三维基因组数据分析方法进展

对染色质三维结构的探究逐渐成为了解基因组功能与基因调控关系的必要手段.近年来,随着高通量染色体构象捕获(Hi-C)等技术的发展和高通量测序成本的降低,全基因组交互作用的数据量快速增长,交互作用图谱分辨率不断提高.这给三维基因组学发展带来机遇的同时,也给计算建模带来了挑战.当前,三维基因组数据的分析方法覆盖面广,包括了数据前期处理、标准化、可视化、特征提取、三维建模等环节,但是如何从中选择高效、准确的方法却成为制约研究者们开展研究的一项关键因素.本文根据这些方法的适用场景、原理及特点进行系统地归纳,并重点关注了针对新技术或新需求的分析方法,以期促进这一领域中信息学方法的应用和开发,助力三维基因组学的研究.     

槐种子发育中胚乳细胞半乳甘露聚糖积累的研究

槐 ( Sophora japonica L.)开花约 60 d至种子成熟 ,为胚乳半乳甘露聚糖积累期。用组织化学方法 ,对储藏于胚乳细胞壁上的半乳甘露聚糖的形成积累进行了观察 ,结果表明 ,半乳甘露聚糖最先在邻近胚的胚乳细胞的粗面内质网的囊泡腔内形成 ,并通过细胞质膜分泌至细胞壁周围。此后 ,半乳甘露聚糖的积累逐渐向种皮方向扩展 ,及至种子成熟时 ,除糊粉层外 ,所有胚乳细胞几乎全由多糖所填充。此外 ,对半乳甘露聚糖发生部位及其积累过程的消长变化进行了讨论     

单分子纳米孔测序技术及其应用研究进展

测序技术在通量和成本方面有了较大的改进,以单分子纳米孔测序技术为代表的第三代测序技术更是以其超长读长、实时检测和可以直接检测碱基甲基化修饰等优势在医学及生命科学等领域作出了较大贡献。文中就单分子纳米孔测序技术的原理进行了简要描述,并对其在临床、动物、植物、细菌及病毒等领域的应用和其未来的发展方向进行了讨论。     

国槐叶黄酮的抗氧化活性研究

本文采用ABTS清除体系、DPPH清除体系、H2O2/Fe2+/水杨酸检测体系、亚硝基清除体系、普鲁士蓝法、邻苯三酚自氧化法研究了国槐叶黄酮的抗氧化活性,并同芦丁、Vc进行了比较。结果表明,国槐叶黄酮对几种自由基均有不同的清除效果,在质量浓度为50μg/mL时,国槐叶黄酮对羟基自由基(·OH)、ABTS、DPPH、亚硝基自由基(NO2-)和超氧阴离子自由基(O2-·)的清除率为分别62.09%、47.70%、43.28%、22.11%、21.83%;与芦丁、Vc相比较,国槐叶黄酮清除ABTS、DPPH自由基的能力低于芦丁和Vc,而清除NO2-、.OH的能力高于芦丁和Vc,对O2-·的清除能力低于Vc而高于芦丁,其次国槐叶黄酮具有很好的还原力。由此说明,国槐叶提取物可以作为天然抗氧化剂,可以应用在医药食品领域。     

国槐（Sophora japonica）种子成分分析

为更深入了解国槐种子的生理特性及其综合利用价值,对种子主要成分进行研究,结果表明,国槐种子中蛋白质含量最高,其次为总糖和脂肪;谷氨酸,精氨酸和天冬氨酸是组成种子蛋白质的主要成分;种子油脂以不饱和脂肪酸油酸和亚油酸为主,各种维生素Ｖｃ含量最高,各种化学成分在叶和胚轴＋胚根中含量存在差异。     

槐种子发育过程中子叶细胞显微结构的变化和过氧化物酶同工酶变化的动态

槐（SophorajaponicaL．）种子发育过程中,子叶细胞大量合成和积累储藏物质,光镜和电镜下用组织化学方法观察到开花后30d,叶肉细胞高度液泡化,其中分布着大量的质体、粗面内质网、一些线粒体和小脂体。淀粉粒开始积累。开花后60d,淀粉粒和脂体不断长大,数量明显增多,液泡中蛋白体开始形成。从花后90d开始,液泡中有大量蛋白体形成且不断长大,有些蛋白体变得不规则形。至种子成熟期,叶肉细胞几乎完全被蛋白体及脂体所填充。淀粉粒及大多数细胞器消失。基于上述观察,还对种子发育过程中子叶细胞过氧化物酶活力及同工酶港的变化进行了观察和分析。     

槐果皮中的脂溶性成分

首次对槐（Sophora japonica)果皮进行了化学成分研究,从其石油醚部分分离得到了7个化合物,它们的结构经波谱和化学方法确定为：（Z）－1,1′－biindenyliden(Ⅰ),lupenone(Ⅰ),β-sitosterol(Ⅲ),p-ethoxybenzoic acid(Ⅳ),hexacosoic acid(Ⅴ),nonadecyl alcohol(Ⅵ)和eicosanol(Ⅶ),其中化合物Ⅰ为新天然产物,其它均为首次从该植物中分离得到。     

槐树组织培养中再生植株的比较解剖学研究

本文对组织培养过程中,槐树(Sophora japonica L.)再生植株正常苗和玻璃苗的叶、茎及茎端的解剖结构进行了比较研究。结果表明:正常苗结构基本类似于实生苗,玻璃苗结构变异较大;玻璃苗叶片变厚,表皮细胞形状不规则,气孔保卫细胞萎缩变形,叶肉无明显的栅栏组织与海绵组织分化,叶绿体含量较少,叶维管组织发育不良;茎横切面形状不规则,表皮上气孔数目较多,皮层厚角组织不明显,维营束大致分布成一轮,形成不规则维管柱;茎端分生组织细胞层数较少,不呈现典型的原套原体结构。     

利用改进的3DMax算法重构染色体3D结构

近年来,随着高通量染色体构象捕获(Hi-C)等技术的发展和高通量测序成本的降低,全基因组交互作用的数据量快速增长,交互作用图谱分辨率不断提高,促使染色体和基因组三维结构建模的研究取得了很大进展,已经提出了几种从染色体构象捕捉数据中构建单个染色体或整个基因组结构的方法。文中通过对在 Hi-C 数据基础上对染色体三维结构重建的相关文献进行分析,总结了重建染色体三维空间结构的经典算法3DMax的原理,并且提出了一种新的随机梯度上升算法:XNadam,是Nadam优化方法的一个变体,将其应用于3DMax算法中,以便提高3DMax算法的性能,从而用于预测染色体三维结构。     

Fungal regulatory evolution: cis and trans in the balance

Regulatory divergence is likely a major driving force in evolution. Comparative genomics is being increasingly used to infer the evolution of gene regulation. Ascomycota fungi are uniquely suited among eukaryotes for regulatory evolution studies, due to broad phylogenetic scope, many sequenced genomes, and tractability of genomic analysis. Here we review recent advances in the identification of the contribution of cis- and trans-factors to expression divergence. Whereas current strategies have led to the discovery of surprising signatures and mechanisms, we still understand very little about the adaptive role of regulatory evolution. Empirical studies including experimental evolution, comparative functional genomics and hybrid and engineered strains are showing early promise toward deciphering the contribution of regulatory divergence to adaptation.     

Molecular cloning of the bark and seed lectins from the Japanese pagoda tree (Sophora japonica)

cDNA clones encoding the bark and seed lectins from Sophora japonica were isolated and their sequences analyzed. Screening of a cDNA library constructed from polyA RNA isolated from the bark resulted in the isolation of three different lectin cDNA clones. The first clone encodes the GalNAc-specific bark lectin which was originally described by Hankins et al. whereas the other clones encode the two isoforms of the mannose/glucose-specific lectin reported by Ueno et al.. Molecular cloning of the seed lectin genes revealed that Sophora seeds contain only a GalNAc-specific lectin which is highly homologous to though not identical with the GalNAc-specific lectin from the bark. All lectin polypeptides are translated from mRNAs of ca. 1.3 kb encoding a precursor carrying a signal peptide. In the case of the mannose/glucose-specific bark lectins this precursor is post-translationally processed in two smaller peptides. Alignment of the deduced amino acid sequences of the different clones revealed striking sequence similarities between the mannose/glucose-binding and the GalNAc-specific lectins. Furthermore, there was a high degree of sequence homology with other legume lectins which allowed molecular modelling of the Sophora lectins using the coordinates of the Pisum sativum, Lathyrus ochrus and Erythrina corallodendron lectins.     

国槐新害虫——竖鳞条麦蛾的初步研究

竖鳞条麦蛾AnarsiasquamerectaLietZheng是国槐上新发现的害虫 ,该文首次报道了其寄主及生物学特性。该虫在山东商河 1年发生 1代 ,以 3龄幼虫在枝条芽缝内越冬 ,用 40 %久效磷 1 0 0 0倍液喷雾防治 ,防治效果较好     

Evolution of follistatin in teleosts revealed through phylogenetic, genomic and expression analyses

Follistatin (Fst) inhibits transforming growth factor-β (TGF-B) proteins and is a known regulator of amniote myogenesis. Here, we used phylogenetic, genomic and experimental approaches to study its evolution in teleosts. Phylogenetic analyses suggested that one fst gene (fst1) is common to euteleosts, but a second gene (fst2) is conserved specifically within the Ostariophysi. Zebrafish fst1/2 respectively appear on chromosomes 5 and 10 in two genomic regions, each with conserved synteny to a single region in tetrapods. Interestingly, other teleosts have two corresponding chromosomal regions with a similar repertoire of paralogues. Phylogenetic reconstruction clustered these gene duplicates into two sister clades branching from tetrapod sequences. We suggest that an ancestral fst-containing chromosome was duplicated during the teleost whole genome duplication, but that fst2 was lost in lineages external to the Ostariophysi. We show that Fst1 of teleosts/mammals has evolved under strong purifying selection, but the N-terminal of Fst2 may have evolved under positive selection. Furthermore, the tissue-specific expression of zebrafish fst2 was restricted to fewer tissues compared to its paralogue and the single fst1 orthologue of Atlantic salmon (Salmo salar). Zebrafish fst1/2 may have subfunctionalized relative to non-duplicated vertebrate lineages, as several regions in the fst promoter of tetrapods were conserved with one paralogue, but not both. Finally, we examined the embryonic expression of fst1 in a teleost outside the Ostariophysi (Atlantic salmon). During segmentation, fst1 was expressed in the anterior somite compartment but was excluded from muscle progenitors that strongly expressed myogenic regulatory factors (MRFs). Later, fst1 was expressed in myogenic progenitors of the pectoral fin buds and also within the pax7 ⁺ cell layer external to the myotome. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.