Primary genome scan for complex body shape‐related traits in the common carp Cyprinus carpio

To identify quantitative trait loci (QTL) that affect body shape in common carp Cyprinus carpio, a linkage map, 2159·23 cM long, was constructed with a total of 307 markers covering 51 linkage groups (LG). The map included 167 new single nucleotide polymorphism (SNP) markers derived from expressed sequence tags (EST) together with 140 microsatellite markers reported earlier. A primary genome scan was conducted for QTL for standard length (L_S), head length (L_H), body height (H_B), body width (W_B) and tail length (L_TAIL) in an F1 line containing 92 offspring. A total of 15 suggestive QTL on six LGs were found to associate with L_S, L_H, H_B, W_B and L_TAIL which explained 10·7–17·4% of the variance. Five significant QTL were detected for body‐shape related traits and located for LGs (lg1, 12 and 20). These QTL included: one associated with L_S (21·1% variance explained), three for H_B (almost 20% variance explained) and one for W_B (20·7% variance explained).     

Moisture adsorption capacity and surface area as deduced from vapour pressure isotherms in relation to hygroscopic water of soils

Six calcareous and alluvial soil profiles differing in their texture, CaCO₃ and salinity were chosen from west and middle Nile Delta for the present study. The 1^st and 2^nd profiles from Borg El-Arab area were sandy loam in texture and > 30% CaCO₃, while the 3^rd and 4^th profiles (from Nubaria area) were sandy clay loam and < 30% CaCO₃. The 2^nd and 4^th profiles were taken from cultivated area with maize. The 5^th profile from Epshan area was non-saline clay alluvial soil and the 6^th from El-Khamsen was saline clay alluvial soil. The relation between soil moisture content (W%) and water vapour pressure (P/P _o) was established for the mentioned soils. Data showed that the specific surface area (S) values were 34–53 and 44–60 m²/g for calcareous soils of Borg El-Arab and Nubaria areas, 206–219 and 206–249 m²/g for non-saline and saline clay alluvial soils of Epshan and El-Khamsen areas, respectively. The corresponding values of the external specific surface area (S _e) were 16–21, 14–22, 72–86 and 92–112 m²/g. Submitting W _m+W _me as an adsorption boundary of moisture films (W _c) (where W _m is mono-adsorbed layer of water vapour on soil particles and W _me is the external mono-adsorbed layer), the maximum water adsorption capacity (W _a) was found to be W _c + W _me or W _m + 2W _me. It was ranged from 1.88 to 2.70%, 1.97 to 2.95%, 9.70–10.70% and 10.80 to 13.12% while the maximum hygroscopic water (M _H) values were 2.43–3.78%, 2.91–4.65%, 16–17% and 18.30–21.9% for the studied soil profiles respectively. The residual moisture content (θ _r) at pF 7 and P/P _o = 0 was ranged from 0.0005–0.0010%, 0.0007–0.0019% and 0.0043–0.0048% in Borg El-Arab, Nubaria and Epshan soil profiles, respectively. The inter-relations between the surface area and the hygroscopic moisture parameters of the soils under investigation were as follows Calcareous soils; W _m = 0.40 M _H, W _c = 0.55 M _H, W _a = 0.70 M _H, S = 14 M _H Non-saline soil; W _m = 0.35 M _H, W _c = 0.49 M _H, W _a = 0.63 M _H, S = 13 M _H Saline soil; W _m = 031 M _H, W _c = 0.45 M _H, W _a = 0.59 M _H, S = 12 M _H These relations give possibility to deduce the soil moisture adsorption capacities and specific surface area via maximum hygroscopic water, which can be obtained through the experimental determination of water vapor adsorption isotherms.     

Diminished Confidence Levels in the Interval Estimation of an Unknown Regressor in Model I of Linear Regression

For the model y=β₀ + β₁ x + e (model I of linear regression) in the literature confidence estimators of an unknown position x₀ are given at which either the expectation of y is given (see FIELLER, 1944; FINNEY, 1952), or realizations of y are given (see GRAYBILL, 1961). These confidence regions with level 1—α need not be intervals. The occurrence of interval shape is a random event. Its probability is equal to the power of the t test for the examination of the hypothesis H: β₁ = 0. The papers mentioned above claim to provide confidence intervals with level 1 ? α. But because of the restriction of (1 —α)—confidence regions to intervals the true confidence probability is the conditional probability W_c: W_c = P (the confidence region covers x₀| the region has interval shape). Here this conditional probability is shown to be less than 1 —α. Evidence on the possible deviations from 1 —α has been obtained by simulations.     

Sensitivity Analyses of a Population Projection Model of Ring-Necked Pheasants

Abstract A large literature exists on population dynamics of ring-necked pheasant (Phasianus colchicus) in North America, but there has not been an attempt to formulate a matrix model nor a sensitivity analysis of the relationships between vital rates and population finite growth rate (Λ) that can be used to guide management. We summarized demographic data available from a 5-year field study in Iowa, USA, collected in Kossuth County (low composition of perennial habitat) and Palo Alto County (high composition of perennial habitat) into a 2-stage (young and adult) matrix projection model. We estimated Λ₁ (the dominant eigenvalue of the deterministic matrix), the stable age distribution (ω), relative reproductive value vector (n̈), other demographic parameters, and Λ_iid, a bootstrap estimate of growth that includes interannual variation in life history parameters. We analyzed the relative importance of vital rates on population growth rate using sensitivity and elasticity of both matrix elements and lower-level parameters such as winter survival and nest success. We first characterized general life history using averaged data from both areas and all years that yielded Λ₁ = 1.086, and a stable stage distribution of. Minimum success of the initial nesting attempt (H₁) that would maintain Λ ≥ 1 under average conditions was estimated to be 42%. Changes in Λ₁ were most sensitive to survival of chicks during brood rearing (S_B), followed in importance by survival during the subsequent winter (S_W), followed by H₁. We followed the general analyses with analyses that helped us to focus on the differences in the landscapes of northwest Iowa. Λ_iid was ≥1 in only 9% of simulations of data from Kossuth whereas estimated Λ_iid was ≥1 in 88% of simulations from Palo Alto. Our analyses of the relative importance and interactions between S_B, S_W, and total recruitment (M, including H₁ and renesting), if combined with data more specific to a local area, would guide management aimed at affecting multiple life history stages whose relative importance will vary across the landscape.     

An Unbalanced Nested Model with Random Effects Having Unequal Variances

Consider the model Y_ijk=μ + a_i + b_ij + e_ijk (i=1, 2,…, t; j=1,2,…, B_i; k=1,2…,n_ij), where μ is a constant and a¹,b_ij and e_ijk are distributed independently and normally with zero means and variances σ²_ad_ij and σ², respectively, where it is assumed that the d_i's and d_ij's are known. In this paper procedures for estimating the variance components (σ², σ²_a and σ²_b) and for testing the hypothesis σ²_b = 0 and σ²_a = 0 are presented. In the last section the mixed model y_ijk, where x_ijkkm are known constants and β_m's are unknown fixed effects (m = 1, 2,…,p), is transformed to a fixed effect model with equal variances so that least squares theory can be used to draw inferences about the β_m's.     

Hydrophobic hydration processes thermal and chemical denaturation of proteins

The hydrophobic hydration processes have been analysed under the light of a mixture model of water that is assumed to be composed by clusters (W₅)_I, clusters (W₄)_II and free water molecules W_III. The hydrophobic hydration processes can be subdivided into two Classes A and B. In the processes of Class A, the transformation A(− ξ_wW_I → ξ_wW_II + ξ_wW_III + cavity) takes place, with expulsion from the bulk of ξ_w water molecules W_III, whereas in the processes of Class B the opposite transformation B(− ξ_wW_III − ξ_wW_II → ξ_wW_I − cavity) takes place, with condensation into the bulk of ξ_w water molecules W_III. The thermal equivalent dilution (TED) principle is exploited to determine the number ξ_w. The denaturation (unfolding) process belongs to Class A whereas folding (or renaturation) belongs to Class B. The enthalpy ΔH_den and entropy ΔS_den functions can be disaggregated in thermal and motive components, ΔH_den = ΔH_therm + ΔH_mot, and ΔS_den = ΔS_therm + ΔS_mot, respectively. The terms ΔH_therm and ΔS_therm are related to phase change of water molecules W_III, and give no contribution to free energy (ΔG_therm = 0). The motive functions refer to the process of cavity formation (Class A) or cavity reduction (Class B), respectively and are the only contributors to free energy ΔG_mot. The folded native protein is thermodynamically favoured (ΔG_fold ≡ ΔG_mot < 0) because of the outstanding contribution of the positive entropy term for cavity reduction, ΔS_red ? 0. The native protein can be brought to a stable denatured state (ΔG_den ≡ ΔG_mot < 0) by coupled reactions. Processes of protonation coupled to denaturation have been identified. In thermal denaturation by calorimetry, however, is the heat gradually supplied to the system that yields a change of phase of water W_III, with creation of cavity and negative entropy production, ΔS_for ? 0. The negative entropy change reduces and at last neutralises the positive entropy of folding. In molecular terms, this means the gradual disruption by cavity formation of the entropy-driven hydrophobic bonds that had been keeping the chains folded in the native protein. The action of the chemical denaturants is similar to that of heat, by modulating the equilibrium between W_I, W_II, and W_III toward cavity formation and negative entropy production. The salting-in effect produced by denaturants has been recognised as a hydrophobic hydration process belonging to Class A with cavity formation, whereas the salting-out effect produced by stabilisers belongs to Class B with cavity reduction.Some algorithms of denaturation thermodynamics are presented in the Appendices.     

Gram-Schmidt Orthogonalization of Multinormal Variates: Applications in Genetics

The computation of an N-variate normal density function requires the inversion of an N × N co-variance matrix. Furthermore, if each mean depends on u unobservable factors, a mixture of u^N N-variate normal densities must be computed, making likelihood calculations impractical even for moderate N. The Gram-Schmidt orthogonalization process is used to express a multinormal density as a product of univariate normal densities. When the pattern of the correlation matrix is taken into account the formulas may be considerably simplified. In some cases each of the orthogonal variates can be written as a linear combination of only a few of the original variates. Such results are crucial for applications of multinormal distributions and of mixtures of multinormal distributions. An intraclass correlation model and a genetic variance components model applicable to family data are discussed as examples.     

QSAR models on H4 receptor antagonists associated with inflammation and anaphylaxis

Histamine, an endogenous amine is implicated in hypersensitivity (allergic) responses, gastric acid secretion, neurotransmission, immuno-modulation, cell differentiation, and embryonic development. It exerts its effects via four histamine receptor subtypes, termed H₁ to H₄ receptors (H₁R–H₄R) belonging to the superfamily of G-protein coupled receptors. The latest discovered histamine receptor, H₄R, is implicated in the chemotaxis of several cell types and strongly associated with immune and inflammatory responses. Thus, we found interesting to analyze in terms of 2D-QSAR a number of H₄ antagonists in order to highlight the most important physicochemical properties implicated in their mechanism of action and in continuation to suggest structural modifications. The C-QSAR platform of Biobyte has been used in this study. The study reveals that lipophilicity, clog P (linear or bilinear model) as well as steric factors such as the overall molar refractivity (CMR), molar volume or the substitutents molar refractivity (linear) or the sterimol parameters B₁ and B₅ are important. Electronic effects appear only in one model. The study shows that log P as calculated from the C-QSAR program of Biobyte is suitable for this form of QSAR study.     

Estimates of subtropical forest biomass based on airborne LiDAR and Landsat 8 OLI data

 快速、定量、精确地估算区域森林生物量一直是森林生态功能评价以及碳储量研究的重要问题。该研究基于机载激光雷达(LiDAR)点云与Landsat 8 OLI多光谱数据, 借助江苏省常熟市虞山地区55块调查样地数据, 首先提取并分析了87个特征变量(53个OLI特征变量, 34个LiDAR特征变量)与森林地上、地下生物量的Pearson’s相关系数以进行变量优选, 然后利用多元逐步回归法建立森林生物量估算模型(OLI生物量估算模型和LiDAR生物量估算模型), 并与基于两种数据建立的综合生物量估算模型的结果进行比较, 讨论预测结果及其精确性。结果表明: 3种模型(OLI模型、LiDAR模型和综合模型)在所有样地无区分分析时, 地上和地下生物量的估算精度均达到0.4以上, 基于不同森林类型(针叶林、阔叶林、混交林)分析时地上和地下生物量的估算精度均有明显提高, 达到0.67及以上。利用分森林类型模型估算生物量, 综合生物量估算模型精度(地上生物量: R²为0.88; 地下生物量: R²为0.92)优于OLI生物量估算模型(地上生物量: R²为0.73; 地下生物量: R²为0.81)和LiDAR生物量估算模型(地上生物量: R²为0.86; 地下生物量: R²为0.83)。     

Estimated genetic parameters for growth‐related traits in large yellow croaker Larimichthys crocea using microsatellites to assign parentage

To estimate the heritabilities of growth‐related traits in large yellow croaker, Larimichthys crocea, three independent full‐factorial crosses were created by crossing four males × four females, seven males × three females and four males × three females (set 1, set 2 and set 3). At 13 months post‐hatch, the juveniles were collected from three cross sets and measured for body mass (M), standard length (L_S) and body height (H_B). In addition, the parentage of the juveniles was assigned by genotyping six or seven polymorphic microsatellite loci. Out of the 959 juveniles, 99·6% could be assigned to a single parental pair. Heritabilities of growth‐related traits were estimated for individual and combined sets with the pedigrees reconstructed by using microsatellite genotypes. The heritability estimates at 13 month‐old were 0·02–0·30 for M, 0·02–0·25 for L_S and 0·03–0·36 for H_B. These results showed that the heritabilities of M, L_S and H_B were different among three sets, which suggested that different breeding strategies should be adopted for different sets.     

Testing Hypotheses about Regression Parameters,When the Error Term Is Heteroscedastic

The paper considers methods for testing H₀: β₁ = … = β_p = 0, where β₁, … ,β_p are the slope parameters in a linear regression model with an emphasis on p = 2. It is known that even when the usual error term is normal, but heteroscedastic, control over the probability of a type I error can be poor when using the conventional F test in conjunction with the least squares estimator. When the error term is nonnormal, the situation gets worse. Another practical problem is that power can be poor under even slight departures from normality. Liu and Singh (1997) describe a general bootstrap method for making inferences about parameters in a multivariate setting that is based on the general notion of depth. This paper studies the small-sample properties of their method when applied to the problem at hand. It is found that there is a practical advantage to using Tukey's depth versus the Mahalanobis depth when using a particular robust estimator. When using the ordinary least squares estimator, the method improves upon the conventional F test, but practical problems remain when the sample size is less than 60. In simulations, using Tukey's depth with the robust estimator gave the best results, in terms of type I errors, among the five methods studied.     

A Stochastic Compartmental Model with Long Lasting Infusion

Most of the compartmental models in current use to model pharmacokinetic systems are deterministic. Stochastic formulations of pharmacokinetic compartmental models introduce stochasticity through either a probabilistic transfer mechanism or the randomization of the transfer rate constants. In this paper we consider a linear stochastic differential equation (LSDE) which represents a stochastic version of a one‐compartment linear model when input function undergoes random fluctuations. The solution of the LSDE, its mean value and covariance structure are derived. An explicit likelihood function is obtained either when the process is observed continuously over a period of time or when sampled data are available, as it is generally feasible. We discuss some asymptotic properties of the maximum likelihood estimators for the model parameters. Furthermore we develop expressions for two random variables of interest in pharmacokinetics: the area under the time‐concentration curve, M₀(T), and the plateau concentration, x_ss. Finally the estimation procedure is illustrated by an application to real data.     

Effect of environmental factors on tenuazonic acid production by Alternaria alternata on soybean-based media

Aims: To determine the effects of water activity (a_W; 0·995–0·90), temperature (5, 18, 25 and 30°C), time of incubation (7–35 days) and their interactions on tenuazonic acid (TA) production on 2% soybean‐based agar by two Alternaria alternata strains isolated from soybean in Argentina. Methods and Results: TA production by two isolates of A. alternata was examined under interacting conditions of a_W, temperature and time of incubation on 2% soybean‐based agar. Maximum TA production was obtained for both strains at 0·98 a_W, but at 30 and 25°C for the strains for RC 21and RC 39, respectively. The toxin concentration varied considerably depending on a_W, temperature, incubation time and strain interactions. TA was produced over the temperature range from 5 to 30°C and a_W range from 0·92 to 0·995, however at 5 and 18°C little TA was produced at a_W below 0·94. Contour maps were developed from these data to identify areas where conditions indicate a significant risk for TA accumulation. Conclusions: The optimum and marginal conditions for TA production by A. alternata on soybean‐based agar were identified. The results indicated that TA production by A. alternata is favoured by different temperatures in different strains. Significance and Impact of the Study: Data obtained provide very useful information for predicting the possible risk factors for TA contamination of soybean as the a_W and temperature range used in this study simulate those occurring during grain ripening. The knowledge of TA production under marginal or sub‐optimal temperature and a_W conditions for growth are relevant as improper storage conditions accompanied by elevated temperature and moisture content in the grain can favour further mycotoxin production and lead to reduction in grain quality.     

Comparative analysis of surface electrostatic potentials of carbon, boron/nitrogen and carbon/boron/nitrogen model nanotubes

We have extended an earlier study, in which we characterized in detail the electrostatic potentials on the inner and outer surfaces of a group of carbon and B_xN_x model nanotubes, to include several additional ones with smaller diameters plus a new category, C_2xB_xN_x. The statistical features of the surface potentials are presented and analyzed for a total of 19 tubes as well as fullerene and a small model graphene. The potentials on the surfaces of the carbon systems are relatively weak and rather bland; they are much stronger and more variable for the B_xN_x and C_2xB_xN_x. A qualitative correlation with free energies of solvation indicates that the latter two categories should have considerably greater water solubilities. The inner surfaces are generally more positive than the corresponding outer ones, while both positive and negative potentials are strengthened by increasing curvature. The outsides of B_xN_x tubes have characteristic patterns of alternating positive and negative regions, while the insides are strongly positive. In the closed C_2xB_xN_x systems, half of the C–C bonds are double-bond-like and have negative potentials above them; the adjacent rows of boron and nitrogens show the usual B_xN_x pattern. When the C_2xB_xN_x tubes are open, with hydrogens at the ends, the surface potentials are dominated by the B⁺–H^– and N^––H⁺ linkages.Figure Calculated electrostatic potential on the molecular surface of closed (6,0) B₄₈N₄₈; a is an outside view, while b shows the interior. Color ranges, in kcal mol^–1: red, greater than 20; yellow, between 20 and 0; green, between 0 and –10; blue, between –10 and –20; purple, more negative than –20     

Validated annual band‐pair periodicity and growth parameters of blue‐spotted maskray Neotrygon kuhlii from south‐east Queensland,Australia

Age and growth parameters were derived for blue‐spotted maskray Neotrygon kuhlii from Moreton Bay in subtropical eastern Australia. Maximum age estimates of 13 and 10 years were obtained from female (n = 76) and male (n = 44) N. kuhlii, respectively. Estimated ages at maturity for 50% of females and males were 6·32 and 3·95 years, respectively. A three‐parameter power function provided the best statistical fit to size at age data in both sexes, providing parameter estimates of y⁰ = 163·13, a = 58·52 and b = 0·58 for females and y⁰ = 165·13, a = 59·02 and b = 0·54 in males. The two‐parameter von Bertalanffy growth function was used to estimate biological parameters based on disc width (W_D) for both female (W_D∞ = 465·81 mm, K = 0·13 year^?1, b = 0·63) and male N. kuhlii (W_D∞ = 385·19 mm, K = 0·20 year^?1, b = 0·54). Annual band‐pair deposition was observed in three calcein‐injected N. kuhlii after periods of liberty ranging from 631 to 1081 days. Centrum edge analysis indicated that annual band‐pair formation was generally consistent within this population, with translucent bands formed over spring and summer and opaque bands formed in autumn and winter. Individual growth rates obtained from tagged specimens were similar to power function growth predictions. These results support previous characterizations of this common trawl by‐catch species as comparatively resilient to non‐targeted catches, although higher catch rates outside Australia infer a need for cautious management.     

Effects of amino acid and trace element supplementation on pneumocandin production by Glarea lozoyensis: impact on titer, analogue levels, and the identification of new analogues of pneumocandin B0

Addition of the amino acids threonine, serine, proline, and arginine to fermentations of the fungus Glarea lozoyensis influenced both the pneumocandin titer and the spectrum of analogues produced. Addition of threonine or serine altered the levels of the “serine analogues” of pneumocandins B₀ and B₅ and allowed for their isolation and identification. Proline supplementation resulted in a dose-dependent increase in the levels of pneumocandins B₀ and E₀, whereas pneumocandins C₀ and D₀ decreased as a function of proline level. Moreover, proline supplementation resulted in an overall increase in the synthesis of both trans-3- and trans-4-hydroxyproline while maintaining a low trans-4-hydroxyproline to trans-3-hydroxyproline ratio compared to the unsupplemented culture. Pneumocandin production and the synthesis of hydroxyprolines was also affected by addition of the proline-related amino acid arginine but not by the addition of glutamine or ornithine. Zinc, cobalt, copper, and nickel, trace elements that are known to inhibit α-ketoglutarate-dependent dioxygenases, affected the pneumocandin B₀ titer and altered the levels of pneumocandins B₁, B₂, B₅, B₆, and E₀, analogues that possess altered proline, ornithine, and tyrosine hydroxylation patterns. Journal of Industrial Microbiology & Biotechnology (2001) 26, 216–221. Received 05 November 2000/ Accepted in revised form 27 January 2001     

Interrelationships between water and cellular metabolism inArtemia cysts

Cysts of the crustaceanArtemia are a useful model for studies on intracellular water because they are capable of essentially complete and reversible desiccation. We have used a variety of techniques on this system, the present work being an attempt to estimate the density of intracellular water (ρ_w). The density of individual cysts was evaluated from sedimentation velocity. Heptane displacement methods were used to determine the volume of a known mass of cysts, from which the density was calculated. The two methods produce comparable results. It was shown that the densities and water contents of large masses of cysts accurately reflect those of individual cysts. Cyst densities (ρ_c) were determined over the entire range of water content from 0 to 0.63 weight fraction of water (W _f), and temperature dependence was measured for 0.61W _f over 2–41°C. The following refer to 25°C. No marked change was detected in ρ_c until the water content exceeded 0.15W _f, at which ρ_c decreased as a linear function of Wf to maximum water content. However, the cyst does not behave ideally in the sense that the densities of the nonaqueous components and added water are not additive as a function ofW _f. The partial specific volume of water in cysts at maximum hydration was estimated to be 3% larger than that of pure water. These observations are compared with density measurements on other systems, and with previous findings on the physical properties of water in this system.     

F-tests for Hypotheses with Block Matrices and Under Conditions of Orthogonality in the General Multivariate Gauss-Markoff Model

The multivariate general Gauss-Markoff (MGM) model (U, XB, ∑?σ²V) when the matrices V ≥ 0 and ∑ > 0 are known and the scalar σ² > 0 is unknown, is considered. The present paper is a continuation of two earlier works (Oktaba, 1988a, b). If XB = X₁Σ + X₂Δ, then the F-test for verification the hypothesis WΣA = 0 is presented. Moreover, under conditions of orthogonality the decomposition of the matrix S_A (?BCA)′L^?(?BCA) into the sum of s = r(L) matrices is given, where ?BCA is the estimator of the parametric estimable functions ?BCA, Cov (?BCA) = A′ ∑?σ²L = ?C₄?′, B? = (X′T^?X)^?X′T^?U, C₄ = (X′T^?X)^?M, where M = M′ is any arbitrary matrix such that R(X) ? R(T), T=V+XMX′; T^? is any c-inverse. R(A) is the linear space generated by the colums of A. Then under additional assumption on normality of U the statistics F for testing ?BA = 0 is deduced. Under conditions of normality of U and decomposition of S_A, the statistics F₁, …, F_s for the hypotheses jⁱ BA = 0 (i = 1,…, s) are established.     

Complex Segregation Analysis on Multi-Modal Distributions

By using sib-pairs and parent-pairs data, Tai and Gross (1988) proposed a method to test the existence of a 2-allele major locus for a quantitative trait. This method is extended to include three alleles at a major locus in this paper. One may perform this extension in a feasible and practical manner. To show the advantage of this extension, a simulated data set of nuclear families from a 3-allele ordered dominant (i.e., A > B, A > W and B > W in our notation) major locus model for a quantitative trait is analyzed by a 2-allele codominant major locus mixed model and a 3-allele ordered dominant major locus mixed model. The result shows that our method can distinguish between ambiguous trimodal distributions.