Identifying G-protein coupled receptors using weighted Levenshtein distance and the nearest neighbor method

G-protein coupled receptors （GPCRs） are a class of seven-helix transmembrane proteins that have been used in bioinformatics as the targets to facilitate drug discovery for human diseases. Although thousands of GPCR sequences have been collected, the ligand specificity of many GPCRs is still unknown and only one crystal structure of the rhodopsin-like family has been solved. Therefore, identifying GPCR types only from sequence data has become an important research issue. In this study, a novel technique for identifying GPCR types based on the weighted Levenshtein distance between two receptor sequences and the nearest neighbor method （NNM） is introduced, which can deal with receptor sequences with different lengths directly. In our experiments for classifying four classes （acetylcholine, adrenoceptor, dopamine, and serotonin） of the rhodopsin-like family of GPCRs, the error rates from the leave-one-out procedure and the leave-half-out procedure were 0.62% and 1.24%, respectively. These results are prior to those of the covariant discriminant algorithm, the support vector machine method, and the NNM with Euclidean distance.     

密云水库上游流域生态系统服务功能空间特征及其与居民福祉的关系

生态系统管理的一个重要挑战是在区域尺度上管理生态系统服务并提高当地居民福祉。以2009年土地利用数据和社会经济数据为基础,利用InVEST模型和空间制图在乡镇尺度上对密云水库上游流域水资源供给服务、土壤保持服务、水质净化服务、产品供给服务以及居民福祉进行了定量评估和空间特征刻画,并探讨了生态系统服务与居民福祉的不同关系模式。结果表明,流域内各乡镇土壤保持服务从上游到下游呈逐渐递增的趋势,水质净化服务从上游到下游整体上也呈逐渐递增的趋势,流域内水质净化服务功能与水资源供给服务、粮食供给服务、蔬菜供给服务以及畜牧产品供给服务在空间上呈显著负相关;基于生态系统服务与居民福祉在空间上的聚集特征,可将56个乡镇划分为低服务低福祉模式、供给服务依赖模式和高服务高福祉模式,针对这3种关系模式特点,可分别提出改善生态系统服务功能和居民福祉的管理措施。案例研究可为其他区域实施分区管理、协调生态系统服务功能保护与居民福祉的关系提供借鉴。     

泛素化修饰与植物免疫应答

植物暴露在细菌、病毒和真菌等病原微生物环境中,病虫害是限制农作物产量和品质的主要因素,而植物病虫害的防治依赖于对植物抗病机制的深入认识。近年来的研究表明,蛋白质泛素化广泛地参与植物防御调节。蛋白质泛素化是真核生物中重要的翻译后修饰方式之一,在植物中,泛素化修饰在多种信号传导途径中发挥作用,如激素、光、糖应答,发育调节和病原菌防御信号途径等。综述了蛋白质泛素化修饰在植物免疫应答中的调控作用。     

Scalable GMP compliant suspension culture system for human ES cells

Suspension bioreactors are an attractive alternative to static culture of human embryonic stem cells (hESCs) for the generation of clinically relevant cell numbers in a controlled system. In this study, we have developed a scalable suspension culture system using serum-free defined media with spinner flasks for hESC expansion as cell aggregates. With optimized cell seeding density and splitting interval, we demonstrate prolonged passaging and expansion of several hESC lines with overall expansion, yield, viability and maintenance of pluripotency equivalent to adherent culture. Human ESCs maintained in suspension as aggregates can be passaged at least 20 times to achieve over 1×10(13) fold calculated expansion with high undifferentiation rate and normal karyotype. Furthermore, the aggregates are able to differentiate to cardiomyocytes in a directed fashion. Finally, we show that the cells can be cryopreserved in serum-free medium and thawed into adherent or suspension cultures to continue passaging and expansion. We have successfully used this method under cGMP or cGMP-equivalent conditions to generate cell banks of several hESC lines. Taken together, our suspension culture system provides a powerful approach for scale-up expansion of hESCs under defined and serum-free conditions for clinical and research applications.     

马传染性贫血病毒基因非编码区LTR嵌合克隆的构建

在已有全长感染性克隆pLGFD3-8和pD70344的基础上,根据马传贫弱毒疫苗致弱过程中不同代次毒株LTR序列的分析,在LTR U3区选取特定的酶切位点对EIAV非编码区LTR基因进行了部分替换.将替换的全基因克隆转染驴胎皮肤细胞(FDD)并以驴白细胞(DL)传代,用逆转录酶活性检测、RT-PCR方法及Real-time RT-PCR验证其感染性.结果发现,其衍生病毒感染上述两种细胞均出现明显的细胞病变;细胞培养上清可检测到RT酶活性和RT-PCR阳性.电镜下可见大量典型的EIAV颗粒.pLGFD9-12嵌合克隆衍生病毒与其父本克隆衍生病毒pLGFD3-8具有相似的复制水平,pLGFD9-12嵌合克隆衍生病毒在DL细胞上复制水平略高于FDD细胞.此结果为进一步深入研究LTR对马传染性贫血病毒复制水平和毒力的影响奠定了基础.     

黄猄蚁对橡胶盔蚧种群消长的影响

调查西双版纳地区黄猄蚁OecophyllasmaragdinaFabricius对橡胶盔蚧Parasaissetianigra(Nietner)种群数量和寄生蜂的影响。结果表明:黄猄蚁对橡胶盔蚧种群消长及寄生蜂均有影响。"有蚂蚁"枝条上介壳虫种群数量显著高于"无蚂蚁"枝条。"有蚂蚁"枝条介壳虫死亡率和寄生蜂都显著低于"无蚂蚁"枝条。说明黄猄蚁的存在影响了橡胶树介壳虫的种群繁殖率和死亡率。建议在今后综合防治中,充分利用蚂蚁与橡胶树介壳虫关系。通过驱逐橡胶树上的蚂蚁来有效遏制介壳虫的发生。     

Tat-MANF融合蛋白的制备及生物活性研究

目的：构建用于表达具有Tat序列的新型神经营养因子MANF（mesencephalic astrocyte-derived neurotrophic factor）融合蛋白（Tat-MANF）的重组质粒;利用原核细胞表达系统表达该重组蛋白,并检测其生物学活性。方法：以MANF cDNA为模板,利用PCR技术在上下游分别添加TAT序列和His标签及合适的限制性酶切位点,构建TAT-MANF融合基因。插入表达载体Pet22b⁺后,转化大肠杆菌BL21进行表达和纯化,用SDS-PAGE及Western印迹鉴定表达的重组蛋白。为了验证Tat-MANF的生物学活性,用30μmol/L浓度的6-羟多巴胺（6-OHDA）对神经母胶质瘤细胞（SH-SY5Y）进行毒性诱导,同时加入2μg/ml的TAT-MANF及对照MANF蛋白,24h后用流式细胞仪检测细胞的凋亡率。用脑微血管内皮细胞（B-endo3）体外模拟血脑屏障,与FITC标记的Tat-MANF共孵育4h,荧光显微镜下观察。结果：成功构建TAT-MANF融合基因,表达产物与目的蛋白大小相符,能与MANF抗体发生结合反应。重组蛋白可减少由6-OHDA导致的SH-SY5Y细胞凋亡,Tat-MANF-FITC与B-end3细胞共孵育4h后,可见细胞内明显荧光。结论：获得的重组蛋白Tat-MANF具有神经细胞保护作用及跨膜功能,为进一步开展帕金森症的体内治疗研究奠定了物质基础。     

Cryopreservation of <Emphasis Type="Italic">Panax ginseng</Emphasis> Adventitious Roots

We tested desiccation and/or vitrification procedures to cryopreserve the adventitious roots of Panax ginseng, the source of commercially produced ginsenosides. When only desiccation was applied, the post-freeze survival of 3- to 4-mm root tips was <14% regardless of the composition of the preculture medium or the explant origin. Callus formation was frequently observed after cryopreservation. In contrast, 90% survival and 32.5% root formation efficiency were achieved after cryopreservation when a vitrification protocol was followed. Adventitious root cultures in flasks and bioreactors were reestablished from root tips cryopreserved by vitrification. A prolonged lag-phase and lower biomass production were recorded in post-freeze-regenerated cultures compared with control roots that were subcultured four times in flasks. However, biomass accumulations did not differ between control and regenerated roots at the end of the sixth subculturing period. After 40 days of culture in bioreactors, a mean value of 12.5 g dw L⁻¹ was recorded for post-freeze-regenerated cultures versus 9.1 g dw L⁻¹ for the control roots. Production of triol and diol ginsenosides in our bioreactor cultures also was enhanced after cryopreservation, by 41.0% and 89.8%, respectively. These results suggest that the vitrification method is successful for cryopreservation of P. ginseng adventitious roots.     

抗禽流感病毒多表位DNA疫苗的构建及其免疫效力研究

多表位DNA疫苗是建立在常规DNA疫苗基础上的一种新型疫苗。它是用表位作免疫原,这样就比较容易在一个表达载体上克隆病原体的多个抗原基因中具有免疫活性的部分。本试验以H5N1亚型禽流感病毒的HA和NP基因及其表位为基础构建了4个重组质粒：1 pIRES/HA（表达全长的HA基因）;2 pIRES/tHA（只表达HA基因的主要抗原表位区）;3 pIRES/tHANpep（融合表达HA基因的抗原表位区和NP基因的3个CTL表位）;4 pIRES/tHANpep-IFN-γ（用鸡的IFN-γ基因取代质粒pIRES/tHANpep中的neo基因）。分别用这4个重组质粒和空载体质粒pIRES1neo肌注免疫30日龄SPF鸡。免疫3次,间隔为2周,每次每只鸡的剂量为200μg。第3次免疫后两周以高致病性禽流感病毒H5N1强毒攻击,免疫及攻毒前后均采血检测HI抗体效价和外周血CD4⁺、CD8⁺T细胞的变化。结果发现,攻毒前各质粒免疫组均检测不到HI抗体,攻毒后1周存活鸡HI抗体效价迅速升高到64～256。流式细胞仪检测显示外周血CD4⁺、CD8⁺T细胞在疫苗免疫后都有不同程度的升高。空载体质粒对照组鸡（10只）在攻毒后3～8 d内全部死亡,其他各重组质粒免疫组鸡都获得了部分保护,保护率分别是：pIRES/HA组为545%（6/11）,pIRES/tHA组为30%（3/10）,pIRES/tHANPep组为36.3%（4/11）, pIRES/tHANPepIFNγ组为50%（5/10）。这些结果表明我们构建的多表位DNA疫苗能够诱导机体产生特异性免疫应答,并在同型禽流感强毒攻击时对鸡只提供了一定的保护。     

丹霞地貌沟谷生态效应

以广东省丹霞山为研究实例,探讨丹霞地貌特殊的沟谷生态效应.结果表明,丹霞地貌的特殊沟谷生态效应体现在以下两个方面:第一是丹霞地貌演变过程中形成了众多石峰隆起和沟谷凹陷,特殊的地貌环境使得沟谷中的生态因子与其它非丹霞地貌开阔区域产生差异,小气候相对封闭,水湿条件极好,为喜高温高湿的热带物种提供了较好的生存环境;沟谷所处位置的地理环境,如四周崖壁的光滑程度会影响到太阳光反射到沟谷的光强,这些都会对沟谷中的温湿度产生影响.第二是丹霞地貌特殊的生态条件,为沟谷地带孕育出一批热带性较强的分类群提供了可能,与相近纬度的诸多植被相比,丹霞地貌植物区系热带性明显增强,热带分布区类型所占比重比同纬度区域要大10%以上,大多数沟谷中热带性物种分布现象比较明显,藤本分布较多,蕨类植物也较丰富,耐水湿的植物区系发育良好;这实际上造成了植物水平分布上的移位,使中亚热带区域中分布有南亚热带甚至热带区域的物种,出现了由于其特殊的沟谷地貌效应而形成的与其地貌条件保持协调和平衡的演替顶级群落类型,称为地貌顶级群落.