Thomas Clandinin

All Publications

• Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science (New York, N.Y.) Li, H., Janssens, J., De Waegeneer, M., Kolluru, S. S., Davie, K., Gardeux, V., Saelens, W., David, F. P., Brbic, M., Spanier, K., Leskovec, J., McLaughlin, C. N., Xie, Q., Jones, R. C., Brueckner, K., Shim, J., Tattikota, S. G., Schnorrer, F., Rust, K., Nystul, T. G., Carvalho-Santos, Z., Ribeiro, C., Pal, S., Mahadevaraju, S., Przytycka, T. M., Allen, A. M., Goodwin, S. F., Berry, C. W., Fuller, M. T., White-Cooper, H., Matunis, E. L., DiNardo, S., Galenza, A., O'Brien, L. E., Dow, J. A., FCA Consortium, Jasper, H., Oliver, B., Perrimon, N., Deplancke, B., Quake, S. R., Luo, L., Aerts, S., Agarwal, D., Ahmed-Braimah, Y., Arbeitman, M., Ariss, M. M., Augsburger, J., Ayush, K., Baker, C. C., Banisch, T., Birker, K., Bodmer, R., Bolival, B., Brantley, S. E., Brill, J. A., Brown, N. C., Buehner, N. A., Cai, X. T., Cardoso-Figueiredo, R., Casares, F., Chang, A., Clandinin, T. R., Crasta, S., Desplan, C., Detweiler, A. M., Dhakan, D. B., Dona, E., Engert, S., Floc'hlay, S., George, N., Gonzalez-Segarra, A. J., Groves, A. K., Gumbin, S., Guo, Y., Harris, D. E., Heifetz, Y., Holtz, S. L., Horns, F., Hudry, B., Hung, R., Jan, Y. N., Jaszczak, J. S., Jefferis, G. S., Karkanias, J., Karr, T. L., Katheder, N. S., Kezos, J., Kim, A. A., Kim, S. K., Kockel, L., Konstantinides, N., Kornberg, T. B., Krause, H. M., Labott, A. T., Laturney, M., Lehmann, R., Leinwand, S., Li, J., Li, J. S., Li, K., Li, K., Li, L., Li, T., Litovchenko, M., Liu, H., Liu, Y., Lu, T., Manning, J., Mase, A., Matera-Vatnick, M., Matias, N. R., McDonough-Goldstein, C. E., McGeever, A., McLachlan, A. D., Moreno-Roman, P., Neff, N., Neville, M., Ngo, S., Nielsen, T., O'Brien, C. E., Osumi-Sutherland, D., Ozel, M. N., Papatheodorou, I., Petkovic, M., Pilgrim, C., Pisco, A. O., Reisenman, C., Sanders, E. N., Dos Santos, G., Scott, K., Sherlekar, A., Shiu, P., Sims, D., Sit, R. V., Slaidina, M., Smith, H. E., Sterne, G., Su, Y., Sutton, D., Tamayo, M., Tan, M., Tastekin, I., Treiber, C., Vacek, D., Vogler, G., Waddell, S., Wang, W., Wilson, R. I., Wolfner, M. F., Wong, Y. E., Xie, A., Xu, J., Yamamoto, S., Yan, J., Yao, Z., Yoda, K., Zhu, R., Zinzen, R. P. 2022; 375 (6584): eabk2432

  Abstract

  For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

  View details for DOI 10.1126/science.abk2432

  View details for PubMedID 35239393

• Mechanosensory input during circuit formation shapes Drosophila motor behavior through patterned spontaneous network activity. Current biology : CB Carreira-Rosario, A., York, R. A., Choi, M., Doe, C. Q., Clandinin, T. R. 2021

  Abstract

  Neural activity sculpts circuit wiring in many animals. In vertebrates, patterned spontaneous network activity (PaSNA) generates sensory maps and establishes local circuits.1-3 However, it remains unclear how PaSNA might shape neuronal circuits and behavior in invertebrates. Previous work in the developing Drosophila embryo discovered intrinsic muscle activity that did not require synaptic transmission, and hence was myogenic, preceding PaSNA.4-6 These studies, however, monitored muscle movement, not neural activity, and were therefore unable to observe how myogenic activity might relate to subsequent neural network engagement. Here we use calcium imaging to directly record neural activity and characterize the emergence of PaSNA. We demonstrate that the spatiotemporal properties of PaSNA are highly stereotyped across embryos, arguing for genetic programming. Neural activity begins well before it becomes patterned, emerging during the myogenic stage. Remarkably, inhibition of mechanosensory input, as well as inhibition of muscle contractions, results in premature and excessive PaSNA, demonstrating that muscle movement serves as a brake on this process. Finally, transient mechanosensory inhibition during PaSNA, followed by quantitative modeling of larval behavior, shows that mechanosensory modulation during development is required for proper larval foraging. This work provides a foundation for using the Drosophila embryo to study the role of PaSNA in circuit formation, provides mechanistic insight into how PaSNA is entrained by motor activity, and demonstrates that spontaneous network activity is essential for locomotor behavior. These studies argue that sensory feedback during the earliest stages of circuit formation can sculpt locomotor behaviors through innate motor learning.

  View details for DOI 10.1016/j.cub.2021.08.022

  View details for PubMedID 34478644

• Coupling of activity, metabolism and behaviour across the Drosophila brain. Nature Mann, K., Deny, S., Ganguli, S., Clandinin, T. R. 2021

  Abstract

  Coordinated activity across networks of neurons is a hallmark of both resting and active behavioural states in many species1-5. These global patterns alter energy metabolism over seconds to hours, which underpins the widespread use of oxygen consumption and glucose uptake as proxies of neural activity6,7. However, whether changes in neural activity are causally related to metabolic flux in intact circuits on the timescales associated with behaviour is unclear. Here we combine two-photon microscopy of the fly brain with sensors that enable the simultaneous measurement of neural activity and metabolic flux, across both resting and active behavioural states. We demonstrate that neural activity drives changes in metabolic flux, creating a tight coupling between these signals that can be measured across brain networks. Using local optogenetic perturbation, we demonstrate that even transient increases in neural activity result in rapid and persistent increases in cytosolic ATP, which suggests that neuronal metabolism predictively allocates resources to anticipate the energy demands of future activity. Finally, our studies reveal that the initiation of even minimal behavioural movements causes large-scale changes in the pattern of neural activity and energy metabolism, which reveals a widespread engagement of the brain. As the relationship between neural activity and energy metabolism is probably evolutionarily ancient and highly conserved, our studies provide a critical foundation for using metabolic proxies to capture changes in neural activity.

  View details for DOI 10.1038/s41586-021-03497-0

  View details for PubMedID 33911283

• The connectome predicts resting-state functional connectivity across the Drosophila brain. Current biology : CB Turner, M. H., Mann, K., Clandinin, T. R. 2021

  Abstract

  Anatomical connectivity can constrain both a neural circuit's function and its underlying computation. This principle has been demonstrated for many small, defined neural circuits. For example, connectome reconstructions have informed models for direction selectivity in the vertebrate retina1,2 as well as the Drosophila visual system.3 In these cases, the circuit in question is relatively compact, well-defined, and has known functions. However, how the connectome constrains global properties of large-scale networks, across multiple brain regions or the entire brain, is incompletely understood. As the availability of partial or complete connectomes expands to more systems and species4-8 it becomes critical to understand how this detailed anatomical information can inform our understanding of large-scale circuit function.9,10 Here, we use data from the Drosophila connectome4 in conjunction with whole-brain invivo imaging11 to relate structural and functional connectivity in the central brain. We find a strong relationship between resting-state functional correlations and direct region-to-region structural connectivity. We find that the relationship between structure and function varies across the brain, with some regions displaying a tight correspondence between structural and functional connectivity whereas others, including the mushroom body, are more strongly dependent on indirect connections. Throughout this work, we observe features of structural and functional networks in Drosophila that are strikingly similar to those seen in mammalian cortex, including in the human brain. Given the vast anatomical and functional differences between Drosophila and mammalian nervous systems, these observations suggest general principles that govern brain structure, function, and the relationship between the two.

  View details for DOI 10.1016/j.cub.2021.03.004

  View details for PubMedID 33770490

• Neuroscience: Convergence of biological and artificial networks. Current biology : CB Turner, M. H., Clandinin, T. R. 2021; 31 (18): R1079-R1081

  Abstract

  A new study shows that an artificial neural network trained to predict visual motion reproduces key properties of motion detecting circuits in the fruit fly.

  View details for DOI 10.1016/j.cub.2021.07.051

  View details for PubMedID 34582814

• SPARC enables genetic manipulation of precise proportions of cells. Nature neuroscience Isaacman-Beck, J., Paik, K. C., Wienecke, C. F., Yang, H. H., Fisher, Y. E., Wang, I. E., Ishida, I. G., Maimon, G., Wilson, R. I., Clandinin, T. R. 2020

  Abstract

  Many experimental approaches rely on controlling gene expression in select subsets of cells within an individual animal. However, reproducibly targeting transgene expression to specific fractions of a genetically defined cell type is challenging. We developed Sparse Predictive Activity through Recombinase Competition (SPARC), a generalizable toolkit that can express any effector in precise proportions of post-mitotic cells in Drosophila. Using this approach, we demonstrate targeted expression of many effectors in several cell types and apply these tools to calcium imaging of individual neurons and optogenetic manipulation of sparse cell populations in vivo.

  View details for DOI 10.1038/s41593-020-0668-9

  View details for PubMedID 32690967

• Drosophila Vision: An Eye for Change. Current biology : CB Wienecke, C. F., Clandinin, T. R. 2020; 30 (2): R66–R68

  Abstract

  Two new studies show that neuronal adaptation to changes in visual contrast is widespread in the early Drosophila visual system, improving velocity estimation in downstream motion detectors.

  View details for DOI 10.1016/j.cub.2019.11.069

  View details for PubMedID 31962077

• Transcriptional Feedback Links Lipid Synthesis to Synaptic Vesicle Pools in Drosophila Photoreceptors. Neuron Tsai, J. W., Kostyleva, R., Chen, P., Rivas-Serna, I. M., Clandinin, M. T., Meinertzhagen, I. A., Clandinin, T. R. 2019

  Abstract

  Neurons can maintain stable synaptic connections across adult life. However, the signals that regulate expression of synaptic proteins in the mature brain are incompletely understood. Here, we describe a transcriptional feedback loop between the biosynthesis and repertoire of specific phospholipids and the synaptic vesicle pool in adult Drosophila photoreceptors. Mutations that disrupt biosynthesis of a subset of phospholipids cause degeneration of the axon terminal and loss of synaptic vesicles. Although degeneration of the axon terminal is dependent on neural activity, activation of sterol regulatory element binding protein (SREBP) is both necessary and sufficient to cause synaptic vesicle loss. Our studies demonstrate that SREBP regulates synaptic vesicle levels by interacting with tetraspanins, critical organizers of membranous organelles. SREBP is an evolutionarily conserved regulator of lipid biosynthesis in non-neuronal cells; our studies reveal a surprising role for this feedback loop in maintaining synaptic vesicle pools in the adult brain.

  View details for PubMedID 30737130

• Sequential Nonlinear Filtering of Local Motion Cues by Global Motion Circuits. Neuron Barnhart, E. L., Wang, I. E., Wei, H., Desplan, C., Clandinin, T. R. 2018

  Abstract

  Many animals guide their movements using optic flow, the displacement of stationary objects across the retina caused by self-motion. How do animals selectively synthesize a global motion pattern from its local motion components? To what extent does this feature selectivity rely on circuit mechanisms versus dendritic processing? Here we used invivo calcium imaging to identify pre- and postsynaptic mechanisms for processing local motion signals in global motion detection circuits in Drosophila. Lobula plate tangential cells (LPTCs) detect global motion by pooling input from local motion detectors, T4/T5 neurons. We show that T4/T5 neurons suppress responses to adjacent local motion signals whereas LPTC dendrites selectively amplify spatiotemporal sequences of local motion signals consistent with preferred global patterns. We propose that sequential nonlinear suppression and amplification operations allow optic flow circuitry to simultaneously prevent saturating responses to local signals while creating selectivity for global motion patterns critical to behavior.

  View details for PubMedID 30220510

• Linear Summation Underlies Direction Selectivity in Drosophila. Neuron Wienecke, C. F., Leong, J. C., Clandinin, T. R. 2018

  Abstract

  While linear mechanisms lay the foundations of feature selectivity in many brain areas, direction selectivity in the elementary motion detector (EMD) of the fly has become a paradigm of nonlinear neuronal computation. We have bridged this divide by demonstrating that linear spatial summation cangenerate direction selectivity in the fruit fly Drosophila. Using linear systems analysis and two-photon imaging of a genetically encoded voltage indicator, we measure the emergence of direction-selective (DS) voltage signals in the Drosophila OFF pathway. Our study is a direct, quantitative investigation of the algorithm underlying directional signals, with the striking finding that linear spatial summation is sufficient for the emergence of direction selectivity. A linear stage of the fly EMD strongly resembles similar computations in vertebrate visual cortex, demands a reappraisal of the role of upstream nonlinearities, and implicates the voltage-to-calcium transformation in the refinement of feature selectivity in this system.

  View details for PubMedID 30057202

• Elementary Motion Detection in Drosophila: Algorithms and Mechanisms. Annual review of vision science Yang, H. H., Clandinin, T. R. 2018

  Abstract

  Motion in the visual world provides critical information to guide the behavior of sighted animals. Furthermore, as visual motion estimation requires comparisons of signals across inputs and over time, it represents a paradigmatic and generalizable neural computation. Focusing on the Drosophila visual system, where an explosion of technological advances has recently accelerated experimental progress, we review our understanding of how, algorithmically and mechanistically, motion signals are first computed. Expected final online publication date for the Annual Review of Vision Science Volume 4 is September 15, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  View details for PubMedID 29949723

• Developmental Biology: Neurons That Divide Together Wire Together. Current biology : CB Pang, M. M., Clandinin, T. R. 2018; 28 (12): R715–R717

  Abstract

  Retinotopic maps represent a fundamental organizing principle of visual system wiring. A recent study illustrates how careful coordination of developmental strategies can simultaneously create a diverse array of cell types and establish a complex wiring diagram.

  View details for PubMedID 29920268

• Ben Barres (1954-2017) Obituary NEURON Liddelow, S. A., Eroglu, C., Clandinin, T. R. 2018; 97 (6): 1211–13

  View details for DOI 10.1016/j.neuron.2018.03.005

  View details for Web of Science ID 000428235400006

• Ben Barres (1954-2017). Neuron Liddelow, S. A., Eroglu, C., Clandinin, T. R. 2018; 97 (6): 1211-1213

  View details for DOI 10.1016/j.neuron.2018.03.005

  View details for PubMedID 33245869

• Glia put visual map in sync. Science (New York, N.Y.) Isaacman-Beck, J., Clandinin, T. R. 2017; 357 (6354): 867-868

  View details for DOI 10.1126/science.aao2991

  View details for PubMedID 28860369

• Whole-Brain Calcium Imaging Reveals an Intrinsic Functional Network in Drosophila. Current biology : CB Mann, K., Gallen, C. L., Clandinin, T. R. 2017; 27 (15): 2389-2396.e4

  Abstract

  A long-standing goal of neuroscience has been to understand how computations are implemented across large-scale brain networks. By correlating spontaneous activity during "resting states" [1], studies of intrinsic brain networks in humans have demonstrated a correspondence with task-related activation patterns [2], relationships to behavior [3], and alterations in processes such as aging [4] and brain disorders [5], highlighting the importance of resting-state measurements for understanding brain function. Here, we develop methods to measure intrinsic functional connectivity in Drosophila, a powerful model for the study of neural computation. Recent studies using calcium imaging have measured neural activity at high spatial and temporal resolution in zebrafish, Drosophila larvae, and worms [6-10]. For example, calcium imaging in the zebrafish brain recently revealed correlations between the midbrain and hindbrain, demonstrating the utility of measuring intrinsic functional connections in model organisms [8]. An important component of human connectivity research is the use of brain atlases to compare findings across individuals and studies [11]. An anatomical atlas of the central adult fly brain was recently described [12]; however, combining an atlas with whole-brain calcium imaging has yet to be performed in vivo in adult Drosophila. Here, we measure intrinsic functional connectivity in Drosophila by acquiring calcium signals from the central brain. We develop an alignment procedure to assign functional data to atlas regions and correlate activity between regions to generate brain networks. This work reveals a large-scale architecture for neural communication and provides a framework for using Drosophila to study functional brain networks.

  View details for DOI 10.1016/j.cub.2017.06.076

  View details for PubMedID 28756955

  View details for PubMedCentralID PMC5967399

• Dynamic structure of locomotor behavior in walking fruit flies ELIFE Katsov, A. Y., Freifeld, L., Horowitz, M., Kuehn, S., Clandinin, T. R. 2017; 6

  Abstract

  The function of the brain is unlikely to be understood without an accurate description of its output, yet the nature of movement elements and their organization remains an open problem. Here, movement elements are identified from dynamics of walking in flies, using unbiased criteria. On one time scale, dynamics of walking are consistent over hundreds of milliseconds, allowing elementary features to be defined. Over longer periods, walking is well described by a stochastic process composed of these elementary features, and a generative model of this process reproduces individual behavior sequences accurately over seconds or longer. Within elementary features, velocities diverge, suggesting that dynamical stability of movement elements is a weak behavioral constraint. Rather, long-term instability can be limited by the finite memory between these elementary features. This structure suggests how complex dynamics may arise in biological systems from elements whose combination need not be tuned for dynamic stability.

  View details for PubMedID 28742018

• How Does Familiarity Breed Contempt? Cell Mann, K., Clandinin, T. R. 2017; 169 (5): 775-776

  Abstract

  Classifying sensory experiences as either novel or familiar represents a fundamental challenge to neural processing. In this issue of Cell, Hattori et al. describe a circuit mechanism by which a novel stimulus that initially interests a fruit fly turns into a familiar one.

  View details for DOI 10.1016/j.cell.2017.05.007

  View details for PubMedID 28525749

• . eLife Fisher, Y. E., Yang, H. H., Isaacman-Beck, J., Xie, M., Gohl, D. M., Clandinin, T. R. 2017; 6

  Abstract

  Manipulating gene function cell type-specifically is a common experimental goal in Drosophila research and has been central to studies of neural development, circuit computation, and behavior. However, current cell type-specific gene disruption techniques in flies often reduce gene activity incompletely or rely on cell division. Here we describe FlpStop, a generalizable tool for conditional gene disruption and rescue in post-mitotic cells. In proof-of-principle experiments, we manipulated apterous, a regulator of wing development. Next, we produced conditional null alleles of Glutamic acid decarboxylase 1 (Gad1) and Resistant to dieldrin (Rdl), genes vital for GABAergic neurotransmission, as well as cacophony (cac) and paralytic (para), voltage-gated ion channels central to neuronal excitability. To demonstrate the utility of this approach, we manipulated cac in a specific visual interneuron type and discovered differential regulation of calcium signals across subcellular compartments. Thus, FlpStop will facilitate investigations into the interactions between genes, circuits, and computation.

  View details for DOI 10.7554/eLife.22279

  View details for PubMedID 28211790

  View details for PubMedCentralID PMC5342825

• FlpStop, a tool for conditional gene control in Drosophila ELIFE Fisher, Y. E., Yang, H. H., Isaacman-Beck, J., Xie, M., Gohl, D. M., Clandinin, T. R. 2017; 6

  View details for DOI 10.7554/eLife.22279

  View details for Web of Science ID 000396174800001

• Fast two-photon imaging of subcellular voltage dynamics in neuronal tissue with genetically encoded indicators. eLife Chamberland, S. n., Yang, H. H., Pan, M. M., Evans, S. W., Guan, S. n., Chavarha, M. n., Yang, Y. n., Salesse, C. n., Wu, H. n., Wu, J. C., Clandinin, T. R., Toth, K. n., Lin, M. Z., St-Pierre, F. n. 2017; 6

  Abstract

  Monitoring voltage dynamics in defined neurons deep in the brain is critical for unraveling the function of neuronal circuits but is challenging due to the limited performance of existing tools. In particular, while genetically encoded voltage indicators have shown promise for optical detection of voltage transients, many indicators exhibit low sensitivity when imaged under two-photon illumination. Previous studies thus fell short of visualizing voltage dynamics in individual neurons in single trials. Here, we report ASAP2s, a novel voltage indicator with improved sensitivity. By imaging ASAP2s using random-access multi-photon microscopy, we demonstrate robust single-trial detection of action potentials in organotypic slice cultures. We also show that ASAP2s enables two-photon imaging of graded potentials in organotypic slice cultures and inDrosophila. These results demonstrate that the combination of ASAP2s and fast two-photon imaging methods enables detection of neural electrical activity with subcellular spatial resolution and millisecond-timescale precision.

  View details for PubMedID 28749338

  View details for PubMedCentralID PMC5584994

• Drosophila Connectomics: Mapping the Larval Eye's Mind. Current biology : CB Friedrich-Reed Wienecke, C. n., Clandinin, T. R. 2017; 27 (21): R1161–R1163

  Abstract

  A new study has mapped the connectome - the shapes and connections of all the neurons- of the visual system of a Drosophila larva, providing a structural basis for understanding the neural circuitry of larval vision.

  View details for PubMedID 29112868

• Editorial overview: Microcircuit evolution and computation 2016. Current opinion in neurobiology Clandinin, T. R., Marder, E. 2016; 41: 188-190

  View details for DOI 10.1016/j.conb.2016.10.001

  View details for PubMedID 27810767

• The Influence of Wiring Economy on Nervous System Evolution. Current biology Wang, I. E., Clandinin, T. R. 2016; 26 (20): R1101-R1108

  Abstract

  The activity and maintenance of neurons requires substantial metabolic energy, resulting in selective pressure to decrease resource consumption by the nervous system. The wiring economy principle proposes that animals have evolved mechanisms that wire circuits efficiently by minimizing neurite length. Computational modeling of neuronal morphology, microcircuit organization, and neural networks reveals that wiring economy is a significant determinant of nervous system layout. The strategies for reducing wiring costs are shared across phyla and point to the possibility of generalizable rules that specify the development of efficient nervous systems. As the developmental mechanisms underpinning wiring economy are only now being elucidated, whether the molecular basis of this phenomenon is the result of conserved genetic programs or convergent evolution remains to be determined.

  View details for DOI 10.1016/j.cub.2016.08.053

  View details for PubMedID 27780051

• Hedgehog signaling regulates gene expression in planarian glia. eLife Wang, I. E., Lapan, S. W., Scimone, M. L., Clandinin, T. R., Reddien, P. W. 2016; 5

  Abstract

  Hedgehog signaling is critical for vertebrate central nervous system (CNS) development, but its role in CNS biology in other organisms is poorly characterized. In the planarian Schmidtea mediterranea, hedgehog (hh) is expressed in medial cephalic ganglia neurons, suggesting a possible role in CNS maintenance or regeneration. We performed RNA sequencing of planarian brain tissue following RNAi of hh and patched (ptc), which encodes the Hh receptor. Two misregulated genes, intermediate filament-1 (if-1) and calamari (cali), were expressed in a previously unidentified non-neural CNS cell type. These cells expressed orthologs of astrocyte-associated genes involved in neurotransmitter uptake and metabolism, and extended processes enveloping regions of high synapse concentration. We propose that these cells are planarian glia. Planarian glia were distributed broadly, but only expressed if-1 and cali in the neuropil near hh(+) neurons. Planarian glia and their regulation by Hedgehog signaling present a novel tractable system for dissection of glia biology.

  View details for DOI 10.7554/eLife.16996

  View details for PubMedID 27612382

  View details for PubMedCentralID PMC5055395

• Direction Selectivity in Drosophila Emerges from Preferred-Direction Enhancement and Null-Direction Suppression. journal of neuroscience Leong, J. C., Esch, J. J., Poole, B., Ganguli, S., Clandinin, T. R. 2016; 36 (31): 8078-8092

  Abstract

  Across animal phyla, motion vision relies on neurons that respond preferentially to stimuli moving in one, preferred direction over the opposite, null direction. In the elementary motion detector of Drosophila, direction selectivity emerges in two neuron types, T4 and T5, but the computational algorithm underlying this selectivity remains unknown. We find that the receptive fields of both T4 and T5 exhibit spatiotemporally offset light-preferring and dark-preferring subfields, each obliquely oriented in spacetime. In a linear-nonlinear modeling framework, the spatiotemporal organization of the T5 receptive field predicts the activity of T5 in response to motion stimuli. These findings demonstrate that direction selectivity emerges from the enhancement of responses to motion in the preferred direction, as well as the suppression of responses to motion in the null direction. Thus, remarkably, T5 incorporates the essential algorithmic strategies used by the Hassenstein-Reichardt correlator and the Barlow-Levick detector. Our model for T5 also provides an algorithmic explanation for the selectivity of T5 for moving dark edges: our model captures all two- and three-point spacetime correlations relevant to motion in this stimulus class. More broadly, our findings reveal the contribution of input pathway visual processing, specifically center-surround, temporally biphasic receptive fields, to the generation of direction selectivity in T5. As the spatiotemporal receptive field of T5 in Drosophila is common to the simple cell in vertebrate visual cortex, our stimulus-response model of T5 will inform efforts in an experimentally tractable context to identify more detailed, mechanistic models of a prevalent computation.Feature selective neurons respond preferentially to astonishingly specific stimuli, providing the neurobiological basis for perception. Direction selectivity serves as a paradigmatic model of feature selectivity that has been examined in many species. While insect elementary motion detectors have served as premiere experimental models of direction selectivity for 60 years, the central question of their underlying algorithm remains unanswered. Using in vivo two-photon imaging of intracellular calcium signals, we measure the receptive fields of the first direction-selective cells in the Drosophila visual system, and define the algorithm used to compute the direction of motion. Computational modeling of these receptive fields predicts responses to motion and reveals how this circuit efficiently captures many useful correlations intrinsic to moving dark edges.

  View details for DOI 10.1523/JNEUROSCI.1272-16.2016

  View details for PubMedID 27488629

  View details for PubMedCentralID PMC4971360

• Subcellular Imaging of Voltage and Calcium Signals Reveals Neural Processing In Vivo CELL Yang, H. H., St-Pierre, F., Sun, X., Ding, X., Lin, M. Z., Clandinin, T. R. 2016; 166 (1): 245-257

  Abstract

  A mechanistic understanding of neural computation requires determining how information is processed as it passes through neurons and across synapses. However, it has been challenging to measure membrane potential changes in axons and dendrites in vivo. We use in vivo, two-photon imaging of novel genetically encoded voltage indicators, as well as calcium imaging, to measure sensory stimulus-evoked signals in the Drosophila visual system with subcellular resolution. Across synapses, we find major transformations in the kinetics, amplitude, and sign of voltage responses to light. We also describe distinct relationships between voltage and calcium signals in different neuronal compartments, a substrate for local computation. Finally, we demonstrate that ON and OFF selectivity, a key feature of visual processing across species, emerges through the transformation of membrane potential into intracellular calcium concentration. By imaging voltage and calcium signals to map information flow with subcellular resolution, we illuminate where and how critical computations arise.

  View details for DOI 10.1016/j.cell.2016.05.031

  View details for Web of Science ID 000380254400025

  View details for PubMedID 27264607

• Grabbing brain activity on the go. Proceedings of the National Academy of Sciences of the United States of America Clandinin, T. R., Goodman, M. B. 2016; 113 (8): 1965-7

  View details for DOI 10.1073/pnas.1524219113

  View details for PubMedID 26842834

  View details for PubMedCentralID PMC4776519

• Can You Hear Me Now? Neuron Barnhart, E. L., Clandinin, T. R. 2016; 89 (3): 425-427

  Abstract

  Auditory communication is central to the social interactions of many animals. In fruit flies, males sing to court females. Coen et al. (2016) demonstrate that males can dynamically adjust the loudness of their songs according to the distance to a female.

  View details for DOI 10.1016/j.neuron.2016.01.030

  View details for PubMedID 26844825

• A Class of Visual Neurons with Wide-Field Properties Is Required for Local Motion Detection CURRENT BIOLOGY Fisher, Y. E., Leong, J. C., Sporar, K., Ketkar, M. D., Gohl, D. M., Clandinin, T. R., Silies, M. 2015; 25 (24): 3178-3189

  Abstract

  Visual motion cues are used by many animals to guide navigation across a wide range of environments. Long-standing theoretical models have made predictions about the computations that compare light signals across space and time to detect motion. Using connectomic and physiological approaches, candidate circuits that can implement various algorithmic steps have been proposed in the Drosophila visual system. These pathways connect photoreceptors, via interneurons in the lamina and the medulla, to direction-selective cells in the lobula and lobula plate. However, the functional architecture of these circuits remains incompletely understood. Here, we use a forward genetic approach to identify the medulla neuron Tm9 as critical for motion-evoked behavioral responses. Using in vivo calcium imaging combined with genetic silencing, we place Tm9 within motion-detecting circuitry. Tm9 receives functional inputs from the lamina neurons L3 and, unexpectedly, L1 and passes information onto the direction-selective T5 neuron. Whereas the morphology of Tm9 suggested that this cell would inform circuits about local points in space, we found that the Tm9 spatial receptive field is large. Thus, this circuit informs elementary motion detectors about a wide region of the visual scene. In addition, Tm9 exhibits sustained responses that provide a tonic signal about incoming light patterns. Silencing Tm9 dramatically reduces the response amplitude of T5 neurons under a broad range of different motion conditions. Thus, our data demonstrate that sustained and wide-field signals are essential for elementary motion processing.

  View details for DOI 10.1016/j.cub.2015.11.018

  View details for Web of Science ID 000367233400017

  View details for PubMedID 26670999

• Orientation Selectivity Sharpens Motion Detection in Drosophila. Neuron Fisher, Y. E., Silies, M., Clandinin, T. R. 2015; 88 (2): 390-402

  Abstract

  Detecting the orientation and movement of edges in a scene is critical to visually guided behaviors of many animals. What are the circuit algorithms that allow the brain to extract such behaviorally vital visual cues? Using in vivo two-photon calcium imaging in Drosophila, we describe direction selective signals in the dendrites of T4 and T5 neurons, detectors of local motion. We demonstrate that this circuit performs selective amplification of local light inputs, an observation that constrains motion detection models and confirms a core prediction of the Hassenstein-Reichardt correlator (HRC). These neurons are also orientation selective, responding strongly to static features that are orthogonal to their preferred axis of motion, a tuning property not predicted by the HRC. This coincident extraction of orientation and direction sharpens directional tuning through surround inhibition and reveals a striking parallel between visual processing in flies and vertebrate cortex, suggesting a universal strategy for motion processing.

  View details for DOI 10.1016/j.neuron.2015.09.033

  View details for PubMedID 26456048

  View details for PubMedCentralID PMC4664581

• Neurons Rho to Get in Shape for the Day. Cell Mann, K., Clandinin, T. R. 2015; 162 (4): 699-700

  Abstract

  Linking structural changes in neurons to animal behavior has proven challenging. New findings by Pesakou et al. tie daily cycles of axon arbor extension and retraction, mediated by Rho activity, to circadian and seasonal patterns of behavior in the fruit fly.

  View details for DOI 10.1016/j.cell.2015.07.044

  View details for PubMedID 26276623

• A transcriptional reporter of intracellular Ca(2+) in Drosophila. Nature neuroscience Gao, X. J., Riabinina, O., Li, J., Potter, C. J., Clandinin, T. R., Luo, L. 2015; 18 (6): 917-925

  Abstract

  Intracellular Ca(2+) is a widely used neuronal activity indicator. Here we describe a transcriptional reporter of intracellular Ca(2+) (TRIC) in Drosophila that uses a binary expression system to report Ca(2+)-dependent interactions between calmodulin and its target peptide. We found that in vitro assays predicted in vivo properties of TRIC and that TRIC signals in sensory systems depend on neuronal activity. TRIC was able to quantitatively monitor neuronal responses that changed slowly, such as those of neuropeptide F-expressing neurons to sexual deprivation and neuroendocrine pars intercerebralis cells to food and arousal. Furthermore, TRIC-induced expression of a neuronal silencer in nutrient-activated cells enhanced stress resistance, providing a proof of principle that TRIC can be used for circuit manipulation. Thus, TRIC facilitates the monitoring and manipulation of neuronal activity, especially those reflecting slow changes in physiological states that are poorly captured by existing methods. TRIC's modular design should enable optimization and adaptation to other organisms.

  View details for DOI 10.1038/nn.4016

  View details for PubMedID 25961791

  View details for PubMedCentralID PMC4446202

• A transcriptional reporter of intracellular Ca2+ in Drosophila NATURE NEUROSCIENCE Gao, X. J., Riabinina, O., Li, J., Potter, C. J., Clandinin, T. R., Luo, L. 2015; 18 (6): 917-U373

  Abstract

  Intracellular Ca(2+) is a widely used neuronal activity indicator. Here we describe a transcriptional reporter of intracellular Ca(2+) (TRIC) in Drosophila that uses a binary expression system to report Ca(2+)-dependent interactions between calmodulin and its target peptide. We found that in vitro assays predicted in vivo properties of TRIC and that TRIC signals in sensory systems depend on neuronal activity. TRIC was able to quantitatively monitor neuronal responses that changed slowly, such as those of neuropeptide F-expressing neurons to sexual deprivation and neuroendocrine pars intercerebralis cells to food and arousal. Furthermore, TRIC-induced expression of a neuronal silencer in nutrient-activated cells enhanced stress resistance, providing a proof of principle that TRIC can be used for circuit manipulation. Thus, TRIC facilitates the monitoring and manipulation of neuronal activity, especially those reflecting slow changes in physiological states that are poorly captured by existing methods. TRIC's modular design should enable optimization and adaptation to other organisms.

  View details for DOI 10.1038/nn.4016

  View details for Web of Science ID 000355218300020

  View details for PubMedID 25961791

  View details for PubMedCentralID PMC4446202

• Neuroscience: Internal compass puts flies in their place. Nature Clandinin, T. R., Giocomo, L. M. 2015; 521 (7551): 165-166

  View details for DOI 10.1038/521165a

  View details for PubMedID 25971505

• Extremely Sparse Olfactory Inputs Are Sufficient to Mediate Innate Aversion in Drosophila PLOS ONE Gao, X. J., Clandinin, T. R., Luo, L. 2015; 10 (4)

  Abstract

  Innate attraction and aversion to odorants are observed throughout the animal kingdom, but how olfactory circuits encode such valences is not well understood, despite extensive anatomical and functional knowledge. In Drosophila melanogaster, ~50 types of olfactory receptor neurons (ORNs) each express a unique receptor gene, and relay information to a cognate type of projection neurons (PNs). To examine the extent to which the population activity of ORNs is required for olfactory behavior, we developed a genetic strategy to block all ORN outputs, and then to restore output in specific types. Unlike attraction, aversion was unaffected by simultaneous silencing of many ORNs, and even single ORN types previously shown to convey neutral valence sufficed to mediate aversion. Thus, aversion may rely on specific activity patterns in individual ORNs rather than the number or identity of activated ORNs. ORN activity is relayed into the brain by downstream circuits, with excitatory PNs (ePN) representing a major output. We found that silencing the majority of ePNs did not affect aversion, even when ePNs directly downstream of single restored ORN types were silenced. Our data demonstrate the robustness of olfactory aversion, and suggest that its circuit mechanism is qualitatively different from attraction.

  View details for DOI 10.1371/journal.pone.0125986

  View details for Web of Science ID 000353713100121

  View details for PubMedID 25927233

  View details for PubMedCentralID PMC4416024

• Extremely sparse olfactory inputs are sufficient to mediate innate aversion in Drosophila. PloS one Gao, X. J., Clandinin, T. R., Luo, L. 2015; 10 (4)

  Abstract

  Innate attraction and aversion to odorants are observed throughout the animal kingdom, but how olfactory circuits encode such valences is not well understood, despite extensive anatomical and functional knowledge. In Drosophila melanogaster, ~50 types of olfactory receptor neurons (ORNs) each express a unique receptor gene, and relay information to a cognate type of projection neurons (PNs). To examine the extent to which the population activity of ORNs is required for olfactory behavior, we developed a genetic strategy to block all ORN outputs, and then to restore output in specific types. Unlike attraction, aversion was unaffected by simultaneous silencing of many ORNs, and even single ORN types previously shown to convey neutral valence sufficed to mediate aversion. Thus, aversion may rely on specific activity patterns in individual ORNs rather than the number or identity of activated ORNs. ORN activity is relayed into the brain by downstream circuits, with excitatory PNs (ePN) representing a major output. We found that silencing the majority of ePNs did not affect aversion, even when ePNs directly downstream of single restored ORN types were silenced. Our data demonstrate the robustness of olfactory aversion, and suggest that its circuit mechanism is qualitatively different from attraction.

  View details for DOI 10.1371/journal.pone.0125986

  View details for PubMedID 25927233

  View details for PubMedCentralID PMC4416024

• A Drosophila Toolkit for the Visualization and Quantification of Viral Replication Launched from Transgenic Genomes PLOS ONE Wernet, M. F., Klovstad, M., Clandinin, T. R. 2014; 9 (11)

  View details for DOI 10.1371/journal.pone.0112092

  View details for Web of Science ID 000345250400040

• Differences in Neural Circuitry Guiding Behavioral Responses to Polarized light Presented to Either the Dorsal or Ventral Retina in Drosophila JOURNAL OF NEUROGENETICS Velez, M. M., Gohl, D., Clandinin, T. R., Wernet, M. F. 2014; 28 (3-4): 348-360

  View details for DOI 10.3109/01677063.2014.922556

  View details for Web of Science ID 000344555700017

• Differences in neural circuitry guiding behavioral responses to polarized light presented to either the dorsal or ventral retina in Drosophila. Journal of neurogenetics Velez, M. M., Gohl, D., Clandinin, T. R., Wernet, M. F. 2014; 28 (3-4): 348-360

  Abstract

  Linearly polarized light (POL) serves as an important cue for many animals, providing navigational information, as well as directing them toward food sources and reproduction sites. Many insects detect the celestial polarization pattern, or the linearly polarized reflections off of surfaces, such as water. Much progress has been made toward characterizing both retinal detectors and downstream circuit elements responsible for celestial POL vision in different insect species, yet much less is known about the neural basis of how polarized reflections are detected. We previously established a novel, fully automated behavioral assay for studying the spontaneous orientation response of Drosophila melanogaster populations to POL stimuli presented to either the dorsal, or the ventral halves of the retina. We identified separate retinal detectors mediating these responses: the 'Dorsal Rim Area' (DRA), which had long been implicated in celestial POL vision, as well as a previously uncharacterized 'ventral polarization area' (VPA). In this study, we investigate whether DRA and VPA use the same or different downstream circuitry, for mediating spontaneous behavioral responses. We use homozygous mutants, or molecular genetic circuit-breaking tools (silencing, as well as rescue of synaptic activity), in combination with our behavioral paradigm. We show that responses to dorsal versus ventral stimulation involve previously characterized optic lobe neurons, like lamina monopolar cell L2 and medulla cell types Dm8/Tm5c. However, using different experimental conditions, we show that important differences exist between the requirement of these cell types downstream of DRA versus VPA. Therefore, while the neural circuits underlying behavioral responses to celestial and reflected POL cues share important building blocks, these elements play different functional roles within the network.

  View details for DOI 10.3109/01677063.2014.922556

  View details for PubMedID 24912584

• Processing properties of ON and OFF pathways for Drosophila motion detection. Nature Behnia, R., Clark, D. A., Carter, A. G., Clandinin, T. R., Desplan, C. 2014; 512 (7515): 427-430

  Abstract

  The algorithms and neural circuits that process spatio-temporal changes in luminance to extract visual motion cues have been the focus of intense research. An influential model, the Hassenstein-Reichardt correlator, relies on differential temporal filtering of two spatially separated input channels, delaying one input signal with respect to the other. Motion in a particular direction causes these delayed and non-delayed luminance signals to arrive simultaneously at a subsequent processing step in the brain; these signals are then nonlinearly amplified to produce a direction-selective response. Recent work in Drosophila has identified two parallel pathways that selectively respond to either moving light or dark edges. Each of these pathways requires two critical processing steps to be applied to incoming signals: differential delay between the spatial input channels, and distinct processing of brightness increment and decrement signals. Here we demonstrate, using in vivo patch-clamp recordings, that four medulla neurons implement these two processing steps. The neurons Mi1 and Tm3 respond selectively to brightness increments, with the response of Mi1 delayed relative to Tm3. Conversely, Tm1 and Tm2 respond selectively to brightness decrements, with the response of Tm1 delayed compared with Tm2. Remarkably, constraining Hassenstein-Reichardt correlator models using these measurements produces outputs consistent with previously measured properties of motion detectors, including temporal frequency tuning and specificity for light versus dark edges. We propose that Mi1 and Tm3 perform critical processing of the delayed and non-delayed input channels of the correlator responsible for the detection of light edges, while Tm1 and Tm2 play analogous roles in the detection of moving dark edges. Our data show that specific medulla neurons possess response properties that allow them to implement the algorithmic steps that precede the correlative operation in the Hassenstein-Reichardt correlator, revealing elements of the long-sought neural substrates of motion detection in the fly.

  View details for DOI 10.1038/nature13427

  View details for PubMedID 25043016

• Identifying Functional Connections of the Inner Photoreceptors in Drosophila using Tango-Trace. Neuron Jagadish, S., Barnea, G., Clandinin, T. R., Axel, R. 2014; 83 (3): 630-644

  Abstract

  In Drosophila, the four inner photoreceptor neurons exhibit overlapping but distinct spectral sensitivities and mediate behaviors that reflect spectral preference. We developed a genetic strategy, Tango-Trace, that has permitted the identification of the connections of the four chromatic photoreceptors. Each of the four stochastically distributed chromatic photoreceptor subtypes make distinct connections in the medulla with four different TmY cells. Moreover, each class of TmY cells forms a retinotopic map in both the medulla and the lobula complex, generating four overlapping topographic maps that could carry different color information. Thus, the four inner photoreceptors transmit spectral information through distinct channels that may converge in both the medulla and lobula complex. These projections could provide an anatomic basis for color vision and may relay information about color to motion sensitive areas. Moreover, the Tango-Trace strategy we used may be applied more generally to identify neural circuits in the fly brain.

  View details for DOI 10.1016/j.neuron.2014.06.025

  View details for PubMedID 25043419

  View details for PubMedCentralID PMC4126867

• Motion-detecting circuits in flies: coming into view. Annual review of neuroscience Silies, M., Gohl, D. M., Clandinin, T. R. 2014; 37: 307-327

  Abstract

  Visual motion cues provide animals with critical information about their environment and guide a diverse array of behaviors. The neural circuits that carry out motion estimation provide a well-constrained model system for studying the logic of neural computation. Through a confluence of behavioral, physiological, and anatomical experiments, taking advantage of the powerful genetic tools available in the fruit fly Drosophila melanogaster, an outline of the neural pathways that compute visual motion has emerged. Here we describe these pathways, the evidence supporting them, and the challenges that remain in understanding the circuits and computations that link sensory inputs to behavior. Studies in flies and vertebrates have revealed a number of functional similarities between motion-processing pathways in different animals, despite profound differences in circuit anatomy and structure. The fact that different circuit mechanisms are used to achieve convergent computational outcomes sheds light on the evolution of the nervous system.

  View details for DOI 10.1146/annurev-neuro-071013-013931

  View details for PubMedID 25032498

• Differential Adhesion Determines the Organization of Synaptic Fascicles in the Drosophila Visual System CURRENT BIOLOGY Schwabe, T., Borycz, J. A., Meinertzhagen, I. A., Clandinin, T. R. 2014; 24 (12): 1304-1313

  View details for DOI 10.1016/j.cub.2014.04.047

  View details for Web of Science ID 000337648200019

• Differential adhesion determines the organization of synaptic fascicles in the Drosophila visual system. Current biology Schwabe, T., Borycz, J. A., Meinertzhagen, I. A., Clandinin, T. R. 2014; 24 (12): 1304-1313

  Abstract

  Neuronal circuits in worms, flies, and mammals are organized so as to minimize wiring length for a functional number of synaptic connections, a phenomenon called wiring optimization. However, the molecular mechanisms that establish optimal wiring during development are unknown. We addressed this question by studying the role of N-cadherin in the development of optimally wired neurite fascicles in the peripheral visual system of Drosophila.Photoreceptor axons surround the dendrites of their postsynaptic targets, called lamina cells, within a concentric fascicle called a cartridge. N-cadherin is expressed at higher levels in lamina cells than in photoreceptors, and all genetic manipulations that invert these relative differences displace lamina cells to the periphery and relocate photoreceptor axon terminals into the center.Differential expression of a single cadherin is both necessary and sufficient to determine cartridge structure because it positions the most-adhesive elements that make the most synapses at the core and the less-adhesive elements that make fewer synapses at the periphery. These results suggest a general model by which differential adhesion can be utilized to determine the relative positions of axons and dendrites to establish optimal wiring.

  View details for DOI 10.1016/j.cub.2014.04.047

  View details for PubMedID 24881879

• Walking Drosophila align with the e-vector of linearly polarized light through directed modulation of angular acceleration. Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology Velez, M. M., Wernet, M. F., Clark, D. A., Clandinin, T. R. 2014; 200 (6): 603-614

  Abstract

  Understanding the mechanisms that link sensory stimuli to animal behavior is a central challenge in neuroscience. The quantitative description of behavioral responses to defined stimuli has led to a rich understanding of different behavioral strategies in many species. One important navigational cue perceived by many vertebrates and insects is the e-vector orientation of linearly polarized light. Drosophila manifests an innate orientation response to this cue ('polarotaxis'), aligning its body axis with the e-vector field. We have established a population-based behavioral paradigm for the genetic dissection of neural circuits guiding polarotaxis to both celestial as well as reflected polarized stimuli. However, the behavioral mechanisms by which flies align with a linearly polarized stimulus remain unknown. Here, we present a detailed quantitative description of Drosophila polarotaxis, systematically measuring behavioral parameters that are modulated by the stimulus. We show that angular acceleration is modulated during alignment, and this single parameter may be sufficient for alignment. Furthermore, using monocular deprivation, we show that each eye is necessary for modulating turns in the ipsilateral direction. This analysis lays the foundation for understanding how neural circuits guide these important visual behaviors.

  View details for DOI 10.1007/s00359-014-0910-6

  View details for PubMedID 24810784

• Vision: EM-erging motion-detecting circuits. Current biology Silies, M., Clandinin, T. R. 2014; 24 (10): R390-2

  Abstract

  How does the brain compare visual inputs over space and time to extract motion? Electron microscopic (EM) and molecular analyses reveal a new circuit architecture for motion processing in Drosophila. An offset in the weighting of synaptic connections and differential use of fast and slow nicotinic receptors suggests a mechanism that can implement spatiotemporal comparisons.

  View details for DOI 10.1016/j.cub.2014.03.067

  View details for PubMedID 24845666

• Large-scale mapping of transposable element insertion sites using digital encoding of sample identity. Genetics Gohl, D. M., Freifeld, L., Silies, M., Hwa, J. J., Horowitz, M., Clandinin, T. R. 2014; 196 (3): 615-623

  Abstract

  Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools.

  View details for DOI 10.1534/genetics.113.159483

  View details for PubMedID 24374352

  View details for PubMedCentralID PMC3948795

• Large-scale mapping of transposable element insertion sites using digital encoding of sample identity. Genetics Gohl, D. M., Freifeld, L., Silies, M., Hwa, J. J., Horowitz, M., Clandinin, T. R. 2014; 196 (3): 615-623

  Abstract

  Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools.

  View details for DOI 10.1534/genetics.113.159483

  View details for PubMedID 24374352

  View details for PubMedCentralID PMC3948795

• Generation of infectious virus particles from inducible transgenic genomes. Current biology : CB Wernet, M. F., Klovstad, M., Clandinin, T. R. 2014; 24 (3): R107-8

  Abstract

  Arboviruses like dengue virus, yellow fever virus, and West Nile virus are enveloped particles spread by mosquitoes, infecting millions of humans per year, with neither effective vaccines, nor specific antiviral therapies [1,2]. Previous studies of infection and virus replication utilize either purified virus particles or deficient genomes that do not complete the viral life cycle [1,2]. Here we describe transgenic Drosophila strains expressing trans-complementing genomes (referred to as 'replicons') from the arbovirus Sindbis [2]. We use this binary system to produce, for the first time in any metazoan, infectious virus particles through self-assembly from transgenes. Such cell-type specific particle 'launching' could serve as an attractive alternative for the development of virus-based tools and the study of virus biology in specific tissues.

  View details for DOI 10.1016/j.cub.2013.12.009

  View details for PubMedID 24502780

  View details for PubMedCentralID PMC4110053

• Flies and humans share a motion estimation strategy that exploits natural scene statistics. Nature neuroscience Clark, D. A., Fitzgerald, J. E., Ales, J. M., Gohl, D. M., Silies, M. A., Norcia, A. M., Clandinin, T. R. 2014; 17 (2): 296-303

  Abstract

  Sighted animals extract motion information from visual scenes by processing spatiotemporal patterns of light falling on the retina. The dominant models for motion estimation exploit intensity correlations only between pairs of points in space and time. Moving natural scenes, however, contain more complex correlations. We found that fly and human visual systems encode the combined direction and contrast polarity of moving edges using triple correlations that enhance motion estimation in natural environments. Both species extracted triple correlations with neural substrates tuned for light or dark edges, and sensitivity to specific triple correlations was retained even as light and dark edge motion signals were combined. Thus, both species separately process light and dark image contrasts to capture motion signatures that can improve estimation accuracy. This convergence argues that statistical structures in natural scenes have greatly affected visual processing, driving a common computational strategy over 500 million years of evolution.

  View details for DOI 10.1038/nn.3600

  View details for PubMedID 24390225

• A Drosophila toolkit for the visualization and quantification of viral replication launched from transgenic genomes. PloS one Wernet, M. F., Klovstad, M., Clandinin, T. R. 2014; 9 (11)

  Abstract

  Arthropod RNA viruses pose a serious threat to human health, yet many aspects of their replication cycle remain incompletely understood. Here we describe a versatile Drosophila toolkit of transgenic, self-replicating genomes ('replicons') from Sindbis virus that allow rapid visualization and quantification of viral replication in vivo. We generated replicons expressing Luciferase for the quantification of viral replication, serving as useful new tools for large-scale genetic screens for identifying cellular pathways that influence viral replication. We also present a new binary system in which replication-deficient viral genomes can be activated 'in trans', through co-expression of an intact replicon contributing an RNA-dependent RNA polymerase. The utility of this toolkit for studying virus biology is demonstrated by the observation of stochastic exclusion between replicons expressing different fluorescent proteins, when co-expressed under control of the same cellular promoter. This process is analogous to 'superinfection exclusion' between virus particles in cell culture, a process that is incompletely understood. We show that viral polymerases strongly prefer to replicate the genome that encoded them, and that almost invariably only a single virus genome is stochastically chosen for replication in each cell. Our in vivo system now makes this process amenable to detailed genetic dissection. Thus, this toolkit allows the cell-type specific, quantitative study of viral replication in a genetic model organism, opening new avenues for molecular, genetic and pharmacological dissection of virus biology and tool development.

  View details for DOI 10.1371/journal.pone.0112092

  View details for PubMedID 25386852

  View details for PubMedCentralID PMC4227818

• What can fruit flies teach us about karate? eLife Yang, H. H., Clandinin, T. R. 2014; 3

  Abstract

  Understanding the logic behind how a fruit fly's brain tells it to groom its body parts in a stereotyped order might help us understand other behaviours that also involve a series of actions.

  View details for DOI 10.7554/eLife.04040

  View details for PubMedID 25139958

  View details for PubMedCentralID PMC4136469

• A Network of Cadherin-Mediated Interactions Polarizes Growth Cones to Determine Targeting Specificity CELL Schwabe, T., Neuert, H., Clandinin, T. R. 2013; 154 (2): 351-364

  Abstract

  Neuronal growth cones select synaptic partners through interactions with multiple cell surfaces in their environment. Many of these interactions are adhesive, yet it is unclear how growth cones integrate adhesive cues to direct their movements. Here, we examine the mechanisms that enable photoreceptors in the Drosophila visual system to choose synaptic partners. We demonstrate that the classical cadherin, N-cadherin, and an atypical cadherin, Flamingo, act redundantly to instruct the targeting choices made by every photoreceptor axon. These molecules gradually bias the spatial distribution of growth cone filopodia, polarizing each growth cone toward its future synaptic target before direct contact with the target occurs. We demonstrate that these molecules are localized to distinct subcellular domains and create a network of adhesive interactions distributed across many growth cones. Because this network comprises multiple redundant interactions, a complex wiring diagram can be constructed with extraordinary fidelity, suggesting a general principle.

  View details for DOI 10.1016/j.cell.2013.06.011

  View details for Web of Science ID 000321950700012

  View details for PubMedID 23870124

• Modular Use of Peripheral Input Channels Tunes Motion-Detecting Circuitry NEURON Silies, M., Gohl, D. M., Fisher, Y. E., Freifeld, L., Clark, D. A., Clandinin, T. R. 2013; 79 (1): 111-127

  Abstract

  In the visual system, peripheral processing circuits are often tuned to specific stimulus features. How this selectivity arises and how these circuits are organized to inform specific visual behaviors is incompletely understood. Using forward genetics and quantitative behavioral studies, we uncover an input channel to motion detecting circuitry in Drosophila. The second-order neuron L3 acts combinatorially with two previously known inputs, L1 and L2, to inform circuits specialized to detect moving light and dark edges. In vivo calcium imaging of L3, combined with neuronal silencing experiments, suggests a neural mechanism to achieve selectivity for moving dark edges. We further demonstrate that different innate behaviors, turning and forward movement, can be independently modulated by visual motion. These two behaviors make use of different combinations of input channels. Such modular use of input channels to achieve feature extraction and behavioral specialization likely represents a general principle in sensory systems.

  View details for DOI 10.1016/j.neuron.2013.04.029

  View details for Web of Science ID 000321802000013

  View details for PubMedID 23849199

  View details for PubMedCentralID PMC3713415

• Specific Kinematics and Motor-Related Neurons for Aversive Chemotaxis in Drosophila CURRENT BIOLOGY Gao, X. J., Potter, C. J., Gohl, D. M., Silies, M., Katsov, A. Y., Clandinin, T. R., Luo, L. 2013; 23 (13): 1163-1172

  Abstract

  Chemotaxis, the ability to direct movements according to chemical cues in the environment, is important for the survival of most organisms. The vinegar fly, Drosophila melanogaster, displays robust olfactory aversion and attraction, but how these behaviors are executed via changes in locomotion remains poorly understood. In particular, it is not clear whether aversion and attraction bidirectionally modulate a shared circuit or recruit distinct circuits for execution.Using a quantitative behavioral assay, we determined that both aversive and attractive odorants modulate the initiation and direction of turns but display distinct kinematics. Using genetic tools to perturb these behaviors, we identified specific populations of neurons required for aversion, but not for attraction. Inactivation of these populations of cells affected the completion of aversive turns, but not their initiation. Optogenetic activation of the same populations of cells triggered a locomotion pattern resembling aversive turns. Perturbations in both the ellipsoid body and the ventral nerve cord, two regions involved in motor control, resulted in defects in aversion.Aversive chemotaxis in vinegar flies triggers ethologically appropriate kinematics distinct from those of attractive chemotaxis and requires specific motor-related neurons.

  View details for DOI 10.1016/j.cub.2013.05.008

  View details for Web of Science ID 000321605600017

  View details for PubMedID 23770185

• GABAergic Lateral Interactions Tune the Early Stages of Visual Processing in Drosophila NEURON Freifeld, L., Clark, D. A., Schnitzer, M. J., Horowitz, M. A., Clandinin, T. R. 2013; 78 (6): 1075-1089

  Abstract

  Early stages of visual processing must capture complex, dynamic inputs. While peripheral neurons often implement efficient encoding by exploiting natural stimulus statistics, downstream neurons are specialized to extract behaviorally relevant features. How do these specializations arise? We use two-photon imaging in Drosophila to characterize a first-order interneuron, L2, that provides input to a pathway specialized for detecting moving dark edges. GABAergic interactions, mediated in part presynaptically, create an antagonistic and anisotropic center-surround receptive field. This receptive field is spatiotemporally coupled, applying differential temporal processing to large and small dark objects, achieving significant specialization. GABAergic circuits also mediate OFF responses and balance these with responses to ON stimuli. Remarkably, the functional properties of L2 are strikingly similar to those of bipolar cells, yet emerge through different molecular and circuit mechanisms. Thus, evolution appears to have converged on a common strategy for processing visual information at the first synapse.

  View details for DOI 10.1016/j.neuron.2013.04.024

  View details for Web of Science ID 000321026900013

  View details for PubMedID 23791198

  View details for PubMedCentralID PMC3694283

• Mapping and cracking sensorimotor circuits in genetic model organisms. Neuron Clark, D. A., Freifeld, L., Clandinin, T. R. 2013; 78 (4): 583-595

  Abstract

  One central goal of systems neuroscience is to understand how neural circuits implement the computations that link sensory inputs to behavior. Work combining electrophysiological and imaging-based approaches to measure neural activity with pharmacological and electrophysiological manipulations has provided fundamental insights. More recently, genetic approaches have been used to monitor and manipulate neural activity, opening up new experimental opportunities and challenges. Here, we discuss issues associated with applying genetic approaches to circuit dissection in sensorimotor transformations, outlining important considerations for experimental design and considering how modeling can complement experimental approaches.

  View details for DOI 10.1016/j.neuron.2013.05.006

  View details for PubMedID 23719159

• Mapping and Cracking Sensorimotor Circuits in Genetic Model Organisms NEURON Clark, D. A., Freifeld, L., Clandininz, T. R. 2013; 78 (4): 583-595

  View details for DOI 10.1016/j.neuron.2013.05.006

  View details for Web of Science ID 000319491200004

• Optogenetic Stimulation of Escape Behavior in Drosophila melanogaster JOVE-JOURNAL OF VISUALIZED EXPERIMENTS de Vries, S. E., Clandinin, T. 2013

  View details for DOI 10.3791/50192

  View details for Web of Science ID 000209226200047

• Apical-Basal Polarity Proteins Are Required Cell-Type Specifically to Direct Photoreceptor Morphogenesis CURRENT BIOLOGY Hwa, J. J., Clandinin, T. R. 2012; 22 (24): 2319-2324

  Abstract

  Insect photoreceptor function is dependent on precise placement of the rhabdomeres, elaborated apical domains specialized for capturing light, within each facet of a compound eye. In Diptera, an asymmetric arrangement of rhabdomeres, combined with a particular pattern of axonal connections, enhances light sensitivity through the principle of neural superposition. To achieve the necessary retinal geometry, different photoreceptors (R cells) have distinct shapes. The Crumbs and Bazooka complexes play critical roles in directing rhabdomere development, but whether they might direct cell-type-specific apical architectures is unknown. We demonstrate that while mutations in Bazooka complex members cause pleiotropic morphogenesis defects in all R cell subtypes, Crumbs (Crb) and Stardust (Sdt) function cell autonomously to direct early stages in rhabdomere assembly in specific subsets of R cells. This requirement is reflected in the cell-type-specific expression of Crb protein and demonstrates that Sdt and Crb can act independently to similar effect. These two genes are also required for zonula adherens (ZA) assembly but display an unusual pattern of cellular redundancy for this function, as each gene is required in only one of two adjoining cells. Our results provide a direct link between fate specification and morphogenetic patterning and suggest a model for ZA assembly.

  View details for DOI 10.1016/j.cub.2012.10.027

  View details for Web of Science ID 000312760400021

  View details for PubMedID 23159598

  View details for PubMedCentralID PMC3623937

• Loom-Sensitive Neurons Link Computation to Action in the Drosophila Visual System CURRENT BIOLOGY de Vries, S. E., Clandinin, T. R. 2012; 22 (5): 353-362

  Abstract

  Many animals extract specific cues from rich visual scenes to guide appropriate behaviors. Such cues include visual motion signals produced both by self-movement and by moving objects in the environment. The complexity of these signals requires neural circuits to link particular patterns of motion to specific behavioral responses.Through electrophysiological recordings, we characterize genetically identified neurons in the optic lobe of Drosophila that are specifically tuned to detect motion signals produced by looming objects on a collision course with the fly. Using a genetic manipulation to specifically silence these neurons, we demonstrate that signals from these cells are important for flies to efficiently initiate the loom escape response. Moreover, through targeted expression of channelrhodopsin in these cells, in flies that are blind, we reveal that optogenetic stimulation of these neurons is typically sufficient to elicit escape, even in the absence of any visual stimulus.In this compact nervous system, a small group of neurons that extract a specific visual cue from local motion inputs serve to trigger the ethologically appropriate behavioral response.

  View details for DOI 10.1016/j.cub.2012.01.007

  View details for Web of Science ID 000301330200015

  View details for PubMedID 22305754

  View details for PubMedCentralID PMC3298569

• Genetic Dissection Reveals Two Separate Retinal Substrates for Polarization Vision in Drosophila CURRENT BIOLOGY Wernet, M. F., Velez, M. M., Clark, D. A., Baumann-Klausener, F., Brown, J. R., Klovstad, M., Labhart, T., Clandinin, T. R. 2012; 22 (1): 12-20

  Abstract

  Linearly polarized light originates from atmospheric scattering or surface reflections and is perceived by insects, spiders, cephalopods, crustaceans, and some vertebrates. Thus, the neural basis underlying how this fundamental quality of light is detected is of broad interest. Morphologically unique, polarization-sensitive ommatidia exist in the dorsal periphery of many insect retinas, forming the dorsal rim area (DRA). However, much less is known about the retinal substrates of behavioral responses to polarized reflections.Drosophila exhibits polarotactic behavior, spontaneously aligning with the e-vector of linearly polarized light, when stimuli are presented either dorsally or ventrally. By combining behavioral experiments with genetic dissection and ultrastructural analyses, we show that distinct photoreceptors mediate the two behaviors: inner photoreceptors R7+R8 of DRA ommatidia are necessary and sufficient for dorsal polarotaxis, whereas ventral responses are mediated by combinations of outer and inner photoreceptors, both of which manifest previously unknown features that render them polarization sensitive.Drosophila uses separate retinal pathways for the detection of linearly polarized light emanating from the sky or from shiny surfaces. This work establishes a behavioral paradigm that will enable genetic dissection of the circuits underlying polarization vision.

  View details for DOI 10.1016/j.cub.2011.11.028

  View details for Web of Science ID 000299144200016

  View details for PubMedID 22177904

  View details for PubMedCentralID PMC3258365

• The cytoskeletal regulator Genghis khan is required for columnar target specificity in the Drosophila visual system DEVELOPMENT Gontang, A. C., Hwa, J. J., Mast, J. D., Schwabe, T., Clandinin, T. R. 2011; 138 (22): 4899-4909

  Abstract

  A defining characteristic of neuronal cell type is the growth of axons and dendrites into specific layers and columns of the brain. Although differences in cell surface receptors and adhesion molecules are known to cause differences in synaptic specificity, differences in downstream signaling mechanisms that determine cell type-appropriate targeting patterns are unknown. Using a forward genetic screen in Drosophila, we identify the GTPase effector Genghis khan (Gek) as playing a crucial role in the ability of a subset of photoreceptor (R cell) axons to innervate appropriate target columns. In particular, single-cell mosaic analyses demonstrate that R cell growth cones lacking Gek function grow to the appropriate ganglion, but frequently fail to innervate the correct target column. Further studies reveal that R cell axons lacking the activity of the small GTPase Cdc42 display similar defects, providing evidence that these proteins regulate a common set of processes. Gek is expressed in all R cells, and a detailed structure-function analysis reveals a set of regulatory domains with activities that restrict Gek function to the growth cone. Although Gek does not normally regulate layer-specific targeting, ectopic expression of Gek is sufficient to alter the targeting choices made by another R cell type, the targeting of which is normally Gek independent. Thus, specific regulation of cytoskeletal responses to targeting cues is necessary for cell type-appropriate synaptic specificity.

  View details for DOI 10.1242/dev.069930

  View details for Web of Science ID 000296576700009

  View details for PubMedID 22007130

  View details for PubMedCentralID PMC3201660

• Symmetries in stimulus statistics shape the form of visual motion estimators PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Fitzgerald, J. E., Katsov, A. Y., Clandinin, T. R., Schnitzer, M. J. 2011; 108 (31): 12909-12914

  Abstract

  The estimation of visual motion has long been studied as a paradigmatic neural computation, and multiple models have been advanced to explain behavioral and neural responses to motion signals. A broad class of models, originating with the Reichardt correlator model, proposes that animals estimate motion by computing a temporal cross-correlation of light intensities from two neighboring points in visual space. These models provide a good description of experimental data in specific contexts but cannot explain motion percepts in stimuli lacking pairwise correlations. Here, we develop a theoretical formalism that can accommodate diverse stimuli and behavioral goals. To achieve this, we treat motion estimation as a problem of Bayesian inference. Pairwise models emerge as one component of the generalized strategy for motion estimation. However, correlation functions beyond second order enable more accurate motion estimation. Prior expectations that are asymmetric with respect to bright and dark contrast use correlations of both even and odd orders, and we show that psychophysical experiments using visual stimuli with symmetric probability distributions for contrast cannot reveal whether the subject uses odd-order correlators for motion estimation. This result highlights a gap in previous experiments, which have largely relied on symmetric contrast distributions. Our theoretical treatment provides a natural interpretation of many visual motion percepts, indicates that motion estimation should be revisited using a broader class of stimuli, demonstrates how correlation-based motion estimation is related to stimulus statistics, and provides multiple experimentally testable predictions.

  View details for DOI 10.1073/pnas.1015680108

  View details for Web of Science ID 000293385700073

  View details for PubMedID 21768376

  View details for PubMedCentralID PMC3150910

• Defining the Computational Structure of the Motion Detector in Drosophila NEURON Clark, D. A., Bursztyn, L., Horowitz, M. A., Schnitzer, M. J., Clandinin, T. R. 2011; 70 (6): 1165-1177

  Abstract

  Many animals rely on visual motion detection for survival. Motion information is extracted from spatiotemporal intensity patterns on the retina, a paradigmatic neural computation. A phenomenological model, the Hassenstein-Reichardt correlator (HRC), relates visual inputs to neural activity and behavioral responses to motion, but the circuits that implement this computation remain unknown. By using cell-type specific genetic silencing, minimal motion stimuli, and in vivo calcium imaging, we examine two critical HRC inputs. These two pathways respond preferentially to light and dark moving edges. We demonstrate that these pathways perform overlapping but complementary subsets of the computations underlying the HRC. A numerical model implementing differential weighting of these operations displays the observed edge preferences. Intriguingly, these pathways are distinguished by their sensitivities to a stimulus correlation that corresponds to an illusory percept, "reverse phi," that affects many species. Thus, this computational architecture may be widely used to achieve edge selectivity in motion detection.

  View details for DOI 10.1016/j.neuron.2011.05.023

  View details for Web of Science ID 000292410700014

  View details for PubMedID 21689602

  View details for PubMedCentralID PMC3121538

• A versatile in vivo system for directed dissection of gene expression patterns NATURE METHODS Gohl, D. M., Silies, M. A., Gao, X. J., Bhalerao, S., Luongo, F. J., Lin, C., Potter, C. J., Clandinin, T. R. 2011; 8 (3): 231-U71

  Abstract

  Tissue-specific gene expression using the upstream activating sequence (UAS)–GAL4 binary system has facilitated genetic dissection of many biological processes in Drosophila melanogaster. Refining GAL4 expression patterns or independently manipulating multiple cell populations using additional binary systems are common experimental goals. To simplify these processes, we developed a convertible genetic platform, the integrase swappable in vivo targeting element (InSITE) system. This approach allows GAL4 to be replaced with any other sequence, placing different genetic effectors under the control of the same regulatory elements. Using InSITE, GAL4 can be replaced with LexA or QF, allowing an expression pattern to be repurposed. GAL4 can also be replaced with GAL80 or split-GAL4 hemi-drivers, allowing intersectional approaches to refine expression patterns. The exchanges occur through efficient in vivo manipulations, making it possible to generate many swaps in parallel. This system is modular, allowing future genetic tools to be easily incorporated into the existing framework.

  View details for DOI 10.1038/NMETH.1561

  View details for Web of Science ID 000287734800014

  View details for PubMedID 21473015

  View details for PubMedCentralID PMC3079545

• Complex interactions amongst N-cadherin, DLAR, and Liprin-alpha regulate Drosophila photoreceptor axon targeting DEVELOPMENTAL BIOLOGY Prakash, S., McLendon, H. M., Dubreuil, C. I., Ghose, A., Hwa, J., Dennehy, K. A., Tomalty, K. M., Clark, K. L., Van Vactor, D., Clandinin, T. R. 2009; 336 (1): 10-19

  Abstract

  The formation of stable adhesive contacts between pre- and post-synaptic neurons represents the initial step in synapse assembly. The cell adhesion molecule N-cadherin, the receptor tyrosine phosphatase DLAR, and the scaffolding molecule Liprin-alpha play critical, evolutionarily conserved roles in this process. However, how these proteins signal to the growth cone and are themselves regulated remains poorly understood. Using Drosophila photoreceptors (R cells) as a model, we evaluate genetic and physical interactions among these three proteins. We demonstrate that DLAR function in this context is independent of phosphatase activity but requires interactions mediated by its intracellular domain. Genetic studies reveal both positive and, surprisingly, inhibitory interactions amongst all three genes. These observations are corroborated by biochemical studies demonstrating that DLAR physically associates via its phosphatase domain with N-cadherin in Drosophila embryos. Together, these data demonstrate that N-cadherin, DLAR, and Liprin-alpha function in a complex to regulate adhesive interactions between pre- and post-synaptic cells and provide a novel mechanism for controlling the activity of Liprin-alpha in the developing growth cone.

  View details for DOI 10.1016/j.ydbio.2009.09.016

  View details for Web of Science ID 000271849000002

  View details for PubMedID 19766621

  View details for PubMedCentralID PMC2783772

• Making a visual map: mechanisms and molecules CURRENT OPINION IN NEUROBIOLOGY Clandinin, T. R., Feldheim, D. A. 2009; 19 (2): 174-180

  Abstract

  Visual system development utilizes global and local cues to assemble a topographic map of the visual world, arranging synaptic connections into columns and layers. Recent genetic studies have provided new insights into the mechanisms that underlie these processes. In flies, a precise temporal sequence of neural differentiation provides a global organizing cue; in vertebrates, gradients of ephrin-mediated signals, acting with neurotrophin co-receptors and neural activity, play crucial roles. In flies and mice, neural processes tile into precise arrays through homotypic, repulsive interactions, autocrine signals, and cell-intrinsic mechanisms. Laminar targeting specificity is achieved through temporally regulated cell-cell adhesion, as well as combinatorial expression of specific adhesion molecules. Future studies will define the interactions between these global and local cues.

  View details for DOI 10.1016/j.conb.2009.04.011

  View details for Web of Science ID 000269108900011

  View details for PubMedID 19481440

  View details for PubMedCentralID PMC2726114

• More than just glue The diverse roles of cell adhesion molecules in the Drosophila nervous system CELL ADHESION & MIGRATION Schwabe, T., Gontang, A. C., Clandinin, T. R. 2009; 3 (1): 36-42

  Abstract

  Cell adhesion is the fundamental driving force that establishes complex cellular architectures, with the nervous system offering a striking, sophisticated case study. Developing neurons adhere to neighboring neurons, their synaptic partners, and to glial cells. These adhesive interactions are required in a diverse array of contexts, including cell migration, axon guidance and targeting, as well as synapse formation and physiology. Forward and reverse genetic screens in the fruit fly Drosophila have uncovered several adhesion molecules that are required for neural development, and detailed cell biological analyses are beginning to unravel how these factors shape nervous system connectivity. Here we review our current understanding of the most prominent of these adhesion factors and their modes of action.

  View details for DOI 10.4161/cam.3.1.6918

  View details for Web of Science ID 000208234200010

  View details for PubMedID 19372748

  View details for PubMedCentralID PMC2675147

• Reactive oxygen species act remotely to cause synapse loss in a Drosophila model of developmental mitochondrial encephalopathy DEVELOPMENT Mast, J. D., Tomalty, K. M., Vogel, H., Clandinin, T. R. 2008; 135 (15): 2669-2679

  Abstract

  Mitochondrial dysfunction is a hallmark of many neurodegenerative diseases, yet its precise role in disease pathology remains unclear. To examine this link directly, we subtly perturbed electron transport chain function in the Drosophila retina, creating a model of Leigh Syndrome, an early-onset neurodegenerative disorder. Using mutations that affect mitochondrial complex II, we demonstrate that mild disruptions of mitochondrial function have no effect on the initial stages of photoreceptor development, but cause degeneration of their synapses and cell bodies in late pupal and adult animals. In this model, synapse loss is caused by reactive oxygen species (ROS) production, not energy depletion, as ATP levels are normal in mutant photoreceptors, and both pharmacological and targeted genetic manipulations that reduce ROS levels prevent synapse degeneration. Intriguingly, these manipulations of ROS uncouple synaptic effects from degenerative changes in the cell body, suggesting that mitochondrial dysfunction activates two genetically separable processes, one that induces morphological changes in the cell body, and another that causes synapse loss. Finally, by blocking mitochondrial trafficking into the axon using a mutation affecting a mitochondrial transport complex, we find that ROS action restricted to the cell body is sufficient to cause synaptic degeneration, demonstrating that ROS need not act locally at the synapse. Thus, alterations in electron transport chain function explain many of the neurodegenerative changes seen in both early- and late-onset disorders.

  View details for DOI 10.1242/dev.020644

  View details for PubMedID 18599508

• Motion processing streams in Drosophila are behaviorally specialized NEURON Katsov, A. Y., Clandinin, T. R. 2008; 59 (2): 322-335

  Abstract

  Motion vision is an ancient faculty, critical to many animals in a range of ethological contexts, the underlying algorithms of which provide central insights into neural computation. However, how motion cues guide behavior is poorly understood, as the neural circuits that implement these computations are largely unknown in any organism. We develop a systematic, forward genetic approach using high-throughput, quantitative behavioral analyses to identify the neural substrates of motion vision in Drosophila in an unbiased fashion. We then delimit the behavioral contributions of both known and novel circuit elements. Contrary to expectation from previous studies, we find that orienting responses to motion are shaped by at least two neural pathways. These pathways are sensitive to different visual features, diverge immediately postsynaptic to photoreceptors, and are coupled to distinct behavioral outputs. Thus, behavioral responses to complex stimuli can rely on surprising neural specialization from even the earliest sensory processing stages.

  View details for DOI 10.1016/j.neuron.2008.05.022

  View details for Web of Science ID 000258252700016

  View details for PubMedID 18667159

  View details for PubMedCentralID PMC3391501

• Neural circuitry: Seeing the parts that make the picture CURRENT BIOLOGY Velez, M. M., Clandinin, T. R. 2008; 18 (9): R378-R380

  Abstract

  What are the neural correlates of vision? A recent study on Drosophila has described the incredible neuronal diversity in the fly visual system, and traced the circuits that underlie color vision.

  View details for Web of Science ID 000255668400014

  View details for PubMedID 18460316

• The cadherin flamingo mediates level-dependent interactions that guide photoreceptor target choice in Drosophila NEURON Chen, P., Clandinin, T. R. 2008; 58 (1): 26-33

  Abstract

  Quantitative differences in cadherin activity have been proposed to play important roles in patterning connections between pre- and postsynaptic neurons. However, no examples of such a function have yet been described, and the mechanisms that would allow such differences to direct growth cones to specific synaptic targets are unknown. In the Drosophila visual system, photoreceptors are genetically programmed to make a complex, stereotypic set of synaptic connections. Here we show that the atypical cadherin Flamingo functions as a short-range, homophilic signal, passing between specific R cell growth cones to influence their choice of postsynaptic partners. We find that individual growth cones are sensitive to differences in Flamingo activity through opposing interactions between neighboring cells and require these interactions to be balanced in order to extend along the appropriate trajectory.

  View details for DOI 10.1016/j.neuron.2008.01.007

  View details for Web of Science ID 000254946200007

  View details for PubMedID 18400160

  View details for PubMedCentralID PMC2494600

• The agrin/perlecan-related protein eyes shut is essential for epithelial lumen formation in the Drosophila retina DEVELOPMENTAL CELL Husain, N., Pellikka, M., Hong, H., Klimentova, T., Choe, K., Clandinin, T. R., Tepass, U. 2006; 11 (4): 483-493

  Abstract

  The formation of epithelial lumina is a fundamental process in animal development. Each ommatidium of the Drosophila retina forms an epithelial lumen, the interrhabdomeral space, which has a critical function in vision as it optically isolates individual photoreceptor cells. Ommatidia containing an interrhabdomeral space have evolved from ancestral insect eyes that lack this lumen, as seen, for example, in bees. In a genetic screen, we identified eyes shut (eys) as a gene that is essential for the formation of matrix-filled interrhabdomeral space. Eys is closely related to the proteoglycans agrin and perlecan and secreted by photoreceptor cells into the interrhabdomeral space. The honeybee ortholog of eys is not expressed in photoreceptors, raising the possibility that recruitment of eys expression has made an important contribution to insect eye evolution. Our findings show that the secretion of a proteoglycan into the apical matrix is critical for the formation of epithelial lumina in the fly retina.

  View details for DOI 10.1016/j.devcel.2006.08.012

  View details for Web of Science ID 000241123300010

  View details for PubMedID 17011488

• Activity-independent prespecification of synaptic partners in the visual map of Drosophila CURRENT BIOLOGY Hiesinger, P. R., Zhai, R. G., Zhou, Y., Koh, T., Mehta, S. Q., Schulze, K. L., Cao, Y., Verstreken, P., Clandinin, T. R., Fischbach, K., Meinertzhagen, I. A., Bellen, H. J. 2006; 16 (18): 1835-1843

  Abstract

  Specifying synaptic partners and regulating synaptic numbers are at least partly activity-dependent processes during visual map formation in all systems investigated to date . In Drosophila, six photoreceptors that view the same point in visual space have to be sorted into synaptic modules called cartridges in order to form a visuotopically correct map . Synapse numbers per photoreceptor terminal and cartridge are both precisely regulated . However, it is unknown whether an activity-dependent mechanism or a genetically encoded developmental program regulates synapse numbers. We performed a large-scale quantitative ultrastructural analysis of photoreceptor synapses in mutants affecting the generation of electrical potentials (norpA, trp;trpl), neurotransmitter release (hdc, syt), vesicle endocytosis (synj), the trafficking of specific guidance molecules during photoreceptor targeting (sec15), a specific guidance receptor required for visual map formation (Dlar), and 57 other novel synaptic mutants affecting 43 genes. Remarkably, in all these mutants, individual photoreceptors form the correct number of synapses per presynaptic terminal independently of cartridge composition. Hence, our data show that each photoreceptor forms a precise and constant number of afferent synapses independently of neuronal activity and partner accuracy. Our data suggest cell-autonomous control of synapse numbers as part of a developmental program of activity-independent steps that lead to a "hard-wired" visual map in the fly brain.

  View details for DOI 10.1016/j.cub.2006.07.047

  View details for Web of Science ID 000240719800029

  View details for PubMedID 16979562

  View details for PubMedCentralID PMC3351197

• Liprin-alpha is required for photoreceptor target selection in Drosophila PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Choe, K., Prakash, S., Bright, A., Clandinin, T. R. 2006; 103 (31): 11601-11606

  Abstract

  Classical cadherin-mediated interactions between axons and dendrites are critical to target selection and synapse assembly. However, the molecular mechanisms by which these interactions are controlled are incompletely understood. In the Drosophila visual system, N-cadherin is required in both photoreceptor (R cell) axons and their targets to mediate stabilizing interactions required for R cell target selection. Here we identify the scaffolding protein Liprin-alpha as a critical component in this process. We isolated mutations in Liprin-alpha in a genetic screen for mutations affecting the pattern of synaptic connections made by R1-R6 photoreceptors. Using eye-specific mosaics, we demonstrate a previously undescribed, axonal function for Liprin-alpha in target selection: Liprin-alpha is required to be cell-autonomous in all subtypes of R1-R6 cells for their axons to reach their targets. Because Liprin-alpha, the receptor tyrosine phosphatase LAR, and N-cadherin share qualitatively similar mutant phenotypes in R1-R6 cells and are coexpressed in R cells and their synaptic targets, we infer that these three genes act at the same step in the targeting process. However, unlike N-cadherin, neither Liprin-alpha nor LAR is required postsynaptically for R cells to project to their correct targets. Thus, these two proteins, unlike N-cadherin, are functionally asymmetric between axons and dendrites. We propose that the adhesive mechanisms that link pre- and postsynaptic cells before synapse formation may be differentially regulated in these two compartments.

  View details for DOI 10.1073/pnas.0601185103

  View details for Web of Science ID 000239616400033

  View details for PubMedID 16864799

  View details for PubMedCentralID PMC1544216

• Insect vision: Remembering the shape of things CURRENT BIOLOGY Katsov, A., Clandinin, T. R. 2006; 16 (10): R369-R371

  Abstract

  How does the nervous system store a newly experienced visual pattern, and how is that pattern subsequently made available for recognition? Recent work in Drosophila suggests that specific pattern features are stored separately in the nervous system.

  View details for DOI 10.1016/j.cub.2006.04.006

  View details for Web of Science ID 000237874500016

  View details for PubMedID 16713946

• The mechanisms and molecules that connect photoreceptor axons to their targets in Drosophila SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY Mast, J. D., Prakash, S., Chen, P. L., Clandinin, T. R. 2006; 17 (1): 42-49

  Abstract

  The development of the Drosophila visual system provides a framework for investigating how circuits assemble. A sequence of reciprocal interactions amongst photoreceptors, target neurons and glia creates a precise pattern of connections while reducing the complexity of the targeting process. Both afferent-afferent and afferent-target interactions are required for photoreceptor (R cell) axons to select appropriate synaptic partners. With the identification of some critical cell adhesion and signaling molecules, the logic by which axons make choices amongst alternate synaptic partners is becoming clear. These studies also provide an opportunity to examine the molecular basis of neural circuit evolution.

  View details for DOI 10.1016/j.semcdb.2005.11.004

  View details for Web of Science ID 000236492800006

  View details for PubMedID 16337412

• An isoform-specific allele of Drosophila N-cadherin disrupts a late step of R7 targeting PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Nern, A., Nguyen, L. V., Herman, T., Prakash, S., Clandinin, T. R., Zipursky, S. L. 2005; 102 (36): 12944-12949

  Abstract

  Drosophila N-cadherin is required for the formation of precise patterns of connections in the fly brain. Alternative splicing is predicted to give rise to 12 N-cadherin isoforms. We identified an N-cadherin allele, N-cad(18Astop), that eliminates the six isoforms containing alternative exon 18A and demonstrate that it strongly disrupts the connections of R7 photoreceptor neurons. During the first half of pupal development, N-cadherin is required for R7 growth cones to terminate within a temporary target layer in the medulla. N-cadherin isoforms containing exon 18B are sufficient for this initial targeting. By contrast, 18A isoforms are preferentially expressed in R7 during the second half of pupal development and are necessary for R7 to terminate in the appropriate synaptic layer in the medulla neuropil. Transgene rescue experiments suggest that differences in isoform expression, rather than biochemical differences between isoforms, underlie the 18A isoform requirement in R7 neurons.

  View details for DOI 10.1073/pnas.0502888102

  View details for Web of Science ID 000231716700054

  View details for PubMedID 16123134

• Surprising twists to exocyst function NEURON Clandinin, T. R. 2005; 46 (2): 164-166

  Abstract

  What do neurons use the exocyst complex for? In this issue of Neuron, using mutations in one exocyst component, Mehta et al. reach the surprising conclusion that exocyst function is divisible: different components play distinct roles. These studies also suggest that the exocyst may regulate membrane insertion of cell adhesion molecules required for synaptic partner choice.

  View details for DOI 10.1016/j.neuron.2005.04.003

  View details for Web of Science ID 000228674800002

  View details for PubMedID 15848794

• Drosophila N-cadherin mediates an attractive interaction between photoreceptor axons and their targets NATURE NEUROSCIENCE Prakash, S., Caldwell, J. C., Eberl, D. F., Clandinin, T. R. 2005; 8 (4): 443-450

  Abstract

  Classical cadherins have been proposed to mediate interactions between pre- and postsynaptic cells that are necessary for synapse formation. We provide the first direct, genetic evidence in favor of this model by examining the role of N-cadherin in controlling the pattern of synaptic connections made by photoreceptor axons in Drosophila. N-cadherin is required in both individual photoreceptors and their target neurons for photoreceptor axon extension. Cell-by-cell reconstruction of wild-type photoreceptor axons extending within mosaic patches of mutant target cells shows that N-cadherin mediates attractive interactions between photoreceptors and their targets. This interaction is not limited to those cells that will become the synaptic partners of photoreceptors. Multiple N-cadherin isoforms are produced, but single isoforms can substitute for endogenous N-cadherin activity. We propose that N-cadherin mediates a homophilic, attractive interaction between photoreceptor growth cones and their targets that precedes synaptic partner choice.

  View details for DOI 10.1038/nn1415

  View details for Web of Science ID 000228040400014

  View details for PubMedID 15735641

  View details for PubMedCentralID PMC2367251

• Thinking about visual behavior; Learning about photoreceptor function CURRENT TOPICS IN DEVELOPMENTAL BIOLOGY, VOL 69 Choe, K. M., Clandinin, T. R. 2005; 69: 187-?

  Abstract

  Visual behavioral assays in Drosophila melanogaster were initially developed to explore the genetic control of behavior, but have a rich history of providing conceptual openings into diverse questions in cell and developmental biology. Here, we briefly summarize the early efforts to employ three of these behaviors: phototaxis, the UV-visible light choice, and the optomotor response. We then discuss how each of these assays has expanded our understanding of neuronal connection specificity and synaptic function. All of these studies have contributed to the development of sophisticated tools for manipulating gene expression, assessing cell fate specification, and visualizing neuronal development. With these tools in hand, the field is now poised to return to the original goal of understanding visual behavior using genetic approaches.

  View details for DOI 10.1016/S0070-2153(05)69007-2

  View details for Web of Science ID 000233986700007

  View details for PubMedID 16243600

• The protocadherin Flamingo is required for axon target selection in the Drosophila visual system NATURE NEUROSCIENCE Lee, R. C., Clandinin, T. R., Lee, C. H., Chen, P. L., Meinertzhagen, I. A., Zipursky, S. L. 2003; 6 (6): 557-563

  Abstract

  Photoreceptor neurons (R cells) in the Drosophila visual system elaborate a precise map of visual space in the brain. The eye contains some 750 identical modules called ommatidia, each containing eight photoreceptor cells (R1-R8). Cells R1-R6 synapse in the lamina; R7 and R8 extend through the lamina and terminate in the underlying medulla. In a screen for visual behavior mutants, we identified alleles of flamingo (fmi) that disrupt the precise maps elaborated by these neurons. These mutant R1-R6 neurons select spatially inappropriate targets in the lamina. During target selection, Flamingo protein is dynamically expressed in R1-R6 growth cones. Loss of fmi function in R cells also disrupts the local pattern of synaptic terminals in the medulla, and Flamingo is transiently expressed in R8 axons as they enter the target region. We propose that Flamingo-mediated interactions between R-cell growth cones within the target field regulate target selection.

  View details for DOI 10.1038/nn1063

  View details for Web of Science ID 000183140400011

  View details for PubMedID 12754514

• Making connections in the fly visual system NEURON Clandinin, T. R., Zipursky, S. L. 2002; 35 (5): 827-841

  Abstract

  Understanding the molecular mechanisms that regulate formation of precise patterns of neuronal connections within the central nervous system remains a challenging problem in neurobiology. Genetic studies in worms and flies and molecular studies in vertebrate systems have led to an increasingly sophisticated understanding of how growth cones navigate toward their targets and form topographic maps. Considerably less is known about how growth cones recognize their cellular targets and form synapses with them. Here, we review connection formation in the fly visual system, the methodological approaches used to study it, and recent progress in uncovering the molecular basis of connection specificity.

  View details for Web of Science ID 000177779800007

  View details for PubMedID 12372279

• Drosophila LAR regulates R1-R6 and R7 target specificity in the visual system NEURON Clandinin, T. R., Lee, C. H., Herman, T., Lee, R. C., Yang, A. Y., Ovasapyan, S., Zipursky, S. L. 2001; 32 (2): 237-248

  Abstract

  Different classes of photoreceptor neurons (R cells) in the Drosophila compound eye connect to specific targets in the optic lobe. Using a behavioral screen, we identified LAR, a receptor tyrosine phosphatase, as being required for R cell target specificity. In LAR mutant mosaic eyes, R1-R6 cells target to the lamina correctly, but fail to choose the correct pattern of target neurons. Although mutant R7 axons initially project to the correct layer of the medulla, they retract into inappropriate layers. Using single cell mosaics, we demonstrate that LAR controls targeting of R1-R6 and R7 in a cell-autonomous fashion. The phenotypes of LAR mutant R cells are strikingly similar to those seen in N-cadherin mutants.

  View details for Web of Science ID 000171893700009

  View details for PubMedID 11683994

• N-cadherin regulates target specificity in the Drosophila visual system NEURON Lee, C. H., Herman, T., Clandinin, T. R., LEE, R., Zipursky, S. L. 2001; 30 (2): 437-450

  Abstract

  Using visual behavioral screens in Drosophila, we identified multiple alleles of N-cadherin. Removal of N-cadherin selectively from photoreceptor neurons (R cells) causes deficits in specific visual behaviors that correlate with disruptions in R cell connectivity. These defects include disruptions in the pattern of neuronal connections made by all three classes of R cells (R1-R6, R7, and R8). N-cadherin is expressed in both R cell axons and their targets. By inducing mitotic recombination in a subclass of eye progenitors, we generated mutant R7 axons surrounded by largely wild-type R cell axons and a wild-type target. R7 axons lacking N-cadherin mistarget to the R8 recipient layer. We consider the implications of these findings in the context of the proposed role for cadherins in target specificity.

  View details for Web of Science ID 000168962000016

  View details for PubMedID 11395005

• Afferent growth cone interactions control synaptic specificity in the Drosophila visual system NEURON Clandinin, T. R., Zipursky, S. L. 2000; 28 (2): 427-436

  Abstract

  In the Drosophila compound eye, photoreceptors (R cells) that respond to light from the same point in space are distributed across the retina and connect to the same target neurons. This complex connectivity pattern reconstructs visual space in the first optic ganglion, the lamina. We have used mutations that delete specific R cell subtypes or alter their retinal organization to define the cellular mechanisms that generate this pattern. R cell axons are programmed to search for targets within a local region in the lamina but their selection of appropriate postsynaptic targets requires specific interactions among R cell growth cones. The orientation of the projections is controlled both by the spatial arrangement of R cells in the retina and by cues in the target.

  View details for Web of Science ID 000165493700018

  View details for PubMedID 11144353

• Hedgehog and spitz: Making a match between photoreceptor axons and their targets CELL Salecker, I., Clandinin, T. R., Zipursky, S. L. 1998; 95 (5): 587-590

  View details for Web of Science ID 000077253700004

  View details for PubMedID 9845360