Faculty & Student Publications

The faculty members forming the Biochemistry Program at Villanova University are a community of scholars.  In many cases below, the publications reflect collaboration between our faculty and Villanova students.   Villanova faculty members are in bold and underlined,  Villanova Biochemistry undergraduate coauthors (including BS/MS students) are in red, and Villanova graduate coauthors are in blue

  • Lang, Melissa A., Sultan A. Jenkins, Phillip Balzano, Adeyinka Owoyele, Akshay Patel, and Anil K. Bamezai. “Engaging Ly-6A/Sca-1 Triggers Lipid Raft-Dependent and -Independent Responses in CD4(+) T-Cell Lines.” Immunity, Inflammation and Disease, June 28, 2017. 
  • Murphy, Tami, Heather Melville, Eliza Fradkin, Giana Bistany, Gregory Branigan, Kelly Olsen, Catharine R. Comstock, Hayley Hanby, Ellie Garbade, and Angela J. DiBenedetto. “Knockdown of Epigenetic Transcriptional Co-Regulator Brd2a Disrupts Apoptosis and Proper Formation of Hindbrain and Midbrain-Hindbrain Boundary (MHB) Region in Zebrafish.” Mechanisms of Development 146 (August 2017): 10–30.    
  • Shirangi T. "Motor Control: Winging It with a Few Good Muscles.” Current Biology 27, no. 3 (2017): R115–16. 

 

 

  • Coldren GA, Barreto CR, Wykoff DD, Morrissey EM, Langley JA, Feller IC, and Chapman SK. “Chronic Warming Stimulates Growth of Marsh Grasses More than Mangroves in a Coastal Wetland Ecotone.” Ecology 97, no. 11 (2016): 3167–75. doi:10.1002/ecy.1539.
  • Jones, Morgan A., Sean DeWolf, Vimvara Vacharathit, Michelle Yim, Stacey Spencer, and Anil K. Bamezai. “Investigating B Cell Development, Natural and Primary Antibody Responses in Ly-6A/Sca-1 Deficient Mice.” PloS One 11, no. 6 (2016): e0157271.
  • Iosue, Christine L., Nicholas Attanasio, Noor F. Shaik, Erin M. Neal, Sarah G. Leone, Brian J. Cali, Michael T. Peel, Amanda M. Grannas, and Dennis D. Wykoff. “Partial Decay of Thiamine Signal Transduction Pathway Alters Growth Properties of Candida Glabrata.” PloS One 11, no. 3 (2016): e0152042.
  • Reichard, Eden L., Giavanna G. Chirico, William J. Dewey, Nicholas D. Nassif, Katelyn E. Bard, Nickolas E. Millas, and Daniel A. Kraut. “Substrate Ubiquitination Controls the Unfolding Ability of the Proteasome.” The Journal of Biological Chemistry 291, no. 35 (August 26, 2016): 18547–61.
  • Herman, Allison, Jacquelyn Serfecz, Alexandra Kinnally, Kathleen Crosby, Matthew Youngman, Dennis Wykoff, and James W. Wilson. “The Bacterial iprA Gene Is Conserved across Enterobacteriaceae, Is Involved in Oxidative Stress Resistance, and Influences Gene Expression in Salmonella Enterica Serovar Typhimurium.” Journal of Bacteriology 198, no. 16 (August 15, 2016): 2166–79.

 

Kemmerer ZAAder NR, Mulroy SS, & Eggler AL (2015) Comparison of human Nrf2 antibodies: A tale of two proteins. Toxicol. Lett. 238(2): 83–89.

Orlando KA, Iosue CL, Leone SG, Davies DL & Wykoff DD. (2015) A paralog of the phosphomutase-like gene family in Candida glabrata, CgPmu2, gained broad-range phosphatase activity due to a small number of clustered substitutions. Biochemical Journal 471(2):187-198.

Cangelosi C, Hannagan S, Santiago CP & Wilson JW (2015) Transfer of the cloned Salmonella SPI-1 type III secretion system and characterization of its expression mechanisms in Gram negative bacteria in comparison with cloned SPI-2. Microbiol Res.

Johnston EK, Francis MK, & Knepper JE (2015) Recombinant pigment epithelium-derived factor PEDF binds vascular endothelial growth factor receptors 1 and 2. In vitro cellular & developmental biology. Animal.

 (2015) Gupta K & Selinsky BSBacterial and algal orthologs of prostaglandin H(2)synthase: novel insights into the evolution of an integral membrane protein. Biochimica et biophysica acta 1848(1 Pt A):83-94.

 (2015) Estill M, Kerwin-Iosue CL, & Wykoff DDDissection of the PHO pathway in Schizosaccharomyces pombe using epistasis and the alternate repressor adenine. Current genetics 61(2):175-183.

Schieffer D, Naware S, Bakun W, & Bamezai AK (2014) Lipid raft-based membrane order is important for antigen-specific clonal expansion of CD4(+) T lymphocytes. BMC immunology 15(1):58.

Youngman EM & Claycomb JM (2014) From early lessons to new frontiers: the worm as a treasure trove of small RNA biology. Frontiers in genetics 5:416.

Soni A, O'Sullivan L, Quick LN, Ott CM, Nickerson CA, & Wilson JW. (2014) Conservation of the Low-shear Modeled Microgravity Response in Enterobacteriaceae and Analysis of the trp Genes in this Response. The open microbiology journal 8:51-58.

Solomon L, Shah A, Hannagan S, & Wilson JW (2014) Bacterial genus-specific tolerance for YdcI expression. Current microbiology 69(5):640-648.

Nassif NDCambray SE, & Kraut DA (2014) Slipping up: partial substrate degradation by ATP-dependent proteases. IUBMB life 66(5):309-317.

Fuxreiter M, Toth-Petroczy A, Kraut DA, Matouschek AT, Lim R, Xue B, Kurgan L, & Uversky, V. N. (2014) Disordered Proteinaceous Machines. Chemical reviews.

Desmond ME, Knepper JEDiBenedetto AJ, Malaugh E, Callejo S, Carretero R, Alonso MI, Gato A. (2014) Focal adhesion kinase as a mechanotransducer during rapid brain growth of the chick embryo. The International journal of developmental biology 58(1):35-43.

Larru B, Eby J*, & Lowenthal ED (2014) Antiretroviral treatment in HIV-1 infected pediatric patients: focus on efavirenz. Pediatric health, medicine and therapeutics 5:29-42.

(*This work was carried out by Biochemistry major Ms. Jessica Eby while working in a research lab at the University of Pennsylvania. Authors Larru and Lowenthal are from UPenn)

Crabbe A, Nielsen-Preiss SM, Woolley, CM, Barrila J, Buchanan K, McCracken J, Inglis DO, Searles SC, Nelman-Gonzalez MA, Ott CM, Wilson JW, Pierson DL, Stefanyshyn-Piper HM, Hyman LE & Nickerson CA. (2013) Spaceflight enhances cell aggregation and random budding in Candida albicans. PloS one 8(12):e80677.

Cangelosi C, Shank C, Santiago C, & Wilson JW (2013) Engineering large functional plasmids for biosafety. Plasmid 70(3):385-392.

Corrigan MW, Kerwin-Iosue CL, Kuczmarski AS, Amin KB, & Wykoff DD (2013) The Fate of Linear DNA in Saccharomyces cerevisiae and Candida glabrata: The Role of Homologous and Non-Homologous End Joining. PloS one 8(7):e69628.

Kraut DA (2013) Slippery substrates impair ATP-dependent protease function by slowing unfolding. The Journal of biological chemistry 288(48):34729-34735.

Turlington M, Chun A, Tomar S, Eggler A, Grum-Tokars V, Jacobs J, Daniels JS, Dawson E, Saldanha A, Chase P, Baez-Santos YM, Lindsley CW, Hodder P, Mesecar, AD, Stauffer, S. R., et al. (2013) Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: identification of ML300 and noncovalent nanomolar inhibitors with an induced-fit binding. Bioorganic & medicinal chemistry letters 23(22):6172-6177.

Eggler AL and Savinov SN (2013) Chemical and biological mechanisms of phytochemical activation of NRF2 and importance in disease prevention. 50 years of phytochemistry research, Recent advances in phytochemistry, ed. Gang DR (Springer International Publishing), 43:121-155.

Jacobs J, Grum-Tokars V, Zhou Y, Turlington M, Saldanha SA, Chase P, Eggler A, Dawson ES, Baez-Santos YM, Tomar S, Mielech AM, Baker SC, Lindsley CW, Hodder P, Mesecar A, & Stauffer SR (2013) Discovery, synthesis, and structure-based optimization of a series of N-(tert-butyl)-2-(N-arylamido)-2-(pyridin-3-yl) acetamides (ML188) as potent noncovalent small molecule inhibitors of the severe acute respiratory syndrome coronavirus (SARS-CoV) 3CL protease. Journal of medicinal chemistry 56(2):534-546.

Tessema TD, Gassler F, Shu Y, Jones S, & Selinsky BS (2013) Structure-activity relationships in aminosterol antibiotics: the effect of stereochemistry at the 7-OH group. Bioorganic & medicinal chemistry letters 23(11):3377-3381.

Wilson JW, CP Santiago, J Serfecz, and LN Quick. 2013. Recombineering and conjugation as tools for targeted genomic cloning. In "Genetic Manipulation of DNA and Protein - Examples from Current Research", ed. Dr. David Figurski, InTech Publishing.

Carter-O'Connell I, Peel MTWykoff DD, & O'Shea EK (2012) Genome-wide characterization of the phosphate starvation response in Schizosaccharomyces pombe. BMC genomics 13:697.

Comber JD & Bamezai AK (2012) In vitro derivation of interferon-gamma producing, IL-4 and IL-7 responsive memory-like CD4(+) T cells. Vaccine 30(12):2140-2145.

Gu W, Lee HC, Chaves D, Youngman EM, Pazour GJ, Conte D, Jr., & Mello CC (2012) CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors. Cell 151(7):1488-1500.

Hu C, Nikolic D, Eggler AL, Mesecar AD, & van Breemen RB (2012) Screening for natural chemoprevention agents that modify human Keap1. Analytical biochemistry 421(1):108-114.

Jennings ME, Quick LN, Ubol N, Shrom S, Dollahon N, & Wilson JW (2012) Characterization of Salmonella type III secretion hyper-activity which results in biofilm-like cell aggregation. PloS one 7(3):e33080.

Kerwin CL & Wykoff DD (2012) De novo generation of a phosphate starvation-regulated promoter in Candida glabrata. FEMS yeast research 12(8):980-989.

Kraut DA, Israeli E, Schrader EK, Patil A, Nakai K, Nanavati D, Inobe T, & Matouschek A (2012) Sequence- and species-dependence of proteasomal processivity. ACS chemical biology 7(8):1444-1453.

Lee HC, Gu W, Shirayama M, Youngman E, Conte D, Jr., & Mello CC (2012) C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts. Cell 150(1):78-87.

Liu W, Das A, Morales R, Banday M, Aris V, Lukac DM, Soteropoulos P, Wah DA, Palenchar J, & Bellofatto V (2012) Chromatin immunoprecipitation and microarray analysis reveal that TFIIB occupies the SL RNA gene promoter region in Trypanosoma brucei chromosomes. Molecular and biochemical parasitology 186(2):139-142.

Ott, CM, A Crabbé, JW Wilson, J Barrila, SL Castro, and CA Nickerson. 2012. Microbial stress: spaceflight-induced alterations in microbial virulence and infectious disease risks for the crew. In "Stress Challenges and Immunity in Space", ed. A. Chouker. Springer Press, Inc. Pages 203-226.

Palenchar PM Palenchar JB (2012) The evolution of metabolic enzymes in Plasmodium and trypanosomatids as compared to Saccharomyces and Schizosaccharomyces. Molecular and biochemical parasitology 184(1):13-19.

Solnoki KWSing AHSofa CJMiller ROgorzalek PAPenek HV, & Palenchar JB (2012) TbENF is an essential TbTFIIB-interacting trypanosomatid-specific factor. Molecular and biochemical parasitology 181(2):94-101.

Crabbe A, MJ Schurr, P Monsieurs, J Schurr, JW Wilson, CM Ott, et. al. 2011. Transcriptional and proteomic responses of Pseudomonas aeruginosa PAO1 to spaceflight conditions involve Hfq regulation and reveal a role for oxygen. Appl. Environ. Microbiol. 77(4):1221-30

Henry TCPower JE, Kerwin CL, Mohammed A, Weissman JS, Cameron DM, & Wykoff DD (2011) Systematic screen of Schizosaccharomyces pombe deletion collection uncovers parallel evolution of the phosphate signal transduction pathway in yeasts. Eukaryotic cell 10(2):198-206.

Jennings ME, Quick LN, Soni A, Davis RR, Crosby K, Ott CM, Nickerson CA, and JW Wilson. 2011. Characterization of the Salmonella enterica Serovar Typhimurium ydcI Gene, Which Encodes a Conserved DNA Binding Protein Required for Full Acid Stress Resistance. J. Bacteriol. 193(9):2208-17.

Kennedy C, Nelson MD, & Bamezai AK (2011) Analysis of detergent-free lipid rafts isolated from CD4+ T cell line: interaction with antigen presenting cells promotes coalescing of lipid rafts. Cell communication and signaling : CCS 9(1):31.

Middler SL, Gomez S, Parker CD, & Palenchar PM (2011) The effects of combinatorial treatments with stress inducing molecules on growth of E. coli colonies. Current microbiology 63(6):588-595.

Santiago CP, LN Quick, and JW Wilson. 2011. Self-transmissible IncP R995 plasmids with alternative markers and utility for Flp/FRT cloning strategies. J. Microbiol. Biotechnol. 21(11):1123-1126.

Shah TD, Hickey MC, Capasso KE, & Palenchar JB (2011) The characterization of a unique Trypanosoma brucei beta-hydroxybutyrate dehydrogenase. Molecular and biochemical parasitology 179(2):100-106.

Youngman MJ, Rogers ZN, & Kim DH (2011) A decline in p38 MAPK signaling underlies immunosenescence in Caenorhabditis elegans. PLoS genetics 7(5):e1002082.

Kraut DA, Yu H, & Matouschek A (2011) How ClpX unfolds GFP in stages by pulling. Journal of molecular biology 413(1):1-3.

Kraut DA & Matouschek A (2011) Proteasomal degradation from internal sites favors partial proteolysis via remote domain stabilization. ACS chemical biology 6(10):1087-1095

Orkwis BRDavies DL, Kerwin CL, Sanglard D, & Wykoff DD (2010) Novel acid phosphatase in Candida glabrata suggests selective pressure and niche specialization in the phosphate signal transduction pathway. Genetics 186(3):885-895

O'Sullivan LE, CA Nickerson, and JW Wilson. (2010) A series of IncQ-based reporter plasmids for use in a range of Gram negative genera. J. Microbiol. Biotechnol. 20(5):871-874.

Quick LN, A Shah, and JW Wilson. 2010. A series of vectors with alternative antibiotic resistance markers for use in lambda Red recombination. J. Microbiol. Biotechnol. 20(4):666-9.

Radtke AL, JW Wilson, S. Sarker, and C.A. Nickerson. 2010. Analysis of interactions of Salmonella type III secretion mutants with 3-D intestinal epithelial cells. PLoS ONE. 5(12):e15750.

Small E, Eggler A, & Mesecar AD (2010) Development of an efficient E. coli expression and purification system for a catalytically active, human Cullin3-RINGBox1 protein complex and elucidation of its quaternary structure with Keap1. Biochemical and biophysical research communications 400(4):471-475

Vasale, JJ, Gu W, Thivierge C, Batista PJ, Claycomb JM, Youngman EM, Duchaine TF, Mello CC, Conte D, Jr. (2010) Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in the ERGO-1/Argonaute pathway. Proceedings of the National Academy of Sciences of the United States of America107(8):3582-3587.

Kane LA, Youngman MJ, Jensen RE, & Van Eyk JE (2010) Phosphorylation of the F(1)F(o) ATP synthase beta subunit: functional and structural consequences assessed in a model system. Circulation research 106(3):504-513.

Kraut DA & Matouschek A (2010) Pup grows up: in vitro characterization of the degradation of pupylated proteins. The EMBO journal 29(7):1163-1164.

Kraut DA, Sigala PA, Fenn TD, & Herschlag D (2010) Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole. Proceedings of the National Academy of Sciences of the United States of America 107(5):1960-1965.

Banerjee H, Palenchar JB, Lukaszewicz M, Bojarska E, Stepinski J, Jemielity J, Guranowski A, Ng S, Wah DA, Darzynkiewicz E, & Bellofatto V (2009) Identification of the HIT-45 protein from Trypanosoma brucei as an FHIT protein/dinucleoside triphosphatase: substrate specificity studies on the recombinant and endogenous proteins. RNA 15(8):1554-1564.

Ibrahim BS, Kanneganti N, Rieckhof GE, Das A, Laurents DV, Palenchar JB, Bellofatto V, & Wah DA (2009) Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei. Proceedings of the National Academy of Sciences of the United States of America106(32):13242-13247.

Kerwin CL & Wykoff DD (2009) Candida glabrata PHO4 is necessary and sufficient for Pho2-independent transcription of phosphate starvation genes. Genetics 182(2):471-479.

Stomel, J.M., J.W. Wilson, M.A. Leon, P. Stafford, and J.C. Chaput. 2009. A man-made ATP-binding protein evolved independently of nature causes abnormal growth in bacterial cells. PLoS ONE. 4(10):7385.

Timakhov RA, Tan Y, Rao M, Liu Z, Altomare DA, Pei J, Wiest DL, Favorova OO, Knepper JE, & Testa JR (2009) Recurrent chromosomal rearrangements implicate oncogenes contributing to T-cell lymphomagenesis in Lck-MyrAkt2 transgenic mice. Genes, chromosomes & cancer 48(9):786-794.

Gu W, Shirayama M, Conte D, Jr, Vasale J, Batista PJ, Claycomb, JM, Moresco JJ, Youngman EM, Keys J, Stoltz MJ, Chen CC, Chaves DA, Duan S, Kasschau KD, Fahlgren N, Yates JR, 3rd, Mitani S, Carrington JC, Mello CC. (2009) Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Molecular cell36(2):231-244.

Schwans JP, Kraut DA, & Herschlag D (2009) Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase. Proceedings of the National Academy of Sciences of the United States of America 106(34):14271-14275.

Koodathingal P, Jaffe NE, Kraut DA, Prakash S, Fishbain S, Herman C, Matouschek A. (2009) ATP-dependent proteases differ substantially in their ability to unfold globular proteins. The Journal of biological chemistry 284(28):18674-18684.

Villanova Biochemistry at a Glance

mendel science center

Degrees Offered: BS

Core Faculty: 14

Undergraduate Majors: 100 (each incoming class has approximately 25 students)

Equipment: Complete array of modern instrumentation.

Building:  Mendel Science Center

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