Journal ArticleDOI
A guided tour into subcellular colocalization analysis in light microscopy
TLDR
A novel toolbox for subcellular colocalization analysis under ImageJ is created that integrates current global statistic methods and a novel object‐based approach to assess proteins residing on intracellular structures by fluorescence microscopy.Abstract:
Summary It is generally accepted that the functional compartmentalization of eukaryotic cells is reflected by the differential occurrence of proteins in their compartments. The location and physiological function of a protein are closely related; local information of a protein is thus crucial to understanding its role in biological processes. The visualization of proteins residing on intracellular structures by fluorescence microscopy has become a routine approach in cell biology and is increasingly used to assess their colocalization with well-characterized markers. However, imageanalysis methods for colocalization studies are a field of contention and enigma. We have therefore undertaken to review the most currently used colocalization analysis methods, introducing the basic optical concepts important for image acquisition and subsequent analysis. We provide a summary of practical tips for image acquisition and treatment that should precede proper colocalization analysis. Furthermore, we discuss the application and feasibility of colocalization tools for various biological colocalization situations and discuss their respective strengths and weaknesses. We have created a novel toolbox for subcellular colocalization analysis under Image J, named JACoP, that integrates current global statistic methods and a novel object-based approach.read more
Citations
More filters
Journal ArticleDOI
Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness
Michiru Nishita,Seung-Yeol Park,Tadashi Nishio,Koki Kamizaki,ZhiChao Wang,Kota Tamada,Toru Takumi,Ryuju Hashimoto,Hiroki Otani,Gregory J. Pazour,Victor W. Hsu,Yasuhiro Minami +11 more
TL;DR: It is found that intraflagellar transport 20 mediates the ability of Ror2 signaling to induce the invasiveness of tumors that lack primary cilia, and IFT20 regulates the nucleation of Golgi-derived microtubules by affecting the GM130-AKAP450 complex.
Journal ArticleDOI
N6-methyladenosine-dependent regulation of messenger RNA stability
Xiao Wang,Zhike Lu,Adrian Gomez,Gary C. Hon,Yanan Yue,Dali Han,Ye Fu,Marc Parisien,Qing Dai,Guifang Jia,Bing Ren,Tao Pan,Chuan He +12 more
TL;DR: It is shown that m6A is selectively recognized by the human YTH domain family 2 (YTHDF2) ‘reader’ protein to regulate mRNA degradation and established the role of YTH DF2 in RNA metabolism, showing that binding of Y THDF2 results in the localization of bound mRNA from the translatable pool to mRNA decay sites, such as processing bodies.
Journal ArticleDOI
N6-methyladenosine Modulates Messenger RNA Translation Efficiency
Xiao Wang,Xiao Wang,Boxuan Simen Zhao,Boxuan Simen Zhao,Ian A Roundtree,Ian A Roundtree,Zhike Lu,Zhike Lu,Dali Han,Dali Han,Honghui Ma,Honghui Ma,Xiaocheng Weng,Xiaocheng Weng,Kai Chen,Kai Chen,Hailing Shi,Hailing Shi,Chuan He,Chuan He +19 more
TL;DR: In a unified mechanism of m(6)A-based regulation in the cytoplasm, YTHDF2-mediated degradation controls the lifetime of target transcripts, whereasYTHDF1-mediated translation promotion increases translation efficiency, ensuring effective protein production from dynamic transcripts that are marked by m( 6)A.
Journal ArticleDOI
A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation
Jianzhao Liu,Yanan Yue,Dali Han,Xiao Wang,Ye Fu,Liang Zhang,Guifang Jia,Miao Yu,Zhike Lu,Xin Deng,Qing Dai,Weizhong Chen,Chuan He +12 more
TL;DR: It is reported here that human METTL14 catalyzes m6A RNA methylation, and together with METTL3, the only previously known m 6A methyltransferase, these two proteins form a stable heterodimer core complex ofMETTL3-14 that functions in cellular m6 a deposition on mammalian nuclear RNAs.
Journal ArticleDOI
A forty-kilodalton protein of the inner membrane is the mitochondrial calcium uniporter
TL;DR: It is demonstrated that the 40-kDa protein identified is the channel responsible for ruthenium-red-sensitive mitochondrial Ca2+ uptake, thus providing a molecular basis for this process of utmost physiological and pathological relevance.
References
More filters
BookDOI
Molecular fluorescence : principles and applications
TL;DR: In this article, the effects of intermolecular photophysical processes on fluorescence emission are discussed and an analysis of the effect of polarity of fluorescence emissions is presented.
BookDOI
Handbook of biological confocal microscopy
TL;DR: Methods for Three-Dimensional Imaging and Tutorial on Practical Confocal Microscopy and Use of the Confocal Test Specimen.
Journal ArticleDOI
Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking.
Maxime Dahan,Sabine Lévi,Camilla Luccardini,Philippe Rostaing,Béatrice Riveau,Antoine Triller +5 more
TL;DR: The entry of GlyRs into the synapse by diffusion was observed and further confirmed by electron microscopy imaging of QD-tagged receptors.
Journal ArticleDOI
The watershed transform: definitions, algorithms and parallelization strategies
TL;DR: A critical review of several definitions of watershed transform and associated sequential algorithms is presented in this paper, where the need to distinguish between definition, algorithm specification and algorithm implementation is pointed out.