影响RNA芯片探针杂交效率的因素分析

RNA芯片作为研究ncRNA的主要技术之一,已受到广泛关注。然而因RNA芯片中靶序列的单链特征,使得RNA芯片的探针设计比DNA复杂。本研究对加强型绿色荧光蛋白（EGFP）RNA序列进行覆瓦式探针设计,制作了RNA原位合成芯片,研究探针／靶序列杂交双链△G和Tm、靶序列二级结构以及探针的末端碱基对RNA芯片杂交信号强度的影响。结果表明,探针／靶序列杂交双链△G和Tm相同的探针间的杂交信号存在较大差异,探针／靶序列杂交双链△G和,Tm与RNA芯片杂交信号之间未发现明显的规律性;靶序列二级结构的探针PT-sc参数与芯片杂交信号强度间呈较好的线性关系;探针5’末端碱基组成对芯片杂交信号强度也有影响,5’末端碱基为6／C的探针杂交信号总体上高于其邻近的5’末端碱基为A／T的探针的杂交信号,为RNA芯片的探针筛选提供一定的理论基础。     

水稻端粒酶RNA候选序列的克隆及特征解析

端粒酶是由端粒酶反转录酶和端粒酶RNA构成,端粒酶RNA中含有端粒合成所需的模板序列.现仅获得了拟南芥的端粒酶RNA序列.为了建立快速有效的富集植物端粒酶的方法并克隆水稻的端粒酶RNA序列,研究中使用不同浓度的PEG6000选择性的沉淀端粒酶萃取液中的杂蛋白.结果表明当PEG6000浓度为4％时,端粒酶活力最高,并可以有效降低核糖体28S rRNA和18S rRNA的干扰.从端粒酶蛋白液中提取RNA,并在其3′端连接接头,在模板区设计上游引物,PCR扩增获得一条292 bp的未知片段,其中含有端粒模板序列5'-AAACCCTAA-3′.将该片段及拟南芥端粒酶RNA的转录调控区进行序列比对分析发现,两者具有类似的转录调控元件.因此,初步判定292bp的目的片段为水稻端粒酶RNA的模板下游序列.     

RNA二级结构预测算法的设计与实现

本文提出了一个预测RNA二级结构的计算模型和动态规划算法.该算法采用子序列的组合策略和RNA二级结构的内在特性,计算多个平面伪结点和一个非平面伪结点结构.与Rivas算法相比,该算法减少了2n4的空间,并将时间复杂度由O（n6）降为O（n5）.实验结果验证了算法的有效性.     

Algorithms for testing that sets of DNA words concatenate without secondary structure

We present an efficient algorithm for determining whether all moleculesin a combinatorial set of DNA or RNA strandsare structure free, and thus availablefor bonding to their Watson-Crick complements.This work is motivated by the goalof testing whether strands used in DNAcomputations or as molecular bar-codesare structure free, where the strands areconcatenations of short words. We alsopresent an algorithm for determining whetherall words in S*, for some finite setS of equi-length words, are structure free. This revised version was published online in June 2006 with corrections to the Cover Date.     

Hybridization Networks of mRNA and Branched RNA Hybrids

Messenger RNA (mRNA) is emerging as an attractive biopolymer for therapy and vaccination. To become suitable for vaccination, mRNA is usually converted to a biomaterial, using cationic peptides, polymers or lipids. An alternative form of converting mRNA into a material is demonstrated that uses branched oligoribonucleotide hybrids with the ability to hybridize with one or more regions of the mRNA sequence. Two such hybrids with hexamer arms and adamantane tetraol as branching element were prepared by solution-phase synthesis. When a rabies mRNA was treated with the branched hybrids at 1 M NaCl concentration, biomaterials formed that contained both of the nucleic acids. These results show that branched oligoribonucleotides are an alternative to the often toxic reagents commonly used to formulate mRNA for medical applications.     

Long Non-Coding RNAs: Critical Players in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a complex disease with multiple underlying pathogenic mechanisms caused by a variety of etiologic factors. Emerging evidence showed that long non-coding RNAs (lncRNAs), with size larger than 200 nucleotides (nt), play important roles in various types of cancer development and progression. In recent years, some dysregulated lncRNAs in HCC have been revealed and roles for several of them in HCC have been characterized. All these findings point to the potential of lncRNAs as prospective novel therapeutic targets in HCC. In this review, we summarize known dysregulated lncRNAs in HCC, and review potential biological roles and underlying molecular mechanisms of lncRNAs in HCC. Additionally, we discussed prospects of lncRNAs as potential biomarker and therapeutic target for HCC. In conclusion, this paper will help us gain better understanding of molecular mechanisms by which lncRNAs perform their function in HCC and also provide general strategies and directions for future research.     

Molecular Mechanisms Underlying TDP-43 Pathology in Cellular and Animal Models of ALS and FTLD

Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are neurodegenerative disorders that exist on a disease spectrum due to pathological, clinical and genetic overlap. In up to 97% of ALS cases and ~50% of FTLD cases, the primary pathological protein observed in affected tissues is TDP-43, which is hyperphosphorylated, ubiquitinated and cleaved. The TDP-43 is observed in aggregates that are abnormally located in the cytoplasm. The pathogenicity of TDP-43 cytoplasmic aggregates may be linked with both a loss of nuclear function and a gain of toxic functions. The cellular processes involved in ALS and FTLD disease pathogenesis include changes to RNA splicing, abnormal stress granules, mitochondrial dysfunction, impairments to axonal transport and autophagy, abnormal neuromuscular junctions, endoplasmic reticulum stress and the subsequent induction of the unfolded protein response. Here, we review and discuss the evidence for alterations to these processes that have been reported in cellular and animal models of TDP-43 proteinopathy.     

Effect of biohydrogen by overexpressing small RNA RyhB combined with ldh impairment in novel Klebsiella sp. FSoil 024

Biotechnological hydrogen production is considered as an environmentally sustainable alternative to petrochemical sources or electrolysis. Here, disruption of lactate dehydrogenase (LDH) and metabolic regulation via the small RNA RyhB were adopted to improve hydrogen production in the novel Klebsiella sp. strain FSoil 024. The hydrogen production of FSoil 024-L (Δldh) and FSoil 024-L/R (Δldh/RyhB) from glucose in a 5-L fermenter respectively increased by 40 and 50% compared to the wild type. When glycerol was adopted as a more favorable substrate, FSoil 024-L generated 3.3 L/L of hydrogen after 52 h of fermentation, implying its great potential for the utilization of crude glycerol to produce hydrogen. Overexpression of RyhB downregulated formate biosynthesis in FSoil 024, thereby redirecting NADH toward the hydrogen production pathway. This finding provides new insights into the role of cellular reducing power in hydrogen metabolism and establishes a rationale for improving hydrogen production.