生物组织电导率图像的热声重建

本文以微波热声效应为基础,报道了一种重建生物组织电导率相对分布图像的方法。和传统的微波热声像相比,重建得到的组织电导率图像消除了由于微波场能量密度分布不均匀带来的影响,能够准确的反映组织的介电特性差异,实现对肿瘤的早期发现。本文首先从理论上详细推导了获得生物组织电导率分布图像的原理,然后在实验中通过结合已有的脉冲微波成像系统,重建得到了一块肌肉组织的电导率分布图像。实验结果表明利用热声成像技术,组织的电导率分布图像能够被清晰的重建,本研究为推进热声成像技术的实用性打下了理论和实验基础。     

基于VTK和MFC的医学图像三维重建研究与实现

VTK是医学可视化领域的主流工具,MFC是Windows平台下的应用程序框架。尝试将两者进行结合编程,以实现二维医学图像的三维重建。实现医学图像三维重建的主要方法是面绘制和体绘制。将利用多组医学图像数据进行三维重建研究,其中面绘制用移动立方体法,体绘制用光线投射法、最大密度投影法和合成体绘制法实现。最后比较两种绘制技术的结果并讨论了它们的特点。结果表明,VTK作为一种图像处理和三维可视化工具其功能是十分强大的。     

利用散射光声微分成像技术实现弱吸收物质显微成像

光声显微成像技术依赖于样品的内源性光吸收,对强散射弱吸收样品成像效果差,甚至无法进行成像。为了实现强散射弱吸收高透明生物样品的光声显微成像,以及获得图像的边缘增强效果,使光声显微成像技术在实际的生物医学研究中更有应用价值,本文首次将散射光声技术引入到光声微分显微技术中,研制了新型的散射光声微分成像技术。该技术不仅可以获得强散射弱吸收高透明生物样品的散射光声显微图像,还可以获得对应的边缘清晰的散射光声微分图像,对在生物医学研究领域有重要的应用意义。     

Stokes参量共焦显微术用于弱各向异性物质的成像研究

提出将基于Stokes参量的偏振共焦显微成像技术应用于弱各向异性物质的成像研究。通过将分振幅Stokes参量测量法与共焦扫描成像技术相结合的方法,得到了基于Stokes参量测量的偏振共焦显微成像系统。利用该系统对具有弱各向异性的生物组织样品进行逐点测量,通过四个通道同时测量获得全部的Stokes参量。再以计算得到的偏振参量作为成像物理量进行图像重建,获得对应Stokes参量、偏振度、相位差、方位角和椭率角的空间分布图像,从而对生物组织实现细胞水平的偏振显微成像研究。实验结果表明:基于Stokes参量的偏振共焦显微成像技术能够获得弱各向异性的生物组织样品的显微图像,并通过比较样品的Stokes参量及相关偏振参量的分布图像,提取样品全部的偏振信息,从而为生物组织的特性研究提供更丰富的信息。     

编者按

生物光子学是近几年来迅速崛起的一门生物物理学新技术, 它通过生物光子与物质的相互作用, 以图像的方式提供生物组织、细胞、分子的结构和功能信息。在医学无损伤诊断、细胞内分子过程的探测和脑功能成像方面,展示了良好的应用前景。本期刊登的王进军、王毅和屈军乐等的三篇论文反映了生物光子学研究在我国的兴起。王进军等应用荧光共振能量转移（简称FRET）研究了活细胞内蛋白激酶RKA活性的时空变化; 屈军乐等介绍了一种新型光学相干层析成像技术,并用它得到了视网膜上单个锥状细胞的图像; 王毅等则报道了一种新的研究生物组织结构的光声成像方法。我们希望,这三篇论文的发表能激起读者对生物光子成像技术的兴趣,并使这一技术在生命科学研究中受到更多的 关注。     

基于H分量旋转的色盲矫正方法

为提高色盲患者的色彩分辨力，提出一种基于H分量旋转的色盲矫正方法。在颜色的HSI空间，利用H分量的连续性和周期性特点，在保持S、I分量不变的情况下，通过旋转H分量得到矫正图像，该图像以降低低频颜色的分辨率来换取高频颜色的分辨率提高。实验表明：在色盲类型给定且图像颜色是给定色盲易混淆的情况下，对H分量旋转120度能得到色彩分辨效果很好的矫正图像。     

液晶空间光调制器在生物光学显微中的应用

利用液晶空间光调制器(LCSLM)对光学显微中的成像光进行实时的相位/振幅调制,不仅可以实现各种传统的生物样品相位显微,而且能够以更复杂的相位调制方式,如螺旋相位滤波,得到新的显微图像。该方式已经和荧光显微、光镊技术结合,丰富了生物显微技术。     

核酸物质蛋白单分子层电镜技术

在研究核酸等遗传活性物质的电子显微镜技术过程中,蛋白单分子层技术是最基本而且最重要的方法。它不只用来研究核酸物质的物理特性、核酸的复制,而且能在体外观察转录的位置、方向和过程。用这个方法还能使生物颗粒(如噬菌体、病毒)直接释放出核酸物质,进而鉴别生物材料中所含的核酸是双股还是单股,以及了解生物材料所含核酸的量。特别是异源双股体方法应用以来,可以通过核酸异源双股体的观察,来精确地计算和绘制出两个噬菌     

冷冻电子断层成像技术及其在生物研究领域的应用

冷冻电子断层成像可以在纳米级尺度上研究那些结构不具有均一性的分子、病毒、细胞器以及它们之间组成的复合体的三维结构。在过去的十年中,电子显微镜硬件、冷冻制样设备和技术,以及自动化断层数据收集方法的进步使得本研究领域得到快速发展。本文对冷冻电子断层成像的方法,包括基本原理、样品制备、断层数据采集和图像处理、三维重构以及重建信息的理解和展示、近年来在生物样品领域的一些典型应用以及前景作一简单介绍。     

活体细胞三维图像科学可视化方法的研究

科学可视化是指运用计算机图形学和图像处理技术,将科学计算过程中或者是计算结果的数据转换为图形或图像,在屏幕上显示出来并进行交互式处理的理论技术或方法。介绍了用反卷积荧光显微成像技术获得活体大鼠胰腺B细胞三维图像及对其进行科学可视化的主要过程和两种常用可视化算法,并运用这两种方法对所得到的三维图像进行处理以分析和研究细胞内分泌囊泡的空间分布。结果显示,当仅观察细胞三维图像的二维切片时,三维图像中的某些重要信息会被忽略,而使用科学可视化方法则可以从三维角度直观观察活体细胞内分泌囊泡的空间分布,并且可以观察到分泌囊泡的释放趋势和整体分布,从而为细胞生物学研究提供重要的信息。     

Discrimination between BI and BII conformational substates of B-DNA based on sugar-base interproton distances

Molecular dynamics (MD) simulations of four water-solvated DNA duplexes were used to generate a database of approximately 27000 dinucleotide conformations. Analyzing this database, we investigated the relationship between so-called BI-BII transitions and short-range interproton distances. Four H-H distances were found particularly sensitive to BI-BII transitions: internucleotide H1'(n)-H68(n+1), H2'(n)-H68(n+1), and H2"(n)-H68(n+1), and intranucleotide H2"(n)-H68(n). Determination of these distances using classical NOESY spectroscopy can thus provide valuable indications on the existence of BII substates, complementing the existing method based on (31)P chemical shifts and (31)P-(1)H spin-spin coupling constants.     

Visualizing the principal component of 1H,15N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C

Laboratories often repeatedly determine the structure of a given protein under a variety of conditions, mutations, modifications, or in a number of states. This approach can be cumbersome and tedious. Given then a database of structures, identifiers, and corresponding (1)H,(15)N-HSQC NMR spectra for homologous proteins, we investigated whether structural information could be ascertained for a new homolog solely from its (1)H,(15)N-HSQC NMR spectrum. We addressed this question with two different approaches. First, we used a semi-automated approach with the program, ORBplus. ORBplus looks for patterns in the chemical shifts and correlates these commonalities to the explicit property of interest. ORBplus ranks resonances based on consistency of the magnitude and direction of the chemical shifts within the database, and the chemical shift correlation of the unknown protein with the database. ORBplus visualizes the results by a histogram and a vector diagram, and provides residue specific predictions on structural similarities with the database. The second method we used was partial least squares (PLS), which is a multivariate statistical technique used to correlate response and predictor variables. We investigated the ability of these methods to predict the tertiary structure of the contractile regulatory protein troponin C. Troponin C undergoes a closed-to-open conformational change, which is coupled to its function in muscle. We found that both ORBplus and PLS were able to identify patterns in the (1)H,(15)N-HSQC NMR data from different states of troponin C that correlated to its conformation.     

抗口蹄疫病毒相关基因的筛选及分析

口蹄疫是一种烈性传染病，其广泛流行给社会造成了巨大经济损失。为了研究口蹄疫灭活疫苗免疫的分子机制，同时也为抗口蹄疫病毒药物的研制奠定基础，本研究应用mRNA差异显示技术，以PK-15细胞为材料，系统比较了口蹄疫疫苗刺激组（A组）和正常的PK-15细胞（B组）的基因表达情况，回收差异片段，经二次扩增并纯化后，得到30条ESTs。将30条ESTs采用以地高辛标记的反向Northern点杂交鉴定，将阳性条带克隆测序，筛选出8条ESTs，编号E1~E8，应用BLASTn工具将8条ESTs对核酸数据库nr和dbEST中所有序列进行了同源性分析，其中E1，E2分别与猪的热休克蛋白基因、猪的MHCⅠ类基因同源，序列相似性都达到100%。E3，E4，E5，E7分别与已有核酸数据库中的基因克隆或EST具有较高同源性，为已知的EST，但功能未知；E6，E8在数据库中没有发现与其相似性较高的序列，为新的EST。应用数据库资源将E5、E7进行电子延伸后，将延伸序列进行开放阅读框分析，又经TBLASTx分析发现E7蛋白质序列与猪的精氨酸酶Ⅰ类蛋白序列有很高同源性。将E1、E2、E4、E5序列进行了基因表达谱分析，对E6、E8用BLASTx工具对非冗余蛋白质数据库nr进行了相似性搜索，在其他物种中找到了相似的基因序列。本研究筛选出的热休克蛋白基因、MHCⅠ类基因、精氨酸酶Ⅰ类基因和其他未知功能基因可以作为抗口蹄疫病毒研究中的侯选基因，其具体的功能有待今后进一步研究。     

Discrimination Between BI and BII Conformational Substates of B-DNA Based on Sugar-base Interproton Distances

Abstract

Molecular dynamics (MD) simulations of four water-solvated DNA duplexes were used to generate a database of ～27000 dinucleotide conformations. Analyzing this database, we investigated the relationship between so-called BI-BII transitions and short-range interproton distances. Four H-H distances were found particularly sensitive to BI-BII transitions: inter- nucleotide H1′(n)-H68(n+1), H2′(n)-H68(n+1), and H2″(n)-H68(n+1), and intranucleotide H2″(n)-H68(n). Determination of these distances using classical NOESY spectroscopy can thus provide valuable indications on the existence of BII substates, complementing the existing method based on ³¹P chemical shifts and ³¹P-¹H spin-spin coupling constants.     

Histone Sequence Database: a compilation of highly-conserved nucleoprotein sequences.

By searching the current protein sequence databases using sequences from human and chicken histones H1/H5, H2A, H2B, H3 and H4, a database of aligned histone protein sequences with statistically significant sequence similarity to the search sequence was constructed. In addition, a nucleotide sequence database of the corresponding coding regions for these proteins has been assembled. The region of each of the core histones containing the histone fold motif is identified in the protein alignments. The database contains >1300 protein and nucleotide sequences. All sequences and alignments in this database are available through the World Wide Web at http://www.ncbi.nlm.nih.gov/Baxevani/HISTO NES.     

NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database

Compound identification and support for computer-assisted structure elucidation via a free community-built web database for organic structures and their NMR data is described. The new database NMRShiftDB is available on . As the first NMR database, NMRShiftDB allows not only open access to the database but also open and peer reviewed submission of datasets, enabling the natural products community to build its first free repository of assigned 1H and 13C NMR spectra. In addition to the open access, the underlying database software is built solely from free software and is available under an open source license. This allows collaborating laboratories to fully replicate the database and to create a highly available network of NMRShiftDB mirrors. The database contains about 10,000 structures and assigned spectra, with new datasets constantly added. Its functionality includes (sub-) spectra and (sub-) structure searches as well as shift prediction of 13C spectra based on the current database material.     

Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database

Precise annotation of genes or open reading frames is still a difficult task that results in divergence even for data generated from the same genomic sequence. This has an impact in further proteomic studies, and also compromises the characterization of clinical isolates with many specific genetic variations that may not be represented in the selected database. We recently developed software called multistrain mass spectrometry prokaryotic database builder (MSMSpdbb) that can merge protein databases from several sources and be applied on any prokaryotic organism, in a proteomic-friendly approach. We generated a database for the Mycobacterium tuberculosis complex (using three strains of Mycobacterium bovis and five of M. tuberculosis), and analyzed data collected from two laboratory strains and two clinical isolates of M. tuberculosis. We identified 2561 proteins, of which 24 were present in M. tuberculosis H37Rv samples, but not annotated in the M. tuberculosis H37Rv genome. We were also able to identify 280 nonsynonymous single amino acid polymorphisms and confirm 367 translational start sites. As a proof of concept we applied the database to whole-genome DNA sequencing data of one of the clinical isolates, which allowed the validation of 116 predicted single amino acid polymorphisms and the annotation of 131 N-terminal start sites. Moreover we identified regions not present in the original M. tuberculosis H37Rv sequence, indicating strain divergence or errors in the reference sequence. In conclusion, we demonstrated the potential of using a merged database to better characterize laboratory or clinical bacterial strains.     

Overpassing an aberrant V(kappa) gene to sequence an anti-idiotypic abzyme with (beta)-lactamase-like activity that could have a linkage with autoimmune diseases.

A monoclonal antibody 9G4H9 that exhibits a beta-lactamase-like activity was previously obtained in accordance with the idiotypic network theory. This abzyme presents the most catalytic efficiency in amidase activity described in literature (kcat = 0.9 min-1). Some reports have demonstrated that functionality as complex as catalysis may be mimicked in this way. Comparison of the catalytic properties of both enzyme and abzyme previously allowed us to obtain better knowledge about 9G4H9 abzymatic machinery. In attempt to characterize this abzyme, the variable regions of kappa and heavy chain were cloned. We present a 'universal' method to clone the correct Vkappa gene to bypass aberrant Vkappa (abVkappa) produced by MOPC-21-derived hybridomas. Sequences obtained are compared in the GenBank database. The VH and Vkappa genes present some important sequence homology with autoantibodies suggesting a direct relationship between catalytic anti-idiotypic antibody and autoimmunity.     

Safety of Pandemic (H1N1) 2009 Monovalent Vaccines in Taiwan: A Self-Controlled Case Series Study

In Taiwan, new H1N1 monovalent vaccines without adjuvant and with MF59® adjuvant were used in the nationwide vaccination campaign beginning on November 1, 2009. From November 2009 through February 2010, the authors identified recipients of H1N1 vaccines who were diagnosed with adverse events of special interest (AESIs) in a large-linked safety database, and used the self-controlled case series (SCCS) method to examine the risk of each AESI in the 0–42 days after H1N1 vaccination. Of the 3.5 million doses of H1N1 vaccines administered and captured in the linked database, the SCCS analysis of Guillain-Barré syndrome (GBS) found an incidence rate ratio of 3.81 (95% confidence interval 0.43–33.85) within 0–42 days after nonadjuvanted H1N1 vaccination and no cases after MF59®-adjuvanted H1N1 vaccination. The risks of other AESIs were, in general, not increased in any of the predefined postvaccination risk periods and age groups. The databases and infrastructure created for H1N1 vaccine safety evaluation may serve as a model for safety, effectiveness and coverage studies of licensed vaccines in Taiwan.