12 research outputs found
Evaluation of metabolomics profiles of grain from maize hybrids derived from near-isogenic GM positive and negative segregant inbreds demonstrates that observed differences cannot be attributed unequivocally to the GM trait
Introduction: Past studies on plant metabolomes have highlighted the influence of growing environments and varietal differences in variation of levels of metabolites yet there remains continued interest in evaluating the effect of genetic modification (GM). Objectives: Here we test the hypothesis that metabolomics differences in grain from maize hybrids derived from a series of GM (NK603, herbicide tolerance) inbreds and corresponding negative segregants can arise from residual genetic variation associated with backcrossing and that the effect of insertion of the GM trait is negligible. Methods: Four NK603-positive and negative segregant inbred males were crossed with two different females (testers). The resultant hybrids, as well as conventional comparator hybrids, were then grown at three replicated field sites in Illinois, Minnesota, and Nebraska during the 2013 season. Metabolomics data acquisition using gas chromatography–time of flight-mass spectrometry (GC–TOF-MS) allowed the measurement of 367 unique metabolite features in harvested grain, of which 153 were identified with small molecule standards. Multivariate analyses of these data included multi-block principal component analysis and ANOVA-simultaneous component analysis. Univariate analyses of all 153 identified metabolites was conducted based on significance testing (α = 0.05), effect size evaluation (assessing magnitudes of differences), and variance component analysis. Results: Results demonstrated that the largest effects on metabolomic variation were associated with different growing locations and the female tester. They further demonstrated that differences observed between GM and non-GM comparators, even in stringent tests utilizing near-isogenic positive and negative segregants, can simply reflect minor genomic differences associated with conventional back-crossing practices. Conclusion: The effect of GM on metabolomics variation was determined to be negligible and supports that there is no scientific rationale for prioritizing GM as a source of variation.</p
Tracing Phenolic Metabolism in Vitis vinifera Berries with <sup>13</sup>C<sub>6</sub>‑Phenylalanine: Implication of an Unidentified Intermediate Reservoir
Understanding
the regulation of phenolic compounds in agricultural
products has been a topic of great interest. In V.
vinifera berries, phenolics are responsible for important
sensory and functional characteristics. To elucidate the ripening
profile of phenolic compounds in Cabernet Sauvignon berries, the stable-isotope
tracer l-phenyl-<sup>13</sup>C<sub>6</sub>-alanine (Phe<sup>13</sup>) was incorporated in situ, and the development of labeled
and unlabeled phenolics was tracked in the vineyard at different stages
of maturity over two vintages. Phenolic profiles during ripening were
consistent with previous research. However, individual anthocyanins
accumulated with different profiles during ripening; malvidin species
continually climbed in concentration, whereas other anthocyanins tended
to plateau or drop near the end of the growing season. The isotopic
label was predominantly incorporated into anthocyanins, presumably
because of their dominant accumulation during ripening. Notably, the
incorporation of label continued long after levels of Phe<sup>13</sup> had dropped to below 1 nmol/berry, preventing an accurate assessment
of the hypothesized turnover of anthocyanins. Although our tracer
did not perform exactly as we had expected, the results of this study
suggest the presence of a previously unreported pool of substrate
in the phenolic pathway
Tracing Phenolic Metabolism in Vitis vinifera Berries with <sup>13</sup>C<sub>6</sub>‑Phenylalanine: Implication of an Unidentified Intermediate Reservoir
Understanding
the regulation of phenolic compounds in agricultural
products has been a topic of great interest. In V.
vinifera berries, phenolics are responsible for important
sensory and functional characteristics. To elucidate the ripening
profile of phenolic compounds in Cabernet Sauvignon berries, the stable-isotope
tracer l-phenyl-<sup>13</sup>C<sub>6</sub>-alanine (Phe<sup>13</sup>) was incorporated in situ, and the development of labeled
and unlabeled phenolics was tracked in the vineyard at different stages
of maturity over two vintages. Phenolic profiles during ripening were
consistent with previous research. However, individual anthocyanins
accumulated with different profiles during ripening; malvidin species
continually climbed in concentration, whereas other anthocyanins tended
to plateau or drop near the end of the growing season. The isotopic
label was predominantly incorporated into anthocyanins, presumably
because of their dominant accumulation during ripening. Notably, the
incorporation of label continued long after levels of Phe<sup>13</sup> had dropped to below 1 nmol/berry, preventing an accurate assessment
of the hypothesized turnover of anthocyanins. Although our tracer
did not perform exactly as we had expected, the results of this study
suggest the presence of a previously unreported pool of substrate
in the phenolic pathway
Tracing Phenolic Metabolism in Vitis vinifera Berries with <sup>13</sup>C<sub>6</sub>‑Phenylalanine: Implication of an Unidentified Intermediate Reservoir
Understanding
the regulation of phenolic compounds in agricultural
products has been a topic of great interest. In V.
vinifera berries, phenolics are responsible for important
sensory and functional characteristics. To elucidate the ripening
profile of phenolic compounds in Cabernet Sauvignon berries, the stable-isotope
tracer l-phenyl-<sup>13</sup>C<sub>6</sub>-alanine (Phe<sup>13</sup>) was incorporated in situ, and the development of labeled
and unlabeled phenolics was tracked in the vineyard at different stages
of maturity over two vintages. Phenolic profiles during ripening were
consistent with previous research. However, individual anthocyanins
accumulated with different profiles during ripening; malvidin species
continually climbed in concentration, whereas other anthocyanins tended
to plateau or drop near the end of the growing season. The isotopic
label was predominantly incorporated into anthocyanins, presumably
because of their dominant accumulation during ripening. Notably, the
incorporation of label continued long after levels of Phe<sup>13</sup> had dropped to below 1 nmol/berry, preventing an accurate assessment
of the hypothesized turnover of anthocyanins. Although our tracer
did not perform exactly as we had expected, the results of this study
suggest the presence of a previously unreported pool of substrate
in the phenolic pathway
Evaluation of metabolomics profiles of grain from maize hybrids derived from near-isogenic GM positive and negative segregant inbreds demonstrates that observed differences cannot be attributed unequivocally to the GM trait
INTRODUCTION: Past studies on plant metabolomes have highlighted the influence of growing environments and varietal differences in variation of levels of metabolites yet there remains continued interest in evaluating the effect of genetic modification (GM). OBJECTIVES: Here we test the hypothesis that metabolomics differences in grain from maize hybrids derived from a series of GM (NK603, herbicide tolerance) inbreds and corresponding negative segregants can arise from residual genetic variation associated with backcrossing and that the effect of insertion of the GM trait is negligible. METHODS: Four NK603-positive and negative segregant inbred males were crossed with two different females (testers). The resultant hybrids, as well as conventional comparator hybrids, were then grown at three replicated field sites in Illinois, Minnesota, and Nebraska during the 2013 season. Metabolomics data acquisition using gas chromatography–time of flight-mass spectrometry (GC–TOF-MS) allowed the measurement of 367 unique metabolite features in harvested grain, of which 153 were identified with small molecule standards. Multivariate analyses of these data included multi-block principal component analysis and ANOVA-simultaneous component analysis. Univariate analyses of all 153 identified metabolites was conducted based on significance testing (α = 0.05), effect size evaluation (assessing magnitudes of differences), and variance component analysis. RESULTS: Results demonstrated that the largest effects on metabolomic variation were associated with different growing locations and the female tester. They further demonstrated that differences observed between GM and non-GM comparators, even in stringent tests utilizing near-isogenic positive and negative segregants, can simply reflect minor genomic differences associated with conventional back-crossing practices. CONCLUSION: The effect of GM on metabolomics variation was determined to be negligible and supports that there is no scientific rationale for prioritizing GM as a source of variation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-016-1017-6) contains supplementary material, which is available to authorized users
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Evaluation of metabolomics profiles of grain from maize hybrids derived from near-isogenic GM positive and negative segregant inbreds demonstrates that observed differences cannot be attributed unequivocally to the GM trait
IntroductionPast studies on plant metabolomes have highlighted the influence of growing environments and varietal differences in variation of levels of metabolites yet there remains continued interest in evaluating the effect of genetic modification (GM).ObjectivesHere we test the hypothesis that metabolomics differences in grain from maize hybrids derived from a series of GM (NK603, herbicide tolerance) inbreds and corresponding negative segregants can arise from residual genetic variation associated with backcrossing and that the effect of insertion of the GM trait is negligible.MethodsFour NK603-positive and negative segregant inbred males were crossed with two different females (testers). The resultant hybrids, as well as conventional comparator hybrids, were then grown at three replicated field sites in Illinois, Minnesota, and Nebraska during the 2013 season. Metabolomics data acquisition using gas chromatography-time of flight-mass spectrometry (GC-TOF-MS) allowed the measurement of 367 unique metabolite features in harvested grain, of which 153 were identified with small molecule standards. Multivariate analyses of these data included multi-block principal component analysis and ANOVA-simultaneous component analysis. Univariate analyses of all 153 identified metabolites was conducted based on significance testing (α = 0.05), effect size evaluation (assessing magnitudes of differences), and variance component analysis.ResultsResults demonstrated that the largest effects on metabolomic variation were associated with different growing locations and the female tester. They further demonstrated that differences observed between GM and non-GM comparators, even in stringent tests utilizing near-isogenic positive and negative segregants, can simply reflect minor genomic differences associated with conventional back-crossing practices.ConclusionThe effect of GM on metabolomics variation was determined to be negligible and supports that there is no scientific rationale for prioritizing GM as a source of variation
Associations of Trimethylamine N-Oxide With Nutritional and Inflammatory Biomarkers and Cardiovascular Outcomes in Patients New to Dialysis.
ObjectivesTrimethylamine N-oxide (TMAO) is a product of metabolism of phosphatidylcholine (lecithin) and carnitine by the intestinal microbiome. Elevated serum concentrations of TMAO have been linked to adverse cardiovascular outcomes in the general population. We examined correlates of serum TMAO and the relations among serum TMAO concentrations, all-cause mortality, and cardiovascular mortality and hospitalizations in a nationally derived cohort of patients new to hemodialysis (HD).MethodsWe quantified serum TMAO by liquid chromatography and online tandem mass spectrometry and assessed nutritional and cardiovascular risk factors in 235 patients receiving HD and measured TMAO in pooled serum from healthy controls. We analyzed time to death and time to cardiovascular death or hospitalization using Cox proportional hazards regression.ResultsSerum TMAO concentrations of patients undergoing HD (median, 43 μM/L; 25th-75th percentile, 28-67 μM/L) were elevated compared with those with normal or near-normal kidney function (1.41 ± 0.49 μM/L). TMAO was directly correlated with serum albumin (Spearman rank correlation, 0.24; 95% CI, 0.12-0.35; P <.001), prealbumin (Spearman rank correlation, 0.19; 95% CI, 0.07-0.31; P = .003), and creatinine (Spearman rank correlation, 0.21; 95% CI, 0.08-0.33; P = .002) and inversely correlated with log C-reactive protein (Spearman rank correlation, -0.18; 95% CI, -0.30 to -0.06; P = .005). Higher serum concentrations of TMAO were not significantly associated with time to death (Spearman rank correlation, 0.84; CI, 0.65-1.09; P = .19) or time to cardiovascular hospitalization or cardiovascular death (Spearman rank correlation, 0.88; CI, 0.57-1.35; P = .55).ConclusionsSerum TMAO concentrations were markedly elevated and correlated directly with biochemical markers of nutritional status and inversely with markers of inflammation in patients receiving HD. There was no significant association between serum TMAO concentrations and all-cause mortality, cardiovascular death, or hospitalizations. In patients receiving dialysis-in contrast with the general population-adverse vascular effects of TMAO may be counterbalanced by associations with nutritional or inflammatory status
Metabolomic Assessment of Key Maize Resources: GC-MS and NMR Profiling of Grain from B73 Hybrids of the Nested Association Mapping (NAM) Founders and of Geographically Diverse Landraces
The
present study expands metabolomic assessments of maize beyond
commercial lines to include two sets of hybrids used extensively in
the scientific community. One set included hybrids derived from the
nested association mapping (NAM) founder lines, a collection of 25
inbreds selected on the basis of genetic diversity and used to investigate
the genetic basis of complex plant traits. A second set included 24
hybrids derived from a collection of landraces representative of native
diversity from North and South America that may serve as a source
of new alleles for improving modern maize hybrids. Metabolomic analysis
of grain harvested from these hybrids utilized gas chromatography–time-of-flight
mass spectrometry (GC-TOF-MS) and <sup>1</sup>H nuclear magnetic resonance
spectroscopy (<sup>1</sup>H NMR) techniques. Results highlighted extensive
metabolomic variation in grain from both hybrid sets, but also demonstrated
that, within each hybrid set, subpopulations could be differentiated
in a pattern consistent with the known genetic and compositional variation
of these lines. Correlation analysis did not indicate a strong association
of the metabolomic data with grain nutrient composition, although
some metabolites did show moderately strong correlations with agronomic
features such as plant and ear height. Overall, this study provides
insights into the extensive metabolomic diversity associated with
conventional maize germplasm
Metabolomic Assessment of Key Maize Resources: GC-MS and NMR Profiling of Grain from B73 Hybrids of the Nested Association Mapping (NAM) Founders and of Geographically Diverse Landraces
The
present study expands metabolomic assessments of maize beyond
commercial lines to include two sets of hybrids used extensively in
the scientific community. One set included hybrids derived from the
nested association mapping (NAM) founder lines, a collection of 25
inbreds selected on the basis of genetic diversity and used to investigate
the genetic basis of complex plant traits. A second set included 24
hybrids derived from a collection of landraces representative of native
diversity from North and South America that may serve as a source
of new alleles for improving modern maize hybrids. Metabolomic analysis
of grain harvested from these hybrids utilized gas chromatography–time-of-flight
mass spectrometry (GC-TOF-MS) and <sup>1</sup>H nuclear magnetic resonance
spectroscopy (<sup>1</sup>H NMR) techniques. Results highlighted extensive
metabolomic variation in grain from both hybrid sets, but also demonstrated
that, within each hybrid set, subpopulations could be differentiated
in a pattern consistent with the known genetic and compositional variation
of these lines. Correlation analysis did not indicate a strong association
of the metabolomic data with grain nutrient composition, although
some metabolites did show moderately strong correlations with agronomic
features such as plant and ear height. Overall, this study provides
insights into the extensive metabolomic diversity associated with
conventional maize germplasm
Untargeted Profiling of Tracer-Derived Metabolites Using Stable Isotopic Labeling and Fast Polarity-Switching LC–ESI-HRMS
An untargeted metabolomics workflow
for the detection of metabolites
derived from endogenous or exogenous tracer substances is presented.
To this end, a recently developed stable isotope-assisted LC–HRMS-based
metabolomics workflow for the global annotation of biological samples
has been further developed and extended. For untargeted detection
of metabolites arising from labeled tracer substances, isotope pattern
recognition has been adjusted to account for nonlabeled moieties conjugated
to the native and labeled tracer molecules. Furthermore, the workflow
has been extended by (i) an optional ion intensity ratio check, (ii)
the automated combination of positive and negative ionization mode
mass spectra derived from fast polarity switching, and (iii) metabolic
feature annotation. These extensions enable the automated, unbiased,
and global detection of tracer-derived metabolites in complex biological
samples. The workflow is demonstrated with the metabolism of <sup>13</sup>C<sub>9</sub>-phenylalanine in wheat cell suspension cultures
in the presence of the mycotoxin deoxynivalenol (DON). In total, 341
metabolic features (150 in positive and 191 in negative ionization
mode) corresponding to 139 metabolites were detected. The benefit
of fast polarity switching was evident, with 32 and 58 of these metabolites
having exclusively been detected in the positive and negative modes,
respectively. Moreover, for 19 of the remaining 49 phenylalanine-derived
metabolites, the assignment of ion species and, thus, molecular weight
was possible only by the use of complementary features of the two
ion polarity modes. Statistical evaluation showed that treatment with
DON increased or decreased the abundances of many detected metabolites