New methods for estimating the numbers of synonymous and nonsynonymous substitutions

New methods for estimating the numbers of synonymous and nonsynonymous substitutions per site were developed. The methods are unweighted pathway methods based on Kimura's two-parameter model. Computer simulations were conducted to evaluate the accuracies of the new methods, Nei and Gojobori's (NG) method, Miyata and Yasunaga's (MY) method, Li, Wu, and Luo's (LWL) method, and Pamilo, Bianchi, and Li's (PBL) method. The following results were obtained: (1) The NG, MY, and LWL methods give overestimates of the number of synonymous substitutions and underestimates of the number of nonsynonymous substitutions. The major cause for the biased estimation is that these three methods underestimate the number of synonymous sites and overestimate the number of nonsynonymous sites. (2) The PBL method gives better estimates of the numbers of synonymous and nonsynonymous substitutions than those obtained by the NG, MY, and LWL methods. (3) The new methods also give better estimates of the numbers of synonymous and nonsynonymous substitutions than those obtained by the NG, MY, and LWL methods. In addition, estimates of the numbers of synonymous and nonsynonymous sites obtained by the new methods are reasonably accurate. (4) In some cases, the new methods and the PBL method give biased estimates of substitution numbers. However, from the number of nucleotide substitutions at the third position of codons, we can examine whether estimates obtained by the new methods are good or not, whereas we cannot make an examination of estimates obtained by the PBL method. (5) When there are strong transition/transversion and nucleotide-frequency biases like mitochondrial genes, all of the above methods give biased estimates of substitution numbers. In such cases, Kondo et al.'s method is recommended to be used for estimating the number of synonymous substitutions, although their method cannot estimate the number of nonsynonymous substitutions and is time-consuming. These results, particularly result (1), call for reexaminations of some genes. This is because evolutionary pictures of genes have often been discussed on the basis of results obtained by the NG, MY, and LWL methods, which are favorable for the neutral theory of molecular evolution.     

氯喹导致大鼠肌组织载脂蛋白E大量表达

载脂蛋白E(ApoE)与迟发的家族性及孤发性阿尔茨海默(Alzheimer)病密切相关. 氯喹慢性中毒可诱发某些肌病理改变, 出现β淀粉样蛋白(βAP)与tau蛋白等的沉积, 与Alzheimer脑中见到的病理改变类似. 为分析这一改变的机制, 用逆转录结合多聚酶链反应技术(RT-PCR)对氯喹处理的大鼠肌肉中ApoE表达的改变进行了研究. 在PCR定量中采用了一种稳定表达的内源性甘油醛-3-磷酸脱氢酶mRNA作为内部参照. PCR扩增在很宽的循环数范围内成线性, 且靶mRNA与参照mRNA的扩增效率相当. 氯喹处理后大鼠肌肉中ApoE mRNA的表达从第6周开始增加, 第8周后超过对照组的20多倍. 结果提示, ApoE在氯喹慢性中毒所致的大鼠肌病理改变中发挥某些作用.     

Analysis of the NH2-Terminal 83rd Amino Acid of Escherichia coli GyrA in Quinolone-Resistance

Artificial mutations of Gyrase A protein (GyrA) in Escherichia coli by site-directed mutagenesis were generated to analyze quinolone-resistant mechanisms. By genetic analysis of gyrA genes in a gyrA temperature sensitive (Ts) background, exchange of Ser at the NH₂-terminal 83rd position of GyrA to Trp, Leu, Phe, Tyr, Ala, Val, and Ile caused bacterial resistance to the quinolones, while exchange to Gly, Asn, Lys, Arg and Asp did not confer resistance. These results indicate that it is the most important for the 83rd amino acid residue to be hydrophobic in expressing the phenotype of resistance to the quinolones. These findings also suggest that the hydroxyl group of Ser would not play a major role in the quinolone-gyrase interaction and Ser83 would not interact directly with other amino acid residues.     

Establishment and maintenance of the breeding territory in the polygynous great reed warbler

Settlement of male great reed warblers in the breeding ground was highly asynchronous at Lake Biwa in Japan. It took over 1 month from the appearance of the first male to a saturation in number of males. In resource-defense-polygyny, males are expected to try to defend as large an area as possible in the optimal habitat. In fact, a small number of the earliest settling males divided up the breeding ground almost completely as territories among themselves and these were later reduced in size with the addition of later settlers. The reduction was not due to a seasonal decline of aggressiveness on the part of the owners but to a higher level of intrusion pressure by later arriving males. The neighbor-neighbor relationship, once established, was rather stable. Home range overlap was small and territorial contacts were few between neighbors. Territorial boundaries seem not to shift despite the addition of new males as long as the neighbors were the same. The stable relationships between neighbors are expected to help the earlier resident to maintain his large and good territories throughout the breeding season and hence polygyny is favored in this species.     

N-2′-Acetoxybenzoyl derivatives of chitosan, N-desulphated heparin and 2-amino-2-deoxy-d-glucose

N-2′-Acetoxybenzoyl (aspirin) derivatives (degree of substitution 0·35–1·00) of chitosan, N-desulphated heparin and 2-amino-2-deoxy-d-glucose were prepared by methods that gave yields in the range 65–86%. The salicylate of chitosan was isolated with a 98% yeild. Aspirin or salicylic acid was released much more slowly from N-(2′-acetoxybenzoyl)-chitosan than from the salicylate of chitosan, and much faster at 37°C in 0·1 m NaOH solution than in 2% aqueous acetic acid solution. Salicylic acid was isolated from the dialysate (0·1 m NaOH solution) of N-(2′-acetoxybenzoyl)-chitosan.     

Matter production processes ofReineckia carnea Kunth,an evergreen forest floor herb in the warm-temperate region of Japan

The growth and matter production were examined forReineckia carnea, an evergreen herb growing on the forest floor in a warm-temperate region. Seasonal change in the biomass of plants growing in the field was estimated from the harvested sample plants. Carbohydrate contents and respiration rates were measured for analysis of dry matter economy. Light intensity and temperature on the forest floor were periodically measured. In mid-spring the biomass reached a maximum which was about half again its minimum value, found in autumn. Two phases, the productive phase in cooler seasons and the developmental phase in warmer seasons, were distinguished from the annual growth pattern of this plant. In cooler seasons, positive net production was found without any morphological changes, resulting in active accumulation of reserves which were mainly soluble sugars. This high net production seems to be closely related to the favorable light conditions and low respiratory losses. In warmer seasons, though new organs were developed, net production remained low or was even negative. The morphological development of this plant in these seasons depended mostly on reserves previously accumulated. This characteristic feature of annual matter economy is considered to be common to evergreen plants on the forest floor in warm regions.     

Nitrogen fixation by immobilized Azotobacter chroococcum

A nitrogen-fixing bacterium, Azotobacter chroococcum, was immobilized in 2% agar gel. The optimum partial oxygen pressure, pO₂, of immobilized cells was 0.2 atm, wherea s that of native cells was 0.05 atm. When continual nitrogen fixation was performed under aerobic conditions, the nitrogenase activity of immobilized cells increased with increasing time. On the other hand, the activity of native cells decreased rapidly. Increase of nitrogenase activity was attributed to growth of the bacteria in the gel matrix. The production rate of total nitrogen compounds by the immobilized bacteria was also increased during the first 4 days. Nitrogen compounds produced by the immobilized cells were mainly amino acids such as γ-aminobutyrate, glutamate and arginine.     

Circadian alterations in tubular structures on the outer mitochondrial membrane of rat hepatocytes

Summary The ontogeny and distribution of immunoreactive motilin and secretin were studied in the gastro-entero-pancreatic (GEP) system of human fetuses, aged 5–24 weeks, using an indirect immunocytochemical method. Several controls to check for the specificity of the immunoperoxidase staining were performed. The first motilin- and secretin-containing cells were observed in the duodenal and jejunal mucosa in fetuses at a gestational age of 16 weeks. These immunoreactive cells were located in the glands of Lieberkühn and in the villi. No immunoreactive cells were present in the oxyntic and pyloric mucosa, ileum, colon and endocrine pancreas. These observations indicate that the motilin- and secretin-containing cells detected by our antisera appear (i) in the same organs of the fetus where they are also detectable in the adult, and (ii) after the completion of histogenesis of the gastro-entero-pancreatic (GEP) system.