Peeling and sliding in nucleosome repositioning

We investigate the mechanisms of histone sliding and detachment with a stochastic model that couples thermally induced, passive histone sliding with active motor-driven histone unwrapping. Analysis of a passive loop or twist defect-mediated histone sliding mechanism shows that diffusional sliding is enhanced as larger portions of the DNA is peeled off the histone. The mean times to histone detachment and the mean distance traveled by the motor complex prior to histone detachment are computed as functions of the intrinsic speed of the motor. Fast motors preferentially induce detachment over sliding. However, for a fixed motor speed, increasing the histone-DNA affinity (and thereby decreasing the passive sliding rate) increases the mean distance traveled by the motor.

Exact steady-state velocity of ratchets driven by random sequential adsorption

We solve the problem of discrete translocation of a polymer through a pore, driven by the irreversible, random sequential adsorption of particles on one side of the pore. Although the kinetics of the wall motion and the deposition are coupled, we find the exact steady-state distribution for the gap between the wall and the nearest deposited particle. This result enables us to construct the mean translocation velocity demonstrating that translocation is faster when the adsorbing particles are smaller. Monte-Carlo simulations also show that smaller particles gives less dispersion in the ratcheted motion. We also define and compare the relative efficiencies of ratcheting by deposition of particles with different sizes and we describe an associated "zone-refinement" process.

Stochastic entry of enveloped viruses: fusion versus endocytosis

Infection by membrane-enveloped viruses requires the binding of receptors on the target cell membrane to glycoproteins, or "spikes," on the viral membrane. The initial entry mechanism is usually classified as fusogenic or endocytotic. However, binding of viral spikes to cell surface receptors not only initiates the viral adhesion and the wrapping process necessary for internalization, but can simultaneously initiate direct fusion with the cell membrane. Both fusion and internalization have been observed to be viable pathways for many viruses. We develop a stochastic model for viral entry that incorporates a competition between receptor-mediated fusion and endocytosis. The relative probabilities of fusion and endocytosis of a virus particle initially nonspecifically adsorbed on the host cell membrane are computed as functions of receptor concentration, binding strength, and number of spikes. We find different parameter regimes where the entry pathway probabilities can be analytically expressed. Experimental tests of our mechanistic hypotheses are proposed and discussed.

Long-Term Effect of Xylitol Gum Use on Mutans Streptococci in Adults

Many studies have shown the effects of chewing xylitol gum on mutans streptococci (MS) over short- and long-term periods in children; however, few studies have addressed long-term periods in adults. The objective of this investigation was to examine for 6 months the effects of chewing xylitol gum on MS in saliva and plaque in 127 adults (mean age 28.0 years). The participants were assigned to three groups according to gum type, in part taking preference for flavor into account and in part at random: xylitol (XYL), maltitol (MAL) and control (CR); 33, 34 and 27 subjects in each group, respectively, completed the trial. Daily gum use of the XYL and MAL groups was 7.9 and 7.1 g, respectively. MS levels, which declined significantly in saliva (p < 0.05) and plaque (p < 0.001) in the XYL group after 6 months, exhibited a significant increase in plaque in the MAL group (p < 0.001). Differences in relative changes of MS levels in plaque during the experimental period were significant between the XYL group and the CR (p < 0.05) and MAL groups (p < 0.001). Differences in relative change of amount of plaque during the experimental period were not statistically significant between the groups. The present study demonstrated that chewing xylitol gum for 6 months continued to inhibit the growth of mutans streptococci in adults.

Band gaps and the Kelvin-Helmholtz instability

We consider the linear stability of two inviscid fluids, in the presence of gravity, sheared past each other and separated by a flexible plate. Conditions for exponential growth of velocity perturbations are found as functions of the flexural rigidity of the plate and the shear rate. This Kelvin-Helmholtz instability is then analyzed in the presence of plates with spatially periodic (with period a) flexural rigidity arising from, for example, a periodic material variation. The eigenvalues of this periodic system are computed using Bloch's theorem (Floquet theory) that imposes specific Fourier decompositions of the velocity potential and plate deformations. We derive the non-Hermitian matrix whose eigenvalues determine the dispersion relation. Our dispersion relation shows that plate periodicity generally destabilizes the flow, compared to a uniform plate with the same mean flexural rigidity. However, enhanced destabilization and stabilization can occur for disturbances with wavelengths near an even multiple of the plate periodicity. The sensitivity of flows with such wavelengths arises from the nonpropagating, "Bragg reflected" modes coupled to the plate periodicity through the boundary condition at the plate.

Pulmonary embolism: accuracy and safety of a negative CT pulmonary angiogram and value of a negative D-dimer assay to exclude CT pulmonary angiogram-detectable pulmonary embolism

This is a retrospective study to determine the accuracy and safety of a negative CT pulmonary angiogram (CTPA) based on clinical outcome and to determine the usefulness of a negative D-dimer assay before CTPA. A total of 483 patients with a negative CTPA study were followed up for 3 months, with the aim of detecting episodes of venous thromboembolism and mortality. Three hundred and forty-nine patients had an immunochromatographic D-dimer assay called 'Simplify', carried out before a CTPA examination. Seventy-eight patients had a negative D-dimer assay and a negative CTPA. Three patients had a negative D-dimer assay and a positive CTPA. All three patients had a moderate pretest clinical probability. Of the 483 patients who had a negative CTPA and a 3-month follow up, 444 (92%) were alive and 39 (8%) had died. Of the 444 patients who were alive, none had any further suspected episode of thromboembolism or had received anticoagulation therapy within the follow-up period. Of those who died, none of the deaths was thought to be as a result of pulmonary embolism (PE). Single-detector helical CT can be used safely as the primary diagnostic test to evaluate PE. Negative Simplify D-dimer assay and low pretest clinical probability exclude CTPA-detectable PE, and a CTPA is unnecessary in this cohort of patients.

First passage and cooperativity of queuing kinetics

We model the kinetics of ligand-receptor systems, where multiple ligands may bind and unbind to the receptor, either randomly or in a specific order. Equilibrium occupation and first occurrence of complete filling of the receptor are determined and compared. At equilibrium, receptors that bind ligands sequentially are more likely to be saturated than those that bind in random order. Surprisingly however, for low cooperativity, the random process first reaches full occupancy faster than the sequential one. This is true except near a critical binding energy where a "kinetic trap" arises and the random process dramatically slows down when the number of binding sites N > or = 8. These results demonstrate the subtle interplay between cooperativity and sequentiality for a wide class of kinetic phenomena, including chemical binding, nucleation, and assembly line strategies.

First passage times of driven DNA hairpin unzipping

We model the dynamics of voltage-driven transport of DNA hairpins through transmembrane channels. A two-dimensional stochastic model of the DNA translocation process is fit to the measurements of Mathé, who pulled self-hybridized DNA hairpins through lipid-embedded alpha-hemolysin channels. As the channel was too narrow to accommodate hybridized DNA, dehybridization of the hairpin became the rate-limiting step of the transport process. We show that the mean first passage time versus voltage curve for the escape of the DNA from the transmembrane channel can be divided into two regions: (1) a low-voltage region where the DNA slides out of the pore in reverse and without undergoing significant dehybridization, and (2) a region where the DNA dehybridizes under the influence of the applied voltage and translocates across the membrane.

Isolation and transplantation of highly purified autologous peripheral CD34+ progenitor cells: purging efficacy, hematopoietic reconstitution in non-Hodgkin's lymphoma (NHL): results of Japanese phase II study

The purging efficacy of positive selection of autologous CD34+ PBSC with a clinical scale method of magnetic-activated cell sorting system (CliniMACS) was investigated in 48 patients with non-Hodgkin's lymphoma (NHL). The median purity and recovery rate of the CD34+ cells post-selection were 93.3% (range 32.6-99.3) and 72.2% (range 20.5-309.8), respectively. The real-time PCR method to detect the patient-specific monoclonal immunoglobulin heavy chain gene rearrangement (minimal residual tumor; MRT) and CD19 and CD20 positivities were used for the detection of contaminating NHL cells before and after CD34+ selection. After selection, the median (range) depletion rate of MRT was 2.53 (1.52-4.78) log, and that of CD19+ cell and CD20+ cell was 2.46 (0.74-3.64) log and 2.32 (0.40-4.01) log, respectively. In 41 patients, high-dose chemotherapy was performed, followed by the transplantation of the isolated CD34+ cells. Rapid neutrophil recovery as well as platelet recovery was seen with a median time to reach 0.5 x 10(9)/l neutrophils of 10 days (range 8-13) and 20 x 10(9)/l platelets of 14 days (range 10-34), respectively. The present study demonstrated that CliniMACS is a highly effective positive selection method and a high purging efficacy could be obtained without compromising the hematopoietic reconstitution capacity of the graft in NHL patients undergoing high-dose chemotherapy.

Physics of RecA-mediated homologous recognition

To accomplish its DNA strand exchange activities, the Escherichia coli protein RecA polymerizes onto DNA to form a stiff helical nucleoprotein filament within which the DNA is extended by 50%. Homology search and recognition occurs between ssDNA within the filament and an external dsDNA molecule. We show that stretching the internal DNA greatly enhances homology recognition by increasing the probability that the homologous regions of a stretched DNA molecule and a parallel, unstretched DNA molecule will be "in register" at some position. We also show that the stretching and stiffness of the filament act together to ensure that initiation of homologous exchange between the substrate DNA molecules at one position precludes initiation of homologous exchange at any other position. This prevents formation of multiple exchange site "topological traps" which would prevent completion of the exchange reaction and resolution of the products.

Steady-state properties of a totally asymmetric exclusion process with periodic structure

We study the steady-state behavior of totally asymmetric simple exclusion processes (TASEPs) that contain periodically varying movement rates. In this model, particles move to the right at one of two rates: p(2) if the particle occupies one of a periodically arranged set of lattice sites; p(1) otherwise. Approximate mean field approaches are used to study the steady-state currents and bulk densities of this model. These mean field methods are found to provide results in good agreement with data derived from Monte Carlo simulations. Finally, the condition for particle-hole symmetry in the TASEP with periodically varying movement rates is specified, and the changes in the locations of the boundary-limited to maximal-current transition lines due to symmetry violation are investigated.

Water alignment, dipolar interactions, and multiple proton occupancy during water-wire proton transport

A discrete multistate kinetic model for water-wire proton transport is constructed and analyzed using Monte Carlo simulations. In the model, each water molecule can be in one of three states: oxygen lone-pairs pointing leftward, pointing rightward, or protonated (H(3)O(+)). Specific rules for transitions among these states are defined as protons hop across successive water oxygens. Our model also includes water-channel interactions that preferentially align the water dipoles, nearest-neighbor dipolar coupling interactions, and Coulombic repulsion. Extensive Monte Carlo simulations were performed and the observed qualitative physical behaviors discussed. We find the parameters that allow the model to exhibit superlinear and sublinear current-voltage relationships, and show why alignment fields, whether generated by interactions with the pore interior or by membrane potentials, always decrease the proton current. The simulations also reveal a "lubrication" mechanism that suppresses water dipole interactions when the channel is multiply occupied by protons. This effect can account for an observed sublinear-to-superlinear transition in the current-voltage relationship.

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.

Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance

'Hot zones' are areas that have >5% prevalence (or incidence) of multidrug-resistant tuberculosis (MDRTB). We present a new mathematical model (the amplifier model) that tracks the emergence and evolution of multiple (pre-MDR, MDR and post-MDR) strains of drug-resistant Mycobacterium tuberculosis. We reconstruct possible evolutionary trajectories that generated hot zones over the past three decades, and identify the key causal factors. Results are consistent with recently reported World Health Organization (WHO) data. Our analyses yield three important insights. First, paradoxically we found that areas with programs that successfully reduced wild-type pansensitive strains often evolved into hot zones. Second, some hot zones emerged even when MDR strains were substantially less fit (and thus less transmissible) than wild-type pansensitive strains. Third, levels of MDR are driven by case-finding rates, cure rates and amplification probabilities. To effectively control MDRTB in the hot zones, it is essential that the WHO specify a goal for minimizing the amplification probability.

Physical mechanisms of gas and perfluoron retinopexy and sub-retinal fluid displacement

Injection of gas into the eye, followed by face-down positioning, is a common protocol for the reseating of the retina in posterior and superior retinal tears and breaks. The physical mechanism by which injected gas helps reattach retinal flaps is often ascribed to the 'buoyancy' force of the injected gas bubble. The various forces at play in this system (surface tension and buoyancy) were calculated and compared. The results are extended to the case in which the retina is intact (pneumatic displacement of blood) and to the use of intraocular perfluoron (n-perfluorooctane). We show that buoyancy forces are applicable only for gas or n-perfluorooctane bubbles that are smaller than the detached retina and that do not invade underneath the retina. For larger bubbles, as is normally used in reattachment protocols, we show that it is the interfacial tension that reattaches the retina. The range of angles within which patients can position, and still maintain a gas-vitreous interface along a tear is calculated as a function of the volume of injected gas and size of the tear. The maximum retinal flap size that can be reattached using surface tension forces is also estimated.

Chiral molecule adsorption on helical polymers

We present a lattice model for helicity induction on an optically inactive polymer due to the adsorption of exogenous chiral amine molecules. The system is mapped onto a one-dimensional Ising model characterized by an on-site polymer helicity variable and an amine occupancy one. The equilibrium properties are analyzed in the limits of strong coupling between helicity induction and amine adsorption and in that of noninteracting adsorbant molecules. We discuss our results in the context of recent experimental results.

Ribosome recycling, diffusion, and mRNA loop formation in translational regulation

We explore and quantify the physical and biochemical mechanisms that may be relevant in the regulation of translation. After elongation and detachment from the 3' termination site of mRNA, parts of the ribosome machinery can diffuse back to the initiation site, especially if it is held nearby, enhancing overall translation rates. The elongation steps of the mRNA-bound ribosomes are modeled using exact and asymptotic results of the totally asymmetric exclusion process. Since the ribosome injection rates of the totally asymmetric exclusion process depend on the local concentrations at the initiation site, a source of ribosomes emanating from the termination end can feed back to the initiation site, leading to a self-consistent set of equations for the steady-state ribosome throughput. Additional mRNA binding factors can also promote loop formation, or cyclization, bringing the initiation and termination sites into close proximity. The probability distribution of the distance between the initiation and termination sites is described using simple noninteracting polymer models. We find that the initiation, or initial ribosome adsorption binding required for maximal throughput, can vary dramatically depending on certain values of the bulk ribosome concentration and diffusion constant. If cooperative interactions among the loop-promoting proteins and the initiation/termination sites are considered, the throughput can be further regulated in a nonmonotonic manner. Experiments that can potentially test the hypothesized physical mechanisms are discussed.

Interplay of chemotaxis and chemokinesis mechanisms in bacterial dynamics

Motivated by observations of the dynamics of Myxococcus xanthus, we present a self-interacting random walk model that describes the competition between chemokinesis and chemotaxis. Cells are constrained to move in one dimension, but release a chemical chemoattractant at a steady state. The bacteria sense the chemical that they produce. The probability of direction reversals is modeled as a function of both the absolute level of chemoattractant sensed directly under each cell as well as the gradient sensed across the length of the cell. If the chemical does not degrade or diffuse rapidly, the one-dimensional trajectory depends on the entire past history of the trajectory. We derive the corresponding Fokker-Planck equations, use an iterative mean-field approach that we solve numerically for short times, and perform extensive Monte Carlo simulations of the model. Cell positional distributions and the associated moments are computed in this feedback system. Average drift and mean squared displacements are found. Crossover behaviors among different diffusion regimes are found.