2,609 research outputs found
Secondary or Specialized Metabolites, or Natural Products: A Case Study of Untargeted LC–QTOF Auto-MS/MS Analysis
No full textThe large structural diversity of specialized metabolites represents a substantial challenge in untargeted metabolomics. Modern LC–QTOF instruments can provide three- to four-digit numbers of auto-MS/MS spectra from sample sets. This case study utilizes twelve structurally closely related flavonol glycosides, characteristic specialized metabolites of plant tissues, some of them isomeric and isobaric, to illustrate the possibilities and limitations of their identification. This process requires specific software tools that perform peak picking and feature alignment after spectral deconvolution and facilitate molecular structure base searching with subsequent in silico fragmentation to obtain initial ideas about possible structures. The final assignment of a putative identification, so long as spectral databases are not complete enough, requires structure searches in a chemical reference database, such as SciFindern, in attempts to obtain additional information about specific product ions of a metabolite candidate or check its feasibility. The highlighted problems in this process not only apply to specialized metabolites in plants but to those occurring in other organisms as well. This case study is aimed at providing guidelines for all researchers who obtain data from such analyses but are interested in deeper information than just Venn diagrams of the feature distribution in their sample groups
MS-FINDER analyses
No full textFor import into MS-FINDER all files have to be located in one project folder. Retention times of flavonoids can be found in file names as exemplified: 6.78 as 6_78
GC-MS analyses in ABF Format
No full textThe ABF files can be opened by the Software MS-DIal to perform deconvolution, peak picking and alignment. I recommend version 4. Alkane standrad files for all three sampling years are provided
SIRIUS analyses
No full textAll files have to be places into one folder for import into SIRIUS. Retention times of flavonoids can be found in file names as exemplified: 6.78 as 6_78
Flavonol glycoside chemical structures
No full textStructures, CAS, and SMILES for 12 flavonol glycoside
GC-MS analysis, MS-Dial output after deconvolution peak picking and alignment
No full textYou can view any spectum in the MS-Dial output by copying it into a ms.txt file and running the R Script mass spectrum.R thereafter
The oxidative damage initiation hypothesis for meiosis
No full textThe maintenance of sexual reproduction in eukaryotes is still a major enigma in evolutionary biology. Meiosis represents the only common feature of sex in all eukaryotic kingdoms, and thus, we regard it a key issue for discussing its function. Almost all asexuality modes maintain meiosis either in a modified form or as an alternative pathway, and facultatively apomictic plants increase frequencies of sexuality relative to apomixis after abiotic stress. On the physiological level, abiotic stress causes oxidative stress. We hypothesize that repair of oxidative damage on nuclear DNA could be a major driving force in the evolution of meiosis. We present a hypothetical model for the possible redox chemistry that underlies the binding of the meiosis-specific protein Spo11 to DNA. During prophase of meiosis I, oxidized sites at the DNA molecule are being targeted by the catalytic tyrosine moieties of Spo11 protein, which acts like an antioxidant reducing the oxidized target. The oxidized tyrosine residues, tyrosyl radicals, attack the phosphodiester bonds of the DNA backbone causing DNA double strand breaks that can be repaired by various mechanisms. Polyploidy in apomictic plants could mitigate oxidative DNA damage and decrease Spo11 activation. Our hypothesis may contribute to explaining various enigmatic phenomena: first, DSB formation outnumbers crossovers and, thus, effective recombination events by far because the target of meiosis may be the removal of oxidative lesions; second, it offers an argument for why expression of sexuality is responsive to stress in many eukaryotes; and third, repair of oxidative DNA damage turns meiosis into an essential characteristic of eukaryotic reproduction
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