Design, synthesis and biological evaluation of cycloalkyl arylpyrimidines (CAPYs) as HIV-1 NNRTIs

A series of 18 cycloalkyl arylpyrimidines (CAPYs) were designed from lead compounds diarylpyrimidines (DAPYs), synthesized and evaluated for in vitro anti-HIV activity. Among them, the compound 1p displayed potent anti-HIV-1 activity against WT HIV-1 with an EC(50) value of 0.055 μM and a selectivity index (SI) >7290. The preliminary structure-activity relationship (SAR) of this new series of compounds was also investigated, which enriched the SAR of diarylpyrimidines (DAPYs).     

扎龙湿地不同生境的昆虫多样性

为了探讨湿地不同生境对昆虫物种多样性的影响,对扎龙湿地8种生境的昆虫进行了系统调查.共捕获昆虫5822只,分属11目58科143种,其中直翅目、双翅目、蜻蜒目为扎龙湿地的优势类群.不同生境中,草原草甸昆虫多样性最高,湖边生境多样性指数和均匀度指数均较高,杂草甸均最低.聚类分析和主分量分析结果表明,不同生境的昆虫群落相似性与水资源状况和植被类型有关,捕食性类群种类数和个体数量对昆虫群落稳定性具有重要的调控作用.湖边生境昆虫群落稳定性最强,湿草甸稳定性最弱.湿地水资源状况能影响昆虫生存生境,进而影响昆虫群落的组成和分布格局.     

Supramolecular assemblies of histidinylated α-cyclodextrin in the presence of DNA scaffold during CDplexes formation

α-Cyclodextrin was transformed in a cationic unit after per substitution with histidine (His-α-CD) and lysine (Lys-α-CD) molecules on the primary face. His-α-CD and Lys-α-CD were used to form electrostatic complexes (CDplexes) with a plasmid DNA encoding luciferase gene, and the ability of CDplexes to transfect mammalian cells was examined using HEK293-T7 cells. The luciferase activity in cells transfected with His-α-CDplexes was 8-fold higher than that obtained Lys-α-CDplexes. When the transfection was carried out in the presence of chloroquine, the luciferase activity with His-α-CDplexes and Lys-α-CDplexes increased 6 and 25 times, respectively. The lower enhancement with His-α-CDplexes confirmed that histidine induced a proton sponge effect inside endosomes upon imidazole protonation, favoring DNA delivery in the cytosol. At the same time, we found that the condensation of DNA with His-α-CD was unexpectedly stronger than that obtained with the lysyl-α-CD counterpart. Moreover, it was as strong as that observed with high molecular weight polylysine. NMR (ROESY and DOSY) investigations in the absence of DNA showed that an inclusion complex is formed between the imidazole ring of histidine and the hydrophobic cavity of CD but no His-α-CD polymers can be formed by intermolecular interactions. These results suggest that intermolecular interactions between imidazole and His-α-CD cavity could be involved to form supramolecular assemblies in the presence of a DNA scaffold leading to DNA condensation into low diameter particles.     

Evaluation of 64Cu-labeled bifunctional chelate-bombesin conjugates

Several bifunctional chelates (BFCs) were investigated as carriers of (64)Cu for PET imaging. The most widely used chelator for (64)Cu labeling of BFCs is DOTA (1,4,7,10-tetraazacyclododecane-N,N',N″,N'-tretraacetic acid), even though this complex exhibits only moderate in vivo stability. In this study, we prepared a series of alternative chelator-peptide conjugates labeled with (64)Cu, measured in vitro receptor binding affinities in human breast cancer T47D cells expressing the gastrin-releasing peptide receptor (GRPR) and compared their in vivo stability in mice. DOTA-, NOTA-(1,4,7-triazacyclononane-1,4,7-triacetic acid), PCTA-(3,6,9,15-tetraazabicyclo[9.3.1]pentadeca-1(15),11,13-triene-3,6,9-triacetic acid), and Oxo-DO3A-(1-oxa-4,7,10-triazacyclododecane-4,7,10-triacetic acid) peptide conjugates were prepared using H(2)N-Aoc-[d-Tyr(6),βAla(11),Thi(13),Nle(14)]bombesin(6-14) (BBN) as a peptide template. The BBN moiety was selected since it binds with high affinity to the GRPR, which is overexpressed on human breast cancer cells. A convenient synthetic approach for the attachment of aniline-BFC to peptides on solid support is also presented. To facilitate the attachment of the aniline-PCTA and aniline-Oxo-DO3A to the peptide via an amide bond, a succinyl spacer was introduced at the N-terminus of BBN. The partially protected aniline-BFC (p-H(2)N-Bn-PCTA(Ot-Bu)(3) or p-H(2)N-Bn-DO3A(Ot-Bu)(3)) was then coupled to the resulting N-terminal carboxylic acid preactivated with DEPBT/ClHOBt on resin. After cleavage and purification, the peptide-conjugates were labeled with (64)Cu using [(64)Cu]Cu(OAc)(2) in 0.1 M ammonium acetate buffer at 100 °C for 15 min. Labeling efficacy was >90% for all peptides; Oxo-DO3A-BBN was incubated an additional 150 min at 100 °C to achieve this high yield. Specific activities varied from 76 to 101 TBq/mmol. Competition assays on T47D cells showed that all BFC-BBN complexes retained high affinity for the GRPR. All BFC-BBN (64)Cu-conjugates were stable for over 20 h when incubated at 37 °C in mouse plasma samples. However, in vivo, only 37% of the (64)Cu/Oxo-DO3A complex remained intact after 20 h while the (64)Cu/DOTA-BBN complex was completely demetalated. In contrast, both (64)Cu/NOTA- and (64)Cu/PCTA-BBN conjugates remained stable during the 20 h time period. Our results indicate that it is possible to successfully conjugate aniline-BFC with peptide on solid support. Our data also show that (64)Cu-labeled NOTA- and PCTA-BBN peptide conjugates are promising radiotracers for PET imaging of many human cancers overexpressing the GRP receptor.     

Stromal upregulation of lateral epithelial adhesions: Gene expression analysis of signalling pathways in prostate epithelium

Background  

Stromal signalling increases the lateral cell adhesions of prostate epithelial cells grown in 3D culture. The aim of this study was to use microarray analysis to identify significant epithelial signalling pathways and genes in this process.     

Sensitivity analysis of periprosthetic healing to cell migration, growth factor and post-operative gap using a mechanobiological model

A theoretical rationale, which could help in the investigation of mechanobiological factors affecting periprosthetic tissue healing, is still an open problem. We used a parametric sensitivity analysis to extend a theoretical model based on reactive transport and computational cell biology. The numerical experimentation involved the drill hole, the haptotactic and chemotactic migrations, and the initial concentration of an anabolic growth factor. Output measure was the mineral fraction in tissue surrounding a polymethymethacrylate (PMMA) canine implant (stable loaded implant, non-critical gap). Increasing growth factor concentration increased structural matrix synthesis. A cell adhesion gradient resulted in heterogeneous bone distribution and a growth factor gradient resulted in homogeneous bone distribution in the gap. This could explain the radial variation of bone density from the implant surface to the drill hole, indicating less secure fixation. This study helps to understand the relative importance of various host and clinical factors influencing bone distribution and resulting implant fixation.     

The E-cadherin (CDH1) -160C>A polymorphism associated with gastric cancer among Asians but not Europeans

E-cadherin (CDH1) is a tumor suppressor gene involved in epithelial cell-cell interactions and plays important roles in the etiology of gastric cancer. Studies reporting conflicting results on the role of -160C>A polymorphism in the CDH1 promoter region on gastric cancer risk led us to perform a meta-analysis to investigate this relationship. Thirteen published case-control studies including 2509 gastric cancer cases and 3687 controls were identified. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of the association. Overall, individuals with the variant genotypes were not associated with a significant gastric cancer risk (AA vs. CC: OR?=?1.04, 95% CI: 0.74-1.48; CA vs. CC: 1.02, 0.85-1.21; AA/CA vs. CC: 1.03, 0.86-1.22; AA vs. CA/CC: 1.03, 0.74-1.43). However, in the stratified analysis by ethnicity, significantly decreased gastric cancer risk was found among Asians in dominant model (AA/CA vs. CC: 0.84, 0.72-0.99). Further, when stratified by clinicopathologic characteristics of gastric cancer, no statistically significant result was observed for any analysis. The results suggested that the CDH1 -160C>A polymorphism may contribute to susceptibility to gastric cancer among Asians. Additional well-designed large studies will be required to validate this association in different populations.     

PCR相关技术在植物病毒检疫检测中的应用

PCR和建立在PCR基础上的分子生物学技术以其灵敏、快速、简便等优点广泛应用于植物病毒的检测。阐述反转录聚合酶链式反应、免疫捕捉反转录PCR、PCR-单链构型多态性、实时荧光定量PCR、差异显示PCR和巢式PCR等相关技术的原理及其在植物病毒检测中的应用现状,以期为我国植物病毒的检疫检测提供有益参考。     

Role of magnesium and a phagosomal P-type ATPase in intracellular bacterial killing

Bacterial ingestion and killing by phagocytic cells are essential processes to protect the human body from infectious microorganisms. However, only few proteins implicated in intracellular bacterial killing have been identified to date. We used Dictyostelium discoideum, a phagocytic bacterial predator, to study intracellular killing. In a random genetic screen we identified Kil2, a type V P-ATPase as an essential element for efficient intracellular killing of Klebsiella pneumoniae bacteria. Interestingly, kil2 knockout cells still killed efficiently several other species of bacteria, and did not show enhanced susceptibility to Mycobacterium marinum intracellular replication. Kil2 is present in the phagosomal membrane, and its structure suggests that it pumps cations into the phagosomal lumen. The killing defect of kil2 knockout cells was rescued by the addition of magnesium ions, suggesting that Kil2 may function as a magnesium pump. In agreement with this, kil2 mutant cells exhibited a specific defect for growth at high concentrations of magnesium. Phagosomal protease activity was lower in kil2 mutant cells than in wild-type cells, a phenotype reversed by the addition of magnesium to the medium. Kil2 may act as a magnesium pump maintaining magnesium concentration in phagosomes, thus ensuring optimal activity of phagosomal proteases and efficient killing of bacteria.     

HDX-analyzer: a novel package for statistical analysis of protein structure dynamics

BACKGROUND: HDX mass spectrometry is a powerful platform to probe protein structure dynamics during ligand binding, protein folding, enzyme catalysis, and such. HDX mass spectrometry analysis derives the protein structure dynamics based on the mass increase of a protein of which the backbone protons exchanged with solvent deuterium. Coupled with enzyme digestion and MS/MS analysis, HDX mass spectrometry can be used to study the regional dynamics of protein based on the m/z value or percentage of deuterium incorporation for the digested peptides in the HDX experiments. Various software packages have been developed to analyze HDX mass spectrometry data. Despite the progresses, proper and explicit statistical treatment is still lacking in most of the current HDX mass spectrometry software. In order to address this issue, we have developed the HDXanalyzer for the statistical analysis of HDX mass spectrometry data using R, Python, and RPY2. IMPLEMENTATION AND RESULTS: HDXanalyzer package contains three major modules, the data processing module, the statistical analysis module, and the user interface. RPY2 is employed to enable the connection of these three components, where the data processing module is implemented using Python and the statistical analysis module is implemented with R. RPY2 creates a low-level interface for R and allows the effective integration of statistical module for data processing. The data processing module generates the centroid for the peptides in form of m/z value, and the differences of centroids between the peptides derived from apo and ligand-bound protein allow us to evaluate whether the regions have significant changes in structure dynamics or not. Another option of the software is to calculate the deuterium incorporation rate for the comparison. The two types of statistical analyses are Paired Student's t-test and the linear combination of the intercept for multiple regression and ANCOVA model. The user interface is implemented with wxpython to facilitate the data visualization in graphs and the statistical analysis output presentation. In order to evaluate the software, a previously published xylanase HDX mass spectrometry analysis dataset is processed and presented. The results from the different statistical analysis methods are compared and shown to be similar. The statistical analysis results are overlaid with the three dimensional structure of the protein to highlight the regional structure dynamics changes in the xylanase enzyme. CONCLUSION: Statistical analysis provides crucial evaluation of whether a protein region is significantly protected or unprotected during the HDX mass spectrometry studies. Although there are several other available software programs to process HDX experimental data, HDXanalyzer is the first software program to offer multiple statistical methods to evaluate the changes in protein structure dynamics based on HDX mass spectrometry analysis. Moreover, the statistical analysis can be carried out for both m/z value and deuterium incorporation rate. In addition, the software package can be used for the data generated from a wide range of mass spectrometry instruments.