Comparison of dipeptidyl carboxypeptidase and endopeptidase activities in the three enkephalin-hydrolysing metallopeptidases: "angiotensin-converting enzyme", thermolysin and "enkephalinase"

Angiotensin-converting enzyme (ACE), thermolysin and "enkephalinase", three metallopeptidases cleaving the Gly3-Phe4 amide bond of enkephalins, were compared regarding substrate specificity and effects of butanedione, an arginyl-directed reagent. The hydrolysis of enkephalins and analogues was more affected by the nature of P1 and P2 residues in the case of thermolysin than in those of ACE or "enkephalinase"; amidation of the C-terminal carboxylate decreased drastically the hydrolysis by ACE but only marginally by thermolysin and the effect was intermediate for "enkephalinase". With adequate model substrates, the ratio of dipeptidylcarboxypeptidase to tripeptidylcaroxypeptidase (endopeptidase) activities were of 25 for ACE, 3 for "enkephalinase" and only 0.3 for thermolysin. Finally a butanedione treatment increased thermolysin activity, but abolished ACE activity; it reduced "enkephalinase" activity by 80% when measured with a free C-terminal carboxylate enkephalin analogue but only slightly with the corresponding amidated derivative. A critical role of an Arg residue in ACE and, to a lesser extent, in "enkephalinase" (but not in thermolysin) is suggested to be responsible for the preferential dipeptidylcarboxypeptidase activity of these two enzymes.     

A model for the formation of ring-shaped structures in colonies of mycelial fungi

Mathematical model of the development of the pattern of colonies is considered. The model represents the systems of differential equations of the first order. It includes non-dimensional parameters characterizing the following features: concentration of substrate, concentration of metabolic products--growth inhibitor, mycelium and spores, radial and specific rate of mycelium growth, rate of substrate consumption and production of metabolic products, coefficients of diffusion of substrate and metabolic products, initial concentration of mycelium and substrate, time of delay of mycelium reaction on metabolic products and spore formation, threshold concentration of metabolic products. The model is adequate to the experiments with cultivation of Penicillium chrysogenum. It was shown that necessary condition for the formation of the circle periodical structures (zoning) in the colonies is an ability for the production of growth inhibitors (antibiotics, etc.). It was proved that formation of colonies of "continuous lawn" type is caused by restrictions on growth because of mycelium satiation or exhaustion of substrate. Such growth scenario is realized in experiments either on reach substrate or on hungry agar. For the appearance of regulating of "zone structure" type limitation on critical level of metabolic product concentration is very important. The number of periodical zone structures and their widths are determined by the above parameters.     

The importance of predation,substrate and spatial refugia in determining lotic insect distributions

An experiment was conducted to evaluate the interaction between predation, substrate, and spatial refugia in the organization of a stream insect community (Reeds Creek, Pendleton Co., West Virginia). Patterns of insect colonization were compared between fish exclusion cages and open controls that allowed access to vertebrate predators. Each cage contained 4 different substrates that varied in the relative amount of spatial refugia. Fish had little influence on the diversity or abundance of any insect taxa, even when spatial refugia were limited. The only significant effect due to predation, was an increased diversity of large (>8 mm) invertebrates in the absence of predators. However, because these taxa were relatively rare, the overall role of fish predation on insect community structure was minimal.In contrast, substrate had a marked effect on insect colonization. Insects were always more abundant (number/basket) on loose substrates containing large numbers of interstitial spaces, compared to cement-embedded substrates with few refuges available. In addition, invertebrates were more abundant on loose gravel compared to loose cobbles. Howver, when substrate preferencesrd were examined according to insect density (number/m²), loose cobbles were generally the preferred substrate. The present experiment rejects the hypothesis that patterns of substrate colonization can be explained as differential insect mortality by predators, due to varying amounts of refugia. Alternative mechanisms such as differing amounts of trapped detritus and substrate surface area may account for substrate preference.     

Accounting for roughness of circular processes: using Gaussian random processes to model the anisotropic spread of airborne plant disease

Variables with values in the circle or indexed by the circle have been studied in order to investigate questions in ecology, epidemiology, climatology and oceanography for example. To model circular variables with rough behaviors, the use of Gaussian random processes (GRPs) can be particularly convenient as will be seen in this paper. The roughness of a GRP being mainly determined by its correlation function, a circular correlation function convenient for rough processes is proposed. These mathematical tools are applied to describe the anisotropic spread of an airborne plant disease from a point source: a hierarchical model including two circular GRPs is built and used to analyze data coming from a field experiment. This random-effect model is fitted to data using a Monte-Carlo expectation-maximization (MCEM) algorithm.     

Monitoring histone deacetylase inhibition in vivo: noninvasive magnetic resonance spectroscopy method

Histone deacetylase inhibitors (HDACis) are emerging as promising and selective antitumor agents. However, HDACis can lead to tumor stasis rather than shrinkage, in which case, traditional imaging methods are not adequate to monitor response. Consequently, novel approaches are needed. We have shown in cells that (19)F magnetic resonance spectroscopy (MRS)-detectable levels of the HDAC substrate Boc-Lys-TFA-OH (BLT) are inversely correlated with HDAC activity. We extended our investigations to a tumor xenograft model. Following intraperitoneal injection of BLT, its accumulation within the tumor was monitored by in vivo (19)F MRS. In animals treated with the HDACi suberoylanilide hydroxamic acid (SAHA), tumoral BLT levels were higher by 77% and 132% on days 2 and 7 of treatment compared with pretreatment levels (n = 6; p < .05). In contrast, tumoral BLT levels remained unchanged in control animals and in normal tissue. Thus, (19)F MRS of BLT detected the effect of HDACi treatment as early as day 2 of treatment. Importantly, tumor size confirmed that SAHA treatment leads to inhibition of tumor growth. However, difference in tumor size reached significance only on day 6 of treatment. Thus, this work identifies BLT as a potential molecular imaging agent for the early noninvasive MRS detection of HDAC inhibition in vivo.     

Membrane perturbation induced by interfacially adsorbed peptides

The structural and energetic characteristics of the interaction between interfacially adsorbed (partially inserted) alpha-helical, amphipathic peptides and the lipid bilayer substrate are studied using a molecular level theory of lipid chain packing in membranes. The peptides are modeled as "amphipathic cylinders" characterized by a well-defined polar angle. Assuming two-dimensional nematic order of the adsorbed peptides, the membrane perturbation free energy is evaluated using a cell-like model; the peptide axes are parallel to the membrane plane. The elastic and interfacial contributions to the perturbation free energy of the "peptide-dressed" membrane are evaluated as a function of: the peptide penetration depth into the bilayer's hydrophobic core, the membrane thickness, the polar angle, and the lipid/peptide ratio. The structural properties calculated include the shape and extent of the distorted (stretched and bent) lipid chains surrounding the adsorbed peptide, and their orientational (C-H) bond order parameter profiles. The changes in bond order parameters attendant upon peptide adsorption are in good agreement with magnetic resonance measurements. Also consistent with experiment, our model predicts that peptide adsorption results in membrane thinning. Our calculations reveal pronounced, membrane-mediated, attractive interactions between the adsorbed peptides, suggesting a possible mechanism for lateral aggregation of membrane-bound peptides. As a special case of interest, we have also investigated completely hydrophobic peptides, for which we find a strong energetic preference for the transmembrane (inserted) orientation over the horizontal (adsorbed) orientation.     

Ultrastructural cytochemistry of non-specific esterase in murine peritoneal macrophages

Summary Non-specific esterase (NSE) activity was demonstrated in glutaraldehyde-fixed monolayers of murine peritoneal macrophages. Using 2-naphthylthiol acetate (NTA) as substrate and Fast Blue BB as coupling agent a strong osmiophilic reaction product was obtained. The reaction product was observed as electron-dense dots covering cisterns of the rough endoplasmic reticulum, Golgi saccules and vesicles, or as large aggregates in lysosomes. Using -naphthyl butyrate (ANB) as substrate and hexazotized pararosaniline as coupling agent the osmiophilic reaction product was observed extracellularly on the plasma membrane as an electron-dense continuous layer, whereas intracytoplasmic staining of lysosomes was rare. Substitution of the coupling agents in the respective media resulted in a slight reaction with the ANB medium whereas with the NTA medium reaction product was observed only in lysosomal structures. The substrate specificity of the different types of esterases was confirmed after isoelectric focusing on thin-layer polyacrylamide gels. The results indicate that in murine peritoneal macrophages different types on NSE are detected with NTA and ANB, having distinct ultrastructural localizations.     

Rate theory models for ion transport through rigid pores. I. Time-dependent analysis in the case of vanishing interactions

In this first of a series of papers concerning the theoretical analysis of rate theory models for ion transport through rigid pores, the case of vanishing interactions is investigated. "Rigidity" means that ions crossing membranes through pores see a fixed structure of the pores, not changing in time. A single pore is considered to be a sequence of (n + 1) activation barriers separated by n energy minima. The explicit analytical treatment is restricted to pores with regular internal barrier structure, including the nonequilibrium situation of an applied electric field. In this case the connection with continuum diffusion models is demonstrated by performing in the limit n leads to infinity (n = number of binding sites within the pores) the transition to continuum. Thus, from diffusion equations describing a discrete number of jumps, the corresponding diffusion-like partial differential equations and boundary conditions are generated. For regular pores, from the time dependent solutions of the discrete equations, the corresponding solutions of the continuum equations are explicitly generated. The time-dependent relaxation behaviour of the discrete model is in good agreement with the continuum model if one assumes more than two binding sites in the pores.     

Role of plasma membrane proteins and cell wall in meridional arrangement of cortical microtubules inBoodlea coacta

Summary The effects of 2,6-dichlorobenzonitrile (DCB, an agent which inhibits cellulose synthesis) and cycloheximide (CHI, a known inhibitor of protein synthesis) on the construction and stability of the cortical microtubule (MT) cytoskeleton in two kinds of protoplasts (smaller protoplasts and larger ones) prepared fromBoodlea coacta (Dickie) Murray et De Toni were examined by immunofluorescence microscopy. In smaller protoplasts which develop from released protoplasmic masses in culture media, parental cortical MTs assume a convoluted configuration, but new cortical MTs appear following disassembly of convoluted MTs. New cortical MTs initially have a random arrangement but later, a rough meridional arrangement following development of cell polarity and finally, a high density meridional arrangement. In larger protoplasts which are formed within cell wall cylinders of thalli cut at 500 m length, longitudinally oriented parental cortical MTs are preserved. Each exhibits a curving configuration just after protoplast formation, but a straight configuration after 3 h of culture. In smaller protoplasts, cortical MT orientation changes from random to rough meridional orientation but never to a high density meridional orientation following treatment with 10 M CHI, and MT density decreases after 12 h. However, rough meridional and high density meridional arrangements of MTs ceased to be formed and MT density decreased following treatment with 10 M DCB. In larger protoplasts, high density meridional arrangements of MTs were noted not to be affected by treatment with CHI; instead, they continued to remain oriented meridionally, but the length and density were decreased after treatment with DCB for 3–4 h. After 10 h, the MTs became fragmented and orientation was random. From these findings it is summarized that: (1) There are no putative anchors in the plasma membrane of nascent smaller protoplasts, but the meridional orientation of cortical MTs requires anchors which may be distributed in the plasma membrane following the establishment of cell polarity. (2) Plasma membranes in larger protoplasts contain parental anchors oriented meridionally. Anchors stabilize cortical MTs via their close relation to cell walls (especially to cellulose). Anchors are detached from the plasma membrane when cellulose is not formed. (3) Cellulose regeneration may be indispensable to the formation and stabilization of the MT cytoskeleton inBoodlea.Abbreviations CHI cycloheximide - DCB 2,6-dichlorobenzonitrile - DMSO dimethylsulfoxide - MT microtubule     

Predicting the performance of immobilized enzyme reactors using reversible Michaelis–Menten kinetics

A general mathematical model is developed in the present work for predicting the steady state performance of immobilized enzyme reactor performing reversible Michaelis - Menten kinetics. The model takes into account the effect of external diffusional limitations, the axial dispersion and the equilibrium constant on reactor performance quantified as relative substrate conversion and yield. The performance of reactor is characterized using the dimensionless parameters of Damkohler number, Stanton number, Peclet number, the equilibrium constant and the dimensionless input substrate concentration. The reactor performance is described for the two extreme cases of plug flow reactor (PFR) and continuous stirred tank reactor (CSTR) in addition to the intermediate case of dispersed plug flow reactor (DPFR). The performance of reactor is compared for the two cases of zero order and reversible first order kinetics.     

Event-driven time-optimal control for a class of discontinuous bioreactors

Discontinuous bioreactors may be further optimized for processing inhibitory substrates using a convenient fed-batch mode. To do so the filling rate must be controlled in such a way as to push the reaction rate to its maximum value, by increasing the substrate concentration just up to the point where inhibition begins. However, an exact optimal controller requires measuring several variables (e.g., substrate concentrations in the feed and in the tank) and also good model knowledge (e.g., yield and kinetic parameters), requirements rarely satisfied in real applications. An environmentally important case, that exemplifies all these handicaps, is toxicant wastewater treatment. There the lack of online practical pollutant sensors may allow unforeseen high shock loads to be fed to the bioreactor, causing biomass inhibition that slows down the treatment process and, in extreme cases, even renders the biological process useless. In this work an event-driven time-optimal control (ED-TOC) is proposed to circumvent these limitations. We show how to detect a "there is inhibition" event by using some computable function of the available measurements. This event drives the ED-TOC to stop the filling. Later, by detecting the symmetric event, "there is no inhibition," the ED-TOC may restart the filling. A fill-react cycling then maintains the process safely hovering near its maximum reaction rate, allowing a robust and practically time-optimal operation of the bioreactor. An experimental study case of a wastewater treatment process application is presented. There the dissolved oxygen concentration was used to detect the events needed to drive the controller.     

Effects of mood stabilizers on hippocampus BDNF levels in an animal model of mania

There is an emerging body of data suggesting that mood disorders are associated with decreased brain-derived neurotrophic factor (BDNF). The present study aims to investigate the effects of the mood stabilizers lithium (Li) and valproate (VPT) in an animal model of bipolar disorder. In the first experiment (acute treatment), rats were administered D-amphetamine (AMPH) or saline for 14 days, and then between day 8 and 14, rats were treated with either Li, VPT or saline. In the second experiment (maintenance treatment), rats were pretreated with Li, VPT or saline, and then between day 8 and 14, rats were administered AMPH or saline. In both experiments, locomotor activity was measured using the open-field test and BDNF levels were measured in rat hippocampus by sandwich-ELISA. Li and VPT reversed AMPH-induced behavioral effects in the open-field test in both experiments. In the first experiment, Li increased BDNF levels in rat hippocampus. In the second experiment, AMPH decreased BDNF levels and Li and VPT increased BDNF levels in rat hippocampus. Our results suggest that the present model fulfills adequate face, construct and predictive validity as an animal model of mania.     

Sticking coefficient-orchestrated selection in a kinetic model for the first origin

The mathematical formalism of the steady-state Poisson equation is applied to a variant of Freeman Dyson's "Toy Model" for a first origin. Our kinetic approach allows for an examination of the requisite conditions under which metabolism is quantized into discrete eigenstates (e.g. Dyson's disordered, saddle point, and metabolically active toy cell states). The surface reaction machinery additionally allows for more realistic modeling, whence the crucial role of sticking coefficients (catalyst precursors) as prebiotic selectors emerges. In our interior source model, a steady influx of vent nutrients fuels the intracellular synthesis of (impermeable) monomers within a rock-encradled cavity. Random adsorptions and desorptions occur at inactive "cell" wall sites (where the inert monomers remain impermeable until their eventual return to the intracellular metabolite pool). Occasionally, metabolizing reactions also occur due to endogeneous source monomers adsorbing at their "active" sites. Dyson's mean field approach is used to simplify the species-specific sticking coefficients at empty active (substrate) sites to functions of the fraction x of sites occupied by (catalytically) active monomers. In short, our work suggests that disorder-order transition models based on random drift between discrete metabolic eigenstates (Dyson's Toy Model) do not, in general, extend to more realistic metabolisms. From a perspective based on quasi-random feedback kinetics, the contraindication for discretization (spontaneous generation) in non-autocatalytic metabolisms is consistent with the emergence of ordered metabolism under hydrothermal driving forces, a provisio the occurrence of each period of vent dormancy coincides with a discrete zero-source (dormant) metabolic state. Cell drift to higher order is induced by the random reactions which happen to enhance the substrate specificity (chemical selectivity) of the sticking coefficients for active monomers. The result is stronger sink effects for metabolizing species, whence active adsorptions are promoted in favor of inactive adsorptions at substrate sites. Positive feedback plays a crucial role in preserving ("propagating") order in the cell wall reaction kinetics and is held in check by negative feedback inhibition of excessive cell growth. Finally, the eventual desorption of randomly growing dysfunctional proteins is postulated as a deterrent to deterioration catastrophes.     

Modelling of continuous microbial cultivation taking into account the memory effects

The problem of chemostat dynamics modelling for the purpose of control is considered. The "memory" of the culture is explicitly taken into account. Two possibilities for improving the quality of the proposed modelling approaches are discussed. A general model that accounts for the culture `memory' by means of different `memory' functions in the expressions of the specific growth rate and of the specific consumption rate and a polynomial function of the substrate concentration for the yield factor is proposed. The case where the maintenance energy is taken into account is also discussed. Two modifications of the general model (w-type and S-type) are presented. A zero-order `memory' function and a i-function with delay are applied in order to describe the `memory' effects. Continuous growth of the strain Saccharomyces cerevisiae on a glucose limited medium is considered as a case study. Detailed investigations of the variety of models, derived from the general model by applying different `memory' functions and different assumptions are carried out. The results are compared with those previously reported for the same process. It is shown that a significant improvement in predicting the substrate dynamics (not accompanied by any decrease in the quality of the model with respect to the biomass concentration) could be achieved, involving a first- or second-order polynomial function for the yield factor. It is also shown that the quality of the model mainly depends on the way that `memory' function is incorporated. The detailed investigations give priority to the w-type models. In this case past values of both biomass and substrate variables are considered. The time delay models with pure (constant) delay and those which account for the culture `memory' by zero-order `memory' function (adaptability parameter) are compared with respect to their utilization for the purpose of model-based control.     

Analytical effectiveness calculations concerning the degradation of an inhibitive substrate by a steady-state biofilm

A reaction engineering model for the degradation of an inhibitory substrate by a steady-state biofilm is presented. The model describes both the metabolic rate controlling behavior of this substrate in the biofilm and the effect of diffusion limitation caused by an arbitrary substrate on the active biofilm thickness. An analytical expression for the biocatalyst effectiveness factor is presented on the basis of Pirt kinetics for cell maintenance, first order substrate inhibition kinetics, and zero order substrate consumption kinetics. The proposed expression for the biocatalyst effectiveness factor is much more convenient to incorporate into a macroreactor model than the numerical alternatives. Simple criteria are presented to check the applicability of the model in case of true Monod kinetics. The analytical solution is expected to be particularly applicable to processes where a low soluble organic substrate controls the biomass growth, a situation which is often met in wastewater purification processes of industrial importance. The degradation of phenol by Pseudomonas sp. is treated as an example. (c) 1993 John Wiley & Sons, Inc.     

Criterion for aerobic biological treatment design

Examples of the aerobic biological reactor treatment design in accordance with generalized model, suggested earlier by the author, are presented. The generalized model is shown to be most adequate to experiments, in a wide range of the level of treatment. The coefficients of the generalized model can be determined graphically. Two simple limiting cases follow from the generalized model corresponding to the rough and high level treatment from complex pollutant. A criterion, which helps to distinguish these two cases, is suggested.     

Effects of substrate roughening on the swimming performance of Schizothorax wangchiachii (Fang, 1936) in the Heishui River: Implications for vertical slot fishway design

Re-establishing the natural connectivity of rivers using fishways may mitigate the unfavourable effects of dam construction on riverine biodiversity and freshwater fish populations. Knowledge of the swimming performance of target species in specific regions is critical for designing fishways with a high passage efficiency. Substrate roughening with river stones of fishways is considered to improve fish swimming capacity by benefiting from reduced-velocity zones with lower energetic costs. However, the effectiveness of rough substrates in energy metabolism is rarely tested. We investigated the effect of substrate roughening on the swimming capacity, oxygen consumption and behaviour of Schizothorax wangchiachii from the Heishui River in a flume-type swimming respirometer. The results showed that substrate roughening improved critical and burst swimming speed by ~12.9% and ~15.0%, respectively, compared to the smooth substrate. Our results demonstrate that increased reduced-velocity zones, lowered metabolic rate and tail-beat frequency support our hypothesis that lower energetic costs improve fish swimming performance in rough substrate compared to smooth treatment. The traversable flow velocity model predicted that maximum traversable flow velocity and maximum ascent distance were higher over rough compared to smooth substrate fishways. Fishway substrate roughening may be a practical approach to improve fish swimming upstream for demersal riverine fish.     

Interactions substrat-flavine-hemoproteine et stabilite thermique du cytochrome b(2) (L-lactate deshydrogenase de la levure)

We studied the thermal inactivation of yeast cytochrome b(2), the native flavohaemoprotein (FHP(n)) and its derivatives, the haemoprotein (HP) obtained by dissociation of FMN from FHP(n) and the reconstituted flavohaemoprotein (FHP(r)) (haemoprotein + FMN). The initial velocity of inactivation is faster in the presence of FMN. The substrate (L-lactate) or the competitive inhibitor (oxolate) protects only the flavohaemoproteins (FHP(n) and FHP(r)) from thermal inactivation by decreasing this velocity. In each case, the "protection constant", K(p), is determined.Several interpretations can be proposed to explain the lack of protection of the haemoprotein by its substrate: 1) the structure of the substrate-binding site depends on the presence of the FMN; 2) the substrate binding site exists, but the affinity is too small to be detected; 3) a hypothetical scheme is proposed, suggesting that the protein can exist under different thermally sensitive forms following whether FMN or substrate is present.     

Effect of alternating milieu changes on specific substrate consumption in microorganisms]

In technical microbiology microorganisms often undergo alternating milieu changes. For instance, this is the case in recirculation reactors. The organisms react on these changes with an increase of entropy production and in connection with this with increasing substrate consumption. This increasing substrate consumption contradicts the aim of an optimum yield from a given substrate. Thus, studies of the reaction of microbial growth to alternating milieu changes are of great importance. A simple model of the influence of alternating milieu changes on specific substrate consumption is given. In it the biological conversion of substances is built up by an irreversible consecutive reaction. After preliminary examinations on the analogue computer the reaction of the model to alternating perturbations is simulated on the digital computer. The results of the stimulations are compared with experimental data. The good agreement of experiment and model justifies the use of the simple formulation in the preparation of technical processes.     

Construction of mathematical model for high-level expression of foreign genes in pPIC9 vector and its verification

In this report, we introduced a mathematical model for high-level expression of foreign genes in pPIC9 vector. At first, we collected 40 heterologous genes expressed in pPIC9 vector, and these 40 genes were classified into high-level expression group (expression level >100mg/L, 12 genes) and low-level expression group (expression level <100mg/L, 28 genes). Then, the Naive Bayes method was used to construct the model with RNA secondary structure profile of 3'-end of foreign genes as features. The classification accuracy from leave-one-out cross-validation was 100%. Finally, another five genes collected from literatures were used to test the ability of the model. The results indicated that there were four genes correctly predicted. In addition, the model was also verified by expressing human neutrophil gelatinase-associated lipocalin (NGAL) gene with expression level more than 100mg/L. Therefore, we propose that the model can be used to predict the expression level of heterologous genes before experiments and optimize the experiment designs to obtain the high-level expression. Furthermore, we have developed a web server for evaluation and design for high-level expression of foreign genes, which is accessible at http://ppic9.med.stu.edu.cn/ppic9.