Energetic Macroevolution of Vertebrates

An analysis of our own data and published data on comparable standard metabolism in vertebrates has been carried out. It was shown that within each family and most of the orders this parameter varies insignificantly and the mean values for the comparable standard metabolism are grouped around certain values presumably corresponding to the stationary states to which organisms aspire in the course of evolution. There was a significant difference in the comparable standard metabolism in poikilothermic and homeothermic animals, apparently related to the existence of a heat barrier, which is overcome by the appearance of thermoregulation. In total, seven levels of stationary states were distinguished for vertebrates and 12 of them for all animals. It was established that the ratio of the values of the comparable standard metabolism for neighboring levels varies insignificantly and is ~2.2. It was noted that in the process of macroevolution of phyla and classes, their constituent units occupy ever higher stationary levels. A possible mechanism of transition from one stationary level to another is discussed.     

Rates of evolution on the time scale of the evolutionary process

A generational time scale, involving change from one generation to the next, is the time scale of evolution by natural selection. Microevolutionary and macroevolutionary patterns reflect this process on longer time scales. Rates of evolution are most efficiently expressed in haldane units, H, in standard deviations per generation, indexed by the log of the time interval. Rates from replicated selection experiments and simulations have rate-interval [RI] and log rate-log interval [LRI] scaling relations enabling directional, stationary, and random time series to be distinguished. Empirical microevolutionary and macroevolutionary data exhibit stationary scaling, but point to generational rates of evolution (H ₀) conservatively on the order of 0.2 standard deviations per generation on the time scale of the evolutionary process. This paradox of long-term stationary scaling and short-term high rates of change can be explained by considering the shape of an heuristic time-form evolutionary lattice. Cenozoic mammals occupy a lattice that is about four orders of magnitude longer in time than it has ever been wide in form. The evolutionary process is dynamic but operates within relatively narrow morphological constraints compared to the time available for change.     

Lifetime energy budgets in mammals and birds.

1. Two data sets for standard energy metabolism (351 and 320 species, respectively) and one for maximal lifespan (494 species) in mammals have been assembled from the literature. 2. In addition smaller data sets of active (field) energy metabolism in mammals (36 species) and in birds (25 species) have been drawn on. 3. The products of the respective regression parameters as well as the products of energy metabolism and maximal lifespan in individual species have been computed in order to estimate lifetime energy metabolism in mammals generally and in various mammalian orders. 4. It is found that lifetime energy budgets in mammals generally, whether standard or active, very systematically with body mass with slopes between 0.87 and 0.93, significantly different from unity (P less than 0.001 or P less than 0.01). 5. In birds, lifetime energy budgets, whether standard or active, vary with slopes of 0.94 +/- 0.05 and 0.88 +/- 0.09, which are not significantly different from unity (P greater than 0.1). 6. In carnivores, artiodactyls, primates and bats the slopes for lifetime standard as well as lifetime active energy budgets are not significantly different from one in any of the investigated data sets. 7. In rodents the lifetime standard energy budgets have slope significantly different from one; in marsupials one data set for lifetime standard and the one for lifetime active energy budget lead to slopes significantly different from one. 8. It is concluded from this analysis that current data do not support the hypothesis that lifetime energy budgets, whether standard or active, vary as the first power of body mass in mammals generally.(ABSTRACT TRUNCATED AT 250 WORDS)     

Control of oxidative phosphorylation by the extramitochondrial ATP/ADP ratio

The control of mitochondrial ATP synthesis by the extramitochondrial adenine nucleotide pattern was investigated with rat liver mitochondria. It is demonstrated that any stationary state between the two limit states of maximum activity (state 3) and of resting activity (state 4) can be obtained by a hexokinase-glucose trap as an ADP-regenerating system. These intermediate states are characterized by stationary respiratory rates, stationary redox levels of the cytochromes b and c and stationary levels of extramitochondrial ATP and ADP between the rates and levels of the limit states. At a constant concentration of inorganic phosphate the activity of mitochondria between the limit states is controlled by the extramitochondrial ATP/ADP ratio independent of the total concentration of adenine nucleotides present. The control range was found to be between ratios of about 5 and 100 at 10 mM phosphate. At lower ratios the mitochondria are in their maximum phosphorylating state. With succinate + rotenone and glutamate + malate the same control range was observed, indicating that it is independent of the nature of substrate oxidized.The results suggest that in the control range the mitochondrial activity is limited by the competition of ADP and ATP for the adenine nucleotide translocator.     

Stabilization of energy charge, generation of oscillations and multiple steady states in energy metabolism as a result of purely stoichiometric regulation.

A simple kinetic model of cell energy metabolism with autocatalytic reaction sequences has beepn analysed. The model accounts for the fact that part of energy produced in the form of ATP, or any other equivalent form, is utilized in "sparking" reactions to activate initial substrates. Analysis of the model shows that energy metabolism, in the absen-e of all non-stoichiometric (i.e. isosteric, cooperative, and allosteric) regulations, is capable of (a) stabilizing, to a high degree of accuracy, the relative concentration of the "charged form" of the energy-transferring cofactor (ATP); (b) alternating between two stable stationary states by means of hysteretic transitions; (c) generating self-oscillations in energy production. It is proposed that energy metabolism can be a source of very slow, in particular circadian (of about a one-day period), oscillations which may serve as the basis for temporal organization of the cell.     

Estimating kinetic constants from single channel data.

The process underlying the opening and closing of ionic channels in biological or artificial lipid membranes can be modeled kinetically as a time-homogeneous Markov chain. The elements of the chain are kinetic states that can be either open or closed. A maximum likelihood procedure is described for estimating the transition rates between these states from single channel data. The method has been implemented for linear kinetic schemes of fewer than six states, and is suitable for nonstationary data in which one or more independent channels are functioning simultaneously. It also provides standard errors for all estimates of rate constants and permits testing of smoothly parameterized subhypotheses of a general model. We have illustrated our approach by analysis of single channel data simulated on a computer and have described a procedure for analysis of experimental data.     

Flow birefringence of xanthan and other polysaccharide solutions

A xanthan sample with molecular weight M = 2.2 x 10(6) was investigated in three solvents: bidistilled water, 0.2 M aqueous NaCl and cadoxen by flow birefringence and viscometry methods in dilute solutions. It was shown that the optical shear rate coefficients of xanthan in aqueous and cadoxen media differ by two orders of magnitude. An estimation of xanthan optical anisotropy in different conformational states has been made and compared with values for other polysaccharides: dextran, pullulan, cellulose and chitosan. The process of denaturation and the flow birefringence of renaturated xanthan in aqueous solutions (after heat treatment at 121 degrees C) have also been studied.     

Trace element content in fingernails and hair of a nonindustrialized US control population

The concentrations of 17 elements in the nail and hair of 117 subjects from a nonindustrialized environment were determined by instrumental neutron activation analysis (INAA). A new method of statistical treatment that allows for more meaningful use of detection limit values was used to process the concentration data. Geometric means and standard errors are presented for each element, along with a summary of the effects of age, sex, and treatment on the concentration of each element. For nails, these data represent the first comprehensive study for several important elements. Correlations for each element between hair and nail were determined. With few exceptions, concentrations of nonessential trace elements were positively correlated in hair and nail, whereas concentrations of essential elements showed no correlations. The factors affecting concentrations and control levels must be considered in studying alterations in disease states.     

Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis

A fundamental problem in DNA microarray analysis is the lack of a common standard to compare the expression levels of different samples. Several normalization protocols have been proposed to overcome variables inherent in this technology. As yet, there are no satisfactory methods to exchange gene expression data among different research groups or to compare gene expression values under different stimulus–response profiles. We have tested a normalization procedure based on comparing gene expression levels to the signals generated from hybridizing genomic DNA (genomic normalization). This procedure was applied to DNA microarrays of Mycobacterium tuberculosis using RNA extracted from cultures growing to the logarithmic and stationary phases. The applied normalization procedure generated reproducible measurements of expression level for 98% of the putative mycobacterial ORFs, among which 5.2% were significantly changed comparing the logarithmic to stationary growth phase. Additionally, analysis of expression levels of a subset of genes by real time PCR technology revealed an agreement in expression of 90% of the examined genes when genomic DNA normalization was applied instead of 29–68% agreement when RNA normalization was used to measure the expression levels in the same set of RNA samples. Further examination of microarray expression levels displayed clusters of genes differentially expressed between the logarithmic, early stationary and late stationary growth phases. We conclude that genomic DNA standards offer advantages over conventional RNA normalization procedures and can be adapted for the investigation of microbial genomes.     

SVM-Cabins: prediction of solvent accessibility using accumulation cutoff set and support vector machine

A number of methods for predicting levels of solvent accessibility or accessible surface area (ASA) of amino acid residues in proteins have been developed. These methods either predict regularly spaced states of relative solvent accessibility or an analogue real value indicating relative solvent accessibility. While discrete states of exposure can be easily obtained by post prediction assignment of thresholds to the predicted or computed real values of ASA, the reverse, that is, obtaining a real value from quantized states of predicted ASA, is not straightforward as a two-state prediction in such cases would give a large real valued errors. However, prediction of ASA into larger number of ASA states and then finding a corresponding scheme for real value prediction may be helpful in integrating the two approaches of ASA prediction. We report a novel method of obtaining numerical real values of solvent accessibility, using accumulation cutoff set and support vector machine. This so-called SVM-Cabins method first predicts discrete states of ASA of amino acid residues from their evolutionary profile and then maps the predicted states onto a real valued linear space by simple algebraic methods. Resulting performance of such a rigorous approach using 13-state ASA prediction is at least comparable with the best methods of ASA prediction reported so far. The mean absolute error in this method reaches the best performance of 15.1% on the tested data set of 502 proteins with a coefficient of correlation equal to 0.66. Since, the method starts with the prediction of discrete states of ASA and leads to real value predictions, performance of prediction in binary states and real values are simultaneously optimized.     

Necessary conditions for a minimal model of receptor to show adaptive response over a wide range of levels of stimulus

Sensory systems respond to temporal changes in the stimulus and adapt to the new level when it persists, this pattern of response being maintained in a wide range of levels of stimulus. Here we use a simple model of adaptation developed by Segel et al. (J. Theor. Biol. 120 (1986) 151-179) and extended by Hauri and Ross (Biophys. J. 68 (1995) 708-722) to study the conditions in which it shows wide range of response. The model consists of a receptor that switches between a variable number of states, either by mass action law or by covalent modification. Using a global optimization procedure, we have optimized the adaptive response of the alternatives of the model with different number of states. We find that it is impossible to obtain a wide range of response if the receptor switches between states following mass-action laws, irrespective of the number of states. Instead, a wide range (of five orders of magnitude of ligand concentration) can be obtained if the receptor switches between several states by irreversible covalent modification, in agreement with previous models. Therefore, in this model, expenditure of energy to maintain a large number of covalent modification cycles operating outside equilibrium is necessary to achieve a wide range of response. The optimal values of the parameters present similar patterns to those reported for specific receptors, but there is no quantitative agreement. For instance, ligand affinity varies several orders of magnitude between the different states of the receptor, what is unlikely to be fulfilled by real systems. To see if the minimal model can show adaptive response and range with quantitatively plausible parameter values a sub-optimal receptor was studied, finding that adaptive response of high intensity can still be obtained in at least three orders of magnitude.     

Thermodynamic Analysis of Energy Transfer in Acidogenic Cultures

A global thermodynamic analysis, normally used for pure cultures, has been performed for steady‐state data sets from acidogenic mixed cultures. This analysis is a combination of two different thermodynamic approaches, based on tabulated standard Gibbs energy of formation, global stoichiometry and medium compositions. It takes into account the energy transfer efficiency, ?, together with the Gibbs free energy dissipation, ΔG_o, analysis of the different data. The objective is to describe these systems thermodynamically without any heat measurement. The results show that ? is influenced by environmental conditions, where increasing hydraulic retention time increases its value all cases. The pH effect on ? is related to metabolic shifts and osmoregulation. Within the environmental conditions analyzed, ? ranges from 0.23 for a hydraulic retention time of 20 h and pH 4, to 0.42 for a hydraulic retention time of 8 h and a pH ranging from 7–8.5. The estimated values of ΔG_o are comparable to standard Gibbs energy of dissipation reported in the literature. For the data sets analyzed, ΔG_o ranges from –1210 kJ/mol_x, corresponding to a stirring velocity of 300 rpm, pH 6 and a hydraulic retention time of 6 h, to –20744 kJ/mol_x for pH 4 and a hydraulic retention time of 20 h. For average conclusions, the combined approach based on standard Gibbs energy of formation and global stoichiometry, used in this thermodynamic analysis, allows for the estimation of Gibbs energy dissipation values from the extracellular medium compositions in acidogenic mixed cultures. Such estimated values are comparable to the standard Gibbs energy dissipation values reported in the literature. It is demonstrated that ? is affected by the environmental conditions, i.e., stirring velocity, hydraulic retention time and pH. However, a relationship that relates this parameter to environmental conditions was not found and will be the focus of further research.     

Prolonged lidocaine metabolizing activity of primary hepatocytes with spheroid culture using polyurethane foam as a culture substratum

Primary rat hepatocytes formed spheroids in the pores of polyurethane foam (PUF) used as a culture substratum. The hepatocytes in monolayer and spheroid stationary culture converted lidocaine to monoethylglycinexylidide (MEGX) which was N-deethylation of lidocaine. The metabolic activity of the hepatocytes/spheroid stationary culture system was 1.5∼2.0-fold higher than that of monolayer culture for 10 days. The activity of albumin production and cell survival of hepatocytes in monolayer and spheroid cultures decrease due to lidocaine treatment dependend on the lidocaine concentration, but the activity and cell survival in PUF/spheroid stationary culture were maintained at a higher level than that in monolayer culture under the lidocaine treatment. We developed a device for an in vitro liver model, drug metabolism simulator (DMS), using a PUF/spheroid packed-bed module including 4.00 ± 0.68 × 10⁷ hepatocytes and analyzed pharmacokinetics of lidocaine in a one-compartment model. Lidocaine clearance and extraction ratio of hepatocytes in the DMS corresponded to 1.354 ± 0.318 ml/min/g-liver and 0.677 ± 0.0159/g-liver, respectively (N=4). These values were comparable with in vivo values, 1.930 ml/min g-liver and 0.965/g-liver reported by Nyberg (1977). Consequently, PUF/spheroid culture maintained high lidocaine metabolizing activity over a long term and seems to provide a promising culture system as a drug metabolism simulator which will be used for drug screening, cytotoxicity tests and prediction of pharmacokinetics. This revised version was published online in July 2006 with corrections to the Cover Date.     

Growth-related fluctuation in messenger RNA utilization in animal cells

Monkey fibroblasts maintained in culture regulate their levels of intracellular protein throughout the growth cycle by means of variations in the rate of protein biosynthesis. Cytoplasmic mRNA in stationary phase cells was compared to that in exponential phase cells. In stationary phase cells 56% of the cytoplasmic polyadenylated RNA was found in the 40--90S postpolysomal region of sucrose sedimentation gradients, while only 23% was found in this region in exponential phase cells. Analysis of electron micrographs of sectioned exponential and stationary phase cells revealed that this shift in polyadenylated RNA location is accompanied by a loss of polysome-like aggregates of ribosomes. Most if not all of this species of postpolysomal polyadenylated RNA is not being translated by single ribosomes since no detectable amounts of nascent peptide were present in this region. This nonpolysomal polyadenylated RNA is comparable in size to polysomal polyadenylated RNA. The length of the 3'-poly(A) tract was also comparable for these two species. The extent of capping of poly(A)- containing molecules was also comparable for these two species. The template activity of nonpolysomal RNA in a wheat germ extract was comparable to that of polysomal RNA. The peptides produced by these two preparations were of a similar large size. Furthermore, most of the nonpolysomal polyadenylated RNA of stationary phase cells was driven into polysomes in the presence of a low dose of cycloheximide. Therefore, we conclude that the untranslated mRNA that accumulates in stationary phase cells is structurally intact, is fully capable of being translated, and is not being translated due to the operation of a translational initiation block.     

Micro-determination of clonazepam in plasma or serum by electron-capture gas—liquid chromatography

A rapid method is described for the electron-capture gas chromatographic determination of clonazepam in plasma or serum using methyl-clonazepam as an internal standard. The analysis is performed isothermally on the silicone stationary phase SP-2510DA (Supelco). With this liquid phase, gas chromatographic properties are comparable to methods involving acid hydrolysis or derivatisation. A short pre-column containing another phase is added to enhance resolution. The method involves a single extraction, requires 100 μl of sample and has a detection limit of 3 nmol/l. Response is linear at concentrations from 5–900 nmol/l and thus clonazepam analysis both during therapy and after overdosage is possible. Plasma and serum clonazepam levels are interchangeable.     

Comparison of ovalbumin quantification using forward-phase protein microarrays and suspension arrays

We employed ovalbumin (a simulant used for ricin and botulism toxins in biodefense applications) and its high affinity polyclonal antibody as a model system to examine the sensitivity, dynamic range, linearity, and reproducibility of forward-phase array results in comparison to suspension arrays. It was found that protein microarrays had a dynamic range of 4 orders of magnitude and a sensitivity of less than 1 pg/mL, respectively. The dynamic range and sensitivity of suspension arrays were close to 2 orders of magnitude and 0.25 ng/mL, respectively. The sensitivity we observed for the suspension arrays is comparable to that reported for enzyme-linked immunosorbent assays (ELISAs) in the literature. We used ovalbumin samples with two different purities, 38.0% and 76.0% (w/w), as determined by polyacrylamide gel electrophoresis (PAGE). These samples were used to evaluate the effect of impure samples on detection. The data obtained from the forward-phase protein arrays gave values that were consistent with the PAGE data. The data from the suspension arrays were not as consistent and may indicate that this format may not give as reliable data with impure samples. Knowledge of the advantages and disadvantages of the two proteomic methods would allow their more rational use in clinical diagnosis.     

Macroscopic modelling of overflow metabolism and model based optimization of hybridoma cell fed-batch cultures

A macroscopic model that takes into account phenomena of overflow metabolism within glycolysis and glutaminolysis is proposed to simulate hybridoma HB-58 cell cultures. The model of central carbon metabolism is reduced to a set of macroscopic reactions. The macroscopic model describes three metabolism states: respiratory metabolism, overflow metabolism and critical metabolism. The model parameters and confidence intervals are obtained via a non linear least squares identification. It is validated with experimental data of fed-batch hybridoma cultures and successfully predicts the dynamics of cell growth and death, substrate consumption (glutamine and glucose) and metabolites production (lactate and ammonia). Based on a sensitivity analysis of the model outputs with respect to the parameters, a model reduction is proposed. Finally, the maximization of biomass productivity of hybridoma cell fed-batch cultures is analyzed. This model allows, on the one hand, quantitatively describing overflow metabolism in mammalian cell cultures and, on the other hand, will be valuable for monitoring and control of fed-batch cultures in order to optimize the process. This is illustrated in this contribution with the determination of optimal feeding profiles aiming at maximizing biomass productivity.     

Self-organizing maps: stationary states,metastability and convergence rate

We investigate the effect of various types of neighborhood function on the convergence rates and the presence or absence of metastable stationary states of Kohonen's self-organizing feature map algorithm in one dimension. We demonstrate that the time necessary to form a topographic representation of the unit interval [0, 1] may vary over several orders of magnitude depending on the range and also the shape of the neighborhood function, by which the weight changes of the neurons in the neighborhood of the winning neuron are scaled. We will prove that for neighborhood functions which are convex on an interval given by the length of the Kohonen chain there exist no metastable states. For all other neighborhood functions, metastable states are present and may trap the algorithm during the learning process. For the widely-used Gaussian function there exists a threshold for the width above which metastable states cannot exist. Due to the presence or absence of metastable states, convergence time is very sensitive to slight changes in the shape of the neighborhood function. Fastest convergence is achieved using neighborhood functions which are "convex" over a large range around the winner neuron and yet have large differences in value at neighboring neurons.     

A procedure for the detection of pollution by fish movements.

An "alarm" system using fish movements has recently been developed to provide rapid information about accidental spills of pollutants. The data are the realization of a non-stationary stochastic process which takes on discrete values. By the use of the Camp-Paulson approximation, the process is transformed to a strictly stationary one for which calculations are tractable. A procedure is then presented to detect the presence of pollutants. Tests with real data indicate that it detects them sooner than the method used previously.     

Mathematical modelling of the purine metabolism of the rat liver

The regulation of the purine metabolism of the rat liver is studied on the basis of a mathematical model which comprises rate laws and kinetic constants of all physiologically relevant reactions. The computed stationary and time-dependent concentrations are in good accordance with experimental data obtained in the ischaemic rat liver and in isolated hepatocytes. In particular, model-based simulations of the adenine nucleotide metabolism have been performed for situations where ATP-deficient states of the cell (hypoxia, anoxia or ischaemia) of various length are followed by onset of ATP production (reoxygenation). These simulations confirm the experimentally observed incomplete recovery of ATP and of the total pool of adenine nucleotides within a few hours of reoxygenation after long-term ATP depletion. Therefore, it can be concluded that this phenomenon is an intrinsic regulatory property of the purine metabolism and not necessarily due to some irreversible changes in the activity of the enzymes involved.