比较蛋白质组研究方法学进展

比较蛋白质组学针对不同空间、不同时间上动态变化着的蛋白质组的整体进行比较,分析不同蛋白质组之间在表达数量、表达水平和修饰状态上的差异,可以发现与病变相关的特异蛋白质,对疾病的诊断和治疗具有重要意义.本文对比较蛋白质组研究在方法学方面的最新进展加以系统综述,引用文献33篇.     

基于生物质谱的蛋白质组学绝对定量方法研究进展

蛋白质组学定量方法包括相对定量和绝对定量两部分。相对定量蛋白质组学（也称比较蛋白质组学）是指对不同生理病理状态下细胞、组织或体液蛋白质表达量的相对变化进行比较分析;绝对定量蛋白质组学是测定细胞、组织或体液蛋白质组中每种蛋白质的绝对量或浓度。目前蛋白质组学的绝对定量方法主要有基于内标法的蛋白质组学绝对定量方法和基于质谱数据统计分析的非标记方法。蛋白质组学定量的信息可以帮助了解蛋白质在相互作用网络中所起的作用;通过对临床生物标记物绝对量的分析,可以帮助直观地判断疾病的发生和发展过程,这对于临床诊断和疾病治疗都具有现实的指导意义。     

蛋白质组

蛋白质组研究是近来兴起的生命科学的前沿领域,是生命科学进入后基因组时代的标志之一。蛋白质组是指基因组表达的全部蛋白质,蛋白质组研究在细胞或组织水平上对蛋白质进行大规模的分离和分析。目前蛋白质组研究采用的主要技术是双向凝胶电泳和质谱方法。本文就蛋白质组研究和蛋白质组学的发展过程,研究意义,所涉及的研究范围及主要的研究策略,及最新的进展作一综述。     

基于质谱的蛋白质组学方法新进展

蛋白质组学是后基因组时代的科研热点,其研究方向主要涵盖蛋白质表达谱、蛋白质翻译后修饰谱、蛋白质相互作用谱和单细胞蛋白质组等定性分析以及相对和绝对定量分析,现已广泛应用于生物、医药及病理研究中。由于质谱具有灵敏、准确、高通量等特点,是蛋白质组学研究必不可少的工具。本文综述了近年来基于质谱技术的蛋白质组鉴定及定量方法,并展望未来蛋白质组学研究的发展方向。     

RPLC—SDS—PAGE整体蛋白质分离与纳升毛细管液相色谱-串联质谱联用技术的研究及应用

采用RPLC-SDS-PAGE与纳升毛细管液相色谱-串联质谱联用技术对国际人类蛋白质组织(HUPO)提供的法国人肝脏蛋白质组表达谱的构建及其理化性质的统计分析,鉴定了2552条肽段,归结于402种蛋白质和240个蛋白质簇.蛋白质的pI分布范围为4.29～11.57,分子量范围为8,593～3,816,218Da,其中大于100kDa的蛋白质占到所鉴定蛋白质的10%,二者皆高于两维凝胶电泳的等电点和分子量范围(一般等电点3～10;分子量10～100kDa).另外,蛋白质组中不同蛋白质的疏水性分布显示大部分蛋白质为可溶性蛋白质,其中疏水性蛋白质占15%(GRAVY＞0的蛋白质).实验结果表明该技术路线兼顾了反相色谱分离度高和SAS-PAGE兼容性好的优点,可用于复杂组织或细胞中蛋白质组表达谱的构建或比较蛋白质组的研究,为蛋白质组学的方法学研究奠定了基础.     

不同产地太子参的iTRAQ定量蛋白质组学研究

采用同位素标记相对和绝对定量（iTRAQ）技术对不同产地的太子参进行定量蛋白质组学研究,探讨蛋白质组表达水平的差异。所提取的太子参蛋白质样品经FASP酶解、iTRAQ试剂标记、高pH-RPLC分离、RPLC-MS分离分析,获取的串联质谱数据通过Protein Pilot 5.0软件搜库进行蛋白质鉴定,通过蛋白质相对定量的比较寻找差异表达蛋白;再对差异蛋白质进行GO（gene ontology）、KEGG代谢通路和STRING网络通路分析。实验共鉴定出3 775个蛋白质,其中3676个蛋白质具有定量信息,与传统产区相比,种植基地太子参上调差异蛋白质54个,下调差异蛋白质86个;通过生物信息学分析得到44个目标差异蛋白,主要分为9类：热休克蛋白、氧化还原酶、转移酶、水解酶、裂解酶、异构酶、Rubisco大亚基结合蛋白、伴侣蛋白质、胞腔结合蛋白。结果显示,传统产区太子参中氧化还原酶和转移酶的分解代谢、碳水化合物代谢以及抗应激能力比种植基地太子参强,但热休克蛋白、异构酶、Rubisco大亚基结合蛋白、伴侣蛋白质和胞腔结合蛋白中的蛋白质折叠和抗应激能力比种植基地太子参弱,水解酶和裂解酶的分解代谢能力与种植基地太子参相差不大;ADG1和TKTA可能是调节不同产地太子参蔗糖变化的2个关键蛋白;MFP2是导致不同产地太子参脂肪酸差异的关键蛋白。本研究可为解析不同产地太子参次生代谢物差异的成因及其药材品质形成的蛋白质机制提供参考。     

在微生物中生产重组蛋白质的方法

随着科学技术的提高和人们物质世界和精神世界的飞速提高,人们迎来了基因组的时代,这不仅代表了人们的创新思想和创新思维的逐步提高,也代表了在基因组时代下重组蛋白质应用的重要性。在重组蛋白质的帮助下,科学家们可以更好地研究微生物的生理特征、生命活动及其它的细胞功能等其他指标。而我们应该重点研究在微生物的角度生产重组蛋白质的方法,分析从上而下的蛋白质组学和从下而生的蛋白质组学,掌握蛋白质组定量分析技术和蛋白质芯片技术等。     

利用蛋白质组学技术探究叶绿素含量对植物生长的影响

本研究基于蛋白质组学技术，结合主成分分析和偏最小二乘法判别分析等方法探究叶绿素含量对植物生长的影响。依次收集冷处理前、冷处理后和复性3个阶段的水稻幼苗叶片，测定叶绿素含量，同时进行蛋白质组学分析。将蛋白质组与叶绿素含量的变化结合进行差异蛋白质组学分析，通过通路分析富集出淀粉蔗糖代谢、糖酵解途径等7个代谢途径，筛选出与叶绿素含量强相关的近30种酶。通过探寻与叶绿素含量变化相关的代谢途径，从蛋白质组学角度证明叶绿素含量可以作为植物生长健康状况的重要指标。     

植物逆境生物学中的蛋白质组学技术运用

逆境胁迫会对植物生长发育造成制约,并且对作物产量、质量等造成影响,植物应答胁迫分子机理的分析为人们尤为重视的内容。植物蛋白质组学的研究能够系统性的揭露在胁迫条件不同时,植物蛋白质表达的情况,以此对基于环境胁迫下植物基因表达调控机制进行掌握。以此,简单分析了蛋白质组学技术在植物逆境生物学中的使用。     

Intracellular and extracellular roles of S100 proteins

S100, a multigenic family of non-ubiquitous Ca(2+)-modulated proteins of the EF-hand type expressed in vertebrates exclusively, has been implicated in intracellular and extracellular regulatory activities. Members of this protein family have been shown to interact with several effector proteins within cells thereby regulating enzyme activities, the dynamics of cytoskeleton constituents, cell growth and differentiation, and Ca(2+) homeostasis. Structural information indicates that most of S100 proteins exist in the form of antiparallelly packed homodimers (in some cases heterodimers), capable of functionally crossbridging two homologous or heterologous target proteins in a Ca(2+)-dependent (and, in some instances, Ca(2+)-independent) manner. In addition, extracellular roles have been described for several S100 members, although secretion (via an unknown mechanism) has been documented for a few of them. Extracellular S100 proteins have been shown to exert regulatory effects on inflammatory cells, neurons, astrocytes, microglia, and endothelial and epithelial cells, and a cell surface receptor, RAGE, has been identified as a potential S100A12 and S100B receptor transducing the effects of these two proteins on inflammatory cells and neurons. Other cell surface molecules with ability to interact with S100 members have been identified, suggesting that RAGE might not be a universal S100 protein receptor and/or that a single S100 protein might interact with more than one receptor. Collectively, these data indicate that members of the S100 protein family are multifunctional proteins implicated in the regulation of a variety of cellular activities.     

New separation tools for comprehensive studies of protein expression by mass spectrometry

Mass spectrometry has emerged as a core technique for protein identification and characterization because of its high sensitivity, accuracy, and speed of analysis. The most widespread strategy for studying global protein expression in biological systems employs analytical two-dimensional polyacrylamide gel electrophoresis (2D PAGE) followed by enzymatic degradation of isolated protein spots, peptide mapping, and bioinformatics searches. Using this method, thousands of proteins can be resolved in a gel and their expression quantified. However, certain types of proteins possessing important cellular functions are not easily analyzed using this strategy. These proteins include membrane, low copy number, highly basic, and very large (> 150 kDa) and small (< 10 kDa) proteins. To meet the growing need to simultaneously monitor all types of proteins in a biological system, new separation strategies have emerged that are amenable to hyphenation to mass spectrometric techniques. This article will review these new techniques and examine their usefulness in studies of protein expression.     

使用非正交曲线座标和非正交速度分量的叶轮机械三元流动基本方程及其解法

本文使用张量方法推导了使用任意非正交曲线座标和非正交速度倒分量的叶轮机械内部三元流动的基本气动热力学方程,详细考虑了适用于S1和S2相对流面的各种座标的取法及其相应的方程。最后讨论了适用于反问题（设计问题）和正问题（分析、和变工况计算问题）的两类求解方法。第一类方法是作者以前提出的中心流线法的发展,属于流线推广法范畴。第二类方法是过去使用的矩阵法和迭代法的继续。这一套非正交曲线座标的方程组及其解法可以用来更准确地设计或计算分析具有任意弯曲通道和任意倾斜的以及具有任意前、后缘形状的叶片的叶轮机械内部三元流动。     

Deaccelerating films for picosecond new generation dissectors

This paper describes the selection of deaccelerating films made of aluminum of various thicknesses (300–500 nm) and intended for deacceleration of electrons (with an energy of tens of kiloelectron volts to tens of electron volts) in the developed new generation picosecond dissectors. The designed dissectors should be different by a higher temporal resolution as compared to the maximum reached (~20 ps) in LI-602 dissecting image-tube converters used for diagnosing synchrotron radiation. This paper also presents the results of comparative measurements of emission characteristics of manufactured films in the models of image-tube converters similar in design to a PIF-01/S1 device, which is the basis of the developed dissectors and which provides the maximum temporal resolution of up to 1 ps in the streak mode with the streak speed of ~10¹⁰ cm/s. It is established that, when the energy of the incident electron beam equals 10 to 12 keV, the optimum thickness of the deaccelerating aluminum film is 400 nm with the effective secondary emission coefficient equal to 0.7.     

S-100 proteins in the human peripheral nervous system

This article reviews the distribution of S100 proteins in the human peripheral nervous system. The expression of S100 by peripheral glial cells seems to be a distinctive fact of these cells, independently of their localization and their ability to myelinate or not. S100 proteins expressing cells include satellite cells of sensory, sympathetic and enteric ganglia, supporting cells of the adrenal medulla, myelinating and non-myelinating Schwann cells in the nerve trunks, and the Schwann-related cells of sensory corpuscles. In addition, S100 proteins are expressed in peripheral neurons. Most of them express S100alpha protein, and a subpopulation of sensory neurons in dorsal root ganglia contains S100beta protein or S100alpha plus S100beta proteins.     

全系统动态测量精度理论的基本问题

动态测量已成为现代测量技术发展的主流趋势,但对动态测量系统的描述和评价仍沿用传统的静态测量理论,本文提出全系统动态测量精度理论新概念,并论述了传递链函数和全系统动态测量误差等基本问题,为深入研究这种新颖理论建立了必要基础     

基于健康指标的设备动态预防维护策略研究

设备维护目前主要采用传统的矫正维护或计划性预防保养，在系统运行前就设定出阈值，在应用阶段不随时间变化，故策略的静态特性不符合实际的生产控制过程。因此，基于设备健康状态的可测性，且利用维护后设备的健康状态更新能力，通过采用离散马尔可夫随机过程描述设备衰退趋势，建立了一类新的设备动态预防维护优化模型，并引入威布尔失效函数进行验证和分析。通过实验，验证了该基于设备健康指标的动态预防维护优化策略是实用而有效的。     

Proteomics analysis provides novel biomarkers and therapeutic target candidates in the treatment of the Huang-Pu-Tong-Qiao formula in an AD rat model

Background: Huang-Pu-Tong-Qiao formula (HPTQ), a traditional Chinese herbal formula, has a variety of pharmacological effects. It has been used to treat Alzheimer’s disease (AD) for decades. This study aimed to screen differentially expressed proteins in the hippocampus of AD model rats treated with HPTQ. Proteomic studies of the effects of HPTQ on AD are key to understanding the therapeutic mechanisms of HPTQ and identifying potential therapeutic targets. Methods: We hence used the isobaric tags for relative and absolute quantification (ITRAQ) approach to investigate the differentially expressed proteins in the hippocampus of AD model rats before and after HPTQ administration and to identify the potential therapeutic target proteins of HPTQ. In this study, the learning and memory abilities of AD rats were examined by the Morris water maze test. After HPTQ administration, the differentially expressed proteins in the hippocampus of AD rats were quantified and analyzed in silico. Furthermore, western blotting was used to verify the expression of related proteins. Results: The Morris water maze results showed that HPTQ could improve the learning and memory ability of AD model rats. The proteomics analysis results showed that 57 proteins were differentially expressed, of which 35 were up-regulated and 22 were down-regulated. Bioinformatics analysis indicated that proteins with altered expression after HPTQ treatment were involved in several biological processes that have the potential to exert neuroprotective effects. These included promoting the translation of ribosomes, improving the deposition of amyloid-beta (Aβ), regulating autophagy, regulating neuronal synaptic function and plasticity, and alleviating oxidative stress. Conclusion: In conclusion, we identified several potential therapeutic target proteins and related mechanistic pathways of HPTQ in the treatment of AD, laying the foundation for further investigation of the therapeutic effects of HPTQ.     

Assessment of In vivo behavior of polymer tube nerve grafts simultaneously with the peripheral nerve regeneration process using scanning electron microscopy technique

In this study, scanning electron microscopy (SEM) has been applied for instantaneous assessment of processes occurring at the site of regenerating nerve. The technique proved to be especially useful when an artificial implant should have been observed but have not yet been extensively investigated before for assessment of nerve tissue. For in vivo studies, evaluation of implant's morphology and its neuroregenerative properties is of great importance when new prototype is developed. However, the usually applied histological techniques require separate and differently prepared samples, and therefore, the results are never a 100% comparable. In our research, we found SEM as a technique providing detailed data both on an implant behavior and the nerve regeneration process inside the implant. Observations were carried out during 12‐week period on rat sciatic nerve injury model reconstructed with nerve autografts and different tube nerve grafts. Samples were analyzed with haematoxylin‐eosin (HE), immunocytochemical staining for neurofillament and S‐100 protein, SEM, TEM, and the results were compared. SEM studies enabled to obtain characteristic pictures of the regeneration process similarly to TEM and histological studies. Schwann cell transformation and communication as well as axonal outgrowth were identified, newly created and matured axons could be recognized. Concurrent analysis of biomaterial changes in the implant (degradation, collapsing of the tube wall, migration of alginate gel) was possible. This study provides the groundwork for further use of the described technique in the nerve regeneration studies. SCANNING 35: 232‐245, 2013. © 2012 Wiley Periodicals, Inc.     

Multivariate statistical analysis of electron probe microanalytical data on cell nuclear constituents

A multivariate statistical analysis (the principal component analysis) has been used to process electron probe microanalytical data from cell nuclei. Fifty-seven measurements from different areas of chromatin and nucleolus in follicular rat cells have been studied. The variables are the X-ray characteristic signals for P, S, Al, Fe, Cu and Zn. This method demonstrates three groups of individuals - the chromatin area which is associated with a stronger concentration of P and two groups of nucleolar areas, one of them being connected with a higher content in S, Al and Zn. This high degree of correlation between these three elements proves the chemical affinity of the metals with the protein, S being the signature for proteins.