代谢组学方法研究水飞蓟宾对四氯化碳致小鼠肝损伤的保护作用

运用代谢组学方法研究四氯化碳(CCl4)致小鼠肝损及水飞蓟宾肝保护作用的机理. 通过气相色谱-质谱(GC-MS)技术分析CCl4及水飞蓟宾作用下的小鼠肝组织匀浆及血浆代谢物谱. 使用正交偏最小二乘判别分析法研究正常组与CCl4模型组之间的代谢物谱差异, 并通过变量重要性投影(VIP)选取肝组织与血浆中各12种标志性代谢物. 使用主成分分析法研究水飞蓟宾预防性及治疗性给药对CCl4肝损的干预效果. 通过比较选取的标志性代谢物的含量的差异, 探讨了水飞蓟宾对CCl4致小鼠肝损的保护机理. 结果表明, CCl4作用后, 小鼠机体能量代谢、氨基酸代谢及脂类代谢都受到不同程度的影响. 水飞蓟宾能有效地缓解CCl4所造成的体内线粒体功能及氨基酸代谢紊乱. 采用代谢组学方法能较全面地反应生物体的生理及代谢状态, 并可应用于物质毒性和药效评价研究.     

基于修饰组和探针分子的重要途径代谢物筛选和注释新方法北大核心CSCD

植物次生代谢物在抵御生物/非生物胁迫、生物间互作以及信息传递等方面发挥重要作用,次生代谢途径解析对植物分子育种、天然产物合成等方面具有重要意义。液相色谱-高分辨串联质谱(LC-HRMS/MS)为次生代谢物鉴定及途径表征提供了技术手段。非靶向LC-HRMS/MS方法可获得丰富的质谱信号,包括一级质谱和二级质谱(MS,MS/MS),但受质谱数据库规模以及次生代谢物复杂性的制约,次生代谢物注释十分困难。该研究以玉米叶片中苯丙烷途径代谢物为例,发展用于非靶向代谢组数据中重要途径代谢物的高效筛选和注释新方法。首先,利用公共代谢途径数据库及文献获取参与苯丙烷代谢途径的61种修饰反应类型,进而从非靶向实验数据中筛选出修饰代谢组。其次,获取开源串联质谱数据中的苯丙烷类化合物作为探针分子,构建探针分子质谱数据库。将探针分子与修饰代谢组共建分子网络,锁定目标途径代谢物并注释结构。该方法在正、负离子模式下分别筛选出玉米叶片中392个和417个苯丙烷途径候选代谢物,去冗余后共注释出129个代谢物,涉及苯丙烷代谢的主要分支途径,如黄酮途径的8个类黄酮、19个氧苷类黄酮和32个碳苷类黄酮,31个羟基肉桂酸途径代谢物以及22个木脂素途径代谢物;其中26个在PubChem和SciFinder数据库中未见收录。该研究利用探针分子结合修饰组可快速锁定途径代谢物,且有助于快速、准确的网络传播注释,可显著提高目标途径代谢物筛选与注释效率,为植物次生代谢途径的深入解析提供分析手段。     

硫酸铵提高裂殖壶菌不饱和脂肪酸积累的代谢组学研究

采用基于气相色谱-质谱(GC-MS)联用技术的代谢组学方法,通过分析裂殖壶菌胞内代谢物的变化,研究(NH4)2SO4提高裂殖壶菌不饱和脂肪酸积累的作用机制.利用GC-MS技术对添加0,1.5,2.5和3.5g/L (NH4)2SO4的发酵样品进行分析,结合K-Means算法对数据进行聚类分析,得到胞内代谢物的热图.主成分分析(PCA)和偏最小二乘判别分析(OPLS-DA)得分图可将不同添加条件下裂殖壶菌胞内物质明显区分.运用PLS-DA载荷图及模型的变量重要性因子(VIP)值,发现了7种代谢物可作为区别4种不同条件下的生物标志物.经NIST和Wiley谱库检索,它们分别为葡萄糖、肌醇、甘露醇、果糖、磷酸、乙醇胺、乙胺.代谢途径分析结果表明,(NH4)2SO4是通过弱化糖酵解途径和乙酸合成支路,提高苹果酸酶的活力,强化氨基酸代谢和NADPH的积累,从而提高不饱和脂肪酸积累.     

基于气相色谱-飞行时间质谱技术的佐剂性关节炎大鼠尿液代谢组学的研究

采用弗氏完全佐剂(FCA)诱导佐剂性关节炎(AA)大鼠模型,观察大鼠足趾肿胀度和踝关节组织的病理学形态变化。应用气相色谱-飞行时间质谱(GC-TOF MS)技术检测AA大鼠尿液代谢物谱,并对数据进行主成分分析(PCA)、偏最小二乘法-判别分析(PLS-DA)及正交偏最小二乘法-判别分析(OPLS-DA),探讨可能的发病机制。通过变量重要性投影值(VIP>1)和P值(<0.05),筛选出尿液中的差异代谢物。在模型组大鼠的尿液中共发现异柠檬酸、α-酮戊二酸、柠康酸、肌酸、3-羟基丁酸等20种差异代谢物。推断AA代谢组学的发病机制可能与能量代谢、氨基酸代谢、脂肪酸代谢途径有关。     

蛋白质组学和代谢组学在微生物代谢工程中的应用

构建微生物细胞工厂是化学品、生物能源以及药物分子可持续生产的可行性策略。然而，微生物的代谢复杂、调控严谨，制约着目标产物高效合成。蛋白质组学和代谢组学可以从系统生物学角度分析酶和代谢物组分，从而理解复杂的生物系统，为微生物代谢工程改造提供重要线索。该文介绍了蛋白质组学和代谢组学在微生物代谢工程中的应用，包括基因组尺度代谢模型构建、菌株生物合成优化、指导菌株耐受性改造、限速步骤预测、植物次级代谢途径挖掘，从而为微生物合成天然产物提供新的基因或途径。在此基础上，该文还展望了生物大数据未来的发展方向。     

基于核磁共振技术的临床尿毒症的代谢组学研究

采用核磁共振技术与统计学分析方法,结合尿液的生化指标,进行临床尿毒症尿样的代谢组学研究。结果表明,尿毒症患者和健康对照人群尿样的代谢轮廓存在明显差异,通过核磁共振氢谱鉴定出70种代谢物,其中20种具有显著差异。与健康人群相比,尿毒症患者尿液中2-羟基异丁酸、3-羟基丁酸、丙酮、丁酸、谷氨酸、肌氨酸、肌酐、赖氨酸、N,N-二甲基组氨酸、柠檬酸、天冬酰胺、乙醇和乙醇胺的含量明显偏低,而支链氨基酸(包括亮氨酸、缬氨酸、异亮氨酸)、牛磺酸、乳酸、α-葡萄糖和β-葡萄糖的含量明显偏高。这些代谢物涉及氨基酸代谢、能量代谢和脂质代谢中的多条代谢途径,可作为尿毒症代谢影响的潜在的生物标志物,有助于理解尿毒症发病的生化机制。     

基于气相色谱-质谱的烟草根部代谢组学方法建立及应用

建立了一种基于气相色谱-质谱的烟草根部代谢组学研究方法,方法采用甲基叔丁基醚-甲醇-水和二氯甲烷分别作为极性和非(弱)极性代谢物的萃取溶剂,采用10 mg冻干烟草根粉末对应1.5 m L甲基叔丁基醚-甲醇-水和100 mg冻干烟草根粉末对应5 m L二氯甲烷分别作为极性和非极性代谢物的最佳萃取方案。方法建立了烟草根部代谢物定性信息库,信息库包含了100个极性代谢物和32个非极性代谢物的质谱谱图、保留指数、化学结构等信息。将所建立的方法应用于红大与TN90根部代谢组差异研究,发现缬氨酸等8种氨基酸、乙醇酸等7种有机酸、果糖等4种糖类物质等在两种烟草根中含量有显著性差异。     

基于气相色谱-质谱法的广泛靶向代谢组学方法开发

气相色谱-质谱法(GC-MS)的四极杆检测器具有扫描速率低、离子流失率高、浓度检测范围窄的特点，这些缺陷限制了该技术在代谢组学领域的广泛应用，因此亟需建立一种基于GC-MS的高覆盖率代谢组学分析方法。本文提出了一种基于GC-MS的广泛靶向代谢组学方法，广泛靶向代谢组学结合了靶向和非靶向的优点，可以实现对代谢物质的定性和半定量检测，该方法以The Fiehn library(FiehnLib)数据库中的代谢物质信息为基础，建立直链脂肪酸甲酯(FAMEs)的保留时间与FiehnLib数据库中的保留指数(RI)的关系，根据FiehnLib数据库中的保留指数计算数据库中代谢物质在具体实验条件下的保留时间；对比分析并确定保留时间的阈值为0.15 min,优化最佳扫描间隔为0.20 s;优化代谢物质的定量离子以避免出峰时间相近离子的干扰；最终构建了含有611种代谢物质的选择离子监测(SIM)方法表，这611种代谢物质覆盖了KEGG(Kyoto Encyclopedia of Genes and Genomes)中65%的代谢通路。与全扫描非靶向GC-MS方法相比，该广泛靶向GC-MS方法所检测的代...     

液相色谱-质谱联用结合化学计量学方法分析冠心病及冠心病合并高血压患者的代谢特征

以51例健康人、 21例冠心病患者以及16例冠心病合并高血压患者的血浆为样本,采用超高效液相色谱-高分辨质谱联用技术,分析两类患者的血浆代谢特征。在定性和定量分析104个内源性代谢物的基础上,进行主成分分析、偏最小二乘-判别分析,并结合变量重要性投影与单因素方差分析,分别筛选出8、 41和26种可区分健康人与冠心病患者、健康人与冠心病合并高血压患者、冠心病与冠心病合并高血压患者的潜在特征代谢物。代谢通路分析结果表明,在冠心病与冠心病合并高血压患者中,亚油酸等脂肪酸代谢途径以及苯丙氨酸、酪氨酸、色氨酸的生物合成等氨基酸代谢途径发生了明显变化。其中,氨基酸代谢在冠心病合并高血压患者中表现出更加显著的变化。     

微生物代谢组学的样品前处理

微生物代谢组学是指全面分析(定性和定量)细胞生长或生产周期某一时刻细胞内和细胞周围的所有低分子量代谢物.微生物代谢组学研究需要可靠和重现地分析细胞内较宽动力学浓度范围(nmol～mmol)、化学功能各异的代谢产物,因此,需要对从生物量培养、灭活和代谢产物的提取到代谢物的定量分析这整个实验过程提出耐用、可重现和可靠的实验方案.本文介绍了灭活过程中细胞内代谢产物泄漏的处理方法,较为详细地论述了通过灭活草案捕获代谢反应活性方法和代谢物提取方法的优化,并对微生物代谢组学样品前处理的目前发展趋势提出初步见解.     

Zingiber officinale var. rubrum: Red Ginger’s Medicinal Uses

Zingiber officinale var. rubrum (red ginger) is widely used in traditional medicine in Asia. Unlike other gingers, it is not used as a spice in cuisines. To date, a total of 169 chemical constituents have been reported from red ginger. The constituents include vanilloids, monoterpenes, sesquiterpenes, diterpenes, flavonoids, amino acids, etc. Red ginger has many therapeutic roles in various diseases, including inflammatory diseases, vomiting, rubella, atherosclerosis, tuberculosis, growth disorders, and cancer. Scientific evidence suggests that red ginger exhibits immunomodulatory, antihypertensive, antihyperlipidemic, antihyperuricemic, antimicrobial, and cytotoxic activities. These biological activities are the underlying causes of red ginger’s therapeutic benefits. In addition, there have been few reports on adverse side effects of red ginger. This review aims to provide insights in terms the bioactive constituents and their biosynthesis, biological activities, molecular mechanisms, pharmacokinetics, and qualitative and quantitative analysis of red ginger.     

Chemotaxonomic Identification of Key Taste and Nutritional Components in ‘Shushanggan Apricot’ Fruits by Widely Targeted Metabolomics

The chemotypic and the content variation in taste substances and nutrients in ‘Shushanggan apricot’ fruits were detected by UPLC-MS/MS. A total of 592 compounds were identified, of which sucrose contributed mainly to the sweet taste and malic acid and citric acid were important organic acids affecting sweet–sour taste. γ-linolenic acid, α-linolenic acid and linoleic acid were the dominant free fatty acids, and neochlorogenic acid and chlorogenic acid were the predominant phenolic acids. Fruit taste was positively correlated with sucrose and negatively correlated with malic acid and citric acid. The differential metabolites were significantly enriched in the biosynthesis of amino acids and 2-oxocarboxylic acid metabolism pathways, regulating the sugar and organic acid biosynthesis. Taste and nutrient differences could be revealed by variations in composition and abundance of carbohydrates, organic acids and amino acids. The purpose of this study was to provide a comprehensive chemical characterization of taste and nutrient compounds in ‘Shushanggan apricot’ fruits.     

Metabolomic Analysis and MRM Verification of Coarse and Fine Skin Tissues of Liaoning Cashmere Goat

One of the critical elements in evaluating the quality of cashmere is its fineness, but we still know little about how it is regulated at the metabolic level. In this paper, we use UHPLC–MS/MS detection and analysis technology to compare the difference in metabolites between coarse cashmere (CT_LCG) and fine cashmere (FT_LCG) skin of Liaoning cashmere goats. According to the data, under positive mode four metabolites were significantly up-regulated and seven were significantly down-regulated. In negative mode, seven metabolites were significantly up-regulated and fourteen metabolites were significantly down-regulated. The two groups’ most significant metabolites, Gly–Phe and taurochenodeoxycholate, may be crucial in controlling cashmere’s growth, development, and fineness. In addition, we enriched six KEGG pathways, of which cholesterol metabolism, primary bile acid biosynthesis, and bile secretion were enriched in positive and negative modes. These findings offer a new research idea for further study into the critical elements influencing cashmere’s fineness.     

Neuroprotective Effects of the Psychoactive Compound Biatractylolide (BD) in Alzheimer’s Disease

Mitochondria play a central role in the survival or death of neuronal cells, and they are regulators of energy metabolism and cell death pathways. Many studies support the role of mitochondrial dysfunction and oxidative damage in the pathogenesis of Alzheimer’s disease. Biatractylolide (BD) is a kind of internal symmetry double sesquiterpene novel ester compound isolated from the Chinese medicinal plant Baizhu, has neuroprotective effects in Alzheimer’s disease. We developed a systematic pharmacological model based on chemical pharmacokinetic and pharmacological data to identify potential compounds and targets of Baizhu. The neuroprotective effects of BD in PC12 (rat adrenal pheochromocytoma cells) and SH-SY5Y (human bone marrow neuroblastoma cells) were evaluated by in vitro experiments. Based on the predicted results, we selected 18 active compounds, which were associated with 20 potential targets and 22 signaling pathways. Compound-target, target-disease and target-pathway networks were constructed using Cytoscape 3.2.1. And verified by in vitro experiments that BD could inhibit Aβ by reducing oxidative stress and decreasing CytC release induced mPTP opening. This study provides a theoretical basis for the development of BD as an anti-Alzheimer’s disease drug.     

Ex vivo Application of δ-Aminolevulinic Acid Induces High and Specific Porphyrin Levels in Human Skin Tumors: Possible Basis for Selective Photodynamic Therapy

Abstract— In photodynamic therapy with topically applied δ-aminolevulinic acid porphyrins are acting as photosensitiz-ers. The profile of porphyrin metabolites in normal or in neoplastic skin after administration of δ-aminolevulinic acid has not been determined in detail yet. Thus, to study porphyrin biosynthesis in human skin an organ culture model was developed. Explant pieces of normal skin, ker-atoacanthoma, and basal cell carcinoma were incubated with 1 niM δ-aminolevulinic acid for 36 h. Levels of δ-aminolevulinic acid, porphyrins and porphyrin metabolites were measured in tissues and supernatants. After incubation with δ-aminolevulinic acid, higher porphyrin levels were demonstrated in tumors as compared to normal skin. In supernatants, most of formed porphyrins, preferentially highly carboxylated porphyrin metabolites, were measured. The pattern of synthesized porphyrins differed between normal and neoplastic skin explants. In tissues of basal cell carcinomas protoporphyrin was preferentially shown and tissues of keratoacanthomas were characterized by a predominance of coproporphyrin as compared to normal skin. The results show that explant cultures offer an easy approach to examine the porphyrin biosynthesis of various tissues. The tumor-specific δ-aminolevulinic acid metabolism indicates additional porphyrin metabolites such as coproporphyrin apart from protoporphyrin as effective photosensitizers and may offer a novel approach to tumor-selective photodynamic damage.     

Evaluation of the Chemical Composition,Bioactive Substance,Gas Production,and Rumen Fermentation Parameters of Four Types of Distiller’s Grains

Distiller’s grain is rich in natural active ingredients and can be used as an excellent antioxidant feed for goats. The current study aimed to assess the feeding value of four different types of distiller’s grains with an in vitro gas production trial. The chemical composition, total phenols, total anthocyanins, dry matter degradability, methane, hydrogen, and rumen fermentation parameters were evaluated. The results indicated that red distiller’s grain and glutinous rice distiller’s grain had higher (p < 0.05) levels of crude protein than the other two types. There were significantly (p < 0.05) higher concentrations of dry matter, ether extract, hemicellulose, and total carbohydrate in corn distiller’s grain than in the other three types of distiller’s grain. In addition, red distiller’s grain showed a higher (p < 0.05) gas production rate constant (c) and ruminal outflow rate, as well as higher (p < 0.05) concentrations of total phenol, total anthocyanins and 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity, than the other three types of distiller’s grains. In contrast, red distiller’s grain displayed the lowest (p < 0.05) immediately soluble fraction (a) and half the time of maximum gas production relative to the other samples. In particular, the levels of methane (%) in white distiller’s grain and glutinous rice distiller’s grain were greater (p < 0.05) than that in red distiller’s grain. Moreover, the ammonia nitrogen content in red distiller’s grain was greater (p < 0.05) than that in white distiller’s grain and corn distiller’s grain. In contrast, red distiller’s grain exhibited a lower (p < 0.05) level of ruminal fluid acetic acid relative to that found in white distiller’s grain and corn distiller’s grain. Taken together, the results showed that red distiller’s grain and glutinous rice distiller’s grain could be used as protein feed, red distiller’s grain had higher levels of total phenols and total anthocyanins and a high DPPH scavenging activity; corn distiller’s grain might be considered as an alternative energy source feed, and white distiller’s grain exhibited higher total gas production.     

Rapid Identification of 3,6′-Disinapoyl Sucrose Metabolites in Alzheimer’s Disease Model Mice Using UHPLC–Orbitrap Mass Spectrometry

Alzheimer’s disease (AD) is a degenerative disease of the central nervous system characterized by the progressive impairment of neural activity. Studies have shown that 3,6′-disinapoyl sucrose (DISS) can alleviate the pathological symptoms of AD through the activation of the cAMP/CREB/BDNF signaling pathway. However, the exact biochemical mechanisms of action of DISS are not clear. This study explores metabolism of DISS in an AD mouse model, induced by the microinjection of a lentiviral expression plasmid of the APPswe₆₉₅ gene into CA1 of the hippocampus. After gavage administration of DISS (200 mg/kg), the kidneys, livers, brains, plasma, urine, and feces were collected for UHPLC–Orbitrap mass spectrometry analysis. Twenty metabolites, including the prototype drug of DISS, were positively or tentatively identified based on accurate mass measurements, characteristic fragmentation behaviors, and retention times. Thus, the metabolic pathways of DISS in AD mice were preliminarily elucidated through the identification of metabolites, such as ester bond cleavage, demethoxylation, demethylation, and sinapic acid-related products. Furthermore, differences in the in vivo distribution of several metabolites were observed between the model and sham control groups. These findings can provide a valuable reference for the pharmacological mechanisms and biosafety of DISS.     

Quercetin’s Effects on Glutamate Cytotoxicity

The potentially therapeutic effects of the naturally abundant plant flavonoid quercetin have been extensively studied. An extensive body of literature suggests that quercetin’s powerful antioxidant effects may relate to its ability to treat disease. Glutamate excitotoxicity occurs when a neuron is overstimulated by the neurotransmitter glutamate and causes dysregulation of intracellular calcium concentrations. Quercetin has been shown to be preventative against many forms of neuronal cell death resulting from glutamate excitotoxicity, such as oncosis, intrinsic apoptosis, mitochondrial permeability transition, ferroptosis, phagoptosis, lysosomal cell death, parthanatos, and death by reactive oxygen species (ROS)/reactive nitrogen species (RNS) generation. The clinical importance for the attenuation of glutamate excitotoxicity arises from the need to deter the continuous formation of tissue infarction caused by various neurological diseases, such as ischemic stroke, seizures, neurodegenerative diseases, and trauma. This review aims to summarize what is known concerning glutamate physiology and glutamate excitotoxic pathophysiology and provide further insight into quercetin’s potential to hinder neuronal death caused by cell death pathways activated by glutamate excitotoxicity. Quercetin’s bioavailability may limit its use clinically, however. Thus, future research into ways to increase its bioavailability are warranted.