The kinetics of cometabolism

Experimental observations indicate that the rates of cometabolic transformation are linked to the consumption of growth substrate during growth and to the consumption of cell mass and/or energy substrate in the absence of growth substrate. Three previously proposed models (models 1 through 3) describing the kinetics of cometabolism by resting cells are compared, and the interrelationships and underlying assumptions for these models are explored. Models 1 to 3 are shown to converge at high concentrations of the nongrowth substrate. An expression describing nongrowth substrate transformation in the presence of growth substrate is proposed, and this expression is integrated with an expression for cell growth to give a single unstructured model (model 4) that encompasses models 1 to 3 and describes cometabolism by both resting and growing cells. Model 4 couples transformation of nongrowth substrate to consumption of growth substrate and biomass, and predicts that cometabolism will result, and decreased specific growth rates for a cometabolizing population. Competitive inhibition can also be incorporated in the model. Experimental aspects of model calibration and verification are discussed. The need for models that distinguish between the exhaustion of cell activity and cell death is emphasized. (c) 1993 Wiley & Sons, Inc.     

Determination of maintenance coefficients of Saccharomyces cerevisiae cultures with cell recycle by cross-flow membrane filtration

The fermentation of glucose by a strain of Saccharomyces cerevisiae was studied in a continuous single-stage process with recycle of the cells via cross-flow micro-filtration membranes. Operating conditions were selected such that the culture was not carbon limited and inhibition by ethanol and cell death were minimized.Steady states were obtained for various biomass bleeding rates, i.e., various specific growth rates. From the experimental data, the stoichiometry of the simultaneous reactions, cell growth, ethanol production and maintenance were established using mass and degree of reduction balance relative to substrates (carbon source and oxygen) and products (biomass, ethanol, carbon dioxide etc.), and the growth parameters, yields, and maintenance cofficients were determined. It was shown that the oxygen consumption was not linked to the kinetics of the fermentation. The calculated growth constants were discussed and compared to the currently reported values.     

Biases in the estimation of the demographic parameters of a snowshoe hare population

1. Survival rates and natalities for a population of snowshoe hares in the Yukon were estimated independently of and simultaneously with estimates of population change during the increase phase of a hare cycle.
2. Simple demographic models are used to show that even though the estimated survival rates and natalities were high relative to previously published estimates, the observed demographic parameters are unable to explain the extent of population increase, and we conclude that some of these parameters must be underestimates.
3. A sensitivity analysis is used to examine the potential influence of changes in these demographic parameters on the population growth rate. During most years of the hare cycle the population growth rate is potentially most sensitive to changes in juvenile postweaning survival. Only during crash years is adult survivorship likely to be a more important determinant of the rate of population change.
4. Examination of previously published data sets on two full population cycles suggests that while survival rates are positively correlated with population growth rates, their incorporation into demographic models results in frequent underestimation of the rate of population increase.     

Assessment of macroenergetic parameters for an anaerobic upflow biomass bed and filter (UBF) reactor

This article reports the steady-state performance of two hybrid anaerobic digesters treating soluble synthetic sugar wastes of 1 and 0.5% strength and the assessment of the associated macroenergetic parameters (growth yield, so-called maintenance coefficient). A theoretical development shows a "nongrowth" parameter concept to be more appropriate than maintenance or decay. Combined energy and mass balances are used to develop a model for growth rate which compares well with experimental data. The COD removal efficiency had no significant effect on growth yield and the maintenance parameter, although a dual combined balance indicated the possibility of such an effect. Macroenergetic parameters did not vary significantly with the specific feeding rate of the system. We thus conclude that a single model may be used over a broad range of feeding and performance conditions.     

A cometabilic kinetics model incorporating enzyme inhbition, inactivation, and recovery: I. Model development, analysis, and testing

Cometabolic biodegradation prcesses are important for bioremediation of hazardous waste sites. However, these proceeses are not well understood and have not been modeled thoroughly. Traditional Michaelis-Menten kinetics models often are used, but toxic effects and bacterial responses to toxicity may cause changes in enzyme levels, rendering such models inappropriate. In this article, a conceptual and mathematical model of cometabolic enzyme kinetics i described. Model derivation is based on enzyme/growth-substrate/nongrowth-substrate interaction and incorporates enzyme inhibition (caused by the presence of a cometabolic compound), inactivation (resulting from toxicity of a cometabolic product), and recovery (associated with bacterial synthesis of new enbzyme in response to inactivation). The mathematical model consists of a system of two, nonlinear ordinary differential equations that can be solved implicitly using numerical methods, providing estimates of model parameters. Model analysis shows that growth substraate adn nongrowth substrate oxidation rates are related by a dimensionless constant. Reliability of tehy model solution prcedure is verifiedl by abnalyzing data ses, containing random error, from simulated experimentss with trichhloroethyylene (TCE) degradation by ammonia-oxidizing bacterialunder various conditions. Estimation of the recovery rate contant is deterimined to be sensitive to intial TCE concentration. Model assumptions are evaluated in a companion article using data from TCE degradation experiments with amoniaoxidizing bacteria. (c) 1995 John Wiley & Sons, Inc.     

Estimating age at maturation and energy-based life-history traits from individual growth trajectories with nonlinear mixed-effects models

A new method is presented to estimate individuals’ (1) age at maturation, (2) energy acquisition rate, (3) energy expenditure for body maintenance, and (4) reproductive investment, and the multivariate distribution of these traits in a population. The method relies on adjusting a conceptual energy allocation model to individual growth curves using nonlinear mixed-effects modelling. The method’s performance was tested using simulated growth curves for a range of life-history types. Individual age at maturation, energy acquisition rate and the sum of maintenance and reproductive investment rates, and their multivariate distribution, were accurately estimated. For the estimation of maintenance and reproductive investment rates separately, biases were observed for life-histories with a large imbalance between these traits. For low reproductive investment rates and high maintenance rates, reproductive investment rate estimates were strongly biased whereas maintenance rate estimates were not, the reverse holding in the opposite situation. The method was applied to individual growth curves back-calculated from otoliths of North Sea plaice (Pleuronectes platessa) and from scales of Norwegian spring spawning herring (Clupea harengus). For plaice, maturity ogives derived from our individual estimates of age at maturation were almost identical to the maturity ogives based on gonad observation in catch samples. For herring, we observed 51.5 % of agreement between our individual estimates and those directly obtained from scale reading, with a difference lower than 1 year in 97 % of cases. We conclude that the method is a powerful tool to estimate the distribution of correlated life-history traits for any species for which individual growth curves are available.     

Analysis and validation of a predictive model for growth and death of Aeromonas hydrophila under modified atmospheres at refrigeration temperatures

Specific growth and death rates of Aeromonas hydrophila were measured in laboratory media under various combinations of temperature, pH, and percent CO(2) and O(2) in the atmosphere. Predictive models were developed from the data and validated by means of observations obtained from (i) seafood experiments set up for this purpose and (ii) the ComBase database (http://www.combase.cc; http://wyndmoor.arserrc.gov/combase/). Two main reasons were identified for the differences between the predicted and observed growth in food: they were the variability of the growth rates in food and the bias of the model predictions when applied to food environments. A statistical method is presented to quantitatively analyze these differences. The method was also used to extend the interpolation region of the model. In this extension, the concept of generalized Z values (C. Pin, G. García de Fernando, J. A. Ordó?ez, and J. Baranyi, Food Microbiol. 18:539-545, 2001) played an important role. The extension depended partly on the density of the model-generating observations and partly on the accuracy of extrapolated predictions close to the boundary of the interpolation region. The boundary of the growth region of the organism was also estimated by means of experimental results for growth and death rates.     

Spatial Variation in Lesser Prairie-Chicken Demography: A Sensitivity Analysis of Population Dynamics and Management Alternatives

ABSTRACT The lesser prairie-chicken (Tympanuchus pallidicinctus) is currently considered a candidate for protection under the Endangered Species Act. To identify potential limiting factors for lesser prairie-chicken populations, we developed an age-based matrix model of lesser prairie-chicken population dynamics to compare the relative importance of components of reproduction and survival, and determine if various management alternatives stabilize or increase rates of population change. We based our analyses on an intensive 6-year population study from which demographic rates were estimated for each age class in Kansas. We used deterministic models and elasticity values to identify parameters predicted to have the greatest effect on the rate of population change (λ) at 2 study sites. Last, we used life-stage simulation analysis to simulate various management alternatives. Lambda was <1 for both populations (site 1: λ = 0.54, site 2: λ = 0.74). However, we found differences in sensitivity to nest success and chick survival between populations. The results of the simulated management scenarios complemented the lower-level elasticity analysis and indicated the relative importance of female survival during the breeding season compared with winter. If management practices are only capable of targeting a single demographic rate, changes to either nest success or chick survival had the greatest impact on λ at site 1 and 2, respectively. Management that simultaneously manipulated both nest success and chick survival was predicted to have a greater effect on λ than changes in survival of adult females. In practice, our demographic analyses indicate that effective management should be based on habitat conservation measures to increase components of fecundity.     

What can genetics tell us about population connectivity?

Genetic data are often used to assess ‘population connectivity’ because it is difficult to measure dispersal directly at large spatial scales. Genetic connectivity, however, depends primarily on the absolute number of dispersers among populations, whereas demographic connectivity depends on the relative contributions to population growth rates of dispersal vs. local recruitment (i.e. survival and reproduction of residents). Although many questions are best answered with data on genetic connectivity, genetic data alone provide little information on demographic connectivity. The importance of demographic connectivity is clear when the elimination of immigration results in a shift from stable or positive population growth to negative population growth. Otherwise, the amount of dispersal required for demographic connectivity depends on the context (e.g. conservation or harvest management), and even high dispersal rates may not indicate demographic interdependence. Therefore, it is risky to infer the importance of demographic connectivity without information on local demographic rates and how those rates vary over time. Genetic methods can provide insight on demographic connectivity when combined with these local demographic rates, data on movement behaviour, or estimates of reproductive success of immigrants and residents. We also consider the strengths and limitations of genetic measures of connectivity and discuss three concepts of genetic connectivity that depend upon the evolutionary criteria of interest: inbreeding connectivity, drift connectivity, and adaptive connectivity. To conclude, we describe alternative approaches for assessing population connectivity, highlighting the value of combining genetic data with capture‐mark‐recapture methods or other direct measures of movement to elucidate the complex role of dispersal in natural populations.     

Variation in and correlation between intrinsic rate of increase and carrying capacity

Intrinsic population growth rate and density dependence are fundamental components of population dynamics. Theory suggests that variation in and correlations between these parameters among patches within a population can influence overall population size, but data on the degree of variation and correlation are rare. Replicate populations of a specialist aphid (Chaetosiphon fragaefolii) were followed on 11 genotypes of host plant (Fragaria chiloensis) in the greenhouse. Population models fit to these census data provide estimates of intrinsic growth rate and carrying capacity for aphid populations on each plant genotype. Growth rate and carrying capacity varied substantially among plant genotypes, and these two parameters were not significantly correlated. These results support the existence of spatial variation in population dynamic parameters; data on frequency distributions and correlations of these parameters in natural populations are needed for evaluation of the importance of variation in growth rate and density dependence for population dynamics in the field.     

Kinetics of competitive inhibition and cometabolism in the biodegradation of benzene, toluene, and p-xylene by two Pseudomonas isolates

Two Pseudomonas species (designated strains B1 and X1) were isolated from an aerobic pilot-scale fluidized bed reactor treating groundwater containing benzene, toluene, and p-xylene (BTX). Strain B1 grew with benzene and toluene as the sole sources of carbon and energy, and it cometabolized p-xylene in the presence of toluene. Strain X1 grew on toluene and p-xylene, but not benzene. In single substrate experiments, the appearance of biomass lagged the consumption of growth substrates, suggesting that substrate uptake may not be growth-rate limiting for these substrates. Batch tests using paired substrates (BT, TX, or BX) revealed competitive inhibition and cometabolic degradation patterns. Competitive inhibition was modeled by adding a competitive inhibition term to the Monod expression. Cometabolic transformation of nongrowth substrate (p-xylene) by strain B1 was quantified by coupling xylene transformation to consumption of growth substrate (toluene) during growth and to loss of biomass during the decay phase. Coupling was achieved by defining two transformation capacity terms for the cometabolizing culture: one that relates consumption of growth substrate to the consumption of nongrowth substrate, and second that relates consumption of biomass to the consumption of nongrowth substrate. Cometabolism increased decay rates, and the observed yield for strain B1 decreased in the presence of p-xylene. (c) 1993 Wiley & Sons, Inc.     

Potentially lethal damage repair is due to the difference of DNA double-strand break repair under immediate and delayed plating conditions

Cells plated immediately after irradiation on nutrient agar (immediate plating) exhibit a lower survival than cells which are kept under nongrowth conditions before plating (delayed plating). The difference between the survival curves obtained after immediate plating and delayed plating is considered to exhibit the cell's capacity to repair potentially lethal damage. In yeast evidence has been presented previously for the DNA double-strand break (DSB) as the molecular lesion involved in the repair of potentially lethal damage observed at the cellular level. Radiation-induced DSB are repaired in cells plated on nutrient agar, i.e., under growth conditions, as well as in cells kept under nongrowth conditions. In this paper DSB repair under growth and nongrowth conditions is studied with the help of the yeast mutant rad54-3 which is temperature conditional for DSB repair. It is shown that the extent of repair of potentially lethal damage can be varied by shifting the relative fractions of repair of DSB under growth conditions versus nongrowth conditions. Repair of DSB in cells plated on nutrient agar is promoted when glucose is substituted by Na-succinate as an energy source. As a result the immediate plating survival curve approaches the delayed plating survival curve, thus reducing the operationally defined repair of potentially lethal damage. We show that this reduced potentially lethal damage repair is caused, however, by a higher amount of DSB repair in cells immediately plated on succinate agar as compared to glucose agar.     

Cladoceran birth and death rates estimates: experimental comparisons of egg-ratio methods

I. Birth and death rates of natural cladoceran populations cannot be measured directly. Estimates of these population parameters must be calculated using methods that make assumptions about the form of population growth. These methods generally assume that the population has a stable age distribution.
2. To assess the effect of variable age distributions, we tested six egg ratio methods for estimating birth and death rates with data from thirty-seven laboratory populations of Daphnia pulicaria. The populations were grown under constant conditions, but the initial age distributions and egg ratios of the populations varied. Actual death rates were virtually zero, so the difference between the estimated and actual death rates measured the error in both birth and death rate estimates.
3. The results demonstrate that unstable population structures may produce large errors in the birth and death rates estimated by any of these methods. Among the methods tested, Taylor and Slatkin's formula and Paloheimo's formula were most reliable for the experimental data.
4. Further analyses of three of the methods were made using computer simulations of growth of age-structured populations with initially unstable age distributions. These analyses show that the time interval between sampling strongly influences the reliability of birth and death rate estimates. At a sampling interval of 2.5 days (equal to the duration of the egg stage), Paloheimo's formula was most accurate. At longer intervals (7.5–10 days), Taylor and Slatkin's formula which includes information on population structure was most accurate.     

Dynamical Model of Drug Accumulation in Bacteria: Sensitivity Analysis and Experimentally Testable Predictions

We present a dynamical model of drug accumulation in bacteria. The model captures key features in experimental time courses on ofloxacin accumulation: initial uptake; two-phase response; and long-term acclimation. In combination with experimental data, the model provides estimates of import and export rates in each phase, the time of entry into the second phase, and the decrease of internal drug during acclimation. Global sensitivity analysis, local sensitivity analysis, and Bayesian sensitivity analysis of the model provide information about the robustness of these estimates, and about the relative importance of different parameters in determining the features of the accumulation time courses in three different bacterial species: Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. The results lead to experimentally testable predictions of the effects of membrane permeability, drug efflux and trapping (e.g., by DNA binding) on drug accumulation. A key prediction is that a sudden increase in ofloxacin accumulation in both E. coli and S. aureus is accompanied by a decrease in membrane permeability.     

A New Method for Assessing How Sensitivity and Specificity of Linkage Studies Affects Estimation

Background

While the importance of record linkage is widely recognised, few studies have attempted to quantify how linkage errors may have impacted on their own findings and outcomes. Even where authors of linkage studies have attempted to estimate sensitivity and specificity based on subjects with known status, the effects of false negatives and positives on event rates and estimates of effect are not often described.

Methods

We present quantification of the effect of sensitivity and specificity of the linkage process on event rates and incidence, as well as the resultant effect on relative risks. Formulae to estimate the true number of events and estimated relative risk adjusted for given linkage sensitivity and specificity are then derived and applied to data from a prisoner mortality study. The implications of false positive and false negative matches are also discussed.

Discussion

Comparisons of the effect of sensitivity and specificity on incidence and relative risks indicate that it is more important for linkages to be highly specific than sensitive, particularly if true incidence rates are low. We would recommend that, where possible, some quantitative estimates of the sensitivity and specificity of the linkage process be performed, allowing the effect of these quantities on observed results to be assessed.     

Reduction of porous media permeability from in situ Leuconostoc mesenteroides growth and dextran production

In situ growth of bacteria in a porous medium can alter the permeability of that media. This article reveals that the rate of permeability alteration can be controlled by the inoculation strategy, nutrient concentrations, and injection rates. Based on experimental observations a phenomenological model has been developed to describe the inoculation of the porous medium, the in situ growth of bacteria, and the permeability decline of the porous medium. This model consists of two phases that describe the bacteria in the porous medium: (1) the nongrowth phase in which cell transport and retention are occurring; and (2) the growth phase in which the retained cells grow and plug the porous media. Transition from the transport phase to the growth phase is governed by the growth lag time of the cells within the porous medium. The importance of the inoculum injection strategy and the nutrient injection strategy is illustrated by the model. (c) 1996 John Wiley & Sons, Inc.     

Apoptosis as a mechanism of T-regulatory cell homeostasis and suppression

Activation-induced cell death is a general mechanism of immune homeostasis through negative regulation of clonal expansion of activated immune cells. This mechanism is involved in the maintenance of self- and transplant tolerance through polarization of the immune responses. The Fas/Fas-ligand interaction is a major common executioner of apoptosis in lymphocytes, with a dual role in regulatory T cell (Treg) function: Treg cell homeostasis and Treg cell-mediated suppression. Sensitivity to apoptosis and the patterns of Treg-cell death are of outmost importance in immune homeostasis that affects the equilibrium between cytolytic and suppressor forces in activation and termination of immune activity. Naive innate (naturally occurring) Treg cells present variable sensitivities to apoptosis, related to their turnover rates in tissue under steady state conditions. Following activation, Treg cells are less sensitive to apoptosis than cytotoxic effector subsets. Their susceptibility to apoptosis is influenced by cytokines within the inflammatory environment (primarily interleukin-2), the mode of antigenic stimulation and the proliferation rates. Here, we attempt to resolve some controversies surrounding the sensitivity of Treg cells to apoptosis under various experimental conditions, to delineate the function of cell death in regulation of immunity.     

Competition coefficients in a marine epibenthic assemblage depend on spatial structure

We investigated the importance of the spatial context of interactions in a multispecies marine epibenthic assemblage with respect to the outcomes of interspecific interactions, neighbour-specific growth rates, and the dynamics of spatial and mean-field models of the system. We compared the outcomes of interactions and overgrowth rates of pair-wise combinations of species in spatially simplified contrived interactions with the same combinations in an unmanipulated assemblage. While estimates of neighbour-specific growth rates were similar in both sets of interactions, the probability of a species winning a particular interaction was strongly dependent on whether the interaction was contrived or occurred in the unmanipulated assemblage. The dynamics of a spatial model and its mean-field equivalent parameterised from estimates of interaction outcome and neighbour-specific growth from contrived interactions were significantly different to the dynamics of models based on estimates of interaction outcome and neighbour-specific growth obtained from non-manipulated assemblages. Differences in the dynamics of models based on parameters from unmanipulated and contrived interactions are primarily due to differences in outcomes of interspecific interactions, while fluctuations in growth rates contribute to the variability around these dynamics. Our results suggest that conclusions about interspecific interactions and community dynamics examined in simplified spatial associations (e.g. in manipulative experiments) is likely to be limited to assemblages with a similarly simplified spatial structure, which is an unlikely occurrence in nature.     

On maintenance models in severely and long-term limited membrane bioreactor cultivations

Membrane bioreactors (MBRs) are combinations of common bioreactors and membrane separation units for biomass retention. Through increased biomass concentration, they allow increased productivity (or smaller reactor volume, respectively). Besides high biomass concentrations, operation at very low growth rates is typical for MBRs. In this regime, maintenance metabolism where substrate uptake only yields energy for cell survival becomes of higher importance than in processes run at higher growth rates. While thermodynamically based correlations for the prediction of maintenance coefficients are available for chemostat or other medium growth rate processes, some authors have mentioned a change in energy demand in MBRs and a dependence of maintenance parameters on operating conditions. Due to the fact that often mixed cultures are used and resulting from the different evaluation methods used by different authors, views on the possible influences on maintenance parameters differ. However, it is accepted that common models describing microbial growth and production of metabolites or degradation of pollutants do not consider the effects caused by severe limitations and therefore cannot sufficiently be applied to MBRs. In this study, maintenance parameters were determined for a model organism (Ustilago maydis) and results from different evaluation methods were compared. A continuous fit of respiration data gave more consistent results than the traditional method of plotting specific uptake versus growth rate. They suggest that below micro = 10% micro(max) the maintenance coefficient drops to a third of the value in short-term limited cultures.     

Estimating cell death in G(2)M using bivariate BrdUrd/DNA flow cytometry.

BACKGROUND: In an accompanying paper (Asmuth et al.) it was found necessary to include cell death explicitly to estimate parameters of cell proliferation. The use of bivariate flow cytometry to estimate the phase durations and the doubling times of cells labeled with thymidine analogues is well established. However, these methods of analysis do not consider the possibility of cell death. This report demonstrates that estimating cell death in G(2)/M is possible. METHODS: Mathematical models for the experimental quantities, the fraction of labeled undivided cells, the fraction of labeled divided cells, and the relative movement were developed. These models include the possibility that, of the cells with G(2)/M DNA content, only a certain fraction will divide, with the remainder dying after some time T(R). Simulation studies were conducted to test the possibility of using simple methods to estimate phase durations and cell death rates. RESULTS: Cell death alters the estimates of phase transit times in a rather complex manner that depends on the lifetime of the doomed cells. However, it is still possible to obtain estimates of the phase durations of cells in S and G(2)/M and the death rates of cells in G(2)/M. CONCLUSIONS: The methods presented herein provide a new way to characterize cell populations that includes cell death rates and common measurements of cell proliferation.