An algorithm for searching RNA motifs in genomic sequences

RNA molecules, which are found in all living cells, fold into characteristic structures that account for their diverse functional activities. Many of these RNA structures consist of a collection of fundamental RNA motifs. The various combinations of RNA basic components form different RNA classes and define their unique structural and functional properties. The availability of many genome sequences makes it possible to search computationally for functional RNAs. Biological experiments indicate that functional RNAs have characteristic RNA structural motifs represented by specific combinations of base pairings and conserved nucleotides in the loop regions. The searching for those well-ordered RNA structures and their homologues in genomic sequences is very helpful for the understanding of RNA-based gene regulation. In this paper, we consider the following problem: given an RNA sequence with a known secondary structure, efficiently determine candidate segments in genomic sequences that can potentially form RNA secondary structures similar to the given RNA secondary structure. Our new bottom-up approach searches all potential stem-loops similar to ones of the given RNA secondary structure first, and then based on located stem-loops, detects potential homologous structural RNAs in genomic sequences.     

A Vesicular Stomatitis Virus-Based Vaccine Carrying Zika Virus Capsid Protein Protects Mice from Viral Infection

<正>Dear Editor,Zika virus (ZIKV) is a mosquito-borne virus that belongs to the Flavivirus family along with dengue virus (DENV),yellow fever virus, West Nile virus, and Japanese encephalitis virus (Ming et al. 2016). ZIKV is a singlestranded positive-sense RNA virus encoding three structural proteins, including nucleocapsid protein C, prM/M,envelope glycoprotein E, and seven non-structural proteins.Since 2015, over 70 countries and territories had reported     

细菌素Paracin 1.7的纯化与性质研究

摘要：【目的】分离纯化（Lactobacillus paracasei）HD1.7所产生的细菌素并分析其特性。【方法】细菌素Paracin 1.7的纯化采用色谱技术,其分子量检测采用十二烷基磺酸钠－聚丙烯酰胺凝胶电泳（SDS-PAGE）,利用琼脂扩散法测定细菌素活力。【结果】Paracin 1.7分离于我国传统发酵食品酸菜发酵液中,其产生菌为副干酪乳杆菌。 Paracin 1.7可以抑制其它微生物的生长,为细菌素。该菌在稳定期可产生大量Paracin 1.7。经过阳离子交换层析、凝胶过滤层析以及高效液相色谱（HPLC）,对该细菌素进行了初步纯化,并经Tricine-SDS-PAGE检测其分子量大约为11 kDa。Paracin 1.7抑菌谱较广,其抑菌范围包括Proteus, Bacillus, Enterobacter, Staphylococcus, Escherichia, Lactobacillus, Microccus, Pseudomonas, Salmonella, Saccharomyces,其中有些为食品源致病菌。该细菌素在酸性及高温下稳定,对几种蛋白质酶敏感。该细菌素对敏感菌株的作用方式为抑菌。在4oC保存4个月后,Paracin 1.7的抑菌活性保持稳定。【结论】基于细菌素Paracin 1.7的性质,该细菌素可用作食品防腐剂。     

谱系年代研究进展

谱系年代学是结合化石记录和分子钟方法计算"生命树"(Tree of Life)上各分歧点时间的一个新兴交叉学术领域.由于化石记录的不完整性,各类生物的起源年代和支系分化时间的确定可借助于部分化石记录和通过计算现生生物类群之间的遗传距离转换得出的相对分歧时间相结合的办法进行讨论.化石记录可代表部分生物类群起源时间的保守估计值,而分子钟方法可为那些不易保存为化石的生物类群与其姊妹群的分化时间提供依据.如果使用得当的话,两者可进行相互验证.在分子谱系年代分析中,正确使用化石校准方案是获得准确分歧时间的关键,这需要:1)正确确定化石物种在谱系树上的位置;2)正确解释化石记录所代表的时间含义(最小值、确定值、最大值及其标准差).分子钟估算分歧时间的技术在不断改进,目前常用的分子分歧时间估算法(宽松分子钟法,如贝叶斯法、补偿性似然法等)包容分子演化速率在谱系间和随时间的变化.随着谱系年代研究的不断深入,长期困扰人们的化石记录时间与分子钟计算结果悬殊的问题正在逐渐趋于和谐并得到正确诠释.文中还讨论了有关动物起源与早期分化时间以及早期陆生节肢动物的谱系年代学研究进展.我们强调,化石记录和分子钟分析可以优势互补,两者的整合无疑将提高生物演化历史时间格架的准确度和精度,以利更好地将生命演化事件置于地球系统科学及地球环境演化史之中.     

The Recombination Protein RAD52 Cooperates with the Excision Repair Protein OGG1 for the Repair of Oxidative Lesions in Mammalian Cells

Oxidized bases are common types of DNA modifications. Their accumulation in the genome is linked to aging and degenerative diseases. These modifications are commonly repaired by the base excision repair (BER) pathway. Oxoguanine DNA glycosylase (OGG1) initiates BER of oxidized purine bases. A small number of protein interactions have been identified for OGG1, while very few appear to have functional consequences. We report here that OGG1 interacts with the recombination protein RAD52 in vitro and in vivo. This interaction has reciprocal functional consequences as OGG1 inhibits RAD52 catalytic activities and RAD52 stimulates OGG1 incision activity, likely increasing its turnover rate. RAD52 colocalizes with OGG1 after oxidative stress to cultured cells, but not after the direct induction of double-strand breaks by ionizing radiation. Human cells depleted of RAD52 via small interfering RNA knockdown, and mouse cells lacking the protein via gene knockout showed increased sensitivity to oxidative stress. Moreover, cells depleted of RAD52 show higher accumulation of oxidized bases in their genome than cells with normal levels of RAD52. Our results indicate that RAD52 cooperates with OGG1 to repair oxidative DNA damage and enhances the cellular resistance to oxidative stress. Our observations suggest a coordinated action between these proteins that may be relevant when oxidative lesions positioned close to strand breaks impose a hindrance to RAD52 catalytic activities.Oxidative DNA damage is generated at high levels in mammalian cells, even in cells not exposed to exogenous sources of reactive oxygen species. Several kinds of DNA modifications are formed upon oxidative stress (8). The most prevalent modifications, quantitatively, are single-strand breaks and oxidized bases. Clustered DNA damage, when two or more modifications are closely positioned in opposite strands, is detectable after gamma irradiation and has recently been shown to be generated by normal oxidative metabolism (3, 35). One unique aspect of such clustered lesions is that they can be converted into double-strand breaks (DSB) if a DNA glycosylase removes the two opposite bases and an apurinic/apyrimidinic (AP)-endonuclease cleaves the resulting abasic sites. Thus, although quantitatively minor, DSB are possible outcomes of oxidative DNA damage.Oxidized DNA bases are repaired primarily by the base excision repair pathway (BER) (22, 39). BER is initiated by a lesion-specific DNA N-glycosylase that recognizes and excises the damaged base. Eight-hydroxyguanine (8-oxoG) is one of the most abundant oxidized bases detected in cellular DNA. This adduct is easily bypassed by replicative polymerases; however, it can direct the misincorporation of adenine opposite 8-oxoG, thus leading to G·C-to-T·A transversion mutations (31). 8-oxoG accumulation has been causally associated with carcinogenesis and aging in several experimental models (1, 12). In eukaryotes, oxoguanine DNA glycosylase (OGG1) is the major 8-oxoG DNA glycosylase. OGG1 possesses an associated AP-lyase activity, such that it removes 8-oxoG and cleaves the DNA backbone. Human cells express two distinct OGG1 isoforms, α and β, which share the first 316 amino acids but differ significantly in their C termini (25). While OGG1-α is a bone fide DNA glycosylase (5) and localizes both to nuclei and mitochondria, OGG1-β localizes exclusively to mitochondria. We recently showed that the recombinant OGG1-β protein has no DNA glycosylase activity (13). The high degree of conservation of repair pathways for 8-oxoG, from bacteria to humans, along with epidemiological data correlating OGG1 polymorphisms and activity with predisposition to some cancers (11, 27, 33) attest to the biological importance of the repair of 8-oxoGs and other oxidative DNA lesions.Until recently, distinct classes of DNA lesions were believed to be metabolized by different and independent repair pathways. However, experimental evidence indicates that these pathways can interact and that there is a considerable degree of overlap in their substrate specificity and in the proteins that participate in each pathway. Experiments using yeast strains lacking one or more distinct DNA repair genes suggest that DSB repair pathways may play a role in repair of oxidative DNA damage. Swanson et al. showed that while yeast cells lacking ntg1 and ntg2 (homologues of Escherichia coli endonuclease III, a DNA glycosylase specific for pyrimidine lesions formed by oxidation) and apn1 (the major yeast abasic site endonuclease) are not overtly sensitive to oxidative stress, the additional disruption of the rad52 gene significantly increases sensitivity to H₂O₂ and menadione (36). Similarly, yeast cells expressing decreased levels of frataxin, which leads to elevated oxidative stress, show accumulation of oxidative damage in nuclear DNA only in a rad52 mutant background (18). RAD52 is a member of the RAD51 epistatic group. These proteins are believed to be involved in the early steps of homologous recombination, contributing to homology search and strand invasion; disruption of the corresponding genes renders cells deficient in DSB repair and hyper-recombinogenic (19).These results suggested a possible role for RAD52 in the repair of oxidative DNA damage. Moreover, an in vitro screening of protein partners that interact physically with OGG1-β performed in our lab (unpublished data) showed that human RAD52 strongly interacted with this glycosylase, again suggesting a possible function for RAD52 in the oxidative DNA damage response. Thus, we investigated whether RAD52 plays a role in the repair of oxidative DNA damage in human cells. We show here that human RAD52 physically interacts with both OGG1-α and -β, in vitro and in cell extracts. We also show that OGG1-α and -β inhibit RAD52 enzymatic activities. Conversely, RAD52 stimulates OGG1-α 8-oxoG incision activity. RAD52 colocalizes with OGG1-α in cells, and this colocalization increases after oxidative stress. Moreover, lower RAD52 expression, via gene knockdown (KD) or disruption of the RAD52 gene, render cells sensitive to oxidative stress. Based on our results, we discuss a model in which OGG1 and RAD52 cooperate to repair 8-oxoG lesions.     

Sorcin在鳗鱼免疫器官的组织化学研究

目的:探究sorcin蛋白在鳗鱼主要免疫器官中的分布情况,为应用sorcin蛋白研制药用新靶点和应用鱼用疫苗奠定理论基础.方法:运用组织学和组织化学技术,在鳗鱼的主要免疫器官中进行sorcin蛋白的免疫组化定位研究.结果:sorcin蛋白在鳗鱼的心脏、肠、肝脏中均有分布.结论:sorcin蛋白在鳗鱼免疫器官中的分布情况与其功能密切相关.     

国内外作物种植制度的计算机模型与系统分析的研究动态与现状

国内外作物种植制度的计算机模型与系统分析的研究动态与现状杨京平（浙江农业大学农业生态研究所,杭州３１００２９）ＲｅｓｅａｒｃｈＡｃｔｉｖｉｔｙａｎｄＳｉｔｕａｔｉｏｎｏｆＣｏｍｐｕｔｅｒＭｏｄｅｌｌｉｎｇａｎｄＳｙｓｔｅｍＡｎａｌｙｓｉｓｉｎＣｒｏｐ...     

姜属植物种子的解剖学和组织化学研究

本文报道以斑蝉姜、珊瑚姜和多穗姜为材料的姜属种子解剖学和组织化学研究结果。结果表明,姜属种子较大,基部具一膨大的种阜状结构,膜质假种皮２－５裂,裂片指状或瓣状。种皮黑褐色,一般平滑,由外种皮、中种皮与内种皮组成。外种皮为一层表皮细胞。中种皮由各含一层细胞的下皮层和半透明细胞层与含（２）３－４层薄壁细胞的色素层组成。半透明细胞体积很大,细胞内的不定形块状物含有脂类;色素层细胞体积小,不含或仅含少许色     

利用杂种F_2世代鉴定数量性状主基因-多基因混合遗传模型并估计其遗传效应

大量实验数据和OTL作图结果表明:控制数量性状的基因中既有遗传效应较大的主基因,又有遗传效应较小的多基因,其分离世代表现出多峰性,即出现多个分布混合的特征。本文利用混合模型理论的AIC信息准则在F_2世代中鉴定影响数量性状的主基因的存在,当主基因存在时通过分离分析估计主基因的遗传效应以及主基因的遗传变异占总变异的分量;同时还提出利用P_1、P_2、F_2和F_2 4个世代鉴定多基因存在的方法。以大豆开花期性状为例说明了该方法的应用,在所分析的骨绿豆×上海红芒早杂交组合的F_2世代数据中发现有主基因的存在,主基因表现出完全显性(晚开花),并且有多基因存在。     

CPPU对猕猴桃果实组织发育及内源细胞分裂素含量的影响

对经生长调节剂ＣＰＰＵ处理的猕猴桃果帝进行了组织学及内源细胞分裂素含量变化的研究。结果表明：处理后的果帝细胞分裂时期延长,细胞的数目增多,体积增大;处理果实中,内源细胞分裂素的含量在果肉细胞分裂盛期及其之后都有所增高。