Three-Dimensional Stochastic Off-Lattice Model of Binding Chemistry in Crowded Environments

Molecular crowding is one of the characteristic features of the intracellular environment, defined by a dense mixture of varying kinds of proteins and other molecules. Interaction with these molecules significantly alters the rates and equilibria of chemical reactions in the crowded environment. Numerous fundamental activities of a living cell are strongly influenced by the crowding effect, such as protein folding, protein assembly and disassembly, enzyme activity, and signal transduction. Quantitatively predicting how crowding will affect any particular process is, however, a very challenging problem because many physical and chemical parameters act synergistically in ways that defy easy analysis. To build a more realistic model for this problem, we extend a prior stochastic off-lattice model from two-dimensional (2D) to three-dimensional (3D) space and examine how the 3D results compare to those found in 2D. We show that both models exhibit qualitatively similar crowding effects and similar parameter dependence, particularly with respect to a set of parameters previously shown to act linearly on total reaction equilibrium. There are quantitative differences between 2D and 3D models, although with a generally gradual nonlinear interpolation as a system is extended from 2D to 3D. However, the additional freedom of movement allowed to particles as thickness of the simulation box increases can produce significant quantitative change as a system moves from 2D to 3D. Simulation results over broader parameter ranges further show that the impact of molecular crowding is highly dependent on the specific reaction system examined

SAXS signature of the lamellar ordering of ionic domains of perfluorinated sulfonic acid ionomers by electric and magnetic field assisted casting

At present, small angle X ray scattering SAXS studies of perfluorinated sulfonic acid ionomers PFSAs are unable to fully determine the true shape of their building blocks, as recent SAXS modelling predicts disk and rod like nanoionic domains as being equally possible. This scenario requires evidence based findings to unravel the real shape of PFSA building blocks. Herein, a SAXS pattern signature for a lamellar nanophase separation of the ionic domains of Nafion is presented, backed by mid and far infrared spectroscopy MIR and FIR and wide angle X ray scattering WAXS data of Nafion in different ionic forms, a broad range of ionic phase contents EW amp; 8764; 859 42 amp; 8198;252 g eq amp; 8722;1 and temperatures. The study indicates that the lamellar arrangement of the ionic domains is the most representative morphology that accounts for the physical properties of this ionomer. The lamellar SAXS reflections of Nafion are enhanced in electric and magnetic field aligned membranes, as confirmed by atomic force microscopy AFM . Electric and magnetic field assisted casting of Nafion allowed producing nanostructured and anisotropic films with the lamellas stacked perpendicularly to the field vector, which is the direction of interest for several applications. Such nanostructured Nafion membranes are bestowed with advanced optical and proton transport properties, making them promising materials for solar and fuel cell

Synaptic Connections of the Neurokinin 1 Receptor-Like Immunoreactive Neurons in the Rat Medullary Dorsal Horn

The synaptic connections between neurokinin 1 (NK1) receptor-like immunoreactive (LI) neurons and γ-aminobutyric acid (GABA)-, glycine (Gly)-, serotonin (5-HT)- or dopamine-β-hydroxylase (DBH, a specific marker for norepinephrinergic neuronal structures)-LI axon terminals in the rat medullary dorsal horn (MDH) were examined under electron microscope by using a pre-embedding immunohistochemical double-staining technique. NK1 receptor-LI neurons were observed principally in laminae I and III, only a few of them were found in lamina II of the MDH. GABA-, Gly-, 5-HT-, or DBH-LI axon terminals were densely encountered in laminae I and II, and sparsely in lamina III of the MDH. Some of these GABA-, Gly-, 5-HT-, or DBH-LI axon terminals were observed to make principally symmetric synapses with NK1 receptor-LI neuronal cell bodies and dendritic processes in laminae I, II and III of the MDH. The present results suggest that neurons expressing NK1 receptor within the MDH might be modulated by GABAergic and glycinergic inhibitory intrinsic neurons located in the MDH and 5-HT- or norepinephrine (NE)-containing descending fibers originated from structures in the brainstem

The Use of PRV-Bartha to Define Premotor Inputs to Lumbar Motoneurons in the Neonatal Spinal Cord of the Mouse

The neonatal mouse has become a model system for studying the locomotor function of the lumbar spinal cord. However, information about the synaptic connectivity within the governing neural network remains scarce. A neurotropic pseudorabies virus (PRV) Bartha has been used to map neuronal connectivity in other parts of the nervous system, due to its ability to travel trans-neuronally. Its use in spinal circuits regulating locomotion has been limited and no study has defined the time course of labelling for neurons known to project monosynaptically to motoneurons.Here we investigated the ability of PRV Bartha, expressing green and/or red fluorescence, to label spinal neurons projecting monosynaptically to motoneurons of two principal hindlimb muscles, the tibialis anterior (TA) and gastrocnemius (GC). As revealed by combined immunocytochemistry and confocal microscopy, 24-32 h after the viral muscle injection the label was restricted to the motoneuron pool while at 32-40 h the fluorescence was seen in interneurons throughout the medial and lateral ventral grey matter. Two classes of ipsilateral interneurons known to project monosynaptically to motoneurons (Renshaw cells and cells of origin of C-terminals) were consistently labeled at 40 h post-injection but also a group in the ventral grey matter contralaterally. Our results suggest that the labeling of last order interneurons occurred 8-12 h after motoneuron labeling and we presume this is the time taken by the virus to cross one synapse, to travel retrogradely and to replicate in the labeled cells.The study establishes the time window for virally-labelling monosynaptic projections to lumbar motoneurons following viral injection into hindlimb muscles. Moreover, it provides a good foundation for intracellular targeting of the labeled neurons in future physiological studies and better understanding the functional organization of the lumbar neural networks

The Mechanism of Stress-Relief Cracking in a Ferritic Alloy Steel

A novel stress-relaxation technique and extensive microstructural characterization of the carbide precipitation, elemental segregation, and fracture modes were used to investigate stress-relief cracking in a ferritic alloy steel ABSTRACT. Stress-relief cracking is a major cause of weld failures in creepresistant, precipitation-strengthened materials such as ferritic alloy steels, stainless steels, and Ni-based superalloys. Stressrelief cracking occurs primarily in the coarse-grained heat-affected zone of weldments. Although the general causes of stress-relief cracking are known, the underlying mechanisms are very much a topic of debate. The mechanism of stressrelief cracking in the coarse-grained heataffected zone (CGHAZ) of a new ferritic alloy steel (HCM2S) was investigated through stress-relaxation testing and detailed microstructural characterization. The CGHAZ simulation and stress-relaxation testing was performed using Gleeble techniques. The time to failure exhibited C-curve behavior as a function of temperature. A balance of intergranular and intragranular carbide precipitation controlled the stress-relief cracking susceptibility. Cracking initiated at prior austenite grain boundaries by cavity nucleation on incoherent, Fe-rich M3C carbides. The grain interiors were resistant to plastic deformation due to precipitation strengthening by small (5-40 nm) alloy carbides. Elemental segregation played no detectable role in the stress-relief cracking failures. Much of the microstructural characterization was performed using a VG603 FEG STEM having a probe size of about 1.5 nm. The small probe size allowed nano-sized precipitates to be individually analyzed by using EDS and elemental EDS traces taken across prior austenite grain boundaries. In addition, SE STEM imaging with the VG603 FEG STEM was able to resolve small precipitates that were previously unobservable using conventional TEM and STEM techniques. The results of this study form a basis for heat treatment and welding process variables for HCM2S to avoid stress-relief cracking. In addition, these procedures and analytical results can be applied to other materials to avoid microstructures that are susceptible to stress-relief cracking