Techniques for staining fungal nuclei and appendages

PUNITHALINGAM, E., 1989. Techniques for staining fungal nuclei and appendages. The use of HCl-Giemsa stain for staining nuclei and a modified Leifson's flagellum staining technique for staining appendages in Coelomycetes has produced useful information which could further our knowledge of fungi and help to reappraise earlier concepts.     

外源激素在西洋参种胚后熟中的作用研究

西洋参(Panax Quinquefolium L.)种胚需经形态后熟和生理后熟后才能萌发.经过激素(GA100ppm+KT50ppm+BA20ppm)处理的西洋参种子,在后熟过程中鲜重增加,β—淀粉酶活性增强,过氧化物酶活性保持较高水平.在生理后熟期,可溶性蛋白量逐渐增多.激素处理加速了胚体内物质的分解和合成,促使胚迅速发育和分化,缩短了种胚完成形态和生理后熟的时间,使种子提早一年萌发.     

Genome-wide analysis of Nilaparvata lugens nymphal responses to high-density and low-quality rice hosts

The brown planthopper （BPH） Nilaparvata lugens is an economically impor- tant pest on rice plants. In this study, the higher population density and yellow-ripe stage of rice plants were used to construct adverse survival conditions （ASC） against BPH nymphs. Simultaneously, the low population density and tillering stage of rice plants were used to establish a suitable survival condition （SSC） as a control. Solexa/Illumina sequencing was used to identify genes of BPH nymphs responding to ASC. Significantly longer duration development of BPH nymphs and significantly lower brachypterous ratio of BPH adults were observed by ASC compared with SSC. A total of 2 544 differentially expressed genes （DEGs） were obtained and analyzed by BLASTx, Gene Ontology and KEGG Orthology. Gene ontology analysis revealed that the DEGs were mainly involved in categories of cell, cell part, cellular process, binding, catalytic, organelle and metabolic processes. 1138 DEGs having enzyme commission numbers were assigned to different metabolic pathways. The largest clusters were neurodegenerative diseases （137, 12.0%）, followed by carbohy- drate metabolism （113, 9.9%）, amino acid metabolism （94, 8.3%）, nucleotide metabolism （76, 6.7%）, energy metabolism （64, 5.6%）, translation （60, 5.3%）, lipid metabolism （58, 5.1%）, and folding, sorting and degradation （52, 4.6%）. Expressing profile of 11 DEGs during eight nymphal developmental stages of BPH were analyzed by quantitative real- time polymerase chain reaction. The 11 genes exhibited differential expression between ASC and SSC during at least one developmental stage. The DEGs identified in this study provide molecular proof of how BPH reconfigures its gene expression profile to adapt to overcrowding and low-quality hosts.     

钠氢交换体1在病理性心肌肥厚大鼠心肌组织及血浆中的表达

目的：研究异丙肾上腺素诱导的病理性心肌肥厚大鼠心肌组织及血浆中钠氢交换体1（sodium—hydrogen exchanger1,NHE—1）的表达,探讨NHE1在心肌肥厚发生和发展中的作用。方法：30只雄性SD大鼠随机并平均分为2组：病理性心肌肥厚组和对照组,每组15只,病理性心肌肥厚组（以下简称ISO组）予以ISO（异丙肾上腺素）连续每日以20、10和5mg／kg的剂量递减皮下注射,再以3mg／kg的剂量维持皮下注射7d,对照组予相同剂量生理盐水皮下注射。给药结束后进行心脏超声检测左室舒张末径（LVEDD）、左室收缩末径（LVESD）、室间隔厚度（IVST）、短轴缩短率（FS）、左室射血分数（LVEF）。分别测定各组大鼠体重（Bw）、心室重量（VW）、左心室重量（LVW）,计算心室重量指数VWI（VW／BW）、左心室重量指数LVWI（LVW／BW）。取血检测血浆中NHE．1的浓度,并取心肌组织观察病理形态学特征,用免疫组化法检测心肌组织中NHE—1的表达量。结果：与对照组相比,ISO组大鼠LVEF、IVST显著增加（P〈0．05）,LVESD明显降低（P〈0．05）,VWI、LVWI明显增加（P〈0．01）,血浆NHE—1浓度明显升高（P〈0．01）,心肌组织NHE-1表达增多（P〈0．01）。结论：NHE-1可能在病理性心肌肥厚的发生和发展过程中起着重要作用。     

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

The identification of proteins by mass spectrometry is a standard technique in the field of proteomics, relying on search engines to perform the identifications of the acquired spectra. Here, we present a user-friendly, lightweight and open-source graphical user interface called SearchGUI (http://searchgui.googlecode.com), for configuring and running the freely available OMSSA (open mass spectrometry search algorithm) and X!Tandem search engines simultaneously. Freely available under the permissible Apache2 license, SearchGUI is supported on Windows, Linux and OSX.     

宁南退耕还草区近地面湍流通量观测初报

根据 2 0 0 2～ 2 0 0 3年小气候考察资料 ,分别分析了四季晴天条件下宁南退耕还草区净辐射、感热、潜热和土壤热通量比例和变化特征。结果表明 ,近地层各通量有较规则的日变化。白天 ,感热通量占净辐射的 5 0 %以上 ,一般达 80 %～ 10 0 %。只有夏季全天和秋季白天的潜热通量为正 ,在春季的早晨和秋季的傍晚潜热通量为负。冬春季节土壤的热量收支大于夏秋季节。     

Tandem mass spectrometry of human tryptic blood peptides calculated by a statistical algorithm and captured by a relational database with exploration by a general statistical analysis system

A goodness of fit test may be used to assign tandem mass spectra of peptides to amino acid sequences and to directly calculate the expected probability of mis-identification. The product of the peptide expectation values directly yields the probability that the parent protein has been mis-identified. A relational database could capture the mass spectral data, the best fit results, and permit subsequent calculations by a general statistical analysis system. The many files of the Hupo blood protein data correlated by X!TANDEM against the proteins of ENSEMBL were collected into a relational database. A redundant set of 247,077 proteins and peptides were correlated by X!TANDEM, and that was collapsed to a set of 34,956 peptides from 13,379 distinct proteins. About 6875 distinct proteins were only represented by a single distinct peptide, 2866 proteins showed 2 distinct peptides, and 3454 proteins showed at least three distinct peptides by X!TANDEM. More than 99% of the peptides were associated with proteins that had cumulative expectation values, i.e. probability of false positive identification, of one in one hundred or less. The distribution of peptides per protein from X!TANDEM was significantly different than those expected from random assignment of peptides.     

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

LC‐MS experiments can generate large quantities of data, for which a variety of database search engines are available to make peptide and protein identifications. Decoy databases are becoming widely used to place statistical confidence in result sets, allowing the false discovery rate (FDR) to be estimated. Different search engines produce different identification sets so employing more than one search engine could result in an increased number of peptides (and proteins) being identified, if an appropriate mechanism for combining data can be defined. We have developed a search engine independent score, based on FDR, which allows peptide identifications from different search engines to be combined, called the FDR Score. The results demonstrate that the observed FDR is significantly different when analysing the set of identifications made by all three search engines, by each pair of search engines or by a single search engine. Our algorithm assigns identifications to groups according to the set of search engines that have made the identification, and re‐assigns the score (combined FDR Score). The combined FDR Score can differentiate between correct and incorrect peptide identifications with high accuracy, allowing on average 35% more peptide identifications to be made at a fixed FDR than using a single search engine.     

XTandem Parser: An open‐source library to parse and analyse X!Tandem MS/MS search results

Identification of proteins by MS plays an important role in proteomics. A crucial step concerns the identification of peptides from MS/MS spectra. The X!Tandem Project ( http://www.thegpm.org/tandem ) supplies an open‐source search engine for this purpose. In this study, we present an open‐source Java library called XTandem Parser that parses X!Tandem XML result files into an easily accessible and fully functional object model ( http://xtandem‐parser.googlecode.com ). In addition, a graphical user interface is provided that functions as a usage example and an end‐user visualization tool.     

Altered expression of the Na+/H+ exchanger isoform-3 in experimental colitis: Effect of garlic

The sodium-hydrogen exchanger isoform, NHE-3 is essential for the absorption of sodium and water from intestine. Whether this protein plays any role in inflammatory bowel disease is less understood. To address this issue, NHE-3 mRNA and protein levels were estimated in the terminal ileum and colon of the rats having colitis induced with trinitrobenzenesulphonic acid (TNBS). The effect of garlic (Allium sativum) was also evaluated on the expression of NHE-3. The animals were treated with garlic extract intraperitoneally starting 2 h before the TNBS administration until day 4 post-TNBS administration and were sacrificed on day 5. In control animals, the levels of NHE-3 in colon was higher than the ileum. As a result of colitis, the levels of NHE-3 protein and mRNA increased both in the colon and terminal ileum. Garlic treatment of the colitic animals resulted in a selective suppression of NHE-3 in the terminal ileum. Colitis caused an induction of the myeloperoxidase activity, the marker of inflammation in the colon but not in the ileum. These findings suggest that induction of NHE-3 is not primarily due to inflammation. Selective suppression of this protein in ileum by garlic may cause loss of sodium chloride and water during colitis.