一个设立海洋保护区的捕鱼模型的生物经济分析

考虑一个设立海洋保护区的捕鱼模型．从生物学和经济学两个角度研究海洋保护区的作用．给出所研究系统的生物和经济平衡点以及平衡点的局部稳定性,不稳定性,全局稳定性的条件．研究结果说明设立海洋保护区对于保护海洋资源是一种有效途径,保护区内的鱼群即使在对非保护区进行连续捕捞的情形下也能够保持在一个适当的水平．进一步研究了最优收获策略,并对所得结果的生物经济解释予以说明．     

A Model for Multi-site Pacing of Fibrillation Using Nonlinear Dynamics Feedback

Traditionally, cardiac defibrillation requires a strong electric shock. Many unwanted side effects of this shock could be eliminated if defibrillation were performed using weak stimuli applied to several locations throughout the heart. Such multi-site pacing algorithms have been shown to defibrillate both experimentally (Pak et al., Am J Physiol 285:H2704–H2711, 2003) and theoretically (Puwal and Roth, J Biol Systems 14:101–112, 2006). Gauthier et al. (Chaos, 12:952–961, 2002) proposed a method to pace the heart using an algorithm based on nonlinear dynamics feedback applied through a single electrode. Our study applies a related but simpler algorithm, which essentially configures each electrode as a demand pacemaker, to simulate the multi-site pacing of fibrillating cardiac tissue. We use the numerical model developed by Fenton et al. (Chaos, 12:852–892, 2002) as the reaction term in a reaction–diffusion equation that we solve over a two-dimensional sheet of tissue. The defibrillation rate after pacing for 3 s is about 30%, which is significantly higher than the spontaneous defibrillation rate and is higher than observed in previous experimental and theoretical studies. Tuning the algorithm period can increase this rate to 45%. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A Mathematical Model of a Fishery with Variable Market Price: Sustainable Fishery/Over-exploitation

We present a mathematical bioeconomic model of a fishery with a variable price. The model describes the time evolution of the resource, the fishing effort and the price which is assumed to vary with respect to supply and demand. The supply is the instantaneous catch while the demand function is assumed to be a monotone decreasing function of price. We show that a generic market price equation (MPE) can be derived and has to be solved to calculate non trivial equilibria of the model. This MPE can have 1, 2 or 3 equilibria. We perform the analysis of local and global stability of equilibria. The MPE is extended to two cases: an age-structured fish population and a fishery with storage of the resource.     

DNA Polymorphism in a Subdivided Population: The Expected Number of Segregating Sites in the Two-Subpopulation Model

Using the two subpopulation model, the expected numbers of segregating sites in a number of DNA sequences randomly sampled from a subdivided population were examined for several types of population subdivisions. It is shown that, in the case where the pattern of migration is symmetrical such as the finite island model, the expected number of segregating sites is independent of the migration rate when two or three DNA sequences are randomly sampled from the same subpopulation, but depends on the migration rate when more than three DNA sequences are sampled. It is also shown that the population subdivision can increase the amount of DNA polymorphism even in a subpopulation in some cases.     

具有阶段结构和非线性接触率的SI传染病模型的渐近性态

研究了一类具有阶段结构和非线性接触率的传染病模型的渐近性态,得到了传染病最终消除和成为地方病的阀值．     

Design and Chemoenzymatic Synthesis of A Tissue Plasminogen Activator Gene with Unique Restriction Sites: A Model for Studying Protein Domain Function

Abstract

We have designed and constructed a cassette tPA gene with unique restriction sites in the interdomain regions. Each domain was chemoenzymatically assembled, cloned and sequenced. We have constructed and expressed the full-length molecule and some deletion mutants.     

Modulation of Habitat-Based Conservation Plans by Fishery Opportunity Costs: A New Caledonia Case Study Using Fine-Scale Catch Data

Numerous threats impact coral reefs and conservation actions are urgently needed. Fast production of marine habitat maps promotes the use of habitat-only conservation plans, where a given percentage of the area of each habitat is set as conservation objectives. However, marine reserves can impact access to fishing grounds and generate opportunity costs for fishers that need to be minimized. In New Caledonia (Southwest Pacific), we used fine-scale fishery catch maps to define nineteen opportunity costs layers (expressed as biomass catch loss) considering i) total catches, ii) target fish families, iii) local marine tenure, and iv) gear type. The expected lower impacts on fishery catch when using the different cost constraints were ranked according to effectiveness in decreasing the costs generated by the habitat-only scenarios. The exercise was done for two habitat maps with different thematic richness. In most cases, habitat conservation objectives remained achievable, but effectiveness varied widely between scenarios and between habitat maps. The results provide practical guidelines for coral reef conservation and management. Habitat-only scenarios can be used to initiate conservation projects with stakeholders but the costs induced by such scenarios can be lowered by up to 50–60% when detailed exhaustive fishery data are used. When using partial data, the gain would be only in the 15–25% range. The best compromises are achieved when using local data.     

A Case of Greenlandic Fisheries Co-Politics: Power and Participation in Total Allowable Catch Policy-Making

Greenlandic governance institutions have been criticised for their colonial heritage of centralisation and lack of democratic participation. In the same manner, Greenlandic fisheries management is notorious in the academic literature for its centralised and locally illegitimate character. While recognising the lack of localised co-management fisheries governance institutions in Greenland, we argue that something has yet to be said about power and user participation in the centralised institutions that have developed. From a symbolic interactionist perspective we dissect the centralised institutions in terms of a differentiated cast of actors and their interaction and argue that participation and power come in many institutional guises as the complex cast of actors within the centralised system represent themselves and others. If we are to understand power and participation in Greenlandic fisheries governance, we need to understand the creation of alliances of the subject-positions that seek control of the self-rule fisheries governance decision-making.     

The Nucleotide-Binding Sites of SUR1: A Mechanistic Model

ATP-sensitive potassium (K_ATP) channels comprise four pore-forming Kir6.2 subunits and four modulatory sulfonylurea receptor (SUR) subunits. The latter belong to the ATP-binding cassette family of transporters. K_ATP channels are inhibited by ATP (or ADP) binding to Kir6.2 and activated by Mg-nucleotide interactions with SUR. This dual regulation enables the K_ATP channel to couple the metabolic state of a cell to its electrical excitability and is crucial for the K_ATP channel’s role in regulating insulin secretion, cardiac and neuronal excitability, and vascular tone. Here, we review the regulation of the K_ATP channel by adenine nucleotides and present an equilibrium allosteric model for nucleotide activation and inhibition. The model can account for many experimental observations in the literature and provides testable predictions for future experiments.     

Qualitative and Dynamical Analysis of a Bionomic Fishery Model with Prey Refuge

Acta Biotheoretica - Viruses are the simplest of pathogens, but possess sophisticated molecular mechanisms to manipulate host behavior, frequently utilizing molecular mimicry. Severe acute...     

Induced Abscission Sites in Internodal Explants of Impatiens sultani: A New System for Studying Positional Control: with an Appendix: A Mathematical Model for Abscission Sites

Intemodes from Impatiens sultani shoots, explanted into sterileculture, often developed a transverse separation layer afterone to two weeks and the top then abscised from the bottom ofthe explant. Such abscission occurred more rapidly and in agreater proportion of explants when 00001 per cent auxin (IAA)was provided basally and when younger intemodes and shorterexplants were used. The distance of the separation layer fromthe base of the explant varied little with explant length, butincreased with the concentration of auxin applied basally. It seems that in this adventitious abscission the processesof positional definition and differentiation proceed withoutpause, whereas in normal abscission the position is definedearly in development but the final stage of differentiationof the separation layer is delayed until much later when theorgan senesces. To account for the results from the internodal explants andfrom surgical operations on shoots as well as for the characteristicposition of abscission sites of leaves and fruits, we suggestthat the position of abscission is controlled primarily by auxinacting as a morphogen: abscission sites occur at Y-junctionsjust above the base of the arm with the lower activity and auxinstatus, or in single axes above a region of higher auxin status.In both sites, the auxin concentration decreases in the apicaldirection. This hypothesis is supported by a mathematical model (see Appendix)of the interaction of diffusive and polar transport in controllingthe concentration gradient along intemodes with specified auxinconcentrations maintained basally. The model allows predictionsconcerning the site and timing of abscission which accord withobservations on intemodal explants. Impatiens sultani Hook., abscission, auxin, differentiation, diffusion coefficient, IAA, morphogen, polar transport coefficient, positional control, separation layer     

物种总数的一类Bayes区间估计的改进

通常所使用的由传统方法得到的物种总数的一类Bayes置信区间不是最短的,就此意义而言也不是最优的。本文得到改进后的Bayes区间估计,并在各种有代表性的自由度情形下通过对比指出它相对于传统的Bayes区间估计的优越性所在,由分析可见,改进后的区间估计更能满足生产实践的需要,得到的物种总数的区间估计更为精确。     

On the Reproduction Number of a Gut Microbiota Model

A spatially structured linear model of the growth of intestinal bacteria is analysed from two generational viewpoints. Firstly, the basic reproduction number associated with the bacterial population, i.e. the expected number of daughter cells per bacterium, is given explicitly in terms of biological parameters. Secondly, an alternative quantity is introduced based on the number of bacteria produced within the intestine by one bacterium originally in the external media. The latter depends on the parameters in a simpler way and provides more biological insight than the standard reproduction number, allowing the design of experimental procedures. Both quantities coincide and are equal to one at the extinction threshold, below which the bacterial population becomes extinct. Optimal values of both reproduction numbers are derived assuming parameter trade-offs.     

Estimating the Age of the Common Ancestor of a DNA Sample Using the Number of Segregating Sites

The number of segregating sites in a sample of DNA sequences and the age of the most recent common ancestor (MRCA) of the sequences in the sample are positively correlated. The value of the former can be used to estimate the value of the latter. Using the coalescent approach, we derive in this paper the joint probability distribution of the number of segregating sites and the age of the MRCA of a sample under the neutral Wright-Fisher model. From this distribution, we are able to compute the likelihood function of the number of segregating sites and the posterior probability of the age of the MRCA of a sample. Three point estimators and one interval estimator of the age of the MRCA are developed; their relationships and properties are investigated. The estimation of the age of the MRCA of human Y chromosomes from a sample of no variation is discussed.     

To the Theory of the Supercompensation Phenomenon with a Nonlinear Overdamped Oscillator Model

Biophysics - An analytical approach was proposed to describe the supercompensation phenomenon on the basis of a nonlinear overdamped Duffing oscillator equation. An expression was obtained for the...     

Pulmonary Surfactant Model Systems Catch the Specific Interaction of an Amphiphilic Peptide with Anionic Phospholipid

Interfacial behavior was studied in pulmonary surfactant model systems containing an amphiphilic α-helical peptide (Hel 13-5), which consists of 13 hydrophobic and five hydrophilic amino acid residues. Fully saturated phospholipids of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylglycerol (DPPG) were utilized to understand specific interactions between anionic DPPG and cationic Hel 13-5 for pulmonary functions. Surface pressure (π)-molecular area (A) and surface potential (ΔV)-A isotherms of DPPG/Hel 13-5 and DPPC/DPPG (4:1, mol/mol)/Hel 13-5 preparations were measured to obtain basic information on the phase behavior under compression and expansion processes. The interaction leads to a variation in squeeze-out surface pressures against a mole fraction of Hel 13-5, where Hel 13-5 is eliminated from the surface on compression. The phase behavior was visualized by means of Brewster angle microscopy, fluorescence microscopy, and atomic force microscopy. At low surface pressures, the formation of differently ordered domains in size and shape is induced by electrostatic interactions. The domains independently grow upon compression to high surface pressures, especially in the DPPG/Hel 13-5 system. Under the further compression process, protrusion masses are formed in AFM images in the vicinity of squeeze-out pressures. The protrusion masses, which are attributed to the squeezed-out Hel 13-5, grow larger in lateral size with increasing DPPG content in phospholipid compositions. During subsequent expansion up to 35 mN m⁻¹, the protrusions retain their height and lateral diameter for the DPPG/Hel 13-5 system, whereas the protrusions become smaller for the DPPC/Hel 13-5 and DPPC/DPPG/Hel 13-5 systems due to a reentrance of the ejected Hel 13-5 into the surface. In this work we detected for the first time, to our knowledge, a remarkably large hysteresis loop for cyclic ΔV-A isotherms of the binary DPPG/Hel 13-5 preparation. This exciting phenomenon suggests that the specific interaction triggers two completely independent processes for Hel 13-5 during repeated compression and expansion: 1), squeezing-out into the subsolution; and 2), and close packing as a monolayer with DPPG at the interface. These characteristic processes are also strongly supported by atomic force microscopy observations. The data presented here provide complementary information on the mechanism and importance of the specific interaction between the phosphatidylglycerol headgroup and the polarized moiety of native surfactant protein B for biophysical functions of pulmonary surfactants.     

In Defense of a Folk Model: The "Skipper Effect" in the Icelandic Cod Fishery

The Icelandic folk model of fishing success emphasizes the importance of the skipper. The validity of this folk model has recently been hotly debated in the social science literature. In this study an attempt is made to estimate the role of the skipper in fishing success. First, we document by a national survey the composition of the folk model of fishing success held by the Icelandic public. Second, drawing on extensive interview data we outline the model of fishing success proposed by skippers themselves. Third, we test this folk science of the skipper by means of visual and statistical analysis against a social science model that emphasizes the role of material factors. The results show that fishing success is not determined by technological and material factors, leaving plenty of room for human factors, such as the skills and knowledge of the skipper. These results are consistent with folk notions of the skipper effect, but contradictory to earlier results of social science. Finally, the results are discussed in a theoretical context with reference to resource management and the nature of folk models.     

DNA Apurinic Sites: Synthesis of a Model Compound and Study of its Reactivity with 3-Aminocarbazole

Abstract

The mechanism of breakage of apurinic DNA with 3-aminocarbazole was determinated on a short oligonucleotide model. The results founded contrast with those reported in the literature.¹     

Phosphatidylinositol 4,5-Bisphosphate Alters the Number of Attachment Sites between Ezrin and Actin Filaments: A COLLOIDAL PROBE STUDY*

Direct linkage between the plasma membrane and the actin cytoskeleton is controlled by the protein ezrin, a member of the ezrin-radixin-moesin protein family. To function as a membrane-cytoskeleton linker, ezrin needs to be activated in a process that involves binding of ezrin to phosphatidylinositol 4,5-bisphosphate (PIP₂) and phosphorylation of a conserved threonine residue. Here, we used colloidal probe microscopy to quantitatively analyze the interaction between ezrin and F-actin as a function of these activating factors. We show that the measured individual unbinding forces between ezrin and F-actin are independent of the activating parameters, in the range of approximately 50 piconewtons. However, the cumulative adhesion energy greatly increases in the presence of PIP₂ demonstrating that a larger number of bonds between ezrin and F-actin has formed. In contrast, the phosphorylation state, represented by phosphor-mimetic mutants of ezrin, only plays a minor role in the activation process. These results are in line with in vivo experiments demonstrating that an increase in PIP₂ concentration recruits more ezrin to the apical plasma membrane of polarized cells and significantly increases the membrane tension serving as a measure of the adhesion sites between the plasma membrane and the F-actin network.     

A Unified Model of the GABAA Receptor Comprising Agonist and Benzodiazepine Binding Sites

We present a full-length α₁β₂γ₂ GABA receptor model optimized for agonists and benzodiazepine (BZD) allosteric modulators. We propose binding hypotheses for the agonists GABA, muscimol and THIP and for the allosteric modulator diazepam (DZP). The receptor model is primarily based on the glutamate-gated chloride channel (GluCl) from C. elegans and includes additional structural information from the prokaryotic ligand-gated ion channel ELIC in a few regions. Available mutational data of the binding sites are well explained by the model and the proposed ligand binding poses. We suggest a GABA binding mode similar to the binding mode of glutamate in the GluCl X-ray structure. Key interactions are predicted with residues α₁R66, β₂T202, α₁T129, β₂E155, β₂Y205 and the backbone of β₂S156. Muscimol is predicted to bind similarly, however, with minor differences rationalized with quantum mechanical energy calculations. Muscimol key interactions are predicted to be α₁R66, β₂T202, α₁T129, β₂E155, β₂Y205 and β₂F200. Furthermore, we argue that a water molecule could mediate further interactions between muscimol and the backbone of β₂S156 and β₂Y157. DZP is predicted to bind with interactions comparable to those of the agonists in the orthosteric site. The carbonyl group of DZP is predicted to interact with two threonines α₁T206 and γ₂T142, similar to the acidic moiety of GABA. The chlorine atom of DZP is placed near the important α₁H101 and the N-methyl group near α₁Y159, α₁T206, and α₁Y209. We present a binding mode of DZP in which the pending phenyl moiety of DZP is buried in the binding pocket and thus shielded from solvent exposure. Our full length GABA_A receptor is made available as Model S1.