Estimation of steady-state flux rates in metabolic systems by computer simulations of radioactive tracer experiments

The dynamics of radioactive tracers in metabolic systems canbe mathematically modelled by coupled systems of differentialequations for both the concentrations and the specific radio-activitiesof the metabolites involved. Computer simulations, i.e. directfitting of numerical solutions of these equations to observedtime-courses of metabolites and spec jflc radioactivities, enablesone to estimate unknown kinetic parameters of the system. Thetheoretical fundamentals of this approach and the main stepstowards the quantitative assessment of flux rates in stationarymetabolic systems are outlined. An application of the methodto the purine nucleotide metabolism of Ehrlich ascites twnorcells is given based on a simp4fied model of this pathway. Theobtained steady-state flux rates indicate a marked increasein the metabolism of the adenine nucleotides during the proliferatingphase in comparison to the resting phase of tumor growth.     

Model‐based identifiable parameter determination applied to a simultaneous saccharification and fermentation process model for bio‐ethanol production

In this work, a methodology for the model‐based identifiable parameter determination (MBIPD) is presented. This systematic approach is proposed to be used for structure and parameter identification of nonlinear models of biological reaction networks. Usually, this kind of problems are over‐parameterized with large correlations between parameters. Hence, the related inverse problems for parameter determination and analysis are mathematically ill‐posed and numerically difficult to solve. The proposed MBIPD methodology comprises several tasks: (i) model selection, (ii) tracking of an adequate initial guess, and (iii) an iterative parameter estimation step which includes an identifiable parameter subset selection (SsS) algorithm and accuracy analysis of the estimated parameters. The SsS algorithm is based on the analysis of the sensitivity matrix by rank revealing factorization methods. Using this, a reduction of the parameter search space to a reasonable subset, which can be reliably and efficiently estimated from available measurements, is achieved. The simultaneous saccharification and fermentation (SSF) process for bio‐ethanol production from cellulosic material is used as case study for testing the methodology. The successful application of MBIPD to the SSF process demonstrates a relatively large reduction in the identified parameter space. It is shown by a cross‐validation that using the identified parameters (even though the reduction of the search space), the model is still able to predict the experimental data properly. Moreover, it is shown that the model is easily and efficiently adapted to new process conditions by solving reduced and well conditioned problems. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1064–1082, 2013     

Two-dimensional electrophoretic protein patterns of reciprocal hybrids of the mouse strains DBA and C57BL

Two-dimensional electrophoretic patterns of cytoplasmic liver proteins of the mouse were investigated in reciprocal hybrids of the two inbred mouse strains DBA and C57BL in order to establish whether strain-specific protein variants reveal a mode of inheritance compatible with the concept of genomic imprinting. Variants of this type were found to account for about 11% of approximately 200 variant protein spots scrutinized. Transmission of the maternal form of a variant protein was more frequent than transmission of the paternal form. Maternal/paternal transmission was observed only for proteins showing strain variations in their amount. The results are discussed in terms of the frequency of imprinted genes.     

PHOSPHATE AND SILICATE GROWTH AND UPTAKE KINETICS OF THE DIATOMS ASTERIONELLA FORMOSA AND CYCLOTELLA MENEGHINIANA IN BATCH AND SEMICONTINUOUS CULTURE1

Information on the nutrient kinetics of Asterionella formosa Hass. and Cyclotella meneghiniana Kutz. under either phosphate or silicate limitation was obtained for use in a Monod model and in a variable internal stores model of growth. Short-term batch culture growth experiments were fit to the Monod model and long-term semicontinuous culture experiments and short-term uptake experiments were fit to the variable internal stores model. Mathematical analysis indicates that the parameters of the 2 models may be expressed in terms of each other at steady state. The qualitative results of both batch and steady state culture methods agree. For limiting phosphate experiments. A. formosa is better able to grow at low PO₄-P concentrations than C. meneghiniana, as shown by its lower K for PO₄-P limited growth. The k_Q of A. formosa compared to C. meneghiniana found in long-term semicontinuous culture indicates that A. formosa is almost an order of magnitude more efficient at using internal phosphate for growth. The qualitative results under silicate-limited growth of C. meneghiniana is less than that of A. formosa. The k_Q from semicontinuous culture experiments indicates that C. meneghiniana is the more efficient at using internal silicate for growth. Nutrient uptake experiments showed more variability from a Michaelis-Menten relationship than short-term growth experiments. There were no significant differences between the 2 species in half saturation constants for either phosphate or silicate uptake. We observed a marked dependence of the coefficient of luxury consumption (R) of phosphate on the steady state growth rate. A. formosa has a higher R than C. meneghiniana.     

Estimation of metabolic flux rates in liver purine catabolism of tumour-bearing mice by computer simulation of radioactive tracer experiments

Mouse hepatocytes from healthy control mice and from Ehrlich ascites tumour-bearing mice were used for tracer-kinetic studies of purine catabolism of liver cells during different periods of tumour growth. The dynamics of the radioactive tracers were modelled mathematically by a system of differential equations. Computer simulations, i.e. direct fitting of numerical solutions of these equations to the observed time-courses of metabolites and specific radioactivites, enables one to estimate unknown kinetic parameters of a simplified model of pathways of hepatic purine catabolism in tumour-bearing mice. There occurred great differences of metabolic flux rates between control hepatocytes, hepatocytes of mice during the proliferating period of tumour growth (6th day after inoculation of the tumour) and hepatocytes of mice during the resting period of tumour growth (12th day after inoculation of the tumour). The final purine degradation of hepatocytes prepared during the proliferating period was lower in comparison with that of control hepatocytes, but it was markedly higher in hepatocytes prepared during the resting period of tumour growth. The changes in hepatocyte purine catabolism during the proliferating period of tumour growth argue for transitions which aim at the maintenance of high purine nucleotide levels in the liver itself rather than for an increased nucleoside and nucleobase supply for the tumour. This suggestion is in accordance with the increased ATP level of the liver during the proliferating phase of tumour growth. The drastic acceleration of the final steps of hepatic purine catabolism forming uric acid and allantoin during the resting period of tumour growth was predominantly due to increased flux rate from xanthosine and guanine in accordance with increased catabolism of monophosphorylated nucleotides.     

Substance P- and choline acetyltransferase immunoreactivities in somatostatin-containing, human submucosal neurons

The submucous layers of human small and large intestines contain at least two separate neuron populations. Besides morphological features, they differ in their immunoreactivities for calretinin (CALR) and somatostatin (SOM), respectively. In this study, submucosal wholemounts of 23 patients or body donors (including all segments of small intestine and colon) were immunohistochemically quadruple stained for CALR and SOM as well as for substance P (SP) and choline acetyltransferase (ChAT). We found that all SOM-positive neurons co-stained for ChAT and the majority for SP [between 50 % in the small intestinal external submucosal plexus (ESP) and 75 % in the colonic ESP]. In contrast, a majority of CALR-neurons contained ChAT (between 77 % in the small intestinal ESP and 92 % in the large intestinal ESP) whereas less than 4 % of CALR-neurons were co-immunoreactive for SP. Another set of wholemounts was co-stained for peripherin, a marker enabling morphological analysis. Where identifiable, both SOM alone- and SOM/SP-neurons displayed a uniaxonal (supposed pseudouniaxonal) morphology. We suggest that the chemical code of SOM-immunoreactive, human submucosal neurons may be “ChAT+/SOM+/SP±”. In additional sections double stained for SOM and SP, we regularly found double-labelled nerve fibres only in the mucosa. In contrast, around submucosal arteries mostly SOM alone- fibres were found and the muscularis propria contained numerous SP-alone fibres. We conclude that the main target of submucosal SOM(/SP)-neurons may be the mucosa. Due to their morpho-chemical similarity to human myenteric type II neurons, we further suggest that one function of human submucosal SOM-neurons may be a primary afferent one.