scholarly journals Cortical Cell Types and their Distribution in Wool Fibres

1984 ◽  
Vol 37 (4) ◽  
pp. 237 ◽  
Author(s):  
Donald FG Orwin ◽  
Joy L Woods ◽  
Stephen L Ranford
Keyword(s):  
Cross Section ◽  
Cortical Cell ◽  
Cell Types ◽  
Blue Staining ◽  
Cell Type ◽  
Predominant Cell Type ◽  
Percentage Area ◽  
Log Linear ◽  
The Relationship ◽  
Linear Manner

A method of determining cell types in wool fibres by methylene-blue staining has been extended to allow relationships between cortical cell type and cortical diameter to be studied in wools from individual sheep. Application of the method to wools from 12 sheep from six breeds showed that orthocortical cells were the predominant cell type produced. The percentage area occupied by orthocortical cells in a fibre cross-section increased with increasing cortical diameter in either a curvilinear (log-linear) or a linear manner. Nutritional stress or season may have affected the relationship in some sheep.

Varied interactions between proviruses and adjacent host chromatin

1986 ◽  
Vol 6 (11) ◽  
pp. 3999-4007
Author(s):  
K F Conklin ◽  
M Groudine
Keyword(s):  
Cell Types ◽  
Chromatin Conformation ◽  
Cell Type ◽  
Chromatin Domains ◽  
Site Structure ◽  
The Relationship ◽  
Structure And Activity ◽  
Different Levels ◽  
Host Chromatin ◽  
Nuclease Sensitivity

Retroviruses integrated at unique locations in the host genome can be expressed at different levels. We have analyzed the preintegration sites of three transcriptionally competent avian endogenous proviruses (evs) to determine whether the various levels of provirus expression correlate with their location in active or inactive regions of chromatin. Our results show that in three of four cell types, the chromatin conformation (as defined by relative nuclease sensitivity) of virus preintegration sites correlates with the level of expression of the resident provirus in ev+ cells: two inactive proviruses (ev-1 and ev-2) reside in nuclease-resistant chromatin domains and one active provirus (ev-3) resides in a nuclease-sensitive domain. Nuclear runoff transcription assays reveal that the preintegration sites of the active and inactive viruses are not transcribed. However, in erythrocytes of 15-day-old chicken embryos (15d RBCs), the structure and activity of the ev-3 provirus is independent of the conformation of its preintegration site. In this cell type, the ev-3 preintegration site is organized in a nuclease-resistant conformation, while the ev-3 provirus is in a nuclease-sensitive conformation and is transcribed. In addition, the nuclease sensitivity of host sequences adjacent to ev-3 is altered in ev-3+ 15d RBCs relative to that found in 15d RBCs that lack ev-3. These data suggest that the relationship between preintegration site structure and retrovirus expression is more complex than previously described.

SOME OBSERVATIONS ON THE ULTRASTRUCTURE OF THE ADENOHYPOPHYSIS OF THE RABBIT

1965 ◽  
Vol 31 (3) ◽  
pp. 279-287 ◽  
Author(s):  
B. A. YOUNG ◽  
C. L. FOSTER ◽  
E. CAMERON
Keyword(s):  
Granular Cell ◽  
Pars Intermedia ◽  
Pars Tuberalis ◽  
Pars Distalis ◽  
Cell Type ◽  
Cytoplasmic Rna ◽  
Large Numbers ◽  
Predominant Cell Type ◽  
Relationship Of ◽  
The Relationship

SUMMARY The ultrastructure of the adenohypophysis of the rabbit is described preliminary to reporting changes after experimental procedures. Fixation by perfusing with gluteraldehyde enabled selected regions of the gland to be removed with accuracy. Separate descriptions of the pars distalis proper, zona tuberalis, pars tuberalis and pars intermedia are therefore included. In the pars distalis proper four types of granular cell were recognized although their function cannot be accurately determined. For convenience, therefore, they have been designated 1, 2, 3 and 4. In addition a fifth type of cell (type 5) is described which is also present in the other areas. This cell, as well as having possible phagocytic functions, appears to be concerned in the formation of a perivascular channel. Two types of cell are recognized in the zona tuberalis, which are similar in appearance to the 3 and 4 cells of the pars distalis, although not necessarily identical in function. The characteristic cells of the pars tuberalis are rich in cytoplasmic RNA and contain large numbers of intracellular fibrils. It is suggested that the ribosomes are concerned in the synthesis of a sedentary protein which may take the form of the microfibrils. The pars intermedia contains a predominant cell type with large granules of varying density. The relationship of these granules to the specific hormone is discussed.

scholarly journals Accurate imputation of histone modifications using transcription

2020 ◽  
Author(s):  
Zhong Wang ◽  
Alexandra G. Chivu ◽  
Lauren A. Choate ◽  
Edward J. Rice ◽  
Donald C. Miller ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Cell Type ◽  
Active Chromatin ◽  
Histone Marks ◽  
Repressive Mark ◽  
Cell Type Specific ◽  
The Relationship ◽  
Machine Learning Tool

AbstractWe trained a sensitive machine learning tool to infer the distribution of histone marks using maps of nascent transcription. Transcription captured the variation in active histone marks and complex chromatin states, like bivalent promoters, down to single-nucleosome resolution and at an accuracy that rivaled the correspondence between independent ChIP-seq experiments. The relationship between active histone marks and transcription was conserved in all cell types examined, allowing individual labs to annotate active functional elements in mammals with similar richness as major consortia. Using imputation as an interpretative tool uncovered cell-type specific differences in how the PRC2-dependent repressive mark, H3K27me3, corresponds to transcription, and revealed that transcription initiation requires both chromatin accessibility and an active chromatin environment demonstrating that initiation is less promiscuous than previously thought.

scholarly journals Automatic identification of informative regions with epigenomic changes associated to hematopoiesis

2016 ◽  
Author(s):  
Enrique Carrillo-de-Santa-Pau ◽  
David Juan ◽  
Vera Pancaldi ◽  
Felipe Were ◽  
Ignacio Martin-Subero ◽  
...  
Keyword(s):  
Cell Lineage ◽  
Cell Types ◽  
Automatic Identification ◽  
Epigenetic Alterations ◽  
Cell Type ◽  
Lineage Differentiation ◽  
Orthogonal Dimension ◽  
Genomic Regions ◽  
The Relationship ◽  
Nih Roadmap

AbstractHematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate a chromatin space that allows to classify forty-two human healthy blood epigenomes from the BLUEPRINT, NIH ROADMAP and ENCODE consortia by their cell type. This approach let us to distinguish different cells types based on their epigenomic profiles, thus recapitulating important aspects of human hematopoiesis. The analysis of the orthogonal dimension of the chromatin space identify 32,662 chromatin determinant regions (CDRs), genomic regions with different epigenetic characteristics between the cell types. Functional analysis revealed that these regions are linked with cell identities. The inclusion of leukemia epigenomes in the healthy hematological chromatin sample space gives us insights on the healthy cell types that are more epigenetically similar to the disease samples. Further analysis of tumoral epigenetic alterations in hematopoietic CDRs points to sets of genes that are tightly regulated in leukemic transformations and commonly mutated in other tumors. Our method provides an analytical approach to study the relationship between epigenomic changes and cell lineage differentiation. Method availability: https://github.com/david-juan/ChromDet

scholarly journals Differential DNA methylation and changing cell-type proportions as fibrotic stage progresses in NAFLD

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Nicholas D. Johnson ◽  
Xiumei Wu ◽  
Christopher D. Still ◽  
Xin Chu ◽  
Anthony T. Petrick ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Types ◽  
Disease Stage ◽  
Rna Seq ◽  
Cell Type ◽  
Alcoholic Fatty Liver ◽  
Cell Composition ◽  
Cpg Sites ◽  
Plausible Mechanism ◽  
The Relationship

Abstract Background Non-alcoholic fatty liver disease (NAFLD) is characterized by changes in cell composition that occur throughout disease pathogenesis, which includes the development of fibrosis in a subset of patients. DNA methylation (DNAm) is a plausible mechanism underlying these shifts, considering that DNAm profiles differ across tissues and cell types, and DNAm may play a role in cell-type differentiation. Previous work investigating the relationship between DNAm and fibrosis in NAFLD has been limited by sample size and the number of CpG sites interrogated. Results Here, we performed an epigenome-wide analysis using Infinium MethylationEPIC array data from 325 individuals with NAFLD, including 119 with severe fibrosis and 206 with no histological evidence of fibrosis. After adjustment for latent confounders, we identified 7 CpG sites whose DNAm associated with fibrosis (p < 5.96 × 10–8). Analysis of RNA-seq data collected from a subset of individuals (N = 56) revealed that gene expression at 288 genes associated with DNAm at one or more of the 7 fibrosis-related CpGs. DNAm-based estimates of cell-type proportions showed that estimated proportions of natural killer cells increased, while epithelial cell proportions decreased with disease stage. Finally, we used an elastic net regression model to assess DNAm as a biomarker of fibrotic stage and found that our model predicted fibrosis with a sensitivity of 0.93 and provided information beyond a model based solely on cell-type proportions. Conclusion These findings are consistent with DNAm as a mechanism underpinning or marking fibrosis-related shifts in cell composition and demonstrate the potential of DNAm as a possible biomarker of NAFLD fibrosis.

scholarly journals Comprehensive in situ mapping of human cortical transcriptomic cell types

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Christoffer Mattsson Langseth ◽  
Daniel Gyllborg ◽  
Jeremy A. Miller ◽  
Jennie L. Close ◽  
Brian Long ◽  
...  
Keyword(s):  
Brain Function ◽  
Cortical Cell ◽  
Cell Types ◽  
Cell Type ◽  
Cortical Cells ◽  
Human Cortex ◽  
Single Nucleus ◽  
Genetic Signatures ◽  
Cell Typing

AbstractThe ability to spatially resolve the cellular architecture of human cortical cell types over informative areas is essential to understanding brain function. We combined in situ sequencing gene expression data and single-nucleus RNA-sequencing cell type definitions to spatially map cells in sections of the human cortex via probabilistic cell typing. We mapped and classified a total of 59,816 cells into all 75 previously defined subtypes to create a first spatial atlas of human cortical cells in their native position, their abundances and genetic signatures. We also examined the precise within- and across-layer distributions of all the cell types and provide a resource for the cell atlas community. The abundances and locations presented here could serve as a reference for further studies, that include human brain tissues and disease applications at the cell type level.

scholarly journals Saturating Single-Cell atlas Datasets

2017 ◽  
Author(s):  
Aparna Bhaduri ◽  
Tomasz J. Nowakowski ◽  
Alex A. Pollen ◽  
Arnold R. Kriegstein
Keyword(s):  
Population Structure ◽  
Single Cell ◽  
Mouse Brain ◽  
Large Scale ◽  
Single Cells ◽  
Cost Effective ◽  
Cell Types ◽  
Cell Number ◽  
Cell Type ◽  
The Relationship

AbstractHigh throughput methods for profiling the transcriptomes of single cells have recently emerged as transformative approaches for large-scale population surveys of cellular diversity in heterogeneous primary tissues. Efficient generation of such an atlas will depend on sufficient sampling of the diverse cell types while remaining cost-effective to enable a comprehensive examination of organs, developmental stages, and individuals. To examine the relationship between cell number and transcriptional heterogeneity in the context of unbiased cell type classification, we explicitly explored the population structure of a publically available 1.3 million cell dataset from the E18.5 mouse brain. We propose a computational framework for inferring the saturation point of cluster discovery in a single cell mRNA-seq experiment, centered around cluster preservation in downsampled datasets. In addition, we introduce a “complexity index”, which characterizes the heterogeneity of cells in a given dataset. Using Cajal-Retzius cells as an example of a limited complexity dataset, we explored whether biological distinctions relate to technical clustering. Surprisingly, we found that clustering distinctions carrying biologically interpretable meaning are achieved with far fewer cells (20,000). Together, these findings suggest that most of the biologically interpretable insights from the 1.3 million cells can be recapitulated by analyzing 50,000 randomly selected cells, indicating that instead of profiling few individuals at high “cellular coverage”, the much anticipated cell atlasing studies may instead benefit from profiling more individuals, or many time points at lower cellular coverage.Recent efforts seek to create a comprehensive cell atlas of the human body1,2 Current technology, however, makes it precipitously expensive to perform analysis of every cell. Therefore, designing effective sampling strategies be critical to generate a working atlas in an efficient, cost-effective, and streamlined manner. The advent of single cell and single nucleus mRNA sequencing (RNAseq) in droplet format3,4 now enables large scale sampling of cells from any tissue, and a recently released publicly available dataset of 1.3 million single cells from the E18.5 mouse brain generated with the 10X Chromium5 provides an opportunity to explore the relationship between population structure and the number of sampled cells necessary to reveal the underlying diversity of cell types. Here, we present a framework for how researchers can evaluate whether a dataset has reached saturation, and we estimate how many cells would be required to generate an atlas of the sample analyzed here. This framework can be applied to any organ or cell type specific atlas for any organism.

scholarly journals Varied interactions between proviruses and adjacent host chromatin.

1986 ◽  
Vol 6 (11) ◽  
pp. 3999-4007 ◽  
Author(s):  
K F Conklin ◽  
M Groudine
Keyword(s):  
Cell Types ◽  
Chromatin Conformation ◽  
Cell Type ◽  
Chromatin Domains ◽  
Site Structure ◽  
The Relationship ◽  
Structure And Activity ◽  
Different Levels ◽  
Host Chromatin ◽  
Nuclease Sensitivity

Retroviruses integrated at unique locations in the host genome can be expressed at different levels. We have analyzed the preintegration sites of three transcriptionally competent avian endogenous proviruses (evs) to determine whether the various levels of provirus expression correlate with their location in active or inactive regions of chromatin. Our results show that in three of four cell types, the chromatin conformation (as defined by relative nuclease sensitivity) of virus preintegration sites correlates with the level of expression of the resident provirus in ev+ cells: two inactive proviruses (ev-1 and ev-2) reside in nuclease-resistant chromatin domains and one active provirus (ev-3) resides in a nuclease-sensitive domain. Nuclear runoff transcription assays reveal that the preintegration sites of the active and inactive viruses are not transcribed. However, in erythrocytes of 15-day-old chicken embryos (15d RBCs), the structure and activity of the ev-3 provirus is independent of the conformation of its preintegration site. In this cell type, the ev-3 preintegration site is organized in a nuclease-resistant conformation, while the ev-3 provirus is in a nuclease-sensitive conformation and is transcribed. In addition, the nuclease sensitivity of host sequences adjacent to ev-3 is altered in ev-3+ 15d RBCs relative to that found in 15d RBCs that lack ev-3. These data suggest that the relationship between preintegration site structure and retrovirus expression is more complex than previously described.

Lung redox homeostasis: emerging concepts

2000 ◽  
Vol 279 (3) ◽  
pp. L413-L417 ◽  
Author(s):  
Marilyn P. Merker ◽  
Bruce R. Pitt ◽  
Augustine M. Choi ◽  
Paul M. Hassoun ◽  
Christopher A. Dawson ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Electron Transport ◽  
Nadph Oxidase ◽  
Redox Homeostasis ◽  
Cell Types ◽  
Xanthine Dehydrogenase ◽  
Zinc Binding ◽  
Cell Type ◽  
Predominant Cell Type ◽  
Lung Endothelium

This symposium was organized to present some aspects of current research pertaining to lung redox function. Focuses of the symposium were on roles of pulmonary endothelial NADPH oxidase, xanthine oxidase (XO)/xanthine dehydrogenase (XDH), heme oxygenase (HO), transplasma membrane electron transport (TPMET), and the zinc binding protein metallothionein (MT) in the propagation and/or protection of the lung or other organs from oxidative injury. The presentations were chosen to reflect the roles of both intracellular (metallothionein, XO/XDH, and HO) and plasma membrane (NADPH oxidase, XO/XDH, and unidentified TPMET) redox proteins in these processes. Although the lung endothelium was the predominant cell type under consideration, at least some of the proposed mechanisms operate in or affect other cell types and organs as well.

Distribution of leucocyte populations, and milk composition, in milk fractions of healthy quarters in dairy cows

2005 ◽  
Vol 72 (4) ◽  
pp. 486-492 ◽  
Author(s):  
Hande Sarikaya ◽  
Claudia Werner-Misof ◽  
Melanie Atzkern ◽  
Rupert M Bruckmaier
Keyword(s):  
Dairy Cows ◽  
Cell Types ◽  
Milk Composition ◽  
Polymorphonuclear Neutrophils ◽  
Cell Type ◽  
Maximum Value ◽  
Predominant Cell Type ◽  
Teat Canal ◽  
Main Entrance

The goal of the study was to evaluate the composition of leucocyte populations in different milk fractions as a basis on which to judge their possible role in the immune response in different compartments of the udder. The milk of one healthy quarter of nine dairy cows (SCC/quarter [les ]125000/ml; bacteriologically negative) was removed separately and during the course of milking divided into: cisternal milk (C), alveolar milk 0–25%, 25–50%, 50–75%, 75–100% (A25; A50; A75; A100, respectively) and residual milk (R). Each fraction was analysed for the main constituents, SCC and distribution of leucocyte populations and their viability. The content of fat increased steadily during milking and reached highest values in R. Protein and lactose increased from C to A25, decreased from A25 to A100 and reached their minimum in R. Na and Cl ion levels diminished from C to A25 and thereafter increased from A50 to R. Electrical Conductivity (EC) also decreased from C to A25 but remained similar within the alveolar samples and reached a minimum in R. SCC decreased from C to a minimum in A25 and increased subsequently to a significant maximum in R. Somatic cell viability increased throughout consecutive fractions with a maximum value in R. The ratio of cell populations in the various milk fractions showed a reverse trend of macrophages (M) and polymorphonuclear neutrophils (PMN). M values were highest in C while PMN levels increased to their maximum in the R fraction. The lymphocyte (L) fraction remained similar in C, A25, A50, A75 and R but was higher in A100. Proportions of L, PMN and M were, respectively, 9·3%, 38·2%, 52·3% in C, 10·9%, 64%, 25·1% in A25–A100 and 10·2%, 64·9%, 24·8% in R. Numbers of L, PMN and M in milk showed a similar pattern for all three cell types: high levels in C decreased to a minimum at A25 and increased steadily thereafter to their maxima in R. It is concluded that, for healthy quarters, M, the predominant cell type in C, are located near the teat canal, the main entrance of pathogens. Obviously they are the first immunological barriers for invading pathogens. In contrast, PMN are the most important population in the alveolar compartment. However, each leucocyte fraction had a higher concentration in C than in early alveolar fractions, thus indicating the crucial role of immune defence in the cisternal compartment.

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