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2449 Publications

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    08/01/11 | Shedding light on the system: studying embryonic development with light sheet microscopy.
    Tomer R, Khairy K, Keller PJ
    Current Opinion in Genetics and Development. 2011 Aug;21(5):558-65. doi: 10.1016/j.gde.2011.07.003

    Light sheet-based fluorescence microscopy (LSFM) is emerging as a powerful imaging technique for the life sciences. LSFM provides an exceptionally high imaging speed, high signal-to-noise ratio, low level of photo-bleaching and good optical penetration depth. This unique combination of capabilities makes light sheet-based microscopes highly suitable for live imaging applications. There is an outstanding potential in applying this technology to the quantitative study of embryonic development. Here, we provide an overview of the different basic implementations of LSFM, review recent technical advances in the field and highlight applications in the context of embryonic development. We conclude with a discussion of promising future directions.

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    Tjian Lab
    08/01/11 | Sub-nuclear compartmentalization of core promoter factors and target genes.
    Yao J, Tjian R
    Cell Cycle. 2011 Aug 1;10(15):2405-6
    Looger Lab
    08/01/11 | Two-photon calcium imaging of evoked activity from L5 somatosensory neurons in vivo.
    Mittmann W, Wallace DJ, Czubayko U, Herb JT, Schaefer AT, Looger LL, Denk W, Kerr JN
    Nature Neuroscience. 2011 Aug;14(8):1089-93. doi: 10.1038/nn.2879

    Multiphoton imaging (MPI) is widely used for recording activity simultaneously from many neurons in superficial cortical layers in vivo. We combined regenerative amplification multiphoton microscopy (RAMM) with genetically encoded calcium indicators to extend MPI of neuronal population activity into layer 5 (L5) of adult mouse somatosensory cortex. We found that this approach could be used to record and quantify spontaneous and sensory-evoked activity in populations of L5 neuronal somata located as much as 800 μm below the pia. In addition, we found that RAMM could be used to simultaneously image activity from large (80) populations of apical dendrites and follow these dendrites down to their somata of origin.

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    07/17/11 | Precise olfactory responses tile the sniff cycle.
    Shusterman R, Smear MC, Koulakov AA, Rinberg D
    Nature Neuroscience. 2011 Jul 17;14(8):1039-44. doi: 10.1038/nn.2877

    In terrestrial vertebrates, sniffing controls odorant access to receptors, and therefore sets the timescale of olfactory stimuli. We found that odorants evoked precisely sniff-locked activity in mitral/tufted cells in the olfactory bulb of awake mouse. The trial-to-trial response jitter averaged 12 ms, a precision comparable to other sensory systems. Individual cells expressed odor-specific temporal patterns of activity and, across the population, onset times tiled the duration of the sniff cycle. Responses were more tightly time-locked to the sniff phase than to the time after inhalation onset. The spikes of single neurons carried sufficient information to discriminate odors. In addition, precise locking to sniff phase may facilitate ensemble coding by making synchrony relationships across neurons robust to variation in sniff rate. The temporal specificity of mitral/tufted cell output provides a potentially rich source of information for downstream olfactory areas.

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    Cui Lab
    07/04/11 | Phase resolved interferometric spectral modulation (PRISM) for ultrafast pulse measurement and compression.
    Wu T, Tang J, Hajj B, Cui M
    Optics Express. 2011 Jul 4;19(14):12961-8. doi: 10.1364/OE.19.012961

    We show through experiments and simulations that parallel phase modulation, a technique developed in the field of adaptive optics, can be employed to quickly determine the spectral phase profile of ultrafast laser pulses and to perform phase compensation as well as pulse shaping. Different from many existing ultrafast pulse measurement methods, the technique reported here requires no spectrum measurements of nonlinear signals. Instead, the power of nonlinear signals is used directly to quickly measure the spectral phase, a convenient feature for applications such as two-photon fluorescence microscopy. The method is found to work with both smooth and even completely random distortions. The experimental results are verified with MIIPS measurements.

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    Baker Lab
    07/01/11 | Direct targets of the D. melanogaster DSXF protein and the evolution of sexual development.
    Luo SD, Shi GW, Baker BS
    Development. 2011 Jul;138(13):2761-71. doi: 10.1242/dev.065227

    Uncovering the direct regulatory targets of doublesex (dsx) and fruitless (fru) is crucial for an understanding of how they regulate sexual development, morphogenesis, differentiation and adult functions (including behavior) in Drosophila melanogaster. Using a modified DamID approach, we identified 650 DSX-binding regions in the genome from which we then extracted an optimal palindromic 13 bp DSX-binding sequence. This sequence is functional in vivo, and the base identity at each position is important for DSX binding in vitro. In addition, this sequence is enriched in the genomes of D. melanogaster (58 copies versus approximately the three expected from random) and in the 11 other sequenced Drosophila species, as well as in some other Dipterans. Twenty-three genes are associated with both an in vivo peak in DSX binding and an optimal DSX-binding sequence, and thus are almost certainly direct DSX targets. The association of these 23 genes with optimum DSX binding sites was used to examine the evolutionary changes occurring in DSX and its targets in insects.

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    Sternson Lab
    07/01/11 | Flip-flop memory circuit uses a synaptic AMPK-dependent positive feedback loop and is switched by hunger state.
    Y.Yang , D.Atasoy , S.Sternson
    Appetite. 2011 Jul 01;57(1):47. doi: 10.1016/j.appet.2011.05.296

    Synaptic plasticity in response to changes in physiologic state is coordinated by hormonal signals across multiple neuronal cell types, but the significance and underlying mechanisms are unclear. Here, we combine cell type-specific electrophysiological, pharmacological, and optogenetic techniques to dissect neural circuits and molecular pathways controlling synaptic plasticity onto AGRP neurons, a population that regulates feeding. We find that food deprivation elevates excitatory synaptic input, which is mediated by a presynaptic positive feedback loop involving AMP-activated protein kinase. Potentiation of glutamate release was triggered by the orexigenic hormone ghrelin and exhibited hysteresis, persisting for hours after ghrelin removal. Persistent activity was reversed by the anorexigenic hormone leptin, and optogenetic photostimulation demonstrated involvement of opioid release from POMC neurons. Based on these experiments, we propose a memory storage device for physiological state constructed from bistable synapses that are flipped between two sustained activity states by transient exposure to hormones signaling energy levels. Supported by: Howard Hughes Medical Institute.

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    Eddy/Rivas Lab
    07/01/11 | HMMER web server: interactive sequence similarity searching.
    Finn RD, Clements J, Eddy SR
    Nucleic Acids Research. 2011 Jul;39:W29-37. doi: 10.1093/nar/gkr367

    HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server ( has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.

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    Baker Lab
    06/24/11 | Functional dissection of the neural substrates for sexual behaviors in Drosophila melanogaster.
    Meissner GW, Manoli DS, Chavez JF, Knapp J, Lin TL, Stevens RJ, Mellert DJ, Tran DH, Baker BS
    Genetics. 2011 Jun 24;189(1):195-211. doi: 10.1534/genetics.111.129940

    The male-specific Fruitless proteins (Fru(M)) act to establish the potential for male courtship behavior in Drosophila melanogaster and are expressed in small groups of neurons throughout the nervous system. We screened  1000 GAL4 lines, using assays for general courtship, male-male interactions, and male fertility to determine the phenotypes resulting from the GAL4 driven inhibition of Fru(M) expression in subsets of these neurons. A battery of secondary assays showed that the phenotypic classes of GAL4 lines could be divided into subgroups based on additional neurobiological and behavioral criteria. For example, in some lines restoration of Fru(M) expression in cholinergic neurons restores fertility or reduces male-male courtship. Persistent chains of males courting each other in some lines results from males courting both sexes indiscriminately whereas in other lines this phenotype result from apparent habituation deficits. Inhibition of ectopic Fru(M) expression in females, in populations of neurons where Fru(M) is necessary for male fertility, can rescue female infertility. To identify the neurons responsible for some of the observed behavioral alterations, we determined the overlap between the identified GAL4 lines and endogenous Fru(M) expression in lines with fertility defects. The GAL4 lines causing fertility defects generally had widespread overlap with Fru(M) expression in many regions of the nervous system suggesting likely redundant Fru(M)-expressing neuronal pathways capable of conferring male fertility. From associations between the screened behaviors, we propose a functional model for courtship initiation.

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    06/24/11 | Studying sensorimotor integration in insects.
    Huston* SJ, Jayaraman V
    Current Opinion in Neurobiology. 2011 Jun 24;21(4):527-34. doi: 10.1016/j.conb.2011.05.030

    Sensorimotor integration is a field rich in theory backed by a large body of psychophysical evidence. Relating the underlying neural circuitry to these theories has, however, been more challenging. With a wide array of complex behaviors coordinated by their small brains, insects provide powerful model systems to study key features of sensorimotor integration at a mechanistic level. Insect neural circuits perform both hard-wired and learned sensorimotor transformations. They modulate their neural processing based on both internal variables, such as the animal’s behavioral state, and external ones, such as the time of day. Here we present some studies using insect model systems that have produced insights, at the level of individual neurons, about sensorimotor integration and the various ways in which it can be modified by context.

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