牡竹属三竹种的秆形质量与材性比较

通过牡竹属(Dendrocalamus) 3个竹笋品质佳的竹种（勃氏甜龙竹(D.brandisii)、马来麻竹(D. asper)、花吊丝竹(D. minor var. amoenus)）竹材形态质量及材性比较的研究,结果表明：种间立竹枝下高、相对全高差异显著或极显著,勃氏甜龙竹相对枝下高最小,立竹胸径、全高、枝下高、尖削度值、壁厚率均为最大;竹秆含水率随立竹年龄增大而下降,3年立竹竹秆含水率花吊丝竹>勃氏甜龙竹>马来麻竹,种间差异极显著;相对材积勃氏甜龙竹（1771.35cm 3 cm-1）>马来麻竹（1166.66 cm3 cm-1）>花吊丝竹（659.78 cm3 cm-1）,种间差异极显著;竹材密度随立竹年龄增大而提高,3a立竹竹材密度花吊丝竹（0.914 g.cm-3）>勃氏甜龙竹(0.812 g.cm-3)>马来麻竹（0.749 g.cm-3）,种间差异显著。综合分析勃氏甜龙竹、马来麻竹可作为优良的笋材兼用竹种,花吊丝竹宜作为笋用、观赏竹种推广应用。     

几种模式生物基因组中最适密码对和稀有密码对使用的规律性

以6种模式生物基因组为样本,从密码对的碱基组成及密码子的使用两方面,分析了最适密码对与稀有密码对的使用。结果显示:6种生物的最适密码对rP双碱基TA出现的频数都是最低的,而出现频率最大的双碱墓对于古菌、细菌、真核是不同的;稀有密码对中双碱基TA出现的频数却是最高的,而出现频率最低的双碱基刘·于古菌、细菌、真核是不同的。这说明双碱基的分布与密码对的偏好性有很强的相关性,同时也与基因组进化存在关联。另外,我们也分析了本文的6种生物编码序列叶,最适密码对与稀有密码对的出现频数与密码了的相对使用频率的关系,发现密码对的出现频数与其密码子的使用存在相关性。     

The imprint of codons on protein structure

The "central dogma" of biology outlines the unidirectional flow of interpretable data from genetic sequence to protein sequence. This has led to the idea that a protein's structure is dependent only on its amino acid sequence and not its genetic sequence. Recently, however, a more than transient link between the coding genetic sequence and the protein structure has become apparent. The two interact at the ribosome via the process of co-translational protein folding. Evidence for co-translational folding is growing rapidly, but the influence of codons on the protein structure attained is still highly contentious. It is theorised that the speed of codon translation modulates the time available for protein folding and hence the protein structure. Here, past and present research regarding synonymous codons and codon translation speed are reviewed within the context of protein structure attainment.     

Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis

Patterns of codon usage have been extensively studied among Bacteria and Eukaryotes, but there has been little investigation of species from the third domain of life, the Archaea. Here, we examine the nature of codon usage bias in a methanogenic archaeon, Methanococcus maripaludis. Genome-wide patterns of codon usage are dominated by a strong A + T bias, presumably largely reflecting mutation patterns. Nevertheless, there is variation among genes in the use of a subset of putatively translationally optimal codons, which is strongly correlated with gene expression level. In comparison with Bacteria such as Escherichia coli, the strength of selected codon usage bias in highly expressed genes in M. maripaludis seems surprisingly high given its moderate growth rate. However, the pattern of selected codon usage differs between M. maripaludis and E. coli: in the archaeon, strongly selected codon usage bias is largely restricted to twofold degenerate amino acids (AAs). Weaker bias among the codons for fourfold degenerate AAs is consistent with the small number of tRNA genes in the M. maripaludis genome.     

Optimality of codon usage in Escherichia coli due to load minimization

The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslational errors and point mutations, an ability which in term is designated "load minimization". One parameter involved in calculating the load minimizing property of the genetic code is codon usage. In most bacteria, synonymous codons are not used with equal frequencies. Different factors have been proposed to contribute to codon usage preference. It has been shown that the codon preference is correlated with the composition of the tRNA pool. Selection for translational efficiency and translational accuracy both result in such a correlation. In this work, it is shown that codon usage bias in Escherichia coli works so as to minimize the consequences of translational errors, i.e. optimized for load minimization.     

Correspondence regarding October 31, 2003, Breakthroughs and Views by K. Brown and P.L. Carmichael

A. Fuglsang [Biochem. Biophys. Res. Commun. 317 (2004) 957-964] suggested that effective number of codons for individual amino acids (Nc-values) should be re-adjusted to the number of synonymous codons of those amino acids, in order to prevent the overestimation of the effective number of codons. Here, it is shown that re-adjustment at the level of individual amino acids results in loss of considerable amounts of information. Furthermore, we have shown that theoretical Nc-values are functions of GC3s (and GC1s); as a result, when an amino acid Nc-value exceeds the related theoretical Nc-value, the implication of re-adjustment depends on the GC composition of the gene.     

Modulation of Base-Specific Mutation and Recombination Rates EnablesFunctional Adaptation Within the Context of the Genetic Code

The persistence of life requires populations to adapt at a rate commensurate with the dynamics of their environment. Successful populations that inhabit highly variable environments have evolved mechanisms to increase the likelihood of successful adaptation. We introduce a 64 × 64 matrix to quantify base-specific mutation potential, analyzing four different replicative systems, error-prone PCR, mouse antibodies, a nematode, and Drosophila. Mutational tendencies are correlated with the structural evolution of proteins. In systems under strong selective pressure, mutational biases are shown to favor the adaptive search of space, either by base mutation or by recombination. Such adaptability is discussed within the context of the genetic code at the levels of replication and codon usage.Supplementary material to this paper is available in electronic form.Reviewing Editor: Dr. Edward Trifonov     

Serpins in Unicellular Eukarya, Archaea, and Bacteria: Sequence Analysis and Evolution

Most serpins irreversibly inactivate specific serine proteinases of the chymotrypsin family. Inhibitory serpins are unusual proteins in that their native structure is metastable, and rapid conversion to a relaxed state is required to trap target enzymes in a covalent complex. The evolutionary origin of the serpin fold is unresolved, and while serpins in animals are known to be involved in the regulation of a remarkable diversity of metabolic processes, the physiological functions of homologues from other phyla are unknown. Addressing these questions, here we analyze serpin genes identified in unicellular eukaryotes: the green alga Chlamydomonas reinhardtii, the dinoflagellate Alexandrium tamarense, and the human pathogens Entamoeba spp., Eimera tenella, Toxoplasma gondii, and Giardia lamblia. We compare these sequences to others, particularly those in the complete genome sequences of Archaea, where serpins were found in only 4 of 13 genera, and Bacteria, in only 9 of 56 genera. The serpins from unicellular organisms appear to be phylogenetically distinct from all of the clades of higher eukaryotic serpins. Most of the sequences from unicellular organisms have the characteristics of inhibitory serpins, and where multiple serpin genes are found in one genome, variability is displayed in the region of the reactive-center loop important for specificity. All the unicellular eukaryotic serpins have large hydrophobic or positively charged residues at the putative P₁ position. In contrast, none of the prokaryotic serpins has a residue of these types at the predicted P₁ position, but many have smaller, neutral residues. Serpin evolution is discussed.[Reviewing Editor: Dr. Peer Bork]     

Inferring parameters shaping amino acid usage in prokaryotic genomes via Bayesian MCMC methods

Molar content of guanine plus cytosine (G + C) and optimal growth temperature (OGT) are main factors characterizing the frequency distribution of amino acids in prokaryotes. Previous work, using multivariate exploratory methods, has emphasized ascertainment of biological factors underlying variability between genomes, but the strength of each identified factor on amino acid content has not been quantified. We combine the flexibility of the phylogenetic mixed model (PMM) with the power of Bayesian inference via Markov Chain Monte Carlo (MCMC) methods, to obtain a novel evolutionary picture of amino acid usage in prokaryotic genomes. We implement a Bayesian PMM which incorporates the feature that evolutionary history makes observed data interdependent. As in previous studies with PMM, we present a variance partition; however, attention is also given to the posterior distribution of "systematic effects" that may shed light about the relative importance of and relationships between evolutionary forces acting at the genomic level. In particular, we analyzed influences of G + C, OGT, and respiratory metabolism. Estimates of G + C effects were significant for amino acids coded by G + C or molar content of adenine plus thymine (A + T) in first and second bases. OGT had an important effect on 12 amino acids, probably reflecting complex patterns of protein modifications, to cope with varying environments. The effect of respiratory metabolism was less clear, probably due to the already reported association of G + C with aerobic metabolism. A "heritability" parameter was always high and significant, reinforcing the importance of accommodating phylogenetic relationships in these analyses. "Heritable" component correlations displayed a pattern that tended to cluster "pure" G + C (A + T) in first and second codon positions, suggesting an inherited departure from linear regression on G + C.