Determination of cell volume as part of metabolomics experiments.

Cells regulate their cell volume, but cell volumes may change in response to metabolic and other perturbations. Many metabolomics experiments use cultured cells to measure changes in metabolites in response to physiological and other experimental perturbations, but the metabolomics workflow by mass spectrometry only determines total metabolite amounts in cell culture extracts. To convert metabolite amount to metabolite concentration requires knowledge of the number and volume of the cells. Measuring only metabolite amount can lead to incorrect or skewed results in cell culture experiments because cell size may change due to experimental conditions independent of change in metabolite concentration. We have developed a novel method to determine cell volume in cell culture experiments using a pair of stable isotopically labeled phenylalanine internal standards incorporated within the normal liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics workflow. This method relies on the flooding-dose technique where the intracellular concentration of a particular compound (in this case phenylalanine) is forced to equal its extracellular concentration. We illustrate the LC-MS/MS technique for two different mammalian cell lines. Although the method is applicable in general for determining cell volume, the major advantage of the method is its seamless incorporation within the normal metabolomics workflow.

Total Retention Liquid Chromatography-Mass Spectrometry to Achieve Maximum Protein Sequence Coverage.

Peptide identification by liquid chromatography-mass spectrometry (LC-MS) requires retention and elution of peptides from the LC column. Although medium and hydrophobic peptides are readily retained by the C18 columns that are commonly used in proteomics, short and hydrophilic peptides are not retained nor measured by MS due to their elution in the void volume after sample injection. These nonretained peptides can possess important post-translational modifications, such as glycosylation or phosphorylation. We describe a total retention LC-MS method that employs a reverse phase C18 column and porous graphitic carbon (PGC) column to retain both hydrophobic and hydrophilic peptides for LC-MS analysis. Our setup uses a single valve with a trapping column and two LC pumps run at low microliter/minute flow rates to deliver separate gradients to parallel capillary C18 and PGC columns. Our capillary LC system balances the need for high sensitivity with ease of implementation as compared to other 2D LC systems that use nanocolumns with multiple trapping columns and multiport valves. We demonstrate the utility of the method identifying hydrophilic peptides that went undetected when only a C18 nanocolumn was used. These missed hydrophilic peptides include tripeptides and N-glycosylated species.

Differential effects of the cystic fibrosis lung inflammatory environment on mesenchymal stromal cells.

Growing evidence demonstrates that human mesenchymal stromal cells (MSCs) modify their in vivo anti-inflammatory actions depending on the specific inflammatory environment encountered. Understanding this better is crucial to refine MSC-based cell therapies for lung and other diseases. Using acute exacerbations of cystic fibrosis (CF) lung disease as a model, the effects of ex vivo MSC exposure to clinical bronchoalveolar lavage fluid (BALF) samples, as a surrogate for the in vivo clinical lung environment, on MSC viability, gene expression, secreted cytokines, and mitochondrial function were compared with effects of BALF collected from healthy volunteers. CF BALF samples that cultured positive for Aspergillus sp. (Asp) induced rapid MSC death, usually within several hours of exposure. Further analyses suggested the fungal toxin gliotoxin as a potential mediator contributing to CF BALF-induced MSC death. RNA sequencing analyses of MSCs exposed to either Asp+ or Asp- CF BALF samples identified a number of differentially expressed transcripts, including those involved in interferon signaling, antimicrobial gene expression, and cell death. Toxicity did not correlate with bacterial lung infections. These results suggest that the potential use of MSC-based cell therapies for CF or other lung diseases may not be warranted in the presence of Aspergillus.

Review of Lysine Metabolism with a Focus on Humans.

Lysine cannot be synthesized by most higher organisms and, therefore, is an indispensable amino acid (IAA) that must be consumed in adequate amounts to maintain protein synthesis. Although lysine is an abundant amino acid in body proteins, lysine is limited in abundance in many important food sources (e.g. grains). Older observations assigned importance to lysine because animals fed a lysine-deficient diet did not lose weight as fast as animals placed upon other IAA-deficient diets, leading to the theory that there may be a special pool of lysine or metabolites that could be converted to lysine. The first step in the lysine catabolic pathway is the formation of saccharopine and then 2-aminoadipic acid, processes that are mitochondrial. The catabolism of 2-aminoadipic acid proceeds via decarboxylation to a series of CoA esters ending in acetyl-CoA. In mammals, the liver appears to be the primary site of lysine catabolism. In humans, the metabolic and oxidative response of lysine to diets either restricted in protein or in lysine is consistent with what has been measured for other IAAs with isotopically labeled tracers. Intestinal microflora are known to metabolize urea to ammonia and scavenge nitrogen (N) for the synthesis of amino acids. Studies feeding 15N-ammonium chloride or 15N-urea to animals and to humans, demonstrate the appearance of 15N-lysine in gut microbial lysine and in host lysine. However, the amount of 15N-lysine transferred to the host is difficult to assess directly using current methods. It is important to understand the role of the gut microflora in human lysine metabolism, especially in conditions where dietary lysine intake may be limited, but better methods need to be devised.

An N-terminally truncated form of cyclic GMP-dependent protein kinase Iα (PKG Iα) is monomeric and autoinhibited and provides a model for activation.

The type I cGMP-dependent protein kinases (PKG I) serve essential physiological functions, including smooth muscle relaxation, cardiac remodeling, and platelet aggregation. These enzymes form homodimers through their N-terminal dimerization domains, a feature implicated in regulating their cooperative activation. Previous investigations into the activation mechanisms of PKG I isoforms have been largely influenced by structures of the cAMP-dependent protein kinase (PKA). Here, we examined PKG Iα activation by cGMP and cAMP by engineering a monomeric form that lacks N-terminal residues 1-53 (Δ53). We found that the construct exists as a monomer as assessed by whole-protein MS, size-exclusion chromatography, and small-angle X-ray scattering (SAXS). Reconstruction of the SAXS 3D envelope indicates that Δ53 has a similar shape to the heterodimeric RIα-C complex of PKA. Moreover, we found that the Δ53 construct is autoinhibited in its cGMP-free state and can bind to and be activated by cGMP in a manner similar to full-length PKG Iα as assessed by surface plasmon resonance (SPR) spectroscopy. However, we found that the Δ53 variant does not exhibit cooperative activation, and its cyclic nucleotide selectivity is diminished. These findings support a model in which, despite structural similarities, PKG Iα activation is distinct from that of PKA, and its cooperativity is driven by in trans interactions between protomers.

Uricase Inhibits Nitrogen Dioxide-Promoted Allergic Sensitization to Inhaled Ovalbumin Independent of Uric Acid Catabolism.

Nitrogen dioxide (NO2) is an environmental air pollutant and endogenously generated oxidant that contributes to the exacerbation of respiratory disease and can function as an adjuvant to allergically sensitize to an innocuous inhaled Ag. Because uric acid has been implicated as a mediator of adjuvant activity, we sought to determine whether uric acid was elevated and participated in a mouse model of NO2-promoted allergic sensitization. We found that uric acid was increased in the airways of mice exposed to NO2 and that administration of uricase inhibited the development of OVA-driven allergic airway disease subsequent to OVA challenge, as well as the generation of OVA-specific Abs. However, uricase was itself immunogenic, inducing a uricase-specific adaptive immune response that occurred even when the enzymatic activity of uricase had been inactivated. Inhibition of the OVA-specific response was not due to the capacity of uricase to inhibit the early steps of OVA uptake or processing and presentation by dendritic cells, but occurred at a later step that blocked OVA-specific CD4(+) T cell proliferation and cytokine production. Although blocking uric acid formation by allopurinol did not affect outcomes, administration of ultra-clean human serum albumin at protein concentrations equivalent to that of uricase inhibited NO2-promoted allergic airway disease. These results indicate that, although uric acid levels are elevated in the airways of NO2-exposed mice, the powerful inhibitory effect of uricase administration on allergic sensitization is mediated more through Ag-specific immune deviation than via suppression of allergic sensitization, a mechanism to be considered in the interpretation of results from other experimental systems.

Increased palmitate intake: higher acylcarnitine concentrations without impaired progression of ß-oxidation.

Palmitic acid (PA) is associated with higher blood concentrations of medium-chain acylcarnitines (MCACs), and we hypothesized that PA may inhibit progression of FA ß-oxidation. Using a cross-over design, 17 adults were fed high PA (HPA) and low PA/high oleic acid (HOA) diets, each for 3 weeks. The [1-(13)C]PA and [13-(13)C]PA tracers were administered with food in random order with each diet, and we assessed PA oxidation (PA OX) and serum AC concentration to determine whether a higher PA intake promoted incomplete PA OX. Dietary PA was completely oxidized during the HOA diet, but only about 40% was oxidized during the HPA diet. The [13-(13)C]PA/[1-(13)C]PA ratio of PA OX had an approximate value of 1.0 for either diet, but the ratio of the serum concentrations of MCACs to long-chain ACs (LCACs) was significantly higher during the HPA diet. Thus, direct measurement of PA OX did not confirm that the HPA diet caused incomplete PA OX, despite the modest, but statistically significant, increase in the ratio of MCACs to LCACs in blood.

Disulfide reduction abolishes tissue factor cofactor function.

BACKGROUND: Tissue factor (TF), an in vivo initiator of blood coagulation, is a transmembrane protein and has two disulfides in the extracellular domain. The integrity of one cysteine pair, Cys186-Cys209, has been hypothesized to be essential for an allosteric "decryption" phenomenon, presumably regulating TF procoagulant function, which has been the subject of a lengthy debate. The conclusions of published studies on this subject are based on indirect evidences obtained by the use of reagents with potentially oxidizing/reducing properties. METHODS: The status of disulfides in recombinant TF1-263 and natural placental TF in their non-reduced native and reduced forms was determined by mass-spectrometry. Functional assays were performed to assess TF cofactor function. RESULTS: In native proteins, all four cysteines of the extracellular domain of TF are oxidized. Reduced TF retains factor VIIa binding capacity but completely loses the cofactor function. CONCLUSION: The reduction of TF disulfides (with or without alkylation) eliminates TF regulation of factor VIIa catalytic function in both membrane dependent FX activation and membrane independent synthetic substrate hydrolysis. GENERAL SIGNIFICANCE: Results of this study advance our knowledge on TF structure/function relationships.

Determination of steady-state protein breakdown rate in vivo by the disappearance of protein-bound tracer-labeled amino acids: a method applicable in humans.

A method to determine the rate of protein breakdown in individual proteins was developed and tested in rats and confirmed in humans, using administration of deuterium oxide and incorporation of the deuterium into alanine that was subsequently incorporated into body proteins. Measurement of the fractional breakdown rate of proteins was determined from the rate of disappearance of deuterated alanine from the proteins. The rate of disappearance of deuterated alanine from the proteins was calculated using an exponential decay, giving the fractional breakdown rate (FBR) of the proteins. The applicability of this protein-specific FBR approach is suitable for human in vivo experimentation. The labeling period of deuterium oxide administration is dependent on the turnover rate of the protein of interest.

Increased total daily energy expenditure in mild to moderate ALS: greater contribution from physical activity energy expenditure than hyper-metabolism.

Objective: It is unknown whether the relative contribution to energy imbalance in amyotrophic lateral sclerosis (ALS) is due to decreased energy intake, or increased energy expenditure from hyper-metabolism and/or physical activity, or both. Methods: We studied 10 free-living sporadic ALS subjects with mild to moderate disease and 10 matched healthy controls to address this question. We estimated energy intake by 24-h recall in ALS subjects and three-day food diary in all. We estimated body composition by dual energy X-ray absorptiometry and resting metabolic rate by indirect calorimetry; and measured total daily energy expenditure (TEE) and physical activity-energy expenditure using doubly labeled water. Results: Daily energy intake was no different between ALS subjects and controls. Despite lower fat-free mass, unadjusted TEE was higher in ALS subjects than controls (2844 ± 319 vs. 2505 ± 261 kcal/d, p = 0.005 by paired t-test). Compared to controls, hyper-metabolism occurred in 80% of ALS subjects. Physical activity-energy expenditure was higher in ALS subjects than controls (718 ± 262 kcal/d vs. 487 ± 196 kcal/d, p = 0.04). In controls, energy intake matched TEE; in ALS subjects TEE was higher than energy intake. Conclusions: We found higher TEE in ALS subjects than controls, with larger contribution to difference from physical activity-energy expenditure than hyper-metabolism. Although daily energy intake in ALS subjects was similar to that in controls, they were unable to compensate for increased energy needs. To accurately determine energy balance and optimize nutrition in ALS, future studies should consider measuring energy intake, energy expenditure, and physical activity.

Differences in the fractional abundances of carbohydrates of natural and recombinant human tissue factor.

BACKGROUND: Tissue factor (TF) is a single polypeptide integral membrane glycoprotein composed of 263 residues and is essential to life in its role as the initiator of blood coagulation. Previously we have shown that the activity of the natural placental TF (pTF) and the recombinant TF (rTF) from Sf9 insect cells is different (Krudysz-Amblo, J. et al (2010) J. Biol. Chem. 285, 3371-3382). METHODS: In this study, using mass spectrometry, we show by quantitative analysis that the extent of glycosylation varies on each protein. RESULTS AND CONCLUSIONS: Fractional abundance of each glycan composition at each of the three glycosylation sites reveals the most pronounced difference to be at asparagine (Asn) 11. This residue is located in the region of extensive TF-factor VIIa (FVIIa) interaction. Carbohydrate fractional abundance at Asn11 revealed that glycosylation in the natural placental TF is much more prevalent (~76%) than in the recombinant protein (~20%). The extent of glycosylation on Asn124 and Asn137 is similar in the two proteins, despite the pronounced differences in the carbohydrate composition. Additionally, 77% of rTF exists as TF des-1, 2 (missing the first two amino acids from the N-terminus). In contrast, only 31% of pTF is found in the des-1, 2 form. CONCLUSION: These observations may attribute to the difference in the ability of TF-FVIIa complex to activate factor X (FX). GENERAL SIGNIFICANCE: Structural and functional comparison of the recombinant and natural protein advances our understanding and knowledge on the biological activity of TF.

Simple, Rapid Spectrophotometric Assay of Dispensed Methadone for Diversion Control.

OBJECTIVES: Treatment of opioid use disorder with methadone is highly effective. Methadone is dispensed from opioid treatment programs under regulated circumstances. However, diversion of take-home doses can occur and is difficult to detect. We wanted to test the application of a handheld ultraviolet light absorption spectrometer to detect the concentration of methadone in take-home bottles that were suspected of being altered by the patient. METHODS: Standardized dilutions of methadone hydrochloride oral concentrate were used to calibrate absorption wavelengths and then compared to take homes from suspected and unsuspected bottles to see if measured concentrations differed from expected doses. RESULTS: Ten standardized "control" doses were analyzed to determine 99% confidence intervals. These were compared to 104 samples "not-of-concern" obtained randomly over a 10-month period. An additional 103 methadone bottles of concern from 27 patients showed 15 bottles with <25 % and 8 with <75 % of expected concentrations. CONCLUSIONS: A handheld, low-cost ultraviolet light spectrometer detected altered take-home doses of methadone. This assay presents a simple and effective method for methadone clinics to perform inhouse analysis on "call back" methadone doses. It allows individual clinics to define diversion rates of their patient body, while allowing state and federal agencies to better understand how much prescribed methadone is diverted for illicit uses.