Dynamics of a stage-structured predator-prey model: cost and benefit of fear-induced group defense.

In the predator-prey system, predators can affect the prey population (1) by direct killing and (2) by inducing predation fear, which ultimately force preys to adopt some anti-predator strategies. However, the anti-predator strategy is not the same for all individual preys of different life stages. Also, anti-predator behavior has both cost and benefit, but most of the mathematical models observed the dynamics by incorporating its cost only. In the present study, we formulate a predator-prey model dividing the prey population into two stages: juvenile and adult. We assume that adult preys are only adapting group defense as an anti-predator strategy when they are sensitive to predation. Group defense plays a positive role for adult prey by reducing their predation, but, on the negative side, it simultaneously decreases their reproductive potential. A parameter, anti-predator sensitivity is introduced to interlink both the benefit and cost of group defense. Our result shows that when adult preys are not showing anti-predator behavior, with an increase of maturation rate, the system exhibits a population cycle of abruptly increasing amplitude, which may drive all species of the system to extinction. Anti-predator sensitivity may exclude oscillation through homoclinic bifurcation and avert the prey population for any possible random extinction. Anti-predator sensitivity also decreases the predator population density and produces bistable dynamics. Higher values of anti-predator sensitivity may lead to the extinction of the predator population and benefit adult preys to persist with large population density. Below a threshold value of anti-predator sensitivity, it may possible to retain the predator population in the system by increasing the fear level of the predator. We also observe our fear-induced stage-structured model exhibits interesting and rich dynamical behaviors, various types of bistabilities in different bi-parameter planes. Finally, we discuss the potential impact of our findings.

Disease control through removal of population using Z-control approach.

Present study considers the situation where the removal of population is adopted as a prevention measure for isolating the susceptible population from an infected region to reduce the disease prevalence. To investigate the scenario, a dynamic error based method, Z-type control is applied in an SI type disease model with the aim of achieving a predetermined disease prevalence. The controlled system is designed by introducing a new compartment (the population in an infection-free region) in the uncontrolled system to capture the removal of susceptible population from the infected region to an infection free region. By performing numerical simulations, our study shows that using Z-control mechanism, the removal of susceptible to an infection free region can effectively achieve a predetermined disease prevalence. The removal rates required for achieving a specific reduction in infected population for different levels of disease endemicity are quantified. Furthermore, the global sensitivity analysis (PRCC) is also performed to have a more clear insights on the correlations of the control parameter with the model parameters.

Chaos in a nonautonomous eco-epidemiological model with delay.

In this paper, we propose and analyze a nonautonomous predator-prey model with disease in prey, and a discrete time delay for the incubation period in disease transmission. Employing the theory of differential inequalities, we find sufficient conditions for the permanence of the system. Further, we use Lyapunov's functional method to obtain sufficient conditions for global asymptotic stability of the system. We observe that the permanence of the system is unaffected due to presence of incubation delay. However, incubation delay affects the global stability of the positive periodic solution of the system. To reinforce the analytical results and to get more insight into the system's behavior, we perform some numerical simulations of the autonomous and nonautonomous systems with and without time delay. We observe that for the gradual increase in the magnitude of incubation delay, the autonomous system develops limit cycle oscillation through a Hopf-bifurcation while the corresponding nonautonomous system shows chaotic dynamics through quasi-periodic oscillations. We apply basic tools of non-linear dynamics such as Poincaré section and maximum Lyapunov exponent to confirm the chaotic behavior of the system.

Fear effect in prey and hunting cooperation among predators in a Leslie-Gower model.

The predation strategy for predators and the avoidance strategy of prey are important topics in ecology and evolutionary biology. Both prey and predators adjust their behaviours in order to gain the maximal benefits and to increase their biomass for each. In the present paper, we consider a modified Leslie-Gower predator-prey model where predators cooperate during hunting and due to fear of predation risk, prey populations show anti-predator behaviour. We investigate step by step the impact of hunting cooperation and fear effect on the dynamics of the system. We observe that in the absence of fear effect, hunting cooperation can induce both supercritical and subcritical Hopf- bifurcations. It is also observed that fear factor can stabilize the predator-prey system by excluding the existence of periodic solutions and makes the system more robust compared to hunting cooperation. Moreover, the system shows two different types of bi-stabilities behaviour: one is between coexisting equilibrium and limit cycle oscillation, and another is between prey-free equilibrium and coexisting equilibrium. We also observe generalized Hopf-bifurcation and Bogdanov-Takens bifurcation in two parameter bifurcation analysis. We perform extensive numerical simulations for supporting evidence of our analytical findings.

Transmission dynamics and optimal control of stage-structured HLB model.

Citrus Huanglongbing (HLB) is one of severe quarantine diseases affecting citrus pro-duction both in abroad and domestic. Based on the mechanism and characteristics of citrus HLB transmission, we establish a vector-borne model with stage structure and integrated strategy and inves-tigate the effect of the strategy in controlling the spread of HLB. By calculating, we obtain the basic reproductive number R0, and prove that the disease can be eradicated if R0 < 1, whereas the disease will persist if R0 > 1. Meanwhile, we apply the optimal control theory to obtain an optimal integrated strategy. Finally, we use our model to simulate the data of the numbers of inspected and infected citrus trees in "Yuan Orchard", located in Ganzhou City, Jiangxi Province in the southeast of P.R China. We also give some numerical simulations for our theoretical findings.

Backward bifurcation, oscillations and chaos in an eco-epidemiological model with fear effect.

This paper considers an eco-epidemiological model with disease in the prey population. The disease in the prey divides the total prey population into two subclasses, susceptible prey and infected prey. The model also incorporates fear of predator that reduces the growth rate of the prey population. Furthermore, fear of predator lowers the activity of the prey population, which reduces the disease transmission. The model is well-posed with bounded solutions. It has an extinction equilibrium, susceptible prey equilibrium, susceptible prey-predator equilibrium, and coexistence equilibria. Conditions for local stability of equilibria are established. The model exhibits fear- induced backward bifurcation and bistability. Extensive numerical simulations show the presence of oscillations and occurrence of chaos due to fear induced lower disease transmission in the prey population.

A simple SI-type model for HIV/AIDS with media and self-imposed psychological fear.

Infectious diseases can have a large impact on society, as they cause morbidity, mortality, unemployment, inequality and other adverse effects. Mathematical models are invaluable tools in understanding and describing disease dynamics with preventive measures for controlling the disease. The roles of media coverage and behavioral changes due to externally imposed factors on the disease dynamics are well studied. However, the effect of self-imposed psychological fear on the disease transmission has not been considered in extant research, and this gap is addressed in the present investigation. We propose a simple SI-type model for HIV/AIDS to assess the effects of media and self-imposed psychological fear on the disease dynamics. Local and global dynamics of the system are studied. Global sensitivity analysis is performed to identify the most influential parameters that have significant impact on the basic reproduction number. After calibrating our model using HIV case data-sets for Uganda and Tanzania, we calculate the basic reproduction numbers in the study period using the estimated parameters. Furthermore, a comparison of the effects of awareness and self-imposed psychological fear effects reveals that awareness is more effective in eliminating the burden of HIV infection.

Chaos control via feeding switching in an omnivory system.

Tanabe and Namba (Ecology, 86, 3411-3414) studied a three species Lotka-Volterra model with omnivory and explored that omnivory can create chaos. It is well documented that predator switching is a similar biological phenomenon to omnivory and likely to occur simultaneously. In the present paper, the tri-trophic Lotka-Volterra food web model with omnivory and predator switching is re-investigated. We observe that if we incorporate predator switching in the system and the intensity of predator switching increases above a threshold value, then the system will be stable from chaotic dynamics. To study the global dynamics of the system extensive numerical simulations are performed. Our analytical and numerical results suggest that predator switching mechanism enhances the stability and the persistence of a food chain system.

A delayed eco-epidemiological system with infected prey and predator subject to the weak Allee effect.

We consider a system of delay differential equations to represent predator-prey eco-epidemic dynamics with weak Allee effect in the growth of predator population. The basic aim of the paper is to observe the dynamics of such system under the influence of gestation delay of predator and Allee parameter. We analyze essential mathematical features of the proposed model such as uniform persistence, stability and Hopf-bifurcation at the interior equilibrium point of the system. Global asymptotic stability analysis of the positive equilibrium points by constructing a suitable Lyapunov function for the delayed model is carried out separately. We perform several numerical simulations to illustrate the applicability of the proposed mathematical model and our analytical findings. We observe that the system exhibits chaotic oscillation due to increase of the delay parameter τ. We also observe that there is a threshold of Allee parameter above which the predator population will be washed away from the system.

The effect of nanoparticles on plankton dynamics: a mathematical model.

A simple modification of the Rosenzweig-MacArthur predator (zooplankton)-prey (phytoplankton) model with the interference of the predators by adding the effect of nanoparticles is proposed and analyzed. It is assumed that the effect of these particles has a potential to reduce the maximum physiological per-capita growth rate of the prey. The dynamics of nanoparticles is assumed to follow a simple Lotka-Volterra uptake term. Our study suggests that nanoparticle induce growth suppression of phytoplankton population can destabilize the system which leads to limit cycle oscillation. We also observe that if the contact rate of nanoparticles and phytoplankton increases, then the equilibrium densities of phytoplankton as well as zooplankton decrease. Furthermore, we observe that the depletion/removal of nanoparticles from the aquatic system plays a crucial role for the stable coexistence of both populations. Our investigation with various types of functional response suggests that Beddington functional response is the most appropriate representation of the interaction of phytoplankton-nanoparticles in comparison to other widely used functional responses.

How posttranslational modification of nitrogenase is circumvented in Rhodopseudomonas palustris strains that produce hydrogen gas constitutively.

Nitrogenase catalyzes the conversion of dinitrogen gas (N(2)) and protons to ammonia and hydrogen gas (H(2)). This is a catalytically difficult reaction that requires large amounts of ATP and reducing power. Thus, nitrogenase is not normally expressed or active in bacteria grown with a readily utilized nitrogen source like ammonium. nifA* mutants of the purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris have been described that express nitrogenase genes constitutively and produce H(2) when grown with ammonium as a nitrogen source. This raised the regulatory paradox of why these mutants are apparently resistant to a known posttranslational modification system that should switch off the activity of nitrogenase. Microarray, mutation analysis, and gene expression studies showed that posttranslational regulation of nitrogenase activity in R. palustris depends on two proteins: DraT2, an ADP-ribosyltransferase, and GlnK2, an NtrC-regulated P(II) protein. GlnK2 was not well expressed in ammonium-grown NifA* cells and thus not available to activate the DraT2 nitrogenase modification enzyme. In addition, the NifA* strain had elevated nitrogenase activity due to overexpression of the nif genes, and this increased amount of expression overwhelmed a basal level of activity of DraT2 in ammonium-grown cells. Thus, insufficient levels of both GlnK2 and DraT2 allow H(2) production by an nifA* mutant grown with ammonium. Inactivation of the nitrogenase posttranslational modification system by mutation of draT2 resulted in increased H(2) production by ammonium-grown NifA* cells.

A stability-indicating liquid chromatographic method for Lomustine.

A simple, inexpensive and rapid liquid chromatography (LC) method has been developed for the quantitative determination of Lomustine, an chemotherapy drug. Degradation studies were performed on the bulk drug by heating to 60 °C, exposure to UV light at an energy of 200 Wh/m(2)and to visible light at an illumination of not less than 1.2 million lux hours, acid (0.1N hydrochloric acid), base (0.1N sodium hydroxide) aqueous hydrolysis and oxidation with 6.0% (v/v) hydrogen peroxide. Good resolution between the peaks corresponding to impurities produced during synthesis, degradation products and the analyte was achieved on a Symmetry C 8 LC column using a mobile phase consisting of a mixture of aqueous potassium dihydrogen phosphate and acetonitrile. The degradation samples were assayed against the reference standard of Lomustine and the mass balance in each case was close to 99.9%. Validation of the method was carried out as per International Conference on Harmonization (ICH) requirements.

Investigative mining of sequence data for novel enzymes: a case study with nitrilases.

Mining sequence data is increasingly important for biocatalysis research. However, when relying on sequence data alone, prediction of the reaction catalyzed by a specific protein sequence is often elusive, and substrate specificity is far from trivial. The present study demonstrated an approach of combining sequence data and structures from distant homologs to target identification of new nitrilases that specifically utilize hindered nitrile substrates like mandelonitrile. A total of 212 non-identical target nitrilases were identified from GenBank. Evolutionary trace and sequence clustering methods were used combinatorily to identify a set of nitrilases with presumably distinct substrate specificities. Selected encoding genes were cloned into Escherichia coli. Recombinant E. coli expressing NitA (gi91784632) from Burkholderia xenovorans LB400 was capable of growth on glutaronitrile or adiponitrile as the sole nitrogen source. Purified NitA exhibited highest activity with mandelonitrile, showing a catalytic efficiency (k(cat)/K(m)) of 3.6 x 10(4)M(-1)s(-1). A second nitrilase predicted from our studies from Bradyrhizobium zaponicum USDA 110 (gi27381513) was likewise shown to prefer mandelonitrile [Zhu, D., Mukherjee, C., Biehl, E.R., Hua, L., 2007. Discovery of a mandelonitrile hydrolase from Bradyrhizobium japonicum USDA110 by rational genome mining. J. Biotechnol. 129 (4), 645-650]. Thus, predictions from sequence analysis and distant superfamily structures yielded enzyme activities with high selectivity for mandelonitrile. These data suggest that similar data mining techniques can be used to identify other substrate-specific enzymes from published, unannotated sequences.

Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris.

The photosynthetic bacterium Rhodopseudomonas palustris is one of just a few prokaryotes described so far that has vnf and anf genes for alternative vanadium cofactor (V) and iron cofactor (Fe) nitrogenases in addition to nif genes for a molybdenum cofactor (Mo) nitrogenase. Transcriptome data indicated that the 32 genes in the nif gene cluster, but not the anf or vnf genes, were induced in wild-type and Mo nitrogenase-expressing strains grown under nitrogen-fixing conditions in Mo-containing medium. Strains that were unable to express a functional Mo nitrogenase due to mutations in Mo nitrogenase structural genes synthesized functional V and Fe nitrogenases and expressed vnf and anf genes in nitrogen-fixing growth media that contained Mo and V at concentrations far in excess of those that repress alternative nitrogenase gene expression in other bacteria. Thus, not only does R. palustris have multiple enzymatic options for nitrogen fixation, but in contrast to reports on other nitrogen-fixing bacteria, the expression of its alternative nitrogenases is not repressed by transition metals. Between 95 and 295 genes that are not directly associated with nitrogenase synthesis and assembly were induced under nitrogen-fixing conditions, depending on which nitrogenase was being used by R. palustris. Genes for nitrogen acquisition were expressed at particularly high levels during alternative nitrogenase-dependent growth. This suggests that alternative nitrogenase-expressing cells are relatively starved for nitrogen and raises the possibility that fixed nitrogen availability may be the primary signal that controls the synthesis of the V and Fe nitrogenases.

Use of the Rhodopseudomonas palustris genome sequence to identify a single amino acid that contributes to the activity of a coenzyme A ligase with chlorinated substrates.

Rhodopseudomonas palustris strain RCB100 degrades 3-chlorobenzoate (3-CBA) anaerobically. We purified from this strain a coenzyme A ligase that is active with 3-CBA and determined its N-terminal amino acid sequence to be identical to that of a cyclohexanecarboxylate-CoA ligase encoded by aliA from the R. palustris strain (CGA009) that has been sequenced. Strain CGA009 differs from strain RCB100 in that it does not use 3-CBA as a sole carbon source. The aliA gene from the 3-CBA degrading strain differed by a single nucleotide from the aliA gene from strain CGA009, causing the substitution of a serine for a threonine at position 208. Both AliA enzymes, purified as His-tagged fusion proteins, had comparable activities with cyclohexanecarboxylate. However, AliA from the 3-CBA degrading strain was 10-fold more active with 3-CBA (kcat/Km of 4.3 x 10(4) M(-1) s(-1)) than the enzyme from the sequenced strain (kcat/Km 0.32 x 10(4) M(-1) s(-1)). The CGA009 enzyme was not sufficiently active with 3-CBA to complement an RCB100 aliA mutant for growth on this compound. Here, whole genome sequence information enabled us to identify a single nucleotide among 5.4 million nucleotides that contributes to the substrate preference of a coenzyme A ligase.

The role of the central nucleus of the amygdala in nociception and aversion.

The role of the central nucleus of the amygdala in nociception--conditioned and unconditioned aversion--was studied. Rats received microinjection of vehicle or the N-type Ca2+ channel blocker omega-conotoxin GVIA (0.2 microg/250 nl) into the central amygdaloid nucleus prior to intra-plantar injection of formalin, ultrasound exposure or immediately prior to the acquisition phase of an aversive conditioning trial. Intra-amygdala omega-conotoxin GVIA resulted in an earlier onset of nociceptive response to formalin and increased nociceptive behaviour during the first 5 min. Omega-conotoxin GVIA significantly reduced conditioned freezing behaviour with no effect on ultrasound-induced unconditioned aversive behaviour. These data indicate that N-type Ca2+ channels in the central amygdaloid nucleus play a role in mediating behavioural responses to nociceptive and conditioned aversive stimuli.

Chemotaxis of a Ralstonia sp. SJ98 toward co-metabolizable nitroaromatic compounds.

We have earlier reported chemotaxis of a Gram-negative, motile Ralstonia sp. SJ98 towards p-nitrophenol (PNP), 4-nitrocatechol (NC), o-nitrobenzoate (ONB), p-nitrobenzoate (PNB), and 3-methyl-4-nitrophenol (MNP) that also served as sole source of carbon and energy to the strain [S.K. Samanta, B. Bhushan, A. Chauhan, R.K. Jain, Biochem. Biophy. Res. Commun. 269 (2000) 117; B. Bhushan, S.K. Samanta, A. Chauhan, A.K. Chakraborti, R.K. Jain, Biochem. Biophy. Res. Commun. 275 (2000) 129]. In this paper, we report chemotaxis of a Ralstonia sp. SJ98 toward seven different nitroaromatic compounds (NACs) by drop assay, swarm plate assay, and capillary assay. These NACs do not serve as sole carbon and energy source to strain SJ98 but are partially transformed in the presence of an alternate carbon source such as succinate. This is the first report showing chemotaxis of a bacterial strain toward co-metabolizable NACs.

Polycyclic aromatic hydrocarbons: environmental pollution and bioremediation.

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed and relocated in the environment as a result of the incomplete combustion of organic matter. Many PAHs and their epoxides are highly toxic, mutagenic and/or carcinogenic to microorganisms as well as to higher systems including humans. Although various physicochemical methods have been used to remove these compounds from our environment, they have many limitations. Xenobiotic-degrading microorganisms have tremendous potential for bioremediation but new modifications are required to make such microorganisms effective and efficient in removing these compounds, which were once thought to be recalcitrant. Metabolic engineering might help to improve the efficiency of degradation of toxic compounds by microorganisms. However, efficiency of naturally occurring microorganisms for field bioremediation could be significantly improved by optimizing certain factors such as bioavailability, adsorption and mass transfer. Chemotaxis could also have an important role in enhancing biodegradation of pollutants. Here, we discuss the problems of PAH pollution and PAH degradation, and relevant bioremediation efforts.