Seasonal dynamics of atmospheric methane oxidation in gray forest soils

Seasonal fluctuations in the methane flow in the soil-atmosphere system were determined for gray forest soils of Central Russia. Consumption of atmospheric methane was found to exceed methane emission in gray forest soils under forest and in agrocenosis. The average annual rates of atmospheric methane consumption by the soil under forest and in agrocenosis were 0.026 and 0.008 mg CH4-C/(m2 h), respectively. The annual rate of atmospheric methane oxidation in the gray forest soils of Moscow oblast was estimated to be 0.68 kton. Seasonal fluctuations in the methane oxidation activity were due to changes in the hydrothermal conditions and in the reserves of readily decomposable organic matter and mineral nitrogen, as well as to changes in the activity of methane oxidizers.     

Seasonal Variation in Low Density Lipoprotein Oxidation and Antioxidant Status

Accumulating evidence indicates that oxidative modification of low-density lipoproteins is atherogenic and that antioxidants may play a role in protection of LDL against oxidation. Several studies have reported a seasonal fluctuation in antioxidant levels, but to date nothing is known about seasonal fluctuations in parameters of oxidizability. We collected blood from 10 volunteers at four different periods over one year (February, May, September and December), and measured the amount of plasma lip ids, plasma antioxidants, lipid and fatty acid composition of the LDL particle, LDL antioxidant content, LDL particle size and oxidation parameters (lag time and propagation rate). No seasonal fluctuation for lag time and propagation rate of copper ion-induced LDL oxidation was found. Small seasonal fluctuations were observed for some determinants of LDL oxidation, e.g. plasma and LDL vitamin E and LDL particle size, and for plasma lipids, plasma and LDL lutein and LDL p-carotene. Fatty acid composition of LDL did not change during the year. The main determinant of oxidation susceptibility was the fatty acid composition of LDL. We conclude that LDL oxidation parameters do not change over the year.     

Seasonal Dynamics of Atmospheric Methane Oxidation in Gray Forest Soils

Seasonal fluctuations in the methane fluxes in the soil–atmosphere system were determined for gray forest soils of Central Russia. Consumption of atmospheric methane was found to exceed methane emission in gray forest soils under forest and in the agrocenosis. The average annual rates of atmospheric methane consumption by the soil under forest and in the agrocenosis were 0.026 and 0.008 mg C-CH₄/(m² h), respectively. The annual rate of atmospheric methane oxidation in the gray forest soils of Moscow oblast was estimated to be 0.68 kton. Seasonal fluctuations in the methane oxidation activity were due to changes in the hydrothermal conditions and in the reserves of readily decomposable organic matter and mineral nitrogen, as well as to changes in the activity of methane oxidizers.     

Seasonal Changes in Organic Matter Mineralization in a Sublittoral Sediment and Temperature-Driven Decoupling of Key Processes

Seasonal changes in the mineralization of organic compounds in sediments were investigated in temperate, sublittoral zone sediments (Tokyo Bay, Japan). The total mineralization rate and sulfate reduction rate showed large seasonal variations over the year, and although the fluctuations in both rates correlated with temperature, the latter was irregularly high in May. The concentration of organic carbon dissolved in interstitial water was specifically high in April. A culture-based experiment was also conducted under temperatures corresponding to the seasonal changes. In the culture incubated at a temperature corresponding to April (13 °C), hydrolysis and fermentation proceeded, but terminal oxidation was hindered, thereby resulting in acetate accumulation. At a temperature corresponding to May (22 °C), acetate oxidation coupled with sulfate reduction was observed. The temperature-related differences were also reflected in the bacterial community structure in the cultures analyzed by DGGE. In the culture incubated at the lower temperature, sulfate-reducing bacterium of incomplete oxidizer was detected, while sequence found in the culture incubated at the higher temperature was related to complete oxidizers. These results suggest that complete and incomplete-oxidizing sulfate-reducing bacteria act as distinct functional groups, responding to temperature in different ways, particularly in environments characterized by large temperature fluctuations.     

Diurnal response in endogenous amino acid oxidation of meal-fed rats.

A model has been developed to measure the effects of dietary protein on daily fluctuations in the rate of endogenous amino acid oxidation in meal-fed and starved rats. In addition, N tau-methylhistidine and hydroxyproline were utilized to determine changes in the rate of degradation of myofibrillar and collagen proteins. In rats meal-fed a normal diet of 18% (w/w) casein, a diurnal response was observed in rate of oxidation of radioactive amino acids contained in endogenous labelled body protein, with a nadir 16--20 h and maximum 4--8 h after beginning the feeding. This observation in part may be related to alterations in flux of amino acids from non-hepatic tissues to site of oxidation in liver, as well as alterations in rates of amino acid oxidation after a protein meal. When meal-fed a 70% protein diet, the maximal rates of endogenous amino acid oxidation were significantly increased by 4--8 h after meal-feeding, with no change in fractional rates of degradation of myofibrillar- or collagen-protein breakdown. This could suggest increases in activities of enzymes involved in amino acid oxidation, in rats meal-fed 70% compared with 18% dietary protein. In contrast, meal-feeding of a protein-free diet muted the diurnal response in the rate of oxidation of endogenously labelled amino acids, which correlated with a decrease in the fractional rate of degradation of myofibrillar or collagen protein. Thus dietary protein is apparently responsible for the observed diurnal rhythm rhythms in the rate of amino acid oxidation, whereas carbohydrates tend to mute the response.     

Molecular dynamics simulations and oxidation rates of methionine residues of granulocyte colony-stimulating factor at different pH values

To understand the connection between the conformation of a protein molecule and the oxidation of its methionine residues, we measured the rates of oxidation of methionine residues by H(2)O(2) in granulocyte colony-stimulating factor (G-CSF) as a function of pH and also studied the structural properties of this protein as a function of pH via molecular dynamics simulations. We found that each of the four methionine groups in G-CSF have significant and different rates of oxidation as a function of pH. Moreover, Met(1), in the unstructured N-terminal region, has a rate of oxidation as low as half that of free methionine. The structural properties of G-CSF as a function of pH are evaluated in terms of properties such as hydrogen bonding, deviations from X-ray structure, helical/helical packing, and the atomic covariance fluctuation matrix of alpha-carbons. We found that dynamics (structural fluctuations) are essential in explaining oxidation and that a static picture, such as that resulting from X-ray data, fails in this regard. Moreover, the simulation results also indicate that the solvent-accessible area, traditionally used to measure solvent accessibility of a protein site, of the sulfur atom of methionine residues does not correlate well with the rate of oxidation. Instead, we identified a structural property, average two-shell water coordination number, that correlates well with measured oxidation rates.     

Oxidative activity of poikilotherm mitochondria as a function of temperature

In Newell & Northcroft (1967) evidence was presented which showed that the metabolism of certain intertidal invertebrates at rest does not vary greatly with temperature change. The following work was undertaken to determine whether temperature-independent metabolism could be demonstrated in suspensions of mitochondria extracted from poikilotherm tissue and whether it could be inferred that there was any difference in the ability of poikilotherms from different habitats to adjust to short-term temperature change.
It was found that the rate of reaction/temperature curve of mitochondria isolated from the skate Raia had a flattened region below 10C but above this the rate of oxidation of succinate and pyruvate increased regularly with temperature. The curve for intertidal forms had a gradual slope extending as high as 20C in the mussel Mytilus edulis while in the terrestrial snail Helix aspersa the gradual slope reached 27.5C after which the rate of oxidation of substrate increased sharply before declining towards higher temperatures. Finally, the curve for mitochondria isolated from the desert locust Schistocerca gregaria showed a gradual slope up to 35C after which a sharp increase in the rate of oxidation of substrate occurred. Thus the extent of the gradual slope corresponds with the normal environmental temperature range to which the tissues of the poikilotherms are subjected and the general form of the R-T curve is such that rapid fluctuations within the normal environmental temperature range have relatively little effect on the rate of mitochondrial activity.     

Oxidative activity of poikilotherm mitochondria as a function of temperature

In Newell & Northcroft (1967) evidence was presented which showed that the metabolism of certain intertidal invertebrates at rest does not vary greatly with temperature change. The following work was undertaken to determine whether temperature-independent metabolism could be demonstrated in suspensions of mitochondria extracted from poikilotherm tissue and whether it could be inferred that there was any difference in the ability of poikilotherms from different habitats to adjust toshort-term temperature change.
It was found that the rate of reaction/temperature curve of mitochondria isolated from the skate Raia had a flattened region below 10°C but above this the rate of oxidation of succinate and pyruvate increased regularly with temperature. The curve for intertidal forms had a gradual slope extending as high as 20°C in the mussel Mytilus edulis while in the terrestrial snail Helix aspersa the gradual slope reached 27.5°C after which the rate of oxidation of substrate increased sharply before declining towards higher temperatures. Finally, the curve for mitochondria isolated from the desert locust Schistocerca gregaria showed a gradual slope up to 35°C after which a sharp increase in the rate of oxidation of substrate occurred. Thus the extent of the gradual slope corresponds with the normal environmental temperature range to which the tissues of the poikilotherms are subjected and the general form of the R-T curve is such that rapid fluctuations within the normal environmental temperature range have relatively little effect on the rate of mitochondrial activity.     

A spectral analysis of the periodic components in the heart rhythm structure of newborn infants

Spectral analysis of spontaneous heart rate fluctuations were assessed in 12 healthy newborn infants and in 14 low birth weight newborns. The orthostatic test was performed by the change of newborns posture. High-frequency fluctuations at the respiratory rate were detected in healthy infants and orthostatic reactions of heart rate resembled the same reactions in healthy adults. High-frequency (respiratory) fluctuations were diminished in low-birth weight infants. It is supposed that respiratory fluctuations can be used as a sign of newborn infants well-being and maturation.     

The dynamics of giant unilamellar vesicle oxidation probed by morphological transitions

We have studied the dynamics of Lissamine Rhodamine B dye sensitization-induced oxidation of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) giant unilamellar vesicles (GUVs), where the progression of the underlying chemical processes was followed via vesicle membrane area changes. The surface-area-to-volume ratio of our spherical GUVs increased after as little as ten seconds of irradiation. The membrane area expansion was coupled with high amplitude fluctuations not typical of GUVs in isoosmotic conditions. To accurately measure the area of deformed and fluctuating membranes, we utilized a dual-beam optical trap (DBOT) to stretch GUV membranes into a geometrically regular shape. Further oxidation led to vesicle contraction, and the GUVs became tense, with micron-scale pores forming in the bilayer. We analyzed the GUV morphological behaviors as two consecutive rate-limiting steps. We also considered the effects of altering DOPC and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(lissamine rhodamine B sulfonyl) (RhDPPE) concentrations. The resulting kinetic model allows us to measure how lipid molecular area changes during oxidation, as well as to determine the rate constants controlling how quickly oxidation products are formed. Controlled membrane oxidation leading to permeabilization is also a potential tool for drug delivery based on engineered photosensitizer-containing lipid vesicles.     

Macroscopic fluctuations of the kinetic activity of alcohol dehydrogenase

Macroscopic fluctuations of liver alcohol dehydrogenase enzymic activity in complex reaction consisting in ethanol oxidation and butyraldehyde reduction were studied. It was found that maximal fluctuation amplitude was observed when the rates of both reactions were equal. Such dependence indicates connection between macroscopic fluctuations in alcohol dehydrogenase reaction and oscillations of relative affinity of the enzyme to oxidized and reduced coenzyme forms.     

Hydrogen exchange and proteolytic degradation of ribonuclease A. Similarities and distinctions of the kinetic mechanisms

The studies by IR spectroscopy of the temperature dependence of the H-D exchange rate of the RNase A peptide NH atoms permit one to characterize two types of conformation fluctuations, local and global. A comparison with the temperature dependence of the proteolytic degradation rate of RNase A shows that similar in nature fluctuations allow for the H-D exchange of NH atoms and the splitting of peptide bonds of the native protein. In the low temperature region, both processes occur through local fluctuations, by way of the EX2 mechanism, and in the high temperature region, they occur through global fluctuations with the overall denaturation desorganization of the native structure, by way of the EX1 mechanism. The biphasic dependence of the rate of H-D exchange and proteolytic degradation of RNase A on urea concentration is also explained by the combination of local and global fluctuations.     

Actual and potential rates of substrate oxidation and product formation in continuous cultures ofChromatium vinosum

Kinetics of electron-donor oxidation, storage-polymer formation and growth were studied in continuous cultures ofChromatium under conditions of balanced growth as well as during transient states.Under steady-state conditions, glycogen was accumulated at all dilution rates. This observation is consistent with previously postulated ideas about an ineffective glycogen-synthesis regulation.Upon perturbing the steady states, brought about by injection of extra sulfide into steady-state cultures, the following phenomena were observed immediately, irrespective of the dilution rate: the specific rate of sulfide oxidation increased to the value found in batch cultures, the sulfur-oxidation rate was decreased, the specific glycogen-synthesis rate increased, the increment being higher the lower the dilution rate, but an increase in the specific growth rate, if any, was below the limit of detection. The inverse relationship between the specific rates of glycogen synthesis and growth after removing the substrate limitation is to be explained by a shortage of intermediates, rather than by a growth-rate dependent intrinsic glycogen-synthesis limitation, because upon complete inhibition of growth a further increase in the rate of glycogen synthesis was observed. Essayed in this way, identical glycogen-synthesis rates were found at all dilution rates.Competitive advantages of such an apparently not adapted metabolism in environments with diurnal fluctuations in substrate concentrations are discussed.Non-Standard Abbreviations N_c cell nitrogen - TS total sugar - PHB poly--hydroxybutyrate - D dilution rate - S_R reservoir concentration of the growth-limiting substrate - CAP chloramphenicol     

Regulatory control and the costs and benefits of biochemical noise

Experiments in recent years have vividly demonstrated that gene expression can be highly stochastic. How protein concentration fluctuations affect the growth rate of a population of cells is, however, a wide-open question. We present a mathematical model that makes it possible to quantify the effect of protein concentration fluctuations on the growth rate of a population of genetically identical cells. The model predicts that the population's growth rate depends on how the growth rate of a single cell varies with protein concentration, the variance of the protein concentration fluctuations, and the correlation time of these fluctuations. The model also predicts that when the average concentration of a protein is close to the value that maximizes the growth rate, fluctuations in its concentration always reduce the growth rate. However, when the average protein concentration deviates sufficiently from the optimal level, fluctuations can enhance the growth rate of the population, even when the growth rate of a cell depends linearly on the protein concentration. The model also shows that the ensemble or population average of a quantity, such as the average protein expression level or its variance, is in general not equal to its time average as obtained from tracing a single cell and its descendants. We apply our model to perform a cost-benefit analysis of gene regulatory control. Our analysis predicts that the optimal expression level of a gene regulatory protein is determined by the trade-off between the cost of synthesizing the regulatory protein and the benefit of minimizing the fluctuations in the expression of its target gene. We discuss possible experiments that could test our predictions.     

Parametric spectral analysis of nonstationary fluctuations of excitatory synaptic currents

We assessed on Monte-Carlo simulated excitatory post-synaptic currents the ability of autoregressive (AR)-model fitting to evaluate their fluctuations. AR-model fitting consists of a linear filter describing the process that generates the fluctuations when driven with a white noise. Its fluctuations provide a filtered version of the signal and have a spectral density depending on the properties of the linear filter. When the spectra of the non-stationary fluctuations of excitatory post-synaptic currents were estimated by fitting AR-models to the segments of current fluctuations, assumed to be stationary and independent, the parameter and spectral estimates were scattered. The scatter was much reduced if the time-variant AR-models were fitted using stochastic adaptive estimators (Kalman, recursive least squares and least mean squares). The ability of time-variant AR-models to accurately fit the current fluctuations was monitored by comparing the fluctuations with predicted fluctuations, and by evaluating the model-learning rate. The median frequency of current fluctuations, which could be rapidly tracked and estimated from the individual quantal events (either Monte-Carlo simulated or recorded from pyramidal neurons of rat hippocampus), rose during the rise phase, before declining to a lower steady-state level during the decay phase of quantal event, whereas the variance showed a broad peak. The closing rate of AMPA channels directly affects the steady-state median frequency, whereas the transient peak can be modulated by a variety of factors—number of molecules released, ability of glutamate molecules to re-enter the synaptic cleft, diffusion constant of glutamate in the cleft and opening rate of AMPA channels. In each case, the effect on the amplitude and decay time of mEPSCs and on the current fluctuations differs. Each factor thus leaves its own kinetic fingerprint arguing that the contribution of such factors can be inferred from the combined kinetic properties of individual mEPSCs.     

Fluctuations in tension during contraction of single muscle fibers.

We have searched for fluctuations in the steady-state tension developed by stimulated single muscle fibers. Such tension "noise" is expected to be present as a result of the statistical fluctuations in the number and/or state of myosin cross-bridges interacting with thin filament sites at any time. A sensitive electro-optical tension transducer capable of resolving the expected fluctuations in magnitude and frequency was constructed to search for the fluctuations. The noise was analyzed by computing the power spectra and amplitude of stochastic fluctuations in the photomultiplier counting rate, which was made proportional to muscle force. The optical system and electronic instrumentation together with the minicomputer software are described. Tensions were measured in single skinned glycerinated rabbit psoas muscle fibers in rigor and during contraction and relaxation. The results indicate the presence of fluctuations in contracting muscles and a complete absence of tension noise in eith rigor or relaxation. Also, a numerical method was developed to simulate the power spectra and amplitude of fluctuations, given the rate constants for association and dissociation of the cross-bridges and actin. The simulated power spectra and the frequency distributions observed experimentally are similar.     

Fluctuations in continuous mammalian cell bioreactors with retention.

Continuous flow bioreactors with cell retention have been increasingly used for the cultivation of mammalian cells. The potential advantages of such bioreactors are high cell concentrations and volumetric productivities. In many reported cases, these systems have shown fluctuations in cell concentrations of various frequency and magnitude. To analyze the dynamics of the fluctuations, a model-based approach is followed. Simulations showed that large fluctuations in biomass resulted in response to fluctuations in the retention ratio when the system is operated at high dilution rate and high cell retention. The dependence of cell concentration fluctuations on variations in dilution rate and retention ratio was established by a cross-correlation statistical analysis on available experimental data. The slower dynamics and the fluctuation propensity of retention systems suggest that continuous culture without retention is more convenient for kinetic studies. In all likelihood, continuous culture with retention can be stabilized by controlling both the retention ratio and the dilution rate.     

Persistence of the control of the fluctuations of heart rate in the anesthetized and pithed adult rat. Effect of enteraminergic drugs]

Spontaneous fluctuations in heart rate were analyzed by spectral analysis in the ether anesthetized and pithed adult rat. In order to investigate the changes in the spectral pattern of the fluctuations, the selective 5HT-2 and -3 isoreceptor blockers ritanserin and BRL 43694A were used. In both the experimental conditions, ritanserin blockade led to dose-dependent increased fluctuations in HR low and high frequencies. In both the anesthetized and pithed rats, the low frequency range HR fluctuations were drastically reduced by BRL 43694A.     

Pharmacology of atriopeptin in the adult rat: power spectra of the fluctuations in heart rate]

The persistence of the cardiac beat-to-beat control is studied in the anesthetized and the pithed adult rat by means of spectral analysis. The data show that atriopeptin affects the amplitude of the heart rate low frequency fluctuations, significantly increasing the spectral patterns both in the anesthetized and the pithed rat. The atriopeptin enhancement of the low frequency range in heart rate fluctuations provides further insight into the hypothesis that beat to beat variability in hemodynamic parameters reflects a compensatory response in the short term cardiovascular control.     

Dynamical systems analysis of arterial blood pressure signals in relation to heart rate fluctuations in chick embryos

We attempted a new approach based on a modern dynamical system theory to reconstruct the arterial blood pressure signals in relation to heart rate fluctuations of developing chick embryos. The dynamical systems approach in general is to model a phenomenon that is presented by a single time series record and approximate the dynamical property (e.g. heart rate fluctuations) of a system based only on information contained in a single-variable (arterial blood pressure) of the system. The time-series data of the arterial blood pressure was reconstructed in 3-dimensional space to draw characteristic orbits. Since the reconstructed orbits of the blood pressure should retain information contained in the pressure signals, we attempted to derive instantaneous heart rate (IHR) from the reconstructed orbits. The derived IHR presenting HR fluctuations coincided well with the IHR obtained conventionally from the peak-to-peak time intervals of the maximum blood pressure. Movements of the reconstructed orbits of the arterial blood pressure in 3-dimensional space reflected HR fluctuations (i.e. transient decelerations and accelerations).