogenet Evol. (2010) 54(2):627-33. abstract
  • Hodgson JA, Sterner KN, Matthews LJ, Burrell AS, Jani RA, Raaum RL, Stewart CB, Disotell TR. Successive radiations, not stasis, in the South American primate fauna. Proc Natl Acad Sci U S A. (2009) 106(14):5534-9. abstract
  • Karanth KP, Singh L, Collura RV, Stewart CB. Molecular phylogeny and biogeography of langurs and leaf monkeys of South Asia (Primates: Colobinae). Mol Phylogenet Evol. (2008) 46(2):683-94. abstract
  • Schienman JE, Holt RA, Auerbach MR, Stewart CB. Duplication and divergence of 2 distinct pancreatic ribonuclease genes in leaf-eating African and Asian colobine monkeys. Mol Biol Evol. (2006) 1465-79. abstract
  • Sterner KN, Raaum RL, Zhang YP, Stewart CB, Disotell TR. Mitochondrial data support an odd-nosed colobine clade. Mol Phylogenet Evol. (2006) 40: 1-7. abstract
  • Xing J, Wang H, Han K, Ray DA, Huang CH, Chemnick LG, Stewart CB, Disotell TR, Ryder OA, Batzer MA. A mobile element based phylogeny of Old World monkeys. Mol Phylogenet Evol. (2005) 37(3):872-80. abstract
  • Raina SZ, Faith JJ, Disotell TR, Seligmann H, Stewart CB, Pollock DD. Evolution of base-substitution gradients in primate mitochondrial genomes. Genome Res. (2005) 15(5):665-73. abstract
  • Raaum RL, Sterner KN, Noviello CM, Stewart CB, Disotell TR. Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence. J Hum Evol. (2005) 48(3):237-57. abstract
  • Krishnan NM, Seligmann H, Stewart CB, De Koning AP, Pollock DD. Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference. Mol Biol Evol. (2004) 21(10):1871-83. abstract
  • Xing J, Salem AH, Hedges DJ, Kilroy GE, Watkins WS, Schienman JE, Stewart CB, Jurka J, Jorde LB, Batzer MA. Comprehensive analysis of two Alu Yd subfamilies. J Mol Evol. (2003) 57 Suppl 1:S76-89. abstract
  • Brandon-Jones, D., Eudey, A.A., Geissmann, T., Groves, C.P., Melnick, D.J., Morales, J.C., Shekelle, M., Stewart, C.-B., (2003). Asian primate classification. Int. J. Primatol. 25, 97-162.
  • 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.