基于支持向量机的细菌基因组水平转移基因预测

随着各种生物基因组序列测定工作的完成,大量的DNA序列数据涌现出来,为研究在基因组中寻找水平转移基因提供了极大的便利.将基因序列特征分析和支持向量机技术结合起来,通过分析基因序列的特征差异发现水平转移基因.依据以前研究工作的基础,选取了绝对密码子使用频率(FCU)作为序列特征,主要因为它既包含了基因密码子使用偏性的信息,也包含了基因所编码蛋白的氨基酸组成信息,支持向量机利用这些信息进行水平转移基因分析和预测,可以提高预测的准确性.另外,提出了基于分链的水平转移基因预测新方法,即将细菌基因组前导链和滞后链上的基因区别对待,分别进行水平转移基因预测.结果显示,基本预测方法要优于目前预测结果最好的Tsirigos等提出的基于八联核苷酸频率的打分算法,命中率的相对提高率最高达31.47%,而基于分链的方法对水平转移基因的预测取得了更好的结果.     

武汉地区硅质磷片金藻的初步研究

1986年11月,在武汉植物所的3个池塘及东湖附近的池塘内采集的标本中,含有大量的具硅质磷片的金藻,共11种,分别隶属于Spiniferomonas, Paraphysomonas, Chrysosphaevella, Mallomonas和Synura 5个属。本文提供了这些藻的硅质磷片、刺及毛的电镜照片。这些藻在中国研究得很少,许多种都是第一次报道,它们中的大多数在世界上其它一些地区也是普遍出现的,有些则毫无疑问地属于世界性分布。     

Eye drop delivery of nano-polymeric micelle formulated genes with cornea-specific promoters

BACKGROUND: This study evaluates the eye drop delivery of genes with cornea-specific promoters, i.e., keratin 12 (K12) and keratocan (Kera3.2) promoters, by non-ionic poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) polymeric micelles (PM) to mouse and rabbit eyes, and investigates the underlying mechanisms. METHODS: Three PM-formulated plasmids (pCMV-Lac Z, pK12-Lac Z and pKera3.2-Lac Z) containing the Lac Z gene for beta-galactosidase (beta-Gal) whose expression was driven by the promoter of either the cytomegalovirus early gene, the keratin 12 gene or the keratocan gene, were characterized by critical micelle concentration (CMC), dynamic light scattering (DLS), and atomic force microscopy (AFM). Transgene expression in ocular tissue after gene delivery was analyzed by 5-bromo-4-chloro-3-indolyl-beta-D-galactoside (X-Gal) color staining, 1,2-dioxetane beta-Gal enzymatic activity measurement, and real-time polymerase chain reaction (PCR) analysis. The delivery mechanisms of plasmid-PM on mouse and rabbit corneas were evaluated by EDTA and RGD (arginine-glycine-aspartic acid) peptide. RESULTS: The sizes of the three plasmid-PM complexes were around 150-200 nm with unimodal distribution. Enhanced stability was found for three plasmid-PM formulations after DNase I treatment. After six doses of eye drop delivery of pK12-Lac Z-PM three times a day, beta-Gal activity was significantly increased in both mouse and rabbit corneas. Stroma-specific Lac Z expression was only found in pKera3.2-Lac Z-PM-treated animals with pretreatment by 5 mM EDTA, an opener of junctions. Lac Z gene expression in both pK12-Lac Z-PM and pKera3.2-Lac Z-PM delivery groups was decreased by RGD peptide pretreatment. CONCLUSIONS: Cornea epithelium- and stroma-specific gene expression could be achieved using cornea-specific promoters of keratin 12 and keratocan genes, and the gene was delivered with PM formulation through non-invasive, eye drop in mice and rabbits. The transfection mechanism of plasmid-PM may involve endocytosis and particle size dependent paracellular transport.     

糖基化终产物对原代培养乳鼠肾脏细胞损伤的影响

糖基化终产物(AGEs)在糖尿病肾病的发生发展过程中起着重要的作用.但目前其作用机制还不太清楚.通过体外乳鼠肾脏细胞的原代培养,探讨AGEs对肾细胞的损伤作用及可能的作用机制.取出生3天的SD大鼠的乳鼠肾脏进行体外原代细胞培养,并取传代到4-6代的细胞进行实验研究.分别用不同浓度的AGEs(0、1.2、2.5、5、10、20 mg/ml),不同的作用时间(6、12、18、24 h)作用于体外培养的肾细胞,用MTT法检测AGEs对肾细胞的增殖情况,用酶试剂盒法检测AGEs对肾细胞培养液中乳酸脱氢酶(LDH)、β-N-乙酰氨基葡萄糖苷酶(NAG)的含量,以及肾细胞内还原型谷胱甘肽(GSH)和超氧化物歧化酶(SOD)的含量.实验结果表明随着AGEs作用肾细胞时间的延长和浓度的增加,细胞存活率、细胞内GSH含量和SOD活性均逐渐下降,而细胞培养液中LDH和NAG的含量则逐渐升高,与正常培养的对照组细胞相比差异非常显著(P＜0.001),并且AGEs对细胞的作用与其浓度和作用时间呈显著的量效关系.实验结果说明AGEs对原代培养的肾细胞有明显的损伤作用,并随着AGEs作用浓度的增加和作用时间的延长对肾细胞的损伤越来越严重,实验结果也表明.肾细胞对AGEs的作用很敏感,其损伤细胞的途径和作用机制可能是由于改变了肾细胞膜的通透性和降低肾细胞抗氧化能力,该实验研究也进一步提示了AGEs是导致糖尿病肾脏并发症发生的重要原因之一.     

城市化对空气污染人群暴露贡献的定量方法研究

短期快速城市化引发一系列生态环境问题,尤其是近年来以细颗粒物(PM_(2.5))为代表的城市与区域空气污染问题。人群的污染暴露一方面是因为污染区范围的扩张,另外一方面则归因于城市化引发的人口迁移,目前的研究重点关注于前者的贡献,而忽略了后者的贡献。因此,建立了城市化对空气污染人群暴露贡献的定量方法,并选取我国PM_(2.5)污染最为严重的京津冀城市群开展了实证研究,通过利用2000、2005、2010、2015年PM_(2.5)浓度和人口栅格数据以及人口自然增长率数据,定量评估了城市化引发的人口迁移对空气污染人群暴露的贡献。研究结果显示:(1)京津冀地区受污染影响面积和人口变化显著,造成大量的人口暴露于PM_(2.5)污染。(2)城市化引发的人口迁移与自然增长贡献率方面:总体上,2000—2015年,京津冀城市群总的人口迁移贡献率为48%,北京市和天津市总的人口迁移贡献率分别为94%和88%,而河北省污染总的人口迁移贡献率为-32%。其中在污染保持区,北京市和天津市的人口迁移贡献率均接近100%,而河北省的迁移贡献率为-26%,尤其在2010—2015年,河北省衡水市的人口迁移贡献率达到-6613%;在污染新增区,北京市和天津市的人口迁移贡献率分别为86%和84%,而河北省污染的人口迁移贡献率为-757%。本研究建立了定量化的方法揭示了城市化在空气污染人群暴露中的定量贡献,为科学引导城市化发展提供了定量的手段,为合理规划京津冀城市群地区的人口流动与空气污染奠定了数据基础。     

马铃薯卷叶病毒中国株(PLRV-Ch)复制酶基因结构研究

用设计合成的两对特异性引物,以马铃薯卷叶病毒中国分离株PLRV-Ch RNA为模板,经反转录PCR扩增,将复制酶基因3′端0.6 kb和5′端1.2 kb,克隆于pUC19中,分别构建了重组质粒pLR3和pLR5,并分五段进行了序列分析.将获得的核苷酸序列及氨基酸序列与国外报导的四个PLRV分离株的相应区段的序列同源性进行了比较.结果表明具有高度同源性.文中对核苷酸序列中存在的可能移码序列和其下游的茎环结构或假节结构、以及特征性三次重复区及氨基酸序列中复制酶蛋白N端的碱性氨基酸序列以及C端区域中包括GDD在内的8个特征序列进行了讨论.作者发现移码序列上游的三次重复的核苷酸序列可以形成连续折叠的互补双链区和发夹结构,这一结构可能和转译移码有关.此外PLRV复制酶蛋白N端部分氨基酸序列易变,而C端氨基酸序列十分保守,可能和复制酶功能有更重要关系.     

Molecular genetic characterization of rice seed lipoxygenase 3 and assessment of its effects on seed longevity

Lipoxygenases (LOXs) are enzymes involved in lipid peroxidation. Here we reported the identification, molecular and functional characterization of the gene encoding rice (Oryza sativa L.) seed LOX3 (sLOX3). Via a map-based cloning strategy we identified Os03g0700400 as the candidate gene encoding sLOX3. Further functional complementary test and biochemical characterization of the recombinant Os03g0700400 protein verified the identification. The sLOX3 gene was highly expressed in roots, moderately in embryos and very weakly in leaves, leaf sheaths and stems. Transient expression experiment (in rice protoplasts) and subsequent laser confocal microscopic analysis demonstrated that the sLOX3 protein was localized into the cytosol. We next showed that overexpression of sLOX3 in a japonica sLOX3-normal rice cultivar, Wuyunjing 7 accelerated the decrease of seed germination ability when the seeds were routinely stored, which demonstrated that sLOX3 had a negative effect on seed longevity (storability). Meanwhile, an increased occurrence of embryo decay was observed in the same transgenic seeds, suggesting that sLOX3 might negatively affect seed longevity by facilitating colonization of particular seed pathogens. Our result forwarded the understanding of the effects of 9-LOX on rice seed longevity.     

Phosphorylation on tyrosine-15 of p34(Cdc2) by ErbB2 inhibits p34(Cdc2) activation and is involved in resistance to taxol-induced apoptosis

ErbB2 overexpression confers resistance to taxol-induced apoptosis by inhibiting p34(Cdc2) activation. One mechanism is via ErbB2-mediated upregulation of p21(Cip1), which inhibits Cdc2. Here, we report that the inhibitory phosphorylation on Cdc2 tyrosine (Y)15 (Cdc2-Y15-p) is elevated in ErbB2-overexpressing breast cancer cells and primary tumors. ErbB2 binds to and colocalizes with cyclin B-Cdc2 complexes and phosphorylates Cdc2-Y15. The ErbB2 kinase domain is sufficient to directly phosphorylate Cdc2-Y15. Increased Cdc2-Y15-p in ErbB2-overexpressing cells corresponds with delayed M phase entry. Expressing a nonphosphorylatable mutant of Cdc2 renders cells more sensitive to taxol-induced apoptosis. Thus, ErbB2 membrane RTK can confer resistance to taxol-induced apoptosis by directly phosphorylating Cdc2.     

具有中等毒性的马氏钳蝎神经毒素的纯化和初步晶体学研究

运用柱层析技术对产自淅川和常德的马氏钳蝎毒素进行分离纯化,得到８种哺乳动物神经毒素。运用制备型等电聚焦电泳技术,对常德样品中具有中等毒性的蝎神经毒素（ＢｍＫ５）进一步纯化,获得了高纯度样品。两个产地的蝎毒素ＢｍＫ５均已经成功地获得了大晶体。空间群均为Ｐ２１２１２１,晶胞参数分别为：ａ＝３８．４６埃,ｂ＝３７．２８埃,ｃ＝３６．９７埃（淅川）;ａ＝３８．４４埃,ｂ＝３７．５５埃,ｃ＝３６．８３埃（常德）。对两个产地的晶体分别收集了２．１埃（淅川）和１．６２埃（常德）分辨率的衍射数据。