Tom Chou

Clustered bottlenecks in mRNA translation and protein synthesis

Using a model based on the totally asymmetric exclusion process, we investigate the effects of slow codons along messenger RNA. Ribosome density profiles near neighboring clusters of slow codons interact, enhancing suppression of ribosome throughput when such bottlenecks are closely spaced. Increasing the slow codon cluster size beyond approximately 3-4 codons does not significantly reduce the ribosome current. Our results are verified by both extensive Monte Carlo simulations and numerical calculation, and provide a biologically motivated explanation for the experimentally observed clustering of low-usage codons.

Elite suppressor-derived HIV-1 envelope glycoproteins exhibit reduced entry efficiency and kinetics.

Elite suppressors (ES) are a rare subset of HIV-1–infected individuals who are able to maintain HIV-1 viral loads below the limit of detection by ultra-sensitive clinical assays in the absence of antiretroviral therapy. Mechanism(s) responsible for this elite control are poorly understood but likely involve both host and viral factors. This study assesses ES plasma-derived envelope glycoprotein (env) fitness as a function of entry efficiency as a possible contributor to viral suppression. Fitness of virus entry was first evaluated using a novel inducible cell line with controlled surface expression levels of CD4 (receptor) and CCR5 (co-receptor). In the context of physiologic CCR5 and CD4 surface densities, ES envs exhibited significantly decreased entry efficiency relative to chronically infected viremic progressors. ES envs also demonstrated slow entry kinetics indicating the presence of virus with reduced entry fitness. Overall, ES env clones were less efficient at mediating entry than chronic progressor envs. Interestingly, acute infection envs exhibited an intermediate phenotypic pattern not distinctly different from ES or chronic progressor envs. These results imply that lower env fitness may be established early and may directly contribute to viral suppression in ES individuals.

A Quantitative Affinity-Profiling System That Reveals Distinct CD4/CCR5 Usage Patterns among Human Immunodeficiency Virus Type 1 and Simian Immunodeficiency Virus Strains

ABSTRACT The affinity of human immunodeficiency virus (HIV) envelope for CD4 and CCR5 appears to be associated with aspects of R5 virus (virus using the CCR5 coreceptor) pathogenicity. However, entry efficiency results from complex interactions between the viral envelope glycoprotein and both CD4 and CCR5, which limits attempts to correlate viral pathogenicity with surrogate measures of envelope CD4 and CCR5 affinities. Here, we present a system that provides a quantitative and comprehensive characterization of viral entry efficiency as a direct interdependent function of both CD4 and CCR5 levels. This receptor affinity profiling system also revealed heretofore unappreciated complexities underlying CD4/CCR5 usage. We first developed a dually inducible cell line in which CD4 and CCR5 could be simultaneously and independently regulated within a physiologic range of surface expression. Infection by multiple HIV type 1 (HIV-1) and simian immunodeficiency virus isolates could be examined simultaneously for up to 48 different combinations of CD4/CCR5 expression levels, resulting in a distinct usage pattern for each virus. Thus, each virus generated a unique three-dimensional surface plot in which viral infectivity varied as a function of both CD4 and CCR5 expression. From this functional form, we obtained a sensitivity vector along with corresponding metrics that quantified an isolates overall efficiency of CD4/CCR5 usage. When applied to viral isolates with well-characterized sensitivities to entry/fusion inhibitors, the vector metrics were able to encapsulate their known biological phenotypes. The application of the vector metrics also indicated that envelopes derived from elite suppressors had overall-reduced entry efficiencies compared to those of envelopes derived from chronically infected viremic progressors. Our affinity-profiling system may help to refine studies of R5 virus tropism and pathogenesis.

Totally asymmetric exclusion processes with particles of arbitrary size

The steady-state currents and densities of a one-dimensional totally asymmetric exclusion process (TASEP) with particles that occlude an integer number (d) of lattice sites are computed using various mean-field approximations and Monte Carlo simulations. TASEPs featuring particles of arbitrary size are relevant for modelling systems such as mRNA translation, vesicle locomotion along microtubules and protein sliding along DNA. We conjecture that the nonequilibrium steady-state properties separate into low-density, high-density, and maximal current phases similar to those of the standard (d = 1) TASEP. A simple mean-field approximation for steady-state particle currents and densities is found to be inaccurate. However, we find local equilibrium particle distributions derived from a discrete Tonks gas partition function yield apparently exact currents within the maximal current phase. For the boundary-limited phases, the equilibrium Tonks gas distribution cannot be used to predict currents, phase boundaries, or the order of the phase transitions. However, we employ a refined mean-field approach to find apparently exact expressions for the steady-state currents, boundary densities, and phase diagrams of the d ≥ 1 TASEP. Extensive Monte Carlo simulations are performed to support our analytic, mean-field results.

Measurement of the Optic Disc Vertical Tilt Angle With Spectral-Domain Optical Coherence Tomography and Influencing Factors

PURPOSE To report a novel method for measuring the vertical tilt angle of the optic nerve (ON) head and to investigate the associated factors. DESIGN Cross-sectional diagnostic study. METHODS One hundred and twelve normal, glaucomatous, and glaucoma suspect eyes (99 patients) were enrolled in this study. Subjects underwent a full eye examination, biometry, and spectral-domain optical coherence tomography (SDOCT). The vertical tilt angle was measured on high-resolution cross-sectional SDOCT images passing through the ON head and foveal centers using the inner edges of the Bruch membrane opening as the reference plane. The correlation between the vertical tilt angle with the ovality index and the potential associated factors was estimated with univariate and multivariate linear regression analyses. RESULTS The median (interquartile range, [IQR]) axial length and visual field mean deviation were 24.5 (23.8-25.3) mm and -0.9 (-2.76 to 0.26) dB. The median (IQR) tilt angle was 3.5 (1.2-11.2) degrees. There was a moderate correlation between the ovality index and tilt angle (Spearman ρ = 0.351; P < .001). In univariate analyses, axial length, spherical equivalent, and mean deviation were correlated with the tilt angle (P = .002, P = .011, and P = .013, respectively). Axial length, mean deviation, and their interaction showed a statistically significant correlation with the tilt angle in multivariate analyses (P = .044 for axial length, P = .039 for mean deviation, and P = .028 for their interaction). CONCLUSIONS We describe a new method for measuring the ON head vertical tilt angle with high-resolution SDOCT imaging. The ovality index demonstrated only a moderate correlation with the tilt angle measurements and hence is not a good proxy measure for the vertical ON head tilt angle. Axial length and visual field mean deviation are the main factors associated with the ON head vertical tilt angle. The underlying basis for the relationship of vertical tilt angle and glaucoma severity should be further explored.

Electrostatics of lipid bilayer bending

The electrostatic contribution to spontaneous membrane curvature is calculated within Poisson-Boltzmann theory under a variety of assumptions and emphasizing parameters in the physiological range. Asymmetrical surface charges can be fixed with respect to bilayer midplane area or with respect to the lipid-water area, but induce curvatures of opposite signs. Unequal screening layers on the two sides of a vesicle (e.g., multivalent cationic proteins on one side and monovalent salt on the other) also induce bending. For reasonable parameters, tubules formed by electrostatically induced bending can have radii in the 50-100-nm range, often seen in many intracellular organelles. Thus membrane associated proteins may induce curvature and subsequent budding, without themselves being intrinsically curved. Furthermore, we derive the previously unexplored effects of respecting the strict conservation of charge within the interior of a vesicle. The electrostatic component of the bending modulus is small under most of our conditions and is left as an experimental parameter. The large parameter space of conditions is surveyed in an array of graphs.

Kinetics and thermodynamics across single-file pores: Solute permeability and rectified osmosis

We study the effects of solute-membrane interactions on osmotic transport through pores. By extending single-file, single-species kinetic models to include entrance of solute into membrane pores, we model the statistical mechanics of competitive transport of two species across membrane pores. The results have direct applications to water transport across biomembrane pores and particle movement in zeolites, and can be extended to study ion channel transport. Reflection coefficients, the reduction of osmotic fluxes measured using different solutes, are computed in terms of the microscopic kinetic parameters. We find that a reduction in solvent flow due to solute–pore interactions can be modeled by a Langmuir adsorption isotherm. Osmosis experiments are discussed and proposed. Special cases and Onsager relations are presented in the Appendixes.

Enhancement of charged macromolecule capture by nanopores in a salt gradient.

Nanopores spanning synthetic membranes have been used as key components in proof-of-principle nanofluidic applications, particularly those involving manipulation of biomolecules or sequencing of DNA. The only practical way of manipulating charged macromolecules near nanopores is through a voltage difference applied across the nanopore-spanning membrane. However, recent experiments have shown that salt concentration gradients applied across nanopores can also dramatically enhance charged particle capture from a low concentration reservoir of charged molecules at one end of the nanopore. This puzzling effect has hitherto eluded a physically consistent theoretical explanation. Here, we propose an electrokinetic mechanism of this enhanced capture that relies on the electrostatic potential near the pore mouth. For long pores with diameter much greater than the local screening length, we obtain accurate analytic expressions showing how salt gradients control the local conductivity which can lead to increased local electrostatic potentials and charged analyte capture rates. We also find that the attractive electrostatic potential may be balanced by an outward, repulsive electro-osmotic flow that can in certain cases conspire with the salt gradient to further enhance the analyte capture rate.

First passage times in homogeneous nucleation and self-assembly

Motivated by nucleation and molecular aggregation in physical, chemical, and biological settings, we present a thorough analysis of the general problem of stochastic self-assembly of a fixed number of identical particles in a finite volume. We derive the backward Kolmogorov equation (BKE) for the cluster probability distribution. From the BKE, we study the distribution of times it takes for a single maximal cluster to be completed, starting from any initial particle configuration. In the limits of slow and fast self-assembly, we develop analytical approaches to calculate the mean cluster formation time and to estimate the first assembly time distribution. We find, both analytically and numerically, that faster detachment can lead to a shorter mean time to first completion of a maximum-sized cluster. This unexpected effect arises from a redistribution of trajectory weights such that upon increasing the detachment rate, paths that take a shorter time to complete a cluster become more likely.

Buckling instabilities of a confined colloid crystal layer.

A model predicting the structure of repulsive, spherically symmetric, monodisperse particles confined between two walls is presented. We study the buckling transition of a single flat layer as the double layer state develops. Experimental realizations of this model are suspensions of stabilized colloidal particles squeezed between glass plates. By expanding the thermodynamic potential about a flat state of \( N \) confined colloidal particles, we derive a free energy as a functional of in-plane and out-of-plane displacements. The wavevectors of these first buckling instabilities correspond to three different ordered structures. Landau theory predicts that the symmetry of these phases allows for second order phase transitions. This possibility exists even in the presence of gravity or plate asymmetry. These transitions lead to critical behavior and phases with the symmetry of the three-state and four-state Potts models, the X-Y model with 6-fold anisotropy, and the Heisenberg model with cubic interactions. Experimental detection of these structures is discussed.