scholarly journals An optimized procedure for quantitative analysis of mitophagy with the mtKeima system using flow cytometry

BioTechniques ◽  
2020 ◽  
Vol 69 (4) ◽  
pp. 249-256
Author(s):  
Nathaniel J Winsor ◽  
Samuel A Killackey ◽  
Dana J Philpott ◽  
Stephen E Girardin

Mitophagy is the process by which mitochondria are selectively targeted and removed via autophagic machinery to maintain mitochondrial homeostasis in the cell. Recently, flow cytometry-based assays that utilize the fluorescent mtKeima reporter system have allowed for quantitative assessment of mitophagy at a single-cell level. However, clear guidelines for appropriate flow cytometry workflow and downstream analysis are lacking and studies using flow cytometry in mtKeima-expressing cells often display incorrect and arbitrary binary mitophagic or nonmitophagic cutoffs that prevent proper quantitative analyses. In this paper we propose a novel method of mtKeima data analysis that preserves subtle differences present within flow cytometry data in a manner that ensures reproducibility.

Author(s):  
Zilong Zhang ◽  
Feifei Cui ◽  
Chen Lin ◽  
Lingling Zhao ◽  
Chunyu Wang ◽  
...  

Abstract Single-cell RNA sequencing (scRNA-seq) has enabled us to study biological questions at the single-cell level. Currently, many analysis tools are available to better utilize these relatively noisy data. In this review, we summarize the most widely used methods for critical downstream analysis steps (i.e. clustering, trajectory inference, cell-type annotation and integrating datasets). The advantages and limitations are comprehensively discussed, and we provide suggestions for choosing proper methods in different situations. We hope this paper will be useful for scRNA-seq data analysts and bioinformatics tool developers.


2014 ◽  
Vol 115 (suppl_1) ◽  
Author(s):  
Konstantina Ioanna Sereti ◽  
Paniz Kamran Rashani ◽  
Peng Zhao ◽  
Reza Ardehali

It has been proposed that cardiac development in lower vertebrates is driven by the proliferation of cardiomyocytes. Similarly, cycling myocytes have been suggested to direct cardiac regeneration in neonatal mice after injury. Although, the role of cardiomyocyte proliferation in cardiac tissue generation during development has been well documented, the extent of this contribution as well as the role of other cell types, such as progenitor cells, still remains controversial. Here we used a novel stochastic four-color Cre-dependent reporter system (Rainbow) that allows labeling at a single cell level and retrospective analysis of the progeny. Cardiac progenitors expressing Mesp1 or Nkx2.5 were shown to be a source of cardiomyocytes during embryonic development while the onset of αMHC expression marked the developmental stage where the capacity of cardiac cells to proliferate diminishes significantly. Through direct clonal analysis we provide strong evidence supporting that cardiac progenitors, as opposed to mature cardiomyocytes, are the main source of cardiomyocytes during cardiac development. Moreover, we have identified quadri-, tri-, bi, and uni-potent progenitors that at a single cell level can generate cardiomyocytes, fibroblasts, endothelial and smooth muscle cells. Although existing cardiomyocytes undergo limited proliferation, our data indicates that it is mainly the progenitors that contribute to heart development. Furthermore, we show that the limited proliferation capacity of cardiomyocytes observed during normal development was enhanced following neonatal cardiac injury allowing almost complete regeneration of the scared tissue. However, this ability was largely absent in adult injured hearts. Detailed characterization of dividing cardiomyocytes and proliferating progenitors would greatly benefit the development of novel therapeutic options for cardiovascular diseases.


2011 ◽  
Author(s):  
Laimonas Kelbauskas ◽  
Shashanka Ashili ◽  
Jeff Houkal ◽  
Dean Smith ◽  
Aida Mohammadreza ◽  
...  

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Nicolas Lemus-Diaz ◽  
Kai O. Böker ◽  
Ignacio Rodriguez-Polo ◽  
Michael Mitter ◽  
Jasmin Preis ◽  
...  

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Filippos Porichis ◽  
Meghan G. Hart ◽  
Morgane Griesbeck ◽  
Holly L. Everett ◽  
Muska Hassan ◽  
...  

2017 ◽  
Vol 9 (2) ◽  
pp. 123-134 ◽  
Author(s):  
Henriette Christie Ertsås ◽  
Garry P. Nolan ◽  
Mark A. LaBarge ◽  
James B. Lorens

A novel microsphere-based flow cytometry approach to study adherent cell signaling responses in different microenvironmental contexts at the single cell level.


2019 ◽  
Vol 97 (7) ◽  
pp. 713-726 ◽  
Author(s):  
Cristina García‐Timermans ◽  
Peter Rubbens ◽  
Jasmine Heyse ◽  
Frederiek‐Maarten Kerckhof ◽  
Ruben Props ◽  
...  

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