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      RIBEYE B-Domain Is Essential for RIBEYE A-Domain Stability and Assembly of Synaptic Ribbons

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          Abstract

          Synaptic ribbons are presynaptic specializations that define eponymous ribbon synapses. Synaptic ribbons are largely composed of RIBEYE, a protein containing an N-terminal A-domain and a carboxyterminal B-domain that is identical with CtBP2, a NAD(H)-binding transcriptional co-repressor. Previously we showed that synaptic ribbons are completely absent in RIBEYE knockout mice in which the RIBEYE A-domain-encoding exon had been deleted, but CtBP2 is still made, demonstrating that the A-domain is required for synaptic ribbon assembly. In the present study, we asked whether the RIBEYE B-domain also has an essential role in the assembly of synaptic ribbons. For this purpose, we made use of RIBEYE knockin mice in which the RIBEYE B-domain was replaced by a fluorescent protein domain, whereas the RIBEYE A-domain was retained unchanged. We found that replacing the RIBEYE B-domain with a fluorescent protein module destabilizes the resulting hybrid protein and causes a complete loss of synaptic ribbons. Our results thus demonstrate an essential role of the RIBEYE B-domain in enabling RIBEYE assembly into synaptic ribbons, reinforcing the notion that RIBEYE is the central organizer of synaptic ribbons.

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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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            NIH Image to ImageJ: 25 years of image analysis

            For the past twenty five years the NIH family of imaging software, NIH Image and ImageJ have been pioneers as open tools for scientific image analysis. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
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              Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.

              Patterns of gene expression can be used to characterize and classify neuronal types. It is challenging, however, to generate taxonomies that fulfill the essential criteria of being comprehensive, harmonizing with conventional classification schemes, and lacking superfluous subdivisions of genuine types. To address these challenges, we used massively parallel single-cell RNA profiling and optimized computational methods on a heterogeneous class of neurons, mouse retinal bipolar cells (BCs). From a population of ∼25,000 BCs, we derived a molecular classification that identified 15 types, including all types observed previously and two novel types, one of which has a non-canonical morphology and position. We validated the classification scheme and identified dozens of novel markers using methods that match molecular expression to cell morphology. This work provides a systematic methodology for achieving comprehensive molecular classification of neurons, identifies novel neuronal types, and uncovers transcriptional differences that distinguish types within a class.
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                Author and article information

                Contributors
                Journal
                Front Mol Neurosci
                Front Mol Neurosci
                Front. Mol. Neurosci.
                Frontiers in Molecular Neuroscience
                Frontiers Media S.A.
                1662-5099
                28 January 2022
                2022
                : 15
                : 838311
                Affiliations
                [1] 1Institute of Anatomy and Cell Biology, Saarland University, Medical School , Homburg, Germany
                [2] 2Institute of Medical Biochemistry and Molecular Biology, Saarland University, Medical School , Homburg, Germany
                [3] 3Department of Molecular and Cellular Physiology, Stanford University School of Medicine , Stanford, CA, United States
                Author notes

                Edited by: Jaewon Ko, Daegu Gyeongbuk Institute of Science and Technology (DGIST), South Korea

                Reviewed by: Wallace B. Thoreson, University of Nebraska Medical Center, United States; Didier Dulon, Institut Pasteur, France

                *Correspondence: Soni Shankhwar sonikk27@ 123456gmail.com Frank Schmitz frank.schmitz@ 123456uks.eu

                Specialty section: This article was submitted to Molecular Signalling and Pathways, a section of the journal Frontiers in Molecular Neuroscience

                Article
                10.3389/fnmol.2022.838311
                8831697
                3bfb8edb-8bd0-4e40-b2ac-48d09992e131
                Copyright © 2022 Shankhwar, Schwarz, Katiyar, Jung, Maxeiner, Südhof and Schmitz.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 17 December 2021
                : 03 January 2022
                Page count
                Figures: 13, Tables: 2, Equations: 0, References: 68, Pages: 26, Words: 1495
                Funding
                Funded by: Dr. Rolf M. Schwiete Stiftung, doi 10.13039/501100020027;
                Funded by: Deutsche Forschungsgemeinschaft, doi 10.13039/501100001659;
                Categories
                Molecular Neuroscience
                Original Research

                Neurosciences
                retina,inner ear,ribbon synapse,synaptic ribbon,ribeye a-domain,ribeye b-domain,ctbp2,presynaptic active zone

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