PCR-based methods for <Emphasis Type="Italic">CDA</Emphasis> K27Q and A70T genotyping: genotypes and alleles distribution in a central Italy population

Cytidine deaminase (CDA) is a pyrimidine salvage pathway enzyme that catalyzes the hydrolytic deamination of cytidine and deoxycytidine to their corresponding uracil nucleosides. CDA also catalyzes the inactivation of some chemotherapeutic nucleoside analogues such as cytosine arabinoside and gemcitabine. CDA 79A > C (K27Q, rs2072671) and 208G > A (A70T, rs60369023) were found to be associated either with clinical outcomes as well as with pharmacokinetics and toxicity of drugs administered to different subsets of patients. In this paper we reported two PCR-based methods for CDA 79A > C (K27Q) and 208G > A (A70T) genotyping and tested their feasibility using DNA extracted from whole blood as well as from buccal swabs. The aim of this study was also to assess the distribution of genotypic variants in a central Italy population. The allele frequencies were 56.3% (K*) and 43.7% (Q*) for K27Q and 100% (A*) and 0% (T*) for A70T. The genotype frequencies were 32.8% (K*/K*), 46.9% (K*/Q*) and 20.3% (Q*/Q*) for K27Q. The genotype frequencies did not deviate from Hardy–Weinberg equilibrium. The results were compared with those of other reported populations. They showed marked ethnic group differences.     

CORRELATION OF PAIRWISE GENETIC AND GEOGRAPHIC DISTANCE MEASURES: INFERRING THE RELATIVE INFLUENCES OF GENE FLOW AND DRIFT ON THE DISTRIBUTION OF GENETIC VARIABILITY

Attempts to relate estimates of regional F_ST to gene flow and drift via Wright's (1931) equation F_ST ≈ 1/ (4Nm + 1) are often inappropriate because most natural sets of populations probably are not at equilibrium (McCauley 1993), as assumed by the island model upon which the equation is based, or ineffective because the influences of gene flow and drift are confounded in the product Nm. Evaluations of the association between genetic (F_ST) and geographic distances separating all pairwise populations combinations in a region allows one to test for regional equilibrium, to evaluate the relative influences of gene flow and drift on population structure both within and between regions, and to visualize the behavior of the association across all degrees of geographic separation. Tests of the model using microsatellite data from 51 populations of eastern collared lizards (Crotaphytus collaris collaris) collected from four distinct geographical regions gave results highly consistent with predicted patterns of association based on regional differences in various historical and ecological factors that affect the amount of drift and gene flow. The model provides a prerequisite for and an alternative to regional F_ST analyses, which often simply assume regional equilibrium, thus potentially leading to erroneous and misleading inferences regarding regional population structure.     

Status,trends, and equilibrium abundance estimates of the translocated sea otter population in Washington State

Sea otters (Enhydra lutris kenyoni) historically occurred in Washington State, USA, until their local extinction in the early 1900s as a result of the maritime fur trade. Following their extirpation, 59 sea otters were translocated from Amchitka Island, Alaska, USA, to the coast of Washington, with 29 released at Point Grenville in 1969 and 30 released at La Push in 1970. The Washington Department of Fish and Wildlife has outlined 2 main objectives for sea otter recovery: a target population level and a target geographic distribution. Recovery criteria are based on estimates of population abundance, equilibrium abundance (K), and geographic distribution; therefore, estimates of these parameters have important management implications. We compiled available survey data for sea otters in Washington State since their translocation (1977–2019) and fit a Bayesian state-space model to estimate past and current abundance, and equilibrium abundance at multiple spatial scales. We then used forward projections of population dynamics to explore potential scenarios of range recolonization and as the basis of a sensitivity analysis to evaluate the relative influence of movement behavior, frontal wave speed, intrinsic growth, and equilibrium density on future population recovery potential. Our model improves upon previous analyses of sea otter population dynamics in Washington by partitioning and quantifying sources of estimation error to estimate population dynamics, by providing robust estimates of K, and by simulating long-term population growth and range expansion under a range of realistic parameter values. Our model resulted in predictions of population abundance that closely matched observed counts. At the range-wide scale, the population size in our model increased from an average of 21 independent sea otters (95% CI = 13–29) in 1977 to 2,336 independent sea otters (95% CI = 1,467–3,359) in 2019. The average estimated annual growth rate was 12.42% and varied at a sub-regional scale from 6.42–14.92%. The overall estimated mean K density of sea otters in Washington was 1.71 ± 0.90 (SD) independent sea otters/km² of habitat (1.96 ± 1.04 sea otters/km², including pups), and estimated densities within the current range correspond on average to 87% of mean sub-regional equilibrium values (range = 66–111%). The projected value of K for all of Washington was 5,287 independent sea otters (95% CI = 2,488–8,086) and 6,080 sea otters including pups (95% CI = 2,861–9,300), assuming a similar range of equilibrium densities in currently un-occupied habitats. Sensitivity analysis of simulations of sea otter population growth and range expansion suggested that mean K density estimates in currently occupied sub-regions had the largest impact on predicted future population growth (r² = 0.52), followed by the rate of southward range expansion (r² = 0.26) and the mean K density estimate of currently unoccupied sub-regions to the south of the current range (r² = 0.04). Our estimates of abundance and sensitivity analysis of simulations of future population abundance and geographic range help determine population status in relation to population recovery targets and identify the most influential parameters affecting future population growth and range expansion for sea otters in Washington State.     

Organization and function of cytochromeb and ubiquinone in the cristae membrane of beef heart mitochondria

The arrangement and function of the redox centers of the mammalianbc ₁ complex is described on the basis of structural data derived from amino acid sequence studies and secondary structure predictions and on the basis of functional studies (i.e., EPR data, inhibitor studies, and kinetic experiments). Two ubiquinone reaction centers do exist—a QH₂ oxidation center situated at the outer, cytosolic surface of the cristae membrane (Q₀ center), and a Q reduction center (Q _i center) situated more to the inner surface of the cristae membrane. The Q₀ center is formed by theb-566 domain of cytochromeb, the FeS protein, and maybe an additional small subunit, whereas the Q _i center is formed by theb-562 domain of cytochromeb and presumably the 13.4kDa protein (QP-C). The Q binding proteins are proposed to be protein subunits of the Q reaction centers of various multiprotein complexes. The path of electron flow branches at the Q₀ center, half of the electrons flowing via the high-potential cytochrome chain to oxygen and half of the electrons cycling back into the Q pool via the cytochromeb path connecting the two Q reaction centers. During oxidation of QH₂, 2H⁺ are released to the cytosolic space and during reduction of Q, 2H⁺ are taken up from the matrix side, resulting in a net transport across the membrane of 2H⁺ per e^– flown from QH₂ to cytochromec, the H⁺ being transported across the membrane as H (H⁺ + e^–) by the mobile carrier Q. The authors correct their earlier view of cytochromeb functioning as a H⁺ pump, proposing that the redox-linkedpK changes of the acidic groups of cytochromeb are involved in the protonation/deprotonation processes taking place during the reduction and oxidation of Q. The reviewers stress that cytochromeb is in equilibrium with the Q pool via the Q _i center, but not via the Q₀ center. Their view of the mechanisms taking place at the reductase is a Q cycle linked to a Q-pool where cytochromeb is acting as an electron pump.     

On the stock estimation for some fishery systems

In this work we address the stock estimation problem for two fishery models. We show that a tool from nonlinear control theory called “observer” can be helpful to deal with the resource stock estimation in the field of renewable resource management. It is often difficult or expensive to measure all the state variables characterising the evolution of a given population system, therefore the question arises whether from the observation of certain indicators of the considered system, the whole state of the population system can be recovered or at least estimated. The goal of this paper is to show how some techniques of control theory can be applied for the approximate estimation of the unmeasurable state variables using only the observed data together with the dynamical model describing the evolution of the system. More precisely we shall consider two fishery models and we shall show how to built for each model an auxiliary dynamical system (the observer) that uses the available data (the total of caught fish) and which produces a dynamical estimation of the unmeasurable stock state x(t). Moreover the convergence speed of towards x(t) can be chosen.     

Backward bifurcations and strong Allee effects in matrix models for the dynamics of structured populations

In nonlinear matrix models, strong Allee effects typically arise when the fundamental bifurcation of positive equilibria from the extinction equilibrium at r=1 (or R₀=1) is backward. This occurs when positive feedback (component Allee) effects are dominant at low densities and negative feedback effects are dominant at high densities. This scenario allows population survival when r (or equivalently R₀) is less than 1, provided population densities are sufficiently high. For r>1 (or equivalently R₀>1) the extinction equilibrium is unstable and a strong Allee effect cannot occur. We give criteria sufficient for a strong Allee effect to occur in a general nonlinear matrix model. A juvenile–adult example model illustrates the criteria as well as some other possible phenomena concerning strong Allee effects (such as positive cycles instead of equilibria).     

Local consideration of polymorphisms for populations coexisting in stable ecosystems

Summary The stability problem for multiallelic genetic polymorphisms for n populations coexisting in stable ecosystems is considered. Taking into account only density-dependent interactions a generalization of Fisher's theorem is obtained. Specifically, the average fitness of a population must be locally maximized subject to the constraint that the equilibrium population sizes are fixed if the polymorphism is stable. Further, the quasi-equilibrium population sizes N _i ^* corresponding to fixing the genetic structure of all populations in the ecosystem at various values have extrema at the equilibrium point. Such an equilibrium can be a maximum, minimum or saddle point depending upon the type of ecosystem under consideration. A simple test separating these cases on the basis of the so-called ecosystem matrix is suggested. The general equilibrium problem is reformulated as a maximization problem under some restrictions. Conditions under which the maximized function can be expressed as ₌₁ ⁿ N_i are formulated.     

Divalent cations as probes for structure-function relationships of cloned voltage-dependent sodium channels

1. Several cloned sodium channels were expressed in oocytes and compared with respect to their sensitivity to internal Mg²⁺ concerning the open-channel block and to external Ca²⁺ concerning open-channel block and shifts in steady-state activation. 2. A quantitative comparison between wild-type II channels and a mutant with a positive charge in the S4 segment of repeat I neutralized (K226Q) revealed no significant differences in the Mg²⁺ block. 3. The blocking effect of extracellular Ca²⁺ ions on single-channel inward currents was studied for type II, mutant K226Q and type III. A quantitative comparison showed that all three channel types differ significantly in their Ca⁺ sensitivity. 4. The influence of extracellular Ca²⁺ on the voltage dependence of steady-state activation of macroscopic currents was compared for type II and K226Q channels. Extracellular Ca⁺ increases the voltage of half-maximal activation, V_1/2, more for K226Q than for wild-type II channels; a plot of V _1/2 against [Ca] _o , is twice as steep for the mutant K226Q as for the wild-type on a logarithmic concentration scale. 5. The differential effects of extracellular Ca⁺ and intracellular Mg²⁺ on wild-type II and K226Q channels are discussed in terms of structural models of the Na⁺ channel protein.Abbreviations [Na] _i intracellular Na⁺ concentration - [Mg] intracellular Mg²⁺ concentration - [Ca] _o extracellular Ca²⁺ concentration     

K121Q PC‐1 Gene Polymorphism Is Not Associated with Insulin Resistance in a Spanish Population

Objective : To investigate the effect of the K121Q plasma cell membrane glycoprotein (PC‐1) polymorphism on the components of the insulin resistance syndrome in a population‐based nationwide multicenter study in Spain. Research Methods and Procedures : The subjects of the study were 293 nonrelated adults (44.7% men and 55.3% women) ages 35 to 64 years randomly chosen from a nationwide population‐based survey on obesity and related conditions, including insulin resistance and cardiovascular risk factors. Obesity‐related anthropometric measurements included blood pressure, oral glucose tolerance test, lipid profile (total cholesterol, high‐density lipoprotein‐ and low‐density lipoprotein‐cholesterol, and triglycerides), plasma leptin, insulin levels by radioimmunoassay, and insulin resistance (homeostasis model assessment). K121Q PC‐1 genotypes were determined by restriction fragment‐length polymorphism‐polymerase chain reaction. Results : Overall Q allele frequency was 0.14, with no differences between obese and nonobese individuals (0.15 vs. 0.13). After adjustment for sex, age, BMI, and degree of glucose tolerance, the Q allele was associated with high plasma leptin and triglyceride levels, but not with insulin resistance. Discussion : The results showed that the K121Q PC‐1 polymorphism in the Spanish population has no significant impact on insulin sensitivity.     

Genetic analysis of two weak dormancy mutants derived from strong seed dormancy wild type rice N22 (Oryza sativa)

Two weak dormancy mutants, designated Q4359 and Q4646, were obtained from the rice cultivar N22 after treatment with 400 Gy ⁶⁰Co gamma‐radiation. Compared to the N22 cultivar, the dormancy of the mutant seeds was more readily broken when exposed to a period of room temperature storage. The mutants also showed a reduced level of sensitivity to abscisic acid compared to the N22 cultivar, although Q4359 was more insensitive than Q4646. A genetic analysis indicated that in both mutants, the reduced dormancy trait was caused by a single recessive allele of a nuclear gene, but that the mutated locus was different in each case. The results of quantitative trait locus (QTL) mapping, based on the F₂ population from Q4359 x Nanjing35, suggested that Q4359 lacks the QTL qSdn‐1 and carries a novel allele at QTL qSdn‐9, while a similar analysis of the Q4646 x Nanjing35 F₂ population suggested that Q4646 lacks QTL qSdn‐5, both qSdn‐1 and qSdn‐5 are major effect seed dormancy QTL in N22. Therefore, these two mutants were helpful to understand the mechanism of seed dormancy in N22.     

Dry matter production, population structure and environmental conditions of the spring ephemeralErythronium japonicum growing in various habitats differing in sunlight exposure in cool temperate Japan

Phenology, dry matter production, population structure and environmental conditions were examined inErythronium japonicum Decne plants growing on the floor of a deciduous broad-leavedQuercus mongolica forest (Q.m. stand), an evergreen coniferousCryptomeria japonica plantation (C. j. stand) and bare ground left for 3 years after the clearing of a forest composed of youngQ. mongolica andPinus densiflora trees (bare stand) in the cool temperate zone of Japan. The average population density of the plants growing at theQ.m. stand was much higher than that observed at the bare stand, whereas the average number of flowering plants at the former stand was less than half of that at the latter. The population density and number of flowering plants growing at theC. j. stand were both less than 30% of those at theQ. m. stand. The number of seedlings at theQ. m. stand was much more than that at the bare andC. j. stands. Their survivorship rate over 1 year at the former stand also seems to be significantly higher than those at the other stands. Their aboveground and belowground parts at the bare stand were exposed to more severe heat and water stress than those at the other two stands. The net production per leaf area of the plants growing at theQ. m. stand was two and six times larger than those at the bare andC. j. stands, respectively. The plants at the bare stand did not use the available solar radiation as efficiently for dry matter production through photosynthesis as those growing at theQ. m. stand, whereas those at theC. j. stand are strongly restricted in their photosynthetic process by the significantly limited light condition on the floor of the evergreen coniferous plantation. The differences in the number of plants reaching sexual maturity, the density and structure of the population and the net production between their three habitats are discussed here from the standpoint of differences in environmental conditions.     

Distribution patterns of the Q and B biotypes of Bemisia tabaci in the Mediterranean Basin based on microsatellite variation

At least five of the biotypes described in the Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae) complex are known to be present in the Mediterranean Basin area. Only two of them, however, are economically relevant, that is, biotypes B and Q. Biological and genetic differences between the two biotypes have been well studied, but less is known about their patterns of genetic variation and population structure. To address these issues, a study was undertaken based on variation at six microsatellite loci among a subset of nine B. tabaci populations (five belonging to the Q and four to the B biotype). The data obtained show that (i) these loci showed considerable polymorphism in the Q and B biotypes populations although the presence of null alleles can obscure the picture; (ii) the Iberian‐Q, Canarian‐Q, and Egyptian‐B populations exhibit heterozygosity excess as a result of bottleneck events; (iii) the low genetic differentiation between the Israeli, Iberian Peninsula, and Italian populations suggest that these populations share a common gene pool; (iv) the genetic distances between the Canarian‐Q population and the geographically close population from Morocco indicates spatial isolation and a limited gene flow; and finally (v) the microsatellite data for the B populations indicate that the whiteflies from Egypt and Israel have a close phylogenetic relationship, but the source of these biotype B invasions into the Mediterranean area remains unknown.     

Equilibrium state of molecular breeding

We investigate the equilibrium state of the model of Peng, et al. for molecular breeding. In the model, a population of DNA sequences is successively culled by removing the sequences with the lowest binding affinity to a particular target sequence. The remaining sequences are then amplified to restore the original population size, undergoing some degree of point-substitution of nucleotides in the process. Working in the infinite population size limit, we derive an equation for the equilibrium distribution of binding affinity, here modeled by the number of matches to the target sequence. The equation is then solved approximately in the limit of large sequence length, in the three regimes of strong, intermediate and weak selection. The approximate solutions are verified via comparison to exact numerical results.     

The effect of epistasis on the excess of the additive and nonadditive variances after population bottlenecks

The effect of population bottlenecks on the components of the genetic variance generated by two neutral independent epistatic loci has been studied theoretically (VA, additive; VD, dominant; VAA, additive x additive; VAD, additive x dominant; VDD; dominant x dominant components of variance). Nonoverdominance and overdominance models were considered, covering all possible types of marginal gene action at the single locus level. The variance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium, after t consecutive bottlenecks of equal size N (derived components). Formulae were obtained in terms of allele frequencies and effects at each locus and the corresponding epistatic value. An excess of VA after bottlenecks can be assigned to two sources: (1) the spatiotemporal changes in the marginal average effects of gene substitution alpha(i), which are equal to zero only for additive gene action within and between loci; and (2) the covariance between alpha2(i) and the heterozygosity at the loci involved, which is generated by dominance, with or without epistasis. Numerical examples were analyzed, indicating that an increase in VA after bottlenecks will only occur if its ancestral value is minimal or very small. For the nonoverdominance model with weak reinforcing epistasis, that increase has been detected only for extreme frequencies of the negative allele at one or both loci. With strong epistasis, however, this result can be extended to a broad range of intermediate frequencies. With no epistasis, the same qualitative results were found, indicating that dominance can be considered as the primary cause of an increase in VA following bottlenecks. In parallel, the derived total nonadditive variance exceeded its ancestral value (V(NA) = V(D) + V(AA) + V(AD) + V(DD)) for a range of combinations of allele frequencies covering those for an excess of VA and for very large frequencies of the negative allele at both loci. For the overdominance model, an increase in V(A) and V(NA) was respectively observed for equilibrium (intermediate) frequencies at one or both loci or for extreme frequencies at both loci. For all models, the magnitude of the change of V(A) and V(NA) was inversely related to N and t. At low levels of inbreeding, the between-line variance was not affected by the type of gene action. For the models considered, the results indicate that it is unlikely that the rate of evolution may be accelerated after population bottlenecks, in spite of occasional increments of the derived V(A) over its ancestral value.     

The use of isotope effects to determine enzyme mechanisms

Isotope effects are one of the most powerful kinetic tools for determining enzyme mechanisms. There are three methods of measurement. First, one can compare reciprocal plots with labeled and unlabeled substrates. The ratio of the slopes is the isotope effect on V/K, and the ratio of the vertical intercepts is the isotope effect on V(max). This is the only way to determine V(max) isotope effects, but is limited to isotope effects of 5% or greater. The second method is internal competition, where the labeled and unlabeled substrates are present at the same time and the change in their ratio in residual substrate or in product is used to calculate an isotope effect, which is that on V/K of the labeled reactant. This is the method used for tritium or (14)C, or with the natural abundances of (13)C, (15)N, or (18)O. The third method involves perturbations from equilibrium when a labeled substrate and corresponding unlabeled product are present at chemical equilibrium. This also gives just an isotope effect on V/K for the labeled reactant. The chemistry is typically not fully rate limiting, so that the isotope effect on V/K is given by: (x)(V/K)=((x)k+c(f)+c(r)(x)K(eq))/(1+c(f)+c(r)) where x defines the isotope (D, T, 13, 15, 18 for deuterium, tritium, (13)C, (15)N, or (18)O), and (x)(V/K), (x)k, and (x)K(eq) are the observed isotope effect, the intrinsic one on the chemical step, and the isotope effect on the equilibrium constant, respectively. The constants c(f) and c(r) are commitments in forward and reverse directions, and are the ratio of the rate constant for the chemical reaction and the net rate constant for release from the enzyme of the varied substrate (direct comparison) or labeled substrate (internal competition and equilibrium perturbation) for c(f), or the first product released or the one involved in the perturbation for c(r). The intrinsic isotope effect, (x)k, can be estimated by comparing deuterium and tritium isotope effects on V/K, or by comparing the deuterium isotope effect with (13)C ones with deuterated and undeuterated substrates. Adding a secondary deuterium isotope effect and its effect on the (13)C one can give an exact solution for all intrinsic isotope effects and commitments. The effect of deuteration on a (13)C isotope effect allows one to tell if the two isotope effects are on the same or different steps. Applications of these methods to several enzyme systems will be presented.     

NMR structure of the calflagin Tb24 flagellar calcium binding protein of Trypanosoma brucei

Flagellar calcium binding proteins are expressed in a variety of trypanosomes and are potential drug targets for Chagas disease and African sleeping sickness. The flagellar calcium binding protein calflagin of Trypanosoma brucei (called Tb24) is a myristoylated and palmitoylated EF‐hand protein that is targeted to the inner leaflet of the flagellar membrane. The Tb24 protein may also interact with proteins on the membrane surface that may be different from those bound to flagellar calcium binding proteins (FCaBPs) in T. cruzi. We report here the NMR structure of Tb24 that contains four EF‐hand motifs bundled in a compact arrangement, similar to the overall fold of T. cruzi FCaBP (RMSD = 1.0 Å). A cluster of basic residues (K22, K25, K31, R36, and R38) located on a surface near the N‐terminal myristoyl group may be important for membrane binding. Non‐conserved residues on the surface of a hydrophobic groove formed by EF2 (P91, Q95, D103, and V108) and EF4 (C194, T198, K199, Q202, and V203) may serve as a target protein binding site and could have implications for membrane target recognition.     

不同放牧强度季节调控下荒漠草原主要植物种群点格局及空间关联性

种群空间格局是种群自身特性、种间相互关系及环境条件综合作用的结果。以短花针茅荒漠草原为研究对象,运用Programita软件,采用Ripley's K函数和Monte Carlo随机模拟方法,对短花针茅、无芒影子草和碱韭种群点格局及空间关联性进行了研究。结果表明:短花针茅在禁牧和过度放牧下集群分布的尺度在增加,禁牧和过度放牧两种草地利用方式下短花针茅种群的格局具有趋同的趋势;并且,随着放牧强度的增大或者是持续放牧的影响,使得随机分布尺度在逐渐的增大,短花针茅在更大的尺度上才可能为集群分布。春季重牧+夏季重牧+秋季轻牧和全年重度放牧利用下无芒隐子草在较大尺度上才表现为集群分布,并且尺度转化的临界点在放牧的影响下有增大的趋势;重度放牧下碱韭为了适应放牧干扰逐渐向集群分布方向发展,集群分布的尺度在减小以提高种群的稳定性从而抵御过度的干扰。在不同的放牧干扰强度下植物种群具有明显的响应策略,大致表现为物种的群居性在增强,物种集群分布的尺度在减小以提高种群的稳定性从而抵御过度的干扰。春季休牧+夏季重牧+秋季轻牧处理下种群斑块化的尺度较大,有利于群落的稳定,因此荒漠草原采用这种利用方法较为合理。     

A size dependent predator-prey interaction: who pursues whom?

We investigate the properties of an (age, size) -structured model for a population of Daphnia that feeds on a dynamical algal food source. The stability of the internal equilibrium is studied in detail and combined with numerical studies on the dynamics of the model to obtain insight in the relation between individual behaviour and population dynamical phenomena. Particularly the change in the (age, size)-relation with a change in the food availability seems to be an important behavioural mechanism that strongly influences the dynamics. This influence is partly stabilizing and partly destabilizing and leads to the coexistence of a stable equilibrium and a stable limit cycle or even coexistence of two stable limit cycles for the same parameter values. The oscillations in this case are characterized by drastic changes in the size-structure of the population during a cycle. In addition the model exhibits the usual predator-prey oscillations that characterize Lotka-Volterra models.