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Lee Tzumin Lab / Publications
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17 Publications

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    06/30/13 | TALE-mediated modulation of transcriptional enhancers in vivo.
    Crocker J, Stern DL
    Nature Methods. 2013 Jun 30;10(8):762-7. doi: 10.1038/nmeth.2543

    We tested whether transcription activator-like effectors (TALEs) could mediate repression and activation of endogenous enhancers in the Drosophila genome. TALE repressors (TALERs) targeting each of the five even-skipped (eve) stripe enhancers generated repression specifically of the focal stripes. TALE activators (TALEAs) targeting the eve promoter or enhancers caused increased expression primarily in cells normally activated by the promoter or targeted enhancer, respectively. This effect supports the view that repression acts in a dominant fashion on transcriptional activators and that the activity state of an enhancer influences TALE binding or the ability of the VP16 domain to enhance transcription. In these assays, the Hairy repression domain did not exhibit previously described long-range transcriptional repression activity. The phenotypic effects of TALER and TALEA expression in larvae and adults are consistent with the observed modulations of eve expression. TALEs thus provide a novel tool for detection and functional modulation of transcriptional enhancers in their native genomic context.

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    06/19/13 | Imaging a population code for odor identity in the Drosophila mushroom body.
    Campbell RA, Honegger KS, Qin H, Li W, Demir E, Turner GC
    The Journal of Neuroscience : the official journal of the Society for Neuroscience. 2013 Jun 19;33(25):10568-81. doi: 10.1523/JNEUROSCI.0682-12.2013

    The brain represents sensory information in the coordinated activity of neuronal ensembles. Although the microcircuits underlying olfactory processing are well characterized in Drosophila, no studies to date have examined the encoding of odor identity by populations of neurons and related it to the odor specificity of olfactory behavior. Here we used two-photon Ca(2+) imaging to record odor-evoked responses from >100 neurons simultaneously in the Drosophila mushroom body (MB). For the first time, we demonstrate quantitatively that MB population responses contain substantial information on odor identity. Using a series of increasingly similar odor blends, we identified conditions in which odor discrimination is difficult behaviorally. We found that MB ensemble responses accounted well for olfactory acuity in this task. Kenyon cell ensembles with as few as 25 cells were sufficient to match behavioral discrimination accuracy. Using a generalization task, we demonstrated that the MB population code could predict the flies' responses to novel odors. The degree to which flies generalized a learned aversive association to unfamiliar test odors depended upon the relative similarity between the odors' evoked MB activity patterns. Discrimination and generalization place different demands on the animal, yet the flies' choices in these tasks were reliably predicted based on the amount of overlap between MB activity patterns. Therefore, these different behaviors can be understood in the context of a single physiological framework.

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    06/17/13 | Decoupled roles for the atypical, bifurcated binding pocket of the ybfF hydrolase.
    Ellis EE, Adkins CT, Galovska NM, Lavis LD, Johnson RJ
    Chembiochem : A European Journal of Chemical Biology. 2013 Jun 17;14(9):1134-44. doi: 10.1002/cbic.201300085

    Serine hydrolases have diverse intracellular substrates, biological functions, and structural plasticity, and are thus important for biocatalyst design. Amongst serine hydrolases, the recently described ybfF enzyme family are promising novel biocatalysts with an unusual bifurcated substrate-binding cleft and the ability to recognize commercially relevant substrates. We characterized in detail the substrate selectivity of a novel ybfF enzyme from Vibrio cholerae (Vc-ybfF) by using a 21-member library of fluorogenic ester substrates. We assigned the roles of the two substrate-binding clefts in controlling the substrate selectivity and folded stability of Vc-ybfF by comprehensive substitution analysis. The overall substrate preference of Vc-ybfF was for short polar chains, but it retained significant activity with a range of cyclic and extended esters. This broad substrate specificity combined with the substitutional analysis demonstrates that the larger binding cleft controls the substrate specificity of Vc-ybfF. Key selectivity residues (Tyr116, Arg120, Tyr209) are also located at the larger binding pocket and control the substrate specificity profile. In the structure of ybfF the narrower binding cleft contains water molecules prepositioned for hydrolysis, but based on substitution this cleft showed only minimal contribution to catalysis. Instead, the residues surrounding the narrow binding cleft and at the entrance to the binding pocket contributed significantly to the folded stability of Vc-ybfF. The relative contributions of each cleft of the binding pocket to the catalytic activity and folded stability of Vc-ybfF provide a valuable map for designing future biocatalysts based on the ybfF scaffold.

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    06/17/13 | Vertebrate versus invertebrate neural circuits.
    Katz P, Grillner S, Wilson R, Borst A, Greenspan R, Buzsáki G, Martin K, Marder E, Kristan W, Friedrich R, Chklovskii DM
    Current Biology. 2013 Jun 17;23(12):R504-6
    06/15/13 | Juvenile hormone and insulin suppress lipolysis between periods of lactation during tsetse fly pregnancy.
    Baumann AA, Benoit JB, Michalkova V, Mireji PO, Attardo GM, Moulton JK, Wilson TG, Aksoy S
    Molecular and Cellular Endocrinology. 2013 Jun 15;372(1-2):30-41. doi: 10.1016/j.mce.2013.02.019

    Tsetse flies are viviparous insects that nurture a single intrauterine progeny per gonotrophic cycle. The developing larva is nourished by the lipid-rich, milk-like secretions from a modified female accessory gland (milk gland). An essential feature of the lactation process involves lipid mobilization for incorporation into the milk. In this study, we examined roles for juvenile hormone (JH) and insulin/IGF-like (IIS) signaling pathways during tsetse pregnancy. In particular, we examined the roles for these pathways in regulating lipid homeostasis during transitions between non-lactating (dry) and lactating periods. The dry period occurs over the course of oogenesis and embryogenesis, while the lactation period spans intrauterine larvigenesis. Genes involved in the JH and IIS pathways were upregulated during dry periods, correlating with lipid accumulation between bouts of lactation. RNAi suppression of Forkhead Box Sub Group O (FOXO) expression impaired lipolysis during tsetse lactation and reduced fecundity. Similar reduction of the JH receptor Methoprene tolerant (Met), but not its paralog germ cell expressed (gce), reduced lipid accumulation during dry periods, indicating functional divergence between Met and gce during tsetse reproduction. Reduced lipid levels following Met knockdown led to impaired fecundity due to inadequate fat reserves at the initiation of milk production. Both the application of the JH analog (JHA) methoprene and injection of insulin into lactating females increased stored lipids by suppressing lipolysis and reduced transcripts of lactation-specific genes, leading to elevated rates of larval abortion. To our knowledge, this study is the first to address the molecular physiology of JH and IIS in a viviparous insect, and specifically to provide a role for JH signaling through Met in the regulation of lipid metabolism during insect lactation.

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    06/14/13 | Parallel neural pathways mediate CO2 avoidance responses in Drosophila.
    Lin H, Chu L, Fu T, Dickson BJ, Chiang A
    Science. 2013 Jun 14;340(6138):1338-41. doi: 10.1126/science.1236693

    Different stimulus intensities elicit distinct perceptions, implying that input signals are either conveyed through an overlapping but distinct subpopulation of sensory neurons or channeled into divergent brain circuits according to intensity. In Drosophila, carbon dioxide (CO2) is detected by a single type of olfactory sensory neuron, but information is conveyed to higher brain centers through second-order projection neurons (PNs). Two distinct pathways, PN(v)-1 and PN(v)-2, are necessary and sufficient for avoidance responses to low and high CO2 concentrations, respectively. Whereas low concentrations activate PN(v)-1, high concentrations activate both PN(v)s and GABAergic PN(v)-3, which may inhibit PN(v)-1 pathway-mediated avoidance behavior. Channeling a sensory input into distinct neural pathways allows the perception of an odor to be further modulated by both stimulus intensity and context.

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    Riddiford Lab
    06/11/13 | Microarrays reveal discrete phases in juvenile hormone regulation of mosquito reproduction.
    Riddiford LM
    Proceedings of the National Academy of Sciences of the United States of America. 2013 Jun 11;110(24):9623-4. doi: 10.1073/pnas.1307487110
    06/08/13 | Essential role of the mushroom body in context-dependent CO2 avoidance in Drosophila.
    Bräcker LB, Siju KP, Varela N, Aso Y, Zhang M, Hein I, Vasconcelos ML, Grunwald Kadow IC
    Current Biology. 2013 Jul 8;23(13):1228-34. doi: 10.1016/j.cub.2013.05.029

    Internal state as well as environmental conditions influence choice behavior. The neural circuits underpinning state-dependent behavior remain largely unknown. Carbon dioxide (CO2) is an important olfactory cue for many insects, including mosquitoes, flies, moths, and honeybees [1]. Concentrations of CO2 higher than 0.02% above atmospheric level trigger a strong innate avoidance in the fly Drosophila melanogaster [2, 3]. Here, we show that the mushroom body (MB), a brain center essential for olfactory associative memories [4-6] but thought to be dispensable for innate odor processing [7], is essential for CO2 avoidance behavior only in the context of starvation or in the context of a food-related odor. Consistent with this, CO2 stimulation elicits Ca(2+) influx into the MB intrinsic cells (Kenyon cells: KCs) in vivo. We identify an atypical projection neuron (bilateral ventral projection neuron, biVPN) that connects CO2 sensory input bilaterally to the MB calyx. Blocking synaptic output of the biVPN completely abolishes CO2 avoidance in food-deprived flies, but not in fed flies. These findings show that two alternative neural pathways control innate choice behavior, and they are dependent on the animal’s internal state. In addition, they suggest that, during innate choice behavior, the MB serves as an integration site for internal state and olfactory input.

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    06/07/13 | Imaging morphogenesis: technological advances and biological insights.
    Keller PJ
    Science. 2013 Jun 7;340(6137):1234168. doi: 10.1126/science.1234168

    Morphogenesis, the development of the shape of an organism, is a dynamic process on a multitude of scales, from fast subcellular rearrangements and cell movements to slow structural changes at the whole-organism level. Live-imaging approaches based on light microscopy reveal the intricate dynamics of this process and are thus indispensable for investigating the underlying mechanisms. This Review discusses emerging imaging techniques that can record morphogenesis at temporal scales from seconds to days and at spatial scales from hundreds of nanometers to several millimeters. To unlock their full potential, these methods need to be matched with new computational approaches and physical models that help convert highly complex image data sets into biological insights.

    Science Profile: A Research Career in Focus

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    06/06/13 | Two-photon calcium imaging during fictive navigation in virtual environments.
    Ahrens MB, Huang KH, Narayan S, Mensh BD, Engert F
    Frontiers in Neural Circuits. 2013 Jun 6;7:104. doi: 10.3389/fncir.2013.00104 *equal contribution

    A full understanding of nervous system function requires recording from large populations of neurons during naturalistic behaviors. Here we enable paralyzed larval zebrafish to fictively navigate two-dimensional virtual environments while we record optically from many neurons with two-photon imaging. Electrical recordings from motor nerves in the tail are decoded into intended forward swims and turns, which are used to update a virtual environment displayed underneath the fish. Several behavioral features-such as turning responses to whole-field motion and dark avoidance-are well-replicated in this virtual setting. We readily observed neuronal populations in the hindbrain with laterally selective responses that correlated with right or left optomotor behavior. We also observed neurons in the habenula, pallium, and midbrain with response properties specific to environmental features. Beyond single-cell correlations, the classification of network activity in such virtual settings promises to reveal principles of brainwide neural dynamics during behavior.

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