Exploring the Arabidopsis sulfur metabolome

Sulfur plays a crucial role in protein structure and function, redox status and plant biotic stress responses. However, our understanding of sulfur metabolism is limited to identified pathways. In this study, we used a high‐resolution Fourier transform mass spectrometric approach in combination with stable isotope labeling to describe the sulfur metabolome of Arabidopsis thaliana. Databases contain roughly 300 sulfur compounds assigned to Arabidopsis. In comparative analyses, we showed that the overlap of the expected sulfur metabolome and the mass spectrometric data was surprisingly low, and we were able to assign only 37 of the 300 predicted compounds. By contrast, we identified approximately 140 sulfur metabolites that have not been assigned to the databases to date. We used our method to characterize the γ‐glutamyl transferase mutant ggt4‐1, which is involved in the vacuolar breakdown of glutathione conjugates in detoxification reactions. Although xenobiotic substrates are well known, only a few endogenous substrates have been described. Among the specifically altered sulfur‐containing masses in the ggt4‐1 mutant, we characterized one endogenous glutathione conjugate and a number of further candidates for endogenous substrates. The small percentage of predicted compounds and the high proportion of unassigned sulfur compounds identified in this study emphasize the need to re‐evaluate our understanding of the sulfur metabolome.     

EPR study of hydrated testosterone monoclinic and orthorhombic single crystals gamma-irradiated at 295 K

The molecular structure of free radicals formed in gamma-irradiated monoclinic and orthorhombic single crystals of hydrated testosterone were investigated by EPR spectroscopy. Two different types of radical were observed. In the monoclinic form, the radical arises by the loss of a hydrogen atom from the carbon atom C(2), whereas, in the orthorhombic form, it arises by addition of a hydrogen atom to the oxygen atom O(3). The hyperfine spectrum of the radical formed in the monoclinic single crystal originates from the interaction of the unpaired electron with one alpha-proton in position 2 and two non equivalent beta-protons in position 1. In the orthorhombic single crystal, we observed interaction of the unpaired electron, which is delocalized on the carbons C(3), C(4) and C(5) with one alpha-proton in position 4 and with four nonequivalent beta-protons connected with the carbon atoms C(2) and C(6). The hyperfine tensors of the coupling and the g-tensor of the radicals are given.     

Yeast tRNAPhe conformation wheels: a novel probe of the monoclinic and orthorhombic models.

A series of conformation wheels is constructed from the recently refined X-ray crystallographic data of monoclinic and orthorhombic yeast tRNAPhe. These circular plots relate the primary chemical structure (i.e., base sequence) directly to the secondary and tertiary structure of the molecule. The circular sequence of backbone torsion angles displays a unique pattern that is useful both in distinguishing the ordered and disordered regions of the molecule and in comparing the three sets of experimental data. Composite conformation wheels describe the fluctuations in the "fixed" parameters (phi', phi, chi) and independent conformation wheels reveal the changes in the "variable" parameters (omega', omega, psi, psi') of the three different yeast tRNAPhe models. Additional plots of base-stacking parameters help to visualize the intimate interrelationship between chemical sequence and three-dimensional folding of yeast tRNAPhe. The composite data illustrate several conformational schemes that position the bases of adjacent nucleosides in a parallel stacked array and reveal an even larger number of conformations that introduce bends or turns in the polynucleotide chain.     

Effects of dietary macronutrients on the hepatic transcriptome and serum metabolome in mice

Dietary macronutrient composition influences both hepatic function and aging. Previous work suggested that longevity and hepatic gene expression levels were highly responsive to dietary protein, but almost unaffected by other macronutrients. In contrast, we found expression of 4005, 4232, and 4292 genes in the livers of mice were significantly associated with changes in dietary protein (5%–30%), fat (20%–60%), and carbohydrate (10%–75%), respectively. More genes in aging‐related pathways (notably mTOR, IGF‐1, and NF‐kappaB) had significant correlations with dietary fat intake than protein and carbohydrate intake, and the pattern of gene expression changes in relation to dietary fat intake was in the opposite direction to the effect of graded levels of caloric restriction consistent with dietary fat having a negative impact on aging. We found 732, 808, and 995 serum metabolites were significantly correlated with dietary protein (5%–30%), fat (8.3%–80%), and carbohydrate (10%–80%) contents, respectively. Metabolomics pathway analysis revealed sphingosine‐1‐phosphate signaling was the significantly affected pathway by dietary fat content which has also been identified as significant changed metabolic pathway in the previous caloric restriction study. Our results suggest dietary fat has major impact on aging‐related gene and metabolic pathways compared with other macronutrients.     

Modelling of processes in nerve fibres at the interface of physiology and mathematics

Biomechanics and Modeling in Mechanobiology - The in silico simulations are widely used in contemporary systems biology including the analysis of nerve pulse propagation. As known from numerous...     

Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model

Background  

Modelling of time series data should not be an approximation of input data profiles, but rather be able to detect and evaluate dynamical changes in the time series data. Objective criteria that can be used to evaluate dynamical changes in data are therefore important to filter experimental noise and to enable extraction of unexpected, biologically important information.     

代谢组与转录组联合解析赤皮青冈叶片黄化变异机制

为揭示赤皮青冈叶色黄化变异机制,该研究以赤皮青冈叶色变异植株和正常植株的叶片为试验材料,采用超高效液相色谱串联质谱法和高通量RNA测序技术分别进行代谢组和转录组分析。结果表明:(1)代谢组在正离子(POS)、负离子(NEG)模式下分别检测出正常植株和突变体之间存在257个和357个显著差异代谢物(SCMs),其中槲皮素、白矢车菊素、杨梅素等多种黄酮类化合物及其糖苷衍生物(吡喃酮啡肽A、异鼠李素3-葡糖苷酸等)在突变体中显著上调,而叶绿素a、叶绿素b、类胡萝卜素等色素含量则显著下降。(2)转录组测序检测出4 146个差异表达基因(DEGs),其中1 711个基因上调表达,2 435个基因下调表达。(3)KEGG富集分析表明,SCMs和DEGs显著富集到光合作用、卟啉与叶绿素代谢、类黄酮生物合成等途径。综上表明,突变体叶色黄化可能是受到叶绿素合成受阻、叶绿体发育异常及黄酮物质合成增加等因素的综合影响。此外,MYB和bHLH家族基因在突变体中显著上调,证实该两类转录因子参与调控类黄酮生物合成。该研究结果为植物黄化突变的分子机制研究提供了新的见解,也为叶色功能基因挖掘与园林植物育种工作提供了参考。     

基于代谢组和转录组的白蜡虫吊糖成分及其作用分析

【目的】白蜡虫Ericerus pela Chavannes在育卵期会大量分泌吊糖(蜜露),前期研究发现吊糖容易受到真菌的侵染,但是白蜡虫吊糖的生物学意义并不清楚。本研究旨在了解白蜡虫吊糖的成分以及该时期雌成虫基因表达特点,为更深入的了解白蜡虫分泌吊糖对于白蜡虫发育的意义奠定基础。【方法】对吊糖分泌期的白蜡虫雌虫进行转录组测序分析,对吊糖组分进行代谢组学分析,并对转录组与代谢组进行联合分析。【结果】在白蜡虫吊糖组分中,麦芽糖醇含量最高,其次为半乳糖醇,之后为海藻糖、水苏糖等其他种类糖物质,此外,还含有多种少量氨基酸、脂肪、维生素等代谢物质或次生代谢物质;关联分析表明,代谢途径(Metabolic pathways)、碳代谢(Carbon metabolism)和氨基酸合成(Biosynthesis of amino acids)占主要部分;与N-聚糖生物合成(Various types of N-glycan biosynthesis)相关通路的基因家族在白蜡虫发生了收缩;与代谢产物关联的基因Q96JB1家族也发生了收缩,该基因与吊糖中的L-谷氨酸、乳清酸盐以及柠檬酸盐相关。【结论】白蜡虫吊糖主要成分不利于天敌寄生或者与其它昆虫形成互利共生,一些与吊糖成分相关的基因家族在白蜡虫中发生了收缩,说明白蜡虫吊糖可能是其分泌的不利的或多余的代谢物。