High-Resolution FluoRespirometry and OXPHOS Protocols for Human Cells, Permeabilized Fibers from Small Biopsies of Muscle, and Isolated Mitochondria

Author(s):  
Carolina Doerrier ◽  
Luiz F. Garcia-Souza ◽  
Gerhard Krumschnabel ◽  
Yvonne Wohlfarter ◽  
András T. Mészáros ◽  
...  
2018 ◽  
Author(s):  
Jie Zhang ◽  
Massimo Cavallaro ◽  
Daniel Hebenstreit

Transcription of many genes in metazoans is subject to polymerase pausing, which corresponds to the transient arrest of transcriptionally engaged polymerase. It occurs mainly at promoter proximal regions and is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been lacking.We present here an extension of PRO-seq, time variant PRO-seq (TV-PRO-seq), that allowed us to estimate genome-wide pausing times at single base resolution. Its application to human cells reveals that promoter proximal pausing is surprisingly short compared to other regions and displays an intricate pattern. We also find precisely conserved pausing profiles at tRNA and rRNA genes and identified DNA motifs associated with pausing time. Finally, we show how chromatin states reflect differences in pausing times.


1997 ◽  
Vol 3 (S2) ◽  
pp. 1251-1252
Author(s):  
B. Panessa-Warren ◽  
G. Tortora ◽  
J. Warren

This paper uses high resolution scanning electron microscopy (SEM) with a LaB6 gun and the newest commercial field emission guns, to obtain high magnification images of intact clostridial spores throughout the activation/germination/outgrowth process. by high resolution SEM, the clostridial exosporial membrane can be seen to produce numerous delicate projections (following activation), that extend from the exosporial surface to a nutritive substrate (agar), or cell surface when anaerobically incubated in the presence of human cells (embryonic fibroblasts and colon carcinoma cells). Magnifications of 20,000 to 200,000Xs at accelerating voltages low enough to minimize or eliminate specimen damage (1-5 kV) have permitted the entire surface of C.sporogenes and C.difficile endospores to be examined during all stages of germination. The relationships between the spore and the agar or human cell surface were also clearly visible.Clostridium sporogenes ATCC 3584 and C.difficile ATCC 43594 and 9689 were grown in cooked meat media, filtered and cleaned.


Mitochondrion ◽  
2010 ◽  
Vol 10 (2) ◽  
pp. 238
Author(s):  
Hélène Lemieux ◽  
Mariana G. Rosca ◽  
Edwin J. Vazquez ◽  
Erich Gnaiger ◽  
Charles L. Hoppel

2013 ◽  
Vol 305 (9) ◽  
pp. R1065-R1075 ◽  
Author(s):  
Anaïs Fongy ◽  
Caroline Romestaing ◽  
Coralie Blanc ◽  
Nicolas Lacoste-Garanger ◽  
Jean-Louis Rouanet ◽  
...  

The ontogeny of pectoralis muscle bioenergetics was studied in growing Adélie penguin chicks during the first month after hatching and compared with adults using permeabilized fibers and isolated mitochondria. With pyruvate-malate-succinate or palmitoyl-carnitine as substrates, permeabilized fiber respiration markedly increased during chick growth (3-fold) and further rose in adults (1.4-fold). Several markers of muscle fiber oxidative activity (cytochrome oxidase, citrate synthase, hydroxyl-acyl-CoA dehydrogenase) increased 6- to 19-fold with age together with large rises in intermyofibrillar (IMF) and subsarcolemmal (SS) mitochondrial content (3- to 5-fold) and oxidative activities (1.5- to 2.4-fold). The proportion of IMF relative to SS mitochondria increased with chick age but markedly dropped in adults. Differences in oxidative activity between mitochondrial fractions were reduced in adults compared with hatched chicks. Extrapolation of mitochondrial to muscle respirations revealed similar figures with isolated mitochondria and permeabilized fibers with carbohydrate-derived but not with lipid-derived substrates, suggesting diffusion limitations of lipid substrates with permeabilized fibers. Two immunoreactive fusion proteins, mitofusin 2 (Mfn2) and optic atrophy 1 (OPA1), were detected by Western blots on mitochondrial extracts and their relative abundance increased with age. Muscle fiber respiration was positively related with Mfn2 and OPA1 relative abundance. Present data showed by two complementary techniques large ontogenic increases in muscle oxidative activity that may enable birds to face thermal emancipation and growth in childhood and marine life in adulthood. The concomitant rise in mitochondrial fusion protein abundance suggests a role of mitochondrial networks in the skeletal muscle processes of bioenergetics that enable penguins to overcome harsh environmental constraints.


2020 ◽  
Author(s):  
Natália C. Romeiro ◽  
Caroline M. Ferreira ◽  
Marcus F. Oliveira

AbstractWhite adipose tissue (WAT) is classically associated with energy storage in the form of triacylglycerol and is directly associated with metabolic disorders, including obesity. Mitochondria regulates cellular expenditure and are active in WAT. Although isolated mitochondria have been classically used to assess their functions, several artifacts can be introduced by this approach. Although methods to assess mitochondrial physiology in permeabilized WAT were proposed, important limitations that affect organelle function exist. Here, we established and validated a method for functional evaluation of mice mesenteric WAT (mWAT) mitochondria by using mechanical permeabilization in combination with lipid depletion and high-resolution respirometry. We observed that mild stirring of mWAT for 20 minutes at room temperature with 4% fatty acid-free albumin selectively permeabilized white adipocytes plasma membrane. In these conditions, mWAT mitochondria were intact and coupled, exhibiting succinate-induced respiratory rates that were sensitive to classical modulators of oxidative phosphorylation. Finally, the respiratory capacity of mWAT in females was significantly higher than in males, an observation that agrees with reported data using isolated mitochondria. The functional assessment of mWAT mitochondria through mild mechanical permeabilization, lipid depletion and high resolution respirometry proposed here will contribute to a better understanding of WAT biology in several pathophysiological contexts.


2019 ◽  
Author(s):  
Michaela Krafcikova ◽  
Simon Dzatko ◽  
Coralie Caron ◽  
Anton Granzhan ◽  
Radovan Fiala ◽  
...  

High-resolution studies of DNA–ligand interactions in the cellular environment are problematic due to the lack of suitable biophysical tools. To address this issue, we developed an in-cell NMR-based approach for monitoring DNA–ligand interactions inside the nuclei of living human cells. Our method relies on the acquisition of high-resolution NMR data of cells electroporated with pre-formed DNA-ligand complex. The impact of the intracellular environment on the integrity of the complex is assessed on the basis of in-cell NMR signals from unbound and ligand-bound forms of a given DNA target. By using this technique, we studied complexes of model DNA fragments and four ligands, representative of DNA minor-groove binders (netropsin) or ligands binding to DNA pairing defects (naphthalenophanes). We demonstrate that some of the <i>in vitro</i> validated ligands retain their ability to form stable on-target DNA interactions <i>in situ</i>, while other<i> </i>lose this ability due to off-target interactions with genomic DNA as well as cellular metabolic components. Collectively, our data suggest that direct evaluation of behavior of drug-like molecules in the intracellular environment provides important insights for the design and development of DNA-binding ligands with the desired biological action and minimal side effects resulting from off-target binding.<br><div><br></div>


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