Publication Highlights in the Biological Sciences

Each year, faculty in the Department of Biological Sciences publish scores of research papers, book chapters and other scholarly articles. While a comprehensive list is provided at the bottom of this page, here we would like to draw your attention to a few notable papers which you may find of interest.

Paper published so far this year

  1. Acilan, C., D.M. Potter, and W.S. Saunders (2007) DNA repair pathways involved in anaphase bridge formation. Gene Chromosome Canc. 46:522-531
  2. Ahner, A., K. Nakatsukasa, H. Zhang, R.A. Frizzell, and J.L. Brodsky (2007) Small Heat Shock Proteins Select DF508-CFTR for ER Associated Degradation (ERAD). Mol. Biol. Cell 18:806-814
  3. An, P., and P.J. Grabowski (2007) Exon silencing by UAGG motifs in response to neuronal excitation. PLoS Biol. 5:e36
  4. Arana, M.E., K. Takata, M. Garcia-Diaz, R.D. Wood, and T.A. Kunkel (2007) A unique error signature for human DNA polymerase nu. DNA Repair 6:213-223
  5. Ashman, T.-L., and L. Penet (2007) Direct and indirect effects of a sex-biased antagonist on male and female fertility: consequences for reproductive trait evolution in a gender dimorphic plant. Am. Nat. 169:595-608
  6. Azad, R.K., and J.G. Lawrence (2007) Detecting laterally-transferred genes: Use of entropic clustering methods and genome position. Nucleic Acids Res. 35:4629-4639
  7. Bittner, A.N., A. Foltz, and V. Oke (2007) Only one of five groEL genes is required for viability and successful symbiosis in Sinorhizobium meliloti. J. Bacteriol. 189:1884-1889
  8. Bochman, M.L., and A. Schwacha (2007) Differences in the single-stranded DNA binding activities of MCM2-7 and MCM467: MCM2 and 5 define a slow ATP-dependent step. J Biol Chem 282:33795-33804
  9. Braun, M.A., P.J. Costa, E.M. Crisucci, and K.M. Arndt (2007) Identification of Rkr1, a nuclear RING domain protein with functional connections to chromatin modification in Saccharomyces cerevisiae. Mol. Cell. Biol. 27:2800-2811
  10. Brodsky, J.L. (2007) The protective and destructive roles played by molecular chaperones during ERAD (endoplasmic-reticulum-associated degradation). Biochem. J. 404:353-363
  11. Brodsky, J.L., and C.M. Scott (2007) Tipping the delicate balance: Defining how proteasome maturation affects the degradation of a substrate for autophagy and endoplasmic reticulum associated degradation (ERAD). Autophagy 3:623-625
  12. Case, A.L., and T.-L. Ashman (2007) An experimental test of the effects of resource and sex ratio on maternal fitness and phenotypic selection in gynodioecious Fragaria virginiana. Evolution 61:1900-1911
  13. Chu, Y., R. Simic, M.H. Warner, K.M. Arndt, and G. Prelich (2007) Regulation of histone modification and cryptic transcription by the Bur1 and Paf1 complexes. EMBO J. 26:4646-4656
  14. Conway, J.F., N. Cheng, P.D. Ross, R.W. Hendrix, R.L. Duda, and A.C. Steven (2007) A thermally induced phase transition in a viral capsid transforms the hexamers, leaving the pentamers unchanged. J. Struct. Biol. 158:224-232
  15. Feng, D., X. Zhao, C. Soromani, J. Toikkanen, K. Romisch, S.S. Vembar, J.L. Brodsky, S. Keranen, and J. Jantti (2007) The trans-membrane domain is sufficient for Sbh1p function, its association with the Sec61 complex and its interaction with Rtn1p. J. Biol. Chem. 282:30618-30628
  16. Friedberg, E.C., and R.D. Wood (2007) New insights into the combined Cockayne/xeroderma pigmentosum complex: human XPG protein can function in transcription factor stability. Mol. Cell 26:162-164
  17. Grabe, M., H.C. Lai, M. Jain, Y.N. Jan, and L.Y. Jan (2007) Structure prediction for the down state of a potassium channel voltage sensor. Nature 445:550-553
  18. Grabowski, P.J. (2007) RNA-binding proteins switch gears to drive alternative splicing in neurons. Nat. Struct. Mol. Biol. 14:577-579
  19. Gusarova, V., J. Seo, M.L. Sullivan, S.C. Watkins, J.L. Brodsky, and E.A. Fisher (2007) Golgi-associated maturation of very low density lipoproteins involves conformational changes of apolipoprotein B, but is not dependent on apolipoprotein E. J. Biol. Chem. 282:19453-19462
  20. Hatfull, G.F. (2007) Host-microbe interactions: matters of life and death. Curr. Opin. Microbiol. 0:
  21. Hendrickson, H., and J.G. Lawrence (2007) Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites. Mol. Microbiol. 64:42-56
  22. Hoverman, J.T., and R.A. Relyea (2007) How flexible is phenotypic plasticity? Developmental windows for trait induction and reversal. Ecology 88:693-705
  23. Hoverman, J.T., and R.A. Relyea (2007) The rules of engagement: How prey respond to multiple predators. Oecologia 154:551-560
  24. Hrizo, S.L., V. Gusarova, D.M. Habiel, J.L. Goeckeler, E.A. Fisher, and J.L. Brodsky (2007) The Hsp110 molecular chaperone stabilizes apolipoprotein B from endoplasmic reticulum associated degradation (ERAD). J. Biol. Chem. 282:32665-32675
  25. Jelenska, J., N. Yao, B.A. Vinatzer, C.M. Wright, J.L. Brodsky, and J.T. Greenberg (2007) A J domain virulence effector of Pseudomonas syringae remodels host chloroplasts and suppresses defenses. Curr. Biol. 17:499-508
  26. Kashlan, O.B., G.M. Mueller, M.Z. Qamar, P.A. Poland, A. Ahner, R.C. Rubenstein, R.P. Hughey, J.L. Brodsky, and T.R. Kleyman (2007) Small heat shock protein alpha A-crystallin regulates epithelial sodium channel expression. J. Biol. Chem. 282:28149-28156
  27. Kim, H.J., Q. Li, S. Tjon-Kon-Sang, I. So, K. Kiselyov, and S. Muallem (2007) Gain-of-function mutation in TRPML3 causes the mouse varitint-waddler phenotype. J. Biol. Chem. 0:
  28. Kiselyov, K., D.M. Shin, J.Y. Kim, J.P. Yuan, and S. Muallem (2007) TRPC channels: interacting proteins. Handb. Exp. Pharmacol. 2007:559-574
  29. Kiselyov, K., J.J. .J.r. Jennigs, Y. Rbaibi, and C.T. Chu (2007) Autophagy, mitochondria and cell death in lysosomal storage diseases. Autophagy 3:259-262
  30. Krzysiak, T.C., M. Grabe, and S.P. Gilbert (2007) Getting in sync with dimeric Eg5: Initiation and regulation of the processive run. J. Biol. Chem. 0:
  31. Majetic, C.J., R.A. Raguso, S.J. Tonsor, and T.-L. Ashman (2007) Flower color-flower scent associations in polymorphic Hesperis matronalis (Brassicaceae). Phytochemistry 68:865-874
  32. Mandal, A.K., P. Lee, J.A. Chen, N. Nillegoda, A. Heller, S. Distasio, H. Oen, J. Victor, D.M. Nair, J.L. Brodsky, and A.J. Caplan (2007) Cdc37 has distinct roles in protein kinase quality control that protect nascent chains from degradation and promote posttranslational maturation. J. Cell. Biol. 176:319-328
  33. Masuda, K., R. Ouchida, M. Hikida, T. Kurosaki, M. Yokoi, C. Masutani, M. Seki, R.D. Wood, F. Hanaoka, and J. O-Wang (2007) DNA Polymerases {eta} and {theta} Function in the Same Genetic Pathway to Generate Mutations at A/T during Somatic Hypermutation of Ig Genes. J. Biol. Chem. 282:17387-17394
  34. Mondal, G., S. Sengupta, C.K. Panda, C.K. Gollin, W.S. Saunders, and S. Roychoudhury (2007) Overexpression of Cdc20 leads to impairment of the spindle assembly checkpoint and aneuploidization in oral cancer. Carcinogenesis 28:81-92
  35. Ojha, A., and G.F. Hatfull (2007) The role of iron in Mycobacterium smegmatis biofilm formation: the exochelin siderophore is essential in limiting iron conditions for biofilm formation but not for planktonic growth. Mol. Microbiol. 66:468-483
  36. Parikh, R.A., J.S. White, X. Huang, D.W. Schoppy, B.E. Baysal, R. Baskaran, C.J. Bakkenist, W.S. Saunders, L.C. Hsu, M. Romkes, and S.M. Gollin (2007) Loss of distal 11q is associated with DNA repair deficiency and reduced sensitivity to ionizing radiation in head and neck squamous cell carcinoma. Gene Chromosome Canc. 46:761-775
  37. Park, S.O., Y.J. Lee, T. Seki, K.H. Hong, N. Fliess, Z. Jiang, A. Park, X. Wu, V. Kaartinen, B.L. Roman, and S.P. Oh (2007) ALK5- and TGFBR2-independent role of ALK1 in the pathogenesis of hereditary hemorrhagic telangiectasia type 2 (HHT2). Blood :In Press
  38. Peebles, C.L., and S. Finkbeiner (2007) RNA decay back in play. Nat. Neurosci. 10:1083-1084
  39. Perlmutter, D.H., J.L. Brodsky, W.F. Balistreri, and B.C. Trapnell (2007) Molecular pathogenesis of alpha-1-antitrypsin deficiency-associated liver disease: A meeting review. Hepatology 45:1313-1323
  40. Pham, T.T., D. Jacobs-Sera, M.L. Pedulla, R.W. Hendrix, and G.F. Hatfull (2007) Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site-specific integration vectors for mycobacteria. Microbiology 153:2711-2723
  41. Pope, W.H., P.R. Weigele, J. Chang, M.L. Pedulla, M.E. Ford, J.M. Houtz, W. Jiang, W. Chiu, G.F. Hatfull, R.W. Hendrix, and J. King (2007) Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine synechococcus. J. Mol. Biol. 368:966-981
  42. Rathi, A.V., M.T. Sáenz-Robles, and J.M. Pipas (2007) Enterocyte proliferation and intestinal hyperplasia induced by simian virus 40 T antigen require a functional j domain. J Virol 81:9481-9489
  43. Rathi, A.V., M.T. Sáenz-Robles, and J.M. Pipas (2007) Enterocyte proliferation and intestinal hyperplasia induced by simian virus 40 T antigen require a functional J domain. J. Virol. 81:9481-9489
  44. Relyea, R.A. (2007) Getting out alive: How predators affect metamorphic decisions. Oecologia 152:389-400
  45. Reshmi, S.C., S. Roychoudhury, Z. Yu, E. Feingold, D. Potter, W.S. Saunders, and S.M. Gollin (2007) Inverted duplication pattern in anaphase bridges confirms the breakage-fusion-bridge (BFB) cycle model for 11q13 amplification. Cytogenet. Genome Res. 116:46-52
  46. Reshmi, S.C., X. Huang, D.W. Schoppy, R.C. Black, W.S. Saunders, D.I. Smith, and S.M. Gollin (2007) Relationship between FRA11F and 11q13 gene amplification in oral cancer. Gene Chromosome Canc. 46:143-154
  47. Retchless, A.C., and J.G. Lawrence (2007) Temporal fragmentation of speciation in bacteria. Science 317:1093-1096
  48. Rodina, A., M. Vilenchik, K. Moulick, J. Aguirre, J. Kim, A. Chiang, J. Litz, C.C. Clement, Y. Kang, Y. She, N. Wu, S. Felts, P. Wipf, J. Massague, X. Jiang, J.L. Brodsky, G.W. Krystal, and G. Chiosis (2007) Selective compounds define Hsp90 as a major inhibitor of apoptosis in small-cell lung cancer. Nat. Chem. Biol. 3:498-507
  49. Rubenstein, E.M., R.R. McCartney, C. Zhang, K.M. Shokat, M.K. Shirra, K.M. Arndt, and M.C. Schmidt (2007) Access denied: Snf1 activation loop phosphorylation is controlled by availability of the phosphorylated threonine 210 to the PP1 phosphatase. J Biol Chem :In Press
  50. Sáenz-Robles, M.T., D. Toma, P. Cantalupo, J. Zhou, H. Gong, C. Edwards, J.M. Pipas, and W. Xie (2007) Repression of Intestinal Drug Metabolizing Enzymes by the SV40 Large T Antigen. Oncogene :In Press
  51. Sáenz-Robles, M.T., J.A. Markovics, J.L. Chong, R. Opavsky, R.H. Whitehead, G. Leone, and J.M. Pipas (2007) Intestinal hyperplasia induced by simian virus 40 large tumor antigen requires E2F2. J. Virol. 81:13191-13199
  52. Saenz-Robles, M.T., J.A. Markovics, J.L. Chong, R. Opavsky, R.H. Whitehead, G. Leone, and J.M. Pipas (2007) Intestinal hyperplasia induced by simian virus 40 large tumor antigen requires E2F2. J. Virol. 81:13191-13199
  53. Sapienza, P.J., J.M. Rosenberg, and L. Jen-Jacobson (2007) Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease. Structure 15:1368-1382
  54. Scott, C.M., K.B. Kruse, B.Z. Schmidt, D.H. Perlmutter, A.A. McCracken, and J.L. Brodsky (2007) ADD66, a gene involved in the endoplasmic reticulum associated degradation (ERAD) of alpha-1-antitrypsin-Z in yeast, facilitates proteasome activity and assembly. Mol. Biol. Cell 18:3776-3787
  55. Selva, E.M., and B.E. Stronach (2007) Germline clone analysis for maternally acting Drosophila hedgehog components. Methods Mol. Biol. 397:129-144
  56. Sparvero, L.J., S. Patz, J.L. Brodsky, and C.M. Coughlan (2007) Proteomic analysis of the amyloid precursor protein fragment C99: expression in yeast. Anal. Biochem. 370:162-170
  57. Spring, J.H., S.R. Robichaux, N. Kaufmann, and J.L. Brodsky (2007) Localization of a Drosophila DRIP-like aquaporin in the malpighian tubules of the house cricket, Acheta domesticus. Comp. Biochem. Phys. A 148:92-100
  58. Spring, J.H., S.R. Robichaux, N. Kaufmann, and J.L. Brodsky (2007) Localization of a Drosophila DRIP-like aquaporin in the Malpighian tubules of the house cricket, Acheta domesticus. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 148:92-100
  59. Steets, J.A., D.E. Wolf, J.R. Auld, and T.-L. Ashman (2007) The role of natural enemies in the expression and evolution of mixed mating in hermaphrodite plants and animals. Evolution 61:2043-2055
  60. Steets, J.A., T.M. Knight, and T.-L. Ashman (2007) The interactive effects of herbivory and mixed mating for the population dynamics of Impatiens capensis. Am. Nat. 170:113-127
  61. Sullivan, C.S., A. Grundhoff, R. Treisman, J.M. Pipas, and D. Ganem (2007) Expression and function of microRNAs in viruses great and small. Cold Spring Harb. Sym. 71:351-365
  62. Szewczyk, N.J., B.K. Peterson, S.J. Barmada, L.P. Parkinson, and L.A. Jacobson (2007) Opposed growth factor signals control protein degradation in muscles of Caenorhabditis elegans. EMBO J 26:935-943
  63. Tonsor, S.J., and S.M. Scheiner (2007) Plastic trait integration across a CO2 gradient in Arabidopsis thaliana. Am. Nat. :In Press
  64. Traw, M.B., J.M. Kniskern, and J. Bergelson (2007) Sar increases fitness of Arabidopsis thaliana in the presence of natural bacterial pathogens. Evolution 61:2444-2449
  65. VanDemark, A.P., M. Kasten, E. Ferris, A. Heroux, C.P. Hill, and B.R. Cairns (2007) Autoregulation of the Rsc4 Tandem Bromodomain by Gcn5 acetylation. Mol. Cell :In Press
  66. Vergarajauregui, S., R. Oberdick, K. Kiselyov, and R. Puertollano (2007) Mucolipin-1 channel activity is regulated by protein kinase A mediated phosphorylation. Biochem. J. 0:
  67. Wahlman, J., G.N. Demartino, W.R. Skach, N.J. Bulleid, J.L. Brodsky, and A.E. Johnson (2007) Real-Time fluorescence detection of ERAD substrate retrotranslocation in a mammalian in vitro system. Cell 129:943-955
  68. Warner, M.H., K.L. Roinick, and K.M. Arndt (2007) Rtf1 is a multifunctional component of the Paf1 complex that regulates gene expression by directing cotranscriptional histone modification. Mol. Cell Biol. 27:6103-6115
  69. Weigele, P.R., W.H. Pope, M.L. Pedulla, J.M. Houtz, A.L. Smith, J.F. Conway, J. King, G.F. Hatfull, J.G. Lawrence, and R.W. Hendrix (2007) Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus. Environ. Microbiol. 9:1675-1695
  70. Weigele, P.R., W.H. Pope, M.L. Pedulla, J.M. Houtz, A.L. Smith, J.F. Conway, J. King, G.F. Hatfull, J.G. Lawrence, and R.W. Hendrix (2007) Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus. Environ. Microbiol. 9:1675-1695
  71. Welch, B., A.P. VanDemark, A. Heroux, C.P. Hill, and M.S. Kay (2007) Potent D-peptide inhibitor of HIV-1 entry. Proc. Natl. Acad. Sci., USA :
  72. Werner, E.E., D.K. Skelly, R.A. Relyea, and K.L. Yurewicz (2007) Amphibian species richness across environmental gradients. Oikos 116:1697-1712
  73. Werner, E.E., K.L. Yurewicz, D.K. Skelly, and R.A. Relyea (2007) Turnover in an amphibian metacommunity: the role of local and regional factors. Oikos 116:1713-1725
  74. Wildschutte, H., and J.G. Lawrence (2007) Differential Salmonella survival against communities of intestinal amoebae. Microbiology 1789:1781
  75. Worley, P.F., W. Zeng, G. Huang, J.Y. Kim, D.M. Shin, M.S. Kim, J.P. Yuan, K. Kiselyov, and S. Muallem (2007) Homer proteins in Ca2+ signaling by excitable and non-excitable cells. Cell Calcium 42:363-371
  76. Wright, C.M., S.W. Fewell, M.L. Sullivan, J.M. Pipas, S.C. Watkins, and J.L. Brodsky (2007) The hsp40 molecular chaperone, Ydj1p, along with the protein kinase C pathway, impact cell wall integrity in the yeast Saccharomyces cerevisiae. Genetics 175:1649-1664
  77. Wymore, T., D.W. Ii, and J. Hempel (2007) Mechanistic implications of the cysteine-nicotinamide adduct in aldehyde dehydrogenase based on quantum mechanical/molecular mechanical simulations. Biochemistry 46:9495-9506
  78. Yoder, M., and J.D. Hildebrand (2007) Shroom4 (KIAA1202) is an actin-associated protein implicated in cytoskeletal organization. Cell Motil. Cytoskel. 64:49-63

 
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