基于模拟退火法由脑磁图推测电流偶极子参数

利用模拟退火（Ｓｉｍｕｌａｔｅｄ Ａｎｎｅａｌｉｎｇ） 算法,由脑磁图（ ＭＥＧ） 数据反演脑内作为磁源的单电流偶极子参数,可以得到理想的结果。在上述工作的基础上,对脑内多电流偶极子参数的反演,则呈现如下状况：即以少于实际源数目的偶极子为源假设反演,目标函数得不到极小优化。反之,目标函数可以得到极小优化, 但出现多余的伪偶极子, 且这些伪偶极子在多次不同条件的反演结果中,处于不稳定状态。若将多次反演结果中处于不稳定状态的偶极子作为伪偶极子的判据而将其排除,则可以得到一种判断磁源偶极子数目的方法     

Reproduction of correct electrostatic field by charges and dipoles on a closed surface

A general algorithm based on the Green function theorem has been developed to correctly reproduce electrostatic fields inside a closed space by point charges and point dipoles on the surface surrounding the space. For actual computations, limited numbers of point charges, including charge pairs replacing point dipoles, are enough to approximate the inner fields. As examples, reaction fields were reproduced by the current surface charges and dipoles for the dielectric models, where a monopole, dipole, or quadrupole was individually set at the center in a vacuum sphere surrounded by high dielectric continuum. The potentials due to those reaction fields agree well with the analytical ones. As an application of this method to the analysis of the electronic structure of the active site of a protein, a combination of the continuum dielectric model and ab initio molecular orbital calculation was carried out. Other applications to molecular dynamics and quantum mechanical calculations are also discussed.     

Spatial Covariance Reconstructive (SCORE) Super-Resolution Fluorescence Microscopy

Super-resolution fluorescence microscopy has become a powerful tool to resolve structural information that is not accessible to traditional diffraction-limited imaging techniques such as confocal microscopy. Stochastic optical reconstruction microscopy (STORM) and photoactivation localization microscopy (PALM) are promising super-resolution techniques due to their relative ease of implementation and instrumentation on standard microscopes. However, the application of STORM is critically limited by its long sampling time. Several recent works have been focused on improving the STORM imaging speed by making use of the information from emitters with overlapping point spread functions (PSF). In this work, we present a fast and efficient algorithm that takes into account the blinking statistics of independent fluorescence emitters. We achieve sub-diffraction lateral resolution of 100 nm from 5 to 7 seconds of imaging. Our method is insensitive to background and can be applied to different types of fluorescence sources, including but not limited to the organic dyes and quantum dots that we demonstrate in this work.     

Precise nanometer localization analysis for individual fluorescent probes

Calculation of the centroid of the images of individual fluorescent particles and molecules allows localization and tracking in light microscopes to a precision about an order of magnitude greater than the microscope resolution. The factors that limit the precision of these techniques are examined and a simple equation derived that describes the precision of localization over a wide range of conditions. In addition, a localization algorithm motivated from least-squares fitting theory is constructed and tested both on image stacks of 30-nm fluorescent beads and on computer-generated images (Monte Carlo simulations). Results from the algorithm show good agreement with the derived precision equation for both the simulations and actual images. The availability of a simple equation to describe localization precision helps investigators both in assessing the quality of an experimental apparatus and in directing attention to the factors that limit further improvement. The precision of localization scales as the inverse square root of the number of photons in the spot for the shot noise limited case and as the inverse of the number of photons for the background noise limited case. The optimal image magnification depends on the expected number of photons and background noise, but, for most cases of interest, the pixel size should be about equal to the standard deviation of the point spread function.     

几种超分辨率荧光显微技术的原理和近期进展

在生命科学领域,人们常常需要在细胞内精确定位特定的蛋白质以研究其位置与功能的关系．多年来,宽场/共聚焦荧光显微镜的分辨率受限于光的阿贝/瑞利极限,不能分辨出200 nm以下的结构．近年来,随着新的荧光探针和成像理论的出现,研究者开发了多种实现超出普通共聚焦显微镜分辨率的三维超分辨率成像方法．主要介绍这些方法的原理、近期进展和发展趋势．介绍了光源的点扩散函数(point spread function, PSF)的概念和传统分辨率的定义,阐述了提高xy平面分辨率的方法．通过介绍单分子荧光成像技术,引入了单分子成像定位精度的概念,介绍了基于单分子成像的超分辨率显微成像方法,包括光激活定位显微技术(photoactivated localization microscopy, PALM)和随机光学重构显微技术(stochastic optical reconstruction microscopy, STORM)．介绍了两大类通过改造光源的点扩散函数来提高成像分辨率的方法,分别是受激发射损耗显微技术(stimulated emission depletion, STED)和饱和结构照明显微技术(saturated structure illumination microscopy, SSIM)．比较了不同的z轴提取信息的方法,并阐述了这些方法与xy平面上的超分辨率显微成像技术相结合所得到的各种三维超分辨率显微成像技术的优劣．探讨了目前超分辨率显微成像的发展极限和方向．     

Simultaneous suppression of disturbing fields and localization of magnetic markers by means of multipole expansion

BACKGROUND: Magnetically marked capsules serve for the analysis of peristalsis and throughput times within the intestinal tract. Moreover, they can be used for the targeted disposal of drugs. The capsules get localized in time by field measurements with a superconducting quantum interference device (SQUID) magnetometer array. Here it is important to ensure an online localization with high speed and high suppression of disturbing fields. In this article we use multipole expansions for the simultaneous localization and suppression of disturbing fields. METHODS: We expand the measurement data in terms of inner and outer multipoles. Thereby we obtain directly a separation of marker field and outer disturbing fields. From the inner dipoles and quadrupoles we compute the magnetization and position of the capsule. The outer multipoles get eliminated. RESULTS: The localization goodness has been analyzed depending on the order of the multipoles used and depending on the systems noise level. We found upper limits of the noise level for the usage of certain multipole moments. Given a signal to noise ratio of 40 and utilizing inner dipoles and quadrupoles and outer dipoles, the method enables an accuracy of 5 mm with a speed of 10 localizations per second. CONCLUSION: The multipole localization is an effective method and is capable of online-tracking magnetic markers.     

基于混合遗传算法的偶极子源定位的仿真计算

首先提出一种新的混合遗传算法。在基于实数编码的基础上,通过嵌入一个最速下降算子,结合遗传算法和最速下降法两者的优点,并引入模拟退火的思想,即可改善原算法的局部搜索能力,又能进一步提高优化效率。为了验证算法的可行性,通过对脑电偶极子源定位的仿真计算,证明所提出的新算法与其它优化算法相比,在达到最优解的效率上有了明显的提高。     

Chromatin investigation in the nucleus using a phasor approach to structured illumination microscopy

Chromatin in the nucleus is organized in functional sites at variable level of compaction. Structured illumination microscopy (SIM) can be used to generate three-dimensional super-resolution (SR) imaging of chromatin by changing in phase and in orientation a periodic line illumination pattern. The spatial frequency domain is the natural choice to process SIM raw data and to reconstruct an SR image. Using an alternative approach, we demonstrate that the additional spatial information encoded in the knowledge of the position of the illumination pattern can be efficiently decoded using a generalized version of separation of photon by lifetime tuning (SPLIT) that does not require lifetime measurements. In the resulting SPLIT-SIM, the SR image is obtained by isolating a fraction of the intensity corresponding to the center of the diffraction-limited point spread function. This extends the use of the SPLIT approach from stimulated emission depletion microscopy to SIM. The SPLIT-SIM algorithm is based only on phasor analysis and does not require deconvolution. We show that SPLIT-SIM can be used to generate SR images of chromatin organizational motifs with tunable resolution and can be a valuable tool for the imaging of functional sites in the nucleus.     

Single molecule localization deep within thick cells; a novel super‐resolution microscope

A novel 3D imaging system based on single‐molecule localization microscopy is presented to allow high‐accuracy drift‐free (<0.7 nm lateral; 2.5 nm axial) imaging many microns deep into a cell. When imaging deep within the cell, distortions of the point‐spread function result in an inaccurate and very compressed Z distribution. For the system to accurately represent the position of each blink, a series of depth‐dependent calibrations are required. The system and its allied methodology are applied to image the ryanodine receptor in the cardiac myocyte. Using the depth‐dependent calibration, the receptors deep within the cell are spread over a Z range that is many hundreds of nanometers greater than implied by conventional analysis. We implemented a time domain filter to detect overlapping blinks that were not filtered by a stringent goodness of fit criterion. This filter enabled us to resolve the structure of the individual (30 nm square) receptors giving a result similar to that obtained with electron tomography.

High‐accuracy deep imaging of the ryanodine receptor in the cardiac myocyte, using single‐molecule localization microscopy. Depth‐dependent calibrations are performed for accurate depth localization. The optical design featuring two independent and variable focal planes allows real‐time feedback for drift‐free deep imaging.     

Bidirectional Lipid Droplet Velocities Are Controlled by Differential Binding Strengths of HCV Core DII Protein

Host cell lipid droplets (LD) are essential in the hepatitis C virus (HCV) life cycle and are targeted by the viral capsid core protein. Core-coated LDs accumulate in the perinuclear region and facilitate viral particle assembly, but it is unclear how mobility of these LDs is directed by core. Herein we used two-photon fluorescence, differential interference contrast imaging, and coherent anti-Stokes Raman scattering microscopies, to reveal novel core-mediated changes to LD dynamics. Expression of core protein’s lipid binding domain II (DII-core) induced slower LD speeds, but did not affect directionality of movement on microtubules. Modulating the LD binding strength of DII-core further impacted LD mobility, revealing the temporal effects of LD-bound DII-core. These results for DII-core coated LDs support a model for core-mediated LD localization that involves core slowing down the rate of movement of LDs until localization at the perinuclear region is accomplished where LD movement ceases. The guided localization of LDs by HCV core protein not only is essential to the viral life cycle but also poses an interesting target for the development of antiviral strategies against HCV.     

The SpoIIQ landmark protein has different requirements for septal localization and immobilization

Bacillus subtilis sporulation depends on the forespore membrane protein SpoIIQ, which interacts with the mother cell protein SpoIIIAH at the septum to localize other sporulation proteins. It has remained unclear how SpoIIQ localizes. We demonstrate that localization of SpoIIQ is achieved by two pathways: SpoIIIAH and the SpoIID, SpoIIM, SpoIIP engulfment proteins. SpoIIQ shows diffuse localization only in a mutant lacking both pathways. Super‐resolution imaging shows that in the absence of SpoIIIAH, SpoIIQ forms fewer, slightly larger foci than in wild type. Surprisingly, photobleaching experiments demonstrate that, although SpoIIQ localizes without SpoIIIAH, it is no longer immobilized, and is therefore able to exchange subunits within a localized pool. SpoIIQ mobility is further increased by the additional absence of the engulfment proteins. However an enzymatically inactive SpoIID protein immobilizes SpoIIQ even in the absence of SpoIIIAH, indicating that complete septal thinning is not required for SpoIIQ localization. This suggests that SpoIIQ interacts with both SpoIIIAH and the engulfment proteins or their peptidoglycan cleavage products. They further demonstrate that apparently normal localization of a protein without a binding partner can mask dramatic alterations in protein mobility. We speculate that SpoIIQ assembles foci along the path defined by engulfment proteins degrading peptidoglycan.     

The nuclear import of protein kinase D3 requires its catalytic activity

The protein kinase D (PKD) family consists of three serine/threonine protein kinases termed PKD, PKD2, and PKD3, which are similar in overall structure and primary amino acid sequence. However, each isozyme displays a distinctive intracellular localization. Taking advantage of the structural homology and opposite nuclear localization of PKD2 and PKD3, we generated an extensive set of chimeric proteins between both isozymes to determine which PKD3 domain(s) mediates its nuclear localization. We found that the C-terminal region of PKD3, which contains its catalytic domain, is necessary but not sufficient for its nuclear localization. Real time imaging of a photoactivatable green fluorescent protein fused to PKD3 revealed that point mutations that render PKD3 catalytically inactive completely prevented its nuclear import despite its interaction with importin alpha and beta. We also found that activation loop phosphorylation of PKD3 did not require its nuclear localization, and it was not sufficient to promote the nuclear import of PKD3. These results identify a novel function for the kinase activity of PKD3 in promoting its nuclear entry and suggest that the catalytic activity of PKD3 may regulate its nuclear import through autophosphorylation and/or interaction with another protein(s).     

An enhanced method for accessory pathway localization in case of Wolff-Parkinson-White syndrome

This paper presents an analysis of the Arruda accessory pathway localization method for patients suffering from Wolff-Parkinson-White syndrome, with modifications to increase the overall accuracy. The Arruda method was tested on a total of 79 cases, and 91.1% localization performance was reached. After a deeper analysis of each decision point of the Arruda localization method, we considered that the lead aVF was not as relevant as other leads (I, II, III, V1) used. The branch of the decision tree, which evaluates the left ventricle positions, was entirely replaced using different decision criteria based on the same biological parameters. The modified algorithm significantly improves the localization accuracy in the left ventricle, reaching 94.9%. An accurate localization performance of non-invasive methods is relevant because it can enlighten the necessary invasive interventions, and it also reduces the discomfort caused to the patient.     

A novel 500,000 Da, linear, single chain extracellular protein synthesized by several childhood tumors

A high molecular weight extracellular protein has been purified from cell culture medium of Ewing's sarcoma cell lines, by high performance liquid chromatography and electroelution from SDS-PAGE electrophoresis. This protein has an apparent molecular mass of about 500,000 Da on SDS-PAGE. Immunoprecipitation studies with several extracellular matrix glycoproteins (laminin, fibronectin) specific antisera indicate it is a separate protein. Reduction of disulphide bonds with 2-ME or DTT fails to significantly alter its migration on SDS-PAGE gels, other than a slight apparent increase in molecular mass, indicating an apparent single polypeptide chain structure. The slightly greater mobility observed in unreduced gels suggests one or more regions of intrachain disulfide bonding. It is sensitive to pepsin and trypsin, but resistant to bacterial collagenase indicating that it does not contain collagenous domains. Metabolic labelling with 3H-proline, 3H-leucine, and 35S-methionine indicate that this protein is proline-poor, but leucine, and especially methionine, rich. Sodium 35S-sulfate incorporation is totally negative and treatment with glycosaminoglycan degrading enzymes has no effect on the mobility of the protein on gels, unlike typical proteoglycans. This protein appears by rotary shadowing electron microscopy as a long, thin, filamentous molecule at least 500 nm (0.5 um) in length. The tissue localization and function are unknown at this time, but are under active investigation.     

Point-vortex approach in two-dimensional turbulence

The properties of two-dimensional turbulence in a circular domain are investigated within the framework of the punctuated point-vortex model. Vortex dynamics is governed by Hamiltonian equations, and it is interrupted by instantaneous events resulting in vortex merging. Motion of about 100 point vortices is simulated using an accurate, symplectic integration method. Ensembles of like-sign vortices relax to a quasi-lattice state. Vortices with zero total vorticity tend to be randomized. Their motion still does not become fully chaotic. We observe emergence of long lived large dipoles (co-propagating pairs of vortices with opposite signs), which affect the evolution of the whole vortex ensemble. The presence of such dipoles accelerate the vortex decay rate. The decay exponent has been estimated as ξ ? 1.7, which is much larger than ξ ? 0.7, reported in previous studies of decaying turbulence. Since dipole dynamics depends on specific properties of the point vortex system, our findings suggest that a universal decay exponent in such systems does not exist.     

Theory of electrostatic effects in soft biological interfaces using atomic force microscopy.

We calculated the electrostatic force between a planar interface, such as a planar-supported lipid bilayer membrane, and the tip of a stylus on which another lipid bilayer or some other biomacromolecular system might be deposited. We considered styli with rounded tips as well as conical tips. To take into account the effect of dynamical hydrogen-bonded structures in the aqueous phase, we used a theory of nonlocal electrostatics. We used the Derjaguin approximation and identified the systems for which its use is valid. We pointed out where our approach differs from previous calculations and to what extent the latter are inadequate. We found that 1) the nonlocal interactions have significant effects over distances of 10-15 A from the polar zone and that, at the surface of this zone, the effect on the calculated force can be some orders of magnitude; 2) the lipid dipoles and charges are located a distance L from the hydrophobic layer in the aqueous medium and this can have consequences that may not be appreciated if it is ignored; 3) dipoles, located in the aqueous region, can give rise to forces even though the polar layer is unchanged, and if this is ignored the interpretation of force data can be erroneous if an attempt is made to rationalize an observed force with a knowledge of an uncharged surface; 4) the shape of the stylus tip can be very important, and a failure to take this into account can result in incorrect conclusions, a point made by other workers; and 5) when L is nonzero, the presence of charges and dipoles can yield a force that can be nonmonotonic as a function of ionic concentration.     

Biochemical characterization of pKi67 with the identification of a mitotic-specific form associated with hyperphosphorylation and altered DNA binding.

Although widely used as an operational marker of proliferation, the cell cycle-regulated Ki67 protein is of unknown function. pKi67 is found predominantly in the nucleolus in cycling interphase cells and moves to become perichromosomal during mitosis. We have performed a detailed immunochemical analysis of pKi67 in HeLa cells and report the existence of a novel hyperphosphorylated form in mitosis. Two isoforms can be identified on immunoblots as a consequence of the previously described alternative splicing. In extracts from mitotic cells both these isoforms have considerably reduced mobility. Treatment with phosphatase converts the mitotic form to the interphase form. Immunoprecipitated pKi67 can be phosphorylated in vitro both by cdc2/cyclin B and by protein kinase C, and treatment by PKC leads to the full mobility shift. Treatment of nocodazole-arrested mitotic HeLa cells with staurosporine causes a dephosphorylation of pKi67 to the interphase state and a concomitant change in the localization of pKi67 with movement away from the perichromosomal layer to cytoplasmic dots that colocalize with nucleolin. These data indicate that pKi67 localization is regulated by the action of cell cycle-specific kinase(s) and phosphatase(s). The data presented here provide a starting point for the analysis of pKi67 function and regulation.     

A count-dependent filter for smoothing flow cytometric histograms

An adaptive count-dependent algorithm for smoothing statistically limited histograms has been developed. It considers both the spatial frequency limitations of the measurement system (described by the measurement system point spread function) and the reliability of the measured data (indicated by the effective number of counts influencing each channel of the histogram. Windows for smoothing flow cytometric histograms are derived from an assumed Gaussian-shaped point spread function (PSF) with a constant coefficient of variation. The windows are developed by scaling the variances of the Gaussian functions inversely with the statistical reliability of the data contained in each channel of the measured histogram. The reliability of this data is determined by taking the square root of the number of counts influencing the value tabulated for each channel. Using the algorithm, a smoothed version of the measured histogram may be developed from a linear sum of the products of the individual scaled Gaussian functions and the original measured histogram. Data are presented demonstrating the advantages of count-dependent smoothing over non-count-dependent smoothing using synthesized DNA histograms as a function of sample size.     

MPB2C, a microtubule-associated plant factor, is required for microtubular accumulation of tobacco mosaic virus movement protein in plants

Movement protein binding 2C (MPB2C) is a plant endogenous microtubule-associated protein previously identified as an interaction partner of tobacco (Nicotiana tabacum) mosaic virus movement protein (TMV-MP). In this work, the role of MPB2C in cell-to-cell transport of TMV-MP, viral spread of TMV, and subcellular localization of TMV-MP was examined. To this end, plants with reduced MPB2C levels were generated by a gene-silencing strategy. Local and systemic spread of TMV and cell-to-cell movement of TMV-MP were unimpaired in MPB2C-silenced plants as compared to nonsilenced plants, indicating that MPB2C is not required for intercellular transport of TMV-MP itself or spread of TMV. However, a clear change in subcellular distribution of TMV-MP characterized by a nearly complete loss of microtubular localization was observed in MPB2C-silenced plants. This result shows that the MPB2C is a central player in determining the complex subcellular localization of TMV-MP, in particular its microtubular accumulation, a phenomenon that has been frequently observed and whose role is still under discussion. Clearly, MPB2C mediated accumulation of TMV-MP at microtubules is not required for intercellular spread but may be a means to withdraw the TMV-MP from the cell-to-cell transport pathway.     

Assessing the capabilities of a 4kx4k CCD camera for electron cryo-microscopy at 300kV

CCD cameras have numerous advantages over photographic film for detecting electrons; however the point spread function of these cameras has not been sufficient for single particle data collection to subnanometer resolution with 300kV microscopes. We have adopted spectral signal to noise ratio (SNR) as a parameter for assessing detector quality for single particle imaging. The robustness of this parameter is confirmed under a variety of experimental conditions. Using this parameter, we demonstrate that the SNR of images of either amorphous carbon film or ice embedded virus particles collected on a new commercially available 4kx4k CCD camera are slightly better than photographic film at low spatial frequency (<1/5 Nyquist frequency), and as good as photographic film out to half of the Nyquist frequency. In addition it is slightly easier to visualize ice embedded particles on this CCD camera than on photographic film. Based on this analysis it is realistic to collect images containing subnanometer resolution data (6-9A) using this CCD camera at an effective magnification of approximately 112000x on a 300kV electron microscope.