A selective metabolite array for the detection of phosphometabolites

Immobilised metal ion affinity (IMA) has been traditionally used specifically for the separation of phosphorylated proteins and nucleic acids, in proteomics and genomics, respectively. This report describes the novel application of IMA in metabolomics for the development of metabolite arrays to detect phosphometabolites using a plasma polymer-modified surface. Immobilisation of gallium, zirconium, cobalt, copper, zinc, nickel, iron, and chromium to acrylic acid plasma polymer followed by subsequent exposure to metabolites (phospho- and non-phosphometabolites) was investigated. Results analysed using ToF-SIMS suggests that gallium and zirconium exhibit higher phosphometabolite affinity and specificity compared to other metals, and can be used to develop metabolite arrays for the detection of phosphometabolites.     

Parameter selection for peak alignment in chromatographic sample profiling: objective quality indicators and use of control samples

In chromatographic profiling applications, peak alignment is often essential as most chromatographic systems exhibit small peak shifts over time. When using currently available alignment algorithms, there are several parameters that determine the outcome of the alignment process. Selecting the optimum set of parameters, however, is not straightforward, and the quality of an alignment result is at least partly determined by subjective decisions. Here, we demonstrate a new strategy to objectively determine the quality of an alignment result. This strategy makes use of a set of control samples that are analysed both spiked and non-spiked. With this set, not only the system and the method can be checked but also the quality of the peak alignment can be evaluated. The developed strategy was tested on a representative metabolomics data set using three software packages, namely Markerlynx™, MZmine and MetAlign. The results indicate that the method was able to assess and define the quality of an alignment process without any subjective interference of the analyst, making the method a valuable contribution to the data handling process of chromatography-based metabolomics data.     

Hyperpolarized 13C NMR Spectroscopy of Urine Samples at Natural Abundance by Quantitative Dissolution Dynamic Nuclear Polarization

Hyperpolarized nuclear magnetic resonance (NMR) offers an ensemble of methods that remarkably address the sensitivity issues of conventional NMR. Dissolution Dynamic Nuclear Polarization (d-DNP) provides a unique and general way to detect ¹³C NMR signals with a sensitivity enhanced by several orders of magnitude. The expanding application scope of d-DNP now encompasses the analysis of complex mixtures at natural ¹³C abundance. However, the application of d-DNP in this area has been limited to metabolite extracts. Here, we report the first d-DNP-enhanced ¹³C NMR analysis of a biofluid -urine- at natural abundance, offering unprecedented resolution and sensitivity for this challenging type of sample. We also show that accurate quantitative information on multiple targeted metabolites can be retrieved through a standard addition procedure.     

Integration of metabolomics and network pharmacology to validate the mechanism of Schisandra chinensis（Turcz.）Baill - Acorus tatarinowii Schott ameliorating the Alzheimer's disease by regulating the aromatase activity to affect local estrogen in brain of AD model rats

Alzheimer's disease (AD) is a latent and progressive neurodegenerative disease. Schisandra chinensis（Turcz.）Baill - Acorus tatarinowii Schott (Sc-At) are effective in treating neurological disorders.Purpose of this study is to explore the mechanism of Sc-At in AD treatment. First, untargeted ultra-performance liquid chromatography quadrupole-time of flight/mass spectrometer (UPLC-QTOF/MS) metabolomics was employed to detect the rat brain metabolism. Then, network pharmacology was used to determine the potential anti-AD targets. Bioinformatics, and molecular docking were conducted for further analysis. A MetScape study examined the association between differential metabolites and potential targets. Finally, the targeted ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) metabolomics and the potential protein activity studies were carried out to elucidate the mechanisms. The results showed that Sc-At improved the neuronal cell alignment disorder in hippocampal CA1 region of AD rats. In brain metabolomics, 30 differential metabolites were screened in the study model versus blank group. The network pharmacology analyzed 54 targets of Sc-At anti-AD where, 14 were correlated with amyloid β-protein (Aβ). Aromatase was selected as an important hub target having the best binding power in molecular docking simulation predictions and also correlated with Aβ. Further tests showed that the brain aromatase activity, and the downstream product 17β-Estradiol levels were elevated in AD rats treated with Sc-At. This work may provide new perspectives for the pharmacological effects and the action mechanisms of natural compounds extracts in treating AD progression.     

Chemical Modification of a Bacterial Siderophore by a Competitor in Dual-Species Biofilms

Chemical communication between competing bacteria in multi-species environments often enables both species to adapt and survive, and perhaps even thrive. P. aeruginosa and S. aureus are two bacterial pathogens found in natural biofilms, especially in the lungs of cystic fibrosis (CF) patients, where recent studies showed that there is often cooperation between the two species, leading to increased disease severity and antibiotic resistance. However, the mechanisms behind this cooperation are poorly understood. In this study, we analyzed co-cultured biofilms in various settings, and we applied untargeted mass spectrometry-based metabolomics analyses, combined with synthetic validation of candidate compounds. We unexpectedly discovered that S. aureus can convert pyochelin into pyochelin methyl ester, an analogue of pyochelin with reduced affinity for iron (III). This conversion allows S. aureus to coexist more readily with P. aeruginosa and unveils a mechanism underlying the formation of robust dual-species biofilms.