Lipoprotein
profiling of human blood by 1H nuclear magnetic
resonance (NMR) spectroscopy is a rapid and promising approach to
monitor health and disease states in medicine and nutrition. However,
lack of standardization of measurement protocols has prevented the
use of NMR-based lipoprotein profiling in metastudies. In this study,
a standardized NMR measurement protocol was applied in a ring test
performed across three different laboratories in Europe on plasma
and serum samples from 28 individuals. Data was evaluated in terms
of (i) spectral differences, (ii) differences in LPD predictions obtained
using an existing prediction model, and (iii) agreement of predictions
with cholesterol concentrations in high- and low-density lipoproteins
(HDL and LDL) particles measured by standardized clinical assays.
ANOVA-simultaneous component analysis (ASCA) of the ring test spectral
ensemble that contains methylene and methyl peaks (1.4–0.6
ppm) showed that 97.99% of the variance in the data is related to
subject, 1.62% to sample type (serum or plasma), and 0.39% to laboratory.
This interlaboratory variation is in fact smaller than the maximum
acceptable intralaboratory variation on quality control samples. It
is also shown that the reproducibility between laboratories is good
enough for the LPD predictions to be exchangeable when the standardized
NMR measurement protocol is followed. With the successful implementation
of this protocol, which results in reproducible prediction of lipoprotein
distributions across laboratories, a step is taken toward bringing
NMR more into scope of prognostic and diagnostic biomarkers, reducing
the need for less efficient methods such as ultracentrifugation or
high-performance liquid chromatography (HPLC).
Lactic acid bacteria with antifungal properties are applied for biopreservation of food. In order to further our understanding of their antifungal mechanism, there is an ongoing search for bioactive molecules. With a focus on the metabolites formed, bioassay-guided fractionation and comprehensive screening have identified compounds as antifungal. Although these are active, the compounds have been found in concentrations that are too low to account for the observed antifungal effect. It has been hypothesized that the formation of metabolites and consumption of nutrients during bacterial fermentations form the basis for the antifungal effect, i.e., the composition of the exometabolome. To build a more comprehensive view of the chemical changes induced by bacterial fermentation and the effects on mold growth, a strategy for correlating the exometabolomic profiles with mold growth was applied. The antifungal properties were assessed by measuring mold growth of two Penicillium strains on cell-free ferments of three strains of Lactobacillus paracasei pre-fermented in a chemically defined medium. Exometabolomic profiling was performed by reversed-phase liquid chromatography in combination with mass spectrometry in electrospray positive and negative modes. By multivariate data analysis, the three strains of Lb. paracasei were readily distinguished by the relative difference of their exometabolomes. The relative differences correlated with the relative growth of the two Penicillium strains. Metabolic footprinting proved to be a supplement to bioassay-guided fractionation for investigation of antifungal properties of bacterial ferments. Additionally, three previously identified and three novel antifungal metabolites from Lb. paracasei and their potential precursors were detected and assigned using the strategy.
Difficulty in obtaining
bone
tissue is an obstacle to studying epigenetics to understand gene–environment interactions, and their role in disease pathogenesis. Blood is an obvious alternative and in this proof of principle study, our aim was to systematically investigate whether blood is a viable surrogate for bone. We measured epigenome-wide DNA methylation at 850 K CpG sites in matched trabecular bone and peripheral blood collected from the same patients at the same time-point (n = 12 women; 66–85y), to investigate the between-tissue correspondence. What constituted a CpG site with corresponding methylation in both tissues was stringently defined. Only sites highly correlated (r
2
> 0.74; FDR
q
-value <0.05) and at least 80% similarity in methylation level (Δβ <0.2) between paired samples were retained. In total, 28,549 CpG sites were similarly methylated in bone and blood. Between 33% and 49% of loci associated with bone phenotypes through GWAS were represented among these sites, and major pathways relevant to bone regulation were enriched. The results from this study indicate that blood can mirror the bone methylome and capture sites related to bone regulation. This study shows that in principal, peripheral blood is a feasible surrogate for bone tissue in DNA methylation investigations. As the first step, this will provide a platform for future studies in bone epigenetics, and possibly for larger-scale epidemiological studies.
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