基于几丁质酶特征序列预测其最适pH的研究

基于Z标度法对C/18家族几丁质酶的特征序列PS01095和PS00232进行数字转换,将得到的数据集采用逐步回归方法回归预测,构建了几丁质酶特征序列与其最适pH间关系的数学模型.当模型的相关系数为R＝0.964,显著水平P<0.001,得到了最佳的预测效果.模型对pH值拟合的平均绝对百分比误差为0.05 %,同时具有良好的预测效果,预测的平均绝对误差为0.26 个pH单位,比基于几丁质酶氨基酸组成的支持向量机模型更好.     

木聚糖酶氨基酸组成与其最适pH的神经网络模型

籍均匀设计（UD）方法,构建了G/11家族木聚糖酶氨基酸组成和最适pH的神经网络（NNs）模型。当学习速率为0.09、动态参数为0.4、Sigmoid参数为0.98,隐含层结点数为10时,该模型对最适pH的拟合和预测平均绝对百分比误差可分别达到3.02%和4.06%,均方根误差均为0.19个pH单位,平均绝对误差分别为0.11和0.19个pH单位。该结果比文献报道的用逐步回归方法好。     

响应面法优化金针菇栽培工艺的研究

以提高金针菇单瓶产量为目的,以常规生产为对照,通过单因素试验、Plackett-Burman试验、响应面优化法、验证试验分析培养基装瓶量、灭菌前pH、接种量、搔菌深度、搔菌补水量对金针菇单瓶平均产量的影响。单因素试验结果表明,单瓶平均产量分别在装瓶量1 000 g、灭菌前pH值 6.80、接种量35 mL、搔菌深度10 mm、搔菌补水量10 mL时达到最大值;Plackett-Burman试验表明装瓶量、灭菌前pH和搔菌补水量是影响金针菇单瓶平均产量的关键因素;响应面优化法预测的最优化条件为培养基装瓶量1 004.05 g、灭菌前pH值6.83、搔菌补水量11.41 mL,金针菇单瓶平均产量为473.81 g;结合单因素试验及响应面预测,将验证试验设置为培养基装瓶量(1 000±5) g、灭菌前pH值(6.80±0.10)、搔菌补水量(11±1) mL、搔菌深度(10±2) mm、接种量(35±5) mL,金针菇单瓶平均产量为466.36 g,比对照组提高11.63 g,与预测值接近,相对误差为1.57%,试验设计符合生产需求。     

基于SVM 的药物靶点预测方法及其应用

目的:基于已知药物靶点和潜在药物靶点蛋白的一级结构相似性,结合SVM技术研究新的有效的药物靶点预测方法。方法:构造训练样本集,提取蛋白质序列的一级结构特征,进行数据预处理,选择最优核函数,优化参数并进行特征选择,训练最优预测模型,检验模型的预测效果。以G蛋白偶联受体家族的蛋白质为预测集,应用建立的最优分类模型对其进行潜在药物靶点挖掘。结果:基于SVM所建立的最优分类模型预测的平均准确率为81.03%。应用最优分类器对构造的G蛋白预测集进行预测,结果发现预测排位在前20的蛋白质中有多个与疾病相关。特别的,其中有两个G蛋白在治疗靶点数据库(TTD)中显示已作为临床试验的药物靶点。结论:基于SVM和蛋白质序列特征的药物靶点预测方法是有效的,应用该方法预测出的潜在药物靶点能够为发现新的药靶提供参考。     

嗜热和常温蛋白模式识别的研究

采用主成分分析、偏最小二乘回归和BP神经网络三种方法对嗜热和常温蛋白进行模式识别。结果表明,三种方法对训练集拟合的平均正确率分别为92％、95％和98％,对测试集进行预测的平均正确率分别为60％、72.5％和72.5％,对嗜热蛋白预测正确率最高为75％,常温蛋白最高为85％。构建了数学模型并对其生物学意义进行了解释,建立了一种基于序列的识别嗜热和常温蛋白的新方法。     

基因表达数据小波降噪与肿瘤识别

建立了基于小波降噪和支持向量机的结肠癌基因表达数据肿瘤识别模型.对试验数据进行小波分解,并利用交叉验证的方法计算试验样本的平均分类准确率,确定小波函数与小波分解层数;引入能量阈值方法对小波分解系数进行阈值处理,达到降噪的目的;提出了基因分类贡献率与主成分分析结合的方法,提取结肠癌样本数据特征;利用支持向量机强大的非线性映射能力,实现对结肠癌样本数据的非线性分类.为了减弱样本集的划分对分类准确率的影响,本文采取Jackknife检验方法对支持向量分类器的分类器检验,其分类准确率为96.77%.试验结果证明了该方法的有效性,该方法对结肠癌的识别具有一定的参考价值.     

大肠杆菌内源性转录终止子的支持向量机预测方法

内源性转录终止子的计算预测是基因转录调控研究的重要内容,但当前方法的预测特异性偏低.在深入分析大肠杆菌内源性终止子中RNA发夹结构和多聚胸腺嘧啶区域等特征信号的基础上,为内源性终止子建立了一个由5个特征变量组成的包含序列组分、局部构象和能量分布信息的特征集,并根据此特征集实现了一种基于支持向量机的内源性终止子计算预测方法.针对大肠杆菌内源性终止子数据集和编码区阴性对照集的六重交叉验证测试证实了预测方法的有效性,对已知数据的预测平均正确率达到了99.4%.在对大肠杆菌全基因组限定范围内的搜索中,该预测方法可以成功地识别出绝大多数已知内源性终止子,与其他几种常用方法相比,预测结果总数大幅度减少,预测的特异性有了明显提高.     

多基因模型在肝细胞癌预后中的应用

利用较少分子信息预测肝细胞癌类型对患者的个性化治疗十分关键。探索已知的与肝细胞癌预后相关的信号通路,共发现41个关键基因。随后,运用机器学习的方法对其构建风险预测模型,并在4个肝细胞癌数据集上进行验证。结果显示,该模型能将肝细胞癌患者分成两个预后差异显著的类型:癌症基因图谱(The cancer genome atlas,TCGA)数据集交叉验证的平均log rank P值为0.03;其他测试数据集的log rank P 值分别为0.000 38、0.002 1和0.01。生物信息学分析显示肝细胞癌的预后与细胞周期等信号通路显著相关,并筛选出12个潜在的肝细胞癌分子标志物。研究结果表明,基于41个基因构建的肝细胞癌预后模型具有较好的稳健性和准确的风险预测能力。     

GM(1,1)模型和等维递补GM(1,1)模型在流动人口结核病预测中的应用

目的:探讨流动人口结核病疫情预测方法,为结核病控制提供依据.方法:利用2000～2009年深圳市宝安区流动人口初治涂阳结核病发病人数,建立GM(1,1)模型和等维递补GM(1,1)模型进行预测,并用多种方法检验两模型的拟合效果.结果:GM(1,1)模型参数α值为-0.173,μ值为210.815,其拟合精度指标均方差比值为0.183,平均相时误差为7.839,小误差概率为1.等维递补GM(1,1)模型的一阶递补参数α值为-0.174,μ值为249.856,二阶递补参数α值为-0.172,μ值为310.436,拟合精度指标均方差比值和平均相对误差均较GM(1,1)模型小,小误差概率均为1.后者预测到2010、2011和2012年深圳市宝安区流动人口初治涂阳结核病发病人数分为1316人、1570人和1851人.结论:两模型均能合理地对流动人口结核病疫情进行预测,但动态等维递补GM(1,1)模型拟合效果优于普通的静态GM(1,1)模型;深圳市宝安区流动人口初治涂阳结核病人数在今后三年有明显增加趋势,结核病疫情形势严峻,需进一步加强流动人口结核病的防控.     

梨不同DNA提取方法的效果研究

以7个梨品种为实验材料,比较分析了SDS法、CTAB法、SDSCTAB法、改良的CTAB法、高盐低pH值法、分步离心法对梨总DNA提取的效果。结果表明:利用以上6种方法提取的梨总DNA在纯度和量上有很大的差别。所得到的平均DNA量从大到小依次为:分步离心法、SDS法、SDSCTAB法、改良的CTAB法、CTAB法、高盐低pH值法。DNA提取纯度依次为分步离心法、SDSCTAB法、改良的CTAB法、高盐低pH值法、CTAB法、SDS法。RAPD和自交不亲和基因(S基因)特异性引物扩增实验结果都比较理想,但分步离心法和SDSCTAB法提取的DNA双酶切效果较好。分步离心法提取的梨总DNA更适用于后续的分子生物学实验操作。     

Ambient pH Is a Major Determinant in the Expression of Cuticle-Degrading Enzymes and Hydrophobin by Metarhizium anisopliae

Secretion of proteolytic and chitinolytic enzymes is a hallmark of infection processes of Metarhizium anisopliae in response to host (insect) cuticular signals. The regulation of these enzymes (subtilisin-like proteases [Pr1a and Pr1b], trypsin-like proteases [Pr2], metalloproteases, aspartyl proteases, aminopeptidase, and chitinases) and a hydrophobin was investigated by Northern analysis and/or enzyme assay. The production of each enzyme showed a differential expression pattern in response to ambient pH; enzymes were synthesized only at pHs at which they function effectively, irrespective of whether the medium contained an inductive cuticle substrate. Three aspartyl proteases (pH optimum, 3), and chitinase (pH optimum, 5) showed maximal accumulation at acidic pHs. The highest level of aminopeptidase (pH optimum, 7) was detected at pH 7. The highest levels of five metalloproteases (pH optima, ca. 7) were detected over the pH range 6 to 8. Two trypsins and several subtilisin-like Pr1 isoforms with pH optima of ca. 8 were produced only under alkaline conditions. Northern analysis of RNA species corresponding to seven cDNA sequences encoding proteases and chitinase confirmed that the ambient pH played a major role in gene expression of secreted proteins. Hydrophobin was expressed almost equally at pHs 5 and 8 but was not expressed at pH 3. During fungal penetration, the pH of infected cuticle rises from about 6.3 to 7.7. Consistent with pH regulation of enzyme production, serine and metalloproteases were produced in situ during infection, but no production of aspartyl proteases was found. We propose that the alkalinity of infected cuticle represents a physiological signal that triggers the production of virulence factors.     

Chitinase profiles in mature carrot (Daucus carota) roots and purification and characterization of a novel isoform

The profile of chaitinases (EC 3.2.1.14) in mature carrot ( Daucus carota L. cv. Eagle) roots was studied. Multiple chitinase bands (8–10) were observed in native and sodium dodecylsulfate-denaturing polyacrylamide gels. The molecular masses of these chitinases were estimated to be from 20 000 to 40 000. One major chitinase was purified and found to be an acidic protein with pI at 4.3 and a molecular mass of 39 500. The optimum pH for enzymatic activity was around 5 and the optimum temperature was 25°C. The enzyme was stable at pHs below 8 and temperatures below 60°C. The protein did not have a chitin-binding domain, but showed some similarity to the amino acid composition of tobacco class I chitinase. The N-terminal amino acid sequence did not resemble any of the described classes of chitimases. This chitinase did not possess lysozyme activity and showed antifungal activity when tested against Trichoderma sp.     

Kinetic analysis of a chitinase from red sea bream, Pagrus major

Kinetic analysis was done on the 46-kDa chitinase (EC 3.2.1.14) purified from the stomach of red sea bream, Pagrus major, using glycolchitin and N-acetylchitooligosaccharides (GlcNAc(n), n=2-6) as substrates. High activity was observed at two pHs, such as 2.5 and 9.0, toward glycolchitin as seen in other insect chitinases, and also at both pH 2.5 and 5.0 even toward a short substrate, N-acetylchitopentasaccharide. Allosamidin competitively inhibited chitinase with Ki value of 0.0214 microM at pH 2.5 and 0.0024 microM at pH 9.0 in the reaction of glycolchitin. Substrate inhibition was observed in the reaction of N-acetylchitopentasaccharide. The anomeric forms of the products from N-acetylchitooligosaccharides were analyzed to be beta anomer by the high pressure liquid chromatography (HPLC) method. The data for both beta-anomer formation and allosamidin inhibition suggest that red sea bream chitinase belongs to family 18 of glycosyl hydrolases. This suggestion is also supported by the results for the N-terminal amino acid sequence.     

Removal of hexavalent chromium by fungal biomass of <Emphasis Type="Italic">Mucor racemosus</Emphasis>: influencing factors and removal mechanism

This study reported the hexavalent chromium removal by untreated Mucor racemosus biomass and the possible mechanism of Cr (VI) removal to the biomass. The optimum pH, biomass dose, initial Cr (VI) concentration and contact time were investigated thoroughly to optimize the removal condition. The metal removal by the biomass was strongly affected by pH and the optimum pH ranged from 0.5 to 1.0. The residual total Cr was determined. It was found that dichromate reduction occurred at a low very low pH value. At biomass dose 6 g/l, almost all the Cr (VI) ions were removed in the optimum condition. Higher removal percentage was observed at lower initial concentrations of Cr (VI) ions, while the removal capacity of the biomass linearly depended on the initial Cr (VI) concentration. More than half of Cr (VI) ions were diminished within 1 h of contact and removal process reached a relative equilibrium in approximately 8 h. Almost all of the Cr (VI) ions were removed in 24 h when initial concentrations were below 100 mg/l. The equilibrium data were fitted in to the Langmuir and the Freundlich isotherm models and the correlated coefficients were gained from the models. A Fourier transform infrared spectra was employed to elucidate clearly the possible biosorption mechanism as well.     

Purification and characterization of goose type lysozyme from cassowary (Casuarius casuarius) egg white

A novel goose-type lysozyme was purified from egg white of cassowary bird (Casuarius casuarius). The purification step was composed of two fractionation steps: pH treatment steps followed by a cation exchange column chromatography. The molecular mass of the purified enzyme was estimated to be 20.8 kDa by SDS-PAGE. This enzyme was composed of 186 amino acid residues and showed similar amino acid composition to reported goose-type lysozymes. The N-terminal amino acid sequencing from transblotted protein found that this protein had no N-terminal. This enzyme showed either lytic or chitinase activities and had some different properties from those reported for goose lysozyme. The optimum pH and temperature on lytic activity of this lysozyme were pH 5 and 30 degrees C at ionic strength of 0.1, respectively. This lysozyme was stable up to 30 degrees C for lytic activity and the activity was completely abolished at 80 degrees C. The chitinase activity against glycol chitin showed dual optimum pH around 4.5 and 11. The optimum temperature for chitinase activity was at 50 degrees C and the enzyme was stable up to 40 degrees C.     

Statistical modelling and forecasting annual sugarcane production in India: Using various time series models

This paper proposes a comparison of various time series forecasting models to forecast annual data on sugarcane production over 63 years from 1960 to 2022. In this research, the Mean Forecast Model, the Naive Model, the Simple Exponential Smoothing Model, Holt's model, and the Autoregressive Integrated Moving Average time series models have all been used to make effective and accurate predictions for sugarcane. Different scale-dependent error forecasting techniques and residual analysis have been used to examine the forecasting accuracy of these time series models. SE of Residuals, Root Mean Squared Error (RMSE), Mean Absolute Error (MAE) and Akaike's Information Criterion (AIC) are used to analyse the forecast's accuracy. The best model has been selected based on the predictions with the lowest value, according to the three-performance metrics of RMSE, MAE, and AIC. The estimated sugarcane production shows an increasing trend for the next 10 years and is projected to be 37,763.38 million tonnes in the year 2032. Further, empirical results support the plan and execution of viable strategies to advance sugarcane production in India to fulfil the utilisation need of the increasing population and further improve food security.     

Formulation of medium constituents by multiresponse analysis of central composite design to enhance chitinase production in Pantoea dispersa

In the present study, a high chitinase producing strain Pantoea dispersa was isolated from the sea dumps at Bhavnagar, India. Chitin, urea, CaCl2 and MgSO4 x 7H2O were variables used in central composite design for chitinase production. Chitinase, biomass and pH were the responses used in different models to evaluate individually fit ones. Quadratic model was found to be fit for chitinase response whereas in the case of biomass and pH, linear model was found to be fit without the effect of others. Chitinase production was optimized with respect to other responses such as biomass and pH in multiresponse analysis of response surface design by using desirability approach. In multiresponse analysis, following medium formulation (g/l), chitin, 15; urea, 0.32; CaCl2, 0.10 and MgSO4 x 7H2O, 0.08 was found to predict optimum chitinase production of 482.77 units/ml with overall highest desirability of 0.854 as compared to other formulations. The selection of model was done on the basis of high Adjusted R-squared value and lowered p-value for each model in individual analysis of each response. In multiresponse experiment, it was found that for response chitinase quadratic model and for responses pH and biomass linear models were well fit. Through desirability analysis, it was found that in the chitinase production, pH was essential as compared to biomass in P. dispersa. Endochitinase and chitobiase actvities were also studied.     

Molecular Cloning of a Genomic DNA Encoding Yam Class IV Chitinase

Genomic DNA for a class IV chitinase was cloned from yam (Dioscorea opposita Thunb) leaves and sequenced. The deduced amino acid sequence shows 50 to 59% identity to class IV chitinases from other plants. The yam chitinase, however, has an additional sequence of 8 amino acids (a C-terminal extension) following the cysteine that was reported as the last amino acid for other class IV chitinases; this extension is perhaps involved in subcellular localization. A homology model based on the structure of a class II chitinase from barley was used as an aid to interpreting the available data. The analysis suggests that the class IV enzyme recognizes an even shorter segment of the substrate than class I or II enzymes. This observation might help to explain why class IV enzymes are better suited to attack against pathogen cell walls.