ORCID Profile
0000-0002-1789-8000
Current Organisations
Institut National de Recherche pour l’Agriculture l’Alimentation et l’Environnement Centre Clermont-Auvergne-Rhône-Alpes
,
Iowa State University
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Publisher: Springer Science and Business Media LLC
Date: 29-05-2013
DOI: 10.1007/S00249-012-0822-8
Abstract: q-Space plots obtained experimentally using pulsed field-gradient stimulated echo (PGSTE) nuclear magnetic resonance (NMR) spectroscopy from water diffusing in red blood cells (RBCs) of different canonical (distinct variant) morphologies have "signature" features. The experimental q-space plots from suspensions of stomatocytes, echinocytes and spherocytes generated chemically had no diffraction features in contrast a s le of blood from a patient with hereditary spherocytosis showed diffraction minima. To understand the forms of q-space plots, mathematical/geometrical models of discocytes, stomatocytes, echinocytes and spherocytes were used as restricting boundaries in simulations of water diffusion with Monte Carlo random walks. These simulations indicated that diffusion-diffraction minima are expected for each of the cell shapes considered. The absence of diffusion-diffraction minima in stomatocytes generated by dithiothreitol treatment was surmised to be due to non-alignment of the cells with the magnetic field of the NMR spectrometer. Differential interference contrast microscopy images of the chemically generated spherocyte and echinocyte suspensions showed them to be heterogeneous in cell shape. Therefore, we concluded that the shape heterogeneity caused the loss of the diffusion-diffraction features, which were observed in the more homogeneous s le from a patient with hereditary spherocytosis, and in the simulations of homogeneous cell suspensions. This understanding of factors that affect q-space plots from RBC suspensions will assist morphological studies of other cell and tissue types.
Publisher: Wiley
Date: 11-08-2014
DOI: 10.1002/NBM.3176
Abstract: Hyperpolarized [1,(13)C]pyruvate was injected rapidly into haemolysates in which hydrolysis of nicotinamide adenine dinucleotide (phosphate) (NAD(P))/NAD(P)H had been inhibited with nicotinamide. Haemolysates provide a stable glycolytic system in which membrane permeability is not a flux-controlling step, and they enable the concentration of NADH to be adjusted experimentally while keeping the rest of the s le with the same composition as that of the cytoplasm of the cell (albeit diluted twofold at the time of injection of the [1,(13)C]pyruvate). We showed that the maximum litude of the (13)C NMR signal from the [1,(13)C]L-lactate, produced from [1,(13)C]pyruvate, and the time at which it occurred was dependent on NADH concentration, as predicted by enzyme-kinetic analysis. The main feature of such curves was dictated by the immediacy of the supply of the co-substrate of lactate dehydrogenase (LDH, EC 1.1.1.27), and we posit that this also pertains in vivo in various tissues including neoplasms. By constructing an appropriate mathematical model and by using a Markov-chain Monte Carlo approach, we fitted experimental data to estimate LDH and NADH concentrations. Experiments carried out with only endogenous NADH present enabled the estimation of its effective concentration in human RBCs the ability to make this estimate is a special feature of the rapid-dissolution dynamic nuclear polarization method. We found an endogenous NADH concentration in human RBCs two to four times higher than previously reported.
Publisher: Elsevier BV
Date: 02-2011
Publisher: Springer Science and Business Media LLC
Date: 21-03-2009
DOI: 10.1007/S00249-009-0433-1
Abstract: The hERG K(+) channel undergoes rapid inactivation that is mediated by 'collapse' of the selectivity filter, thereby preventing ion conduction. Previous studies have suggested that the pore-helix of hERG may be up to seven residues longer than that predicted by homology with channels with known crystal structures. In the present work, we determined structural features of a peptide from the pore loop region of hERG (residues 600-642) in both sodium dodecyl sulfate (SDS) and dodecyl phosphocholine (DPC) micelles using NMR spectroscopy. A complete structure calculation was done for the peptide in DPC, and the localization of residues inside the micelles were analysed by using a water-soluble paramagnetic reagent with both DPC and SDS micelles. The pore-helix in the hERG peptide was only two-four residues longer at the N-terminus, compared with the pore helices seen in the crystal structures of other K(+) channels, rather than the seven residues suggested from previous NMR studies. The helix in the peptide spanned the same residues in both micellar environments despite a difference in the localization inside the respective micelles. To determine if the extension of the length of the helix was affected by the hydrophobic environment in the two types of micelles, we compared NMR and X-ray crystallography results from a homologous peptide from the voltage gated potassium channel, KcsA.
Publisher: Springer Science and Business Media LLC
Date: 21-12-2018
DOI: 10.1038/S42003-018-0241-1
Abstract: Methylglyoxal is a faulty metabolite. It is a ubiquitous by-product of glucose and amino acid metabolism that spontaneously reacts with proximal amino groups in proteins and nucleic acids, leading to impairment of their function. The glyoxalase pathway evolved early in phylogeny to bring about rapid catabolism of methylglyoxal, and an understanding of the role of methylglyoxal and the glyoxalases in many diseases is beginning to emerge. Metabolic processing of methylglyoxal is very rapid in vivo and thus notoriously difficult to detect and quantify. Here we show that 13 C nuclei in labeled methylglyoxal can be hyperpolarized using dynamic nuclear polarization, providing 13 C nuclear magnetic resonance signal enhancements in the solution state close to 5,000-fold. We demonstrate the applications of this probe of metabolism for kinetic characterization of the glyoxalase system in isolated cells as well as mouse brain, liver and lymphoma in vivo.
Publisher: Wiley
Date: 22-05-2013
DOI: 10.1016/J.FEBSLET.2013.05.025
Abstract: We introduce the concept of 'chiral compartmentation' in metabolism that emerges from the stereo-specificity of enzymes for their substrate(s). The fully differentiated mammalian erythrocyte has no sub-cellular organelles and yet it displays compartmentation of lactic acid that is generated either by glycolysis or the glyoxalase pathway. A form of 'operational compartmentation' exists, based not on the chemistry of the reactive groups in the molecules but their stereoisomerism. This we call 'chiral compartmentation', and the rationale for its 'natural selection' in the erythrocyte (and presumably in the cytoplasm of other cells) is discussed. Increasing awareness of the presence of d-amino acids in proteins in the otherwise dominant 'L-chiral biosphere', and of the preferential use of one enantiomer of a metabolite versus the other is largely due to recent developments in rapidly-applicable, analytical-chemical methods. We confirmed that the glyoxalase pathway yields D-lactic acid by using nuclear magnetic resonance (NMR) spectroscopy of stretched chiral hydrogels. The activities of the two lactate-producing pathways have been described by numerical integration of simultaneous non-linear differential equations, based on enzyme models like that introduced by Michaelis and Menten in 1913.
Publisher: Elsevier BV
Date: 11-2013
Publisher: Cold Spring Harbor Laboratory
Date: 05-2021
DOI: 10.1101/2021.04.30.440339
Abstract: Experimental data about known gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a ten-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills. The primary scientific literature catalogs the results from publicly funded scientific research about gene function in human-readable format. Information captured from those studies in a widely adopted, machine-readable standard format comes in the form of Gene Ontology annotations about gene functions from all domains of life. Manual annotations based on inferences directly from the scientific literature, including the evidence used to make such inferences, represents the best return on investment by improving data accessibility across the biological sciences. To supplement professional curation, our CACAO project enabled annotation of the scientific literature by community annotators, in this case undergraduates, which resulted in contribution of thousands of validated entries to public resources. These annotations are now being used by scientists worldwide.
Publisher: American Chemical Society (ACS)
Date: 09-03-2009
DOI: 10.1021/BM8014413
Abstract: A (1)H NMR method is presented that monitors the initial and later stages of in vitro enzymatic digestion of starch suspensions. It allows, for the first time to our knowledge, the accurate analysis of the initial 5% of the extent of hydrolysis. This is significant because rapidly digested starch produces glucose that determines the blood glucose concentration immediately after ingestion of food. The two key hydrolytic enzymes, alpha-amylase and amyloglucosidase, showed clear systematic deviation from Michaelis-Menten kinetics as the starch or wheat flour substrate that was used changed its character during the reaction. Estimates of Michaelis-Menten parameters for amyloglucosidase and alpha-amylase were successfully found by analyzing two stages of digestion separately. The Michaelis-Menten constants for purified starch were (6.4 +/- 0.8) and (1.1 +/- 0.3) g dL(-1) (% w/v), respectively and the maximum velocities of glucose release by amyloglucosidase, and short oligoglucosides and glucose by alpha-amylase were (1.9 +/- 0.4) x 10(-2) and (1.6 +/- 0.2) x 10(-2) mmol L(-1) s(-1) for the first stage of digestion, and (9.0 +/- 1.0) x 10(-3) and (4.7 +/- 1.4) x 10(-3) mmol L(-1) s(-1) for the second stage, giving a ratio of the two V(max) values of 2.1 and 3.4, respectively.
Publisher: Springer Science and Business Media LLC
Date: 27-01-2013
DOI: 10.1038/NMETH.2340
Publisher: Wiley
Date: 25-08-2010
DOI: 10.1002/MRM.22457
Abstract: Pulsed field-gradient spin-echo (PGSE) NMR spectroscopy via q-space plots can characterize erythrocyte shapes and their evolution. The present study employed PGSE NMR to investigate shape reversion from advanced echinocytic to normal discocytic shapes due to depletion and then readdition of Mg(2+). In q-space plots of the data, the diffusion-diffraction minima disappeared for Mg(2+)-depleted erythrocytes and reappeared during the shape recovery process, but with lower definition than for control cells. Shape estimates from PGSE NMR spectra and light microscopy were in excellent agreement after application of a scaling/correction factor. (31)P NMR was used to probe the biochemical processes activated in erythrocytes after depletion or addition of Mg(2+) it showed the activation of the nonoxidative part of the pentose phosphate pathway. Experimental conditions were optimized to bypass this pathway without any influence on the q-space plots. The release of choline from phosphatidylcholine in the outer leaflet of the plasma membrane of the cells, observed using (1)H spin-echo NMR, showed a higher rate for shape-recovered than for control cells. This points to a change in phospholipid asymmetry in the plasma membrane. This variation in asymmetry affected the mean cell shape and hence influenced the average alignment of the erythrocytes with the static magnetic field and so affected the shapes of the q-space plots.
Publisher: Elsevier BV
Date: 05-2014
DOI: 10.1016/J.MRI.2014.01.001
Abstract: Foot dorsi and plantar flexion affects the pennation angle of skeletal muscle fibers and changes the fiber direction with respect to the main magnetic field, thereby affecting MR spectrum of the muscle. In order to analyze the effect that foot flexion has on the MR spectrum, tibialis anterior (TA) and soleus muscles were studied in humans and rats. Localized MRS was performed at different foot angles in clinical and pre-clinical settings using a 3T MRI/MRS GE Excite HD and 7T Bruker Clinscan scanner, respectively. In this study we show the effect of foot angle variation on total Creatine (tCr) resonance of (1)H spectrum at 3.03 and 3.93ppm for TA and soleus muscles. In addition to this, we observe a 4-line splitting pattern for methylene resonance of tCr in the rat TA spectrum for a specific foot angle. This observation is attributed to the in idual splitting of creatine and phosphocreatine of the tCr signal. Novel hydrogel application is demonstrated and used to support our in vivo observations and for the first time splitting of in idual resonances of Cr and PCr has been shown in an in vitro set-up.
Publisher: Elsevier BV
Date: 09-2012
DOI: 10.1016/J.JMR.2012.06.006
Abstract: In NMR spectroscopy of the liquid state T(1) is typically measured using an inversion recovery pulse sequence but with hyperpolarized spins use is made of a sequence of multiple small radiofrequency (RF) induced nutations, α. Depending on the values of α and τ, the time interval between the pulses, the estimate of T(1) can be artifactually smaller than the real value so without knowing the value of α the estimate of T(1) can be incorrect. Thus, we propose a method that involves a series of pulses with timing governed by a geometric sequence (or in general, any mathematically specified non-uniformly spaced sequence). This approach enables the simultaneous estimation of both the intrinsic T(1) value and α. The method was successfully applied to obtain T(1)=(44.9 ± 0.3)s and α=(4.0 ± 0.2)° (n=3) for a s le of hyperpolarized (13)C-urea in solution, matching with the inversion recovery pulse sequence estimate of T(1)=44 ± 2s using non-hyperpolarized (13)C-urea in solution.
Publisher: Elsevier BV
Date: 10-2011
Publisher: Wiley
Date: 09-2012
DOI: 10.1002/CMR.A.21241
Publisher: Elsevier BV
Date: 2009
Publisher: Springer Science and Business Media LLC
Date: 19-11-2019
DOI: 10.1186/S13059-019-1835-8
Abstract: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster , which we suspected of being involved in long-term memory. We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster , it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.
Publisher: Springer Science and Business Media LLC
Date: 03-05-2013
DOI: 10.1007/S00249-012-0808-6
Abstract: The unique gating kinetics of hERG K(+) channels are critical for normal cardiac repolarization, and patients with mutations in hERG have a markedly increased risk of cardiac arrhythmias and sudden cardiac arrest. HERG K(+) channels are also remarkably promiscuous with respect to drug binding, which has been a very significant problem for the pharmaceutical industry. Here, we review the progress that has been made in understanding the structure and function of hERG K(+) channels with a particular focus on nuclear magnetic resonance studies of the domains of the hERG K(+) channel.
Publisher: Wiley
Date: 30-03-2014
DOI: 10.1016/J.FEBSLET.2014.03.044
Abstract: The three-dimensional structure of a chemically synthesized peptide that we have called 'intermediate' defensin-like peptide (Int-DLP), from the platypus genome, was determined by nuclear magnetic resonance (NMR) spectroscopy and its antimicrobial activity was investigated. The overall structural fold of Int-DLP was similar to that of the DLPs and β-defensins, however the presence of a third antiparallel β-strand makes its structure more similar to the β-defensins than the DLPs. Int-DLP displayed potent antimicrobial activity against Staphylococcus aureus and Pseudomonas aeruginosa. The four arginine residues at the N-terminus of Int-DLP did not affect the overall fold, but were important for its antimicrobial potency.
Publisher: Springer Science and Business Media LLC
Date: 14-03-2014
DOI: 10.1007/S10858-014-9821-7
Abstract: The longitudinal (T 1), transverse (T 2), and singlet state (T s) relaxation times of the geminal backbone protons (CH2) of L-Leu-Gly-Gly were studied by NMR spectroscopy at 9.4 T in a bovine hide gelatin gel composed in D2O at 25 °C. Gelatin granules were dissolved in a hot solution of the tripeptide and then the solution was allowed to gel inside a flexible silicone tubing. With increases in gelatin content, the T 2 and T s of the CH2 protons correspondingly decreased (T s/T 2 ~ constant), while the change in T 1 was relatively small. The largest observed T s/T 1 value was 3.3 at 46% w/v gelatin that was the lowest gelatin content examined. Stretching the tubing, and hence the gel, brought about anisotropic alignment of the constituents resulting in residual quadrupolar splitting of the resonance from D2O in (2)H NMR spectra, and residual dipolar splitting of the CH2 resonance in (1)H NMR spectra. WALTZ-16 decoupling during the relaxation intervals extended the singlet state relaxation time, but the efficacy diminished as the gels were stretched. Theoretically predicted T 1, T 2, and T s values, assuming intramolecular dipolar coupling as the only source of relaxation, were within the same order of magnitude as the experimentally observed values. Overall we showed that it is possible to observe a long-lived spin state in an anisotropic medium when T 2 is shorter than T 1 in the presence of non-zero residual dipolar couplings.
Publisher: Elsevier BV
Date: 05-05-2010
Publisher: SAGE Publications
Date: 15-05-2013
Abstract: 2-Deoxy-D-glucose (2DG) is a known surrogate molecule that is useful for inferring glucose uptake and metabolism. Although 13 C-labeled 2DG can be detected by nuclear magnetic resonance (NMR), its low sensitivity for detection prohibits imaging to be performed. Using chemical exchange saturation transfer (CEST) as a signal- lification mechanism, 2DG and the phosphorylated 2DG-6-phosphate (2DG6P) can be indirectly detected in 1 H magnetic resonance imaging (MRI). We showed that the CEST signal changed with 2DG concentration, and was reduced by suppressing cerebral metabolism with increased general anesthetic. The signal changes were not affected by cerebral or plasma pH, and were not correlated with altered cerebral blood flow as demonstrated by hypercapnia neither were they related to the extracellular glucose amounts as compared with injection of D- and L-glucose. In vivo 31 P NMR revealed similar changes in 2DG6P concentration, suggesting that the CEST signal reflected the rate of glucose assimilation. This method provides a new way to use widely available MRI techniques to image deoxyglucose/glucose uptake and metabolism in vivo without the need for isotopic labeling of the molecules.
Publisher: Wiley
Date: 02-07-2015
DOI: 10.1002/MRM.25345
Abstract: To introduce a direct method for estimating relaxation and kinetic parameter values from rapid dissolution dynamic nuclear polarization (RD-DNP) NMR time courses. The analysis relied on a kinetic model that is often used to analyze data in these studies-a unidirectional (bio)chemical reaction with rate constant k1 , coupled to longitudinal relaxation of the magnetization of substrate and product that is characterized by the time constant T1 . The latter value was estimated from the width of the product curve (peak) at the height α relative to the maximum height. We showed α ∼ 0.8 under most conditions, so we measured the interval between the falling and rising parts of the curve at the relative height 0.8. We called this the "fall-minus-rise time at height α," or FmRα , and found that FmR0.8 ∼ T1 . The ratio β = (product signal/substrate signal) when the product is maximal was shown to be equal to k1 T1 . Therefore, k1 = β/FmR0.8 . FmRα analysis was demonstrated with (13) C NMR RD-DNP data recorded from hemolysates and from previously published data. FmRα analysis enables immediate estimates of kinetic and relaxation parameters from (13) C NMR RD-DNP data. The values can be used as initial estimates in more extensive computer-based data-regression analysis.
Publisher: Wiley
Date: 24-11-2008
DOI: 10.1002/JMRI.21588
Abstract: To monitor red blood cell (RBC) shape evolution by (1)H(2)O diffusion-diffraction NMR in time steps comparable to those required for the acquisition of a (31)P NMR spectrum thus, to correlate RBC mean diameter with ATP concentration after poisoning with NaF. Pulsed-field gradient-stimulated echo (PFGSTE) diffusion experiments were recorded on (1)H(2)O in RBC suspensions. Under conditions of restricted diffusion, q-space experiments report on mean RBC diameter. To decrease experiment time, the phase cycling of radiofrequency (RF) pulses was cut to two transients by using unbalanced pairs of gradient pulses. Data processing used a recent digital filter. Differential interference contrast (DIC) light microscopy also recorded shape changes. (31)P NMR spectroscopy gave estimates of mean ATP concentration. NaF caused RBC-shape evolution from discocytes, through various forms of echinocytes, to spherocytes, over approximately 6 h and approximately 10 h at 37 degrees C and 25 degrees C, respectively. ATP declined to approximately 0.5 its normal concentration before the first stage of discocyte transformation the concentration was 0.0 after approximately 1.5 h and 3.0 h, respectively, at the two temperatures. RBC shape was readily monitored by NMR with a temporal resolution that was useful for correlations with both DIC microscopy and (31)P NMR spectra.
Publisher: Springer Science and Business Media LLC
Date: 07-09-2016
Location: United States of America
Location: France
Location: No location found
Location: United States of America
No related grants have been discovered for Iddo Friedberg.