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4 Janelia Publications

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    09/14/18 | Probing synaptic transmission and behavior in Drosophila with optogenetics: a laboratory exercise
    Vilinksy I, Hibbard KL, Johnson Bruce R , Deitcher DL
    Journal of Undergraduate Neuroscience Education. 2018 Summer;16(3):A289-95

    Optogenetics is possibly the most revolutionary advance in neuroscience research techniques within the last decade. Here, we describe lab modules, presented at a workshop for undergraduate neuroscience educators, using optogenetic control of neurons in the fruit fly Drosophila melanogaster. Drosophila is a genetically accessible model system that combines behavioral and neurophysiological complexity, ease of use, and high research relevance. One lab module utilized two transgenic Drosophila strains, each activating specific circuits underlying startle behavior and backwards locomotion, respectively. The red-shifted channelrhodopsin, CsChrimson, was expressed in neurons sharing a common transcriptional profile, with the expression pattern further refined by the use of a Split GAL4 intersectional activation system. Another set of strains was used to investigate synaptic transmission at the larval neuromuscular junction. These expressed Channelrhodopsin 2 (ChR2) in glutamatergic neurons, including the motor neurons. The first strain expressed ChR2 in a wild type background, while the second contained the SNAP-25ts mutant allele, which confers heightened evoked potential amplitude and greatly increased spontaneous vesicle release frequency at the larval neuromuscular junction. These modules introduced educators and students to the use of optogenetic stimulation to control behavior and evoked release at a model synapse, and establish a basis for students to explore neurophysiology using this technique, through recapitulating classic experiments and conducting independent research. 

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    03/13/18 | Genetic reagents for making split-GAL4 lines in Drosophila.
    Dionne H, Hibbard KL, Cavallaro A, Kao J, Rubin GM
    Genetics . 2018 March;209(1):31-5. doi: 10.1101/197509

    The ability to reproducibly target expression of transgenes to small, defined subsets of cells is a key experimental tool for understanding many biological processes. The Drosophila nervous system contains thousands of distinct cell types and it has generally not been possible to limit expression to one or a few cell types when using a single segment of genomic DNA as an enhancer to drive expression. Intersectional methods, in which expression of the transgene only occurs where two different enhancers overlap in their expression patterns, can be used to achieve the desired specificity. This report describes a set of over 2,800 transgenic lines for use with the split-GAL4 intersectional method.

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    08/28/15 | The transgenic RNAi project at Harvard Medical School: resources and validation.
    Perkins LA, Holderbaum L, Tao R, Hu Y, Sopko R, McCall K, Yang-Zhou D, Flockhart I, Binari R, Shim H, Miller A, Housden A, Foos M, Randkelv S, Kelley C, Namgyal P, Villalta C, Liu L, Jiang X, Huan-Huan Q, Xia W, Fujiyama A, Toyoda A, Ayers K, Blum A, Czech B, Neumuller R, Yan D, Cavallaro A, Hibbard K, Hall D, Cooley L, Hannon GJ, Lehmann R, Parks A, Mohr SE, Ueda R, Kondo S, Ni J, Perrimon N
    Genetics. 2015 Aug 28;201(3):843-52. doi: 10.1534/genetics.115.180208

    To facilitate large scale functional studies in Drosophila, the Drosophila Transgenic RNAi Project (TRiP) at Harvard Medical School (HMS) was established along with several goals: developing efficient vectors for RNAi that work in all tissues, generating a genome scale collection of RNAi stocks with input from the community, distributing the lines as they are generated through existing stock centers, validating as many lines as possible using RT-qPCR and phenotypic analyses, and developing tools and web resources for identifying RNAi lines and retrieving existing information on their quality. With these goals in mind, here we describe in detail the various tools we developed and the status of the collection, which is currently comprised of 11,491 lines and covering 71% of Drosophila genes. Data on the characterization of the lines either by RT-qPCR or phenotype is available on a dedicated web site, the RNAi Stock Validation and Phenotypes Project (RSVP; www.flyrnai.org/RSVP.html), and stocks are available from three stock centers, the Bloomington Drosophila Stock Center (USA), National Institute of Genetics (Japan), and TsingHua Fly Center (China).

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    08/01/09 | A Drosophila resource of transgenic RNAi lines for neurogenetics.
    Ni J, Liu L, Binari R, Hardy R, Shim H, Cavallaro A, Booker M, Pfeiffer BD, Markstein M, Wang H, Villalta C, Laverty TR, Perkins LA, Perrimon N
    Genetics. 2009 Aug;182(4):1089-100. doi: 10.1534/genetics.109.103630

    Conditional expression of hairpin constructs in Drosophila is a powerful method to disrupt the activity of single genes with a spatial and temporal resolution that is impossible, or exceedingly difficult, using classical genetic methods. We previously described a method (Ni et al. 2008) whereby RNAi constructs are targeted into the genome by the phiC31-mediated integration approach using Vermilion-AttB-Loxp-Intron-UAS-MCS (VALIUM), a vector that contains vermilion as a selectable marker, an attB sequence to allow for phiC31-targeted integration at genomic attP landing sites, two pentamers of UAS, the hsp70 core promoter, a multiple cloning site, and two introns. As the level of gene activity knockdown associated with transgenic RNAi depends on the level of expression of the hairpin constructs, we generated a number of derivatives of our initial vector, called the "VALIUM" series, to improve the efficiency of the method. Here, we report the results from the systematic analysis of these derivatives and characterize VALIUM10 as the most optimal vector of this series. A critical feature of VALIUM10 is the presence of gypsy insulator sequences that boost dramatically the level of knockdown. We document the efficacy of VALIUM as a vector to analyze the phenotype of genes expressed in the nervous system and have generated a library of 2282 constructs targeting 2043 genes that will be particularly useful for studies of the nervous system as they target, in particular, transcription factors, ion channels, and transporters.

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