Relationships between genotype x environment interactions and rank orders for a set of genotypes tested in different environments

Multilocation trials in plant breeding lead to cross-classified data sets with rows=genotypes and columns=environments, where the breeder is particularly interested in the rank orders of the genotypes in the different environments. Non-identical rank orders are the result of genotype x environment interactions. Not every interaction, however, causes rank changes among the genotypes (rank-interaction). From a breeder's point of view, interaction is tolerable only as long as it does not affect the rank orders. Therefore, the question arises of under which circumstances does interaction become rank-interaction. This paper contributes to our understanding of this topic. In our study we emphasized the detection of relationships between the similarity of the rank orders (measured by Kendall's coefficient of concordance W) and the functions of the diverse variance components (genotypes, environments, interaction, error). On the basis of extensive data sets on different agricultural crops (faba bean, fodder beet, sugar beet, oats, winter rape) obtained from registration trials (1985–1989) carried out in the Federal Republic of Germany, we obtained the following as main result: W ₂ ^g /( ₂ ^g + ₂ ^v ) where ₂ ^g =genotypic variance and ₂ ^v = ₂ ^ge + ₂ ^o /L with ₂ ^ge =interaction variance, ₂ ^o =error variance and L=number of replications.     

Probabilities of negative estimates of genetic variances

Summary The probability of negative analysis of variance estimates of genetic variance components due to sampling error (Ps) was investigated. The objectives were to evaluate the magnitude of Ps, to compare Ps for estimates of _A ² and _D ² , and to compare Ps for genetic variance component estimates from the nested and factorial mating designs. Ps was defined in terms of ratios of mean squares and the F distribution was used to calculate probabilities of the negative estimates. The results indicated that Ps is often greater than 0.20 for _D ² . It is generally lower for _A ² than for _D ² , and lower for the factorial mating design than the nested mating design.Technical Contribution No. 2589 from the South Carolina Agricultural Experiment Station, Clemson University     

Theoretical studies on the necessary number of components in mixtures

Summary Theoretical studies on the optimal numbers of components in mixtures (for example multiclonal varieties or mixtures of lines) have been performed according to phenotypic yield stability (measured by the parameter variance). For each component i, i = 1, 2,..., n, a parameter u_i with 0 u_i 1 has been introduced reflecting the different survival and yielding ability of the components. For the stochastic analysis the mean of each u_i is denoted by u ₁ and its variance by _i ² For the character total yield the phenotypic variance V can be explicitly expressed dependent on 1) the number n of components in the mixture, 2) the mean of the _i ² 3) the variance of the _i ² 4) the ratio and 5) the ratio _i ² /² where denotes the mean of the u _i and _u ² is the variance of the u _j. According to the dependence of the phenotypic stability on these factors some conclusions can be easily derived from this V-formula. Furthermore, two different approaches for a calculation of necessary or optimal numbers of components using the phenotypic variance V are discussed: A. Determination of optimal numbers in the sense that a continued increase of the number of components brings about no further significant effect according to stability. B. A reduction of b % of the number of components but nevertheless an unchanged stability can be realized by an increase of the mean of the u _i by 1% (with and _u ² assumed to be unchanged). Numerical results on n (from A) and 1 (from B) are given. Computing the coefficient of variation v for the character total yield and solving for the number n of components one obtains an explicit expression for n dependent on v and the factors 2.-5. mentioned above. In the special case of equal variances, _i ² = _o ² for each i, the number n depends on v, x = (₀/)² and y = (_u/)². Detailed numerical results for n = n (v, x, y) are given. For x 1 and y 1 one obtains n = 9, 20 and 79 for v = 0.30, 0.20 and 0.10, respectively while for x 1 and arbitrary y-values the results are n = 11, 24 and 95.This publication is an extended version of a lecture given at the 1984-EUCARPIA meeting (Section Biometrics in Plant Breeding) in Stuttgart-Hohenheim (Federal Republic of Germany)     

Genetic architecture of a heterotic cross between two populations of maize

Summary The nature and magnitude of variability in the interpopulation cross of Mezcla Amarillo Selection (MAS), an introduction from CIMMYT, Mexico, and J607, a population developed in India using indigenous, American, and Yugoslavian germplasm, were studied. Interpopulation progenies developed by following the North Carolina Design I were evaluated at two locations. The additive genetic variance component in interpopulation cross, _A(12) ² , and in one population assuming the other population as tester, _A12 ² and _A21 ² were significant for all the traits evaluated, namely ear length, ear girth, kernel rows and days to silk, with one exception. For kernel rows, the dominance variance component, _A(12) ² , was also significant but it was smaller than _A(12) ² . The variance component due to dominance X location interaction, _DL(12) ² , was significant for all traits except kernel rows. In the case of ear length and ear girth, _DL(12) ² was greater than the other components. _AL(12) ² , _AL12 ² and _AL21 ² were not significant for any trait. Expected genetic advance indicated a superiority of half-sib reciprocal recurrent selection over full-sib reciprocal recurrent selection.     

The<Emphasis Type="Italic"> ssgB</Emphasis> gene,encoding a member of the regulon of stress-response sigma factor σ<Superscript>H</Superscript>, is essential for aerial mycelium septation in<Emphasis Type="Italic"> Streptomyces coelicolor</Emphasis> A3(2)

The Streptomyces coelicolor A3(2) gene ssgB belongs to the regulon of stress-response sigma factor ^H. By integrative transformation via double cross-over, a stable null mutant of ssgB was obtained. This mutation had no obvious effect on vegetative growth, but critically affected aerial mycelium septation. The S. coelicolor ssgB mutant produced aerial hyphae without any signs of septation into spore compartments. The mutation was complemented in trans by wild-type ssgB including the ^H-dependent ssgBp promoter. The results proved that ssgB belongs a developmental branch of the ^H regulon.     

Foam behavior of biological media

Summary The surface tension and foaminess of (a) unlimited, (b) substrate limited, and (c) oxygen transfer limited growth media of Hansenula polymorpha were measured using methanol, ethanol or glucose as a substrate.The time dependence of can be described by the Avrami-Überreiter relationship: log (2.3 log V)=n log t+log b, where V = (_O – _eq/(_t – _eq, and _O, _t and _eq are at t_M=0, t_M=t and t_M (equilibrium value).The constants n and b are functions of the fermentation time t_F as long as the growth is unlimited but they are constant in the state of limited growth. With glucose substrate, the foaminess can be presented as a definite function of the time, t_DG, which is necessary to attain _eq. With alcohol as a substrate no definite (t_DG) function was found.Symbols b constant in Eq. (1) - n constant in Eq. (1) - S substrate concentration - T temperature - t_M time h (measured from the beginning of the determination of the surface tension ) - t_F cultivation time h (measured from the time of inoculation) - t_DG time (min) necessary to attain the equilibrium surface tension ) - X dry biomass concentration (gl^–1) - V (_O – _eq)/(_t – _eq) - V_S equilibrium volume of the foam (cm³) - V_G volumetric gas flow rate during the estimation of (cm³ s^–1) - vvm volumetric gas flow rate with regard to the volume of the medium (min^–1) - w_SG superficial gas velocity (cm s^–1) - _m maximum specific growth rate (h^–1) - V_S/V_G foaminess (s) - surface tension, mMm^–1 (milli Newton m^–1) - _O at t_M=0 - _eq equilibrium surface tension ( at t_M) - _t at t_M=t - HP probes from Hansenula polymorpha cultivation - NLG non limited growth - OTLG oxygen transfer limited growth - SLG substrate limited growth     

Membrane pathways for water and solutes in the toad bladder: II. Reflection coefficients of the water and solute channels

Summary Urea and water transport across the toad bladder can be separately activated by low concentrations of vasopressin or 8 Br-cAMP. Employing this method of selective activation, we have determined the reflection coefficient () of urea and other small molecules under circumstances in which the bladder was transporting urea or water. An osmotic method for the determination of was used, in which the ability of a given solute to retard water efflux from the bladder was compared to that of raffinose (=1.0) or water (=0). When urea transport was activated (low concentration of vasopressin), for urea and other solutes was low, (_urea,0.08–0.39;_acetamide, 0.55; _{ethylene glycol}, 0.60). When water transport was activated (0.1mm 8 Br-cAMP) _urea approached 1.0 _urea also approached 1.0 at high vasopressin concentrations. In a separate series of studies, _urea was determined in the presence of 2×10^–5 m KMnO₄ in the luminal bathing medium. Under these conditions, when urea transport is selectively blocked, _urea rose from a value of 0.12 to 0.89. Thus, permanganate appears to close the urea transport channel. These findings indicate that the luminal membrane channels for water and solutes differ significantly in their dimensions. The solute channels, limited in number, have relatively large radii. They carry a small fraction (approximately 10%) of total water flow. The water transport channels, on the other hand, have small radii, approximately the size of a water molecule, and exclude solutes as small as urea.     

A method for the estimation of gene flow parameters from a population structure caused by restricted gene flow and genetic drift

Summary A method has been developed which enables the estimation of the plant gene flow parameters _p (pollen dispersal), _s (seed dispersal) and t (outcrossing rate) from a selection-free continuously structured population in equilibrium. The method uses Wright's F-coefficients and introduces a new F-function which describes the genetic similarity as a function of the spatial distance. The method has been elaborated for wind pollinated plant species but can be modified for insect pollination and for animal species. In practice allozymes will provide for the necessary neutral genetic variation. The more loci used and the more intermediate the gene frequencies, the more reliable the results. For the estimation of _p and t together (when the outcrossing rate is not known) at least two chromosomally unlinked loci are required. The method for estimating _s depends on whether the plant species is annual or perennial. The mechanism of selfing has been analysed by the explanation of the value of t by three components: population density (d), pollen flow (_p) and relative fertilization potential of own pollen (Z). The concepts of neighbourhood size and isolation by distance, developed by Wright, who used a single gene flow parameter , have been extended to the situation which is realistic for seed plants, using all three parameters _p, _s and t. When _p is large with respect to _s, _s largely determines the value of the neighbourhood size, whereas _p is the most dominating factor in isolation by distance. The use of local effective population size and mean gene transport per generation instead of neighbourhood size and neighbourhood area, respectively, is proposed to avoid confusion. Computer simulations have been carried out to check the validity and the reliability of the method. Populations of 200 plants, using two or three loci with intermediate allele frequencies, gave good results in the calculation of _p with known value of t and of _s and N_e. With unknown t, especially with lower values of t, larger populations of at least 1,000 plants are necessary to obtain reasonably accurate results for _p and mean gene transport per generation M.Grassland Species Research Group Publication No. 81     

Free sigma subunit of Bacillus subtilis RNA polymerase binds to DNA

Summary The affinity of Bacillus subtilis RNA polymerase and subunits to DNA was examined by a non-denaturing polyacrylamide slab gel electrophoresis method which made it possible to resolve DNA-bound and free subunits. The results revealed that subunit, but not subunit had a relatively high affinity for double stranded DNA. The subunit was bound maximally to super-coiled pGR1-3 plasmid DNA at a mass ratio of /DNA of 0.7. With B. subtilis double stranded linear DNA one subunit was bound per approximately 1,000 base pairs. The -DNA complex was sufficiently stable for isolation by a molecular gel filtration column. The subunit had much higher affinity for super-coiled than for linear pGR1-3 DNA or for linear double stranded or denatured DNA from B. subtilis, E. coli, and calf thymus. These results indicate that the free B. subtilis subunit, in contrast to the E. coli subunit, can bind by itself to DNA.     

Simple diagnostic statistical tests of models for DNA substitution

The accuracy of models for DNA substitution used in phylogenetic analyses is becoming more important with the increasing availability and analysis of molecular sequence data. It is natural to look for ways of improving these models, and to do this in a planned manner it is useful to be able to identify features of sequences that may not be described adequately. In this paper, I describe three statistics which may give useful diagnostic information on departures from models' predictions. The statistical distributions of these statistics are discussed and simple significance tests are derived. These tests are based on the (estimated) phylogeny of the sequences and so have the advantage of using the information contained in this tree. Examples are given of the application of the new tests to Markov chain models describing the evolution of primate pseudogene sequences and small-subunit RNA sequences.Abbreviations b(N,p) binomial distribution of N trials, each with probability p of success - m(N,p ₁,p ₂, ..., p _r ) multinomial distribution of N trials, with r possible outcomes having probabilities p ₁, p ₂, ..., p_r, respectively - N(, ²) Normal distribution with mean and variance ² - p() Poisson distribution with mean - bp base pairs - cdf cumulative distribution function - i.i.d. independent, identical distribution     

Electric field-induced breakdown of lipid bilayers and cell membranes: A thin viscoelastic film model

Summary A simple viscoelastic film model is presented, which predicts a breakdown electric potential having a dependence on the electric pulse length which approximates the available experimental data for the electric breakdown of lipid bilayers and cell membranes (summarized in the reviews of U. Zimmermann and J. Vienken, 1982,J. Membrane Biol. 67:165 and U. Zimmermann, 1982,Biochim. Biophys. Acta 694:227). The basic result is a formula for the time of membrane breakdown (up to the formation of pores): =(/C)/( _m ² ₀ ² U ⁴/24Gh ³+T ²/Gh–1), where is a proportionality coefficient approximately equal to ln(h/2₀),h being the membrane thickness and ₀ the amplitude of the initial membrane surface shape fluctuation ( is usually of the order of unity), represents the membrane shear viscosity,G the membranes shear elasticity modules, _m the membrane relative permittivity, ₀=8.85×10^–12 Fm,U the electric potential across the membrane, the membrane surface tension andT the membrane tension. This formula predicts a critical potentialU _c ;U _c =(24Gh ³/ _m ² ₀ ² )^1/4 (for = andT=0). It is proposed that the time course of the electric field-induced membrane breakdown can be divided into three stages: (i) growth of the membrane surface fluctuations, (ii) molecular rearrangements leading to membrane discontinuities, and (iii) expansion of the pores, resulting in the mechanical breakdown of the membrane.     

Selection studies in sugarcane (Saccharum sp. hybrids)

Summary An approximate method to determine sample size for the estimation of population variance, ², is given. The estimate of ² is denoted as s² . Based on the assumption of a normal distribution for (s²/²–1), the sample size is approximately equal to 20,000 z² _p,/k²; where z is a standard normal deviate, p is the probability that s² ( 100¦s² – ²¦/²) is less than, or equal to, a critical value k, and k (measured as gDs²) is the desired precision of s² .The expected value of s², with respect to sample size, and the expected cumulative frequencies of s² over sample size for various k values are given. Their goodness of fit to the observed results was satisfactory except for populations that were different from normal. The observed values were taken from a study on four yield components in five sugarcane polycross progenies, grown in two contrasting environments over 2 years in three selection stages.The expected s² was found to be independent of the population coefficient of variance.Research suppoted in part by USDA, ARS, grant #12-14-5001-34. Published with the approval of the Director as Paper No. 412 in the Journal Series of the Experiment Station, Hawaiian Sugar Planters' Association.     

An experimental approach to evaluation of the relative hydrophobic character of biological liquids and tissues

Summary Total proteins extractable from a number of rat tissues were partitioned in the aqueous Ficoll-400-Dextran-70 biphasic system. The partition coefficient of the total proteins extractable from a given tissue, K, was shown to be a tissue-specific constant. The free energy of transfer of a CH₂ group from water to the aqueous solution of a given protein extract, (gCH₂), was calculated from the corresponding K-value using the correlation relationship between K and (gCH₂) reported earlier. It is suggested to use the parameter (gCH₂)-value as a measure of the relative hydrophobic character of biological fluids and tissues. The difference between the (gCH₂)-values for blood plasma medium and for a given tissue medium is used to quantify the difference in the relative hydrophobic character of the biological tissues and fluids under study. The possibilities to use the above characteristics in drug research are considered.     

Amber mutations in the structural gene for RNA polymerase sigma factor of Escherichia coli

Summary Amber mutants of Escherichia coli K-12 affected in the structural gene (rpoD) for th subunit of RNA polymerase have been obtained from a strain harboring a temperature-sensitive amber suppressor (supF-Ts6) which is active only at low temperatures. These mutants grow normally at low temperature (30°C) but do not grow at high temperature (42°C) due to the inability to synthesize factor. In one mutant studied in detail (rpoD40), the rate of -factor synthesis at 30°C is about half that of the wild type and is decreased to 10%–15% within 1 h of incubation at 42°C. The synthesis of core polymerase subunits or bulk protein is virtually unaffected at least for 2 h. The defect of the mutant in synthesis and growth at high temperature can be suppressed by any of the amber suppressors tested (supD, supE or supF). RNA-polymerase holoenzymes prepared from the mutant cells carrying each of the suppressors (grown at 42°C) exhibit different thermostabilities attributable to alterations in the factor. The reduced synthesis in the mutant is accompanied by the synthesis of polypeptide tentatively identified as amber fragment. These results as well as the genetic mapping data indicate that the amber mutation (rpoD40) resides within the structural gene for the factor and directly affects synthesis upon inactivation of the suppressor at high temperature.     

RNA polymerase sigma-related proteins in Escherichia coli: detection by antibodies against a synthetic peptide

Summary Antibodies were raised against a synthetic tetradecameric peptide with an amino acid sequence, DLIQEGNIGLMKAV, which corresponds to the most highly conserved region of bacterial RNA polymerase factors. In a Western-blot analysis of total Escherichia coli proteins, the antiserum reacted specifically with at least three proteins with apparent molecular weights of 75 kDa, 27 kDa and 23 kDa, in addition to the known factors (⁷⁰ and ³²). The majorities of ⁷⁰ and ³² were recovered as associated forms with the RNA polymerase on glycerol gradient centrifugation, while the other cross-reacting proteins were not. Unambiguous evidence was obtained which indicated that the intracellular level of ³² increased rapidly upon heatshock, at least in the strain containing high copy numbers of the rpoH gene.     

A comparative study of variation in codon 33 of the<Emphasis Type="Italic"> rpoS</Emphasis> gene in<Emphasis Type="Italic"> Escherichia coli</Emphasis> K12 stocks: implications for the synthesis of σ<Superscript>s</Superscript>

The Escherichia coli rpoS gene encodes an RNA polymerase sigma factor (sigma S or ^S) required for the expression of stationary-phase genes. In the first published rpoS sequence from E. coli K-12 codon 33 is given as CAG. However, several subsequent independent studies found the amber codon TAG at this position ( rpoSAm). Besides this amber codon, other codons such as TAT have also been found at this location in rpoS. Comparative genome analysis now leads us to propose TAG as the parental codon 33 in rpoS in E. coli K-12. Five different stocks of the strain W3110, which differ in the levels of ^S protein they express, were investigated. We sequenced the rpoS gene from these, and found a T at nucleotide position 97 in four out of the five stocks and a G at position 99 in three out of the five. W1485, a parental strain of W3110, and W3350, a derivative of W3110, are also rpoSAm mutants. Such rpoSAm mutants would be expected to show no RpoS activity. The retention of partial or intermediate ^S activity by suppressor-free rpoSAm mutants is therefore puzzling. We propose that a functional, N-terminally truncated, ^S (1–53^S) can be translated from a Secondary Translation Initiation Region (STIR) located downstream of the amber codon 33. It has recently been reported that a fragment of RpoS (1–53^S) that lacks the first 53 amino acids is functional when synthesized in vivo. Taken together, our results support the hypothesis that the original codon 33 of the rpoS gene in E. coli K-12 strains is the amber codon TAG.Communicated by W. Goebel     

Converging catabolism of 2,4,6-trinitrophenol (picric acid) and 2,4-dinitrophenol by Nocardioides simplex FJ2-1A

Initial F₄₂₀-dependent hydrogenation of 2,4,6-trinitrophenol(picric acid) generated the hydride -complex of picrate and finally the dihydride complex.With 2,4-dinitrophenol the hydride -complex of 2,4-dinitrophenolis generated. The hydride transferring enzyme system showed activity against several substituted2,4-dinitrophenols but not with mononitrophenols. A K_m-value of0.06 mM of the hydride transfer for picrate as substrate was found. The pH optimaof the NADPH-dependent F₄₂₀ reductase and for the hydride transferase were 5.5and 7.5, respectively. An enzymatic activity has been identified catalyzing the releaseof stoichometric amounts of 1 mol nitrite from 1 mol of the dihydride -complexof picrate. This complex was synthesized by chemical reduction of picrate and characterizedby ¹H and ¹³C NMR spectroscopy. The hydride -complex of 2,4-dinitrophenolhas been identified as the denitration product. The nitrite-eliminating activitywas enriched and clearly separated from the hydride transferring enzyme system byFPLC. 2,4-Dinitrophenol has been disproven as a metabolite of picrate (Ebert et al. 1999)and a convergent catabolic pathway for picrate and 2,4-dinitrophenol with thehydride -complex of 2,4-dinitrophenol as the common intermediate has been demonstrated.     

The distribution of genetic parameter estimates and confidence intervals from small disconnected diallels

The distributions of genetic variance components and their ratios (heritability and type-B genetic correlation) from 105 pairs of six-parent disconnected half-diallels of a breeding population of loblolly pine (Pinus taeda L.) were examined. A series of simulations based on these estimates were carried out to study the coverage accuracy of confidence intervals based on the usual t-method and several other alternative methods. Genetic variance estimates fluctuated greatly from one experiment to another. Both general combining ability variance (²_g) and specific combining ability variance (²_s) had a large positive skewness. For ²_g and ²_s, a skewness-adjusted t-method proposed by Boos and Hughes-Oliver (Am Stat 54:121–128, 2000) provided better upper endpoint confidence intervals than t-intervals, whereas they were similar for the lower endpoint. Bootstrap BCa-intervals (Efron and Tibshirani, An introduction to the bootstrap. Chapman & Hall, London 436 p, 1993) and Halls transformation methods (Zhou and Gao, Am Stat 54:100–104, 2000) had poor coverages. Coverage accuracy of Fiellers interval endpoint(J R Stat Soc Ser B 16:175–185, 1954) and t-interval endpoint were similar for both h² and r_B for sample sizes n10, but for n=30 the Fiellers method is much better.     

Calculations of one-, two- and three-bond nuclear spin-spin couplings in a model peptide and correlations with experimental data

Summary We present ab initio calculations of the Fermi contact term and experimental correlations of six coupling constants, ³J_H ^N _H , ¹J_{C H} , ²J_CH , ¹J_{C N}, ²J_{C N} and ¹J_CN, in a peptide as functions of the backbone dihedral angles, and . Given estimates of experimental uncertainties, we find semiquantitative experimental correlations for ³J_H ^N _H , ¹J_{C N} and ²J_{C N}, qualitative correlations for ¹J_{C H} and ²J_CH , but no experimental correlations of practical utility for ¹J_CN, owing to its complex dependence on at least four dihedral angles. Errors in the estimation of dihedral angles from X-ray crystallographic data for proteins, which result from uncertainties in atom-to-atom distances, place substantial limitations on the quantitative reliability of coupling constant calculations fitted to such data. In the accompanying paper [Edison, A.S. et al., J. Biomol. NMR, 4, 543–551] we apply the results of the coupling constant calculations presented here to the estimation of and angles in staphylococcal nuclease from experimental coupling constants.Abbreviations AO atomic orbital - BPTI basic pancreatic trypsin inhibitor (bovine) - CI-2 chymotrypsin inhibitor 2 - E.COSY exclusive correlation spectroscopy (Griesinger et al., 1986) - ⁿJ_AB single bond (n=1), geminal (n=2), or vicinal (n=3) coupling constant between nuclei A and B - LCAO linear combination of atomic orbitals - NBO natural bond orbital - n lone pair orbitals - bonding orbitals - ^* antibonding orbitals - dihedral angle or molecular orbital wave function; r², correlation coefficient - RHF restricted Hartree-Fock; rmsd, root-mean-square deviation - 3-21G and 6-31G^* molecular orbital basis set designations (Hehre et al., 1986)