Main Pathway Discovery in Metabolic Pathways

Author(s):  
Katsumi Inoue ◽  
Andrei Doncescu ◽  
Gabriel Synaeve ◽  
Nabil Kabbak
2017 ◽  
Vol 39 (1) ◽  
pp. 147-162 ◽  
Author(s):  
Niamh M Denihan ◽  
Jennifer A Kirwan ◽  
Brian H Walsh ◽  
Warwick B Dunn ◽  
David I Broadhurst ◽  
...  

Elucidating metabolic effects of hypoxic-ischaemic encephalopathy (HIE) may reveal early biomarkers of injury and new treatment targets. This study uses untargeted metabolomics to examine early metabolic alterations in a carefully defined neonatal population. Infants with perinatal asphyxia who were resuscitated at birth and recovered (PA group), those who developed HIE (HIE group) and healthy controls were all recruited at birth. Metabolomic analysis of cord blood was performed using direct infusion FT-ICR mass spectrometry. For each reproducibly detected metabolic feature, mean fold differences were calculated HIE vs. controls (ΔHIE) and PA vs. controls (ΔPA). Putative metabolite annotations were assigned and pathway analysis was performed. Twenty-nine putatively annotated metabolic features were significantly different in ΔPA after false discovery correction ( q < 0.05), with eight of these also significantly altered in ΔHIE. Altered putative metabolites included; melatonin, leucine, kynurenine and 3-hydroxydodecanoic acid which differentiated between infant groups (ΔPA and ΔHIE); and D-erythrose-phosphate, acetone, 3-oxotetradecanoic acid and methylglutarylcarnitine which differentiated across severity grades of HIE. Pathway analysis revealed ΔHIE was associated with a 50% and 75% perturbation of tryptophan and pyrimidine metabolism, respectively. We have identified perturbed metabolic pathways and potential biomarkers specific to PA and HIE, which measured at birth, may help direct treatment.


1991 ◽  
Vol 278 (1) ◽  
pp. 299-304 ◽  
Author(s):  
A R Schulz

A computer program is described that derives the Flux and Concentration Control Coefficients for linear and branched metabolic pathways. The program prompts the user to enter a concise description of the metabolic pathway. From this description, the program constructs the appropriate equations in matrix form. The algorithm employed to obtain the symbolic determinants is described, and this algorithm also provides a convenient method for manual derivation of the Control Coefficients. The computer-based method will accommodate unlimited feed-forward and feed-backward loops and a maximum of two branches from each metabolite on the main pathway. The utility of the method is illustrated with a linear path with feed-forward and feed-backward loops, and with a substrate cycle as an example of a path with two branches.


2010 ◽  
Author(s):  
Sohan Lal ◽  
Kolin Paul ◽  
James Gomes
Keyword(s):  

Planta Medica ◽  
2016 ◽  
Vol 81 (S 01) ◽  
pp. S1-S381
Author(s):  
E Vikeved ◽  
R Buonfiglio ◽  
T Kogej ◽  
A Backlund

1965 ◽  
Vol 49 (3) ◽  
pp. 427-435 ◽  
Author(s):  
K. D. Voigt ◽  
J. Tamm ◽  
U. Volkwein ◽  
H. Schedewie

ABSTRACT Pregnenolone-sulphate (400 mg) was perfused through isolated dog livers. The following steroids were isolated in the perfusate: pregnenolone, progesterone, dehydroepiandrosterone, androst-5-ene-diol and the two steroid conjugates, i. e. pregnenolone-sulphate and dehydroepiandrosterone-sulphate. Two »free« steroids and one steroid conjugate could not be characterized. A tentative scheme for the metabolic pathways of pregnenolone-sulphate is presented.


Author(s):  
Kamila B. Muchowska ◽  
Sreejith Jayasree VARMA ◽  
Joseph Moran

How core biological metabolism initiated and why it uses the intermediates, reactions and pathways that it does remains unclear. Life builds its molecules from CO<sub>2 </sub>and breaks them down to CO<sub>2 </sub>again through the intermediacy of just five metabolites that act as the hubs of biochemistry. Here, we describe a purely chemical reaction network promoted by Fe<sup>2+ </sup>in which aqueous pyruvate and glyoxylate, two products of abiotic CO<sub>2 </sub>reduction, build up nine of the eleven TCA cycle intermediates, including all five universal metabolic precursors. The intermediates simultaneously break down to CO<sub>2 </sub>in a life-like regime resembling biological anabolism and catabolism. Introduction of hydroxylamine and Fe<sup>0 </sup>produces four biological amino acids. The network significantly overlaps the TCA/rTCA and glyoxylate cycles and may represent a prebiotic precursor to these core metabolic pathways.


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