Student Theses

See a list of past thesis titles by majors.

*Middlebury student author​


Choudoir MJ, Eggleston EM (2022) Reciprocal Inclusion of Microbiomes and Environmental Justice Contributes Solutions to Global Environmental Health Challenges. mSystems


Ruxin, T.R*., J.A. Schwartzman*, C.R. Davidowitz*, Z. Peters*, A. Holtz*, R.A. Haney and G.A. Spatafora. 2021. Regulatory involvement of the PerR and SloR metalloregulators in the Streptococcus mutans oxidative stress response.  J. Bacteriol.  doi:10.1128/JB.00678-20.


Parker KE, Ward JO, Eggleston EM, Fedorov E*, Parkinson JE, Dahlgren CP, Cunning R (2020) Characterization of a thermally tolerant Orbicella faveolata reef in Abaco, The Bahamas. Coral Reefs 39, 675–685. 

C. Merenstein*, J. Ward, and D. Allen. Diplorickettsia in the microbiome of an Ixodes scapularis tick in western Vermont. Emerging Infectious Diseases. 2020.


Allen D, Borgmann-Winter B, Bashor L, Ward J. The Density of the Lyme Disease Vector, Ixodes scapularis (Blacklegged Tick), Differs Between the Champlain Valley and Green Mountains, Vermont. Northeast Nat (Steuben). 2019 Jul;26(3):545-560.

Brahmstedt ES, Zhou H, Eggleston EM, Holsen TM, Twiss MR (2019) Assessment of mercury mobilization potential in Upper St. Lawrence River riparian wetlands under new water level regulation management. Journal of Great Lakes Research 45, 735–741. 

Kajfasz, J.K., Katrak, C., Gaguly, T., Vargas, J., Wright, L.*, Peters, Z.T.*, Spatafora, G.A., Abranches, J., and Lemos, J.A. 2019. Manganese Uptake, Mediated by SloABC and MntH, is Essential for the Fitness of Streptococcus mutans. mSphere 5:e00764-19.

O’Brien, J*, Patora, A.*, Stoner, A., and Spatafora, G.A. 2019. The S. mutans mntE gene encodes a manganese efflux transporter. Mol. Oral Microbiol. 35:129-140. doi:10.1111/omi.12286  


*Monette, P., R. Brach*, A. Cowan*, R. Winters*, J. Weisman, F. Seybert, K. Goguen*, J. Chen, A. Glasfeld, and G. Spatafora. 2018. Autoregulation of the Streptococcus mutans SloR metalloregulator is constitutive and driven by an independent promoter. J. Bacteriol. doi:10.1128/JB.00214-18.

Joshua T. Yuan, Daniel M. Gatti, Vivek M. Philip, Steven Kasparek, Andrew M. Kreuzman, Benjamin Mansky, Kayvon Sharif, Dominik Taterra, Walter M. Taylor, Mary Thomas, Jeremy O. Ward, Andrew Holmes, Elissa J. Chesler, and Clarissa C. Parker. Genome-wide association for testis weight in the diversity outbred mouse population. Mamm Genome (2018) 29: 310.


Spatafora, G., J. Corbett*, L. Cornacchione*, W. Daly*, D. Galan-Donlo*, M. Wysota*, P. Tivnan*, J. Collins*, D. Nye, T. Levitz, W. Breyer, and A. Glasfeld.  2015.  Interactions of the Metalloregulatory Protein SloR from Streptococcus mutans with its Metal Ion Effectors and DNA Binding Site.  J. Bacteriol. 197:3601-3615.


Merchant, A.T.* and G. Spatafora2014. A role for the DtxR family of metalloregulators in gram positive pathogenesis.  Mol. Oral Microbiol. 29:1-10. Invited review.

Qiao, H., Prasada Rao, H. B. D., Yang, Y., Fong, J. H., Cloutier, J. M.*, Deacon, D. C.*, Nagel, K. E.*, Swartz, R.K.*Strong, E., Holloway, J.K., Cohen, P.E., Schimenti, J., Ward, J., and Hunter, N.(2014). Antagonistic roles of ubiquitin ligase HEI10 and SUMO ligase RNF212 regulate meiotic recombination. Nat Genet, 2014 Jan 5. doi:10.1038/ng.2858

Qiao, H., Prasada Rao, H. B. D., Yang, Y., Fong, J. H., Cloutier, J. M., Deacon, D. C., Nagel, K. E., Swartz R.K., Strong, E., Holloway, J.K., Cohen, P.E., Schimenti, J., Ward, J., and Hunter, N.(2014). Antagonistic roles of ubiquitin ligase HEI10 and SUMO ligase RNF212 regulate meiotic recombination. Nat Genet, 2014 Jan 5. doi:10.1038/ng.2858


Hennet*, M.L., Yu*, H.Y., and Combelles, C.M.H.  2013.  Follicular fluid hydrogen peroxide and lipid hydroperoxide in bovine antral follicles of various size, atresia, and dominance status. Journal of Assisted Reproduction and Genetics, 30, 333-340.

Haswell, J.R.*, B.W. Pruitt*, L.P. Cornacchione*, C.L. Coe*, E.G. Smith* and G. Spatafora. 2013.  Characterization of the functioinal domains of the SloR metalloregulatory protein in Streptococcus mutans.  J. Bacteriol. 195:126-134.

Schimenti, K. J., Feuer, S. K*., Griffin, L. B*., Graham, N. R., Bovet, C. A*., Hartford, S., Pendola, J., Lessard C, Schimenti JC, Ward JO (2013). AKAP9 is essential for spermatogenesis and sertoli cell maturation in mice. Genetics,194(2), 447-57. 2013 Jun. 

Machtinger^, R.B., Combelles^, C.M.H., Missmer, S.A., Hauser, R., and Racowsky, C.  2013. The effect of bisphenol A on human oocyte maturation. Human Reproduction July 30, Epub ahead of print.  ^ denotes equal first author contribution

Combelles^, C.M.H. and Rawe^, V.Y. 2013. Determinants of oocyte quality: impact on in vitro fertilization failures. In Mammalian Oogenesis. Editors: Coticchio, G., De Santis, L., and Albertini, D.F. Springer Science and Business Media. ^ denotes equal author contribution

Schimenti, K. J., Feuer, S. K., Griffin, L. B., Graham, N. R., Bovet, C. A., Hartford, S., Pendola, J., et al. (2013). AKAP9 is essential for spermatogenesis and sertoli cell maturation in mice. Genetics,194(2), 447-57. 2013 Jun. doi:10.1534/genetics.113.150789


Combelles, C.M.H., Holick*, E.A., and Racowsky, C.  2012.  Release of superoxide dismutase-1 by day 3 embryos of varying quality and implantation potential.  Journal of Assisted Reproduction and Genetics 29, 305-311.

Combelles, C.M.H. and Hennet*, M.L. 2012. Media composition: antioxidants/chelators and   cellular function. In Embryo Culture: Advances, Controversies, and Future Considerations. Methods in Molecular Biology. Editors: Smith, G.D., Swain, J.E., and Pool, T.B.  912, 129-159.

Combelles, C.M.H. and Chateau*, G. 2012. The use of immature oocytes in the fertility preservation for cancer patients: current promises and challenges. Special issue on Female Germ Cells in Development and Cancer, Editors: Garagna, S., Redi, C.A., and Zuccotti, M. International Journal of Developmental Biology 56, 919-929.

Combelles, C.M.H.  2012. Over 40 years of mentoring, educating, and researching in the world of oocytes- an interview with David Albertini.  Special issue on Female Germ Cells in Development and Cancer, Editors: Garagna, S., Redi, C.A., and Zuccotti, M. International Journal of Developmental Biology 56, 765-770.

Hennet*, M.L. and Combelles, C.M.H. 2012. The antral follicle: a microenvironment for oocyte differentiation.  Special issue on Female Germ Cells in Development and Cancer, Editors: Garagna, S., Redi, C.A., and Zuccotti, M. International Journal of Developmental Biology 56, 819-831.

Combelles, C.M.H. and Hennet*, M.L., 2012. Oxidative stress in assisted reproductive technologies.  In Studies on Women’s Health: Oxidative Stress in Applied Basic Research and Clinical Practice. Editors: Agarwal, A., Rizk, B, and Aziz, N. Humana Press, Springer Science and Business Media.

Wang, H., Racowsky, C., and Combelles, C.M.H., 2012.  Is it best to cryopreserve human cumulus-free immature oocytes before or after in vitro maturation? Cryobiology 65, 79-87. 

Machtinger, R.B., Combelles, C.M.H., Missmer, S.A., Correia, K.F., Fox, J.F., and Racowsky, C.  2012.  The association between severe obesity and characteristics of failed fertilized oocytes.  Human Reproduction 27, 3198-3207.

Combelles, C.M.H.  2012. Unique patient issues: early interventions and  management.  Seminars in Reproductive Medicine. Special issue on the Safety, Efficacy, and Complexities in the ART Laboratory. Editors: Carrell, D. and Racowsky. C. 30, 243-251.


Gupta, S., Choi, A., Yu*, H., Czerniak*, S.M., Holick*, E.A., Paolella*, L.J., Agarwal, A., and Combelles, C.M.H. 2011. Fluctuations in total antioxidant capacity, catalase activity and hydrogen peroxide levels of follicular fluid during bovine folliculogenesis. Reproduction, Fertility, and Development 23, 673-680.

Combelles, C.M.H., Kearns, W.G., Fox, J.H., and Racowsky, C. 2011. Cellular and genetic analysis of oocytes and embryos in a human case of spontaneous oocyte activation. Human Reproduction 26, 545-552.

Heindryckx, B., Lierman, S., Combelles, C.M.H., Cuvelier, C., Gerris, J, and DeSutter, P.  2011. Aberrant meiotic spindle structures responsible for recurrent human metaphase-I oocyte arrest with attempts to induce meiosis artificially. Human Reproduction 26, 791-800.

Alvarez Sedó C., Schatten H., Combelles C.M.H, and Rawe, V.Y. 2011. The nuclear mitotic apparatus (NuMA) protein: localization and dynamics in human oocytes, fertilization and early embryos. Molecular Human Reproduction 17, 392-398.

Combelles, C.M.H., Ceyhan, T.S., Wang, H., and Racowsky, C. 2011. Maturation outcomes are improved following vitrification of immature human oocytes when compared to slow-freezing. Journal of Assisted Reproduction and Genetics 281183-1192. Work featured as the journal’s cover.

Smith, E.G.* and G. Spatafora2011. Gene Regulation in Streptococcus mutans: Complex Control in a Complex Environment. J. Dent. Res. 91(2):133-141. Invited review.

Townson, D.H. and Combelles, C.M.H. 2011. Ovarian follicular atresia. In Basic Gynecology-Some Related Issues. Editors: Darwish, A. InTech-Open Access Publisher.


Combelles, C.M.H, Holick*, E.A., Paolella*, L.J., Walker*, D.C., and Wu*, Q.  2010.  Profiling of superoxide dismutase isoenzymes in compartments of the developing bovine antral follicle. Reproduction 139, 871-881.

O’Rourke, K.P.*, J.D. Shaw*, M.W. Pesesky*, B.T. Cook*. S.M. Roberts*, J. P. Bond and G. Spatafora. 2010. Genome-wide characterization of the SloR metalloregulome in Streptococcus mutans.  J. Bacteriol. 192:1433-1443.

Levine, R.B.*, M.S. Constanza-Robinson and G. Spatafora2010.  Neochloris oleoabundans grown on anaerobically digested dairy manure for concomitant nutrient removal and biodiesel feedstock production. Biomass and Bioenergy, 35:40-49

Combelles, C.M.H., Morozumi, K., Yanagimachi, R., Zhu, L., Fox, J.H., and Racowsky C.  2010.  Diagnosing cellular defects in an unexplained case of total fertilization failure. Human Reproduction 25, 1666-1671.


Hackert, M.L. and Sandwick, R.K. Study Guide and Solutions Manual for Chemistry and Life, An Introduction to General, Organic, and Biological Chemistry, Prentice Hall, Englewood Cliffs., NJ (in press)


Combelles, C.M.H. 2008. What are the trade-offs between one-cell and two-cell biopsies of preimplantation embryos?  Human Reproduction 23, 493-498.

Choi, S.; Vastag, L.; Larrabee, Y. C.;* Personick, M. L.;* Schaberg, K. B.;* Fowler, B. J.;* Sandwick, R. K.; Rawji, G. “The Importance of Pt(II) Catalyzed Pt(IV) Substitution for the Oxidation of Guanosine Derivatives by Pt(IV) Complexes” Inorg. Chem.200847, 1352-1360.

Dunning, D.W., L.W. McCall*, W.F. Powell*, W.Tristram Arscott*, Erin M. McConocha*, Cheryl J. McClurg*, Steven D. Goodman, and Grace A. Spatafora.  2008.  SloR modulation of the Streptococcus mutans acid tolerance response involves the GcrR response regulator as an essential intermediary.  Microbiology, 154:1132-1143.


Combelles, C.M.H. and Racowsky, C.  2007. Gamete quality and assisted reproductive     technologies. In The Endometrium: Molecular, Cellular, and Clinical Perspectives, Second Edition (Reproductive Medicine & Assisted Reproductive Techniques series). Editors: Aplin, J.D., Fazleabas, A.T., Glasser, S.R., and Giudice, L.C. Informa Healthcare.  

Ward JO, Reinholdt LG, Motley WW*, Niswander LM*, Deacon DC*, Griffin LB* et al. 2007. Mutation in Mouse Hei10, an E3 Ubiquitin Ligase, Disrupts Meiotic Crossing Over. PLoS Genet 3(8): e139 doi:10.1371/journal.pgen.0030139

Kim S, Namekawa SH, Niswander LM*, Ward JO, Lee JT, et al. 2007. A mammal-specific Doublesex homolog associates with male sex chromatin and is required for male meiosis. PLoS Genet 3(4): e62. doi:10.1371/journal.pgen.0030062


Combelles, C.M.H. and Racowsky, C.  2006. Protein expression profiles of early embryos- an important step in the right direction: just note quite ready for prime time. Letters to the Editor, Fertility and Sterility 86, 493-494.

“Radical Reactions Mediated by Cyclobutadieneiron Tricarbonyl” Byers, J. H.; Sontum, S. F.; Dimitrova, T. S.*; Huque, S.*; Zhang, Y.*; Zegarelli, B. M.*; Jasinski, J. P; Butcher, R. P. Organometallics 200625, 3787.

Senadheera, D.*, A. Lee, D. Hung, G. Spatafora, S. Goodman, and D. Cvitkovitch. 2006. The Streptococcus mutans vicX gene product modulates gtfB/C expression, biofilm formation, genetic competence and oxidative stress tolerance. J. Bacteriol. Accepted.

Rolerson, E., A. Swick, L. Newlon*, C. Palmer*, Y. Pan*, B. Keeshan*, and G. Spatafora2006. The SloR/Dlg metalloregulator modulates Streptococcus mutans virulence gene expression. J. Bacteriol. 188:5033-5044.


Combelles, C.M.H., and Racowsky, C. 2005. Assessing and optimizing oocyte quality during ART treatment. Seminars in Reproductive Medicine 3: 277-284.

Combelles, C.M.H., Orasanu, B., Ginsburg, E.S., and Racowsky, C. 2005. Optimum number of embryos to transfer in women more than 40 years of age undergoing treatment with assisted reproductive technologies. Fertility and Sterility 84: 1637-1642.

Ibanez, E., Sanfins, A., Combelles, C.M.H., Overstrom, E.W., and Albertini, D.F. 2005. Genetic strain variations in the metaphase-II phenotype of mouse oocytes matured in vivo or in vitroReproduction 130: 845-855.

Combelles, C.M.H., Albertini, D.F., Fissore, R.A., and Racowsky, C. 2005. In-vitro maturation of human oocytes and cumulus cells using a coculture three-dimensional collagen gel system. Human Reproduction 20: 1349-1358.

Sandwick, R.K., Johanson, M.*, Breuer, E.*, 2005. in The Maillard Reaction: Chemistry at the Interface of Nutrition, Aging, and Disease, Baynes, J., Monnier, V.M., Ames, J.M., and Thorpe, S.R. (eds), Annals of the New York Academy of Sciences, New York, 1043, 85 - 96

Senadheera, M.D., B. Guggenheim, G.A. Spatafora, Y.-C.C. Huang, J. Choi, D.C.I. Hung, J.S. Treglown, S.D. Goodman, R.P. Ellen and D.G. Cvitkovitch. 2005. A VicRK signal transduciton system in Streptococcus mutans affects gtfBCDgbpB, and ftf expression, biofilm formation, and genetic competence development. J. Bacteriol. 187:4064-4076.

Mahaffy, P. and C. Watters. 2005. Seeing and Understanding: Guiding Visualization Research in Science and Education. Paper presented to the Annual Meeting of Principal Investigators, NSF, Directorate of Education and Human Resources, Division of Research, Evaluation and Communication; Arlington VA, 8-9 December.

Watters, C., D. Guertin, D. Conache*, and D. Koparov*. 2005. Visualizing the Structure and Function of Integral Membrane Proteins. A poster presented to the Gordon Research Conference on Visualization in Science and Education, Queens College, Oxford University, 1-6 July 2005.


Cluss, R. G., Silverman*, D. A., and T. R. Stafford*. 2004. Extracellular secretion of the Borrelia burgdorferi Oms28 Porin and Bgp, a glycosaminoglycan binding protein. Infect. Immun. 62:6279-6286.

Combelles, C.M.H., Carabatsos, M.J. Kumar, T.R., Matzuk, M.M.M., and Albertini, D.F. 2004. Hormonal control of somatic cell polarity during ovarian follicle development. Molecular Reproduction and Development 69: 347-355.


Albertini, D.F., Sanfins, A., and Combelles, C.M.H. 2003. Origins and manifestations of oocyte maturation competencies. Reproductive BioMedicine Online 6: 410-415.

Combelles, C.M.H., Albertini, D.F., and Racowsky, C. 2003. Distinct microtubule and chromatin characteristics of human oocytes after failed in vivo and in vitro meiotic maturation. Human Reproduction 18: 2124-2130.

Racowsky, C., Combelles, C.M.H., Nureddin, A., Pan, Y., Finn, A., Miles, L., Gale, S., O’Leary, T., and Jackson, K.V. 2003. Day 3 and day 5 morphological predictors of embryo quality. Reproductive BioMedicine Online 6: 323-331.

Combelles, C.M.H., and Albertini, D.F. 2003. Assessment of oocyte quality following repeated gonadotropin stimulation in the mouse. Biology of Reproduction 68: 812-821.

Meola,M, Yamen,B., Weaver,K., and Sandwick,RK. (2003) “The Catalytic Effect of Mg2+ and Imidazole on the Decomposition of 5-Phosphoribosyl-a-1-pyrophosphate in Aqueous Solution” (in press)

Ward JO, Reinholdt LG, Hartford SA, Wilson LA, Munroe RJ, Schimenti KJ, Libby BL, O’Brien M, Pendola JK, Eppig J and Schimenti JC. 2003. Toward the genetics of mammalian reproduction: Induction and mapping of gametogenesis mutants in mice. Biol Reprod. 69:1615-1625


Combelles, C.M.H., Cekleniak, N.A., Racowsky, C., and Albertini, D.F. 2002. Assessment of nuclear and cytoplasmic maturation in in-vitro matured human oocytes. Human Reproduction 17: 1006-1016.

Spatafora, G., N. Van Hoeven*, K. Wagner and P. Fives-Taylor. 2002. Evidence that ORF3 at the S. parasanguis fimA locus codes for a thiol-specific antioxidant. Microbiology 148:755-762.


Combelles, C.M.H., and Albertini, D.F. 2001. Microtubule patterning during meiotic maturation in mouse oocytes is determined by cell cycle-specific sorting and redistribution of ?-tubulin. Developmental Biology 239: 281-294.

Albertini, D.F., Combelles, C.M.H., Benecchi, E., and Carabatsos, M.J. 2001. Cellular basis for paracrine regulation of ovarian follicle development. Reproduction 121: 647-653.

Cekleniak, N.A., Combelles, C.M.H., Ganz, D.A., Fung, J., Albertini, D.F., and Racowsky, C. 2001. A novel system for in vitro maturation of human oocytes. Fertility and Sterility 75: 1185-1193.

Spatafora, G., M. Moore*, S. Landgren, E. Stonehouse* and S. Michalek. 2001. Expression of S. mutans fimA is iron-responsive and regulated by a DtxR homolog. Microbiology 147:1599-1610.

Ward JO, McConnell M, Licht J, Freedman LP. 2001. The acute promyelocytic leukemia-associated protein, promyelocytic leukemia zinc finger, regulates 1,25-dihydroxyvitamin D3-induced monocytic differentiation of U937 cells through a physical interaction with vitamin D3 receptor. Blood. 98:3290-3300.


Combelles, C.M.H., Carabatsos, M.J., London, S.N., Mailhes, J.B., and Albertini, D.F. 2000. Centrosome-specific perturbations during in vitro maturation of mouse oocytes exposed to cocaine. Experimental Cell Research 260: 116-126.

Carabatsos, M.J., Combelles, C.M.H., Messinger, S.M., and Albertini, D.F. 2000. Sorting and reorganization of centrosomes during oocyte maturation in the mouse. Microscopy and Research Techniques 49: 435-444.

Dennis, A., Puskas, M., Stasaitis, S., and Sandwick, R.K. (2000) “The Formation of a 1-5 Phosphodiester Linkage in the Spontaneous Breakdown of 5-Phosphoribosyl-a-1-Pyrophosphate”, J. Inorg. Biochem., 81, 73 - 80