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      Opportunities and Challenges for Genomic Data Analyses in Biobanks: A Call for Papers

      The GSA Journals are calling for submissions of papers on biobank-scale genomic data analyses. The closing date for submissions is May 31 2024.

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      A Drosophila LexA Enhancer-Trap Resource for Developmental Biology and Neuroendocrine Research

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      * , , , , , , , , , , , , , , , , , , , , , , , , , , § , * , ** , ** , ** , * , †† , 2
      G3: Genes|Genomes|Genetics
      Genetics Society of America
      Drosophila melanogaster, Drosophila neuro-endocrine system enhancer trap, LexA-LexAop binary expression system

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          Abstract

          Novel binary gene expression tools like the LexA-LexAop system could powerfully enhance studies of metabolism, development, and neurobiology in Drosophila. However, specific LexA drivers for neuroendocrine cells and many other developmentally relevant systems remain limited. In a unique high school biology course, we generated a LexA-based enhancer trap collection by transposon mobilization. The initial collection provides a source of novel LexA-based elements that permit targeted gene expression in the corpora cardiaca, cells central for metabolic homeostasis, and other neuroendocrine cell types. The collection further contains specific LexA drivers for stem cells and other enteric cells in the gut, and other developmentally relevant tissue types. We provide detailed analysis of nearly 100 new LexA lines, including molecular mapping of insertions, description of enhancer-driven reporter expression in larval tissues, and adult neuroendocrine cells, comparison with established enhancer trap collections and tissue specific RNAseq. Generation of this open-resource LexA collection facilitates neuroendocrine and developmental biology investigations, and shows how empowering secondary school science can achieve research and educational goals.

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          Most cited references39

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          Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31.

          The phiC31 integrase functions efficiently in vitro and in Escherichia coli, yeast, and mammalian cells, mediating unidirectional site-specific recombination between its attB and attP recognition sites. Here we show that this site-specific integration system also functions efficiently in Drosophila melanogaster in cultured cells and in embryos. Intramolecular recombination in S2 cells on transfected plasmid DNA carrying the attB and attP recognition sites occurred at a frequency of 47%. In addition, several endogenous pseudo attP sites were identified in the fly genome that were recognized by the integrase and used as substrates for integration in S2 cells. Two lines of Drosophila were created by integrating an attP site into the genome with a P element. phiC31 integrase injected into embryos as mRNA functioned to promote integration of an attB-containing plasmid into the attP site, resulting in up to 55% of fertile adults producing transgenic offspring. A total of 100% of these progeny carried a precise integration event at the genomic attP site. These experiments demonstrate the potential for precise genetic engineering of the Drosophila genome with the phiC31 integrase system and will likely benefit research in Drosophila and other insects.
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            Motor control in a Drosophila taste circuit.

            Tastes elicit innate behaviors critical for directing animals to ingest nutritious substances and reject toxic compounds, but the neural basis of these behaviors is not understood. Here, we use a neural silencing screen to identify neurons required for a simple Drosophila taste behavior and characterize a neural population that controls a specific subprogram of this behavior. By silencing and activating subsets of the defined cell population, we identify the neurons involved in the taste behavior as a pair of motor neurons located in the subesophageal ganglion (SOG). The motor neurons are activated by sugar stimulation of gustatory neurons and inhibited by bitter compounds; however, experiments utilizing split-GFP detect no direct connections between the motor neurons and primary sensory neurons, indicating that further study will be necessary to elucidate the circuitry bridging these populations. Combined, these results provide a general strategy and a valuable starting point for future taste circuit analysis.
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              Genetic applications of an inverse polymerase chain reaction.

              A method is presented for the rapid in vitro amplification of DNA sequences that flank a region of known sequence. The method uses the polymerase chain reaction (PCR), but it has the primers oriented in the reverse direction of the usual orientation. The template for the reverse primers is a restriction fragment that has been ligated upon itself to form a circle. This procedure of inverse PCR (IPCR) has many applications in molecular genetics, for example, the amplification and identification of sequences flanking transposable elements. In this paper we show the feasibility of IPCR by amplifying the sequences that flank an IS1 element in the genome of a natural isolate of Escherichia coli.
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                Author and article information

                Journal
                G3 (Bethesda)
                Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes|Genomes|Genetics
                Genetics Society of America
                2160-1836
                15 August 2016
                October 2016
                : 6
                : 10
                : 3017-3026
                Affiliations
                [* ]Department of Developmental Biology, Stanford University School of Medicine, California 94305
                [†† ]Department of Medicine (Oncology Division), Stanford University School of Medicine, California 94305
                []Phillips Exeter Academy, New Hampshire 03833
                [** ]Science Department, Phillips Exeter Academy, New Hampshire 03833
                []Palo Alto High School, California 94306
                [§ ]Pinewood School, Los Altos, California 94022
                Author notes
                [1]

                These authors contributed equally to this work.

                [2 ]Corresponding author: Department of Developmental Biology, Stanford University School of Medicine, Beckman B300, 279 Campus Drive, Stanford CA 94305-5329. E-mail: seungkim@ 123456stanford.edu
                Article
                GGG_031229
                10.1534/g3.116.031229
                5068927
                27527793
                03b47fdd-775d-4ee7-abf5-941ccd594bc7
                Copyright © 2016 Kockel et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 13 May 2016
                : 12 July 2016
                Page count
                Figures: 5, Tables: 0, Equations: 0, References: 53, Pages: 10
                Categories
                Investigations

                Genetics
                drosophila melanogaster,drosophila neuro-endocrine system enhancer trap,lexa-lexaop binary expression system

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