Synonymous Codon Usage Bias in Plant Mitochondrial Genes Is Associated with Intron Number and Mirrors Species Evolution

Synonymous codon usage bias (SCUB) is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons) are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes.     

根癌农杆菌转化紫草的研究

紫草 (ＬｉｔｈｏｓｐｅｒｍｕｍｅｒｙｔｈｒｏｒｈｉｚｏｎＳｉｅｂ .ｅｔＺｕｃｃ)是传统中药。其根部含有萘醌类化合物—紫草素及其衍生物 ,具有显著的抗菌、抗炎、抗癌以及促进伤口愈合等生理活性。紫草素同时也是一种名贵化妆品染料。科学家对紫草的研究兴趣是基于其资源的缺乏及紫草植物本身所具有的一些特点 ;如 :紫草素及其衍生物的颜色特性可凭借肉眼观察 ,紫草素及其衍生物只在紫草的根部积累 ,紫草素合成的次生代谢途径受多种酶和外界条件 (光照 ,营养等 )的调节等。紫草细胞培养 (Ｆｕｊｉｔａ等 ,1983;叶和春等 ,1991)可以产…     

宁夏枸杞的大、小孢子发生和雌、雄配子体发育

在幼小花药横切面上,每个角隅处可见一层拱形孢原细胞,其经过平周分裂形成初生造孢细胞、次生造孢细胞,发育为小孢子母细胞。减数分裂过程中胞质分裂为同时型。四分体为四面体型。成熟花粉粒含二细胞,具三孔沟型萌发孔。花药绒毡层由二部分组成:药壁区的绒毡层由初生壁细胞所产生,药隔区的由药隔细胞直接转化成,为双重起源,呈二型性,属分泌型。雌蕊由二个心皮构成二室子房,中轴胎座。倒生胚珠具单珠被、薄珠心,珠被绒毡层。胚囊发育为蓼型。在胚囊细胞分化后,组成胚囊的四种细胞继续发育,表现出各自的形态学变化。     

Development of new transformation-competent artificial chromosome vectors and rice genomic libraries for efficient gene cloning

The transformation-competent artificial chromosome vector (TAC) system has been shown to be very useful for efficient gene isolation in Arabidopsis thaliana (Proc. Natl. Acad. Sci. USA 96 (1998) 6535). To adapt the vector system for gene isolation in crops, two new TAC vectors and rice genomic libraries were developed. The new vectors pYLTAC17 and pYLTAC27 use the Bar gene and Hpt gene driven by the rice Act1 promoter as the plant selectable markers, respectively, and are suitable for transformation of rice and other grasses. Two representative genomic libraries (I and II) of an Indica rice variety Minghui63, a fertility restorer line for hybrid rice, were constructed with pYLTAC17 using different size classes of partially digested DNA fragments. Library I and library II consisted of 34,560 and 1.2 x 10(5) clones, with average insert sizes of approximately 77 and 39 kb, respectively. The genome coverage of the libraries I and II was estimated to be about 5 and 11 haploid genome equivalents, respectively. Clones of the library I were stored individually in ninety 384-well plates, and those of the library II were collected as bulked pools each containing 30-50 clones and stored in eight 384-well plates. A number of probes were used to hybridize high-density colony filters of the library I prepared by an improved replicating method and each detected 2-9 positive clones. A method for rapid screening of the library II by pooled colony hybridization was developed. A TAC clone having an 80 kb rice DNA insert was successfully transferred into rice genome via Agrobacterium-mediated transformation. The new vectors and the genomic libraries should be useful for gene cloning and genetic engineering in rice and other crops.     

Enhanced chemiluminescence enzyme‐linked immunoassay for the determination of DNA methyltransferase 1 in human serum

The occurrence of many diseases is closely related to the high expression of DNA methyltransferase 1 (DNMT1). However, most studies are focused on the detection of DNMT1 activity, a few are concerned with the detection of DNMT1 content. In this study, we developed a simple and highly sensitive chemiluminescence (CL) assay for the detection of DNMT1 content. In this method, anti‐DNMT1 monoclonal antibody was coated on a polystyrene microplate to capture DNMT1. Then anti‐DNMT1 polyclonal antibody and goat anti‐rabbit immunoglobulin G with horseradish peroxidase (IgG‐HRP) were respectively added to combine with captured DNMT1 to form a sandwich structure. Finally, the HRP could catalyze CL substrate and achieve CL signal response. Based on this novel sensitive strategy, the recovery percents were in the ranges from 71.5% to 91.0%. The precision of intra‐assays and inter‐assays were 5.45%–11.29% and 7.03%–11.25%, respectively. The method was successfully applied for the determination of DNMT1 in human serum. The detection results of serum samples showed that the proposed assay had a high correlation with enzyme‐linked immunosorbent assay (ELISA) kit. Compared with the ELISA kit (limit of detection = 0.1 ng/mL), the method has a lower limit of detection of 0.042 ng/mL. Therefore, our method has the potential for the detection of DNMT1 content in clinical diagnosis.     

Comprehensive metabolomic,proteomic and physiological analyses of grain yield reduction in rice under abrupt drought–flood alternation stress

Abrupt drought–flood alternation (T1) is a meteorological disaster that frequently occurs during summer in southern China and the Yangtze river basin, often causing a significant loss of rice production. In this study, the response mechanism of yield decline under abrupt drought–flood alternation stress at the panicle differentiation stage was analyzed by looking at the metabolome, proteome as well as yield and physiological and biochemical indexes. The results showed that drought and flood stress caused a decrease in the yield of rice at the panicle differentiation stage, and abrupt drought–flood alternation stress created a synergistic effect for the reduction of yield. The main reason for the decrease of yield per plant under abrupt drought–flood alternation was the decrease of seed setting rate. Compared with CK0 (no drought and no flood), the net photosynthetic rate and soluble sugar content of T1 decreased significantly and its hydrogen peroxidase, superoxide dismutase, peroxidase activity increased significantly. The identified differential metabolites and differentially expressed proteins indicated that photosynthesis metabolism, energy metabolism pathway and reactive oxygen species response have changed strongly under abrupt drought–flood alteration stress, which are factors that leads to the rice grain yield reduction.     

细菌萜类合成酶的生物信息学分析

【目的】目前对于萜类合成酶(Terpenoid synthase,TPS)的研究主要集中在植物和真菌中,而对细菌TPS的系统研究尚少。建立在大量已经被测序的细菌基因组基础上,利用生物信息学方法,对细菌TPS在全基因组范围内进行识别、分类和功能分析。【方法】利用TPS的隐马尔科夫模型(Pfam编号为PF03936)搜索自建的细菌蛋白质组数据库,预测出细菌TPS。对这些候选TPS的蛋白序列用MAFFT 7.130b进行多序列比对,并利用MEGA 6.0对多序列比对结果进行进化分析。利用MEME和PredictProtein分别进行细菌TPS的基序(Motifs)和点突变分析。【结果】建立在生物信息学分析的基础上,1 423条细菌TPS被识别,它们分布在8个门中,即放线菌门(Actinobacteria)、变形菌门(Proteobacteria)、蓝藻门(Cyanobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)、绿弯菌门(Chloroflexi)、酸杆菌门(Acidobacteria)和衣原体门(Chlamydiae)。进化分析表明细菌TPS可分为4大类,Motifs分析表明除了各类之间保守的基序(Motifs)外,还有特异的Motifs,这暗示着细菌TPS在不同类别之间的功能分化。点突变分析表明,细菌TPS不同位点的氨基酸突变对TPS功能的影响不同。【结论】细菌TPS主要分布于8个门中,其中在2个门中细菌TPS尚未见报道,即厚壁菌门(Firmicutes)与酸杆菌门(Acidobacteria)。基于进化分析,可以把细菌TPS分为4类,各类之间的差异可能是由类特异的Motifs决定的,另外细菌TPS不同氨基酸位点的突变分析为今后验证TPS的功能提供了很好的理论基础。     

Effects of europium ions (Eu3+) on the distribution and related biological activities of elements in Lathyrus sativus L. roots

Scanning electron microscopic and energy-dispersive X-ray analyses were used to study the distributions of different types of elements in the epidermis, exodermis, endodermis, and vascular cylinder of the fracture face in the Lathyrus sativus L. roots in the presence or absence of Eu³⁺. Some index of the biological activity related to the elements binding with protein were determined also. The results showed that the tissular distributions of elements in the fracture face are different in the presence and absence of Eu³⁺. The atomic percentages of P, S, Ca, and Mn were influenced more than those of other elements. Eu³⁺ promoted the biological activities of various kinds of element. The one possible mechanism changing the biological activities was that the reaction of Eu³⁺ Eu²⁺ would influence the electron capture or transport in elements of binding protein. Another mechanism was that CaM-Ca²⁺ becoming CaM-Eu³⁺ through Eu³⁺ instead of Ca²⁺ would affect the biological activity of elements by regulating the Ca²⁺ level in the plant cell.