家蚕磷酸吡哆醇氧化酶基因的表达谱分析

【目的】了解家蚕Bombyx mori维生素B6关键代谢酶磷酸吡哆醇氧化酶（pyridoxine- 5′-phosphate oxidase, PNPO）基因在家蚕不同发育阶段及5龄幼虫不同组织中的表达差异。【方法】将家蚕PNPO基因的重组表达质粒pET-22b(+)-PNPO转化入大肠杆菌Escherichia coli Rosetta中诱导表达, 纯化蛋白制备多克隆抗体。分别采用荧光定量PCR和Western blot方法对家蚕PNPO基因进行了转录水平和翻译水平的表达分析。【结果】在家蚕发育水平上, 5龄幼虫的PNPO翻译量为最高。PNPO基因在5龄幼虫各组织中的转录水平由高到低依次为精巢、 头、 中肠、 马氏管、 卵巢、 表皮、 脂肪体、 丝腺; 翻译量也以精巢为最高, 其次是头、 中肠和马氏管。【结论】明确了PNPO在家蚕各发育阶段及5龄幼虫各组织中的表达情况。     

三棱内酯B调控人冠状动脉内皮细胞基因表达谱的生物信息学分析

目的:分析三棱内酯B在人冠状动脉内皮细胞中的表达谱数据集,寻找三棱内酯B调控血管内皮功能的关键作用靶点。方法:基于GEO公共数据库,下载原始表达谱数据集(GSE44598),经过差异基因筛选,功能注释,通路富集,信号通路网络以及基因互作网络分析,找出三棱内酯B对人冠状动脉内皮细胞基因表达谱产生影响的关键基因和信号通路。结果:同对照组相比,三棱内酯B给药组共有5224个基因有显著性差异,包括2628个上调基因和2596个下调基因。基因功能注释和信号通路富集分析表明,差异基因主要参与了细胞周期过程。网络分析显示,MAPK信号通路、细胞周期通路以及PLCG2,PRKACA和ADCY4等为关键信号通路和基因。结论:三棱内酯B通过影响PLCG2,PRKACA,ADCY4等基因的表达,参与MAPK和细胞周期等信号通路,从而调节人冠状内皮细胞的功能。这些关键基因和信号通路是三棱内酯B在心血管疾病治疗应用中潜在的作用靶点。     

Improving profile HMM discrimination by adapting transition probabilities

Profile hidden Markov models (HMMs) are used to model protein families and for detecting evolutionary relationships between proteins. Such a profile HMM is typically constructed from a multiple alignment of a set of related sequences. Transition probability parameters in an HMM are used to model insertions and deletions in the alignment. We show here that taking into account unrelated sequences when estimating the transition probability parameters helps to construct more discriminative models for the global/local alignment mode. After normal HMM training, a simple heuristic is employed that adjusts the transition probabilities between match and delete states according to observed transitions in the training set relative to the unrelated (noise) set. The method is called adaptive transition probabilities (ATP) and is based on the HMMER package implementation. It was benchmarked in two remote homology tests based on the Pfam and the SCOP classifications. Compared to the HMMER default procedure, the rate of misclassification was reduced significantly in both tests and across all levels of error rate.     

长期施肥对红壤稻田氮储量的影响

稻田背景氮高是我国氮肥利用率低的主要原因之一,减少氮肥施用量对提高氮肥的农学利用率和缓解环境压力具有重要的意义。研究采用长期定位试验(19902006年)土壤全氮、稻谷产量等数据,分析施肥模式对稻田耕层土壤氮储量、氮肥农学利用率的影响,探讨在降低常规施用氮量的33.3%而不明显减产措施的可行性。结果表明:长期有机物质循环利用能显著提高耕层土壤全氮含量,氮储量与试验前相比平均提高了18.8%,仅施用化肥对土壤全氮含量没有显著影响,减量施肥处理(JS)对耕层土壤氮的积累效应一直优于仅施化肥的处理(NP、NPK)。17a的JS处理并没有降低稻谷产量,与常量NPK储量相比年际产量相对误差仅为3.2%,而输入N的农学利用率提高了12%。在半量稻草还田的条件下减少氮肥的施用量到180kg·hm-2是可行的,红壤稻田产量可维持在10t·hm-2左右。     

基于流形学习的基因表达谱数据可视化

基因表达谱的可视化本质上是高维数据的降维问题。采用流形学习算法来解决基因表达谱的降维数据可视化,讨论了典型的流形学习算法（Isomap和LLE）在表达谱降维中的适用性。通过类内／类间距离定量评价数据降维的效果,对两个典型基因芯片数据集（结肠癌基因表达谱数据集和急性白血病基因表达谱数据集）进行降维分析,发现两个数据集的本征维数都低于3,因而可以用流形学习方法在低维投影空间中进行可视化。与传统的降维方法（如PCA和MDS）的投影结果作比较,显示Isomap流形学习方法有更好的可视化效果。     

表皮生长因子诱导人成纤维细胞基因表达谱的变化

深入研究EGF对靶细胞的作用有助于揭示细胞增殖、转化、凋亡以及胚胎发育的分子机理。本文采用cDNA微阵列技术,检测EGF持续作用48小时后人胚肺二倍体成纤维细胞基因表达谱的变化。结果显示:EGF长期作用诱导广泛的基因表达变化,在所检测的4096种人类基因中,有855种发生了变化,这些表达变化的基因参与细胞的能量代谢、生物合成、细胞周期调控及受体酪氨酸激酶和G蛋白耦连受体信号转导等细胞反应,其中最显著的变化趋势是GPCR及其相关蛋白基因表达的下调。     

甲型流感病毒基因组进化事件检测软件的实现

目的 流感病毒通过跨宿主迁移和基因组重配作用等进化事件引起抗原转换是造成流感大流行的主要原因;传统上利用系统发生树通过进化分析检测这些事件,而进化分析过程复杂并且算法参数较难设定.方法 作者曾提出了一种利用基因型谱检测甲型流感病毒基因组进化事件的新方法,弥补了进化分析的这些缺陷.在本文中,利用C++ Builder开发工具在Windows平台上实现了基因型谱分析方法.结果 利用甲型流感病毒进化事件检测软件,可以快速的检测跨宿主迁移和基因组重配作用等甲型流感病毒基因组进化事件.结论 甲型流感病毒进化事件检测软件可以作为流感病毒疫情监测控制中进化分析的辅助工具,无论在病毒基因组进化的基础研究和疾控实践中都将具有很强的应用价值.     

Risk factors in autism spectrum disorder: A Tunisian case-control study

BackgroundAutism spectrum disorder (ASD) is a neurodevelopmental condition that causes disability in social interaction, communication, and restrictive and repetitive behaviors. Common environmental factors like prenatal, perinatal, and/or postnatal factors play a key role in ASD etiologies. Moreover, specific metabolic disorders can be associated with ASD.Subjects and methodsWe performed a retrospective case-control study in child psychiatry clinics, involving 51 children with ASD and 40 typical development controls (TDC).ResultsWe found a correlation between children being breastfed for less than 6 months, having fathers more than 40 years old at childbirth in ASD compared to TDC group. Our study also associated low blood cholesterol and low erythrocyte magnesium levels with increased risk for ASD.ConclusionFindings support the implication of total cholesterol (TC) and erythrocyte magnesium level in defining autism outcome.     

不同土地利用方式土壤氨氧化微生物和反硝化微生物时空分布特征

研究不同土地利用方式下氮循环相关微生物在不同土壤剖面的分布,可为认识和理解土壤氮转化过程提供科学依据。土壤氨氧化微生物和反硝化微生物在调节氮肥利用率、硝态氮淋溶和氧化亚氮(N₂O)排放等方面有着重要作用。以北京郊区农田和林地两种土地利用方式为研究对象,分析土壤氨氧化潜势和亚硝酸盐氧化潜势在0—100 cm土壤剖面上的季节分布(春季和秋季),并通过实时荧光定量PCR方法表征土壤氨氧化和反硝化微生物的时空分布特征。结果表明,农田土壤氨氧化潜势、亚硝酸盐氧化潜势、氨氧化微生物和反硝化微生物丰度均显著高于林地土壤,且随土壤深度增加而显著降低。除氨氧化古菌amoA基因丰度在不同季节间无显著差异外,春季土壤氨氧化细菌(amoA基因)、反硝化微生物nirS、nirK和典型nosZ I基因的丰度均显著高于秋季。土壤有机质、总氮、NH~+₄-N、NO~-₃-N含量与氨氧化微生物和反硝化微生物的功能基因丰度显著相关。综上,不同土地利用方式下土壤氮循环相关微生物的丰度与土壤氮素的可利用性和转化过程紧密相关,研究结果对土壤氮素利用和养分管理提供...     

Study on the effects of sulfur fumigation on chemical constituents and antioxidant activity of Chrysanthemum morifolium cv. Hang-ju

The traditional after-harvesting drying method of C. morifolium cv. Hang-ju (HJ) is sun drying, but recently sulfur fumigation is increasingly used as a cheap and convenient method. However, the effects of sulfur fumigation on chemical constituents and potential activities of HJ were unknown. A comprehensively comparison of the chemical profiles between non-fumigated HJ (NHJ) and sulfur-fumigated HJ (SHJ) was conducted by HPLC fingerprints analysis and the discrepant peaks were identified or tentatively assigned by HPLC–ESI/MSⁿ. Dramatic chemical changes were found that the contents of 4 flavonoid aglycones remarkably increased while those of 7 glycosides significantly reduced which suggested that sulfur-fumigation induced flavonoid glycosides transformed into aglycons by hydrolysis reaction. A significant loss of hydroxycinnamoylquinic acids showed the sulfur fumigation was a destructive effect on HJ. Principal component analysis (PCA) was employed to rapidly discriminate NHJ and SHJ samples. By ICP-OES analysis, it was found that the residue of sulfur of SHJ were three times higher than NHJ (p < 0.05). The antioxidant activity of NHJ and SHJ were evaluated by DPPH and FRAP assay, and the results showed that NHJ had much stronger antioxidant activities than SCF (p < 0.05). Combining the results of chemical analysis, residue of sulfur and pharmacological evaluation, it showed that the sulfur fumigation was a destructive effect on HJ.