Isolation and characterization of phenanthrene-degrading <Emphasis Type="Italic">Sphingomonas paucimobilis</Emphasis> strain ZX4

Phenanthrene-degrading bacterium strain ZX4 was isolated from an oil-contaminated soil, and identified as Sphingomonas paucimobilis based on 16S rDNA sequence, cellular fatty acid composition, mol% G + C and Biolog-GN tests. Besides phenanthrene, strain ZX4 could also utilize naphthalene, fluorene and other aromatic compounds. The growth on salicylic acid and catechol showed that the strain degraded phenanthrene via salicylate pathway, while the assay of catechol 2, 3-dioxygenase revealed catechol could be metabolized through meta-cleavage pathway. Three genes, including two of meta-cleavage operon genes and one of GST encoding gene were obtained. The order of genes arrangement was similar to S-type meta-pathway operons. The phylogenetic trees based on 16S rDNA sequence and meta-pathway gene both revealed that strain ZX4 is clustered with strains from genus Sphingomonas.     

DGGE analysis of 16S rDNA of ammonia-oxidizing bacteria in chemical–biological flocculation and chemical coagulation systems

Microbial community DNA was extracted from activated sludge samples taken from a chemical bioflocculation process and a chemical coagulation process in Shanghai, China. 16S rDNA of ammonia-oxidizing bacteria (AOB)was amplified by nested polymerase chain reaction and fingerprinted by denaturing gradient gel electrophoresis for microbial structure analysis. The Shannon diversity index of each sample was determined. The results indicated that the microbial structure of AOB in chemical bioflocculation process was comparable at two operational conditions. The ammonia-oxidizing bacterial communities were similar in three channels of the chemical bioflocculation process and in three serial tanks in the chemical coagulation process at the same condition. The diversity of microbial structures in the chemical bioflocculation process was higher than in the chemical coagulation process, in which the microbial structure was similar to that in the influent. Although the microbial study provides insights to the nitrification removal, higher microbial diversity of AOB does not necessarily mean higher ammonia oxidization. Molecular analysis should be combined with chemical assays to optimize operational conditions.     

Towards precise classification of cancers based on robust gene functional expression profiles

Background

Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method.

Results

We performed experimental evaluation by RT-PCR of three different computational gene finders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was computed and each component of it was evaluated. The results showed that de novo comparative methods can identify up to about 700 chicken genes with no previous evidence of expression, and can correctly extend about 40% of homology-based predictions at the 5' end.

Conclusions

De novo comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.     

中国粮食和农业植物遗传资源状况报告（Ⅰ）

10多年来,中国政府十分重视粮食和农业植物遗传资源的保护和可持续利用,并根据<粮食和农业植物遗传资源全球行动计划>20项优先领域,通过制定和完善相关的法律法规,加强了粮食和农业植物遗传资源的管理;通过培训和科普宣传,提高了公众意识;通过国际合作和协作网建设,实现了信息、人员和植物遗传资源的交流与交换;通过各种国家计划和项目的实施,建立和完善了植物遗传资源保护体系,实现了植物遗传资源的安全保存和可持续利用,为中国乃至世界植物育种和粮食安全发挥了较大作用. (1)对主要粮食和农业植物野生种进行了系统调查和编目,建立了116个原生境保护点,包括野生稻、野生大豆、小麦野 生近缘植物、野生蔬菜等,有效遏制了野生植物遗传资源的快速灭绝现象. (2)建成和完善了1座国家长期库、1座国家复份库、10座国家中期库、29座省级中期库、32个国家种质资源圃(含2个 试管苗库),另外7个种质圃正在建设中.基本形成了较为完善的国家植物遗传资源保护体系,长期保存植物遗传资源 397067份. (3)繁殖更新了286604份植物遗传资源,充实了中期库,极大地提高了植物遗传资源分发和供种能力.仅2001-2007年 就向全国2650个单位,提供了13.2万份次植物遗传资源. (4)国家投资1.8亿元人民币,于2003年建成了"作物基因资源与基因改良国家重大科学工程",为植物遗传资源具有重 大应用前景新基因的基因型鉴定、发掘提供了条件平台. (5)通过植物遗传资源的深入鉴定与评价,创造了一大批优异种质,培育了大量植物新品种并应用于生产,提高了植物遗 传资源的利用率.同时,中国政府十分重视植物遗传资源的多样性利用,通过不同作物间作套种、同一作物不同品种混合种 植.保护了品种的多样性,减少了病虫杂草危害. (6)通过加强植物遗传资源的管理,实现了国内植物遗传资源的共享,扩大了对外交流与交换,为中国乃至世界粮食安 全、国民经济又快又好地发展、减少贫困、增加农民收入做出了较大贡献. 尽管中国在粮食和农业植物遗传资源保护和利用方面取得了显著成绩,但还面临许多挑战.需要加强与其他国家和国 际组织的合作,获得国外植物遗传资源和相关技术;继续进行植物遗传资源,特别是野生植物遗传资源、边远地区古老农家品 种的调查及考察与收集,进一步建设和完善植物遗传资源保护体系,实现本国植物遗传资源的全面保护;系统深入地鉴定评 价已保存的植物遗传资源,提供育种家利用,拓宽育种材料的遗传基础;实现更加充分的资源共享和利益分享.进一步提高资 源利用效率.     

Variation in mutation rates caused by RB69pol fidelity mutants can be rationalized on the basis of their kinetic behavior and crystal structures

We have previously observed that stepwise replacement of amino acid residues in the nascent base-pair binding pocket of RB69 DNA polymerase (RB69pol) with Ala or Gly expanded the space in this pocket, resulting in a progressive increase in misincorporation. However, in vivo results with similar RB69pol nascent base-pair binding pocket mutants showed that mutation rates, as determined by the T4 phage rI forward assay and rII reversion assay, were significantly lower for the RB69pol S565G/Y567A double mutant than for the Y567A single mutant, the opposite of what we would have predicted. To investigate the reasons for this unexpected result, we have determined the pre-steady-state kinetic parameters and crystal structures of relevant ternary complexes. We found that the S565G/Y567A mutant generally had greater base selectivity than the Y567A mutant and that the kinetic parameters for dNMP insertion, excision of the 3′-terminal nucleotide residue, and primer extension beyond a mispair differed not only between these two mutants but also between the two highly mutable sequences in the T4 rI complementary strand. Comparison of the crystal structures of these two mutants with correct and incorrect incoming dNTPs provides insight into the unexpected increase in the fidelity of the S565G/Y567A double mutant. Taken together, the kinetic and structural results provide a basis for integrating and interpreting in vivo and in vitro observations.     

酪氨酸羟化酶与视网膜疾病

酪氨酸羟化酶（tyrosine hydroxylase,TH）是儿茶酚胺（catech01amines,CAs）合成过程中的限速酶,提高或抑制该酶的活性可大幅度影响CAs的合成。近年来对于TH的关注越来越多,大量的研究表明,TH含量及活性的异常改变能通过影响CAs的含量而导致相应生理功能的异常,从而导致疾病。本文将TH的结构功能、分布、表达变化及其与视网膜疾病关系做一综述。     

棉株上烟粉虱若虫种群的垂直分布与统计方法研究

对烟粉虱Bemisiatabaci在棉花植株上的垂直分布调查发现 ,烟粉虱在棉株各部位均有分布 ,且分布极不均匀 ,统计分析表明棉株各部位间烟粉虱的种群数量存在显著的差异。棉花顶部烟粉虱的若虫数量约占全棉株若虫总量的 1 6%,通过对棉株各部位烟粉虱的若虫数量与整株若虫总量的回归分析 ,建立了相应的回归方程式     

玫烟色拟青霉对小菜蛾致病力的时间-剂量-死亡率模型模拟

小菜蛾Plutella xylostella是我国南方十字花科蔬菜上的重要害虫,已对田间常用的化学杀虫剂产生了严重的抗性。为寻找有效的小菜蛾生物防治措施,本实验研究了一株分离自家白蚁的玫烟色拟青霉Paecilomyces fumosoroseus (SCAU-PFCF01)对小菜蛾2～4龄幼虫的致病力。实验采用浸液法,供试浓度为1×10³、1×10⁴、1×10⁵、1×10⁶和1×10⁷个孢子/mL。结果表明：随玫烟色拟青霉孢子浓度的升高,小菜蛾的感病死亡率增加,在浓度为1×10⁷ /mL时,小菜蛾2、3和4龄幼虫的累计死亡率分别为96%、85%和80%。玫烟色拟青霉对小菜蛾各龄幼虫的致病力与供试龄期有关,其感病的敏感顺序为2龄、3龄和4龄。用时间 剂量 死亡率模型（time-dose-mortality model,TDM）对各龄幼虫的致病力数据进行模拟,所建模型均顺利通过Hosmer-Lemeshow拟合异质性检验,表明模型拟合良好,并由模型估计出了该菌株对小菜蛾各龄幼虫的致死剂量与致死时间。2龄幼虫接种后第7天、3龄幼虫接种后第5天、4龄幼虫接种后第4天的LC₅₀估计值分别为1.17×10⁴、1.44×10⁴和5.21×10⁴ /mL,LC₉₀估计值分别为1.98×10⁶、3.82×10⁷和1.29×10⁸ /mL。玫烟色拟青霉对小菜蛾幼虫的致死时间与浓度相关,供试各龄幼虫的LT₅₀值随着孢子悬浮液浓度的增加而递减,在1×10⁵～1×10⁷ /mL的范围内,2龄幼虫的LT₅₀值从3.16天降低到1.72天,3龄幼虫的LT₅₀从3.21天降低到1.83天,4龄幼虫的LT₅₀从3.69天降低到2.04天。即2龄幼虫致死所需的时间最短,其次为3龄幼虫,4龄幼虫致死所需的时间最长。结果显示了该株玫烟色拟青霉在小菜蛾的生物防治中具较强的应用潜力。     

黑木耳多糖对急性脑缺血/再灌注损伤影响的研究

目的:观察黑木耳多糖(APP)对急性脑缺血大鼠的保护作用并探讨其相关机制。方法:成年雄性SD大鼠给予不同浓度的AAP灌胃20d,每天1次,腹腔注射银杏叶提取物(ginkgo biloba extract,EGb671)作为阳性对照,20d后实施右侧大脑中动脉栓塞(MCAO)建立局灶性脑缺血模型。MCAO60min后复灌,复灌24h后进行Longa神经功能损伤评分,并用2,3,5-氯化三苯基四氮唑(TTC)染色法测定脑梗死面积。复灌48h后用TUNEL免疫组化检测神经元凋亡,测定脑组织线粒体内活性氧簇(ROS)的生成量判断氧化应激水平。结果:黑木耳多糖能降低神经功能损伤评分,减小脑梗死面积,减少神经元凋亡,并且能够使缺血复灌脑组织线粒体ROS生成显著减少。高剂量AAP组的凋亡神经元数量、ROS生成量和阳性对照组相比有显著性差异。结论:黑木耳多糖能够对抗大鼠的局灶性脑缺血损伤,其保护作用和减轻氧化应激水平有关,并优于银杏叶提取物。     

Piperazine sulfonamide BACE1 inhibitors: Design,synthesis, and in vivo characterization

With collaboration between chemistry, X-ray crystallography, and molecular modeling, we designed and synthesized a series of novel piperazine sulfonamide BACE1 inhibitors. Iterative exploration of the non-prime side and S2′ sub-pocket of the enzyme culminated in identification of an analog that potently lowers peripheral Aβ₄₀ in transgenic mice with a single subcutaneous dose.