Colocalization of dihydropyridine (DHPR) and ryanodine (RyR) receptors, a key determinant of Ca(2+)-induced Ca2+ release, was previously estimated in 3-, 6-, 10-, and 20-day-old rabbit ventricular myocytes by immunocytochemistry and confocal microscopy. We now report on the effects of deconvolution (using a maximum-likelihood estimation algorithm) on the calculation of colocalization indexes. Clusters of DHPR and RyR can be accurately represented as point sources of fluorescence, which enables a model of their relative distributions to be constructed using images of point spread functions to simulate their fluorescence inside a cell. This model was used to investigate the effects of deconvolution on colocalization as a function of separation distance. Deconvolution resulted in significant improvements in both axial and transverse resolutions, producing significant increases in clarity. Comparisons of intensity profiles (full-width half-maximum) pre- and postdeconvolution showed decreased dispersion of the fluorescent signal and a corresponding decrease in false colocalization as determined by fluorescence modeling. This hypothesis was extended to physiological data previously collected. The number of colocalized voxels was quantified after deconvolution, and the degree of colocalization of DHPR with RyR decreased significantly after deconvolution in all age groups: 3 days (62 +/- 2% before deconvolution, 43 +/- 3 after deconvolution) to 20 days old (79 +/- 1% before deconvolution, 63 +/- 2% after deconvolution). The data demonstrate that confocal images should be deconvolved before any quantitative analysis, such as colocalization index determination, to minimize the detrimental effects of out-of-focus light in coincident voxels.
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http://dx.doi.org/10.1152/japplphysiol.00089.2004 | DOI Listing |
J Am Soc Mass Spectrom
January 2025
Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland, 20899, United States.
The Mass Spectrometry Data Center (MSDC) has recently started improving existing libraries and creating new ones for identifying and analyzing plastics-related compounds (PRC) and materials (PRM) as part of the NIST circular economy program. PRC are small molecules of dissimilar chemical nature; hence, to increase coverage, we have used three types of ionizations: EI, ESI, and APCI. PRM are solids that include polymers, polymer mixtures, and commercial plastics, so we have used pyrolysis-gas chromatography (py-GC-MS) to create a new searchable library.
View Article and Find Full Text PDFCancer Immunol Immunother
January 2025
Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Tampere, Finland.
The tumor immune microenvironment (TiME) of human central nervous system (CNS) tumors remains to be comprehensively deciphered. Here, we employed flow cytometry and RNA sequencing analysis for a deep data-driven dissection of a diverse TiME and to uncover noncanonical immune cell types in human CNS tumors by using seven tumors from five patients. Myeloid subsets comprised classical microglia, monocyte-derived macrophages, neutrophils, and two noncanonical myeloid subsets: CD3 myeloids and CD19 myeloids.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Columbia University Irving Medical Center, New York, NY, USA.
Background: Glial cells exhibit distinct transcriptional responses to β-amyloid pathology in Alzheimer's disease (AD). While sophisticated single-cell based methods have revealed heterogeneous glial subpopulations in the human AD brain, the histological localization of these multicellular responses to AD pathology has not been fully characterized due to the loss of spatial information. Here, we combined spatial transcriptomics (ST) with immunohistochemistry to explore the molecular mechanisms in the neuritic plaque niche.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
Background: Progressive supranuclear palsy (PSP) is a neurodegenerative disorder involving pathological deposition of tau that includes glial inclusions and specific regional vulnerability patterns. Therapeutic developments are hampered by incomplete understanding of disease mechanisms. Few studies have examined its cell type-specific effects.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Cleveland Clinic, Cleveland, OH, USA.
Background: Cell-type specific expression quantitative trait loci (eQTLs) can help dissect cellular heterogeneity in the impact of genetic variation on gene expression for Alzheimer's disease (AD) and AD-related dementia (ADRD). However, due to the high cost and stringent sample collection criteria, it is challenging to obtain large single-nuclei RNA sequencing (snRNA-seq) data with sufficient cohort size to match genotyping data to systematically identify human brain-specific eQTLs for AD/ADRD.
Method: In this study, we presented a deep learning-based deconvolution framework on large-scale bulk RNA sequencing (RNA-seq) data to infer cell-type specific eQTLs in the human brains with AD/ADRD.
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