Amino acid compositions and evolutionary relationships with protein families.

We have examined the merits of the three functions based on amino acid compositions which have been proposed to indicate the similarity in amino acid sequences of two proteins; the difference index, the composition divergence and the composition coefficient. We have taken the amino acid compositions and sequences of 41 cytochrome c's and used the 820 values from all possible comparisons in the evaluation. We conclude that the functions do have a limited value in predicting proteins which are closely related in sequence and that the three functions are equivalent in this predictive ability. We have used the composition divergence values obtained from available pyruvate kinase amino acid compositions to generate a phylogenetic tree for this glycolytic enzyme.     

Classification of eubacteria based on their complete genome: where does Mycoplasmataceae belong?

The amino acid compositions of 11 Gram-positive and 12 Gram-negative eubacteria were determined from their complete genomes. They were classified into two groups, 'S-type' represented by Staphylococcus aureus and 'E-type' represented by Escherichia coli, based on their patterns of amino acid compositions determined from the complete genome. These two groups were characterized by their concentrations of Arg, Ala and Lys. Mycoplasmas, which lack a cell wall, belonged to the 'S-type', while Gram-positive mycobacteria belonged to the 'E-type'. Rickettsia prowazekii, Borrelia burgdorferi, Campylobacter jejuni and Helicobacter pylori, which are Gram-negative, belong to the 'S-type'. The classification into two groups based on their amino acid compositions determined from the complete genome was independent of Gram staining. In addition, the amino acid composition based on the plasmid resembled that based on the parent complete genome.     

The use of equilibrium density-gradient ultracentrifugation in the isolation and characterisation of glycoproteins with blood group P1 activity from sheep hydatid-cyst fluid.

Equilibrium density-gradient ultracentrifugation in caesium choride and caesium sulphate has been used in the isolation and fractionation of the glycoproteins specific for blood-group P1 from hydatid cyst fluids. The fractions obtained have distinct and systematic differences specifically related to their buoyant densities, chemical compositions and specific-activities for group P1. High levels of specific-activity were maintained over a large range of chemical compositions. The peptide content varied systematically from 2.5% for the densest fraction to 37% for the least dense fraction. The amino acid composition was essentially constant over all fractions. The proportion of glucosamine decreased and the proportions of galactosamine, mannose and glucose increased with increasing peptide content of the fractions. The data presented suggest the present of oligosaccharide side-chains of various lengths and compositions and/or the presence of oligosaccharide side-chains with very different chemical compositions, of which only some are associated with the specificity for group P1. The properties of the glycoproteins from hydatid cyst fluids have been compared with those of the glycoproteins from human ovarian cysts. Although some similarities have been demonstrated there are significant differences.     

Detecting thermophilic proteins through selecting amino acid and dipeptide composition features

Detecting thermophilic proteins is an important task for designing stable protein engineering in interested temperatures. In this work, we develop a simple but efficient method to classify thermophilic proteins from mesophilic ones using the amino acid and dipeptide compositions. Since most of the amino acid and dipeptide compositions are redundant, we propose a new forward floating selection technique to select only a useful subset of these compositions as features for support vector machine-based classification. We test the proposed method on a benchmark data set of 915 thermophilic and 793 mesophilic proteins. The results show that our method using 28 amino acid and dipeptide compositions achieves an accuracy rate of 93.3% evaluated by the jackknife cross-validation test, which is higher not only than the existing methods but also than using all amino acid and dipeptide compositions.     

FROG SCIATIC NERVE MYELIN: A CHEMICAL CHARACTERIZATION

Abstract— The lipid and protein compositions of PNS myelin from two species of frogs, Xenopus laevis and Rana catesbiana , are compared with each other and with those of the rat. The relative proportions of PNS myelin lipids in the two frog species and rat are very similar except for a somewhat higher phosphatidyl choline content in frog myelin. The protein compositions of frog PNS myelin of the two species are also much alike, but a protein smaller than P₂ is found in Xenopus , which is not seen in Rana . The results are discussed in terms of results found by others in other species and the compositions are compared with those of the corresponding CNS myelin.     

Polysaccharide compositions of primary cell walls of the palms Phoenix canariensis and Rhopalostylis sapida

The polysaccharide compositions of unlignified primary cell walls from two species of palms were examined. Cell-wall preparations were isolated from the stem apex, including the pre-emergent leaflets and rachides, of Phoenix canariensis (Canary Island date palm), and from leaflets and rachides dissected from pre-emergent leaves in the stem apex of Rhopalostylis sapida (Nikau palm). The non-cellulosic polysaccharides in the cell-wall preparations from both species had similar monosaccharide compositions, with arabinose and galactose being the predominant neutral monosaccharides, together with large amounts of galacturonic acid. These monosaccharide compositions indicated the presence of large proportions of pectic polysaccharides, including homogalacturonans. This was confirmed by linkage analyses of the cell-wall preparations which showed the presence of large proportions of pectic arabinans, together with pectic galactans and/or Type I arabinogalactans. Evidence for rhamnogalacturonan I and small amounts of rhamnogalacturonan II was also obtained. In addition to pectic polysaccharides, the cell-wall preparations contained smaller amounts of xyloglucans and even smaller amounts of heteroxylans, probably glucuronoarabinoxylans, and glucomannans and/or galactoglucomannans; (1→3,1→4)-β-D-glucans were not present. Although palms (Arecaceae) are commelinoid monocotyledons, the polysaccharide compositions of their primary cell walls resemble those of non-commelinoid monocotyledons and dicotyledons. These compositions contrast with those of primary cell walls of other commelinoid families which have glucuronoarabinoxylans rather than pectic polysaccharides as the major non-cellulosic polysaccharides. The results are discussed in relation to the possible evolution of the composition of primary cell walls of monocotyledons.     

A review of the use of copepods in marine fish larviculture

In spite of the growing interest and success obtained using cultured-copepods, their use in marine aquaculture remains sporadic. Besides, mass culture of several marine copepods has been well established by several authors. However, the upscale of copepod cultures to commercial levels is still a challenge. The practice of using wild copepods from natural ponds which thus increases the risk of parasitic infections of most species has limited their application in aquaculture. The present paper thus emphasizes on recent research efforts focused on the use of chemical treatments and freeze-thawing methods to eradicate procercoids from copepods. Research efforts focused on copepod culture systems which subsequently improved and refined their culture in marine fish larviculture are also well discussed. Advances in the use of copepod eggs as potential source of nauplii for marine fish larvae with special emphasis on the viability, storage conditions and biochemical compositions of the copepod eggs are underscored. Additionally, recent advances in the biochemical compositions (protein, amino acids, pigments, and vitamins) of copepods, which has received relatively little attention compared to researches on the lipid and fatty acid compositions are well emphasized. Specific recommended areas for further research are also proffered.     

The amino acid composition of mammalian and bacterial cells

Summary High performance liquid chromatography was used to analyze the amino acid composition of cells. A total of 17 amino acids was analyzed. This method was used to compare the amino acid compositions of the following combinations: primary culture and established cells, normal and transformed cells, mammalian and bacterial cells, andEscherichia coli andStaphylococcus aureus. The amino acid compositions of mammalian cells were similar, but the amino acid compositions ofEscherichia coli andStaphylococcus aureus differed not only from mammalian cells, but also from each other. It was concluded that amino acid composition is almost independent of cell establishment and cell transformation, and that the amino acid compositions of mammalian and bacterial cells differ. Thus, it is likely that changes in amino acid composition due to cell transformation or species differences between mammalian cells are negligible compared with the differences between mammalian and bacterial cells, which are more distantly related.     

矮依兰油化学成份分析

采用色谱—质谱—计算机(GC/MS)联用分析仪对矮依兰油、高依兰油和进口依兰油的主要化学成份进行了鉴定,尽管它们的成份及其含量有较大差异,但其整体香气特征无明显的差异,均可用作调香原料。     

福建省樟树叶精油的主成分分析及其化学型

对来源于福建省28个县（市）的329份樟树[Cinnamomum camphora（L．）Presl]叶精油的21个主要化学成分（占总化学成分含量的90．735％）进行了主成分分析和聚类分析。提取出12个主成分因子,累计贡献率达到84．342％,可基本描述樟树叶精油21个主要化学成分的变异情况。取λ=5．5,329份叶精油样品可被分为5个化学型：芳樟型（主要成分为芳樟醇）、脑樟型（主要成分为樟脑）、桉樟型（主要成分为1,8-桉叶油素）、黄樟型（主要成分为黄樟油素）和杂樟型（无明显主要成分）。除杂樟型外,其他化学型樟树叶精油的主要化学成分均较一致。     

Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins

A compact mitochondrial gene contains all essential information about the synthesis of mitochondrial proteins which play their roles in a small compartment of the mitochondrium. Almost no noncoding regions have been found through the gene, but a necessary set of tRNAs for the 20 amino acids is provided for biosynthesis, some of them coding different amino acids from those in a usual cell. Since the gene is so compact that the produced proteins would have some characteristic aspects for the mitochondrium, amino acid compositions of mitochondrial proteins (mt-proteins) were examined in the 20-dimensional composition space. The results show that compositions of proteins translated from the mitochondrial genes have a distinct character having more hydrophobic content than others, which is illustrated by a clustered distribution in the multidimensional composition space. The cluster is located at the tail edge of the global distribution pattern of a Gaussian shape for other various kinds of proteins in the space. The mt-proteins are rich in hydrophobic amino acids as is a membrane protein, but are different from other membrane proteins in a lesser content of Val. A good correlation found between the base and amino acid compositions for the mitochondria was examined in comparison to those of organisms such as thermophilic bacterium having an extreme G-C-rich base composition.     

Influence of selective processes on the amino acid compositions of proteins: collagen, cytochrome c, ferredoxin and alpha-crystallin

Deviations in the compositions of homologous proteins from a standard composition which minimizes these differences are characterized by two measures, the information gain and a generalization of the Dayhoff PAMs measure. It is shown that protein compositions cannot be understood as generated by a random process alone and that the proposed compositional analysis is sensitive enough to detect, in favourable cases, also the existence of specific adaptive processes. For α-crystallin A a previously unknown adaption of the composition is found and an explanation in terms of protein function proposed.     

Reciprocal amino acid substitutions in the evolution of homologous peptides

Amino acid sequences of peptides are often inferred from their amino acid compositions by comparison with homologous peptides of known sequence. The probabilities are considered that by such an approach errors are made due to the occurrence of balanced double changes, i.e. reciprocal substitutions, between two homologous peptides of identical compositions. Formulae are derived for the calculation of these probabilities, depending on peptide length and evolutionary distance. However, such calculations requiring too much computer time, the probabilities for reciprocal substitutions are estimated by simulation of evolutionary changes in peptides. It can be concluded from the resulting data that for many purposes the possible errors in amino acid sequences partially inferred from amino acid compositions are acceptably small.     

Comparison of fatty acid compositions in birds feeding in aquatic and terrestrial ecosystems

Fatty acid (FA) contents and compositions in the pectoral muscles of 18 bird species from Novosibirsk, Volgograd, and Yaroslavl oblasts were studied. Three groups of birds that had significantly different FA compositions were distinguished based on a multivariate statistical analysis: Passeriformes, Columbiformes, and a group of waterfowl and waterbird species (Charadriiformes, Anseriformes, Podicipediformes, and Ciconiiformes). The highest content of physiologically important docosahexaenoic acid (22:6n-3, DHA), which is considered a marker of aquatic food, was surprisingly found in the biomass of Passeriformes, which are terrestrial feeders, rather than in the biomass of waterfowls and waterbirds. It was suggested that Passeriformes species had the ability to synthesize large quantities of DHA from short-chain omega-3 FAs, which is rare among animals.     

玫瑰精油的提取和理化性质分析

采用水蒸汽蒸馏法从江西首次引种的大马士革玫瑰(Rose damascene Miller)花中提取获得精油,得率为0.023％.按照ISO 9842:2003玫瑰精油标准方法测定精油的物理指标和主要组分,结果表明:该精油为黄色液体,具有天然的玫瑰花香,其物理指标和特征组分的百分含量符合标准要求,且主要组分构成与标准中保加利亚玫瑰精油相似.气相色谱-质谱(GC-MS)结合直观推导式演进特征投影法(HELP)分析江西大马士革玫瑰精油,共鉴定出73个组分,其中香质组分较为完整,高品质玫瑰精油的标识成分β-突厥烯酮也被检出.     

Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria

One of the well-known observations of proteins from thermophilic bacteria is the bias of the amino acid composition in which charged residues are present in large numbers, and polar residues are scarce. On the other hand, it has been reported that the molecular surfaces of proteins are adapted to their subcellular locations, in terms of the amino acid composition. Thus, it would be reasonable to expect that the differences in the amino acid compositions between proteins of thermophilic and mesophilic bacteria would be much greater on the protein surface than in the interior. We performed systematic comparisons between proteins from thermophilic bacteria and mesophilic bacteria, in terms of the amino acid composition of the protein surface and the interior, as well as the entire amino acid chains, by using sequence information from the genome projects. The biased amino acid composition of thermophilic proteins was confirmed, and the differences from those of mesophilic proteins were most obvious in the compositions of the protein surface. In contrast to the surface composition, the interior composition was not distinctive between the thermophilic and mesophilic proteins. The frequency of the amino acid pairs that are closely located in the space was also analyzed to show the same trend of the single amino acid compositions. Interestingly, extracellular proteins from mesophilic bacteria showed an inverse trend against thermophilic proteins (i.e. a reduced number of charged residues and rich in polar residues). Nuclear proteins from eukaryotes, which are known to be abundant in positive charges, showed different compositions as a whole from the thermophiles. These results suggest that the bias of the amino acid composition of thermophilic proteins is due to the residues on the protein surfaces, which may be constrained by the extreme environment.     

琼南与琼北沿海低山丘陵植物物种组成的比较分析

在对海南岛南端与北端沿海低山丘陵植物区系进行实地调查的基础上,对两个地区植物物种组成进行了比较研究。结果显示两地物种组成既有相似性也有差异性：琼南有种子植物876种,隶属于112科484属,植物区系以热带成分为主,兼有一定的温带成分和中国特有成分,且海南特有成分较高,具有一定的过渡性;琼北有种子植物934种,隶属于141科580属,植物区系以热带分布类型为主,同时有一定的温带成分,海南特有成分较高;两地植物区系的共同点是：均具有种类丰富、地理成分多样、优势成分明显、热带性质较强等。     

Possible evolutionary relationships of the nitrogenase proteins

Comparisons of the amino acid compositions of the nitrogenase proteins from different organisms and their correlation with cross-reactivities and taxonomical data suggest an evolution within bacterial genomes rather than within plasmids. Comparisons of the amino acid compositions of nitrogenases and other ATP-ases show similarities which might be due to the evolution of these ATP-ases from a common ancestral protein.     

Amino acids dissolved in stream water as possible home stream odorants for masu salmon

It is well established that salmon return to their home stream by sensing the odors of the stream water. In this study we have attempted to identify the home stream odorants used by masu salmon in Lake Toya. The salmon in Lake Toya return to the home stream which flows into the lake after lake life for 2-3 years. Besides water from the home stream, waters from two other streams which flow into Lake Toya were also used in the experiments. We analyzed the compositions of amino acids, inorganic cations and bile acids in waters from the three streams. Application of mixtures of inorganic cations or bile acids, reconstituted based on the compositions of the stream waters, to the olfactory epithelium induced only very small responses. On the other hand, application of mixtures of amino acids induced large responses. The response to artificial stream water reconstituted based on the compositions of amino acids and salts closely resembles that to the corresponding stream water. Cross-adaptation experiments with three combinations of the mixtures were carried out. The response pattern for each combination closely resembled that to the corresponding combination of stream waters. Based on the results obtained, we concluded that amino acids dissolved in the home stream water are possible home stream odorants.     

The tryptic peptides of coyote (Canis latrans) hemoglobin

The tryptic peptides from α- and β-chains of coyote (Canis latrans) hemoglobin have been isolated and their amino acid compositions determined. The compositions are identical to those previously found for dog hemoglobin in all respects except one: the αT-13 peptide of coyote has only threonine at residue 130 of the chain. This indicates only one α-chain in coyote instead of two as in dog, which has one α-chain with threonine and one α-chain with alanine at this position. The α-chain from wolf (Canis lupus) is like that from coyote in having only threonine at residue 130.