大肠杆菌基因组水平蛋白质-RNA相互作用初步研究

目的初步研究大肠杆菌中基因组水平的蛋白质-RNA相互作用（protein-RNA interactions,PRI）。方法通过RNA酶消化细菌裂解液,提取与蛋白质相互作用的RNA片段,构建cDNA文库,进行高通量测序,并通过生物信息学分析获得与蛋白质结合的转录本。结果获得了与蛋白质结合的3193条转录本,涉及2234个mRNA、47个sRNA（small regulatory RNAs）、39个tRNA、11个rRNA以及862个基因间区（intergenic region,IGR）。结论初步获得大肠杆菌中与蛋白质相互作用的转录本信息,为进一步开展PRI研究提供了支持。     

串联MS2衣壳蛋白和MS2特异结合RNA表达载体构建及应用

目的构建体内研究RNA-蛋白相互作用的表达载体。方法利用MS衣壳蛋白可与MS2结合位点（MS2bs）RNA特异性结合的特点,通过设计特异引物,构建pcDNA3．0-Flag．2XMS2和pcDNA3．0—12XMS2％s表达载体,以及表达MEG3非编码RNA的表达载体pcDNA3．0-EG3V1—12XMS2bs。共转染细胞,进行RNA免疫沉淀,所得RNA进行实时定量PCR分析验证。结果成功构建了pcDNA3．0-Flag-2XMS2和pcDNA3．0．12XMS2bs表达载体,实时定量PCR结果表明,与对照相比能明显富集MEG3V1非编码RNA分子。结论成功构建了体内研究RNA-蛋白质相互作用的表达载体,为RNA一蛋白相互作用研究提供了新的技术方法。     

蛋白质-RNA相互作用预测研究进展

蛋白质-RNA相互作用(PRI)与基因表达调控等多种生物过程密切相关.目前一般从实验和计算机预测两方面研究PRI.虽然X射线晶体衍射和核磁共振等实验方法可获得蛋白质-RNA复合物结构,但这些方法具有耗时长与花费高等缺点,并且有些蛋白质-RNA复合物结晶很难获得.特别是,随着高通量测序技术的应用,有大量的PRI需要分析,实验方法已不能满足日益增长的分析需求.为此,现已发展了4类PRI预测方法,分别为结合RNA的蛋白质残基预测、结合蛋白质的RNA小片段预测、基于序列水平的PRI预测和基于结合位点水平的PRI预测.为使有关研究人员系统了解这些预测方法,该文对上述预测方法进行了评述,并探讨其进一步发展方向.     

BLAP75蛋白与DNA螺旋酶BLM以及拓扑异构酶TopoⅢα的相互作用

目的确定BLAP75蛋白与BLM蛋白及TopoⅢα蛋白的相互作用及作用位点。方法构建一系列携带MBP标记的不同BLAP75载体,通过体外纯化蛋白结合实验检测BLAP75与BLM、TopoⅢα的相互作用位点,并在真核细胞中通过免疫共沉淀方法进行验证;运用RNA干扰(RNAi)技术特异性抑制BLAP75的表达,并利用West-ern印迹法检测其对BLM和TopoⅢα蛋白表达的影响。结果 BLAP75与BLM和TopoⅢα蛋白的结合位点位于BLAP75的N端区域;BLAP75与BLM的直接相互作用需要DNA的介导;当BLAP75蛋白表达量减少时,BLM和TopoⅢα蛋白量也随之减少。结论细胞内BLM和TopoⅢα蛋白均结合在BLAP75的氨基端部分;BLAP75对TopoⅢα和BLM的蛋白水平具有重要影响。     

精子蛋白质的合成及意义

Bhargara(1957)发现射出体外的牛精子,可以结合氨基酸形成蛋白质,并且蛋白质的合成与活力具有平行关系。但是没有发现RNA的存在,因此他错误地提到了精子细胞中蛋白质的合成是不需要RNA的观点,并得到一些研究者的承认。直到60年代许多研究者还认为精于内不含RNA。他于1959年还发现洗涤精子和非洗涤精子,结合     

基于SVM方法构建细菌sRNA靶标预测模型

目的:为实验方法鉴定细菌sRNA靶标和研究sRNA功能提供生物信息学支持.方法:首先以实验证实的132个sRNA与靶标相互作用数据为训练集,其中包含46个阳性数据和86个阴性数据;其次,以实验证实的22个阳性数据和随机生成的1 700个阴性数据为测试集;最后以RNA二级结构谱等特征为变量,运用支持向量机(SVM)方法构建sRNA靶标预测数学模型.结果和结论:构建的模型对训练集的敏感性和特异性均为100%,对测试集的敏感性和特异性分别为72.73%和80.65%.所构建的数学模型为实验发现sRNA靶标提供了生物信息学支持.     

G蛋白偶联受体及其配体的结构与功能分析

Ｇ蛋白偶联的受体是介导跨膜信号转导的一组多样性蛋白质，它们具有显著的同源性及由七个跨膜螺旋组成的相同的膜结构。异源基因表达和位点诱变相结合的方法是将来对Ｇ蛋白偶联受体进行结构－功能分析的起点。通过对结合配体的主要结构进行研究，已建立了受体蛋白异源表达的模型，并结合位点诱变实验认证了配体结合中有功能作用的氨基酸序列。这些研究以及试图得到受体晶体结构的努力，为设计更适用于放射性核素显像和治疗的配体提供了可能性     

人血管生成素-1基因cDNA的克隆及结构分析

 目的 克隆人血管生成素-1基因,并分析其结构特征,为研究生理及病理性血管生成奠定基础。方法 提取人胎盘组织总RNA,用逆转录聚合酶链式反应(RT-PCR)技术扩增逆转录产物,经克隆及序列测定获得人血管生成素-1 cD-NA;用计算机软件分析基因序列及编码蛋白质结构。结果 获得高质量的胎盘组织总RNA。RT-PCR扩增出—1.5 kb的cD-NA片段,将PCR产物的阳性克隆测序,显示含1534 bp的插入片段,可编码503个氨基酸的蛋白质,与小鼠的血管生成素-1氨基酸高度同源。编码的氨基酸中含3个功能结构域。结论 为从基因及蛋白质水平研究人血管生成素-1与生理、病理性血管生成奠定了基础。     

多物种A-to-I编辑事件的可视化注释数据库

目的 构建涵盖多物种,并提供精确、可视化注释信息的A-to-I编辑事件的数据库.方法 用多种方法收集9个项目中包含7个物种超过230万个RNA编辑位点,将数据整合并上传至MySQL数据库.利用Django、Boot-strap和Echarts等框架,在阿里云服务器搭建数据库平台.结果 dbRED数据库(https://...     

基于文献挖掘的蛋白质相互作用信息数据库设计及实现

目的针对目前数据库在提供组织、存储和展示文献来源的蛋白质相互作用知识和数据支撑方面的不足,设计并构建了蛋白质相互作用信息数据库系统（protein—proteininteractioninformationdatabase,dbPPII）。方法根据文献来源的蛋白质相互作用数据的特点,使用MySQL设计包含蛋白质相互作用、文献及本体三方面信息的数据库结构,引入本体工具展示数据,并使用JSP等技术开发实现。结果数据库系统实现了基于本体的信息组织和展示,提供多种数据查询方式及丰富的文献信息,并具有数据下载功能。目前,dbPPll系统已经应用于组织、存储和展示人及小鼠肝脏相关文献挖掘得到的蛋白质相互作用信息。结论dbPPll系统具有存储和检索文献来源的蛋白质相互作用信息的多种优势,并有效地利用了蛋白质相互作用本体信息框架组织和展示蛋白质相互作用数据odbPPII访问i页：http：／／ppii．hupo．org．cn,     

Modeling one complete versus triplicate analyses in low template DNA typing

There are generally two strategies for low template DNA typing: the complete strategy, which uses all available DNA in a single PCR and subsequent typing, and the consensus strategy, in which the biological sample is divided into two or more aliquots and the genotype profile is determined by consensus from these “replicates.” In this study, the consensus and complete strategies are compared by a statistical approach in terms of the accuracy of obtaining the correct genotype at a single locus for single source samples. Logistic models were employed to describe the allele drop-out and drop-in events. The parameters of the models were estimated with empirical or hypothetical data. The probabilities of obtaining the true genotype and the chances to observe drop-out and drop-in alleles were estimated and compared for both strategies. Consistent with a previous experimental study, this study found that, with relatively high input DNA (e.g., ≥100 pg), the complete strategy performs better than the consensus strategy to obtain the true genotype and the complete strategy will display less dropped out alleles. The consensus strategy had less drop-in alleles for ≤100 pg DNA samples. Moreover, the limitations of the logistic models were discussed. Ideal models with better fit of empirical data approximating casework conditions were proposed for future studies.     

Dynamic contrast-enhanced CT of intracranial meningioma: comparison of distributed and compartmental tracer kinetic models--initial results

Dynamic contrast material-enhanced computed tomographic images of intracranial meningioma were analyzed by using both distributed-parameter and conventional compartmental tracer kinetic models. The distributed-parameter models were found to yield consistently better fitting of data sets than were conventional compartmental models. Although linear correlations were found between the kinetic parameters of the two models, some of these parameters (such as perfusion and mean transit time) did not correspond quantitatively. For all models, the kinetic parameters associated with the extravasation of tracer were found to be distinctly higher in meningiomas than in normal white- and gray-matter tissues.     

Der praktische Schußhandnachweis Die PVAL-Methode im Vergleich zu Abzügen mit Folie

The polyvinylalcohol (PVAL) method for sampling gunshot residues from the hands was used in 30 investigations involving 22 suicides, 3 accidents and 5 homicides. In these cases 16 pistols, 7 revolvers, 2 shotguns and 2 rifles had been used. The small calibres (.22 lr to 7.65 mm) represented 75% of the arms. In two cases lead-free primers had deposited zink-containing residues. PVAL gloves were examined by microradiography and chemographical analysis. The PVAL method was successful in 29 cases and assisted in the majority of cases to reconstruct the position of the arm during shooting. Additionally, 16 other pairs of hands were treated with adhesive films. In 6 cases of suicide the films showed lead-containing traces and gave evidence of shooting. It was also possible to reconstruct an accident with lead-free ammunition. In 3 out of the 9 cases of criminal shooting the adhesive films did not contain gunshot residues. The amount of traces on the films did not reach the yield of traces fixed by PVAL. PVAL gloves showed better and more stable staining results. The adhesive films did not work if there was too much blood on the hands. The staining results of these bloody films were not satisfactory.     

MPSproto: An extension of EuroForMix to evaluate MPS-STR mixtures

We have developed MPSproto as an extension of EuroForMix to improve handling of stutter artefacts and other typing errors that commonly occur in MPS-STR data. MPSproto implements two models for read depth: gamma and negative binomial. It differs from EuroForMix in that calibration is required before mixtures are interpreted. In this study a mixture dataset (2–4 persons) was revisited, where EuroForMix interpretation of MPS-STR mixtures using the LUS+ format was first described; the performance of this model was compared to the MPSproto models. Results indicated that, overall, the MPSproto models performed better than the conventional EuroForMix model, and the gamma model implemented in MPSproto performed best. Differences were highlighted and further investigated to establish causality. Goodness of fit tests showed that the MPSproto models were adequate for the sequence reads when a low analytical threshold was applied.     

Intestinal preparation with an osmotic solution for edema with double contrast media

PURPOSE: To evaluate the most effective way of cleansing the colon lumen for double contrast colon enema with a single preparation at osmotic effect. MATERIAL AND METHODS: We examined 80 patients (age range: 29-84 years) and divided them into two groups. Group 1: patients (no. 41) were prepared with the traditional method consisting of a residue-free diet in the three days before the examination followed by the administration of a sennoside-based laxative the morning of the day before and a dose of magnesium sulphate in the afternoon, after the Genoa School method. Group 2: patients (no. 39) were prepared with a Phospholax solution according to the following administration schedule: one dose in the evening two days before the examination and four doses the day before, that is two in the afternoon and two in the evening, followed by abundant hydratation. The examination was performed in a double blind fashion and graded as follows: excellent, good, sufficient, poor. The statistical analysis of all data was performed with Student's t-test and the chi-square test. RESULTS: We obtained better results with the new protocol than with the traditional one, where some patients discontinued the preparation because of intolerance (nausea, abdominal pain and swelling). In addition, more fecal residues were found in the colon with the first preparation, which however provided better contrast agent coating than the new protocol. The second preparation provided better mucosal cleansing, with more cases graded as excellent-good, and there were no cases of poor coating or electrolyte disturbances. DISCUSSION AND CONCLUSIONS: Intestinal preparation with Phospholax was better than the conventional method relative to compliance, intestinal cleansing and side-effects (in both the latter two cases, the difference is statistically significant, p < 0.01). In conclusion the new protocol is a possible alternative to the traditional method thanks to its ease of preparation and effective results.     

Validation procedures in radiologic diagnostic models. Neural network and logistic regression.

OBJECTIVE: To compare the performance of two predictive radiologic models, logistic regression (LR) and neural network (NN), with five different resampling methods. METHODS: One hundred sixty-seven patients with proven calvarial lesions as the only known disease were enrolled. Clinical and CT data were used for LR and NN models. Both models were developed with cross-validation, leave-one-out, and three different bootstrap algorithms. The final results of each model were compared with error rate and the area under receiver operating characteristic curves (Az). RESULTS: The NN obtained statistically higher Az values than LR with cross-validation. The remaining resampling validation methods did not reveal statistically significant differences between LR and NN rules. CONCLUSIONS: The NN classifier performs better than the one based on LR. This advantage is well detected by three-fold cross-validation but remains unnoticed when leave-one-out or bootstrap algorithms are used.     

Comparison of three physiologically-based pharmacokinetic models for the prediction of contrast agent distribution measured by dynamic MR imaging

PURPOSE: To compare the performance of three physiologically-based pharmacokinetic (PBPK) models for predicting gadolinium contrast agent concentration-time curves (Gd-CTCs) obtained in superior sagittal sinus (SSS), cerebral cortex, and psoas muscle. MATERIALS AND METHODS: Three published whole-body PBPK models were modified to predict Gd-CTCs in normal-appearing tissue. The models differed in the number of organs modeled and total number of compartments, and were designated as the "well-mixed," "delay," and "dispersion" models. The suitability of the three models to predict Gd-CTC was studied using data from dynamic contrast-enhanced MR perfusion imaging obtained at 1.5T from 10 patients with glioblastoma multiforme and at 3.0T from five patients with liver metastases. RESULTS: The dispersion model produced better fits than the delay model in the SSS (P < 0.0001) and cerebral cortex (P < 0.0001), and better fits than the well-mixed model in psoas muscle (P < 0.005). No model produced better fits than the dispersion model at any of the three locations. CONCLUSION: In this evaluation, the dispersion model was most robust for prediction of Gd-CTCs derived from dynamic contrast-enhanced (DCE)-MRI. This represents a preliminary step in the development of a PBPK model useful for predicting Gd-CTCs at a time resolution appropriate for dynamic MRI applications.     

缺血性脑白质病变DCE-MRI药代动力学模型选择

目的:探讨动态对比增强磁共振成像不同计算模型在缺血性脑白质病中的应用价值.方法:2016年4月-10月共搜集57例受试者,根据Fazekas评分分为两组:0～2分为对照组(共18例,男10例,女8例),3～6分为病例组(共39例,男17例,女22例).所有研究对象进行DCE-MRI检查,通过两种不同的计算模型(Patlak模型、Extended Tofts双室模型)测量研究对象脑白质病变区域的容积转运常数(Ktrans),采用Mann-Whitney U检验比较两组Ktrans值的差异,并应用ROC曲线分析不同计算模型所得Ktrans值的敏感度及特异度.结果:Patlak模型计算所得两组的Ktrans值分别为0.20(0.05,0.31)×10-4 min-1,0.62(0.39,1.12)×10-4 min-1,Extended Tofts模型计算所得两组的Ktrans值的分别为4.00(1.80,5.99)×10-4 min-1、7.20(4.60,13.20)×10-4 min-1,两种模型计算所得Ktrans值病例组均明显高于对照组,差异有统计学意义(P＜0.001).Patlak模型所得Ktrans值的诊断效能较Extended Tofts模型所得Ktrans值诊断效能高,敏感度为74.36％,特异度94.44％.结论:应用DCE-MRI可以为缺血性脑白质病变发病机制提供重要参考,Patlak模型更适用于评价缺血性脑白质病.     

Quantification of forensic genetic evidence: Comparison of results obtained by qualitative and quantitative software for real casework samples

To overcome the multifactorial complexity associated with the analysis and interpretation of the capillary electrophoresis results of forensic mixture samples, probabilistic genotyping methods have been developed and implemented as software, based on either qualitative or quantitative models. The former considers the electropherograms’ qualitative information (detected alleles), whilst the latter also takes into account the associated quantitative information (height of allele peaks). Both models then quantify the genetic evidence through the computation of a likelihood ratio (LR), comparing the probabilities of the observations given two alternative and mutually exclusive hypotheses.In this study, the results obtained through the qualitative software LRmix Studio (v.2.1.3), and the quantitative ones: STRmix™ (v.2.7) and EuroForMix (v.3.4.0), were compared considering real casework samples. A set of 156 irreversibly anonymized sample pairs (GeneMapper files), obtained under the scope of former cases of the Portuguese Scientific Police Laboratory, Judiciary Police (LPC-PJ), were independently analyzed using each software. Sample pairs were composed by (i) a mixture profile with either two or three estimated contributors, and (ii) a single contributor profile associated. In most cases, information on 21 short tandem repeat (STR) autosomal markers were considered, and the majority of the single-source samples could not be a priori excluded as belonging to a contributor to the paired mixture sample. This inter-software analysis shows the differences between the probative values obtained through different qualitative and quantitative tools, for the same input samples. LR values computed in this work by quantitative tools showed to be generally higher than those obtained by the qualitative. Although the differences between the LR values computed by both quantitative software showed to be much smaller, STRmix™ generated LRs are generally higher than those from EuroForMix. As expected, mixtures with three estimated contributors showed generally lower LR values than those obtained for mixtures with two estimated contributors.Different software products are based on different approaches and mathematical or statistical models, which necessarily result in the computation of different LR values. The understanding by the forensic experts of the models and their differences among available software is therefore crucial. The better the expert understands the methodology, the better he/she will be able to support and/or explain the results in court or any other area of scrutiny.