Nuclear magnetic resonance-based quantification of organic diphosphates

Phosphorylated compounds are ubiquitous in life. Given their central role, many such substrates and analogs have been prepared for subsequent evaluation. Prior to biological experiments, it is typically necessary to determine the concentration of the target molecule in solution. Here we describe a method where concentrations of stock solutions of organic diphosphates and bisphosphonates are quantified using ³¹P nuclear magnetic resonance (NMR) spectroscopy with standard instrumentation using a capillary tube with a secondary standard. The method is specific and is applicable down to a concentration of 200 μM. The capillary tube provides the reference peak for quantification and deuterated solvent for locking.     

Utility of magnetic resonance imaging and nuclear magnetic resonance-based metabolomics for quantification of inflammatory lung injury

Magnetic resonance imaging (MRI) and metabolic nuclear magnetic resonance (NMR) spectroscopy are clinically available but have had little application in the quantification of experimental lung injury. There is a growing and unfulfilled need for predictive animal models that can improve our understanding of disease pathogenesis and therapeutic intervention. Integration of MRI and NMR could extend the application of experimental data into the clinical setting. This study investigated the ability of MRI and metabolic NMR to detect and quantify inflammation-mediated lung injury. Pulmonary inflammation was induced in male B6C3F1 mice by intratracheal administration of IL-1beta and TNF-alpha under isoflurane anesthesia. Mice underwent MRI at 2, 4, 6, and 24 h after dosing. At 6 and 24 h lungs were harvested for metabolic NMR analysis. Data acquired from IL-1beta+TNF-alpha-treated animals were compared with saline-treated control mice. The hyperintense-to-total lung volume (HTLV) ratio derived from MRI was higher in IL-1beta+TNF-alpha-treated mice compared with control at 2, 4, and 6 h but returned to control levels by 24 h. The ability of MRI to detect pulmonary inflammation was confirmed by the association between HTLV ratio and histological and pathological end points. Principal component analysis of NMR-detectable metabolites also showed a temporal pattern for which energy metabolism-based biomarkers were identified. These data demonstrate that both MRI and metabolic NMR have utility in the detection and quantification of inflammation-mediated lung injury. Integration of these clinically available techniques into experimental models of lung injury could improve the translation of basic science knowledge and information to the clinic.     

Nuclear magnetic resonance-based dissection of a glycosyltransferase specificity for the mucin MUC1 tandem repeat

The human glycoprotein MUC1 mucin plays a critical role in cancer progression. Breast, ovarian, and colon cancer cells often display unique cell-surface antigens corresponding to aberrantly glycosylated forms of the MUC1 tandem repeat. In this report, (15)N- and (13)C-labeled forms of a recombinant MUC1 construct containing five tandem repeats were used as substrates to define the order and kinetics of addition of N-acetylgalactosamine (GalNAc) moieties by a recombinant active form of the human enzyme UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase I (ppGalNAc-T1; residues 40-559). Heteronuclear NMR experiments were performed to assign resonances associated with the two serines (Ser5 and Ser15) and three threonines (Thr6, Thr14, and Thr19) present in the 20-residue long MUC1 repeat. The kinetics and order of addition of GalNAc moieties (Tn antigen) on the MUC1 construct by human ppGalNAc-T1 were subsequently dissected by NMR spectroscopy. Threonine 14 was shown to be rapidly glycosylated by ppGalNAc-T1 with an initial rate of 25 microM/min, followed by Thr6 (8.6 microM/min). The enzyme also modified Ser5 at a slower rate (1.7 microM/min), an event that started only after the glycosylation of Thr14 and Thr6 side chains was mostly completed. Ser15 and Thr19 remained unglycosylated by ppGalNAc-T1. Corresponding O-glycosylation sites within all five tandem repeats were simultaneously modified by ppGalNAc-T1, suggesting that each repeat behaves as an independent substrate unit. This study demonstrated that the hydroxyl oxygens of Thr14 and to a lesser extent Thr 6 represent the two dominant substrates modified by ppGalNAc-T1 within the context of a complex MUC1 peptide substrate. More importantly, the availability of defined isotopically labelled MUC1 glycopeptide substrates and the relative simplicity of their NMR spectra will facilitate the analysis of other transferases within the O-glycosylation pathways and the rational design of tumor-associated MUC1 antigens.     

Nuclear transfer-mediated rescue of the nuclear genome of nonviable mouse cells frozen without cryoprotectant

Nuclear transfer (NT) provides an opportunity for clonal amplification of a nuclear genome of interest. Here, we report NT-mediated reprogramming with frozen mouse cells that were nonviable because they were frozen at -80 degrees C for up to 342 days without a cryoprotectant. We derived eight embryonic stem (ES) cell lines from cloned blastocysts by conventional NT procedure and five ntES (nuclear transfer embryonic stem) cell lines by a modified NT procedure in which a whole cell instead of a nucleus was injected into an enucleated oocyte. Chromosome analysis revealed that 12 of 13 ntES cell lines have normal karyotypes. On injection of ntES cells into tetraploid blastocysts to generate clonal mice that are nearly completely ntES-cell derived, live pups were obtained; four clonal mice survived until adulthood. On injection of ntES cells into diploid blastocysts, chimeric mice with a high somatic ES cell contribution were generated; germ-line transmission was obtained. Our findings indicate that chromosome stability and genomic integrity can be maintained in mouse somatic cells after freezing without cryoprotection and that NT and ES cell techniques can rescue the genome of these cells.     

Nuclear magnetic resonance imaging (MRI) of diesel oil migration in estuarine sediment samples

Magnetic resonance imaging (MRI) provides a means of monitoring the change in position and the eventual breakdown of oil within sediments. The multidimensional technique allows the position of nuclei (most commonly protons) to be located within a known volume of substrate, e.g. sediment, hence offering a method of assessing the harming potential of oils in near-shore environments. Two-dimensional (2D) and three-dimensional (3D) MRI analyses of the measurement and movement of oil in estuarine sediments show that, using appropriate parameters, movement of the oil can be both observed and quantified. To aid the quantification a sample holder fabricated from polyvinylsiloxane, an inert material visible in magnetic resonance images has been used as an internal intensity standard. The results show the great potential of MRI in studying protonated contaminants in these materials, notwithstanding the presence of paramagnetic species in estuarine sediments which might distort the image. Sediments studied thus far have been collected from the Tay Estuary, Northeast Scotland. Journal of Industrial Microbiology & Biotechnology (2001) 26, 77–82. Received 26 January 2000/ Accepted in revised form 07 June 2000     

State-of-the-art non-targeted metabolomics in the study of chronic kidney disease

Here we report a metabolomics discovery study conducted on blood serum samples of patients in different stages of chronic kidney disease (CKD). Metabolites were monitored on a quality controlled holistic platform combining reversed-phase liquid chromatography coupled to high-resolution quadrupole time-of-flight mass spectrometry in both negative and positive ionization mode and gas chromatography coupled to quadrupole mass spectrometry. A substantial portion of the serum metabolome was thereby covered. Eighty-five metabolites were shown to evolve with CKD progression of which 43 metabolites were a confirmation of earlier reported uremic retention solutes and/or uremic toxins. Thirty-one unique metabolites were revealed which were increasing significantly throughout CKD progression, by a factor surpassing the level observed for creatinine, the currently used biomarker for kidney function. Additionally, 11 unique metabolites showed a decreasing trend.     

Nuclear magnetic resonance analysis of water in natural and deuterated mouse muscle above and below freezing.

Measurements of absolute proton signal intensities, free induction decays, spin-spin relaxation times, and local fields in the rotating frame in natural and fully deuterated mouse muscle at five temperatures in the range 293-170 K are reported. The analysis is carried out at three time windows on the free induction decay. The contribution to the magnetization from protons on large molecules and water are analyzed.     

Genetic deficiency in tissue kallikrein activity in mouse and man: effect on arteries, heart and kidney

Tissue kallikrein (KLK1) is a kinin-forming serine protease synthesized in many organs including arteries and kidney. Study of the physiological role of KLK1 has benefited from the availability of mouse and human genetic models of KLK1 deficiency, through engineering of KLK1 mouse mutants and discovery of a major polymorphism in the human KLK1 gene that induces a loss of enzyme activity. Studies in KLK1-deficient mice and human subjects partially deficient in KLK1 have documented its critical role in arterial function in both species. KLK1 is also involved in the control of ionic transport in the renal tubule, an action that may not be kinin-mediated. Studies of experimental diseases in KLK1-deficient mice have revealed cardio- and nephro-protective effects of KLK1 and kinins in acute cardiac ischemia, post-ischemic heart failure, and diabetes. Potential clinical and therapeutic developments are discussed.     

Tuberculosis metabolomics reveals adaptations of man and microbe in order to outcompete and survive

Despite numerous research efforts to control tuberculosis, it is still regarded as a global pandemic. It is clear that the infectious agent responsible and its associated disease mechanisms remain poorly understood. Alternative research strategies are therefore urgently needed to better characterize active-TB, especially the adaptations of the host and microbe as they compete to survive. Using a GCxGC-TOFMS metabolomics approach, we identified new urinary TB metabolite markers induced by adaptations of the host metabolome and/or host-pathogen interactions. The most significant of these were the TB-induced changes resulting in abnormal host fatty acid and amino acid metabolism, in particular to tryptophan, phenylalanine and tyrosine, inducing a metabolite profile similar to that of patients suffering from phenylketonuria, mediated through changes to INF-γ and possibly insulin. This subsequently also explains some of the symptoms associated with TB and provides clues to better treatment approaches.     

Alterations in the metabolomics of sulfur-containing substances in rat kidney by betaine

Earlier studies have shown that betaine administration may modulate the metabolism of sulfur amino acids in the liver. In this study, we determined the changes in the metabolomics of sulfur-containing substances induced by betaine in the kidney, the other major organ actively involved in the transsulfuration reactions. Male rats received betaine (1 %) in drinking water for 2 weeks before killing. Betaine intake did not affect betaine–homocysteine methyltransferase activity or its protein expression in the renal tissue. Expression of methionine synthase was also unchanged. However, methionine levels were increased significantly both in plasma and kidney. Renal methionine adenosyltransferase activity and S-adenosylmethionine concentrations were increased, but there were no changes in S-adenosylhomocysteine, homocysteine, cysteine levels or cystathionine β-synthase expression. γ-Glutamylcysteine synthetase expression or glutathione levels were not altered, but cysteine dioxygenase and taurine levels were decreased significantly. In contrast, betaine administration induced cysteine sulfinate decarboxylase and its metabolic product, hypotaurine. These results indicate that the metabolomics of sulfur-containing substances in the kidney is altered extensively by betaine, although the renal capacity for methionine synthesis is unresponsive to this substance unlike that of the liver. It is suggested that the increased methionine availability due to an enhancement of its uptake from plasma may account for the alterations in the metabolomics of sulfur-containing substances in the kidney. Further studies need to be conducted to clarify the physiological/pharmacological significance of these findings.     

Cancer gene discovery in mouse and man

The elucidation of the human and mouse genome sequence and developments in high-throughput genome analysis, and in computational tools, have made it possible to profile entire cancer genomes. In parallel with these advances mouse models of cancer have evolved into a powerful tool for cancer gene discovery. Here we discuss the approaches that may be used for cancer gene identification in both human and mouse and discuss how a cross-species ‘oncogenomics’ approach to cancer gene discovery represents a powerful strategy for finding genes that drive tumourigenesis.     

Left-right axis malformations in man and mouse

The study of left-right axis malformations in man and mouse has greatly advanced understanding of the mechanisms regulating vertebrate left-right axis formation. Recently, the roles of the TGF-beta family, Sonic hedgehog and fibroblast growth factor signaling, homeobox genes, and cilia in left-right axis determination have been more clearly defined. The identification of genes and environmental factors affecting left-right axis formation has important implications for understanding human laterality defects.