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SURROGATE SELECTION OVERSAMPLES EXPANDED T CELL CLONOTYPES.

Surrogate selection is an experimental design that without sequencing any DNA can restrict a sample of cells to those carrying certain genomic mutations. In immunological disease studies, this design may provide a relatively easy approach to enrich a lymphocyte sample with cells relevant to the disease response because the emergence of neutral mutations associates with the proliferation history of clonal subpopulations. A statistical analysis of clonotype sizes provides a structured, quantitative perspective on this useful property of surrogate selection. Our model specification couples within-clonotype birth-death processes with an exchangeable model across clonotypes. Beyond enrichment questions about the surrogate selection design, our framework enables a study of sampling properties of elementary sample diversity statistics; it also points to new statistics that may usefully measure the burden of somatic genomic alterations associated with clonal expansion. We examine statistical properties of immunological samples governed by the coupled model specification, and we illustrate calculations in surrogate selection studies of melanoma and in single-cell genomic studies of T cell repertoires.

Bayes’s rule↗

Diastolic calcium release controls the beating rate of rabbit sinoatrial node cells: numerical modeling of the coupling process.

Recent studies employing Ca2+ indicators and confocal microscopy demonstrate substantial local Ca2+ release beneath the cell plasma membrane (subspace) of sinoatrial node cells (SANCs) occurring during diastolic depolarization. Pharmacological and biophysical experiments have suggested that the released Ca2+ interacts with the plasma membrane via the ion current (INaCa) produced by the Na+/Ca2+ exchanger and constitutes an important determinant of the pacemaker rate. This study provides a numerical validation of the functional importance of diastolic Ca2+ release for rate control. The subspace Ca2+ signals in rabbit SANCs were measured by laser confocal microscopy, averaged, and calibrated. The time course of the subspace [Ca2+] displayed both diastolic and systolic components. The diastolic component was mainly due to the local Ca2+ releases; it was numerically approximated and incorporated into a SANC cellular electrophysiology model. The model predicts that the diastolic Ca2+ release strongly interacts with plasma membrane via INaCa and thus controls the phase of the action potential upstroke and ultimately the final action potential rate.

Animals↗

Numerical model to predict settlements coupled with landfill gas pressure in bioreactor landfills.

Landfills settle due to its weight and biodegradation of waste. Biodegradation-induced settlement is a direct result of rearrangement of waste skeleton in response to the conversion of waste mass into landfill gases. Traditionally, the compressibility index based on settlement of clays is used to explain the settlement of waste. Literature review showed that there are limited research attempts of landfill settlement predictions by coupling with landfill gas generation and transport. This research describes a model which couples settlement in a bioreactor landfill with the generation and subsequent upward movement of landfill gases. The mass balance of the landfill gas was used to link settlement and gas pressures. In the absence of a closed-formed analytical solution, a computer program was developed to numerically predict the settlements and gas pressures in a bioreactor landfill using landfill geometry and waste properties. Explicitly computed settlement values were then used to predict the pressure profile implicitly. To test the mathematical formulations, a numerical exercise was performed using a single-cell hypothetical bioreactor landfill. The numerical simulation produced satisfactory trends of the settlement and the landfill gas pressure profiles.

Bioreactors↗

Equilibrium and steady-state models of the coupling between the amino acid gradient and the sodium electrochemical gradient in mouse ascites- tumour cells.

1. The tumour cells were incubated at 37 degrees C in Ringer solutions containing glucose, 1 mM-methionine, various concentrations of Na+ and K+ and, in some instances, ouabain or valinomycin to lower the membrane potential generated by the Na+ pump. After about 30 min, when the system had reached a steady state, the ratio [extracellular Na+]/[cellular Na+] varied from about 0.6 to 3.2 with the ionic conditions. The membrane potential, determined by means of the fluorescent probe 3,3'-dipropyloxadicarbocyanine, also varied systemically from about zero to--55mV.2. the ratio [cellular methionine]/[extra-cellular methionine] varied from about 1 to 35 in these circumstances. The Na+ electrochemical gradient, measured in the same units, varied from about 1 to 30. Its magnitude in 46 assays was almost directly proportional to, though slightly smaller than, the methionine gradient. 3. A mathematical model was used to define the relation between these two gradients, which were not in equilibrium, owing to the presence of a leak pathway for the amino acid. On the assumption that the values of [cellular Na+] were correct, the methionine gradient was about 1.8 times larger than this version of the gradient hypothesis predicted.

Amino Acids↗

A multi-substrate single-file model for ion-coupled transporters.

Ion-coupled transporters are simulated by a model that differs from contemporary alternating-access schemes. Beginning with concepts derived from multi-ion pores, the model assumes that substrates (both inorganic ions and small organic molecules) hop a) between the solutions and binding sites and b) between binding sites within a single-file pore. No two substrates can simultaneously occupy the same site. Rate constants for hopping can be increased both a) when substrates in two sites attract each other into a vacant site between them and b) when substrates in adjacent sites repel each other. Hopping rate constants for charged substrates are also modified by the membrane field. For a three-site model, simulated annealing yields parameters to fit steady-state measurements of flux coupling, transport-associated currents, and charge movements for the GABA transporter GAT1. The model then accounts for some GAT1 kinetic data as well. The model also yields parameters that describe the available data for the rat 5-HT transporter and for the rabbit Na(+)-glucose transporter. The simulations show that coupled fluxes and other aspects of ion transport can be explained by a model that includes local substrate-substrate interactions but no explicit global conformational changes.

Animals↗

MPR.

Mathematical Principles of Reinforcement (MPR) is a theory of reinforcement schedules. This paper reviews the origin of the principles constituting MPR: arousal, association and constraint. Incentives invigorate responses, in particular those preceding and predicting the incentive. The process that generates an associative bond between stimuli, responses and incentives is called coupling. The combination of arousal and coupling constitutes reinforcement. Models of coupling play a central role in the evolution of the theory. The time required to respond constrains the maximum response rates, and generates a hyperbolic relation between rate of responding and rate of reinforcement. Models of control by ratio schedules are developed to illustrate the interaction of the principles. Correlations among parameters are incorporated into the structure of the models, and assumptions that were made in the original theory are refined in light of current data.

Journal Article↗

Computational modelling of H+-coupled peptide transport via human PEPT1.

H+-coupled peptide transporter 1 (PEPT1) mediates the transport of small peptides and peptide-like drugs in a pH- and voltage-dependent manner. Here, we investigated the transport mechanisms of PEPT1 for neutral and charged substrates by experimental studies and computational simulation. Uptake studies revealed that the Michaelis-Menten constant (Km) of glycylsarcosine (Gly-Sar), a neutral substrate, decreased with a fall in pH from 7.4 to 5.5, but at pH 5.0, the Km increased again. In contrast, the Km value of an anionic substrate, ceftibuten, declined steadily with decreasing pH. Based on these findings and information from the literature, we hypothesized the transport mechanisms in which (1) H+ binds to not only the H+-binding site, but also the substrate-binding site; and (2) H+ at the substrate-binding site inhibits the interaction of neutral and cationic substrates, but is necessary for that of anionic substrates. To validate these hypotheses, a computational model was constructed and various properties of substrate transport by PEPT1 were simulated. Our model reproduced the voltage dependence, hyperbolic saturation and bell-shaped pH-profile of Gly-Sar transport. Moreover, the various transport properties of negatively and positively charged substrates were also reconstructed. These findings indicated that the inferred mechanisms are able to sufficiently interpret the transport of both neutral and charged substrates by PEPT1.

Anions↗

Parameterization and testing of a coupled photosynthesis-stomatal conductance model for boreal trees.

A coupled photosynthesis-stomatal conductance model was parameterized and tested with branches of black spruce (Picea mariana (Mill.) B.S.P.) and jack pine (Pinus banksiana Lamb.) trees growing in the Northern Study Area of the Boreal Ecosystem-Atmosphere Study (BOREAS) in Manitoba, Canada. Branch samples containing foliage of all age-classes were harvested from a lowland old black spruce (OBS) and an old jack pine (OJP) stand and the responses of photosynthesis (A(n)) and stomatal conductance (g(s)) to temperature, CO(2), light, and leaf-to-air vapor pressure difference (VPD) were determined under controlled laboratory conditions at the beginning, middle, and end of the growing season (Intensive Field Campaigns (IFC) 1, 2, and 3, respectively). The parameterized model was then tested against in situ field gas-exchange measurements in a young jack pine (YJP) and an upland black spruce (UBS) stand as well as in the OBS and OJP stands. Parameterization showed that Rubisco capacity (V(max)), apparent quantum yield (alpha') and Q(10) for sink limitation were the most crucial parameters for the photosynthesis sub-model and that V(max) varied among different measurement series in the laboratory. Verification of the model against the data used to parameterize it yielded correlation coefficients (r) of 0.97 and 0.93 for black spruce and jack pine, respectively, when IFC-specific parameters were used, and 0.77 and 0.87 when IFC-2 parameters were applied to all IFCs. For both measured and modeled g(s), the stomatal conductance sub-model, which linearly relates g(s) to (A(n)h(s))/c(s) (where h(s) and c(s) are relative humidity and CO(2) mole fraction at the leaf surface, respectively), had significantly steeper slopes and higher r values when only the VPD response data were used for parameterization than when all of the response data were used for parameterization. Testing the photosynthesis sub-model against upper canopy field data yielded poor results when laboratory estimates of V(max) were used. Use of the mean V(max) estimated for all upper canopy branches measured on a given day improved model performance for jack pine (from a nonsignificant correlation between measured and modeled A(n) to r = 0.45), but not for black spruce (r = 0.45 for both cases). However, when V(max) was estimated for each branch sample individually, the model accurately predicted the 23 to 137% diurnal variation in A(n) for all stands for both the upper and lower canopy. This was true both when all of the other parameters were IFC-specific (r = 0.93 and 0.92 for black spruce and jack pine, respectively) and when only mid-growing season (IFC-2) values were used (r = 0.92 for both species). Branch-specific V(max) estimates also permitted accurate prediction of field g(s) (r = 0.75 and 0.89 for black spruce and jack pine, respectively), although parameterization with all of the response data overestimated g(s) in the field, whereas parameterization with only the VPD response data provided unbiased predictions. Thus, after parameterization with the laboratory data, accurately modeling the range of A(n) and g(s) encountered in the field for both black spruce and jack pine was reduced to a single unknown parameter, V(max).

Journal Article↗

Antidiabetic effect of novel modulating peptides of G-protein-coupled kinase in experimental models of diabetes.

AIMS/HYPOTHESIS: G-protein-coupled receptor kinases (GRKs) play a key role in agonist-induced desensitisation of G-protein-coupled receptors (GPCRs) that are involved in metabolic regulation and glucose homeostasis. Our aim was to examine whether small peptides derived from the catalytic domain of GRK2 and -3 would ameliorate Type 2 diabetes in three separate animal models of diabetes. METHODS: Synthetic peptides derived from a kinase-substrate interaction site in GRK2/3 were initially screened for their effect on in vitro melanogenesis, a GRK-mediated process. The most effective peptides were administered intraperitoneally, utilising a variety of dosing regimens, to Psammomys obesus gerbils, Zucker diabetic fatty (ZDF) rats, or db/db mice. The metabolic effects of these peptides were assessed by measuring fasting and fed blood glucose levels and glucose tolerance. RESULTS: Two peptides, KRX-683(107) and KRX-683(124), significantly reduced fed-state blood glucose levels in the diabetic Psammomys obesus. In animals treated with KRX-683(124) at a dose of 12.5 mg/kg weekly for 7 weeks, ten of eleven treated animals responded with mean blood glucose significantly lower than controls (4.7+/-0.4 vs 16.8+/-0.8 mmol/l, p</=0.0001). Significant reductions in blood glucose compared with controls were also seen in ZDF rats administered KRX-683(124) and in db/db mice, which had significantly reduced fasting and 2-hour postprandial glucose levels after the treatment. CONCLUSIONS/INTERPRETATION: Sequence-based peptides derived from GRK2/3 have an antidiabetic effect demonstrated in three different animal models of Type 2 diabetes. By modulating GRK2/3 activity, these peptides enhance GPCR-initiated signal transduction, resulting in improved glucose homeostasis. Sequence-based peptide modulation of GRK could prove useful in the treatment of Type 2 diabetes.

Animals↗

Link between truncated fractals and coupled oscillators in biological systems.

This article aims at providing a new theoretical insight into the fundamental question of the origin of truncated fractals in biological systems. It is well known that fractal geometry is one of the characteristics of living organisms. However, contrary to mathematical fractals which are self-similar at all scales, the biological fractals are truncated, i.e. their self-similarity extends at most over a few orders of magnitude of separation. We show that nonlinear coupled oscillators, modeling one of the basic features of biological systems, may generate truncated fractals: a truncated fractal pattern for basin boundaries appears in a simple mathematical model of two coupled nonlinear oscillators with weak dissipation. This fractal pattern can be considered as a particular hidden fractal property. At the level of sufficiently fine precision technique the truncated fractality acts as a simple structure, leading to predictability, but at a lower level of precision it is effectively fractal, limiting the predictability of the long-term behavior of biological systems. We point out to the generic nature of our result.

Animals↗

Gaze control in the cat: studies and modeling of the coupling between orienting eye and head movements in different behavioral tasks.

1. Orienting movements, consisting of coordinated eye and head displacements, direct the visual axis to the source of a sensory stimulus. A recent hypothesis suggests that the CNS may control gaze position (gaze = eye-relative-to-space = eye-relative-to-head + head-relative-to-space) by the use of a feedback circuit wherein an internally derived representation of gaze motor error drives both eye and head premotor circuits. In this paper we examine the effect of behavioral task on the individual and summed trajectories of horizontal eye- and head-orienting movements to gain more insight into how the eyes and head are coupled and controlled in different behavioral situations. 2. Cats whose heads were either restrained (head-fixed) or unrestrained (head-free) were trained to make orienting movements of any desired amplitude in a simple cat-and-mouse game we call the barrier paradigm. A rectangular opaque barrier was placed in front of the hungry animal who either oriented to a food target that was visible to one side of the barrier or oriented to a location on an edge of the barrier where it predicted the target would reappear from behind the barrier. 3. The dynamics (e.g., maximum velocity) and duration of eye- and head-orienting movements were affected by the task. Saccadic eye movements (head-fixed) elicited by the visible target attained greater velocity and had shorter durations than comparable amplitude saccades directed toward the predicted target. A similar observation has been made in human and monkey. In addition, when the head was unrestrained both the eye and head movements (and therefore gaze movements) were faster and shorter in the visible- compared with the predicted-target conditions. Nevertheless, the relative contributions of the eye and head to the overall gaze displacement remained task independent: i.e., the distance traveled by the eye and head movements was determined by the size of the gaze shift only. This relationship was maintained because the velocities of the eye and head movements covaried in the different behavioral situations. Gaze-velocity profiles also had characteristic shapes that were dependent on task. In the predicted-target condition these profiles tended to have flattened peaks, whereas when the target was visible the peaks were sharper. 4. Presentation of a visual cue (e.g., reappearance of food target) immediately before (less than 50 ms) the onset of a gaze shift to a predicted target triggered a midflight increase in first the eye- and, after approximately 20 ms, the head-movement velocity.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

Model of the dynamics of receptor potential in a mechanoreceptor.

Mechanoreceptors are physiological units that convert mechanical stimuli to neural responses. An important one in the skin is the Pacinian corpuscle, which consists of a nerve ending surrounded by a capsule that is made up of alternating layers of fluid and elastic shells. In this paper a capsule model is coupled to a model for the dendrite via a variable representing the hoop strain imposed by the capsule on the receptor membrane of the dendrite. The transient behavior of the receptor potential due to step and periodic displacement-type stimuli imposed on the outer membrane of the capsule is investigated, and the results are compared to those of analogous experiments. The model is used to develop hypotheses concerning the role of the capsule as a filter for mechanical stimuli.

Animals↗

Coupling of computer modeling with in vitro methodologies to reduce animal usage in toxicity testing.

The use of in vitro data to support the development of physiologically based pharmacokinetic (PBPK) models and to reduce the requirement for in vivo testing is demonstrated by three examples. In the first example, polychlorotrifluoroethylene, in vitro studies comparing metabolism and tissue response in rodents and primates made it possible to obtain definitive data for a human risk assessment without resorting to additional in vivo studies with primates. In the second example, a PBPK model for organophosphate esters was developed in which the parameters defining metabolism, tissue partitioning, and enzyme inhibition were all characterized by in vitro studies, and the rest of the model parameters were established from the literature. The resulting model was able to provide a coherent description of enzyme inhibition following both acute and chronic exposures in mice, rats, and humans. In the final example, the carcinogenic risk assessment for methylene chloride was refined by the incorporation of in vitro data on human metabolism into a PBPK model.

Animal Testing Alternatives↗

Simple modeling of dipolar coupled 7Li spins and stimulated-echo spectroscopy of single-crystalline beta-eucryptite.

Stimulated-echo spectroscopy has recently been applied to study the ultra-slow dynamics of nuclear spin-3/2 probes such as 7Li and 9Be in solids. Apart from the dominant first-order quadrupolar interaction in the present article also the impact of the homonuclear dipolar interactions is considered in a simple way: the time evolution of a dipole coupled pair of spins with I = 3/2 is calculated in an approximation, which takes into account that the satellite transitions usually do not overlap. Explicit analytical expressions describing various aspects of a coupled quadrupolar pair subjected to a Jeener-Broekaert pulse sequence are derived. Extensions to larger spin systems are also briefly discussed. These results are compared with experimental data on a single-crystalline Li ion conductor.

Journal Article↗

Chemiluminescence of luminol in the presence of iron(II) and oxygen: oxidation mechanism and implications for its analytical use.

The validity of chemiluminescence-based methods relies upon the uniqueness of the relationship between the concentration of the analyte and the intensity of chemiluminescence produced. We have examined the chemiluminescence of luminol (5-amino-2,3-dihydro-1,4-phthalazinedione) in the presence of O2, without added H202, to measure nanomolar concentrations of total Fe(II) (both inorganically and organically complexed) in aqueous samples. To test the validity of the method, we have developed a kinetic model that describes the two-step oxidation of luminol by superoxide and hydroxyl (or hydroxyl-like) radicals produced from the oxidation of Fe-(II) by O2 by synthesis of existing published data. This model was coupled with a model for Fe(II) oxidation by O2 in the presence and absence of the naturally occurring Suwannee River fulvic acid (SRFA). The production of chemiluminescence depended upon the concentrations of free radicals in both the sample and luminol reagent and the pH at which the reactions were performed. The relationship between Fe(II) concentration and chemiluminescence intensity was found to be unique at Fe(II) concentrations from 1 nM to 1 microM without organic complexation and from 1 to 32 nM in the presence of SRFA despite strong signal quenching in the latter case. This type of behavior will likely ensure a similarly unique relationship in the presence of a wide range of organic compounds; however, when other systems are being investigated, the technique should be carefully evaluated.

Benzopyrans↗

Phenomenology of boiling: A coupled map lattice model.

A minimal model for boiling is proposed. With increasing temperature of a bottom plate, the model shows three successive phases; conduction, nucleate, and film boiling. In the nucleate regime the heat flux increases with the temperature of the bottom plate, while it decreases in the film boiling regime. In the boiling phase, the maximum Lyapunov exponent is positive, implying that the boiling phenomena are spatiotemporally chaotic.

Journal Article↗