Endosomal localization and receptor dynamics determine tyrosine phosphorylation of hepatocyte growth factor-regulated tyrosine kinase substrate

Hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs) is a prominent substrate for activated tyrosine kinase receptors that has been proposed to play a role in endosomal membrane trafficking. The protein contains a FYVE domain, which specifically binds to the lipid phosphatidylinositol (PI) 3-phosphate (PI 3-P). We show that this interaction is required both for correct localization of the protein to endosomes that only partially coincides with early endosomal autoantigen 1 and for efficient tyrosine phosphorylation of the protein in response to epidermal growth factor stimulation. Treatment with wortmannin reveals that Hrs phosphorylation also requires PI 3-kinase activity, which is necessary to generate the PI 3-P required for localization. We have used both hypertonic media and expression of a dominant-negative form of dynamin (K44A) to inhibit endocytosis; under which conditions, receptor stimulation fails to elicit phosphorylation of Hrs. Our results provide a clear example of the coupling of a signal transduction pathway to endocytosis, from which we propose that activated receptor (or associated factor) must be delivered to the appropriate endocytic compartment in order for Hrs phosphorylation to occur.

Biosensor analysis of dynamics of interleukin 5 receptor subunit beta(c) interaction with IL5:IL5R(alpha) complexes

To gain insight into IL5 receptor subunit recruitment mechanism, and in particular the experimentally elusive pathway for assembly of signaling subunit beta(c), we constructed a soluble beta(c) ectodomain (s(beta)(c)) and developed an optical biosensor assay to measure its binding kinetics. Functionally active s(beta)(c) was anchored via a C-terminal His tag to immobilized anti-His monoclonal antibodies on the sensor surface. Using this surface, we quantitated for the first time direct binding of s(beta)(c) to IL5R(alpha) complexed to either wild-type or single-chain IL5. Binding was much weaker if at all with either R(alpha) or IL5 alone. Kinetic evaluation revealed a moderate affinity (0.2-1 microM) and relatively fast off rate for the s(beta)(c) interaction with IL5:R(alpha) complexes. The data support a model in which beta(c) recruitment occurs with preformed IL5:R(alpha) complex. Dissociation kinetics analysis suggests that the IL5-alpha-beta(c) complex is relatively short-lived. Overall, this study solidifies a model of sequential recruitment of receptor subunits by IL5, provides a novel biosensor binding assay of beta(c) recruitment dynamics, and sets the stage for more advanced characterization of the roles of structural elements within R(alpha), beta(c), and cytokines of the IL5/IL3/GM-CSF family in receptor recruitment and activation.

Molecular dynamics simulation (MDS) to study nanoscale machining processes

Molecular Dynamics Simulations (MDS) are constantly being used to make important contributions to our fundamental understanding of material behaviour, at the atomic scale, for a variety of thermodynamic processes. This chapter shows that molecular dynamics simulation is a robust numerical analysis tool in addressing a range of complex nanofinishing (machining) problems that are otherwise difficult or impossible to understand using other methods. For example the mechanism of nanometric cutting of silicon carbide is influenced by a number of variables such as machine tool performance, machining conditions, material properties, and cutting tool performance (material microstructure and physical geometry of the contact) and all these variables cannot be monitored online through experimental examination. However, these could suitably be studied using an advanced simulation based approach such as MDS. This chapter details how MD simulation can be used as a research and commercial tool to understand key issues of ultra precision manufacturing research problems and a specific case was addressed by studying diamond machining of silicon carbide. While this is appreciable, there are a lot of challenges and opportunities in this fertile area. For example, the world of MD simulations is dependent on present day computers and the accuracy and reliability of potential energy functions [109]. This presents a limitation: Real-world scale simulation models are yet to be developed. The simulated length and timescales are far shorter than the experimental ones which couples further with the fact that contact loading simulations are typically done in the speed range of a few hundreds of m/sec against the experimental speed of typically about 1 m/sec [17]. Consequently, MD simulations suffer from the spurious effects of high cutting speeds and the accuracy of the simulation results has yet to be fully explored. The development of user-friendly software could help facilitate molecular dynamics as an integral part of computer-aided design and manufacturing to tackle a range of machining problems from all perspectives, including materials science (phase of the material formed due to the sub-surface deformation layer), electronics and optics (properties of the finished machined surface due to the metallurgical transformation in comparison to the bulk material), and mechanical engineering (extent of residual stresses in the machined component) [110]. Overall, this chapter provided key information concerning diamond machining of SiC which is classed as hard, brittle material. From the analysis presented in the earlier sections, MD simulation has helped in understanding the effects of crystal anisotropy in nanometric cutting of 3C-SiC by revealing the atomic-level deformation mechanisms for different crystal orientations and cutting directions. In addition to this, the MD simulation revealed that the material removal mechanism on the (111) surface of 3C-SiC (akin to diamond) is dominated by cleavage. These understandings led to the development of a new approach named the “surface defect machining” method which has the potential to be more effective to implement than ductile mode micro laser assisted machining or conventional nanometric cutting.

Molecular dynamics simulation investigation on the plastic flow behaviour of silicon during nanometric cutting

Molecular dynamics (MD) simulation was carried out to acquire an in-depth understanding of the flow behaviour of single crystal silicon during nanometric cutting on three principal crystallographic planes and at different cutting temperatures. The key findings were that (i) the substrate material underneath the cutting tool was observed for the first time to experience a rotational flow akin to fluids at all the tested temperatures up to 1200 K. (ii) The degree of flow in terms of vorticity was found higher on the (1 1 1) crystal plane signifying better machinability on this orientation in accord with the current pool of knowledge (iii) an increase in the machining temperature reduces the springback effect and thereby the elastic recovery and (iv) the cutting orientation and the cutting temperature showed significant dependence on the location of the stagnation region in the cutting zone of the substrate.

Biofilm Complexity Controls Fine Particle Dynamics in Streams

Most models of riverine eco-hydrology and biogeochemistry rely upon bulk parameterization of fluxes. However, the transport and retention of carbon and nutrients in headwater streams is strongly influenced by biofilms (surface-attached microbial communities), which results in strong feedbacks between stream hydrodynamics and biogeochemistry. Mechanistic understanding of the interactions between streambed biofilms and nutrient dynamics is lacking. Here we present experimental results linking microscale observations of biofilm community structure to the deposition and resuspension of clay-sized mineral particles in streams. Biofilms were grown in identical 3 m recirculating flumes over periods of 14-50 days. Fluorescent particles were introduced to each flume, and their deposition was traced over 30 minutes. Particle resuspension from the biofilms was then observed under an increased stream flow, mimicking a flood event. We quantified particle fluxes using flow cytometry and epifluorescence microscopy. We directly observed particle adhesion to the biofilm using a confocal laser scanning microscope. 3-D Optical Coherence Tomography was used to determine biofilm roughness, areal coverage and void space in each flume. These measurements allow us to link biofilm complexity to particle retention during both baseflow and floodflow. The results suggest that increased biofilm complexity favors deposition and retention of fine particles in streams.

Electron dynamics and frequency coupling in a radio-frequency capacitively biased planar coil inductively coupled plasma system

The electron dynamics in a planar coil inductively coupled plasma (ICP) system with a capacitively biased electrode is investigated using space and phase resolved optical emission spectroscopy. The two power source frequencies are exact multiple of each other and phase-locked. In this configuration, the system is investigated when the coil is operated in both E-mode and H-mode. The results show that in a phase synchronized RF biased ICP, the electrode bias power couples with the capacitive contribution of the coil, in both E-mode and H-modes, similar to dual-frequency capacitively coupled plasmas (2f-CCPs). It is also demonstrated that in H-mode, the phase between the electrode bias frequency and the ICP coil frequency influences the electron heating, similar to the electrical asymmetry effect in 2f-CCPs.

Electron-scale dissipative electrostatic solitons in multi-species plasmas

The linear and nonlinear properties of small-amplitude electron-acoustic solitary waves are investigated via the fluid dynamical approach. A three-component plasma is considered, composed of hot electrons, cold electrons, and ions (considered stationary at the scale of interest). A dissipative (wave damping) effect is assumed due to electron-neutral collisions. The background (hot) electrons are characterized by an energetic (excessively superthermal) population and are thus modeled via a κ-type nonthermal distribution. The linear characteristics of electron-acoustic excitations are discussed, for different values of the plasma parameters (superthermality index κ and cold versus hot electron population concentration β). Large wavelengths (beyond a threshold value) are shown to be overdamped. The reductive perturbation technique is used to derive a dissipative Korteweg de-Vries (KdV) equation for small-amplitude electrostatic potential disturbances. These are expressed by exact solutions in the form of dissipative solitary waves, whose dynamics is investigated analytically and numerically. Our results should be useful in elucidating the behavior of space and experimental plasmas characterized by a coexistence of electron populations at different temperatures, where electron-neutral collisions are of relevance.

An evaluation of strain softening of glacial tills as a result of pore pressure dynamics.

Deep-seated progressive failures of cuttings in heavily overconsolidated clays have been observed in the field and are well documented, especially for London Clays (Potts, Kovacevic, & Vaughan, 1997; Smethurst, Powrie, & Clarke, 2006; Take, 2003), however, the process of softening and the development of a rupture surface in other clays, including the clay fraction of glacial tills, is still to be established. Recent decades have witnessed extreme weather conditions in Northern Ireland with dry summers and wet winters. The dynamics of this pore pressure variation can trigger strength reduction and progressive plastic straining, both of which will lead to slope failure. The aim of this research is to evaluate the effect of pore pressure variations on the deformation and long-term stability of large cuttings in glacial tills in Northern Ireland. This paper outlines the overall research program and presents initial laboratory findings (Carse, 2013).

Irish language education and the national ideal: The dynamics of nationalism in Northern Ireland

Since the beginning of the Northern Ireland conflict in the late 1960s, Irish nationalism has been identified as a prominent force in the political culture of the state. Recent studies have suggested, however, that the ‘Nationalist’ population has become increasingly content within the new political framework created by the peace process and the aspiration for Irish unity diminished. In placing the Northern Ireland situation within the theoretical framework of nationalism, this paper will analyse how these changing priorities have been possible. Through an analysis of Irish language study in Northern Ireland's schools, the paper will examine how the political ideals espoused by the nationalist Sinn Féin Party reflected the priorities of the ‘nationalist community’. It will be contended that the relationship between the ideology and ‘the people’ is much more complex than is often allowed for and that educational inequalities are a significant contributing factor to this.

Performance Limits of MIMO Systems with Nonlinear Power Amplifiers

The development of 5G enabling technologies brings new challenges to the design of power amplifiers (PAs). In particular, there is a strong demand for low-cost, nonlinear PAs which, however, introduce nonlinear distortions. On the other hand, contemporary expensive PAs show great power efficiency in their nonlinear region. Inspired by this trade-off between nonlinearity distortions and efficiency, finding an optimal operating point is highly desirable. Hence, it is first necessary to fully understand how and how much the performance of multiple-input multiple-output (MIMO) systems deteriorates with PA nonlinearities. In this paper, we first reduce the ergodic achievable rate (EAR) optimization from a power allocation to a power control problem with only one optimization variable, i.e. total input power. Then, we develop a closed-form expression for the EAR, where this variable is fixed. Since this expression is intractable for further analysis, two simple lower bounds and one upper bound are proposed. These bounds enable us to find the best input power and approach the channel capacity. Finally, our simulation results evaluate the EAR of MIMO channels in the presence of nonlinearities. An important observation is that the MIMO performance can be significantly degraded if we utilize the whole power budget.

Nonconservative current-driven dynamics: beyond the nanoscale

Long metallic nanowires combine crucial factors for nonconservative current-driven atomic motion. These systems have degenerate vibrational frequencies, clustered about a Kohn anomaly in the dispersion relation, that can couple under current to form nonequilibrium modes of motion growing exponentially in time. Such motion is made possible by nonconservative current-induced forces on atoms, and we refer to it generically as the waterwheel effect. Here the connection between the waterwheel effect and the stimulated directional emission of phonons propagating along the electron flow is discussed in an intuitive manner. Nonadiabatic molecular dynamics show that waterwheel modes self-regulate by reducing the current and by populating modes in nearby frequency, leading to a dynamical steady state in which nonconservative forces are counter-balanced by the electronic friction. The waterwheel effect can be described by an appropriate effective nonequilibrium dynamical response matrix. We show that the current-induced parts of this matrix in metallic systems are long-ranged, especially at low bias. This nonlocality is essential for the characterisation of nonconservative atomic dynamics under current beyond the nanoscale.

Structure and dynamics of aqueous 2-propanol: A THz-TDS, NMR and neutron diffraction study

Aqueous liquid mixtures, in particular, those involving amphiphilic species, play an important role in many physical, chemical and biological processes. Of particular interest are alcohol/water mixtures; however, the structural dynamics of such systems are still not fully understood. Herein, a combination of terahertz time-domain spectroscopy (THz-TDS) and NMR relaxation time analysis has been applied to investigate 2-propanol/water mixtures across the entire composition range; while neutron diffraction studies have been carried out at two specific concentrations. Excellent agreement is seen between the techniques with a maximum in both the relative absorption coefficient and the activation energy to molecular motion occurring at ∼90 mol% H₂O. Furthermore, this is the same value at which well-established excess thermodynamic functions exhibit a maximum/minimum. Additionally, both neutron diffraction and THz-TDS have been used to provide estimates of the size of the hydration shell around 2-propanol in solution. Both methods determine that between 4 and 5 H₂O molecules per 2-propanol are found in the 2-propanol/water clusters at 90 mol% H₂O. Based on the acquired data, a description of the structure of 2-propanol/water across the composition range is presented.

Dynamics and structure of self-generated magnetics fields on solids following high contrast, high intensity laser irradiation

The dynamics of self-generated magnetic B-fields produced following the interaction of a high contrast, high intensity (I > 10¹⁹W cm^-2) laser beam with thin (3 μm thick) solid (Al or Au) targets is investigated experimentally and numerically. Two main sources drive the growth of B-fields on the target surfaces. B-fields are first driven by laser-generated hot electron currents that relax over ∼10-20 ps. Over longer timescales, the hydrodynamic expansion of the bulk of the target into vacuum also generates B-field induced by non-collinear gradients of density and temperature. The laser irradiation of the target front side strongly localizes the energy deposition at the target front, in contrast to the target rear side, which is heated by fast electrons over a much larger area. This induces an asymmetry in the hydrodynamic expansion between the front and rear target surfaces, and consequently the associated B-fields are found strongly asymmetric. The sole long-lasting (>30 ps) B-fields are the ones growing on the target front surface, where they remain of extremely high strength (∼8-10 MG). These B-fields have been recently put by us in practical use for focusing laser-accelerated protons [B. Albertazzi et al., Rev. Sci. Instrum. 86, 043502 (2015)]; here we analyze in detail their dynamics and structure.

The dynamics of murid gammaherpesvirus 4 within wild, sympatric populations of bank voles and wood mice

Murid gammaherpesvirus 4 (MuHV-4) is widely used as a small animal model for understanding gammaherpesvirus infections in man. However, there have been no epidemiological studies of the virus in wild populations of small mammals. As MuHV-4 both infects cells associated with the respiratory and immune systems and attempts to evade immune control via various molecular mechanisms, infection may reduce immunocompetence with potentially serious fitness consequences for individuals. Here we report a longitudinal study of antibody to MuHV-4 in a mixed assemblage of bank voles (Clethrionomys glareolus) and wood mice (Apodemus sylvaticus) in the UK. The study was conducted between April 2001 and March 2004. Seroprevalence was higher in wood mice than bank voles, supporting earlier work that suggested wood mice were the major host even though the virus was originally isolated from a bank vole. Analyses of both the probability of having antibodies and the probability of initial seroconversion indicated no clear seasonal pattern or relationship with host density. Instead, infection risk was most closely associated with individual characteristics, with heavier males having the highest risk. This may reflect individual variation in susceptibility, potentially related to variability in the ability to mount an effective immune response.