A multiscale model of the role of microenvironmental factors in cell segregation and heterogeneity in breast cancer development.

We analyzed a quantitative multiscale model that describes the epigenetic dynamics during the growth and evolution of an avascular tumor. A gene regulatory network (GRN) formed by a set of ten genes that are believed to play an important role in breast cancer development was kinetically coupled to the microenvironmental agents: glucose, estrogens, and oxygen. The dynamics of spontaneous mutations was described by a Yule-Furry master equation whose solution represents the probability that a given cell in the tissue undergoes a certain number of mutations at a given time. We assumed that the mutation rate is modified by a spatial gradient of nutrients. The tumor mass was simulated by means of cellular automata supplemented with a set of reaction diffusion equations that described the transport of microenvironmental agents. By analyzing the epigenetic state space described by the GRN dynamics, we found three attractors that were identified with cellular epigenetic states: normal, precancer and cancer. For two-dimensional (2D) and three-dimensional (3D) tumors we calculated the spatial distribution of the following quantities: (i) number of mutations, (ii) mutation of each gene and, (iii) phenotypes. Using estrogen as the principal microenvironmental agent that regulates cell proliferation process, we obtained tumor shapes for different values of estrogen consumption and supply rates. It was found that he majority of mutations occurred in cells that were located close to the 2D tumor perimeter or close to the 3D tumor surface. Also, it was found that the occurrence of different phenotypes in the tumor are controlled by estrogen concentration levels since they can change the individual cell threshold and gene expression levels. All results were consistently observed for 2D and 3D tumors.

Bacteria-instructed B cells cross-prime naïve CD8+ T cells triggering effective cytotoxic responses.

In addition to triggering humoral responses, conventional B cells have been described in vitro to cross-present exogenous antigens activating naïve CD8+ T cells. Nevertheless, the way B cells capture these exogenous antigens and the physiological roles of B cell-mediated cross-presentation remain poorly explored. Here, we show that B cells capture bacteria by trans-phagocytosis from previously infected dendritic cells (DC) when they are in close contact. Bacterial encounter "instructs" the B cells to acquire antigen cross-presentation abilities, in a process that involves autophagy. Bacteria-instructed B cells, henceforth referred to as BacB cells, rapidly degrade phagocytosed bacteria, process bacterial antigens and cross-prime naïve CD8+ T cells which differentiate into specific cytotoxic cells that efficiently control bacterial infections. Moreover, a proof-of-concept experiment shows that BacB cells that have captured bacteria expressing tumor antigens could be useful as novel cellular immunotherapies against cancer.

Extrasynaptic Communication.

Streams of action potentials or long depolarizations evoke a massive exocytosis of transmitters and peptides from the surface of dendrites, axons and cell bodies of different neuron types. Such mode of exocytosis is known as extrasynaptic for occurring without utilization of synaptic structures. Most transmitters and all peptides can be released extrasynaptically. Neurons may discharge their contents with relative independence from the axon, soma and dendrites. Extrasynaptic exocytosis takes fractions of a second in varicosities or minutes in the soma or dendrites, but its effects last from seconds to hours. Unlike synaptic exocytosis, which is well localized, extrasynaptic exocytosis is diffuse and affects neuronal circuits, glia and blood vessels. Molecules that are liberated may reach extrasynaptic receptors microns away. The coupling between excitation and exocytosis follows a multistep mechanism, different from that at synapses, but similar to that for the release of hormones. The steps from excitation to exocytosis have been studied step by step for the vital transmitter serotonin in leech Retzius neurons. The events leading to serotonin exocytosis occur similarly for the release of other transmitters and peptides in central and peripheral neurons. Extrasynaptic exocytosis occurs commonly onto glial cells, which react by releasing the same or other transmitters. In the last section, we discuss how illumination of the retina evokes extrasynaptic release of dopamine and ATP. Dopamine contributes to light-adaptation; ATP activates glia, which mediates an increase in blood flow and oxygenation. A proper understanding of the workings of the nervous system requires the understanding of extrasynaptic communication.

Dynamics of Neuromuscular Transmission Reproduced by Calcium-Dependent and Reversible Serial Transitions in the Vesicle Fusion Complex.

Neuromuscular transmission, from spontaneous release to facilitation and depression, was accurately reproduced by a mechanistic kinetic model of sequential maturation transitions in the molecular fusion complex. The model incorporates three predictions. First, calcium-dependent forward transitions take vesicles from docked to preprimed to primed states, followed by fusion. Second, prepriming and priming are reversible. Third, fusion and recycling are unidirectional. The model was fed with experimental data from previous studies, whereas the backward (ß) and recycling (ρ) rate constant values were fitted. Classical experiments were successfully reproduced with four transition states in the model when every forward (α) rate constant had the same value, and both backward rate constants were 50-100 times larger. Such disproportion originated an abruptly decreasing gradient of resting vesicles from docked to primed states. By contrast, a three-state version of the model failed to reproduce the dynamics of transmission by using the same set of parameters. Simulations predict the following: (1) Spontaneous release reflects primed to fusion spontaneous transitions. (2) Calcium elevations synchronize the series of forward transitions that lead to fusion. (3) Facilitation reflects a transient increase of priming following the calcium-dependent maturation transitions. (4) The calcium sensors that produce facilitation are those that evoke the transitions form docked to primed states. (5) Backward transitions and recycling restore the resting state. (6) Depression reflects backward transitions and slow recycling after intense release. Altogether, our results predict that fusion is produced by one calcium sensor, whereas the modulation of the number of vesicles that fuse depends on the calcium sensors that promote the early transition states. Such finely tuned kinetics offers a mechanism for collective non-linear transitional adaptations of a homogeneous vesicle pool to the ever-changing pattern of electrical activity in the neuromuscular junction.

Author Correction: Conventional CD4+ T cells present bacterial antigens to induce cytotoxic and memory CD8+ T cell responses.

The original version of this Article contained an error in the spelling of the author José María González-Granado, which was incorrectly given as José María Gozález-Granado. This has now been corrected in both the PDF and HTML versions of the Article.

Conventional CD4+ T cells present bacterial antigens to induce cytotoxic and memory CD8+ T cell responses.

Bacterial phagocytosis and antigen cross-presentation to activate CD8+ T cells are principal functions of professional antigen presenting cells. However, conventional CD4+ T cells also capture and kill bacteria from infected dendritic cells in a process termed transphagocytosis (also known as transinfection). Here, we show that transphagocytic T cells present bacterial antigens to naive CD8+ T cells, which proliferate and become cytotoxic in response. CD4+ T-cell-mediated antigen presentation also occurs in vivo in the course of infection, and induces the generation of central memory CD8+ T cells with low PD-1 expression. Moreover, transphagocytic CD4+ T cells induce protective anti-tumour immune responses by priming CD8+ T cells, highlighting the potential of CD4+ T cells as a tool for cancer immunotherapy.

Clathrin regulates lymphocyte migration by driving actin accumulation at the cellular leading edge.

Lymphocyte migration, which is essential for effective immune responses, belongs to the so-called amoeboid migration. The lymphocyte migration is up to 100 times faster than between mesenchymal and epithelial cell types. Migrating lymphocytes are highly polarized in three well-defined structural and functional zones: uropod, medial zone, and leading edge (LE). The actiomyosin-dependent driving force moves forward the uropod, whereas massive actin rearrangements protruding the cell membrane are observed at the LE. These actin rearrangements resemble those observed at the immunological synapse driven by clathrin, a protein normally involved in endocytic processes. Here, we used cell lines as well as primary lymphocytes to demonstrate that clathrin and clathrin adaptors colocalize with actin at the LE of migrating lymphocytes, but not in other cellular zones that accumulate both clathrin and actin. Moreover, clathrin and clathrin adaptors, including Hrs, the clathrin adaptor for multivesicular bodies, drive local actin accumulation at the LE. Clathrin recruitment at the LE resulted necessary for a complete cell polarization and further lymphocyte migration in both 2D and 3D migration models. Therefore, clathrin, including the clathrin population associated to internal vesicles, controls lymphocyte migration by regulating actin rearrangements occurring at the LE.

Spatio-temporal dynamics of a cell signal pathway with negative feedbacks: the MAPK/ERK pathway.

We studied the spatio-temporal dynamics of a cell signal cascade with negative feedback that quantitatively emulates the regulative process that occurs in the Mitogen Activated Protein Kinase/Extracellular Regulated Kinase (MAPK/ERK) pathway. The model consists of a set of six coupled reaction-diffusion equations that describes the dynamics of the six-module pathway. In the basic module the active form of the protein transmits the signal to the next pathway's module. As suggested by experiments, the model considers that the fifth module's kinase down-regulates the first and third modules. The feedback parameter is defined as, µ(r)( j)= k(kin)5/k(kin)(j), (j = 1, 3). We analysed the pathway's dynamics for µ(r)( j) = 0.10, 1.0, and 10 in the kinetic regimes: i) saturation of both kinases and phosphatases, ii) saturation of the phosphatases and iii) saturation of the kinases. For a regulated pathway the Total Activated Protein Profiles (TAPPs) as a function of time develop a maximum during the transient stage in the three kinetic regimes. These maxima become higher and their positions shift to longer times downstream. This scenario also applies to the TAPP's regulatory kinase that sums up its inhibitory action to that of the phosphatases leading to a maximum. Nevertheless, when µ(r)(j)= 1.0 , the TAPPs develop two maxima, with the second maximum being almost imperceptible. These results are in qualitative agreement with experimental data obtained from NIH 3T3 mouse fibroblasts. In addition, analyses of the stationary states as a function of position indicate that in the kinetic regime i) which is of physiological interest, signal transduction occurs with a relatively large propagation length for the three values of the regulative parameter. However, for µ(r)(j)= 0.10 , the sixth module concentration profile is transmitted with approximately 45% of its full value. The results obtained for µ(r)(j) = 10 , indicate that the first five concentration profiles are small with a short propagation length; nonetheless, the last concentration profile, c6, attains more than 90% of its full value with a relatively large propagation length as an indication of signal transduction. Signal transduction also occurred favourably in the kinetic regimes ii) and iii), but the signal was longer-ranged in the regime ii).

T Cells Capture Bacteria by Transinfection from Dendritic Cells.

Recently, we have shown, contrary to what is described, that CD4(+) T cells, the paradigm of adaptive immune cells, capture bacteria from infected dendritic cells (DCs) by a process called transinfection. Here, we describe the analysis of the transinfection process, which occurs during the course of antigen presentation. This process was unveiled by using CD4(+) T cells from transgenic OTII mice, which bear a T cell receptor (TCR) specific for a peptide of ovoalbumin (OVAp), which therefore can form stable immune complexes with infected dendritic cells loaded with this specific OVAp. The dynamics of green fluorescent protein (GFP)-expressing bacteria during DC-T cell transmission can be monitored by live-cell imaging and the quantification of bacterial transinfection can be performed by flow cytometry. In addition, transinfection can be quantified by a more sensitive method based in the use of gentamicin, a non-permeable aminoglycoside antibiotic killing extracellular bacteria but not intracellular ones. This classical method has been used previously in microbiology to study the efficiency of bacterial infections. We hereby explain the protocol of the complete process, from the isolation of the primary cells to the quantification of transinfection.

Phase behavior of Langmuir monolayers with ionic molecular heads: Molecular simulations.

We carried out Monte Carlo simulations in the N,Π,T ensemble of a Langmuir monolayer coarse-grained molecular model. Considering that the hydrophilic groups can be ionized by modulating acid-base interactions, here we study the phase behavior of a model that incorporates the short-range steric and long-range ionic interactions. The simulations were carried out in the reduced temperature range 0.1≤T*<4.0, where there is a competition of these interactions. Different order parameters were calculated and analyzed for several values of the reduced surface pressure in the interval, 1≤Π*≤40. For most of the surface pressures two directions of molecular tilt were found: (i) towards the nearest neighbor (NN) at low temperatures, T*<0.7, and most of the values of Π* and (ii) towards next-nearest neighbors (NNN) in the temperature interval 0.7≤T*<1.1 for Π*<25. We also found the coexistence of the NN and NNN at intermediate temperatures and Π*>25. A low-temperature reentrant disorder-order-disorder transition in the positions of the molecular heads and in the collective tilt of the tails was found for all the surface pressure values. It was also found that the molecular tails arranged forming "rotating patterns" in the temperature interval, 0.5

T cells kill bacteria captured by transinfection from dendritic cells and confer protection in mice.

Dendritic cells (DCs) phagocytose, process, and present bacterial antigens to T lymphocytes to trigger adaptive immunity. In vivo, bacteria can also be found inside T lymphocytes. However, T cells are refractory to direct bacterial infection, leaving the mechanisms by which bacteria invade T cells unclear. We show that T cells take up bacteria from infected DCs by the process of transinfection, which requires direct contact between the two cells and is enhanced by antigen recognition. Prior to transfer, bacteria localize to the immunological synapse, an intimate DC/T cell contact structure that activates T cells. Strikingly, T cells efficiently eliminate the transinfecting bacteria within the first hours after infection. Transinfected T cells produced high levels of proinflammatory cytokines and were able to protect mice from bacterial challenge following adoptive transfer. Thus, T lymphocytes can capture and kill bacteria in a manner reminiscent of innate immunity.

Phase and interfacial behavior of partially miscible symmetric Lennard-Jones binary mixtures.

We have carried out extensive equilibrium molecular-dynamics simulations to study quantitatively the topology of the temperature versus density phase diagrams and related interfacial phenomena in a partially miscible symmetric Lennard-Jones binary mixture. The topological features are studied as a function of miscibility parameter, alpha = epsilonAB/epsilonAA. Here epsilonAA = epsilonBB and epsilonAB stand for the parameters related to the attractive part of the intermolecular interactions for similar and dissimilar particles, respectively. When the miscibility varies in the range 0 < alpha < 1, a continuous critical line of consolute points Tcons(rho)--critical demixing transition line--appears. This line intersects the liquid-vapor coexistence curve at different positions depending on the values of alpha, yielding mainly three different topologies for the phase diagrams. These results are in qualitative agreement to those found previously for square-well and hard-core Yukawa binary mixtures. The main contributions of the present paper are (i) a quantitative analysis of the phase behavior and (ii) a detailed study of the liquid-liquid interfacial and liquid-vapor surface tensions, as function of temperature and miscibility as well as its relationship to the topological features of the phase diagrams.

Wetting phenomenon in the liquid-vapor phase coexistence of a partially miscible Lennard-Jones binary mixture.

We have carried out extensive equilibrium molecular dynamics simulations to study the structure and the interfacial properties in the liquid-vapor phase coexistence of partially miscible binary Lennard-Jones mixtures. By analyzing the structural properties as a function of the miscibility parameter, alpha, we found that at relatively low temperatures the system separates forming a liquid A-liquid B interface in coexistence with the vapor phase. At higher temperatures and, 0< alpha < or =0.5 , we found a temperature range, T*w (alpha) < or =T*< T*Cons (alpha) , where the liquid phases are wet by the vapor phase. Here, T*w (alpha) represents the wetting transition temperature and T*Cons (alpha) is the consolute temperature of the mixture. However, for 0.5< alpha <1 , no wetting phenomenon occurs. For the particular value, alpha=0.25 , we analyzed quantitatively the T* versus rho* , and P* versus T* phase diagrams and found, T*c approximately 1.25 , and T*Cons approximately 1.25 . We also studied quantitatively, as a function of temperature, the surface tension and the adsorption of molecules at the liquid-liquid interface. It was found that the adsorption shows a jump from a finite negative value up to minus infinity, when the vapor wets the liquid phases, suggesting that the wetting transition is of first order. The calculated phase diagram, together with the wetting phenomenon, strongly suggests the existence of a tricritical point. These results agree well with some experiments carried out in fluid binary mixtures.

Metastable liquid lamellar structures in binary and ternary mixtures of Lennard-Jones fluids.

We have carried out extensive equilibrium molecular dynamics simulations to investigate the liquid-vapor coexistence in partially miscible binary and ternary mixtures of Lennard-Jones fluids. We have studied in detail the time evolution of the density profiles and the interfacial properties in a temperature region of the phase diagram where the condensed phase is demixed. The composition of the mixtures is fixed, 50% for the binary mixture and 33.33% for the ternary mixture. The results of the simulations clearly indicate that in the range of temperatures 78