Comparing and identifying matching metabolites, reactions, and compartments in genome-scale reconstructed metabolic networks can be difficult due to inconsistent naming in different networks. In this paper, we propose metabolite and reaction matching techniques for matching metabolites and reactions in a given metabolic network to metabolites and reactions in another metabolic network. We employ a variety of techniques that include approximate string matching, similarity score functions and multi-step filtering techniques, all enhanced by a set of rules based on the underlying metabolic biochemistry. The proposed techniques are evaluated by an empirical study on four pairs of metabolic networks, and significant accuracy gains are achieved using the proposed metabolite and reaction identification techniques.
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http://dx.doi.org/10.1016/j.ymeth.2014.06.007 | DOI Listing |
New Phytol
January 2025
Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark.
Lupins are promising protein crops that accumulate toxic quinolizidine alkaloids (QAs) in the seeds, complicating their end-use. QAs are synthesized in green organs (leaves, stems, and pods) and a subset of them is transported to the seeds during fruit development. The exact sites of biosynthesis and accumulation remain unknown; however, mesophyll cells have been proposed as sources, and epidermal cells as sinks.
View Article and Find Full Text PDFFront Microbiol
December 2024
Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Hangzhou, China.
Long COVID is an often-debilitating condition with severe, multisystem symptoms that can persist for weeks or months and increase the risk of various diseases. Currently, there is a lack of diagnostic tools for Long COVID in clinical practice. Therefore, this study utilizes plasma proteomics and metabolomics technologies to understand the molecular profile and pathophysiological mechanisms of Long COVID, providing clinical evidence for the development of potential biomarkers.
View Article and Find Full Text PDFAnal Chim Acta
February 2025
Department of Pharmacy, College of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan. Electronic address:
Background: Chemical derivatization is a common technique in liquid chromatography-mass spectrometry (LC-MS) metabolomics used to improve the ionizability and chromatographic properties of metabolites in complex biological samples. This process facilitates better detection and separation of a wide array of compounds. The reagent 2-(4-boronobenzyl) isoquinolin-2-ium bromide (BBII), developed as a glucose labeling reagent for matrix-assisted laser desorption/ionization MS, enhances ionization for glucose and other hydroxyl metabolites.
View Article and Find Full Text PDFMolecules
December 2024
Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata 990-9585, Japan.
Leucine, isoleucine, and valine are collectively known as branched chain amino acids (BCAAs) and are often discussed in the same physiological and pathological situations. The two consecutive initial reactions of BCAA catabolism are catalyzed by the common enzymes referred to as branched chain aminotransferase (BCAT) and branched chain α-keto acid dehydrogenase (BCKDH). BCAT transfers the amino group of BCAAs to 2-ketoglutarate, which results in corresponding branched chain 2-keto acids (BCKAs) and glutamate.
View Article and Find Full Text PDFToxicol Lett
January 2025
Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, PR China; State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou 550025, PR China; Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550025, PR China. Electronic address:
Osthole (OST), a coumarin derivative, is one of the major components of Cnidium monnieri (L.) Cussion. OST was reported to induce apoptosis in hepatocytes.
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