An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites

MOTIVATION: Analysis of the conversion of (13)C glucose within the metabolic network allows the evaluation of the biochemical fluxes in interconnecting metabolic pathways. Such analyses require solving hundreds of equations with respect to individual isotopomer concentrations, and this assumes applying special software even for constructing the equations. The algorithm, proposed by others could be improved. METHOD: A C-code linked to the program written in Mathematica (Wolfram Research Inc.), constructs and solves differential equations for all isotopomer concentrations, using the general enzyme characteristics (K(m), equilibrium constant, etc.). This code uses innovative algorithm of determination for the isotopomers-products, thus essentially decreasing the computation time. Feasible metabolic fluxes are provided by the parameters of enzyme kinetics found from the data fitting. RESULTS: The software effectively evaluates metabolic fluxes based on the measured isotopomer distribution, as was illustrated by the analysis of glycolysis and pentose phosphate cycle. The mechanism of transketolase and transaldolase catalysis was shown to induce a specific kind of isotopomer re-distribution, which, despite the significance of its effect, usually is not taken into account. AVAILABILITY: The software could be freely downloaded from the site: http://bq.ub.es/bioqint/label_distribution/.     

Coupling of cell energetics with membrane metabolic sensing. Integrative signaling through creatine kinase phosphotransfer disrupted by M-CK gene knock-out

Transduction of metabolic signals is essential in preserving cellular homeostasis. Yet, principles governing integration and synchronization of membrane metabolic sensors with cell metabolism remain elusive. Here, analysis of cellular nucleotide fluxes and nucleotide-dependent gating of the ATP-sensitive K+ (K(ATP)) channel, a prototypic metabolic sensor, revealed a diffusional barrier within the submembrane space, preventing direct reception of cytosolic signals. Creatine kinase phosphotransfer, captured by 18O-assisted 31P NMR, coordinated tightly with ATP turnover, reflecting the cellular energetic status. The dynamics of high energy phosphoryl transfer through the creatine kinase relay permitted a high fidelity transmission of energetic signals into the submembrane compartment synchronizing K(ATP) channel activity with cell metabolism. Knock-out of the creatine kinase M-CK gene disrupted signal delivery to K(ATP) channels and generated a cellular phenotype with increased electrical vulnerability. Thus, in the compartmentalized cell environment, phosphotransfer systems shunt diffusional barriers and secure regimented signal transduction integrating metabolic sensors with the cellular energetic network.     

NMR spectroscopy for studying structure and intramolecular dynamics of modified analogs of steroid hormones

Special features of the use of homo- and heteronuclear correlation methods of NMR in one and two dimensions for studying the spatial structure and intramolecular dynamics of modified analogues of steroid hormones (MASH) are considered. The application of these methods to the assignment of resonances in the high-field 1H NMR region and to the determination of the most stereospecifically important parameters, such as the vicinal constants of spin-spin coupling (3JH-H) and nuclear Overhauser effects (NOE), are discussed using the example of NMR studies of some estrogens and androgens at 300 MHz and on the basis of literature data. The most efficient combination of the methods and the necessary modification of each of them may be chosen considering the spectral and relaxation parameters of MASH in liquid medium, including the anisotropy of the overall diffusive motion. The characteristics of MASH are the wide use of correlations through long-range couplings (COSY-45 and DQF-COSY), the application of the 4,5JH-H constants for the determination of spatial structure, and the advantage of heteronuclear HSQC methods with and without 13C decoupling over the corresponding HMQC methods in both resolution and sensitivity. In the conformationally rigid MASH molecules, the anisotropy of the MASH diffusive motion in liquid adversely affects the determination of interproton distances by the calibrating processing method for the NOE difference and NOESY spectra: it results in both overestimated and underestimated distance values depending on the polar angle ratios of the reference and the determined distances. Under certain conditions, conformationally mobile MASH demonstrate the additional contribution of the scalar relaxation mechanism between the indirectly (scalarly) bound protons. This mechanism is responsible for the underestimated values of NOE and the corresponding errors in the distance determination.     

Radiologic diagnosis of bone metastases recurrence in patients with prostate cancer treated strontium-89

Aiming to evaluate efficiency of 89SrCl (Metastron) in patients with metastatic lesion of the skeleton in prostate cancer we have performed a follow-up scintigraphy of the skeleton with 99mTc-methylendiphosphonate (MDP) and MRI with quantitative study of metastatic foci. 12 patients with prostate cancer (on the average 11 +/- 6 bone metastases were examined using scintigraphy of the skeleton with 99mTc-MDP and MRI study in T1, T2 and proton density modes. Investigations were performed before injected as a single dose of 150 MBq (4 mCi). At all the stages there was made a quantitative study of foci of pathological uptake of 99mTc-MDP compromising numbers of foci, focus parameters, intensity of 99mTc-MDP accumulation in the pathological part relatively the contralateral region as well as quantification of MRI signals from metastatic areas in signal intensity units. In 3 month 4 patients with extensive metastatic skeletal lesion (> 12) showed a considerable decrease of number of foci of pathological 99mTc-MDP uptake (on average to 6 +/- 3). In the remained metastatic foci there was noted a decrease of dimensions and 99mTc-MDP uptake intensity at an average by 29.8 +/- 15%, improvement in T1 intensity by 113 +/- 55.6 units. In 2 patients who initially presented a "superscan" pattern on 99mTc-MDP bone scintigraphy the 89SrCl treatment converted this of low intensity had demonstrated their complete regression. Results of radiologic follow-up of bone metastases in prostate cancer using MRI and bone scintigraphy with 99mTc-MDP argue that systemic radiotherapy with 89SrCl induces significant regress of metastatic process that involves all volume of the metastases.     

Synthesis and study on activity in vitro of the high purity human butyrylcholinesterase conjugated with gold nanoparticles

The aim of this research was to design a method of immobilization of high-purity human butyrylcholinesterase on the surface of gold nanoparticles preserving the activity of the enzyme. In order to achieve this aim, the method of fractionation and purification of human butyrylcholinesterase from plasma was modified. The synthesis of 15-nm gold nanoparticles was carried out by citrated method. A method of conjugation of the high-purity butyrylcholinesterase with gold nanoparticles was developed. It was found that the Immobilization of butyrylcholinesterase on the surface of gold nanoparticles resulted in a significant (to 23%) increase in the specific activity of the enzyme.     

Photosynthetic generation of O2 and H2 by photosystem I-deficient chlamydomonas mutants

A comparative study of aerobic generation of O2 and anaerobic photoproduction of H2 in whole cells of a wild-type strain of Chlamydomonas reinhardtii and its photosystem I-deficient mutants B4 and F8 found no contribution of photosystem II to ferredoxin photoreduction, which is not consistent with data of recent studies by Greenbaum et al. (Nature, 1995, 376, 438-441; and Science, 1996, 273, 364-367) who reported that they had discovered such a capacity in these mutant strains. In the wild-type and mutant strains, action spectra showed that O2 was evolved by photosystem II, whereas photoinhibition of chlororespiration and evolution of H2 depended on the activity of photosystem I. Single-turnover flash measurements of H2 evolution showed that the contents of photosystem I in mutant strains amounted to 3-35% of that in the wild-type strain. This fraction of photosystem I in "leaky" mutants displayed abnormal kinetic features and was highly sensitive to photoinhibition.     

Detection of two loci involved in (1-->3)-beta-glucan (curdlan) biosynthesis by Agrobacterium sp. ATCC31749, and comparative sequence analysis of the putative curdlan synthase gene

Genes essential for the production of a linear, bacterial (1-->3)-beta- glucan, curdlan, have been cloned for the first time from Agrobacterium sp. ATCC31749. The genes occurred in two, nonoverlapping, genomic fragments that complemented different sets of curdlan( crd )-deficient transposon-insertion mutations. These were detected as colonies that failed to stain with aniline blue, a (1-->3)-beta-glucan specific dye. One fragment carried a biosynthetic gene cluster (locus I) containing the putative curdlan synthase gene, crdS, and at least two other crd genes. The second fragment may contain only a single crd gene (locus II). Determination of the DNA sequence adjacent to several locus I mutations revealed homology to known sequences only in the cases of crdS mutations. Complete sequencing of the 1623 bp crdS gene revealed highest similarities between the predicted CrdS protein (540 amino acids) and glycosyl transferases with repetitive action patterns. These include bacterial cellulose synthases (and their homologs), which form (1-->4)-beta-glucans. No similarity was detected with putative (1-->3)- beta-glucan synthases from yeasts and filamentous fungi. Whatever the determinants of the linkage specificity of these beta-glucan synthases might be, these results raise the possibility that (1-->3)-beta-glucans and (1-->4)-beta-glucans are formed by related catalytic polypeptides.      

A state and transition model for the eastern Monte Phytogeographycal Province in Rio Negro

We developed a functional model for a shrub steppe vegetation of the eastern Monte Phytogeographical Province in Río Negro (Argentina) with six stable states and 12 transitions, based on the woody encroachment degree, characteristics of the herbaceous layer and the soil surface, and biological crust cover. Information was obtained from letters of naturalists and travelers along the region since the late eighteenth century, reports of old settlers, and our own research work. On the Monte, different functional groups can be distinguished. Our work focused on the three most conspicuous to analyze the dynamics of the system: shrubs, grasses and biological crust. The shrub layer is only affected by large-scale disturbances (fire, mechanical clearing) which maintain the balance between grasses and shrubs in the system. Mechanical clearing with soil removal also causes a decrease in grass cover and vegetation diversity. This layer, however, is most frequently affected by intensive and continuous grazing, which reduces the occurrence of fires and shifts the equilibrium toward the shrubs. All disturbances in general deteriorate the biological crust that covers the soil, which offers situations of facilitation for the regeneration of the herbaceous layer. Grazing and mechanical clearing reduce soil cover and promote the development of soil compaction, which reduce water infiltration and germination and/or seedling establishment, and this creates deteriorated states difficult to reverse. Those states can also be produced by tillage for agriculture and stubble grazing. Some of the transitions that we describe can be favored through grassland management strategies, in order to reach higher states of pastoral value and reverse deteriorating situations.     

A multi-population phenome-wide association study of genetically-predicted height in the Million Veteran Program

BackgroundHeight has been associated with many clinical traits but whether such associations are causal versus secondary to confounding remains unclear in many cases. To systematically examine this question, we performed a Mendelian Randomization-Phenome-wide association study (MR-PheWAS) using clinical and genetic data from a national healthcare system biobank.Methods and findingsAnalyses were performed using data from the US Veterans Affairs (VA) Million Veteran Program in non-Hispanic White (EA, n = 222,300) and non-Hispanic Black (AA, n = 58,151) adults in the US. We estimated height genetic risk based on 3290 height-associated variants from a recent European-ancestry genome-wide meta-analysis. We compared associations of measured and genetically-predicted height with phenome-wide traits derived from the VA electronic health record, adjusting for age, sex, and genetic principal components. We found 345 clinical traits associated with measured height in EA and an additional 17 in AA. Of these, 127 were associated with genetically-predicted height at phenome-wide significance in EA and 2 in AA. These associations were largely independent from body mass index. We confirmed several previously described MR associations between height and cardiovascular disease traits such as hypertension, hyperlipidemia, coronary heart disease (CHD), and atrial fibrillation, and further uncovered MR associations with venous circulatory disorders and peripheral neuropathy in the presence and absence of diabetes. As a number of traits associated with genetically-predicted height frequently co-occur with CHD, we evaluated effect modification by CHD status of genetically-predicted height associations with risk factors for and complications of CHD. We found modification of effects of MR associations by CHD status for atrial fibrillation/flutter but not for hypertension, hyperlipidemia, or venous circulatory disorders.ConclusionsWe conclude that height may be an unrecognized but biologically plausible risk factor for several common conditions in adults. However, more studies are needed to reliably exclude horizontal pleiotropy as a driving force behind at least some of the MR associations observed in this study.