A graph-theoretic approach to modeling metabolic pathways

Summary The metabolic pathways of medazepam, oxazepam, and diazepam were modeled using graph-theoretic transforms which are incorporable into computer-assisted metabolic analysis programs. The information, represented in the form of a graph-theoretic transform kit, which was obtained from these pathways was then used to predict the metabolites of other benzodiazepine compounds. The transform kits gave statistically significant predictions with respect to a statistical method for evaluating the performance of the transform kits.     

Taura 综合征病毒主要结构蛋白的表达与纯化

根据Taura综合征病毒(TSV)基因组,设计特异性引物,从感染病毒组织中提取组织总RNA后扩增,分别将3个主要结构蛋白基因VP1、VP2和VP3克隆到pGEM TEasyVector.与表达载体连接后,导入大肠杆菌中诱导表达,并纯化目的蛋白.诱导表达的融合蛋白分子量分别为54.2×103、43×103和57.1×103,在变性条件下过柱纯化VP1和VP2,一次可以纯化10mg以上纯度较高的蛋白.     

The role of TLC in the screening of inherited metabolic diseases

Summary Thin-layer chromatography (TLC) is a rapid, reliable and inexpensive screening technique for diagnosis of inherited metabolic diseases (IMD). Our screening program encompasses five main situations where the use of TLC is considered to be vindicated: (i) analysis of amino acids; (ii) screening for sugar defects; (iii) detection of pathological oligosaccharidurias; (iv) screening for organic acid disorders; and (v) detection of abnormalities in tryptophan metabolism. Examples are presented of chromatograms obtained from pathological samples. Presented at the 21^st ISC held in Stuttgart, Germany, 15^th–20^th September, 1996     

湿热证动物模型微量元素、维生素E变化及清香散的调节作用

采用多因素造模方法复制成湿热证动物模型，观察了动物模型微量元素Zn、Cu、Fe、Se和维生素E代谢水平的变化。结果显示，模型动物血清Zn下降（P＜0．05），Cu升高（P＜0．05或P＜0．01），Fe变化不大（P＞0．05），血Se水平下降（P＜0．05），血浆维生素E含量减少（P＜0．01）。经清热祛湿的经验方清香散治疗后，治疗I组动物血清Zn、血Se、血浆维生素E明显升高（P＜0．05），血清Cu下降（P＜0．05）；治疗Ⅱ组血浆血清Cu有变化（P＜0．05）外，其余变化不大。     

Interpretation of the Metabolic Enthalpy Change, ΔHmet,Calculated for Microbial Growth Reactions in Soils

The microcalorimetric method was used to calculate the metabolic enthalpy change per mol of glucose degraded by soil microorganisms, ΔH _met. This parameter has been calculated by microcalorimetry for many organic, inorganic and biochemical reactions, but there is only some information about its quantification for microbial growth reactions in soils. Values of ΔH _met were calculated for different soil samples collected in Galicia (Spain) and Campinas (Săo Paolo, Brazil). Exponential microbial growth was stimulated in all soil samples by the addition of glucose and power-time curves were recorded. Results showed changes in the values of ΔH _met calculated for all the soil samples, suggesting a dependence of this value with the microbial growth rate constant, with the percentage of growth, with the initial number of microorganisms of soil samples, with the quantity of glucose added and with the strain of bacteria growing in soil. The interpretation of variations of ΔH _met provides important qualitative and quantitative information. It reports data that allow to interpret from a qualitative point of view, the increase in biomass as a consequence of the degradation of the organic matter in soil, to understand changes in the percentages of soil organic matter and to know if the microbial population growing in differential soil samples is homogeneous. Therefore, to report that value would be very important in ecological studies, but beforehand, it is necessary to solve some problems that can appear in the experiments done to make the quantification . This revised version was published online in August 2006 with corrections to the Cover Date.     

A molecular docking model of SARS-CoV S1 protein in complex with its receptor, human ACE2

The exact residues within severe acute respiratory syndrome coronavirus (SARS-CoV) S1 protein and its receptor, human ACE2, involved in their interaction still remain largely undetermined. Identification of exact amino acid residues that are crucial for the interaction of S1 with ACE2 could provide working hypotheses for experimental studies and might be helpful for the development of antiviral inhibitor. In this paper, a molecular docking model of SARS-CoV S1 protein in complex with human ACE2 was constructed. The interacting residue pairs within this complex model and their contact types were also identified. Our model, supported by significant biochemical evidence, suggested receptor-binding residues were concentrated in two segments of S1 protein. In contrast, the interfacial residues in ACE2, though close to each other in tertiary structure, were found to be widely scattered in the primary sequence. In particular, the S1 residue ARG453 and ACE2 residue LYS341 might be the key residues in the complex formation.     

Biochemical reaction engineering for redox reactions

Redox reactions are still a challenge for biochemical engineers. A personal view for the development of this field is given. Cofactor regeneration was an obstacle for quite some time. The first technical breakthrough was achieved with the system formate/formate dehydrogenase for the regeneration of NADH2. In cases where the same enzyme could be used for chiral reduction as well as for cofactor regeneration, isopropanol as a hydrogen source proved to be beneficial. The coproduct (acetone) can be removed by pervaporation. Whole-cell reductions (often yeast reductions) can also be used. By proper biochemical reaction engineering, it is possible to apply these systems in a continuous way. By cloning a formate dehydrogenase and an oxidoreductase "designer bug" can be obtained where formate is used instead of glucose as the hydrogen source. Complex sequences of redox reactions can be established by pathway engineering with a focus on gene overexpression or with a focus on establishing non-natural pathways. The success of pathway engineering can be controlled by measuring cytosolic metabolite concentrations. The optimal exploitation of such systems calls for the integrated cooperation of classical and molecular biochemical engineering.     

Genomic variation and point mutations analysis of Indian COVID-19 patient samples submitted in GISAID database

Corona virus disease 2019 (COVID-19) endemic has havoc on the world; the causative virus of the pandemic is SARS CoV-2. Pharmaceutical companies and academic institutes are in continuous efforts to identify anti-viral therapy or vaccines, but the most significant challenge faced is the highly evolving genome of SARS CoV-2, which is imparting evolutionary selective benefits to the virus. To understand the viral mutations, we have retrieved nine hundred and thirty-four samples from different states of India via the GISAID database and analyzed the frequency of all types of point mutation in all structural, non-structural proteins, and accessory factors of SARS CoV-2. Spike glycol protein, nsp3, nsp6, nsp12, N and NS3 were the most evolving proteins. High frequency point mutations were Q496P (nsp2), A380V (nsp4), A994D (nsp3), L37F (nsp6), P323L & A97V (nsp12), Q57H (ns3), D614G (S), P13L (N), R203K (N), G204R (N) and S194L (N).     

治疗小儿厌食症中药强壮灵冲剂微量元素测定及其与疗效关系探讨

已证明小儿厌食症除与缺乏微量元素锌关系密切外,还与其他多种微量元素和宏量元素的缺乏或低下也有关。本院以自行研制的中药强壮灵冲剂治疗小儿厌食症疗效显著。其于浸膏粉经２０余种微量元素测定表明含有锌、铁、钴、铜、镍、锰、铬、锗、锶、铝、钡、硒、硅、钛等多种人体必需且品种齐全,含量适度的微量元素。上述元素又恰是患儿体内所缺乏和低下的品种,无疑对患儿全面适度的补充大有裨益．中药强壮灵与西药硫酸锌临床对比研究表明,无论比发锌回升数值以及从厌食等全面疗效统计,中药组均明显优于西药组,并且发现疗效与药物的补锌量不成正相关。说明中药的调理脾胃功能及综合整体治疗作用是其突出优点,值得推广．     

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。