Study on a prolyl endopeptidase from the skeletal muscle of common carp (Cyprinus carpio)

A prolyl endopeptidase (PEP) was purified to homogeneity from the skeletal muscle of common carp using a procedure involving ammonium sulfate fractionation and column chromatography involving DEAE-Sephacel, Phenyl-Sepharose, DEAE-Sepharose Fast Flow, and hydroxyapatite. The molecular weight of the PEP was 82 kDa as determined by SDS-PAGE. Using Suc-Gly-Pro-MCA as a substrate, the optimal pH and temperature of the purified enzyme were pH 6.0 and 35 °C, respectively, and the K_m and k_cat were 8.33 μM and 1.71 S^?1, respectively. The activity of the PEP was inhibited by SUAM-14746, a specific inhibitor of prolyl endopeptidases, and was partially inhibited by the serine proteinase inhibitors PMSF and Pefabloc SC. According to peptide mass fingerprinting, 12 peptide fragments with a total of 134 amino acid residues were obtained, which were highly identical to prolyl endopeptidases from zebrafish (Danio rerio) and sponge (Amphimedon queenslandica), confirming the purified enzyme was a prolyl endopeptidase. Our present study for the first time reported the existence of a prolyl endopeptidase in fish muscle.     

Purification, characterization and cDNA cloning of a trypsin from the hepatopancreas of snakehead (Channa argus)

A trypsin was purified from the hepatopancreas of snakehead (Channa argus) by ammonium sulfate fractionation and a series of column chromatographies including DEAE-Sepharose, Sephacryl S-200 HR and Hi-Trap Capto-Q. The molecular mass of the purified trypsin was about 22 kDa, as estimated by SDS-PAGE. The optimum pH and temperature of the purified trypsin were 9.0 and 40 °C, respectively. The trypsin was stable in the pH range of 7.5-9.5 and below 45 °C. The enzymatic activity was strongly inhibited by serine proteinase inhibitors, such as MBTI, Pefabloc SC, PMSF, LBTI and benzamidine. Peptide mass fingerprinting (PMF) of the purified protein obtained 2 peptide fragments with 25 amino acid residues and were 100% identical to the trypsinogen from pufferfish (Takifugu rubripes). The activation energy (Ea) of this enzyme was 24.65 kJ·M^− 1. Apparent K_m was 1.02 μM and k_cat was 148 S^− 1 for fluorogenic substrate Boc-Phe-Ser-Arg-MCA. A trypsinogen gene encoding 247 amino acid residues was further cloned on the basis of the sequence obtained from PMF and the conserved site peptide of trypsinogen together with 5′-RACE and 3′-RACE. The deduced amino acid sequence contains a signal peptide of 15 residues and an activation peptide of 9 amino acid residues with a mature protein of 223 residues. The catalytic triad His-64, Asp-107, Ser-201 and 12 Cys residues which may form 6 disulfide bonds were conserved. Compared with the PMF data, only 2 amino acid residues difference were identified, suggesting the cloned trypsinogen is quite possibly the precursor of the purified trypsin.     

Identification of microRNA precursors with support vector machine and string kernel

MicroRNAs （miRNAs） are one family of short （21-23 nt） regulatory non-coding RNAs processed from long （70-110 nt） miRNA precursors （pre-miRNAs）. Identifying true and false precursors plays an important role in computational identification of miRNAs. Some numerical features have been extracted from precursor sequences and their secondary structures to suit some classification methods; however, they may lose some usefully discriminative information hidden in sequences and structures. In this study, pre-miRNA sequences and their secondary structures are directly used to construct an exponential kernel based on weighted Levenshtein distance between two sequences. This string kernel is then combined with support vector machine （SVM） for detecting true and false pre-miRNAs. Based on 331 training samples of true and false human pre-miRNAs, 2 key parameters in SVM are selected by 5-fold cross validation and grid search, and 5 realizations with different 5-fold partitions are executed. Among 16 independent test sets from 3 human, 8 animal, 2 plant, 1 virus, and 2 artificially false human pre-miRNAs, our method statistically outperforms the previous SVM-based technique on 11 sets, including 3 human, 7 animal, and 1 false human pre-miRNAs. In particular, premiRNAs with multiple loops that were usually excluded in the previous work are correctly identified in this study with an accuracy of 92.66%.     

嗜热四膜虫——具有发展潜力的功能基因组学研究模型

在真核生物的分子生物学和遗传学研究方面,纤毛类原生动物嗜热四膜虫(Tetrahymenathermophila)已经被证明是一种有价值的生物学模型。通过对它的研究,人们发现并且掌握了核酶的分子机制、RNA的自我拼接、端粒的结构和功能、DNA序列重组等机理。这种原生动物的基因组功能分别由两个细胞核执行,即二倍体的小核与生殖过程有关,而多倍体的大核决定细胞的基因转录,并为转化基因的表达提供了强有力的手段。     

壶菌病与两栖动物的种群衰退

两栖类种群全球性衰退是21世纪最紧迫的环境问题之一。越来越多的证据表明壶菌(Batrachochytrium dendrobatidis)与澳大利亚、美洲北部、中部、南部及欧洲的两栖类种群衰退有关。由壶菌引起的壶菌病是变态后的无尾类所患的一种显性传染病,其令人质疑的快速传播及广泛爆发对世界范围内的两栖类种群构成重大威胁。本文对这种致病壶菌的病理学、生态学、生物地理学及其治疗方面的进展进行了综述。     

植物乳杆菌PC518质粒pLP224的发现以及pMV158家族质粒的保守性和多样性分析

【背景】植物乳杆菌含有丰富的天然质粒,分析这些质粒的序列特征有利于分析质粒所携带的遗传信息。【目的】分析从植物乳杆菌PC518分离的新质粒pLP224,聚类分析其所属家族质粒的保守性与多样性。【方法】提取植物乳杆菌PC518的质粒,酶切后构建质粒DNA文库,测序和BLAST鉴定文库中的新序列;通过反向PCR完成质粒全序列测定,注释新质粒;使用进化树软件MEGA X构建质粒的Rep蛋白进化树,并分析结合序列的变化。【结果】从植物乳杆菌PC518分离出一个质粒pLP224,大小为1 766 bp,其中(G+C)mol%含量为41.39%,与已知质粒的最大序列相似性为86.85%。推定其复制方式为滚环复制,属于pMV158家族成员。17个pMV158家族质粒的Rep蛋白分析表明：pMV158家族质粒的Rep蛋白进化距离越近,其dso位点的结合序列相似性越高,进化距离越远则其序列相似性越低。【结论】 pLP224是pMV158家族的新成员。pMV158家族质粒在dso位点的切开序列上保守,在结合序列上多样。其Rep蛋白随结合序列变化而不同。这种差异有利于pMV158家族不同成员在同一宿主的共存,是家族成员持续存在并稳定进化的基础。     

Modeling the water use efficiency of soybean and maize plants under environmental stresses: application of a synthetic model of photosynthesis-transpiration based on stomatal behavior

Understanding the variability of plant WUE and its control mechanism can promote the comprehension to the coupling relationship of water and carbon cycle in terrestrial ecosystem, which is the foundation for developing water-carbon coupling cycle model. In this paper, we made clear the differences of net assimilation rate, transpiration rate, and WUE between the two species by comparing the experiment data of soybean (Glycine max Merr.) and maize (Zea mays L.) plants under water and soil nutrient stresses. WUE of maize was about two and a half times more than that of soybean in the same weather conditions. Enhancement of water stresses led to the marked decrease of Am and Em of two species, but water stresses of some degree could improve WUE, and this effect was more obvious for soybean. WUE of the two species changed with psiL in a second-order curve relation, and the WUE at high fertilization was higher than that at low fertilization, this effect was especially obvious for maize. Moreover, according to the synthetic model of photosynthesis-transpiration based on stomatal behavior (SMPTSB) presented by Yu et al. (2001), the WUE model and its applicability were discussed with the data measured in this experiment. The WUE estimated by means of the model accorded well with the measured values. However, this model underestimated the WUE for maize slightly, thus further improvement on the original model was made in this study. Finally, by discussing some physiological factors controlling Am and WUE, we made clear the physiological explanation for differences of the relative contributions of stomata- and mesophyll processes to control of Am and WUE, and the applicability of WUE model between the two species. Because the requirement to stomatal conductance by unit change of net assimilation rate is different, the responses of opening-closing activity of stomata to environmental stresses are different between the two species. To obtain the same level of net assimilation rate, soybean has to open its stomata more widely to keep small stomatal resistance, as compared with maize.     

中条山混沟地区森林乔木种的数量分类与环境解释

通过对中条山混沟地区森林植被调查资料的多元分析——TWINSPAN分类、CCA排序与环境解释,划分了该地区的植被类型,给出了植被与环境因子的定量关系。结果如下:1)40个样地可划分为青檀林(Form.Pteroceltis tatarinowii)、栾树林(Form. Koelreuteria paniculata)、槲栎林(Form. Quercus aliena)、栓皮栎林(Form. Quercus variabilis)、鹅耳枥+葛萝槭林(Form. Carpinus turczaninowii+Acer grosseri)、元宝槭+千金榆林(Form. Acer truncatum+Carpinus cordata)和辽东栎林(Form. Quercus liaotungensis)7种群落类型,体现了中条山地带性植被类型为暖温带落叶阔叶林的特点。2)群落类型的划分主要反映了CCA排序第一、二轴的环境梯度,CCA排序第一轴突出反映了海拔与土壤养分梯度,第二轴与土壤pH值、湿度指数和坡度显著相关。总体来说,海拔和土壤因子是影响混沟地区乔木物种分布分异的最主要环境因子。3)环境因子和空间因子解释了物种格局变化的46.14%,其中环境因子占30.79%,空间因子占8.48%,空间因子和环境因子交互作用解释的部分占6.87%。良好的环境解释反映了调查取样和环境因子选取的合理性,同时也体现了混沟地区植被的原始性。     

细胞周期检控点

细胞周期是高度有组织的时序调控过程,受到DNA损伤检控点、DNA复制检控点和纺锤体检控点等细胞周期检控点的精确调控。细胞周期检控点的作用主要是调节细胞周期的时序转换,以确保DNA复制、染色体分离等细胞重要生命活动的高度精确性,并对DNA损伤、DNA复制受阻、纺锤体组装和染色体分离异常等细胞损伤及时做出反应,以防止突变和遗传不稳定的发生。细胞周期检控点的功能缺陷,将导致细胞基因组的不稳定,与细胞癌变密切相关。因此细胞周期检控点对于维持细胞遗传信息的稳定性和完整性以及防止细胞癌变和遗传疾病的发生起着至关重要的作用。     

不同植物叶片水分利用效率对光和CO2的响应与模拟

植物叶片水分利用效率的高低取决于气孔控制的光合作用和蒸腾作用两个相互耦合的过程,模拟水分利用效率对环境变化的响应特征和机制是理解生态系统碳循环和水循环及其耦合关系的基础.研究通过人工控制光强和CO2浓度,对叶片水分利用效率进行了研究.提出了植物水分利用效率在光强和CO2浓度共同作用下的估算模型.数据分析表明,该模型在包括C3和C4植物、草本和木本植物在内的9种植物上能很好地模拟水分利用效率对光强和CO2浓度共同作用的响应.该模型可以用于估算CO2浓度升高条件下光合速率的提高和蒸腾速率的降低对水分利用效率提高的贡献量.CO2浓度变化条件下,水分利用效率在不同植物之间有巨大差异,研究区域尺度植物的水分利用效率时至少需要将植物区分为C4植物和C3植物,其中C3植物区分为草本和木本植物3种生态功能型才能较为准确地估算植物的整体水分利用效率.应用本研究提出的水分利用效率估算模型和植物水分利用效率生态功能型分类标准,可以为建立以植物的水分利用效率为基本参数的陆地生态系统水循环模型和陆地生态系统生产力模型提供重要依据.