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。

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

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.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

Since the discovery of mechanically exfoliated graphene in 2004, research on ultrathin two-dimensional (2D) nanomaterials has grown exponentially in the fields of condensed matter physics, material science, chemistry, and nanotechnology. Highlighting their compelling physical, chemical, electronic, and optical properties, as well as their various potential applications, in this Review, we summarize the state-of-art progress on the ultrathin 2D nanomaterials with a particular emphasis on their recent advances. First, we introduce the unique advances on ultrathin 2D nanomaterials, followed by the description of their composition and crystal structures. The assortments of their synthetic methods are then summarized, including insights on their advantages and limitations, alongside some recommendations on suitable characterization techniques. We also discuss in detail the utilization of these ultrathin 2D nanomaterials for wide ranges of potential applications among the electronics/optoelectronics, electrocat...

Recent Advances in Ultrathin Two-Dimensional Nanomaterials

Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. Here we describe these techniques and illustrate them with examples highlighting current capabilities and limitations.

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

In the Raman effect, incident light is inelastically scattered from a sample and shifted in frequency by the energy of its characteristic molecular vibrations. Since its discovery in 1927, the effect has attracted attention from a basic research point of view as well as a powerful spectroscopic technique with many practical applications. The advent of laser light sources with monochromatic photons at high flux densities was a milestone in the history of Raman spectroscopy and resulted in dramatically improved scattering signals (for a general overview of modern Raman spectroscopy, see refs 1-5). In addition to this so-called spontaneous or incoherent Raman scattering, the development of lasers also opened the field of stimulated or coherent Raman spectroscopies, in which molecular vibrations are coherently excited. Whereas the intensity of spontaneous Raman scattering depends linearly on the number of probed molecules, the coherent Raman signal is proportional to the square of this number (for an overview, see refs 6 and 7). Coherent Raman techniques can provide interesting new opportunities such as vibrational imaging of biological samples,8 but they have not yet advanced the field of ultrasensitive trace detection. Therefore, in the following article, we shall focus on the spontaneous Raman effect, in the following simply called Raman scattering. Today, laser photons over a wide range of frequencies from the near-ultraviolet to the near-infrared region are used in Raman scattering studies, allowing selection of optimum excitation conditions for each sample. By choosing wavelengths which excite appropriate electronic transitions, resonance Raman studies of selected components of a sample or parts of a molecule can be performed.9 In the past few years, the range of excitation wavelengths has been extended to the near-infrared (NIR) region, in which background fluorescence is reduced and photoinduced degradation from the sample is diminished. High-intensity NIR diode lasers are easily available, making this region attractive for compact, low cost Raman instrumentation. Further, the development of low noise, high quantum efficiency multichannel detectors (chargecoupled device (CCD) arrays), combined with highthroughput single-stage spectrographs used in combination with holographic laser rejection filters, has led to high-sensitivity Raman spectrometers (for an overview on state-of-the-art NIR Raman systems, see ref 10). As we shall show in section 2, the nearinfrared region also has special importance for ultrasensitive Raman spectroscopy at the singlemolecule level. As with optical spectroscopy, the Raman effect can be applied noninvasively under ambient conditions in almost every environment. Measuring a Raman spectrum does not require special sample preparation techniques, in contrast with infrared absorption spectroscopy. Optical fiber probes for bringing excitation laser light to the sample and transporting scattered light to the spectrograph enable remote detection of Raman signals. Furthermore, the spatial and temporal resolution of Raman scattering are determined by the spot size and pulse length, respectively, of the excitation laser. By using a confocal microscope, Raman signals from femtoliter volumes (∼1 μm3) can by observed, enabling spatially resolved measurements in chromosomes and cells.11 Techniques such as multichannel Hadamard transform Raman microscopy12,13 or confocal scanning Fourier transform Raman microscopy14 allow generation of high-resolution Raman images of a sample. Recently, Raman spectroscopy was performed using near-field optical microscopy.15-17 Such techniques overcome the diffraction limit and allow volumes significantly smaller than the cube of the wavelength to be investigated. In the time domain, Raman spectra can be measured on the picosecond time scale, providing information on short-lived species such as excited 2957 Chem. Rev. 1999, 99, 2957−2975

Ultrasensitive Chemical Analysis by Raman Spectroscopy

Enzymatic turnovers of single cholesterol oxidase molecules were observed in real time by monitoring the emission from the enzyme's fluorescent active site, flavin adenine dinucleotide (FAD). Statistical analyses of single-molecule trajectories revealed a significant and slow fluctuation in the rate of cholesterol oxidation by FAD. The static disorder and dynamic disorder of reaction rates, which are essentially indistinguishable in ensemble-averaged experiments, were determined separately by the real-time single-molecule approach. A molecular memory phenomenon, in which an enzymatic turnover was not independent of its previous turnovers because of a slow fluctuation of protein conformation, was evidenced by spontaneous spectral fluctuation of FAD.

https://science.sciencemag.org/content/sci/282/5395/1877.full.pdf

Single-Molecule Enzymatic Dynamics

RECENT advances in near-field1and far-field2,3 fluorescence microscopy have made it possible to image single molecules and measure their emission3,4 and excitation5 spectra and fluorescence lifetimes3,6–8 at room temperature. These studies have revealed spectral shifts4 and intensity fluctuations6,7, the origins of which are not clear. Here we show that spontaneous fluctuations in the spectra of immobilized single dye molecules occur on two different timescales: hundreds of milliseconds and tens of seconds, indicating that these fluctuations have two distinct activation energies. In addition, we see photoinduced spectral fluctuations on repeated photoexcitation of single molecules. We suggest that all of these fluctuations can be understood as transitions between metastable minima in the molecular potential-energy surface.

Single-molecule spectral fluctuations at room temperature

To characterize the roles of cytochromes MtrC and OmcA of Shewanella oneidensis MR-1 in Cr(VI) reduction, the effects of deleting the mtrC and/or omcA gene on Cr(VI) reduction and the cellular locations of reduced Cr(III) precipitates were investigated. Compared to the rate of reduction of Cr(VI) by the wild type (wt), the deletion of mtrC decreased the initial rate of Cr(VI) reduction by 43.5%, while the deletion of omcA or both mtrC and omcA lowered the rate by 53.4% and 68.9%, respectively. In wt cells, Cr(III) precipitates were detected by transmission electron microscopy in the extracellular matrix between the cells, in association with the outer membrane, and inside the cytoplasm. No extracellular matrix-associated Cr(III) precipitates, however, were found in the cytochrome mutant cell suspension. In mutant cells without either MtrC or OmcA, most Cr(III) precipitates were found in association with the outer membrane, while in mutant cells lacking both MtrC and OmcA, most Cr(III) precipitates were found inside the cytoplasm. Cr(III) precipitates were also detected by scanning election microscopy on the surfaces of the wt and mutants without MtrC or OmcA but not on the mutant cells lacking both MtrC and OmcA, demonstrating that the deletion of mtrC and omcA diminishes the extracellular formation of Cr(III) precipitates. Furthermore, purified MtrC and OmcA reduced Cr(VI) with apparent k(cat) values of 1.2 ± 0.2 (mean ± standard deviation) and 10.2 ± 1 s(-1) and K(m) values of 34.1 ± 4.5 and 41.3 ± 7.9 μM, respectively. Together, these results consistently demonstrate that MtrC and OmcA are the terminal reductases used by S. oneidensis MR-1 for extracellular Cr(VI) reduction where OmcA is a predominant Cr(VI) reductase.

https://aem.asm.org/content/aem/77/12/4035.full.pdf

Extracellular Reduction of Hexavalent Chromium by Cytochromes MtrC and OmcA of Shewanella oneidensis MR-1

Real-time observation of enzymatic turnovers of single molecules has revealed non-Markovian dynamical behavior. Although chemical kinetics (such as the Michaelis-Menten mechanism) are sufficient to describe the average behavior of an ensemble of molecules, statistical analysis of the single-molecule fluorescence time trace reveals fluctuations in the rate of the activation step. These fluctuations are attributed to slow fluctuations of protein conformations. In this paper, we discuss models of the dynamical disorder behavior and relate them to observables of single molecule experiments. Simulations based on a discrete multistate model and a diffusive model are compared with experiment data. The role of various correlation functions, including higher order time correlation functions, in the interpretation of the underlying dynamics is discussed.

Statistical Analyses and Theoretical Models of Single-Molecule Enzymatic Dynamics

Electric field enhancement distributions encountered in atomic force microscopy (AFM) tip-enhanced surface-enhanced Raman spectroscopy (SERS) experiments (AFM-SERS) are simulated using a frequency-domain three-dimensional finite element method to solve Maxwell's equations of electric field distributions. We simulated an electromagnetic field enhancement in the vicinity of an AFM tip in close proximity to silver spherical nanoparticles under the illumination of a laser beam of various incident angles under different geometric arrangements. Maximum electric field enhancement is discussed in terms of the relative position of the tip and nanoparticles, as well as the direction of excitation laser propagation. Our results suggest new approaches for using AFM-SERS tip-enhanced near-field technique to image samples on surfaces.

H. Peter Lu

Papers

Single-Molecule Enzymatic Dynamics

Single-molecule spectral fluctuations at room temperature

Extracellular Reduction of Hexavalent Chromium by Cytochromes MtrC and OmcA of Shewanella oneidensis MR-1

Statistical Analyses and Theoretical Models of Single-Molecule Enzymatic Dynamics

Finite Element Method Simulation of the Field Distribution for AFM Tip-Enhanced Surface-Enhanced Raman Scanning Microscopy