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      A Functional SMAD2/3 Binding Site in the PEX11β Promoter Identifies a Role for TGFβ in Peroxisome Proliferation in Humans

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          Abstract

          In mammals, peroxisomes perform crucial functions in cellular metabolism, signaling and viral defense which are essential to the viability of the organism. Molecular cues triggered by changes in the cellular environment induce a dynamic response in peroxisomes, which manifests itself as a change in peroxisome number, altered enzyme levels and adaptations to the peroxisomal morphology. How the regulation of this process is integrated into the cell’s response to different stimuli, including the signaling pathways and factors involved, remains unclear. Here, a cell-based peroxisome proliferation assay has been applied to investigate the ability of different stimuli to induce peroxisome proliferation. We determined that serum stimulation, long-chain fatty acid supplementation and TGFβ application all increase peroxisome elongation, a prerequisite for proliferation. Time-resolved mRNA expression during the peroxisome proliferation cycle revealed a number of peroxins whose expression correlated with peroxisome elongation, including the β isoform of PEX11, but not the α or γ isoforms. An initial map of putative regulatory motif sites in the respective promoters showed a difference between binding sites in PEX11α and PEX11β, suggesting that these genes may be regulated by distinct pathways. A functional SMAD2/3 binding site in PEX11β points to the involvement of the TGFβ signaling pathway in expression of this gene and thus peroxisome proliferation/dynamics in humans.

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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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            Genome engineering using the CRISPR-Cas9 system.

            Targeted nucleases are powerful tools for mediating genome alteration with high precision. The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA. Here we describe a set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells, as well as generation of modified cell lines for downstream functional studies. To minimize off-target cleavage, we further describe a double-nicking strategy using the Cas9 nickase mutant with paired guide RNAs. This protocol provides experimentally derived guidelines for the selection of target sites, evaluation of cleavage efficiency and analysis of off-target activity. Beginning with target design, gene modifications can be achieved within as little as 1-2 weeks, and modified clonal cell lines can be derived within 2-3 weeks.
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              TGFβ signalling in context.

              The basic elements of the transforming growth factor-β (TGFβ) pathway were revealed more than a decade ago. Since then, the concept of how the TGFβ signal travels from the membrane to the nucleus has been enriched with additional findings, and its multifunctional nature and medical relevance have relentlessly come to light. However, an old mystery has endured: how does the context determine the cellular response to TGFβ? Solving this question is key to understanding TGFβ biology and its many malfunctions. Recent progress is pointing at answers.
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                Author and article information

                Contributors
                Journal
                Front Cell Dev Biol
                Front Cell Dev Biol
                Front. Cell Dev. Biol.
                Frontiers in Cell and Developmental Biology
                Frontiers Media S.A.
                2296-634X
                23 October 2020
                2020
                : 8
                : 577637
                Affiliations
                [1] 1Biosciences, College of Life and Environmental Sciences, University of Exeter , Exeter, United Kingdom
                [2] 2Institute of Molecular Health Sciences, Swiss Federal Institute of Technology in Zürich (ETH Zürich) , Zurich, Switzerland
                [3] 3Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, University of Amsterdam , Amsterdam, Netherlands
                Author notes

                Edited by: Sigrun Reumann, University of Hamburg, Germany

                Reviewed by: Ralf Erdmann, Ruhr University Bochum, Germany; Xuequn Chen, Wayne State University, United States; Andrew Simmonds, University of Alberta, Canada

                *Correspondence: Michael Schrader, m.schrader@ 123456exeter.ac.uk

                These authors have contributed equally to this work

                ORCID: Ruth E. Carmichael, orcid.org/0000-0003-2665-2966; Werner J. Kovacs, orcid.org/0000-0002-4440-4344; Michael Schrader, orcid.org/0000-0003-2146-0535

                This article was submitted to Membrane Traffic, a section of the journal Frontiers in Cell and Developmental Biology

                Article
                10.3389/fcell.2020.577637
                7644849
                33195217
                a8689ff3-954d-4a7f-ac4b-bc27303c20d3
                Copyright © 2020 Azadi, Carmichael, Kovacs, Koster, Kors, Waterham and Schrader.

                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
                : 29 June 2020
                : 01 October 2020
                Page count
                Figures: 8, Tables: 0, Equations: 0, References: 101, Pages: 18, Words: 0
                Funding
                Funded by: Biotechnology and Biological Sciences Research Council 10.13039/501100000268
                Award ID: BB/R016844/1
                Funded by: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung 10.13039/501100001711
                Funded by: FP7 People: Marie-Curie Actions 10.13039/100011264
                Funded by: Medical Research Council 10.13039/501100000265
                Categories
                Cell and Developmental Biology
                Original Research

                peroxisomes,organelle dynamics,transcriptional regulation,peroxin,pex11,transforming growth factor beta

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