Topological classification of RNA structures

We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number whose value quantifies the topological complexity of the folded RNA structure. In such a representation, planar diagrams correspond to pure RNA secondary structures and have zero genus, whereas non-planar diagrams correspond to pseudoknotted structures and have higher genus. The topological genus allows for the definition of topological folding motifs, similar in spirit to those introduced and commonly used in protein folding. We analyze real RNA structures from the databases Worldwide Protein Data Bank and Pseudobase and classify them according to their topological genus. For simplicity, we limit our analysis by considering only Watson-Crick complementary base pairs and G-U wobble base pairs. We compare the results of our statistical survey with existing theoretical and numerical models. We also discuss possible applications of this classification and show how it can be used for identifying new RNA structural motifs.     

世界栽培水杉的调查(1947～2007年)

自第一批种子于1947年12月底走出中国国门,著名‘活化石’水杉已在世界上栽培了60年。过去的5年间通过各种调查方式获得了6大洲近50个国家的2535份资料。调查结果显示,水杉除在欧美及东亚等国家栽培非常普遍外,阿根廷、澳大利亚、智利、印度、墨西哥、尼泊尔、新西兰、南非、泰国、土耳其、津巴布韦等国也有成功的栽培。生长最好的是北美植物耐寒带5-9及欧洲和东亚相似气候地区的栽培水杉,植株最高已达38m,最大胸围已达6.2m。调查内容包括引种的时间、栽培地点、株数、高度及胸围,调查单位不仅包括公立的单位,还包括不对外开放的私人住宅。另外,还讨论了栽培用途、限制因子以及原生种群的资源保护等。     

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank

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Biology of the freshwater diatom <Emphasis Type="Italic">Didymosphenia</Emphasis>: a review

Features of the colonial diatom Didymosphenia are reviewed, especially D. geminata. Although there is a long record of its occurrence in north temperate regions, mass growths have been reported much more widely in recent years. Contrary to some statements in the literature, there are also reliable older records for the southern hemisphere, though the first report of mass growth was in New Zealand in 2004. The annual cycle of morphological changes in D. geminata in northern England, and probably elsewhere, includes a winter period when motile cells are attached to the substratum followed by spring when stalks start to develop. These raise cells into the water column and provide a site for phosphatase activity. Environmental factors associated with success include absence of extreme floods, high light, pH above neutral and nutrient chemistry. D. geminata often, but not always, occurs in waters where the N:P ratio is high for much of the year, but the key factor is the ratio of organic to inorganic phosphate. D. geminata thrives where organic P is predominant and the overall P concentration is low enough for organic P to be an important P source. It is unknown whether organic N can be used. Environmental changes increasing the relative importance of organic P are likely to favour D. geminata. Likely examples are increased N:P due to atmospheric N deposition and changes in form and seasonality of P release from organic-rich soils due to climatic warming. The nutrient chemistry of deep water released from dams to rivers also needs investigation. To what extent are genetic changes occurring in response to environmental changes and are new ecotypes spreading round the world? In spite of many adverse reports about D. geminata, such as detached mats blocking water pipes, there is still doubt about the extent to which it causes problems, particularly for fish. There have been few adverse effects on migratory salmonids in Europe and North America, but at least one report of harm to a brown trout population in USA. In New Zealand, it has caused serious problems for water sports, although it remains open to question how much adverse effect it has had on fish populations. If the presence of microcystins in or associated with D. geminata, as indicated recently for two populations, proves to be widespread and at sufficiently high concentration, their possible accumulation in fish requires study. Where control is required, this could be achieved by enhancing the ratio of inorganic to organic phosphate in the water early in the growth season. Practical ways to achieve this are suggested.     

弓背叶蝉属分类研究（同翅目：叶蝉科）

记述全世界弓背叶蝉属Cyrta Melichar昆虫10种,其中包括8个新种。编制了分种检索表,绘制了新种头、胸部及雄性外生殖器特征图。研究标本中,已知种金弓背叶蝉C.blattina Jacobi的正模标本保存于德国Zoologisches Forschungsinstitut und Museum Alexander Koening (ZFMK),Bonn,但标本标签为Staatliches Museum fuer Tierkunde,Dresden;新种逆毛弓背叶蝉C.recusetosa,sp.nov.模式标本保存于中国南开大学（NKU）;具毛弓背叶蝉C.setosa,sp.nov.正模保存于西北农林科技大学昆虫博物馆（NWSUAF）,副模保存于中国天津自然历史博物馆（TJNHM）;版纳弓背叶蝉C.banna,sp.nov.、尖齿弓背叶蝉C.dentata,sp.nov.和异额弓背叶蝉C.parafrons,sp.nov.模式标本保存于中国科学院动物研究所（IZAS）;异色弓背叶蝉C.bicolor,sp.nov.正模保存于中国科学院上海昆虫研究所（SHIE）;长突弓背叶蝉C.longiloba,sp.nov.正模及1副模保存于中国科学院动物研究所（IZAS）,1副模保存于天津自然历史博物馆（TJNHM）;双斑弓背叶蝉C.bimaculata,sp.nov.正模及2副模保存于天津自然历史博物馆（TJNHM),1副模保存于英国Comm.Inst.Ent.(CIE)。     

2型糖尿病易感候选基因在世界不同人群中的多样性比较分析

近10年来兴起的全基因组关联分析（Genome-wide association study, GWAS）相关研究结果获得了大量与2型糖尿病相关的候选易感基因,了解这些候选基因在正常人群中的遗传多样性程度以及在不同人群间的遗传差异,不但有助于阐明2型糖尿病的遗传机理,而且对于今后在特定人群中进行2型糖尿病发病机制的深入研究具有指导意义。本研究通过对GWAS数据库和相关文献的搜索和整理确定了170个与2型糖尿病相关的基因或基因区域;随后基于千人基因组计划的全基因组测序数据对这些候选基因在世界范围内14个人群间的遗传多样性进行了比较分析;进一步确定了在人群间存在显著差异的易感基因,并分析了这些基因的多样性特征。在所研究的14个世界人群中,2型糖尿病候选易感基因的遗传多样性与基因组范围的平均水平没有显著差异;但其中8个易感基因IL20RA、RNMTL1-NXN、NOTCH2、ADRA2A-BTBD7P2、TBC1D4、RBM38-HMGB1P1、UBE2E2和PPARD在群体间呈现显著差异,其中最明显的是IL20RA基因 (FST=0.152),该易感基因在非洲人群和非非洲人群间存在显著等位基因频率和单倍型频率差异。14个人群中易感基因遗传结构差异的主要原因是由于非洲人群与非非洲人群之间的群体遗传结构的不同所造成的。进一步比较东西方人群间的2型糖尿病候选基因遗传结构差异,发现在东西方人群中同样存在明显的群体遗传结构差别,其中DGKB-AGMO(FST=0.173)和JAZF1(FST=0.182)是差异最显著的易感基因。本研究通过对群体间2型糖尿病易感基因遗传结构进行比较,鉴别出一些差异特别显著的易感基因,对今后2型糖尿病易感基因与不同人群间发病率和易感性差异的相关研究提供重要参考。     

The Occurrence and Economic Impact of <Emphasis Type="Italic">Plasmodiophora brassicae</Emphasis> and Clubroot Disease

The significance of Plasmodiophora brassicae Woronin and clubroot disease which it incites in members of the family Brassicaceae is reviewed as the focus for this special edition of the Journal of Plant Growth Regulation. This is a monographic treatment of recent research into the pathogen and disease; previous similar treatments are now well over half a century old. Vernacular nomenclature of the disease indicates that it had a well-established importance in agriculture and horticulture from at least the Middle Ages onward in Europe and probably earlier. Subsequently, the pathogen probably spread worldwide as a result of transfer on and in fodder taken by colonists as livestock feed. It is a moot point, however, whether there was much earlier spread by P. brassicae into China and subsequently Japan as Brassica rapa (Chinese cabbage and many variants) colonized those lands in archaeological time. Symptoms, worldwide distribution, and economic impact are briefly described here to provide a basis for understanding subsequent papers. Clubroot disease devastates both infected field and protected vegetable and agricultural Brassica crops. Particular importance is placed on recent reports of crop losses in tropical countries, albeit where the crops are grown in cooler altitudes, and in the Canadian prairie land canola crops. The latter is of enormous importance because this crop is the single most important and essential source of vegetable oils used in human foodstuffs and in industrial lubricants where mineral oils are inappropriate.     

Present status of Accelerator-Based BNCT

Aim

This work aims at giving an updated report of the worldwide status of Accelerator-Based BNCT (AB-BNCT).

Background

There is a generalized perception that the availability of accelerators installed in hospitals, as neutron sources, may be crucial for the advancement of BNCT. Accordingly, in recent years a significant effort has started to develop such machines.

Materials and methods

A variety of possible charged-particle induced nuclear reactions and the characteristics of the resulting neutron spectra are discussed along with the worldwide activity in suitable accelerator development.

Results

Endothermic ⁷Li(p,n)⁷Be and ⁹Be(p,n)⁹B and exothermic ⁹Be(d,n)¹⁰B are compared. In addition to having much better thermo-mechanical properties than Li, Be as a target leads to stable products. This is a significant advantage for a hospital-based facility. ⁹Be(p,n)⁹B needs at least 4–5 MeV bombarding energy to have a sufficient yield, while ⁹Be(d,n)¹⁰B can be utilized at about 1.4 MeV, implying the smallest possible accelerator. This reaction operating with a thin target can produce a sufficiently soft spectrum to be viable for AB-BNCT. The machines considered are electrostatic single ended or tandem accelerators or radiofrequency quadrupoles plus drift tube Linacs.

Conclusions

⁷Li(p,n)⁷Be provides one of the best solutions for the production of epithermal neutron beams for deep-seated tumors. However, a Li-based target poses significant technological challenges. Hence, Be has been considered as an alternative target, both in combination with (p,n) and (d,n) reactions. ⁹Be(d,n)¹⁰B at 1.4 MeV, with a thin target has been shown to be a realistic option for the treatment of deep-seated lesions.