The probability of contact between the immunocompetent cell and antigen

The present work is an attempt to make a mathematical formulation of the first part of a well-known hypothesis (Šterzl, 1967) dealing with the course of differentiation of an immunocompetent cell into an antibody-producing cell, namely with the early event—the contact between the cell and antigen. The probability of an event, namely that during the given time interval the contact between the immunocompetent cell and antigen will take place, was studied. The corresponding probability distribution depends substantially on the function describing the fate of antigen following its injection into the organism and further, on the amount of active antigen that is present in the organism in dependence on the length of time after the antigen injection. In addition to a general formula, formula were even obtained describing one particular important function of the decrease in the amount of antigen (exponential).     

Extracting multi-way chromatin contacts from Hi-C data

There is a growing realization that multi-way chromatin contacts formed in chromosome structures are fundamental units of gene regulation. However, due to the paucity and complexity of such contacts, it is challenging to detect and identify them using experiments. Based on an assumption that chromosome structures can be mapped onto a network of Gaussian polymer, here we derive analytic expressions for n-body contact probabilities (n > 2) among chromatin loci based on pairwise genomic contact frequencies available in Hi-C, and show that multi-way contact probability maps can in principle be extracted from Hi-C. The three-body (triplet) contact probabilities, calculated from our theory, are in good correlation with those from measurements including Tri-C, MC-4C and SPRITE. Maps of multi-way chromatin contacts calculated from our analytic expressions can not only complement experimental measurements, but also can offer better understanding of the related issues, such as cell-line dependent assemblies of multiple genes and enhancers to chromatin hubs, competition between long-range and short-range multi-way contacts, and condensates of multiple CTCF anchors.     

On the distribution of the epoch of the first contact of immunocompetent cell with antigen

A hypothesis on the dynamics of the immune reaction at a cellular level is considered, as was presented by Šterzl (1967). According to this hypothesis, the onset of the immune response depends on the first contact of a so-called virgin immunocompetent cell with the antigen. In the present paper a conditional probability distribution of the epoch of this first contact is derived, assuming that such a contact occurs at all (probability of non-occurrence of the contact being, in the general case, positive); the density of this distribution (7) is then specified (8) for the case that decrease of the quantity of an active antigen follows an exponential curve, and moments of this distribution are calculated (12).     

Rab35 regulates cadherin-mediated adherens junction formation and myoblast fusion

Cadherins are homophilic cell–cell adhesion molecules implicated in many fundamental processes, such as morphogenesis, cell growth, and differentiation. They accumulate at cell–cell contact sites and assemble into large macromolecular complexes named adherens junctions (AJs). Cadherin targeting and function are regulated by various cellular processes, many players of which remain to be uncovered. Here we identify the small GTPase Rab35 as a new regulator of cadherin trafficking and stabilization at cell–cell contacts in C2C12 myoblasts and HeLa cells. We find that Rab35 accumulates at cell–cell contacts in a cadherin-dependent manner. Knockdown of Rab35 or expression of a dominant-negative form of Rab35 impaired N- and M-cadherin recruitment to cell–cell contacts, their stabilization at the plasma membrane, and association with p120 catenin and led to their accumulation in transferrin-, clathrin-, and AP-2–positive intracellular vesicles. We also find that Rab35 function is required for PIP5KIγ accumulation at cell–cell contacts and phosphatidyl inositol 4,5-bisphosphate production, which is involved in cadherin stabilization at contact sites. Finally, we show that Rab35 regulates myoblast fusion, a major cellular process under the control of cadherin-dependent signaling. Taken together, these results reveal that Rab35 regulates cadherin-dependent AJ formation and myoblast fusion.     

Multi-type branching models to describe cell differentiation programs

Cell proliferation and differentiation is described by a multi-type branching process, a probability model that defines the inheritance of cell type. Cell type is defined by (i) a repression index related to the time required for S-phase entry and (ii) phenotype as determined by cell markers and division history. The inheritance of cell type is expressed as the expected number and type of progeny cells produced by a mother cell given her type. Expressions for the expected number and type of cells produced by a multi-cellular (bulk culture) system are derived from the general model by making the simplifying assumption that cell generation times are independent. The multi-type Smith-Martin model (MSM) makes the further assumption that cell generation times are lag-exponentially distributed with phenotype transitions occurring just before entry into S-phase. The inheritance-modified MSM (IMSM) model includes the influence of generation time memory so that mother and daughter generation times are correlated. The expansion of human cord blood CD34⁺ cells by haematopoietic growth factors was division tracked in bulk culture using carboxyfluorescein diacetate, succinimidyl ester (CFDA-SE). The MSM model was fitted to division tracking data to indentify cell cycle length, and the rates of CD34 antigen down-regulation and apoptosis. The IMSM model was estimated for mouse granulocyte-macrophage progenitors using live cell imaging data. Multi-type branching models describe cell differentiation dynamics at both single- and multi-cell scales, providing a new paradigm for systematic analysis of stem and progenitor cell development.     

Ultrastructure of interstitial cells of Cajal at the gastro-oesophageal junction of the monkey (Macaca fascicularis)

The ultrastructure of the interstitial cells of Cajal (ICC) in the oesophagus of the monkey resembled that described in the oesophagus of other mammalian species but differed in their paucity and almost lack of smooth endoplasmic reticulum, caveolae and filaments. The plasmalemma of the ICC was in close contact (20- to 30-nm gaps) with that of smooth muscle cells. This may occasionally take the form of a desmosome, but gap junctions have not been observed. Vesiculated axon profiles, containing large granular or agranular vesicles were in close contact (20- to 30-nm gaps) with the plasmalemma of ICC. In a few vesiculated profiles a presynaptic density could be recognized. The intercalation of the ICC between the vesiculated axon profiles and the smooth muscle cells suggest a role in oesophageal motility. Between 3 and 21 days following bilateral vagotomy some ICC showed regressive changes such as increased electron density and shrinkage of the cytoplasm, crowding of the organelles and dissolution of the nuclear chromatin material. Axon profiles in the vicinity of the affected ICC contained glycogen granules suggesting injury. In late stages, the number of ICC and smooth muscle contacts was reduced. The results suggest that the vagus nerves exert a trophic influence on the ICC and that the intercellular relationships between ICC and smooth muscle cells possess a degree of plasticity. It is tentatively suggested that these vagal effects may be mediated via the oesophageal myenteric ganglia.     

Evaluation of CD8 T cell killing models with computer simulations of 2-photon imaging experiments

In vivo imaging of cytotoxic T lymphocyte (CTL) killing activity revealed that infected cells have a higher observed probability of dying after multiple contacts with CTLs. We developed a three-dimensional agent-based model to discriminate different hypotheses about how infected cells get killed based on quantitative 2-photon in vivo observations. We compared a constant CTL killing probability with mechanisms of signal integration in CTL or infected cells. The most likely scenario implied increased susceptibility of infected cells with increasing number of CTL contacts where the total number of contacts was a critical factor. However, when allowing in silico T cells to initiate new interactions with apoptotic target cells (zombie contacts), a contact history independent killing mechanism was also in agreement with experimental datasets. The comparison of observed datasets to simulation results, revealed limitations in interpreting 2-photon data, and provided readouts to distinguish CTL killing models.     

Monoclonal antibodies against contact sites A of Dictyostelium discoideum: detection of modifications of the glycoprotein in tunicamycin-treated cells

Tunicamycin acts on cell aggregation in Dictyostelium discoideum by changing cell movement and by inhibiting the EDTA-stable type of intercellular adhesion. Tunicamycin-treated cells show unco-ordinated pseudopodial activity such that pseudopods are simultaneously extended from all parts of the cell surface, and the cells are unable to move in straight paths. Concurrent with the inhibition of formation of EDTA-stable contacts, N-glycosylation of a glycoprotein specific for aggregation-competent cells is inhibited. This glycoprotein, previously called contact site A, has an apparent mol. wt. of 80 kilodaltons (kd). In membranes of tunicamycin-treated cells, two components are detected that react with certain monoclonal antibodies against contact sites A: one component of 66 kd, the other of 53 kd apparent mol. wt. Another group of monoclonal antibodies reacts only with the 80-kd glycoprotein and the 66-kd component. These results are in accord with the assumption that the glycoprotein carries two carbohydrate chains, and that the antibodies differ in their requirement for glycosylation of the antigen. Despite the coincidence between blockage of EDTA-stable cell adhesion and inhibited glycosylation of contact sites A, direct involvement of the carbohydrate moieties of this glycoprotein in intercellular adhesion seems questionable. EDTA-stable cell adhesion has not been blocked by Fab fragments from antibodies that specifically react with the glycosylated protein.     

Adenoviral Transduction of Naive CD4 T Cells to Study Treg Differentiation

Regulatory T cells (Tregs) are essential to provide immune tolerance to self as well as to certain foreign antigens. Tregs can be generated from naive CD4 T cells in vitro with TCR- and co-stimulation in the presence of TGFβ and IL-2. This bears enormous potential for future therapies, however, the molecules and signaling pathways that control differentiation are largely unknown.Primary T cells can be manipulated through ectopic gene expression, but common methods fail to target the most important naive state of the T cell prior to primary antigen recognition. Here, we provide a protocol to express ectopic genes in naive CD4 T cells in vitro before inducing Treg differentiation. It applies transduction with the replication-deficient adenovirus and explains its generation and production. The adenovirus can take up large inserts (up to 7 kb) and can be equipped with promoters to achieve high and transient overexpression in T cells. It effectively transduces naive mouse T cells if they express a transgenic Coxsackie adenovirus receptor (CAR). Importantly, after infection the T cells remain naive (CD44^low, CD62L^high) and resting (CD25^-, CD69^-) and can be activated and differentiated into Tregs similar to non-infected cells. Thus, this method enables manipulation of CD4 T cell differentiation from its very beginning. It ensures that ectopic gene expression is already in place when early signaling events of the initial TCR stimulation induces cellular changes that eventually lead into Treg differentiation.     

Ultrastructural changes in the connective tissue of the gastric region during the metamorphosis of Xenopus laevis

Development of the gastric connective tissue of Xenopus laevis during metamorphosis was investigated by electron microscopy. Throughout the larval period to stage 60, the layer of connective tissue underlying the gastric epithelium consists of immature fibroblasts surrounded by a sparse extracellular matrix. At the beginning of the transition from the larval to the adult epithelial form, at about stage 60, extensive changes occur in the connective tissue. The number of cells suddenly increses and different cell types appear. Numerous contacts between epithelial and connective tissue cells are established through random gaps in the thickened basal lamina. During stages 62–63, just after the beginning of the morphogenesis of adult-type glands, the basal lamina lining the glandular epithelium becomes thinner, and the number of contacts decreases rapidly except near the tips of the glands. After the glandular cells begin to produce zymogen granules at stage 64, contacts become rare. From stage 63, when the muscularis mucosae develops, until the completion of metamorphosis, the connective tissue consists mainly of typical fibroblasts. Outside the muscularis mucosae, the fibroblasts of the lamina propria are aligned in parallel with the curvature of the glands. These observations indicate that developmental changes in the connective tissue are closely related spatiotemporally to those of the epithelial transition from larval to adult form during metamorphic climax. Although some changes are similar to those in the intestine (Ishizuya-Oka and Shimozawa, '87b), others are specific to the gastric region, which suggests that connective tissue may have a role in organ-specific differentiation of the gastric epithelium.     

Predicting epidemics on directed contact networks

Contact network epidemiology is an approach to modeling the spread of infectious diseases that explicitly considers patterns of person-to-person contacts within a community. Contacts can be asymmetric, with a person more likely to infect one of their contacts than to become infected by that contact. This is true for some sexually transmitted diseases that are more easily caught by women than men during heterosexual encounters; and for severe infectious diseases that cause an average person to seek medical attention and thereby potentially infect health care workers (HCWs) who would not, in turn, have an opportunity to infect that average person. Here we use methods from percolation theory to develop a mathematical framework for predicting disease transmission through semi-directed contact networks in which some contacts are undirected-the probability of transmission is symmetric between individuals-and others are directed-transmission is possible only in one direction. We find that the probability of an epidemic and the expected fraction of a population infected during an epidemic can be different in semi-directed networks, in contrast to the routine assumption that these two quantities are equal. We furthermore demonstrate that these methods more accurately predict the vulnerability of HCWs and the efficacy of various hospital-based containment strategies during outbreaks of severe respiratory diseases.     

Quantitative analysis of the 51Cr release cytotoxicity assay for cytotoxic lymphocytes

Using ⁵¹Cr-labelled P-815 mastocytoma cells as target cells and CS7BL/6 spleen cells sensitized against DBA/2 antigens as effector cells, it is shown that the variation in the observed specific ⁵¹Cr release over a broad range of experimental conditions can be explained on the basis of a simple physical model of the interaction process. The model assumes that a target cell can be destroyed only after contact with an effector cell, contact takes place on a random basis, one contact is sufficient, and that one effector cell can kill several targets with unchanged efficiency. The fraction of target cells destroyed (f) depends only on the incubation time (t), the number of effector cells (n) and a constant interaction probability (δ). Thus f = 1 ? e^?nδt. However, the experimental measurement, the fraction of ⁵¹Cr specifically released into the supernatant during the assay, may not be the same as the fraction of target cells destroyed because it takes considerable time for the releasable ⁵¹Cr to be released from a damaged target cell. This can be overcome experimentally by following the standard 37 °C incubation with a further incubation at 45 °C during which there are no new lytic events but all previously damaged target cells release the remainder of their releasable ⁵¹Cr. The model enables one to obtain accurate measurements of relative effector cell frequency over a broad range of experimental conditions.     

Intercellular contacts at the epithelial-mesenchymal interface during the prenatal development of the rat submandibular gland

During the investigation of the embryogenesis of the rat submandibular gland (SMG), direct epithelial-mesenchymal and epithelial-nerve contacts were observed by light and electron microsopy. These contacts were seen at the epithelial-mesenchymal interface of the end buds of the initial four to twelve branches of the glandular rudiment during the period of rapid branching and budding of the analage. The epithelial-mesenchymal contacts were made by either mesenchymal or epithelial cell extensions which penetrated small gaps in the basal lamina to contact an apposing cell. The epithelial-mesenchymal contact zones showed several morphologic variations, but no septate or gap junctions were seen. The epithelial-nerve contacts were primarily of the intermediate contact zone variety although some tight-type contacts were seen. They were not typical synaptic junctions. The fine structure and importance of these unusual contact zones in the prenatal differentiation of the submandibular gland rudiment are discussed.     

Mouse versions of fly developmental control genes: legitimate or illegitimate relatives?

Embryo development requires a complex order of events that must occur at the correct time and in the correct space. A series of decisions takes place as cells divide and become committed to increasingly specialized and limited domains of the embryo. Many genes that are important in orchestrating this process were originally identified in the fruitfly Drosophila melanogaster. Conserved sequences from the fly genes have been used to clone homologous genes in vertebrates, including mice. Studies of the pattern of expression of these genes during murine development in conjunction with the use of new functional assays suggest that not only DNA sequences, but also functional roles during embryogenesis, have been conserved. Thus, we may have the tools in hand to begin to understand how vertebrate development and cell differentiation take place.     

Development of neurons in the abdominal ganglion of Aplysia californica. I. Axosomatic synaptic contacts.

The development of mariculture techniques for the raising of Aplysia californica in the laboratory from fertilized egg to reproductively mature adult permits the study of the developmental program whereby individual identified neurons in the abdominal ganglion acquire their specific adult properties. In this paper, we describe one of the early steps of this developmental program: the outgrowth of axonal processes by neurons of the abdominal ganglion. Axonal outgrowth is correlated with and may be triggered by the transient appearance of morphologically identifiable axosomatic contacts between the as yet undifferentiated cell body of specific neurons and an axon terminal from an incoming nerve fiber from the pleuroabdominal connective. The evidence that transient axosomatic contacts may signal neuronal differentiation is the following: (1) Axosomatic contacts have not been observed in the abdominal ganglion of adult animals, whereas they are commonly observed during the early stages of development. (2) Cells that receive axosomatic contacts are undifferentiated morphologically and do not as yet have axons. By contrast, cells with axons do not have soma contacts. (3) Individual cells that can be identified from animal to animal in the same and succeeding developmental stages receive axosomatic contacts on similar topographic postions of the cell body at one point in development. Axon outgrowth then occurs at the site of contact. Later in development, with further axon extension, these cells no longer have synaptic contacts on the cell body or axon.     

Cell-type specific dendritic contacts between retinal ganglion cells during development.

The extent of a neuron's dendritic field defines the region within which information is processed. The dendritic fields of functionally distinct ON and OFF center retinal ganglion cells (RGCs) form separate mosaics across the retina. Within each mosaic, neighboring dendritic fields overlap by a constant amount, sampling the visual field with the appropriate coverage. Contact-mediated lateral inhibition between neighboring RGCs has long been thought to regulate both the extent and overlap of dendritic fields during development. Here we show that dendro-dendritic contact exists between developing RGCs and occurs in a manner that would regulate the formation of ON and OFF mosaics separately. Dye-filled neighboring ON and OFF ferret alpha RGCs were reconstructed using multiphoton microscopy. At all neonatal ages examined, we observed dendro-dendritic contacts between RGCs of the same sign (ON/ON; OFF/OFF), but never between cells of opposite signs (ON/OFF). Terminal dendrites of one cell often touched a dendrite of its neighbor as they intersected. In some instances, the distal dendrite of one cell formed a fascicle with the proximal process of its neighbor. Alpha cells did not form contacts with neighboring beta cells of the same sign. Together, these observations suggest that dendro-dendritic contact between RGCs is cell-type specific. Dendritic contacts were observed even before the alpha cell arbors were completely stratified, suggesting that cell-cell recognition may take place early in their development. For each cell type, the relative overlap of dendritic fields was constant with age, despite a two-fold increase in field area. We suggest that dendro-dendritic contacts may be sites of intercellular signaling that could regulate local extension of dendrites to maintain the relative overlap of RGCs within a mosaic during development.     

Residue-residue contact substitution probabilities derived from aligned three-dimensional structures and the identification of common folds.

We report the derivation of scores that are based on the analysis of residue-residue contact matrices from 443 3-dimensional structures aligned structurally as 96 families, which can be used to evaluate sequence-structure matches. Residue-residue contacts and the more than 3 x 10(6) amino acid substitutions that take place between pairs of these contacts at aligned positions within each family of structures have been tabulated and segregated according to the solvent accessibility of the residues involved. Contact maps within a family of structures are shown to be highly conserved (approximately 75%) even when the sequence identity is approaching 10%. In a comparison involving a globin structure and the search of a sequence databank (> 21,000 sequences), the contact probability scores are shown to provide a very powerful secondary screen for the top scoring sequence-structure matches, where between 69% and 84% of the unrelated matches are eliminated. The search of an aligned set of 2 globins against a sequence databank and the subsequent residue contact-based evaluation of matches locates all 618 globin sequences before the first non-globin match. From a single bacterial serine proteinase structure, the structural template approach coupled with residue-residue contact substitution data lead to the detection of the mammalian serine proteinase family among the top matches in the search of a sequence databank.     

Calcium response of helper T lymphocytes to antigen-presenting cells in a single-cell assay.

We developed a dynamic, single-cell assay involving alternating differential interference contrast and fluorescence microscopy, together with digital imaging, for both viewing the physical interaction of live helper T lymphocytes (Th cells) with antigen-presenting cells (APCs) and monitoring the increases in the intracellular free calcium concentration of the Th cell, an early event in Th cell activation. We obtained Th-APC conjugates by allowing the Th cells to migrate toward and interact with APCs that either settled nearby or had been micromanipulated in close proximity to the Th cells. Th cell motility played an important role in initiating Th-APC contacts but not in determining the Th cell calcium response. We found that the intracellular calcium responses of individual Th cells are heterogeneous and an all-or-none phenomenon, independent of antigen concentration. However, the fraction of Th-APC conjugates involving responding Th cells is an increasing function of the antigen concentration. Finally, we measured some characteristics of the developing Th-APC contact area. We used all of these data together with previously developed mathematical models to estimate that only 1 to 20 major histocompatibility class II-antigen complexes are required in the initial Th-APC contact area to elicit a Th cell calcium response.     

Stochastic branching model for hemopoietic progenitor cell differentiation

We present algebraic expressions describing the predictions of a stochastic branching model for differentiation of hemopoietic progenitor cells. The model assumes that there is a fixed probability, p (0 less than or equal to p less than or equal to 1), that commitment to a differentiative event occurs per progenitor cell division for each daughter cell. The model describes properties of in vitro hemopoietic cell differentiation including the population structure at the time the first progenitor cell becomes committed, the number of committed progenitor cells engendered by a single progenitor cell, and the probability of eventual commitment of all daughter cells derived from a single progenitor or stem cell. Application of the model to experimental data obtained from erythroid cultures suggests that the observed data can be explained by the stochastic branching model alone without making the deterministic assumption that there is a differentiative hierarchy in the lineage of the progenitors of erythropoiesis (BFU-E). The qualitative and quantitative aspects of the proposed stochastic model are discussed in conjunction with other analogous stochastic branching models.