MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution

Background  

MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution.     

药（毒）物对尸食性蝇类生长发育影响的研究进展

药（毒）物对尸食性蝇类生长发育影响是法医昆虫毒理学领域里一个十分重要的研究方向,其研究结果可对与药（毒）物相关死亡案件的死亡时间作出修正。随着近年来全球毒品及药物滥用情况的日趋严重,其所导致的死亡案件也越来越多。这类案件常常需要应用尸食性蝇类生长发育历期来推算死后经历时间（postmortem interval, PMI）。为了阐明该领域的研究进展以及未来研究的焦点和难点,本文在阐述法医昆虫毒理学概念和特点的基础上,按照不同的药（毒）物分类,对近年来药（毒）物对尸食性蝇类生长发育影响在国内外的研究进展进行了综述。研究表明,某些药（毒）物对尸食性蝇类生长发育具有一定的影响,且这种影响存在种属差异。目前,该领域的研究尚限于宏观现象观察阶段,其研究范围在不断拓宽,既有的研究也在进一步深化,但还有许多问题有待进一步探讨。     

相思子属三种药材中的氨基酸分析比较

利用全自动氨基酸分析仪和高效液相色谱仪分析比较相思子属三种药材中氨基酸成分及含量。结果9个样品都检测出17种氨基酸和2种色氨酸衍生物。结论:不同样品中的氨基酸含量有所差异,但其中门冬氨酸、谷氨酸、亮氨酸和赖氨酸的含量相对较高。     

DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes

Different patterns of strand asymmetry have been documented in a variety of prokaryotic genomes as well as mitochondrial genomes. Because different replication mechanisms often lead to different patterns of strand asymmetry, much can be learned of replication mechanisms by examining strand asymmetry. Here I summarize the diverse patterns of strand asymmetry among different taxonomic groups to suggest that (1) the single-origin replication may not be universal among bacterial species as the endosymbionts Wigglesworthia glossinidia, Wolbachia species, cyanobacterium Synechocystis 6803 and Mycoplasma pulmonis genomes all exhibit strand asymmetry patterns consistent with the multiple origins of replication, (2) different replication origins in some archaeal genomes leave quite different patterns of strand asymmetry, suggesting that different replication origins in the same genome may be differentially used, (3) mitochondrial genomes from representative vertebrate species share one strand asymmetry pattern consistent with the strand-displacement replication documented in mammalian mtDNA, suggesting that the mtDNA replication mechanism in mammals may be shared among all vertebrate species, and (4) mitochondrial genomes from primitive forms of metazoans such as the sponge and hydra (representing Porifera and Cnidaria, respectively), as well as those from plants, have strand asymmetry patterns similar to single-origin or multi-origin replications observed in prokaryotes and are drastically different from mitochondrial genomes from other metazoans. This may explain why sponge and hydra mitochondrial genomes, as well as plant mitochondrial genomes, evolves much slower than those from other metazoans.     

氮气气腹制作腹内高压对肝脏功能的影响

目的研究腹内压升高及持续时间对肝脏功能的影响。方法选择SD大鼠45只,随机分为正常对照组,10mmHg腹内压(IAP)模型组,20mmHg腹内压(IAP)模型组,每组15只。各IAP组大鼠以头皮针于腹腔穿刺,通过三通管连接压力计及氮气袋,运用氮气气腹法制作SD大鼠腹内高压动物模型,对照组不充气。各组动物按腹内压持续时间分别于1、2、4h处死,使用全自动生化分析仪检测每个动物的天门冬氨酸转氨酶(AST)、丙氨酸转氨酶(ALT)。结果 10mmHg和20mmHg IAP持续4h组的血清AST、ALT含量均明显高于持续1h和2h组(P<0.01,P<0.05);20mmHg IAP 2h组血清AST、ALT含量亦明显高于1h组(P<0.05);但10mmHg IAP持续2h组血清AST、ALT含量与1h相比,差异无统计学意义(P>0.05)。IAP维持1h的3组(10mmHg组,20mmHg组,对照组)大鼠的血清AST、ALT含量差异无统计学意义(P>0.05);IAP持续2h,20mmHg IAP组的AST、ALT含量明显高于10mmHg IAP组和对照组;IAP维持4h,20mmHg IAP组血清AST、ALT含量均显著高于对照组(P<0.01),较10mmHg IAP组血清AST含量增高(P<0.05),而ALT间比较无统计学意义(P>0.05);10mmHg IAP组持续4h组血清AST、ALT含量高于对照组4h组(P<0.01,P<0.05)。结论腹内高压可致肝损伤,并与腹腔压力和时间密切相关。SD大鼠腹内高压动物模型的制作简易、稳定可靠,且可重复。     

细胞粘附分子群相互作用网络模型研究

通过相互作用网络可视化软件Cytoscape对整联蛋白粘合体156种成份及相互间的690个反应实现网络可视化,并通过网络分析软件network analyser得到该网络节点间的平均连接并不复杂是一个不可分割的整体网络,网络较稳定,信息传递很快等。直接可视化的网络通过节点的形状改变视图有助于我们在原始数据的基础上更好的认识这一复杂的作用网络的相关信息。     

某私营木制家具制造企业2004 年与2010 年职业病危害因素检测 与评价报告比较和分析

目的:通过比较2个年份职业病危害因素检测与评价报告,评估职业病防治工作的效果。方法:选取两份有代表性的报告,比较和分析职业病危害防护设施的安装、个人防护用品发放与使用、警示标示以及各项检测结果的合格率。结果:该企业2010年各项调查指标相比2004年明显提高。结论:该企业各项职业病防治工作效果显著,劳动环境明显改善,但仍需注意噪声、木粉尘的危害。     

GC skew in protein-coding genes between the leading and lagging strands in bacterial genomes: new substitution models incorporating strand bias

The DNA strands in most prokaryotic genomes experience strand-biased spontaneous mutation, especially C→T mutations produced by deamination that occur preferentially in the leading strand. This has often been invoked to account for the asymmetry in nucleotide composition, typically measured by GC skew, between the leading and the lagging strand. Casting such strand asymmetry in the framework of a nucleotide substitution model is important for understanding genomic evolution and phylogenetic reconstruction. We present a substitution model showing that the increased C→T mutation will lead to positive GC skew in one strand but negative GC skew in the other, with greater C→T mutation pressure associated with greater differences in GC skew between the leading and the lagging strand. However, the model based on mutation bias alone does not predict any positive correlation in GC skew between the leading and lagging strands. We computed GC skew for coding sequences collinear with the leading and lagging strands across 339 prokaryotic genomes and found a strong and positive correlation in GC skew between the two strands. We show that the observed positive correlation can be satisfactorily explained by an improved substitution model with one additional parameter incorporating a general trend of C avoidance.     

SIMULATING SEASONAL AND INTERANNUAL VARIATIONS OF ECOSYSTEM EVAPOTRANSPIRATION AND ITS COMPONENTS IN INNER MONGOLIA STEPPE WITH VIP MODEL

 利用内蒙古羊草草原(Leymus chinensis)生态系统通量观测站的气象数据、野外实测和MODIS叶面积指数(Leaf area index, LAI), 应用基于生态系统过程的VIP(Vegetation interface process)模型, 以半小时为步长, 模拟分析了羊草草原生态系统2003～2005年(分别为平水年、平水年和干旱年)蒸散及其分量的变化过程。通过与通量数据对比, VIP模型能够很好地模拟羊草草原生态系统的蒸散过程(R² = 0.80), 在峰值大小和变化趋势上, 模拟值与实测值有较好的一致性。模拟结果显示: 3年蒸散量分别为337、338和223 mm; 在降水相对充沛的2003和2004年, 蒸腾量为192和171 mm, 而降水相对较少的2005年, 蒸腾量仅为96 mm; 年平均蒸腾和蒸发对蒸散的贡献基本持平; 生长季蒸散占全年的83%, 6月开始, 蒸腾大于蒸发, 蒸散和蒸腾的月总值均在7、8月达到最大值,两月蒸散占全年的43%。LAI是影响蒸散的主要因素, 其次是降水, 而净辐射对蒸散的影响较小。在生长季, 蒸发的季节变化平缓, 蒸散的差异主要体现在蒸腾的差异。