James A. Coffman, Ph.D.

James Coffman, Ph.D.Associate ProfessorMDI Biological Laboratory

Research Areas

Human and Environmental SustainabilityRegenerative Biology and Medicine


Ph.D., Duke University, Zoology, 1990 B.A., Carleton College, Biology, 1981


207-288-9880 ext 444

159 Old Bar Harbor RD
PO Box 35
Salisbury Cove, ME 04672

Chronic early life stress can have lifelong effects that predispose an individual to a variety of inflammatory diseases and more rapid aging, a phenomenon known as ‘developmental programming’ of health and disease.  We are investigating the mechanisms underlying these effects, focusing on (1) how stressful conditions experienced during early development program responsiveness to the stress hormone cortisol, an important physiological regulator of inflammation, and (2) the long-term effects of that programming on the body’s capacity for tissue repair and regeneration.   We are using zebrafish as a model system to investigate these issues, as the cortisol-mediated stress response is conserved between zebrafish and humans, and zebrafish are exceptionally amenable to detailed mechanistic studies of both early development and adult regeneration.

Selected Publications

Developmental control of transcriptional and proliferative potency during the evolutionary emergence of animals. Arenas-Mena, C. and Coffman, J.A. (2015). Dev. Dyn., In press.

Gene expression changes associated with the developmental plasticity of sea urchin larvae in response to food availability.  Carrier, T.J., King, B.L., and Coffman, J.A. (2015). Biological Bulletin, 228: 171-180.

On the meaning of chance in biologyCoffman, J.A. (2014). Biosemiotics 7: 377-388.

Oral-aboral axis specification in the sea urchin embryo IV. Hypoxia radializes embryos by preventing the initial spatialization of nodal activity. Coffman, J.A., Wessels, A., DeSchiffart, C., and Rydlizky, K. (2014). Dev. Biol. 386: 302-307.

Developmental cis-regulatory analysis of the cyclin D gene in the sea urchin Strongylocentrotus purpuratus. McCarty, C.M., and Coffman, J.A. (2013). Biochem. Biophys. Research Comm. 440: 413-418.

Sea urchin akt activity is Runx-dependent and required for post-cleavage stage cell division. Robertson, A.J., Coluccio, A., Jensen, S., Rydlizky, K., and Coffman, J.A. (2013). Biology Open, 2: 472-478.

Global Insanity: How Homo sapiens Lost Touch with Reality while Transforming the World. Coffman, J.A. and Mikulecky, D.C. (2012). Emergent Publications (ISBN 9781938158049).

Nodal-mediated epigenesis requires dynamin-mediated endocytosis. Ertl, R.P., Robertson, A.J., Saunders, D., and Coffman, J.A. (2011). Dev. Dyn. 240: 704-711.

Oxygen, pH, and oral-aboral axis specification in the sea urchin embryo. Coluccio, A.E., LaCasse, T.J., and Coffman, J.A. (2011). Mol. Rep. & Dev. 78: 68.

Information as a manifestation of development. Coffman, J.A. (2011). Information 2 (1): 102-116. (In the Special Issue “What is Information?”)

On causality in non-linear complex systems: the developmentalist perspective. Coffman, J.A. (2011). In: Philosophy of Complex Systems (Cliff Hooker, ed.): pp. 287-309. North Holland/Elsevier, Oxford, UK (ISBN 9780444520760).

The evolution of Runx genes. II. The C-terminal Groucho recruitment motif is present in both eumetazoans and homoscleromorphs but absent in a haplosclerid demosponge. Robertson, A.J., Larroux, C., Degnan, B.M., and Coffman, J.A. (2009). BMC Research Notes 2: 59.

Oral-aboral axis specification in the sea urchin embryo III. Role of mitochondrial redox signaling via H2O2. Coffman, J.A., Coluccio, A., Planchart, A., and Robertson, A.J. (2009). Dev. Biol. 330: 123-130.

Is Runx a linchpin for developmental signaling in metazoans? Coffman, J.A. (2009). J. Cellular Biochem. 107: 194-202.

Mitochondria and metazoan epigenesis. Coffman, J.A. (2009). Semin. Cell Dev. Biol. 20: 321-329.

Runx expression is mitogenic and mutually linked to wnt activity in blastula-stage sea urchin embryos. Robertson, A.J., Coluccio, A., Knowlton, P., Dickey-Sims, C., and Coffman, J.A. (2008). PLoS One 3: 11.

Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network. Nam, J., Su, Y.-H., Lee, P.Y., RobertsonA. J., Coffman, J.A., and Davidson, E.H. (2007). Dev. Biol. 306: 860-869.

Mitochondria, redox signaling, and axis specification in metazoan embryos. Coffman, J.A. and Denegre, J.M. (2007). Dev. Biol. 308: 266-280.

CBF-beta is a facultative Runx partner in the sea urchin embryo. Robertson, A.J., Dickey-Sims, C., Ransick, A., Rupp, D.E., McCarthy, J.J., and Coffman, J.A. (2006). BMC Biol. 4: 4.

Developmental ascendency: from bottom-up to top-down control. Coffman, J.A. (2006). Biological Theory 1 (2):165-178.

The genome of the sea urchin Strongylocentrotus purpuratus. Sodergren E., Weinstock G. M., Davidson E. H., Cameron R. A., Gibbs R. A., Angerer R. C., Angerer L. M., Arnone M. I., Burgess D. R., Burke R. D., Coffman J.A., et al. (The Sea Urchin Genome Sequencing Consortium) (2006). Science 314: 941-952.

The genomic underpinnings of apoptosis in Strongylocentrotus purpuratus. Robertson, A.J., Croce, J., Carbonneau, S., Voronina, E., Miranda, E., McClay, D.R. and Coffman, J.A. (2006). Dev. Biol. 300: 321-334.

The sea urchin kinome: a first look.  Bradham, C.A., Beane, W.S., Arnone, M.I., Rizzo, F., Coffman, J.A., Mushegian, A., Goel, M., Morales, J., Geneviere, A-M., Lapraz, F., Robertson, A.J., Kelkar, H., Loza-Coll, M., Townley, I.R., Raisch, M., Roux, M.M., Lepage, T., Gache, C., McClay, D.R., and Foltz, K.R. (2006). Dev. Biol. 300: 180-193.

Protein tyrosine and ser-thr phosphatases in the sea urchin, Strongylocentrotus purpuratus: identification and potential functions. Byrum, C.A., Walton, K., Robertson, A.J., Carbonneau, S., Thomason, R., Bradham, C.A., Coffman, J.A., and McClay, D.R. (2006). Dev. Biol. 300: 194-218.

The genomic repertoire for cell cycle control and DNA metabolism in S. purpuratus. Fernandez-Guerra, A., Aze, A., Morales, J., Mulner-Lorillon, O., Cosson, B., Cormier, P., Bradham, C.,Adams, N., Robertson, A.J., Marzluff, W.F., Coffman, J.A., and Genevière, A.M. (2006). Dev. Biol. 300: 238-251.

Runx-dependent expression of PKC is critical for cell survival in the sea urchin embryo. Dickey-Sims, C., Robertson, A.J., Rupp, D.E., McCarthy, J.J., and Coffman, J.A. (2005). BMC Biol. 3: 18.

Sea urchin vault structure, composition, and differential localization during development. Stewart, P.L., Makabi, M., Lang, J., Dickey-Sims, C., Robertson, A.J., Coffman, J.A., and Suprenant, K.A. (2005). BMC Dev. Biol. 5: 3.

Oral-aboral axis specification in the sea urchin embryo. II. Mitochondrial distribution and redox state contribute to establishing polarity in Strongylocentrotus purpuratus. Coffman, J.A., McCarthy, J.J., Dickey-Sims, C., and Robertson, A.J. (2004). Dev. Biol. 273: 160-171.

Evaluation of developmental phenotypes produced by morpholino antisense targeting of a sea urchin Runx gene. Coffman, J.A., Dickey-Sims, C., Haug, J.S., McCarthy, J.J., and Robertson, A.J. (2004). BMC Biol. 2: 6.

Cell cycle development. Coffman, J.A. (2004). Dev. Cell 6: 321-327.

Runx transcription factors and the developmental balance between cell proliferation and differentiation. Coffman, J.A. (2003). Cell Biol. Int. 27: 315-324.

The expression of SpRunt during sea urchin embryogenesis. Robertson, AJ., Dickey, C.E., McCarthy, J.J., and Coffman, J.A. (2002). Mech. Dev. 117: 327-330.

Oral-aboral axis specification in the sea urchin embryo. I. Axis entrainment by respiratory asymmetry.  Coffman, J.A., and Davidson, E.H. (2001). Dev. Biol. 230: 18-28.

SpMyb functions as an intramodular repressor to regulate spatial expression of CyIIIa in sea urchin embryos. Coffman, J.A., Kirchhamer, C.V., Harrington, M.G., and Davidson, E.H. (1997). Development 124:4717-4727.

SpRunt-1, a new member of the runt-domain family of transcription factors, is a positive regulator of the aboral ectoderm-specific CyIIIa gene in sea urchin embryos. Coffman, J.A., Kirchhamer, C.V., Harrington, M.G., and Davidson, E.H. (1996). Dev. Biol. 174: 43-54.

SpGCF1, a sea urchin embryo DNA binding protein, exists as five nested variants encoded by a single mRNA. Zeller, R.W., Coffman, J.A., Harrington, M.G., Britten, R.J., and Davidson, E.H. (1995). Dev. Biol. 169: 713-727.

SpOct, a gene encoding the major octamer-binding protein in sea urchin embryos: Expression profile, evolutionary relationships, and DNA binding of expressed protein. Char, B.R., Bell, J.R., Dovola, J., Coffman, J.A., Harrington, M., Beccerra, J.C., Davidson, E.H., Calzone, F.J., and Maxson, R. (1993). Dev. Biol. 158: 350-363.

Complexity of sea urchin embryo nuclear proteins that contain basic domains. Harrington, M.G., Coffman, J.A., Calzone, F.J., Hood, L.E., Britten, R.J., and Davidson, E.H. (1992). Proc. Natl. Acad. Sci. USA 89: 6252-6256.

Automated sequential affinity chromatography of sea urchin embryo DNA binding proteins. Coffman, J.A., Moore, J.G., Calzone, F.J., Britten, R.J., Hood, L.E., and Davidson, E.H. (1992). Mol. Mar. Biol. Biotechnol. 1: 136-146.

Commitment along the dorsoventral axis of the sea urchin embryo is altered in response to NiCl2. Hardin, J., Coffman, J.A., Black, S.D., and McClay, D.R. (1992). Development 116: 671-685.

A hyaline layer protein that becomes localized to the oral ectoderm and foregut of sea urchin embryos. Coffman, J.A. and McClay, D.R. (1990). Dev. Biol. 140: 93-104.

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  • Shusen Zhu, M.S., Research Assistant
  • Ellen Hartig, B.S., B.A., Research Assistant