Equilibrium unfolding thermodynamics of beta2-microglobulin analyzed through native-state H/D exchange

The exchange rates for the amide hydrogens of β₂-microglobulin, the protein responsible for dialysis-related amyloidosis, were measured under native conditions at different temperatures ranging from 301 to 315 K. The pattern of protection factors within different regions of the protein correlates well with the hydrogen-bonding pattern of the deposited structures. Analysis of the exchange rates indicates the presence of mixed EX1- and EX2-limit mechanisms. The measured parameters are consistent with a two-process model in which two competing pathways, i.e., global unfolding in the core region and partial openings of the native state, determine the observed exchange rates. These findings are analyzed with respect to the amyloidogenic properties of the protein.     

Solutions for the kinetic analysis of 45calcium uptake curves

The classic solutions based on specific activity curves for the kinetic analysis of ⁴⁵Ca movements in three compartment cellular systems cannot be used when the extracellular compartment is one to two orders of magnitude larger than the cellular or tissue compartments. However if the relative radioactivity curve (tracer uptake curve) is analyzed it is possible to calculate all the relevant kinetic parameters. This paper offers the solutions based on relative radioactivity measurements for the calculation of exchange rates, rate constants and compartment sizes of three compartment systems, for series and parallel cases, for closed and open systems.     

Nutrient dynamics and ecosystem metabolism in the Bay of Blanes (NW Mediterranean)

The dynamics of the nutrient pools and their stoichiometry as well as their control by ecosystem metabolism (benthic and planktonic) and benthic–pelagic exchanges (sedimentation rates and sediment waterfluxes) were examined in the Mediterranean littoral (Blanes Bay, NE Spain). Dissolved organic nitrogen comprised about half of the nitrogen present in the water column and the carbon pool was dominated by the inorganic pool (95% of the carbon present in the water column). The dissolved and particulate organic pools were deficient in P relative to C and N, indicating a rapid recycling of P from organic matter. The pelagic compartment was heterotrophic, supported by significant allochthonous inputs of land material, which also contributed greatly to the sedimentary inputs (37% of total sedimenting carbon). In contrast, the benthic compartment was autotrophic, with the excess net benthic community production balancing the deficit in pelagic community production, leading to metabolic equilibrium at the station studied. Sedimentary inputs of nitrogen, phosphorus and silicon exceeded the benthic release, indicating that the benthic compartment acted as a sink for nutrients, consistent with its autotrophic nature. Carbon inputs to the benthic compartment also exceeded requirements, due to the allochthonous subsidies to the system, so that the benthic compartment stored or exported organic carbon. An erratum to this article can be found at .     

Impact of phosphorus availability on modelling phytoplankton dynamics

Regulation of phosphorus loading is considered to be the primary method of eutrophication control for many lake systems. It is therefore necessary to have accurate estimates of the forms and bioavailability of all phosphorus sources in order to develop the most cost effective load control measures. Research at Clarkson University, aimed at improving the accuracy of estimates of the form and reactivity of phosphorus loadings to Lake Erie, has revealed a significant difference between the algal-availability of allochthonous and autochthonous particulate phosphorus. This paper presents the results of modifying an existing multi-nutrient phytoplankton model by separating allochthonous phosphorus into three forms: soluble reactive phosphorus (SRP) — immediately available for algal uptake; external ultimately-available phosphorus—not immediately available but converted to an available form at a specific rate; an external refractory phosphorus (ERP)—not available while in the water column. Comparisons between the original and modified models showed that the modified phosphorus dynamics proved to be a viable alternative to the concept of invoking an unexplained soluble phosphorus water column loss term, employed in the original model. The work also demonstrates that the distinction is significant for lakes receiving a significant portion of their external phosphorus load in a particulate (not immediately available) form and having a morphometry and hydrology such that this particulate phosphorus remains in the water column for longer than about two weeks.     

Computer Solutions for Photosynthesis Rates from a Two Pigment Model

A kinetic model for a two pigment mechanism of photosynthesis based on observations made on the red alga Porphyridium cruentum is developed. The model supposes that different products are formed by chlorophyll and phycobilin pigments and that these products react to produce oxygen. The product of the chlorophyll reaction is also rapidly utilized for O₂ consumption both in light and in the dark. Rate equations based on the model reactions were derived and put into an analog computer. The effect of varying parameters on the time course curves for oxygen exchange resulting from the model was studied. Appropriate selection of parameters yielded computer curves which resembled fairly closely the oxygen exchange curves obtained using Porphyridium. The model showed the Emerson enhancement effect, chromatic transients, “respiratory stimulation,” and other effects observed with live algae.     

Dopamine Uptake by Rat Striatal Synaptosomes: A Compartmental Analysis

Abstract: Dopamine (DA) uptake into synaptosomes from rat corpus striatum was studied in the presence of a monoamine oxidase (MAO) inhibitor and dithiothreitol, by means of a filtration technique. Under these conditions a steady state develops rapidly in which the synaptosomal DA content remains constant while the continuing DA uptake is counterbalanced by DA efflux from the synaptosome. Exchange of synaptosomal [³H]DA and [¹⁴C]DA was measured under these conditions. In timecourse experiments it was found that exchange could be described significantly better by a three-compartment model than by a two-compartment model. However, if synaptosomes from reserpine-pretreated animals were used, analysis according to a three-compartment model did not result in a significantly better fit compared with a two-compartment model. Subsequently, kinetic transfer parameters describing DA fluxes between compartments at different DA concentrations were calculated from the fitted exchange curves. A Michaelis-Menten kinetic analysis indicated that only the in-series three-compartment configuration, in which DA is taken up from the medium into one synaptosomal compartment, from which it can subsequently be transferred to a second compartment without direct access to the medium, gave kinetically acceptable results. Transfer parameters in synaptosomes from reserpine-treated rats were comparable to those parameters describing DA transport between the medium and the first intrasynaptosomal compartment as measured under control conditions. Morover, it was found that potassium depolarization of synaptosomes resulted in a release of DA in a quantity similar to that found in the second intrasynaptosomal compartment. It is suggested that the two intrasynaptosomal compartments found correspond to a cytoplasmatic and vesicular DA pool, respectively. The functional significance of these findings is discussed in terms of the regulation of DA levels within the nerve terminal.     

The relationship of intercompartmental excitation transfer rate constants to those of an underlying physical model

In studies on photosynthetic systems it is common practice to interpret the results of time-resolved fluorescence experiments on the basis of compartmental, or target, models. Each compartment represents a group of molecules with similar fluorescence characteristics. In cases of practical interest, the members of each compartment are spatially contiguous and make up part of an overall energy-transferring system. Since a rate constant describing the overall transfer between compartments is not that of any pair of molecules in the system, this question naturally rises: what do we learn about the microscopic structure from these data? In this note we introduce ‘compartment melting’, a smooth mathematical connection between the compartmental and microscopic levels. We then show, on the basis of model calculations on finite lattices in one, two, and three dimensions, that average microscopic rates at the interfaces between compartments may be estimated from observed intercompartmental rates. The estimate involves a modest number of structural assumptions about the system. As examples of the method, which is applicable mainly to systems containing homogeneous pigment pools, some recent chlorophyll-protein antenna studies are analyzed.     

Repeated injection (continuous labelling) experiments in mouse epidermis

Theoretical labelling index curves for epidermis have been generated under conditions of repeated tritiated thymidine injection. These curves take into account different injection intervals, circadian fluctuations in labelling and two different models for epidermal proliferation; one based on a homogeneous basal layer with “random” loss initially (later, loss was restricted to late G₁), and the other based on a programmed sequential aging of proliferative cells in a compartment derived from a minority class of stem cells. These curves have been compared with previously published experimental results and with results from some new experiments. Both models fit the data to some extent provided a mean value of T_c of about 140 h is assumed. However, the sequential aging model provides a slightly better overall fit. A further conclusion is that it is impossible to make any accurate statements on the epidermal growth fraction from repeated labelling data.     

Estimating bioavailability of soil particulate phosphorus to Microcystis aeruginosa

Bioavailable phosphorus has been reported to include not only phosphorus in dissolved form but also the fraction of particulate phosphorus that is readily usable. Here, a chemical extraction scheme in combination with an algal bioassay was conducted to estimate the potential bioavailability of particulate phosphorus in soil collected from a Chinese cabbage field. Microcystis aeruginosa was cultured in a medium containing the soils sequentially extracted with 1?M NH₄Cl, 0.11?M bicarbonate dithionite, 1?M NaOH, and 0.5?M HCl as the sole source of phosphorus. Analyses of chlorophyll-a, suspended solids, particulate organic carbon, and particulate organic nitrogen showed that M. aeruginosa could utilize some of the phosphorus present in each soil extract. These results imply that bioavailable phosphorus includes not only aluminum/iron-bound P and clay-bound P but also carbonate/apatite-bound P and residual P which have been considered not to be available to algae.     

Fatty acid metabolism by a particulate fraction from germinating peas

The incorporation of fatty acids into lipid fractions was studied using a high-speed particulate fraction from germinating peas (Pisum sativum cv Feltham First). The acids were incorporated principally into the acyl-CoA and polar lipid fractions, with unsaturated fatty acids labelling the latter fraction at higher rates than saturated substrates. α-Hydroxylation also occurred. Oleate from oleoyl-CoA or oleoyl-acyl carrier protein was incorporated into polar lipids faster than from ammonium oleate. The incorporation of fatty acids into polar lipids was dependent on the presence of CoA and ATP in the medium and on the consequent generation of acyl-CoA's. Time-course studies and experiments when two fatty acid substrates were added consecutively confirmed the role of acyl-CoA's in the transfer of acyl groups to phospholipids. Although CoA was necessary when acyl-CoA's had to be generated, high concentrations were found to inhibit the rate ofacyl transfer. The results are discussed in terms ofthe ‘witching mechanism’ for controlling the fate of fatty acids in the plant cell.     

Particulate phosphorus in the Humber estuary

The biogeochemical controls on particulate phosphorus distribution in the Humber estuary have been investigated with regard to salinity and season. Surveys of the Humber were conducted in August 1991 and January, March and June 1992. Samples were collected for particulate phosphorus, dissolved phosphorus, suspended load and salinity analysis. Particulate phosphorus forms 16 to 93% of the total phosphorus present in the water column of the Humber estuary. Total particulate phosphorus concentrations in the Humber ranged from 1 to 45 μmol l⁻¹. This range is comparable to that observed in similar sized industrialized estuaries of the U.S.A. and northern Europe. Flocculation at low salinities was found to be a major influence on particulate phosphorus concentrations. Highest concentrations of particulate phosphorus were found in reaches below a salinity of 5 and may result in phosphorus being trapped in the sediments of the estuary. There is evidence that this phosphorus may be released as oxygen concentrations decrease during the summer. Suspended load, adsorption/desorption equilibrium and external inputs were also found to influence the particulate phosphorus concentrations.     

Mathematical modeling of pulmonary tuberculosis therapy: Insights from a prototype model with rifampin

There is a critical need for improved and shorter tuberculosis (TB) treatment. Current in vitro models of TB, while valuable, are poor predictors of the antibacterial effect of drugs in vivo. Mathematical models may be useful to overcome the limitations of traditional approaches in TB research. The objective of this study was to set up a prototype mathematical model of TB treatment by rifampin, based on pharmacokinetic, pharmacodynamic and disease submodels.The full mathematical model can simulate the time-course of tuberculous disease from the first day of infection to the last day of therapy. Therapeutic simulations were performed with the full model to study the antibacterial effect of various dosage regimens of rifampin in lungs.The model reproduced some qualitative and quantitative properties of the bactericidal activity of rifampin observed in clinical data. The kill curves simulated with the model showed a typical biphasic decline in the number of extracellular bacteria consistent with observations in TB patients. Simulations performed with more simple pharmacokinetic/pharmacodynamic models indicated a possible role of a protected intracellular bacterial compartment in such a biphasic decline.This modeling effort strongly suggests that current dosage regimens of RIF may be further optimized. In addition, it suggests a new hypothesis for bacterial persistence during TB treatment.     

Mechanics of the compression wood response: I. Preliminary analyses

Righting of two tilted white pine (Pinus strobus L.) stem leaders by compression wood formation was followed for 16 weeks. The natural curves and three deflection curves under added end loads were determined from weekly field photographs. Data for self-loading and cross sectional diameters were interpolated from original estimated and final measurements. A mechanical-mathematical model was developed to predict curves under zero gravity for each stem each week. The model estimated stiffness of the leaders independently for each week, and the stiffnesses were consistent throughout the experiment. A second model was developed to simulate the deflection curves assumed when the zero gravity curves were subjected to different end loads. These predicted curves were nearly identical to the observed curves from the photographs, thus verifying the assumptions in the first model. Data from this study will be used to investigate the mechanical aspects of compression wood induction and action as the stem is bent upward toward the vertical.     

Optimal foraging in bumblebees: Calculation of net rate of energy intake and optimal patch choice

To test many predictions of “optimal foraging theory” it is necessary to calculate the rate of net energy intake of a foraging animal. Equations are derived for the calculation of the rate of net energy intake of a foraging bumblebee. The assumptions that form the basis of these energy equations are discussed. As examples, the rates of net energy intake are calculated for Bombus flavifrons workers foraging on neighboring patches of Aconitum columbianum and Delphinium barbeyi. If the bumblebees forage optimally, their net rates of energy intake in the two patches should be equal. The observed rates are consistent with this hypothesis. The application of an optimality approach to pollination biology is briefly discussed.     

Estimation of phosphorus metabolic rates of Daphnia galeata using a three-compartment model

A compartment model to estimate the different phosphorus metabolicrates in Daphnia galeata is presented. The model has three compartments:gut, metabolic pool and structural pool. Existing two-compartmentmodels used for carbon and phosphorus turnover in Daphnia donot allow estimation of ingestion and egestion rates. We extendedexisting two-compartment models with one more compartment, thegut, which allowed us to estimate both the ingestion and theegestion rates. Parameters of the model are estimated from asingle experiment of feeding unlabelled Daphnia with ³²P-labelledScenedesmus obliquus. Separate experiments with juvenile andadult daphnids were carried out in order to compare their metabolisms.This model permits a reliable estimation of the different metabolicrates of Daphrna in a single experiment and discriminates clearlybetween animals of different sizes.     

Enhancement models at high light intensities

The separate package and spillover models of photosynthetic enhancement are generalized and extended to light saturation assuming hyperbolic or exponential rate versus intensity curves. The available data are more consistent with the exponential model at high light intensities. Two significant conclusions follow: (a) the decreases in enhancement observed at high light intensities are accounted for by the curvatures of the light intensity curves for photosynthesis, and (b) nonlinearity of rate versus intensity curves may be sufficient to reduce enhancement greatly even when the intensity curves appear linear.     

Decomposition of Blue-Green Algal (Cyanobacterial) Blooms in Lake Mendota, Wisconsin

Decomposition of natural populations of Lake Mendota phytoplankton dominated by blue-green algae (cyanobacteria) was monitored by using oxygen uptake and disappearance of chlorophyll, algal volume (fluorescence microscopy), particulate protein, particulate organic carbon, and photosynthetic ability (¹⁴CO₂ up-take). In some experiments, decomposition of ¹⁴C-labeled axenic cultures of Anabaena sp. was also measured. In addition to decomposition, mineralization of inorganic nitrogen and phosphorus were followed in some experiments. Decomposition could be described as a first-order process, and the rate of decomposition was similar to that found by others using pure cultures of eucaryotic algae. Nitrogen and phosphorus never limited the decomposition process, even when the lake water was severely limited in soluble forms of these nutrients. This suggests that the bacteria responsible for decomposition can obtain all of their key nutrients for growth from the blue-green algal cells. Filtration of lake water through plankton netting that removed up to 90% of the algal biomass usually did not cause a similar decrease in oxygen demand, suggesting that most of the particulate organic matter used for respiration of the decomposing bacteria was in a small-particle fraction. Short-term oxygen demand correlated well with the particulate chlorophyll concentration of the sample, and a relationship was derived that could be used to predict community respiration of the lake from chlorophyll concentration. Kinetic analysis showed that not all analyzed components disappeared at the same rate during the decomposition process. The relative rates of decrease of the measured parameters were as follows: photosynthetic ability > algal volume > particulate chlorophyll > particulate protein. Decomposition of ¹⁴C-labeled Anabaena occurred at similar rates with aerobic epilimnetic water and with anaerobic sediment, but was considerably slower with anaerobic hypolimnetic water. Of the various genera present in the lake, Aphanizomenon and Anabaena were more sensitive to decomposition than was Microcystis. In addition to providing a general picture of the decomposition process, the present work relates to other work on sedimentation to provide a detailed picture of the fate of blue-green algal biomass in a eutrophic lake ecosystem.     

Linear n-compartment catenary models: Formulas to describe tracer amount in any compartment and identification of parameters from a concentration-time curve

Resolution of kinetic equations and parameter identification are discussed for n-compartment linear catenary models with elimination allowed from any compartment. For a given input, general formulas are derived to describe the tracer amount in any compartment as a function of the model parameters. Conversely, explicit procedures are given to identify the model parameters when the concentration-time curve is known in one arbitrary compartment, the tracer being injected into the same compartment. In this inverse problem, the solution is not unique: the model transfer rate constants can only be localized in a finite set of intervals.     

On transfer times in tracer experiments

A compartment is defined as a pool of material whose behavior can be described by a deterministic or by a stochastic equation; these two equations are used to define the transit time through the compartment, the total residence time, the time of entrance and the time of exit.If in a complex system one or more compartments are accessible, the transport of material through it can be studied using a tracer. Then the transfer time between any two compartments, or through the cycle around a compartment, can be analyzed under certain hypotheses, even if the transport along the route considered cannot be described by compartment equations.