The accuracy of varietal selection using factor analytic models for multi-environment plant breeding trials

Modeling of cultivar x trial effects for multienvironment trials (METs) within a mixed model framework is now common practice in many plant breeding programs. The factor analytic (FA) model is a parsimonious form used to approximate the fully unstructured form of the genetic variance-covariance matrix in the model for MET data. In this study, we demonstrate that the FA model is generally the model of best fit across a range of data sets taken from early generation trials in a breeding program. In addition, we demonstrate the superiority of the FA model in achieving the most common aim of METs, namely the selection of superior genotypes. Selection is achieved using best linear unbiased predictions (BLUPs) of cultivar effects at each environment, considered either individually or as a weighted average across environments. In practice, empirical BLUPs (E-BLUPs) of cultivar effects must be used instead of BLUPs since variance parameters in the model must be estimated rather than assumed known. While the optimal properties of minimum mean squared error of prediction (MSEP) and maximum correlation between true and predicted effects possessed by BLUPs do not hold for E-BLUPs, a simulation study shows that E-BLUPs perform well in terms of MSEP.

Molecular characterisation, pathogenesis and fungicide sensitivity of Pythium spp. from table beet (Beta vulgaris var. vulgaris) grown in the Lockyer Valley, Queensland

Table beet production in the Lockyer Valley of south-eastern Queensland is known to be adversely affected by soilborne root disease from infection by Pythium spp. However, little is known regarding the species or genotypes that are the causal agents of both pre- and post-emergence damping off. Based on RFLP analysis with HhaI, HinfI and MboI of the PCR amplified ITS region DNA from soil and diseased plant samples, the majority of 130 Pythium isolates could be grouped into three genotypes, designated LVP A, LVP B and LVP C. These groups comprised 43, 41 and 7% of all isolates, respectively. Deoxyribonucleic acid sequence analysis of the ITS region indicated that LVP A was a strain of Pythium aphanidermatum, with greater than 99% similarity to the corresponding P. aphanidermatum sequences from the publicly accessible databases. The DNA sequences from LVP B and LVP C were most closely related to P. ultimum and P. dissotocum, respectively. Lower frequencies of other distinct isolates with unique RFLP patterns were also obtained with high levels of similarity (>97%) to P. heterothallicum, P. periplocum and genotypes of P. ultimum other than LVP B. Inoculation trials of 1- and 4-week-old beet seedlings indicated that compared with isolates of the LVP B genotype, a higher frequency of LVP A isolates caused disease. Isolates with the LVP A, LVP B and LVP C genotypes were highly sensitive to the fungicide Ridomil MZ, which suppressed radial growth on V8 agar between approximately four and thirty fold at 5 μg/mL metalaxyl and 40 μg/mL mancozeb, a concentration far lower than the recommended field application rate.

Bearing capacity factor N-c under phi=0 condition for piles in clays

Bearing capacity factor N-c for axially loaded piles in clays whose cohesion increases linearly with depth has been estimated numerically under undrained (phi=0) condition. The Study follows the lower bound limit analysis in conjunction With finite elements and linear programming. A new formulation is proposed for solving an axisymmetric geotechnical stability problem. The variation of N-c with embedment ratio is obtained for several rates of the increase of soil cohesion with depth; a special case is also examined when the pile base was placed on the stiff clay stratum overlaid by a soft clay layer. It was noticed that the magnitude of N-c reaches almost a constant value for embedment ratio greater than unity. The roughness of the pile base and shaft affects marginally the magnitudes of N-c. The results obtained from the present study are found to compare quite well with the different numerical solutions reported in the literature.

Improved bounds on the radius and curvature of the K pi scalar form factor and implications to low-energy theorems

We obtain stringent bounds in the < r(2)>(K pi)(S)-c plane where these are the scalar radius and the curvature parameters of the scalar K pi form factor, respectively, using analyticity and dispersion relation constraints, the knowledge of the form factor from the well-known Callan-Treiman point m(K)(2)-m(pi)(2), as well as at m(pi)(2)-m(K)(2), which we call the second Callan-Treiman point. The central values of these parameters from a recent determination are accomodated in the allowed region provided the higher loop corrections to the value of th form factor at the second Callan-Treiman point reduce the one-loop result by about 3% with F-K/F-pi = 1.21. Such a variation in magnitude at the second Callan-Treiman point yields 0.12 fm(2) less than or similar to < r(2)>(K pi)(S) less than or similar to 0.21 fm(2) and 0.56 GeV-4 less than or similar to c less than or similar to 1.47 GeV-4 and a strong correlation between them. A smaller value of F-K/F-pi shifts both bounds to lower values.

New constraints on the pion EM form factor using Pi `(-Q(2))

We study the constraints arising on the expansion parameters c and d of the pion electromagnetic form factor from the inclusion of pure spacelike data and the phase of timelike data along with one spacelike datum, using as input the first derivative of the QCD polarization amplitude Pi'(-Q(2)). These constraints when combined with other analyses, provide a valuable check on a determination of c due to Guo et al. and on our previous work where pionic contribution to the (g - 2) of the muon was used as the input. This work further illustrates the power of analyticity techniques in form factor analysis.

Type II beta-turn conformation of pivaloyl-L-prolyl-alpha-aminoisobutyryl-N-methylamide: Theoretical, spectroscopic, and X-ray studies

Pivaloyl-L-Pro-Aib-N-methylamide has been shown to possess one intramolecular hydrogen bond in (CD3)2SO solution, by 1H-nmr methods, suggesting the existence of beta -turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II beta-turn conformations are about 2 kcal mol-1 more stable than Type III structures. A crystallographic study has established the Type II beta-turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, beta = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II -turn conformation is stabilized by an intramolecular 4 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are Pro = -57.8°, Pro = 139.3°, Aib = 61.4°, and Aib = 25.1°. The Type II beta-turn conformation for Pro-Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.

Isolation and functional characterization of a lycopene beta-cyclase gene that controls fruit colour of papaya (Carica papaya L.).

The colour of papaya fruit flesh is determined largely by the presence of carotenoid pigments. Red-fleshed papaya fruit contain lycopene, whilst this pigment is absent from yellow-fleshed fruit. The conversion of lycopene (red) to beta-carotene (yellow) is catalysed by lycopene beta-cyclase. This present study describes the cloning and functional characterization of two different genes encoding lycopene beta-cyclases (lcy-beta1 and lcy-beta2) from red (Tainung) and yellow (Hybrid 1 B) papaya cultivars. A mutation in the lcy-beta2 gene, which inactivates enzyme activity, controls lycopene production in fruit and is responsible for the difference in carotenoid production between red and yellow-fleshed papaya fruit. The expression level of both lcy-beta1 and lcy-beta2 genes is similar and low in leaves, but lcy-beta2 expression increases markedly in ripe fruit. Isolation of the lcy-beta2 gene from papaya, that is preferentially expressed in fruit and is correlated with fruit colour, will facilitate marker-assisted breeding for fruit colour in papaya and should create possibilities for metabolic engineering of carotenoid production in papaya fruit to alter both colour and nutritional properties.

Theoretical studies on the conformation of beta-D-N-acetyl neuraminic acid (sialic acid)

The possible conformations of sialic acid were analysed using semi-empirical potential functions. The solid state conformation has approx. 0.2 kcal/mol higher energy than the minimum energy conformation. These studies suggest that in solution sialic acid may exist preponderantly in two different conformations which differ in the orientation of the terminal hydroxymethyl group of glycerol side-chain. The present model is consistent with 1H- and 13C-NMR data, but differs from the earlier models.

beta.-Turn conformation of N-acetyl-L-prolylglycyl-L-phenylalanine. Crystal structure and solution studies

Pro-Gly segments in peptides and proteins are prone to adopt the 0-turn conformation. This paper reports experimental data for the presence of this conformation in a linear tripeptide N-acetyl-L-prolylglycyl-L-phenylalanineb oth in the solid state and in solution. X-ray diffraction data on the tripeptide crystal show that it exists in the type I1 0-turn conformation. CD and proton NMR data show that this conformation persists in trifluoroethanol and methanol solutions in equilibrium with the nonhydrogen-bonded structures. Isomerization around the acetyl-prolyl bond is seen to take place in dimethyl sulfoxide solutions of the tripeptide.

Constant factor incremental delta modulator

This paper presents a new algorithm for the step-size change of instantaneous adaptive delta modulator. The present strategy is such that the step-size at any sampling instant can increase or decrease by either of the two constant factors or can remain the same, depending upon the combination of three or four most recent output bits. The quantizer has been simulated on a digital computer, and its performance compared with other quantizers. The figure of merit used is the SNR with gaussian signals as the input. The results indicate that the new design can give an improved SNR over a wider dynamic range and fast response to step inputs, as compared to the earlier systems.

Determination of mode 1 notch stress intensity factor by the photoelastic technique

The structural integrity of any member subjected to a load gets impaired due to the presence of cracks or crack-like defects. The notch severity is one of the several parameters that promotes the brittle fracture. The most severe one is an ideal crack with infinitesimal width and infinitesimal or zero root radius. Though analytical investigations can handle an ideal crack, experimental work, either to validate the analytical conclusions or to impose the bounds, needs to be carried out on models or specimens containing the cracks which are far from the ideal ones. Thus instead of an ideal crack with infinitesimal width the actual model will have a slot or a slit of finite width and instead of a crack ending in zero root radius, the model contains a slot having a finite root radius. Another factor of great significance at the root is the notch angle along which the transition from the slot to the root takes place. This paper is concerned with the photoelastic determination of the notch stress intensity factor in the case of a “crack” subjected to Mode 1 deformation.

The modes of binding methyl-alpha (and beta)-D-glucopyranosides and some of their derivatives to concanavalin A--a theoretical approach

The probable modes of binding of Methyl--alpha (and beta)-D-glucopyranosides and some of their derivatives to concanavalin A have been proposed from theoretical studies. Theory predicts that beta-MeGlcP can bind to ConA in three different modes whereas alpha-MeGlcP can bind only in one mode. beta-MeGlcP in its most favourable mode of binding differs from alpha-MeGlcP in its alignment in the active-site of the lectin where it binds in a flipped or inverted orientation. Methyl substitution at the C-2 atom of the alpha-MeGlcP does not significantly affect the possible orientations of the sugar in the active-site of the lectin. Methyl substitution at C-3 or C-4, however, affects the allowed orientations drastically leading to the poor inhibiting power of Methyl-3-O-methyl-alpha-D-glucopyranoside and the inactivity of Methyl-4-O-methyl-alpha-D-glycopyranoside. These studies suggest that the increased activity of the alpha-MeGlcP over beta-MeGlcP may be due to the possibility of formation of better hydrogen bonds and to hydrophobic interactions rather than to steric factors as suggested by earlier workers. These models explain the available NMR and other binding studies.