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| [[Image:Stuff_banner.jpg]]
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| <div style="padding: 20px; color: #ffffff; background-color: #000; width: 757px">
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| <center>
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| [http://openwetware.org/wiki/Bateman <font face="trebuchet ms" style="color:#ffffff"> '''Home''' </font>]
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| [http://openwetware.org/wiki/Bateman:Research <font face="trebuchet ms" style="color:#ffffff"> '''Research''' </font>]
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| [http://openwetware.org/wiki/Bateman:Labmembers <font face="trebuchet ms" style="color:#ffffff"> '''Lab Members''' </font>]
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| [http://openwetware.org/wiki/Bateman:Reprints <font face="trebuchet ms" style="color:#ffffff"> '''Publications''' </font>]
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| [http://openwetware.org/wiki/Bateman:Links <font face="trebuchet ms" style="color:#ffffff"> '''Links''' </font>]
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| [http://openwetware.org/wiki/Bateman:LabStuff <font face="trebuchet ms" style="color:#ffffff"> '''Lab Stuff''' </font>]
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| [http://openwetware.org/wiki/Bateman:Tools <font face="trebuchet ms" style="color:#ffffff"> '''Tools''' </font>]
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| </center>
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| </div><br>
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| == Links ==
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| [http://www.kcep.co.uk/swl/kcep_index.html KCL purchasing]
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| == Files ==
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| [[Media: Fly_stock_template.xls]]
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| [[Media: Antibody stocks template.xls]]
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| [[Media: Bacterial stocks template.xls]]
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| [[Media: Plasmids template.xls]]
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| [[Media: Vector_data_sheet.doc]]
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| [[Media: Imaging_files_database_template.xls]]
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| == Journal Club articles ==
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| '''2015'''
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=26641712 Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt.
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| Murn J, Teplova M, Zarnack K, Shi Y1,, Patel DJ. Nat Struct Mol Biol. 2016 Jan;23(1):16-23. doi: 10.1038/nsmb.3140]
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=26783299 Loss of OMA1 delays neurodegeneration by preventing stress-induced OPA1 processing in mitochondria. Korwitz A, Merkwirth C, Richter-Dennerlein R, Tröder SE, Sprenger HG, Quirós PM, López-Otín C, Rugarli EI, Langer T. J Cell Biol. 2016 Jan 18;212(2):157-66]
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=24807906 γ-Tubulin controls neuronal microtubule polarity independently of Golgi outposts Michelle M. Nguyena, Christie J. McCrackena,*, E. S. Milnera,†, Daniel J. Goetschiusa, Alexis T. Weinera, Melissa K. Longa, Nick L. Michaela, Sean Munrob, and Melissa M. Rolls Mol Biol Cell. 2014 Jul 1;25(13):2039-50]
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=26219626 Changes in neuronal CycD/Cdk4 activity affect aging, neurodegeneration, and oxidative stress. Icreverzi A1, de la Cruz AF2, Walker DW1, Edgar BA3. Aging Cell. 2015 Oct;14(5):896-906]
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| [http://www.ncbi.nlm.nih.gov/pubmed/26143260 S6K Promotes Dopaminergic Neuronal Differentiation Through PI3K/Akt/mTOR-Dependent Signaling Pathways in Human Neural Stem Cells. Lee JE1,2, Lim MS1,3, Park JH1,2, Park CH4,5, Koh HC6,7. Mol Neurobiol. 2015]
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| [http://www.ncbi.nlm.nih.gov/pubmed/25418722 Defining the role of oxygen tension in human neural progenitor fate.
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| Xie Y1, Zhang J2, Lin Y3, Gaeta X3, Meng X3, Wisidagama DR4, Cinkornpumin J1, Koehler CM5, Malone CS4, Teitell MA6, Lowry WE7. Stem Cell Reports. 2014 Nov 11;3(5):743-57]
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=25451918 Topoisomerase II Regulates the Maintenance of DNA Methylation. Lin-Yu Lu, Henry Kuang, Gautam Korakavi and Xiaochun Yu. (2014). The Journal of Biological Chemistry, 290, 851-860]
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=25642965 Mitochondrial DNA stress primes the antiviral innate immune response. West AP1, Khoury-Hanold W2, Staron M2, Tal MC2, Pineda CM1, Lang SM1, Bestwick M1, Duguay BA3, Raimundo N1, MacDuff DA4, Kaech SM5, Smiley JR3, Means RE1, Iwasaki A5, Shadel GS6. Nature. 2015 Feb 2. doi: 10.1038/nature14156]
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| [http://www.ncbi.nlm.nih.gov/pubmed/25126791 Ecdysone and mediator change energy metabolism to terminate proliferation in Drosophila neural stem cells.
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| Homem CC, Steinmann V, Burkard TR, Jais A, Esterbauer H, Knoblich JA Cell 2014 874-88]
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| [http://www.sciencemag.org/content/344/6179/97. Neuronal Control of Drosophila Walking Direction. Salil S. Bidaye*, Christian Machacek, Yang Wu†, Barry J. Dickson†‡ Science 4 April 2014: Vol. 344 no. 6179 pp. 97-101]
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| [http://www.ncbi.nlm.nih.gov/pubmed/23172145 Autism-related deficits via dysregulated eIF4E-dependent translational control. Gkogkas CG1, Khoutorsky A, Ran I, Rampakakis E, Nevarko T, Weatherill DB, Vasuta C, Yee S, Truitt M, Dallaire P, Major F, Lasko P, Ruggero D, Nader K, Lacaille JC, Sonenberg N. Nature. 2013 Jan 17;493(7432):371-7]
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=25192935 Progressive increase in mtDNA 3243A>G heteroplasmy causes abrupt transcriptional reprogramming. Picard M, Zhang J2, Hancock S, Derbeneva O, Golhar R, Golik P, O'Hearn S, Levy S, Potluri P, Lvova M, Davila A, Lin CS, Perin JC, Rappaport EF, Hakonarson H, Trounce IA, Procaccio V, Wallace DC.Proc Natl Acad Sci U S A. 2014 Sep 23;111(38):E4033-42]
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| '''2014'''
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=24899720 Genetic reduction of mammalian target of rapamycin ameliorates Alzheimer's disease-like cognitive and pathological deficits by restoring hippocampal gene expression signature J Neurosci. 2014 Jun 4;34(23):7988-9]
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| [http://www.ncbi.nlm.nih.gov/pubmed/24979777 An uncoupling channel within the c-subunit ring of the F1FO ATP synthase is the mitochondrial permeability transition pore Alavian KN1, Beutner G2, Lazrove E3, Sacchetti S3, Park HA3, Licznerski P3, Li H3, Nabili P3, Hockensmith K2, Graham M4, Porter GA Jr5, Jonas EA6. Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10580-5]
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| [http://www.cell.com/neuron/abstract/S0896-6273%2813%2901087-8 Insulin/IGF1 Signaling Inhibits Age-Dependent Axon Regeneration Alexandra B. Byrne, Trent Walradt, Kathryn E. Gardner, Austin Hubbert, Valerie Reinke, Marc Hammarlund (2014) Neuron 81 561-573]
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| [http://www.ncbi.nlm.nih.gov/pubmed/24912190 Genome-wide RNAi screen identifies the Parkinson disease GWAS risk locus SREBF1 as a regulator of mitophagy Ivatt RM, Sanchez-Martinez A1, Godena VK, Brown S, Ziviani E, Whitworth AJ. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8494-9]
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| [http://www.sciencedirect.com/science/article/pii/S1550413113001459 Epigenetic Silencing Mediates Mitochondria Stress-Induced Longevity Elizabeth A. Schroeder, Nuno Raimundo, Gerald S. Shadel Cell Metabolism 17 4 Pages 954–964]
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| [http://www.ncbi.nlm.nih.gov/pubmed/24645666 PI3K-p110-alpha-subtype signalling mediates survival, proliferation and neurogenesis of cortical progenitor cells via activation of mTORC2 Wahane SD, Hellbach N, Prentzell MT, Weise SC, Vezzali R, Kreutz C, Timmer J, Krieglstein K, Thedieck K, Vogel T. J Neurochem. 2014 Mar 19. doi: 10.1111/jnc.12718]
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| [http://www.ncbi.nlm.nih.gov/pubmed/24768297 PTENα, a PTEN Isoform Translated through Alternative Initiation, Regulates Mitochondrial Function and Energy Metabolism.
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| Liang H1, He S1, Yang J1, Jia X2, Wang P1, Chen X1, Zhang Z2, Zou X1, McNutt MA1, Shen WH3, Yin Y4.Cell Metab. 2014 May 6;19(5):836-48]
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| [http://www.ncbi.nlm.nih.gov/pubmed/23827738 Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system.Bassett AR, Tibbit C, Ponting CP, Liu JL. Cell Rep. 2013 4:220-8]
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=24553947 Loss of PINK1 Attenuates HIF-1α Induction by Preventing 4E-BP1-Dependent Switch in Protein Translation under Hypoxia. Lin W, Wadlington NL, Chen L, Zhuang X, Brorson JR, Kang UJ. J Neurosci. 2014 Feb 19;34(8):3079-89]
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=24485457 Sensing of amino acids in a dopaminergic circuitry promotes rejection of an incomplete diet in Drosophila. Bjordal M, Arquier N, Kniazeff J, Pin JP, Léopold P. Cell. 2014 Jan 30;156(3):510-21]
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| [http://www.ncbi.nlm.nih.gov/pubmed/23665475 A temporal mechanism that produces neuronal diversity in the Drosophila visual center
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| Suzuki T, Kaido M, Takayama R, Sato M. Dev Biol. 2013 Aug 1;380(1):12-24]
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| '''2013'''
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| [http://www.ncbi.nlm.nih.gov/pubmed/24206664 mTORC1 Controls Mitochondrial Activity and Biogenesis through 4E-BP-Dependent Translational Regulation. Morita M, Gravel SP, Chénard V, Sikström K, Zheng L, Alain T, Gandin V, Avizonis D, Arguello M, Zakaria C, McLaughlan S, Nouet Y, Pause A, Pollak M, Gottlieb E, Larsson O, St-Pierre J, Topisirovic I, Sonenberg N. Cell Metab. 2013 Nov 5;18(5):698-711]
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| [http://www.ncbi.nlm.nih.gov/pubmed/24026126 midlife crisis encodes a conserved zinc-finger protein required to maintain neuronal differentiation in Drosophila. Carney TD, Struck AJ, Doe CQ. Development. 2013 Oct;140(20):4155-64]
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=23516108 Bigenomic transcriptional regulation of all thirteen cytochrome c oxidase subunit genes by specificity protein 1. Dhar SS, Johar K, Wong-Riley MT. Open Biol. 2013 Mar 20;3(3):120176]
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| [http://www.ncbi.nlm.nih.gov/pubmed/?term=23509287 The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo. Proc Natl Acad Sci U S A. 2013 Mar 18]
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| [http://www.ncbi.nlm.nih.gov/pubmed/23307869 A secreted decoy of InR antagonizes insulin/IGF signaling to restrict body growth in Drosophila. Okamoto N, Nakamori R, Murai T, Yamauchi Y, Masuda A, Nishimura T. Genes Dev. 2013 Jan 1;27(1):87-97. doi: 10.1101/gad.204479.112]
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| [http://www.ncbi.nlm.nih.gov/pubmed/23312286 Adenosine Nucleotide Biosynthesis and AMPK Regulate Adult Life Span and Mediate the Longevity Benefit of Caloric Restriction in Flies. Stenesen D, Suh JM, Seo J, Yu K, Lee KS, Kim JS, Min KJ, Graff JM. Cell Metab. 2013 Jan 8;17(1):101-12]
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| '''2012'''
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| [http://www.ncbi.nlm.nih.gov/pubmed?term=22691499 Analysis of neural subtypes reveals selective mitochondrial dysfunction in dopaminergic neurons from parkin mutants. Burman JL, Yu S, Poole AC, Decal RB, Pallanck L. Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10438-43]
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| [http://www.ncbi.nlm.nih.gov/pubmed?term=22514691 Mitochondria-specific accumulation of amyloid β induces mitochondrial dysfunction leading to apoptotic cell death. Cha MY, Han SH, Son SM, Hong HS, Choi YJ, Byun J, Mook-Jung I. PLoS One. 2012;7(4):e34929]
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| [http://www.ncbi.nlm.nih.gov/pubmed/22068330 Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Glatter T, Schittenhelm RB, Rinner O, Roguska K, Wepf A, Jünger MA, Köhler K, Jevtov I, Choi H, Schmidt A, Nesvizhskii AI, Stocker H, Hafen E, Aebersold R, Gstaiger M. Mol Syst Biol. 2011 Nov 8;7:547. doi: 10.1038/msb.2011.79]
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| [http://www.ncbi.nlm.nih.gov/pubmed/22750943 Metabolic differentiation in the embryonic retina. Agathocleous M, Love NK, Randlett O, Harris JJ, Liu J, Murray AJ, Harris WA. Nat Cell Biol. 2012 Aug;14(8):859-64]
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| [http://www.ncbi.nlm.nih.gov/pubmed/22219285 Mitochondrial dynamics and bioenergetic dysfunction is associated with synaptic alterations in mutant SOD1 motor neurons. Magrané J, Sahawneh MA, Przedborski S, Estévez ÁG, Manfredi G. J Neurosci. 2012 Jan 4;32(1):229-42]
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| [http://www.ncbi.nlm.nih.gov/pubmed/22132213 Insulin receptor-mediated signaling via phospholipase C-γ regulates growth and differentiation in Drosophila. Murillo-Maldonado JM, Zeineddine FB, Stock R, Thackeray J, Riesgo-Escovar JR. PLoS One. 2011;6(11):e28067]
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| [http://www.ncbi.nlm.nih.gov/pubmed/22242018 The Yeast Complex I Equivalent NADH Dehydrogenase Rescues pink1 Mutants.Vilain S, Esposito G, Haddad D, Schaap O, Dobreva MP, Vos M, Van Meensel S, Morais VA, De Strooper B, Verstreken P.PLoS Genet. 2012 Jan;8(1):e1002456.]
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| '''2011'''
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| [http://dev.biologists.org/content/138/23/5201.long Regulation of Drosophila glial cell proliferation by Merlin-Hippo signaling. B. V. V. G. Reddy and Kenneth D. Irvine Development. 2011 Dec;138(23):5201-12.]
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| [http://www.sciencedirect.com/science/article/pii/S0092867411012244 PINK1 and Parkin Target Miro for Phosphorylation and Degradation to Arrest Mitochondrial Motility Xinnan Wang1, 3, Dominic Winter2, Ghazaleh Ashrafi1, 4, Julia Schlehe5, Yao Liang Wong6, Dennis Selkoe5, Sarah Rice6, Judith Steen1, 2, Matthew J. LaVoie5, Thomas L. Schwarz. Cell Volume 147, Issue 4, 11 November 2011, Pages 893–906]
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| [http://www.ncbi.nlm.nih.gov/pubmed/19707574 Glia and muscle sculpt neuromuscular arbors by engulfing destabilized synaptic boutons and shed presynaptic debris. Fuentes-Medel Y, Logan MA, Ashley J, Ataman B, Budnik V, Freeman MR. PLoS Biol. 2009 Aug;7(8):e1000184]
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| [http://www.ncbi.nlm.nih.gov/pubmed/21478857 During autophagy mitochondria elongate, are spared from degradation and sustain cell viability. Gomes LC, Di Benedetto G, Scorrano L. Nat Cell Biol. 2011, 13 :589-98]
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| [http://www.ncbi.nlm.nih.gov/pubmed/20935173 Drosophila FMRP regulates microtubule network formation and axonal transport of mitochondria. Yao A, Jin S, Li X, Liu Z, Ma X, Tang J, Zhang YQ. Hum Mol Genet. 2011 Jan 1;20(1):51-63.]
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| [http://www.ncbi.nlm.nih.gov/pubmed/21183078 Nutrition-responsive glia control exit of neural stem cells from quiescence. Chell JM, Brand AH. Cell. 2010 Dec 23;143(7):1161-73.]
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| '''2010'''
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| [http://www.ncbi.nlm.nih.gov/pubmed/20435911 Expression of the yeast NADH dehydrogenase Ndi1 in Drosophila confers increased lifespan independently of dietary restriction. Sanz A, Soikkeli M, Portero-Otín M, Wilson A, Kemppainen E, McIlroy G, Ellilä S, Kemppainen KK, Tuomela T, Lakanmaa M, Kiviranta E, Stefanatos R, Dufour E, Hutz B, Naudí A, Jové M, Zeb A, Vartiainen S, Matsuno-Yagi A, Yagi T, Rustin P, Pamplona R, Jacobs HT. Proc Natl Acad Sci U S A. 2010 107:9105-9110]
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| [http://www.ncbi.nlm.nih.gov/sites/pubmed Initiation of neuronal differentiation requires PI3-kinase/TOR signalling in the vertebrate neural tube.Fishwick KJ, Li RA, Halley P, Deng P, Storey KG. Dev Biol. 2010 Feb 15;338(2):215-225.]
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| [http://www.ncbi.nlm.nih.gov/pubmed/20200521 Heteroplasmic mitochondrial DNA mutations in normal and tumour cells. He Y, Wu J, Dressman DC, Iacobuzio-Donahue C, Markowitz SD, Velculescu VE, Diaz LA Jr, Kinzler KW, Vogelstein B, Papadopoulos N. Nature. 2010 Mar 25;464(7288):610-4.]
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| [http://www.ncbi.nlm.nih.gov/pubmed/20421993 Combined inactivation of pRB and hippo pathways induces dedifferentiation in the Drosophila retina.Nicolay BN, Bayarmagnai B, Moon NS, Benevolenskaya EV, Frolov MV. PLoS Genet. 2010 Apr 22;6(4):e1000918.]
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| [http://www.ncbi.nlm.nih.gov/pubmed/19684592 Rapamycin activation of 4E-BP prevents parkinsonian dopaminergic neuron loss. Tain LS, Mortiboys H, Tao RN, Ziviani E, Bandmann O, Whitworth AJ. Nat Neurosci. 2009 Sep;12(9):1129-35]
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| [http://www.ncbi.nlm.nih.gov/pubmed/18299344? FOXO-regulated transcription restricts overgrowth of Tsc mutant organs. J Cell Biol. 2008 Feb 25;180(4):691-6]
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| '''2009'''
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| [http://www.ncbi.nlm.nih.gov/pubmed/8929534?ordinalpos=191&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Reiterative use of the EGF receptor triggers differentiation of all cell types in the Drosophila eye.Freeman M.Cell. 1996 Nov 15;87(4):651-60]
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| [http://www.ncbi.nlm.nih.gov/pubmed/11390358?ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum TSC1 and TSC2 tumor suppressors antagonize insulin signaling in cell growth.Gao X, Pan D. Genes Dev. 2001 Jun 1;15(11):1383-92]
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| [http://www.ncbi.nlm.nih.gov/pubmed/19019992?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Neuronal programmed cell death induces glial cell division in the adult Drosophila brain. Kato K, Awasaki T, Ito K. Development. 2009 Jan;136(1):51-9. Epub 2008 Nov 19]
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