John Bechhoefer

Bio: John Bechhoefer is an academic researcher from Simon Fraser University. The author has contributed to research in topics: DNA replication & Liquid crystal. The author has an hindex of 36, co-authored 133 publications receiving 7487 citations. Previous affiliations of John Bechhoefer include University of Chicago & University of British Columbia.

Nucleation and growth in one dimension. II. Application to DNA replication kinetics

Abstract: Inspired by recent experiments on DNA replication, we apply a one-dimensional nucleation-and-growth model to DNA-replication kinetics, focusing on how to extract the time-dependent nucleation rate $I(t)$ and growth speed $v$ from data. We discuss generic experimental problems: namely, spatial inhomogeneity, measurement noise, and finite-size effects. After evaluating how each of these affects the measurements of $I(t)$ and $v$, we give guidelines for the design of experiments. These ideas are then discussed in the context of the DNA-replication experiments.

Virtual potentials for feedback traps.

Abstract: The recently developed feedback trap can be used to create arbitrary virtual potentials, to explore the dynamics of small particles or large molecules in complex situations. Experimentally, feedback traps introduce several finite time scales: There is a delay between the measurement of a particle's position and the feedback response, the feedback response is applied for a finite update time, and a finite camera exposure integrates motion. We show how to incorporate such timing effects into the description of particle motion. For the test case of a virtual quadratic potential, we give the first accurate description of particle dynamics, calculating the power spectrum and variance of fluctuations as a function of feedback gain, testing against simulations. We show that for small feedback gains, the motion approximates that of a particle in an ordinary harmonic potential. Moreover, if the potential is varied in time, for example by varying its stiffness, the work that is calculated approximates that done in an ordinary changing potential. The quality of the approximation is set by the ratio of the update time of the feedback loop to the relaxation time of motion in the virtual potential.

Regulation of DNA Replication within the Immunoglobulin Heavy-Chain Locus During B Cell Commitment

Abstract: The temporal order of replication of mammalian chromosomes appears to be linked to their functional organization, but the process that establishes and modifies this order during cell differentiation remains largely unknown. Here, we studied how the replication of the Igh locus initiates, progresses, and terminates in bone marrow pro-B cells undergoing B cell commitment. We show that many aspects of DNA replication can be quantitatively explained by a mechanism involving the stochastic firing of origins (across the S phase and the Igh locus) and extensive variations in their firing rate (along the locus). The firing rate of origins shows a high degree of coordination across Igh domains that span tens to hundreds of kilobases, a phenomenon not observed in simple eukaryotes. Differences in domain sizes and firing rates determine the temporal order of replication. During B cell commitment, the expression of the B-cell-specific factor Pax5 sharply alters the temporal order of replication by modifying the rate of origin firing within various Igh domains (particularly those containing Pax5 binding sites). We propose that, within the Igh CH-3′RR domain, Pax5 is responsible for both establishing and maintaining high rates of origin firing, mostly by controlling events downstream of the assembly of pre-replication complexes.

How Xenopus laevis embryos replicate reliably: investigating the random-completion problem.

Abstract: DNA synthesis in Xenopus frog embryos initiates stochastically in time at many sites origins along the chromosome. Stochastic initiation implies fluctuations in the time to complete and may lead to cell death if replication takes longer than the cell cycle time 25 min. Surprisingly, although the typical replication time is about 20 min, in vivo experiments show that replication fails to complete only about 1 in 300 times. How is replication timing accurately controlled despite the stochasticity? Biologists have proposed two solutions to this “random-completion problem.” The first solution uses randomly located origins but increases their rate of initiation as S phase proceeds, while the second uses regularly spaced origins. In this paper, we investigate the random-completion problem using a type of model first developed to describe the kinetics of first-order phase transitions. Using methods from the field of extreme-value statistics, we derive the distribution of replicationcompletion times for a finite genome. We then argue that the biologists’first solution to the problem is not only consistent with experiment but also nearly optimizes the use of replicative proteins. We also show that spatial regularity in origin placement does not alter significantly the distribution of replication times and, thus, is not needed for the control of replication timing.

Crystal growth at long times : critical behavior at the crossover from diffusion to kinetics-limited regimes

Abstract: We simulate one-dimensional crystal growth from an undercooled melt using a phase-field model and find interesting behavior when the liquid is undercooled by L/${\mathit{c}}_{\mathit{p}}$ degrees (``unit undercooling''). L is the latent heat and ${\mathit{c}}_{\mathit{p}}$ the specific heat. For smaller undercoolings, the diffusion of latent heat limits growth and the velocity of the solid-liquid interface decays with time as ${\mathit{t}}^{\mathrm{\ensuremath{-}}1/2}$. For larger undercoolings, non- equilibrium interface kinetics limits growth, and the interface velocity is constant. At unit undercooling, there are two scenarios, depending on the ratio of order parameter to thermal diffusivity (p). If p is small, the front-decay velocity is very well described by a power law ${\mathit{t}}^{\mathrm{\ensuremath{-}}\ensuremath{ u}}$, with \ensuremath{ u}\ensuremath{\approxeq}0.3. If p is large, the velocity at unit undercooling is finite. The branch of steady-state solutions then extends to smaller undercoolings, where the solid created is superheated. At the end of the branch, the solution jumps to a ${\mathit{t}}^{\mathrm{\ensuremath{-}}1/2}$ velocity-decay law. Although pure materials have small p's, impure materials can have large p's, so that the two scenarios at unit undercooling should be observable experimentally. Although our simulations apply strictly only to one-dimensional fronts, similar behavior is expected in two and three dimensions. The presence of the Mullins-Sekerka instability is unlikely to change our conclusions.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Pattern formation outside of equilibrium

Abstract: A comprehensive review of spatiotemporal pattern formation in systems driven away from equilibrium is presented, with emphasis on comparisons between theory and quantitative experiments. Examples include patterns in hydrodynamic systems such as thermal convection in pure fluids and binary mixtures, Taylor-Couette flow, parametric-wave instabilities, as well as patterns in solidification fronts, nonlinear optics, oscillatory chemical reactions and excitable biological media. The theoretical starting point is usually a set of deterministic equations of motion, typically in the form of nonlinear partial differential equations. These are sometimes supplemented by stochastic terms representing thermal or instrumental noise, but for macroscopic systems and carefully designed experiments the stochastic forces are often negligible. An aim of theory is to describe solutions of the deterministic equations that are likely to be reached starting from typical initial conditions and to persist at long times. A unified description is developed, based on the linear instabilities of a homogeneous state, which leads naturally to a classification of patterns in terms of the characteristic wave vector q0 and frequency ω0 of the instability. Type Is systems (ω0=0, q0≠0) are stationary in time and periodic in space; type IIIo systems (ω0≠0, q0=0) are periodic in time and uniform in space; and type Io systems (ω0≠0, q0≠0) are periodic in both space and time. Near a continuous (or supercritical) instability, the dynamics may be accurately described via "amplitude equations," whose form is universal for each type of instability. The specifics of each system enter only through the nonuniversal coefficients. Far from the instability threshold a different universal description known as the "phase equation" may be derived, but it is restricted to slow distortions of an ideal pattern. For many systems appropriate starting equations are either not known or too complicated to analyze conveniently. It is thus useful to introduce phenomenological order-parameter models, which lead to the correct amplitude equations near threshold, and which may be solved analytically or numerically in the nonlinear regime away from the instability. The above theoretical methods are useful in analyzing "real pattern effects" such as the influence of external boundaries, or the formation and dynamics of defects in ideal structures. An important element in nonequilibrium systems is the appearance of deterministic chaos. A greal deal is known about systems with a small number of degrees of freedom displaying "temporal chaos," where the structure of the phase space can be analyzed in detail. For spatially extended systems with many degrees of freedom, on the other hand, one is dealing with spatiotemporal chaos and appropriate methods of analysis need to be developed. In addition to the general features of nonequilibrium pattern formation discussed above, detailed reviews of theoretical and experimental work on many specific systems are presented. These include Rayleigh-Benard convection in a pure fluid, convection in binary-fluid mixtures, electrohydrodynamic convection in nematic liquid crystals, Taylor-Couette flow between rotating cylinders, parametric surface waves, patterns in certain open flow systems, oscillatory chemical reactions, static and dynamic patterns in biological media, crystallization fronts, and patterns in nonlinear optics. A concluding section summarizes what has and has not been accomplished, and attempts to assess the prospects for the future.

Calibration of atomic‐force microscope tips

Abstract: Images and force measurements taken by an atomic‐force microscope (AFM) depend greatly on the properties of the spring and tip used to probe the sample’s surface. In this article, we describe a simple, nondestructive procedure for measuring the force constant, resonant frequency, and quality factor of an AFM cantilever spring and the effective radius of curvature of an AFM tip. Our procedure uses the AFM itself and does not require additional equipment.

Stochastic Processes in Physics and Chemistry

Abstract: N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.