Quantification of heart fatty acid binding protein as a biomarker for drug-induced cardiac and musculoskeletal necroses

Heart fatty acid binding protein (Fabp3) is a cytosolic protein expressed primarily in heart, and to a lesser extent in skeletal muscle, brain, and kidney. During myocardial injury, the Fabp3 level in serum is elevated rapidly, making it an ideal early marker for myocardial infarction. In this study, an MS‐based selected reaction monitoring method (LC‐SRM) was developed for quantifying Fabp3 in rat serum. Fabp3 was enriched first through an immobilized antibody, and the protein was digested on beads directly. A marker peptide of Fabp3 was quantified using LC‐SRM with a stable isotope‐labeled peptide standard. For six quality control samples with Fabp3 ranging from 0.256 to 25 ng, the average recovery following the procedure was about 73%, and the precision (%CV) between replicates was less than 7%. The Fabp3 concentrations in rat serum peaked 1 h after isoproterenol treatment, and returned to baseline levels 24 h after the dose. Elevated Fabp3 levels were also detected in rats administered with a PPAR α/δ agonist, which has shown to cause skeletal muscle necrosis. Fabp3 can be used as a biomarker for both cardiac and skeletal necroses. The cross‐validation of the LC‐SRM method with an existing ELISA method is described.     

The discovery of biomarkers for type 2 diabetic nephropathy by serum proteome analysis

Diabetic nephropathy (DN) is a serious kidney complication of diabetes, and constitutes the leading cause of end-stage renal disease. The earliest clinical evidence of DN is microalbuminuria, a term which refers to the appearance of small but abnormal amounts of albumin in the urine. However, screening methods for DN, such as biomarker assays, are yet to be developed for type 2 DN. In the present study, in an attempt to identify the biomarkers for initial diagnoses of type 2 DN, the protein profiles of human sera collected from 30 microalbuminuric type 2 diabetic patients were compared with those collected from 30 normoalbuminuric type 2 diabetic patients, via 2-DE. As a result, a total of 18 spots were determined to have different protein levels in the microalbuminuric patients. Twelve spots had lower protein levels of approximately 50%, and the other six had higher levels of approximately 100-300% as compared to the spots of normoalbuminuric patients. These spots were identified with ESI-Q-TOF (ESI-quadrupole-TOF) MS. Among the identified proteins, vitamin D-binding protein (DBP) and pigment epithelium-derived factor (PEDF) were verified by Western blotting. The results of this study indicate that the DBP may be employed as diagnostic and monitoring biomarkers of type 2 DN, contingent on further study into the matter.     

Texture analysis of poly-adenylated mRNA staining following global brain ischemia and reperfusion

Texture analysis provides a means to quantify complex changes in microscope images. We previously showed that cytoplasmic poly-adenylated mRNAs form mRNA granules in post-ischemic neurons and that these granules correlated with protein synthesis inhibition and hence cell death. Here we utilized the texture analysis software MaZda to quantify mRNA granules in photomicrographs of the pyramidal cell layer of rat hippocampal region CA3 around 1 h of reperfusion after 10 min of normothermic global cerebral ischemia. At 1 h reperfusion, we observed variations in the texture of mRNA granules amongst samples that were readily quantified by texture analysis. Individual sample variation was consistent with the interpretation that animal-to-animal variations in mRNA granules reflected the time-course of mRNA granule formation. We also used texture analysis to quantify the effect of cycloheximide, given either before or after brain ischemia, on mRNA granules. If administered before ischemia, cycloheximide inhibited mRNA granule formation, but if administered after ischemia did not prevent mRNA granulation, indicating mRNA granule formation is dependent on dissociation of polysomes. We conclude that texture analysis is an effective means for quantifying the complex morphological changes induced in neurons by brain ischemia and reperfusion.     

串联质谱谱库搜索鉴定技术综述

介绍蛋白质质谱鉴定领域的串联质谱谱库搜索技术,分析谱库搜索技术的基本原理,从多个角度阐述当前主流的谱库搜索方法,并对其优缺点进行比较,针对目前蛋白质质谱鉴定技术所存在的优缺点,设计其改进思路,论述目前谱库搜索技术所面临的问题以及未来的研究趋势。     

酵母蛋白网络的功能模块与关键蛋白研究

蛋白交互网络在各种细胞功能和生命过程中发挥着至关重要的作用。对它的结构特征进行分析吸引了众多科研人员的关注,功能模块与关键蛋白的识别是其中的重要研究主题。本文主要使用模拟退火算法分析了酵母蛋白交互网络的功能模块,同时结合使用多种中心化指标识别了其中的关键蛋白,并讨论了这些功能模块和关键蛋白的生物学意义。     

基于Z曲线的SARS冠状病毒特征的研究

刺突（Spike）蛋白是SARS（Severe Acute Respiratory Syndmme）冠状病毒表面最重要的膜蛋白，它通过与被感染细胞的受体结合来作为感染的媒介。受此启发，该文利用Z曲线方法，对S蛋白及SARS受体序列进行探究，捕捉到一种SARS病毒的可视化特征。大量序列比对的结果证明该特征是SARS病毒所特有的。将这种特征图谱应用到SARS病毒的检测中，可以提供一种非标准的、简单、直观的检验方法，能够诊断一些利用标准方法难以判断的SARS病例。由此可见，Z曲线作为一种基因序列的几何学研究途径是一种有效的研究方法。     

利用奇异值分解最小二乘法(SVDLS)解析蛋白质的现场光谱电化学圆二色(CD)谱

圆二色谱仪是研究蛋白质二级结构的有力工具，能在远紫外区测出蛋白质的二级结构的各种构象。通常的蛋白质二级结构有α-螺旋、β-折叠、反β-折叠、β-转角及无规则卷曲五种构象，实际观测到的CD谱是这几种二级结构构象CD谱的线性加和。本文利用了奇异值分解最小二乘算法(SVDLS)，并编译相关程序解析现场外加电压电解条件下的蛋白质溶液的CD谱，得到几种二级结构构象的组分分布。所得结果与文献报道上的其他方法如SELCON3等相比较，证明是一种快速和有效的方法。     

Orphan gene finding—an exon assembly approach

This paper introduces an algorithm for finding eukaryotic genes. It particularly addresses the problem of orphan genes, that is of genes that cannot, based on homology alone, be connected to any known gene family and to which it is therefore not possible to apply traditional gene finding methods. To the best of our knowledge, this is also the first algorithm that attempts to compare in an exact way two DNA sequences that contain both coding (i.e. exonic) and non-coding (i.e. intronic and, possibly, intergenic) parts. The comparison is performed following an algorithmical model of a gene that is as close as possible to the biological one (we consider in this paper the “one ORF, one gene” problem only). A gene is seen as a set of exons that are pieces of an assembly and are not independent. The algorithm is efficient enough: although the constants are higher than for usual sequence comparison, its time complexity is proportional to the product of the sequences lengths while its space complexity scales linearly with the length of the smallest sequence.     

用同步辐射X荧光分析血浆蛋白质的微量元素

用同步辐射X荧光(SRXRF)分析技术与凝胶色谱生化分离相结合，分析了用抗肿瘤药物顺铂处理过的和未处理过的小鼠血浆的大分子蛋白质。对以轻元素为基体的小量样品，用X荧光谱中的康普顿散射强度作为质量的因子，获得了在大于22ku分子量的蛋白质中Pt、S、Ca、Fe、Ni、Cu、Zn、Se、Br和Sr等元素含量在不同样品问的相对变化。由此推测，经顺铂处理后，Pt元素可与血浆中的大分子蛋白结合，含CM和S的大分子蛋白含量明显升高，而含Zn的减少。     

GigaMatrix: an ultra high-throughput tool for accessing biodiversity

Recombinant approaches for tapping into the biodiversity present in nature for the discovery of novel enzymes and biosynthetic pathways can result in large gene libraries. Likewise, laboratory evolution techniques can result in large but potentially valuable libraries. Thorough screening of these libraries requires ultra high-throughput methods. The GigaMatrix^™ screening platform addresses this opportunity using reusable high-density plates with 100,000 to 1,000,000 through-hole wells in a microplate footprint. In addition to throughputs of over 10⁷ wells per day, the platform offers a significant reduction in reagent use and waste, has fully integrated automated “cherry picking,” and uses no complicated dispensing equipment. Wells containing putative hits from targeted fluorescent liquid phase assays are revealed by a fluorescent imaging system. Vision-guided robotics are utilized to recover hits by accessing individual 200 μm and smaller wells with a disposable sterile needle. The GigaMatrix platform has proven to be an effective and efficient tool for screening gene libraries for both discovery and evolution applications.