Pattern formation in Dictyostelium discoideum

Development ◽  
1977 ◽  
Vol 40 (1) ◽  
pp. 229-243
Author(s):  
D. Forman ◽  
D. R. Garrod
Keyword(s):  
Life Cycle ◽  
Pattern Formation ◽  
Single Cells ◽  
Cell Mass ◽  
Positional Information ◽  
Cell Types ◽  
Immunofluorescent Staining ◽  
Cell Contact ◽  
Slime Mould ◽  
Normal Life

Cells of the cellular slime mould D. discoideum were allowed to form into spherical aggregates, by shaking vegetative cells as a suspension in phosphate buffer. In such conditions, grex polarity is never established and surface sheath is not formed (Loomis, 1975 a). Despite the absence of such characteristics of normal development, differentiation of prespore cells, as tested for by immunofluorescent staining, and the organization of such cells into a patterned structure still occurred within the aggregates. Differentiation of prespore cells was found to occur within the cultures at times equivalent to those in the normal life cycle; such differentiation could be advanced by pulsation of the cultures with cyclic-AMP. When cell contact and aggregate formation was prevented, differentiation never occurred within the single cells. Our results suggest that the prespore cells develop randomly within the aggregate and that a pattern is subsequently formed as a result of sorting out of cell types within the cell mass. Aggregates shaken for extended periods of time showed development into cyst-like structures. The process of pattern formation that occurred within these aggregates which possess neither polarity nor a grex tip, would be unlikely to involve any mechanism of positional information signalling. The relevance of polar organization in the generation of pattern in the normal life cycle may therefore be questionable. We present a model of pattern formation in the slime mould in which sorting out of predetermined cell types is viewed as the major mechanism in bringing about patterned organization of the grex precursor cells.

Applications of a Theory of Biological Pattern Formation Based on Lateral Inhibition

1974 ◽  
Vol 15 (2) ◽  
pp. 321-346 ◽  
Author(s):  
H. MEINHARDT ◽  
A. GIERER
Keyword(s):  
Pattern Formation ◽  
Lateral Inhibition ◽  
Molecular Mechanisms ◽  
Positional Information ◽  
Cell Types ◽  
Model Calculations ◽  
Slime Moulds ◽  
Biological Pattern Formation ◽  
Pattern Forming ◽  
Differentiation And Proliferation

Model calculations are presented for various problems of development on the basis of a theory of primary pattern formation which we previously proposed. The theory involves short-range autocatalytic activation and longer-range inhibition (lateral inhibition). When a certain criterion is satisfied, self-regulating patterns are generated. The autocatalytic features of the theory are demonstrated by simulations of the determination of polarity in the Xenopus retina. General conditions for marginal and internal activation, and corresponding effects of symmetry are discussed. Special molecular mechanisms of pattern formation are proposed in which activator is chemically converted into inhibitor, or an activator precursor is depleted by conversion into activator. The (slow) effects of primary patterns on differentiation can be included into the formalism in a straightforward manner. In conjunction with growth, this can lead to asymmetric steady states of cell types, cell differentiation and proliferation as found, for instance, in growing and budding hydra. In 2 dimensions, 2 different types of patterns can be obtained. Under some assumptions, a single pattern-forming system produces a ‘bristle’ type pattern of peaks of activity with rather regular spacings on a surface. Budding of hydra is treated on this basis. If, however, gradients develop under the influence of a weak external or marginal asymmetry, a monotonic gradient can be formed across the entire field, and 2 such gradient-forming systems can specify ‘positional information’ in 2 dimensions. If inhibitor equilibrates slowly, a spatial pattern may oscillate, as observed with regard to the intracellular activation of cellular slime moulds. The applications are intended to demonstrate the ability of the proposed theory to explain properties frequently encountered in developing systems.

Position dependent control of cell fate in the Fucus embryo: role of intercellular communication

Development ◽  
1998 ◽  
Vol 125 (11) ◽  
pp. 1999-2008 ◽  
Author(s):  
F.Y. Bouget ◽  
F. Berger ◽  
C. Brownlee
Keyword(s):  
Cell Wall ◽  
Pattern Formation ◽  
Cell Fate ◽  
Intercellular Communication ◽  
Cell Types ◽  
Early Embryo ◽  
Cell Contact ◽  
Dependent Manner ◽  
Intact Cells ◽  
Cell Fate Decisions

The early embryo of the brown alga Fucus comprises two cell types, i. e. rhizoid and thallus which are morphogically and cytologically distinguishable. Previous work has pointed to the cell wall as a source of position-dependent information required for polarisation and fate determination in the zygote and 2-celled embryo. In this study we have analysed the mechanism(s) of cell fate control and pattern formation at later embryonic stages using a combination of laser microsurgery and microinjection. The results indicate that the cell wall is required for maintenance of pre-existing polarity in isolated intact cells. However, all cell types ultimately have the capacity to re-differentiate or regenerate rhizoid cells in response to ablation of neighbouring cells. This regeneration is regulated in a position-dependent manner and is strongly influenced by intercellular communication, probably involving transport or diffusion of inhibitory signals which appear to be essential for regulation of cell fate decisions. This type of cell-to-cell communication does not involve symplastic transport or direct cell-cell contact inhibition. Apoplastic diffusible gradients appear to be involved in pattern formation in the multicellular embryo.

Pattern formation in Dictyostelium discoideum

Development ◽  
1977 ◽  
Vol 40 (1) ◽  
pp. 215-228
Author(s):  
D. Forman ◽  
D. R. Garrod
Keyword(s):  
Life Cycle ◽  
Pattern Formation ◽  
Dictyostelium Discoideum ◽  
Cell Population ◽  
Growth Conditions ◽  
Total Cell ◽  
Immunofluorescent Staining ◽  
Fruiting Bodies ◽  
Fluorescent Intensity ◽  
Total Cell Population

Immunofluorescent staining of the prespore cells of the cellular slime mould Dictyostelium discoideum was carried out using a heterologous spore antibody. The highly specific staining of the prespore vesicles (PSVs) within the prespore cells enabled quantitative determinations to be made of the rate and extent of development of these cells throughout the life cycle. The results showed that PSVs first appeared in a large proportion of the cells shortly after the cells had chemotactically aggregated into multicellular masses. During the later phases of the life cycle, the proportion of cells containing PSV increased, as did the fluorescent intensity of their PSVs, until the early culmination stage of development when 85–90 % of the total cell population contained PSVs. Lowering the temperature of development delayed the onset of vesicle formation and decreased the proportion of prespore cells in the total cell population. Changing the growth conditions of the cells prior to multicellular development also had a significant effect on the proportions of prespore cells, as did the use of a mutant known to give rise to fruiting bodies with a reduced number of spores. The comparability between these estimates of prespore cell proportions at culmination and previously reported spore:stalk ratios within fruiting bodies confirms the view that PSVs are reliable indicators of prespore cells. The finding that temperature and growth conditions and the use of mutants all of which are known to affect spore:stalk ratios, also all affected prespore proportions in the expected direction, adds further weight to this argument. The fact that prespore cells are beginning to differentiate early in the multicellular phase of the life cycle and the related finding that such differentiation always precedes formation of the grex tip are results of considerable importance to the development of a model for pattern formation in D. discoideum.

scholarly journals A Quantitative Single-Cell Proteomics Approach to Characterize an Acute Myeloid Leukemia Hierarchy

2019 ◽  
Author(s):  
Erwin M. Schoof ◽  
Nicolas Rapin ◽  
Simonas Savickas ◽  
Coline Gentil ◽  
Eric Lechman ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Cell Mass ◽  
Science Research ◽  
Cell Types ◽  
Cellular Heterogeneity ◽  
Significant Shift ◽  
Cell Analysis ◽  
Computational Pipeline

AbstractIn recent years, cellular life science research has experienced a significant shift, moving away from conducting bulk cell interrogation towards single-cell analysis. It is only through single cell analysis that a complete understanding of cellular heterogeneity, and the interplay between various cell types that are fundamental to specific biological phenotypes, can be achieved. Single-cell assays at the protein level have been predominantly limited to targeted, antibody-based methods. However, here we present an experimental and computational pipeline, which establishes a comprehensive single-cell mass spectrometry-based proteomics workflow.By exploiting a leukemia culture system, containing functionally-defined leukemic stem cells, progenitors and terminally differentiated blasts, we demonstrate that our workflow is able to explore the cellular heterogeneity within this aberrant developmental hierarchy. We show our approach is capable to quantifying hundreds of proteins across hundreds of single cells using limited instrument time. Furthermore, we developed a computational pipeline (SCeptre), that effectively clusters the data and permits the extraction of cell-specific proteins and functional pathways. This proof-of-concept work lays the foundation for future global single-cell proteomics studies.

Morphogenesis in the cellular slime mould Dictyostelium discoideum; the formation and regulation of aggregate tips and the specification of developmental axes

Development ◽  
1973 ◽  
Vol 29 (2) ◽  
pp. 253-266
Author(s):  
P. Farnsworth
Keyword(s):  
Morphological Changes ◽  
Cell Mass ◽  
Staging System ◽  
Positional Information ◽  
Cell Labelling ◽  
Slime Mould ◽  
Impermeable Barrier ◽  
A Cell ◽  
Cellular Slime

A general discussion of ‘organizing regions’ and the specification of biological patterns is followed by introducing the idea that the tip of the slime mould cell mass is such an ‘organizer’. This view is supported by a discussion of the developmental ubiquity of the tip and its effects. A staging system is described which assigns numbers to sequential morphological changes during development. A set of experiments investigating the role of the tip are described, using techniques of cell labelling, grafting and bisection of cell masses with barriers, and the manufacture and use of cylindrical barriers of permeable cellulose. The results of such experiments show: (1) That the tip of the cell mass is made of the same group of cells from stage 10 (late aggregate) to stage 20+ (culmination). (2) That a stage 10 aggregate will regenerate a new tip in an average time of 32 min. (3) That if a stage 10 aggregate is bisected by an impermeable barrier two tips, indicating two new developmental axes, develop in an average time of 34 min. (4) That if a stage 10 aggregate is bisected for 40 min, the barrier removed and one of the tips removed, the remaining tip inhibits the re-formation of the second tip, and the polarity of the aggregate is again reorganized with respect to the remaining tip. (5) That if experiments (3), (4) and (5) are repeated with a stage 9 aggregate, which is an hour younger, all the regulation times are increased by about 60 min. Similarly a stage 8 aggregate takes over 120 min longer to show the effect. (6) That if part or all of a cell mass from any stage is placed inside a cellulose tube, all the enclosed cells differentiate into stalk cells. These results are then discussed in relation to pattern formation and the role of the tip in polarization and the specification of new developmental axes in cell masses. A model for culmination in the slime mould is proposed which takes account of the above results. The essence of this model is that at no time are stalk and spore cells ‘determined’ in the classical sense, and that, by a non-signalling positional information system, the size invariance of the ratio of stalk to spore cells seen in the fruiting body is a result of the mechanical process of culmination.

A boundary model for pattern formation in vertebrate limbs

Development ◽  
1983 ◽  
Vol 76 (1) ◽  
pp. 115-137
Author(s):  
Hans Meinhardt
Keyword(s):  
Pattern Formation ◽  
Positional Information ◽  
Cell Types ◽  
Cooperative Interaction ◽  
Main Body ◽  
Polar Coordinate ◽  
Coordinate Model ◽  
Supernumerary Limbs ◽  
Boundary Model

We postulate that positional information for secondary embryonic fields is generated by a cooperative interaction between two pairs of differently determined cell types. Positional information is thus generated at the boundaries between cells of different determination. The latter are assumed to result from the primary pattern formation in the embryo. The application of this model to vertebrate limbs accounts for the pairwise determination of limbs at a particular location, with a particular handedness and alignment to the main body axes of the embryo. It accounts further for the gross difference in the regeneration of double anterior and double posterior amphibian limbs as well as for the formation of supernumerary limbs after certain graft experiments including supernumeraries in which the dorsoventral polarity changes or which consist of two anterior or two posterior halves. Our model provides a feasible molecular basis for the polar coordinate model and successfully handles recently found violations, for instance formation of supernumerary limbs after ipsilateral grafting with 90° rotation. The most frequent types of developmental malformations become explicable. The models allow specific predictions which are fully supported by recent experiments (see the accompanying paper of M. Maden).

scholarly journals DGCyTOF:  deep learning with graphic cluster visualization to predict cell types of single cell mass cytometry data

2021 ◽  
Author(s):  
Lijun Cheng ◽  
Pratik Karkhanis ◽  
Birkan Gokbag ◽  
Lang Li
Keyword(s):  
Deep Learning ◽  
Single Cell ◽  
3D Visualization ◽  
Single Cells ◽  
Cell Mass ◽  
Cell Types ◽  
Learning System ◽  
Cell Populations ◽  
Calibration System ◽  
Mass Cytometry

Background :  Single-cell mass cytometry, also known as cytometry by time of flight (CyTOF) is a powerful high-throughput technology that allows analysis of up to 50 protein markers per cell for the quantification and classification of single cells. Traditional manual gating utilized to identify new cell populations has been inadequate, inefficient, unreliable, and difficult to use, and no algorithms to identify both calibration and new cell populations has been well established. Methods :   A deep learning with graphic cluster (DGCyTOF) visualization is developed as a new integrated embedding visualization approach in identifying canonical and new cell types. The DGCyTOF combines deep-learning classification and hierarchical stable-clustering methods to sequentially build a tri-layer construct for known cell types and the identification of new cell types. First, deep classification learning is constructed to distinguish calibration cell populations from all cells by softmax classification assignment under a probability threshold, and graph embedding clustering is then used to identify new cell populations sequentially. In the middle of two-layer, cell labels are automatically adjusted between new and unknown cell populations via a feedback loop using an iteration calibration system to reduce the rate of error in the identification of cell types, and a 3-dimensional (3D) visualization platform is finally developed to display the cell clusters with all cell-population types annotated. Results : Utilizing two benchmark CyTOF databases comprising up to 43 million cells, we compared accuracy and speed in the identification of cell types among DGCyTOF, DeepCyTOF, and other technologies including dimension reduction with clustering, including Principal Component Analysis ( PCA ) , Factor Analysis ( FA ), Independent Component Analysis ( ICA ), Isometric Feature Mapping ( Isomap ), t-distributed Stochastic Neighbor Embedding ( t-SNE ), and Uniform Manifold Approximation and Projection ( UMAP ) with k -means clustering and Gaussian mixture clustering. We observed the DGCyTOF represents a robust complete learning system with high accuracy, speed and visualization by eight measurement criteria. The DGCyTOF displayed F-scores of 0.9921 for CyTOF1 and 0.9992 for CyTOF2 datasets, whereas those scores were only 0.507 and 0.529 for the t-SNE + k-means ; 0.565 and 0.59, for UMAP + k-means . Comparison of DGCyTOF with t-SNE and UMAP visualization in accuracy demonstrated its approximately 35% superiority in predicting cell types. In addition, observation of cell-population distribution was more intuitive in the 3D visualization in DGCyTOF than t-SNE and UMAP visualization. Conclusions :  The DGCyTOF model can automatically assign known labels to single cells with high accuracy using deep-learning classification assembling with traditional graph-clustering and dimension-reduction strategies. Guided by a calibration system, the model seeks optimal accuracy balance among calibration cell populations and unknown cell types, yielding a complete and robust learning system that is highly accurate in the identification of cell populations compared to results using other methods in the analysis of single-cell CyTOF data. Application of the DGCyTOF method to identify cell populations could be extended to the analysis of single-cell RNASeq data and other omics data.

scholarly journals ECM-mediated positional cues are able to induce pattern, but not new positional information, during axolotl limb regeneration

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248051
Author(s):  
Warren A. Vieira ◽  
Shira Goren ◽  
Catherine D. McCusker
Keyword(s):  
Pattern Formation ◽  
Connective Tissue ◽  
Limb Regeneration ◽  
Positional Information ◽  
Cell Types ◽  
Induce Pattern ◽  
Tissue Cells ◽  
Pattern Information

The Mexican Axolotl is able to regenerate missing limb structures in any position along the limb axis throughout its life and serves as an excellent model to understand the basic mechanisms of endogenous regeneration. How the new pattern of the regenerating axolotl limb is established has not been completely resolved. An accumulating body of evidence indicates that pattern formation occurs in a hierarchical fashion, which consists of two different types of positional communications. The first type (Type 1) of communication occurs between connective tissue cells, which retain memory of their original pattern information and use this memory to generate the pattern of the regenerate. The second type (Type 2) of communication occurs from connective tissue cells to other cell types in the regenerate, which don’t retain positional memory themselves and arrange themselves according to these positional cues. Previous studies suggest that molecules within the extracellular matrix (ECM) participate in pattern formation in developing and regenerating limbs. However, it is unclear whether these molecules play a role in Type 1 or Type 2 positional communications. Utilizing the Accessory Limb Model, a regenerative assay, and transcriptomic analyses in regenerates that have been reprogrammed by treatment with Retinoic Acid, our data indicates that the ECM likely facilities Type-2 positional communications during limb regeneration.

scholarly journals Individual and collective behaviour in cellular slime mould development: contributions of John Bonner (1920-2019)

2019 ◽  
Vol 63 (8-9-10) ◽  
pp. 333-342
Author(s):  
Vidyanand Nanjundiah
Keyword(s):  
Single Cells ◽  
Cell Types ◽  
Spatial Patterning ◽  
Multicellular Aggregate ◽  
Slime Mould ◽  
Slime Moulds ◽  
Cellular Slime ◽  
The Right ◽  
Evolutionary And Developmental Biology ◽  
Cellular Slime Moulds

John Bonner used the cellular slime moulds to address issues that lie at the heart of evolutionary and developmental biology. He did so mostly by combining acute observation and a knack for asking the right questions with the methods of classical embryology. The present paper focusses on his contributions to understanding two phenomena that are characteristic of development in general: chemotaxis of single cells to an external attractant, and spatial patterning and proportioning of cell types in the multicellular aggregate. Brief mention is also made of other areas of slime mould biology where he made significant inputs. He saw cellular slime moulds as exemplars of development and worthy of study in their own right. His ideas continue to inspire researchers.

Use of F9 teratocarcinoma STEM cells to study cell-matrix interactions in the early mouse embryo

1992 ◽  
Vol 50 (1) ◽  
pp. 602-603
Author(s):  
Marc Lenburg ◽  
Rulang Jiang ◽  
Lengya Cheng ◽  
Laura Grabel
Keyword(s):  
Mouse Embryo ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Cell Types ◽  
Embryoid Bodies ◽  
F9 Cells ◽  
Cell Matrix ◽  
Matrix Interactions ◽  
Cell Matrix Interactions ◽  
F9 Teratocarcinoma

We are interested in defining the cell-cell and cell-matrix interactions that help direct the differentiation of extraembryonic endoderm in the peri-implantation mouse embryo. At the blastocyst stage the mouse embryo consists of an outer layer of trophectoderm surrounding the fluid-filled blastocoel cavity and an eccentrically located inner cell mass. On the free surface of the inner cell mass, facing the blastocoel cavity, a layer of primitive endoderm forms. Primitive endoderm then generates two distinct cell types; parietal endoderm (PE) which migrates along the inner surface of the trophectoderm and secretes large amounts of basement membrane components as well as tissue-type plasminogen activator (tPA), and visceral endoderm (VE), a columnar epithelial layer characterized by tight junctions, microvilli, and the synthesis and secretion of α-fetoprotein. As these events occur after implantation, we have turned to the F9 teratocarcinoma system as an in vitro model for examining the differentiation of these cell types. When F9 cells are treated in monolayer with retinoic acid plus cyclic-AMP, they differentiate into PE. In contrast, when F9 cells are treated in suspension with retinoic acid, they form embryoid bodies (EBs) which consist of an outer layer of VE and an inner core of undifferentiated stem cells. In addition, we have established that when VE containing embryoid bodies are plated on a fibronectin coated substrate, PE migrates onto the matrix and this interaction is inhibited by RGDS as well as antibodies directed against the β1 integrin subunit. This transition is accompanied by a significant increase in the level of tPA in the PE cells. Thus, the outgrowth system provides a spatially appropriate model for studying the differentiation and migration of PE from a VE precursor.

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