Cynthia K. Larive

Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana.

Cellular oxygen deprivation (hypoxia/anoxia) requires an acclimation response that enables survival during an energy crisis. To gain new insights into the processes that facilitate the endurance of transient oxygen deprivation, the dynamics of the mRNA translation state and metabolites were quantitatively monitored in Arabidopsis thaliana seedlings exposed to a short (2 h) or prolonged (9 h) period of oxygen and carbon dioxide deprivation and following 1 h of re-aeration. Hypoxia stress and reoxygenation promoted adjustments in the levels of polyribosomes (polysomes) that were highly coordinated with cellular ATP content. A quantitative comparison of steady-state and polysomal mRNA populations revealed that over half of the cellular mRNAs were restricted from polysome complexes during the stress, with little or no change in abundance. This selective repression of translation was rapidly reversed upon reoxygenation. Comparison of the adjustment in gene transcripts and metabolites demonstrated that profiling of polysomal mRNAs strongly augments the prediction of cellular processes that are altered during cellular oxygen deprivation. The selective translation of a subset of mRNAs promotes the conservation of ATP and facilitates the transition to anaerobic metabolism during low-oxygen stress.

Quantitative NMR for bioanalysis and metabolomics

Over the last several decades, significant technical and experimental advances have made quantitative nuclear magnetic resonance (qNMR) a valuable analytical tool for quantitative measurements on a wide variety of samples. In particular, qNMR has emerged as an important method for metabolomics studies where it is used for interrogation of large sets of biological samples and the resulting spectra are treated with multivariate statistical analysis methods. In this review, recent developments in instrumentation and pulse sequences will be discussed as well as the practical considerations necessary for acquisition of quantitative NMR experiments with an emphasis on their use for bioanalysis. Recent examples of the application of qNMR for metabolomics/metabonomics studies, the characterization of biologicals such as heparin, antibodies, and vaccines, and the analysis of botanical natural products will be presented and the future directions of qNMR discussed.

Analysis and characterization of heparin impurities

AbstractThis review discusses recent developments in analytical methods available for the sensitive separation, detection and structural characterization of heparin contaminants. The adulteration of raw heparin with oversulfated chondroitin sulfate (OSCS) in 2007–2008 spawned a global crisis resulting in extensive revisions to the pharmacopeia monographs on heparin and prompting the FDA to recommend the development of additional physicochemical methods for the analysis of heparin purity. The analytical chemistry community quickly responded to this challenge, developing a wide variety of innovative approaches, several of which are reported in this special issue. This review provides an overview of methods of heparin isolation and digestion, discusses known heparin contaminants, including OSCS, and summarizes recent publications on heparin impurity analysis using sensors, near-IR, Raman, and NMR spectroscopy, as well as electrophoretic and chromatographic separations. FigureSchematic illustrating the process for heparin impurity characterization

Two Rumex Species from Contrasting Hydrological Niches Regulate Flooding Tolerance through Distinct Mechanisms

Rumex palustris and Rumex acetosa are two closely related species that survive flooding using distinct strategies. Using a genomics approach, this study identifies novel molecular components and processes that contribute to the survival of these plant species that normally complete their life cycle in flood-prone environments. Global climate change has increased flooding events, which affect both natural vegetation dynamics and crop productivity. The flooded environment is lethal for most plant species because it restricts gas exchange and induces an energy and carbon crisis. Flooding survival strategies have been studied in Oryza sativa, a cultivated monocot. However, our understanding of plant adaptation to natural flood-prone environments remains scant, even though wild plants represent a valuable resource of tolerance mechanisms that could be used to generate stress-tolerant crops. Here we identify mechanisms that mediate the distinct flooding survival strategies of two related wild dicot species: Rumex palustris and Rumex acetosa. Whole transcriptome sequencing and metabolite profiling reveal flooding-induced metabolic reprogramming specific to R. acetosa. By contrast, R. palustris uses the early flooding signal ethylene to increase survival by regulating shade avoidance and photomorphogenesis genes to outgrow submergence and by priming submerged plants for future low oxygen stress. These results provide molecular resolution of flooding survival strategies of two species occupying distinct hydrological niches. Learning how these contrasting flood adaptive strategies evolved in nature will be instrumental for the development of stress-tolerant crop varieties that deliver enhanced yields in a changing climate.

Heparin characterization: Challenges and solutions

Although heparin is an important and widely prescribed pharmaceutical anticoagulant, its high degree of sequence microheterogeneity and size polydispersity make molecular-level characterization challenging. Unlike nucleic acids and proteins that are biosynthesized through template-driven assembly processes, heparin and the related glycosaminoglycan heparan sulfate are actively remodeled during biosynthesis through a series of enzymatic reactions that lead to variable levels of O- and N-sulfonation and uronic acid epimers. As summarized in this review, heparin sequence information is determined through a bottom-up approach that relies on depolymerization reactions, size- and charge-based separations, and sensitive mass spectrometric and nuclear magnetic resonance experiments to determine the structural identity of component oligosaccharides. The structure-elucidation process, along with its challenges and opportunities for future analytical improvements, is reviewed and illustrated for a heparin-derived hexasaccharide.

Comparison of GC-MS and NMR for Metabolite Profiling of Rice Subjected to Submergence Stress.

Natural disasters such as drought, extreme temperatures, and flooding can severely impact crop production. Understanding the metabolic response of crops threatened with these disasters provides insights into biological response mechanisms that can influence survival. In this study, a comparative analysis of GC-MS and (1)H NMR results was conducted for wild-type and tolerant rice varieties stressed by up to 3 days of submergence and allowed 1 day of postsubmergence recovery. Most metabolomics studies are conducted using a single analytical platform. Each platform, however, has inherent advantages and disadvantages that can influence the analytical coverage of the metabolome. In this work, a more thorough analysis of the plant stress response was possible through the use of both (1)H NMR and GC-MS. Several metabolites, such as S-methyl methionine and the dipeptide alanylglycine, were only detected and quantified by (1)H NMR. The high dynamic range of NMR, as compared with that of the GC-TOF-MS used in this study, provided broad coverage of the metabolome in a single experiment. The sensitivity of GC-MS facilitated the quantitation of sugars, organic acids, and amino acids, some of which were not detected by NMR, and provided additional insights into the regulation of the TCA cycle. The combined metabolic information provided by (1)H NMR and GC-MS was essential for understanding the complex biochemical and molecular response of rice plants to submergence.

Analysis of Diffusion Coefficient Distributions in Humic and Fulvic Acids by Means of Diffusion Ordered NMR Spectroscopy

The use of the computer program CONTIN to analyze pulsed-field gradient NMR (PFG-NMR) data for several standard humic and fulvic acids is described. An advantage of PFG-NMR analysis is that integration of different spectral regions provides a picture of how the diffusion coefficients vary with functional group composition for a given sample. Using prior knowledge of the sample and the principle of parsimony, CONTIN approximates a solution to the inverse Laplace transform applied to the decay of peak intensity with gradient area in the PFG-NMR experiment. Thus, a continuous distribution of diffusion coefficients is resolved for the polydisperse humic and fulvic acids. The results of the CONTIN analyses are in the form of a distribution function and a two-dimensional DOSY plot. The 2D DOSY spectrum displays chemical shifts along one axis and diffusion coefficients along the other, while a number-average diffusion coefficient, D(N), a weight-average diffusion coefficient, D(W), and a most probable diffusion coefficient, D(P), are realized from the diffusion coefficient distribution. For all spectral regions of each humic sample, D(W) was greater than D(N), which in turn was greater than or equal to the D(P), suggesting that the diffusion coefficient distribution is weighted toward smaller, more rapidly diffusing molecules. Polydispersities, estimated from the ratio D(W)/D(N), were less than the reported M(W)/M(N) values for similar humic substances. Thus, the D(W)/D(N) ratio obtained by CONTIN analysis of PFG-NMR data can be at least a qualitative, and at best a semiquantitative, indication of the polydispersity of the humic sample, but should not be used as a quantitative measure of polydispersity.

A comparison of metabolite extraction strategies for 1H-NMR-based metabolic profiling using mature leaf tissue from the model plant Arabidopsis thaliana

Metabolite analysis is recognized as an important facet of systems biology, however complete metabolome characterization has not been realized due to challenges in sample preparation, inherent instrumental limitations and the labor intensive task of data interpretation. This work aims to compare several commonly used metabolite extraction strategies for their effect on the 1H nuclear magnetic resonance (NMR) metabolic profile of extracts of the model plant Arabidopsis thaliana. Extractions were carried out on aliquots from a pool of homogenized plant tissue using CD3CN/D2O, buffered D2O, perchloric acid in D2O, CD3OD/D2O and CD3OD/D2O/CDCl3 as the extraction solvents. The effects of lyophilization as a sample pretreatment, solvent evaporation and extract fractionation for removal of interfering species were studied. Representative spectra are presented for qualitative interpretation. Analytical reproducibility was evaluated by principal components analysis. Perchloric acid facilitated acid‐catalyzed cleavage of sucrose, further complicating biological interpretation of the resulting metabolite profile. The solvent system CD3OD/D2O/CDCl3 gave the least reproducible results in our hands. D2O extracts suffered from poor stability probably due to contamination by soluble enzymes, which were not denatured in this solvent. CD3CN/D2O extracts showed greater stability than D2O alone, but problems were encountered due to degradation of 1H NMR spectral resolution during lengthy acquisitions due to partial phase separation. In addition, this solvent system produced spectra with significant contamination by lipids that obscured spectral regions containing the resonances of the aliphatic amino acids. These problems were solved by speedvacuuming the CD3CN/D2O extract and reconstituting in D2O solution. Copyright

Measurement of SDS Micelle-Peptide Association Using 1H NMR Chemical Shift Analysis and Pulsed-Field Gradient NMR Spectroscopy

The binding of two simple tripeptides, glycyl-histidyl-glycine (GHG) and phenylalanyl-histidyl-phenylalanine (FHF) with SDS micelles was examined using (1)H NMR chemical shift analysis and self-diffusion coefficients measured with pulsed-field gradient NMR spectroscopy. The presence of GHG or FHF did not appear to significantly affect the critical micelle concentration (cmc) or the average size of the SDS micelles formed. The chemical shifts of several of the GHG resonances change as a function of SDS concentration, indicating an interaction between the peptide and the micelles. In addition, the concentration-dependent decrease observed for the GHG diffusion coefficients suggests association of the peptide with SDS micelles. The free and micelle-associated GHG are in fast exchange on both the (1)H chemical shift and diffusion time scales. The equilibrium constant for the binding of GHG to SDS micelles was determined from the analysis of the concentration dependence of the histidine C2 and C4 resonances to be 17 ± 5 and 24 ± 6 M(-)(1), respectively. The precision of the equilibrium constants obtained by analysis of the chemical shift data is limited by the small chemical shift changes observed. Analysis of the concentration dependence of the diffusion coefficients produced an equilibrium constant of 17 ± 1 M(-)(1). The more hydrophobic peptide, FHF is strongly associated with the SDS micelles. Because the fraction of free FHF is small in these solutions, it was not possible to determine a formation constant for the interaction of FHF with the SDS micelles by analysis of either the (1)H chemical shift or diffusion coefficient data. The cmc of SDS in 0.10 M Na(2)C(2)O(4) buffer was determined to be 5.4 ± 0.1 mM by analysis of the SDS diffusion coefficients in the absence of the peptides. The SDS cmc could also be extracted from the GHG and FHF diffusion coefficients measured as a function of the SDS concentration. The cmc determined from the GHG diffusion data, 5.7 ± 0.2 mM, is in good agreement with the value determined from analysis of the SDS diffusion coefficients in the 5.0 mM GHG solution, 5.2 ± 0.1 mM. The smaller cmc determined from the FHF diffusion data, 4.1 ± 0.1 mM, may reflect some association of the SDS with the peptide prior to micelle formation in bulk solution.

Quantitative analysis of peptides with NMR spectroscopy

The determination of peptide concentration with 1H nuclear magnetic resonance (NMR) spectroscopy using an internal standard or an external standard in a sealed glass capillary was investigated for three tyrosine-containing tripeptides. Trimethylsilylpropionic acid (TSP) and maleic acid were tested as external standards for quantitation by proton NMR. Although comparable results were obtained for either standard, the performance of maleic acid was found to be superior because of its better long-term stability in the sealed capillary. Loss of TSP from solution occurred over time due to adsorption onto the walls of the capillary, necessitating frequent recalibration against the primary standard, potassium acid phthalate (KHP). The peptide contents of solid peptides determined with 1H NMR are compared with those obtained from ultraviolet (UV) absorbance measurements of the tyrosine chromophore. The versatility of NMR for the quantitative analysis of peptides that do not contain an appropriate UV chromophore make it well-suited for the determination of peptide concentration in aggregation studies or for the preparation of solutions for high-throughput screening of biological activity.