FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2115198483> ?p ?o ?g. }

• W2115198483 endingPage "3564" @default.
• W2115198483 startingPage "3558" @default.
• W2115198483 abstract "Motivation: Addition of labeled substrates and the measurement of the subsequent distribution of the labels in isotopomers in reaction networks provide a unique method for assessing metabolic fluxes in whole cells. However, owing to insufficiency of information, attempts to quantify the fluxes often yield multiple possible sets of solutions that are consistent with a given experimental pattern of isotopomers. In the study of the pentose phosphate pathways, the need to consider isotope exchange reactions of transketolase (TK) and transaldolase (TA) (which in past analyses have often been ignored) magnifies this problem; but accounting for the interrelation between the fluxes known from biochemical studies and kinetic modeling solves it. The mathematical relationships between kinetic and equilibrium constants restrict the domain of estimated fluxes to the ones compatible not only with a given set of experimental data, but also with other biochemical information. Method: We present software that integrates kinetic modeling with isotopomer distribution analysis. It solves the ordinary differential equations for total concentrations (accounting for the kinetic mechanisms) as well as for all isotopomers in glycolysis and the pentose phosphate pathway (PPP). In the PPP the fluxes created in the TK and TA reactions are expressed through unitary rate constants. The algorithms that account for all the kinetic and equilbrium constant constraints are integrated with the previously developed algorithms, which have been further optimized. The most time-consuming calculations were programmed directly in assembly language; this gave an order of magnitude decrease in the computation time, thus allowing analysis of more complex systems. The software was developed as C-code linked to a program written in Mathematica (Wolfram Research, Champaign, IL), and also as a C++ program independent from Mathematica. Results: Implementing constraints imposed by kinetic and equilibrium constants in the isotopomer distribution analysis in the data from the cancer cells eliminated estimates of fluxes that were inconsistent with the kinetic mechanisms of TK and TA. Fluxes measured experimentally in cells can be used to estimate better the kinetics of TK and TA as they operate in situ. Thus, our approach of integrating various methods for in situ flux analysis opens up the possibility of designing new types of experiments to probe metabolic interrelationships, including the incorporation of additional biochemical information. Availability: Software is available freely at: http://www.bq.ub.es/bioqint/selivanov.htm Contact:martacascante@ub.edu" @default.
• W2115198483 created "2016-06-24" @default.
• W2115198483 creator A5009596579 @default.
• W2115198483 creator A5028264139 @default.
• W2115198483 creator A5040662322 @default.
• W2115198483 creator A5062483693 @default.
• W2115198483 creator A5063235088 @default.
• W2115198483 creator A5081563103 @default.
• W2115198483 creator A5086729497 @default.
• W2115198483 creator A5089973047 @default.
• W2115198483 date "2005-07-07" @default.
• W2115198483 modified "2023-09-23" @default.
• W2115198483 title "Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells" @default.
• W2115198483 cites W1485030470 @default.
• W2115198483 cites W1582190823 @default.
• W2115198483 cites W1940014006 @default.
• W2115198483 cites W1969560495 @default.
• W2115198483 cites W2022008424 @default.
• W2115198483 cites W2074424962 @default.
• W2115198483 cites W2096767559 @default.
• W2115198483 cites W2111602998 @default.
• W2115198483 cites W79437885 @default.
• W2115198483 doi "https://doi.org/10.1093/bioinformatics/bti573" @default.
• W2115198483 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/16002431" @default.
• W2115198483 hasPublicationYear "2005" @default.
• W2115198483 type Work @default.
• W2115198483 sameAs 2115198483 @default.
• W2115198483 citedByCount "34" @default.
• W2115198483 countsByYear W21151984832012 @default.
• W2115198483 countsByYear W21151984832013 @default.
• W2115198483 countsByYear W21151984832014 @default.
• W2115198483 countsByYear W21151984832017 @default.
• W2115198483 countsByYear W21151984832018 @default.
• W2115198483 countsByYear W21151984832019 @default.
• W2115198483 countsByYear W21151984832020 @default.
• W2115198483 crossrefType "journal-article" @default.
• W2115198483 hasAuthorship W2115198483A5009596579 @default.
• W2115198483 hasAuthorship W2115198483A5028264139 @default.
• W2115198483 hasAuthorship W2115198483A5040662322 @default.
• W2115198483 hasAuthorship W2115198483A5062483693 @default.
• W2115198483 hasAuthorship W2115198483A5063235088 @default.
• W2115198483 hasAuthorship W2115198483A5081563103 @default.
• W2115198483 hasAuthorship W2115198483A5086729497 @default.
• W2115198483 hasAuthorship W2115198483A5089973047 @default.
• W2115198483 hasBestOaLocation W21151984831 @default.
• W2115198483 hasConcept C103432212 @default.
• W2115198483 hasConcept C127124265 @default.
• W2115198483 hasConcept C147597530 @default.
• W2115198483 hasConcept C178790620 @default.
• W2115198483 hasConcept C181199279 @default.
• W2115198483 hasConcept C185592680 @default.
• W2115198483 hasConcept C186060115 @default.
• W2115198483 hasConcept C20251656 @default.
• W2115198483 hasConcept C32909587 @default.
• W2115198483 hasConcept C3409486 @default.
• W2115198483 hasConcept C38706188 @default.
• W2115198483 hasConcept C41008148 @default.
• W2115198483 hasConcept C55493867 @default.
• W2115198483 hasConcept C86803240 @default.
• W2115198483 hasConceptScore W2115198483C103432212 @default.
• W2115198483 hasConceptScore W2115198483C127124265 @default.
• W2115198483 hasConceptScore W2115198483C147597530 @default.
• W2115198483 hasConceptScore W2115198483C178790620 @default.
• W2115198483 hasConceptScore W2115198483C181199279 @default.
• W2115198483 hasConceptScore W2115198483C185592680 @default.
• W2115198483 hasConceptScore W2115198483C186060115 @default.
• W2115198483 hasConceptScore W2115198483C20251656 @default.
• W2115198483 hasConceptScore W2115198483C32909587 @default.
• W2115198483 hasConceptScore W2115198483C3409486 @default.
• W2115198483 hasConceptScore W2115198483C38706188 @default.
• W2115198483 hasConceptScore W2115198483C41008148 @default.
• W2115198483 hasConceptScore W2115198483C55493867 @default.
• W2115198483 hasConceptScore W2115198483C86803240 @default.
• W2115198483 hasIssue "17" @default.
• W2115198483 hasLocation W21151984831 @default.
• W2115198483 hasLocation W21151984832 @default.
• W2115198483 hasOpenAccess W2115198483 @default.
• W2115198483 hasPrimaryLocation W21151984831 @default.
• W2115198483 hasRelatedWork W190286435 @default.
• W2115198483 hasRelatedWork W2001340534 @default.
• W2115198483 hasRelatedWork W2015247318 @default.
• W2115198483 hasRelatedWork W2026448567 @default.
• W2115198483 hasRelatedWork W2028995352 @default.
• W2115198483 hasRelatedWork W2072049884 @default.
• W2115198483 hasRelatedWork W2111602998 @default.
• W2115198483 hasRelatedWork W2115198483 @default.
• W2115198483 hasRelatedWork W2289707431 @default.
• W2115198483 hasRelatedWork W75334843 @default.
• W2115198483 hasVolume "21" @default.
• W2115198483 isParatext "false" @default.
• W2115198483 isRetracted "false" @default.
• W2115198483 magId "2115198483" @default.
• W2115198483 workType "article" @default.