On the Effect of Unbalancedness and Heteroscedasticity on the ANOVA Estimator of Group Variance Component in One-Way Random Model

The expression for rth cumulant of ANOVA estimator of group variance component is derived in the One-way unbalanced random model under heteroscedasticity. The expression is used to study the effect of unbalancedness and heteroscedasticity on the mean and variance of the estimator, numerically. The computed results reveal that the unbalancedness and heteroscedasticity have a combined effect on the mean and variance of the estimator. For certain situations of unequal group sizes and error variances, the mean and variance of the estimator are increased and for certain other situations the values are decreased.     

On Two Measures of Unbalancedness in a One-Way Model and Their Relation to Efficiency

This paper discusses two measures of unbalancedness in a one-way model and shows that for a given statistical procedure they may serve as measures of efficiency of a design. They also allow to compare for example estimation methods for variance components in designs with a fixed level of unbalancedness.     

On the Estimation of Heritability from Unbalanced Data

The distribution and moments, of ANOVA estimator of heritability are given under unbalanced random model. These expressions are used to investigate the effect of unbalancedness on the bias and variance/MSE of the estimator and also the validity of certain approximations for its variance, numerically. The computed results reveal that the unbalancedness increases both the bias and variance/MSE of the estimator and the Smith-approximation for the variance of the estimator provides better accuracy.     

Almost Unbiased Ratio and Product Type Estimators: A New Approach

In this paper, we have proposed a new method, consisting of a linear variety of the estimators and a linear constraint to remove the bias appearing in the estimators of the ratio R = Y/X and product P = YX. The percent relative efficiency of proposed estimators has also been demonstrated with numerical illustrations.     

Imbalance and its Influence on Variance Component Estimation

A measure of imbalance has been defined for the one-way classification (Model II) in order to quantify the degree of imbalance. Using the ANOVA and MINQUE procedures we consider the variances and relative efficiencies of the estimators of σ²_a as functions of the measure of imbalance. We propose a method for generating all the designs which are possible from a given number of observations and a given number of groups. Numerical results for special types of designs show the influence of imbalance on the variance and relative efficiency of an estimator for σ^z_a.     

Activity, stability, and unfolding of reconstituted horseradish peroxidase with modified heme

Heme-propionates of horseradish peroxidase (HRP) were esterified by p-nitrophenol, phenol and p-methylphenol to change its electron character and to increase its hydrophobicity. These synthetic hemes were inserted apo-HRP to give a novel HRP, respectively. Of the three reconstituted HRPs, reconstituted HRP with p-nitrophenol-modified heme derivative had a larger initial rate, affinity, catalytic efficiency and substrate-binding efficiency than native HRP in aqueous buffer and some solvents. The reconstituted HRPs showed higher thermostability and tolerance of DMF because of the increase of the hydrophobicity of the active site. Changing the electron character of the aromatic moieties linked at each terminal of the two heme-propionates can control activity and stability of HRP. The initial rate, affinity, catalytic efficiency and substrate-binding efficiency increased with the increases of electron-withdrawing efficiency of substituents at 4-position of the phenolic used to synthesize the heme derivatives, contrariwise, the stability decreased. The modifications resulted in the increase in the temperature (T_m) at the midpoint of thermal denaturation and the decreases in both enthalpy and entropy change at T_m. The changes of catalytic properties and stabilities are related to the changes of the conformation of HRP. The modification changed the environment of heme and tryptophan, increased α-helix content of HRP. The present work demonstrates that enhancement of the hydrophobicity and the electron-withdrawing efficiency of heme improves the activity and stability of HRP.     

Effect of a Bacillus subtilis strain on flax protection against Fusarium oxysporum and its impact on the root and stem cell walls

In Normandy, flax is a plant of important economic interest because of its fibres. Fusarium oxysporum, a telluric fungus, is responsible for the major losses in crop yield and fibre quality. Several methods are currently used to limit the use of phytochemicals on crops. One of them is the use of plant growth promoting rhizobacteria (PGPR) occurring naturally in the rhizosphere. PGPR are known to act as local antagonists to soil‐borne pathogens and to enhance plant resistance by eliciting the induced systemic resistance (ISR). In this study, we first investigated the cell wall modifications occurring in roots and stems after inoculation with the fungus in two flax varieties. First, we showed that both varieties displayed different cell wall organization and that rapid modifications occurred in roots and stems after inoculation. Then, we demonstrated the efficiency of a Bacillus subtilis strain to limit Fusarium wilt on both varieties with a better efficiency for one of them. Finally, thermo‐gravimetry was used to highlight that B. subtilis induced modifications of the stem properties, supporting a reinforcement of the cell walls. Our findings suggest that the efficiency and the mode of action of the PGPR B. subtilis is likely to be flax variety dependent.     

Carbon isotopes and water use efficiency: sense and sensitivity

We revisit the relationship between plant water use efficiency and carbon isotope signatures (δ¹³C) of plant material. Based on the definitions of intrinsic, instantaneous and integrated water use efficiency, we discuss the implications for interpreting δ¹³C data from leaf to landscape levels, and across diurnal to decadal timescales. Previous studies have often applied a simplified, linear relationship between δ¹³C, ratios of intercellular to ambient CO₂ mole fraction (C _i/C _a), and water use efficiency. In contrast, photosynthetic ¹³C discrimination (Δ) is sensitive to the ratio of the chloroplast to ambient CO₂ mole fraction, C _c/C _a (rather than C _i/C _a) and, consequently, to mesophyll conductance. Because mesophyll conductance may differ between species and over time, it is not possible to determine C _c/C _a from the same gas exchange measurements as C _i/C _a. On the other hand, water use efficiency at the leaf level depends on evaporative demand, which does not directly affect Δ. Water use efficiency and Δ can thus vary independently, making it difficult to obtain trends in water use efficiency from δ¹³C data. As an alternative approach, we offer a model available at to explore how water use efficiency and ¹³C discrimination are related across leaf and canopy scales. The model provides a tool to investigate whether trends in Δ indicate changes in leaf functional traits and/or environmental conditions during leaf growth, and how they are associated with trends in plant water use efficiency. The model can be used, for example, to examine whether trends in δ¹³C signatures obtained from tree rings imply changes in tree water use efficiency in response to atmospheric CO₂ increase. This is crucial for predicting how plants may respond to future climate change. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A novel strategy for analysis of gene homologues and segmental genome duplications

Transformation-associated recombination (TAR) cloning allows selective isolation of a desired chromosomal region or gene from complex genomes. The method exploits a high level of recombination between homologous DNA sequences during transformation in the yeast Saccharomyces cerevisiae. We investigated the effect of nonhomology on the efficiency of gene capture and found that up to 15% DNA divergence did not prevent efficient gene isolation. Such tolerance to DNA divergence greatly expands the potential applications of TAR cloning for comparative genomics. In this study, we were able to use the technique to isolate nonidentical chromosomal duplications and gene homologues.     

Some features of feeding,respiration and energy conversion of Dapnia Magna

Some results of studies with Daphnia magna are presented. These results can be used as background information for toxicologists, but the techniques referred to might well be used for toxicity tests. Daphnia magna is a filter-feeder. With the Coulter Counter it was shown that the feeding mechanism is aselective for size of the food particles. It was also shown that algal cells can pass the gut of Daphnia magna several times before being completely digested. The uptake of food is proportional to the food concentration up to a critical concentration. Above this concentration the food uptake is constant. Respiration is also dependent on the food concentration, and has a maximum value at food concentrations near the critical concentration of the feeding process. Growth efficiency is independent of the food concentration. The effect of temperature on the feeding process is different for low and high food concentrations. Growth efficiency is maximal at 10°C and above 22°C growth efficiency was negative, which means that the population cannot survive under the experimental conditions used, at temperatures above 22°C.     

Determination of aphid transmission efficiencies for N, NTN and Wilga strains of Potato virus Y

Potato virus Y (PVY, genus Potyvirus, family Potyviridae) causes high economic losses worldwide, especially in the production of seed potatoes (Solanum tuberosum). PVY control systems rely on measuring virus pressure and vector pressure in the field. Calculation of the vector pressure is based on the relative efficiency factors (REFs) of aphid species. These REFs express the transmission efficiency of aphid species in relation to the transmission efficiency of Myzus persicae, the most efficient vector of PVY. In this paper, we report on the determination of aphids' relative transmission efficiency factors (REFs) for isolates of the PVY strains PVY^N, PVY^NTN and PVY^N-Wi. Biotype Mp2 of M. persicae was tested for its transmission efficiency for six PVY isolates (one PVY^N, three PVY^NTN and two PVY^N-Wi isolates) and showed comparable average transmission efficiencies for all isolates. The transmission rate of this biotype for the six PVY isolates was set to 1 and Mp2 was used as an internal control in transmission experiments to determine the REFs of three other biotypes of M. persicae and 16 other aphid species (three biotypes per species when available) for the six PVY isolates. Comparing the calculated REFs for PVY^N with the REFs reported in the previous century for PVY^N, we observe overall comparable REFs, except for Aphis fabae, Aphis spp., Hyperomyzus lactucae, Macrosiphum euphorbiae and Rhopalosiphum padi, which have a lower REF in our experiments, and Aphis frangulae and Phorodon humuli, which have now a higher REF. Comparing the new REFs found for the PVY^NTN strains with the new REFs for PVY^N, we observe that they are overall comparable, except for A. frangulae (0.17 compared with 0.53) and Schizaphis graminum (0.05 compared with 0.00). Comparing the REFs calculated for PVY^N-Wi with those calculated for PVY^N, we can observe six aphid species with higher REFs (Acyrthosiphon pisum, A. fabae, Aphis nasturtii, Aphis spp., P. humuli and R. padi). Only the species A. frangulae shows a lower REF for PVY^N-Wi compared with the transmission efficiency of PVY^N. Three aphid species (Aulacorthum solani, Myzus ascalonicus and S. graminum) for which no REF was determined earlier were found to be capable to transmit PVY and their REFs were determined.     

贵州喀斯特森林三种植物对不同坡位环境的光合生理响应

该研究以贵州普定喀斯特森林中、下坡位生长的构树( Broussonetia papyrifera)、朴树( Celtis sinensis)和光滑悬钩子( Rubus tsangii)为材料,通过对碳酸酐酶( CA)活性、光合作用日变化、净光合速率对CO2与光的响应曲线、叶绿素荧光特性以及稳定碳同位素组成等指标的测定,进而对比分析三种植物不同的光合生理响应特性。结果表明：构树光合作用过程的无机碳源既可来自大气中的CO2,也可以在气孔部分闭合的情况下利用细胞内的HCO3－,下坡位的构树较高的CA活性使其利用HCO3－的效率会更高,并能在较低光强下具有较高的光能利用效率。这可能与下坡位的构树具有较高的CA活性有关,对下坡位具有更好的适应性。朴树光合无机碳的同化能力最低,且光合无机碳源较单一,主要利用大气CO2,其较慢的生长速率使其对无机碳的需求最低,且能保持较稳定的无机碳同化速率。相对来说,中坡位的朴树具有相对较高的净光合速率和光能利用效率,对中坡位表现出较好的适应性。光滑悬钩子主要利用大气中的CO2进行光合作用。中坡位的光滑悬钩子具有较强的光能利用效率,并表现出较高的净光合速率,光滑悬钩子对中坡位同样表现出较好的适应性。该研究结果为喀斯特生态脆弱区植被重建过程中树种的选择及合理配置提供了科学依据。     

Enhancing plasmid transformation efficiency and enabling CRISPR-Cas9/Cpf1-based genome editing in Clostridium tyrobutyricum

Clostridium tyrobutyricum ATCC 25755 is known as a natural hyper-butyrate producer with great potentials as an excellent platform to be engineered for valuable biochemical production from renewable resources. However, limited transformation efficiency and the lack of genetic manipulation tools have hampered the broader applications of this micro-organism. In this study, the effects of Type I restriction-modification system and native plasmid on conjugation efficiency of C. tyrobutyricum were investigated through gene deletion. The deletion of Type I restriction endonuclease resulted in a 3.7-fold increase in conjugation efficiency, while the additional elimination of the native plasmid further enhanced conjugation efficiency to 6.05 ± 0.75 × 10³ CFU/ml-donor, which was 15.3-fold higher than the wild-type strain. Fermentation results indicated that the deletion of those two genetic elements did not significantly influence the end-products production in the resultant mutant ΔRMIΔNP. Thanks to the increased conjugation efficiency, the CRISPR-Cas9/Cpf1 systems, which previously could not be implemented in C. tyrobutyricum, were successfully employed for genome editing in ΔRMIΔNP with an efficiency of 12.5–25%. Altogether, approaches we developed herein offer valuable guidance for establishing efficient DNA transformation methods in nonmodel micro-organisms. The ΔRMIΔNP mutant can serve as a great chassis to be engineered for diverse valuable biofuel and biochemical production.     

单碱基编辑系统介导欧拉藏绵羊GDF9、FecB多胎基因的定点突变

本研究旨在利用单碱基编辑系统(single base editing system)实现欧拉藏绵羊成纤维细胞FecB和GDF9基因靶位点A到G和C到T的碱基替换并检测其编辑效率。首先设计合成靶向欧拉藏绵羊FecB和GDF9基因的sgRNA序列,再分别连接至epi-ABEmax、epi-BE4max质粒,构建载体并电转至欧拉藏绵羊成纤维细胞,最后对阳性细胞FecB和GDF9基因进行Sanger测序鉴定靶位点突变结果,并通过T-A克隆估算单碱基编辑系统的编辑效率。结果显示获得了靶向欧拉藏绵羊FecB和GDF9基因的sgRNA,并构建使欧拉藏绵羊FecB和GDF9基因单碱基突变的载体,FecB基因靶位点编辑效率为39.13%,GDF9基因靶位点(G260、G721、G1184)编辑效率分别为10.52%、26.67%和8.00%。本研究运用单碱基编辑系统在欧拉藏绵羊成纤维细胞上实现了FecB和GDF9基因靶位点突变,为改良欧拉藏绵羊一胎多羔的繁殖性状奠定理论基础。     

Testing the resource‐matching hypothesis in the mast seeding tree Nothofagus truncata (Fagaceae)

Abstract: The genus Nothofagus in New Zealand and Australia exhibits strong mast seeding (i.e. highly variable seed crops between years). Seed crop variation is synchronized within and between species over large spatial scales, and results in greatly increased wind pollination efficiency which could provide a selective benefit favouring the maintenance of mast seeding. However, the null hypothesis (that plants simply match their reproductive effort to the variable resources available each year) has not been tested in Nothofagus. Here we use a 33‐year dataset on seedfall and wood ring increments for 19 individual Nothofagus truncata trees at Orongorongo, New Zealand, to test for the presence of switching (exaggeration of seedfall variability by diverting resources into, then out of, reproduction). A generalized least squares model explained 40.7% of the variance in standardized ring widths, using six weather variables (absolute minimum temperatures in March (lag 0) April (lag 0 and lag 1), May (lag 0) and rainfall in November and February (lag 0) ) and seedfall. Seedfall had a negative relationship with the current year's ring widths even after controlling for all significant weather variables. This shows that switching is occurring in N. truncata within individuals among years, and therefore that masting in this species is the result of selective forces such as increased wind pollination efficiency. As this result has been demonstrated for very few masting species, we call for this test to be applied more widely.     

High efficiency transformation by electroporation of <Emphasis Type="Italic">Yarrowia lipolytica</Emphasis>

Yarrowia lipolytica was usually transformed by heat shock, but linearized integrative vectors always resulted in a low transformation efficiency when electroporation was used. To develop a high efficiency integrative transformation method by electroporation of F. lipolytica, we report here that pretreatment of F. lipolytica with 150 mM LiAc for 1 h before electroporation will approximately 30-fold of increase transformation efficiency. A cell concentration of 10¹⁰/ml and instrument settings of 1.5 kV will generate the highest transformation efficiencies. We have developed a procedure to transform F. lipolytica that will be able to yield an efficiency of 2.1 × 10⁴ transformants/ug for integrative linear DNA. With our modifications, the electroporation procedures became a very efficient and reliable tool for F. lipolytica transformation.     

Functional tuning of the catalytic residue pKa in a de novo designed esterase

AlleyCatE is a de novo designed esterase that can be allosterically regulated by calcium ions. This artificial enzyme has been shown to hydrolyze p‐nitrophenyl acetate (pNPA) and 4‐nitrophenyl‐(2‐phenyl)‐propanoate (pNPP) with high catalytic efficiency. AlleyCatE was created by introducing a single‐histidine residue (His¹⁴⁴) into a hydrophobic pocket of calmodulin. In this work, we explore the determinants of catalytic properties of AlleyCatE. We obtained the pK_a value of the catalytic histidine using experimental measurements by NMR and pH rate profile and compared these values to those predicted from electrostatics pK_a calculations (from both empirical and continuum electrostatics calculations). Surprisingly, the pK_a value of the catalytic histidine inside the hydrophobic pocket of calmodulin is elevated as compared to the model compound pK_a value of this residue in water. We determined that a short‐range favorable interaction with Glu¹²⁷ contributes to the elevated pK_a of His¹⁴⁴. We have rationally modulated local electrostatic potential in AlleyCatE to decrease the pK_a of its active nucleophile, His¹⁴⁴, by 0.7 units. As a direct result of the decrease in the His¹⁴⁴ pK_a value, catalytic efficiency of the enzyme increased by 45% at pH 6. This work shows that a series of simple NMR experiments that can be performed using low field spectrometers, combined with straightforward computational analysis, provide rapid and accurate guidance to rationally improve catalytic efficiency of histidine‐promoted catalysis. Proteins 2017; 85:1656–1665. © 2017 Wiley Periodicals, Inc.     

武汉市医院效率动态变化的Malmquist指数分析

目的 了解武汉市医院2006—2008年3年间运行效率变化的情况,找出引起其效率变化的原因,有针对性地采取措施,以提高医院的整体效率。方法 通过Malmquist指数法分析了武汉市23家医院3年间的全要素生产率、技术效率、技术变化等方面的变化趋势。结果 23家医院全要素生产率普遍下降主要是由于技术退步所致,医院的纯技术效率和规模效率趋于稳定,发挥的促进作用较小。结论 医院不但需要提高管理水平、引进先进的管理模式、控制合适的规模以保证技术效率的提高;更应引进人才,加强技术培训与进修,鼓励医务人员在诊疗技术、诊疗过程上有所创新,以此来提高医疗技术水平,进而提升医院的运行效率。

     

The ant Lasius niger shows no relationship between task efficiency and body size variation among workers

In ants, workers of different sizes may perform various tasks, even in so-called monomorphic species with relatively low body size variation. However, it is unclear if the body size diversity of monomorphic workers correlates with task efficiency, especially in stressful contingencies. Here we tested if the body size variation of workers corresponds with its efficiency in transferring pupae. Transferring brood is a pre-set behavioral response to stress, e.g. suboptimal temperature. Here we applied a laboratory experiment simulating nest damage. The study was performed on the common garden ant (Lasius niger (Linnaeus, 1758)) – a species with no distinct worker subcastes. The efficiency of workers was measured as the latency of transferring pupae from a lit part of the experimental colony to a darkened part, while the body size diversity was expressed as the within-colony coefficient of variation in head width. We did not find any significant correlation between efficiency and body size variation. Summarizing the existing studies and the present results, we propose the hypothesis that the body size diversity of L. niger may have implications for workers’ division of labor but not for their task efficiency in a stressful contingency.