Design,synthesis and antithrombotic evaluation of novel dabigatran prodrugs containing methyl ferulate

A novel series of prodrugs containing dabigatran and methyl (E)-3-(4-hydroxy-2-methoxyphenyl)propenoate (methyl ferulate) were synthesized. All of them reveal the effect of thrombin-induced anti-platelet aggregation in vitro. In addition, in vivo experiment shows that one of the target compounds, X-2 (ED₅₀ = 3.7 ± 1.0 μmol/kg) possesses a more potent activity for inhibiting venous thrombosis than that of dabigatran etexilate (ED₅₀ = 7.8 ± 1.5 μmol/kg).     

Imidazo[4,5-b]pyridine inhibitors of B-Raf kinase

This Letter details the synthesis and evaluation of imidazo[4,5-b]pyridines as inhibitors of B-Raf kinase. These compounds bind in a DFG-in, αC-helix out conformation of B-Raf, which is a binding mode associated with significant kinase selectivity. Structure–activity relationship studies involved optimization of the ATP-cleft binding region of these molecules, and led to compound 23, an inhibitor with excellent enzyme/cell potency, and kinase selectivity.     

Glutamate transporter type 3 knockout leads to decreased heart rate possibly via parasympathetic mechanism

Parasympathetic tone is a dominant neural regulator for basal heart rate. Glutamate transporters (EAAT) via their glutamate uptake functions regulate glutamate neurotransmission in the central nervous system. We showed that EAAT type 3 (EAAT3) knockout mice had a slower heart rate than wild-type mice when they were anesthetized. We design this study to determine whether non-anesthetized EAAT3 knockout mice have a slower heart rate and, if so, what may be the mechanism for this effect. Young adult EAAT3 knockout mice had slower heart rates than those of their littermate wild-type mice no matter whether they were awake or anesthetized. This difference was abolished by atropine, a parasympatholytic drug. Carbamylcholine chloride, a parasympathomimetic drug, equally effectively reduced the heart rates of wild-type and EAAT3 knockout mice. Positive immunostaining for EAAT3 was found in the area of nuclei deriving fibers for vagus nerve. There was no positive staining for the EAATs in the sinoatrial node. These results suggest that EAAT3 knockout mice have a slower heart rate at rest. This effect may be caused by an increased parasympathetic tone possibly due to increased glutamate neurotransmission in the central nervous system. These findings indicate that regulation of heart rate, a vital sign, is one of the EAAT biological functions.     

TOPS-MODE model of multiplexing neuroprotective effects of drugs and experimental-theoretic study of new 1,3-rasagiline derivatives potentially useful in neurodegenerative diseases

The interest on computational techniques for the discovery of neuroprotective drugs has increased due to recent fail of important clinical trials. In fact, there is a huge amount of data accumulated in public databases like CHEMBL with respect to structurally heterogeneous series of drugs, multiple assays, drug targets, and model organisms. However, there are no reports of multi-target or multiplexing Quantitative Structure–Property Relationships (mt-QSAR/mx-QSAR) models of these multiplexing assay outcomes reported in CHEMBL for neurotoxicity/neuroprotective effects of drugs. Accordingly, in this paper we develop the first mx-QSAR model for multiplexing assays of neurotoxicity/neuroprotective effects of drugs. We used the method TOPS-MODE to calculate the structural parameters of drugs. The best model found correctly classified 4393 out of 4915 total cases in both training and validation. This is representative of overall train and validation Accuracy, Sensitivity, and Specificity values near to 90%, 98%, and 80%, respectively. This dataset includes multiplexing assay endpoints of 2217 compounds. Every one compound was assayed in at least one out of 338 assays, which involved 148 molecular or cellular targets and 35 standard type measures in 11 model organisms (including human). The second aim of this work is the exemplification of the use of the new mx-QSAR model with a practical case of study. To this end, we obtained again by organic synthesis and reported, by the first time, experimental assays of the new 1,3-rasagiline derivatives 3 different tests: assay (1) in absence of neurotoxic agents, (2) in the presence of glutamate, and (3) in the presence of H₂O₂. The higher neuroprotective effects found for each one of these assays were for the stereoisomers of compound 7: compound 7b with protection = 23.4% in assay (1) and protection = 15.2% in assay (2); and for compound 7a with protection = 46.2% in assay (3). Interestingly, almost all compounds show protection values >10% in assay (3) but not in the other 2 assays. After that, we used the mx-QSAR model to predict the more probable response of the new compounds in 559 unique pharmacological tests not carried out experimentally. The results obtained are very significant because they complement the pharmacological studies of these promising rasagiline derivatives. This work paves the way for further developments in the multi-target/multiplexing screening of large libraries of compounds potentially useful in the treatment of neurodegenerative diseases.     

Structural Mechanism of CCM3 Heterodimerization with GCKIII Kinases

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Highlights? Crystal structure of CCM3-MST4 heterodimeric complex ? Structural mechanism driving CCM3-GCKIII heterodimerization ? Conformational changes required for CCM3-GCKIII heterodimerization ? Synergistic effects of CCM3-MST4 complex on cell proliferation and migration     

Impact of GC content on gene expression pattern in chicken

Background

GC content varies greatly between different genomic regions in many eukaryotes. In order to determine whether this organization named isochore organization influences gene expression patterns, the relationship between GC content and gene expression has been investigated in man and mouse. However, to date, this question is still a matter for debate. Among the avian species, chicken (Gallus gallus) is the best studied representative with a complete genome sequence. The distinctive features and organization of its sequence make it a good model to explore important issues in genome structure and evolution.

Methods

Only nuclear genes with complete information on protein-coding sequence with no evidence of multiple-splicing forms were included in this study. Chicken protein coding sequences, complete mRNA sequences (or full length cDNA sequences), and 5^′ untranslated region sequences (5^′ UTR) were downloaded from Ensembl and chicken expression data originated from a previous work. Three indices i.e. expression level, expression breadth and maximum expression level were used to measure the expression pattern of a given gene. CpG islands were identified using hgTables of the UCSC Genome Browser. Correlation analysis between variables was performed by SAS Proprietary Software Release 8.1.

Results

In chicken, the GC content of 5^′ UTR is significantly and positively correlated with expression level, expression breadth, and maximum expression level, whereas that of coding sequences and introns and at the third coding position are negatively correlated with expression level and expression breadth, and not correlated with maximum expression level. These significant trends are independent of recombination rate, chromosome size and gene density. Furthermore, multiple linear regression analysis indicated that GC content in genes could explain approximately 10% of the variation in gene expression.

Conclusions

GC content is significantly associated with gene expression pattern and could be one of the important regulation factors in the chicken genome.     

丰水期长江感潮河口段网采浮游植物的分布与长期变化

于2009年6、8月对长江口门至江阴的河口段浮游植物进行了拖网采集,共检出浮游植物6门99属239种。其中:硅藻123种,甲藻19种,绿藻和蓝藻各42种,裸藻9种,黄藻4种。河口段网采浮游植物丰度以蓝藻占绝对优势,硅藻次之,两者合计在群落中的比例超过了95%。优势种也主要以蓝藻(水华鱼腥藻Anabaena flos-aquae、柔软腔球藻Coelosphaerium kuetzingiarum、微囊藻Microcystis spp.、颤藻Oscillatoria spp.和席藻Phorimidium spp.)构成,硅藻仅有2种(骨条藻Skeletonema spp.和颗粒直链藻Aulacoseira granulata)。口门内盐度均<0.5,群落基本以淡水类群为主,口门附近则以半咸水类群为主,海水类群主要位于口门外(盐度>13)。随着水温和营养盐水平的升高,8月浮游植物平均丰度(347.75×10⁴ 个/m³)明显高于6月(204.19×10⁴ 个/m³)。根据多维尺度和相似性分析,丰水期长江河口段浮游植物群落组成与分布存在显著(P<0.01)的时空差异。对比20世纪80年代以来的历史资料发现,长江口门内网采浮游植物丰度显著升高,且优势种也从硅藻(骨条藻、直链藻和圆筛藻)转变为蓝藻(颤藻、鱼腥藻和微囊藻)。     

城市不同地表覆盖类型对土壤呼吸的影响

采用Licor-6400-09的土壤呼吸测量系统对北京市区3种不同覆盖类型地表(全硬地表、半透砖地表、草坪覆盖地表)的土壤呼吸速率及其影响因子进行了测定和分析。结果表明:(1)不同地表覆盖类型的土壤呼吸速率年均值分别为7.928 μmol·m^-2·s^-1(全硬地表),5.592 μmol·m^-2·s^-1(部分硬化地表)、2.625 μmol·m^-2·s^-1(草坪覆盖地表);土壤呼吸日均值最高均出现在夏季(14.785,10.296,5.143 μmol·m^-2·s^-1),最低为冬季(0.490,0.319,0.239 μmol·m^-2·s^-1);(2)3种地表类型的土壤呼吸速率有显著差异(P<0.05),大小排序为:草坪覆盖地表<部分硬化地表<全硬地表;(3)3种地表类型土壤呼吸速率均与土壤温度呈显著的指数相关,Q₁₀值排序为:草坪覆盖地表<部分硬化地表<全硬地表;(4)土壤含水率和土壤电导率与土壤呼吸均有一定的相关性,但关系较为复杂,有待于进一步研究。     

气相色谱-质谱联用技术及其在代谢组学中的应用

代谢组学是以高通量、高灵敏度、高分辨率的现代仪器分析方法为手段,对细胞、体液、组织中所有代谢物进行无偏向的定性与定量分析的一门学科。气相色谱-质谱联用技术具有较高的检测灵敏度和鉴定准确度,通过标准谱图库的比对可对代谢物进行快速的鉴定,因此被广泛应用于生物样品的代谢产物的检测中。文中对近年来气相色谱-质谱联用技术的发展以及在代谢组学研究中取得的成果进行了综述。首先介绍了气相色谱-质谱联用技术的分类和常用的样品衍生化方法;继而从样品预处理、定性与定量分析、数据分析三方面介绍了气相色谱-质谱联用技术分析代谢物的方法,并系统地对该技术在微生物、植物、疾病诊断领域的应用实例进行了评述;最后提出了当前气相色谱-质谱联用技术在代谢组学研究中存在的问题并对后续的研究进行了展望。