An Efficient Statistic for Determining the Diameter of Thin Sectioned Uniform Spheres from Measurements of Biological Samples

1974 ◽  
Vol 32 ◽  
pp. 114-115
Author(s):  
W. R. Schucany ◽  
G. H. Kelsoe ◽  
V. F. Allison
Keyword(s):  
Biological Samples ◽  
Traditional Method ◽  
Cell Types ◽  
Accurate Estimation ◽  
Morphological Identification ◽  
Sectioned Material ◽  
Maximal Diameter ◽  
Similar Cell

Accurate estimation of the size of spheroid organelles from thin sectioned material is often necessary, as uniquely homogenous populations of organelles such as vessicles, granules, or nuclei often are critically important in the morphological identification of similar cell types. However, the difficulty in obtaining accurate diameter measurements of thin sectioned organelles is well known. This difficulty is due to the extreme tenuity of the sectioned material as compared to the size of the intact organelle. In populations where low variance is suspected the traditional method of diameter estimation has been to measure literally hundreds of profiles and to describe the “largest” as representative of the “approximate maximal diameter”.

scholarly journals Hyperspectral imaging-based exosome microarray for rapid molecular profiling of extracellular vesicles

Lab on a Chip ◽  
2021 ◽  
Vol 21 (1) ◽  
pp. 196-204
Author(s):  
Yifei Wang ◽  
Qinming Zhang ◽  
Wang Yuan ◽  
Yixuan Wang ◽  
Hannah J. Loghry ◽  
...  
Keyword(s):  
Hyperspectral Imaging ◽  
Extracellular Vesicles ◽  
High Throughput ◽  
Hyperspectral Image ◽  
Cell Types ◽  
Molecular Profiling ◽  
Microarray Technology ◽  
Similar Cell

A high-throughput hyperspectral image-based exosome (EV) microarray technology to differentiate EVs released by similar cell types or phenotypes.

Gene expression analysis of osteoblasts and calcifying vascular cells: Similar cell types or similar mechanisms?

Bone ◽  
2011 ◽  
Vol 48 ◽  
pp. S119
Author(s):  
R.D.A.M. Alves⁎ ◽  
M. Koedam ◽  
J. van de Peppel ◽  
M. Eijken ◽  
J.P.T.M. van Leeuwen
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Cell Types ◽  
Vascular Cells ◽  
Similar Cell ◽  
Calcifying Vascular Cells

scholarly journals OSCAR: a framework to identify and quantify cells in densely packed three-dimensional biological samples

2021 ◽  
Author(s):  
Mario ledesma-terron ◽  
Diego perez-dones ◽  
david G Miguez
Keyword(s):  
Biological Samples ◽  
Object Segmentation ◽  
Three Dimensional ◽  
Cell Types ◽  
Biological Tissues ◽  
Nuclear Marker ◽  
Quantitative Characterization ◽  
3D Space ◽  
Immunofluorescence Labeling

We have developed an Object Segmentation, Counter and Analysis Resource (OSCAR) that is designed specifically to quantify densely packed biological samples with reduced signal-to-background ratio. OSCAR uses as input three dimensional images reconstructed from confocal 2D sections stained with dies such as nuclear marker and immunofluorescence labeling against specific antibodies to distinguish the cell types of interest. Taking advantage of a combination of arithmetic, geometric and statistical algorithms, OSCAR is able to reconstruct the objects in the 3D space bypassing segmentation errors due to the typical reduced signal to noise ration of biological tissues imaged in toto. When applied to the zebrafish developing retina, OSCAR is able to locate and identify the fate of each nuclei as a cycling progenitor or a terminally differentiated cell, providing a quantitative characterization of the dynamics of the developing vertebrate retina in space and time with unprecedented accuracy.

Phase Contrast Microscopy with Modified Hansel's Staining: Mast Cell Identification and Activity-Related Changes in Cell Membrane Refractivity in Allergic Nasal Smears

2003 ◽  
Vol 17 (2) ◽  
pp. 101-106
Author(s):  
Masatoshi Masuko ◽  
Fumiyuki Goto
Keyword(s):  
Cell Membrane ◽  
Phase Contrast ◽  
Early Stage ◽  
Japanese Cedar ◽  
Cell Types ◽  
New Technique ◽  
Morphological Identification ◽  
Phase Contrast Microscopy ◽  
Contrast Microscopy ◽  
Japanese Cedar Pollinosis

Background A new technique called phase contrast microscopy with modified Hansel's staining (used with bright field microscopy) was developed to identify mast cells (MCs) and granulocytes (eosinophil/neutrophil/basophil [E/N/B]). Methods Nasal scratching smears from 618 patients with Japanese cedar pollinosis were examined using this new technique. Results This technique permitted accurate morphological identification. MCs can be discriminated from E/N/Bs. The surface of the cell membrane appeared as low refractile (lr), moderately refractile (mr), or high refractile (hr). This was caused by the light, which is not related to the phase difference, but rather originated from the difference in the refraction of the direct light. In specimens from the onset stage (i.e., 1–3 days after onset), lr-MC and mr/hr-E/N/B were dominant. In specimens from the early stage (i.e., 4–7 days after onset), lr-E/N/B significantly increased in number. Conclusion The phospholipid bilayers of the cell membrane exhibit a phase transition after the onset, and phase refractivity of the cell membrane is closely related to the activity of the cell. This indicates that in the onset stage, MCs are already activated, whereas most of the E/N/Bs are not. In contrast, the latter cell types become activated subsequently in the early stage.

Separation of two phenotypically similar cell types via a single common marker in microfluidic channels

Lab on a Chip ◽  
2012 ◽  
Vol 12 (18) ◽  
pp. 3399 ◽  
Author(s):  
Dwayne A. L. Vickers ◽  
Emma J. Chory ◽  
Shashi K. Murthy
Keyword(s):  
Cell Types ◽  
Microfluidic Channels ◽  
Common Marker ◽  
Similar Cell

scholarly journals Tannic acid-stained microtubules with 12, 13, and 15 protofilaments

1975 ◽  
Vol 65 (1) ◽  
pp. 227-233 ◽  
Author(s):  
PR Burton ◽  
RE Hinkley ◽  
GB Pierson
Keyword(s):  
Cross Section ◽  
Tannic Acid ◽  
Nerve Cord ◽  
Ventral Nerve Cord ◽  
Cell Types ◽  
Subunit Structure ◽  
Meristematic Cells ◽  
Sectioned Material ◽  
Cytoplasmic Microtubules ◽  
Neuronal Systems

Subunit structure in the walls of sectioned microtubules was first noted by Ledbetter and Porter (6), who clearly showed that certain microtubules of plant meristematic cells have 13 wall protofilaments when seen in cross section. Earlier, protofilaments of microtubular elements had been described in negatively stained material, although exact counts of their number were difficult to obtain. In microtubular elements of axonemes, some success has been achieved in visualizing protofilaments in conventionally fixed and sectioned material (8, 10); much less success has been achieved in identifying and counting protofilaments of singlet cytoplasmic microtubules. By using glutaraldehyde-tannic acid fixation, as described by Misuhira and Futaesaku (7), Tilney et al. (12) studied microtubules from a number of sources and found that all have 13 protofilaments comprising their walls. These authors note that "...the number of subunits and their arrangement as protofilaments appear universal...". Preliminary studies of ventral nerve cord of crayfish fixed in glutaraldehyde-tannic acid indicated that axonal microtubules in this material possess only 12 protofilaments (4). On the basis of this observation, tannic acid preparations of several other neuronal and non-neuronal systems were examined. Protofilaments in microtubules from these several cell types are clearly demonstrated, and counts have been made which show that some kinds of microtubules have more or fewer protofilaments than the usual 13 and that at least one kind of microtubule has an even rather than an odd number.

scholarly journals A minibead method for detection of membrane lectins.

1989 ◽  
Vol 37 (1) ◽  
pp. 91-96 ◽  
Author(s):  
T Matsuoka ◽  
M Tavassoli
Keyword(s):  
Soluble Sugar ◽  
Cell Types ◽  
Cell Populations ◽  
Morphological Identification ◽  
Cell Systems ◽  
Biological Phenomena ◽  
Homogeneous Cell ◽  
Different Cell Types ◽  
Derivatives Of ◽  
Scanning Electron

Membrane lectins are being increasingly implicated in many biological phenomena. Previous methods for detection of these substances are applicable only to homogeneous cell populations. We have now developed a method that permits morphological identification of lectin-bearing cells in heterogeneous cell populations. Amide-modified latex minibeads (0.345 or 0.532 micron) were activated with glutaraldehyde and then covalently bound to p-aminophenyl derivatives of various sugars. When the probe thus constructed was incubated with cell systems known to bear well-defined membrane lectins (galactosyl receptors in hepatocytes, mannosyl receptors in macrophages), binding occurred and could be visualized by scanning electron microscopy. Binding was inhibited in the presence of excess soluble sugar, indicating the specificity of reaction. Incubation of a mixture of two different-sized probes with two different cell types led to segregation of the probes. This method also permits semiquantification of binding.

scholarly journals Method: Isolation of Epithelial Cell RNA from Frozen Jejunum Segments While Minimizing Smooth Muscle Cell RNA Contamination

2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1182-1182
Author(s):  
Shumao Ye ◽  
Nirupa Matthan ◽  
Stefania Lamon-Fava ◽  
Gloria Solano-Aguilar ◽  
Jerrold Turner ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Epithelial Cell ◽  
Smooth Muscle Cells ◽  
Traditional Method ◽  
Rna Isolation ◽  
Current Method ◽  
Muscle Cells ◽  
Cell Types ◽  
Enrichment Score ◽  
Rna Quality

Abstract Objectives High RNA quality is a prerequisite for accurate PCR and sequencing results. Dissecting a specific tissue fraction from frozen samples while maintaining RNA quality is challenging. Starting with frozen pig jejunum segments, we describe a novel method to isolate epithelial cell RNA while minimizing contamination with smooth muscle cell RNA. Methods Jejunum tissue segments from Ossabaw pigs (N = 30) were snap-frozen in liquid nitrogen upon harvest from a diet-statin study and stored at −80°C. At the time of RNA isolation samples were incubated in prechilled RNAlater-ICE at −20°C for 24 hours, opened longitudinally, and epithelium cleanly separated from the muscle layer using a scalpel and tweezers. Total RNA was extracted from the epithelium using TRI-reagent. RNA Quality Indicator (RQI) of total RNA was measured using Experion RNA StdSens Analysis kit. RNA-sequencing was performed on Illumina NextSeq 500 platform. Raw sequencing data were aligned to the domestic pig (sus scrofa 11.1) reference genome and applied to subsequent analyses. xCell, a gene signature-based tool trained by thousands of single cell types from various sources, was used to estimate enrichment of epithelial cells (target) and smooth muscle cells (contamination) across samples. A Student t-test was used to compare the enrichment scores of these two cell types between the current method and a traditional method (small jejunal pieces collected at necropsy and stored frozen until RNA isolation). Results RQI ranged from 8.6 to 9.7, above the standard for RNA sequencing (RQI > 8). The enrichment score of epithelial cells was significantly higher in the current method (mean = 0.030, SD = 0.006) compared to the traditional method (mean = 0.016, SD = 0.013) (P < 0.0001). The enrichment score of smooth muscle cells was significantly lower in the current method (mean = 0.043, SD = 0.035) compared to the traditional method (mean = 0.13, SD = 0.093) (P < 0.0001). Conclusions The current method effectively maintained RNA quality and minimized contamination of epithelial with smooth muscle cells. This method may be applicable to other frozen archived tissues that require a single tissue source of RNA. Funding Sources USDA-ARS-NEA, JM-USDA-HNRCA, and Tufts University.

Nitrogen estimation in biological samples by use of chemiluminescence.

1980 ◽  
Vol 26 (9) ◽  
pp. 1336-1339 ◽  
Author(s):  
M W Ward ◽  
C W Owens ◽  
M J Rennie
Keyword(s):  
Renal Failure ◽  
Renal Function ◽  
Nitrogen Balance ◽  
Biological Samples ◽  
Traditional Method ◽  
Surgical Patients ◽  
Clinical Samples ◽  
Chemiluminescence Method ◽  
Chemical Substances ◽  
Kjeldahl Method

Abstract We describe an apparatus modified for the chemiluminescent estimation of nitrogen in biological and clinical samples. Analytical characteristics have been assessed and results compared with those by the traditional Kjeldahl method. The chemiluminescence method, much faster and more sensitive than the traditional method, is at least as accurate, precise, and reproducible. Costs are low, and the method should find a place in laboratories needing, for example, rapid assessments of nitrogen balance in surgical patients and renal function in patients with renal failure, or estimations of small amounts of specific nitrogen-containing chemical substances in biological samples.

scholarly journals Accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments

2017 ◽  
Author(s):  
Viktor Petukhov ◽  
Jimin Guo ◽  
Ninib Baryawno ◽  
Nicolas Severe ◽  
David Scadden ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Biological Tissues ◽  
Droplet Microfluidics ◽  
Accurate Estimation ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Sequencing Errors ◽  
Powerful Means

AbstractSingle-cell RNA-seq protocols provide powerful means for examining the gamut of cell types and transcriptional states that comprise complex biological tissues. Recently-developed approaches based on droplet microfluidics, such as inDrop or Drop-seq, use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data also creates challenges for subsequent computational processing and troubleshooting of these experiments, with few software options currently available. Here we describe a flexible pipeline for processing droplet-based transcriptome data that implements barcode corrections, classification of cell quality, and diagnostic information about the droplet libraries. We introduce advanced methods for correcting composition bias and sequencing errors affecting cellular and molecular barcodes to provide more accurate estimates of molecular counts in individual cells.

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