A systematic approach to determine the impact of elevated CO2 levels on the chemical composition of wheat (Triticum aestivum)

Two wheat genetic lines (responsive and non-responsive to elevated CO₂) grown under ambient and free-air CO₂ enrichment (FACE) conditions were compared using fuzzy chromatography mass spectrometry (FCMS) metabolite fingerprinting. A more comprehensive survey of the changes in their chemical composition was made on selected samples using ultra-high-performance liquid chromatography (UHPLC) metabolomic profiling with high resolution accurate mass/tandem mass spectrometry (HRAM/MSⁿ). Principal component analysis (PCA) of the metabolite fingerprints showed four clusters for the two genetic lines (responsive and non-responsive) and the two CO₂ levels (ambient and elevated) in score plots. Metabolite profiling of representative samples for each of the four clusters identified 25 and 16 compounds from negative and positive data, respectively, including amino acids, saccharides, phenolic acids, flavonoids, and lipids. Loading plots demonstrated that some saccharides and lipids were responsible for discriminating between not only two genetic lines but also two CO₂ levels. Analysis of free amino acids (not bound) showed a clear pattern of reduced concentration for both lines with elevated CO₂. After acid hydrolysis, the responsive line 6 (41% increase in yield) showed the same pattern observed for free amino acids, but the non-responsive line 5 (6% increase in yield) showed different trends in concentrations of amino acids with elevated CO₂.     

粒径对平菇栽培用玉米芯发酵料代谢物的影响

为了解玉米芯粒径对平菇栽培用发酵料中代谢物的影响,采用代谢组学技术分析添加不同粒径玉米芯的发酵料中微生物代谢物及其代谢通路。结果表明,添加小粒径玉米芯(D₅₀=0.5 cm)和大粒径玉米芯(D₅₀=1.5 cm)的发酵料中微生物代谢物差异显著。在正离子(POS)和负离子(NEG)模式下分别筛选得到464种和201种差异代谢物,包括芳香族化合物、氨基酸、糖及醇类、脂质、生物碱等。差异代谢物分别富集到90条(POS模式)和94条(NEG模式)代谢通路,差异显著的有2条,分别为源自鸟氨酸、赖氨酸、烟酸生物合成生物碱和组氨酸代谢。说明不同粒径玉米芯发酵料中微生物代谢物具有显著差异,为发酵料栽培平菇原料选择提供了理论依据。     

Preliminary study of patients with chronic mountain sickness by GC-TOF-MS based serum metabolomics analysis

AIM: To evaluate specific metabolomics profiles in the serum of patients with chronic mountain sickness (CMS) and to explore the potential metabolic biomarkers in the native Tibetans living on the Qinghai-Tibet Pla-teau.METHODS: A gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) approach as a metabolomics technique was used to evaluate metabolic differences. The native Tibetan CMS patients (n=10) and healthy Tibetan controls (n=10) were enrolled from YuShu in Qinghai province in this study. The serum samples were collected and analyzed by GC-TOF-MS coupled with a series of multivariate statistical analyses such as principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA).RESULTS: The intergroup differences between CMS patients and control subjects have been observed. A list of differential metabolites and several top altered metabolic pathways have been identified. The levels of fumaric acid, an intermediate in the tricarboxylic acid (TCA) cycle, and inosine were highly upregulated in the CMS patients, suggesting a greater effort to hypoxic adaptation in high elevation area. Other differential metabolites, such as methyl phosphate, 2-ketoadipate, lyxose and phytanic acid were also identified. Importantly, the differential metabolites possessed higher area under the ROC curve (AUC) values, indicating an excellent clinical ability for the prediction of CMS. Increased levels of amino acids (isoleucine, glycine, serine, L-cysteine, citrulline and trimethyllysine) were detected in CMS group, yet significantly decreased levels of sulfuric acid, oxamic acid, lyxose and glutamine were also detected in CMS group than those in control group. At the same time, the levels of ribose and glucose-1-phosphate were markedly elevated in CMS group (P<0.05).CONCLUSION: The metabolic activities are significantly altered in the serum of CMS patients. High altitude hypoxia may act on the disturbed glucose metabolism and amino acid metabolism in part of the Tibetan triggered by CMS.     

Where systems biology meets postharvest

According to the dictionary, a system is something like “a group or combination of interrelated, interdependent, or interacting elements forming a collective entity”. In postharvest, fresh harvested food crops can be considered isolated small scale systems. Postharvest research aims to understand the quality of these ‘systems’ as influenced by postharvest conditions. The phenotypic quality of horticultural produce is based on genetic traits that are expressed through a cascade of reactions subject to complex regulatory mechanisms and diverse environmental conditions. Ultimately, to fully understand postharvest phenomena, a systemic approach that links genetic and environmental responses and identifies the underlying biological networks is required. Thanks to the development of high throughput omics techniques such system-wide approaches have become a viable option to support traditional postharvest research. This review provides an overview of systems biology and how it can lead postharvest research into a new era.     

A correlation network approach to metabolic data analysis for tomato fruits

Network analysis of correlations between abundances of metabolites across tomato genotypes can help in unraveling the biological basis of organoleptic variation in tomato. We illustrate how to construct and interpret simple correlations networks using metabolic data collected on a diverse set of tomato genotypes. Various types of correlations are calculated and displayed in the form of networks. Interpretations on the basis of network analyses are compared to interpretations following principal components analysis.     

Effects of PM2.5 on metabolic pathways based on metabolomics

As one of the common air pollutants, fine particulate matter/particulate matter 2.5 (PM_2.5) is an important risk factor affecting human health. Many epidemiological studies have shown that PM_2.5 increases the risk of various diseases. However, its underlying biological mechanisms have not been well understood. Metabolomics is an emerging field that has been used to identify the metabolic pathways involved in pathogenesis by analyzing changes in metabolite levels for disease diagnosis and treatment development. Many metabolomics-based studies have shown that the pathophysiological changes caused by PM_2.5 exposure may involve disturbances in various metabolites and metabolic pathways. In this paper, a brief review of the research progress of the effects of PM_2.5 on the metabolic pathways using metabolomics is presented.     

From classical taxonomy to genome and metabolome: towards comprehensive quality standards for medicinal herb raw materials and extracts

Fundamental to herbal medicine quality is the use of 'authentic' medicinal herb species. Species, however, 'represent more or less arbitrary and subjective man-made units'. Against this background, we discuss, with illustrative examples, the importance of defining species boundaries by accommodating both the fixed (shared) diagnostic and varying (within-species) traits in medicinal herb populations. We emphasize the role of taxonomy, floristic information and genomic profiling in authenticating medicinal herb species, in addition to the need to include within species phytochemical profile variations while developing herbal extract identification protocols. We outline the application of species-specific genomic and phytochemical markers, chemoprofiling and chemometrics as additional tools to develop qualifying herbal extract references. We list the diagnostic traits available subsequent to each step during the medicinal herb extract manufacturing process and delineate limits to qualification of extract references.     

代谢组学在牧草与草坪草抗逆性中的研究进展

牧草和草坪草的生长和发育常常面临着严重的盐碱、干旱、高温等非生物胁迫的影响。代谢组学是功能基因组学和系统生物学研究的重要技术，它涉及不同物种的细胞调控过程中代谢物的识别和定量，能够在代谢水平上有效地筛选与植物产量和抗逆性等相关的重要代谢物。目前随着色谱和质谱等技术的发展，牧草和草坪草对胁迫响应的代谢组研究也取得了许多重大进步。本文总结了近5年来代谢组学在牧草与草坪草抗逆性研究中的进展，详细描述和讨论了在水分、温度、盐分等非生物胁迫下草类植物中重要响应代谢物的鉴定以及不同代谢通路的调节与变化过程，以期为牧草和草坪草抗逆性研究及认识其内在逆境适应机制提供理论基础。     

Correlation between fecal metabolites and body weight/food intake in rats after chronic immobilization stress

AIM:To explore the correlation between fecal metabolites and body weight/food intake in rats after chronic immobilization stress (CIS). METHODS:Healthy male Sprague-Dawley (SD) rats (n=48) were randomly divided into control group and CIS group. The rats in CIS group were subjected to 3 h of immobilization stress a day for 21 consecutive days, and the rats in control group were kept for 21 d without stress intervention. The behaviors in open-field test (OFT) and elevated plus-maze test (EPM test), the sucrose consumption, the serum D-xylose content, and the small bowel transit rate were detected. The fecal metabolites were determined by ¹H-nuclear magnetic resonance spectroscopy (¹H-NMR) technique, and differential metabolites in the rats of 2 groups were analyzed by multivariate statistics. The correlation between body weight/food intake and above indexes of CIS rats were observed by Pearson correlation analysis. RESULTS:Compared with the control rats, the body weight of CIS rats was increased slowly and the food intake was decreased significantly (P<0.01). In the OFT, both the total and central distance covered in CIS rats were reduced significantly than those in control group within 5 min (P<0.01). In the EPM test, the residence time in open-arms of CIS rats within 5 min was shortened dramatically than those in the control group (P<0.01). The content of serum D-xylose and the sucrose consumption of the rats after stress for 21 d were decreased markedly (P<0.05). The small bowel transit rate of CIS rats was lower than that of control rats, but no statistical difference was observed (P>0.05). Acetate, butyrate, glucose, propionate, glutamate, ribose, pimelate, lactate, alanine, valerate, total 10 kinds of differential metabolites in fecal samples were detected, and the 10 kinds of metabolites in CIS rats were higher than that of the control rats (P<0.05). Pearson correlation analysis showed that food intake of CIS rats was negatively correlated with metabolites of acetate and pimelate (P<0.05), and no correlation between body weight and above indexes was found. CONCLUSION:Under the CIS condition, there are certain correlations between food intake and metabolites of acetate and pimelate, but the mechanism still need further study.