Spatial Arrangement Of Cells Research Articles

Three-dimensional computational modeling of high-frequency ultrasound imaging of murine liver and liver metastases.

High-frequency ultrasound images of preclinical cancer models are sensitive to variations in microanatomy that accompany tumor growth, but the relationships between high-frequency backscattering and tumor microstructure are incompletely understood. To investigate these relationships, a 3-D microanatomical model that incorporates cell number density, sizes of cells and nuclei, and spatial arrangement of cells is used to represent a healthy mouse liver and an experimental liver metastasis. A first-order k-space method is used to synthesize B-mode images by computing linear 3-D propagation of focused 40-MHz pulses through the simulated tissues. Simulated images are compared to corresponding experimental images by constructing gray-level histograms with 13 bins evenly spaced over 256 gray levels. Simulated and experimental speckle distributions for a healthy liver match within one standard deviation in all 13 histogram bins when the sound speed and mass density of the cell nuclei are set to 1503 m/s and 1.43 g/cm3, respectively. Simulated and experimental speckle distributions for the liver metastasis match in 11 of 13 bins when the sound speed and density of the nuclei are set to 1527 m/s and 1.14 g/cm3. These simulations suggest that changes in first-order speckle statistics during tumor development reflect variations in both tissue acoustic and microstructural properties.

Inhibition of neuronal cell–cell adhesion measured by the microscopic aggregation assay and impedance sensing

Microscopic aggregation assay and impedance sensing (IS) were used to monitor a change in in vitro neuron–neuron adhesion in response to blocking of cell adhesion molecules. By blocking neuron–neuron adhesion, migration and aggregation of neuronal cells can be inhibited. This leads to better control of spatial arrangement of cells in culture. In the literature N-CAM, L1 and N-cadherin proteins are pointed out as main regulators of neuronal adhesion. In this study, these three main cell adhesion molecules were used to inhibit neuron-to-neuron adhesion and aggregation. Both soluble extracellular domains and antigen antibodies were added to these adhesion molecules. They were investigated for their blocking ability in neuronal cultures. First, in a 96 h aggregation assay on a low-adhesive substrate, the effect of inhibition of the three proteins on aggregation of cortical neurons was investigated optically. Both L1 antibody and L1 protein had no effect on the degree of aggregation. An N-cadherin antibody however was shown to be effective in aggregation inhibition at concentrations of 1 and 3 µg ml−1. Up to 96 h no aggregation occurred. A similar effect was achieved by the N-cadherin protein, although less distinct. N-CAM blocking revealed no inhibition of aggregation. Second, results from IS corresponded to those of the aggregation assays. In these experiments neuron–neuron adhesion was also inhibited by blocking N-CAM L1 and N-cadherin. Cortical neurons were cultured in small wells containing circular 100 µm diameter gold electrodes, so small changes in cell–cell interactions in monolayers of neurons could be monitored by IS. Impedances of neuron-covered electrodes were significantly lower in the presence of the N-cadherin antibody and protein at concentrations of 1, 3 and 10 µg ml−1, indicating a less profound binding between adjacent neurons. Results from the aggregation assays and impedance measurements demonstrate the applicability of blocking cell adhesion molecules for inhibition of cell–cell adhesion and aggregation.

Learning modular representations from global sparse coding networks

The introduction of the efficient coding hypothesis by Barlow in 1961 marked the beginning of a detailed investigation into how neurons could adapt their receptive field (RF) profiles to represent their external sensory environment more efficiently. The efficiency of the neural code was originally studied in the context of a single neuron, primarily with respect to the amount of information that could be sent from a single cell across an axonal communication channel. With the development of techniques to examine the activity of multiple neurons in intact neural circuits, our view of information processing in sensory systems has shifted from a neuron-centric view to a network-centric one. The sparse coding hypothesis attempts to describe how efficient coding can be performed at the network level. In sparse coding models, a network’s representation is deemed efficient if the number of neurons that are active within a population is small relative to the size of the population. Mounting evidence shows that sensory systems employ sparse population coding, both in experimental [1] and computational modeling [2] studies. While these studies have focused on testing the sparse coding hypothesis with respect to the development of RF profiles in different sensory environments, predictions of information processing in mature neural sparse coding circuits have yet to be studied in detail, let alone tested experimentally. To determine relevant predictions of sparse coding models for mature neural circuits, we began by studying current neurally plausible models for sparse coding [3],4 that employ a number of processes known to take place within cortical networks, including recurrent inhibition, stimulus-driven excitation, and thresholding of each cell’s membrane potential. These models also predict that in order to perform sparse approximation across a network of neurons, the strength of inhibition amongst any pair of neurons is given by the coherence between the RF profiles of the preand post-synaptic cell. This implies that as a cell’s RF profile changes over time, the cell would need to alert all interneurons that synapse onto excitatory cells with overlapping receptive fields of the precise changes in its RF profile. Furthermore, predictions made about the spatial arrangement of cells differ from observations of the spatial organization of cells in the cortex. To move towards a more biologically accurate model for sparse coding in sensory systems, we incorporated a simple Hebbian learning rule into the locally competitive sparse coding model described in [3]. We found that as connections are strengthened amongst all the cells that become active in response to a given stimuli, the networks that emerge exhibit modularity (akin to columnar architectures) and small-world topologies (high clustering with small average path length), both of which have been observed in networks in the cortex. Using this model, we go on to show that under certain assumptions, orientation maps emerge. In addition to suggesting that sparse coding must be refined to incorporate stimulus-dependent plasticity, our results suggest that analyzing the structure of the coherence amongst the RFs of neighboring neurons should enable a more principled investigation of the sparse coding hypothesis in intact mature neural circuits.

Visualization of initial attachment of bioleaching bacteria using combined atomic force and epifluorescence microscopy

Bioleaching is the dissolution of metal sulfides, such as pyrite and chalcopyrite, by bacterial oxidation processes. It has been found that attachment of leaching bacteria to the mineral surface enhances the metal sulfide dissolution. The interaction of mixed cultures with respect to initial attachment processes has not been investigated. Therefore in this study we quantified and visualized initial colonization on pyrite by pure and mixed cultures. Strains of the genera Acidithiobacillus and Leptospirillum were tested. Sessile and planktonic cells were visualized by fluorescence microscopy using DAPI, FISH, Syto™ 9, lectin- and calcofluor-staining. Additionally, atomic force microscopy (AFM) was used for the investigations on cell morphology, spatial arrangement of cells on pyrite and mineral surface topography. The morphology of planktonic and sessile cells is different. Moreover, planktonic cells show differences in morphology due to the use of different substrata. By using different visualization methods it could be proven that colonization and biofilm formation on pyrite in mixed cultures is mostly dominated by Leptospirillum spp. Interactions of different species resulted in increased production of extracellular polymeric substances (EPS) or caused bacteria showing little tendency to attach when in monoculture to be incorporated into a biofilm by those that attach preferentially. Consequently, biofilm formation and metabolic diversity were furthered. One of the most important results is the finding that not all bioleaching bacteria are involved to the same extent in biofilm formation. Thus, further work shall allow us elucidate the important bacteria for biotechnological use, thereby leaching processes can be faster, more efficient and costs can be reduced.

Receptive Field Mosaics of Retinal Ganglion Cells Are Established Without Visual Experience

A characteristic feature of adult retina is mosaic organization: a spatial arrangement of cells of each morphological and functional type that produces uniform sampling of visual space. How the mosaics of visual receptive fields emerge in the retina during development is not fully understood. Here we use a large-scale multielectrode array to determine the mosaic organization of retinal ganglion cells (RGCs) in rats around the time of eye opening and in the adult. At the time of eye opening, we were able to reliably distinguish two types of ON RGCs and two types of OFF RGCs in rat retina based on their light response and intrinsic firing properties. Although the light responses of individual cells were not yet mature at this age, each of the identified functional RGC types formed a receptive field mosaic, where the spacing of the receptive field centers and the overlap of the receptive field extents were similar to those observed in the retinas of adult rats. These findings suggest that, although the light response properties of RGCs may need vision to reach full maturity, extensive visual experience is not required for individual RGC types to form a regular sensory map of visual space.

EGFL7 meets miRNA-126: an angiogenesis alliance

Blood vessels form de novo through the tightly regulated programs of vasculogenesis and angiogenesis. Both processes are distinct but one of the steps they share is the formation of a central lumen, when groups of cells organized as vascular cords undergo complex changes to achieve a tube-like morphology. Recently, a protein termed epidermal growth factor-like domain 7 (EGFL7) was described as a novel endothelial cell-derived factor involved in the regulation of the spatial arrangement of cells during vascular tube assembly. With its impact on tubulogenesis and vessel shape EGFL7 joined the large family of molecules governing blood vessel formation. Only recently, the molecular mechanisms underlying EGFL7's effects have been started to be elucidated and shaping of the extracellular matrix (ECM) as well as Notch signaling might very well play a role in mediating its biological effects. Further, findings in knock-out animal models suggest miR-126, a miRNA located within the egfl7 gene, has a major role in vessel development by promoting VEGF signaling, angiogenesis and vascular integrity. This review summarizes our current knowledge on EGFL7 and miR-126 and we will discuss the implications of both bioactive molecules for the formation of blood vessels.

Attachment Behavior of Leaching Bacteria to Metal Sulfides Elucidated by Combined Atomic Force and Epifluorescence Microscopy

The aim of the study was to quantify and to visualize colonization of metal sulfides by pure and mixed cultures. Strains of the genera Acidithiobacillus and Leptospirillum were tested. Sessile and planktonic cells were visualized by fluorescence microscopy using 4',6-diamidino-2-phenylindole (DAPI) and FISH. Additionally, atomic force microscopy was used for the investigations on cell morphology, spatial arrangement of cells on metal sulfides and mineral surface topography. It was shown that the morphology of sessile cells was totally different as compared with planktonic ones. Interactions of different species resulted in increased production of extracellular polymeric substances (EPS) or caused negligible-attaching bacteria to be incorporated into a biofilm by the good attaching ones. Consequently, biofilm formation was furthered.

Contraction-induced cluster formation in cardiac cell culture

The evolution of the spatial arrangement of cells in a primary culture of cardiac tissue derived from newborn rats was studied experimentally over an extended period. It was found that cells attract each other spontaneously to form a clustered structure over the timescale of several days. These clusters exhibit spontaneous rhythmic contraction and have been confirmed to consist of cardiac muscle cells. The addition of a contraction inhibitor (2,3-butanedione-2-monoxime) to the culture medium resulted in the inhibition of both the spontaneous contractions exhibited by the cells as well as the formation of clusters. Furthermore, the formation of clusters is suppressed when high concentrations of collagen are used for coating the substratum to which the cells adhere. From these experimental observations, it was deduced that the cells are mechanically stressed by the tension associated with repeated contractions and that this results in the cells becoming compact and attracting each other, finally resulting in the formation of clusters. This process can be interpreted as modulation of a cellular network by the activity associated with contraction, which could be employed to control cellular networks by modifying the dynamics associated with the contractions in cardiac tissue culture.

Localized PEM mRNA and Protein Are Involved in Cleavage-Plane Orientation and Unequal Cell Divisions in Ascidians

Orientation and positioning of the cell division plane are essential for generation of invariant cleavage patterns and for unequal cell divisions during development. Precise control of the division plane is important for appropriate partitioning of localized factors, spatial arrangement of cells for proper intercellular interactions, and size control of daughter cells. Ascidian embryos show complex but invariant cleavage patterns mainly due to three rounds of unequal cleavage at the posterior pole. The ascidian embryo is an emerging model for studies of developmental and cellular processes. The maternal Posterior End Mark (PEM) mRNA is localized within the egg and embryo to the posterior region. PEM is a novel protein that has no known domain. Immunostaining showed that the protein is also present in the posterior cortex and the in centrosome-attracting body (CAB) and that the localization is extraction-resistant. Here we show that PEM of Halocynthia roretzi is required for correct orientation of early-cleavage planes and subsequent unequal cell divisions because it repeatedly pulls a centrosome toward the posterior cortex and the CAB, respectively, where PEM mRNA and protein are localized. When PEM activity is suppressed, formation of the microtubule bundle linking the centrosome and the posterior cortex did not occur. PEM possibly plays a role in anchoring microtubule ends to the cortex. In our model of orientation of the early-cleavage planes, we also amend the allocation of the conventional animal-vegetal axis in ascidian embryos, and discuss how the newly proposed A-V axis provides the rationale for various developmental events and the fate map of this animal. The complex cleavage pattern in ascidian embryos can be explained by a simple rule of centrosome attraction mediated by localized PEM activity. PEM is the first gene identified in ascidians that is required for multiple spindle-positioning events.

Control of growth and positional information by the graded vestigial expression pattern in the wing of Drosophila melanogaster

The size and shape of organs depend on cellular processes such as cell proliferation, cell survival, and spatial arrangement of cells. In turn, all of these processes are a consequence of positional identity of individual cells in whole organs. Links of positional information with organ growth and pattern expression of genes is a little-addressed question. We show that differences in vestigial expression between neighboring cells of the wing blade autonomously and nonautonomously affect cell proliferation along the proximo-distal axis. On the other hand, uniform expression of vestigial inhibits cell proliferation and also perturbs the shape of wing blade altering the preferential orientation of cell divisions. Our observations provide evidence that local cell interactions, triggered by differences in vestigial expression between neighboring cells, confer positional values operating in the control of growth and shape of the wing.

Granulometric analysis of corneal endothelium specular images by using a germ–grain model

Specular microscopy is widely used to study the human corneal endothelium status in vivo. In this paper, the corneal endothelium is represented as a binary image composed of the cell inscribed circles. The granulometric distribution function of the complement of this image is used as a functional descriptor, which provides information about the shape, size and spatial arrangement of cells. Experimental evaluation using bootstrap techniques shows its ability to discriminate between controls and pathological cases. It represents a reliable and graphical alternative to the classical indices (cell density, hexagonality and coefficient of variation of cell areas), which behave poorly when detecting subtle abnormalities.

Texture Pattern Generation Using Clonal Mosaic

In this paper, an effective system for synthesizing animal skin patterns on arbitrary polygonal surfaces is developed. To accomplish the task, a system inspired by the Clonal Mosaic (CM) model is proposed. The CM model simulates cells’ reactions on arbitrary surface. By controlling the division, mutation and repulsion of cells, a regulated spatial arrangement of cells is formed. This arrangement of cells shows appealing result, which is comparable with those natural patterns observed from animal skin. However, a typical CM simulation process incurs high computational cost, where the distances among cells across a polygonal surface are measured and the movements of cells are constrained on the surface. In this framework, an approach is proposed to transform each of the original 3D geometrical planes of the surface into its Canonical Reference Plane Structure. This structure helps to simplify a 3D computational problem into a more manageable 2D problem. Furthermore, the concept of Local Relaxation is developed to optimally enhance the relaxation process for a typical CM simulation. The performances of the proposed solution methods have been verified with extensive experimental results.

The Orientation of Cell Divisions Determines the Shape of Drosophila Organs

Organ shape depends on the coordination between cell proliferation and the spatial arrangement of cells during development. Much is known about the mechanisms that regulate cell proliferation, but the processes by which the cells are orderly distributed remain unknown. This can be accomplished either by random division of cells that later migrate locally to new positions (cell allocation) or through polarized cell division (oriented cell division; OCD). Recent data suggest that the OCD is involved in some morphogenetic processes such as vertebrate gastrulation, neural tube closure, and growth of shoot apex in plants; however, little is known about the contribution of OCD during organogenesis. We have analyzed the orientation patterns of cell division throughout the development of wild-type and mutant imaginal discs of Drosophila. Our results show a causal relationship between the orientation of cell divisions in the imaginal disc and the adult morphology of the corresponding organs, indicating a key role of OCD in organ-shape definition. In addition, we find that a subset of planar cell polarity genes is required for the proper orientation of cell division during organ development.

In vitro cartilage tissue engineering with 3D porous aqueous-derived silk scaffolds and mesenchymal stem cells

Adult cartilage tissue has limited self-repair capacity, especially in the case of severe damages caused by developmental abnormalities, trauma, or aging-related degeneration like osteoarthritis. Adult mesenchymal stem cells (MSCs) have the potential to differentiate into cells of different lineages including bone, cartilage, and fat. In vitro cartilage tissue engineering using autologous MSCs and three-dimensional (3-D) porous scaffolds has the potential for the successful repair of severe cartilage damage. Ideally, scaffolds designed for cartilage tissue engineering should have optimal structural and mechanical properties, excellent biocompatibility, controlled degradation rate, and good handling characteristics. In the present work, a novel, highly porous silk scaffold was developed by an aqueous process according to these criteria and subsequently combined with MSCs for in vitro cartilage tissue engineering. Chondrogenesis of MSCs in the silk scaffold was evident by real-time RT-PCR analysis for cartilage-specific ECM gene markers, histological and immunohistochemical evaluations of cartilage-specific ECM components. Dexamethasone and TGF-β3 were essential for the survival, proliferation and chondrogenesis of MSCs in the silk scaffolds. The attachment, proliferation, and differentiation of MSCs in the silk scaffold showed unique characteristics. After 3 weeks of cultivation, the spatial cell arrangement and the collagen type-II distribution in the MSCs-silk scaffold constructs resembles those in native articular cartilage tissue, suggesting promise for these novel 3-D degradable silk-based scaffolds in MSC-based cartilage repair. Further in vivo evaluation is necessary to fully recognize the clinical relevance of these observations.

Morphological and molecular analysis of the early developing chick requires an expanded series of primitive streak stages

A detailed analysis of the gastrulating chick embryo was performed using three methods : time-lapse videotaping of embryos in culture, histological semithin sections, and in situ hybridization with 10 mRNA signals expressed during gastrulation. The results suggest that the gene expression pattern of Goosecoid, Hex, Crescent, and Bmp7 may be involved in the axial establishment of the temporal and spatial arrangement of cells forming the prechordal plate endoderm, and that Chordin, cNot1, Noggin, and Brachyury are precocious markers of cells coming from Hensen's node, which contribute to the rostralmost tip of the notochord, its arrowhead, the head process, and, later, the elongating notochord. These results explain several earlier descriptions based only on morphological analyses of the axial mesodermal structures characteristic of the gastrulation stages. The data, carefully observed and compared with the whole-mount observation in time-lapse video, show that the changes in cell populations, movements, and cell differentiation occur step-by-step over a precise temporal range, which requires the establishment of a subdivision of the stages usually employed. Knowledge of new aspects of avian gastrulation, including gene expression patterns, immunocytochemical analyses, and the great number of recent experiments based on microinjections or transplants of groups of cells to analyze processes of induction or regulation, need the support of a precisely defined scheme of primitive streak stages (PS-stages), and a correlation of these stages with other approaches to provide a finer resolution of the staging steps, and thus to facilitate a better understanding of the initial gastrulation period.

Architectural analysis of oral cancer, dysplastic, and normal epithelia

We present a novel, automated, and quantitative approach to evaluate local epithelial tissue architecture based on mathematical graph theory. Four hundred forty-one images of three diagnostic classes of oral epithelium (normal, dysplastic, and neoplastic) were analysed. The epithelial compartment was partitioned into exclusive areas associated with each nucleus to approach the theoretical cell extents. The spatial arrangement of cells in neighbourhoods of two sizes was characterised by constructing graph networks based on the cell centroids and recording 29 statistical properties. We analysed 104,627 and 67,590 neighbourhoods of diameters 37.5 and 75 microm, respectively. The discrimination power of the architectural descriptors was evaluated by using discriminant analysis. The best neighbourhood discrimination rate was 75% for normal versus carcinoma. For the pooled data, discrimination into three classes based on largest number of neighbourhoods associated with each class was 100% correct. Case-wise, discrimination rates were 67%, 100%, and 80% correct for normal, premalignant, and malignant. When considering two classes, discrimination rates was 89% (normal) and 100% (malignant) correct, with 71% of premalignant cases assigned to the malignant class. The results indicate that unbiased and reproducible quantification of tissue architectural features is possible and may provide valuable morphological information for diagnostic purposes.

Minimally invasive tissue engineering composites and cell printing.

Injectable composites combined with tissue-printing technology for improved bioengineered devices. The invisible engineering problem, the one often ignored, is the design of a readily implantable, precisely assembled cellular construct. Previous studies have consistently shown that composite tissue-engineered devises are readily implanted via minimally invasive means and, in the systems tested, produce minimal inflammation and fibrous encapsulation. Gels of optimal viscosity are able to maintain separation between the cellular scaffold and allow tissue growth. Studies with the cell/substrate printing system have shown that it is possible to define, in a controlled manner, spatial arrangement of cells within a gel substrate.

MORPHOMETRIC ANALYSIS OF HUMAN CORNEAL ENDOTHELIUM BY MEANS OF SPATIAL POINT PATTERNS

This paper presents a method for detecting abnormalities in spatial arrangements of cells within any tissue that can be described by different sets of relevant points. The method has been applied to the detection of subtle abnormalities in corneal endothelia. Images of this type of tissue can be characterized by two types of points: cell centroids and triple points associated with the apical intersections as it was proposed by Díaz.7 Both types of points jointly considered are modeled using a bivariate spatial point process; then a statistical analysis based on certain distributional descriptors proposed by Doguwa4,9 is carried out to discriminate severe and subtle abnormalities from controls. According to the results, the method constitutes a valid alternative to currently used techniques, which involve statistical descriptions of cell density, cell area and hexagonality, that fail in the detection of these subtle abnormalities.

Population dynamics and habitat connectivity affecting the spatial spread of populations – a simulation study

In this paper we show how the spatialconfiguration of habitat quality affects the spatial spread of apopulation in a heterogeneous environment. Our main result is thatfor species with limited dispersal ability and a landscape withisolated habitats, stepping stone patches of habitat greatlyincrease the ability of species to disperse. Our results showthat increasing reproductive rate first enables and thenaccelerates spatial spread, whereas increasing the connectivity has aremarkable effect only in case of low reproductive rates. Theimportance of landscape structure varied according to thedemographic characteristics of the population. To show this wepresent a spatially explicit habitat model taking into accountpopulation dynamics and habitat connectivity. The population dynamicsare based on a matrix projection model and are calculated on eachcell of a regular lattice. The parameters of the Leslie matrix dependon habitat suitability as well as density. Dispersal between adjacentcells takes place either unrestricted or with higher probability inthe direction of a higher habitat quality (restricted dispersal).Connectivity is maintained by corridors and stepping stones ofoptimal habitat quality in our fragmented model landscape containinga mosaic of different habitat suitabilities. The cellular automatonmodel serves as a basis for investigating different combinations ofparameter values and spatial arrangements of cells with high and lowquality.

An image analysis method for the study of cell adhesion to biomaterials.

This fluorescence image analysis method for the quantitative determination of cell adhesion on biomaterials allows bone cells labelled with propidium iodide to be counted automatically, directly on their support. The reliability of the estimation by fluorescence image analysis was validated by comparison with visual counting and with results obtained by an electronic particle counter. In this way it was possible to demonstrate that the adhesive properties of bone cells are dependent on the type of substrate--enstatite (MgO, SiO2, CaO-P2O5-Al2O3), Thermanox (modified polyethyleneterephthalate), or glass. In contrast, the spread of the cell cytoplasm, labelled with fluorescein isothiocyanate and measured by image analysis, does not vary significantly according to the substrate. The characterisation by SKIZ tessellation of the spatial cell arrangement shows that the bone cells have a random organisation on Thermanox and glass, whereas they form aggregates on enstatite.