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

Chemical analysis of acoustically levitated drops by Raman spectroscopy

An experimental apparatus combining Raman spectroscopy with acoustic levitation, Raman acoustic levitation spectroscopy (RALS), is investigated in the field of physical and chemical analytics. Whereas acoustic levitation enables the contactless handling of microsized samples, Raman spectroscopy offers the advantage of a noninvasive method without complex sample preparation. After carrying out some systematic tests to probe the sensitivity of the technique to drop size, shape, and position, RALS has been successfully applied in monitoring sample dilution and preconcentration, evaporation, crystallization, an acid–base reaction, and analytes in a surface-enhanced Raman spectroscopy colloidal suspension

The optical properties of In2S3 films in the far infrared spectral range

Optical reflection spectra of In2S3 thin films 180 730 nm deposited on glass substrates are measured by infrared spectroscopy using the synchrotron radiation of BESSY II storage ring in the spectral range of 30 8000 cm amp; 8722;1. The aim of the study is to find the influence of different substrate and post annealing temperatures on the electron and phonon systems of In2S3 films deposited on glass. Clear features in the reflectance spectra for the studied films have been found mainly in the phonon excitation range 100 400 cm amp; 8722;1. The experimental dielectric functions amp; 949; amp; 969; of In2S3 films are found to be in good agreement with the calculated ones obtained for In2S3 crystals within the density functional theory. The dielectric functions amp; 949; amp; 969; of the films in the range of 100 400 cm amp; 8722;1 depend substantially on the post annealing temperature. This indicates a transition of the film from the amorphous to the crystalline state. The thorough analysis of the frequency dependence of the reflection coefficient R amp; 969; and optical conductivity amp; 963; amp; 969; in the wavenumber range of 30 130 cm amp; 8722;1 allowed us to reveal the distributed electron states in In2S3 film

Stretched or noded orbital densities and self-interaction correction in density functional theory

Semilocal approximations to the density functional for the exchange-correlation energy of a many-electron system necessarily fail for lobed one-electron densities, including not only the familiar stretched densities but also the less familiar but closely related noded ones. The Perdew-Zunger (PZ) self-interaction correction (SIC) to a semilocal approximation makes that approximation exact for all one-electron ground- or excited-state densities and accurate for stretched bonds. When the minimization of the PZ total energy is made over real localized orbitals, the orbital densities can be noded, leading to energy errors in many-electron systems. Minimization over complex localized orbitals yields nodeless orbital densities, which reduce but typically do not eliminate the SIC errors of atomization energies. Other errors of PZ SIC remain, attributable to the loss of the exact constraints and appropriate norms that the semilocal approximations satisfy, suggesting the need for a generalized SIC. These conclusions are supported by calculations for one-electron densities and for many-electron molecules. While PZ SIC raises and improves the energy barriers of standard generalized gradient approximations (GGAs) and meta-GGAs, it reduces and often worsens the atomization energies of molecules. Thus, PZ SIC raises the energy more as the nodality of the valence localized orbitals increases from atoms to molecules to transition states. PZ SIC is applied here, in particular, to the strongly constrained and appropriately normed (SCAN) meta-GGA, for which the correlation part is already self-interaction-free. This property makes SCAN a natural first candidate for a generalized SIC. Published under license by AIP Publishing.Peer reviewe

Unified regression model of binding equilibria in crowded environments

Molecular crowding is a critical feature distinguishing intracellular environments from idealized solution-based environments and is essential to understanding numerous biochemical reactions, from protein folding to signal transduction. Many biochemical reactions are dramatically altered by crowding, yet it is extremely difficult to predict how crowding will quantitatively affect any particular reaction systems. We previously developed a novel stochastic off-lattice model to efficiently simulate binding reactions across wide parameter ranges in various crowded conditions. We now show that a polynomial regression model can incorporate several interrelated parameters influencing chemistry under crowded conditions. The unified model of binding equilibria accurately reproduces the results of particle simulations over a broad range of variation of six physical parameters that collectively yield a complicated, non-linear crowding effect. The work represents an important step toward the long-term goal of computationally tractable predictive models of reaction chemistry in the cellular environment

Detection of a MicroRNA Signal in an In Vivo Expression Set of mRNAs

Background. microRNAs (miRNAs) are approximately 21 nucleotide non-coding transcripts capable of regulating gene expression. The most widely studied mechanism of regulation involves binding of a miRNA to the target mRNA. As a result, translation of the target mRNA is inhibited and the mRNA may be destabilized. The inhibitory effects of miRNAs have been linked to diverse cellular processes including malignant proliferation, apoptosis, development, differentiation, and metabolic processes. We asked whether endogenous fluctuations in a set of mRNA and miRNA profiles contain correlated changes that are statistically distinguishable from the many other fluctuations in the data set. Methodology/Principal Findings. RNA was extracted from 12 human primary brain tumor biopsies. These samples were used to determine genome-wide mRN

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

How to reduce household costs for people with tuberculosis : a longitudinal costing survey in Nepal

The aim of this study was to compare costs and socio-economic impact of tuberculosis (TB) for patients diagnosed through active (ACF) and passive case finding (PCF) in Nepal. A longitudinal costing survey was conducted in four districts of Nepal from April 2018 to October 2019. Costs were collected using the WHO TB Patient Costs Survey at three time points: intensive phase of treatment, continuation phase of treatment and at treatment completion. Direct and indirect costs and socio-economic impact (poverty headcount, employment status and coping strategies) were evaluated throughout the treatment. Prevalence of catastrophic costs was estimated using the WHO threshold. Logistic regression and generalized estimating equation were used to evaluate risk of incurring high costs, catastrophic costs and socio-economic impact of TB over time. A total of 111 ACF and 110 PCF patients were included. ACF patients were more likely to have no education (75% vs 57%, P = 0.006) and informal employment (42% vs 24%, P = 0.005) Compared with the PCF group, ACF patients incurred lower costs during the pretreatment period (mean total cost: US$55 vs US$87, P < 0.001) and during the pretreatment plus treatment periods (mean total direct costs: US$72 vs US$101, P < 0.001). Socio-economic impact was severe for both groups throughout the whole treatment, with 32% of households incurring catastrophic costs. Catastrophic costs were associated with ‘no education’ status [odds ratio = 2.53(95% confidence interval = 1.16–5.50)]. There is a severe and sustained socio-economic impact of TB on affected households in Nepal. The community-based ACF approach mitigated costs and reached the most vulnerable patients. Alongside ACF, social protection policies must be extended to achieve the zero catastrophic costs milestone of the End TB strategy