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61.
Hucka M Finney A Bornstein BJ Keating SM Shapiro BE Matthews J Kovitz BL Schilstra MJ Funahashi A Doyle JC Kitano H 《Systems biology》2004,1(1):41-53
Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today. 相似文献
62.
F. Vovelle J. M. Goodfellow H. F. J. Savage P. Barnes J. L. Finney 《European biophysics journal : EBJ》1985,11(4):225-237
Both the ordered and disordered solvent networks of vitamin B12 coenzyme crystal hydrate have been generated by Monte Carlo simulation techniques. Several different potential functions have been use to model both water-water and water-solute (i.e., water-coenzyme) interactions. The results have been analysed in terms of the structural properties of the water networks, such as mean water oxygen and hydrogen positions, coordination of each water molecule, and maxima of probability density maps in all four asymmetric units of this crystal.The following results were found: (I) Within each asymmetric unit only one hydrogen bonding network was predicted although there were several hydrogen atom positions for any one solvent molecule (defined as maxima in probability density). (II) Reasonable agreement was obtained between predicted and experimental positions in the ordered solvent region, independent of the potential function used. (III) The positions of the calculated probability density maxima for the disordered channel region were different in different asymmetric units; this led to different simulated hydrogen bond networks which were not always consistent with the experimentally determined alternative (lower occupancy) sites.The results suggest that it is advisable to simulate more than one asymmetric unit if one wishes to look at disorder in the solvent regions. Probability density maps were qualitatively very useful for picturing these disordered regions. However, there were no significant differences between quantitative results predicted using either average atomic positions or maxima of the probability density distributions.Problems in quantifying agreement between experimental and predicted disordered solvent networks are discussed. The potential which included hydrogen atoms explicitly (EMPWI) seemed to give the best overall agreement, mainly because it was successful in predicting the unusually short hydrogen bonds which are found in this crystal. 相似文献
63.
Sarah C. Brennan Brenda A. Finney Maria Lazarou Anne E. Rosser Caroline Scherf Dirk Adriaensen Paul J. Kemp Daniela Riccardi 《PloS one》2013,8(11)
Airway branching morphogenesis in utero is essential for optimal postnatal lung function. In the fetus, branching morphogenesis occurs during the pseudoglandular stage (weeks 9–17 of human gestation, embryonic days (E)11.5–16.5 in mouse) in a hypercalcaemic environment (∼1.7 in the fetus vs. ∼1.1–1.3 mM for an adult). Previously we have shown that fetal hypercalcemia exerts an inhibitory brake on branching morphogenesis via the calcium-sensing receptor. In addition, earlier studies have shown that nifedipine, a selective blocker of L-type voltage-gated Ca2+ channels (VGCC), inhibits fetal lung growth, suggesting a role for VGCC in lung development. The aim of this work was to investigate the expression of VGCC in the pseudoglandular human and mouse lung, and their role in branching morphogenesis. Expression of L-type (CaV1.2 and CaV1.3), P/Q type (CaV2.1), N-type (CaV2.2), R-type (CaV2.3), and T-type (CaV3.2 and CaV3.3) VGCC was investigated in paraffin sections from week 9 human fetal lungs and E12.5 mouse embryos. Here we show, for the first time, that Cav1.2 and Cav1.3 are expressed in both the smooth muscle and epithelium of the developing human and mouse lung. Additionally, Cav2.3 was expressed in the lung epithelium of both species. Incubating E12.5 mouse lung rudiments in the presence of nifedipine doubled the amount of branching, an effect which was partly mimicked by the Cav2.3 inhibitor, SNX-482. Direct measurements of changes in epithelial cell membrane potential, using the voltage-sensitive fluorescent dye DiSBAC2(3), demonstrated that cyclic depolarisations occur within the developing epithelium and coincide with rhythmic occlusions of the lumen, driven by the naturally occurring airway peristalsis. We conclude that VGCC are expressed and functional in the fetal human and mouse lung, where they play a role in branching morphogenesis. Furthermore, rhythmic epithelial depolarisations evoked by airway peristalsis would allow for branching to match growth and distension within the developing lung. 相似文献
64.
65.
Selectivity in biomineralization of barium and strontium 总被引:1,自引:0,他引:1
Krejci MR Wasserman B Finney L McNulty I Legnini D Vogt S Joester D 《Journal of structural biology》2011,176(2):192-202
The desmid green alga Closterium moniliferum belongs to a small number of organisms that form barite (BaSO4) or celestite (SrSO4) biominerals. The ability to sequester Sr in the presence of an excess of Ca is of considerable interest for the remediation of 90Sr from the environment and nuclear waste. While most cells dynamically regulate the concentration of the second messenger Ca2+ in the cytosol and various organelles, transport proteins rarely discriminate strongly between Ca, Sr, and Ba. Herein, we investigate how these ions are trafficked in C. moniliferum and how precipitation of (Ba,Sr)SO4 crystals occurs in the terminal vacuoles. Towards this goal, we simultaneously visualize intracellular dynamics of multiple elements using X-ray fluorescence microscopy (XFM) of cryo-fixed/freeze-dried samples. We correlate the resulting elemental maps with ultrastructural information gleaned from freeze-fracture cryo-SEM of frozen-hydrated cells and use micro X-ray absorption near edge structure (micro-XANES) to determine sulfur speciation. We find that the kinetics of Sr uptake and efflux depend on external Ca concentrations, and Sr, Ba, and Ca show similar intracellular localization. A highly ion-selective cross-membrane transport step is not evident. Based on elevated levels of sulfate detected in the terminal vacuoles, we propose a “sulfate trap” model, where the presence of dissolved barium leads to preferential precipitation of (Ba,Sr)SO4 due to its low solubility relative to SrSO4 and CaSO4. Engineering the sulfate concentration in the vacuole may thus be the most direct way to increase the Sr sequestered per cell, an important consideration in using desmids for phytoremediation of 90Sr. 相似文献
66.
Anthony H Taylor Mark Finney Patricia MW Lam Justin C Konje 《Reproductive biology and endocrinology : RB&E》2011,9(1):1-18
Background
In early pregnancy, increased plasma levels of the endocannabinoid anandamide (AEA) are associated with miscarriage through mechanisms that might affect the developing placenta or maternal decidua.Methods
In this study, we compare AEA levels in failed and viable pregnancies with the levels of the trophoblastic hormones (beta-human chorionic gonadotrophin (beta-hCG), progesterone (P4) and (pregnancy-associated placental protein-A (PAPP-A)) essential for early pregnancy success and relate that to the expression of the cannabinoid receptors and enzymes that modulate AEA levels.Results
The median plasma AEA level in non-viable pregnancies (1.48 nM; n = 20) was higher than in viable pregnancies (1.21 nM; n = 25; P = 0.013), as were progesterone and beta-hCG levels (41.0 vs 51.5 ng/mL; P = 0.052 for P4 and 28,650 vs 6,560 mIU/L; P = 0.144 for beta-hCG, respectively, but were not statistically significant). Serum PAPP-A levels in the viable group were approximately 6.8 times lower than those in the non-viable group (1.82 vs 12.25 mg/L; P = 0.071), but again these differences were statistically insignificant. In the spontaneous miscarriage group, significant correlations between P4 and beta-hCG, P4 and PAPP-A and AEA and PAPP-A levels were observed. Simultaneously, immunohistochemical distributions of the two main cannabinoid receptors and the AEA-modifying enzymes, fatty acid amide hydrolase (FAAH) and N-acylphosphatidylethanolamine-phospholipase D (NAPE-PLD), changed within both the decidua and trophoblast.Conclusions
The association of higher AEA levels with early pregnancy failure and with beta-hCG and PAPP-A, but not with progesterone concentrations suggest that plasma AEA levels and pregnancy failure are linked via a mechanism that may involve trophoblastic beta-hCG, and PAPP-A, but not, progesterone production. Although the trophoblast, decidua and embryo contain receptors for AEA, the main AEA target in early pregnancy failure remains unknown. 相似文献67.
E. N. Jack Brookshire Paul C. Stoy Bryce Currey Bruce Finney 《Global Change Biology》2020,26(10):5404-5413
Vegetation greenness has increased across much of the global land surface over recent decades. This trend is projected to continue—particularly in northern latitudes—but future greening may be constrained by nutrient availability needed for plant carbon (C) assimilation in response to CO2 enrichment (eCO2). eCO2 impacts foliar chemistry and function, yet the relative strengths of these effects versus climate in driving patterns of vegetative greening remain uncertain. Here we combine satellite measurements of greening with a 135 year record of plant C and nitrogen (N) concentrations and stable isotope ratios (δ13C and δ15N) in the Northern Great Plains (NGP) of North America to examine N constraints on greening. We document significant greening over the past two decades with the highest proportional increases in net greening occurring in the dries and warmest areas. In contrast to the climate dependency of greening, we find spatially uniform increases in leaf‐level intercellular CO2 and intrinsic water use efficiency that track rising atmospheric CO2. Despite large spatial variation in greening, we find sustained and climate‐independent declines in foliar N over the last century. Parallel declines in foliar δ15N and increases in C:N ratios point to diminished N availability as the likely cause. The simultaneous increase in greening and decline in foliar N across our study area points to increased N use efficiency (NUE) over the last two decades. However, our results suggest that plant NUE responses are likely insufficient to sustain observed greening trends in NGP grasslands in the future. 相似文献
68.
Guangjie Chen Daniel T. Selbie Bruce P. Finney Daniel E. Schindler Lynda Bunting Peter R. Leavitt Irene Gregory‐Eaves 《Oikos》2011,120(9):1317-1326
Migratory animals, such as Pacific salmon, can significantly shape communities in recipient habitats both by altering the flux of resources, and changing community composition and subsequent trophic interactions. Here we mainly used paleoecological records from natural sockeye salmon nursery lakes to quantify the response of plankton communities to the influx of salmon‐derived nutrients and consumers (juvenile salmon). Our long‐term data show that increases in the density of spawning salmon often elevated influx of nutrients, and, in turn, zooplankton production over the past few centuries. In contrast, significant correlations were not detected in two lakes with extremely low or high average spawner densities (i.e. 1.5 and 34.7 × 103 spawners km?2 year?1 respectively). With increasing spawner densities across lakes, analysis of the size structure of subfossils in sediments revealed a strong decrease in body size of a main juvenile salmon prey item (Eubosmina longispina; r2= 0.36, p < 0.001, n = 67), consistent with an overriding effect of predation in lakes with high salmon densities. These long‐term data not only highlight the key role of salmon‐derived nutrients in stimulating plankton communities, but also suggest that the relative effect of nutrient and consumer subsidies varies along gradients of lake production, despite a single ultimate causal mechanism (migrating fish). 相似文献
69.