The analysis of spatial distributions in mixed cell populations: a statistical method for detecting sorting out

Development ◽  
1971 ◽  
Vol 26 (1) ◽  
pp. 135-156
Author(s):  
R. A. Elton ◽  
C. A. Tickle
Keyword(s):  
Plant Communities ◽  
Quantitative Measure ◽  
Cell Types ◽  
Limb Bud ◽  
Cell Populations ◽  
Spatial Distributions ◽  
Mixed Cell ◽  
Mixed Aggregates ◽  
Chick Heart ◽  
Gyratory Shaker

1. This work presents a quantitative measure, α, of the degree of segregation of two cell types in sections of aggregates, and some results obtained with the measure relating to ‘sorting out’. The method is designed particularly for the case where labelling of one type of cell is incomplete, and the importance of this effect is assessed. Possible problems in formulating such a model are discussed. The measure α is compared with methods used in investigations of segregation in plant communities. 2. Segregation of chick heart and limb-bud cells in mixed aggregates has been analysed using α. In control aggregates of mixtures of labelled and unlabelled cells of one type, α is near to its random value of 1, and we suggest that the departure from random can be adequately accounted for by cell division. In mixed aggregates, significant segregation is consistently found, even in aggregates formed after 2 and 4 h. Both disaggregation procedures (EDTA, trypsin or trypsin + EDTA) and reaggregation methods (reciprocating or gyratory shaker) are found to have an effect on the degree of segregation. Possible reasons for these findings are discussed. 3. Positioning of the cells relative to the outside of aggregates is also investigated for some of the aggregates.

Cell contacts and sorting out in vivo: the behaviour of some embryonic tissues implanted into the developing chick wing

Development ◽  
1978 ◽  
Vol 48 (1) ◽  
pp. 225-237
Author(s):  
C. Tickle ◽  
M. Goodman ◽  
L. Wolpert
Keyword(s):  
Neural Tube ◽  
Cell Types ◽  
Neural Retina ◽  
Limb Bud ◽  
Embryonic Liver ◽  
Malignant Cells ◽  
Embryonic Tissues ◽  
Mixed Aggregates ◽  
Wing Bud

The interaction of cells from embryonic liver, neural retina and mesonephros with cells from limb-bud mesenchyme has been investigated in vivo by grafting these tissues into the developing chick wing-bud. The implanted cells were in all cases from quail tissue which can be recognized histologically. As embryonic liver and neural tube are tissues that sort externally to limb-bud mesenchyme in mixed aggregates, it would be expected, from a differential adhesiveness hypothesis, that heterotypic adhesions along the borders of graft and host would be favoured over cell-cell adhesions in the graft. No morphological signs of this were evident: rather the grafted cells maximized like-like contacts. The cells of the grafts, including those from control mesenchyme, did not invade into the wing. The results were the same irrespective of whether the graft was a fragment of tissue or a pellet of reaggregated cells. This supports the idea that cells within tissues are not actively moving around and also provides controls for assaying the invasiveness of other cell types, such as malignant cells into the wing.

Cell autonomous functions of the receptor tyrosine kinase TIE in a late phase of angiogenic capillary growth and endothelial cell survival during murine development

Development ◽  
1996 ◽  
Vol 122 (10) ◽  
pp. 3013-3021 ◽  
Author(s):  
J. Partanen ◽  
M.C. Puri ◽  
L. Schwartz ◽  
K.D. Fischer ◽  
A. Bernstein ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Endothelial Cell ◽  
Tyrosine Kinase ◽  
Receptor Tyrosine Kinase ◽  
Late Phase ◽  
Cell Lineage ◽  
Cell Types ◽  
Limb Bud ◽  
Cell Populations ◽  
Cell Integrity

TIE is a receptor tyrosine kinase expressed in both mature endothelial cells and their precursors, as well as in some hematopoietic cells. Mouse embryos homozygous for a disrupted Tie allele die at midgestation due to impaired endothelial cell integrity and resulting hemorrhage. Here we have performed chimeric analysis to study further the function of the murine TIE in the development of embryonic vasculature and in the hematopoietic system. Cells lacking a functional Tie gene (tie(lcz)/tie(lczn-) cells) contributed to the embryonic vasculature at E10.5 as efficiently as cells heterozygous for a targeted Tie allele (tie(lcz)/+ cells). Thus, TIE does not play a significant role in vasculogenesis or in early angiogenic processes, such as formation of the intersomitic arteries and limb bud vascularization. At E15.5 tie(lcz)/tie(lczn-) cells still readily contributed to major blood vessels and to endothelial cells of organs such as lung and heart, which have been suggested to be vascularized by angioblast differentiation. In contrast, the tie(lcz)/tie(lczn-) cells were selected against in the capillary plexuses of several angiogenically vascularized tissues, such as brain and kidney. Our results thus support a role for TIE in late phases of angiogenesis but not vasculogenesis. Furthermore, the results suggest that different mechanisms regulate early and late angiogenesis and provide support for a model of differential organ vascularization by vasculogenic or angiogenic processes. Analysis of adult chimeras suggested that TIE is required to support the survival or proliferation of certain types of endothelial cells demonstrating heterogeneity in the growth/survival factor requirements in various endothelial cell populations. Chimeric analysis of adult hematopoietic cell populations, including peripheral platelets and bone marrow progenitor cells, revealed that tie(lcz)/tie(lczn-) cells were able to contribute to these cell types in a way indistinguishable from tie(lcz)/+ or wild-type cells. Thus, the primary function of TIE appears to be restricted to the endothelial cell lineage.

Histotypic Cell Aggregation in the Presence of Cytochalasin B

1974 ◽  
Vol 16 (3) ◽  
pp. 651-663
Author(s):  
D. E. MASLOW ◽  
E. MAYHEW
Keyword(s):  
Cell Suspension ◽  
Cytochalasin B ◽  
Cell Aggregation ◽  
Cell Types ◽  
Neural Retina ◽  
Heart Cell ◽  
Heart Cells ◽  
Cell Type ◽  
Mixed Aggregates ◽  
Gyratory Shaker

A study was made of the effects of cytochalasin B on (a) specific sorting of reaggregating cells; (b) redistribution of cell types after treatment of preformed aggregates; and (c) the ability of aggregates of one cell type to incorporate and sort cells of another type. Freshly disaggregated neural retina and heart cells were cultured on a gyratory shaker at 70 rev/min and the aggregates formed analysed for sorting of cell types. Cytochalasin B disrupted the sorting of forming aggregates at concentrations of 1 µg/ml and greater. The distribution of cell types in aggregates that were treated with cytochalasin after 24 h of culture was more random than the control. Untreated cultures of retinal aggregates and heart cell suspension resulted in pure retinal and pure heart aggregates, but with more than 50 % mixed and sorted aggregates. Cytochalasin B treatment resulted in fewer mixed aggregates and a higher proportion of pure retina and pure heart aggregates.

scholarly journals Clonal Populations of Amniotic Cells by Dilution and Direct Plating: Evidence for Hidden Diversity

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Patricia G. Wilson ◽  
Lorna Devkota ◽  
Tiffany Payne ◽  
Laddie Crisp ◽  
Allison Winter ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Amniotic Fluid ◽  
Ex Vivo ◽  
Cell Types ◽  
Cell Populations ◽  
Mixed Cell ◽  
Differentiation Potential ◽  
Direct Plating ◽  
Fetal Cells ◽  
Amniotic Cells

Fetal cells are widely considered a superior cell source for regenerative medicine; fetal cells show higher proliferative capacity and have undergone fewer replicative cycles that could generate spontaneous mutations. Fetal cells in amniotic fluid were among the first normal primary cells to be cultured ex vivo, but the undefined composition of amniotic fluid has hindered advance for regenerative applications. We first developed a highly efficient method to generate clonal populations by dilution of amniocentesis samples in media and direct plating without intervening refrigeration, centrifugation, or exposure of cells to the paracrine effects in mixed cell cultures. More than 40 clonal populations were recovered from 4 amniocentesis samples and representative clones were characterized by flow cytometry, conventional assays for differentiation potential, immunofluorescence imaging, and transcript analysis. The results revealed previously unreported diversity among stromal and epithelial cell types and identified unique cell types that could be lost or undetected in mixed cell populations. The differentiation potential of amniotic cells proved to be uncoupled from expression of definitive cell surface or cytoplasmic markers for stromal and epithelial cells. Evidence for diversity among stromal and epithelial cells in amniotic fluid bears on interpretations applied to molecular and functional tests of amniotic cell populations.

scholarly journals Single-cell transcriptomic analysis of mIHC images via antigen mapping

2021 ◽  
Vol 7 (10) ◽  
pp. eabc5464
Author(s):  
Kiya W. Govek ◽  
Emma C. Troisi ◽  
Zhen Miao ◽  
Rachael G. Aubin ◽  
Steven Woodhouse ◽  
...  
Keyword(s):  
Single Cell ◽  
Spatial Patterns ◽  
Cell Types ◽  
Level Of Detail ◽  
Cell Populations ◽  
Sequencing Data ◽  
Spatially Resolved ◽  
Murine Spleen ◽  
Single Cell Rna Sequencing ◽  
Antibody Panel

Highly multiplexed immunohistochemistry (mIHC) enables the staining and quantification of dozens of antigens in a tissue section with single-cell resolution. However, annotating cell populations that differ little in the profiled antigens or for which the antibody panel does not include specific markers is challenging. To overcome this obstacle, we have developed an approach for enriching mIHC images with single-cell RNA sequencing data, building upon recent experimental procedures for augmenting single-cell transcriptomes with concurrent antigen measurements. Spatially-resolved Transcriptomics via Epitope Anchoring (STvEA) performs transcriptome-guided annotation of highly multiplexed cytometry datasets. It increases the level of detail in histological analyses by enabling the systematic annotation of nuanced cell populations, spatial patterns of transcription, and interactions between cell types. We demonstrate the utility of STvEA by uncovering the architecture of poorly characterized cell types in the murine spleen using published cytometry and mIHC data of this organ.

scholarly journals Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Seyed Ali Madani Tonekaboni ◽  
Benjamin Haibe-Kains ◽  
Mathieu Lupien
Keyword(s):  
Transposable Elements ◽  
Histone Modifications ◽  
Cell Types ◽  
Regulatory Elements ◽  
Cell Populations ◽  
Genomic Features ◽  
Differentiated Cells ◽  
Chromatin Interactions ◽  
Topologically Associating Domains ◽  
Highly Expressed Genes

AbstractThe human genome is partitioned into a collection of genomic features, inclusive of genes, transposable elements, lamina interacting regions, early replicating control elements and cis-regulatory elements, such as promoters, enhancers, and anchors of chromatin interactions. Uneven distribution of these features within chromosomes gives rise to clusters, such as topologically associating domains (TADs), lamina-associated domains, clusters of cis-regulatory elements or large organized chromatin lysine (K) domains (LOCKs). Here we show that LOCKs from diverse histone modifications discriminate primitive from differentiated cell types. Active LOCKs (H3K4me1, H3K4me3 and H3K27ac) cover a higher fraction of the genome in primitive compared to differentiated cell types while repressive LOCKs (H3K9me3, H3K27me3 and H3K36me3) do not. Active LOCKs in differentiated cells lie proximal to highly expressed genes while active LOCKs in primitive cells tend to be bivalent. Genes proximal to bivalent LOCKs are minimally expressed in primitive cells. Furthermore, bivalent LOCKs populate TAD boundaries and are preferentially bound by regulators of chromatin interactions, including CTCF, RAD21 and ZNF143. Together, our results argue that LOCKs discriminate primitive from differentiated cell populations.

Cytogenetic, anatomical and blood group studies of sheep twin chimaeras

1970 ◽  
Vol 175 (1039) ◽  
pp. 183-200 ◽  
Keyword(s):  
Blood Cell ◽  
Blood Group ◽  
Sex Chromosomes ◽  
Cell Types ◽  
In Utero ◽  
Red Cells ◽  
Cell Populations ◽  
Red Cell ◽  
X Protein ◽  
Blood Grouping

Karyotyping and blood grouping methods were used to identify sheep twin chimaeras. Evidence that an exchange of blood cell precursors (the origin of chimaerism) had taken place in utero was obtained by examining lymphocytes in culture and finding the chromosomes of both sexes in one individual, or by finding admixture of red cell antigens, haemoglobin or ‘X ’ protein. Where chimaerism of sex chromosomes was found the pairs had identical red cell types, but two separate populations of red cells were not always identifiable. The four females in the pairs studied were freemartins. No correlation was found between the relative proportions of the two red cell populations and those of the two white cell populations. In one pair of chimaeric ewes, breeding tests showed that the major red cell populations in each case were the true genetic type. In the freemartins no correlation was found between the degree of masculinity and the numbers of male lymphocytes. A possible correlation of masculinity with red cell proportions is discussed.

scholarly journals Characterization and Regulation of Type A Endothelin Receptor Gene Expression in Bovine Luteal Cell Types

Endocrinology ◽  
1999 ◽  
Vol 140 (5) ◽  
pp. 2110-2116 ◽  
Author(s):  
Roni Mamluk ◽  
Nitzan Levy ◽  
Bo Rueda ◽  
John S. Davis ◽  
Rina Meidan
Keyword(s):  
Gene Expression ◽  
Receptor Gene ◽  
Cell Types ◽  
Cell Populations ◽  
Mrna Levels ◽  
Factor I ◽  
Receptor Mrna ◽  
Progesterone Production ◽  
Eta Receptor ◽  
Receptor Gene Expression

Abstract Our previous studies demonstrated that endothelin-1 (ET-1), a 21-amino acid vasoconstrictor peptide, has a paracrine regulatory role in bovine corpus luteum (CL). The peptide is produced within the gland where it inhibits progesterone production by acting via the selective type A endothelin (ETA) receptors. The present study was designed to characterize ETA receptor gene expression in different ovarian cell types and its hormonal regulation. ETA receptor messenger RNA (mRNA) levels were high in follicular cells as well as in CL during luteal regression. At this latter stage, high ETA receptor expression concurred with low prostaglandin F2α receptor mRNA. The ETA receptor gene was expressed by all three major cell populations of the bovine CL; i.e. small and large luteal cells, as well as in luteal endothelial cells. Among these various cell populations, the highest ETA receptor mRNA levels were found in endothelial cells. cAMP elevating agents, forskolin and LH, suppressed ETA receptor mRNA expression in luteinized theca cells (LTC). This inhibition was dose dependent and was evident already after 24 h of incubation. In luteinized granulosa cells (LGC), 10 and 100 ng/ml of insulin-like growth factor I and insulin (only at a concentration of 2000 ng/ml) markedly decreased ETA receptor mRNA levels. In both LGC and LTC there was an inverse relationship between ETA receptor gene expression and progesterone production; insulin (in LGC) and forskolin (in LTC) enhanced progesterone production while inhibiting ETA receptor mRNA levels. Our findings may therefore suggest that, during early stages of luteinization when peak levels of both LH and insulin-like growth factor I exist, the expression of ETA receptors in the gland are suppressed. This study demonstrates physiologically relevant regulatory mechanisms controlling ETA receptor gene expression and further supports the inhibitory role of ET-1 in CL function.

The application of aqueous two-phase partition to the study of chick limb mesenchymal diversification

Development ◽  
1986 ◽  
Vol 94 (1) ◽  
pp. 267-275
Author(s):  
C. P. Cottrill ◽  
Paul T. Sharpe ◽  
Lewis Wolpert
Keyword(s):  
Pattern Formation ◽  
Limb Development ◽  
Developmental Stages ◽  
Proximal Region ◽  
Limb Bud ◽  
Cell Populations ◽  
Two Phase ◽  
Phase Partition ◽  
Surface Character ◽  
Two Phase Partition

A technique which identifies cells differing in surface character, aqueous two-phase partition using thin-layer countercurrent distribution (TLCCD), has been used to study differentiation and pattern formation in the developing chick limb bud. The TLCCD profiles of cell populations, derived from various regions of morphologically undifferentiated mesenchyme from three different stages of limb development, have been compared. At no stage, or location, has the population been found to be homogeneous. Cells from progress zones and more proximal regions could all be resolved into several populations. The populations from progress zones at three different developmental stages were qualitatively similar but differed in the proportions of cells in each. The most striking differences in cell populations were those obtained from the most proximal region of the limb, closest to the flank, which represents the developmentally most advanced region.

scholarly journals Single Cell, Single Nucleus and Spatial RNA Sequencing of the Human Liver Identifies Hepatic Stellate Cell and Cholangiocyte Heterogeneity

2021 ◽  
Author(s):  
Tallulah S Andrews ◽  
Jawairia Atif ◽  
Jeff C Liu ◽  
Catia T Perciani ◽  
Xue-Zhong Ma ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Human Liver ◽  
Stellate Cell ◽  
Parenchymal Cell ◽  
Cell Types ◽  
Cell Populations ◽  
Healthy Human ◽  
Single Nucleus

The critical functions of the human liver are coordinated through the interactions of hepatic parenchymal and non-parenchymal cells. Recent advances in single cell transcriptional approaches have enabled an examination of the human liver with unprecedented resolution. However, dissociation related cell perturbation can limit the ability to fully capture the human liver's parenchymal cell fraction, which limits the ability to comprehensively profile this organ. Here, we report the transcriptional landscape of 73,295 cells from the human liver using matched single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq). The addition of snRNA-seq enabled the characterization of interzonal hepatocytes at single-cell resolution, revealed the presence of rare subtypes of hepatic stellate cells previously only seen in disease, and detection of cholangiocyte progenitors that had only been observed during in vitro differentiation experiments. However, T and B lymphocytes and NK cells were only distinguishable using scRNA-seq, highlighting the importance of applying both technologies to obtain a complete map of tissue-resident cell-types. We validated the distinct spatial distribution of the hepatocyte, cholangiocyte and stellate cell populations by an independent spatial transcriptomics dataset and immunohistochemistry. Our study provides a systematic comparison of the transcriptomes captured by scRNA-seq and snRNA-seq and delivers a high-resolution map of the parenchymal cell populations in the healthy human liver.

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