Basic Image Analysis and Manipulation in ImageJ

Hartig, Sean M.

doi:10.1002/0471142727.mb1415s102

Cited by 285 publications

(219 citation statements)

References 7 publications

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“…Fibrosis image analysis. We quantified the amount of post-MI myocardial fibrosis in mutant and control mice using a color segmentation method in ImageJ (NIH) that has been previously described (83). Briefly, serial sections from the coronary ligature to the cardiac apex in mutant and control mice after MI were stained for Masson's trichrome to mark fibrotic tissue.…”

Section: Methodsmentioning

confidence: 99%

Epicardial YAP/TAZ orchestrate an immunosuppressive response following myocardial infarction

Ramjee¹,

Li²,

Manderfield³

et al. 2017

Journal of Clinical Investigation

134

106

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Section: Methodsmentioning

confidence: 99%

Epicardial YAP/TAZ orchestrate an immunosuppressive response following myocardial infarction

Ramjee¹,

Li²,

Manderfield³

et al. 2017

Journal of Clinical Investigation

134

106

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“…5 µl of the suspension was placed under a coverslip and imaged using DeltaVision Elite widefield microscope, GE, USA at room temperature. The images were processed using ImageJ (63,64). The Pearson's correlation coefficient (PCC) was obtained using the Coloc2 plugin from Fiji (65) P. berghei culturing and genetic manipulationIntra-erythrocytic asexual stages of P. berghei ANKA (procured from MR4) were maintained in BALB/c mice.…”

Section: Complementation Of Fh Deficiency In ∆Fumacb Strain With Pffhmentioning

confidence: 99%

Biochemical characterization and essentiality of fumarate hydratase

Jayaraman¹,

Suryavanshi²,

Kalale

et al. 2018

Journal of Biological Chemistry

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Plasmodium falciparum (Pf), the causative agent of malaria, has an iron-sulfur cluster-containing class I fumarate hydratase (FH) that catalyzes the interconversion of fumarate to malate, a wellknown reaction in the tricarboxylic acid cycle. In humans, the same reaction is catalyzed by class II FH that has no sequence or structural homology with the class I enzyme from Plasmodium. Fumarate is generated in large quantities in the parasite as a byproduct of AMP synthesis and is converted to malate by FH and then used in the generation of the key metabolites oxaloacetate, aspartate, and pyruvate. Previous studies have identified the FH reaction as being essential to P. falciparum, but biochemical characterizations of PfFH that may provide leads for the development of specific inhibitors are lacking. Here, we report on the kinetic characterization of purified recombinant PfFH, functional complementation of fh deficiency in Escherichia coli, and mitochondrial localization in the parasite. We found that the substrate analog mercaptosuccinic acid is a potent PfFH inhibitor, with a K i value in the nanomolar range. The fh gene could not be knocked out in Plasmodium berghei when transfectants were introduced into BALB/c mice; however, fh knockout was successful when C57BL/6 mice were used as host, suggesting that the essentiality of the fh gene to the parasite was mouse strain dependent.Plasmodium falciparum (Pf), the causative agent of the most lethal form of malaria, during its intra-erythrocytic asexual stages, derives ATP primarily from glycolysis with low contribution from mitochondrial pathways (1, 2). The bulk of pyruvate formed is converted to lactic acid with a minor amount entering the tricarboxylic acid (TCA) cycle, the flux through which is upregulated in sexual stages (2). Key intermediates that anaplerotically feed into the TCA cycle are α-ketoglutarate derived from glutamate, oxaloacetate (OAA) from phosphoenolpyruvate, and fumarate from adenosine 5΄-monophosphate (AMP) synthesis. Synthesis of AMP in the parasite is solely from inosine-5΄-monophosphate (IMP) through a pathway involving the enzymes adenylosuccinate synthetase (ADSS) and adenylosuccinate lyase (ASL). The net reaction of ADSS and ASL involves consumption of GTP and aspartate and, generation of GDP, P i and fumarate. In the rapidly dividing parasite with an AT-rich genome and high energy requirements, leading to a high demand for adenine pools, one would expect a high flux of fumarate generation. The parasite does not secrete fumarate but instead, the carbon derived from this metabolite can be traced in malate, OAA, aspartate, pyruvate (through PEP) and lactate (3). The metabolic significance of this fumarate anaplerosis is still obscure. In this context, fumarate hydratase (FH, fumarase) the key enzyme to metabolize fumarate becomes an Fumarate hydratase (fumarase, E.C. 4.2.1.2) catalyzes the reversible conversion of fumarate to malate. The stereospecific reaction involves the anti-addition of a water molecule across the carbon-carbon...

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“…The fluorescence intensity was quantified by laser scanning microscopy (LSM 780 microscope equipped with Plan-Apochromat 20ϫ/0.8 M27 objective and ZEN 2011 software; Carl Zeiss, Germany). The average fluorescence intensity per cell for each treatment was calculated using ImageJ (21,26). Averages of at least 75 cells per field and 3 fields per condition were analyzed.…”

Section: Chemicalsmentioning

confidence: 99%

Major Pathways of Polymyxin-Induced Apoptosis in Rat Kidney Proximal Tubular Cells

Azad

Akter

Rogers

et al. 2015

Antimicrob Agents Chemother

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bIdentifying the pathways involved in the apoptotic cell death that is associated with polymyxin-induced nephrotoxicity is crucial for the development of strategies to ameliorate this dose-limiting side effect and for the development of novel safer polymyxins. The primary aim of this study was to identify the major pathways which lead to polymyxin-induced apoptosis in cultured rat kidney proximal tubular cells (NRK-52E). Caspase-3, -8, and -9 were activated by polymyxin B treatment in a concentrationdependent manner. Concentration-and time-dependent expression of FasL and deformation of mitochondrial morphology were revealed following polymyxin B treatment. The proportion of cells with filamentous mitochondria (regular morphology) following an 8-h treatment with 1.0 mM polymyxin B was 56.2% ؎ 9.7% (n ‫؍‬ 3). This was decreased to 30.7% ؎ 7.5% when the polymyxin B concentration was increased to 2.0 mM. The mitochondrial membrane potential (⌬ m ) decreased to 14.1% ؎ 2.9% in the cells treated with 1.0 mM polymyxin B for 24 h (n ‫؍‬ 3) compared to that in the untreated control group. Concomitantly, concentration-and time-dependent production of mitochondrial superoxide was also observed. This study is the first to have demonstrated that polymyxin-induced apoptosis is mediated through both the death receptor and mitochondrial pathways in cultured renal tubular cells. It provides key information not only for the amelioration of polymyxin-induced nephrotoxicity but also for the discovery of novel safer polymyxin-like antibiotics against Gram-negative "superbugs."

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Basic Image Analysis and Manipulation in ImageJ

Cited by 285 publications

References 7 publications

Epicardial YAP/TAZ orchestrate an immunosuppressive response following myocardial infarction

Epicardial YAP/TAZ orchestrate an immunosuppressive response following myocardial infarction

Biochemical characterization and essentiality of fumarate hydratase

Major Pathways of Polymyxin-Induced Apoptosis in Rat Kidney Proximal Tubular Cells

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