J S de Ropp

University of California, Davis, Davis, California, United States

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Publications (47)107.53 Total impact

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    ABSTRACT: Several fundamental requirements must be met so that NMR-based metabolomics and the related technique of metabonomics can be formally adopted into environmental monitoring and chemical risk assessment. Here we report an intercomparison exercise which has evaluated the effectiveness of 1H NMR metabolomics to generate comparable data sets from environmentally derived samples. It focuses on laboratory practice that follows sample collection and metabolite extraction, specifically the final stages of sample preparation, NMR data collection (500, 600, and 800 MHz), data processing, and multivariate analysis. Seven laboratories have participated from the U.S.A., Canada, U.K., and Australia, generating a total of ten data sets. Phase 1 comprised the analysis of synthetic metabolite mixtures, while Phase 2 investigated European flounder (Platichthys flesus) liver extracts from clean and contaminated sites. Overall, the comparability of data sets from the participating laboratories was good. Principal components analyses (PCA) of the individual data sets yielded ten highly similar scores plots for the synthetic mixtures, with a comparable result for the liver extracts. Furthermore, the same metabolic biomarkers that discriminated fish from clean and contaminated sites were discovered by all the laboratories. PCA of the combined data sets showed excellent clustering of the multiple analyses. These results demonstrate that NMR-based metabolomics can generate data that are sufficiently comparable between laboratories to support its continued evaluation for regulatory environmental studies.
    Environmental Science and Technology 02/2009; 43(1):219-25. · 5.26 Impact Factor
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    ABSTRACT: The automated and robust identification of metabolites in a complex biological sample remains one of the greatest challenges in metabolomics. In our experiments, HSQC carbon-proton correlation NMR data with a model that takes intensity information into account improves upon the identification of metabolites that was achieved using COSY proton-proton correlation NMR data with the binary model of [Y. Xi, J.S. de Ropp, M.R. Viant, D.L. Woodruff, P. Yu, Metabolomics, 2 (2006) 221-233]. In addition, using intensity information results in easier-to-interpret "grey areas" for cases where it is not clear if the compound might be present. We report on highly successful experiments that identify compounds in chemically defined mixtures as well as in biological samples, and compare our two-dimensional HSQC analyses against quantification of metabolites in the corresponding one-dimensional proton NMR spectra. We show that our approach successfully employs a fully automated algorithm for identifying the presence or absence of predefined compounds (held within a library) in biological HSQC spectra, and in addition calculates upper bounds on the compound intensities.
    Analytica chimica acta 06/2008; 614(2):127-33. · 4.31 Impact Factor
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    ABSTRACT: We report on the use and applicability of microfabricated radio frequency (r.f.) coils for viscosity measurements of fluid foods. The viscosity of fluid milk and milklike products was measured using nuclear magnetic resonance imaging based on microfabricated r.f. coils coupled to in-line tubing with an inner diameter of 1.4 × 10-3 m. The fluid's apparent viscosity ranged from 0.002 to 0.08 Pa·s. The magnetic resonance-based measurements were limited in shear rate range because of the small size of the coil. Magnetic resonance-based measurements from 2 to 15 s-1 were obtained and were equivalent to off-line rotational rheometry.
    Journal of Texture Studies 11/2006; 37(6):607 - 619. · 1.05 Impact Factor
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    ABSTRACT: One of the greatest challenges in metabolomics is the rapid and unambiguous identification and quantification of metabolites in a biological sample. Although one-dimensional (1D) proton nuclear magnetic resonance (NMR) spectra can be acquired rapidly, they are complicated by severe peak overlap that can significantly hinder the automated identification and quantification of metabolites. Furthermore, it is currently not reasonable to assume that NMR spectra of pure metabolites are available a priori for every metabolite in a biological sample. In this paper we develop and report on tests of methods that assist in the automatic identification of metabolites using proton two-dimensional (2D) correlation spectroscopy (COSY) NMR. Given a database of 2D COSY spectra for the metabolites of interest, our methods provide a list sorted by a heuristic likelihood of the metabolites present in a sample that has been analyzed using 2D COSY NMR. Our models attempt to correct the displacement of the peaks that can occur from one sample to the next, due to pH, temperature and matrix effects, using a statistical and chemical model. The correction of one peak can result in an implied correction of others due to spin–spin coupling. Furthermore, these displacements are not independent: they depend on the relative position of functional groups in the molecule. We report experimental results using defined mixtures of amino acids as well as real complex biological samples that demonstrate that our methods can be very effective at automatically and rapidly identifying metabolites.
    Metabolomics 01/2006; 2(4):221-233. · 4.43 Impact Factor
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    ABSTRACT: Fish embryo toxicity tests for chemical risk assessment have traditionally been based upon non-specific endpoints including morphological abnormalities, hatching success, and mortality. Here we extend the application of 1H NMR-based metabolomics in environmental toxicology by adding a suite of metabolic endpoints to the Japanese medaka (Oryzias latipes) embryo assay, with the goal to provide more sensitive, specific and unbiased biomarkers of toxicity. Medaka were exposed throughout embryogenesis to five concentrations of trichloroethylene (TCE; 0, 8.76, 21.9, 43.8, 87.6, 175mg/L) and the relative sensitivities of the traditional and metabolomic endpoints compared. While the no-observable-adverse-effect-level for hatching success, the most sensitive traditional indicator, was 164mg/L TCE, metabolic perturbations were detected at all exposure concentrations. Principal components analysis (PCA) highlighted a dose-response relationship between the NMR spectra of medaka extracts. In addition, 12 metabolites that exhibited highly significant dose-response relationships were identified, which indicated an energetic cost to TCE exposure. Next, embryos were exposed to 0, 0.88, 8.76mg/L TCE and sampled on each of the 8days of development. Projections of 66 two-dimensional J-resolved NMR spectra were obtained, and PCA revealed developmental metabolic trajectories that characterized the basal and TCE-perturbed changes in the entire NMR-visible metabolome throughout embryogenesis. Although no significant increases in mortality, gross deformity or developmental retardation were observed relative to the control group, TCE-induced metabolic perturbations were observed on day 8. In conclusion, these results support the continued development of NMR-based metabolomics as a rapid and reproducible tool for biomarker discovery and environmental risk assessment.
    Metabolomics 03/2005; 1(2):149-158. · 4.43 Impact Factor
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    ABSTRACT: This work reports on applications of a miniaturized RF coil combined with a capillary tube for the design of a portable on-line/in-line magnetic resonance imaging (MRI) based viscometer. A microfabricated Helmholtz RF coil with the average diameter of 7 mm and a Teflon tube with ID = 1.02 mm were utilized. Tube flows of two aqueous CMC polymer solutions (2% with MW = 250k and 1% with MW = 700k) of different viscosities at 1.99 µL s−1 volumetric flow rate were monitored. It was shown that the RF coil and the capillary permit measurement of shear thinning phenomena during flow. A constitutive power law model was used to analyse the tube flows. Viscosity was successfully measured for both the CMC solutions. The less viscous CMC solution was found to have the power index n = 0.77 ± 0.06 and the flow consistency coefficient K = 1.68, whereas the more viscous CMC solution exhibited n = 0.5 ± 0.03 and K = 7.23. The MRI measurements compared well with measurements of the same samples performed on a conventional rotational rheometer. The range of shear rates covered by the obtained MRI viscosity data was 3–20 s−1.
    Measurement Science and Technology 01/2005; 16(2):513. · 1.44 Impact Factor
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    ABSTRACT: A package of two planar gradient coils combined with an RF coil was microfabricated for low-field MRI measurements of velocity flow profiles. The package generates orthogonal gradients in the radial and velocity encoding directions for standard flow imaging experiments. A commercial 0.6 T superconductive magnet was used to test coil performance. For comparison flow imaging was also performed using a commercial set of gradient coils. Velocity profiles were obtained for several volumetric flow rates of water in tubes with inner diameters of 1.02 mm and 1.4 mm. Velocity resolution was 0.13 mm s−1, comparable to that achieved with commercial gradient coils. The quality of the velocity profile was sufficient for viscosity calculations, and thus permits future utilization of this coil package in the design of a portable MRI viscometer.
    Measurement Science and Technology 01/2005; 16(2):505. · 1.44 Impact Factor
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    ABSTRACT: A miniaturized spiral Helmholtz rf coil was fabricated using standard photolithography and electroplating. A commercial 0.6 T superconductive magnet was used to test the coil performance for both nuclear magnetic resonance (NMR) spectroscopy and imaging applications. NMR spectra of water, methanol, and 1-propanol were obtained as well as static and flow images of a water phantom. The spectral resolution was sufficient to allow chemical identification. Additionally, the viscosity of water was estimated from the experimental velocity profile and was equal to the expected value of 1 cP. Results obtained demonstrated the prospect of using the Helmholtz rf coil as part of a portable low-field NMR system for applications in analytical chemistry and process measurements in industrial settings.
    Review of Scientific Instruments 01/2005; 76(2):024101-024101-6. · 1.60 Impact Factor
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    ABSTRACT: A double-tuned NMR microprobe with dual RF microcoil assemblies was fabricated and tested. The coils for the proton and X (low frequency) nuclei were a variant of a loop gap resonator and Helmholtz pair, respectively. 1-D 31P spectra of phosphoric acid and 13C-labeled spectra of methanol were recorded from 1.4-μL samples. Signal was easily observable in one scan. A COSY spectrum of 13C-labeled acetic acid was acquired in 1 h, demonstrating sufficient sensitivity to perform 2-D 13C direct detect experiments. Thus, the ability to obtain direct detection spectra of low-γ nuclei is demonstrated.
    Analytical Chemistry - ANAL CHEM. 08/2003; 75(19).
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    ABSTRACT: The structures of lipopeptides lobocyclamides A (1), B (2), and C (3) were solved using a combination of mass spectrometry, 2D NMR spectroscopy, and degradative analysis. Lobocyclamides B and C are the first peptides reported with the unusual amino acid 4-hydroxythreonine and also incorporate the rare homologous long-chain beta-amino acids 3-aminooctanoic acid and 3-aminodecanoic acid, respectively. The absolute configurations of the amino acid residues in each compound were assigned, after acid hydrolysis, by either direct chiral HPLC comparison with authentic standards or by prior derivatization by Marfey's method and reversed-phase HPLC. Both compounds exhibited moderate antifungal activity against a panel of Candida spp., including two fluconazole-resistant strains. When tested as a mixture, lobocyclamides A and B displayed synergistic in vitro antifungal activity, a phenomenon noted earlier for the related peptides laxaphycins A and B.
    The Journal of Organic Chemistry 12/2002; 67(23):8210-5. · 4.56 Impact Factor
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    ABSTRACT: The functional higher oxidation states of heme peroxidases have been proposed to be stabilized by the significant imidazolate character of the proximal His. This is induced by a "push-pull" combination effect produced by the proximal Asp that abstracts ("pulls") the axial His ring N(delta)H, along with the distal protonated His that contributes ("pushes") a strong hydrogen bond to the distal ligand. The molecular and electronic structure of the distal His mutant of cyanide-inhibited horseradish peroxidase, H42A-HRPCN, has been investigated by NMR. This complex is a valid model for the active site hydrogen-bonding network of HRP compound II. The (1)H and (15)N NMR spectral parameters characterize the relative roles of the distal His42 and proximal Asp247 in imparting imidazolate character to the axial His. 1D/2D spectra reveal a heme pocket molecular structure that is highly conserved in the mutant, except for residues in the immediate proximity of the mutation. This conserved structure, together with the observed dipolar shifts of numerous active site residue protons, allowed a quantitative determination of the orientation and anisotropies of the paramagnetic susceptibility tensor, both of which are only minimally perturbed relative to wild-type HRPCN. The quantitated dipolar shifts allowed the factoring of the hyperfine shifts to reveal that the significant changes in hyperfine shifts for the axial His and ligated (15)N-cyanide result primarily from changes in contact shifts that reflect an approximately one-third reduction in the axial His imidazolate character upon abolishing the distal hydrogen-bond to the ligated cyanide. Significant changes in side chain orientation were found for the distal Arg38, whose terminus reorients to partially fill the void left by the substituted His42 side chain. It is concluded that 1D/2D NMR can quantitate both molecular and electronic structural changes in cyanide-inhibited heme peroxidase and that, while both residues contribute, the proximal Asp247 is more important than the distal His42 in imparting imidazole character to the axial His 170.
    Journal of the American Chemical Society 10/2002; 124(37):11029-37. · 10.68 Impact Factor
  • Da-Mi Jung, Jeffrey S De Ropp, Susan E Ebeler
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    ABSTRACT: Two diffusion-based NMR techniques are presented and used to investigate the binding of selected flavor compounds to macromolecules. A pulsed field gradient NMR (PFG-NMR) method was applied to measure the apparent diffusion coefficients of four alkanone compounds as they associated with bovine serum albumin (BSA). The change in the apparent diffusion coefficient as a function of the BSA/alkanone ratio was fitted to yield binding constants (K(a)()) and binding stoichiometry (n) for each alkanone. The results showed that the apparent diffusion coefficients of alkanones increased with a decrease in the BSA/alkanone ratios, and the measured values of K(a)() and n were comparable with those obtained with other methods and depended on the alkanone structure. A diffusion-based nuclear Overhauser effect (called diffusion NOE pumping) method was also applied to screen mixtures of flavor compounds and identify those that have a binding affinity to complex macromolecules. Using this technique benzaldehyde and vanillin were observed to bind with bovine serum albumin, whereas 2-phenylethanol was identified as a nonbinding or weakly binding ligand with BSA. The diffusion NOE pumping method was also applied to a hydro alcoholic solution of cacao bean tannin extracts to which a mixture of ethylbenzoate, benzaldehyde, and 2-phenylethanol was added. The diffusion NOE pumping technique clearly indicated that ethylbenzoate had a stronger binding affinity to the polymeric (-)-epicatechin units of the cacao bean tannin extracts than the other two flavor compounds. The results successfully demonstrate the potential applications of diffusion-based NMR techniques for studying flavors and nonvolatile food matrix interactions.
    Journal of Agricultural and Food Chemistry 08/2002; 50(15):4262-9. · 3.11 Impact Factor
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    Journal of The American Chemical Society - J AM CHEM SOC. 04/2002; 115(12).
  • Jeffrey S. De Ropp, Gerd N. La Mar
    Journal of The American Chemical Society - J AM CHEM SOC. 04/2002; 113(11).
  • Journal of The American Chemical Society - J AM CHEM SOC. 04/2002; 116(19).
  • V. Thanabal, Jeffrey S. De Ropp, Gerd N. La Mar
    Journal of The American Chemical Society - J AM CHEM SOC. 04/2002; 109(24).
  • Jeffrey S. De Ropp, V. Thanabal, Gerd N. La Mar
    Journal of The American Chemical Society - J AM CHEM SOC. 04/2002; 107(26).
  • Gerd N. La Mar, Jeffrey S. De Ropp
    Journal of The American Chemical Society - J AM CHEM SOC. 04/2002; 104(19).
  • Inorganic Chemistry - INORG CHEM. 04/2002; 30(17).
  • Inorganic Chemistry - INORG CHEM. 04/2002; 29(10).

Publication Stats

462 Citations
107.53 Total Impact Points

Institutions

  • 1979–2006
    • University of California, Davis
      • • Department of Environmental Toxicology
      • • Department of Chemistry
      • • Department of Food Science and Technology
      Davis, California, United States
  • 1997
    • University of Georgia
      • Department of Food Science and Technology
      Атина, Georgia, United States