Below is a sampling of recent publications by the Biology Faculty, including those co-authored with Amherst College students. For a more complete listing of publications, please see individual faculty member web pages. Jump down page to papers authored by:

Clotfelter, Ethan D.  |  Edwards, Marc A.  |  Emerson, Julie A.  |  Goutte, Caroline E.  |  Henderson-Stull, Nidanie  |  Hood, Michael E.  |  Jeong, Jeeyon  |  Lee, Joohyun |  Levin, Rachel A.  |  Miller, Jill S.  |  Poccia, Dominic L.  |  Purdy, Alexandra E.  |  Ragkousi, Katerina  |  Ratner, David I.  |  Temeles, Ethan J.  |  Trapani, Josef G.  |  Williamson, Patrick L.

Clotfelter, Ethan D.

Matthew D. Cahn ‘13, Alexandria C. Brown and Ethan D. Clotfelter. Guanine-based structural coloration as an indicator of oxidative stress in a cichlid fish. Journal of Experimental Zoology, in press.

Montgomery, T.M.’10, Brown, A.C., Gendelman, H.K.’13, Ota, M.’13 and Clotfelter, E.D. (In press). Exposure to 17α-ethinyl estradiol decreases motility and ATP in sperm of male fighting fish Betta splendensEnvironmental Toxicology.

Stevenson L.M.’09, Brown, A.C., Montgomery T.M.’10, and Clotfelter, E.D. (2011). Reproductive consequences of exposure to waterborne phytoestrogens in male fighting fish Betta splendens. Archives of Environmental Contamination and Toxicology 60: 501-510.

Lin S.M.'08, Nieves-Puigdoller, K., Brown, A.C., McGraw, K J. and Clotfelter, E.D. (2010). Testing the carotenoid trade-off hypothesis in the polychromatic Midas cichlid, Amphilophus citrinellus. Physiological and Biochemical Zoology 83: 333-342.

Ardia, D.R., Pérez J H.'07, and Clotfelter, E.D. (2010). Experimental cooling during incubation leads to reduced innate immunity and body condition in nestling tree swallows. Proceedings of the Royal Society of London B 277: 1881-1888.

Pérez J.H.’07, Ardia, D.R., Chad, E.K.'07E and Clotfelter, E.D. (2008). Experimental heating reveals nest temperature affects nestling condition in tree swallows (Tachycineta bicolor). Biology Letters 4: 468-471.

Edwards, Marc C.


Emerson, Julie A. 

Emerson, J.A., Key, S.C.S., Alvarez, C.J., Mel, S., McNeil, G., Saville, K.J. , Leung, W., Shaffer, C.D.  and Elgin, S.C.R. (2013). Introduction to the Genomics Education Partnership and collaborative genomics research in DrosophilaTested Studies for Laboratory Teaching, Proceedings of the Association for Biology Laboratory Education 34: 135-165.

Emerson, J.A. (2012). Identification of human polymorphisms in the phenylthiocarbamide (PTC) bitter taste receptor gene and protein. Tested Studies for Laboratory Teaching, Proceedings of the Association for Biology Laboratory Education 33: 246-250.

Emerson, J.A. and Ratner, D.I. (2006). From bench top to presentation in seven days: DNA sequencing research projects for summer workshops or undergraduate teaching labs. Developmental Biology 295: 350.

Goutte, Caroline E.  

Agarwal, Ipsita ['13], Farnow, Cassandra  ['13], Jiang, Joshua  ['17], Kim, Kyung-Sik  ['17], Leet, Donna E.  ['15], Solomon, Ruth Z.  ['16], Hale, Valerie A. , Goutte, Caroline.  HOP-1 Presenilin Deficiency Causes a Late-Onset Notch Signaling Phenotype that Affects Adult Germline Function in C. elegans. Genetics2018 Feb;208(2):7. Epub 2017 Dec 14.

Hale, V.A., Guiney, E.L.’06, Goldberg, L.Y.’05, Haduong, J.H.’99, Kwartler, C.S.’07, Scangos, K.W.’02, and Goutte, C. (2012). Notch Signaling is Antagonized by SAO-1, a Novel GYF-Domain Protein That Interacts with the E3 Ubiquitin Ligase SEL-10 in Caenorhabditis elegans.  Genetics 190(3): 1043-57. Epub 2011 Dec 29.

Goutte, C. (2002). Genetics leads the way to the accomplices of presenilins. Developmental Cell 3: 6-7.

Goutte, C., Tsunozaki, M.’00, Hale, V.A. and Priess J.R. (2002). APH-1 is a multipass membrane protein essential for the Notch signaling pathway in Caenorhabditis elegans embryos.  Proceedings of the National Academy of Sciences USA 99:775-779.

Levitan, D., Yu, G., Hyslop, P.St.G. and Goutte, C. (2001).  APH-2/nicastrin functions in LIN-12/Notch signaling in the Caenorhabditis elegans somatic gonad. Developmental Biology 240: 654-661.

Goutte, C., Hepler, W., Mickey, K.M. and Priess, J.R. (2000). Aph-2 encodes a novel extracellular protein required for GLP-1 mediated signaling. Development 127: 2481-2492.

Graf, Ethan R. 

Graf E.R., Valakh V., Wright C.W.’11, Wu C., Liu Z., Zhang Y.Q. and DiAntonio A. (2012). RIM Promotes Calcium Channel Accumulation at Active Zones of the Drosophila Neuromuscular Junction. Journal of Neuroscience 32: 16586-96.

Graf E.R., Heerssen H.M., Wright C.W.’11, Davis G.W., and DiAntonio A. (2011). Stathmin is Required for Stability of the Drosophila Neuromuscular Junction. Journal of Neuroscience 31: 15026-34.

Graf, E.R., Daniels, R.W., Burgess, R.W., Schwarz, T.L., and DiAntonio, A. (2009). Rab3 dynamically controls protein composition at active zones.  Neuron 64:663-677. 

Graf, E.R., Kang, Y., Hauner, A.M.,and Craig, A.M. (2006). Structure-function and splice site analysis of the synaptogenic activity of the neurexin-1b LNS domain.  J. Neurosci. 26:4256-65. 

Graf, E.R., Zhang, X.Z., Jin, S.X., Linhoff, M.W., and Craig, A.M. (2004) Neurexins induce differentiation of GABA and glutamate postsynaptic specializations via neuroligins. Cell 199:1013-26. 

Henderson-Stull, Nidanie


Hood, Michael E. 

Hood, M.E., Petit, E., and Giraud, T. (2013). Extensive divergence between mating type chromosomes of the anther-smut fungus. Genetics 193: 309–315.

Chung, E.'09, Petit, E., Antonovics, J., Pedersen, A.B., and Hood, M.E. (2012). Variation in resistance to multiple pathogen species: anther smuts of Silene unifloraEcology and Evolution 2: 2304–2314.

Horns, F.'11, Petit, E., Yockteng, R., and Hood, M.E. (2012). Patterns of repeat-induced point mutation in transposable elements of basidiomycete fungi. Genome Biology and Evolution 4: 240-247.

Gibson, A.K.'08, Mena-Alí, J.I., and Hood M E. (2010). Loss of pathogens in threatened plant species. Oikos 119: 1919–1928.

Hood, M.E., Mena-Alí, J.I., Gibson, A.K.'08, Oxelman, B., Giraud, T., Yockyeng, R., Arroyo, M. T.K., Conti, F., Pedersen, A., Gladieux, P, and Antonovics, J.(2010). Distribution of the anther-smut pathogen Microbotryum on species of the Caryophyllaceae. New Phytologist 187: 217-229.

Jeong, Jeeyon


Lee, Joohyun


Levin, Rachel A. 

Blank, C.M.'14, Levin. R.A., and Miller, J.S. (2014). Intraspecific variation in gender strategies: associations with ploidy and changes in floral form following the evolution of gender dimorphism. American Journal of Botany 101. 

Levin, R.A., Keyes, E.’12, and Miller, J.S. (In prep). Dimorphism in the Galapagos endemic Lycium minimum.  American Journal of Botany.

Levin, R.A., Bernardello, G., Whiting, C.Smith'10, and Miller, J.S. (2011). A new generic circumscription in tribe Lycieae (Solanaceae). Taxon 60: 681-690.

Levin, R.A., Whelan, A.’08, and Miller, J.S. (2009). The utility of nuclear conserved ortholog set II (COSII) genomic regions for species-level phylogenetic inference in Lycium (Solanaceae). Molecular Phylogenetics and Evolution 53: 881-890.

Levin, R.A., Blanton, J.’05, and Miller, J.S. (2009). Phylogenetic utility of nuclear nitrate reductase: A multi-locus comparison of nuclear and chloroplast sequence data for inference of relationships among American Lycieae (Solanaceae). Molecular Phylogenetics and Evolution 50: 608-617.

Miller, Jill S.

Miller, JS, Blank, CM '14, and RA Levin. 2019. Colonization, Baker's law, and the evolution of gynodioecy in Hawaii: implications from a study of Lycium carolinianum. American Journal of Botany 106:733-743.

Kamath, A '11, RA Levin, and JS Miller. 2017. Floral size and shape evolution following the transition to gender dimorphism. American Journal of Botany 104:451-460.

Miller, JS, A Kamath '11, BC Husband, and RA Levin. 2016. Correlated polymorphism in cytotype and sexual system within a monophyletic species, Lycium californicumAnnals of Botany 117:307-317.

Miller JS and JL Kostyun '09. 2011. Functional self-incompatibility in a peripheral population of Solanum peruvianum (Solanaceae). Heredity 107:30-39.

Miller, JS, A Kamath '11, J Damashek '09, and RA Levin. 2011. Out of America to Africa or Asia: Inference of dispersal histories using nuclear and plastid DNA and the S-RNase self-incompatibility locus. Molecular Biology and Evolution  28:793-801.

Diggle, PK and JS Miller. 2013. Developmental plasticity, genetic assimilation, and the evolutionary diversification of sexual expression in Solanum. American Journal of Botany 100:1050-1060.


Poccia, Dominic L. 

Poccia, D.L. (2016) A Sea Urchin Cell-Free System to Study Male Pronuclear Assembly and Activation.  Int. J. Dev. Biol., in press.

Byrne, R.D., Larijani, B. and Poccia, D.L. (2016)The Use of 2-Photon FLIM/FRET to Study Protein Interactions during Nuclear Envelope Fusion in Vivo and in Vitro.  In, The Nuclear Envelope: Methods and Protocols, Methods in Molecular Biology 1411: (S. Shackleton, P. Collas and E.C. Schirmer, eds.) Springer, doi 10.1007/978-1-4939-3530-7, in press.

Larijani, B, Hamati, F. '14, Kundu, A '13., Chung, G.C., Domart, M.-C., Collinson, L. and Poccia, D.L. (2014). Principle of Duality of Phospholipids: Regulators of Membrane Morphology and Dynamics. Biochem. Soc. Trans. 42: 1335-1342. Included in Essays in Biochemistry: Membrane Nanodomains (2015) I. Parmryd, ed., Portland Press.

Mooney J. '12, Thakur S. '11, Kahng P. '13, Trapani J.G., and Poccia D.L. (2013). Quantification of exocytosis kinetics by DIC image analysis of cortical lawns. Journal of Chemical Biology, in press.

Wang, A.’12, Kundu, A.’13, Fong, B.’08, Fitzgerald, J., Larijani, B. and Poccia, D. (2013). A structural role for lipids in organelle shaping. Biol. Bulletin, in press.

Byrne, R.D., Applebee, C., Poccia, D.L., Larijani, B. (2012). Dynamics of PLCγ and Src Family Kinase 1 Interactions during Nuclear Envelope Formation Revealed by FRET-FLIM. PLoS ONE 7: e40669. doi:10.1371.

Domart, M.C., Hobday, T.M.C., Peddie, C.J., Chung,G.H.C., Wang, A.'12, Yeh, K.'13, Jethwa, N., Zhang, Q., Wakelam, M.J.O.,  Woscholski, R., Byrne, R.D., Collinson, L.M., Poccia, D.L. and Larijani, B. (2012). The function of diacylglycerol in controlling ER morphology and nuclear envelope fusion from echinoderms to mammals, PLoS ONE 7: e51150. doi:10.1371.

Larijani, B. and Poccia, D. (2012). Effects of Phosphoinositides and their Derivatives on Membrane Morphology and Function, Curr. Topics Microbiol Immunol 362: 99-110.

Chatzidimitriadou, Z.’11 and Poccia, D. (2010). Localization of PLCγ and Nuclear Envelopes in Telophase of Sea Urchin Embryos. Molecular Reproduction and Development 77: 737.

Purdy, Alexandra E. 

Wang, Z., Hang, S., Purdy, A.E. and Watnick, P.I. (2013). Mutations in the IMD pathway and Mustard counter Vibrio cholerae suppression of intestinal stem cell division in Drosophila.  mBio. 4(3) e00337-13.

Purdy, A E. and Watnick, P.I. (2011). Spatially-selective colonization of the arthropod intestine through activation of Vibrio cholerae biofilm formation. Proc. Natl. Acad. Sci. USA.108:  19737-19742.

Purdy, A. E., Balch, D., Lizarraga-Partida, M.L., Islam, M.S., Martinez-Urtaza, J., Huq, A., Colwell, R.R.  and Bartlett, D.H.  (2010).  Diversity and distribution of cholix toxin, a novel ADP-ribosylating factor from Vibrio choleraeEnviron. Microbiol. Rep. 2(1): 198–207.

Jorgensen*, R., Purdy, A.E.*, Fieldhouse, R., Kimber, M., Bartlett, D.H. and Merrill, A.R. (2008). Cholix toxin, a novel ADP-ribosylating factor from Vibrio cholerae J. Biol. Chem. 283: 10671-10678.  *These authors contributed equally.

Purdy, A., Rohwer, F., Edwards, R., Azam, F. and Bartlett, D.H. (2005). A glimpse into the genome content of the Vibrio cholerae species through identification of genes present in environmental strains.  J. Bacteriol.187: 2992-3001.

Ragkousi, Katerina


Ratner, David I. 

Tilahun, M.E., Rajagopalan, G., Shah-Mahoney, N., Lawlor, R. G.,Tilahun, A.Y., Xie, C.‘09, Natarajan, K., Margulies, D.H., Ratner, D.I., Osborne, B.A., and Goldsby, R.A., (2010).  Potent neutralization of staphylococcal enterotoxin B by synergistic action of chimeric 
antibodies.  Infection and Immunity 78: 2801-11. 

Pauyo, T.’05, Hilinski, G.J. ’04, Chiu, P.T. ‘02, Hansen, D.E. , Choi, Y.J., Ratner, D.I., Shah-Mahoney, N., Southern, C.A., and O’Hara P.B. (2006). Genetic and fluorescence studies of affinity maturation in related antibodies.  Molecular Immunology 43: 812-821.

Tekinay, T., Ennis, H.L., Wu, M.Y., Nelson, M., Kessin, R.H. and Ratner, D.I. (2003).  Genetic interactions of the E3 ubiquitin ligase component Fbxa with cyclic AMP metabolism and a histidine kinase signaling pathway during Dictyostelium discoideum development. Eukary. Cell 2: 618-626.

Wang, Z., Raifu, M.’97, Howard, M.’96, Smith, L., Hansen D., Goldsby, R. and Ratner, D. (2000).  Universal PCR amplification of mouse immunoglobulin gene variable regions: the design of degenerate primers and an assessment of the effect of DNA polymerase 3’ to 5’ exonuclease activity. J. Immunological Methods 233:167-177.

Nadin, B.M.’98, Mah, C.S.’97, Scharff, J.R.’96 and Ratner, D.I. (2000). The regulative capacity of prespore amoebae as demonstrated by fluorescence activated cell sorting and green fluorescent protein. Developmental Biology 217:173-178.

Temeles, Ethan J.

Temeles, E.J., Rah, Y.J. '11, Andicoechea, J. '09, Byanova, K.L. '09, Giller, Geoffrey S.J. '10, Stolk, S.B. '10, and Kress, W.J. (2013). Pollinator-mediated selection in a specialized hummingbird-Heliconia system in the Eastern Caribbean. Journal of Evolutionary Biology 26: 347-356.

Temeles, E.J. and Kress, W.J. (2010). Mate choice and mate competition by a tropical hummingbird at a floral resource. Proceedings of the Royal Society B 277: 1607-1613.

Temeles, E.J., Miller, J.S., and Rifkin, J.L.’09. (2010). Evolution of sexual dimorphism in bill size and shape of hermit hummingbirds (Phaethornithinae): a role for ecological causation. Philosophical Transactions of the Royal Society B 365: 1053-1063.

Temeles, E.J. and Kress, W.J. (2003). Adaptation in a plant-hummingbird association. Science 300: 630-633.

Temeles E.J., Pan, I.L.’99, Brennan, J.L.’01, and Horwitt, J.N.’01 (2000). Evidence for ecological causation of sexual dimorphism in a hummingbird. Science 289: 441-443. 

Trapani, Josef G.

Troconis EL'15, Ordoobadi AJ'15, Sommers TF'16, Aziz-Bose R'14, Carter AR, Trapani JG (2016). Intensity-dependent timing and precision of startle response latency in larval zebrafish. The Journal of Physiology. DOI: 10.1113/JP272466

Kruger M, Boney R, Ordoobadi AJ'15, Sommers TF'16, Trapani JG, Coffin AB (2016). Natural bizbenzoquinoline derivatives protect zebrafish lateral line sensory hair cells from aminoglycoside toxicity. Frontiers in Cellular Neuroscience, 10:83. DOI: 10.3389/fncel.2016.00083 

Olt J, Ordoobadi AJ'15, Marcotti W, Trapani JG (2016). Physiological recordings from the zebrafish lateral line. Methods in Cell Biology, Vol. 133.

Williamson, Patrick L.  

Stone, A.’12, Chau, C., Eaton, C., Foran, E., Kapur, M., Prevatt, E., Belkin, N.’12, Kerr, D.’14, Kohlin, T. and Williamson, P. (2012). Biochemical Characterization of P4-ATPase Mutations Identified in Patients with Progressive Familial Intrahepatic Cholestasis. J Biol Chem 287: 41139-41151.

Castoldi, E., Collins, P.W., Williamson, P.L. and Bevers, E.M. (2011). Compound heterozygosity for two novel TMEM16F mutations in a patient with Scott syndrome. Blood: 117: 4399-4400 .

Lenoir, G., Williamson, P.L., Puts, C.F., Holthuis, J.C.M. (2009). Cdc50p plays a vital role in the ATPase reaction cycle of the putative aminophospholipid transporter Drs2p J. Biol. Chem. 284: 17956-17967.

Williamson, P.,  Halleck, M.S., Malowitz, J. ‘03, Ng, S. ‘00, Fan, X., Krahling, S., Remaley, A.T.,  Schlegel, R.A. Transbilayer phospholipid movements in ABCA1-deficient cells (2007).  PLoS ONE. 2:e729.

Tang, X., Halleck, M.S., Schlegel, R.A. and Williamson, P. (1996).  A subfamily of P-type ATPases with aminophospholipid transporting activity.  Science 272:1495-1497.

Last Updated: 
3 April 2015 TLR