乳酸菌基因组代谢网络模型的研究进展

基因组代谢网络模型(genome-scale metabolic models,GEMs/GSMM)是基因组规模的细胞生化反应网络,可以定量描述基因与表型的关系,广泛应用于系统生物学、代谢工程、环境科学等领域。微生物基因组代谢网络模型是基于微生物基因组构建的生理生化知识库,通过数学模型实现对目标微生物生理生化反应的模拟,已成为研究微生物代谢调控的重要工具。基因组代谢网络模型的构建步骤通常包括构建模型草图、人工精炼、模型转换、验证评估4个阶段。在介绍以模式微生物(大肠杆菌、枯草芽孢杆菌、酿酒酵母)为代表的微生物基因组代谢网络模型发展过程基础上,重点聚焦乳酸菌基因组代谢网络模型的研究现状,系统介绍了已构建的乳酸菌基因组代谢网络模型及其应用。对乳酸菌基因组代谢网络模型的发展方向进行了展望,提出未来乳酸菌基因组代谢网络模型的研究应在现有模型的基础上构建更高质量的代谢与大分子表达模型和泛基因组模型,为乳酸菌的研究提供更高效的工具。     

FluxExplorer： A general platform for modeling and analyses of metabolic networks based on stoichiometry

An increasing number of genomic and biochemical data make it possible to reconstruct biochemical net-works, especially metabolic networks, of an organelle or even a whole cell. Some methods for metabolism modeling and analyses in this field have been deve…     

一种多级别OBS中评估阻塞概率的精确模型

提出了一种应用于多级别光突发交换(OBS)网络中评估每一种级别业务的阻塞概率的分析模型。该模型可以评估OBS网络中任意突发长度分布和任意偏置时间情形下的阻塞概率,也包括每一级别的平均突发长度不同的OBS系统。这样的OBS系统并不遵从守恒律,因此,不能应用已知的OBS模型进行分析。对一个两级别的OBS系统,业务负载为10-3,高优先级与低优先级业务的比率为1:5时,本模型可以为每一级别精确预测阻塞概率。假定守恒条件下,已知的分析模型所给出的预测结果比仿真结果低将近75%。     

基于气质联用技术的猴头菇多糖抗疲劳代谢组学

猴头菇为珍贵的药食两用大型真菌,有抗炎、抗肿瘤、增加免疫力等功效。应用气相色谱-质谱联用(gas chromatography-mass spectrometer, GC-MS)代谢组学方法考察猴头菇多糖对大鼠负重力竭游泳模型的抗疲劳作用及作用机制。将大鼠随机分为6组(空白组、模型组、猴头菇多糖低、中、高3个剂量实验组、阳性对照组),每组6只,连续灌胃21 d;通过测量各组大鼠体重、比较大鼠力竭游泳时间、分析大鼠血清5-HT含量、比较大鼠外周血血象及胸脾指数等实验指标来评估猴头菇多糖对大鼠疲劳的缓解程度;采用GC-MS技术分析各组大鼠血清中代谢物,并进行多元统计分析获取差异性代谢物信息,构建代谢通路并阐述抗疲劳作用机制。结果表明：猴头菇多糖高剂量组的大鼠负重力竭游泳时间显著长于模型组;猴头菇多糖低、中、高剂量组大鼠代谢轮廓趋近于空白组,表现出一定抗疲劳作用。获得了24个差异性代谢物与负重力竭游泳模型有关,涉及的3条主要代谢通路为：亚油酸代谢、甘油代谢及苯丙氨酸、酪氨酸、色氨酸合成。推测猴头菇多糖可能通过调节脂质代谢以及氨基酸代谢对负重力竭游泳模型大鼠发挥抗疲劳作用。     

Pathway complexity in supramolecular polymerization

Self-assembly provides an attractive route to functional organic materials, with properties and hence performance depending sensitively on the organization of the molecular building blocks. Molecular organization is a direct consequence of the pathways involved in the supramolecular assembly process, which is more amenable to detailed study when using one-dimensional systems. In the case of protein fibrils, formation and growth have been attributed to complex aggregation pathways that go beyond traditional concepts of homogeneous and secondary nucleation events. The self-assembly of synthetic supramolecular polymers has also been studied and even modulated, but our quantitative understanding of the processes involved remains limited. Here we report time-resolved observations of the formation of supramolecular polymers from π-conjugated oligomers. Our kinetic experiments show the presence of a kinetically favoured metastable assembly that forms quickly but then transforms into the thermodynamically favoured form. Quantitative insight into the kinetic experiments was obtained from kinetic model calculations, which revealed two parallel and competing pathways leading to assemblies with opposite helicity. These insights prompt us to use a chiral tartaric acid as an auxiliary to change the thermodynamic preference of the assembly process. We find that we can force aggregation completely down the kinetically favoured pathway so that, on removal of the auxiliary, we obtain only metastable assemblies.     

NMR Dynamic Studies in Living Systems

IntroductionApplications of nuclear magnetic resonance(NMR) spectroscopy in the study of living systemsrepresent an ever-expanding area of researchactively pursued in many universities and researchinstitutions[1 ] .The interestin studying living cellswith NMR techniques stemmed from the exchangeexperiments of human blood cells in D2 Operformed by Odeblad et al.in the mid-1 95 0 s[2 ] .Continued interest in defining and explaining theproperties of water in biological tissue from themid-1 96…     

基于气相色谱—质谱联用代谢组学技术研究保元汤对血虚证小鼠的影响

利用基于气相色谱-质谱联用(gas chromatography-mass spectrometer, GC-MS)的代谢组学方法考察了保元汤治疗血虚证小鼠的作用机制;对昆明种小鼠腹腔注射环磷酰胺(cyclophosphamide, CTX),建立了以白细胞减少为特征的血虚证小鼠模型,设立空白对照组、模型组、阳性对照组以及保元汤低、中、高3个剂量的给药组,连续给药14 d。采用GC-MS技术对各实验组小鼠的血清进行分析,获取差异性代谢物信息;采用主成分分析(principal component analysis, PCA)对空白对照组和模型组的代谢物进行分类,寻找并发现保元汤作用于血虚证模型小鼠后差异性代谢物的含量变化,同时检测各组小鼠血液生化指标,计算脾指数与胸腺指数。结果表明,保元汤能显著提升血虚证小鼠的白细胞数量,修复胸腺和脾脏的损伤,给药组小鼠代谢轮廓趋近空白对照组;血清中有10种差异性代谢物与CTX致免疫低下型血虚证相关,主要涉及亚油酸代谢等三条代谢通路,推测保元汤对血虚证的治疗作用可能通过调控脂肪酸类物质实现。     

Parameter estimation for whole-body kinetic model of FDG metabolism

Based on the radioactive tracer ［¹⁸F］2-fluoro-2-deoxy-D-glucose (FDG), positron emission tomography (PET), and compartment model, the tracer kinetic study has become an important method to investigate the glucose metabolic kinetics in human body. In this work, the kinetic parameters of three-compartment and four-parameter model for the FDG metabolism in the tissues of myocardium, lung, liver, stomach, spleen, pancreas, and marrow were estimated through some dynamic FDG-PET experiments. Together with published brain and skeletal muscle parameters, a relatively complete whole-body model was presented. In the liver model, the dual blood supply from the hepatic artery and the portal vein to the liver was considered for parameter estimation, and the more accurate results were obtained using the dual-input rather than the single arterial-input. The established whole-body model provides the functional information of FDG metabolism in human body. It can be used to further investigate the glucose metabolism, and also be used for the simulation and visualization of FDG metabolic process in human body.     

基于精细碳黑模型的柴油机燃烧模拟

为更好地预测及分析柴油机污染物碳黑的产生特性,需要开发具有广泛应用价值的碳黑模型。该文以正庚烷作为燃料模拟物质,基于正庚烷氧化的气相反应机理,及描述固相碳黑颗粒形成物理、化学过程的详细动力学模型,对直喷式内燃机工作过程中的化学反应流进行了数值模拟计算。计算得到了柴油机燃烧室内多环芳烃质量、碳黑质量、体积分数随转角的变化曲线。在一定燃烧室壁面温度条件下,得到典型的多环芳烃质量、碳黑质量、碳黑体积分数均与测试水平相符,碳黑质量随转角变化曲线也与测试结果吻合较好。     

阿特拉津降解菌Enterobacter sp.的基因差异分析

筛选并分析生物降解菌Enterobacter sp.在阿特拉津作用下的差异基因。以Enterobacter sp.BIDMC 29基因组为参考,利用高通量测序技术,对阿特拉津降解菌株和对照菌株进行转录组测序分析。结果表明,共有368个基因表现出显著差异,其中上调基因231个,下调基因137个。在差异基因GO富集分析的前30个条目中,尿嘧啶分解代谢、氮利用、硝酸盐同化、硫化氢生物合成、裂解酶活性和过氧化物酶活性等相关基因表现富集。Pathway分析显示,差异基因涉及70条代谢途径,与氮代谢、氨基酸合成和代谢、ABC转运蛋白、丙酮酸代谢等过程有关。菌株通过调节基因表达来提高对阿特拉津的降解能力,为进一步解析阿特拉津的代谢机制奠定基础。     

水稻幼苗叶片应答稻瘟病侵染的差异蛋白谱分析

为了探讨水稻感病基因型种质响应稻瘟病侵染的蛋白质表达谱的变化规律和作用途径,以水稻感稻瘟病种质日本晴为材料,采用接种稻瘟病菌分生抱子悬浮液,24,48和72 h后提取叶片蛋白质,采用i TRAQ蛋白质组学技术研究稻瘟病胁迫下水稻叶片蛋白质组的变化.结果表明,稻瘟病侵染诱导了水稻幼苗叶片内涉及氧化还原平衡、防御、信号传导、糖和能量代谢、氨基酸代谢、光合作用,以及蛋白质代谢等代谢途径相关的53个蛋白质的表达量发生了改变.GO分析表明稻瘟病主要调控了植株体内细胞内平衡、代谢过程和蛋白质代谢等生物学过程.稻瘟病侵染激活了活性氧代谢、防御,以及热休克蛋白等相关的途径,而抑制了蛋白质生物合成过程.结合这些差异表达蛋白的丰度变化结合它们可能的功能,描绘了水稻应答稻瘟病侵染的蛋白质代谢网络,有助于在蛋白质水平上了解其应答过程.     

Kinetics of the hydrogen absorption and desorption processes of hydrogen storage alloys: A review

High hydrogen absorption and desorption rates are two significant index parameters for the applications of hydrogen storage tanks.The analysis of the hydrogen absorption and desorption behavior using the isothermal kinetic models is an efficient way to investigate the kinetic mechanism.Multitudinous kinetic models have been developed to describe the kinetic process.However,these kinetic models were de-duced based on some assumptions and only appropriate for specific kinetic measurement methods and rate-controlling steps(RCSs),which sometimes lead to confusion during application.The kinetic analysis procedures using these kinetic models,as well as the key kinetic parameters,are unclear for many researchers who are unfamiliar with this field.These problems will prevent the kinetic models and their analysis methods from revealing the kinetic mechanism of hydrogen storage alloys.Thus,this review mainly focuses on the summarization of kinetic models based on different kinetic measurement methods and RCSs for the chemisorption,surface penetration,diffusion of hydrogen,nucleation and growth,and chemical reaction processes.The analysis procedures of kinetic experimental data are expounded,as well as the effects of temperature,hydrogen pressure,and particle radius.The applications of the kinetic models for different hydrogen storage alloys are also introduced.     

肝脏FDG代谢模型的参数估计

利用房室模型进行肝脏[18F]氟代脱氧葡萄糖([18F]2-fluoro-2-deoxy-D-glucose,FDG)代谢的动力学研究是进行人体功能信息的建模和研究肝脏葡萄糖代谢率的重要手段。动力学研究需要得到血液中的示踪剂浓度随时间变化曲线,将其作为模型的输入,估计出肝脏FDG代谢模型的动力学参数。然而,肝脏存在肝动脉输入和肝门静脉输入。研究分别采用动脉和门静脉的双输入方式和动脉的单输入方式作为血液输入曲线,用这两个输入函数分别进行了肝脏FDG代谢的动力学研究,比较了用两种方法所得到的结果。结果显示,在人体肝脏的FDG代谢研究中,用两种输入曲线得到的结果存在明显的不同,并且用双输入曲线得到的结果更加准确。     

肝脏FDG代谢模型的参数估计

利用房室模型进行肝脏[18F]氟代脱氧葡萄糖([18F]2-fluoro-2-deoxy-D-glucose,FDG)代谢的动力学研究是进行人体功能信息的建模和研究肝脏葡萄糖代谢率的重要手段。动力学研究需要得到血液中的示踪剂浓度随时间变化曲线,将其作为模型的输入,估计出肝脏FDG代谢模型的动力学参数。然而,肝脏存在肝动脉输入和肝门静脉输入。研究分别采用动脉和门静脉的双输入方式和动脉的单输入方式作为血液输入曲线,用这两个输入函数分别进行了肝脏FDG代谢的动力学研究,比较了用两种方法所得到的结果。结果显示,在人体肝脏的FDG代谢研究中,用两种输入曲线得到的结果存在明显的不同,并且用双输入曲线得到的结果更加准确。     

Cross-talk between cellular signalling pathways suggested by phorbol-ester-induced adenylate cyclase phosphorylation

Receptor-mediated activation of both adenylate cyclase and phosphatidylinositide hydrolysis systems occurs through guanine nucleotide regulatory proteins and ultimately leads to specific activation of either cyclic AMP-dependent protein kinase A or Ca2+/phospholipid-dependent protein kinase C. Given the remarkable diversity of agents that influence cellular metabolism through these pathways and the similarities of their components, interactions between the two signalling systems could occur. In fact, stimulation of cells with 12-O-tetradecanoyl phorbol-13-acetate (TPA), a phorbol ester that activates protein kinase C, influences hormone-sensitive adenylate cyclase. In some cells TPA induces desensitization of receptor-mediated stimulation of adenylate cyclase, whereas in others, such as frog erythrocytes, phorbol ester treatment results in increased agonist-stimulated as well as basal, guanine nucleotide- and fluoride ion-stimulated adenylate cyclase activities. We show here that TPA produces phosphorylation of the catalytic unit of adenylate cyclase in frog erythrocytes. Moreover, purified protein kinase C can directly phosphorylate in vitro the catalytic unit of adenylate cyclase purified from bovine brain. These results suggest that phosphorylation of the catalytic unit of adenylate cyclase by protein kinase C may be involved in the phorbol ester-induced enhancement of adenylate cyclase activity. In addition to providing the first direct demonstration of a covalent modification of the catalytic unit of adenylate cyclase, these results provide a potential biochemical mechanism for a regulatory link between the two major transmembrane signalling systems.