Clarifying the signal network of salvianolic acid B using proteomic assay and bioinformatic analysis

Salvianolic acid B (SB) is a natural compound with protective effect against ischemia-reperfusion heart injury. However, the signal network of SB including both direct target proteins and downstream signal-related proteins has not been clarified. In the present study, epidermal growth factor receptor (EGFR) was predicted to be the most possible direct protein target of SB by INVDOCK, a ligand-protein inverse-docking algorithm. Possible signal-related proteins of SB in H9C2 cells, including both under normal condition and under ischemia-reperfusion injury, were searched using 2-DE analysis. Totally, 14 signal-related proteins were found. Finally, signal network from EGFR to the signal-related proteins was established using bioinformatic analysis. Interestingly, 9 of the 14 signal-related proteins could be included in a network together with EGFR through direct interaction or only one intermediate partner. The signal cascade from EGFR to heat shock protein 27 (HSP27) and mitofilin (IMMT, inner membrane mitochondrial protein) might be the most important cascade. The signal network was certified by measuring the binding affinity of SB to EGFR in vitro, the effect of SB on internalization and phosphorylation of EGFR, the effect of SB on viability and proliferation of H9C2 cells, and the expression of inner membrane mitochondrial protein in the presence of EGFR inhibitor AG 1478.     

ER stress-mediated apoptosis induced by celastrol in cancer cells and important role of glycogen synthase kinase-3β in the signal network

HeLa cells treated with celastrol, a natural compound with inhibitive effect on proteasome, exhibited increase in apoptotic rate and characteristics of apoptosis. To clarify the signal network activated by celastrol to induce apoptosis, both the direct target proteins and undirect target proteins of celastrol were searched in the present study. Proteasome catalytic subunit β1 was predicted by computational analysis to be a possible direct target of celastrol and confirmed by checking direct effect of celastrol on the activity of recombinant human proteasome subunit β1 in vitro. Undirect target-related proteins of celastrol were searched using proteomic studies including two-dimensional electrophoresis (2-DE) analysis and iTRAQ-based LC-MS analysis. Possible target-related proteins of celastrol such as endoplasmic reticulum protein 29 (ERP29) and mitochondrial import receptor Tom22 (TOM22) were found by 2-DE analysis of total cellular protein expression profiles. Further study showed that celastrol induced ER stress and ER stress inhibitor could ameliorate cell death induced by celastrol. Celastrol induced translocation of Bax into the mitochondria, which might be related to the upregulation of BH-3-only proteins such as BIM and the increase in the expression level of TOM22. To further search possible target-related proteins of celastrol in ER and ER-related fractions, iTRAQ-based LC-MS method was use to analyze protein expression profiles of ER/microsomal vesicles-riched fraction of cells with or without celastrol treatment. Based on possible target-related proteins found in both 2-DE analysis and iTRAQ-based LC-MS analysis, protein–protein interaction (PPI) network was established using bioinformatic analysis. The important role of glycogen synthase kinase-3β (GSK3β) in the signal cascades of celastrol was suggested. Pretreatment of LiCL, an inhibitor of GSK3β, could significantly ameliorate apoptosis induced by celastrol. On the basis of the results of the present study, possible signal network of celastrol activated by celastrol leading to apoptosis was predicted.     

An assessment of the genetic diversity within Ganoderma strains with AFLP and ITS PCR-RFLP

Ganoderma lucidum is one of the most important medicinal materials and plant pathogens. Because of its specific interhybridization, the genetic background, however, is relatively unclear. It made identification of Ganoderma strains, especially closely related strains difficulty. Amplified fragment length polymorphism (AFLP) using 14 primer combinations and internal transcribed spacer (ITS) PCR-RFLP were used in a comparative study which was designed to investigate the closely related Ganoderma strains genetic relations at molecular level. The analysis of 37 Ganoderma strains showed there were 177 polymorphic AFLP markers and 12 ITS PCR-RFLP markers, and all accessions could be uniquely identified. Among the Ganoderma accessions, similarity coefficients ranged from 0.07692 to 0.99194 in AFLP. The Ganoderma strains formed a tight cluster in nine groups in AFLP whereas seven groups in ITS PCR-RFLP. The cluster analysis revealed that the taxonomical system of subgenus Ganoderma is composed of Sect. Ganoderma and Sect. Phaeonema, and the strain 22 should be a variant form of strain 21. All methods delineated the Ganoderma strains from the different regions seeming to show a greater level of genetic diversity. It indicated that the genotype study at molecular level is a useful complement method to the current classification system of Ganoderma strains based on morphological traits. The congruency of the experiments was analyzed using the biostatistical software DPS V3.01.     

利用PEG法建立药用真菌灵芝的转化系统

本文首次建立了一种通过PEG转化缓冲液将外源基因转入灵芝的方法,转化频率约为5~6个/mg(抗性转化子/质粒+107个原生质体)。转化子在不含HmB的培养基上经5代以上的继代培养后仍可以稳定表达HmB抗性。Southernblot检测证明外源基因已经整合到了灵芝的基因组DNA中。本研究为通过基因工程手段定向、快速改良灵芝药用品质以及利用灵芝发酵方法生产一些具有重大经济价值的外源蛋白等应用奠定基础,并且也有助于我们进一步了解灵芝这一大型真菌中的基因的表达调控机制。     

生物富硒对灵芝营养成分的影响

在人工栽培灵芝中,通过外施硒盐以生物转化法获得富硒灵芝,以不同含硒量的富硒灵芝子实体为试样,系统研究了灵芝生物富硒后对其主要营养成分多糖、蛋白质、氨基酸和矿物质等的影响。结果表明：硒可以明显提高灵芝中多糖、蛋白质以及氨基酸的含量,但并不改变灵芝蛋白质的分布和蛋白质中氨基酸的组成配比,而对矿质元素则有不同的影响,如富硒灵芝子实体中人体必需微量营养元素硒有极明显地增加,而铜和钼等人体必需微量元素的含量有一定量的增加,但铁、钙、锶等矿质元素的含量则有所下降。     

冬虫夏草与韩芝液体发酵混合培养特性研究

平板培养基上比较了冬虫夏草、韩芝及树舌的菌丝生长速度和对淀粉的利用情况,结果显示三者的生长速度分别达到1.28、0.64和0.55 cm/d,且韩芝与树舌对淀粉的利用均优于冬虫夏草;混合培养结果得出菌种的最佳菌龄比为虫草:韩芝=3 d:5 d,最佳的接种比例为2:3;正交试验混合发酵最佳的培养基配方(%):葡萄糖1.0、淀粉2.0、黄豆粉2.0、酵母粉0.5,在此条件下,菌丝生物量达到最大值1.97 g/100 mL。     

The knowledge-integrated network biomarkers discovery for major adverse cardiac events

The mass spectrometry (MS) technology in clinical proteomics is very promising for discovery of new biomarkers for diseases management. To overcome the obstacles of data noises in MS analysis, we proposed a new approach of knowledge-integrated biomarker discovery using data from Major Adverse Cardiac Events (MACE) patients. We first built up a cardiovascular-related network based on protein information coming from protein annotations in Uniprot, protein-protein interaction (PPI), and signal transduction database. Distinct from the previous machine learning methods in MS data processing, we then used statistical methods to discover biomarkers in cardiovascular-related network. Through the tradeoff between known protein information and data noises in mass spectrometry data, we finally could firmly identify those high-confident biomarkers. Most importantly, aided by protein-protein interaction network, that is, cardiovascular-related network, we proposed a new type of biomarkers, that is, network biomarkers, composed of a set of proteins and the interactions among them. The candidate network biomarkers can classify the two groups of patients more accurately than current single ones without consideration of biological molecular interaction.     

Identification of novel 14-3-3ζ interacting proteins by quantitative immunoprecipitation combined with knockdown (QUICK)

The family of 14-3-3 proteins has emerged as critical regulators of diverse cellular responses under both physiological and pathological conditions. To gain insight into the molecular action of 14-3-3ζ in multiple myeloma (MM), we performed a systematic proteomic analysis of 14-3-3ζ-associated proteins. This analysis, recently developed by Matthias Mann, termed quantitative immunoprecipitation combined with knockdown (QUICK), integrates RNAi, SILAC, immunoprecipitation, and quantitative MS technologies. Quantitative mass spectrometry analysis allowed us to distinguish 14-3-3ζ-interacting proteins from background proteins, resulting in the identification of 292 proteins in total with 95 novel interactions. Three 14-3-3ζ-interacting proteins-BAX, HSP70, and BAG3-were further confirmed by reciprocal coimmunoprecipitations and colocalization analysis. Our results therefore not only uncover a large number of novel 14-3-3ζ-associated proteins that possess a variety of cellular functions, but also provide new research directions for the study of the functions of 14-3-3ζ. This study also demonstrated that QUICK is a useful approach to detect specific protein-protein interactions with very high confidence and may have a wide range of applications in the investigation of protein complex interaction networks.     

基于MADS-box诱饵与蛋白质相互作用的拟南芥花瓣发育分子网络拓展

阐明花器官发育调控机理具重要的进化、发育和生态学意义。该文以拟南芥(Arabidopsis thaliana)花瓣发育为例, 整合蛋白质互作、亚细胞定位、基因芯片和基因功能注释等数据库, 通过组建蛋白质互作可信预测模型, 获得拟南芥花瓣蛋白质互作网络, 以含有MADS-box结构域蛋白为诱饵在网络中进行一级拓展, 得到含38个蛋白质和67对互作的拓展网络。基于拓展网络, DAVID基因功能注释表明, 多数蛋白质涉及的生物学过程与花发育调控相关; 提取到19个候选四元互作, 涉及ABCDE模型基因之外的8个基因, 其中含MADS-box结构域的AGL16可能是B类基因新成员或其冗余; SEU、LUH、CHR4、CHR11、CHR17和AT3G04960为拟南芥花瓣AP1-AP3-PI-SEP四聚体的候选靶标基因。研究结果为深入解析拟南芥花瓣发育分子调控网络奠定了基础。     

响应面设计法优化蕨渣基质的灵芝培养条件

探索灵芝在以蕨渣为主要成分的固态基质中的培养条件,可为蕨渣的开发利用提供理论依据。以蕨渣为主要原料,采用响应面法对灵芝培养条件（基质蕨渣比例、基质含水量和培养温度）进行优化。结果表明,基质蕨渣比例、基质含水量和培养温度对灵芝菌丝日平均生长速率均有极显著的影响（p<0.01）,且基质含水量与培养温度之间、基质蕨渣比例与基质含水量之间存在交互作用。优化出灵芝培养条件为蕨渣比例85%,基质含水量62.5%,培养温度27℃,在此条件下,灵芝菌丝日平均生长速率为3.48mm/d。多元回归分析结果显示,基质蕨渣比例、基质含水量、培养温度与菌丝日平均生长速率之间回归模型高度显著,可用于实际生产预测。首次报道了利用蕨渣培养灵芝,为蕨渣进一步的开发研究奠定基础。     

A quantitative approach to study indirect effects among disease proteins in the human protein interaction network

Background  

Systems biology makes it possible to study larger and more intricate systems than before, so it is now possible to look at the molecular basis of several diseases in parallel. Analyzing the interaction network of proteins in the cell can be the key to understand how complex processes lead to diseases. Novel tools in network analysis provide the possibility to quantify the key interacting proteins in large networks as well as proteins that connect them. Here we suggest a new method to study the relationships between topology and functionality of the protein-protein interaction network, by identifying key mediator proteins possibly maintaining indirect relationships among proteins causing various diseases.     

Cloning and characterization of squalene synthase (SQS) gene from Ganoderma lucidum

This report provides the complete nucleotide sequences of the full-length cDNA encoding squalene synthase (SQS) and its genomic DNA sequence from a triterpene-producing fungus, Ganoderma lucidum. The cDNA of the squalene synthase (SQS) (GenBank Accession Number: DQ494674) was found to contain an open reading frame (ORF) of 1,404 bp encoding a 468-amino-acid polypeptide, whereas the SQS genomic DNA sequence (GenBank Accession Number: DQ494675) consisted of 1,984 bp and contained four exons and three introns. Only one gene copy was present in the G lucidum genome. The deduced amino acid sequence of Ganoderma lucidum squalene synthase (Gl-SQS) exhibited a high homology with other fungal squalene synthase genes and contained six conserved domains. A phylogenetic analysis revealed that G. lucidum SQS belonged to the fungi SQS group, and was more closely related to the SQS of U. maydis than to those of other fungi. A gene expression analysis showed that the expression level was relatively low in mycelia incubated for 12 days, increased after 14 to 20 days of incubation, and reached a relatively high level in the mushroom primordia. Functional complementation of Gl-SQS in a SQS-deficient strain of Saccharomyces cerevisiae confirmed that the cloned cDNA encoded a squalene synthase.     

灵芝漆酶催化直接耐晒翠蓝GL脱色条件的优化

采用灵芝菌株发酵所得的漆酶, 对酞菁类染料直接耐晒翠蓝GL进行了催化脱色实验, 确定了脱色反应的最适条件。结果表明: 单独使用灵芝漆酶粗酶液对直接耐晒翠蓝GL具有很好的脱色效果。其最适脱色pH为3.0, 最适脱色温度为40°C, 最适漆酶用量是40 U/mL, 最适染料浓度为60 mg/L。以上述最适脱色条件对直接耐晒翠蓝GL进行脱色实验, 反应70 min, 脱色率可达94.3%。研究结果显示, 所试灵芝漆酶在印染废水治理方面具有良好的应用前景。     

11个灵芝菌株的分子ID构建

[目的]收集11株灵芝菌种为材料,在分子水平上对其进行分类鉴定,并构建分子ID.[方法]采用ITS和SSR分子标记技术,对11株灵芝进行分子鉴定分析.[结果]通过内转录间隔区(ITS)序列测定分析表明,与GenBank上登录的灵芝(Ganoderma lucidum)菌株ITS序列相似度达到99％,在种的水平上证明实验所采用的供试菌株均属灵芝种(Ganoderma lucidum).利用SSR分子标记技术对菌株进行引物扩增,综合多态性条带,用NTSYS软件进行聚类分析,相似度在0.62水平上,1 1个灵芝菌种被分成4个类群,其中GL-2与GL-4各自聚为一类.用ID Analysis 1.0软件进行数据分析表明,用5对SSR引物可将11株灵芝供试菌种完全区分开,并构建其分子身份证.[结论]基于SSR分子标记构建灵芝菌属的分子ID是可行的.     

Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks

Background  

Human cells of various tissue types differ greatly in morphology despite having the same set of genetic information. Some genes are expressed in all cell types to perform house-keeping functions, while some are selectively expressed to perform tissue-specific functions. In this study, we wished to elucidate how proteins encoded by human house-keeping genes and tissue-specific genes are organized in human protein-protein interaction networks. We constructed protein-protein interaction networks for different tissue types using two gene expression datasets and one protein-protein interaction database. We then calculated three network indices of topological importance, the degree, closeness, and betweenness centralities, to measure the network position of proteins encoded by house-keeping and tissue-specific genes, and quantified their local connectivity structure.     

Complex carbohydrate specificity of lectin from fruiting body of Ganoderma lucidum. A surface plasmon resonance study

The thermodynamics and kinetics of binding of glycans and glycoproteins to Ganoderma lucidum lectin was studied using surface plasmon resonance. The lectin showed highest affinity for asialo triantennary N glycan (Ka = 3.52 x 10(5)) among the glycans tested. There was a several fold increase in affinity for glycoproteins compared to their corresponding glycans and coincident increase in contribution from enthalpy (DeltaH), suggesting the involvement of hydrogen bonding in the interaction as well as involvement of protein-protein interactions. Increased affinity also showed increase in unfavorable negative binding entropy (DeltaS) which was compensated with higher enthalpy. The glycoproteins showed faster association rates (k(1)) and the activation energy (E(1)) in the association process was much lower for the glycoproteins than glycans, resulting in their faster associations. These observations elaborate the role of protein matrix in lectin-glycoconjugate interaction.     

纳米级灵芝子实体粉末和破壁灵芝孢子粉体外抗肿瘤活性研究

对纳米级灵芝子实体粉末及破壁灵芝孢子粉石油醚提取物(PE)、氯仿提取物(CE)、丙酮(AE)、甲醇提取物(ME)、水提取物(WE)与灵芝子实体及灵芝孢子提取量进行对比,利用GC-MS联用仪对石油醚提取物进行了成分分析鉴定,对水提物中总糖进行了含量测定,并利用宫颈癌细胞Hela和晶体上皮细胞SRA01/04进行了体外增殖作用和剂量效应关系研究,为灵芝资源的保护及进一步开发利用提供理论基础。结果表明,纳米化灵芝子实体及破壁灵芝孢子不同溶剂提取量显著增加,纳米级灵芝子实体粉末水提取物具有抑制宫颈癌细胞Hela和晶体上皮细胞SRA01/04增殖的作用。破壁灵芝孢子各溶剂提取物对宫颈癌细胞Hela和晶体上皮细胞SRA01/04没有明显的增殖抑制作用。