Exploring QSARs for Inhibitory Activity of Non-peptide HIV-1 Protease Inhibitors by GA-PLS and GA-SVM

The support vector machine (SVM) and partial least square (PLS) methods were used to develop quantitative structure activity relationship (QSAR) models to predict the inhibitory activity of non-peptide HIV-1 protease inhibitors. Genetic algorithm (GA) was employed to select variables that lead to the best-fitted models. A comparison between the obtained results using SVM with those of PLS revealed that the SVM model is much better than that of PLS. The root mean square errors of the training set and the test set for SVM model were calculated to be 0.2027, 0.2751, and the coefficients of determination (R²) are 0.9800, 0.9355 respectively. Furthermore, the obtained statistical parameter of leave-one-out cross-validation test (Q²) on SVM model was 0.9672, which proves the reliability of this model. The results suggest that TE2, Ui, GATS5e, Mor13e, ATS7m, Ss, Mor27e, and RDF035e are the main independent factors contributing to the inhibitory activities of the studied compounds.     

慢病毒介导I型胶原短发夹RNA转染对大鼠系膜细胞生长行为的影响

目的通过观察慢病毒介导的I型胶原（COLI）短发夹（sh）RNA感染大鼠系膜细胞后其增殖、凋亡及细胞周期的变化,探索未来应用于动物实验,甚至临床时RNA干涉（RNAi）药物对靶细胞生长行为的影响。方法利用感染增强剂（对照组）、空慢病毒载体及感染增强剂（pSC-GFP组）、COLIshRNA慢病毒表达载体及感染增强剂（pSC—GFP／COLI组）分别感染大鼠系膜细胞,用噻唑蓝法检测细胞增殖,利用AnnexinV／PE法检测细胞凋亡,利用流式细胞仪检测细胞周期,进而观察慢病毒表达载体对细胞上述能力的影响。结果pSC—GFP／COLI组和pSC—GFP组均能显著抑制细胞增殖,且慢病毒表达载体抑制能力又显著高于空病毒,分别于感染后24h、48h和72h计算抑制效率为22．52％、28．57、33．33％。凋亡实验结果表明,慢病毒感染细胞后一定程度诱导了细胞凋亡,但作为载体携带的COLIshRNA未引起进一步的细胞凋亡加剧。细胞周期实验发现慢病毒引起细胞周期阻滞于G2／M期。而在72hCOLIshRNA对s期的阻滞逐渐突出。结论慢病毒介导I型胶原短发夹RNA转染大鼠系膜细胞后,在一定程度上影响了细胞生长行为,但总体来说仍是安全的,为进一步动物实验及药物研制奠定基础。     

Trait-like individual differences in the human sleep electroencephalogram

We aimed to examine whether commonly observed individual differences in sleep architecture and the sleep electroencephalogram reflect individual traits, which are amenable to a genetic investigation of human sleep. We studied intra-individual stability and inter-individual variation in sleep and sleep electroencephalogram spectra across four baseline recordings of eight healthy young men. A similarity concept based on Euclidean distances between vectors was applied. Visually scored sleep variables served as feature vector components, along with electroencephalogram power spectra in non-rapid-eye-movement and rapid-eye-movement sleep. The distributions of similarity coefficients of feature vectors revealed a clear distinction between high within-subject similarity (i.e. stability), and low between-subject similarity (i.e. variation). Moreover, a cluster analysis based on electroencephalogram spectra in both non-rapid-eye-movement and rapid-eye-movement sleep segregated all four baseline nights of each individual into a distinct cluster. To investigate whether high and low sleep pressure affects the similarity coefficients, normalized non-rapid-eye-movement sleep electroencephalogram spectra of the first and second half of the recordings were compared. Because the electroencephalogram changes systematically in the course of the night, within-subject variation no longer differed from between-subject variation. In conclusion, our data provide evidence for trait-like characteristics in the sleep electroencephalogram. Further studies may help to identify distinct phenotypes to search for genes underlying functional aspects of undisturbed human sleep.     

Intramuscular gene transfer of fibroblast growth factor-1 using improved pCOR plasmid design stimulates collateral formation in a rabbit ischemic hindlimb model

Fibroblast growth factor 1 (FGF1) is an angiogenic factor known to play a role in the growth of arteries. The purpose of this study was to evaluate the usefulness of direct intramuscular injection of an optimized expression plasmid encoding FGF1 to augment collateral formation and tissue perfusion in a rabbit ischemic hindlimb model. Truncated FGF1 fused to the human fibroblast interferon (FIN) signal peptide was expressed from a newly designed plasmid backbone with an improved safety profile for gene therapy applications. In vitro, optimization of plasmid design yielded in a dramatic increase in expression efficiency for FGF1, independent of the presence of a signal peptide, as analyzed by Western Blotting. In vivo, successful transgene expression could be demonstrated by FGF1 immunostaining after gene application. FGF1 plasmid containing FIN signal peptide (100, 500, and 1,000 μg), when injected into ischemic muscle areas of rabbits 10 days after ligation of the external iliac artery, exhibited a pronounced therapeutic effect on collateral formation to the ischemic hindlimb in a dose-depending manner, as assessed by physiological (blood pressure ratio, maximal intra-arterial Doppler flow) and anatomical (angiographic score, histologic evaluation of capillary density) measurements 30 days after therapy, compared to saline or lacZ control plasmid. FGF1 plasmid without a signal peptide sequence resulted in a comparable therapeutic effect on collateral formation at comparable doses (500 and 1,000 μg). Our results indicate that intramuscular FGF1 gene application could be useful to stimulate collateral formation in a situation of chronic peripheral ischemia. The presence of a signal peptide does not seem to be obligatory to achieve bioactivity of intramuscular transfected FGF1. An optimized vector design improved both biosafety of gene transfer and expression efficiency of the transgene, rendering this vector highly suitable for human gene therapy. Therefore, this new generation vector encoding FGF1 might be useful as an alternative treatment for patients with chronic ischemic disorders not amenable to conventional therapy.     

The impact of temporal compression and space selection on SVM analysis of single-subject and multi-subject fMRI data

In the present study, we compared the effects of temporal compression (averaging across multiple scans) and space selection (i.e. selection of "regions of interest" from the whole brain) on single-subject and multi-subject classification of fMRI data using the support vector machine (SVM). Our aim was to investigate various data transformations that could be applied before training the SVM to retain task discriminatory variance while suppressing irrelevant components of variance. The data were acquired during a blocked experiment design: viewing unpleasant (Class 1), neutral (Class 2) and pleasant pictures (Class 3). In the multi-subject level analysis, we used a "leave-one-subject-out" approach, i.e. in each iteration, we trained the SVM using data from all but one subject and tested its performance in predicting the class label of the this last subject's data. In the single-subject level analysis, we used a "leave-one-block-out" approach, i.e. for each subject, we selected randomly one block per condition to be the test block and trained the SVM using data from the remaining blocks. Our results showed that in a single-subject level both temporal compression and space selection improved the SVM accuracy. However, in a multi-subject level, the temporal compression improved the performance of the SVM, but the space selection had no effect on the classification accuracy.     

Transient low pH treatment enhances infection of lentiviral vector pseudotypes with a targeting Sindbis envelope

Efficient transduction of primary hematopoietic cell types by oncoretroviral vectors and lentiviral vectors with a variety of different envelope pseudotypes has proven to be difficult. We recently developed a lentiviral vector based upon a modified Sindbis virus envelope that allows targeted transduction via antibody recognition to specific cells in unfractionated cell populations. However, similar to other envelope pseudotypes, the utility of this vector for some primary hematopoietic cells was limited by low transduction efficiencies. Here, we report that transient treatment of cells with low pH culture medium immediately following infection results in marked enhancements in transduction efficiency for primary hematopoietic cells. In combination with antibody directed targeting, this simple technique expands the utility of targeting transduction to specific cells in mixed populations of primary cells.     

Silk-elastinlike protein polymers for matrix-mediated cancer gene therapy

Silk-elastinlike protein polymers (SELPs) are recombinant polymers designed from silk fibroin and mammalian elastin amino acid repeats. These are versatile materials that have been examined as controlled release systems for intratumoral gene delivery. SELP hydrogels comprise monodisperse and tunable polymers that have the capability to control and localize the release and expression of plasmid DNA and viruses. This article reviews recent developments in the synthesis and characterization of SELP hydrogels and their use for matrix-mediated gene delivery.     

BRD7逆转录病毒稳定系的构建及其功能评价

目的探索BRD7（bromodomain．containingprotein7）是否具有抑癌基因的功能。方法根据NCBI提供的BRD7基因序列设计特异性引物扩增其编码区序列,经酶切、连接转化后进一步挑取单克隆菌落进行菌液PCR筛选及测序鉴定得到阳性重组质粒。共转293T细胞后收集浓缩病毒上清并感染U20S细胞,24h后用嘌呤霉素（puromycin）筛选稳定表达BI①7、的细胞株。结果菌落PCR扩增及DNA测序分析证明重组pMSCV-BRD7．GFP质粒克隆成功。GFP绿色荧光结果显示,绝大部分细胞成功整合了pMSCV-GFP或pMSCV-BRD7．GFP外源质粒;Westernblotting检测发现感染重组质粒pMSCV-BRD7．GFP的细胞株中BRD7蛋白的表达水平显著高于对照组。功能结果显示,过表达BRD7显著抑制U20S细胞的增殖,促进下游靶基因p21与MDM2的表达。结论本研究成功构建了针对BRD7基因的逆转录病毒稳定系,且初步证明了BRD7发挥抑癌基因的功能,为下一步深入研究其被调控的机制与功能奠定了基础。