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。     

Impact of proliferation strategies on food web viability in a model with closed nutrient cycle

A food web model with a closed nutrient cycle is presented and analyzed via Monte Carlo simulations. The model consists of three trophic levels, each of which is populated by animals of one distinct species. While the species at the intermediate level feeds on the basal species, and is eaten by the predators living at the highest level, the basal species itself uses the detritus of animals from higher levels as the food resource. The individual organisms remain localized, but the species can invade new lattice areas via proliferation. The impact of different proliferation strategies on the viability of the system is investigated. From the phase diagrams generated in the simulations it follows that in general a strategy with the intermediate level species searching for food is the best for the survival of the system. The results indicate that both the intermediate and top level species play a critical role in maintaining the structure of the system.     

Exhaled breath condensate: Determination of non-volatile compounds and their potential for clinical diagnosis and monitoring. A review

Exhaled breath condensate is a promising, non-invasive, diagnostic sample obtained by condensation of exhaled breath. Starting from a historical perspective of early attempts of breath testing towards the contemporary state-of-the-art breath analysis, this review article focuses mainly on the progress in determination of non-volatile compounds in exhaled breath condensate. The mechanisms by which the aerosols/droplets of non-volatile compounds are formed in the airways are discussed with methodological consequences for sampling. Dilution of respiratory droplets is a major problem for correct clinical interpretation of the measured data and there is an urgent need for standardization of EBC. This applies also for collection instrumentation and therefore various commercial and in-house built devices are described and compared with regard to their design, function and collection parameters. The analytical techniques and methods for determination of non-volatile compounds as potential markers of oxidative stress and lung inflammation are scrutinized with an emphasis on method suitability, sensitivity and appropriateness. The relevance of clinical findings for each group of possible non-volatile markers of selected pulmonary diseases and methodological recommendations with emphasis on interdisciplinary collaboration that is essential for future development into a fully validated clinical diagnostic tool are given.     

Targeted metabolomic analysis of 33 amino acids and biogenic amines in human urine by ion‐pairing HPLC‐MS/MS: Biomarkers for tacrolimus nephrotoxicity after renal transplantation

Calcineurin inhibitor nephrotoxicity, especially for the widely used tacrolimus, has become a major concern in post‐transplant immunosuppression. Multiparametric amino acid metabolomics is useful for biomarker identification of tacrolimus nephrotoxicity, for which specific quantitative methods are highlighted as a premise. This article presents a targeted metabolomic assay to quantify 33 amino acids and biogenic amines in human urine by high‐performance liquid chromatography coupled with tandem mass spectrometry. Chromatographic separation was carried out on an Agilent Zorbax SB‐C₁₈ column (3.0 × 150 mm, 5 μm) with addition of an ion‐pairing agent in the mobile phase, and MS/MS detection was achieved in both the positive and negative multiple reaction monitoring modes. Good correlation coefficients (r² > 0.98) were obtained for most analytes. Intra‐ and inter‐day precision, stability, carryover and incurred sample reanalysis met with the acceptance criteria of the guidance of the US Food and Drug Administration. Analysis on urine from healthy volunteers and renal transplantation patients with tacrolimus nephrotoxicity confirmed symmetric dimethylarginine and serine as biomarkers for kidney injury, with AUC values of 0.95 and 0.81 in receiver operating characteristic analysis, respectively. Additionally, symmetric dimethylarginine exhibited a tight correlation with serum creatinine, and was therefore indicative of renal function. The targeted metabolomic assay was time and cost prohibitive for amino acid analysis in human urine, facilitating the biomarker identification of tacrolimus nephrotoxicity.     

光电化学技术应用于抗氧化分析的研究进展

在新陈代谢过程中, 机体会产生大量以自由基为主要形式的氧化活性物质, 而抗氧化剂可以通过电子转移的方式捕获并中和自由基, 从而有效抵御自由基引起的细胞损害, 以保障和维护人体健康. 食品作为人体外源性抗氧化剂的重要来源可以有效补充因体内代谢及体液排出而损失的抗氧化物质, 因此对食品中抗氧化物质消除自由基的能力即抗氧化能力的测定和评价具有重要意义. 光电化学技术作为一种简单快捷、 低成本、 低背景且高灵敏度的测定方法, 能够有效克服光学法、 色谱法和电化学法等传统测试手段在抗氧化容量分析中的不足. 本文综述了基于半导体及其复合材料的光电化学传感平台的构建及食品体系抗氧化容量分析的研究进展, 评论了多种检测体系的特点并对其研究前景进行了展望.     

Full physicochemical characterization of malic acid: Emphasis in the potential as food ingredient and application in pectin gels

Malic acid, a carboxylic acid most found in fruits, is a smooth taste substance used as flavoring and preservative agent in foods, although not as used as citric acid. There are no studies focusing in quantitative results or investigations on its physicochemical properties, useful to the food industry, or even the confirmation of its calcium chelating, buffer texturizer and antioxidant alleged properties. Thus, the aim of this work was the assessment of most physicochemical properties of malic acid, solid and in solution, that could be useful to the food industry understand its real potential. The following analyses were carried out: melting point; structure (NMR, XRD, FTIR and SEM/EDS); TGA/DTG; solubility, hygroscopicity; antioxidant activity, iron chelating and antibacterial activities and stability of pectin gels. The melting temperature found was 129.71 °C. TGA/DTG exhibited first loss of mass around 140 °C. In the temperature range of 10 to 55 °C, it exhibited a high solubility in water, from 48.12 to 61.49 (100w), respectively. The tested bacteria, related to food spoilage, were inhibited by DL-malic acid 10% or higher. Chelating and antioxidant activities showed expressive results even in 1% solution. Pectin gels with malic acid had stronger structure and less syneresis than citric acid gels. In addition, calcium chelating, buffer texturizer and antioxidant properties were confirmed. Thus, malic acid has potential to be applied in a wide variety of food products as fortified beverages, frozen and refrigerated items, oils, pectin gels, hard and soft candies, and biofilms, due to all the characteristics quantified.     

The impact of blood on liver metabolite profiling – a combined metabolomic and proteomic approach

Metabolomics has entered the well‐established omic sciences as it is an indispensable information resource to achieve a global picture of biological systems. The aim of the present study was to estimate the influence of blood removal from mice liver as part of sample preparation for metabolomic and proteomic studies. For this purpose, perfused mice liver tissue (i.e. with blood removed) and unperfused mice liver tissue (i.e. containing blood) were compared by two‐dimensional gas chromatography time of flight mass spectrometry (GC × GC‐TOFMS) for the metabolomic part, and by liquid chromatography tandem mass spectrometry (LC‐MS/MS) for the proteomic part. Our data showed significant differences between the unperfused and perfused liver tissue samples. Furthermore, we also observed an overlap of blood and tissue metabolite profiles in our data, suggesting that the perfusion of liver tissue prior to analysis is beneficial for an accurate metabolic profile of this organ. Copyright © 2013 John Wiley & Sons, Ltd.     

Phytochemical Differentiation of Saffron (Crocus sativus L.) by High Resolution Mass Spectrometry Metabolomic Studies

The metabolite profiling of saffron (Crocus sativus L.) from several countries was measured by using ultra-performance liquid chromatography combined with high resolution mass spectrometry (UPLC-HR MS). Multivariate statistical analysis was employed to distinguish among the several samples of C. sativus L. from Greece, Italy, Morocco, Iran, India, Afghanistan and Kashmir. The results of this study showed that the phytochemical content in the samples of C. sativus L. were obviously diverse in the different countries of origin. The metabolomics approach was deemed to be the most suitable in order to evaluate the enormous array of putative metabolites among the saffron samples studied, and was able to provide a comparative phytochemical screening of these samples. Several markers have been identified that aided the differentiation of a group from its counterparts. This can be important for the selection of the appropriate saffron sample, in view of its health-promoting effect which occurs through the modulation of various biological and physiological processes.     

The use of untargeted and widely targeted metabolomics to distinguish between asphyxia and sudden cardiac death as the cause of death in rats: A preliminary study

It is important to determine the cause of death in the case of asphyxia. However, it is difficult to conclude death by asphyxia, especially when the deceased has underlying heart disease, because there are often no specific and representative corpse signs for both asphyxia and sudden cardiac death (SCD). The aim of the present work was to investigate the potential of metabolomics to discriminate asphyxia from SCD as the cause of death. A total of thirty male Sprague–Dawley rats were used to construct models of asphyxia, SCD (interfering cause of death), and cervical dislocation (control). Untargeted and widely targeted metabolomics approaches were used to obtain rat pulmonary metabolic profiles in this study. First, the metabolic alterations resulting from asphyxia were explored. There were significant changes found in carbohydrate metabolism, the endocrine system, and the sensory system. Second, we screened potential biomarkers and built classification models to determine the cause of death. Moreover, some biomarkers remained differentiated at 24 h and 48 h postmortem, so the cause of death could still be determined after death. This study showed the application potential of metabolomics to investigate the metabolic changes occurring in the process of death, as well as to determine the cause of death on the basis of metabolic differences even after death.     

Metabolomics revealed the toxicity of cationic liposomes in HepG2 cells using UHPLC‐Q‐TOF/MS and multivariate data analysis

Cationic liposomes (CLs) are novel nonviral vectors widely used for delivering drugs or genes. However, applications of CLs are largely hampered by their cytotoxicity, partly because the potential mechanism underlying the cytotoxicity of CLs remains unclear. The aim of the present study was to explore the underlying mechanism of cytotoxicity induced by CLs on HepG2 cells. Differential metabolites were identified and quantified using ultra‐liquid chromatography quadrupole time‐of‐flight mass spectrometry (UHPLC‐Q‐TOF/MS). The toxicity of CLs on HepG2 cells was evaluated by multivariate data analysis and statistics. Additionally, CCK‐8 assay, heatmap, pathway and co‐expression network were carried out to explore the relations between the metabolites and the pathways. The results showed a dose‐dependent toxic effect of CLs on HepG2 cells, with an IC₅₀ value of 119.9 μg/mL. Multivariate statistical analysis identified 42 potential metabolites between CLs exposure and control groups. Pathway analysis showed significant changes in pathways involving amino acid metabolism, energy metabolism, lipid metabolism and oxidative stress in the CLs exposure group vs the control group. Metabolites related to the above‐mentioned pathways included phenylalanine, methionine, creatine, oxalacetic acid, glutathione, oxidized glutathione, choline phosphate and several unsaturated fatty acids, indicating that cells were disturbed in amino acid metabolism, energy and lipid supply when CLs exposure‐induced injury occurred. It is concluded that CLs may induce cytotoxicity by enhancing reactive oxygen species in vitro , affect the normal process of energy metabolism, disturb several vital signaling pathways and finally induce cell death.