Some comments on instability of false discovery rate estimation

Some extended false discovery rate (FDR) controlling multiple testing procedures rely heavily on empirical estimates of the FDR constructed from gene expression data. Such estimates are also used as performance indicators when comparing different methods for microarray data analysis. The present communication shows that the variance of the proposed estimators may be intolerably high, the correlation structure of microarray data being the main cause of their instability.     

栗柄金粉蕨的黄酮类成分

从栗柄金粉蕨（ Ｏｎｙｃｈｉｕｍ ｌｕｃｉｄｕｍ ） 地上部分的甲醇抽提物中分到１０ 个成分, 经详细的一维、二维核磁数据分析, 它们被鉴定为： 木犀草甙（１） , ３ , ７ － 二甲基槲皮素（２） , 高山甙Ｂ （３） , 金粉蕨素（４） , 栗柄醇（５） , 金粉蕨醇Ｂ（６） , β－ 谷甾醇（７） , 胡萝卜甙（８） ,齐墩果酸（９） 和蔗糖（１０） 。栗柄醇系新成分。１ , ２, ９ 系首次由金粉蕨属分到。     

Synonymous Codon Usage Bias in Plant Mitochondrial Genes Is Associated with Intron Number and Mirrors Species Evolution

Synonymous codon usage bias (SCUB) is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons) are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes.     

Apple Fruit Diameter and Length Estimation by Using the Thermal and Sunshine Hours Approach and Its Application to the Digital Orchard Management Information System

In apple cultivation, simulation models may be used to monitor fruit size during the growth and development process to predict production levels and to optimize fruit quality. Here, Fuji apples cultivated in spindle-type systems were used as the model crop. Apple size was measured during the growing period at an interval of about 20 days after full bloom, with three weather stations being used to collect orchard temperature and solar radiation data at different sites. Furthermore, a 2-year dataset (2011 and 2012) of apple fruit size measurements were integrated according to the weather station deployment sites, in addition to the top two most important environment factors, thermal and sunshine hours, into the model. The apple fruit diameter and length were simulated using physiological development time (PDT), an indicator that combines important environment factors, such as temperature and photoperiod, as the driving variable. Compared to the model of calendar-based development time (CDT), an indicator counting the days that elapse after full bloom, we confirmed that the PDT model improved the estimation accuracy to within 0.2 cm for fruit diameter and 0.1 cm for fruit length in independent years using a similar data collection method in 2013. The PDT model was implemented to realize a web-based management information system for a digital orchard, and the digital system had been applied in Shandong Province, China since 2013. This system may be used to compute the dynamic curve of apple fruit size based on data obtained from a nearby weather station. This system may provide an important decision support for farmers using the website and short message service to optimize crop production and, hence, economic benefit.     

下行易化系统及其参与神经病理痛的机制

神经病理痛是指由中枢或外周神经系统损伤或疾病引起的疼痛综合征.神经病理痛是临床上常见的一种疾病,但是其发病机制不甚清楚,临床上也缺乏有效的治疗手段.近年来的研究除了集中于痛觉的上行传导及中枢机制,以及痛觉的下行抑制之外,也证明下行易化系统激活参与神经病理痛的发病机制.本文拟对此进行综述,希望为治疗神经病理痛提供新思路.     

大鼠RVLG cDNA的克隆、原核表达和小鼠抗RVLG蛋白多克隆抗体的制备

为了识别大鼠卵巢中的生殖细胞,在原核系统中表达和纯化RVLG蛋白并制备了多克隆抗体.采用RT-PCR方法从大鼠睾丸组织中扩增获得RVLG cDNA片段,然后克隆到pMD19-T载体上进行测序,经双酶切回收目的基因片段后,将其插入到原核表达载体pGEX-4T-1上,转入大肠杆菌BL21(DE3)中诱导表达.纯化后的GST-RVLG融合蛋白免疫昆明(KM)小鼠,最后给小鼠腹腔注射S180细胞制备抗RVLG腹水多克隆抗体.用Western blotting及免疫组织化学法鉴定RVLG腹水多克隆抗体的特异性,间接ELISA法测定该抗体的效价.序列分析表明,所克隆的RVLG cDNA片段比GenBank中报道的大鼠RVLG cDNA(NM_001077647)多60 bp,原因是由于RVLG的可变剪切方式造成的.本研究成功构建了重组表达质粒pGEX-RVLG,且GST-RVLG融合蛋白在大肠杆菌BL21(DE3)中高效表达,表达的目的蛋白占菌体总蛋白的10%以上.制备的抗体可特异性识别RVLG蛋白,其效价达1:20 000.获得的高效价、高特异性的小鼠抗RVLG蛋白腹水多克隆抗体为下阶段研究RVLG的特异性表达奠定了基础.     

昆虫学多媒体信息获取与处理方法的初步研究

该文介绍了多媒体信息包括文字信息、音频信息、视频信息和图象信息的获取及其数字化制作技术。较详细地介绍了制作这些媒体资料所需的软硬件环境及具体的操作步骤。这里包括了文字的录入和处理;声音的录制和处理;数字视频的制作,包括昆虫摄像技术、各种来源的视频信息捕获、视频信息的处理等;数字图象的制作,包括昆虫的摄影技术、图象扫描、图象处理等。     

摇瓶培养条件下雷公藤不定根生长及次生代谢产物含量的研究

以雷公藤(Tripterygium wilfordii Hook. f.)不定根为材料,研究摇瓶悬浮培养条件下接种密度、装液比例、逐级放大、消泡剂、大孔吸附树脂种类及浓度对雷公藤不定根增长量、不定根及培养基中雷公藤内酯醇、雷公藤吉碱、雷公藤次碱含量的影响。结果显示,接种密度在15 g/L (FW)时较适合不定根的继代培养和次生代谢产物的积累。250 m L摇瓶中装入100 m L培养基,即装液量为2/5时,培养基利用率最高。随着摇瓶体积的逐渐放大,不定根增长量和3种次生代谢产物含量略有下降,5 L摇瓶中不定根增长量为对照的91.6%,内酯醇、吉碱和次碱的含量分别为对照的91.8%、91.7%和96.9%。6种大孔吸附树脂中,XAD-7处理对不定根的生长有明显促进作用,培养结束时,3种次生代谢产物产量显著提高,当XAD-7浓度为0.5 g/瓶时不定根增长量为对照的1.2倍,内酯醇、吉碱和次碱产量最高,分别为对照的2.9、2.4和2.2倍。培养基中添加消泡剂后不定根增长量、3种次生代谢产物总产量均不同程度下降,其中,LX-603处理后,虽然不定根增长量为对照的85%,内酯醇、吉碱和次碱产量分别为对照的78%、64%和87%,但明显抑制了培养过程中泡沫的产生。研究结果表明筛选的摇瓶逐级放大培养雷公藤不定根的方法效果较好,可为雷公藤不定根生物反应器放大培养奠定基础。     

Systematic Analysis of Absorbed Anti-Inflammatory Constituents and Metabolites of Sarcandra glabra in Rat Plasma Using Ultra-High-Pressure Liquid Chromatography Coupled with Linear Trap Quadrupole Orbitrap Mass Spectrometry

Ultra-high-pressure liquid chromatography (UHPLC) was coupled with linear ion trap quadrupole Orbitrap mass spectrometry (LTQ-Orbitrap) and was used for the first time to systematically analyze the absorbed components and metabolites in rat plasma after oral administration of the water extract of Sarcandra glabra. This extract is a well-known Chinese herbal medicine for the treatment of inflammation and immunity related diseases. The anti-inflammatory activities of the absorbed components were evaluated by measuring nitric oxide (NO) production and proinflammatory genes expression in lipopolysaccharide (LPS)-stimulated murine RAW 264.7 macrophages. As a result, 54 components in Sarcandra glabra were detected in dosed rat plasma, and 36 of them were positively identified. Moreover, 23 metabolites were characterized and their originations were traced. Furthermore, 20 of the 24 studied components showed anti-inflammatory activities. These results provide evidence that this method efficiency detected constituents in plasma based on the anti-inflammatory mechanism of multiple components and would be a useful technique for screening multiple targets for natural medicine research.     

蛇毒与细胞凋亡

简要介绍了细胞凋亡的形态学变化和生物化学等特性,及其主要的定性、定量检测方法,综述了蛇毒在细胞凋亡和肿瘤研究中的发展概况和国外最新进展。