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2009 McArdle Publications

Click on citation to go to PubMed for article abstract.

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.

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