Dr. J. Robert Macey, Director
Discussing the natural history of Thamnophis elegans terrestris in his herpetology course
Phone: (510) 232-1764
Email: send email
Mailing address:
Genomics Program, Merritt College
860 Atlantic Avenue
Alameda, California, 94501
- 2006- current. Director Merritt Genomics Program and Profile Genomics.
- 2001-2005. Scientist, DOE Joint Genome Institute & Lawrence Berkeley National Laboratory.
- 1999-2001. NSF funded Postdoctoral. Washington University, St. Louis, MO.
- 1992-1999, Ph.D., Washington University, St. Louis, MO, Degree August, 1999.
- 1988, B.A. Biology, University of California at Santa Cruz.
Research foci are broad with concentration on Evolutionary Biololgy at the integration of Genomics and Plate Tectonics. My reseach is largly Asian-based having been the first western biologist to work in western China and Soviet Central Asia, as well as the first western biologist to work in Iran following the Islamic Revolution. I use unique novel samples to derive phylogenetic trees and understand the patterns of complete mitochondrial evolution. This results in better understanding mt-genomic evolution of genes, gene copies, presumed aberrations in encoded transfer RNAs, and alteration of replication origins. In addition, I have worked with Bacterial Artificial Chromosome (BAC) libraries among vertebrates.
book reviews
Macey, J. R. 2003. Review of “Tangled Trees, Phylogeny, Cospeciation, and Coevolution” edited by Roderic D. M. Page (2003), University of Chicago Press, Chicago. 350 p. The Quarterly Review of Biology 78:358.
Macey, J. R. 2002. Review of “Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists” by Barry G. Hall (2001), Sunderland Massachusetts: Sinauer Associates, Inc. 179 p. The Quarterly Review of Biology 77:196-197.
Macey, J. R. 2000. Review of “Describing Species: Practical Taxonomic Procedure for Biologists” by Judith E. Winston (1999), Columbia Univ. Press, New York, 518 p. The Quarterly Review of Biology 75:443.
publications
2013
Weisrock, D. W., J. R. Macey, M. Matsui, D. Mulcahy, and T. J. Papenfuss. 2013. Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata). Zootaxa 3626:77-99.
Böhm, M., et al. (plus 244 co-authors including Macey). 2013. The conservation status of the world's reptiles. Biological Conservation. 157:372–385.
2009
Mulcahy, D. G., and J. R. Macey. 2009. Vicariance and Dispersal form a Ring Distribution in Nightsnakes around the Gulf of California. Molecular Phylogenetics and Evolution. 53:537-546.
2008
Macey, J. R., J. V. Kuehl, A. Larson, M. D. Robinson, I. H. Ugurtas, N. B. Ananjeva, H. Rahman, H. I. Javed, R. M. Osman, A. Doumma, and T. J. Papenfuss. 2008. Socotra Island the forgotten fragment of Gondwana: Unmasking chameleon lizard history with complete mitochondrial genomic data. Molecular Phylogenetics and Evolution. 49:1015- 1018.
2006
Macey, J. R., J. A. Schulte, J. L. Strasburg, J. A. Brisson, A. Larson, N. B. Ananjeva, Yuezhao Wang, J. F. Parham, and T. J. Papenfuss. 2006. Assembly of the Eastern North American herpetofauna: New evidence from lizards and frogs. The Royal Society Biology Letters. 2:388-392.
Macey, J. R., J. A. Schulte, II, J. J. Fong, I. Das, and T. J. Papenfuss. 2006. The complete mitochondrial genome of an agamid lizard from the Afro-Asian subfamily Agaminae and the phylogenetic position of Bufoniceps and Xenagama. Molecular Phylogenetics and Evolution. 39:881-886.
Parham, J. F., J. R. Macey, T. J. Papenfuss, C. R. Feldman, O. Türkozan, R. Polymeni, and J. L. Boore. 2006. The complete mitochondrial genome sequences of Mediterranean tortoises and relatives (Testudona tax. nov.): Implications for phylogeny, taxonomy, and paleobiogeography. Molecular Phylogenetics and Evolution. 38:50-64.
Parham, J. F, O. Türkozan, B. L. Stuart, M. Arakelyan, S. Shafei, J. R. Macey, and T. J. Papenfuss. 2006. Genetic evidence for premature taxonomic inflation in Middle Eastern tortoises. Proceedings of the California Academy of Sciences. 57(33):955-964.
Schulte II, J. A., J. R. Macey, and T. J. Papenfuss. 2006. A genetic perspective on the geographic association of taxa among arid North American lizards of the Sceloporus magister complex (Squamata: Iguanidae: Phrynosomatinae). Molecular Phylogenetics and Evolution. 39:873-880.
Stöck, M., C. Moritz, M. Hickerson, D. Frynta, T. Dujsebayeva, V. Eremchenko, J. R. Macey, T. J. Papenfuss, and D. B. Wake. 2006. Evolution of mitochondrial relationships and biogeography of diploid and polyploid Palearctic green toads (Bufo viridis subgroup) with insights in their genomic plasticity. Molecular Phylogenetics and Evolution. 41:663-689.
Weisrock, D. W., T. J. Papenfuss, J. R. Macey, S. N. Litvinchuk, R. Polymeni, I. H. Ugurtas, E. Zhao, and A. Larson. 2006. A molecular assessment of phylogenetic relationships and lineage accumulation rates within the family Salamandridae (Amphibia, Caudata). Molecular Phylogenetics and Evolution. 41:368-383.
2005
Alexandrino, J., S. J. E. Baird, L. Lawson, J. R. Macey, C. Moritz, and D. B. Wake. 2005. Strong Selection Against Hybrids at a Hybrid Zone in the Ensatina Ring Species Complex and its Evolutionary Implications. Evolution. 59:1334-1347.
Boore, J. L., J. R. Macey, and M. Medina. 2005. Whole mitochondrial genome sequencing and gene order comparisons of animals. In Molecular Evolutiion: Producing the Biochemical Data, Part B, E. A. Zimmer and E. Roalson (eds.), Methods in Enzymology. 395:311-348.
Macey, J. R. 2005. Plethodontid salamander mitochondrial genomics: A parsimony evaluation of character conflict and implications for historical biogeography. Cladistics. 21:194-202.
Macey, J. R., J. J. Fong, J. V. Kuehl, S. Shafiei, N. B. Ananjeva, T. J. Papenfuss, and J. L. Boore. 2005. The complete mitochondrial genome of a gecko and the phylogenetic position of the Middle Eastern Teratoscincus keyserlingii. Molecular Phylogenetics and Evolution. 36:188-193.
2004
Macey, J. R., T. J. Papenfuss, J. V. Kuehl, H. M. Fourcade and J. L. Boore. 2004. Phylogenetic Relationships Among Amphisbaenian Reptiles Based on Complete Mitochondrial Genomic Sequences. Molecular Phylogenetics and Evolution 33:22-31.
Macey, J. R., and Ananjeva. 2004. Genetic Variation Among Agamid Lizards of the Trapelus agilis Complex in the Caspian-Aral Basin. Asiatic Herpetological Research. 10:208-214.
Mueller, R. L., J. R. Macey, M. Jaekel, D. B. Wake, and J. L. Boore. 2004. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proceedings of the National Academy of Sciences. 101(38):13820–13825.
Townsend, T., A. Larson, E. Louis, and J. R. Macey. 2004. A New Hypothesis of Squamate Evolutionary Relationships From Nuclear and Mitochondrial DNA Sequence Data. Systematic Biology. 53:735-757.
2004
Schulte II, J. A., J. R. Macey, R. Pethiyagoda, and A. Larson. 2002. Rostral Horn Evolution Among Agamid Lizards of the Genus Ceratophora Endemic to Sri Lanka. Molecular Phylogenetics and Evolution. 22:111-117.
2001
Papenfuss, T. J., J. R. Macey, and J. A. Schulte. 2001. A New Lizard Species in the Genus Xantusia from Arizona. Scientific Papers, Natural History Museum, The University of Kansas. 23:1-9.
Macey, J. R., J. L. Strasburg, J. A. Brisson, V. T. Vredenburg, M. Jennings, and A. Larson. 2001. Molecular phylogenetics of Western North American frogs of the Rana boylii species group. Molecular Phylogenetics and Evolution. 19:131-143.
Weisrock, D. W., J. R. Macey, I. H. Ugurtas, A. Larson, and T. J. Papenfuss. 2001. Molecular phylogenetics and historical biogeography among salamandrids of the “true” salamander clade: Rapid branching of numerous highly divergent lineages with the rise of Anatolia in Mertensiella luschani. Molecular Phylogenetics and Evolution. 18:434- 448.
2000
Macey, J. R., N. B. Ananjeva, Y. Wang, and T. J. Papenfuss. 2000. Phylogenetic relationships among Asian gekkonid lizards formerly of the genus Cyrtodactylus based on cladistic analyses of allozymic data: Monophyly of Cyrtopodion and Mediodactylus. Journal of Herpetology. 34:258-265.
Macey, J. R., J. A. Schulte II, H. G. Kami, N. B. Ananjeva, A. Larson, and T. J. Papenfuss. 2000. Testing alternative hypotheses of vicariance in the agamid lizard Laudakia caucasia in mountain ranges on the northern Iranian Plateau. Molecular Phylogenetics and Evolution. 14:479-483.
Macey, J. R., J. A. Schulte II, A. Larson. 2000. Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards. Systematic Biology. 49:257-277.
Macey, J. R., J. A. Schulte II, A. Larson, N. B. Ananjeva, Y. Wang, R. Pethiyagoda, N. Rastegar-Pouyani, and T. J. Papenfuss. 2000. Evaluating trans-Tethys migration: An example using acrodont lizard phylogenetics. Systematic Biology. 49:233-256.
Schulte II, J. A., J. R. Macey, R. E. Espinoza, and A. Larson. 2000. Phylogenetic relationships in the iguanid lizard genus Liolaemus: Multiple origins of viviparous reproduction and evidence for recurring Andean vicariance. Biological Journal of the Linnean Society. 69:75-102.
1999
Macey, J. R., J. A. Schulte II, A. Larson, B. S. Tuniyev, N. Orlov, and T. J. Papenfuss. 1999. Molecular phylogenetics, tRNA evolution and historical biogeography in anguid lizards and related taxonomic families. Molecular Phylogenetics and Evolution. 12:250- 272.
Macey, J. R., Y. Wang, N. B. Ananjeva, A. Larson, and T. J. Papenfuss. 1999. Vicariant patterns of fragmentation among gekkonid lizards of the genus Teratoscincus produced by the Indian Collision: A molecular phylogenetic perspective and an area cladogram for Central Asia. Molecular Phylogenetics and Evolution. 12:320-332.
1998
Macey, J. R., J. A. Schulte II, N. B. Ananjeva, A. Larson, N. Rastegar-Pouyani, S. M. Shammakov, and T. J. Papenfuss. 1998. Phylogenetic relationships among agamid lizards of the Laudakia caucasia species group: Testing hypotheses of biogeographic fragmentation and an area cladogram for the Iranian Plateau. Molecular Phylogenetics and Evolution. 10:118-131.
Macey, J. R., J. A. Schulte II, A. Larson, Z. Fang, Y. Wang, B. S. Tuniyev, and T. J. Papenfuss. 1998. Phylogenetic relationships of toads in the Bufo bufo species group from the eastern escarpment of the Tibetan Plateau: A case of vicariance and dispersal. Molecular Phylogenetics and Evolution. 9:80-87.
Macey, J. R., J. A. Schulte II, A. Larson, and T. J. Papenfuss. 1998. Tandem duplication via light-strand synthesis may provide a precursor for mitochondrial genomic rearrangement. Molecular Biology and Evolution. 15:71-75.
Schulte II, J. A., J. R. Macey, A. Larson, and T. J. Papenfuss. 1998. Molecular tests of phylogenetic taxonomies: A general procedure and example using four subfamilies of the lizard family Iguanidae. Molecular Phylogenetics and Evolution. 10:367-376.
1997
Macey, J. R., N. B. Ananjeva, Y. Wang, and T. J. Papenfuss. 1997. A taxonomic reevaluation of the gekkonid lizard genus Teratoscincus in China. Russian Journal of Herpetology. 4:8-16.
Macey, J. R., A. Larson, N. B. Ananjeva, Z. Fang, and T. J. Papenfuss. 1997. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Molecular Biology and Evolution. 14:91-104.
Macey, J. R., A. Larson, N. B. Ananjeva, and T. J. Papenfuss. 1997. Evolutionary shifts in three major structural features of the mitochondrial genome among Iguanian lizards. Journal of Molecular Evolution. 44:660-674.
Macey, J. R., A. Larson, N. B. Ananjeva, and T. J. Papenfuss. 1997. Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs. Molecular Biology and Evolution. 14:30-39.
Macey, J. R., and A. Verma. 1997. Homology in phylogenetic analysis: Alignment of transfer RNA genes and the phylogenetic position of snakes. Molecular Phylogenetics and Evolution. 7:272-279.
1991
Macey, J. R., and T. J. Papenfuss. 1991. The amphibians of the White-Inyo Range. Pp. 277-290. In C. A. Hall, jr. (ed.), Natural History of the White-Inyo Range, Eastern California. University of California Press, Berkeley.
Macey, J. R., and T. J. Papenfuss. 1991. The reptiles of the White-Inyo Range, Pp. 291- 360. In C. A. Hall, jr. (ed.), Natural History of the White-Inyo Range, Eastern California. University of California Press, Berkeley.
1990
Ananjeva, N. B., G. Peters, J. R. Macey, and T. J. Papenfuss. 1990. Stellio sacra (Smith 1935) - a distinct species of Asiatic Rock Agamid from Tibet. Asiatic Herpetological Research. 3:104-115.
1989
Losos, J. B., T. J. Papenfuss, and J. R. Macey. 1989. Correlates of sprinting, jumping, and parachuting performance in the Butterfly Lizard, Leiolepis belliani. Journal of Zoology, London. 217:559-568.
1988
Macey, J. R., T. J. Papenfuss, and E. Zhao. 1988. The snakes of Ningxia Hui Autonomous Region as an indication of a herpetofaunal corridor. Chinese Herpetological Research. 2:4-5.
Zhao, E., J. R. Macey, and T. J. Papenfuss. 1988. A new species of Rana from Ningxia Hui Autonomous Region. Chinese Herpetological Research. 2:1-3.
1986
Macey, J. R. 1986. The biogeography of a herpetofaunal transition between the Great Basin and Mojave deserts. Pp. 119-128 In C. A. Hall, jr. and D. J. Young (eds.), Natural History of the White-Inyo Range, eastern California and western Nevada and high altitude physiology: University of California White Mountain Research Station Symposium, August 23-25, 1985, Bishop, California. Volume 1:i-240.
1983
Macey, R. J. 1983. Charina bottae bottae (Pacific Rubber Boa) food. Life History Notes. Herpetological Review. 14:19.
additional
Macey, J.R. (2005) The Genetics Behind Plate Tectonics in the Middle East and Central Asia - a Lizard's Perspective
Hank Fabian, co-director
My life has been an interesting one. I have a BA in theater, my MS is in Agronomy, and I have earned my Doctor of Arts in Biology. I've been a crop geneticist, a scholar of Native American religion, a commercial cut flower grower and most importantly a teacher. I've taught Human Anatomy and Physiology and Biology for almost twenty years. At Idaho State University, I taught a senior and graduate level anatomy course, and I have also taught a Gross Anatomy Lab at Palmer Chiropractic College in San Jose. As I teach many kinds of biology courses, I consider myself to be a generalist in the biological sciences, including many Natural History courses. As part of the Genomics program, I have been instrumental in developing the pedagogy for our courses and have handling much of the administrative end of developing this new program. Every day new opportunities arise in Genomics and we have much to achieve in the way of original student research. I am happy to be part of developing this program that promises to meet the needs of the Genomics industry while training our students to be top technicians and researchers. I am both humbled and honored to work with such an amazing group of scientists, the like of which has probably never been seen at a community college. We are entering a golden age of Genomics. I consider myself most fortunate to be part of it.
Dr. Brian Rowning, co-director
Office: Merritt College, Room D218
Education
- Shared Postdoctoral Scholar, 1997 – 2001, Howard Hughes Medical Institute - UW Seattle Dept. of Pharmacology, and Advanced Light Source, Lawrence Berkeley National Laboratory (LBNL) / UCSF
- Postdoctoral Fellow, 1995 - 1997 Breast Cancer Biology, LBNL
- PhD, 1993 Molecular Biology, University of California Berkeley
- BA, 1983 Biology, Reed College
Dr. Brian Rowning combines unique expertise in molecular, cell, developmental and cancer biology with advanced imaging skills. He is active in the Genomics, Microscopy and Histotechnology programs, and is excited about the possibilities for transforming biomedical education, strengthening regional scientific and technological capabilities, and expanding student employment opportunities. He has worked as a Scientist at LBNL and UC Berkeley, and did postdoctoral research at LBNL and U.W. Seattle/HHMI. He has published in leading scientific journals on the roles of cytoskeletal mechanisms and critical signaling pathways in cellular dynamics, body pattern formation and cancer. His research interests include comparative signaling pathways in body plan formation and disease, organelle characterization and function, the neurobiology of behavior and evolutionary genomics, and the interface between genomics and imaging technologies for assays and engineering of cells and tissues.
publications currently in preparation
“Ciliogenesis, neurogenesis, and the intersection of aneural and neural larval swimming behaviors in the marine snail Lottia gigantean” (in preparation with Merritt College students) E. Edsinger-Gonzales, J.V. Bredeson, A.V. Leung, C.R. Zimmerman, D.E. Diaz, D.F. Trew, D.G. Brusco, E. Whitburn, G. Martinez, H. Ingle, J.V. Robado-Mejia, L.E. Mugglestone, J. Lazen, M.A. Scott, T.J. Colston, T. Trew, P. Werner, G. Giorgi, B.A. Rowning, and D.S. Rokhsar. Poster presented at Society for Integrative Biology (SICB) meeting January 2013.
“The Endemic Nature of Intrinsic Fluorescence” (in preparation with Merritt College students) Dominique Diaz, Christina Zimmerman, Debbi Brusco, Kelvin Ho, Mary Hogan, Beverly Howard, Jonathan Lathan, Alvin Leung, Gabriela Martinez, Karin Tyson, Kimmy Tucker, Peter Werner, Harris Ingle, Brian Rowning, Gisèle Giorgi. Students received the Second Place award in a poster competition at the Advanced Imaging Methods (AIM) workshop, Berkeley, CA January 2012. Also presented at Stanford Biomedical Imaging Conference, Stanford Center for Biomedical Imaging (CBIS) March 2012, and Bay Area Neuroscience Gathering (BANG) April, 2012
publications
“A PKC wave follows the calcium wave after activation of Xenopus eggs” (2004) Larabell, C.A., Rowning, B.A., Moon, R.T. Differentiation 72:41-47
“GBP binds kinesin light chain and translocates during cortical rotation in Xenopus eggs” (2003) Weaver C, Farr GH 3rd, Pan W, Rowning BA, Wang J, Mao J, Wu D, Li L, Larabell CA, Kimelman D. Development 130(22):5425-36
“From dynamics to details: live cell light microscopy and high-resolution (25 nm) soft X-ray microscopy” (2000) Larabell, C.A., Yager, D., Meyer-Ilse, W. and Rowning, B. Microscopy and Microanalysis. 6, 84-85
“Dishevelled controls cell polarity during Xenopus Gastrulation” (2000) Wallingford, J.B., Rowning, B.A., Vogeli, K.M., Rothbacher, U., Fraser, S.E., and Harland, R.M. Nature, 405, 81-85
“Actin-dependent propulsion of Endosomes and Lysosomes by recruitment of N-WASP” (2000) Taunton, J., Rowning, B.A., Coughlin, M.T., Wu, M., Moon, R.T., Mitchison, T.J., and Larabell, C.A. Journal of Cell Biology, 148,519-530
“Establishment of the dorsal-ventral axis in Xenopus embryos coincides with the dorsal enrichment of Dishevelled that is dependent on cortical rotation” (1999) *Rowning, B.A., *Miller, J.R., Larabell, C.A.; Yang-Snyder, J.A.; Bates, R.L., and Moon, R.T. Journal of Cell Biology, 146, 427-437 (*shared first authorship)
“Lactoferrin expression in mammary epithelial cells is mediated by changes in cell shape and actin cytoskeleton” (1997) Close, M.J., Howlett, A.R., Roskelley, C.D., Desprez, P.Y., Bailey, N., Rowning, B., Teng, C.T., Stampfer, M.R., Yaswen, P. Journal of Cell Science 110, 2861-2871
“Microtubule-mediated transport of organelles and localization of beta-catenin to the future dorsal side of Xenopus eggs” (1997) Rowning B.A., Wells, J., Wu, M., Gerhart,J.C., Moon, R.T., and Larabell, C.A. P.N.A.S.-U.S.A. 94, 1224-1229
“Establishment of the dorso-ventral axis in Xenopus is presaged by early asymmetries in ß-catenin that are modulated by the Wnt signaling pathway” (1997) Larabell, C.A., Torres, M., Rowning B.A., Yost, C., Miller, J.R., Wu, M., Kimelman, D., and Moon, R.T. Journal of Cell Biology, 136, 1123-1136
“Confocal microscopy analysis of living Xenopus eggs and the mechanism of cortical rotation” (1996) Larabell, C.A., Rowning B.A., Wells, J., Wu, M., and Gerhart, J. Development 122, 1281-1289
“Hyperdorsoanterior embryos from Xenopus eggs treated with D2O” (1989) Scharf, S.R., Rowning, B., Wu, M., and Gerhart, J.C. Developmental Biology 134, 175-188
“Cortical rotation of the Xenopus egg: consequences for the anteroposterior pattern of embryonic dorsal development” (1989) Gerhart, J., Danilchik, M., Doniach, T., Roberts, S., Rowning, B., and Stewart, R. Developmental Biology, The Molecular Basis of Positional Signaling. 37-51
“A transient array of parallel microtubules in frog eggs: Potential tracks for a cytoplasmic rotation that specifies the dorso-ventral axis” (1988) Elinson, R.P. and Rowning, B.A. Developmental Biology 128, 185-197
Doug Bruce, Laboratory Manager
Matt Stavis, Chemistry Coordinator
Research Assistants
Clayton Fischer, Senior Research Assistant
Studied biology at UC Santa Cruz and interested in the systematics of Asia-Pacific reptiles and amphibians, using genomics as a tool to put the puzzle pieces together. Member of the IUCN Red List.
Currently working in stem cell genomics for the California Institute for Regenerative Medicine through the UC Santa Cruz Genome Browser team.
Dustin DeMeo
Charles Barbieri, Senior Research Assistant
Originally from Florida, Charles moved to California in 2005 to pursue his career in neurobiology and medicine. He has a worked in graphic design and information technology for over 6 years and strives to integrate these skills with his scientific background.
Angela Lane, Senior Research Associate
Angela’s background includes working with Johnson and Johnson on a prototype blood glucose monitoring device. As a Research Staff Associate at UCSF Medical Center in which her capacity was to work on monitoring the increase of heat shock proteins in Surgical wound healing she contributed in development stages of treatment therapy. Her ambitions are to further her career in Biomedical Sciences with the combination of modern Genomics contributing to her long- term interests in education.
Shetal Sias
A decade of crime lab experience, with specialization in friction ridge analysis, has fueled interest in other forensic disciplines, especially DNA. Forensics is a rapidly expanding field, incorporating science as it relates to law. An active member of the International Association for Identification and California State Division IAI, Shetal is currently the Chairperson over the CSDIAI’s Science and Practices Committee.
Chris Villarreal
Working towards a BSc. in Biology, I appreciate the opportunities and experience Profile Genomics enables, and I am eager to learn about the world of Genomics as it relates to medicine.
Robin Doolin
Lab Affiliates
Crystal Trinh
Pursuing forensic science.
Senait Gebremedhin
Deniz Akgok
Advanced Students and Modified Supplement Instructors (MSIs)
Edixa Sanchez
Monsoon Pandey
Amber Robbins
Working towards a degree in biological sciences, I am excited to have the opportunity to work in this lab and gain hands-on experience through Profile Genomics.
Quang
|