Robin A. de Graaf

Bio: Robin A. de Graaf is an academic researcher from Yale University. The author has contributed to research in topics: Shim (magnetism) & Nuclear magnetic resonance spectroscopy. The author has an hindex of 46, co-authored 128 publications receiving 6699 citations. Previous affiliations of Robin A. de Graaf include Utrecht University & University Medical Center Utrecht.

Impaired Mitochondrial Substrate Oxidation in Muscle of Insulin-Resistant Offspring of Type 2 Diabetic Patients

Abstract: Insulin resistance is the best predictor for the development of diabetes in offspring of type 2 diabetic patients, but the mechanism responsible for it remains unknown. Recent studies have demonstrated increased intramyocellular lipid, decreased mitochondrial ATP synthesis, and decreased mitochondrial density in the muscle of lean, insulin-resistant offspring of type 2 diabetic patients. These data suggest an important role for mitochondrial dysfunction in the pathogenesis of type 2 diabetes. To further explore this hypothesis, we assessed rates of substrate oxidation in the muscle of these same individuals using 13C magnetic resonance spectroscopy (MRS). Young, lean, insulin-resistant offspring of type 2 diabetic patients and insulin-sensitive control subjects underwent 13C MRS studies to noninvasively assess rates of substrate oxidation in muscle by monitoring the incorporation of 13C label into C4 glutamate during a [2-13C]acetate infusion. Using this approach, we found that rates of muscle mitochondrial substrate oxidation were decreased by 30% in lean, insulin-resistant offspring (59.8 ± 5.1 nmol · g−1 · min−1, P = 0.02) compared with insulin-sensitive control subjects (96.1 ± 16.3 nmol · g−1 · min−1). These data support the hypothesis that insulin resistance in skeletal muscle of insulin-resistant offspring is associated with dysregulation of intramyocellular fatty acid metabolism, possibly because of an inherited defect in the activity of mitochondrial oxidative phosphorylation.

In Vivo NMR Spectroscopy: Principles and Techniques

Abstract: Preface. List of Abbreviations and Symbols. 1 Basic Principles. 1.1 Introduction. 1.2 Classical Description. 1.3 Quantum Mechanical Description. 1.4 Macroscopic Magnetization. 1.5 Excitation. 1.6 Bloch Equations. 1.7 Fourier Transform NMR. 1.8 Chemical Shift. 1.9 Digital Fourier Transform NMR. 1.10 Spin-spin Coupling. 1.11 T1 Relaxation. 1.12 T2 Relaxation and Spin-echoes. 1.13 Exercises. References 41 2 In Vivo NMR Spectroscopy - Static Aspects. 2.1 Introduction. 2.2 Proton NMR Spectroscopy. 2.3 Phosphorus-31 NMR Spectroscopy. 2.4 Carbon-13 NMR Spectroscopy. 2.5 Sodium-23 and Potassium-39 NMR Spectroscopy. 2.6 Fluorine-19 NMR Spectroscopy. 2.7 Exercises. 3 In Vivo NMR Spectroscopy - Dynamic Aspects. 3.1 Introduction. 3.2 Relaxation. 3.3 Magnetization Transfer. 3.4 Diffusion. 3.5 Dynamic Carbon-13 NMR Spectroscopy. 3.6 Hyperpolarization. 3.7 Exercises. 4 Magnetic Resonance Imaging. 4.1 Introduction. 4.2 Magnetic Field Gradients. 4.3 Slice Selection. 4.4 Frequency Encoding. 4.5 Phase Encoding. 4.6 Spatial Frequency Space. 4.7 Fast MRI Sequences. 4.8 Contrast in MRI. 4.9 Parallel MRI. 4.10 Exercises. 5 Radiofrequency Pulses. 5.1 Introduction. 5.2 Square RF Pulses. 5.3 Selective RF Pulses. 5.4 Pulse Optimization. 5.5 DANTE RF Pulses. 5.6 Composite RF Pulses. 5.7 Adiabatic RF Pulses. 5.8 Pulse Imperfections and Relaxation. 5.9 Power Deposition. 5.10 Multidimensional RF Pulses. 5.11 Spectral-spatial RF Pulses. 5.12 Exercises. 6 Single Volume Localization and Water Suppression. 6.1 Introduction. 6.2 Single Volume Localization. 6.3 Water Suppression. 6.4 Exercises. 7 Spectroscopic Imaging and Multivolume Localization. 7.1 Introduction. 7.2 Principles of Spectroscopic Imaging. 7.3 Spatial Resolution in MRSI. 7.4 Temporal Resolution in MRSI. 7.5 Lipid Suppression. 7.6 Spectroscopic Imaging Processing and Display. 7.7 Multivolume Localization. 7.8 Exercises. 8 Spectral Editing and Two-dimensional NMR. 8.1 Introduction. 8.2 Scalar Evolution. 8.3 J-difference Editing. 8.4 Practical Considerations of J-difference Editing. 8.5 Multiple Quantum Coherence Editing. 8.6 Heteronuclear Spectral Editing. 8.7 Polarization Transfer - INEPT and DEPT. 8.8 Sensitivity. 8.9 Broadband Decoupling. 8.10 Two-dimensional NMR Spectroscopy. 8.10.1 Correlation Spectroscopy (COSY). 8.10.2 Spin-echo or J-resolved NMR. 8.10.3 Two-dimensional Exchange Spectroscopy. 8.11 Exercises. 9 Spectral Quantification. 9.1 Introduction. 9.2 Data Acquisition. 9.3 Data Pre-processing. 9.4 Data Quantification. 9.5 Data Calibration. 9.6 Exercises. 10 Hardware. 10.1 Introduction. 10.2 Magnets. 10.3 Magnetic Field Homogeneity. 10.4 Magnetic Field Gradients. 10.5 Radiofrequency Coils. 10.6 Radiofrequency Coil Types. 10.7 Complete MR System. 10.8 Exercises. Appendix. A1 Matrix Calculations. A2 Trigonometric Equations. A3 Fourier Transformation. A3.1 Introduction. A3.2 Properties. A3.3 Discrete Fourier Transformation. A4 Product Operator Formalism. A4.1 Cartesian Product Operators. A4.2 Spherical Tensor Product Operators. References. Further Reading. Index.

2-Hydroxyglutarate produced by neomorphic IDH mutations suppresses homologous recombination and induces PARP inhibitor sensitivity.

Abstract: 2-Hydroxyglutarate (2HG) exists as two enantiomers, (R)-2HG and (S)-2HG, and both are implicated in tumor progression via their inhibitory effects on α-ketoglutarate (αKG)-dependent dioxygenases. The former is an oncometabolite that is induced by the neomorphic activity conferred by isocitrate dehydrogenase 1 (IDH1) and IDH2 mutations, whereas the latter is produced under pathologic processes such as hypoxia. We report that IDH1/2 mutations induce a homologous recombination (HR) defect that renders tumor cells exquisitely sensitive to poly(adenosine 5'-diphosphate-ribose) polymerase (PARP) inhibitors. This "BRCAness" phenotype of IDH mutant cells can be completely reversed by treatment with small-molecule inhibitors of the mutant IDH1 enzyme, and conversely, it can be entirely recapitulated by treatment with either of the 2HG enantiomers in cells with intact IDH1/2 proteins. We demonstrate mutant IDH1-dependent PARP inhibitor sensitivity in a range of clinically relevant models, including primary patient-derived glioma cells in culture and genetically matched tumor xenografts in vivo. These findings provide the basis for a possible therapeutic strategy exploiting the biological consequences of mutant IDH, rather than attempting to block 2HG production, by targeting the 2HG-dependent HR deficiency with PARP inhibition. Furthermore, our results uncover an unexpected link between oncometabolites, altered DNA repair, and genetic instability.

The contribution of GABA to glutamate/glutamine cycling and energy metabolism in the rat cortex in vivo

Abstract: Previous studies have shown that the glutamate/glutamine (Glu/Gln) neurotransmitter cycle and neuronal glucose oxidation are proportional (1:1), with increasing neuronal activity above isoelectricity. GABA, a product of Glu metabolism, is synthesized from astroglial Gln and contributes to total Glu/Gln neurotransmitter cycling, although the fraction contributed by GABA is unknown. In the present study, we used 13C NMR spectroscopy together with i.v. infusions of [1,6-13C2]glucose and [2-13C]acetate to separately determine rates of Glu/Gln and GABA/Gln cycling and their respective tricarboxylic acid cycles in the rat cortex under conditions of halothane anesthesia and pentobarbital-induced isoelectricity. Under 1% halothane anesthesia, GABA/Gln cycle flux comprised 23% of total (Glu plus GABA) neurotransmitter cycling and 18% of total neuronal tricarboxylic acid cycle flux. In isoelectric cortex, glucose oxidation was reduced >3-fold in glutamatergic and GABAergic neurons, and neurotransmitter cycling was below detection. Hence, in both cell types, the primary energetic costs are associated with neurotransmission, which increase together as cortical activity is increased. The contribution of GABAergic neurons and inhibition to cortical energy metabolism has broad implications for the interpretation of functional imaging signals.

High magnetic field water and metabolite proton T1 and T2 relaxation in rat brain in vivo.

Abstract: Comprehensive and quantitative measurements of T1 and T2 relaxation times of water, metabolites, and macromolecules in rat brain under similar experimental conditions at three high magnetic field strengths (4.0 T, 9.4 T, and 11.7 T) are presented. Water relaxation showed a highly significant increase (T1) and decrease (T2) with increasing field strength for all nine analyzed brain structures. Similar but less pronounced effects were observed for all metabolites. Macromolecules displayed field-independent T2 relaxation and a strong increase of T1 with field strength. Among other features, these data show that while spectral resolution continues to increase with field strength, the absolute signal-to-noise ratio (SNR) in T1/T2-based anatomical MRI quickly levels off beyond approximately 7 T and may actually decrease at higher magnetic fields.

Proton NMR chemical shifts and coupling constants for brain metabolites.

Abstract: Proton NMR chemical shift and J-coupling values are presented for 35 metabolites that can be detected by in vivo or in vitro NMR studies of mammalian brain. Measurements were obtained using high-field NMR spectra of metabolites in solution, under conditions typical for normal physiological temperature and pH. This information is presented with an accuracy that is suitable for computer simulation of metabolite spectra to be used as basis functions of a parametric spectral analysis procedure. This procedure is verified by the analysis of a rat brain extract spectrum, using the measured spectral parameters. In addition, the metabolite structures and example spectra are presented, and clinical applications and MR spectroscopic measurements of these metabolites are reviewed.

Brain Work and Brain Imaging

Abstract: Functional brain imaging with positron emission tomography and magnetic resonance imaging has been used extensively to map regional changes in brain activity. The signal used by both techniques is based on changes in local circulation and metabolism (brain work). Our understanding of the cell biology of these changes has progressed greatly in the past decade. New insights have emerged on the role of astrocytes in signal transduction as has an appreciation of the unique contribution of aerobic glycolysis to brain energy metabolism. Likewise our understanding of the neurophysiologic processes responsible for imaging signals has progressed from an assumption that spiking activity (output) of neurons is most relevant to one focused on their input. Finally, neuroimaging, with its unique metabolic perspective, has alerted us to the ongoing and costly intrinsic activity within brain systems that most likely represents the largest fraction of the brain's functional activity.

The Human Serum Metabolome

Abstract: Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased interest pressures within the metabolomics community to develop centralized metabolite reference resources for certain clinically important biofluids, such as cerebrospinal fluid, urine and blood. As part of an ongoing effort to systematically characterize the human metabolome through the Human Metabolome Project, we have undertaken the task of characterizing the human serum metabolome. In doing so, we have combined targeted and non-targeted NMR, GC-MS and LC-MS methods with computer-aided literature mining to identify and quantify a comprehensive, if not absolutely complete, set of metabolites commonly detected and quantified (with today's technology) in the human serum metabolome. Our use of multiple metabolomics platforms and technologies allowed us to substantially enhance the level of metabolome coverage while critically assessing the relative strengths and weaknesses of these platforms or technologies. Tables containing the complete set of 4229 confirmed and highly probable human serum compounds, their concentrations, related literature references and links to their known disease associations are freely available at http://www.serummetabolome.ca.