杨树派间不同种的遗传密码子使用频率分析

遗传密码子的简并性特征造成了不同物种使用的密码子存在偏爱性。了解不同物种的密码子使用特点,可以为外源基因导入过程中的基因改造提供依据,从而实现外源基因的高效表达。杨树是世界上广泛栽培的重要造林树种之一,已经成为林木基因工程研究的模式植物。本研究采用高频密码子分析法,对美洲山杨P.tremuloides,毛白杨P.tomentosa,美洲黑杨P.deltoids和毛果杨P.trichocarpa 4种杨树的蛋白质编码基因序列(CDS)进行了分析,计算出了杨树同义密码子相对使用频率(RFSC),确定了4种杨树的高频率密码子,发现虽然不同种类的杨树密码子使用上有一些差别,但是偏爱密码子的差别却很小,共性的密码子占绝大多数。仅有Pro,Thr和Cys等少数几个氨基酸的偏爱密码子有差别。这种“共性”提示我们,用不同种的杨树中任何一种杨树的偏爱密码子所设计的外源基因在其他杨树中也可以使用。     

Lack of Distinction Between Nitrobacter agilis and Nitrobacter winogradskyi

No adequate criteria were established to distinguish between Nitrobacter agilis and N. winogradskyi. However, very gentle preparative techniques permitted demonstration of flagella in N. agilis.     

On the Distinction Between Lag and Delay in Population Growth

The analysis and results presented in this paper provide conclusive evidence to distinguish between the delay effect and the lag as two biologically distinct phenomena. It therefore dispels the incorrect notion that delay effects represented by delay differential equations are the biological reason behind the lag phase in microorganism growth. The resulting consequence so far is that the only other reason for the lag phase is the existence of unstable stationary states. The latter are a result of accounting for the microbial metabolic mass transfer in the population growth process.     

The Codon Statistics Database: A Database of Codon Usage Bias

We present the Codon Statistics Database, an online database that contains codon usage statistics for all the species with reference or representative genomes in RefSeq (over 15,000). The user can search for any species and access two sets of tables. One set lists, for each codon, the frequency, the Relative Synonymous Codon Usage, and whether the codon is preferred. Another set of tables lists, for each gene, its GC content, Effective Number of Codons, Codon Adaptation Index, and frequency of optimal codons. Equivalent tables can be accessed for (1) all nuclear genes, (2) nuclear genes encoding ribosomal proteins, (3) mitochondrial genes, and (4) chloroplast genes (if available in the relevant assembly). The user can also search for any taxonomic group (e.g., “primates”) and obtain a table comparing all the species in the group. The database is free to access without registration at http://codonstatsdb.unr.edu.     

五个鸡群中催乳素基因密码子使用频率与产蛋量的关系分析

通过鸡催乳素基因编码区基因扫描,发现3个SNP位点,分别是外显子2的C1607T、外显子5的C5749T和T5821C,3个SNP均没有改变氨基酸的编码.同时发现不同的单倍型间存在不同的密码子使用频率.对5个鸡群共370只鸡进行SSCP的基因型检测,共发现7种单倍型,结合44周龄产蛋量分析,发现不同单倍型的平均产蛋量存在显著性差异.结合密码子使用频率分析,发现使用高频密码子的单倍型个体产蛋量相对高.通过酶联免疫方法检测催乳素表达量,结果显示,使用高频密码子的个体,激素水平较高,其中使用2个高频密码子的单倍型个体和使用1.5个密码子的单倍型个体之间存在极显著差异.研究结果表明,密码子使用频率与产蛋量在一定的范围内呈现正相关趋势.     

Phenotypic Novelty in EvoDevo: The Distinction Between Continuous and Discontinuous Variation and Its Importance in Evolutionary Theory

The introduction of novel phenotypic structures is one of the most significant aspects of organismal evolution. Yet the concept of evolutionary novelty is used with drastically different connotations in various fields of research, and debate exists about whether novelties represent features that are distinct from standard forms of phenotypic variation. This article contrasts four separate uses for novelty in genetics, population genetics, morphology, and behavioral science, before establishing how novelties are used in evolutionary developmental biology (EvoDevo). In particular, it is detailed how an EvoDevo-specific research approach to novelty produces insight distinct from other fields, gives the concept explanatory power with predictive capacities, and brings new consequences to evolutionary theory. This includes the outlining of research strategies that draw attention to productive areas of inquiry, such as threshold dynamics in development. It is argued that an EvoDevo-based approach to novelty is inherently mechanistic, treats the phenotype as an agent with generative potential, and prompts a distinction between continuous and discontinuous variation in evolutionary theory.     

HYPERTROPHY OF THE HEART—Electrocardiographic Distinction Between Physiologic and Pathologic Enlargement

Electrocardiograms of marathon runners were examined to study hypertrophy of the heart due to prolonged physical exertion and to differentiate this from hypertrophy due to various disease states, especially essential hypertension, aortic valvular disease and coarctation of the aorta. The electrocardiogram of the marathon runners was characterized by a slow cardiac rate, high voltage of the QRS complexes and T waves in the standard and/or precordial leads with normal R/T ratios. There was moderate enlargement of the heart as observed on teleoroentgenogram. These findings are characteristic of physiologic hypertrophy of the heart and should be suspected among patients having a history of athletics calling for endurance. Immediately after running, all waves showed an increased voltage and the heart size decreased. The concept of the secondary T wave in hypertension as a part of the left ventricular strain pattern was challenged by the observation that the increased voltage of the R waves in lead V5 and other leads seen in marathon runners and in certain patients with hypertension, aortic stenosis, aortic insufficiency and coarctation of the aorta were not necessarily associated with typical discordant S-T segments and T waves. There was a higher incidence of dyspnea, angina pectoris and cardiac enlargement among hypertensive patients with discordant T waves than among hypertensive patients without these changes. Thus it is felt that the discordant waves are primary and are not merely secondary to the increased area of the R waves. Primary T waves suggest myocardial disease, possibly anoxia of the subendocardium.     

The Comparative Genomics of Polyglutamine Repeats: Extreme Difference in the Codon Organization of Repeat-Encoding Regions Between Mammals and Drosophila

Polyglutamine repeats within proteins are common in eukaryotes and are associated with neurological diseases in humans. Many are encoded by tandem repeats of the codon CAG that are likely to mutate primarily by replication slippage. However, a recent study in the yeast Saccharomyces cerevisiae has indicated that many others are encoded by mixtures of CAG and CAA which are less likely to undergo slippage. Here we attempt to estimate the proportions of polyglutamine repeats encoded by slippage-prone structures in species currently the subject of genome sequencing projects. We find a general excess over random expectation of polyglutamine repeats encoded by tandem repeats of codons. We nevertheless find many repeats encoded by nontandem codon structures. Mammals and Drosophila display extreme opposite patterns. Drosophila contains many proteins with polyglutamine tracts but these are generally encoded by interrupted structures. These structures may have been selected to be resistant to slippage. In contrast, mammals (humans and mice) have a high proportion of proteins in which repeats are encoded by tandem codon structures. In humans, these include most of the triplet expansion disease genes. Received: 17 August 2000 / Accepted: 20 November 2000     

The Selection-Mutation-Drift Theory of Synonymous Codon Usage

It is argued that the bias in synonymous codon usage observed in unicellular organisms is due to a balance between the forces of selection and mutation in a finite population, with greater bias in highly expressed genes reflecting stronger selection for efficiency of translation. A population genetic model is developed taking into account population size and selective differences between synonymous codons. A biochemical model is then developed to predict the magnitude of selective differences between synonymous codons in unicellular organisms in which growth rate (or possibly growth yield) can be equated with fitness. Selection can arise from differences in either the speed or the accuracy of translation. A model for the effect of speed of translation on fitness is considered in detail, a similar model for accuracy more briefly. The model is successful in predicting a difference in the degree of bias at the beginning than in the rest of the gene under some circumstances, as observed in Escherichia coli, but grossly overestimates the amount of bias expected. Possible reasons for this discrepancy are discussed.     

Reconstitution of Embryo-Like Structures from Sea Urchin Embryo Cells: Distinction Between Cell-Cell and Cell-Substrate Associations

Sea urchin embryos can be dissociated into a suspension of single cells that reconstitute embryo-like structures. When reconstitution is conducted in stationary cultures the first step is attachment of the cells to the culture plate, which requires calcium and metabolic energy but not protein synthesis. We have found that protease treated cells form cell-cell associations in stationary cultures without attaching to the culture plates, and that cell-plate attachments are unaffected by inhibition of protein synthesis. These data suggest that cell surface proteins are needed for cell-plate attachment and that these proteins are present on freshly dissociated cells. We also demonstrated that butanol extracted cells attach to the plates, but do not form functional cell-cell associations unless the butanol extracted material is restored to them. We conclude that sea urchin embryo cells contain two classes of attachment components. The first class functions in the cell-plate attachments, is protease sensitive, and not extracted by butanol; the second class is necessary for cell-cell associations, is protease insensitive, and extracted by butanol. Since protease treated cells reconstitute embryo-like structures without attaching to the culture plates, only the second class of attachment components is necessary for embryo reconstitution.     

Intron Length and Codon Usage

The correlation was shown between the length of introns and the codon usage of the coding sequences of the corresponding genes, which in some cases can be related to the level of gene expression. The link is positive in the unicellular organisms, i.e., genes with the longer introns show the higher bias of codon usage. It is most pronounced in baker's yeast, where it is definitely related to the level of gene expression—genes with the higher level of expression have the longer introns. The correlation is inverted in multicellular organisms as compared to unicellular ones. Some organisms, however, do not show the link. The presence or absence of the link does not seem to be related to the GC percent of the coding sequences. Received: 7 December 1999 / Accepted: 10 May 2000     

Codon usage and genome evolution

The rates and patterns of evolution at silent sites in codons reveal much about the basic features of molecular evolution. Recent increases in the amount of sequence data available for various species and more precise knowledge of the chromosomal locations of those sequences, coming in particular from genome projects, reveal that some features of molecular evolution vary around the genome.     

Codon usage and genome composition

Summary The GC levels of codon third positions from 49 genomes coveering a wide phylogenetic range are linearly correlated with the GC levels of the corresponding genomes. Three different relationships have been found: one for prokaryotes and viruses, one for lower eukaryotes, and one for vertebrates. All points not fitting the first relationship can be brought into quasi coincidence with it when plotted against GC levels of coding sequences.