Atom ordering in cuboctahedral Ni-Al nanoalloys

Energy calculations have been carried out on high-symmetry cuboctahedral Ni-Al nanoalloy clusters, of varying composition, with the interatomic interactions modelled by the Gupta many-body potential. Relaxations of cuboctahedral fragments cut from the bulk lattice of Ni₃Al, with 13-561 atoms, were undertaken, as were relaxations of high symmetry clusters with 55 and 147 atoms. The lowest energy isomers were found to be dominated by three factors: the tendency toward mixing due to the favourable energy of mixing, Δ_mixE; the size difference between nickel and aluminium; and the higher cohesive and surface energy of nickel compared to aluminium. The latter two factors favour Al-segregation to the surface. The most stable Ni:Al composition approaches 3:1 for larger clusters.     

A quantitative structure-activity relationship study for structurally diverse HIV-1 protease inhibitors: contribution of conformational flexibility to inhibitory activity

In this study, we investigated by linear regression model the SAR data of the 15 HIV-1 protease inhibitors possessing structurally diverse scaffolds. First, a regression model was developed only using the enzyme-inhibitor interaction energy as a term of the model, but did not provide a good correlation with the inhibitory activity (R² = 0.580 and Q² = 0.500). Then, we focused on the conformational flexibility of the inhibitors which may represent the diversity of the inhibitors, and added two conformational parameters into the model, respectively: the number of rotatable bonds of ligands (ΔSrot) and the distortion energy of ligands (ΔElig). The regression model by adding ΔElig successfully improved the quality of the model (R² = 0.771 and Q² = 0.713) while the model with ΔSrot was unsuccessful. The prediction for a training inhibitor by the ΔElig model also showed good agreement with experimental activity. These results suggest that the conformational flexibility of HIV-1 protease inhibitors directly contributes to the enzyme inhibition.     

Unusual Role of the 3-OH Group of Oligosaccharide Substrates in the Mechanism of Bacillus 1,3-1,4-β-glucanase

Abstract

In the mechanism of retaining β-glycosidases, the 2-hydroxyl group of the substrate in the monosaccharyl unit involved in catalysis (subsite -1) is beleived to play an important role through hydrogen bonding interactions with protein residues that are optimized at the transition state. Commonly, removal of the 2-OH group of the substrate results in a 10–12 kcal·mol^-1 transition state destabilization. However, this effect seems not to be general as reported here for Bacillus 1,3-1,4-β-glucanase, a family 16 retaining endo-glycosidase. A p-nitrophenol 2-deosxy tetrasaccharide substrate was synthesized to probe the involvement of the 2-OH group in catalysis. Comparative kinetics with wild-type and subsite +1 mutants show that the 2-deoxy analog is a better substrate than the corresponding 2-hydroxy substrate. It is tentatively proposed that the 2-deoxy analog adopts a different conformation upon binding that compensates for the lack of the 2-OH substituent.     

THE GENOMIC TRAJECTORY OF HYBRID SWARMS: OUTCOMES OF REPEATED CROSSES BETWEEN POPULATIONS OF TIGRIOPUS CALIFORNICUS

Introgressive hybridization between genetically divergent populations is an important evolutionary process. The degree to which repeated hybridization events between the same parental taxa lead to similar genomic outcomes is unknown. This study addressed this question by following genomic trajectories of replicate hybrid swarms of the copepod Tigriopus californicus over many generations of free mating. Swarm composition was determined both by differential reproductive success of founder individuals and subsequent selection on hybrid genotypes. For one cross, between two populations showing differential fitness in the laboratory and no hybrid breakdown, the genetic trajectory was highly repeatable: replicates rapidly became dominated by alleles from the fitter parent. In a second cross, between two populations showing similar fitness and significant F2 hybrid breakdown, alleles from alternative populations dominated different replicates. Swarms exhibited a general temporal trend of decreasing cytonuclear mismatch. Some patterns of differential introgression across the genome were strikingly congruent amongst swarm replicates, both within and between cross types, and reflected patterns of segregation distortion previously observed within controlled crosses between the same parental populations. Differences in heterozygosity between the sexes, and evidence for a previously suspected sex‐distortion locus, suggest that complex interactions between sex and genotype influence hybrid swarm outcome.     

Detection of Architectural Distortion in Prior Mammograms via Analysis of Oriented Patterns

We demonstrate methods for the detection of architectural distortion in prior mammograms of interval-cancer cases based on analysis of the orientation of breast tissue patterns in mammograms. We hypothesize that architectural distortion modifies the normal orientation of breast tissue patterns in mammographic images before the formation of masses or tumors. In the initial steps of our methods, the oriented structures in a given mammogram are analyzed using Gabor filters and phase portraits to detect node-like sites of radiating or intersecting tissue patterns. Each detected site is then characterized using the node value, fractal dimension, and a measure of angular dispersion specifically designed to represent spiculating patterns associated with architectural distortion.Our methods were tested with a database of 106 prior mammograms of 56 interval-cancer cases and 52 mammograms of 13 normal cases using the features developed for the characterization of architectural distortion, pattern classification via quadratic discriminant analysis, and validation with the leave-one-patient out procedure. According to the results of free-response receiver operating characteristic analysis, our methods have demonstrated the capability to detect architectural distortion in prior mammograms, taken 15 months (on the average) before clinical diagnosis of breast cancer, with a sensitivity of 80% at about five false positives per patient.     

Improving enantiomeric resolutions by avoiding peak distortion effects in on‐line coupled liquid chromatography to gas chromatography

In this work, we study the effect of different variables affecting elution profile distortion on the enantiomeric resolution eventually achievable when working with on‐line coupled liquid chromatography to gas chromatography (LC‐GC). Specifically, the proposed configuration combines achiral reversed‐phase liquid chromatography (RPLC) and chiral gas chromatography (enantio‐GC), with heptakis‐(2,3,6‐tri‐O‐methyl)‐β‐cyclodextrin as enantioselective stationary phase to analyse target fractions transferred (from LC to GC) via the through oven transfer adsorption desorption (TOTAD) interface. The high degree of orthogonality resulting from the combination of two chromatographic columns having very different separation mechanisms (and also requiring mobile phases in distinct physical states), as well as integration of the sample preparation step in the first dimension of the system, significantly contributed to exploit the performance of the proposed two‐dimensional approach. Occasional adverse effects, which may result in severe peak distortions during LC‐GC analysis and could be explained by flow instabilities due to viscous fingering, are circumvented by using the outstanding capacity of the TOTAD interface for achieving effective elimination of the eluent arriving from the LC preseparation.     

Selfish male‐determining element favors the transition from hermaphroditism to androdioecy

According to the current, widely accepted paradigm, the evolutionary transition from hermaphroditism toward separate sexes occurs in two successive steps: an initial, intermediate step in which unisexual individuals, male or female, sterility mutants coexist with hermaphrodites and a final step that definitively establishes dioecy. Two nonexclusive processes can drive this transition: inbreeding avoidance and reallocation of resources from one sexual function to the other. Here, we report results of controlled crosses between males and hermaphrodites in Phillyrea angustifolia, an androdioecious species with two mutually intercompatible, but intraincompatible groups of hermaphrodites. We observed different segregation patterns that can be explained by: (1) epistatic interactions between two unlinked diallelic loci, determining sex and mating compatibility, and (2) a mutation with pleiotropic effects: female sterility, full compatibility of males with both hermaphrodite incompatibility groups, and complete male‐biased sex‐ratio distortion in one of the two groups. Modeling shows that these mechanisms can explain the high frequency of males in populations of P. angustifolia and can promote the maintenance of androdioecy without requiring inbreeding depression or resource reallocation. We thus argue that segregation distortion establishes the right conditions for the evolution of cryptic dioecy and potentially initiates the evolution toward separate sexes.     

偏分离分子标记的作图方法

对取自MAPMAKER软件小鼠F_2群体(含333个体)的5个RFLP连锁标记数据作了共显性分子标记偏分离的分析。先确定选择类型的方程组(配子或合子),随后采用Newton-Raphson迭代法估算标记间的重组值。在构建分子标记遗传图谱时,如果两个相邻标记均存在偏分离,最好采用纳入偏分离因子的估算方法。在估计F_2群体标记间偏分离重组距离上,用连续x~2检测方法比传统x~2检测更为准确。     

Effects of genotype variation in the cultivated rice species on the biology and galling characteristics of the African rice gall midge,Orseolia oryzivora (Diptera: Cecidomyiidae)

This study assessed the effects of genotype variations in two cultivated rice species: Oryza glaberrima and Oryza sativa on the biology and galling characteristics of the African rice gall midge (AfRGM), Orseolia oryzivora Harris and Gagné. The study was conducted in the screen house at ambient temperature (27 ± 3°C), 70 ± 5% relative humidity and 12:12 h photoperiod. Shoot galling, the most visible response of rice genotypes to attack by the insect, was greatly suppressed, being only 0.7 cm long in the O. glaberrima genotypes compared to 34 cm in the O. sativa species. Larval mortality (70–88%) in the O. glaberrima genotypes was significantly higher at the first instar compared to O. sativa. Gall setting was confirmed to be an irredeemable tiller loss. Even in the susceptible O. sativa genotypes, where many larvae may colonize a tiller, only one survived to the second instar. Resistant and susceptible rice genotypes had significantly different effects on the development and reproductive anatomy of the AfRGM. The female reproductive anatomy which consists of two ovaries, each with a potential complement of 192 eggs was affected by interspecific variation in rice genotypes causing reduced potential fecundity (32); morphological distortion, 60% reduction of egg size of F1 emergent in O. glaberrima compared to emergent from the susceptible O. sativa genotypes.