EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences

Background  

Understanding gene regulatory networks has become one of the central research problems in bioinformatics. More than thirty algorithms have been proposed to identify DNA regulatory sites during the past thirty years. However, the prediction accuracy of these algorithms is still quite low. Ensemble algorithms have emerged as an effective strategy in bioinformatics for improving the prediction accuracy by exploiting the synergetic prediction capability of multiple algorithms.     

长时程增强诱导和维持过程中海马CA1区神经细胞粘附分子蛋白水平与mRNA表达的变化

既往研究发现,神经细胞粘附分子(neural cell adhesion molecules,NCAM)对海马CA1区突触传递长时程增强(longterm potentiation,LTP)的诱导和维持极为关键。本文采用原位杂交法和Western blot法,观察了大鼠海马腑片LTP诱导和维持过程中NCAM mRNA和蛋白水平的动态变化过程。结果显示,强直刺激诱发fEPSP斜率升高10 min时,海马CA1区NCAM mRNA染色阳性神经元数量显著增加(76.6±11.5个),NCAM蛋白水平亦明显升高(7.190±0.64任意单位/50μg蛋白)。强直刺激诱发fEPSP斜率升高1 h时,NCAM mRNA染色阳性神经元数量为73.3±14.0个,NCAM蛋白量为9.031±0.71任意单位/50 μg蛋白;与强直刺激后10 min比较,NCAM mRNA表达无显著变化,而NCAM蛋白水平变化明显。NMDA受体特异阻断剂AP-5在损害LTP的同时,显著抑制NCAM mRNA和蛋白的增加。实验结果表明,在大鼠海马LTP诱导和维持过程中,NCAM mRNA增强的表达相对稳定,而NCAM蛋白水平呈现先低后高的变化。     

Biocidal activity in plant pathogenic Acidovorax, Burkholderia, Herbaspirillum, Ralstonia and Xanthomonas spp.

Antibacterial and antifungal activity was investigated for strains of Acidovorax spp., Burkholderia spp., Herbaspirillum rubrisubalbicans and Ralstonia solanacearum ; strains representing 118 species and pathovars of Xanthomonas were also tested for phytotoxic capacity. Antibacterial activity was present in all Burkholderia spp. except B. andropogonis , in biovars II and III of R. solanacearum but not in biovars I and IV, and in two strains of Xanthomonas. Little antibacterial activity was recorded for Acidovorax spp. Antifungal activity was expressed by most strains of A. avenae ssp. avenae and A. avenae ssp. cattleyae. Weak or variable antifungal reactions were given by strains of A. avenae ssp. citrulli and no activity was expressed by A. konjaci. Most strains of B. caryophylli, B. cepacia, B. gladioli pv. agaricicola, B. gladioli pv. alliicola, B. gladioli pv. gladioli , B. glumae and B. plantari produced extensive inhibition zones against Rhodotorula mucilaginosa. Strains of H. rubrisubalbicans and R. solanacearum gave negative, weak or variable reactions. Strains of Xanthomonas spp. exhibited no antifungal activity. In all cases antifungal activity was caused by a low molecular weight toxin. Three Xanthomonas strains exhibited phytotoxic activity. The ecological implications of these data are discussed.     

大豆异黄酮糖苷酶的纯化及性质研究

利用Absidiasp.R菌株,通过液体发酵的方法,得到了一种高活性的大豆异黄酮糖基水解酶。该酶经硫酸铵分级沉淀、DEAE-Cellocuse(DE-52)离子交换层析纯化,被纯化了11倍,收率为10.9%;经SDS-聚丙烯酰胺凝胶电泳测得该酶的分子量为53kD;该酶的最适反应温度为50℃;最适pH为5.0;温度低于60℃,pH在5.0~7.0范围内该酶较稳定,Co2 、Ca2 对该酶有激活作用;Ag 、Cu2 对该酶有抑制作用。当以染料木甙为底物时该酶的米氏常数(Km)为1.3×10-2mol/L。等电聚焦电泳测得其等电点为3.2。     

Precise Reconstruction of Veins and Bile Ducts in Rat Liver Transplantation

Rat orthotopic liver transplantation (ROLT) remains a technically demanding procedure, especially regarding the reconstruction of the suprahepatic vena cava (SHVC). In this study, a new microsuture technique was developed for anastomosis of the SHVC, and a special single-groove cuff and blade-cut stent were introduced. With these modified techniques, we aimed to make a precise anastomosis of the SHVC and to provide optimal cuffs and stents for the reconstruction of the veins and bile ducts. According to different microsuture techniques for the SHVC and different types of cuffs and stents, three ROLT groups were created to compare the operation times and prognoses. Sham operations were performed as controls in the fourth group. The time expenditures with each step were compared among the transplantation groups. Biochemical parameters were tested at the end of a 1-month observation period. The short- and long-term survival rates of the transplantation groups were recorded and compared. Our new microsuture technique was faster than the conventional continuous suture technique for SHVC anastomosis (P < 0.05). The use of a single-groove cuff for reconstruction of the portal vein and the infrahepatic vena cava shortened the anastomotic time (P < 0.05). The use of blade-cut stents resulted in fewer biliary complications and better survival over the short and long terms (P < 0.05). Our new microsuture technique and the single-groove cuffs proved to be a precise method for venous reconstruction which shortened the anhepatic time and the anastomotic time significantly. The blade-cut stents apparently reduced the incidence of biliary complications. In summary, with this precise microsuture technique and delicate cuffs and stents, excellent long-term survival can be achieved easily and stably for ROLT.     

单穗升麻的柱头和雌配子体发育及胚胎发生

单穗升麻的雌蕊群由1～5枚离生心皮组成。子房单室,4～9枚倒生胚珠,双珠被,厚珠心;大孢子四分体呈线形或T形排列,合点端一个具功能。胚囊发育为蓼型。成熟胚囊中3个单核反足细胞,胞质浓密,在球形胚时期尚能观察到其退化痕迹。极核融合早,次生核位于合点端。胚胎发生为柳叶菜型;核型胚乳。雄蕊凋谢后1～2天花柱顶端腹缝线周围出现乳突细胞,雄蕊凋谢后3～5天延长成柱头毛。讨论了单穗升麻与南川升麻柱头可授期与花粉生活力的差异对传粉效果和结籽率的显著影响。     

雪豹（Uncia uncia）研究的文献计量评价

通过对1950—2010年SCI收录和1989—2010年CSCD收录的雪豹(Uncia uncia)研究文献分析,从年度文献数量变化、国家/地区分布、主要研究机构、期刊分布、发表文献作者、基金资助机构、刊载文献类型、学科类别和语种分布9个方面,对雪豹研究文献的分布规律和研究现状进行了统计分析。结果表明:在SCI上发表雪豹研究论文的国家排名依次是美(50.6%)、英(16.5%)、印度(12.5%)和中国(5.6%);在文献量机构排名方面,国际雪豹基金会和英国爱丁堡大学并列第一,中国科学院排名第五;中国的主要合作国家中包括了美、英和中亚国家(吉尔吉斯斯坦、蒙古)。无论是分布范围还是数量,中国雪豹资源都居于世界第一,而研究却不相匹配,国内在这方面还仍需努力。     

肾素-血管紧张素系统在调节肾脏活动和慢性肾功能不全中的作用

一、肾内RAS的组成、生物学特征及肾内分布;(一)有关RAS的研究进展;(二)肾脏组织局部的RAS;(三)AngⅡ受体的亚型及其在肾内的分布;二、AngⅡ对肾脏血流动力学的影响;三、AngⅡ对肾脏的非血流动力学效应;(一)AngⅡ的促生长作用及促纤维生成效应;(二)AngⅡ作为促炎症因子的作用;四、有关RAS在肾功能不全中的临床研究     

Response of physiological integration in Trifolium repens to heterogeneity of UV-B radiation

Physiological integration has been documented in many clonal plants growing under resource heterogeneity. Little is still known about the response of physiological integration to heterogeneous ultraviolet-B radiation. In this paper, the changes in intensity of physiological integration and of physiological parameters under homogeneous and heterogeneous ultraviolet-B radiation (280-315 nm) were measured in order to test the hypothesis that in addition to resource integration a defensive integration in Trifolium repens might exist as well. For this purpose, homogeneous and heterogeneous ultraviolet-B radiation was applied to pairs of connected and severed ramets of the stoloniferous herb Trifolium repens. Changes in intensity of water and nutrient integration were followed with acid fuchsin dye and ¹⁵N-isotope labeling of the xylem water transport. In order to assess the patterns of physiological integration contents of chlorophyll, ultraviolet-B absorbing compounds, soluble sugar and protein were determined and activities of superoxide dismutase (SOD) and peroxidase (POD) measured. When ramets were connected and exposed to heterogeneous UV-B radiation, the velocity of water transportation from the UV-B treated ramet to its connected sister ramet was markedly lower and the percentage of ¹⁵N left in labelled ramets that suffered from enhanced UV-B radiation was higher and their transfer to unlabelled ramets lower. In comparison with clones under homogeneous ultraviolet-B radiation, the content of chlorophyll, ultraviolet-B absorbing compounds, soluble sugar and activities of SOD and POD increased notably if ultraviolet-B stressed ramets were connected to untreated ramets. Chlorophyll and UV-B absorbing compounds were shared between connected ramets under heterogeneous UV-B radiation. This indicated that physiological connection improved the performance of whole clonal plants under heterogeneous ultraviolet-B radiation. The intensity of physiological integration of T. repens for resources decreased under heterogeneous ultraviolet-B radiation in favor of the stressed ramets. Ultraviolet-B stressed ramets benefited from unstressed ramets by physiological integration, supporting the hypothesis that clonal plants are able to optimize the efficiency of their resistance maintaining their presence also in less favorable sites. The results could be helpful for further understanding of the function of heterogeneous UV-B radiation on growth regulation and microevolution in clonal plants.     

The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins

The New York Consortium on Membrane Protein Structure (NYCOMPS) was formed to accelerate the acquisition of structural information on membrane proteins by applying a structural genomics approach. NYCOMPS comprises a bioinformatics group, a centralized facility operating a high-throughput cloning and screening pipeline, a set of associated wet labs that perform high-level protein production and structure determination by x-ray crystallography and NMR, and a set of investigators focused on methods development. In the first three years of operation, the NYCOMPS pipeline has so far produced and screened 7,250 expression constructs for 8,045 target proteins. Approximately 600 of these verified targets were scaled up to levels required for structural studies, so far yielding 24 membrane protein crystals. Here we describe the overall structure of NYCOMPS and provide details on the high-throughput pipeline.