Predicting siRNA activity based on back-propagation neural network

RNA interference (RNAi) is a phenomenon of gene silence induced by a double-stranded RNA (dsRNA) homologous to a target gene.RNAi can be used to identify the function of genes or to knock down the targeted genes.In RNAi technology,19 bp double-stranded short interfering RNAs (siRNA) with characteristic 3' overhangs are usually used.The effects of siRNAs are quite varied due to the different choices in the sites of target mRNA.Moreover,there are many factors influencing siRNA activity and these factors are usually nonlinear.To find the motif features and the effect on siRNA activity,we carried out a feature extraction on some published experimental data and used these features to train a backpropagation neural network (BP NN).Then,we used the trained BP NN to predict siRNA activity.     

RNAi技术在昆虫功能基因研究中的应用进展

RNA干扰（RNA interference,RNAi）是指外源或内源的双链RNA（dsRNA）特异性地引起基因表达沉默的现象,它作为一种有效的工具用来产生转录后沉默,从而抑制特定基因的表达,成为基因功能研究的一种新方法,除了在模式昆虫如果蝇Drosophila中广泛应用之外,也在非模式昆虫中得到成功应用。近年来,RNAi技术在导入方法和基因功能分析方面都取得了飞速发展,且与转基因技术相结合成功应用于害虫防治领域。本文综述了RNAi技术在导入方法、昆虫功能基因组功能分析及害虫防治等领域新近的研究成果,并展望了该技术的应用前景。     

BP神经网络优化微生物浸矿工艺

以低品位黄铜矿溶液为原料,浸矿制备Cu2＋能有效提高低品位黄铜矿的利用价值。基于浸矿过程中存在多因素影响的现象,通过正交试验与神经网络分析方法,对浸矿条件（接种量、矿石品位、Fe2＋添加量及浸矿溶液pH）实行优化。结果表明：在正交试验组中最佳试验结果为浸矿产128．753mg／LCu^2＋;BP神经网络优化后的最佳实验组合为微生物接种量12％、矿石品位0．3％、添加Fe^2＋24g/L及浸矿溶液pH1．7,该条件下验证试验产Cu^2＋ 141．352mg／L,通过正交试验及神经网络优化提高了微生物浸出低品位黄铜矿酸性溶液Cu^2＋的产量。     

基于BP神经网络的siRNA活性预测

RNA干扰(RNAinterference,RNAi)是由双链RNA(dsRNA)引起的基因沉默现象,它通过降解具有同源序列的mRNA来起作用,特殊设计的siRNA能使靶基因发生特异性沉默,起到确定基因功能或沉默致病基因从而治疗疾病的目的。在RNAi技术的应用中,通常采用的是长度为19bp,正、反义链3'端各有2个不配对碱基的双链RNA(siRNA)。但针对靶基因不同位点设计的siRNA作用效果差别很大。影响siRNA效果的因素是多方面的,这些因素的作用又是非线性的。本文在研究影响siRNA作用效果的各种因素的基础上,对已经公开发表的实验数据进行特征提取,作为BP神经网络的训练数据,并将训练好的BP神经网络用于siRNA活性预测。     

Initial evidence of functional siRNA machinery in dinoflagellates

Dinoflagellates are a major group of protists widely distributed in the aquatic environments. Many species in this lineage are able to form harmful algal blooms (HAB), some even producing toxins, making this phylum the most important contributors of HAB in the marine ecosystem. Despite the ecological importance, the molecular mechanisms underpinning the basic biology and HAB formation of dinoflagellates are poorly understood. While the high-throughput sequencing studies have documented a large and growing number of genes in dinoflagellates, their functions remained to be experimentally proven using a functional genetic tool. Unfortunately, no such tool is yet available. This study was aimed to adopt the RNA interference (RNAi) gene-silencing tool for dinoflagellate research, and to investigate the potential effects of RNAi-based silencing of proton-pump rhodopsin and CO₂-fixing enzyme Rubisco encoding genes in dinoflagellates. It was found that RNAi treatment caused a significant decrease in growth rate in both species. Compared with the non- endogenous target (GFP-siRNA) and the blank control, RNAi treatments also suppressed the expression of the target genes. These results constitute the first experimental evidence of the existence and operation of siRNA in two species of dinoflagellates, present initial evidence that dinoflagellate rhodopsins are functional as a supplemental energy acquisition mechanism, and provide technical information for future functional genetic research on dinoflagellates.     

针对SARS冠状病毒重要蛋白的siRNA设计(英文)

NA干涉 (RNAinterference ,RNAi)是一种特异性地导致转录后基因沉默的现象 ,在哺乳动物细胞中小分子干扰RNA双链体 (smallinterferingRNAduplexes ,siRNAduplexes)可以有效地诱导RNAi现象 ,为一些疾病的治疗开辟了新的途径 .针对SARS冠状病毒 (SARScoronavirus ,SARS CoV)中编码 5个主要蛋白质的基因 ,用生物信息学的方法设计了3 48条候选siRNA靶标 .在理论上 ,相应的siRNA双链体能特异地抑制SARS CoV靶基因的表达 ,同时不会影响人体细胞基因的正常表达 ,这为进一步siRNA类药物的实验研究提供了理论基础     

针对SARS冠状病毒重要蛋白的siRNA设计(英)

RNA干涉(RNA interference, RNAi)是一种特异性地导致转录后基因沉默的现象,在哺乳动物细胞中小分子干扰RNA双链体(small interfering RNA duplexes, siRNA duplexes)可以有效地诱导RNAi现象,为一些疾病的治疗开辟了新的途径.针对SARS冠状病毒(SARS coronavirus, SARS-CoV)中编码5个主要蛋白质的基因,用生物信息学的方法设计了348条候选siRNA靶标.在理论上,相应的siRNA双链体能特异地抑制SARS-CoV靶基因的表达,同时不会影响人体细胞基因的正常表达,这为进一步siRNA类药物的实验研究提供了理论基础.     

Rigid nanoparticle-based delivery of anti-cancer siRNA: Challenges and opportunities

Gene therapy is a promising strategy to treat various genetic and acquired diseases. Small interfering RNA (siRNA) is a revolutionary tool for gene therapy and the analysis of gene function. However, the development of a safe, efficient, and targetable non-viral siRNA delivery system remains a major challenge in gene therapy. An ideal delivery system should be able to encapsulate and protect the siRNA cargo from serum proteins, exhibit target tissue and cell specificity, penetrate the cell membrane, and release its cargo in the desired intracellular compartment. Nanomedicine has the potential to deal with these challenges faced by siRNA delivery. The unique characteristics of rigid nanoparticles mostly inorganic nanoparticles and allotropes of carbon nanomaterials, including high surface area, facile surface modification, controllable size, and excellent magnetic/optical/electrical properties, make them promising candidates for targeted siRNA delivery. In this review, recent progresses on rigid nanoparticle-based siRNA delivery systems will be summarized.     

慢病毒GV115-AIF siRNA 重组表达系统的构建及鉴定

目的:构建高效的慢病毒GV115-AIF si RNA重组表达系统。方法:根据目的基因AIF以及RNA干扰序列设计原则,利用设计软件设计了3个可能的AIF si RNA序列。应用全基因合成技术和亚克隆技术构建GV115-AIF si RNA重组质粒,并采用聚合酶链反应技术(PCR技术)和基因测序技术对GV115-AIF si RNA重组质粒鉴定。利用GV115病毒包装辅助p Helper 1.0质粒和p Helper 2.0质粒进行病毒包装。病毒包装后转染人胚肾293T细胞,通过应用逆转录定量PCR技术(RT-PCR技术)检测转染后对人胚肾293T细胞中AIF基因的敲减效率,筛选最高效的AIF si RNA基因序列。结果:GV115-AIF si RNA质粒PCR鉴定显示位于341bp附近的条带。测序结果与设计的基因序列完全吻合。3个可能的AIF si RNA序列中基因敲减效率最高的可达到88.3%。结论:成功构建高效的慢病毒GV115-AIF si RNA重组表达系统。     

RNA干涉在纤毛虫中的研究进展

RNA干涉是dsRNA介导的基因沉默现象,本文简要介绍了其作用的机制和生物学意义,重点阐述了RNA干涉在原生动物纤毛虫中的发现与应用,比较了RNA干涉与纤毛虫大核基因组重排机理的异同,并对RNA干涉在纤毛虫中传输的技术途径-RNAi喂饲法的原理也做了详细的介绍。     

基于神经网络简单集成的湖库富营养化综合评价模型

根据中国水利部推荐的地表水富营养化控制标准,以叶绿素a、总磷、总氮、化学需氧量和透明度为评价指标,采用线性插值方法生成均匀分布的训练样本,建立了用于湖泊、水库富营养化综合评价的神经网络简单集成模型,其个体网络采用反向传播网络。通过递增法分别确定个体网络隐含层节点数为3,集成规模为40。所有个体网络均采用弹性反传训练算法和带动量的梯度下降学习算法。将该模型应用于巢湖富营养化综合评价,结果表明该模型有效消除了单个反向传播神经网络对初始网络权重的敏感性,泛化能力得到显著的提高。该模型的评价结果与综合营养状态指数法差异极显著,而与插值评分法差异不显著;但相关性较高,相关系数分别为0．9406和0．8891。通过对比分析,表明该模型较好地归纳了评价标准中的潜在评价规则,评价结果客观、可靠。     

Chemically modified siRNA prolonged RNA interference in renal disease

BACKGROUND: We previously demonstrated that transfection of synthetic short interfering RNAs (siRNAs) targeting against TGF-beta1 could be effective and therapeutic in silencing TGF-beta1 expression in glomerulus, thereby ameliorated the progression of matrix expansion in anti-Thy-1 model of glomerulonephritis. However, a major concern in applying RNAi to gene therapy is the prolonged existence of silencing potential in vivo. METHOD: We examined the duration of siRNA stability in kidney and muscle, and checked the tissue distribution of siRNase, eri-1. Thereafter, we tested the effect of chemically modified siRNA called siSTABLE on progressive glomerulosclerosis model. RESULTS: A single introduction of siRNA for EGFP (siEGFP) or its expression vector into kidney resulted in the reduction of masangial EGFP expression only for up to two weeks, while transfection of siEGFP into the pretibial muscle silenced EGFP expression unexpectedly for more than 90 days. These observations could be explained by the different expression of eri-1 between kidney and muscle. In addition, transfection of ERI-1-resistant siSTABLE for TGF-beta1 significantly reduced glomerular matrix deposition in progressive glomerulosclerosis model.Conclusion: Treatment with siRNA resistant to eri-1 may be effective and promising strategy for progressive renal disease.     

Toxoplasma gondii: siRNA can mediate the suppression of adenosine kinase expression

Adenosine kinase (AK) is one of the most important enzymes in the Toxoplasma gondii purine salvage pathway. Three siRNAs specific to the AK gene were designed in the present study. At 24h following electroporation, two of them (siRNA786 and siRNA1200) significantly reduced the mRNA level compared with mock electroporation (P <0.05). The ability to incorporate [3H]-adenosine in the parasites electroporated with 4 microM siRNA786 or 4 microM siRNA1200 was decreased to 39+/-11% and 39+/-7% of the mock electroporation, respectively. At the 48th hour of electroporation, the enzyme's activity was still significantly lower than that of mock electroporation. The data show the siRNAs transfected into cells can work efficiently to regulate gene expression in T. gondii. The application of siRNA in interrupting gene expression in T. gondii would be useful for elucidating gene function as a step toward development of anti-toxoplasmasis vaccines and therapeutic reagents.     

人工神经网络在发酵工业中的应用

人工神经网络技术具有很强的非线性映射能力,用于系统的非线性建模,具有无可比拟的优势,广泛应用于发酵过程中培养基的优化和系统建模与控制方面,本主要介绍了人工神经网络的基本原理与使用方法,以及BP神经网络在非线性函数逼近的优点,详细介绍了其在发酵培养基优化,连续搅拌反应器神经网络估计,分批发酵及补料分批发酵过程建模与控制优化中的应用实例。     

Reconstruction of dopaminergic neural network and locomotion function in planarian regenerates

Planarian, an invertebrate flatworm, has a high capacity for regeneration when compared with other worms and animals. We show here for the first time that the reconstructed dopamine (DA) neural network regulates locomotion and behavior in planarian regenerates. The gene encoding tyrosine hydroxylase in the planarian Dugesia japonica (DjTH) was identified. DjTH protein was coexpressed with aromatic amino acid decarboxylase-like A (DjAADCA) in the planarian central nervous system (CNS). In addition, DjTH-knockdown planarians lost the ability to synthesize DA, but showed no change in 5-hydroxytryptamine synthesis. When the planarian body was amputated, DjTH-positive neurons were regenerated in the brain newly rebuilt from the tail piece at Day 3, and the DjTH-positive axonal and dendritic neural network in the CNS (dopaminergic tiara) was reconstructed at Days 5-7. At that time, autonomic locomotion and methamphetamine-induced hyperkinesia were also suppressed in DjTH-knockdown planarians. Planarian locomotion and behavior seem to be regulated in both cilia- and muscle-dependent manners. In DjTH-knockdown planarians, muscle-mediated locomotion and behavior were significantly attenuated. These results suggest that DA neurons play a key role in the muscle-mediated movement in planarians.     

昆虫RNA干扰中双链RNA的转运方式

昆虫RNA干扰主要指外源双链RNA诱发的,通过阻碍特定基因的翻译或转录,引起内源目标信使RNA沉默的机制。由于RNA干扰的特异性,RNA干扰技术主要应用于昆虫功能基因组和害虫防治的研究。本综述主要对双链RNA引起昆虫体内RNA干扰研究中双链RNA转运的3种方法(显微注射法、喂食法及浸泡与转染法)进行介绍和讨论。这3种方法中,显微注射法能将精确数量的双链RNA迅速转运到目标组织,更适合实验室基因功能的研究;喂食法操作简单快速,适合高通量的基因筛选;浸泡与转染法也适合大规模的基因筛选,但更常见于细胞研究中。     

In vivo electroporation for genetic manipulations of whole Hydra polyps

In vivo electroporation is used to study gene regulation and gene function in the freshwater polyp Hydra. Although this approach has been used successfully by several investigators, efficacy and handling continue to present a problem. Here we show technical aspects of in vivo electroporation for introducing fluorescent dyes, plasmid DNA and double stranded RNA into Hydra polyps. We describe the fundamentals of the electroporation delivery system, discuss recent studies where this approach has been used successfully, compare it to alternative transfection methods such as lipofection, and identify future directions.