Modeling reversible reactions in KFP and rKFP.

<p>(a) A schematic diagram of the toy system considered here; for rKFP two copies of each network are similarly made as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003958#pcbi-1003958-g003" target="_blank">Figure 3a</a>. Parameter values used in generating the simulated data: , , and . (b) Dependence of the summary statistics on in KFP. (c) Dependence of the bias of on of the two conditions in rKFP. The red solid diagonal line corresponds to where there is no bias. The red dashed curves correspond to a five-fold difference in the relative pool size changes between the substrate and product, a range we observe in our data.</p

Estimating Relative Changes of Metabolic Fluxes

<div><p>Fluxes are the central trait of metabolism and Kinetic Flux Profiling (KFP) is an effective method of measuring them. To generalize its applicability, we present an extension of the method that estimates the relative changes of fluxes using only relative quantitation of ¹³C-labeled metabolites. Such features are directly tailored to the more common experiment that performs only relative quantitation and compares fluxes between two conditions. We call our extension rKFP. Moreover, we examine the effects of common missing data and common modeling assumptions on (r)KFP, and provide practical suggestions. We also investigate the selection of measuring times for (r)KFP and provide a simple recipe. We then apply rKFP to ¹³C-labeled glucose time series data collected from cells under normal and glucose-deprived conditions, estimating the relative flux changes of glycolysis and its branching pathways. We identify an adaptive response in which <i>de novo</i> serine biosynthesis is compromised to maintain the glycolytic flux backbone. Together, these results greatly expand the capabilities of KFP and are suitable for broad biological applications.</p></div

Understanding KFP and rKFP.

<p>(a) A schematic diagram of KFP applied to a toy metabolic network. At , the system is switched from a C-labeled environment to C-labeled one, and is measured at a few time points thereafter. (b) For a given trajectory of (the black solid curve), the three time regimes (linear, mixed and constant) are marked and three measurements are made (two in the mixed regime and one in the constant). Normalizing it gives between 0 and 1 (the black dashed curve), parameterized by a single parameter , which can be estimated by comparing the normalized measurements to 's of different 's (the red and blue dashed curves). (c) A schematic diagram of rKFP applied to the same network in (a). Relative quantitation is performed on in two conditions (with subscripts and respectively) with the goal of estimating . (d) The ratio in between and is (Eq. 6), and since 's and are identifiable from relative quantitation, so is .</p

Definitions of variables and their identifiabilities in rKFP.

<p>1: Which one of the two possible meanings is meant should be inferable from the context when not specified; it is a slight abuse of notation customary in the field (<i>e.g.</i>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003958#pcbi.1003958-Gunawardena2" target="_blank">[46]</a>).</p><p>Definitions of variables and their identifiabilities in rKFP.</p

Analysis of experimental data.

<p>(a) The diagram of glycolysis and its two branching pathways used in the analysis, where dashed squares (<i>e.g.</i>, BPG) represent missing metabolites, dashed arrows represent missing pathways, and dashed rectangles containing solid squares represent undistinguished metabolites. Abbreviations for metabolites: GLU: glucose; G6P: glucose-6-phosphate; F6P: fructose-6-phosphate; FBP: fructose-1,6-bisphosphate; DHAP: dihydroxyacetone phosphate; GAP: glyceraldehyde-3-phosphate; BPG: 1,3-biphosphglycerate; 3PG: 3-phosphoglycerate; 2PG: 2-phosphoglycerate; PEP: phosphoenolpyruvate; PYR: pyruvate; PGL: 6-phosphogluconolactone; 6PG: phosphogluconate; R5P: the pool of ribose 5-phosphate, ribulose 5-phosphate and xylulose 5-phosphate; PHP: phosphohydroxypyruvate; 3PS: 3-phosphoserine; SER: serine; GLY: glycine. (b) An exemplary plot of the data of a metabolite and its fit. Plots of all metabolites and their fits can be found in Figure S3. (c) Histograms of 's as generated by sampling the corresponding posterior distributions in a way detailed in the Methods. Glycolysis flux refers to in the diagram, PPP flux , and serine synthesis flux . The three histograms for each flux correspond to three different modeling choices described in the text.</p

Metabolite removal in KFP.

<p>(a) A schematic diagram of getting the reduced model through metabolite removal in KFP. Dashed squares represent metabolites removed in the reduced model; thick dark arrow represents reduction; represents the estimated (potentially biased). (b) The estimation results for the three options. The solid curves represent , the dashed curves represent the cost of fitting (normalized by the number of data points to be comparable across options), and three colors represent the three options. Parameter values used for generating the simulated data: (overall patterns independent of the choice here). (c) The estimation results in (b) in terms of the three summary statistics.</p

Christian values in relation to the life of an adolescent

Resumé ŠMEJKAL, Jiří. Křesťanské hodnoty v životě dospívající mládeže Diplomová práce Diplomová práce Křesťanské hodnoty v životě dospívající mládeže je koncipována jako pracovní materiál pro terapeuty, kněze a další pomáhající profese. Vycházím ze svých zkušeností poradenské praxe v oblasti osobnostního rozvoje a řešení konfliktních situací. Zaměřuji se na problematiku dospívajících a jejich potřeby zvládnout své osobní problémy, vyplývající z disharmonických rodinných vztahů a z různorodých negativních podnětů současné společnosti. Cílem práce je zviditelnit různorodost vlivů na utváření názorů dospívajících a současně nabídnout způsob, jak vytipovat a vybrat vhodné morální hodnoty křesťanského etosu, pro potřeby podpůrného rozhovoru s dospívajícím. V první kapitole vymezuji pojmy hodnota, morální princip a morální norma. Dále navrhuji základní kriteria, která musí být splněna, aby navrhované hodnoty byly přijaty. Téma doplňuji o pohledy hodnotové filosofie, křesťanské antropologie a morální teologie. V závěru kapitoly se zamýšlím nad morálním jednáním člověka ve vztahu ke svobodě a dobru. Ve druhé kapitole shrnuji poznatky současné psychologie o významu a funkci rodiny a jak ovlivňuje své jednotlivé členy. Následně uvádím, jaký význam rodině přikládá křesťanství. V třetí kapitole se zabývám vývojem..