随机光学重构显微成像技术及其应用

光学显微成像技术在生命科学、生物医学、临床医学诊断和材料科学等领域有着非常广泛的应用。但由于光学衍射极限的存在,传统光学显微镜无法观察到纳米尺度的物质及生命活动,极大地限制科学研究和医学的发展。近年来,随着突破光学衍射极限的超分辨成像技术的不断发展,显微成像分辨率得到不同程度的提高。目前在基于不同原理的各种超高分辨率显微镜中,随机光学重构显微镜(STORM)分辨率最高,可达几十纳米,真正实现了单分子水平检测。着重介绍了STORM超分辨显微成像技术的原理、实验方法及其应用。     

远场超分辨随机光重建显微镜(STORM)研究进展

了解细胞内分子尺度的动态和结构的特征是生命科学迫切需要解决的问题,要求远场光学成像要求纳米或亚纳米量级的空间分辨率.介绍了一种实现打破衍射极限的远场荧光显微成像技术--随机光重建显微术(STORM),其分辨率可以达到横向分辨率20 nm,轴向分辨率50 nm,理论上这种方法的空间分辨率可以达到单分子定位的精度.具体介绍...     

利用原子力显微镜研究在单分子水平上DNA与组蛋白的相互作用

核小体是DNA被压缩成染色质的第一级压缩结构. 为了更深刻描述DNA与组蛋白的相互作用,利用透析方法将DNA和组蛋白构建成核小体,并且应用原子力显微镜进行单分子水平上的观察. 实验结果表明利用透析方法得到了核小体的“串珠型排列”,并且对在两种不同的结合条件下DNA与组蛋白的相互作用进行了观察和比较.     

纳米分辨率光学显微成像

光学显微镜发明于17世纪,几百年来其分辨率一直受到光学衍射的限制。进入21世纪,多种超分辨成像技术打破了衍射极限的限制,带来了一场新的显微成像技术革命。其中,基于单分子定位的纳米分辨率光学成像技术近几年更是不断取得突破,达到接近分子尺度的分辨率。文章将简要介绍光学显微镜发展历程及超分辨成像技术基本原理,并着重介绍新型纳米分辨率显微成像技术及应用前景。     

原子尺度材料三维结构、磁性及动态演变的透射电子显微学表征

原子表征与操控是实现原子制造必须突破的物理瓶颈之一.像差校正电子显微学方法因其优异的空间分辨率,为实现原子精细制造提供了有力的表征手段.因此,利用电子显微学手段,在原子尺度对原子制造的材料及器件进行三维结构和性能的协同表征,对于深入理解原子水平材料操控的物理机理具有非常重要的意义.纳米团簇及纳米颗粒是原子制造材料与器件研究的主要对象之一,具有丰富的物理化学性质和较高的可操纵性.本文探讨纳米团簇/颗粒结构三维定量表征、使役条件下纳米团簇/颗粒结构演变定量表征、纳米颗粒/晶粒结构-成分-磁性协同定量表征等诸多方法与实例,阐明了电子显微学表征手段的突破和发展为实现精细控制的原子制造材料提供了坚实基础.     

超分辨定位成像中的像差表征和校正

超分辨定位成像技术凭借对数千甚至数万张采集的原始图像进行单分子定位及重建,可以获得几十纳米的超高分辨率,观察到之前看不到的细胞结构以及生物现象。然而,在实际的成像过程中,采集到的图像会受到像差(来源于光学系统的不完美或样品本身的不均匀性)的影响而导致分辨率下降,甚至会造成错误结果。为此,定量表征了几种典型像差对超分辨定位成像的影响,并提出了一种基于样品图像本身的像差校正方法。仿真和实验结果表明,像差会造成系统点扩展函数的变形以及成像分辨率的下降,使用基于图像本身的像差校正方法可以恢复图像的成像质量。     

沸石分子筛中半导体量子纳米团簇的组装及应用前景

在沸石分子筛中可以形成稳定的、分子尺寸的半导体团簇。这类团簇具有单相性、均匀性好的特点，并可形成三维量子超晶格结构。本文简单介绍沸石分子筛的结构及反应性之后，对团簇的组装技术及表征方法进行了详细的讨论，对半导体团簇的特征、性质反应用前景进行了较系统的论述。并指出了这类团簇材料应用存在的问题及发展方向。     

肿瘤细胞DNA样品基于二次谐波发生(SHG)的非线性光谱学成像

二次谐波的产生是一个二阶非线性光学过程,这个过程只发生在中心对称系数不为零的非中心对称区域。利用二次谐波显微技术可以对各种具有内源性信号的生物组织进行无损伤实时成像,如结缔组织的胶原纤维或肌细胞的肌动球蛋白。在生物化学和结构生物学中,虽然DNA是由脱氧核糖核苷酸构成而蛋白质是由氨基酸残基组成,但是DNA和蛋白质大分子高级结构的形成机制是相似的。利用光谱学成像技术对不同DNA样品进行检测,获取DNA样品的SHG信号并进行高解析度成像。这些DNA样品包括基因组DNA溶液、细胞核提取物以及培养细胞的细胞核。实验结果表明在常规条件下可以获得基因组DNA溶液和细胞核提取物的SHG信号,但几乎观测不到来自培养细胞核区的SHG信号。通过在培养基中添加少量无水乙醇(体积比小于5%),可以在培养细胞的细胞核区域检测到SHG信号。推测在培养细胞中乙醇和DNA相互作用引起DNA分子构象发生变化,这些变化可能导致了DNA分子非线性光学性质的改变。     

DNA与组蛋白相互作用的布朗动力学研究

在真核生物中,DNA按左手手征性的方式,缠绕在组蛋白八聚体的周围,形成稳定的核小体结构.文章作者运用布朗动力学,数值模拟了DNA与组蛋白相互作用最终形成核小体的动力学过程,揭示了DNA与组蛋白相互作用的详细图景,并提出了组蛋白八聚体旋转模型,以解释这一过程.文章作者还计算了组成核小体的DNA在受到拉伸力时,组蛋白被从核小体中剥离下来的动力学过程,得到了组装和剥离过程的详细图像,给出了与前人单分子实验一致的拉伸力与拉伸长度的关系曲线和拉伸台阶.此外,还通过建立的组蛋白手征性模型,模拟了核小体手征性的形成过程,发现DNA的缠绕方向强烈依赖于组蛋白的手征性,显示出环境温度对核小体手征性有重要影响.     

高精度定量相位显微成像方法研究

定量相位显微成像在工业检测、生物医学和光场调控等领域具有重要的应用价值。常用的定量相位显微成像技术通过干涉的方法来获取相位的定量分布,干涉装置的稳定性、光学衍射极限的限制、相位再现时的解包裹问题、激光照明下的相干噪声,以及动态观测过程中的样品离焦等因素都会影响定量相位显微成像的分辨率和精度。本文围绕高精度定量相位显微成像中的上述关键问题展开研究,通过构建物参共路的同步相移数字全息显微结构实现稳定的实时测量;采用结构光照明的超分辨相位成像方法实现对微小物体的超分辨相位成像;利用双波长照明将纵向无包裹相位测量范围扩大到微米量级;使用低相干LED照明解决相干噪声问题;提出了基于结构光照明和双波长照明的数字全息显微自动调焦方法,可以满足对不同类型样品的长时间跟踪观测。     

Cluster analysis of HZE particle tracks as applied to space radiobiology problems

A cluster analysis is performed of ionizations in tracks produced by the most abundant nuclei in the charge and energy spectra of the galactic cosmic rays. The frequency distribution of clusters is estimated for cluster sizes comparable to the DNA molecule at different packaging levels. For this purpose, an improved K-meansbased algorithm is suggested. This technique allows processing particle tracks containing a large number of ionization events without setting the number of clusters as an input parameter. Using this method, the ionization distribution pattern is analyzed depending on the cluster size and particle’s linear energy transfer.     

Comparative analysis of the nucleosome structure of cell nuclei by small-angle neutron scattering

The nucleosome structure in native nuclei of normal (chicken erythrocyte and rat leukocyte nuclei) and anomalously proliferating (the human cervical adenocarcinoma cell line HeLa and the Chinese hamster fibroblast cell line A238) cells has been investigated using small-angle neutron scattering. The experimental results obtained allow one to make the inference that the parameters of the nucleosome structure for the chicken erythrocyte and rat leukocyte nuclei (on average over the nucleus) are close to the universally accepted values and that the distance distribution function is bimodal. The bimodality of the distance distribution function reflects a narrow distribution of distances between nucleosomes (on average over the nucleus) at the fibril level of the chromatin organization. The histone core of the nucleosome structure in the nuclei of the HeLa and A238 cells (on average over the nucleus) is considerably less compact than that in the chicken erythrocyte and rat leukocyte nuclei, and the distance distribution function does not exhibit indications of the bimodality.     

Electronic conduction through 2D arrays of nanometer diameter metal clusters

An experimental study of electrical conduction through arrays of nanometer-diameter metallic clusters linked by organic molecules is presented. Gold clusters, having diameters of ∼4 nm and encapsulated by a monolayer of dodecanethiol, are deposited from solution on to specially prepared substrates to form a close-packed cluster monolayer. Nearest-neighbors in this 2D array of encapsulated clusters are then covalently linked using a conjugated organic molecule approximately 2.2 nm in length having isocyanide groups at both ends. In order to allow both electrical characterization and TEM imaging, the cluster arrays are deposited in 500 nm wide gaps between gold contacts on a free standing, insulating SiO₂ film. Electronic conduction through linked 2D arrays approximately 80 clusters in length has been observed at room temperature. The structure of the arrays and current-voltage relationships for the linked arrays are presented.     

Electron microscopy and atomic force microscopy studies of chromatin and metaphase chromosome structure

The folding of the chromatin filament and, in particular, the organization of genomic DNA within metaphase chromosomes has attracted the interest of many laboratories during the last five decades. This review discusses our current understanding of chromatin higher-order structure based on results obtained with transmission electron microscopy (TEM), cryo-electron microscopy (cryo-EM), and different atomic force microscopy (AFM) techniques.Chromatin isolated from different cell types in buffers without cations form extended filaments with nucleosomes visible as separated units. In presence of low concentrations of Mg²⁺, chromatin filaments are folded into fibers having a diameter of ∼30 nm. Highly compact fibers were obtained with isolated chromatin fragments in solutions containing 1–2 mM Mg²⁺. The high density of these fibers suggested that the successive turns of the chromatin filament are interdigitated. Similar results were obtained with reconstituted nucleosome arrays under the same ionic conditions. This led to the proposal of compact interdigitated solenoid models having a helical pitch of 4–5 nm. These findings, together with the observation of columns of stacked nucleosomes in different liquid crystal phases formed by aggregation of nucleosome core particles at high concentration, and different experimental evidences obtained using other approaches, indicate that face-to-face interactions between nucleosomes are very important for the formation of dense chromatin structures.Chromatin fibers were observed in metaphase chromosome preparations in deionized water and in buffers containing EDTA, but chromosomes in presence of the Mg²⁺ concentrations found in metaphase (5–22 mM) are very compact, without visible fibers. Moreover, a recent cryo-electron microscopy analysis of vitreous sections of mitotic cells indicated that chromatin has a disordered organization, which does not support the existence of 30-nm fibers in condensed chromosomes. TEM images of partially denatured chromosomes obtained using different procedures that maintain the ionic conditions of metaphase showed that bulk chromatin in chromosomes is organized forming multilayered plate-like structures. The structure and mechanical properties of these plates were studied using cryo-EM, electron tomography, AFM imaging in aqueous media, and AFM-based nanotribology and force spectroscopy. The results obtained indicated that the chromatin filament forms a flexible two-dimensional network, in which DNA is the main component responsible for the mechanical strength observed in friction force measurements. The discovery of this unexpected structure based on a planar geometry has opened completely new possibilities for the understanding of chromatin folding in metaphase chromosomes. It was proposed that chromatids are formed by many stacked thin chromatin plates oriented perpendicular to the chromatid axis. Different experimental evidences indicated that nucleosomes in the plates are irregularly oriented, and that the successive layers are interdigitated (the apparent layer thickness is 5–6 nm), allowing face-to-face interactions between nucleosomes of adjacent layers. The high density of this structure is in agreement with the high concentration of DNA observed in metaphase chromosomes of different species, and the irregular orientation of nucleosomes within the plates make these results compatible with those obtained with mitotic cell cryo-sections. The multilaminar chromatin structure proposed for chromosomes allows an easy explanation of chromosome banding and of the band splitting observed in stretched chromosomes.     

Chromatin supraorganization, mitotic abnormalities and proliferation in cells with increased or down-regulated lox expression: Indirect evidence of a LOX-histone H1 interaction in vivo

Lysyl oxidases (LOXs) are enzymes that permit the covalent crosslinking of the component chains of collagen and elastin. These enzymes are present inside the nuclei of certain mammalian cells. Previous studies have proposed LOX binding to histone H1 in vitro, and histone H1 is known to control global chromatin compaction and mitotic chromosome architecture. Therefore, in the present study, we analyzed chromatin supraorganizational changes, mitotic abnormalities, mitotic indices and cell death ratios in COS-7 and NRK-49F cells with high and low lox expression levels, respectively. The objective was to support biochemical data of LOX-H1 interaction, by providing evidence of chromatin remodeling in vivo, under different lox expressions. Chromatin decondensation assessed by image analysis was observed in COS-7 cells with increased lox expression. This decondensation is suggested to be promoted by LOX actions on histone H1, which loosens the DNA-H1 complex. In NRK-49F cells transfected with antisense lox or subjected to treatment with beta-aminopropionitrile (BAPN), chromatin condensation and nuclear phenotypic variability were found, which may be due to reduced LOX-H1 interaction. When lox expression was increased in COS-7 cells, the frequency of irregular chromosome plates was not affected, but cell proliferation decreased and "cell death preceded by multinucleation" increased. In NRK-49F cells there was accelerated proliferation induced by transfection with the antisense lox, and confirmed when cells were treated with BAPN. Apoptosis increased in NRK-49F cells only with BAPN treatment whereas cell death preceded by multinucleation increased only after antisense lox transfection. The data presented herein regarding chromatin remodeling indirectly support the hypothesis that LOX binds to histone H1 in vivo. Cell proliferation in COS-7 and NRK-49F cells and cell death at least in COS-7 cells agree with predicted effects of LOX interference in these processes.     

A view of the chromatin landscape

The microscope has been indispensable to the last century of chromatin structure research. Microscopy techniques have revealed that the three-dimensional location of chromatin is not random but represents a further manifestation of a highly compartmentalized cell nucleus. Moreover, the structure and location of genetic loci display cell type-specific differences and relate directly to the state of differentiation. Advances to bridge imaging with genetic, molecular and biochemical approaches have greatly enhanced our understanding of the interdependence of chromatin structure and nuclear function in mammalian cells. In this review we discuss the current state of chromatin structure research in relationship to the variety of microscopy techniques that have contributed to this field.     

单母体遗传算法优化(H2O)n(n≤14)的结构

在传统遗传算法的基础上提出了单母体遗传算法(single-parent genetic algorithm, SPGA)，通过对母体团簇实施两种不同的变异操作对结构进行优化，给出了分子团簇结构优化的算法实现. 结合TIP3P模型势函数，研究了水分子团簇(H₂O)_n(n≤14)的稳定结构. 优化结构和已有理论及实验结果一致. 计算结果表明当n<8时，平均结合能随n增加较快；当n≥8时有小的起伏. n=4,8,10,12的团簇结构具有较高对称性，比较稳定. 关键词： 单母体遗传算法 水分子团簇 结构优化