Population structure and linkage disequilibrium in diploid and tetraploid potato revealed by genome‐wide high‐density genotyping using the SolCAP SNP array

Genome‐wide association (GWA) mapping in potato requires high‐density genotyping. With the Illumina SolCAP potato single‐nucleotide polymorphism (SNP) array, a first tool for GWA mapping in potato became available. Thirty‐six tetraploid varieties and eight diploid breeding clones were genotyped for 8303 SNPs using this array. The objectives of our study were to examine in this set of germplasm: (i) the degree of polymorphism of the SolCAP SNPs in European germplasm, (ii) the population structure, (iii) temporal trends of genetic diversity and (iv) the genome‐wide extent of linkage disequilibrium (LD). Three‐quarters of the SNPs were polymorphic. In the principal coordinate analysis, a clear separation of tetraploid from diploid genotypes was observed, whereas no distinct subgroups among the tetraploid varieties were detected. The nonlinear trendline of the LD measure vs. the physical map distance decayed within 275 bp to an value of 0.10, indicating that theoretically, about 3 million equally distributed SNPs are required for GWA mapping in this diverse set of germplasm. As the LD decay changes with the population selected for GWA mapping, the number of required markers might be different in other germplasm.     

融合表达淋巴细胞脉络丛脑膜炎病毒和卵清白蛋白CD8+T细胞表位的减毒鼠伤寒沙门氏菌的构建与鉴定

依据淋巴细胞脉络丛脑膜炎病毒(LCMV)主要保护性抗原CD8 T细胞表位VRRPQASGVYMGNLTAQ和卵清白蛋白(OVA)CD8 T细胞表位SIINFEKL,设计、合成两条编码LCMV和OVA CD8 T细胞表位的寡核苷酸片段,经退火后,克隆入绿色荧光蛋白表达质粒pYAGFP,经PCR扩增和序列测定分析,证实成功构建T细胞表位与绿色荧光蛋白融合表达的重组质粒pYAGFPL-O,将此重组质粒pYAGFPL-O转化减毒鼠伤寒沙门氏菌X4550,获得重组沙门氏菌X4550(pYAGFPL-O).用SDS-PAGE电泳测得重组菌表达的融合蛋白约为30kD.同时,荧光显微镜下观察到X4550(pYAGFPL-O)发出黄绿色荧光.这些结果表明LCMV和OVA T细胞表位已成功表达.重组菌X4550(pYAGFPL-O)的获得为研究沙门氏菌载体携带外源抗原的T细胞应答规律及调控机理打下了重要基础.     

Effect of organic matter concentration on agricultural limestone dissolution in laboratory soil–water systems

Laboratory soil – water systems in which soil organic matter was increased by 0.0%, 0.5%, 1.0%, 2.0% and 4.0% by adding dry, chopped ryegrass (Lolium perenne) shoots to sandy soil containing 0.06% organic matter. Agricultural limestone was added to the systems, and pH, alkalinity and hardness of the water were monitored for 65 days. The pH, alkalinity and hardness increased with greater soil organic matter concentration. Amounts of carbon dioxide released by microbial respiration increased at the higher soil organic matter concentrations, and this resulted in more rapid and greater solubility of agricultural limestone. The results suggest that greater soil organic matter concentrations in ponds favour the rate and extent of agricultural limestone dissolution.     

Alkalinity and Hardness: Critical but Elusive Concepts in Aquaculture

Total alkalinity and total hardness are familiar variables in aquatic animal production. Aquaculturists—both scientists and practitioners alike—have some understanding of the two variables and of methods for adjusting their concentrations. The chemistry and the biological effects of alkalinity and hardness, however, are more complex than generally realized or depicted in the aquaculture literature. Moreover, the discussions of alkalinity and hardness—alkalinity in particular—found in water chemistry texts are presented in a rigorous manner and without explanation of how the two variables relate to aquaculture. This review provides a thorough but less rigorous discussion of alkalinity and hardness specifically oriented toward aquaculture. Alkalinity and hardness are defined, their sources identified, and analytical methods explained. This is followed by a discussion of the roles of the two variables in aquaculture, including their relationships with carbon dioxide, pH, atmospheric pollution, ammonia, and other inorganic nitrogen compounds, phytoplankton communities, trace metals, animal physiology, and clay turbidity. Liming and other practices to manage alkalinity and hardness are explained. Changes in alkalinity and hardness concentrations that occur over time in aquaculture systems are discussed. Emphasis is placed on interactions among alkalinity, hardness, water quality, and aquacultural production.     

Measurement of 5-day biochemical oxygen demand without sample dilution or bacterial and nutrient enhancement

A direct method for measuring the 5-day biochemical oxygen demand (BOD₅) of aquaculture samples that does not require sample dilution or bacterial and nutrient enrichment was evaluated. The regression coefficient (R²) between the direct method and the standard method for the analyses of 32 samples from catfish ponds was 0.996. The slope of the regression line did not differ from 1.0 or the Y-intercept from 0.0 at P = 0.05. Thus, there was almost perfect agreement between the two methods. The control limits (three standard deviations of the mean) for a standard solution containing 15 mg/L each of glutamic acid and glucose were 17.4 and 20.4 mg/L. The precision of the two methods, based on eight replicate analyses of four pond water samples did not differ at P = 0.05.     

New approaches in vaccine development

In the last century, vaccines have been one of the most powerful tools for preventing infectious diseases. Smallpox has been eradicated and other diseases such as poliomyelitis or measles have been reduced to very low levels in many regions of the world. However, infectious diseases remain the leading cause of death worldwide. Thus, the development of vaccines to prevent diseases for which no vaccine currently exists such as AIDS or malaria as well as the improvement of efficacy and safety of existing vaccines remains a high priority. Achieving such ambitious goals in a near future will certainly require a strong modification of the methods that have been used so far to identify vaccine candidates. In particular, modern vaccinology could strongly benefit of the latest developments of molecular biology and immunology. Here, we will discuss some potential applications of the increasing knowledge of pathogen genomes as well as the immune system for the discovery of new antigenic targets and the development of new strategies of vaccination.     

Poind Soil pH Measurement

Soil pH often is measured in samples from the bottoms of aquaculture ponds. Several different techniques for soil pH are used. This study considered the differences in pH obtained by the different methods and determined which methods appeared most useful. Dual electrodes (indicating and reference) and a single‐probe combination electrode gave similar pH values when inserted into 1:1 mixtures of dry soil and distilled water. There were slight differences in pH between readings with dual and combination electrodes when the dual electrodes were arranged with the indicating electrode in the sediment phase and the reference electrode in the supernatant phase of the mixture. The two‐phase method with the dual electrode does not appear warranted because of greater difficulty in making measurements. Dry soil: distilled water ratios of 1:2.5, 1:5, and 1:10 had progressively greater pH readings than obtained at a 1:1 ratio. Measurements made in 0.01 M CaCl₂ and 1.0 M KCl had much different values than those made in distilled water. Higher pH resulted when pH was measured without stirring or in filtrates of soil‐water mixtures. A 20‐min period of intermittent stirring before making measurements was necessary for a stable pH value. Particle size did not influence pH in aliquots passing 0.053 to 2.36‐mm sieves. Drying temperature had a strong influence on pH, and measurements made on samples dried at 40 to 60 C are probably most reliable. Measurements of in situ pH in wet soil with standard pH electrode or a portable acidity tester differed greatly from those made in 1:1 dry soil to distilled water mixtures. Pond bottom soil pH measurement should be standardized. Based on findings of this study, the following method is suggested: dry soil at 60 C in a forced‐draft oven; pulverize soil to pass a 2‐mm sieve; mix soil and distilled water in a 1:1 ratio (weight: volume); stir intermittently with glass rod for 30 min; insert dual electrodes or a combination electrode into the mixture; measure pH while stirring.