RBRDetector: Improved prediction of binding residues on RNA‐binding protein structures using complementary feature‐ and template‐based strategies

Computational prediction of RNA‐binding residues is helpful in uncovering the mechanisms underlying protein‐RNA interactions. Traditional algorithms individually applied feature‐ or template‐based prediction strategy to recognize these crucial residues, which could restrict their predictive power. To improve RNA‐binding residue prediction, herein we propose the first integrative algorithm termed RBRDetector (RNA‐Binding Residue Detector) by combining these two strategies. We developed a feature‐based approach that is an ensemble learning predictor comprising multiple structure‐based classifiers, in which well‐defined evolutionary and structural features in conjunction with sequential or structural microenvironment were used as the inputs of support vector machines. Meanwhile, we constructed a template‐based predictor to recognize the putative RNA‐binding regions by structurally aligning the query protein to the RNA‐binding proteins with known structures. The final RBRDetector algorithm is an ingenious fusion of our feature‐ and template‐based approaches based on a piecewise function. By validating our predictors with diverse types of structural data, including bound and unbound structures, native and simulated structures, and protein structures binding to different RNA functional groups, we consistently demonstrated that RBRDetector not only had clear advantages over its component methods, but also significantly outperformed the current state‐of‐the‐art algorithms. Nevertheless, the major limitation of our algorithm is that it performed relatively well on DNA‐binding proteins and thus incorrectly predicted the DNA‐binding regions as RNA‐binding interfaces. Finally, we implemented the RBRDetector algorithm as a user‐friendly web server, which is freely accessible at http://ibi.hzau.edu.cn/rbrdetector . Proteins 2014; 82:2455–2471. © 2014 Wiley Periodicals, Inc.     

角蛋白酶基因gm2886在密旋链霉菌ACT12中的表达及鉴定

通过生物信息学分析,在本实验室分离得到的1株羽毛高效降解菌微白黄链霉菌Fea-10基因组中发现基因gm2886(GenBank Accession Number:KY368946)可能编码一新的角蛋白酶,通过在该基因5'端和3'端分别连接红霉素抗性基因启动子(PermE)和组氨酸标签编码序列并构建在大肠杆菌-链霉菌穿梭质粒pSET152上,接合转入密旋链霉菌Streptomyces pactum ACT12,从而实现了异源表达,蛋白纯化后对其酶学性质进行了研究。实验结果表明,带有组氨酸标签编码序列的gm2886在密旋链霉菌ACT12中可以表达分泌得到1个大小约为36 kDa的蛋白。多种底物检测表明异源表达得到的重组蛋白GM2886-His6具有蛋白酶活性,可以降解水不溶性的天青角蛋白和羽毛粉;其最适温度和pH分别为50℃和pH 10.0。PMSF可抑制GM2886-His6的酶活,而EDTA不能,说明该酶为丝氨酸蛋白酶。本研究为从分子水平上解析羽毛高效降解菌Fea-10的活性机理,从而进一步开发其应用潜力提供了基础,同时可为该类蛋白酶的研究提供借鉴。     

Characterization of culturable bacterial endophytes of switchgrass (Panicum virgatum L.) and their capacity to influence plant growth

Switchgrass (Panicum virgatum L.) is a perennial warm season grass that is native to the plains of North America and is widely grown as a forage, bioenergy or groundcover crop. Despite its importance, a bottleneck in switchgrass production is poor seedling vigor, which as a perennial crop represents an important time for management. Herein, data identify a suite of culturable bacterial microflora extracted from switchgrass, and show their capability to influence host plant growth and development. A total of 307 bacterial isolates were cultured and isolated from surface sterilized switchgrass biomass and sequence identified into 76 strains (subspecies classification), 36 species and 5 phyla. Approximately 58% of bacterial strains, when reintroduced into surface‐sterilized switchgrass seeds, were documented to increase lamina length (cm from base to tip after 60 days growth) relative to uninoculated controls. Ecologically, Phylum Firmicutes was the most abundant bacterial classification and encompassed 75% of all isolates. Although the culturable bacterial community studies herein represent an unknown and assumedly minor proportion of the total microbiome, by focusing on culturable bacteria, we delineate functional feedback between the presence of isolated bacteria and switchgrass seedling growth.     

Enhanced production of Penicillium expansum PED-03 lipase through control of culture conditions and application of the crude enzyme in kinetic resolution of racemic Allethrolone

Alkaline lipase production was performed in submerged fermentation by Penicillium expansum PED-03. It was found that the suitable carbon source and nitrogen source for lipase production were 0.5% starch and 4.0% soybean meal, respectively. The maximal lipase activity (850 U/mL) of production was achieved at initial pH 5.5-6.0, 26 degrees C, 72 h. Tween-80 was an effective enhancer for lipase production. Agitation speed of the fermentor played an important role, and the suitable agitation speed for lipase production was 500 r/min. The lipase was stable within the range of pH 7.0-10.0 and 20-40 degrees C, and the optimum conditions for the enzymatic reaction were 35 degrees C and pH 9.5. The enzymatic resolution of racemic allethrolone (4-hydroxy-3-methyl-2-(2-propenyl)-2- cyclopenten-1-one) was carried out by the lipase from P. expansum PED-03, and the conversion reached 48% with excellent enantioselectivity (E > 100), which showed a good application potential in the production of optically pure allethrolone.     

利用激光扫描共聚焦显微镜研究视皮层脑片长时程增强过程中核酸的变化

本文使用 1 5— 2 0天龄幼年大鼠视皮层脑片的标本 ,在通氧状态下 ,用荧光探针 AO染色 ,激光扫描共聚焦显微镜对全脑片不同层面进行共聚焦断层扫描 ,沿纵轴每 2 0μm扫一次 ,共扫描 1 6次。再利用总值方式的投影算法对其三维重建 ,分析幼年大鼠视皮层脑片长时程增强过程中核酸的变化。     

木质素降解菌Bax的筛选及特性研究

为了高效降解造纸污水中木质素类化合物,采用苯胺兰和鞣酸平板法从腐木分离、筛选得到一株具有高降解木质素活性的丝状真菌,经鉴定为绿色木霉,命名为Bax.最适碳源为葡萄糖和蔗糖,最适氮源为蛋白胨和尿紊,最适酸碱度为pH 5.0,最适温度为30℃.通过对木质素氧化酶系分析,主要起作用的是漆酶和木质素酶,为造纸污水的处理奠定了基础.     

纽氏钝绥螨、尼氏钝绥螨及其猎物—桔全爪螨生态学特性的比较研究

本文从天敌与猎物的种群内禀增长力,天敌对猎物不同密度的功能反应及数值反应三个方面来评价和比较纽氏钝绥螨、尼氏钝绥螨时其猎物——枯全爪螨的控制作用。在五种温度下,两种捕食螨的种群内禀增长力都大于桔全爪螨。它们对猎物的功能反应属HollingⅡ型。尼氏钝绥螨的捕食量大于纽氏钝绥螨,在25℃时两种捕食螨捕食量最大,应用Rogers的模型能较好地对试验结果进行模拟。尼氏钝绥螨对桔全爪不同虫态的取食不存在选择效应,纽氏钝绥螨则嗜食若螨和幼螨。两种捕食螨对桔全爪螨的数值反应表明,仅供给桔全爪螨雌成螨作为食物,对两种捕食螨都不利,尤其对尼氏钝绥螨更为明显。综上所述,两种捕食螨能比较有效地控制桔全爪螨种群,当猎物密度较高时,尼氏钝绥螨控制效果优于纽氏钝绥螨,但纽氏钝绥螨控制效果优于纽氏钝绥螨,但纽氏钝绥螨田间种群数量比尼氏钝绥螨稳定。柑桔园中存在其它补充食物时对这两种捕食敌有利。     

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。     

干旱对浑善达克沙地榆叶片解剖结构的影响

采用石蜡切片法对浑善达克沙地流动沙丘顶部、丘间草地处的浑善达克沙地榆及呼和浩特市白榆叶的解剖结构进行了对比观察和分析,以期探讨浑善达克沙地榆在解剖学方面适应干旱的机理。结果表明,虽然属同种植物,但由于环境条件的不同,叶片的解剖结构表现出明显的差异。生境条件最差的流动沙丘顶部的浑善达克沙地榆的抗旱性最强,具体表现为:叶片厚,表皮细胞大,具有较厚的表皮细胞外壁与角质层;栅栏组织发达,细胞缩小,排列紧密。     

浮毛茛的组织培养与植株再生

1植物名称浮毛茛(Ranunculus natans C.A.Mey.),又称水毛。2材料类别基生茎。3培养条件愈伤组织诱导培养基:(1)MS 6-BA 1mg·L~(-1)(单位下同);(2)MS 6-BA 1 IBA 0.6:(3)MS 6-BA 1 IAA 0.6:(4)MS 6-BA 1 2,4-D 0.6;(5)MS 6-BA 1 NAA 0.6。愈伤组织分化培养基:(6)1/2MS 6-BA 0.2 NAA 0.1;(7)1/2MS 6-