2009 McArdle Publications

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Alexander, C. M., Puchalski, J., Klos, K. S., Badders, N., Ailles, L., Kim, C. F., Dirks, P., and Smalley, M. J.  Separating Stem Cells by Flow Cytometry:  Reducing Variability for Solid Tissues.  Cell Stem Cell, 5:  579-583, 2009.

Badders, N. M., Goel, S., Clark, R. J., Klos, K. S., Kim, S., Bafico, A., Lindvall, C., Williams, B. O., and Alexander, C. M.  The Wnt Receptor, Lrp5, Is Expressed by Mouse Mammary Stem Cells and Is Required to Maintain the Basal Lineage.  PLoS One, 4(8):e6594, 2009.

Bouvard, V., Baan, R., Straif, K., Grosse, Y., Secretan, B., El Ghissassi, F., Benbrahim-Tallaa, L., Guha, N., Freeman, C., Galichet, L., Cogliano, V., WHO International Agency for Research on Cancer Monograph Working Group (35 collaborators, including Paul F. Lambert).  A Review of Human Carcinogens—Part B:  Biological Agents.  Lancet Oncol., 10:  321-322, 2009.

Bristol, J. A., Morrison, T. E., and Kenney, S. C.  CCAAT/Enhancer Binding Proteins α and β Regulate the Tumor Necrosis Factor Receptor 1 Gene Promoter.  Mol. Immunol., 46:  2706-2713, 2009.

Burgess, R. R., and Deutscher, M. P.  Preface.  Methods Enzymol., 463:  xxv-xxvi, 2009.

Burgess, R. R.  Chapter 3: Use of Bioinformatics in Planning a Protein Purification.  Methods Enzymol., 463:  21-28, 2009.

Burgess, R. R.  Chapter 4: Preparing a Purification Summary Table.  Methods Enzymol., 463:  29-34, 2009.

Burgess, R. R.  Chapter 17: Refolding Solubilized Inclusion Body Proteins.  Methods Enzymol., 463:  259-282, 2009.

Burgess, R. R.  Chapter 20: Protein Precipitation Techniques.  Methods Enzymol., 463:  331-342, 2009.

Burgess, R. R.  Chapter 32: Elution of Proteins from Gels.  Methods Enzymol., 463:  565-572, 2009.

Burgess, R. R.  Chapter 44: Important but Little Known (or Forgotten) Artifacts in Protein Biochemistry.  Methods Enzymol., 463:  813-820, 2009.

Chowdhury, G., Dostalek, M., Hsu, E. L., Nguyen, L. P., Stec, D. F., Bradfield, C. A., and Guengerich, F. P.  Structural Identification of Diindole Agonists of the Aryl Hydrocarbon Receptor Derived from Degradation of Indole-3-pyruvic Acid.  Chem. Res. Toxicol., 22:  1905-1912, 2009.

Chung, S.-H., and Lambert, P. F.  Prevention and Treatment of Cervical Cancer in Mice Using Estrogen Receptor Antagonists.  Proc. Natl. Acad. Sci. USA, 106:  19467-19472, 2009.

Cleveland, A. G., Oikarinen, S. I., Bynoté, K. K., Marttinen, M., Rafter, J. J., Gustafsson, J.-Å., Roy, S. K., Pitot, H. C., Korach, K. S., Lubahn, D. B., Mutanen, M., and Gould, K. A.  Disruption of Estrogen Receptor Signaling Enhances Intestinal Neoplasia in ApcMin/+ Mice.  Carcinogenesis, 30: 1581-1590, 2009.

Cotroneo, M. S., Haag, J. D., Stapel, N. R., Waller, J. L., Woditschka, S., and Gould, M. N.  Freund’s Vaccine Adjuvant Promotes Her2/Neu Breast Cancer.  BMC Cancer, 9:19, 2009.

Das, S., Becker, B. N., Hoffmann, F. M., and Mertz, J. E.  Complete Reversal of Epithelial to Mesenchymal Transition Requires Inhibition of Both ZEB Expression and the Rho Pathway.  BMC Cell Biol., 10:94, 2009. 

Dickerson, S. J., Xing, Y., Robinson, A. R., Seaman, W. T., Gruffat, H., and Kenney, S. C.  Methylation-Dependent Binding of the Epstein-Barr Virus BZLF1 Protein to Viral Promoters.  PLoS Pathog., 5(3):e1000356, 2009.

Domenech, M., Yu, H., Warrick, J., Badders, N. M., Meyvantsson, I., Alexander, C. M., and Beebe, D. J.  Cellular Observations Enabled by Microculture:  Paracrine Signaling and Population Demographics.  Integr. Biol., 1:  267-274, 2009.

Dresang, L. R., Vereide, D. T., and Sugden, B.  Identifying Sites Bound by Epstein-Barr Virus Nuclear Antigen 1 (EBNA1) in the Human Genome:  Defining a Position-Weighted Matrix To Predict Sites Bound by EBNA1 in Viral Genomes.  J. Virol., 83:  2930-2940, 2009.

Duellman, S. J., and Burgess, R. R.  Antigen-Binding Properties of Monoclonal Antibodies Reactive with EBNA1 and Use in Immunoaffinity Chromatography.  PLoS One, 4(2):e4614, 2009.

Duellman, S. J., and Burgess, R. R.  Large-Scale Epstein-Barr Virus EBNA1 Protein Purification.  Protein Expr. Purif., 63:  128-133, 2009.

Duellman, S. J., Thompson, K. L., Coon, J. J., and Burgess, R. R.  Phosphorylation Sites of Epstein-Barr Virus EBNA1 Regulate Its Function.  J. Gen. Virol., 90: 2251-2259, 2009.

Durkee, B. Y., Shinki, K., Newton, M. A., Iverson, C. E., Weichert, J. P., Dove, W. F., and Halberg, R. B.  Longitudinal Assessment of Colonic Tumor Fate in Mice by Computed Tomography and Optical Colonoscopy.  Acad. Radiol., 16:  1475-1482, 2009.

Ellison-Zelski, S. J., Solodin, N. M., and Alarid, E. T.  Repression of ESR1 through Actions of Estrogen Receptor Alpha and Sin3A at the Proximal Promoter.  Mol. Cell. Biol., 29: 4949-4958, 2009.

Ewald, J. A., Peters, N., Desotelle, J. A., Hoffmann, F. M., and Jarrard, D. F.  A High-Throughput Method to Identify Novel Senescence-Inducing Compounds.  J. Biomol. Screen., 14: 853-858, 2009.

Glaser, B. T., Bergendahl, V., Anthony, L. C., Olson, B., and Burgess, R. R.  Studying the Salt Dependence of the Binding of σ70 and σ32 to Core RNA Polymerase Using Luminescence Resonance Energy Transfer.  PLoS One, 4(8):e6490, 2009.

Gould, M. N.  The Utility of Comparative Genetics to Inform Breast Cancer Prevention Strategies.  Genetics, 183:  409-412, 2009.

Halberg, R. B., Waggoner, J., Rasmussen, K., White, A., Clipson, L., Prunuske, A. J., Bacher, J. W., Sullivan, R., Washington, M. K., Pitot, H. C., Petrini, J. H. J., Albertson, D. G., and Dove, W. F.  Long-lived Min Mice Develop Advanced Intestinal Cancers through a Genetically Conservative Pathway.  Cancer Res., 69:  5768-5775, 2009.

Hume, A. J., and Kalejta, R. F.  Regulation of the Retinoblastoma Proteins by the Human Herpesviruses.  Cell Div., 4:1, 2009.

Huttlin, E. L., Chen, X., Barrett-Wilt, G. A., Hegeman, A. D., Halberg, R. B., Harms, A. C., Newton, M. A., Dove, W. F., and Sussman, M. R.  Discovery and Validation of Colonic Tumor-Associated Proteins via Metabolic Labeling and Stable Isotopic Dilution.  Proc. Natl. Acad. Sci. USA, 106:  17235-17240, 2009.

Hwang, J., and Kalejta, R. F.  Human Cytomegalovirus Protein pp71 Induces Daxx SUMOylation.  J. Virol., 83:  6591-6598, 2009.

Hyde, J. S., and Mertz, J. E.  Gender, Culture, and Mathematics Performance.  Proc. Natl. Acad. Sci. USA, 106:  8801-8807, 2009.

Jabbar, S. F., Abrams, L., Glick, A., and Lambert, P. F.  Persistence of High-Grade Cervical Dysplasia and Cervical Cancer Requires the Continuous Expression of the Human Papillomavirus Type 16 E7 Oncogene.  Cancer Res., 69:  4407-4414, 2009.

Ju, J., Li, W., Yuan, Q., Peters, N. R., Hoffmann, F. M., Rajski, S. R., Osada, H., and Shen, B.  Functional Characterization of ttmM Unveils New Tautomycin Analogs and Insight into Tautomycin Biosynthesis and Activity.  Org. Lett., 11:  1639-1642, 2009.

Ju, J., Rajski, S. R., Lim, S.-K., Seo, J.-W., Peters, N. R., Hoffmann, F. M., and Shen, B.  Lactimidomycin, Iso-migrastatin and Related Glutarimide-Containing 12-Membered Macrolides Are Extremely Potent Inhibitors of Cell Migration.  J. Am. Chem. Soc., 131:  1370-1371, 2009.

Kamil, J. P., Hume, A. J., Jurak, I., Münger, K., Kalejta, R. F., and Coen, D. M.  Human Papillomavirus 16 E7 Inactivator of Retinoblastoma Family Proteins Complements Human Cytomegalovirus Lacking UL97 Protein Kinase.  Proc. Natl. Acad. Sci. USA, 106:  16823-16828, 2009.

Kim, Y. C., Clark, R. J., Pelegri, F., and Alexander, C. M.  Wnt4 Is Not Sufficient to Induce Lobuloalveolar Mammary Development.  BMC Dev. Biol. 9:55, 2009.

Kuhn, P., and Xu, W.  Protein Arginine Methyltransferases: Nuclear Receptor Coregulators and Beyond.  In:  Progress in Molecular Biology and Translational Science, Vol. 87, Chap. 9, pp. 299-342, 2009.

Kuhn, P., Xu, Q., Cline, E., Zhang, D., Ge, Y., and Xu, W.  Delineating Anopheles gambiae Coactivator Associated Arginine Methyltransferase 1 Automethylation Using Top-Down High Resolution Tandem Mass Spectrometry.  Protein Sci., 18:  1272-1280, 2009.

Kwong, L. N., and Dove, W. F.  APC and Its Modifiers in Colon Cancer.  Adv. Exp. Med. Biol., 656:  85-106, 2009.

Lambert, P.  Oncogenic Viruses.  In:  M. Schaechter, Editor-in-Chief, Encyclopedia of Microbiology, Third Edition, pp. 421-429.  Oxford:  Academic Press, 2009.

Lambert, P. F.  The Interwoven Story of the Small DNA Tumor Viruses.  Virology, 384:  255, 2009.

Lee, D. Y., Lee, J., and Sugden, B.  The Unfolded Protein Response and Autophagy:  Herpesviruses Rule!  J. Virol., 83:  1168-1172, 2009.

Liu, L., Hou, J., Du, J., Chumanov, R. S., Xu, Q., Ge, Y., Johnson, J. A., and Murphy, R. M.  Differential Modification of Cys10 Alters Transthyretin’s Effect on Beta-Amyloid Aggregation and Toxicity.  Protein Eng. Des. Sel., 22:  479-488, 2009.

Liu, L., Westler, W. M., den Boon, J. A., Wang, X., Diaz, A., Steinberg, H. A., and Ahlquist, P.  An Amphipathic α-Helix Controls Multiple Roles of Brome Mosaic Virus Protein 1a in RNA Replication Complex Assembly and Function.  PLoS Pathog., 5(3):e1000351, 2009.

Lodish, H. F., Ghaffari, S., Socolovsky, M., Tong, W., and Zhang, J.  Intracellular Signaling by the Erythropoietin Receptor.  In:  S. G. Elliott, M. A. Foote, and G. Molineux (Eds.), Erythropoietins, Erythropoietic Factors and Erythropoiesis, 2nd Ed., pp. 155-174. Switzerland: Birkhäuser Verlag, 2009. http://www.springerlink.com/content/978-3-7643-8694-8

Méndez-Lago, M., Wild, J., Whitehead, S. L., Tracey, A., de Pablos, B., Rogers, J., Szybalski, W., and Villasante, A.  Novel Sequencing Strategy for Repetitive DNA in a Drosophila BAC Clone Reveals That the Centromeric Region of the Y Chromosome Evolved from a Telomere.  Nucleic Acids Res., 37: 2264-2273, 2009.

Nguyen, L. P., Hsu, E. L., Chowdhury, G., Dostalek, M., Guengerich, F. P., and Bradfield, C. A.  d-Amino Acid Oxidase Generates Agonists of the Aryl Hydrocarbon Receptor from d-Tryptophan.  Chem. Res. Toxicol., 22:  1897-1904, 2009.

Nukaya, M., and Bradfield, C. A.  Conserved Genomic Structure of the Cyp1a1 and Cyp1a2 Loci and Their Dioxin Responsive Elements Cluster.  Biochem. Pharmacol., 77:  654-659, 2009.

Nukaya, M., Moran, S., and Bradfield, C. A.  The Role of the Dioxin-Responsive Element Cluster between the Cyp1a1 and Cyp1a2 Loci in Aryl Hydrocarbon Receptor Biology.  Proc. Natl. Acad. Sci. USA, 106:  4923-4928, 2009.

Peychal, S. E.-M., Bilger, A., Pitot, H. C., and Drinkwater, N. R.  Predominant Modifier of Extreme Liver Cancer Susceptibility in C57BR/cdJ Female Mice Localized to 6 Mb on Chromosome 17.  Carcinogenesis, 30: 879-885, 2009.

Pratt, Z. L., Kuzembayeva, M., Sengupta, S., and Sugden, B.  The microRNAs of Epstein-Barr Virus Are Expressed at Dramatically Differing Levels Among Cell Lines.  Virology, 386:  387-397, 2009.

Pyeon, D., Pearce, S. M., Lank, S. M., Ahlquist, P., and Lambert, P. F.  Establishment of Human Papillomavirus Infection Requires Cell Cycle Progression.  PLoS Pathog., 5(2):e1000318, 2009.

Regehr, K. J., Domenech, M., Koepsel, J. T., Carver, K. C., Ellison-Zelski, S. J., Murphy, W. L., Schuler, L. A., Alarid, E. T., and Beebe, D. J.  Biological Implications of Polydimethylsiloxane-Based Microfluidic Cell Culture.  Lab Chip, 9:  2132-2139, 2009.

Ryan, J. L., Jones, R. J., Elmore, S. H., Kenney, S. C., Miller, G., Schroeder, J. C., and Gulley, M. L.  Epstein-Barr Virus WZhet DNA Can Induce Lytic Replication in Epithelial Cells in vitro, although WZhet Is Not Detectable in Many Human Tissues in vivo.  Intervirology, 52:  8-16, 2009.

Shin, M.-K., Balsitis, S., Brake, T., and Lambert, P. F.  Human Papillomavirus E7 Oncoprotein Overrides the Tumor Suppressor Activity of p21Cip1 in Cervical Carcinogenesis.  Cancer Res., 69:  5656-5663, 2009.

Smith, A. A., Vollrath, A., Bradfield, C. A., and Craven, M.  Clustered Alignments of Gene-Expression Time Series Data.  Bioinformatics, 25:  i119-i127, 2009.

Smits, B. M. G., and Gould, M. N.  Gene Targeting in the Rat?  Cut It Out!  Mol. Interv., 9:  226-229, 2009.

Stanhope, S. A., Sengupta, S., den Boon, J., Ahlquist, P., and Newton, M. A.  Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification.  PLoS Comput. Biol., 5(9):e1000516, 2009.

Stevens, E. A., Mezrich, J. D., and Bradfield, C. A.  The Aryl Hydrocarbon Receptor:  A Perspective on Potential Roles in the Immune System.  Immunology, 127:  299-311, 2009.

Thompson, N.E., Foley, K. M., Stalder, E. S., and Burgess, R. R.  Chapter 28: Identification, Production, and Use of Polyol-Responsive Monoclonal Antibodies for Immunoaffinity Chromatography.  Methods Enzymol., 463:  475-494, 2009.

Thompson, N. E., Glaser, B. T., Foley, K. M., Burton, Z. F., and Burgess, R. R.  Minimal Promoter Systems Reveal the Importance of Conserved Residues in the B-finger of Human Transcription Factor IIB.  J. Biol. Chem., 284: 24754-24766, 2009.

Van Wynsberghe, P. M., and Ahlquist, P.  5’ cis Elements Direct Nodavirus RNA1 Recruitment to Mitochondrial Sites of Replication Complex Formation.  J. Virol., 83:  2976-2988, 2009.

Vereide, D., and Sugden, B.  Proof for EBV’s Sustaining Role in Burkitt’s Lymphomas.  Semin. Cancer Biol., 19:  389-393, 2009.

Vollrath, A. L., and Bradfield, C. A.  An Introduction to Toxicogenomics.  In:  A. F. Nassar, P. F. Hollenberg, and J. Scatina (Eds.), Drug Metabolism Handbook:  Concepts and Applications, Chapter 25, pp. 737-760. John Wiley & Sons, Inc., 2009. http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470118032,descCd-tableOfContents.html

Vollrath, A. L., Smith, A. A., Craven, M., and Bradfield, C. A.  EDGE3:  A Web-Based Solution for Management and Analysis of Agilent Two Color Microarray Experiments.  BMC Bioinformatics, 10:280, 2009.

Wise-Draper, T. M., Morreale, R. J., Morris, T. A., Mintz-Cole, R. A., Hoskins, E. E., Balsitis, S. J., Husseinzadeh, N., Witte, D. P., Wikenheiser-Brokamp, K. A., Lambert, P. F., and Wells, S. I.  DEK Proto-Oncogene Expression Interferes with the Normal Epithelial Differentiation Program.  Am. J. Pathol., 174:  71-81, 2009.

Woditschka, S., Haag, J. D., Sullivan, R., and Gould, M. N.  A Short-term Rat Mammary Carcinogenesis Model for the Prevention of Hormonally Responsive and Nonresponsive In situ Carcinomas.  Cancer Prev. Res., 2:  153-160, 2009.

Xiong, H., Li, S., Yang, Z., Burgess, R. R., and Dynan, W. S.  E. coli Expression of a Soluble, Active Single-Chain Antibody Variable Fragment Containing a Nuclear Localization Signal.  Protein Expr. Purif., 66: 172-180, 2009.

Zehbe, I., Richard, C., DeCarlo, C. A., Shai, A., Lambert, P. F., Lichtig, H., Tommasino, M., and Sherman, L.  Human Papillomavirus 16 E6 Variants Differ in Their Dysregulation of Human Keratinocyte Differentiation and Apoptosis.  Virology, 383:  69-77, 2009.

Zhang, J., Wang, J., Liu, Y., Sidik, H., Young, K. H., Lodish, H. F., and Fleming, M. D.  Oncogenic Kras-Induced Leukemogenesis:  Hematopoietic Stem Cells as the Initial Target and Lineage-Specific Progenitors as the Potential Targets for Final Leukemic Transformation.  Blood, 113:  1304-1314, 2009.