Predicting protein fold types by the general form of Chou's pseudo amino acid composition: approached from optimal feature extractions

Identification on protein folding types is always based on the 27-class folds dataset, which was provided by Ding & Dubchak in 2001. But with the avalanche of protein sequences, fold data is also expanding, so it will be the inevitable trend to improve the existing dataset and expand more folding types. In this paper, we construct a multi-class protein fold dataset, which contains 3,457 protein chains with sequence identity below 35% and could be classified into 76 fold types. It was 4 times larger than Ding & Dubchak's dataset. Furthermore, our work proposes a novel approach of support vector machine based on optimal features. By combining motif frequency, low-frequency power spectral density, amino acid composition, the predicted secondary structure and the values of auto-correlation function as feature parameters set, the method adopts criterion of the maximum correlation and the minimum redundancy to filter these features and obtain a 95-dimensions optimal feature subset. Based on the ensemble classification strategy, with 95-dimensions optimal feature as input parameters of support vector machine, we identify the 76-class protein folds and overall accuracy measures up to 44.92% by independent test. In addition, this method has been further used to identify upgraded 27-class protein folds, overall accuracy achieves 66.56%. At last, we also test our method on Ding & Dubchak's 27-class folds dataset and obtained better identification results than most of the previous reported results.     

A Novel Integrated Method Tor Large-scale Detection,Identification, and Quantification of Widely Targeted Metabolites： Application in the Study of Rice Metabolomics

Liquid chromatography-mass spectrometry （LC-MS）-based metabolomics has been facilitated by the con- struction of MSz spectral tag （MS2T） library from the total scan ESI MS/MS data, and the development of widely targeted metabolomics method using MS/MS data gathered from authentic standards. In this report, a novel strategy called step- wise multiple ion monitoring-enhanced product ions （stepwise MIM-EPI） was developed to construct the MS2T library, in which stepwise MIM was used as survey scans to trigger the acquisition of EPI. A total number of 698 （almost） non- redundant metabolites with MS2 spectra were obtained, of which 135 metabolites were identified/annotated. Integrating the data gathered from our MS2T library and other available multiple reaction monitoring （MRM） information, a widely targeted metabolomics method was developed to quantify 277 metabolites, including some phytohormones. Evaluation of the dehydration responses and natural variations of these metabolites in rice leaf not only suggested the coordinated regulation of abscisic acid （ABA） with metabolites such as serotonin derivative（s）, polyamine conjugates under drought stress, but also revealed some C-glycosylated flavones as the potential markers for the discrimination of indica and japonica rice subspecies. The new MS2T library construction and widely targeted metabolomics strategy could be used as a tool for rice functional genomics.     

Differentiating the 2,3-diols of glucopyranosides by 4,6-O-benzylidene-protected-1,2-d-glucopyranosylorthoesters strategy

A facile and efficient method to differentiate the 2,3-diols of glucopyranosides based on 1,2-orthoesters strategy was developed. Stable thioglucosides were employed as the starting materials to prepare the corresponding 1,2-orthoesters. When treated with HCl aqueous solution and followed with Et₃N, differentiation of the 2,3-diols was efficiently achieved along with the generation of a convertible anomeric hydroxyl group. In addition, an easy and practical method based on NOE was proposed to determine whether the 1,2-orthoesters were endo-type or exo-type.     

去乙酰化酶SIRT1的表达及活性调控机制

SIRT1是哺乳动物中重要的NAD+依赖性去乙酰化酶,参与许多重要的生理和病理过程,如衰老、细胞死亡和肿瘤发生。如何精确调节SIRT1的表达和活性对SIRT1执行其生物学功能至关重要。文章以基因表达的不同阶段为切入点,对调控SIRT1表达及活性的机制进行了论述。     

A combined A431 cell membrane chromatography and online high performance liquid chromatography/mass spectrometry method for screening compounds from total alkaloid of Radix Caulophylli acting on the human EGFR

We have developed an online analytical method that combines A431 cell membrane chromatography (A431/CMC) with high performance liquid chromatography and mass spectrometry (LC/MS) for identifying active components from Radix Caulophylli acting on human EGFR. Retention fractions on A431/CMC model were captured onto an enrichment column and the components were directly analyzed by combining a 10-port column switcher with an LC/MS system for separation and preliminary identification. Using Sorafenib tosylate as a positive control, taspine and caulophine from Radix Caulophylli were identified as the active molecules which could act on the EGFR. This A431/CMC-online-LC/MS method can be applied for screening active components acting on EGFR from traditional Chinese medicines exemplified by Radix Caulophylli and will be of great utility in drug discovery using natural medicinal herbs as a source of novel compounds.     

乐至黑山羊PRLR基因外显子10多态性与产羔数的关系研究

设计2对特异性引物对乐至黑山羊PRLR基因第10外显子进行了PCR-SSCP检测,并研究该基因与产子性能的相关性。结果表明,P1引物扩增片段不存在多态性;P2引物扩增片段存在多态性,表现为AA,AB,AD和CD 4种基因型,测序结果表明,4种基因型都在该片段第89、94、146和157位存在C→T、A→C、C→G、G→C的突变;此外AA型还在61位发生C→T的突变;AD型还在175位发生A→G的突变;CD型还在24位发生T→C的突变,96位发生C→T的突变,通过统计分析发现AD型平均产羔数优于其他3种基因型,并且与AB型差异达到显著水平(P<0.05)。因此认为PRLR基因对于乐至黑山羊产子性能有一定的影响。     

重组干扰素γ的中间试制

用带有表达质粒ＰＢＶ２２０（含有γ干扰素基因）的大肠杆菌ＤＨ５α株进行发酵培养,３批中试的菌产量平均为１４．１克／Ｌ,γ干扰素的表达量平均为１．０２±１０＾９ＩＵ／Ｌ,收集的菌体经高压匀质破菌后收集包涵体,用７ｍｏｌ／Ｌ盐酸胍提取干扰素,此过程中去除７８．４％菌体蛋白,而干扰素活性仅损失１０．４１％,粗制干扰素经复性可使干扰素活性提高４０５％,比活也有明显提高,３批平均为１．７６×１０＾７ＩＵ／ｍ     

55例自身血回收的临床应用探讨

总结和分析在心脏手术中进行自身血回收的经验。1999年1月－2000年3月,上海市胸科医院共进行自身血回收55例,其中男性27例,女性25例。年龄范围19－71岁,体表面积1．3－2．2m^2。本院应用的是意大利dideco公司生产的自身血回收机及其管道,不仅回收手术野血,而且回收体外循环管道内的残余血液。结果：55例患者均康复。自身血回收组患者的术后用血量和ICU时间与对照组相比,均显著降低（P＜0．05）。讨论：自身血回收技术除可减少患者术后用血量和ICU时间与对照组相比,均显著降低（P＜0．05）。讨论：自身回收技术除要减少患者术后用血、缓解血源紧张、避免血源性疾病外,还可提供以下有利条件：①为稀有血型患者提供手术保障;②可提供手术中发生意义大出血时的应急处理手段;③为外地患者就医和手术提供方便,并能减轻经济负担。