Student Publications

2012

Grant TJ, Bishop JA, Christadore LM, Barot G, Chin HG, Woodson S, Kavouris J, Siddiq A, Gredler R, Shen XN, Sherman J, Meehan T, Fitzgerald K, Pradhan S, Briggs LA, Andrews WH, Sarkar D, Schaus SE, Hansen U. (2012). Antiproliferative small molecule inhibitors of the transcription factor LSF reveal oncogene addiction in hepatocellular carcinoma. Proceedings of the National Academy of Sciences, U.S.A., 109:4503-4508.

Youngblut, M., Judd, E. T., Srajer, V., Sayyed, B., Goelzer, T., Elliott, S. J., Schmidt, M., and Pacheco, A. A. (2012) Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system, J Biol Inorg Chem 17, 647-662.

Russell MK, Longoni M, Wells J, Maalouf FI, Tracy AA, Loscertales M, Ackerman KG, Pober BR, Lage K, Bult CJ, Donahoe PK. Congenital diaphragmatic hernia candidate genes derived from embryonic transcriptomes. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2978-83. Epub 2012 Feb 6. PubMed PMID: 22315423; PubMed Central PMCID: PMC328694

Vega, N. M., K. R. Allison, A. S. Khalil. J. J. Collins. (2012). “Signaling-mediated bacterial persister formation.” Nat Chem Biol 8(5): 431-433.

Foti JJ, Devadoss B, Winkler JA, Collins JJ, Walker GC. Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics. Science. 2012 Apr 20; 336(6079):315-9.

2011

Wang H, Guan S, Quimby A, Cohen-Karni D, Pradhan S, Wilson G, Roberts RJ, Zhu Z, Zheng Y. Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine. Nucleic Acids Res. 2011 Nov;39(21):9294-305.

Cohen-Karni D, Xu D, Apone L, Fomenkov A, Sun Z, Davis PJ, Kinney SR, Yamada-Mabuchi M, Xu SY, Davis T, Pradhan S, Roberts RJ, Zheng Y. The MspJI family of modification-dependent restriction endonucleases for epigenetic studies. Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11040-5.

Callard GV, Tarrant AM, Novillo A, Yacci P, Ciaccia L, Vajda S, Chuang GY, Kozakov D, Greytak SR, Sawyer  S, Hoover C, Cotter KA. 2011. Evolutionary origins of the estrogen signaling system: Insights from amphioxus. J Steroid Biochem Mol Biol. [Epub ahead of print].

Doloff JC, Jounaidi Y, and Waxman DJ. 2011. Dual E1A oncolytic adenovirus: Targeting tumor heterogeneity with two independent cancer-specific promoter elements, DF3/MUC1 and hTERT. Cancer Gene Therapy, Mar; 18(3): 153-66

Doloff JC, Jounaidi Y, Waxman DJ. Dual E1A oncolytic adenovirus: targeting tumor heterogeneity with two independent cancer-specific promoter elements, DF3/MUC1 and hTERT. Cancer Gene Ther. 2011 Mar;18(3):153-66. Epub 2010 Sep 24. Erratum in: Cancer Gene Ther. 2011 Mar;18(3):228. Jounaidi, Y [added]. PubMed PMID: 20865021; PubMed Central PMCID: PMC3010505.

Ma J, Chen CS, Blute T, Waxman DJ. Antiangiogenesis enhances intratumoral drug retention. Cancer Res. 2011 Apr 1;71(7):2675-85. Epub 2011 Mar 29. PubMed PMID: 21447737; PubMed Central PMCID: PMC3070759..

Terragni J, Nayak G, Banerjee S, Medrano JL, Graham JR, Brennan JF, Sepulveda S, Cooper GM. The E-box binding factors Max/Mnt, MITF, and USF1 act coordinately with FoxO to regulate expression of proapoptotic and cell cycle control genes by phosphatidylinositol 3-kinase/Akt/glycogen synthase kinase 3 signaling. J Biol Chem. 2011 Oct 21;286(42):36215-27.

Tullai, J.W., Tacheva, S., Owens, L.J., Graham, J.R. and Cooper, G.M. 2011. AP-1 is a component of the transcriptional network regulated by GSK-3 in quiescent cells. PLoS ONE 6:e20150.

Kielbasa OM, Reynolds JG, Wu CL, Snyder CM, Cho MY, Weiler H, Kandarian S, Naya FJ. 2011. Myospryn is a calcineurin-interacting protein that negatively modulates slow-fiber-type transformation and skeletal muscle regeneration. FASEB J. 2011 Mar 22. [Epub ahead of print].

Santos G., Giuliani, M.,  Pizza, M., Rappuoli, R.,  Donnelly, J.   Determination of serum bactericidal titers against group B meningococcus by flow cytometry using fluorescent viability dyes. 11th Meeting of the European Monitoring Group on Meningococci, p. 159, 2011

Tanner, E.A., Blute, T.A. Brachmann, C.B. and McCall, K.  (2011)  Bcl-2 proteins and autophagy regulate mitochondrial dynamics during programmed cell death in the Drosophila ovary. Development 138: 327-338.  *Highlighted article “In This Issue.”

Tanner, E.A. and McCall, K.  (2011) Mitochondrial regulation of cell death in the Drosophila ovary. Autophagy, in press.

Garbati MR, Thompson RC, Haery L, Gilmore TD. A rearranged EP300 gene in the human B-cell lymphoma cell line RC-K8 encodes a disabled transcriptional co-activator that contributes to cell growth and oncogenicity. Cancer Lett. 2011 Mar 1;302(1):76-83. Epub 2011 Jan 12.

Thompson RC, Herscovitch M, Zhao I, Ford TJ, Gilmore TD.NF-kappaB down-regulates expression of the B-lymphoma marker CD10 through a miR-155/PU.1 pathway.
J Biol Chem. 2011 Jan 21;286(3):1675-82. Epub 2010 Oct 14.

2010

Wanunu M, Cohen-Karni D, Johnson RR, Fields L, Benner J, Peterman N, Zheng Y, Klein ML, Drndic M. Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules.  J Am Chem Soc. 2010 Dec 14. [Epub ahead of print]

Zheng Y, Cohen-Karni D, Xu D, Chin HG, Wilson G, Pradhan S, Roberts RJA unique family of Mrr-like modification-dependent restriction endonucleases. Nucleic Acids Res. 2010 Sep;38(16):5527-34.

Swanson HI, Njar VCO, Yu Z, Castro DJ, Gonzalez FJ, Williams DE, Huang Y, Kong AT, Doloff JC, Ma J, Waxman DJ, and Scott EE. 2010. Targeting drug-metabolizing enzymes for effective chemoprevention and chemotherapy.  Drug Metabolism and Disposition. Apr; 38(4): 539-44.

Doloff JC, Su T, and Waxman DJ. 2010. Adenoviral delivery of pan-caspase inhibitor p35 enhances bystander killing by P450 gene-directed enzyme prodrug therapy using cyclophosphamide. BMC Cancer, Sep; 10(1): 487.

Graham, J.R., Tullai, J.R. and Cooper, G.M. 2010. GSK-3 represses growth factor-inducible genes by inhibiting NF-kB in quiescent cells. J. Biol. Chem. 285: 4472-4480.  PMC2836053

Saxena, U.H., Owens, L., Graham, J.R. Cooper, G.M. and Hansen, U. 2010. Prolyl isomerase Pin1 regulates transcription factor LSF (TFCP2) by facilitating dephosphorylation at two serine-proline motifs.  J. Biol. Chem. 285: 31139-31147.  PMC2951187

Graham, J.R., Hendershott, M.C., Terragni, J. and Cooper, G.M. 2010.  mRNA degradation plays a significant role in the program of gene expression regulated by phosphatidylinositol 3-kinase signaling.  Mol. Cell. Biol. 30: 5295-5305.  PMC2976374

McCalmon, S.A., D. Desjardins, S. Ahmad, K. Davidoff, C.M. Snyder, K. Sato, K. Ohashi, O. Kielbasa, M. Mathew, E.P. Ewen, H. Gavras, K. Walsh, and F.J. Naya. 2010. Modulation of angiotensin II-mediated cardiac remodeling by the MEF2A target gene Xirp2. Circ Res. 106(5): 952-60.

Vetterkind, S. Lee E, Sundberg E, Poythress RH, Tao TC, Preuss U, Morgan KG. Par-4: a new activator of myosin phosphotase. Mol Bio Cell, 2010. 1214-24
Santos G.F., Jimenez M., Goodman, R., Giuliani, M.,  Pizza, M., Rappuoli, R.,  Donnelly, J.  Use of immunoglobulin depletion to develop a universal complement source for use in the meningococcal bactericidal assay.  16th  International Pathogenic Neisseria conference, p. 170, 2010.

2009

Doloff JC, Khan N, Ma J, Demidenko E, Swartz HM, and Jounaidi Y. 2009. Increased tumor oxygenation and drug uptake during anti-angiogenic weekly low dose cyclophosphamide enhances the anti-tumor effect of weekly tirapazamine. Current Cancer Drug Targets. Sep; 9(6): 777-88.

Ma J, Waxman DJ. Dominant effect of antiangiogenesis in combination therapy involving cyclophosphamide and axitinib. Clin Cancer Res. 2009; 15(2):578-88.

Repetny KJ, Zhou X, Holodick NE, Rothstein TL, Hansen U. Binding of LBP-1a to specific immunoglobulin switch regions in vivo correlates with specific repression of class switch recombination. Eur J Immunol, 2009; 39:1387-1394.

Bass, B.P., Tanner, E.A., Mateos San Martín, D., Blute, T., Kinser, R.D., Dolph, P.J. and McCall, K. Cell-autonomous requirement for DNaseII in non-apoptotic cell death, Cell Death and Differentiation 2009, in press.

Pritchett, T.L., Tanner, E.A. and McCall, K. Cracking open cell death in the Drosophila ovary, Apoptosis, 2009, in press; invited review

Hansen U, Owens L, Saxena UH Transcription factors LSF and E2Fs: Tandem cyclists driving G0 to S? Cell Cycle 2009, in press; invited review.

Potter, D.R., Jiang, J. & Damiano, E.R. The recovery time course of the endothelial-cell glycocalyx in vivo and its implications in vitro. Circulation Research 2009; in press, invited manuscript.

2008

Terragni J, JR Graham, KW Adams, MW Schaffer, JW Tullai & GM Cooper. 2008. Phosphatidylinositol 3-kinase signaling in proliferating cells maintains an anti-apoptotic transcriptional program mediated by inhibition of FOXO and non-canonical activation of NF-kB transcription factors. BMC Cell Biology 9: 6

Doloff JC, Waxman DJ, & Jounaidi Y. hTERT-promoter driven oncolytic adenovirus with E1B-19 kDa and E1B-55 kDa gene deletions. Human Gene Therapy 2008; 19: 1383-1399

Chin M, Herscovitch M, Zhang N, Waxman DJ, Gilmore TD. Overexpression of an activated REL mutant increases the transformed state of BJAB human B-cell lymphoma cells and alters their gene expression profile. Oncogene. 28: 2100-2111

Holloway MG, Miles GD, Dombkowski AA, Waxman DJ. Liver-specific hepatocyte nuclear factor-4alpha deficiency: greater impact on gene expression in male than in female mouse liver. Mol Endocrinol. 2008; 22(5):1274-86.

Ma J, Waxman DJ. Combination of antiangiogenesis with chemotherapy for more effective cancer treatment. Mol Cancer Ther. 2008; 7(12):3670-84. Review.

Herscovitch M, W Comb, T Ennis, K Coleman, S Yong, B Armstead, D Kalaitzidis, S Chandani & TD Gilmore. 2008. Intermolecular disulfide bond formation in the NEMO dimer requires Cys54 and Cys347. Biochemical and Biophysical Research Communications 367: 103-108

Holloway MG, GD Miles, AA Dombkowski & DJ Waxman. 2008. Liver-specific HNF4{alpha}-deficiency: greater impact on gene expression in male than in female mouse liver. Molecular Endocrinology, in press

Ma J & DJ Waxman. 2008. Modulation of the antitumor activity of metronomic cyclophosphamide by the angiogenesis inhibitor axitinib. Molecular Cancer Therapeutics 7: 79-89

Reynolds JG, SA McCalmon, JA Donaghey & FJ Naya. 2008. Deregulated PKA signaling and myospryn expression in muscular dystrophy. Journal of Biological Chemistry, 283: 8070-8074

2007

Andken BB, I Lim, G Benson, JJ Vincent, MT Ferenc, B Heinrich, LA Jarzylo, HY Man & JO Deshler. 2007. 3′-UTR SIRF: a database for identifying clusters of short interspersed repeats in 3′ untranslated regions. BMC Bioinformatics 8: 274

Adams KW & GM Cooper. 2007. Rapid turnover of Mcl-1 couples translation to cell survival and apoptosis. Journal of Biological Chemistry 282: 6192-6200

Bass BP, K Cullen & K McCall. 2007. The axon guidance gene lola is required for programmed cell death in the Drosophila ovary. Developmental Biology 304: 771-785

Baum JS, E Arama, H Steller & K McCall. 2007. The Drosophila caspases Strica and Droncfunction redundantly in programmed cell death during oogenesis. Cell Death and Differentiation 14: 1508-1517

Jounaidi Y, Doloff JC, Waxman DJ. 2007. Conditionally replicating adenoviruses for cancer treatment. Current Cancer Drug Targets. 7(3): 285-301

Clodfelter KH, GD Miles, V Wauthier, MG Holloway, X Zhang, P Hodor, WJ Ray & DJ Waxman. 2007. Role of STAT5a in regulation of sex-specific gene expression in female but not male mouse liver revealed by microarray analysis. Physiological Genomics 31: 63-74

Holloway MG, Y Cui, EV Laz, A Hosui, L Hennighausen & DJ Waxman. 2007. Loss of sexually dimorphic liver gene expression upon hepatocyte-specific deletion of Stat5a-Stat5b locus. Endocrinology 148 1977-1986

Laz EV, MG Holloway, CS Chen & DJ Waxman. 2007. Characterization of three growth hormone-responsive transcription factors preferentially expressed in adult female liver. Endocrinology 148: 3327-3337

Ma J & DJ Waxman. 2007. Collaboration between hepatic and intratumoral prodrug activation in a P450 prodrug-activation gene therapy model for cancer treatment. Molecular Cancer Therapeutics 6: 2879-2890

O’Lone R, K Knorr, IZ Jaffe, ME Schaffer, PGV Martini, RH Karas, J Bienkowska, ME Mendelsohn & U Hansen. 2007. Estrogen receptors alpha and beta mediate distinct pathways of vascular gene expression, including genes involved in mitochondrial electron transport and generation of reactive oxygen species. Molecular Endocrinology 21:1281-1296

Peterson JS, BP Bass, D Jue, A Rodriguez, JM Abrams & K McCall. 2007. Non-canonical cell death pathways function in Drosophila oogenesis. Genesis 45: 396-404

Pezza JA, JD Stopa, EM Brunyak, KN Allen & DR Tolan. 2007. Thermodynamic analysis shows conformational coupling and dynamics confer substrate specificity in fructose-1,6-bisphosphate aldolase. Biochemistry 46: 13010-13018

Reynolds JG, SA McCalmon, T Tomczyk & FJ Naya. 2007. Identification and mapping of protein kinase A binding sites in the costameric protein myospryn. Biochimica Biophysica Acta 1773: 891-902

Starczynowski DT, H Trautman, C Pott, L Harder, N Arnold, JA Africa, JR Leeman, R Seibert & TD Gilmore. 2007. Mutation of an IKK phosphorylation site within the transactivation domain of REL in two patients with human B-cell lymphoma enhances REL’s in vitro transforming activity. Oncogene 26: 2685-2694

Sullivan JC, D Kalaitzidis, TD Gilmore & JR Finnerty. 2007. Rel homology domain-containing transcription factors in the cnidarian Nematostella vectensis. Development Genes and Evolution 217: 63-72

Tullai JW, J Chen, ME Schaffer, E Kamenetsky, S Kasif & GM Cooper. 2007. GSK-3b mediates repression of CREB target genes in quiescent cells. Journal of Biological Chemistry 282: 9482-9491

Tullai JW, ME Schaffer, S Mullenbrock, G Sholder, S Kasif & GM Cooper. 2007. Immediate-early and delayed primary response genes are distinct in function and genomic architecture. Journal of Biological Chemistry 282: 23981-23995

2006

Clodfelter KH, MG Holloway, P Hodor, SH Park, WJ Raj & DJ Waxman. 2006. Sex-dependent liver gene expression is extensive and largely dependent upon signal transducer and activator of transcription 5b (STAT5b): STAT5b-dependent activation of male genes and repression of female genes revealed by microarray analysis. Molecular Endocrinology 20: 1333-1351

Cronin MA , Lieu M-H, Tsunoda S: Two Stages of Light-Dependent TRPL-Channel Translocation in Drosophila Photoreceptors. J Cell Sci. 2006; 119:2935-2944.

Durham, J. T., O. M. Brand, M. Arnold, J. G. Reynolds , L. Muthukumar, H. Weiler, J. A. Richardson, and F. J. Naya. 2006. Myospryn is a direct transcriptional target for MEF2A that encodes a striated muscle, alpha-actinin-interacting, costamere-localized protein.Journal of Biological Chemistry 281:6841-6849.

Gilmore TD & M Herscovitch . 2006. Inhibitors of NF-kB signaling: 785 and counting.Oncogene 25: 6887-6899.

Holloway MG , Laz EV, Waxman DJ.   2006. Co-dependence of GH-responsive, sexually dimorphic hepatic gene expression on STAT5b and HNF4a.   Molec Endocrinol, Mar;20(3):647-60.

Huang, H.-T., O.M. Brand, M. Mathew, C. Ignatiou, E.P. Ewen, S.A. McCalmon , and F.J. Naya. 2006. Myomaxin is a novel transcriptional target of MEF2A that encodes an alpha-actinin-interacting protein. Journal of Biological Chemistry. In press.

Liang M-C , S Bardhan, EA Pace, D Rosman, JA Beutler, JA Porco Jr & TD Gilmore. 2006. Inhibition of transcription factor NF-kB signaling proteins IKKbeta and p65 through specific cysteine residues by epoxyquinone A monomer: correlation with its anti-cancer cell growth activity. Biochemical Pharmacology: 71: 634-645.

Liang M-C , S Bardhan, JA Porco Jr & TD Gilmore. 2006. The synthetic epoxyquinoids jesterone dimer and epoxyquinone A monomer induce apoptosis and inhibit REL (human c-Rel) DNA binding in an IkBalpha-deficient diffuse large B-cell lymphoma cell line. Cancer Letters 241: 69-78.

Sawyer, S. J ., K. A. Gerstner, and G. V. Callard. 2006. Real-time PCR analysis of cytochrome P450 aromatase expression in zebrafish: Gene specific tissue distribution, sex differences, developmental programming, and estrogen regulation. General and Comparative Endocrinology 147:108-117.

Seo, K.-Y., Nagalingam, A, Shadi Miri, Jun Yin , Alexander Kolbanovskiy, Anant Shastry, and Loechler, E.L. 2006. Mirror Image Stereoisomers of the Major   Benzo[a]pyrene N2-dG Adduct Are Bypassed by Different Lesion-Bypass DNA Polymerases in E. coli DNA Repair 5, 515 – 527.

Starzynowski DT , H Trautmann, C Pott, L Harder, N Arnold, JA Africa, JR Leeman, R Siebert & TD Gilmore. 2006. Mutation of an IKK phosphorylation site within the transactivation domain of REL in two patients with B-cell lymphoma enhances REL’s in vitro transforming activity. Oncogene: in press.

2005

Baum, JS , JP St. George, and K McCall.  Programmed cell death in the germline, Seminars in Cell and Developmental Biology 16:245-59, (2005). Link

Choo, S, B Heinrich, JN Betley, Z Chen, and JO Deshler. Evidence for Common Machinery Utilized by the Early and Late RNA Localization Pathways in Xenopus Oocytes. Developmental Biology   278, 103-117, (2005). Link .

Kalaitzidis D and TD Gilmore. Transcription factor cross-talk: Estrogen receptor and NF-kB. Trends in Endocrinology and Metabolism 16:46-52, (2005). Link

Lee JJ and EP Widmaier. Gene array analysis of the effects of chronic adrenocorticotropic hormone in vivo on immature rat adrenal glands.   J Ster Biochem Mol Biol, 96:31-44, (2005). Link

Liang M-C , S Bardhan, JA Porco Jr & TD Gilmore. The synthetic epoxyquinoids jesterone dimer and epoxyquinone A monomer induce apoptosis and inhibit REL (human c-Rel) DNA binding in an IkBa-deficient diffuse large B-cell lymphoma cell line. Cancer Letters, (2005). Link

Starczynowski DT , JG Reynolds & TD Gilmore. Mutations of tumor necrosis factor alpha-responsive serine residues within the C-terminal transactivation domain of human transcription factor REL can enhance its in vitro transforming ability. Oncogene (2005).Link

Hong, Z, B Chasan, R Bansil, BS Turner , K Bhaskar, N Afdhal. Atomic force microscopy reveals conformational change and aggregation of gastric mucin at low pH Biomacromolecules. November-December (2005) Link