Student Publications

 

 

 

 

 

2012

• Koveal, D., Jayasundera, T.B., Wood, T.K., Peti, W., Page, R. (2012) backbone and sidechain (1)H,(15)N and (13)C assignments of tyrosine phosphatase related to biofilm formation A (TpbA) of Pseudomonas aeruginosa. Biomol NMR Assign. DOI:10.1007/s12104-012-9376-z.
• Le, V.Q., Wharton, K.A. (2012) Hyperactive BMP signaling induced by ALK2(R206H) requires type II receptor function in a Drosophila model for classic fibrodysplasia ossificans progressiva. Dev. Dyn. 241:200-14.
• Delaney, S., Jarem, D.A., Volle, C.B.,Yennie, C.J. (2012) Chemical and biological consequences of oxidatively damaged guanine in DNA. Free Radic. Res. 46:420-41.
• Volle, C.B., Jarem, D.A., Delaney, S. (2012) Trinucleotide repeat DNA alters structure to minimize the thermodynamic impact of 8-0x0-7,8-dihydroguanine. Biochemistry 51(1):52-62.

2011

• Twombly, V., Bangi, E., Le, V., Mainic, B., Singer, M.A., Wharton, K.A. (2011) Functional analysis of saxophone, the Drosophila gene encoding the BMP type I receptor ortholog of human ALK1/ACVRL1 and ACVR1/ALK2. Genetics 183:563-79.
• Eken, A., Ortiz, V. and Wands J.R. (2011) Ethanol inhibits antigen presentation by dendritic cells. Clin. Vaccine Immunol. [Epub ahead of print]
• DiSalvo, S., Serio, T.R. (2011) Insights into prion biology: Integrating a protein misfolding pathway with its cellular environment. Prion 5(2) [Epub ahead of print]
• DiSalvo S, DerdowskiA, Pezza JA and Serio TR (2011) Dominant prion mutants induce curing through pathways that promote chaperone-mediated disaggregation. Nat. Struct. Mol. Biol. 18(4):486-492. 
• Gagnon, J.A., Mowry, K.L. (2011) Molecular motors:directing traffic during RNA localization. Crit. Rev. Biochem. Mol. Biol. 46(3):229-39.
• Staber, C.J., Gell, S., Jepson, J.E., Reenan, R.A. (2011) Perturbing A-to-I RNA editing using genetics and homologous recombination. Methods Mol. Biol. 718:41-73.
• Valm, A.M.,Mark Welch, J.L., Rieken, C.W., Hasegawa, Y., Sogin, M.L., Oldenbourg, R., Dewhirst, F.E., Borisy, G.G. (2011) Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proc. Natl. Acad. Sci. USA 108:4152-7.
• Jones, S.K., Bennett, R.J. (2011) Fungal mating pheromones: Choreographing the dating game. Fungal Genet. Biol. 48:668-76.
• Francis, D.M., Rozycki, B., Koveal, D., Hummer, G., Page, R., Peti, W. (2011) Structural Basis of p38alpha regulation by hematopoietic tyrosine phosphatase. Nat. Chem. Biol. 7(12):916-24.
• Koveal, D., Pinheiro, A.S., Peti, W., Page, R. (2011) Backbone and side chain (1)H,(15)N and (13)C assignments of the KSR1 CA1 domain. Biomol. NMR Assign. 5(1):39-41.
• Porman, A.M., Alby, K., Hirakawa, M.P., Bennett, R.J. (2011) Discovery of a phenotypic switch regulating sexual mating in the opportuistic fungal pathogen Candida tropicalis. Proc. Natl Acad Sci USA 108:21158-63.
• Reich, A., Klatsky, P., Carson, S., Wessel, G. (2011) The transcriptome of a human polar body accurately reflects its sibling oocyte. J. Biol. Chem. 286:40743-9.
• Rieder, L.E., Reenan, R.A. (2011) The intricate relationship between RNA structure, editing and splicing. Semin Cell Dev Biol 23:281-288.
• Jepson, J.E., Savva, Y.A., Yokose, C., Sugden, A.U., Sahin, A., Reenan, R.A. (2011) Engineered alterations in RNA editing modulate complex behavior in Drosophila: regulatory diversity of adenosine deaminase acting on RNA (ADAR) targets. J. Biol. Chem. 286: 8325-37.
• Skottke, K.R., Yoon, G.M., Kieber, J.J., DeLong, A. (2011) Protein Phosphatase 2A Controls Ethylene Biosynthesis by Differentially Regulating the Turnover of ACC Synthase Isoforms. PLoS Genetics. 7(4):e1001370. 
• Antosh,M., Whitaker, R., Kroll, A., Hosier, S., Chang, C., Bauer, J., Cooper, L., Neretti, N., Helfand, S.L. (2011) Comparative transcriptional pathway bioinformati analysis of dietary restriction, Sir2, p53 andresveratrol life span extension in Drosophila. Cell Cycle 10: 904-11. 
• Amenta, A.R., Yilmaz, A., Bogdanovich,S., McKechnie, B.A.,Abedi, M., Khurana, T.S., Fallon, J.R. (2011) Biglycan recruits utrophin to the sarcolemma and counters dystrophic pathology in mdx mice. Proc. Natl. Acad. Sci. USA 108:762-7.   

2010

• Ballard, S.L., Jarolimova, J., Wharton, K.A. (2010) Gbb/BMP signaling is required to maintain energy homeostasis in Drosophila. Dev. Biol. 337: 375-385.
• Terrizzi, S.C., Banh, C., Brossay, L. (2010) A protocol for the production of KLRG1 tetramer. J. Vis. Exp. Jan 12;(35).pii:1701.
• Bronson, M.W.,Hillenmeyer, S., Park, R.W., Brodsky, A.S. (2010 Estrogen Coordinates Translation and Transcription Revealing a Role for NRSF in Human Breast Cancer Cells. (2010) Mol. Endocrinol. Apr 14 [Epubahead of Print]
• Derdowski, A., Sindi, S.S., Klaips, C.L., DiSalvo, S., Serio, T.R. (2010) A size threshold limits prion transmission and establishes phenotypic diversity. Science 330: 680-683.
• Szabo, G., Wands, J.R., Eken, A., Osna, N.A., Weinman, S.A., Machido, K., Joe Wang, H. (2010) Alcohol andhepatitis C virus-interactions in immune dysfunctions and liver damage. Alcohol Clin. Exp. Res. 34(10):1675-86.
• Wintermeyer, P., Gehring, S., Eken, A., Wands, J.R. (2010) Generation of cellular immune responses to HCV NS5 protein through in vivo activation of dendritic cells. J. Viral Hepat. [Epub ahead of print].
• Gagnon, J.A., Mowry, K.A. (2010) Visualizing RNA localization in Xenopus oocytes. J. Vis. Exp. Jan 14;(35). pii:1704.
• Kim, Y., Wang, X., Zhang, X.S., Grigoriu, S., Page, R., Peti, W., Wood, T.K. (2010) Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD. Environ. Microbiol. Jan 26 [Epub ahead of print].
• Gustafson E.A. Wessel, G.M. (2010) DEAD-box helicases: posttranslational regulation and function. Biochem. Biophys. Res. Commun. 395: 1-6.
• Hasegawa, Y., Mark Welch, J., Valm, A.M., Rieken, C., Sogin, M.L., Borisy, G.G. (2010) Imaging marine bacteria with unique 16S rRNA V6 sequences by fluorescence in situ hybridization and spectral analysis. Geomicrobiology J. 27(3).
• Hasegawa, Y., Hobbie, J.E., Schadt, C.W., Wallenstein, M.D., Smemo, K.A., Rich, J., Weintraub, M.N., Allison, S.D., Edmonds, J.W., von Fischer, J.C., Vineis, J.H. (2010) Application of molecular knowledge of microbes to studies of ecological processes: why the integration is so challenging. ESA Bulletin.
• Juliano, C.E., Swartz, S.Z., Wesel, G.M. (2010) A conserved germline multipotency program. Development 137:4113-26.
• Andrade, A., Denome, S., Jiang, Y.Q., Marangoudakis, S., Lipscombe, D. (2010) Opioid inhibition of N-type Ca2+ channels and spinal analgesis couple to alternative splicing. Nat. Neurosci. 13:1249-1256.
• Pratt, C.A., Mowry, K.L. (2010) Preparation of a highly active cell-free translation system from immature Xenopus laevis oocytes. Methods 51: 101-105.
• Ragusa, M.J., Dancheck, B., Critton, D.A., Nairn, A.C., Page, R., Peti, W. (2010) Spinophilin directs protein phosphatase 1 specificity by blocking substrate binding sites. Nat. Struct. Mol. Biol. 17: 459-464.
• Bollen, M., Peti, W., Ragusa, M.J., Beullens, M. (2010) The extended PP1 toolkit: designed to create specificity. Trends Biochem. Sci. Apr 14 [Epub ahead of print]

• Wessel, G.M., Reich, A.M., Klatsky, P.C. (2010) Use of sea stars to study basic reproductive processes. Syst. Biol. Reprod. Med. 56:236-245. Review. 

• Jepson, J.E., Savva, Y.A., Yokose, C., Sugden, A.U., Sahin, A., Reenan, R.A. (2010) Engineered alterations in RNA editing modulate complex behavior in Drosophila: regulatory diversity of adenosine deaminase acting on RNA (ADAR) targets. J. Biol. Chem. [EPub ahead of print] 

• Alby, K., Schaefer, D., Sherwood, R.K., Jones, S.K. Jr., Bennett, R.J. (2010) Identification of a cell death pathway in Candida albicans during the response to pheromone. Eukaryot Cell 9:1690-1701.  

• Yilmaz, M., Kang, I., Beale, S.I. (2010) Heme oxygenase 2 of the cyanobacterium Synechocystis sp. PCC 6803 is induced under a microaerobic atmosphere and is required for microaerobic growth at high light intensity. Photosynth. Res. 103: 47-59.

2009

• Twombley, V., Bangi, E., Le, V., Malnic, B., Singer, M., Wharton, K.A. (2009) Functional analysis of saxophone, the Drosophila BMP type I receptor orthologue of the human ACVRL2/ALK1 and ACVR1/ALK2 genes . Genetics 183(2):563-79.
• Banh, C., Fugere, C., Brossay, L. (2009) Immunoregulatory functions of KLRG1 cadherin interactions are dependent on forward and reverse signaling. Blood 114: 5299-5306.
• Akins, M.R., Berk-Rauch, H.E., Fallon, J.R. (2009) Presynaptic translation: stepping out of the postsynaptic shadow. Front. Neural Circuits 3:17.
• Brown, A., Brown S., Ellisor, D., Hagan, N., Normand, E., Zervas, M. (2009) A practical approach to genetic inducible fate mapping: a visual guide to mark and tracl cells in vivo. J. Vis. Exp. Dec 30;(34). pii:1687.
• Cakir, I., Perello, M. Lansari, O., Messier, N.J., Vaslet, C.A., Nillni, E.A. (2009) Hypothalamic Sirt1 regulates food intake in a rodent model system. PLoS One 4: e8322.
• Gregory, S.T., Carr, J.F., Dahlberg, A.E. (2009) A signal relay between ribosomal protein S12 and elongation factor EF-Tu during decoding of mRNA. RNA 15: 208-214.
• Chung, A.S., Chin, Y.E. (2009) Antibody array platform to monitor protein tyrosine phosphorylation in mammalian cells. Methods Mol. Biol. 527: 247-255.
• Demirci, H., Belardinelli, R., Seri, E., Gregory, S.T., Gualerzi, C., Dahlberg, A.E., Jogl, G. (2009) Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine. J. Mol. Biol. 388:271-282.
• Pezza, J.A., Langseth, S.X., RAupp Yamamoto, R., Doris, S.M., Ulin, S.P., Salomon, A.R., Serio, T.R. (2009) The NatA acetyltransferase couples Sup35 prion complexes to the [PSI+] phenotype. Mol. Biol. Cell 20: 1068-1080.
• Frank, A.C., Johnson, M.A. (2009) Expressing the diphtheria toxin A subunit from the HAP2(GCS1) promoter blocks sperm maturation and produces single sperm-like cells capable of fertilization. Plant Physiol. 151(3):1390-400.
• Gagnon, J.A., Mowry, K.L. (2009) VISIONS: the art of science. Mol. Reproduc. Dev. 76: 1115.
• Gyuris, A., Donovan, D.J., Seymour, K.A., Lovasco, L.A., Smilowitz, N.R., Halperin, A.L., Klysik, J.E., Freiman, R.N. (2009) The chromatin-targeting protein Brd2 is required for neural tube closure and embryogenesis. Biochim Biophys Acta 1789:413-421.
• Juliano, C.E., Yajima, M., Wessel, G.M. (2009) Nanos functions to maintain the fate of small micromere lineage in the sea urchin embryo. Dev. Biol. [Epub ahead of print]
• Juliano, C.E., Wessel, G.M. (2009) An evolutionary transition of vasa regulation in echinoderms. Evolution and Development 11:560-573.
• Ellisor, D., Koveal, D., Hagan, N., Brown, A., Zervas, M. (2009) Comparative analysis of conditional reporter alleles in the developing embryo and embryonic nervous system. Gene Expression Patterns. 9(7):475-489.
• Li, H., Jogl, G. (2009) Structural and biochemical studies of TIGAR (TP53-induced glycolysis and apoptosis regulator). J. Biol. Chem. 284: 1748-1754.
• Lovasco, L.A., Seymour, K.A., Zafra, K., O'Brien, C.W., Schorl, C., Freiman, R.N. (2009) Accelerated ovarian aging in the absence of the transcription regulator TAF4b. Biol. Reprod. [Epub ahead of print]
• Ingleby, L., Maloney, R., Jepson, J., Horn, R., Reenan, R. (2009) Regulated RNA editing and functional epistasis in Shaker potassium channels. J. Gen. Physiol. 133: 17-27.
• Jakubek, L.M., Marangoudakis, S., Raingo, L., Liu, X., Lipscombe, D., Hurt, R.H. (2009) The inhibition of neuronal calcium ion channels by trace levels of yttrium released from carbon nanotubes. Biomaterials 30: 6351-6357.
• Nguyen, V., Cao, L., Lin, J.T., Hung, N., Ritz, A., Yu, K., Jianru R., Ulin, S.P., Raphael, B.J., Laidlaw, D.H., Brossay, L., Salomon, A.R. (2009) A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation. Mol. Cell Proteomics 8: 2418-31.
• Paulo, J.A., Hawrot, E. (2009) Effect of homologous serotonin receptor loop substitutions on the heterologous expression in Pichia of a chimeric acetylcholine-binding protein with alpha-bungarotoxin-binding activity. Protein Expr. Purif. 67:76-81.
• Paulo, J., Brucker, W., Hawrot, E. (2009) Proteomic Analysis of an 7 Nicotinic Acetylcholine Receptor Interactome. J. Proteome Res. 8(4):1849-1858.
• Paulo, J.A., Hawrot, E. (2009) A radioisotope label-free alpha-bungarotoxin-binding assay using BIAcore sensor chip technology for real-time analysis. Anal. Biochem. 389: 86-88.
• Reid, D.C., Chang, B.L., Gunderson, S.I., Alpert, L., Thompson, W.A., Fairbrother, W.G. (2009) Next-generation SELEX identifies sequence andstructural determinants of splicing factor binding in human pre-mRNA sequence. RNA 15: 2385-2397.
• Sherwood, R.K., Bennett, R.J. (2009) Fungal meiosis andparasexual reproduction - lessons from pathogenic yeast. Curr. Opin. Microbiol. 12: 599-607.
• St. Laurent, G. 3rd, Savva, Y.A., Reenan, R. (2009) Enhancing non-coding RNA information content with ADAR editing. Neurosci Lett. [Epub ahead of print]
• Giovannone, B., Tsiaras, W.G., de la Monte, S., Klysik, J., Lautier, C., Karaschuk, G., Goldwurm, S., Smith, R.J. (2009) GIGYF2 gene disruption in mice results in neurodegeneration and altered insulin-like growth factor signaling. Hum. Mol. Genet. 18(23):4629-2639.
• Watkins, K.H., Stewart, A., Fairbrother, W. (2009) A rapid high-throughput method for mapping ribonucleoproteins (RNPs) on human pre-mRNA. J. Vis. Exp. Dec 2;(34) pii:1622.
• Wang, P.Y., Neretti, N., Whitaker, R., Hosier, S., Chang, C., Lu, D., Rogina, B. Helfand, S.L. (2009) Long-lived Indy and calorie restriction interact to extend life span. Proc. Natl. Acad. Sci. USA 106: 9262-9267.
• Wong, J.L., Wessel, G.M. (2009) Extracellular matrix modifications at fertilization: regulation of dityrosine crosslinking by transamidation. Development Development 136:1835-47.

2008

• Romero, A., Cakir, I., Vaslet, C.A., Stuart, R.C., Lansari, O., Lucero, H.A., Nillni, E.A. (2008) Role of a pro-sequence in the secretory pathway of pro thyrotropin releasing hormone (proTRH). J. Biol. Chem. 283:31438-31448.
• Critton, D.A., Tortajada, A., Stetson, G., Peti, W., Page, R. (2008) Structural basis of substrate recopgnition by hematopoietic tyrosine phosphatase. Biochemistry. 47: 13336-13345.
• Flatt, T., Min, K.J., D'Alterio, C., Villa-Cuesta, E., Cumbers, J., Lehmann, R., Jones, D.L., Tatar, M. (2008) Drosophila germ-line modulation of insulin signaling and lifespan. Proc. Natl. Acad. Sci. USA 105: 6368-6373.
• Demirci, H., Gregry, S.T., Dahlberg, A.E., Jogl, G. (2008) Crystal structure of the Thermus thermophilus 16S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine. J. Biol. Chem. 283: 26548-26556.
• Demirci, H., Gregory, S.T., Dahlberg, A.E., Jogl, G. (2008) Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase. Structure. 16: 1059-1066.
• Dugan, A.S., Maginnis, M.S., Jordan, J.A., Gasparovic, M.L., Manley, K., Page, R., Williams, G., Porter, E., O'Hara, B.A., Atwood, W.J. (2008) Human alpha-defensins inhibit BK virus infection by aggregating virions and blocking binding to host cells. J. Biol. Chem. 283:31125-31132.
• Dugan, A.S., Gasparovic, M.L., Atwood, W.J. (2008) Direct correlation between sialic acid binding and infection of cells by two human polyomaviruses (JC virus and BK virus). J. Virol. 82: 2560-2564.
• Gustafson, E.A., Wessel, G.M. (2008) Polycomb group gene expression in the sea urchin. Dev. Dyn. 237: 1851-1861.
• Haley, S.A., Zhao, T., Zou, L., Klysik, J.E., Padbury, J.F., and Kochilas, L.K. (2008) Forced expression of the cell cycle inhibitor p57Kip2 in cardiomyocytes attenuates ischemia-reperfusion injury in the mouse heart. BMC Physiol. 8:4.
• Hazelbaker, D., Azaro, M.A., Landy, A. (2008) A biotin interference assay highlights two different asymmetric interaction profiles for lambda integrase arm-type binding sites in integrative versus excisive recombination. J. Biol. Chem. 283:12402-12414.
• Lewis, R.A., Gagnon, J.A., Mowry, K.L. (2008) PTB/hnRNP I is required for RNP remodeling during RNA localization in Xenopus oocytes. Mol. Cell Biol. 28: 678-686.
• Lizotte, D.L. , Blakeslee, J.J., Siryaporn, A., Heath, J.T., DeLong, A. (2008) A PP2A active site mutant impedes growth and causes misregulation of native catalytic subunit expression. J. Cell Biochem. 103: 1309-1325.
• Ryan, M.Y., Maloney, R., Reenan, R., Horn, R., (2008) Characterization of five RNA editing sites in Shab potassium channels. Channels (Austin)2(3):202-209.
• Manley, K. O'Hara, B.a., Atwood, W.J. (2008) Nuclear factor of activated T-cells (NFAT) plays a role in SV40 infection. Virology 372:48-55.
• Messitt, T.J., Gagnon, J.A., Kreiling, J.A., Pratt, K., Yoon, Y.J. Mowry, K.L. (2008) Multiple kinesin motors coordinate cytoplasmic RNA transport on a subpopulation of microtubules in Xenopus oocytes. Dev. Cell 15: 426-436.
• Li, H., Radford, J.C., Ragusa, M.J., Shea, K.L., McKercher, S.R., Zaremba, J.D., Soussou, W., Nie, Z., Kang, Y.J., Nakanishi, N., Okamoto, S., Roberts, A.J., Schwarz, J.J., Lipton, S.A. (2008) Transcription factor MEF2C influences neural stem/progenitor cell differentiation and maturation in vivo. Proc. Natl. Acad. Sci. USA 105: 9397-0402.
• Rodriguez-Correa, D., Dahlberg, A.E. (2008) Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus. RNA 14: 2314-2318.
• Gruppuso, P.A., Tsai, S.W., Boylan, J.M., Sanders, J.A. (2008) Hepatic translation control in the late-gestation fetal rat. Am. J. Physiol. Regul. Integr. Comp. Physiol. 295: R558-567.
• Sanders, J.A., Lakhani, A., Phornphutkul, C., Wu, K.Y., Gruppuso, P.A. (2008) The effect of rapamycin on DNA sunthesis in multiple tissues from late gestation fetal and postnatal rats. Am. J. Physiol. Cell Physiol. 295: C406-413.
• Yoo, S.J., Jimenez, R.H., Sanders, J.A., Boylan, J.A., Brautigan, D.L., Gruppuso, P.A. (2008) The alpha4-containing form of protein phosphatase 2A in liver and hepatic cells. J. Cell Biochem. 105:290-300.
• Sherwood, R.K., Bennett, R.J. (2008) Microtubule motor protein Kar3 is required for normal mitotic division and morphogenesis in Candida albicans. Eukaryot. Cell 7:1460-1474.
• Blakeslee, J.J., Zhou, H.W., Heath, J.T., Skottke, K.R., Barrios, J.A., Liu, S.Y., DeLong, A. (2008) Specificity of RCN1-mediated protein phosphatase 2A regulation in meristem organization and stress response in roots. Plant Physiol. 146: 539-553.
• Kim, M., Lee, H.C., Tsedensodnom, O., Hartley, R., Lim, Y.S., Yu, E., Merle, P., Wands, J.R. (2008) Functional interaction between Wnt3 and frizzled-7 leads to activation of the Wnt/beta-catenin signaling pathway in helatocellular carcinoma cells. J. Hepatol.48(5):780-791.
• Lautier, C., Goldwurm, S., Durr, A., Givannone, B., Tsiaras, W.G., Pezzoli, G., Brice, A., Smith, R.J. (2008) Mutations in the GIGYF2 (TNRC15) Gene at the PARK11 Locus in Familial Parkinson Disease. Am. J. Hum. Genet. 82(4):822-833,
• Voronina, E., Lopez, M., Juliano, C.E., Gustafson, E., Song, J.L., Extavour, C., George, S., Oliveri, P., McClay, D., Wessel, G. (2008) Vasa protein expression is restricted to the small micromeres of the sea urchin, but is indicible in other lineages early in development. Dev. Biol. 314: 276-286.
• Davis, L.C., Morgan, A.J., Rusa, M., Wong, J.L., Graeff, R.M., Poustka, A.J., Lee, H.C., Wessel, G.M., Parrington, J., Galione, A. (2008) Ca(2+) signaling occurs via sexond messenger release from intraorganelle synthesis sites. Curr. Biol. 18: 1612-1618.
• Wong, J.L., Wessel, G.M.(2008) Free-radical crosslinking of specific proteins alters the function of the egg extracellular matrix at fertilization. Development 135:431-440.
• Wong, J.L., Wessel, G.M. (2008) Renovation of the egg extracellular matrix at fertilization. Int. J. Dev. Biol. 52: 545-550.
• Wong, J.L., Wessel, G.M. (2008) FRAP analysis of secretory granule lipids and proteins in teh sea urchin egg. Methods Mol. Biol. 440: 61-76.
• Drumea, K., Yang, Z.F., Rosmarin, A. (2008) Retinoic acid signaling in myelopoiesis. Curr. Opin. Hematol. 15:37-41.