Publications

2015
Klein, M., et al. Sensory determinants of behavioral dynamics in Drosophila thermotaxis. Proceedings of the National Academy of Sciences USA 112, 2, E220-229 (2015). Publisher's VersionAbstract
Complex animal behaviors are built from dynamical relationships between sensory inputs, neuronal activity, and motor outputs in patterns with strategic value. Connecting these patterns illuminates how nervous systems compute behavior. Here, we study Drosophila larva navigation up temperature gradients towards preferred temperatures (positive thermotaxis). By tracking the movements of animals responding to fixed spatial temperature gradients or random temperature fluctuations, we calculate the sensitivity and dynamics of the conversion of thermosensory inputs into motor responses. We discover three thermosensory neurons in each dorsal organ ganglion (DOG) that are required for positive thermotaxis. Random optogenetic stimulation of the DOG thermosensory neurons evokes behavioral patterns that mimic the response to temperature variations.  In vivo calcium and voltage imaging reveals that the DOG thermosensory neurons exhibit activity patterns with sensitivity and dynamics matched to the behavioral response. Temporal processing of temperature variations carried out by the DOG thermosensory neurons emerges in distinct motor responses during thermotaxis.
2014
Luo, L., et al. Bidirectional thermotaxis in Caenorhabditis elegans is mediated by distinct sensorimotor strategies driven by the AFD thermosensory neurons. Proceedings of the National Academy of Sciences USA 111, 2776-2781 (2014).Abstract
The nematode Caenorhabditis elegans navigates toward a pre- ferred temperature setpoint (Ts) determined by long-term temper- ature exposure. During thermotaxis, the worm migrates down temperature gradients at temperatures above Ts (negative ther- motaxis) and performs isothermal tracking near Ts. Under some conditions, the worm migrates up temperature gradients below Ts (positive thermotaxis). Here, we analyze positive and negative thermotaxis toward Ts to study the role of specific neurons that have been proposed to be involved in thermotaxis using genetic ablation, behavioral tracking, and calcium imaging. We find differ- ences in the strategies for positive and negative thermotaxis. Neg- ative thermotaxis is achieved through biasing the frequency of reorientation maneuvers (turns and reversal turns) and biasing the direction of reorientation maneuvers toward colder temper- atures. Positive thermotaxis, in contrast, biases only the direction of reorientation maneuvers toward warmer temperatures. We find that the AFD thermosensory neuron drives both positive and negative thermotaxis. The AIY interneuron, which is postsyn- aptic to AFD, may mediate the switch from negative to positive thermotaxis below Ts. We propose that multiple thermotactic behaviors, each defined by a distinct set of sensorimotor trans- formations, emanate from the AFD thermosensory neurons. AFD learns and stores the memory of preferred temperatures, detects temperature gradients, and drives the appropriate thermotactic behavior in each temperature regime by the flexible use of downstream circuits.
Luo, L., et al. Dynamic encoding of perception, memory and movement in a C. elegans chemotaxis circuit. Neuron 82, 1115-1128 (2014).Abstract
Brain circuits endow behavioral flexibility. Here, we study circuits encoding flexible 26 chemotaxis in C. elegans, where the animal navigates up or down NaCl gradients (positive or negative chemotaxis) to reach the salt concentration of previous growth (the setpoint). The ASER sensory neuron mediates positive and negative chemotaxis by regulating the frequency and direction of reorientation movements in response to salt gradients. Both salt gradients and setpoint memory are encoded in ASER temporal activity patterns. Distinct temporal activity patterns in interneurons immediately downstream of ASER encode chemotactic movement decisions. Different interneuron combinations regulate positive vs. negative chemotaxis. We conclude that sensorimotor pathways are segregated immediately after the primary sensory neuron in the chemotaxis circuit, and sensory representation is rapidly transformed to motor representation at the first interneuron layer. Our study reveals compact encoding of perception, memory, and locomotion in an experience dependent navigational behavior in C. elegans.
2013
Smith, H.K., et al. Defining specificity determinants of cyclic GMP-mediated gustatory sensory transduction in Caenorhabditis elegans. Genetics 194, 885-901 (2013).Abstract
Cyclic guanosine monophosphate (cGMP) is a key secondary messenger used in signal transduction in various types of sensory neurons. The importance of cGMP in the ASE gustatory receptor neurons of the nematode Caenorhabditis elegans was deduced by the observation that multiple receptor-type guanylyl cyclases (rGCs), encoded by the gcygenes, and two presently known cyclic nucleotide-gated ion channel subunits, encoded by the tax-2 and tax-4 genes, are essential for ASE-mediated gustatory behavior. We describe here specific mechanistic features of cGMP-mediated signal transduction in the ASE neurons. First, we assess the specificity of the sensory functions of individual rGC proteins. We have previously shown that multiple rGC proteins are expressed in a left/right asymmetric manner in the functionally lateralized ASE neurons and are required to sense distinct salt cues. Through domain swap experiments among three different rGC proteins, we show here that the specificity of individual rGC proteins lies in their extracellular domains and not in their intracellular, signal-transducing domains. Furthermore, we find that rGC proteins are also sufficient to confer salt sensory responses to other neurons. Both findings support the hypothesis that rGC proteins are salt receptor proteins. Second, we identify a novel, likely downstream effector of the rGC proteins in gustatory signal transduction, a previously uncharacterized cyclic nucleotide-gated (CNG) ion channel, encoded by the che-6 locus. che-6 mutants show defects in gustatory sensory transduction that are similar to defects observed in animals lacking thetax-2 and tax-4 CNG channels. In contrast, thermosensory signal transduction, which also requires tax-2 and tax-4, does not require che-6, but requires another CNG, cng-3. We propose that CHE-6 may form together with two other CNG subunits, TAX-2 and TAX-4, a gustatory neuron-specific heteromeric CNG channel complex.
Mathew, D., et al. Functional diversity among sensory receptors in a Drosophila olfactory circuit. Proceedings of the National Academy of Sciences USA 110, E2134-43 (2013).Abstract
The ability of an animal to detect, discriminate, and respond to odors depends on the function of its olfactory receptor neurons (ORNs), which in turn depends ultimately on odorant receptors. To understand the diverse mechanisms used by an animal in olfactory coding and computation, it is essential to understand the functional diversity of its odor receptors. The larval olfactory system of Drosophila melanogaster contains 21 ORNs and a comparable number of odorant receptors whose properties have been examined in only a limited way. We systematically screened them with a panel of \~500 odorants, yielding >10,000 receptor-odorant combinations. We identify for each of 19 receptors an odorant that excites it strongly. The responses elicited by each of these odorants are analyzed in detail. The odorants elicited little cross-activation of other receptors at the test concentration; thus, low concentrations of many of these odorants in nature may be signaled by a single ORN. The receptors differed dramatically in sensitivity to their cognate odorants. The responses showed diverse temporal dynamics, with some odorants eliciting supersustained responses. An intriguing question in the field concerns the roles of different ORNs and receptors in driving behavior. We found that the cognate odorants elicited behavioral responses that varied across a broad range. Some odorants elicited strong physiological responses but weak behavioral responses or weak physiological responses but strong behavioral responses.
Donnelly, J.L., et al. Monoaminergic Orchestration of Motor Programs in a Complex C. elegans Behavior. PLoS Biology 11, 4, e1001529 (2013).
Williams, D.C., et al. Rapid and Permanent Neuronal Inactivation In Vivo via Subcellular Generation of Reactive Oxygen with the Use of KillerRed. Cell Reports 5, 553-563 (2013).Abstract
Inactivation of selected neurons in vivo can define their contribution to specific developmental outcomes, circuit functions, and behaviors. Here, we show that the optogenetic tool KillerRed selec- tively, rapidly, and permanently inactivates different classes of neurons in C. elegans in response to a single light stimulus, through the generation of reactive oxygen species (ROS). Ablation scales from individual neurons in single animals to multiple neurons in populations and can be applied to freely behaving animals. Using spatially restricted illumination, we demonstrate that localized KillerRed activation in either the cell body or the axon triggers neuronal degeneration and death of the targeted cell. Finally, targeting KillerRed to mitochondria results in organelle fragmentation without killing the cell, in contrast to the cell death observed when KillerRed is targeted to the plasma membrane. We expect this genetic tool to have wide-ranging applications in studies of circuit function and subcellular responses to ROS.
Kane, E.A., et al. Sensorimotor structure of Drosophila larva phototaxis. Proceedings of the National Academy of Sciences 110, E3868-77 (2013).Abstract
The avoidance of light by fly larvae is a classic paradigm for sensorimotor behavior. Here, we use behavioral assays and video microscopy to quantify the sensorimotor structure of phototaxis using the Drosophila larva. Larval locomotion is composed of sequences of runs (periods of forward movement) that are interrupted by abrupt turns, during which the larva pauses and sweeps its head back and forth, probing local light information to deter- mine the direction of the successive run. All phototactic responses are mediated by the same set of sensorimotor transformations that require temporal processing of sensory inputs. Through functional imaging and genetic inactivation of specific neurons down- stream of the sensory periphery, we have begun to map these sensorimotor circuits into the larval central brain. We find that specific sensorimotor pathways that govern distinct light-evoked responses begin to segregate at the first relay after the photosensory neurons.
Reina, A., Subramaniam, A.B., Laromaine, A., Samuel, A.D. & Whitesides, G.M. Shifts in the distribution of mass densities is a signature of caloric restriction in Caenorhabditis elegans. PLoS ONE 8, e69651 (2013).Abstract
Although the starvation response of the model multicellular organism Caenorhabditis elegans is a subject of much research, there is no convenient phenotypic readout of caloric restriction that can be applicable to large numbers of worms. This paper describes the distribution of mass densities of populations of C. elegans, from larval stages up to day one of adulthood, using isopycnic centrifugation, and finds that density is a convenient, if complex, phenotypic readout in C. elegans. The density of worms in synchronized populations of wildtype N2 C. elegans grown under standard solid-phase culture conditions was normally distributed, with distributions peaked sharply at a mean of 1.091 g/cm3 for L1, L2 and L3 larvae, 1.087 g/cm3 for L4 larvae, 1.081 g/cm3 for newly molted adults, and 1.074 g/cm3 at 24 hours of adulthood. The density of adult worms under starvation stress fell well outside this range, falling to a mean value of 1.054 g/cm3 after eight hours of starvation. This decrease in density correlated with the consumption of stored glycogen in the food-deprived worms. The density of the worms increased when deprived of food for longer durations, corresponding to a shift in the response of the worms: worms sacrifice their bodies by retaining larvae, which consume the adults from within. Density- based screens with the drug Ivermectin on worms cultured on single plates resulted in a clear bimodal (double-peaked) distribution of densities corresponding to drug exposed and non-exposed worms. Thus, measurements of changes in density could be used to conduct screens on the effects of drugs on several populations of worms cultured on single plates.
Mathew, D., et al. Functional diversity among sensory receptors in a Drosophila olfactory circuit. Proceedings of the National Academy of Sciences USA 110, E2134-43 (2013).Abstract

The ability of an animal to detect, discriminate, and respond to odors depends on the function of its olfactory receptor neurons (ORNs), which in turn depends ultimately on odorant receptors. To understand the diverse mechanisms used by an animal in olfactory coding and computation, it is essential to understand the functional diversity of its odor receptors. The larval olfactory system of Drosophila melanogaster contains 21 ORNs and a comparable number of odorant receptors whose properties have been examined in only a limited way. We systematically screened them with a panel of ∼500 odorants, yielding >10,000 receptor-odorant combinations. We identify for each of 19 receptors an odorant that excites it strongly. The responses elicited by each of these odorants are analyzed in detail. The odorants elicited little cross-activation of other receptors at the test concentration; thus, low concentrations of many of these odorants in nature may be signaled by a single ORN. The receptors differed dramatically in sensitivity to their cognate odorants. The responses showed diverse temporal dynamics, with some odorants eliciting supersustained responses. An intriguing question in the field concerns the roles of different ORNs and receptors in driving behavior. We found that the cognate odorants elicited behavioral responses that varied across a broad range. Some odorants elicited strong physiological responses but weak behavioral responses or weak physiological responses but strong behavioral responses.

Reprint.pdf
Donnelly, J.L., et al. Monoaminergic Orchestration of Motor Programs in a Complex C. elegans Behavior. PLoS Biology 11, 4, e1001529 (2013). alkema2013.pdf
2012
Gershow, M., et al. Controlling airborne cues during small animal navigation. Nature Methods 9, 3, 290-296 (2012). Publisher's Version
Pinan-Lucarre, B., et al. The core apoptotic executioner proteins CED-3 and CED-4 promote neuronal regeneration in Caenorhabditis elegans. PLoS Biology 10, e1001331 (2012). Publisher's Version
Omura, D., Clark, D., Samuel, A.D. & Horvitz, H.R. Dopamine signaling sets and maintains a precise rate of locomotion by C. elegans. PLoS ONE 7, e38649 (2012).
Fang-Yen, C., Gabel, C., Samuel, A.D., Bargmann, C. & Avery, L. Laser Microsurgery in Caenorhabditis elegans. Methods in Cell Biology, Vol. 107 177-206 (2012).
Wen, Q., et al. Proprioceptive Coupling within Motor Neurons Drives C. elegans Forward Locomotion. Neuron 76, 4, 750-761 (2012). Publisher's Version
Stavoe, A., et al. Synaptic vesicle clustering and axon arborization require distinct MIG-10/Lamellipodin isoforms downstream of Netrin. Genes and Development 26, 19, 2206-2221 (2012).
Fang-Yen, C., Gabel, C., Samuel, A.D., Bargmann, C. & Avery, L. Laser Microsurgery in Caenorhabditis elegans. Methods in Cell Biology, Vol. 107 177-206 (2012). methods_cell_biol_2012_fang-yen.pdf
Pinan-Lucarre, B., et al. The core apoptotic executioner proteins CED-3 and CED-4 promote neuronal regeneration in Caenorhabditis elegans. PLoS Biology 10, e1001331 (2012). Website plos_biol_2012_pinan-lucarre.pdf
Omura, D., Clark, D., Samuel, A.D. & Horvitz, H.R. Dopamine signaling sets and maintains a precise rate of locomotion by C. elegans. PLoS ONE 7, e38649 (2012). plos_one_2012_omura.pdf

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