2005

Original Research Papers

Alder MN, Rogozin IB, Iyer LM, Glazko GV, Cooper MD, Pancer Z. Diversity and function of adaptive immune receptors in a jawless vertebrate. Science. 2005;310:1970-1973. Abstract

Anderson LK, Royer SM, Page SL, McKim KS, Lai A, Lilly MA, Hawley RS. Juxtaposition of C(2)M and the transverse filament protein C(3)G within the central region of Drosophila synaptonemal complex. Proc Natl Acad Sci U S A. 2005;102:4482-4487. Abstract

Brandman O, Ferrell JE, Jr., Li R, Meyer T. Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science. 2005;310:496-498. Abstract

Bunch JT, Bae NS, Leonardi J, Baumann P. Distinct requirements for pot1 in limiting telomere length and maintaining chromosome stability. Mol Cell Biol. 2005;25:5567-5578. Abstract

Cai Y, Jin J, Florens L, Swanson SK, Kusch T, Li B, Workman JL, Washburn MP, Conaway RC, Conaway JW. The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes. J Biol Chem. 2005:13665-13670. Abstract

Carrozza MJ, Florens L, Swanson SK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex. Biochim Biophys Acta. 2005;1731:77-87; discussion 75-76. Abstract

Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription. Cell. 2005;123:581-592. Abstract

Chen EI, Florens L, Axelrod FT, Monosov E, Barbas CF, 3rd, Yates JR, 3rd, Felding-Habermann B, Smith JW. Maspin alters the carcinoma proteome. FASEB J. 2005;19:1123-1124. Abstract

Cui W, Sproul LR, Gustafson SM, Matthies HJ, Gilbert SP, Hawley RS. Drosophila nod protein binds preferentially to the plus ends of microtubules and promotes microtubule polymerization in vitro. Mol Biol Cell. 2005;16:5400-5409. Abstract

Cui W, Hawley RS. The HhH(2)/NDD Domain of the Drosophila Nod Chromokinesin-Like Protein Is Required for Binding to Chromosomes in the Oocyte Nucleus. Genetics. 2005. Abstract

Delfini MC, Dubrulle J, Malapert P, Chal J, Pourquie O. Control of the segmentation process by graded MAPK/ERK activation in the chick embryo. Proc Natl Acad Sci U S A. 2005;102:11343-11348. Abstract

Dickey-Sims C, Robertson AJ, Rupp DE, McCarthy JJ, Coffman JA. Runx-dependent expression of PKC is critical for cell survival in the sea urchin embryo. BMC Biol. 2005;3:18. Abstract

Egile C, Rouiller I, Xu XP, Volkmann N, Li R, Hanein D. Mechanism of Filament Nucleation and Branch Stability Revealed by the Structure of the Arp2/3 Complex at Actin Branch Junctions. PLoS Biol. 2005;3:e383. Abstract

Ercan S, Reese JC, Workman JL, Simpson RT. Yeast recombination enhancer is stimulated by transcription activation. Mol Cell Biol. 2005;25:7976-7987. Abstract

Ferreira ME, Hermann S, Prochasson P, Workman JL, Berndt KD, Wright AP. Mechanism of transcription factor recruitment by acidic activators. J Biol Chem. 2005. Abstract

Ferretti E, Cambronero F, Tumpel S, Longobardi E, Wiedemann LM, Blasi F, Krumlauf R. Hoxb1 Enhancer and Control of Rhombomere 4 Expression: Complex Interplay between PREP1-PBX1-HOXB1 Binding Sites. Mol Cell Biol. 2005;25:8541-8552. Abstract

Gilliland WD, Wayson S, Hawley RS. The Meiotic Defects of Mutants in the Drosophila mps1 Gene Reveal A Critical Role of Mps1 in the Segregation of Achiasmate Homologs. Curr Biol. 2005;15:672-677. Abstract

Glazko G, Gordon A, Mushegian A. The choice of optimal distance measure in genome-wide datasets. Bioinformatics. 2005;21:iii3-iii11. Abstract

Gong WJ, McKim KS, Hawley RS. All Paired Up with No Place to Go: Pairing, Synapsis, and DSB Formation in a Balancer Heterozygote. PLoS Genet. 2005;1:e67. Abstract

Hall N, Karras M, Raine JD, Carlton JM, Kooij TW, Berriman M, Florens L, Janssen CS, Pain A, Christophides GK, James K, Rutherford K, Harris B, Harris D, Churcher C, Quail MA, Ormond D, Doggett J, Trueman HE, Mendoza J, Bidwell SL, Rajandream MA, Carucci DJ, Yates JR, 3rd, Kafatos FC, Janse CJ, Barrell B, Turner CM, Waters AP, Sinden RE. A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science. 2005;307:82-86. Abstract

Heuze ML, Guibal FC, Banks CA, Conaway JW, Conaway RC, Cayre YE, Benecke A, Lutz PG. ASB2 Is an Elongin BC-interacting Protein That Can Assemble with Cullin 5 and Rbx1 to Reconstitute an E3 Ubiquitin Ligase Complex. J Biol Chem. 2005;280:5468-5474. Abstract

Hilgers V, Pourquie O, Dubrulle J. In vivo analysis of mRNA stability using the Tet-Off system in the chicken embryo. Dev Biol. 2005;284:292-300. Abstract

Huang JK, Phillips GR, Roth AD, Pedraza L, Shan W, Belkaid W, Mi S, Fex-Svenningsen A, Florens L, Yates JR, 3rd, Colman DR. Glial membranes at the node of Ranvier prevent neurite outgrowth. Science. 2005;310:1813-1817. Abstract

Jin J, Cai Y, Yao T, Gottschalk AJ, Florens L, Swanson SK, Gutierrez JL, Coleman MK, Workman JL, Mushegian A, Washburn MP, Conaway RC, Conaway JW. A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex. J Biol Chem. 2005;280:41207-41212. Abstract

Kasemeier-Kulesa JC, Kulesa PM, Lefcort F. Imaging neural crest cell dynamics during formation of dorsal root ganglia and sympathetic ganglia. Development. 2005;132:235-245. Abstract

Kirilly D, Spana EP, Perrimon N, Padgett RW, Xie T. BMP Signaling Is Required for Controlling Somatic Stem Cell Self-Renewal in the Drosophila Ovary. Dev Cell. 2005;9:651-662. Abstract

Kong SE, Banks CA, Shilatifard A, Conaway JW, Conaway RC. ELL-associated factors 1 and 2 are positive regulators of RNA polymerase II elongation factor ELL. Proc Natl Acad Sci U S A. 2005;102:10094-10098. Abstract

Kozbial PZ, Mushegian AR. Natural history of S-adenosylmethionine-binding proteins. BMC Struct Biol. 2005;5:19. Abstract

Kulesa PM, Lu CC, Fraser SE. Time-Lapse Analysis Reveals a Series of Events by Which Cranial Neural Crest Cells Reroute around Physical Barriers. Brain Behav Evol. 2005;66:255-265. Abstract

Lee D, Ezhkova E, Li B, Pattenden SG, Tansey WP, Workman JL. The Proteasome Regulatory Particle Alters the SAGA Coactivator to Enhance Its Interactions with Transcriptional Activators. Cell. 2005;123:423-436.

Lee KK, Florens L, Swanson SK, Washburn MP, Workman JL. The deubiquitylation activity of Ubp8 is dependent upo n Sgf11 and its association with the SAGA complex. Mol Cell Biol. 2005;25:1173-1182. Abstract

Li B, Pattenden SG, Lee D, Gutierrez J, Chen J, Seidel C, Gerton J, Workman JL. Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc Natl Acad Sci U S A. 2005. Abstract

Maroto M, Dale JK, Dequeant ML, Petit AC, Pourquie O. Synchronised cycling gene oscillations in presomitic mesoderm cells require cell-cell contact. Int J Dev Biol. 2005;49:309-315. Abstract

Minakhin L, Semenova E, Liu J, Vasilov A, Severinova E, Gabisonia T, Inman R, Mushegian A, Severinov K. Genome sequence and gene expression of Bacillus anthracis bacteriophage Fah. J Mol Biol. 2005;354:1-15. Abstract

Mushegian A. Protein content of minimal and ancestral ribosome. RNA. 2005;11:1400-1406. Abstract

Page SL, Hawley RS. The Drosophila Meiotic Mutant mei-352 Is an Allele of klp3A and Reveals a Role for a Kinesin-like Protein in Crossover Distribution. Genetics. 2005;170:1797-1807. Abstract

Pourquie O. Segmentation and somitogeneisis in vertebrates. McGraw-Hill Yearbook of Science & Technology 2005. New York ; London: McGraw-Hill; 2004:432.*

Prochasson P, Florens L, Swanson SK, Washburn MP, Workman JL. The HIR corepressor complex binds to nucleosomes generating a distinct protein/DNA complex resistant to remodeling by SWI/SNF. Genes Dev. 2005;19:2534-2539. Abstract

Ren J, Shi M, Liu R, Yang QH, Johnson T, Skarnes WC, Du C. The Birc6 (Bruce) gene regulates p53 and the mitochondrial pathway of apoptosis and is essential for mouse embryonic development. Proc Natl Acad Sci U S A. 2005;102:565-570. Abstract

Ruan C, Workman JL, Simpson RT. The DNA repair protein yKu80 regulates the function of recombination enhancer during yeast mating type switching. Mol Cell Biol. 2005;25:8476-8485. Abstract

Schneider J, Wood A, Lee JS, Schuster R, Dueker J, Maguire C, Swanson SK, Florens L, Washburn MP, Shilatifard A. Molecular regulation of histone H3 trimethylation by COMPASS and the regulation of gene expression. Mol Cell. 2005;19:849-856. Abstract

Serpente P, Tumpel S, Ghyselinck NB, Niederreither K, Wiedemann LM, Dolle P, Chambon P, Krumlauf R, Gould AP. Direct crossregulation between retinoic acid receptor {beta} and Hox genes during hindbrain segmentation. Development. 2005;132:503-513. Abstract

Shia WJ, Osada S, Florens L, Swanson SK, Washburn MP, Workman JL. Characterization of the yeast trimeric-SAS acetyltransferase complex. J Biol Chem. 2005;280:11987-11994. Abstract

Stark DA, Kulesa PM. Photoactivatable green fluorescent protein as a single-cell marker in living embryos. Dev Dyn. 2005;233:983-992. Abstract

Stewart PL, Makabi M, Lang J, Dickey-Sims C, Robertson AJ, Coffman JA, Suprenant KA. Sea urchin vault structure, composition, and differential localization during development. BMC Dev Biol. 2005;5:3. Abstract

Teddy JM, Lansford R, Kulesa PM. Four-Color, 4D Time-Lapse Confocal Imaging of Chick Embryos. Biotechniques. 2005;39:703-710. Abstract

Thummel R, Burket CT, Brewer JL, Sarras MP, Jr., Li L, Perry M, McDermott JP, Sauer B, Hyde DR, Godwin AR. Cre-mediated site-specific recombination in zebrafish embryos. Dev Dyn. 2005;233:1366-1377. Abstract

Tian Q, He XC, Hood L, Li L. Bridging the BMP and Wnt pathways by PI3 kinase/Akt and 14-3-3zeta. Cell Cycle. 2005;4:215-216. Abstract

Trainor PA. Specification of neural crest cell formation and migration in mouse embryos. Semin Cell Dev Biol. 2005;16:683-693. Abstract

Trujillo KM, Bunch JT, Baumann P. Extended DNA binding site in Pot1 broadens sequence specificity to allow recognition of heterogeneous fission yeast telomeres. J Biol Chem. 2005;280:9119-9128. Abstract

Tsuchida T, Berlin WK, Sauer B. Dual chromogenic reporter gene detection in mammalian cells with lacZ and arabinofuranosidase. Biotechniques. 2004;37:896-897. Abstract *

Vermot J, Pourquie O. Retinoic acid coordinates somitogenesis and left-right patterning in vertebrate embryos. Nature. 2005;435:215-220. Abstract

Xi R, Doan C, Liu D, Xie T. Pelota controls self-renewal of germline stem cells by repressing a Bam-independent differentiation pathway. Development. 2005;132:5365-5374. Abstract

Xi R, Kirilly D, Xie T. Molecular mechanisms controlling germline and somatic stem cells: similarities and differences. Curr Opin Genet Dev. 2005;15:381-387. Abstract

Xi R, Xie T. Stem cell self-renewal controlled by chromatin remodeling factors. Science. 2005;310:1487-1489. Abstract

Zybailov B, Coleman MK, Florens L, Washburn MP. Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem. 2005;77:6218-6224. Abstract

Reviews, Commentaries and Chapters

Abmayr SM, Balagopalan L, Galletta BJ, Hong S-J. Myogenesis and Muscle Development. In: L Gilbert, I K., and S Gill, eds. Comprehensive Molecular Insect Science. 1st ed. San Diego, CA: Pergamon; Elsevier LTD; ^©2005;2:p. 1-45. Table of Contents

Baumann P. Taking control of G-quadruplexes. Nat Struct Mol Biol. 2005;12:832-833. Abstract

Coffman JA. On reductionism, organicism, somatic mutations and cancer. Bioessays. 2005;27:459. Abstract

Conaway JW, Florens L, Sato S, Tomomori-Sato C, Parmely TJ, Yao T, Swanson SK, Banks CAS, Washburn MP, Conaway RC. The Mammalian Mediator Complex. FEBS Lett. 2005;579:904-908. Abstract

Conaway RC, Sato S, Tomomori-Sato C, Yao T, Conaway JW. The mammalian Mediator complex and its role in transcriptional regulation. Trends Biochem Sci. 2005;30:250-255. Abstract

Danforth WH, Neaves WB. Using words carefully. Science. 2005;309:1815-1816. Abstract

Dequeant ML, Pourquie O. Chicken genome: new tools and concepts. Dev Dyn. 2005;232:883-886. Abstract

Gerton J. Chromosome cohesion: a cycle of holding together and falling apart. PLoS Biol. 2005;3:e94. Abstract

Gerton JL, Hawley RS. Homologous chromosome interactions in meiosis: diversity amidst conservation. Nat Rev Genet. 2005;6:477-487. Abstract

Gilliland WD, Hawley RS. Cohesin and the maternal age effect. Cell. 2005;123:371-373. Abstract

Glazko GV, Koonin EV, Rogozin IB. Molecular dating: ape bones agree with chicken entrails. Trends Genet. 2005;21:89-92. Abstract

He XC, Li L. Reply to Re-examination of P-PTEN staining patterns in the intestinal crypt. Nat Genet. 2005;37:1017-1018. Abstract

He XC, Zhang J, Li L. Cellular and molecular regulation of hematopoietic and intestinal stem cell behavior. Book Chapter for Ann Rev Cell Dev Biol; In: Stem Cell Biology: Development and Plasticity; 2005;1049:28-38. Abstract

Jin J, Cai Y, Li B, Conaway RC, Workman JL, Conaway JW, Kusch T. In and out: histone variant exchange in chromatin. Trends Biochem Sci. 2005;30:680-687. Abstract

Jones NC, Trainor PA. Role of morphogens in neural crest cell determination. J Neurobiol. 2005;64:388-404. Abstract

Koonin EV, Rogozin IB, Glazko GV. p53 gain-of-function: tumor biology and bioinformatics come together. Cell Cycle. 2005;4:686-688. Abstract

Krull CE, McLennan R, O'Connell S, Chen Y, Trainor PA. In Vivo Electroporation during Embryogenesis In: R Yuste, and A Konnerth, eds. Imaging in Neuroscience and Development: A Llaboratory Manual. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press; 2005:79-94. Table of Contents

Lake CM, Hawley RS. A new target for POLO in meiotic centromere cohesion. Dev Cell. 2005;8:5-7. Abstract

Li B, Ruan C, Workman JL. Histones: should I stay or should I go? Genome Biol. 2005;6:306. Abstract

Li L. Finding the Hematopoietic Stem Cell Niche in Placenta. Dev Cell. 2005;8:297-304. Abstract

Li L, Xie T. Stem Cell Niche: Structure and Function. Annu Rev Cell Dev Biol. 2005;17:605-631. Abstract

Neaves WB. The ends and means of stem cell research. Practical Bioethics. 2005;1:3-5.

Neaves WB. Stem cells from somatic cell nuclear transfer: research to unlock the body's potential for self-repair. Mo Med. 2005;102:14-17. Abstract

Noden DM, Trainor PA. Relations and interactions between cranial mesoderm and neural crest populations. J Anat. 2005;207:575-601. Abstract

Pattenden SG, Chandy MJ, Gutierrez JL, Workman JL. Chromatin dynamics rule the genome. Genome Biol. 2005;6:355. Abstract

Pourquie O. Signal transduction: a new canon. Nature. 2005;433:208-209. Abstract

Rosa-Molinar E, Krumlauf RK, Pritz MB. Hindbrain development and evolution: past, present, and future. Brain Behav Evol. 2005;66:219-221. Abstract  **

Stark D, Kulesa P. In vivo marking of single cells in chick embryos using photoactivation of GFP. Current Protocols in Cell Biology. 2005; Supplement 28:12.18.1-12.18.11.

Swanson SK, Washburn MP. The continuing evolution of shotgun proteomics. Drug Discov Today. 2005;10:719-725. Abstract

Trainor PA. Specification and patterning of neural crest cells during craniofacial development. Brain Behav Evol. 2005;66:266-280. Abstract

Wong MD, Jin Z, Xie T. Molecular Mechanisms of Germline Stem Cell Regulation. Annu Rev Genet. 2005:173-195. Abstract

Xie T, Kawase E, Kirilly D, Wong MD. Intimate relationships with their neighbors: Tales of stem cells in Drosophila reproductive systems. Dev Dyn. 2005;232:775-790. Abstract

Zhang J, Li L. BMP signaling and stem cell regulation. Dev Biol. 2005;284:1-11. Abstract

Zybailov B, Washburn MP. Mass Spectrometry-based Methods of Proteome Analysis. Encyclopedia of molecular cell biology and molecular medicine. 2nd ed. Weinheim: Wiley-VCH Verlag; 2005;8:1-43. Table of Contents and Cover

Books

Richards JE, Hawley RS. The Human Genome: A User's Guide. 2nd Ed. San Diego, Calif.: Elsevier Academic Press; 2005. TOC

 *     This article was published in 2004 and not included in the 2004 SIMR Publications Book.

**   Publisher error. Correct reference:  Rosa-Molinar E, Krumlauf R, Pritz MB. Hindbrain development and evolution: past, present, and future. Brain Behav Evol.
       2005;66:219-221.