Advanced Statistical Methods in Biometric Research.

Root systems of most land plants form arbuscular mycorrhizal (AM) symbioses in the field, and these contribute to nutrient uptake. AM roots have two pathways for nutrient absorption, directly through the root epidermis and root hairs and via AM fungal hyphae into root cortical cells, where arbuscules or hyphal coils provide symbiotic interfaces. New physiological and molecular evidence shows that for phosphorus the mycorrhizal pathway (MP) is operational regardless of plant growth responses (positive or negative). Amounts delivered cannot be determined from plant nutrient contents because when responses are negative the contribution of the direct pathway (DP) is reduced. Nitrogen (N) is also delivered to roots via an MP, but the contribution to total N requirement and the costs to the plant are not clear. The functional interplay between activities of the DP and MP has important implications for consideration of AM symbioses in ecological, agronomic, and evolutionary contexts.

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Roles of Arbuscular Mycorrhizas in Plant Nutrition and Growth: New Paradigms from Cellular to Ecosystem Scales

Urine has long been a “favored” biofluid among metabolomics researchers. It is sterile, easy-to-obtain in large volumes, largely free from interfering proteins or lipids and chemically complex. However, this chemical complexity has also made urine a particularly difficult substrate to fully understand. As a biological waste material, urine typically contains metabolic breakdown products from a wide range of foods, drinks, drugs, environmental contaminants, endogenous waste metabolites and bacterial by-products. Many of these compounds are poorly characterized and poorly understood. In an effort to improve our understanding of this biofluid we have undertaken a comprehensive, quantitative, metabolome-wide characterization of human urine. This involved both computer-aided literature mining and comprehensive, quantitative experimental assessment/validation. The experimental portion employed NMR spectroscopy, gas chromatography mass spectrometry (GC-MS), direct flow injection mass spectrometry (DFI/LC-MS/MS), inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography (HPLC) experiments performed on multiple human urine samples. This multi-platform metabolomic analysis allowed us to identify 445 and quantify 378 unique urine metabolites or metabolite species. The different analytical platforms were able to identify (quantify) a total of: 209 (209) by NMR, 179 (85) by GC-MS, 127 (127) by DFI/LC-MS/MS, 40 (40) by ICP-MS and 10 (10) by HPLC. Our use of multiple metabolomics platforms and technologies allowed us to identify several previously unknown urine metabolites and to substantially enhance the level of metabolome coverage. It also allowed us to critically assess the relative strengths and weaknesses of different platforms or technologies. The literature review led to the identification and annotation of another 2206 urinary compounds and was used to help guide the subsequent experimental studies. An online database containing the complete set of 2651 confirmed human urine metabolite species, their structures (3079 in total), concentrations, related literature references and links to their known disease associations are freely available at http://www.urinemetabolome.ca.

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The Human Urine Metabolome

Plant molecular stress responses face climate change.

icoshift: A versatile tool for the rapid alignment of 1D NMR spectra

Quantification of the degree of blockiness in pectins using 1H NMR spectroscopy and chemometrics

The objective of this study was to develop a calibration model between time-domain low-field nuclear magnetic resonance (LF-NMR) measurements and dry matter (DM) content in single potatoes. An extensive sampling procedure was used to collect 210 potatoes from eight cultivars with a wide range in DM content, ranging from 16 to 28%. The exponential NMR relaxation curves were resolved into four mono-exponential components using a number of solution diagnostics. Partial least-squares (PLS) regression between NMR parameters (relaxation time constants T2,1−4 and magnitudes M0,1−4) and DM content resulted in a model with low error (RMSECV, 0.71; RMSEP, 0.60) and high correlation (rCV, 0.97; rtest, 0.98) between predicted and actual DM content. Correlation between DM content and each of the proton populations revealed that M0,1 (T2,1, 3.6 ms; SD, 0.3 ms; r, 0.95) and M0,4 (T2,4, 508 ms; SD, 53 ms; r, −0.90) were the major contributors to the PLS regression model.

Determination of Dry Matter Content in Potato Tubers by Low-Field Nuclear Magnetic Resonance (LF-NMR)

Summary


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Polyphosphate (polyP) is presumably central to phosphate (P) metabolism of arbuscular mycorrhizal (AM) fungi, but its synthesis, location and chain lengths are poorly characterized. Here, we applied noninvasive and nondestructive nuclear magnetic resonance (NMR) spectroscopy to obtain novel information on AM fungal polyP.

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In vivo31P NMR spectroscopy was used to characterize polyP and other P pools in external hyphae and in mycorrhizal roots of associations between Glomus intraradices and cucumber (Cucumis sativus).

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A time-course study of P-starved external hyphae supplied with additional P showed that polyP appeared more rapidly than vacuolar inorganic P. These P metabolites also appeared in the roots, but later. PolyP considerably exceeded amounts of vacuolar inorganic P, where it was located in acidic, presumably vacuolar compartments, and had a short average chain length.

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The rapid synthesis of polyP might be important for the maintenance of effective hyphal P uptake. Our data support the hypothesis that polyP is the major P species translocated in the tubular vacuolar network, the presence of which was previously demonstrated in AM fungi.

Phosphate pool dynamics in the arbuscular mycorrhizal fungus Glomus intraradices studied by in vivo31P NMR spectroscopy

The metabolome following intake of onion by-products is evaluated. Thirty-two rats were fed a diet containing an onion by-product or one of the two derived onion by-product fractions: an ethanol extract and the residue. A 24 hour urine sample was analyzed using 1H NMR spectroscopy in order to investigate the effects of onion intake on the rat metabolism. Application of interval extended canonical variates analysis (ECVA) proved to be able to distinguish between the metabolomic profiles from rats consuming normal feed and rats fed with an onion diet. Two dietary biomarkers for onion intake were identified as dimethyl sulfone and 3-hydroxyphenylacetic acid. The same two dietary biomarkers were subsequently revealed by interval partial least squares regression (PLS) to be perfect quantitative markers for onion intake. The best PLS calibration model yielded a root mean square error of cross-validation (RMSECV) of 0.97% (w/w) with only 1 latent variable and a squared correlation coefficient of 0.94. This indicates that urine from rats on the by-product diet, the extract diet, and the residue diet all contain the same dietary biomarkers and it is concluded that dimethyl sulfone and 3-hydroxyphenylacetic acid are dietary biomarkers for onion intake. Being able to detect specific dietary biomarkers is highly beneficial in the control of nutritionally enhanced functional foods.

Nanna Viereck

Papers

Quantification of the degree of blockiness in pectins using 1H NMR spectroscopy and chemometrics

Determination of Dry Matter Content in Potato Tubers by Low-Field Nuclear Magnetic Resonance (LF-NMR)

Phosphate pool dynamics in the arbuscular mycorrhizal fungus Glomus intraradices studied by in vivo31P NMR spectroscopy

An exploratory NMR nutri-metabonomic investigation reveals dimethyl sulfone as a dietary biomarker for onion intake

Water mobility in acidified milk drinks studied by low-field 1H NMR