Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities

Detection of different extracellular stimuli leading to functionally distinct outcomes is ubiquitous in cell biology, and is often mediated by differential regulation of positive and negative feedback loops that are a part of the signaling network. In some instances, these cellular responses are stimulated by small numbers of molecules, and so stochastic effects could be important. Therefore, we studied the influence of stochastic fluctuations on a simple signaling model with dueling positive and negative feedback loops. The class of models we have studied is characterized by single deterministic steady states for all parameter values, but the stochastic response is bimodal; a behavior that is distinctly different from models studied in the context of gene regulation. For example, when positive and negative regulation is roughly balanced, a unique deterministic steady state with an intermediate value for the amount of a downstream signaling product is found. However, for small numbers of signaling molecules, stochastic effects result in a bimodal distribution for this quantity, with neither mode corresponding to the deterministic solution; i.e., cells are in "on" or "off" states, not in some intermediate state. For a large number of molecules, the stochastic solution converges to the mean-field result. When fluctuations are important, we find that signal output scales with control parameters "anomalously" compared with mean-field predictions. The necessary and sufficient conditions for the phenomenon we report are quite common. So, our findings are expected to be of broad relevance, and suggest that stochastic effects can enable binary cellular decisions.

Scaffold proteins confer diverse regulatory properties to protein kinase cascades

The assembly of multiple signaling proteins into a complex by a scaffold protein guides many cellular decisions. Despite recent advances, the overarching principles that govern scaffold function are not well understood. We carried out a computational study using kinetic Monte Carlo simulations to understand how spatial localization of kinases on a scaffold may regulate signaling under different physiological conditions. Our studies identify regulatory properties of scaffold proteins that allow them to both amplify and attenuate incoming signals in different biological contexts. These properties are not caused by the well established prozone or combinatorial inhibition effect. These results bring coherence to seemingly paradoxical observations and suggest that cells have evolved design rules that enable scaffold proteins to regulate widely disparate cellular functions.

Phase segregation on different length scales in a model cell membrane system

Lipid rafts are sphingolipid- and cholesterol-enriched domains on cell membranes that have been implicated in many biological functions, especially in T lymphocytes. We used a field theory to examine the forces underlying raft formation on resting living cell membranes. We find that it is difficult to reconcile the observed size of rafts on living cell membranes ( approximately 100 nm) with a mechanism that involves coupling between spontaneous curvature differences and concentration fluctuations. Such a mechanism seems to predict raft domain sizes that are larger and commensurate with those observed on synthetic membranes. Therefore, using a Poisson-Boltzmann approach, we explore whether electrostatic forces originating from transmembrane proteins and net negative charges on cell membranes could play a role in determining the raft size in living cell membranes. We find that a balance among the intrinsic tendency of raft components to segregate, the line tension, and the effective dipolar interactions among membrane constituents leads to a stable phase with a characteristic length scale commensurate with the observed size of rafts on living cell membranes. We calculate the phase diagram of a system in which these three types of forces are important. In a certain region of the parameter space, an interesting phase with mosaic-like morphology consisting of an intertwined pattern of raft and nonraft domains is predicted. Experiments that could further assess the importance of dipolar interactions for lateral organization of the components on multiple length scales in membranes are suggested.

A hybrid deterministic-stochastic algorithm for modeling cell signaling dynamics in spatially inhomogeneous environments and under the influence of external fields

Cell signaling dynamics mediate myriad processes in biology. It has become increasingly clear that inter- and intracellular signaling reactions often occur in a spatially inhomogeneous environment and that it is important to account for stochastic fluctuations of certain species involved in signaling reactions. The importance of these effects enhances the difficulty of gleaning mechanistic information from observations of a few experimental reporters and highlights the significance of synergistic experimental and computational studies. When both stochastic fluctuations and spatial inhomogeneity must be included in a model simultaneously, however, the resulting computational demands quickly become overwhelming. In many situations the failure of standard coarse-graining methods (i.e., ignoring spatial variation or stochastic fluctuations) when applied to all components of a complex system does not exclude the possibility of successfully applying such coarse-graining to some components of the system. Following this approach alleviates computational cost but requires "hybrid" algorithms where some variables are treated at a coarse-grained level while others are not. We present an efficient algorithm for simulation of stochastic, spatially inhomogeneous reaction-diffusion kinetics coupled to coarse-grained fields described by (stochastic or deterministic) partial differential equations (PDEs). The PDEs could represent mean-field descriptions of reactive species present in large copy numbers or evolution of hydrodynamic variables that influence signaling (e.g., membrane shape or cytoskeletal motion). We discuss the approximations made to derive our algorithm and test its efficacy by applying it to problems that include many features typical of realistic cell signaling processes.

A dendronized polymer is a single-molecule glass

The molecular architecture of dendronized polymers can be tuned to obtain nanoscale objects with desired properties. In this paper, we bring together experiments and computer simulations to study the thermodynamic and dynamic properties of a single dendronized polymer chain. We find that, upon changing certain architectural features, dynamic correlations characterizing backbone conformational fluctuations of a dendronized polymer exhibit dynamics akin to glass-forming bulk liquids. Thus, a dendronized polymer chain is a novel macromolecule that is a single-molecule glass. Over a range of conditions that lead to glassy dynamics, there does not appear to be any thermodynamic singularities. We discuss how a dendronized polymer is a molecular system that can directly test different models of glassy dynamics. We also show that defect densities characteristic of typical synthesis conditions do not alter the material properties of dendronized polymers.

Empty class II major histocompatibility complex created by peptide photolysis establishes the role of DM in peptide association

DM catalyzes the exchange of peptides bound to Class II major histocompatibility complex (MHC) molecules. Because the dissociation and association components of the overall reaction are difficult to separate, a detailed mechanism of DM catalysis has long resisted elucidation. UV irradiation of DR molecules loaded with a photocleavable peptide (caged Class II MHC molecules) enabled synchronous and verifiable evacuation of the peptide-binding groove and tracking of early binding events in real time by fluorescence polarization. Empty DR molecules generated by photocleavage rapidly bound peptide but quickly resolved into species with substantially slower binding kinetics. DM formed a complex with empty DR molecules that bound peptide with even faster kinetics than empty DR molecules just having lost their peptide cargo. Mathematical models demonstrate that the peptide association rate of DR molecules is substantially higher in the presence of DM. We therefore unequivocally establish that DM contributes directly to peptide association through formation of a peptide-loading complex between DM and empty Class II MHC. This complex rapidly acquires a peptide analogous to the MHC class I peptide-loading complex.

Sensitivity of T cells to antigen and antagonism emerges from differential regulation of the same molecular signaling module

Activation of T helper cells is necessary for the adaptive immune response to pathogens, and spurious activation can result in organ-specific autoimmunity (e.g., multiple sclerosis). T cell activation is initiated by membrane-proximal signaling that is predicated on the binding of the T cell receptor expressed on the T cell surface to peptide major histocompatibility complex (pMHC) molecules presented on the surface of antigen-presenting cells. These signaling processes regulate diverse outcomes, such as the ability of T cells to discriminate sensitively between stimulatory pMHC molecules and those that are characteristic of "self," and the phenomenon of antagonism (wherein the presence of certain pMHC molecules impairs T cell receptor signaling). We describe a molecular model for membrane-proximal signaling in T cells from which these disparate observations emerge as two sides of the same coin. This development of a unified mechanism that is consistent with diverse data would not have been possible without explicit consideration of the stochastic nature of the pertinent biochemical events. Our studies also reveal that certain previously proposed concepts are not dueling ideas but rather are different stimuli-dependent manifestations of a unified molecular model for membrane-proximal signaling. This model may provide a conceptual framework for further investigations of early events that regulate T cell activation in response to self and foreign antigens and for the development of intervention protocols to inhibit aberrant signaling.

The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse

T cell activation is predicated on the interaction between the T cell receptor and peptide-major histocompatibility (pMHC) ligands. The factors that determine the stimulatory potency of a pMHC molecule remain unclear. We describe results showing that a peptide exhibiting many hallmarks of a weak agonist stimulates T cells to proliferate more than the wild-type agonist ligand. An in silico approach suggested that the inability to form the central supramolecular activation cluster (cSMAC) could underlie the increased proliferation. This conclusion was supported by experiments that showed that enhancing cSMAC formation reduced stimulatory capacity of the weak peptide. Our studies highlight the fact that a complex interplay of factors determines the quality of a T cell antigen.

Effects of quenched and annealed macromolecular crowding elements on a simple model for signaling in T lymphocytes

Biochemical reactions in cells occur in an environment that is crowded in the sense that various macromolecular species and organelles occupy much of the space. The effects of molecular crowding on biochemical reactions have usually been studied in the past in a spatially homogeneous environment. However, signal transduction in cells is often initiated by the binding of receptors and ligands in two apposed cell membranes, and the pertinent biochemical reactions occur in a spatially inhomogeneous environment. We have studied the effects of crowding on biochemical reactions that involve both membrane proteins and cytosolic molecules by investigating a simplified version of signaling in T lymphocytes using a Monte Carlo algorithm. We find that, if signal transduction occurs on time scales that are slow compared to the motility of the molecules and organelles that constitute the crowding elements, the effects of crowding are qualitatively the same as in a homogeneous three-dimensional (3D) medium. In contrast, if signal transduction occurs on a time scale that is much faster than the time over which the crowding elements move, then the effects of varying the extent of crowding are very different when reactions occur in both 2- and 3D space. We discuss these differences and their origin. Since many signaling reactions are fast, our results may be useful for diverse situations in cell biology.

Polarization phase in aberration compensation

A phase/amplitude mask on the aperture of an imaging system results in a pupil function that is multiplicative with the lens function, resulting in a morphological transformation of the imaging wavefront. It was shown that such amplitude and phase functions can be implemented using polarization masks, with the advantage that the phase and amplitude can be controlled in real time and in some cases, independently of each other. The phase and amplitude variation over the mask can be controlled either by changing the polarization of the mask or by changing the input beam parameters. Wavefront tailoring using polarization-masked apertures is therefore feasible and may be utilized for focal shift and partial aberration compensation. For complete compensation of aberration, the phase distribution over the mask should be conjugate to that of the phase error of the aberrant wavefront, which necessitates the use of a continuously variable polarization mask. Since such a mask is difficult to implement, we have considered polarizing masks consisting of discrete polarized zones on the lens aperture, leading to polarization phase steps on the exit pupil of the imaging system. The simulation results presented in this paper show that effects of focal shift, partial compensation of primary spherical aberration and astigmatism can indeed be achieved by the proper use of polarization masked apertures.

Hybridization dynamics of surface immobilized DNA

We model the hybridization kinetics of surface attached DNA oligomers with solubilized targets. Using both master equation and rate equation formalisms, we show that, for surface coverages at which the surface immobilized molecules interact, barriers to penetration create a distribution of target molecule concentrations within the adsorbed layer. By approximately enumerating probe and target conformations, we estimate the probability of overlap between complementary probe and target regions as a function of probe density and chain length. In agreement with experiments, we find that as probe molecules interact more strongly, fewer nucleation sites become accessible and binding rates are diminished relative to those in solution. Nucleation sites near the grafted end of the probes are least accessible; thus targets which preferentially bind to this region show more drastic rate reductions than those that bind near the free end of the probe. The implications of these results for DNA-based biosensors are discussed.

Simple models for extracting mechanical work from the ATP hydrolysis cycle

According to the binding-zipper model, the RecA class of ATPase motors converts chemical energy into mechanical force by the progressive annealing of hydrogen bonds between the nucleotide and the catalytic pocket. The role of hydrolysis is to weaken the binding of products, allowing them to be released so that the cycle can repeat. Molecular dynamics can be used to study the unbinding process, but the binding process is more complex, so that inferences about it are made indirectly from structural, mutation, and biochemical studies. Here we present a series of models of varying complexity that illustrate the basic processes involved in force production during ATP binding. These models reveal the role of solvent and geometry in determining the amount of mechanical work that can be extracted from the binding process.

Kinetic Pathways of Phase Ordering in Lipid Raft Model Systems

We studied kinetic pathways of order-order transitions in bilayer lipid mixtures using a time-dependent Ginzburg-Landau (TDGL) approach. During the stripe-to-hexagonal phase transition in an incompressible two-component system, the stripe phase first develops a pearl-like instability along the phase boundaries, which grows and drives the stripes to break up into droplets that arrange into a hexagonal pattern. These dynamic features are consistent with recent experimental observations. During the disorder-to-hexagonal phase transition in an incompressible three-component system, the disordered state first passes through a transient stripelike structure, which eventually breaks up into a hexagonal droplet phase. Our results suggest experiments with synthetic vesicles where the stripelike patterns could be observed.

Molecular flexibility can influence the stimulatory ability of receptor-ligand interactions at cell-cell junctions

Direct cell-cell communication is crucial for many processes in biology, particularly embryogenesis, interactions between hematopoetic cells, and in the nervous system. This communication is often mediated by the binding of receptors to cognate ligands at a cell-cell junction. One such interaction that is very important for the development of many immune responses is the binding of the alphabeta T cell receptor for antigen (TCR) on T lymphocytes with peptide-MHC complexes on other cells. In general, the stability (e.g., half-life) of TCR-peptide-MHC binding measured in solution correlates with functional responses. Several anomalies have been reported, however. For example, for some anomalous ligands, large changes in heat capacity can apparently substitute for a lack of stability in TCR-ligand interactions. Here, we show that, when there are significant conformational changes during receptor-ligand binding and the receptor/ligand have relatively rigid molecular subdomains, the difference between the half-life of this receptor-ligand complex at a cell-cell junction and that measured using soluble molecules is large. Thus, receptors/ligands with these specific molecular features do not follow correlations between stimulatory potency in the cellular environment and half-lives measured with soluble molecules. Our "first-principles" prescription for correcting the half-life measured in solution to obtain the pertinent value at a cell-cell junction illuminates the origin of correlations of T cell response with thermodynamic properties. Application of our ideas to diverse systems where receptor-ligand interactions occur across juxtaposed cells may help avoid debates about "anomalies" that may simply arise from receptor/ligand-specific differences between half-lives in solution and in the cellular environment.

Advances in methods and algorithms in a modern quantum chemistry program package

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

Community Psychiatry Clinics at Sundarban: a clinical and cultural experience

A series of Community Psychiatric Clinics were conducted in different blocks of Sundarban region of West Bengal. One of the primary objectives of this was to collect clinical epidemiological data on psychiatric morbidity in the region. A total of 26 clinics were conducted in Sagar, Kakdwip, Canning and Gosaba block of the Sundarban region during the period from end 1998 to end 2000. A total of 451 psychiatric cases with diagnostic categories (male 239, female 212) and 215 non-psychiatric cases (male 107 and female 108) were seen in these clinics. Diagnostic Interview Schedules (SCID) and Clinical rating scales like Hamilton Depression Rating Scale and Brief Psychiatric Rating Scales were used to ascertain clinical diagnosis quantitatively. Special emphasis was given on common psychiatric disorders.

Directed migration of positively selected thymocytes visualized in real time

Development of many vertebrate tissues involves long-range cell migrations. In most cases, these migrations have been inferred from analysis of single time points and the migration process has not been directly observed and quantitated in real time. In the mammalian adult thymus, immature CD4⁺CD8⁺ double-positive (DP) thymocytes are found in the outer cortex, whereas after T cell antigen receptor (TCR) repertoire selection, CD4⁺CD8^– and CD4^–CD8⁺ single-positive (SP) thymocytes are found in the central medulla. Here we have used two-photon laser-scanning microscopy and quantitative analysis of four-dimensional cell migration data to investigate the movement of thymocytes through the cortex in real time within intact thymic lobes. We show that prior to positive selection, cortical thymocytes exhibit random walk migration. In contrast, positive selection is correlated with the appearance of a thymocyte population displaying rapid, directed migration toward the medulla. These studies provide our first glimpse into the dynamics of developmentally programmed, long-range cell migration in the mammalian thymus.

Two-photon laser-scanning microscopy reveals the change from random motion to directed migration that occurs when thymocytes undergo positive selection.

Movies, measurement, and modeling: the three Ms of mechanistic immunology

Immunological phenomena that were once deduced from genetic, biochemical, and in situ approaches are now being witnessed in living color, in three dimensions, and in real time. The information in time-lapse imaging can provide valuable mechanistic insight into a host of processes, from cell migration to signal transduction. What we need now are methods to quantitate these new visual data and to exploit computational resources and statistical mechanical methods to develop mechanistic models.

Tuberculosis situation among tribal population of Car Nicobar, India, 15 years after intensive tuberculosis control project and implementation of a national tuberculosis programme

OBJECTIVE

To assess the tuberculosis (TB) situation in the tribal community of Car Nicobar island 15 years after the national TB programme was implemented in this area after an intensive phase of TB control in 1986.

METHODS

The entire population of Car Nicobar was enumerated through a house-to-house survey. Children aged <14 years were tuberculin tested and read for reaction sizes. Individuals aged >15 years were asked about the presence of chest symptoms (cough, chest pain, and unexplained fever for two weeks or longer and haemoptysis), and sputum samples were collected from patients with chest symptoms. Sputum samples were examined for presence of acid-fast bacilli.

FINDINGS

Among the 4,543 children enumerated, 4,351 (95.8%) were tuberculin tested and read. Of the 981 children without bacille Calmette-Guerin scars, 161 (16.4%) were infected with TB. A total of 77 cases who were smear-positive for TB were detected from among 10,570 people aged >15 years; the observed smear-positive case prevalence was 728.5 per 100,000. The standardized prevalence of TB infection, annual risk of TB infection, and prevalence of cases smear-positive for TB were 17.0%, 2.5%, and 735.3 per 100,000, respectively.

CONCLUSION

The prevalence of TB infection and smear-positive cases of TB increased significantly between 1986 and 2002. Such escalation took place despite the implementation of the national TB programme on this island, which was preceded by a set of special anti-TB measures that resulted in sputum conversion in a substantially large proportion of the smear-positive cases prevalent in the community. The most likely reason for the increase seems to be the absence of a district TB programme with enough efficiency to sustain the gains made from the one-time initial phase of special anti-TB measures. High risk of transmission of TB infection currently observed on this island calls for a drastic and sustained improvement in TB control measures.

Epidemiology of tuberculosis: current status in India

India is classified along with the sub-Saharan African countries to be among those with a high burden and the least prospects of a favourable time trend of the disease as of now (Group IV countries). The average prevalence of all forms of tuberculosis in India is estimated to be 5.05 per thousand, prevalence of smear-positive cases 2.27 per thousand and average annual incidence of smear-positive cases at 84 per 1,00,000 annually. The credibility and use of the estimates are discussed in detail. Reports on recent studies on the time trend of the disease from some areas in India, e.g., Chingleput in Tamil Nadu are discussed. They confirm the slow downward trend over a fairly long period of observation, as in the rural areas around Bangalore. It also outlines the serious escalation of disease burden in a tribal population group in Car Nicobar over a period 1986-2002, and highlights the nature and extent of the emerging threats. Some epidemiologists forecast a rise of 20 per cent in incidence in the next 20 yr, for India, with a cumulative rise of 46 million cases of tuberculosis during that period, largely as a consequence of HIV epidemic. The Governmental efforts at intervention through Revised National Tuberculosis Control Programme (RNTCP) and at monitoring the epidemiology of intervention through organising routine reporting are highlighted, and data are presented and evaluated on these. RNTCP needs to be used as an effective instrument to bring a change in epidemiological situation, through fast expansion and achievement of global target. The present review describes the global tuberculosis situation, and views it in the context of the goal of the antituberculosis intervention activities. It presents the epidemiological situation in India, comments on the current trend and discusses the efforts taken towards making projections on the likely burden of disease in India over time.

CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse

How T cells respond with extraordinary sensitivity to minute amounts of agonist peptide and major histocompatibility complex (pMHC) molecules on the surface of antigen-presenting cells bearing large numbers of endogenous pMHC molecules is not understood. Here we present evidence that CD4 affects the responsiveness of T helper cells by controlling spatial localization of the tyrosine kinase Lck in the synapse. This finding, as well as further in silico and in vitro experiments, led us to develop a molecular model in which endogenous and agonist pMHC molecules act cooperatively to amplify T cell receptor signaling. At the same time, activation due to endogenous pMHC molecules alone is inhibited. A key feature is that the binding of agonist pMHC molecules to the T cell receptor results in CD4-mediated spatial localization of Lck, which in turn enables endogenous pMHC molecules to trigger many T cell receptors. We also discuss broader implications for T cell biology, including thymic selection, diversity of the repertoire of self pMHC molecules and serial triggering.

Impact of blast induced transitory vibration and air-overpressure/noise on human brain--an experimental study

Human response to blast induced ground vibration and air-overpressure/noise is a major concern of current mining activity. This is because the fact that mines are fast transgressing the habitats and people are getting educated. Consequently the response of humans is changing and expectedly will increase in days to come with no viable and economic alternative to blasting--an essential component of mining. The response of humans can be purely physiological or psychological in nature or combination of both depending upon the situation and conditions of mining. Where physiological response is documented in terms of effects on ears and lungs there is a meager amount or no literature available regarding effects of blasting on the brain. Moreover, the studies on transitory phenomenon like the effects of blasting on humans are rare in comparison to the whole body vibration studies. This study was designed to address the issues as a precursor to a major initiative. The preliminary investigations conducted with the monitoring of EEG responses of humans to vibration and air-overpressure/noise due to blasting revealed that there is no major response of the brain to transitory vibrations and noise.

Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA

We combine free-energy calculations and molecular dynamics to elucidate a mechanism for DNA base-pair binding and unbinding in atomic detail. Specifically, transition-path sampling is used to overcome computational limitations associated with conventional techniques to harvest many trajectories for the flipping of a terminal cytosine in a 3-bp oligomer in explicit water. Comparison with free-energy projections obtained with umbrella sampling reveals four coordinates that separate true dynamic transition states from stable reactant and product states. Unbinding proceeds via two qualitatively different pathways: one in which the flipping base breaks its intramolecular hydrogen bonds before it unstacks and another in which it ruptures both sets of interactions simultaneously. Both on- and off-pathway intermediates are observed. The relation of the results to coarse-grained models for DNA-based biosensors is discussed.

The Immunological Synapse Balances T Cell Receptor Signaling and Degradation

The immunological synapse is a specialized cell-cell junction between T cell and antigen-presenting cell surfaces. It is characterized by a central cluster of antigen receptors, a ring of integrin family adhesion molecules, and temporal stability over hours. The role of this specific organization in signaling for T cell activation has been controversial. We use in vitro and in silico experiments to determine that the immunological synapse acts as a type of adaptive controller that both boosts T cell receptor triggering and attenuates strong signals.

Effective membrane model of the immunological synapse

The immunological synapse is a patterned collection of different types of receptors and ligands that forms in the intercellular junction between T cells and antigen presenting cells during recognition. The synapse is implicated in information transfer between cells, and is characterized by different spatial patterns of receptors at different stages in the life cycle of T cells. We obtain a minimalist model that captures this experimentally observed phenomenology. A functional renormalization group analysis provides further insights.

Differential gene expression in genetically matched mouse melanoma cells with different metastatic potential

In vitro fusion of weakly metastatic Cloudman S91 melanoma cells with macrophages from DBA/2J mice (syngeneic with Cloudman S91 melanoma) produced hybrids with metastatic potentials ranging from low to high, with more than half showing enhanced metastasis over the parental melanoma [Clin. Exp. Metastasis 16 (1998) 299]. These hybrids, derived from the same parental fusion partners, represent a unique genetically matched model for analyzing differential gene expression regulating the metastatic phenotype. We have examined the differences in gene expression in metastatic fusion hybrid compared to its parental partners, non-/poorly metastatic melanoma cells and normal macrophages. An approach by selective polymerase chain reaction (PCR) amplification and display of 3' end restriction fragments of double-stranded cDNAs was used [Methods Enzymol. 303 (1999) 272]. Gene expression analyses showed an extensive set of transcripts that were up- or down-regulated in the most metastatic hybrid, H95-1, compared to the parental macrophages or melanoma cells. Sequence analyses of more than 60 of these differentially expressed cDNAs revealed significant up- or down-regulation of a number of genes known to be associated with metastasis of melanoma and other solid tumors. Some genes are found to express exclusively either in normal macrophages or in melanoma. Thirteen fragment sequences were found with no matches with GenBank search. Comparison of these gene expression patterns should be of great value in understanding the coordinate programs regulating metastasis. Further, the increased expression of gene(s) common in macrophage and fusion hybrids may be of importance in identifying the regulatory factor(s) related to macrophage-like trait, motility, a critical step of metastatic processes, in hybrids.

GnT-V, macrophage and cancer metastasis: a common link

GnT-V generated, beta1,6-branched polylactosamines are a common feature shared by normal granulocytes, monocytes, and a variety of malignant cells. Furthermore, activation of GnT-V in oncogenic transformation induces invasiveness and metastatic potential in mice as well as in humans. In view of the common expression of lymphocytic/monocytic trait, motility, and GnT-V by metastatic cancer cells, macrophage fusion hybrids were generated in vitro with Cloudman S91 mouse melanoma cells to test whether the parental traits are co-expressed in hybrids and how those are related to altered phenotypes in relation to metastasis. In fact, the fusion hybrids are highly metastatic in vivo, motile in vitro, and express macrophage-associated traits of increased GnT-V activity, beta1,6 branching, and polylactosamine content. A Spontaneously formed lung melanoma metastases have been identified and characterized as host x tumor hybrid containing higher DNA content than parental cells and increased GnT-V activity. The results, taken together, could reflect prior fusion of tumor-associated macrophages with cells of the primary tumor, and therefore establish a possible common link between elevated expression of GnT-V and malignant transformation, a well-known report. Moreover, the fusion hybrids with metastatic potential ranging from high to low offer a genetically matched model system, for identification and characterization of differentially expressed genes in association with metastasis, since the fusion partners are derived from the same species of mouse (DBA/2J).

Low T cell receptor expression and thermal fluctuations contribute to formation of dynamic multifocal synapses in thymocytes

Mature T cell activation and selection of immature T cells (thymocytes) are both initiated by binding of T cell receptor (TCR) molecules on the surface of T cells to MHC peptide (MHCp) molecules on the surface of antigen-presenting cells. Recent experiments have shown that the spatial pattern of receptors and ligands in the intercellular junction (synapse) is different during thymocyte selection compared with mature T cell activation. Using a statistical mechanical model, we show that lower TCR expression in thymocytes contributes to effecting these differences. An analogy with the phase behavior of simple fluids helps clarify how, for low TCR expression, thermal fluctuations lead to the dynamic synapse patterns observed for thymocytes. We suggest that a different synapse pattern resulting from lower TCR expression, which could mediate differential signaling, may be the reason why TCR expression level is low in thymocytes.

The synapse assembly model

A framework for quantitative analysis of the mechanisms underlying immunological synapse assembly has been recently developed. This model uses partial differential equations to describe the binding interactions of receptors and ligands, with the constraint that they are embedded in apposed deformable membranes linked to a cytoskeletal complex.

Correlation of a dynamic model for immunological synapse formation with effector functions: two pathways to synapse formation

During antigen recognition by T cells different receptors and ligands form a pattern in the intercellular junction called the immunological synapse, which might be involved in T-cell activation. Recently, a synapse assembly model has been proposed, which enables the calculation of the propensity for synapse assembly driven by membrane-constrained protein binding interactions. We bring together model predictions of mature synapse assembly with data on the dependence of T-cell responses on T-cell receptor (TCR)-MHC-peptide (pMHC) binding kinetics. Predictions of mature synapse assembly, based on TCR-pMHC binding kinetics, correlate well with observed cytokine responses by T cells bearing the relevant TCR but not with cytotoxic T lymphocyte-mediated killing. We discuss the suggested different role for the synapse in pre- and post-nuclear activation events in T cells. The view of immunological synapse assembly given here emphasizes the importance of both the on and off rates for the TCR-pMHC interaction and in this context recent data on a positive role for analogs of self-peptides in synapse assembly is considered.