Graduate Student Publications 

Department of Neurobiology 

Graduate Student Trainees of Mark Alkema, Ph.D.

Pirri JK, McPherson AD, Donnelly JL, Francis MM, Alkema MJ (2009). A tyramine-gated chloride channel coordinates distinct motor programs of a Caenorhabditis elegans escape response. Neuron 62: 526-538.

Graduate Student Trainees of Vivian Budnik, Ph.D. 

Fuentes-Medel Y, Logan MA, Ashley J, Ataman B, Budnik V, Freeman MR (2009). Glia and muscle sculpt neuromuscular arbors by engulfing destabilized synaptic boutons and shed presynaptic debris. PLoS Biol. 7(8):e1000184.

Korkut C, Ataman B, Ramachandran P, Ashley J, Barria R, Gherbesi N, Budnik V (2009). Trans-Synaptic Transmission of Vesicular Wnt Signals through Evi/Wntless. Cell 139:393-404.

Korkut C, Budnik V (2009) WNTs tune up the neuromuscular junction. Nat Rev Neurosci. 10: 627-634.

Ramachandran P, Barria R, Ashley J, Budnik V (2009). A critical step for postsynaptic F-actin organization: Regulation of Baz/Par-3 localization by aPKC and PTEN. Dev Neurobiol (in press) [Epub ahead of print May 26, 2009].

Mathew D, Ataman B,  Chen J, Zhang Y, Cumberledge S, Budnik V (2005) Wingless signaling at synapses is through cleavage and nuclear import of receptor DFrizzled2. Science 310: 1344-1347.

Ruiz-Canada C, Ashley J, Moeckel-Cole S, Drier E, Yin J, and Budnik V (2004).  New Synapse Formation Disrupted by Misregulation of Microtubule Stability in aPKC Mutants. Neuron 42:567-80. 

Parkard M, Mathew D, Budnik V (2003).  FASt remodeling of synapses in Drosophila.  Curr Opin Neurbiol 13:527-34 

Mathew D, Popescu A, Budnik V (2003). Drosophila amphiphysin functions during synaptic fasciclin II membrane cycling. J Neurosci 23:10710-6 

Packard M,   Mathew D , Budnik V (2003).  Wnts and TGF beta in synaptogenesis: old friends signalling at new places.  Nat Rev Neurosci  4:113-20. 

Packard M, Koo ES, Gorczyca M, Sharpe J, Cumberledge S, Budnik V (2002).  The Drosophila Wnt, wingless, provides an essential signal for pre- and postsynaptic differentiation. Cell  111:319-30. 

Roche JP,  Packard MC, Moeckel-Cole S, Budnik V  (2002).  Regulation of synaptic plasticity and synaptic vesicle dynamics by the PDZ protein Scribble. J Neurosci  22:6471-9. 

Koh YH and Budnik V (2002). The Ras1-mitogen activated protein kinase signal transduction pathway regulates synaptic plasticity through fasciclin II-mediated cell adhesion.  J Neurosci 22:2496-2504 

Mathew D, Gramates LS, Packard M, Gorczyca M, Bilder D, Perrimon N, Budnik V (2002).  GUK-holder, a novel synaptic protein that links the tumor suppressors discs-large and scribble. Curr Biol 12:531-539 

Thomas U, Ebitch S, Gorczycz M, Koh YH, Hough CD, Gundelfinger ED, Budnik V (2000).  Synaptic targeting and localization of DLG at larval neuromuscular junctions: a stepwise process that is controlled by multiple domains. Curr Biol 10:1108-1117. 

Torroja L, Packard M, Gorczyca, M, White K, Budnik V (1999). The ß-amyloid precursor protein promotes synapse differentiation in Drosophila J Neurosci 19:7793-7803. 

Koh YH, Popova E, Thomas U, Griffith L, Budnik V (1999).  Regulation of DLG localization at synapses by CaMKII-dependent phosphorylation. Cell 98: 353-363. 

Zhang, B, Koh YH, Beckstead, RB, Budnik V, Ganetzky B, Bellen HJ (1998). Vesicle size and number are regulated by a novel synaptic protein required for endocytosis Neuron 21:1465-1475. 

Thomas U, Kim E, Kuhlendahl S, Koh YH, Gundelfinger ED, Sheng M, Garner CC, Budnik V (1997).  Synaptic clustering of the cell adhesion molecule fasciclin II by discs large and its role in the regulation of presynaptic Structure. Neuron 19:787-799. 

Budnik V, Koh YH, Guan B, Hartman B, Haugh C, Woods D, Gorczyca M (1996).  Regulation of synapse structure and function by the Drosophila tumor suppressor gene, dlg. Neuron 17:627-640. 

Guan B, Hartmann B, Koh YH, Gorczyca M, Budnik V (1996). The Drosophila tumor suppressor gene, dlg, is involved in structural plasticity at a glutamatergic synapse. Curr Biol 6: 695-706. 

 

Graduate Student Trainees of Patrick Emery, Ph.D. 

Dubruille R, Murad A, Rosbash M, Emery P (2009) A Constant Light-Genetic Screen Identifies KISMET as a Regulator of Circadian Photoresponses. PLoS Genet 5(12): e1000787.

Busza, A., Murad, A. and Emery P. (2007). Interactions between circadian neurons control temperature synchronization of Drosophila behavior. J. Neurosci.,27, 10722-10733.

Kaushik R, Nawathean P, Busza A, Murad A, Emery P, Rosbash M (2007). PER-TIM interactions with the photoreceptor Cryptochrome mediate circadian temperature responses in Drosophila. PLoS Biol 5:e146.

Murad, A., Emery-Le, M., and Emery, P. (2007) A subset of Dorsal Neurons modulates circadian behavior and light responses in Drosophila. Neuron 53, 689-701. 

Rush BL, Murad A,  Emery P, and Giebultowicz JM (2006). Ectopic CRYPTOCHROME renders TIM light sensitive in the Drosophila ovary. J Biol Rhythms  21: 272-278. 

Busza A, Emery-Le M, Rosbash M, Emery P (2004).  Roles of the two Drosophila CRYPTOCHROME structural domains in circadian photoreception.  Science 304: 1503-1506 

 

Graduate Student Trainees of Marc Freeman, Ph.D. 

Fuentes-Medel Y, Logan MA, Ashley J, Ataman B, Budnik V, Freeman MR (2009). Glia and muscle sculpt neuromuscular arbors by engulfing destabilized synaptic boutons and shed presynaptic debris. PLoS Biol. 7(8):e1000184.

Doherty J, Logan MA, Tasdemir OE, Freeman MR (2009). Ensheathing glia function as phagocytes in the adult Drosophila brain. J Neurosci 29: 4768-4781.

Ziegenfuss JS, Biswas R, Avery MA, Hong K, Sheehan AE, Yeung Y-G, Stanley ER, Freeman MR (2008). Draper-dependent glial phagocytic activity is mediated by Src and Syk family kinase signalling. Nature 2008 453:935-939.

Beach M, MacDonald J, Porpiglia E, Sheehan AE, Watts RE, Freeman MR (2006). The Drosophila cell corpse engulfment receptor Draper mediates glial clearance of severed axons. Neuron 50: 869-881.

 

Graduate Student Trainees of Tzumin Lee, M.D., Ph.D. 

Wang, J., Ma, X., Zheng, X., Zugates, C.T., Yang J.S. , Lee, C-H.J., and Lee, T. (2004) “Transmembrane/juxtamembrane domain-dependent Dscam distribution and function during mushroom body neuronal morphogenesis.” Neuron 43: 663-672. 

 

Graduate Student Trainees of Hong-Sheng Li, Ph.D.

Ni L, Guo P, Reddig K, Mitra M and Li HS (2008). Mutation of a TADR protein leads to rhodopsin and Gq-dependent retinal degeneration in Drosophila. J. Neurosci. 28: 13478-13487.

Han J, Gong P, Reddig K, Mitra M, Guo P and Li HS (2006). The fly CAMTA transcription factor potentiates deactivation of rhodopsin, a G protein-coupled light receptor. Cell 127: 847-858.

 

Graduate Student Trainees of Steven M. Reppert, M.D. 

Zhu H, Sauman I, Yuan Q, Casselman A, Emery-Le M, Emery P, Reppert SM (2008). Cryptochromes define a novel circadian clock mechanism in monarch butterflies that may underlie sun compass navigation. PLoS Biol 6, e4.

Yuan Q, Metterville D, Briscoe AD, Reppert SM (2007). Insect cryptochromes: Gene duplication and loss define diverse ways to construct insect circadian clocks. Mol Biol Evol 24: 948-955.

Zhu H, Yuan Q, Briscoe AD, Froy O, Casselman A, Reppert SM (2005). The two CRYs of the butterfly. Curr Biol 15: R953-R954.

Sauman I, Briscoe AD, Zhu H, Shi D, Froy O, Stalleicken J, Yuan Q, Casselman A, Reppert SM (2005). Connecting the navigational clock to sun compass input in monarch butterfly brain. Neuron 46: 457-467.

Chang DC, McWatters HG, Williams JA, Gotter AL, Levine JD, Reppert SM (2003). Constructing a feedback loop with circadian clock molecules from the silkmoth, Antheraea pernyi. J Biol Chem 278:38 149-38158.

Chang DC, Reppert SM (2003). A novel C-terminal domain of drosophila PERIOD inhibits dCLOCK:cYCLE-mediated transcription. Curr Biol 13:758-762.

Froy O,Chang DC, Reppert SM (2002). Redox potential: differential roles in dCRY and mCRY1 functions. Curr Biology 12:147-152.

Chang DC, Reppert SM (2001). The circadian clocks of mice and men. Neuron 29:555-558 (minireview).

Zylka MJ, Reppert SM (1999). Discovery of a putative heme-binding protein family (SOUL/HBP) by two-tissue suppression subtractive hybridization and database searches. Mol Brain Res 74: 175-181.

Kume K, Zylka MJ, Sriram S, Shearman LP, Weaver DR, Jin X, Maywood ES, Hastings MH, Reppert SM (1999). mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell 98:193-205.

Jin X, Shearman LP, Weaver DR, Zylka MJ, De Vries GJ, Reppert SM (1999). A molecular mechanism regulating rhythmic output from the suprachiasmatic circadian clock. Cell 96: 57-68.

Shearman LP, Zylka MJ, Reppert SM, Weaver DR (1999). Expression of basic-helix-loop-helix-PAS genes in the mouse suprachiasmatic nucleus. Neurosci 89: 387-397.

Zylka MJ, Shearman LP, Weaver DR, Reppert SM (1998). Three period homologs in mammals: Differential light regulation in the suprachiasmatic circadian clock and oscillating transcripts outside of brain. Neuron 20:1103-1110.

Zylka MJ, Shearman LP, Levine JD, Jin X, Weaver DR, Reppert SM (1998). Molecular analysis of mammalian timeless. Neuron 21: 1115-1122.

Shearman LP, Zylka MJ, Weaver DR, Kolakawski Jr LF, Reppert SM (1997). Two period homologs: Circadian oscillations and photic regulation in the suprachiasmatic nuclei. Neuron 19: 1261-1269.

Welsh DK, Reppert SM (1996). Gap junctions couple astrocytes but not neurons in dissociated cultures of rat suprachiasmatic nucleus. Brain Res 706: 30-36.

Roca AL, Godson C, Weaver DR, Reppert SM (1996). Structure, characterization and expression of the gene encoding the mouse Mella-melatonin receptor. Endocrinology 137: 3469-3477.

Sauman I, Tsai T, Roca AL, Reppert SM (1996). period protein is necessary for circadian control of egg hatching behavior in the silkmoth Antheraea pernyi. Neuron 17: 901-909.

Slaugenhaupt SA, Roca AL, Liebert CM, Altherr MR, Gusella JF, Reppert SM (1995). Mapping of the gene for the Mella-melatonin receptor to human chromosome 4 (MTNR1a) and mouse chromosome 8 (Mtnr1a). Genomics 27: 355-357.

Welsh DK, Logothetis DE, Meister M, Reppert SM (1995). Individual neurons dissociated from rat suprachiasmatic nucleus express independently phased circadian firing rhythms. Neuron 14: 697-706.

 

Graduate Student Trainees of Scott Waddell, Ph.D. 

Krashes MJ, DasGupta S, Vreede A, White B, Armstrong JD, Waddell S (2009). A neural circuit mechanism integrating motivational state with memory expression in Drosophila. Cell 139: 416-427.

Pitman JL, Dasgupta S, Krashes MJ, Leung B, Perrat PN, Waddell S (2009). There are many ways to train a fly. Fly 3(1). [Epub ahead of print 29 January 2009]

DasGupta S, & Waddell S. (2008). Learned odor discrimination in Drosophila without combinatorial odor maps in the antennal lobe. Curr Biol. 18:1668-74.

Krashes, M.J., and Waddell, S. (2008). Rapid consolidation to a radish and protein synthesis-dependent long-term memory after single-session appetitive olfactory conditioning in Drosophila. J. Neurosci. 28: 3103-3113

Keene AC, Waddell S (2007). Drosophila olfactory memory: from single gene mutants to complex neural circuits. Nature Reviews Neuroscience 8: 341-54.
 
Krashes MJ, Keene AC, Leung B, Armstrong JD, Waddell S (2007). Sequential use of mushroom body neuron subsets during Drosophila odor memory processing. Neuron 53: 103-115.

Rickmyre JL, DasGupta S, Ooi DL, Keel J, Lee E, Kirschner MW, Waddell S, Lee L (2007). The Drosophila homolog of MCPH1, a human microencephaly gene, is required for genomic stability in the early embryo, Journal of Cell Science 120: 3565-3577.

Keene, AC*,  Krashes MJ*, Leung B, Bernard  JA, Waddell S (2006).  Drosophila dorsal paired medial neurons provide a general mechanism for memory consolidation. Current Biology 16:1524-1530. 

Keene AC, Waddell S (2005).  Drosophila memory: dopamine signals punishment?  Curr Biol. 15:R932-934.

Keene AC, Stratmann M, Keller A, Perrat PN, Vosshall LB, Waddell S (2004). Diverse odor-conditioned memories require uniquely timed dorsal paired medial neuron output. Neuron 44: 521-533.

Ding H, Schwarz DS, Keene AC, Affarel B, Fenton L, Xia X, Shi Y, Zamore PD, Xu Z (2003).  Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis. Aging Cell 2: 209-217.

 

Graduate Student Trainees of David Weaver, Ph.D. 

Etchegaray JP, Machida KK, Noton E, Constance CM, Dallmann R, DiNapoli MN, DeBruyne JP, Lambert CM, Yu EA, Reppert SM, Weaver DR (2009). Casein kinase 1 delta regulates the pace of the mammalian circadian clock. Mol Cell Biol [Epub ahead of print May 4, 2009].

Lambert CM, Machida KK, Smale L, Nunez AA, and Weaver DR. Analysis of the prokieticin 2 system in a diurnal rodent, the unstriped Nile grass rat (Arvicanthis niloticus). J Biol Rhythms  20: 206-218. 

 

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