Sedimentation studies of giant DNA molecules present in unsheared whole-cell lysates of D. melanogaster cells.

We have used band sedimentation in shallow density gradients of CsCl in the preparative centrifuge to analyze the distribution of sedimentation coefficients present in tritium labelled DNA from D. melanogaster cells. The cells were lysed according to the method of Kavenoff and Zimm to preserve very high molecular weight DNA. Sedimentation measurements have been carried out as a function of speed of centrifugation. The resulting distribution functions have been interpreted with the aid of the Zimm-Schumaker equation for the speed dependence of the sedimentation coefficient of very high molecular weight DNA. Low-speed centrifugation (3000 rpm) indicates that DNA molecules from the lysate are evenly distributed over values of S_20,w from 0 to 514S. This distribution is very sensitive to changes in speed of centrifugation and is transformed into a bimodal distribution at 12,080 rpm. Analysis of this transformation allows us to postulate that perhaps 55% of the DNA in the lysate may have molecular weights in excess of 40 × 10⁹ g/mol. Some of these molecules may also possess a variety of configurations including partially replicated branched structures.     

Sedimentation Properties of Dextran Sulfate-Low Density Lipoprotein Complexes

The nature of interaction between dextran sulfate and the human plasma low density lipoproteins of S_f 0–10 was investigated in high density media of glycine and glucose. The soluble complex formation between the two components was manifested by sedimentation of the lipoproteins along with dextran sulfate in the glycine and glucose media of density 1.063. The addition of sodium chloride to the mixture caused dissociation of the complex: during subsequent ultracentrifugation, flotation of lipoprotein and sedimentation of dextran sulfate occurred. However, when the complex is in the acidic glycine medium (pH 4.0), the addition of sodium chloride did not induce dissociation of the complex.

Both the solubility and the size of the complex were greatly influenced by the ratio of the two components in solution. At low relative concentrations of dextran sulfate, insoluble aggregates were formed; but the aggregates disintegrated into soluble units upon increasing the dextran sulfate concentrations. From the sedimentation patterns of dextran sulfate lipoprotein mixtures at various ratios, it was possible to estimate the ratio of the two components in the complex. In the presence of excess dextran sulfate a composite biphasic Schlieren diagram was produced as a result of the unusual Johnston-Ogston effect.     

Bivariate Modified Power Series Distribution Some Properties,Estimation and Applications

The class of bivariate modified power series probability distribution (BMPSD) has been defined by P(X = x, Y=y) =a(x, y) (g(?₁ ?₂))^x (h(?₁, ?₂))^xwhere a(x,y) is a sub-set of the Cartesian product of the set of non-negative integers and g(?₁, ?₂), h(?₁ ?₂) and f(?₁, (?₁, ?₂) are positive finite and successively differentiable functions of ?₁and ?₂. It includes a very large number of well known probability distributions. The recurrence relations for central moments and factorial moments have been determined. Also, the M.L. estimators for ?₁ and ?₂ and their asymptotic biases and variances are obtained. Some important properties are discussed. The results of an BMPSD have been applied to derive the corresponding results for the bivariate generalized negative bino-mial distribution and the bivariate Lagrangian Poisson distribution.     

Determination os sedimentation coefficient distributions for cartilage proteoglycans

Sedimentation coefficient distributions of widely polydisperse proteoglycan preparations were made using a previously developed transport sedimentation methodology. Boundary stability was improved by centrifuging samples in a preformed CsCl density gradient (0.016 g/cm⁴). The results were compared with the distributions obtained with an interferometric analytical centrifugation method. When these two techniques were applied to analyze A1 and A1–D1 proteoglycan preparations, results were in substantial agreement with respect to the mean sedimentation coefficients of the peaks, average S value, sedimentation coefficient distribution, skewness, proportion of monomer and aggregates, and linearity of the plot ln(s) versus C extrapolations to zero concentration. The lower solute concentration compatible with the transport (velocity gradient) method makes this technique particularly suitable for studying the details of proteoglycan distribution of molecular sizes, especially for aggregates.     

Optimal Fixing of the Bandwidth-Parameter for the Empirical Regression1,2

The estimator ?₀(x) of the regression r(x) = E (Y | × = x) from measured points (x_i, y_i), i = 1(1) n, of a continuous two-dimensional random variable (X, Y) with unknown continuous density function f(x, y) and with moments up to the second order can be made with the help of a density estimation f?₀(x, y) (see e.g. SCHMERLING and PEIL, 1980). Here f?₀(x, y) still contains free parameters (so-called band-width-parameters), the values of which have to be optimally fixed in the concrete case. This fixing can be done by using a modification of the maximum-likelihood principle including jackknife techniques. The parameter values can be also found from the estimators for r(x). Here the cross-validation principle can be applied. Some numerical aspects of these possibilities for optimally fixing the bandwidth-parameter are discussed by means of examples. If ?₀(x) is used as a smoothing operator for time series the optimal choice of the parameter values is dependent on the purpose of application of the smoothed time series. The fixing will then be done by considering the so-called filter-characteristic of ?C₀(x).     

Interlocked DNA rings. II. Physicochemical studies

Several species of topologically interlocked λb2b5c DNA rings (catenanes) have been prepared in vitro. The sedimentation behavior of dimeric catenanes containing 0, 1, or 2 covalently closed duplex rings has been studied as a function of the superhelical density of the covalently closed ring or rings. In general, if XtpY represents rings X and Y topologically interlocked, the sedimentation coefficient of this species, ^SXtpY, is related to the sedimentation coefficients ^SX and ^SY of the component rings by the empirical relationship ^SXtpY/^SY = [(M_X + M_Y)/M_Y] [1 + (M_X/M_Y)^1.78(^SY/^SX)^1.78]^?0.56 This equation can also be extended to the case where three monomeric rings are topologically linked in a chain. For two topologically interlocked monomeric rings with neither ring covalently closed, the sedimentation coefficient is 1.35 times that of the monomeric ring. This is different from results reported for mitochondrial and P22 catenanes by others. Several possibilities are discussed to account for this discrepancy. The sedimentation coefficient of a species containing one covalently closed duplex ring and a single-stranded ring was also measured in an alkaline medium. This species, which can be easily derived from a dimeric catenane containing two covalently closed duplex rings, is particularly useful for the identification of covalently closed dimeric catenanes. Some electron microscopic studies of these interlocked rings are presented in an accompanying paper.     

Particle properties of parsnip yellow fleck virus

Particle preparations of parsnip yellow fleck virus (PYFV) isolates A-421 and P-121, representing the two major serotypes, were made by clarifying leal extracts with ether or butan-1-ol and concentrating the virus particles by precipitation with polyethylene glycol and differential centrifugation. The preparations contained c. 31 nm-diameter particles comprising two sedimenting components. Top component (T) consisted of stain-penetrable protein shells with A₂₆₀/A₂₈₀= 0.8–0.9, sedimentation coefficient (S₂₀) = 56 S (A-421) or 60 S (P-121), and buoyant density = 1.297 g/cm³. Bottom component (B) consisted of nucleoprotein particles, not penetrable by negative stain, with A₂₆₀/A₂₈₀= 1.9, sedimentation coefficient (S⁰_20.w) = 148 S (A-421) or 153 S (P-121), and buoyant density = 1.520 g/cm³ (A-421) or 1.490 g/cm³ (P-121). Yields of B component particles were up to c. 1 mg/100 g leaf tissue (both isolates); yields of T component particles were up to c. 0.6 mg (A-421) or 5.5 mg (P-121) per 100 g leaf tissue. PYFV particles were found to contain a single RNA species (mol. wt c. 3.4 × 10⁶, c. 9800 nucleotides), constituting 40% of the particle weight, and three polypeptide species, of mol. wt (× 10 ³) 30 , 26 and 24 (A-421) or 31 , 26 and 23 (P-121).     

How to compare fluctuating asymmetry of different traits

Comparing fluctuating asymmetry (FA) between different traits can be difficult because traits vary at different scales. FA is generally quantified either as the variance of the difference between left and right (σ²_L?R) or the mean of the absolute value of this difference (μ_|R?L|). Corrections for scale differences are obtained by dividing by trait size mean. We show that a third index, one minus the correlation coefficient between left and right (1 ? r_L,R), is equivalent to σ²_L?R standardized by trait size variance. The indices are compared with Monte‐Carlo simulations. All achieve the expected correction for scale differences. High type I error rates (false indication of differences) occur only for σ²_L?R and μ_|R?L| if trait sizes close to or below 0 occur. 1 ? r_L,R with a bootstrap test has always low error rates. Recommendation of the index to be used should be based on whether standardization of FA by trait size mean or trait size variance is preferred. A survey of 36 traits in the Speckled Wood Butterfly (Pararge aegeria) indicated that σ²_L?R is slightly higher correlated to trait size variance than to trait size mean. Thus 1 ? r_L,R seems to be the superior index and should be reported when FA of different traits is compared.     

Analysis of self-incompatibility interactions in 30 resynthesized Brassica napus lines. I. Fluorescence microscopic studies

Thirty Brassica napus lines have been developed through interspecific hybridization of B. oleracea and B. campestris lines with defined S-allele constitutions. These lines, which represent 29 different S-allele combinations, were tested in a diallel of test-pollinations to determine the activity of the introgressed S-alleles and intergenomic dominance relationships. Some consistent trends were observed: B. oleracea S-alleles high in the dominance series (e.g. S₈, S₁₄, S₂₉) were always active in the resynthesized B. napus lines, whereas recessive S-alleles (S₂, S₁₅) lost their activity in some test combinations. The B. campestris S-alleles were active in most cases, although 2 alleles were partially inactivated by the recessive B. oleracea allele S₁₅.     

Deoxyribonueleate solutions: Sedimentation in a density gradient,partial specific volumes,density and refractive index increments,and preferential interactions

Density increments (?ρ/?c₂)°_μ in solutions of NaDNA in NaCl and CsDNA in CsCl were determined over a wide range of salt concentrations; calf thymus DNA, fragmented by sonic irradiation to a molecular weight of 4–6 × 10⁵ was used. The partial specific volume v?₂° of NaDNA at 25°C was found to ho 0.500 ml/g in water, and that of CsDNA 0.440 ml/g. Both values increase with increasing NaCl and CsCl concentration. Refractive index increments under various experimental conditions were also determined. The relevance of the density increments (at constant, chemical potential of diffusible solutes) to equilibrium sedimentation in a density gradient and the evaluation of molecular weights is discussed. Distribution coefficients of diffusible components, sometimes referred to as preferential solvation or net hydration, were derived from the density increments and partial volumes and compared with direct experimental results, whenever available, from membrane distribution and isopiestic distillation. The thermo-dynamic significance of the distribution coefficients as well as possible interpretations in terms of specific molecular mechanisms are considered.     

Measurement of non-randomness in spatial distributions

The measurement of departure from randomness in spatial distributions has widespread application in ecological work. Several “indices of non-randomness” are compared with regard to their dependence on sample number, sample size and density. Criteria for the best choice of index for specific situations are discussed. A new coefficient C_x is proposed for use with positively contagious distributions and tests of significance are given. When C_x and another index (S²/m−1) are used for positive and negative contagion respectively, values ranging from −1 through 0 (random) to +1 are obtained, regardless of sample number, sample size or density.     

Empirical regression as a conditional expected value of a special distribution-mixture for a modelfree quantitative recording of stochastical relations

An “empirical” distribution function F?(x, y) is estimated from measured points (xi, yi), i =1(1)n, of a continuous two-dimensional random variable (X, Y) with unknown continuous density function f(x, y). The density function F?(x, y) of F?(x, y) is a mixture of n two-dimensional normal densities. The first order moments of F?(x, y) are the sample means x and y, whilst the second order moments are only proportional to the sample variances and the sample covariance. This “empirical” distribution F?(x, y) is used for evaluation of an empirical regression curve where a free parameter has to be fixed by an optimality criterion. The procedure is demonstrated by an example from morphometrical research.     

Asymptotic line-of-descent distributions

Asymptotic distributions are derived for the number of non-mutant ancestors, at time t in the past, of a sample of n from a neutral infinite alleles model. Either the number of non-mutant ancestors L _n (t) has a normal distribution or n-L_n(t) has a Poisson distribution as n , t 0.     

A new serum lipoprotein found in many rhesus monkeys.

A new serum lipoprotein was found in about 10 out of 30 rhesus monkeys ($\text{Macaca}\text{mulatta}$) which contained 28% by weight of protein, 42% total cholesterol, 22% phospholipid, and 8% triglyceride. This is in contrast to LDL (which the ten monkeys also contained) which had 24% protein, 46% total cholesterol, 24% phospholipid and 7% triglyceride. An S_{f, 1.063} in KBr of 3.0 to 3.7 and molecular weight of 3.5 – 3.7 million were observed compared to means of 8.1 and 3.0 million for normal rhesus LDL. The lower S_f was caused by its higher density. This new lipoprotein was most easily demonstrated and isolated by preparative ultracentrifugation of all serum lipoproteins at density 1.22 g/ml, followed by 6% agarose gel filtration at 6°. The new lipoprotein appeared as a distinct peak eluting before LDL.     

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.     

不同水分处理下喀斯特土层厚度异质性对两种草本叶片解剖结构和光合特性的影响

为了探究不同水分处理下草本植物对喀斯特土层厚度变化的叶片形态建成和光合生理响应,以黑麦草(Lolium perenne L.)和苇状羊茅(Festuca arundinacea Schreb.)为研究对象,通过盆栽水分受控试验,研究了3种水分处理[正常供水(W_(ck)),减水1组(D1)和减水2组(D2)]下3种土层厚度[浅土组(S_S)、对照组(S_(CK))和深土组(S_D)]对两种草本叶片解剖结构和光合特性的影响。结果表明:(1)正常供水下(W_(ck)),黑麦草和苇状羊茅在浅土组(S_S)的气孔密度和气孔限制值(Ls)均显著高于对照组(S_(CK)),净光合速率(Pn)、胞间CO_2浓度(Ci)和蒸腾速率(Tr)降低;在深土组(S_D),两种植物的气孔密度都有所下降,黑麦草的叶脉密度、Pn和Tr均低于对照组,而苇状羊茅的叶脉密度和Pn表现出增加;(2)D1水分条件下,黑麦草在浅土组的气孔密度较对照组增加,叶脉密度、Pn和Tr均降低,而苇状羊茅的气孔密度有所降低,叶脉密度、Pn和Tr未受到显著影响;在深土组中,黑麦草的气孔密度不变,叶脉密度增加,而Pn和Tr均降低;苇状羊茅的气孔密度降低,但叶脉密度、Pn和Tr均升高;(3)D2水分条件下,两种植物在浅土组的叶脉密度较对照组均增加,气孔密度、Pn和Tr均受到抑制;在深土组,黑麦草的远轴面气孔密度较对照组下降,两种植物的其他指标未受到明显影响。可见,在不同水分条件下,植物的叶片解剖结构和光合特性对不同土层厚度的响应不一,且不同物种间也有差异。总体上随着水分减少,土层厚度降低对植物的光合抑制作用增强,而厚度增加对深根植物的光合促进作用和对浅根植物的光合抑制作用先增强后减弱。植物气孔和叶脉性状特征随水分条件的变化在一定程度上与叶面积和叶片宽度的变化有关。     

Gender distribution,sexual size dimorphism and morphometric sexing in ballan wrasse Labrus bergylta

In wild ballan wrasse Labrus bergylta, mass–length relationships were not different between genders, and positive allometry was found in the mixed‐gender population. Male‐biased sexual size dimorphism was significant and the most effective morphometric method for sexing L. bergylta outside of the species spawning window used body mass (M_B in g), total body length (L_T in mm) and Fulton's condition factor (K) as discriminant variables to predict gender with 91% accuracy. The discriminant score (S_D) of a specimen can be calculated as S_D = 0·01 M_B ? 0·016 L_T ? 3·835 K + 6·252 to predict its gender as female or male if S_D is < 1·459 or S_D is > 1·504, respectively. There was a potential trend towards earlier sexual inversion compared to previous studies at comparable latitudes. Sex change is a phenotypically plastic trait under social control in haremic fishes and should be monitored in increasingly exploited L. bergylta.     

Dietary analysis of the herbivorous hemiramphid Hyporhamphus regularis ardelio: an isotopic approach

The stable isotope values for a range of size classes of Hyporhamphus regularis ardelio from Moreton Bay, south‐east Australia were determined. There was a positive linear relationship between δ¹³C and standard length (L_S)(δ¹³C = 0·034 L_S ? 16·23; r² = 0·78). δ¹³C ranged from ?8·48 to ?17·29‰ with the smallest size class (50 mm L_S) being on average 1·04‰ enriched with respect to that of zooplankton (Temora turbinata) and 7·97‰ depleted compared to Zostera capricorni. δ¹³C was positively correlated with L_S(P < 0·01)(more enriched with increasing L_S) with those fish of the largest size class (225 mm L_S) being 9·86 and 0·84‰ enriched than T. turbinata and Z. capricorni, respectively. There was no detectable trend in δ¹⁵N values with L_S(P > 0·01) with δ¹⁵N, ranging from 9·18 to 11·00‰. Fish of all size classes were on average 2·32 and 7·63‰ more enriched than zooplankton and seagrass, respectively. Carbon isotope data indicate that H. r. ardelio commence life as carnivores and change to a diet in which seagrass is the primary carbon source. The dependence on animal matter, however, is always present. Due to the low percentage of nitrogen in Z. capricorni(2·5%) compared to zooplankton (9·1%) it appears that nitrogen from zooplankton is necessary throughout their life history with the carbon requirements for these fish coming chiefly from Z. capricorni.     

The purification and some properties of cocoa necrosis virus, a serotype of tomato black ring virus

Cocoa necrosis virus (CNV) was transmitted by sap inoculation to twelve of twenty-one species tested. It was propagated and assayed in Phaseolus vulgaris. Sap from P. vulgaris was infective after dilution to 10^-3but not 10^-4, after 10 min at 60 d?C but not 65 d?C, and after 4 but not 7 days at 20–24 d?C. Lyophilized sap from P. vulgaris was infective after 2 years in vacuo. Virus was prepared by extracting infected leaves of P. vulgaris with 0.1 M phosphate (pH 7.5) containing 0.05 M ethylene diamine tetra-acetate and 0.02 M thioglycollate. After clarification with n-butanol, virus was purified by precipitation with polyethylene glycol and several cycles of differential centrifugation. Such preparations were very infective and contained numerous particles, 24–26 nm in diameter with a hexagonal profile, which sedimented as two components with sedimentation coefficients (Sd?_20,w) of 101 S and 129 S. The absorption spectra of both components with maximum and minimum absorption at 259 and 240 nm respectively were typical of nucleoproteins (101 S component, A 260/280 = 1.63; A 260/240 = 1.40:129 S component, A260/280 = 1.78; A260/240 = 1.58) and indicated nucleic acid contents of ca. 35% for the 129 S component and ca. 20% for the 101 S component; values calculated from the sedimentation coefficients were 41 and 30% respectively. Only the 129 S component seemed to be infective and was not more so when mixed with 101 S component. Both components contained a single protein subunit weighing ca. 60000 daltons. Under certain conditions sap fractionated without butanol gave virus preparations containing empty protein shells (54 S) and small spherical particles (20–30 S) ca. 12 nm diameter. CNV is a serotype of tomato blackring virus and is distantly related to Hungarian chrome mosaic virus. The cryptogram of CNV is */*:*/(35–41):S/S:S/*.     

Production of precursors for anti-Alzheimer drugs: Asymmetric bioreduction in a packed-bed bioreactor using immobilized D. carota cells

(S)-1-Phenylethanol derivatives, which are the precursors of many pharmacological products, have also been used as anti-Alzheimer drugs. Bioreduction experiments were performed in a batch and packed-bed bioreactor. Then, the kinetics constants were determined by examining the reaction kinetics in the batch system with free and immobilized carrot cells. Also, the effective diffusion coefficient (D_e) of acetophenone in calcium alginate-immobilized carrot cells was investigated. Kinetics constants for free cells, which are intrinsic values, are reaction rate V_max?=?0.052?mmol?L^?1?min^?1, and constants of the Michaelis–Menten K_M?=?2.31?mmol?L^?1. Kinetics constants for immobilized cells, which are considered apparent values, are V_{max, app}?=?0.0407?mmol?L^?1 min^?1, K_{M, app}?=?3.0472?mmol?L^?1 for 2?mm bead diameter, and V_{max, app}?=?0.0453?mmol?L^?1 min^?1, K_{M, app}?=?4.9383?mmol?L^?1 for 3?mm bead diameter. Average value of effective diffusion coefficient of acetophenone in immobilized beads was determined as 1.97?×?10^?6?cm²?s^?1. Using immobilized carrot cells in an up-flow packed-bed reactor, continuous production of (S)-1-phenylethanol through asymmetric bioreduction of acetophenone was performed. The effects of the residence time and concentrations of substrate were investigated at pH 7.6 and 33°C. Enantiomerically pure (S)-1-phenylethanol (ee?>?99%) was produced with 75% conversion at 4-hr residence time.