Identification of superior parents in a potato breeding programme

Summary An incomplete diallel cross was used to study components of genetic variation in potatoes for a range of characters after early and late harvest. The progenies were also used to evaluate five predictors of progeny performance, namely the mean seedling performance, the mid-parent value and the means of the selfed progenies, of the diploid progenies and of the test-cross progenies. For almost all characters, the general combining ability effects were predominant, although the specific combining ability effects present were greater at late than at early harvests. The seedling performance for tuber yield, number of tubers and average tuber weight did not show any relevant relationship to the field performance. The midparent value provided, in general, satisfactory predictions of the mean progeny performance obtained in the diallel, except for ware tuber yield. The selfed and the diploid progenies did not improve the prediction of progeny means compared to the mid-parent value. The predictions based on the test-crosses surpassed those of the mid-parent value, particularly for tuber yield at ware potato harvest. Methods to identify superior parents are discussed.     

Eco-efficiency Trends in the UK Steel and Aluminum Industries

Measures of eco-efficiency—broadly understood as "getting more from less"—often include an economic and an environmental variable. The latter is often seen as the more problematic variable, particularly when used in relation to impacts of public concern. But an analysis of resource and value trends in the U.K. steel and aluminum industries over the last 30 yr showed that there are significant problems associated with using economic variables in measures of eco-efficiency at the sectoral level.
The research found that the U.K. steel and aluminum industries have improved the effectiveness with which they use natural resources, but that this has been accompanied by a decline in the economic output (value added) per unit of material or energy consumed. These seemingly contradictory results can be explained by the fall in the price of metals in real terms, and by the competitive pressures that necessitate the cutting of production costs and indirectly lead to a fall in the measure of economic output of the relevant industry.
The research also suggests a logical terminology to bring consistency and coherence to the broad field of eco-efficiency indicators, with an important distinction made between measures that examine the value output per unit of physical input, and measures that examine the physical output per unit of physical input. Both these types of indicators are important, as they highlight different aspects of eco-efficiency.     

Relationships Among Stop Codon Usage Bias, Its Context, Isochores, and Gene Expression Level in Various Eukaryotes

It is well known that stop codons play a critical role in the process of protein synthesis. However, little effort has been made to investigate whether stop codon usage exhibits biases, such as widely seen for synonymous codon usage. Here we systematically investigate stop codon usage bias in various eukaryotes as well as its relationships with its context, GC3 content, gene expression level, and secondary structure. The results show that there is a strong bias for stop codon usage in different eukaryotes, i.e., UAA is overrepresented in the lower eukaryotes, UGA is overrepresented in the higher eukaryotes, and UAG is least used in all eukaryotes. Different conserved patterns for each stop codon in different eukaryotic classes are found based on information content and logo analysis. GC3 contents increase with increasing complexity of organisms. Secondary structure prediction revealed that UAA is generally associated with loop structures, whereas UGA is more uniformly present in loop and stem structures, i.e., UGA is less biased toward having a particular structure. The stop codon usage bias, however, shows no significant relationship with GC3 content and gene expression level in individual eukaryotes. The results indicate that genomic complexity and GC3 content might contribute to stop codon usage bias in different eukaryotes. Our results indicate that stop codons, like synonymous codons, exhibit biases in usage. Additional work will be needed to understand the causes of these biases and their relationship to the mechanism of protein termination. [Reviewing Editor: Dr. Manyuan Long]     

一种新型一体化防护服的抗荷性能

目的:探讨一种新型一体化防护服(IPS)的抗荷性能.方法:在离心机上首先测定10名受试者的基础 Gz耐力,然后受试者穿IPS充气,测此时的松弛耐力,两者之差即为IPS的抗荷性能.结果:受试者穿IPS时的松弛耐力明显高于基础耐力(P＜0.01),其抗荷性能达到(2.38±0.38)G.结论:IPS的抗荷性能较好,可满足我国高性能战斗机的需要.     

Limit values for decomposition and convergence process of lignocellulose fraction in decomposing leaf litter of 14 tree species in a cool temperate forest

We examined limit values for decomposition and lignocellulose index (LCI, the ratio of acid-soluble holocellulose to acid-soluble holocellulose plus acid-insoluble lignin and lignin-like substances) in leaf litter decomposition of 14 tree species over 3 years. The study was carried out on upper (moder) and lower parts (mull) of a forest slope that showed different humus accumulation forms in a cool temperate forest in Japan. Limit values for accumulated mass loss of litter ranged from 46.8% to 94.1% and were not different between the sites. Limit values were positively correlated to initial LCI and lignin content. Final values of LCI of 14 litter types at the end of the study period showed a convergent trend among litter types at 0.25–0.26 as compared to their initial values (0.41 mean). The final LCI was not different between the sites. A review of limit values and initial and final values of LCI in leaf litter of temperate and boreal forests indicated that the limit values and final LCI in litter types in Japan were lower than those in Europe and North America, which can be primarily ascribed to lower initial LCI in Japan.     

On criteria for evaluating models of absolute risk

Absolute risk is the probability that an individual who is free of a given disease at an initial age, a, will develop that disease in the subsequent interval (a, t]. Absolute risk is reduced by mortality from competing risks. Models of absolute risk that depend on covariates have been used to design intervention studies, to counsel patients regarding their risks of disease and to inform clinical decisions, such as whether or not to take tamoxifen to prevent breast cancer. Several general criteria have been used to evaluate models of absolute risk, including how well the model predicts the observed numbers of events in subsets of the population ("calibration"), and "discriminatory power," measured by the concordance statistic. In this paper we review some general criteria and develop specific loss function-based criteria for two applications, namely whether or not to screen a population to select subjects for further evaluation or treatment and whether or not to use a preventive intervention that has both beneficial and adverse effects. We find that high discriminatory power is much more crucial in the screening application than in the preventive intervention application. These examples indicate that the usefulness of a general criterion such as concordance depends on the application, and that using specific loss functions can lead to more appropriate assessments.     

Phi value analysis of an allosteric transition of GroEL based on a single-pathway model

There are currently two contradictory models for the kinetics of the ATP-induced GroEL allosteric transition occurring around 20 microM ATP. One model, proposed by Horovitz et al. demonstrates the existence of two parallel pathways for the allosteric transition and an abrupt ATP-dependent switch from one pathway to the other. The other model, which was proposed by the present authors, shows no need to assume the parallel pathways, and a combination of the transition-state theory and the Monod-Wyman-Changeux model of allostery can explain the kinetics as well as the equilibrium of the transition. The discrepancy appears to be due to whether we regard the transition as reversible or irreversible. Thus, here we have investigated the reversibility of the allosteric transition between 0 microM and 70 microM ATP by the use of a stopped-flow double-jump technique, which has allowed us to monitor the kinetics of the reverse reaction from the relaxed state at a high ATP concentration to the tense state at a low ATP concentration. The tryptophan fluorescence of a tryptophan-inserted variant of GroEL was used to follow the kinetics. As a result, the allosteric transition was shown to be a reversible process, supporting the validity of our model. We also show that the structural environment around the ATP-binding site of GroEL in the transition state is very similar to that in the relaxed state (Phi=0.9) by using a Phi value analysis in the kinetic Monod-Wyman-Changeux model, which is analogous to the mutational Phi value analysis in protein folding.     

Are residues in a protein folding nucleus evolutionarily conserved?

Protein is the working molecule of the cell, and evolution is the hallmark of life. It is important to understand how protein folding and evolution influence each other. Several studies correlating experimental measurement of residue participation in folding nucleus and sequence conservation have reached different conclusions. These studies are based on assessment of sequence conservation at folding nucleus sites using entropy or relative entropy measurement derived from multiple sequence alignment. Here we report analysis of conservation of folding nucleus using an evolutionary model alternative to entropy-based approaches. We employ a continuous time Markov model of codon substitution to distinguish mutation fixed by evolution and mutation fixed by chance. This model takes into account bias in codon frequency, bias-favoring transition over transversion, as well as explicit phylogenetic information. We measure selection pressure using the ratio omega of synonymous versus non-synonymous substitution at individual residue site. The omega-values are estimated using the PAML method, a maximum-likelihood estimator. Our results show that there is little correlation between the extent of kinetic participation in protein folding nucleus as measured by experimental phi-value and selection pressure as measured by omega-value. In addition, two randomization tests failed to show that folding nucleus residues are significantly more conserved than the whole protein, or the median omega value of all residues in the protein. These results suggest that at the level of codon substitution, there is no indication that folding nucleus residues are significantly more conserved than other residues. We further reconstruct candidate ancestral residues of the folding nucleus and suggest possible test tube mutation studies for testing folding behavior of ancient folding nucleus.     

雷州半岛桉树生物质能源林生长的密度效应研究

以雷州半岛2年生桉树无性系DH201(Eucalyptus grandis  E. tereticornis)能源林为研究对象,对6种不同密度配置下的林分生长量、生物量以及热值等进行了分析,探讨密度对桉树生物质能源林生长的影响。结果表明,密度对桉树胸径和树高生长量影响极显著,在林分不同发育阶段对林分蓄积量的影响不同;单株生物量随密度增大而减小。1年生的林分蓄积量和生物量均以密度为10000 ind. hm-2的最大,分别为52.57 m3 hm-2和32.02 t hm-2;2年生的林分蓄积量和生物量均以密度为2500 ind. hm-2的最大,分别为75.85 m3 hm-2和45.66 t hm-2;密度对热值及灰分含量的影响不显著。因此,1年生和2年生的桉树能源林的最优密度分别为10000 ind. hm-2和2500 ind. hm-2。     

Transformation of recalcitrant turfgrass cultivars through improvement of tissue culture and selection regime

Tissue culture techniques, medium composition, pH value and targeted tissues, agroinfection and co-culture conditions, selection process were optimized for efficient turfgrass transformation. A highly regenerable callus lines were produced in callus induction medium modified from N6 basal medium. Six-week-old calluses were cultured on Pre-regeneration medium I for 4 days and then subjected to Agrobacterium tumefaciens. After co-cultivation at 20±1 °C in a 16 h light/8 h darkness for 3 days, the calluses were cultured on non-selective Pre-regeneration medium II supplemented with 400 mg l⁻¹ l-cysteine for 7 days. Plantlets were regenerated on the Regeneration medium without selection pressure. A selection pressure was given to the regenerated plantlets when they were rooted on the Plantlet rooting medium. Roots appeared within 8–12 days in putative transformed plantlets. Resistant plants obtained were phenotypically normal and fully fertile. Chemical and molecular analyses confirmed that foreign genes were successfully introduced into the genome of perennial ryegrass or tall fescue. The transformation efficiency can attain 23.3% in perennial ryegrass.