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Bibliographies As Submitted by the Departments of the Carnegie Institution for July 1, 2012 – June 30, 2013

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Bibliographies As Submitted by the Departments of the Carnegie Institution for July 1, 2012 – June 30, 2013 Bibliographies as submitted by the departments of the Carnegie Institution for July 1, 2012 – June 30, 2013 Embryology Biau S, Jin S, Fan CM. Gastrointestinal defects of the Gas1 mutant involve dysregulated Hedgehog and Ret signaling. Biol Open. 2013 Feb 15;2(2):144-55. doi: 10.1242/bio.20123186. Epub 2012 Nov 20. Bortvin A. PIWI-Interacting RNAs (piRNAs) - a Mouse Testis Perspective. Biochemistry (Mosc). 2013 Jun;78(6):592-602. doi: 10.1134/S0006297913060059. Chen, H., Chen, X., and Zheng, Y. (2013). The nuclear lamina regulates germline stem cell niche organization via modulation of EGFR signaling. Cell Stem Cell 13, 73-86. Decarvalho TN, Akitake CM, Thisse C, Thisse B, Halpern ME. Aversive cues fail to activate fos expression in the asymmetric olfactory-habenula pathway of zebrafish. Front Neural Circuits. 2013;7:98. doi: 10.3389/fncir.2013.00098. Farber SA, Zeituni EM. We see the light: chemical-genetic protein regulation. Chem Biol. 2012 Mar 23;19(3):311-2. doi: 10.1016/j.chembiol.2012.03.001. Gall JG. Are lampbrush chromosomes unique to meiotic cells? Chromosome Res. 2012 Dec;20(8):905-9. doi: 10.1007/s10577-012-9329-5. Gardner EJ, Nizami ZF, Talbot CC Jr, Gall JG. Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis. Genes Dev. 2012 Nov 15;26(22):2550-9. doi: 10.1101/gad.202184.112. Günther S, Kim J, Kostin S, Lepper C, Fan CM, Braun T.Myf5-Positive Satellite Cells Contribute to Pax7-Dependent Long-Term Maintenance of Adult Muscle Stem Cells. Cell Stem Cell. 2013 Aug 6. doi:pii: S1934-5909(13)00324-X. 10.1016/j.stem.2013.07.016. [Epub ahead of print] Guo Y and Zheng Y (2013). Sculpting the nucleus with dynamic microtubules. Developmental Cell. http://dx.doi.org/10.1016/j.devcel.2013.09.027. Guan L, van der Heijden GW, Bortvin A, Greenberg MM. Intracellular detection of cytosine incorporation in genomic DNA by using 5-ethynyl-2'-deoxycytidine. Chembiochem. 2011 Sep 19;12(14):2184-90. doi: 10.1002/cbic.201100353. Epub 2011 Aug 1. Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell. 2013 Jul 3;154(1):240-51. doi: 10.1016/j.cell.2013.06.009. Epub 2013 Jun 27. PubMed PMID: 23810193; PubMed Central PMCID: PMC3756563. Han JS, Shao S. Circular retrotransposition products generated by a LINE retrotransposon. Nucleic Acids Res. 2012 Nov;40(21):10866-77. doi: 10.1093/nar/gks859. Epub 2012 Sep 12. Jia J, Zheng X, Hu G, Cui K, Zhang A, Zhang J, Du Y, Liu C, Zhao K, and Zheng Y (2012). Regulation of pluripotency and self-renewal of ES cells through epigenetic threshold modulation and mRNA pruning. Cell 151, 576–589. Kim Y, Zheng Z, and Zheng Y (2013). Proliferation and differentiation of mouse embryonic stem cells lacking all lamins. Cell Research. Advance online publication 2013; doi:10.1038/cr.2013.118. Kim Y and Zheng Y (2013). Generation and characterization of a conditional deletion allele for Lmna. Biochemical and Biophysical Research Communications. 2013 Aug 30. doi:pii: S0006-291X(13)01429-0. 10.1016/j.bbrc.2013.08.082. [Epub ahead of print] Lei, L. and Spradling, A.C. (2013). Mouse primordial germ cells produce cysts that partially fragment prior to meiosis. Development 140(10):2075-81. Lei, L. and Spradling, A.C. (2013). Female mice lack adult germline stem cells, but sustain oogenesis using stable primordial follicles. Proc. Natl. Acad. Sci, USA 110(21):8585-90. Morris, L., and Spradling, A.C. (2012). Steroid signaling within Drosophila ovarian epithelial cells sex-specifically modulates early germ cell development and meiotic entry PLoS One 7(10)e46109. Doi:10.1371/journal.pone.0046109 Epub 2012 Oct 2. Nakatsu F, Baskin JM, Chung J, Tanner LB, Shui G, Lee SY, Pirruccello M, Hao M, Ingolia NT, Wenk MR, De Camilli P. PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity. J Cell Biol. 2012 Dec 10;199(6):1003-16. doi: 10.1083/jcb.201206095. Nizami ZF, Gall JG. Pearls are novel Cajal body-like structures in the Xenopus germinal vesicle that are dependent on RNA pol III transcription. Chromosome Res. 2012 Dec;20(8):953-69. doi: 10.1007/s10577-012-9320-1. Otis J.P. and Farber S.A. (2012) Imaging vertebrate digestive function and lipid metabolism in vivo. Drug Discovery Today: Disease Models 10:e11-e16. Sadler KC, Rawls JF, Farber SA.(2013) Getting the inside tract: new frontiers in zebrafish digestive system biology. Zebrafish. 2013 2:129-31. Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H, Mann M, Ingolia NT, Weissman JS. Decoding human cytomegalovirus. Science. 2012 Nov 23;338(6110):1088-93. doi: 10.1126/science.1227919. Subedi A, Macurak M, Gee ST, Monge E, Goll MG, Potter CJ, Parsons MJ, Halpern ME. Adoption of the Q transcriptional regulatory system for zebrafish transgenesis. Methods. 2013 Jun 20. doi:pii: S1046-2023(13)00213-2. 10.1016/j.ymeth.2013.06.012. [Epub ahead of print] Sun, JJ and Spradling, A.C. (2013). Ovulation in Drosophila is controlled by secretory cells of the female reproductive tract. eLife Apr 16;2:e00415. doi: 10.7554. Thorburn RR, Gonzalez C, Brar GA, Christen S, Carlile TM, Ingolia NT, Sauer U, Weissman JS, Amon A. Aneuploid yeast strains exhibit defects in cell growth and passage through START. Mol Biol Cell. 2013 May;24(9):1274-89. doi: 10.1091/mbc.E12-07-0520. Epub 2013 Mar 6. Walters JW, Anderson JL, Bittman R, Pack M, Farber SA. Visualization of lipid metabolism in the zebrafish intestine reveals a relationship between NPC1L1-mediated cholesterol uptake and dietary fatty acid. Chem Biol. 2012 Jul 27;19(7):913-25. doi: 10.1016/j.chembiol.2012.05.018. Epub 2012 Jun 28. Erratum in: Chem Biol. 2012 Aug 24;19(8):1073. Wang SS, Ketcham S, Schön A, Goodman B, Wang Y, Yates III J, Freire E, Schroer TA, and Zheng Y (2013). Lis1 and dynactin regulate spindle morphogenesis by coordinating dynein activities. Molecular Biology of the Cell. Published online before print September 11, 2013, doi: 10.1091/mbc. E13-05-0283. Zheng Y and Iglesias PA (2013). Nucleating new branches from old. Cell 152(4):669-70. doi: 10.1016/j.cell.2013.01.040. GEOPHYSICAL LABORATORY Here updated through September 1, 2013. The list is regularly updated on the Geophysical Laboratory web site (http://www.gl.ciw.edu). 4547 Agee, C. B., N. V. Wilson, F. M. McCubbin, K. Ziegler, V. J. Polyak, Z. D. Sharp, Y. Asmerom, M. H. Nunn, R. Shaheen, M. H. Thiemens, A. Steele, M. L. Fogel, R. Bowden, M. Glamoclija, Z. S. Zhang, and S. M. Elardo, Unique meteorite from early Amazonian Mars: water-rich basaltic breccia Northwest Africa 7034, Science 339, 780-785, 2013. 4532 Ahart, M., S. Sinogeikin, O. Shebanova, D. Ikuta, Z.-G. Ye, H. K. Mao, R. E. Cohen, and R. J. Hemley, Pressure dependence of the monoclinic phase in (1- x)Pb(Mg1/3Nb2/3)O3-xPbTiO3 solid solutions, Phys. Rev. B 86, 224111, 2012. 4507 Bai, L., M. Pravica, Y. Zhao, C. Park, Y. Meng, S. V. Sinogeikin, and G. Shen, Charge transfer in spinel Co3O4 at high pressures, J. Phys.: Cond. Matter 24, 435401, 2012. 4606 Baker, D. M., J. P. Andras, A. G. Jordán-Garza, and M. L. Fogel, Nitrate competition in a coral symbiosis varies with temperature among Symbiodinium clades, ISME J. 7, 1248-1251, 2013. 4576 Baker, D. M., L. Weigt, M. Fogel, and N. Knowlton, Ancient DNA from coral- hosted Symbiodinium reveal a static mutualism over the last 172 years, PLoS One 8(2), e55057, 2013. 4631 Belonoshko, A. B., M. Ramzan, H. K. Mao, and R. Ahuja, Atomic diffusion in solid molecular hydrogen, Sci. Rep. 3, 2340, 2013. 4523 Bishop, M. M., R. S. Chellappa, M. Pravica, J. Coe, Z. Liu, D. Dattlebaum, Y. K. Vohra, and N. Velisavljevic, 1,1-diamino-2,2-dinitroethylene under high pressure- temperature, J. Chem. Phys. 137, 174304, 2012. ____ Boehler, R., M. Guthrie, J. J. Molaison, A. M. dos Santos, S. Sinogeikin, S. Machida, N. Pradhan, and C. A. Tulk, Large-volume diamond cells for neutron diffraction above 90 GPa, High Pressure Res., in press. 4543 Bower, D. M., A. Steele, M. D. Fries, and L. Kater, Micro Raman spectroscopy of carbonaceous material in microfossils and meteorites: improving a method for life detection, Astrobiology 13, 103-113, 2013. 4582 Cadien, A., Q. Y. Hu, Y. Meng, Y. Q. Cheng, M. W. Chen, J. F. Shu, H. K. Mao, and H. W. Sheng, First-order liquid-liquid phase transition in cerium, Phys. Rev. Lett. 110, 125503, 2013. 1 4526 Chen, B., K. Lutker, S. V. Raju, J. Yan, W. Kanitpanyacharoen, J. Lei, S. Yang, H.-R. Wenk, H. K. Mao, and Q. Williams, Texture of nanocrystalline nickel: probing the lower size limit of dislocation activity, Science 338, 1448-1451, 2012. 4650 Cleaves, H. J., II, and J. L. Bada, The prebiotic chemistry of alternative nucleic acids, in Genesis - In the Beginning: Precursors of Life, Chemical Models and Early Biological Evolution, J. Seckbach, ed., pp. 3-33, Springer, Dordrecht, 2012. 4642 Cohen, R. E., I. I. Naumov, and R. J. Hemley, Electronic excitations and metallization of dense solid hydrogen, Proc. Natl. Acad. Sci. USA 110, 13757- 13762, 2013. 4638 Dalton, D. A., W.-P. Hsieh, G. T.
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