Toward an atomistic understanding of the immune synapse:large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex

T-cell activation requires interaction of T-cell receptors (TCR) with peptide epitopes bound by major histocompatibility complex (MHC) proteins. This interaction occurs at a special cell-cell junction known as the immune or immunological synapse. Fluorescence microscopy has shown that the interplay among one agonist peptide-MHC (pMHC), one TCR and one CD4 provides the minimum complexity needed to trigger transient calcium signalling. We describe a computational approach to the study of the immune synapse. Using molecular dynamics simulation, we report here on a study of the smallest viable model, a TCR-pMHC-CD4 complex in a membrane environment. The computed structural and thermodynamic properties are in fair agreement with experiment. A number of biomolecules participate in the formation of the immunological synapse. Multi-scale molecular dynamics simulations may be the best opportunity we have to reach a full understanding of this remarkable supra-macromolecular event at a cell-cell junction.

Close contact fluctuations:the seeding of signalling domains in the immunological synapse

We analyse the size and density of thermally induced regions of close contact in cell : cell contact interfaces within a harmonic potential approximation, estimating these regions to be below one-tenth of a micron across. Our calculations indicate that as the distance between the close contact threshold depth and the mean membrane-membrane separation increases, the density of close contact patches decreases exponentially while there is only a minimal variation in their mean size. The technique developed can be used to calculate the probability of first crossing in reflection symmetry violating systems. © Europhysics Letters Association.

Maternal nutrition modifies trophoblast giant cell phenotype and fetal growth in mice

Mammalian placentation is dependent upon the action of trophoblast cells at the time of implantation. Appropriate fetal growth, regulated by maternal nutrition and nutrient transport across the placenta, is a critical factor for adult offspring long-term health. We have demonstrated that a mouse maternal low-protein diet (LPD) fed exclusively during preimplantation development (Emb-LPD) increases offspring growth but programmes adult cardiovascular and metabolic disease. In this study, we investigate the impact of maternal nutrition on post-implantation trophoblast phenotype and fetal growth. Ectoplacental cone explants were isolated at day 8 of gestation from female mice fed either normal protein diet (NPD: 18% casein), LPD (9% casein) or Emb-LPD and cultured in vitro. We observed enhanced spreading and cell division within proliferative and secondary trophoblast giant cells (TGCs) emerging from explants isolated from LPD-fed females when compared with NPD and Emb-LPD explants after 24 and 48 h. Moreover, both LPD and Emb-LPD explants showed substantial expansion of TGC area during 24-48 h, not observed in NPD. No difference in invasive capacity was observed between treatments using Matrigel transwell migration assays. At day 17 of gestation, LPD- and Emb-LPD-fed conceptuses displayed smaller placentas and larger fetuses respectively, resulting in increased fetal:placental ratios in both groups compared with NPD conceptuses. Analysis of placental and yolk sac nutrient signalling within the mammalian target of rapamycin complex 1 pathway revealed similar levels of total and phosphorylated downstream targets across groups. These data demonstrate that early post-implantation embryos modify trophoblast phenotype to regulate fetal growth under conditions of poor maternal nutrition.

Contact time periods in immunological synapse

This paper resolves the long standing debate as to the proper time scale τ of the onset of the immunological synapse bond, the noncovalent chemical bond defining the immune pathways involving T cells and antigen presenting cells. Results from our model calculations show τ to be of the order of seconds instead of minutes. Close to the linearly stable regime, we show that in between the two critical spatial thresholds defined by the integrin:ligand pair (Δ2∼ 40-45 nm) and the T-cell receptor TCR:peptide-major-histocompatibility-complex pMHC bond (Δ1∼ 14-15 nm), τ grows monotonically with increasing coreceptor bond length separation δ (= Δ2-Δ1∼ 26-30 nm) while τ decays with Δ1 for fixed Δ2. The nonuniversal δ-dependent power-law structure of the probability density function further explains why only the TCR:pMHC bond is a likely candidate to form a stable synapse.

Temporal dynamics in an immunological synapse:role of thermal fluctuations in signaling

The article analyzes the contribution of stochastic thermal fluctuations in the attachment times of the immature T-cell receptor TCR: peptide-major-histocompatibility-complex pMHC immunological synapse bond. The key question addressed here is the following: how does a synapse bond remain stabilized in the presence of high-frequency thermal noise that potentially equates to a strong detaching force? Focusing on the average time persistence of an immature synapse, we show that the high-frequency nodes accompanying large fluctuations are counterbalanced by low-frequency nodes that evolve over longer time periods, eventually leading to signaling of the immunological synapse bond primarily decided by nodes of the latter type. Our analysis shows that such a counterintuitive behavior could be easily explained from the fact that the survival probability distribution is governed by two distinct phases, corresponding to two separate time exponents, for the two different time regimes. The relatively shorter timescales correspond to the cohesion:adhesion induced immature bond formation whereas the larger time reciprocates the association:dissociation regime leading to TCR:pMHC signaling. From an estimate of the bond survival probability, we show that, at shorter timescales, this probability PΔ(τ) scales with time τ as a universal function of a rescaled noise amplitude DΔ2, such that PΔ(τ)∼τ-(ΔD+12),Δ being the distance from the mean intermembrane (T cell:Antigen Presenting Cell) separation distance. The crossover from this shorter to a longer time regime leads to a universality in the dynamics, at which point the survival probability shows a different power-law scaling compared to the one at shorter timescales. In biological terms, such a crossover indicates that the TCR:pMHC bond has a survival probability with a slower decay rate than the longer LFA-1:ICAM-1 bond justifying its stability.

On the shoulders of a giant:his legacy will live on

Editorial

Immunological synapse: a mathematical model of the bond formation process:mathematical modelling of the immature synapse

The cell:cell bond between an immune cell and an antigen presenting cell is a necessary event in the activation of the adaptive immune response. At the juncture between the cells, cell surface molecules on the opposing cells form non-covalent bonds and a distinct patterning is observed that is termed the immunological synapse. An important binding molecule in the synapse is the T-cell receptor (TCR), that is responsible for antigen recognition through its binding with a major-histocompatibility complex with bound peptide (pMHC). This bond leads to intracellular signalling events that culminate in the activation of the T-cell, and ultimately leads to the expression of the immune eector function. The temporal analysis of the TCR bonds during the formation of the immunological synapse presents a problem to biologists, due to the spatio-temporal scales (nanometers and picoseconds) that compare with experimental uncertainty limits. In this study, a linear stochastic model, derived from a nonlinear model of the synapse, is used to analyse the temporal dynamics of the bond attachments for the TCR. Mathematical analysis and numerical methods are employed to analyse the qualitative dynamics of the nonequilibrium membrane dynamics, with the specic aim of calculating the average persistence time for the TCR:pMHC bond. A single-threshold method, that has been previously used to successfully calculate the TCR:pMHC contact path sizes in the synapse, is applied to produce results for the average contact times of the TCR:pMHC bonds. This method is extended through the development of a two-threshold method, that produces results suggesting the average time persistence for the TCR:pMHC bond is in the order of 2-4 seconds, values that agree with experimental evidence for TCR signalling. The study reveals two distinct scaling regimes in the time persistent survival probability density prole of these bonds, one dominated by thermal uctuations and the other associated with the TCR signalling. Analysis of the thermal fluctuation regime reveals a minimal contribution to the average time persistence calculation, that has an important biological implication when comparing the probabilistic models to experimental evidence. In cases where only a few statistics can be gathered from experimental conditions, the results are unlikely to match the probabilistic predictions. The results also identify a rescaling relationship between the thermal noise and the bond length, suggesting a recalibration of the experimental conditions, to adhere to this scaling relationship, will enable biologists to identify the start of the signalling regime for previously unobserved receptor:ligand bonds. Also, the regime associated with TCR signalling exhibits a universal decay rate for the persistence probability, that is independent of the bond length.

Waking the sleeping giant: Beliefs of Brazilian and *American teachers concerning liberation curriculum

The school curriculum is a matter mandated by the educational system rather than determined by the school stakeholders of a community, as Freire (1993) suggests. At the present time, one significant vision of school is challenging the current order of curriculum practice. It focuses on school as a liberating agency grounded on the belief that the abilities to access information and to think critically about it will educate an individual capable of making independent decisions. This dissertation investigates teacher's beliefs concerning curriculum. It was assumed that there is a discrepancy between what has been the position proposed by critical theorists including Freire (1998a, 1993); Apple (1979); Giroux (1998), and the position on curriculum which school systems are typically advancing. ^ There were four purposes of this study. The major purpose of this study was to determine whether or not Brazilian and American Teachers believe that a school curriculum based on Freirean principles could be implemented in the schools in which they worked. Also, this study sought to determine the differences found between teachers' beliefs in the Brazilian and American contexts. Another purpose was to determine how Brazilian and American teachers justify their beliefs and actions when these may represent conflicting values. Finally, this study sought to determine if these teachers believe that the curriculum is in need of change or if they accept the current curriculum as adequate. This study consisted of quantitative and qualitative data collection through multiple methods involving surveys and interviews. The study involved 171 teachers (88 Brazilian and 83 American) from multiple settings with the majority working for public systems. Overall, it seems that Brazilian and American teachers believe that a curriculum based on Freirean principles of education can be implemented in their schools, if ongoing education is provided. The majority of Brazilian teachers believe a curriculum change is necessary while half of the American teachers believe a curriculum change is needed and the other half seems to believe curriculum is adequate. Teachers explain that it is hard to implement a curriculum they believe to be most appropriate for students because the current curriculum is mandated by the school system or by national guidelines. The majority of Brazilian teachers and those American teachers who believed a curriculum change is necessary explained their rationale for change in terms of social justice, problem-solving, collective work, student-centered and context-based curriculum. American teachers, who believed that the curriculum is adequate, explained that they are satisfied with their student's achievements. They stated that their students are doing well on tests and are learning what is required. ^

Giant piezoresistance in silicon-germanium alloys

We use first-principles electronic structure methods to show that the piezoresistive strain gauge factor of single-crystalline bulk n-type silicon-germanium alloys at carefully controlled composition can reach values of G = 500, three times larger than that of silicon, the most sensitive such material used in industry today. At cryogenic temperatures of 4 K we find gauge factors of G = 135 000, 13 times larger than that observed in Si whiskers. The improved piezoresistance is achieved by tuning the scattering of carriers between different (Delta and L) conduction band valleys by controlling the alloy composition and strain configuration.

Giant enhancement of n-type carrier mobility in highly strained germanium nanostructures

First-principles electronic structure methods are used to predict the rate of n-type carrier scattering due to phonons in highly-strained Ge. We show that strains achievable in nanoscale structures, where Ge becomes a direct bandgap semiconductor, cause the phonon-limited mobility to be enhanced by hundreds of times that of unstrained Ge, and over a thousand times that of Si. This makes highly tensile strained Ge a most promising material for the construction of channels in CMOS devices, as well as for Si-based photonic applications. Biaxial (001) strain achieves mobility enhancements of 100 to 1000 with strains over 2%. Low temperature mobility can be increased by even larger factors. Second order terms in the deformation potential of the Gamma valley are found to be important in this mobility enhancement. Although they are modified by shifts in the conduction band valleys, which are caused by carrier quantum confinement, these mobility enhancements persist in strained nanostructures down to sizes of 20 nm.