Founded in 2001, the Department of Neurobiology at the University of Massachusetts Medical School has evolved into a unique and integrated hub of investigators addressing fundamental problems in neurobiology, from single molecules to behavior, primarily using invertebrate model organisms. Combining cell biological, physiological and behavioral analyses with a critical interventionist angle afforded by cutting-edge genetic approaches, the Department aims to understand the complexity of brain development and function. This collection showcases journal articles and other publications and presentations written by faculty and researchers of the Department of Neurobiology.

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Publications from 2013

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Monoaminergic orchestration of motor programs in a complex C. elegans behavior, Jamie L. Donnelly, Christopher M. Clark, Andrew M. Leifer, Jennifer K. Pirri, Marian Haburcak, Michael M. Francis, Aravinthan D. T. Samuel, and Mark J. Alkema

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Coldness triggers northward flight in remigrant monarch butterflies, Patrick A. Guerra and Steven M. Reppert

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Anatomical basis of sun compass navigation II: The neuronal composition of the central complex of the monarch butterfly, Stanley Heinze, Jeremy Florman, Surainder Asokaraj, Basil el Jundi, and Steven M. Reppert

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Torsin mediates primary envelopment of large ribonucleoprotein granules at the nuclear envelope, Vahbiz Jokhi, James A. Ashley, John J. Nunnari, Akiko Noma, Naoto ito, Noriko Wakabayashi-Ito, Melissa J. Moore, and Vivian Budnik

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Regulation of postsynaptic retrograde signaling by presynaptic exosome release, Ceren Korkut, Yihang Li, Kate Koles, Cassandra Brewer, James A. Ashley, Motojiro Yoshihara, and Vivian Budnik

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The c-Jun kinase signaling cascade promotes glial engulfment activity through activation of draper and phagocytic function, Jennifer M. MacDonald, Johnna E. Doherty, Rachel Hackett, and Marc R. Freeman

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Efficient targeted mutagenesis in the monarch butterfly using zinc finger nucleases, Christine Merlin, Lauren E. Beaver, Orley R. Taylor, Scot A. Wolfe, and Steven M. Reppert

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Transposition-driven genomic heterogeneity in the Drosophila brain, Paola N. Perrat, Shamik DasGupta, Jie Wang, William E. Theurkauf, Zhiping Weng, Michael Rosbash, and Scott Waddell

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ACR-12 ionotropic acetylcholine receptor complexes regulate inhibitory motor neuron activity in Caenorhabditis elegans, Hilary A. Petrash, Alison Philbrook, Marian Haburcak, Belinda Barbagallo, and Michael M. Francis

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Increased cell-intrinsic excitability induces synaptic changes in new neurons in the adult dentate gyrus that require npas4, Shuyin Sim, Salome Antolin, Chia-Wei Lin, Yingxi Lin, and Carlos Lois

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A role for Drosophila ATX2 in activation of PER translation and circadian behavior, Yong Zhang, Jinli Ling, Chunyan Yuan, Raphaelle Dubruille, and Patrick Emery

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MonarchBase: the monarch butterfly genome database, Shuai Zhan and Steven M. Reppert

Publications from 2012

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Wld(S) Prevents Axon Degeneration through Increased Mitochondrial Flux and Enhanced Mitochondrial Ca(2+) Buffering., Michelle A. Avery, Timothy M. Rooney, Jignesh D. Pandya, Thomas M. Wishart, Thomas H. Gillingwater, James W. Geddes, Patrick G. Sullivan, and Marc R. Freeman

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The Secreted Immunoglobulin Domain Proteins ZIG-5 and ZIG-8 Cooperate with L1CAM/SAX-7 to Maintain Nervous System Integrity, Claire Y. Benard, Cassandra Blanchette, Janine Recio, and Oliver Hobert

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Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers, Thomas Brody, Amarendra S. Yavatkar, Alexander Kuzin, Mukta Kundu, Leonard J. Tyson, Jermaine Ross, Tzu-Yang Lin, Chi-Hon Lee, Takeshi Awasaki, Tzumin Lee, and Ward F. Odenwald

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Layered reward signalling through octopamine and dopamine in Drosophila, Christopher J. Burke, Wolf Huetteroth, David Owald, Emmanuel Perisse, Michael J. Krashes, Gaurav Das, Daryl Gohl, Marion Silies, Sarah Certel, and Scott Waddell

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Circadian rhythms: An electric jolt to the clock, Patrick Emery

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Integration of a retrograde signal during synapse formation by glia-secreted TGF-beta ligand, Yuly F. Fuentes-Medel, James A. Ashley, Romina Barria, Rachel Maloney, Marc R. Freeman, and Vivian Budnik

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Discordant timing between antennae disrupts sun compass orientation in migratory monarch butterflies, Patrick A. Guerra, Christine Merlin, Robert J. Gegear, and Steven M. Reppert

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Anatomical basis of sun compass navigation I: the general layout of the monarch butterfly brain, Stanley Heinze and Steven M. Reppert

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Protein Gq modulates termination of phototransduction and prevents retinal degeneration, Wen Hu, Didi Wan, Xiaoming Yu, Jinguo Cao, Peiyi Guo, Hong-Sheng Li, and Junhai Han

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Wnt signaling regulates acetylcholine receptor translocation and synaptic plasticity in the adult nervous system, Michael Jensen, Frederic J. Hoerndli, Penelope J. Brockie, Rui Wang, Erica Johnson, Dane Maxfield, Michael M. Francis, David M. Madsen, and Andres V. Maricq

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Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation, Hina Kalra, Vivian Budnik, and Suresh Mathivanan

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Circadian rhythm of temperature preference and its neural control in Drosophila, Haruna Kaneko, Lauren M. Head, Jinli Ling, Xin Tang, Yilin Liu, Paul E. Hardin, Patrick Emery, and Fumika N. Hamada

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Hierarchical deployment of factors regulating temporal fate in a diverse neuronal lineage of the Drosophila central brain, Chih-Fei Kao, Hung-Hsiang Yu, Yisheng He, Jui-Chun Kao, and Tzumin Lee

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Increasing heterogeneity in the organization of synaptic inputs of mature olfactory bulb neurons generated in newborn rats, Wolfgang Kelsch, Shuyin Sim, and Carlos Lois

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Genetic labeling of neuronal subsets through enhancer trapping in mice, Wolfgang Kelsch, Alberto Stolfi, and Carlos Lois

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Wnt Signaling in Neuromuscular Junction Development, Kate Koles and Vivian Budnik

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Mechanism of evenness interrupted (evi)-exosome release at synaptic boutons, Kate Koles, John J. Nunnari, Ceren Korkut, Romina Barria, Cassandra Brewer, Yihang Li, John D. Leszyk, Bing Zhang, and Vivian Budnik

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Inhibitory control of synaptic and behavioral plasticity by octopaminergic signaling, Alex C. Koon and Vivian Budnik

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Antibodies for assessing circadian clock proteins in the rodent suprachiasmatic nucleus, Joseph Lesauter, Christopher M. Lambert, Margaret R. Robotham, Zina Model, Rae Silver, and David R. Weaver

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KAYAK-alpha modulates circadian transcriptional feedback loops in Drosophila pacemaker neurons, Jinli Ling, Raphaelle Dubruille, and Patrick Emery

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Lineage analysis of Drosophila lateral antennal lobe neurons reveals notch-dependent binary temporal fate decisions, Suewei Lin, Chih-Fei Kao, Hung-Hsiang Yu, Ya-ling Huang, and Tzumin Lee

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Generating neuronal diversity in the Drosophila central nervous system, Suewei Lin and Tzumin Lee

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Negative regulation of glial engulfment activity by Draper terminates glial responses to axon injury, Mary A. Logan, Rachel Hackett, Johnna E. Doherty, Amy E. Sheehan, Sean D. Speese, and Marc R. Freeman

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Genetics in non-genetic model systems, Carlos Lois and James O. Groves

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Inwardly rectifying potassium channels in Drosophila, Zhuo Luan and Hong-Sheng Li

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Coincident generation of pyramidal neurons and protoplasmic astrocytes in neocortical columns, Sanjay Magavi, Drew Friedmann, Garrett Banks, Alberto Stolfi, and Carlos Lois

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Unraveling navigational strategies in migratory insects, Christine Merlin, Stanley Heinze, and Steven M. Reppert

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Similarity of Visual Selectivity among Clonally Related Neurons in Visual Cortex, Gen Ohtsuki, Megumi Nishiyama, Takashi Yoshida, Tomonari Murakami, Mark Histed, Carlos Lois, and Kenichi Ohki

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dSarm/Sarm1 is required for activation of an injury-induced axon death pathway, Jeannette M. Osterloh, Jing Yang, Timothy M. Rooney, A. Nicole Fox, Robert Adalbert, Eric H. Powell, Amy E. Sheehan, Michelle A. Avery, Rachel Hackett, Mary A. Logan, Jennifer M. MacDonald, Jennifer S. Ziegenfuss, Stefan Milde, Ying-Ju Hou, Carl Nathan, Aihao Ding, Robert H. Brown Jr., Laura Comforti, Michael Coleman, Marc Tessier-Lavigne, Stephan Zuchner, and Marc R. Freeman

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The neuroethology of C. elegans escape, Jennifer K. Pirri and Mark J. Alkema

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Disruption of gene expression rhythms in mice lacking secretory vesicle proteins IA-2 and IA-2β, Sohan Punia, Kyle K. Rumery, Elizabeth A. Yu, Christopher M. Lambert, Abner L. Notkins, and David R. Weaver

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Intercellular calcium signaling in a gap junction-coupled cell network establishes asymmetric neuronal fates in C. elegans, Jennifer A. Schumacher, Yi-Wen Hsieh, Shiuhwei Chen, Jennifer K. Pirri, Mark J. Alkema, Wen-hong Li, Chieh Chang, and Chiou-Fen Chuang

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Wandering neuronal migration in the postnatal vertebrate forebrain, Benjamin B. Scott, Timothy Gardner, Ni Ji, Michale S. Fee, and Carlos Lois

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Molecular diversity of Dscam and self-recognition, Lei Shi and Tzumin Lee

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Nuclear envelope budding enables large ribonucleoprotein particle export during synaptic Wnt signaling, Sean D. Speese, James A. Ashley, Vahbiz Jokhi, John J. Nunnari, Romina Barria, Yihang Li, Bulent Ataman, Alex C. Koon, Young-Tae Chang, Qian Li, Melissa J. Moore, and Vivian Budnik

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Analysis of glial cell development and function in Drosophila, Tobias Stork, Rebecca Bernardos, and Marc R. Freeman

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Combining comparative proteomics and molecular genetics uncovers regulators of synaptic and axonal stability and degeneration in vivo, Thomas M. Wishart, Timothy M. Rooney, Douglas J. Lamont, Ann K. Wright, A. Jennifer Morgon, Mandy Jackson, Marc R. Freeman, and Thomas H. Gillingwater

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Acute genetic manipulation of neuronal activity for the functional dissection of neural circuits-a dream come true for the pioneers of behavioral genetics, Moto Yoshihara and Kei Ito

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Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus, Haisun Zhu, Rajanikanth Vadigepalli, Rachel Rafferty, Gregory E. Gonye, David R. Weaver, and James S. Schwaber

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Distinct molecular pathways mediate glial activation and engulfment of axonal debris after axotomy, Jennifer S. Ziegenfuss, Johnna E. Doherty, and Marc R. Freeman

Publications from 2011

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Glia instruct developmental neuronal remodeling through TGF-beta signaling, Takeshi Awasaki, Ya-ling Huang, Michael B. O'Connor, and Tzumin Lee

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New tools for the analysis of glial cell biology in Drosophila, Takeshi Awasaki and Tzumin Lee

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Orphan nuclear receptors control neuronal remodeling during fly metamorphosis, Takeshi Awasaki and Tzumin Lee

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Wnt signaling during synaptic development and plasticity, Vivian Budnik and Patricia C. Salinas

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Remembering nutrient quality of sugar in Drosophila, Christopher J. Burke and Scott Waddell

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Photic resetting and entrainment in CLOCK-deficient mice, Robert Dallmann, Jason P. DeBruyne, and David R. Weaver

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From synapse to nucleus and back again--communication over distance within neurons, Mike Fainzilber, Vivian Budnik, Rosalind A. Segal, and Michael R. Kreutz

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Invertebrate glia. Introduction, David Featherstone and Marc R. Freeman

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Human cryptochrome exhibits light-dependent magnetosensitivity, Lauren E. Foley, Robert J. Gegear, and Steven M. Reppert

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Sun compass integration of skylight cues in migratory monarch butterflies, Stanley Heinze and Steven M. Reppert

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Bringing fly brains in line, Wolf Huetteroth and Scott Waddell

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Hungry flies tune to vinegar, Wolf Huetteroth and Scott Waddell

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Autoregulatory and paracrine control of synaptic and behavioral plasticity by octopaminergic signaling, Alex C. Koon, James A. Ashley, Romina Barria, Shamik DasGupta, Ruth Brain, Scott Waddell, Mark J. Alkema, and Vivian Budnik

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Drosophila appetitive olfactory conditioning, Michael Jonathan Krashes and Scott Waddell

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Drosophila aversive olfactory conditioning, Michael Jonathan Krashes and Scott Waddell

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The period of the circadian oscillator is primarily determined by the balance between casein kinase 1 and protein phosphatase 1, Hyeong-min Lee, Rongmin Chen, Hyukmin Kim, Jean-Pierre Etchegaray, David R. Weaver, and Choogon Lee

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Serotonin-mushroom body circuit modulating the formation of anesthesia-resistant memory in Drosophila, Pei-Tseng Lee, Hsuan-Wen Lin, Yu-Hsuan Chang, Tsai-Feng Fu, Josh Dubnau, Jay Hirsh, Tzumin Lee, and Ann-Shyn Chiang

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Optogenetic manipulation of neural activity in freely moving Caenorhabditis elegans, Andrew M. Leifer, Christopher Fang-Yen, Marc Gershow, Mark J. Alkema, and Aravinthan D. T. Samuel

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The C. elegans Touch Response Facilitates Escape From Predacious Fungi, Sean M. Maguire, Christopher M. Clark, Jennifer K. Pirri, John J. Nunnari, and Mark J. Alkema

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Associative memory: without a trace, Emmanuel Perisse and Scott Waddell

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A Pair of Inhibitory Neurons Are Required to Sustain Labile Memory in the Drosophila Mushroom Body, Jena L. Pitman, Wolf Huetteroth, Christopher J. Burke, Michael Jonathan Krashes, Sen-Lin Lai, Tzumin Lee, and Scott Waddell

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Distinct patterns of Period gene expression in the suprachiasmatic nucleus underlie circadian clock photoentrainment by advances or delays, William J. Schwartz, Mahboubeh Tavakoli-Nezhad, Christopher M. Lambert, David R. Weaver, and Horacio O. de la Iglesia

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Anisotropic path searching for automatic neuron reconstruction, Jun Xie, Ting Zhao, Tzumin Lee, Eugene Myers, and Hanchuan Peng

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Disrupting the circadian clock: Gene-specific effects on aging, cancer, and other phenotypes, Elizabeth A. Yu and David R. Weaver

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The monarch butterfly genome yields insights into long-distance migration, Shuai Zhan, Christine Merlin, Jeffrey L. Boore, and Steven M. Reppert

Publications from 2010

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A dominant mutation in a neuronal acetylcholine receptor subunit leads to motor neuron degeneration in Caenorhabditis elegans, Belinda Barbagallo, Hilary A. Prescott, Patrick Boyle, Jason Climer, and Michael M. Francis

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Wallerian degeneration, wld(s), and nmnat, Michael P. Coleman and Marc R. Freeman

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Altered body mass regulation in male mPeriod mutant mice on high-fat diet, Robert Dallmann and David R. Weaver

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A new role for microRNA-9 in human neural progenitor cells, Celine Delaloy and Fen-Biao Gao

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The role of Drosophila Lamin C in muscle function and gene expression, George Dialynas, Sean D. Speese, Vivian Budnik, Pamela K. Geyer, and Lori L. Wallrath

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Casein kinase 1 delta (CK1delta) regulates period length of the mouse suprachiasmatic circadian clock in vitro, Jean-Pierre Etchegaray, Elizabeth A. Yu, Premananda Indic, Robert Dallmann, and David R. Weaver

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Specification and morphogenesis of astrocytes, Marc R. Freeman

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Menage a Trio during BMP-Mediated Retrograde Signaling at the NMJ, Yuly F. Fuentes Medel and Vivian Budnik

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Context-dependent functions of specific microRNAs in neuronal development, Fen-Biao Gao

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Animal cryptochromes mediate magnetoreception by an unconventional photochemical mechanism, Robert J. Gegear, Lauren E. Foley, Amy L. Casselman, and Steven M. Reppert

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MicroRNA-29b regulates the expression level of human progranulin, a secreted glycoprotein implicated in frontotemporal dementia, Jian Jiao, Lauren D. Herl, Robert V. Farese, and Fen-Biao Gao

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Birth time/order-dependent neuron type specification, Chih-Fei Kao and Tzumin Lee

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Clock and cycle limit starvation-induced sleep loss in Drosophila, Alex Carl Keene, Erik R. Duboue, Daniel M. McDonald, Monica Dus, Greg S.B. Suh, Scott Waddell, and Justin Blau

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Lineage-specific effects of Notch/Numb signaling in post-embryonic development of the Drosophila brain, Suewei Lin, Sen-Lin Lai, Hung-Hsiang Yu, Takahiro Chihara, Liqun Luo, and Tzumin Lee

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Activation of autophagy during cell death requires the engulfment receptor Draper, Christina K. McPhee, Mary A. Logan, Marc R. Freeman, and Eric H. Baehrecke

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Activity paradigm to induce Drosophila larval neuromuscular junction growth, Preethi Ramachandran and Vivian Budnik

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Dissection of Drosophila larval body-wall muscles, Preethi Ramachandran and Vivian Budnik

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Electron microscopy of Drosophila larval neuromuscular junctions, Preethi Ramachandran and Vivian Budnik

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Fm1-43 labeling of Drosophila larval neuromuscular junctions, Preethi Ramachandran and Vivian Budnik

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Immunocytochemical staining of Drosophila larval body-wall muscles, Preethi Ramachandran and Vivian Budnik

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Internalization and trafficking assay for Drosophila larvae, Preethi Ramachandran and Vivian Budnik

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Preparation of early Drosophila embryonic fillets (before cuticle deposition), Preethi Ramachandran and Vivian Budnik

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Preparation of late Drosophila embryonic fillets, Preethi Ramachandran and Vivian Budnik