Trends in the codon usage patterns of Chromohalobacter salexigens genes

Chromohalobacter salexigens, a Gammaproteobacterium belonging to the family Halomonadaceae, shows a broad salinity range for growth. In order to reveal the factors influencing architecture of protein coding genes in C. salexigens, pattern of synonymous codon usage bias has been investigated. Overall codon usage analysis of the microorganism revealed that C and G ending codons are predominantly used in all the genes which are indicative of mutational bias. Multivariate statistical analysis showed that the genes are separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. Both NC plot and correspondence analysis on Relative Synonymous Codon Usage (RSCU) indicates that the variation in codon usage among the genes may be due to mutational bias at the DNA level and natural selection acting at the level of mRNA translation. Gene length and the hydrophobicity of the encoded protein also influence the codon usage variation of genes to some extent. A comparison of the relative synonymous codon usage between 10% each of highly and lowly expressed genes determines 23 optimal codons, which are statistically over represented in the former group of genes and may provide useful information for salt-stressed gene prediction and gene-transformation. Furthermore, genes for regulatory functions; mobile and extrachromosomal element functions; and cell envelope are observed to be highly expressed. The study could provide insight into the gene expression response of halophilic bacteria and facilitate establishment of effective strategies to develop salt-tolerant crops of agronomic value.     

绿洲景观中居民地空间分布特征及其影响因子分析

以张掖绿洲居民地为研究对象,用景观格局分析软件FRAGSTATS计算了5个景观格局指标,用GIS计算了形状指数、景观类型空间邻接比例、最邻近指数、最近距离以及居民地的耕作半径,借鉴聚落地理学中的居民地分布研究方法,分析了居民地的空间格局特征及其影响因子。结果表明：①耕地是张掖绿洲内的景观基质,居民地是绿洲内分布最广、斑块数最多的景观类型;居民地的平均斑块面积小、形状简单、聚集度高,与耕地的空间邻接长度和数目均最高,其空间分布类型存在空间差异;②耕地是影响居民地分布格局的重要因子。缓冲区分析方法可以从理论上确定居民地的耕作半径,耕作半径与居民地的空间分布类型紧密相关;③居民地到渠系的平均最临近距离为215m,75．6％的居民地中有渠系穿过;④居民地分布受中心城市——张掖市的影响程度极其明显,两者呈指数相关;⑤景观格局分析、居民地分布研究方法和GIS空间分析方法的有效结合,可以较好的反映居民地的空间分布特征及其影响因子的相关性;⑥借鉴聚落地理学的最近邻点指数具有明确的生态含义,可以作为量化景观聚集度的指标。     

Position dependent expression of GL2-type homeobox gene, Roc1: significance for protoderm differentiation and radial pattern formation in early rice embryogenesis

In early plant embryogenesis, the determination of cell fate in the protodermal cell layer is considered to be the earliest event in radial pattern formation. To elucidate the mechanisms of epidermal cell fate determination and radial pattern formation in early rice embryogenesis, we have isolated a GL2-type homeobox gene Roc1 (Rice outermost cell-specific gene1), which is specifically expressed in the protoderm (epidermis). In early rice embryogenesis, cell division occurs randomly and the morphologically distinct layer structure of the protoderm cannot be observed until the embryo reaches more than 100 microm in length. Nonetheless, in situ hybridization analyses revealed that specific expression of Roc1 in the outermost cells is established shortly after fertilization, much earlier than protoderm differentiation. In the regeneration process from callus, the Roc1 gene is also expressed in the outermost cells of callus in advance of tissue and organ differentiation, and occurs independently of whether the cells will differentiate into epidermis in the future or not. Furthermore, this cell-specific Roc1 expression could be induced flexibly in the newly produced outermost cells when we cut the callus. These findings suggest that the expression of Roc1 in the outermost cells may be dependent on the positional information of cells in the embryo or callus prior to the cell fate determination of the protoderm (epidermis). Furthermore, the Roc1 expression is downregulated in the inner cells of ligule, which have previously been determined as protodermal cells, also suggesting that the Roc1 expression is position dependent and that this position dependent Roc1 expression is important also in post-embryonic protoderm (epidermis) differentiation.     

Spatial associations of tree species in a subtropical evergreen broad-leaved forest

Aims The spatial segregation hypothesis and the low-frequency hypothesis are two important proposed mechanisms that delay or prevent competitive exclusion in ecosystems. Because tree species interact with their neighbors, the importance of these potential processes can be investigated by analyzing the spatial structures of tree species.Methods The distribution of the adults of 27 common tree species in a fully mapped 5-ha subtropical forest plot in Baishanzu, eastern China, was analyzed to investigate the community-level intra- and interspecific spatial association patterns. We first tested for the overall spatial pattern in the 5- to 40-m neighborhoods and classified first-order bivariate associations with a diametric scheme based on Ripley's K and nearest-neighbor statistic (G -function). Then heterogeneous Poisson null models were used to distinguish second-order interactions from overall spatial associations (including first-order effects). Finally, we analyzed correlations between the existence of species interactions and some attributes of the species involved.Important findings Partial overlap and segregation increased with scale, whereas mixing decreased. Nearly 70% of the species pairs occurred less than expected at random, and only 3.4% of the species pairs were well mixed; 11.0% of all species pairs showed significant small-scale interactions, which was a greater frequency than expected by chance if species are abundant or prefer the same habitat, but less frequent than expected if species are highly aggregated. This suggests that both spatial segregation and low frequency of species facilitate species coexistence by reducing the opportunity that trees of two species encounter each other. The study also revealed that positive interactions were more prevalent than negative interactions in the forest, which indicates that positive interactions may have important effects on forest species assemblies.     

Proton-motive force and the motile behavior of Bacillus subtilis

Changes in the proton-motive force cause a transient change in the motile behavior of Bacillus subtilis cells. Both an increase and a decrease in the proton-motive force cause transient tumbling. Simultaneous decrease of proton-motive force and increase of attractant concentration lessens the response toward the attractant. A simultaneous increase of proton-motive force and increase of attractant concentration prolonges the response toward attractant. A hypothesis explaining the various effects is given.Abbreviations KT medium potassium taxis medium - NaT medium sodium taxis medium - HT medium acidic taxis medium - OHT medium alkaline taxis medium - DNP 2,4-dinitrophenol     

祁连山红腹牧草蝗雌雄虫空间格局及关联性

应用地统计学的方法,研究了祁连山北坡石羊河上游,6—10月之间红腹牧草蝗Omocestus haemorrhoidalis(Charpentie)雌雄虫的空间分布格局、动态变化及空间相关性。结果表明:红腹牧草蝗雌雄虫的半变异函数为球状模型与高斯模型,二者空间分布类型相同,均呈聚集分布;随时间的变化均呈现"扩散-聚集-扩散-聚集"的动态特征,7—8月之间雌虫的变化强度明显强于雄虫;二者的模糊贴近度指数在0.53～0.71之间,且指数随红腹牧草蝗的生长呈逐渐增加到减少的变化特征,表明雌雄虫在数量与空间上有较强的跟随关系,且跟随关系随红腹牧草蝗的生长发生明显的阶段性变化。     

肽合成中多对二硫键的形成策略及分析方法

二硫键的正确配对是富含二硫键多肽合成的关键。本文综述了含两对二硫键以上的多肽二硫键的形成策略,优化方法、以及二硫键配对方式的测定方法。     

植物rRNA基因组织模式的荧光原位杂交比较分析

采用荧光原位杂交技术,对分属5个科的10种植物的分生细胞的18S-25S rRNA基因(45S rDNA)的组织模式进行了比较分析.45S rDNA探针在所有供试植物的间期核都产生了两种杂交信号:荧光强、位于核仁周边的纽和荧光较弱分布于核仁内的点,表明不同植物间期核的rDNA染色质的组织模式相似.在每种植物的部分间期细胞都观察到点与纽相连或从纽发出的情况,而且点的数目越多纽就变得越小,点的有无和数目的多少与细胞的活性呈正相关.这些事实表明,纽代表了处于凝缩状态的非活性的rDNA染色质,点是由纽解凝缩而来,rDNA异染色质解凝缩形成点是植物rRNA基因活跃转录的细胞学表现,在同一物种中点的多少代表了间期核rDNA转录活性的强弱.我们的结果支持点是核仁内活性rRNA基因组织的结构单位及rRNA合成发生地点的推论.我们的结果还显示,不同植物间期核的rDNA染色质的组织也存在一些差异,其中核仁内点的最大数目有较大的不同.在所有供试植物的有丝分裂前中期细胞,45S rDNA探针在rDNA位点都产生了松散的信号块和许多点,表明植物的rDNA位点在有丝分裂前中期还有较活跃的转录.     

浙北青冈林群落结构与青冈种群数量特征

本文通过群落和种群的调查,对浙江北部几个地区的青冈林群落结构及青冈种群的数量特征进行了研究,结果表明:青冈常绿阔叶林分层现象明显;各样地的相似是以地域为特征;青冈种群的大小结构有两种类型:纺锤形结构和不典型的金字塔形结构(倒"J"型);青冈种群主要是集群分布格局;从幼苗→大树的时间序列上,有从集群分布到随机分布的变化趋势。