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      Expression of the foraging gene in adult Drosophila melanogaster

      research-article
      a , b , a , c , d
      Journal of Neurogenetics
      Taylor & Francis
      Drosophila melanogaster, foraging gene, expression, promoter analysis, cis-regulatory element, pleiotropy

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          Abstract

          The foraging gene in Drosophila melanogaster, which encodes a cGMP-dependent protein kinase, is a highly conserved, complex gene with multiple pleiotropic behavioral and physiological functions in both the larval and adult fly. Adult foraging expression is less well characterized than in the larva. We characterized foraging expression in the brain, gastric system, and reproductive systems using a T2A-Gal4 gene-trap allele. In the brain, foraging expression appears to be restricted to multiple sub-types of glia. This glial-specific cellular localization of foraging was supported by single-cell transcriptomic atlases of the adult brain. foraging is extensively expressed in most cell types in the gastric and reproductive systems. We then mapped multiple cis-regulatory elements responsible for parts of the observed expression patterns by a nested cloned promoter- Gal4 analysis. The mapped cis-regulatory elements were consistently modular when comparing the larval and adult expression patterns. These new data using the T2A-Gal4 gene-trap and cloned foraging promoter fusion GAL4’s are discussed with respect to previous work using an anti-FOR antibody, which we show here to be non-specific. Future studies of foraging’s function will consider roles for glial subtypes and peripheral tissues (gastric and reproductive systems) in foraging’s pleiotropic behavioral and physiological effects.

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          Fiji: an open-source platform for biological-image analysis.

          Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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            Comprehensive Integration of Single-Cell Data

            Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.
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              Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

              Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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                Author and article information

                Journal
                J Neurogenet
                J Neurogenet
                Journal of Neurogenetics
                Taylor & Francis
                0167-7063
                1563-5260
                12 August 2021
                2021
                12 August 2021
                : 35
                : 3 , Transcending boundaries: from quantitative genetics to single genes. Guest Editors: Jeffrey S. Dason and Ina Anreiter
                : 192-212
                Affiliations
                [a ]Department of Cell and Systems Biology, University of Toronto , Toronto, Canada
                [b ]Centre for Neural Circuits and Behaviour, University of Oxford , Oxford, UK
                [c ]Department of Ecology and Evolutionary Biology, University of Toronto , Toronto, Canada
                [d ]Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) , Toronto, Canada
                Author notes

                Supplemental data for this article can be accessed here .

                CONTACT Aaron M. Allen aaron.allen@ 123456cncb.ox.ac.uk
                Author information
                https://orcid.org/0000-0002-7961-4392
                https://orcid.org/0000-0002-7462-8007
                Article
                1941946
                10.1080/01677063.2021.1941946
                8846931
                34382904
                add1bd13-50bb-4b58-8758-38614092751f
                © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group

                This is an Open Access article distributed under the terms of the Creative Commons Attribution 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
                Page count
                Figures: 7, Tables: 0, Pages: 21, Words: 18485
                Categories
                Research Article
                Original Research Articles

                Genetics
                drosophila melanogaster,foraging gene,expression,promoter analysis,cis-regulatory element,pleiotropy

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