/pdf/inositol-trisphosphate-and-diacylglycerol-as-second-4drzjsg27y.pdf

Inositol trisphosphate and diacylglycerol as second messengers.

A model for receptor-regulated calcium entry

Reactive oxygen species

Metabolism is a vital cellular process, and its malfunction is a major contributor to human disease. Metabolic networks are complex and highly interconnected, and thus systems-level computational approaches are required to elucidate and understand metabolic genotype–phenotype relationships. We have manually reconstructed the global human metabolic network based on Build 35 of the genome annotation and a comprehensive evaluation of >50 years of legacy data (i.e., bibliomic data). Herein we describe the reconstruction process and demonstrate how the resulting genome-scale (or global) network can be used (i) for the discovery of missing information, (ii) for the formulation of an in silico model, and (iii) as a structured context for analyzing high-throughput biological data sets. Our comprehensive evaluation of the literature revealed many gaps in the current understanding of human metabolism that require future experimental investigation. Mathematical analysis of network structure elucidated the implications of intracellular compartmentalization and the potential use of correlated reaction sets for alternative drug target identification. Integrated analysis of high-throughput data sets within the context of the reconstruction enabled a global assessment of functional metabolic states. These results highlight some of the applications enabled by the reconstructed human metabolic network. The establishment of this network represents an important step toward genome-scale human systems biology.

https://www.pnas.org/content/pnas/104/6/1777.full.pdf

Global reconstruction of the human metabolic network based on genomic and bibliomic data

Signaling through phosphatidylcholine breakdown.

https://www.kidney-international.org/article/S0085-2538(15)47462-9/pdf

Contribution of dietary oxalate to urinary oxalate excretion

Background and Purpose: Knowledge of the citric acid content of beverages may be useful in nutrition therapy for calcium urolithiasis, especially among patients with hypocitraturia. Citrate is a naturally-occurring inhibitor of urinary crystallization; achieving therapeutic urinary citrate concentration is one clinical target in the medical management of calcium urolithiasis. When provided as fluids, beverages containing citric acid add to the total volume of urine, reducing its saturation of calcium and other crystals, and may enhance urinary citrate excretion. Information on the citric acid content of fruit juices and commercially-available formulations is not widely known. We evaluated the citric acid concentration of various fruit juices. Materials and Methods: The citric acid content of 21 commercially-available juices and juice concentrates and the juice of three types of fruits was analyzed using ion chromatography. Results: Lemon juice and lime juice are rich sources of citric acid, containing 1.4...

/pdf/quantitative-assessment-of-citric-acid-in-lemon-juice-lime-2fini9y2om.pdf

Quantitative Assessment of Citric Acid in Lemon Juice, Lime Juice, and Commercially-Available Fruit Juice Products

https://www.kidney-international.org/article/S0085-2538(15)46915-7/pdf

Estimation of the oxalate content of foods and daily oxalate intake

Oxalate degradation by the anaerobic bacterium Oxalobacter formigenes is important for human health, helping to prevent hyperoxaluria and disorders such as the development of kidney stones. Oxalate-degrading activity cannot be detected in the gut flora of some individuals, possibly because Oxalobacter is susceptible to commonly used antimicrobials. Here, clarithromycin, doxycycline, and some other antibiotics inhibited oxalate degradation by two human strains of O. formigenes. These strains varied in their response to gut environmental factors, including exposure to gastric acidity and bile salts. O. formigenes strains established oxalate breakdown in fermentors which were preinoculated with fecal bacteria from individuals lacking oxalate-degrading activity. Reducing the concentration of oxalate in the medium reduced the numbers of O. formigenes bacteria. Oxalate degradation was established and maintained at dilution rates comparable to colonic transit times in healthy individuals. A single oral ingestion of O. formigenes by adult volunteers was, for the first time, shown to result in (i) reduced urinary oxalate excretion following administration of an oxalate load, (ii) the recovery of oxalate-degrading activity in feces, and (iii) prolonged retention of colonization.

https://aem.asm.org/content/aem/68/8/3841.full.pdf

Ross P. Holmes

Papers

Contribution of dietary oxalate to urinary oxalate excretion

Quantitative Assessment of Citric Acid in Lemon Juice, Lime Juice, and Commercially-Available Fruit Juice Products

Estimation of the oxalate content of foods and daily oxalate intake

Oxalobacter formigenes and its potential role in human health.

Glyoxylate synthesis, and its modulation and influence on oxalate synthesis