[360] I. Nimmrich, S. Erdmann, U. Melchers, S. Chtarbova, U. Finke, S. Hentsch, I. H<strong>of</strong>fmann, M. Oertel, W. H<strong>of</strong>fmann, and O. Muller. The novel ependymin related gene ucc1 is highly expressed in colorectal tumor cells. Cancer letters, 165(1):71–79, 2001. [361] S. Noctor, A. Flint, T. Weissman, W. Wong, B. Clinton, and A. Kriegstein. Dividing precursor cells <strong>of</strong> the embryonic cortical ventricular zone have morphological and molecular characteristics <strong>of</strong> radial glia. The Journal <strong>of</strong> neuroscience, 22(8):3161, 2002. [362] E. Noetzel, M. Rose, E. Sevinc, R. Hilgers, A. Hartmann, A. Naami, R. Knüchel, and E. Dahl. Intermediate filament dynamics and breast cancer: Aberrant promoter methylation <strong>of</strong> the synemin gene is associated with early tumor relapse. Oncogene, 29(34):4814–4825, 2010. [363] H. Noushmehr, D. Weisenberger, and K. Diefes. Identification <strong>of</strong> a CpG island methylator phenotype that defines a distinct subgroup <strong>of</strong> glioma. Cancer Cell, 2010. [364] J. Novakova, O. Slaby, and R. Vyzula. Microrna involvement in glioblastoma pathogenesis. Biochemical and biophysical research communications, 2009. [365] H. Ohgaki and P. Kleihues. Epidemiology and etiology <strong>of</strong> gliomas. Acta neuropathologica, 109(1):93–108, 2005. [366] K. Ohira, N. Funatsu, K. Homma, Y. Sahara, M. Hayashi, T. Kaneko, and S. Nakamura. Truncated trkb-t1 regulates the morphology <strong>of</strong> neocortical layer i astrocytes in adult rat brain slices. European Journal <strong>of</strong> Neuroscience, 25(2):406–416, 2007. [367] S. Okabe, K. Forsberg-Nilsson, A. Spiro, M. Segal, and R. McKay. Development <strong>of</strong> neuronal precursor cells and functional postmitotic neurons from embryonic stem cells in vitro. Mechanisms <strong>of</strong> development, 59(1):89–102, 1996. [368] Y. Okazaki, M. Furuno, T. Kasukawa, J. Adachi, H. Bono, S. Kondo, I. Nikaido, N. Osato, R. Saito, H. Suzuki, et al. Analysis <strong>of</strong> the mouse transcriptome based on functional annotation <strong>of</strong> 60,770 full-length cdnas. Nature, 420(6915):563–573, 2002. [369] M. Okoniewski, T. Yates, S. Dibben, and C. Miller. An annotation infrastructure for the analysis and interpretation <strong>of</strong> affymetrix exon array data. Genome biology, 8(5):R79, 2007. [370] P. Ongusaha, T. Ouchi, K. Kim, E. Nytko, J. Kwak, R. Duda, C. Deng, and S. Lee. Brca1 shifts p53-mediated cellular outcomes towards irreversible growth arrest. Oncogene, 22(24):3749–3758, 2003. [371] P. C. Orban, D. Chui, and J. D. Marth. Tissue- and site-specific DNA recombination in transgenic mice. Proceedings <strong>of</strong> the National Academy <strong>of</strong> Sciences <strong>of</strong> the United States <strong>of</strong> America, 89(15):6861–6865, Aug. 1992. [372] U. Ørom, T. Derrien, M. Beringer, K. Gumireddy, A. Gardini, G. Bussotti, F. Lai, M. Zytnicki, C. Notredame, Q. Huang, et al. Long noncoding rnas with enhancer-like function in human cells. Cell, 143(1):46–58, 2010. [373] E. Ostrakhovitch, P. Olsson, S. Jiang, and M. Cherian. Interaction <strong>of</strong> metallothionein with tumor suppressor p53 protein. FEBS letters, 580(5):1235–1238, 2006. [374] T. Ozawa, C. W. Brennan, L. Wang, M. Squatrito, T. Sasayama, M. Nakada, J. T. Huse, A. Pedraza, S. Utsuki, Y. Yasui, A. Tandon, E. I. Fomchenko, H. Oka, R. L. Levine, K. Fujii, M. Ladanyi, and E. C. Holland. PDGFRA gene rearrangements are frequent genetic events in PDGFRA-amplified glioblastomas. Genes & Development, 24(19):2205–2218, Oct. 2010. [375] L. Pacey, J. Stead, A. Gleave, K. Tomczyk, and L. Doering. <strong>Neural</strong> stem cell culture: neurosphere generation, microscopical analysis and cryopreservation. Nat. Protoc, 215:1–14, 2006. [376] T. Palmer, P. Schwartz, P. Taupin, B. Kaspar, S. Stein, and F. Gage. Cell culture: Progenitor cells from human brain after death. Nature, 411(6833):42–43, 2001. [377] P. Pandolfi. Breast cancerÂŮloss <strong>of</strong> pten predicts resistance to treatment. New England Journal <strong>of</strong> Medicine, 351(22):2337–2338, 2004. [378] K. Paraiso, Y. Xiang, V. Rebecca, E. Abel, Y. Chen, A. Munko, E. Wood, I. Fedorenko, V. Sondak, A. Anderson, et al. Pten loss confers braf inhibitor resistance to melanoma cells through the suppression <strong>of</strong> bim expression. Cancer research, 71(7):2750–2760, 2011.
[379] D. Park and J. Rich. Biology <strong>of</strong> glioma cancer stem cells. Molecules and cells, 28(1):7– 12, 2009. [380] H. Park, I. Han, H. Kwon, and E. Oh. Focal adhesion kinase regulates syndecan- 2–mediated tumorigenic activity <strong>of</strong> ht1080 fibrosarcoma cells. Cancer research, 65(21):9899–9905, 2005. [381] J. Park, J. Jung, M. Seo, S. Kang, Y. Lee, and K. Kang. Dner modulates adipogenesis <strong>of</strong> human adipose tissue-derived mesenchymal stem cells via regulation <strong>of</strong> cell proliferation. Cell proliferation, 43(1):19–28, 2010. [382] D. Parry, D. Mahony, K. Wills, and E. Lees. Cyclin d-cdk subunit arrangement is dependent on the availability <strong>of</strong> competing ink4 and p21 class inhibitors. Molecular and cellular biology, 19(3):1775, 1999. [383] D. Parsons, S. Jones, X. Zhang, J. Lin, and R. Leary. An integrated genomic analysis <strong>of</strong> human glioblastoma multiforme. Science, 2008. [384] H. Pasantes-Morales and A. Schousboe. Role <strong>of</strong> taurine in osmoregulation in brain cells: mechanisms and functional implications. Amino Acids, 12(3):281–292, 1997. [385] L. Patrawala, T. Calhoun, R. Schneider-Broussard, J. Zhou, K. Claypool, and D. Tang. Side population is enriched in tumorigenic, stem-like cancer cells, whereas abcg2+ and abcg2- cancer cells are similarly tumorigenic. Cancer research, 65(14):6207, 2005. [386] K. Paulsson, M. Kleijmeer, J. Griffith, M. Jevon, S. Chen, P. Anderson, H. Sjögren, S. Li, and P. Wang. Association <strong>of</strong> tapasin and copi provides a mechanism for the retrograde transport <strong>of</strong> major histocompatibility complex (mhc) class i molecules from the golgi complex to the endoplasmic reticulum. Journal <strong>of</strong> Biological Chemistry, 277(21):18266, 2002. [387] G. Paxinos, J. Mai, and S. O. service). The Human Nervous System. Elsevier Academic Press London, 2004. [388] G. Pearson, F. Robinson, T. Gibson, B. Xu, M. Karandikar, K. Berman, and M. Cobb. Mitogen-activated protein (map) kinase pathways: regulation and physiological functions. Endocrine reviews, 22(2):153–183, 2001. [389] L. Pevny and M. Placzek. Sox genes and neural progenitor identity. Current opinion in neurobiology, 15(1):7–13, 2005. [390] H. S. Phillips, S. Kharbanda, R. Chen, W. F. Forrest, R. H. Soriano, T. D. Wu, A. Misra, J. M. Nigro, H. Colman, L. Soroceanu, P. M. Williams, Z. Modrusan, B. G. Feuerstein, and K. Aldape. Molecular subclasses <strong>of</strong> high-grade glioma predict prognosis, delineate a pattern <strong>of</strong> disease progression, and resemble stages in neurogenesis. Cancer Cell, 9(3):157–173, Mar. 2006. [391] J. Phillips, E. Huillard, A. Robinson, A. Ward, D. Lum, M. Polley, S. Rosen, D. Rowitch, and Z. Werb. Heparan sulfate sulfatase sulf2 regulates pdgfrα signaling and growth in human and mouse malignant glioma. The Journal <strong>of</strong> clinical investigation, 122(3):911, 2012. [392] S. Piccirillo, B. Reynolds, N. Zanetti, G. Lamorte, E. Binda, G. Broggi, H. Brem, A. Olivi, F. Dimeco, A. Vescovi, et al. Bone morphogenetic proteins inhibit the tumorigenic potential <strong>of</strong> human brain tumour-initiating cells. Nature, 444(7120):761, 2006. [393] S. G. Piccirillo, E. Binda, R. Fiocco, A. L. Vescovi, and K. Shah. Brain cancer stem cells. Journal <strong>of</strong> molecular medicine, 87(11):1087–95, 2009. [394] R. Piet, L. Vargová, E. Syková, D. Poulain, and S. Oliet. Physiological contribution <strong>of</strong> the astrocytic environment <strong>of</strong> neurons to intersynaptic crosstalk. Proceedings <strong>of</strong> the National Academy <strong>of</strong> Sciences <strong>of</strong> the United States <strong>of</strong> America, 101(7):2151, 2004. [395] D. Pinto and H. Clevers. Wnt control <strong>of</strong> stem cells and differentiation in the intestinal epithelium. Experimental cell research, 306(2):357–363, 2005. [396] A. Pitre, N. Davis, M. Paul, A. Orr, and O. Skalli. Synemin promotes akt-dependent glioblastoma cell proliferation by antagonizing pp2a. Molecular biology <strong>of</strong> the cell, 23(7):1243–1253, 2012. [397] S. Pleasure, C. Page, and V. Lee. Pure, postmitotic, polarized human neurons derived from ntera 2 cells provide a system for expressing exogenous proteins in terminally differentiated neurons. The Journal <strong>of</strong> neuroscience, 12(5):1802, 1992.
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- Page 323 and 324: Bibliography [1] Cell signaling tec
- Page 325 and 326: [38] G. Bain, D. Kitchens, M. Yao,
- Page 327 and 328: [78] S. Bustin, V. Benes, J. Garson
- Page 329 and 330: [112] M. Czystowska, J. Han, M. Szc
- Page 331 and 332: [153] T. Fujiwara, M. Bandi, M. Nit
- Page 333 and 334: [192] M. Hernandez, M. Nieto, and M
- Page 335 and 336: [231] T.-M. Kim, W. Huang, R. Park,
- Page 337 and 338: [268] H. Lemjabbar-Alaoui, A. van Z
- Page 339 and 340: [305] K. MAEDA, S. MATSUHASHI, K. T
- Page 341: [342] H. Moon, M. Ahn, J. Park, K.
- Page 345 and 346: [417] P. Rakic. Guidance of neurons
- Page 347 and 348: [456] T. Shima, N. Okumura, T. Taka
- Page 349 and 350: [490] P. A. C. t’Hoen, Y. Ariyure
- Page 351 and 352: [523] T. Watanabe, A. Takeda, T. Ts