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     

Entamoeba histolytica and Entamoeba dispar: Morphological and Behavioral Differences Induced by Fibronectin through GTPases Activation and Actin‐Binding Proteins

Early steps of tissue invasion by Entamoeba histolytica are mediated by adhesion and migration through matrix components such as fibronectin with the participation of the actin cytoskeleton. Striking differences in their produced structures, movement, and migration were found. These observations suggest differential changes in their ability to organize the actin cytoskeleton and, therefore, to modify its morphology after adhesion to fibronectin. To understand these observations, we explore deeper the cytoskeleton pathway of E. histolytica compared to Entamoeba dispar, analyzing the activation and involvement of actin cytoskeleton regulatory proteins such as small GTPases (Rho, Rac1 and Cdc42), myosin IB, paxillin, alpha‐actinin, and ARP2/3 during interaction with fibronectin. Results showed a higher activation of Rac1 in E. histolytica compared to E. dispar, while Cdc42 and RhoA were equally activated in both amebae; besides, variations in the amount of myosin IB, paxillin, and ARP2/3 were detected among these species, coinciding and reflected in formation of lamellipodia in E. histolytica and filopodia in E. dispar. These could partially explain the higher invasive capacity of E. histolytica compared to E. dispar, due to its pleomorphic ability, high motility, migration, activation, and abundance of proteins involved in the cytoskeleton arrangement.     

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.