Optimum DNA Curvature Using a Hybrid Approach Involving an Artificial Neural Network and Genetic Algorithm

Abstract

In the present paper, a hybrid technique involving artificial neural network (ANN) and genetic algorithm (GA) has been proposed for performing modeling and optimization of complex biological systems. In this approach, first an ANN approximates (models) the nonlinear relationship(s) existing between its input and output example data sets. Next, the GA, which is a stochastic optimization technique, searches the input space of the ANN with a view to optimize the ANN output. The efficacy of this formalism has been tested by conducting a case study involving optimization of DNA curvature characterized in terms of the R_L value. Using the ANN-GA methodology, a number of sequences possessing high R_L values have been obtained and analyzed to verify the existence of features known to be responsible for the occurrence of curvature. A couple of sequences have also been tested experimentally. The experimental results validate qualitatively and also near-quantitatively, the solutions obtained using the hybrid formalism. The ANN-GA technique is a useful tool to obtain, ahead of experimentation, sequences that yield high R_L values. The methodology is a general one and can be suitably employed for optimizing any other biological feature.     

非药物治疗极低出生体重儿喂养不耐受的临床观察

目的:将非药物性干预措施与传统药物方法治疗极低出生体重儿喂养不耐受的临床疗效进行观察比较。方法:选取哈尔滨医科大学附属第二医院2011年1月至2013年4月出生的喂养不耐受极低出生体重儿110例。按入院顺序随机分为药物治疗组(MED)55例、非药物治疗组(NON-MED)55例。药物治疗组采用红霉素;非药物治疗组采用腹部按摩法与非营养性吸吮。结果:两组患儿经治疗后,MED组腹胀消失天数(4.4±0.5)、呕吐天数(2.2±0.5)、每日呕吐次数(3.5±0.8)、胃潴留量占每日喂养量(18.3±0.8)、达全肠道喂养天数(8.2±0.7);NON-MED组腹胀消失天数(3.7±0.1)、呕吐天数(1.9±0.6)、每日呕吐次数(2.8±0.1)、胃潴留量占每日喂养量(12.6±0.4)、达全肠道喂养天数(6.1±0.3)。各项治疗指标的对比中,差异均有统计学意义(P0.05)。MED组治疗有效率76.4%;NON-MED组治疗有效率83.6%。结论:非药物性干预措施可有效改善极低出生体重儿喂养不耐受。     

FXR在胃粘膜肠化生及胃癌中的表达及其意义研究

目的:研究FXR在胃炎,胃粘膜肠化生及胃癌组织中的表达,分析其在胃癌发生中的意义。方法:采用免疫组化方法检测FXR在55例胃炎组织,61例胃黏膜肠化生组织及61例胃癌组织中的表达,利用统计学方法 SPSS17.0软件分析其在三种组织中的表达变化,结合文献回顾,分析FXR在胃癌发生中的意义。结果:FXR在胃黏膜肠化生中的表达明显高于胃炎组织(P0.05),而在胃癌组织中,FXR的表达显著低于胃粘膜肠化生组织(P0.05)。结论:FXR是一个潜在的胃癌发生生物标记物,其具体机制有待于进一步探索。     

球孢白僵菌对四种十字花科蔬菜害虫的兼控潜力评价

研究了分离自小猿叶甲的一株球孢白僵菌(Beauveria bassiana(SCAU-BB01D))对十字花科蔬菜4种非目标害虫烟粉虱Bemisia tabaci、小菜蛾Plutella xylostella、黄曲条跳甲Phyllotreta striolata和菜缢管蚜Lipaphis erysimi的致病能力。结果表明,在实验室条件下,该菌株对以上4种害虫均有不同程度的侵染力。1×108孢子/mL的白僵菌悬浮液对1,2,3,4龄烟粉虱若虫的侵染率分别为84.88,86.81,55.94和38.78%;对小菜蛾2,3和4龄幼虫的侵染率为67,59和44%;对黄曲条跳甲幼虫和成虫分别为63%和60%;对菜缢管蚜成蚜和若蚜的侵染率分别为44%和35%。通过机率值分析,得出该菌株对烟粉虱1~4龄若虫的LT50分别为4.14,3.78,6.24和7.59 d;对小菜蛾2~4龄幼虫的LT50分别为7.29,8.16和9.82d;对黄曲条跳甲成虫和幼虫的LT50分别为11.22和8.11 d;对菜缢管蚜成蚜和若蚜的LT50分别为11.01和12.15 d。说明该球孢白僵菌菌株对烟粉虱、小菜蛾和黄曲条跳甲3种非目标害虫具有一定的兼控作用,在蔬菜害虫的生物防治中具一定的应用潜力。     

猪内源性反转录病毒5′端非编码区的克隆及结构分析

通过五指山猪内源性反转录病毒5′端非编码区(5′UTR)cDNA的克隆,分析其一级结构和调控元件,为进一步研究其在PERV复制、转录中的调控机制奠定基础。本研究采用cDNA末端快速扩增技术(RACE)获得全长约1035bp的PERV 5′UTR。通过NCBI公共数据库BLASTn序列进行同源性分析,并应用KEGG数据库对该转录调控区进行顺式作用元件定位分析,结果发现PERV 5′UTR与GenBank公布的部分PERV 5′UTR相比较,同源性在82.6~94.8%之间。一级结构分析发现PERV 5′UTR由U3、R、U5区、引物结合区(PBS)及前导序列组成,可能的核心启动子序列与具有增强子作用的39bp重复序列分别位于U3区的-67~ 1与-97~-59区段。在5′UTR转录调控区(-428~ 507)鉴定出31个有效的顺式作用元件位点,其中NF-Y、TBP、Oct-1、HSF、GATA-1和GATA-2等与PERV的转录、调控密切相关。     

The 1.13-Å structure of iron-free cytochrome c peroxidase

The iron-free cytochrome c peroxidase (CCP) crystal structure has been determined to 1.13 Å and compared with the 1.2-Å ferric-CCP structure. Quite unexpectedly, removal of the iron has no effect on porphyrin geometry and distortion, indicating that protein–porphyrin interactions and not iron coordination or formation of the axial His–Fe bond determines porphyrin conformation. However, there are changes in solvent structure in the distal pocket, which lead to changes in the distal His52 acid–base catalyst. The observed ability of His52 to move in response to small changes in solvent structure is very likely important for its role as a catalyst in assisting in the heterolytic fission of the peroxide O–O bond.     

人乳头瘤病毒11型L1主要衣壳蛋白的B细胞表位多肽作为疫苗的研究

分析了人乳头瘤病毒11型(HPV11)L1主要衣壳蛋白的B细胞优势表位,并以此为基础研制表位多肽疫苗。研究中采用Goldkey和．PC／Gene软件系统,分析HPV11的L1主要衣壳蛋白的二级结构、抗原性、B细胞表位,并引人氨基酸抗原性指数,综合评估其B细胞优势表位。Fmoc固相合成表位多肽,高效液相层析方法纯化,毛细管电泳分析其纯度。与0．2ml佐剂完全乳化后,按50μg／只的剂量免疫小鼠,进行动物水平的免疫效果评价。取免疫小鼠血清,与HPV11 DNA阳性的尖锐湿疣患者的疣体上清液结合,鉴定免疫后小鼠所产生抗体的特异性。发现HPV11的L1主要衣壳蛋白的第426～439位和第487～501位具有较高的免疫原性,可明显诱导小鼠血清抗体滴度升高,且该抗体与人尖锐湿疣的疣体组织上清液呈阳性反应。说明所选这两个肽段为HPV11的L1主要衣壳蛋白的B细胞优势表位,但是否具有功能特异性,尚需进一步研究。     

TLR3免疫识别dsRNA病毒的分子机制

1984年,果蝇的Toll样蛋白被发现。13年后,人们发现了第一个与果蝇Toll蛋白同源的人Toll样受体(toll like receptor,TLR)蛋白(hTLR4)。迄今,已有10种TLR蛋白(即hTLR1～10)被发现,它们代表了一类保守的受体家族,分别识别不同的抗原。其中TLR3能专一性地识别双链RNA(double stranded RNA,dsRNA),通过依赖MyD88的信号通路及不依赖MyD88的信号通路,     

Surface structure and anatomical aspects of Chinese brake fern (Pteris vittata; Pteridaceae)

The objective of this study was to describe a wide spectrum of surface structural and anatomical details of the Chinese brake fern (Pteris vittata) using scanning electron microscopy (SEM). SEM revealed that the epidermal cells of the pinnae were elongated with raised periclinal and sinuous anticlinal walls. The pinnae were hypostomatous with randomly scattered anomocytic stomatal complexes positioned at the same level as the epidermis. Stomates were large and elliptical (27.4 μm × 10.2 μm). Cross sections from the central regions of the rachis and the stipe revealed V- and U-shaped vascular bundles, respectively. In each vascular bundle, the xylem strands were sea-horse shaped (hippocampus). In contrast, the pinnae possessed a triangular vascular bundle with uniform mesophyll organization comprising of homogenous lobed parenchyma cells. The indumentum consisted of trichomes and scales, which formed various types of vestiture. Trichomes were borne only on the pinnae and scales on the rachis and stipe. The roots developed a dense network of long root hairs averaging 244 μm long, and the xylem consisted of tracheids with scalariform pitting. Sori were submarginal; continuous along both margins of the pinna and were covered with a false indusium. The sporangia were oblong with a short thick stalk and the annulus was positioned vertically resulting in transverse dehiscence of the sporangium. The paraphyses were uniseriate, unbranched, septate and found to be intermixed with the sporangia. The exine of the globose spores was adorned with thick reticulum in which the areoles contained round tubercles. This study describes surface features in detail, which is essential to studies examining the issue of whether morphological characteristics are related to arsenic hyperaccumulation inP. vittata.