Modeling the Effect of Prey Refuge on a Ratio-Dependent Predator–Prey System with the Allee Effect

The extinction of species is a major threat to the biodiversity. The species exhibiting a strong Allee effect are vulnerable to extinction due to predation. The refuge used by species having a strong Allee effect may affect their predation and hence extinction risk. A mathematical study of such behavioral phenomenon may aid in management of many endangered species. However, a little attention has been paid in this direction. In this paper, we have studied the impact of a constant prey refuge on the dynamics of a ratio-dependent predator–prey system with strong Allee effect in prey growth. The stability analysis of the model has been carried out, and a comprehensive bifurcation analysis is presented. It is found that if prey refuge is less than the Allee threshold, the incorporation of prey refuge increases the threshold values of the predation rate and conversion efficiency at which unconditional extinction occurs. Moreover, if the prey refuge is greater than the Allee threshold, situation of unconditional extinction may not occur. It is found that at a critical value of prey refuge, which is greater than the Allee threshold but less than the carrying capacity of prey population, system undergoes cusp bifurcation and the rich spectrum of dynamics exhibited by the system disappears if the prey refuge is increased further.     

Effect of aqueous ethanol on the triple helical structure of collagen

Collagen, the most abundant protein in mammals, is widely used for making biomaterials. Recently, organic solvents have been used to fabricate collagen-based biomaterials for biological applications. It is therefore necessary to understand the behavior of collagen in the presence of organic solvents at low (≤50 %, v/v) and high (≥90 %, v/v) concentrations. This study was conducted to examine how collagen reacts when exposed to low and high concentrations of ethanol, one of the solvents used to make collagen-based biomaterials. Solubility testing indicated that collagen remains in solution at low concentrations (≤50 %, v/v) of ethanol but precipitates (gel-like) thereafter, irrespective of the method of addition of ethanol (single shot or gradual addition); this behavior is different from that observed recently with acetonitrile. Collagen retains its triple helix in the presence of ethanol but becomes thermodynamically unstable, with substantially reduced melting temperature, with increasing concentration of ethanol. It was also found that the CD ellipticity at 222 nm, characteristic of the triple-helical structure, does not correlate with the thermal stability of collagen. Time-dependent experiments reveal that the collagen triple helix is kinetically stable in the presence of 0–40 % (v/v) ethanol at low temperature (5 °C) but highly unstable in the presence of ethanol at elevated temperature (~34 °C). These results indicate that when ethanol is used to process collagen-based biomaterials, such factors as temperature and duration should be done taking into account, to prevent extensive damage to the triple-helical structure of collagen .     

Effect of Biofeedback Training of Sensorimotor and β1EEG Rhythms on Attention Parameters

The effects of the EEG–biofeedback (EEG–BFB) procedure, aimed at increasing the sensorimotor (12–15 Hz) and (15–18 Hz) rhythms on the psychological and electrophysiological parameters of attention, were studied using the methods of scalp recording of evoked potentials in the bistimulus paradigm Go/No–Go and a psychological attention test (Test of Variables of Attention; TOVA). Twenty-five children with attention disorders were included in the study. EEG–BFB sessions significantly improved the attention, behavior, and school study results in 19 (76%) children. In these cases, a significant increase in the amplitude of the inhibitory component in the frontocentral leads and improvement of the TOVA parameters were found.     

The Effect of Transposon P{GUS · p53.259H} on the Frequency of Tumor Clones in Drosophila melanogaster wtsP2/+ Heterozygotes

We showed that transposon P{GUS · p53.259H}, mapped to chromosome 3 and carrying a dominant mutation p53 ^259H.GUS, has a positive effect on the frequency of spontaneous and carcinogen-induced tumor mosaic clones warts ^– in Drosopila melanogaster heterozygotes for the tumor suppressor gene warts located in the same chromosome. The transposon effect could be explained either by the arrest of apoptosis in the cells expressing mutant p53 ^259H.GUS gene and containing carcinogen-induced pre-mutations, and/or by genetic instability introduced into chromosome 3 by the P{GUS · p53.259H} transposon itself. The effect of the P{GUS · p53.259H} appeared to be carcinogen-specific. It substantially increased the frequency of tumors induced by supermutagenic platinum complex, oxoplatin, and did not increase the frequencies of tumors induced by polycyclic aromatic hydrocarbons, benzo()pyrene and pyrene. In the spectrum of mutations induced by all carcinogens tested, somatic recombination events prevailed over somatic mutations. Hence, carcinogen-specificity of the P{GUS · p53.259H} effect cannot be explained by preferential induction of somatic mutations or somatic recombination by one of the carcinogens. Organ-specificity of the increased frequency of mosaic warts ^– clones induced by P{GUS · p53.259H} was established.     

Effect of Silt, Water and Periphyton Quality on Survival and Growth of the Mayfly Heptagenia Sulphurea

The herbivorous mayfly Heptagenia sulphurea is characteristic of rivers with stony bottoms. Records from the 20th century showed that this species had disappeared from the Common Meuse in the Netherlands, probably due to river regulation or changes in water quality. A field survey in 2003 showed that H. sulphurea was present in the Geul tributary, approximately 300 m upstream of its confluence with the Common Meuse. H. sulphurea has not recolonized the Common Meuse despite improvements in water quality over the last decades. Concentration of suspended sediments in the River Meuse, however, is still high, much higher than in the beginning of the 20th century. The presence of a silt layer may limit the return of H. sulphurea in this river by reducing availability and quality of its food. The prime objective of this study was to investigate the impact of silt on survival and growth of H. sulphurea in a laboratory experiment. Furthermore, the impact of water and periphyton quality from the Common Meuse on survival and growth of this mayfly was also investigated. Results showed that neither water quality nor cultured periphyton from the Common Meuse reduced survival and growth of H. sulphurea. The presence of a silt layer resulted in a significantly lower growth rate of the mayfly larvae. It is concluded that the silt layer reduces the accessibility of the food. Covering of food is possibly one of the main factors limiting the recolonization of H. sulphurea and probably other benthic grazers in the Common Meuse.     

Comparative Analysis of the Effects of α-Crystallin and GroEL on the Kinetics of Thermal Aggregation of Rabbit Muscle Glyceraldehyde-3-Phosphate Dehydrogenase

Effects of α-crystallin and GroEL on the kinetics of thermal aggregation of rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH) have been studied using dynamic light scattering and analytical ultracentrifugation. The analysis of the initial parts of the dependences of the hydrodynamic radius of protein aggregates on time shows that in the presence of α-crystallin or GroEL the kinetic regime of GAPDH aggregation is changed from the regime of diffusion-limited cluster–cluster aggregation to the regime of reaction-limited cluster–cluster aggregation, wherein the sticking probability for the colliding particles becomes lower the unity. In contrast to α-crystallin, GroEL does not interfere with formation of the start aggregates which include denatured GAPDH molecules. On the basis of the analytical ultracentrifugation data the conclusion has been made that the products of dissociation of GAPDH and α-crystallin or GroEL play an important role in the interactions of GAPDH and chaperones at elevated temperatures.     

Structures and aromaticity of Cationic closo-$$ B_{n} H_{{n - 3}} {\left( {CO} \right)}^{ + }_{3} $$ (n = 5−12)

Structures and stabilities of tricarbonyl closo-boranes cation, BnHn-3(CO)3+ (n = 5-12), isolobal with cationic closo-carboranes C3Bn-3Hn+, have been investigated at the B3LYP/6-311+G** level of theory. The most stable positional isomers of individual cluster are in agreement with those of closo-C3Bn-3Hn+ clusters except for n = 8 and 10. Energetic analysis identifies closo-B6H3(CO)3+, closo-B10H7(CO)3+ and closo-B12H9(CO)3+ as the most stable cages. It is also found that closo-BnHn-3(CO)3+ is much less strained than closo-C3Bn-3Hn+. The negative nucleus independent chemical shifts (NICS) at the cage center reveal three-dimensional aromaticity of the closo-BnHn-3(CO)3+ cages. The CO stretching frequencies have been computed in advance to aid experimental study.     

Effect of Dephosphorylation on the Self-association and the Precipitation of β-Casein

The pyrolyzate of the nondialyzable melanoidin prepared from glucose-ammonia reaction system (kept in pH 5.3~6.0 during the reaction) was fractionated to volatile fraction and nonvolatile fraction. Among the volatile components, two pyridines and four alkylpyrazines were identified. On the other hand, one imidazole compound and two β-hydroxypyridines isolated from the nonvolatile fraction were identified as 4(5)-methylimidazole, 3-hydroxypyridine and 2-methyl-5-hydroxypyridine, respectively. It is inferred that these compounds are not produced by the fission of the main skeleton in the melanoidin molecule, but formed by pyrolysis of the heterocyclic compounds present as a small moiety in the melanoidin.     

Kinetics of renaturation and self-assembly of intermediates on the pathway of folding of the β2-subunit of Escherichia coli tryptophan-synthetase

The kinetics of renaturation of the β₂-subunit of Escherichia coli tryptophan-synthetase (l-serine hydrolyase (adding indole) E.C. 4.2.1.20) and those of its two proteolytic fragments F₁ and F₂ are studied and compared. Steps corresponding to the refolding of F₁, to the association of the folded F₁ and F₂ fragments, and to an isomerization of the associated protein are identified. These steps are ordered on the pathway of renaturation and some of their kinetic parameters are determined. This leads to a tentative kinetic model for the renaturation of nicked-β₂ starting from the denatured F₁ and F₂ fragments.The step corresponding to the refolding of the F₁ domain, as well as that corresponding to the last rate-limiting isomerization leading to the native protein, is shown to be the same in the refolding of the entire, uncleaved β₂-protein. It is concluded that the refolded F₁ fragment corresponds to a folding intermediate on the pathway of renaturation of the β₂-subunit.     

Effect of pH and Glucose on the Stability of α-lactalbumin

The objective of this study is to understand the influence of pH and effect of cosolvent (glucose) on the stabilization of bovine α-lactalbumin by using ultrasonic techniques. Values of density, ultrasonic velocity and viscosity were measured for bovine α-lactalbumin (5 mg/ml) dissolved in phosphate buffer (pH 2, 5, 7, 9 and 12) solutions mixed with and without the cosolvent at 30 °C. These measurements were used to calculate few thermo-acoustical parameters such as adiabatic compressibility, intermolecular free length, acoustic impedance, relaxation time, relative association constant, the partial apparent specific volume and the partial apparent specific adiabatic compressibility for the said systems. The obtained results revealed a strong comparison between the effects of acidic and alkaline pH values on protein denaturation, i.e., the acidic pH are instantaneous and are of less magnitude whereas alkaline pH are slower but sharper. Further the present study supports the fact that the presence of glucose stabilizes α-lactalbumin against denaturation due to pH variation, which may be due to the strengthening of non-covalent interactions and the steric exclusion effect.     

Analysis of different MMAS ACO algorithms on unimodal functions and plateaus

Recently, the first rigorous runtime analyses of ACO algorithms appeared, covering variants of the MAX–MIN ant system and their runtime on pseudo-Boolean functions. Interestingly, a variant called 1-ANT is very sensitive to the evaporation factor while Gutjahr and Sebastiani proved partly opposite results for their variant MMAS_bs. These algorithms differ in their pheromone update mechanisms and, moreover, 1-ANT accepts equally fit solutions in contrast to MMAS_bs. By analyzing variants of MMAS_bs, we prove that the different behavior of 1-ANT and MMAS_bs results from the different pheromone update mechanisms. Building upon results by Gutjahr and Sebastiani, we extend their analyses of MMAS_bs to the class of unimodal functions and show improved results for test functions using new and specialized techniques; in particular, we present new lower bounds. Finally, we compare MMAS_bs with a variant that also accepts equally fit solutions as this enables the exploration of plateaus. For well-known plateau functions we prove that this drastically reduces the optimization time. Our findings are complemented by experiments that support our asymptotic analyses and yield additional insights. A conference version appeared in SLS 2007 (Neumann et al. 2007).     

Kinetic models of coupling between H+ and Na+-translocation and ATP synthesis/hydrolysis by F0F1-ATPases: Can a cell utilize both\Delta \bar \mu _{H^ + } and\Delta \bar \mu _{Na^ + } for ATP synthesis underin vivo conditions using the same enzyme?

Kinetic models of the F₀F₁-ATPase able to transport H⁺ or/and Na⁺ ions are proposed. It is assumed that (i) H⁺ and Na⁺ compete for the same binding sites, (ii) ion translocation through F₀ is coupled to the rate-limiting step of the F₁-catalyzed reaction. The main characteristics of the dependences of ATP synthesis and hydrolysis rates on Δφ, ΔpH, and ΔpNa are predicted for various versions of the coupling model. The mechanism of the switchover from \(\Delta \bar \mu _{H^ + } \) -dependent synthesis to the \(\Delta \bar \mu _{Na^ + } \) -dependent one is demonstrated. It is shown that even with a drastic drop in \(\Delta \bar \mu _{H^ + } \) , ATP hydrolysis by the proton mode of catalysis can be effectively inhibited by Δφ and ΔpNa. The results obtained strongly support the possibility that the same F₀F₁-ATPase in bacterial cells can utilize both \(\Delta \bar \mu _{H^ + } \) and \(\Delta \bar \mu _{Na^ + } \) for ATP synthesis underin vivo conditions.     

Morphofunctional Analysis of Effect of Short-Term Sleep Deprivation on the Wakefulness–Sleep Cycle in Young and Adult Rats

The work presents comparative data on changes of neurophysiological, time characteristics of the wakefulness–sleep cycle (WSC) and morphofunctional state of neurosecretory cells in supraoptic nucleus of the hypothalamus, which develop under influence of a 6-h long sleep deprivation in adult and one-month old rats. It is shown that the rebound of sleep develops in adult animals with a delay, after the 3rd hour and is characterized by a moderate increase of portions of slow-wave (SSP) and fast-wave (FSP) sleep phases in WSC and by a decrease of the wakefulness portion. Morphological analysis of the hypothalamus nonapeptidergic system has revealed a rise of content of neurosecretory material in fibers of supraoptic nucleus cells an in area of supraoptic-pituitary tract, as well as marked hyperemia that indicates activation of processes of secretion of neurohormones into the general blood flow; these reactions are similar to reactions of this system to stress. In rat pups the sleep rebound develops in 0.5 h after the end of the deprivation procedure and is characterized by more pronounced, statistically significant changes in WSC. Individual WSC become very short and almost all of them are completed with episodes of FSP. A statistically significant rise of power of the -wave band in electrogram spectra of hippocampus and somatosensory cortex in SSP, whereas peak of the activity in FSP is shifted to -waves. Ratios of SSP and FSP to wakefulness in individual WSC in mature animals increase after the deprivation 1.53 and 1.85 times, while they are elevated in one-month old animals 5.25 and 6.75 times, respectively. The obtained morphofunctional data allow believing that deprivation is the stress factor of low intensity for adult animals, whereas it may be considered as the stress action of intermediate and even high intensity for rat pups, which changes essentially the interrelations in WSC. Participation of central mechanisms of regulation of sleep and vigilance, which provide processes of compensation of damaging action of deprivation on WSC in the maturing animals, is discussed.     

Effect of Trifluoroethanol on the Structural and Functional Properties of α-Crystallin

Alpha crystallin is an eye lens protein with a molecular weight of approximately 800 kDa. It belongs to the class of small heat shock proteins. Besides its structural role, it is known to prevent the aggregation of β- and γ-crystallins and several other proteins under denaturing conditions and is thus believed to play an important role in maintaining lens transparency. In this communication, we have investigated the effect of 2,2,2-trifluoroethanol (TFE) on the structural and functional features of the native α-crystallin and its two constituent subunits. A conformational change occurs from the characteristic β-sheet to the α-helix structure in both native α-crystallin and its subunits with the increase in TFE levels. Among the two subunits, αA-crystallin is relatively stable and upon preincubation prevents the characteristic aggregation of αB-crystallin at 20% and 30% (v/v) TFE. The hydrophobicity and chaperone-like activity of the crystallin subunits decrease on TFE treatment. The ability of αA-crystallin to bind and prevent the aggregation of αB-crystallin, despite a conformational change, could be important in protecting the lens from external stress. The loss in chaperone activity of αA-crystallin exposed to TFE and the inability of peptide chaperone—the functional site of αA-crystallin—to stabilize αB-crystallin at 20–30% TFE suggest that the site(s) involved in subunit interaction and chaperone-like function are quite distinct.     

Acetato complexes of molybdenum(V): A novel tetranuclear core based on the metal–metal bonded {Mo2O4}2+ units

A series of acetato complexes of molybdenum(V), based on the singly metal–metal bonded {Mo₂O₄}²⁺ structural fragment, has been prepared. A dinuclear (PyH)₃[Mo₂O₄Cl₄(OOCCH₃)] · CH₃CN (1) (PyH⁺ = pyridinium cation, C₅H₅NH⁺) was obtained upon the reaction of (PyH)₅[MoOCl₄(H₂O)]₃Cl₂ with the equimolar solution of pyridine and acetic acid in acetonitrile at ambient conditions. The acetato ligand in 1 is coordinated to a pair of molybdenum atoms in a syn–syn bidentate bridging manner. (PyH)_n[MoOBr₄]_n afforded in an analogous synthetic procedure a tetranuclear cluster, [Mo₄O₈(OOCCH₃)₃(OH)Py₄] · 1/2CH ₃CN · 1/2H₂O (3), with a novel core which may be envisioned as the acetate- and hydroxide-assisted assembly of {Mo₂O₄}²⁺ building blocks. Its structure is presented in terms of known tetranuclear clusters which are also composed of two {Mo₂O₄}²⁺ units. The acetato ligands in 3 adopted apart from bidentate bridging binding modes also a monodentate one. Partial substitution of chlorido ligands in (PyH)₃[Mo₂O₄Cl₄(OOCCH₃)] · CH₃CN (1) with pyridine resulted in a neutral [Mo₂O₄Cl(OOCCH₃)Py₃] · PrⁱOH · Py (2) which retained the original acetate coordination. The title compounds were fully characterized by X-ray diffraction studies and infrared vibrational spectroscopy.     

Kinetics of in vivo bacteriochlorophyll fluorescence yield and the state of photosynthetic apparatus of purple bacteria

The light-induced electron transport in purple bacterium Rhodobacter sphaeroides was studied in vivo by means of kinetic difference absorption spectroscopy and kinetics of bacteriochlorophyll fluorescence yield. Measurements of redox state of the oxidised primary donor and cytochrome c and the membrane potential revealed a complex pattern of changes of the electron flow. Effects of the membrane potential on the fluorescence yield were also analysed, and a model for the fluorescence induction curve is presented. The data indicate substantial positive effect of the membrane potential on the fluorescence emission in vivo. Moreover, light-induced changes in light scattering were observed, which suggests occurrence of structural changes on the level of the photosynthetic membrane.     

Analyzing and Modeling the Kinetics of Amyloid Beta Pores Associated with Alzheimer’s Disease Pathology

Amyloid beta (Aβ) oligomers associated with Alzheimer’s disease (AD) form Ca²⁺-permeable plasma membrane pores, leading to a disruption of the otherwise well-controlled intracellular calcium (Ca²⁺) homeostasis. The resultant up-regulation of intracellular Ca²⁺ concentration has detrimental implications for memory formation and cell survival. The gating kinetics and Ca²⁺ permeability of Aβ pores are not well understood. We have used computational modeling in conjunction with the ability of optical patch-clamping for massively parallel imaging of Ca²⁺ flux through thousands of pores in the cell membrane of Xenopus oocytes to elucidate the kinetic properties of Aβ pores. The fluorescence time-series data from individual pores were idealized and used to develop data-driven Markov chain models for the kinetics of the Aβ pore at different stages of its evolution. Our study provides the first demonstration of developing Markov chain models for ion channel gating that are driven by optical-patch clamp data with the advantage of experiments being performed under close to physiological conditions. Towards the end, we demonstrate the up-regulation of gating of various Ca²⁺ release channels due to Aβ pores and show that the extent and spatial range of such up-regulation increases as Aβ pores with low open probability and Ca²⁺ permeability transition into those with high open probability and Ca²⁺ permeability.