森林群落物种组成对凋落物组成的影响

在海南铜鼓岭山麓灌木林和季雨矮林固定大样地的基础上,通过收集凋落物,比较两林型的凋落物数量及其器官组成、凋落叶物种组成,探讨森林群落物种组成与凋落物组成的关系。结果表明:(1)两林型的凋落物总量及其器官组成不同,山麓灌木林(6.227 t/hm~2)比季雨矮林的年凋落量大(5.636 t/hm~2);凋落叶是凋落物的主要组成部分,能反映凋落物的凋落情况。(2)山麓灌木林凋落物优势种和主要物种为贡甲、林仔竹、橄树等15个物种,凋落叶总量占77.72%;季雨矮林的凋落物优势种和主要物种为方枝蒲桃、肖蒲桃、贡甲等17个物种,凋落叶总量占71.84%;山麓灌木林中凋落物优势种和主要物种的叶凋落量与其组成物种的株数、总断面积、树冠面积极显著正相关而季雨矮林的凋落物优势种和主要物种的叶凋落量与其组成物种的株数极显著正相关。山麓灌木林中两者的Jaccard相似性系数为20%,季雨矮林为25.93%,两林型的群落物种组成与凋落叶物种组成不一致,热带森林群落优势种不一定是凋落物优势种。     

Relationship between base composition in non-coding DNA of genes and codon composition

The C + G percentage in third position of codons is linearly dependent on the C + G composition of flanking regions and introns. A similar relationship is shown for the first and second position which significantly influence the nature of amino acid sequence. If mutations would be oriented according to the local base composition, this will imply that genes of the same multigenic family would evolve at different rate.     

The relationship of DNA base composition and individual protein composition in micro-organisms

Summary To investigate the dependence of protein composition on DNA base composition, a set of data on individual proteins with known amino acid compositions from a spectrum of bacterial species has been compiled. It is found that similar relationships of amino acid frequency to G + C content exist for these proteins as for the bulk proteins studied by Sueoka (1961). The data are analysed by linear and cubic regression, and a measure of the proportions of A + T-rich and G + C-rich codons in the underlying messenger RNAs is put forward. The theoretical limits on the G + C content of coding DNA are discussed, and inference are made about the various selective forces acting on DNAs of different G + C contents.     

Predicting enzyme subclass by functional domain composition and pseudo amino acid composition

As a continuous effort to use the sequence approach to identify enzymatic function at a deeper level, investigations are extended from the main enzyme classes (Protein Sci. 2004, 13, 2857-2863) to their subclasses. This is indispensable if we wish to understand the molecular mechanism of an enzyme at a deeper level. For each of the 6 main enzyme classes (i.e., oxidoreductase, transferase, hydrolase, lyase, isomerase, and ligase), a subclass training dataset is constructed. To reduce homologous bias, a stringent cutoff was imposed that all the entries included in the datasets have less than 40% sequence identity to each other. To catch the core feature that is intimately related to the biological function, the sample of a protein is represented by hybridizing the functional domain composition and pseudo amino acid composition. On the basis of such a hybridization representation, the FunD-PseAA predictor is established. It is demonstrated by the jackknife cross-validation tests that the overall success rate in identifying the 21 subclasses of oxidoreductases is above 86%, and the corresponding rates in identifying the subclasses of the other 5 main enzyme classes are 94-97%. The high success rates imply that the FunD-PseAA predictor may become a useful tool in bioinformatics and proteomics of the post-genomic era.     

RNA composition in cotton

Nucleotide compositions of soluble (sRNA), whole-cell, and in one instance particulate and nonparticulate, RNA of embryos, cotyledons (dark and light-grown), leaves, stems, and roots of Gossypium hirsutum were compared. Evidence of substantial differences in the overall compositions of the RNAs was not obtained. However, a tendency for some plant parts to differ, particularly in sRNA composition, and that of the cotyledons (including particulate and nonparticulate RNA) to change during the formation of chlorophyll, was indicated by small but statistically significant shifts in certain nucleotide components.     

Ganglioside composition of astrocytes

Short-term and long-term (greater than 7 months) cultured astrocytes from 14-day-old rat brain were analyzed for ganglioside content. Analysis of the extracted gangliosides by HPTLC revealed that ganglioside GM1 was absent in 35 days and 235 days cultured astrocytes, and that the predominant ganglioside was GM3, showing a double band in both cases. A small amount of the disialogangliosides (GD3, GD1a) was also detected. More than 70% of radioactivities into ganglioside fractions by cultured astrocytes, in the presence of N-[3H]-acetylmannosamine, appeared in ganglioside GM3. The upper band component of GM3 increased 60% in long-term astrocyte cultures compared to 35-day-old cultures. Also, an increased GD3 content in long-term astrocyte cultures was detected. These results suggest that the increase of GD3 and upper band GM3 in long-term cultured astrocytes might be related to the appearance of small processes showing strong reactivity against GFAP and vimentin during astrocyte-subculture.     

Exercise and body composition

We assessed changes in body composition in 41 young adults who engaged in various exercise and/or training programs on ad libitum diets. Most of those who gained weight sustained an increase in lean body mass (LBM), and most of those who lost weight lost LBM as well as fat. The change in LBM was directly related to the change in weight, with a regression slope of 0.500. An analysis of published data confirms these findings and, in concert with our data, provides the additional information that the magnitude of the change in body composition in exercising individuals is influenced by body fat content, just as it is for nonexercising individuals.     

Biochemical composition of ctenophores

The biochemical composition of three species of North Sea ctenophores, the beroid Beroe gracilis (Künne), the tentaculate Pleurobrachia pileus (Fabricius) and the lobate Bolinopsis infundibulum (Müller), was analysed in terms of total fractions of protein, lipid, ninhydrin-positive substances (NFS), polysaccharides (PS), and low molecular-weight carbohydrates (LMC). The sum of these biochemical fractions was highest in Beroe (128 mg/g dry wt) and much lower in Pleurobrachia (61 mg/g dry wt) and Bolinopsis (27 mg/g dry wt). Beroe shows higher ratios of NPS/protein and LMC/PS than either of the other species. These findings are explained by differences in the morphology and metabolism of the species.In a 3-wk starvation experiment, Pleurobrachia lost ≈65% of its body mass and ≈80% of its organic content after 14 days at 15°C. However, after 10 days, the biochemical composition of the body tissue changed only slightly indicating that all components of body tissue are consumed without any preference for a specific storage material. Therefore the biochemical composition does not necessarily reflect differences in the nutritional conditions of the ctenophores the field.     

Lipid composition of cyanidium

The major lipids in Cyanidium caldarium Geitler are monogalactosyl diglyceride, digalactosyl diglyceride, plant sulfolipid, lecithin, phosphatidyl glycerol, phosphatidyl inositol, and phosphatidyl ethanolamine. Fatty acid composition varies appreciably among the lipids, but the major ones are palmitic acid, oleic acid, linoleic acid, and moderate amounts of stearic acid. Trace amounts of other acids in the C₁₄ to C₂₀ range were also present. Moderate amounts of linolenic acid were found in two strains, but not in a third. The proportion of saturated acid is relatively high in all lipids ranging from about a third in monogalactosyl diglyceride to three-fourths in sulfolipid. This may be a result of the high growth temperature. Lipases forming lysosulfolipid, and lysophosphatidyl glycerol are active in ruptured cells; galactolipid is degraded with loss of both acyl residues. Thus the lipid and fatty acid composition of Cyanidium more closely resembles that of green algae than that of the blue-green algae, although there are differences of possible phylogenetic interest.     

Macromolecular composition of bacteria

Equations are presented that describe the macromolecular composition in exponential bacterial cultures as functions of five parameters: doubling time of the culture (τ), protein per origin of replication (P₀), chromosome replication time (C-period), peptide chain elongation rate (c_p), and the time between termination of replication and cell division (D-period). Implicit in the value for some of these parameters is a specific macromolecular control system: the control of the growth rate (τ), the timing of initiation of rounds of chromosome replication (P₀), and the regulation of cell division (D). The utility of these relations is illustrated by using updated measurements of the macromolecular composition of E. coli B/r to calculate values for the fundamental parameters and to predict the composition of a mutant which has a defect in the control of DNA replication. Furthermore, the meaning of several often-cited physiological parameters (RNA/protein, RNA/cell and RNA/genome) is examined. The relations presented here show that these parameters and their variation with growth rate are not directly relevant to arguments about control of ribosome synthesis or culture growth.     

Predicting membrane protein type by functional domain composition and pseudo-amino acid composition

Given the sequence of a protein, how can we predict whether it is a membrane protein or non-membrane protein? If it is, what membrane protein type it belongs to? Since these questions are closely relevant to the function of an uncharacterized protein, their importance is self-evident. Particularly, with the explosion of protein sequences entering into databanks and the relatively much slower progress in using biochemical experiments to determine their functions, it is highly desired to develop an automated method that can be used to give a fast answers to these questions. By hybridizing the functional domain (FunD) and pseudo-amino acid composition (PseAA), a new strategy called FunD-PseAA predictor was introduced. To test the power of the predictor, a highly non-homologous data set was constructed where none of proteins has 25% sequence identity to any other. The overall success rates obtained with the FunD-PseAA predictor on such a data set by the jackknife cross-validation test was 85% for the case in identifying membrane protein and non-membrane protein, and 91% in identifying the membrane protein type among the following 5 categories: (1) type-1 membrane protein, (2) type-2 membrane protein, (3) multipass transmembrane protein, (4) lipid chain-anchored membrane protein, and (5) GPI-anchored membrane protein. These rates are much higher than those obtained by the other methods on the same stringent data set, indicating that the FunD-PseAA predictor may become a useful high throughput tool in bioinformatics and proteomics.     

Tissue-specific ribosomal protein composition

Membrane-bound and free polysomes from murine liver and kidney were isolated under identical conditions and their ribosomal proteins were compared by two-dimensional gel electrophoresis. The results demonstrate that these ribosome subpopulations are quantitatively and qualitatively similar except for the presence of one additional protein in the kidney-bound polysomal fraction.