A flexible method to align large numbers of biological sequences

Summary A method for the alignment of two or more biological sequences is described. The method is a direct extension of the method of Taylor (1987) incorporating a consensus sequence approach and allows considerable freedom in the control of the clustering of the sequences. At one extreme this is equivalent to the earlier method (Taylor 1987), whereas at the other, the clustering approaches the binary method of Feng and Doolittle (1987). Such freedom allows the program to be adapted to particular problems, which has the important advantage of resulting in considerable savings in computer time, allowing very large problems to be tackled. Besides a detailed analysis of the alignment of the cytochrome c superfamily, the clustering and alignment of the PIR sequence data bank (3500 sequences approx.) is described.     

Proteolysis of ribulose-1,5-bisphosphate carboxylase/oxygenase in leaves of Citrus explants throughout the annual cycle and its regulation by ethylene

Leaf senescence and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBP carboxylase, EC 4.1.1.39) degradation in orange [ Citrus sinensis (L.) Osbeck cv. Washington Navel] explants have been investigated. Explants consisted of a segment of stem (ca 15 cm) and 5 mature leaves. In vitro RuBP carboxylase degradation was determined by culturing the explants in water for different periods of time (3 days usually) and quantifying the two RuBP carboxylase subunits in the extracts following sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). In vitro RuBP carboxylase degradation was estimated by autodigestion of leaf extracts and SDS-PAGE. The extent of in vivo RuBP carboxylase degradation in explants cultured under 16 h light/8 h dark photoperiod varied throughout the year and showed a cyclic behaviour correlated with the growth cycle of Citrus. The highest proteolytic activity both in vivo and in vitro was found in explants made from April to August coinciding with the maximum vegetative growth period of the tree.
Leaf senescence and abscission could be retarded significantly at any time of the year by maintaining the explants continuously in the dark. Treatment of the explants in the dark with a continuous flow of ethylene enhanced both leaf abscission and rate of RuBP carboxylase degradation, proportionally to ethylene concentration (0.1-0.6 ppm). Ethylene-induced senescence of Citrus leaf explants in the dark appears to be a convenient model system to study the regulation of the proteolytic degradation of RuBP carboxylase.     

Total root length as estimated from small sub-samples

A method is proposed for estimating the total length of a root system from sub-samples. This method is based on the measurement of the length and diameter of small pieces of roots, and on the measurements of the bulk density of root sub-samples. It is assumed that roots are cylinders with a given bulk density. The length and diameter of small root pieces are measured by image analysis. A weighted quadratic mean (W.Q.M.) root diameter is then calculated and used in estimating the root length. This W.Q.M. diameter is defined as the real mean diameter of an equivalent single root with the same length and volume as the tested root system. The accuracy of prediction is demonstrated for one theoretical root system. The standard deviation of estimation can be calculated using sampling simulations.     

Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs)

Summary Preliminary analysis using nuclear RFLPs provided evidence that subspecies within Brassica rapa originated from two different centers. One center is in Europe, represented by turnip and turnip rape from which the oilseed sarson was derived. A second center is in South China containing a variety of Chinese vegetables of which pak choi and narinosa seem to be the most ancient forms. Based on RFLP data, the accessions of B. oleracea examined could be divided into three distinct groups, represented by thousand head kale, broccoli and cabbage. Thousand head kale and Chinese kale appear to be the primitive types. Observations of parallel variation among subspecies of both species are discussed.     

数种昆虫5S rRNA结构特点的比较

比较已知结构的昆虫5S rRNA的核苷酸顺序,发现同科、同目的昆虫比不同科、不同目的昆虫有较少的核苷酸差别.根据Kimura和Ohta(1972)提出的经验公式,绘制了数种昆虫的系统发育图.结果表明,从分子进化得到的结论和经典分类基本上是一致的.根据DeWachter等(1982)提出的二级结构模型,归纳分析这些昆虫5S rRNA,发现保守位点与半保守位点(同一位点仅出现二种核苷酸残基)之和几乎占整个5S rRNA分子的100%.     

图论在中国慈姑属数量分类研究中的应用

慈姑属(Sagittaria L.)是水生单子叶植物泽泻科(Alismataceae)的一个重要属。近年来,陈家宽等对中国慈姑属进行了系统研究。作者应用聚类分析和主成分分析进行了中国慈姑属的数量分类,取得了良好的效果。由于慈姑属分类性状数目较大,因而在压缩后的三维空间中描述分类群间的距离,     

Primary structure of chain I of the heterodimeric hemoglobin from the blood clamBarbatia virescens

The blood clamBarbatia virescens has a heterodimeric hemoglobin in erythrocytes. Interestingly, the congeneric clamsB. reeveana andB. lima contain quite different hemoglobins: tetramer and polymeric hemoglobin consisting of unusual didomain chain. The complete amino acid sequence of chain I ofB. virescens has been determined. The sequence was mainly determined from CNBr peptides and their subpeptides, and the alignment of the peptides was confirmed by sequencing of PCR-amplified cDNA forB. virescens chain I. The cDNA-derived amino acid sequence matched completely with the sequence proposed from protein sequencing.B. virescens chain I is composed of 156 amino acid residues, and the molecular mass was calculated to be 18,387 D, including a heme group. The sequence ofB. virescens chain I showed 35–42% sequence identity with those of the related clamAnadara trapezia and the congeneric clamB. reeveana. An evolutionary tree forAnadara andBarbatia chains clearly indicates that all of the chains are evolved from one ancestral globin gene, and that the divergence of chains has occurred in each clam after the speciation. The evolutionary rate for clam hemoglobins was estimated to be about four times faster than that of vertebrate hemoglobin. We suggest that blood clam hemoglobin is a physiologically less important molecule when compared with vertebrate hemoglobins, and so it evolved rapidly and resulted in a remarkable diversity in quaternary and subunit structure within a relatively short period.     

Nutrient requirements of exotic tree species in Zimbabwe

Pot and field experiments were conducted in the greenhouse and at three field sites (Marondera, Domboshawa and Makoholi) in Zimbabwe to examine the effects of soils and fertilizers on nutrient uptake and growth of 6 exotic tree species (Eucalyptus camaldulensis, E. grandis, E. tereticornis, Leucaena leucocephala, Casuarina cunninghamiana, and Acacia holosericea). Plant growth, N and P contents of all species were increased by the application of N, P, K and micronutrient fertilizers. The effect of individual nutrients (N, P, K and micronutrients) and their combination on Eucalyptus species was further investigated in a pot experiment using soil from Domboshawa. Eucalyptus species responded only to N application and no significant interactions were found between N and the other elements. Nutrient uptake results showed that E. camaldulensis and E. tereticornis removed more cations than the N-fixing trees but only in the fertilized treatments. L. leucocephala and C. cunninghamiana were higher in P, but no clear trends were observed for N. Plant growth and nutrient uptake by E. camaldulensis. C. cunninghamiana and A. holosericea were assessed in the field at the three sites. Plant species grown in the Marondera site had greater height and diameter at breast height (DBH) than those in the two other sites. These results followed trends in soil nutrient contents. The analysis of foliage revealed differences in the nutrient concentration of leaves from different trees, but no effect of site was found. The interrelationships between plant characteristics, soil and foliage nutrients were examined. In a pot experiment, mineral N was the only variable correlated with growth response and nutrient uptake, while in the field the only significant correlation was obtained with soil pH.     

Responses of stomata of senescing and nonsenescing leaves of Nicotians glauca to changes in intercellular concentrations of leaf carbon dioxide

Abstract. Gas exchange measurements were performed to test the hypothesis that failure of stomata to open in senescing leaves of Nicotiana glauca is caused by elevated concentrations of carbon dioxide in the intercellular spaces of leaf mesophyll tissue (c_i). Senescing leaves selected for experiments were completely chlorotic and lacked positive rates of photosynthesis. When stomata in detached epidermis from senescing leaves were illuminated in CO2-free air, they opened to similar apertures as those in detached epidermis from nonsenescing leaves. To compare the effects of changes in c_i on stomatal responses of the two leaf types, leaf 'flags' of either nonsenescing or senescing leaves were illuminated at a photosynthetic photon flux density of 500 μmol m⁻² s⁻¹ in a gas exchange cuvette. Leaf temperatures were maintained at 23.5 ± 0.5°C, and vapour pressure differences between leaves and the air were maintained between 0.70 and 0.75kPa. C_i was adjusted by changing external concentrations of carbon dioxide in air circulating through the cuvette. Conductances and photosynthetic rates of nonsenescing leaves changed in response to changes in c_i, but neither the conductances nor the photosynthetic rates of senescing leaves were affected significantly by changes in q. We conclude that guard cells of senescing leaves of Nicotiana glauca do not lose the capacity to respond to changes in carbon dioxide concentration and that increases in c_i resulting from declining rates of mesophyll photosynthesis are not the sole cause of maintenance of stomatal closure during leaf senescence. The data suggest that factors external to guard cells may prevent them from responding to changes in carbon dioxide concentrations in intact senescing leaves.     

阔叶树的叶形曲线方程：—适于叶面积计算的数学模型

树木的叶形可以看作一个平面几何图形。这种几何图形可用解析方程给予表达,我们把这种解析方程称为叶形曲线方程。由于叶形是一个左右对称,而上下不对称的图形,也就是说叶的最宽处绝大多数不在叶的中部,少数在