判定直系同源关系的进化分析方法

如何正确判定基因之间的直系同源 (ortholog)和旁系同源 (paralog)关系 ,仍是基因组功能诠释和比较基因组学中有待更好解决的关键问题。在以前的工作中 ,曾用进化分析方法解决多基因家族的直系 /旁系同源关系的判定问题 ,现进而完整地展开判定直系同源关系的进化分析方法。从 44个同源蛋白质家族的案例观察表明 ,与流行的COG方法 (直系同源蛋白质的聚类 )比较 ,本方法能一般的判定直系同源关系以及能准确的诠释基因组的分子功能     

比较分析草菇与其他真菌直系同源基因的关系

担子菌类的食用菌种类多、价值高、产量大,然而其产业的升级发展需要对食用菌生长发育相关生物学问题进行深入解析。目前多种食用菌完成了全基因组测序,然而作为非模式种其与模式丝状真菌间的直系同源基因目前尚缺乏全基因组水平的系统研究,在一定程度上限制了其分子生物学研究的深入。本研究以草菇为参照物种,将其与几种食用菌和模式丝状真菌进行两两直系同源基因分析,并对多物种间不同类型的直系同源基因进行功能富集。结果显示：一对一直系同源基因较多富集于基因复制、转录、翻译、修饰、加工等保守的基本功能类别;非一对一直系同源基因多属于基因家族,且包含了65%的转录因子,功能上富集在碳水化合物、脂质、氨基酸、次生代谢物及外源物质的代谢通路。无直系同源基因则较多富集在与基因重组、修复、信号转导相关的功能类别、特导性转录因子以及未知的预测基因。结果为食用菌分子生物学的深入研究提供有价值的参考。     

基因间的同源关系

同源是指从共同祖先的特性遗传下来的通常带有分歧的两个特征之间的关系。同源概念组成了进化基因组学的基础并对功能基因组学有巨大作用,但基于对同源概念的不准确理解,当前对其有诸多模糊表述,因此了解其确切含义具有重要意义。本文就同源、直系同源和旁系同源的概念和性质进行综述。     

基因间的同源关系

同源是指从共同祖先的特性遗传下来的通常带有分歧的两个特征之间的关系。同源概念组成了进化基因组学的基础并对功能基因组学有巨大作用,但基于对同源概念的不准确理解,当前对其有诸多模糊表述,因此了解其确切含义具有重要意义。本文就同源、直系同源和旁系同源的概念和性质进行综述。     

检测番茄BAC序列中paralogs的blastn参数研究

并系同源(paralog)和直系同源(ortholog)是物种进化过程中产生的两种基本的同源序列类型.目前判断ortholog的方法已经基本确立,而paralog的判断却还没有统一的标准.番茄全基因组测序正在进行中,利用GenBank中已有的番茄BAC序列进行一系列不同参数下的比对(blastn),根据比对结果确定了paralog预测的最佳参数,分别是E值为10-40,匹配序列长度为200 bp,序列一致率为80%.这些参数值的确定为以后在番茄BAC序列中进行paralog预测提供了适用的参数.     

水稻全基因组编码抗病基因同源序列分析

利用模糊搜索的方法,在TIGR水稻日本晴基因组数据库(TIGR Rice Genome Annotation-Release5)中识别出565个编码抗病蛋白质的同源序列;利用识别出565个编码抗病蛋白质序列分别与籼稻基因组数据库进行BLASTP联配,共确定320个对应的等位基因。通过在线生物信息学软件,识别了这565个抗病基因的保守结构域、保守模体和DNA序列内转座子元件,其中有14个抗病基因同源序列注释错误。同时绘出了这些基因的基因组分布,并基于这些基因的同源树分析和基因组物理分布,认为基因的原位和远程复制事件产生了抗病基因的现存分布和多样性,其中转座子在复制过程中扮演了重要角色。这些对抗病机制研究和抗病基因进化研究以及抗病基因的转育具有重要意义。     

基于同源基因的病原菌鉴定和分型靶位点的功能基因组学研究

利用病原菌序列差异,对病原菌特定基因和位点进行检测,可以快速发现和鉴别病原菌的分类和特征,对传染病快速诊断和溯源具有基础性意义和重要价值.本文旨在覆盖中国重要传染病的103种病原菌,寻找各分类阶元中特有的同源基因,并从中挑选出适合用于病原菌鉴定、分型的候选基因.利用生物信息学和基因组学方法,对已有全基因组序列的275株病原菌的836415个基因进行比对分析,进一步明确菌株的门、纲、目、科、属各分类阶元中特有的同源基因集合;通过COG功能分类方法,对同源基因集合进行功能注释,并分析在不同分类阶元内的保守基因功能的变化规律.本研究寻找到适合鉴定和分型的不同分类阶元（门、纲、目、科、属）的同源基因集合共19563个（门2891个、纲1016个、目3601个、科10130个、属1925个）.对同源基因功能的分析表明,适合对病原菌进行鉴定的基因在不同分类阶元中,表现的功能存在较大差异.革兰氏阳性和阴性病原菌在不同分类阶元中,同源基因表现出的功能也存在差异.该结果将为对在中国广泛存在的病原菌进行检测所涉及的探针、芯片设计提供理论依据,加快目标探针的筛选工作.同时,研究也是首次将世界范围内的全基因组数据和中国重大传染病涉及的病原菌紧密联系结合,为利用功能基因组学开展区域性、有针对性的病原检测和监测,提供候选基因和位点筛选的新方法.相关结果在细菌的元基因组学研究中也具有一定的应用价值.     

重组工程及其应用

随着功能基因组研究的需要 ,新近建立起一项新型高效的基于体内同源重组的遗传工程技术———重组工程技术。重组工程可定义为 :基于噬菌体短同源序列重组功能的遗传工程 ,或者基于同源重组的遗传工程。λ噬菌体Red系统完全不同于传统的依赖RecA的大肠杆菌重组系统 ,特点是使用长度仅为 <5 0个碱基的同源臂高效率地催化体内同源重组反应。体内重组过程不再需要预先构建含有同源序列的质粒或噬菌体的中间产物 ,只需要简单在体外合成寡核苷酸同源序列 ,或者用PCR方法合成线性打靶序列。重组反应不依赖大肠杆菌RecA系统 ,不需要限制性内切核酸酶和连接酶 ,不需要复杂的体外重组操作 ,可在大肠杆菌体内对染色体DNA、对BAC和PAC质粒或普通质粒载体进行精确的修饰 ,包括真核或原核细胞基因组DNA的基因敲除、基因敲入、基因克隆和各种突变体的引入。由于该技术具有高效率、简单性和应用的广泛性等独特优点 ,将来完全有可能取代传统的遗传工程技术。主要介绍了λ噬菌体Red重组酶系统及重组工程在功能基因组研究方面的应用与进展     

基因组功能预测的进化印记方法

改善基因组功能预测方案是目前功能基因组学的迫切问题,生物进化历程会在分子序列上留下相应进化印记－直系同源簇的特异模体,在这一生物学事实的基础上,提出了一个新的基因缚功能预测方法,首先利用进化分析方法构建直系同源簇,再找到各直系同源簇的功能模体,这样可以形成特异的功能模体库,未知基因的功能预测可望通过搜索该功能模体库而得以高效,准确地完成,对５个家族的检验初步证实该方案是可行的。     

同源建模关键步骤的研究动态

应用同源建模的蛋白质结构预测已经成为一种快速获得蛋白质结构的技术,这种技术也将成为完成结构基因组计划的有力工具.同源建模是指寻找与目标序列同源而且有实验测定结构的蛋白质作为模板,从而构建目标序列的结构模型的方法.限制这种方法的应用主要是同源建模的关键步骤,即目标与模板之间序列比对和环区建模的准确性.当模型的准确性达到令人信服的程度时,更为精确的计算机辅助药物设计和改造蛋白质,甚至设计全新功能的蛋白质将成为可能.综述了从算法和策略上提高同源建模关键步骤准确性的研究进展.     

A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus (2019-nCoV) Potentially Related to Viral Transmissibility

正Dear Editor,In December 2019, a novel human coronavirus caused an epidemic of severe pneumonia(Coronavirus Disease 2019,COVID-19) in Wuhan, Hubei, China(Wu et al. 2020; Zhu et al. 2020). So far, this virus has spread to all areas of China and even to other countries. The epidemic has caused 67,102 confirmed infections with 1526 fatal cases     

Curcuminoids as inhibitors of thioredoxin reductase: A receptor based pharmacophore study with distance mapping of the active site

Curcumin is the yellow pigment of turmeric that interacts irreversibly forming an adduct with thioredoxin reductase (TrxR), an enzyme responsible for redox control of cell and defence against oxidative stress. Docking at both the active sites of TrxR was performed to compare the potency of three naturally occurring curcuminoids, namely curcumin, demethoxy curcumin and bis-demethoxy curcumin. Results show that active sites of TrxR occur at the junction of E and F chains. Volume and area of both cavities is predicted. It has been concluded by distance mapping of the most active conformations that Se atom of catalytic residue SeCYS498, is at a distance of 3.56 from C13 of demethoxy curcumin at the E chain active site, whereas C13 carbon atom forms adduct with Se atom of SeCys 498. We report that at least one methoxy group in curcuminoids is necessary for interation with catalytic residues of thioredoxin. Pharmacophore of both active sites of the TrxR receptor for curcumin and demethoxy curcumin molecules has been drawn and proposed for design and synthesis of most probable potent antiproliferative synthetic drugs.     

Comparative morphology of the carpel in the Liliaceae: Hewardieae, Petrosavieae, and Tricyrteae

The young pistils in the melanthioid tribes, Hewardieae, Petrosavieae and Tricyrteae, are uniformly tricarpellate and syncarpous. They lack raphide idioblasts. All are multiovulate, with bitegmic ovules. The Petrosavieae are marked by the presence of septal glands and incomplete syncarpy. Tepals and stamens adhere to the ovary in the Hewardieae and the Petrosavieae but not in the Tricyrteae. Two vascular bundles occur in the stamens of the Hewartlieae and Tricyrtis latifolia. Ventral bundles in the upper part of the ovary of the Hewardieae are continuous with compound septal bundles and placental bundles in the lower part. Putative ventral bundles occur in the alternate position in the Tricyrteae and putative placental bundles in the opposite. position in the Petrosavieae. The dichtomously branched stigma in each carpel of the Tricyrteae is supplied by a bifurcated dorsal bundle.     

Enterovirus 71 3C proteolytically processes the histone H3 N-terminal tail during infection

Highlights
1. The N-terminal tail of histone H3 is specifically cleaved during EV71 infection.
2. Viral protease 3C is identified as a protease responsible for proteolytically processing the N-terminal H3 tail.
3. Our finding reveals a new epigenetic regulatory mechanism for Enterovirus 71 in virus-host interactions.     

Detection of EBV and HHV6 in the Brain Tissue of Patients with Rasmussen’s Encephalitis

Rasmussen’s encephalitis (RE) is a rare pediatric neurological disorder, and the exact etiology is not clear. Viral infection may be involved in the pathogenesis of RE, but conflicting results have reported. In this study, we evaluated the expression of both Epstein-Barr virus (EBV) and human herpes virus (HHV) 6 antigens in brain sections from 30 patients with RE and 16 control individuals by immunohistochemistry. In the RE group, EBV and HHV6 antigens were detected in 56.7% (17/30) and 50% (15/30) of individuals, respectively. In contrast, no detectable EBV and HHV6 antigen expression was found in brain tissues of the control group. The co-expression of EBV and HHV6 was detected in 20.0% (6/30) of individuals. In particular, a 4-year-old boy had a typical clinical course, including a medical history of viral encephalitis, intractable epilepsy, and hemispheric atrophy. The co-expression of EBV and HHV6 was detected in neurons and astrocytes in the brain tissue, accompanied by a high frequency of CD8⁺ T cells. Our results suggest that EBV and HHV6 infection and the activation of CD8⁺ T cells are involved in the pathogenesis of RE.     

Perinatal Vertical Transmission of Chikungunya Virus in Ruili,a Town on the Border between China and Myanmar

正Dear Editor,Chikungunya virus (CHIKV), an arbovirus in the family of Togaviridae, genus Alphavirus, is transmitted by the A.aegyptii or A. albopictus mosquito, and causes disease in humans characterized by fever, rash, and arthralgia (Silva and Dermody 2017; Suhrbier 2019). It was first reported in 1953 in Tanzania, and caused only a few outbreaks and sporadic cases in Africa and Asia in last century. However, in the epidemic in 2004, CHIKV acquired mutations that conferred enhanced transmission by the A. albopictus mosquito(Schuffenecker et al. 2006). Since then, it has successively caused outbreaks in Africa, the Indian Ocean, South East Asia, the South America, and Europe (Zeller et al. 2016).     

Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2

In conclusion, the novel visual RT-LAMP assay is a simple, rapid, and sensitive approach for detection of SARS-CoV-2, and it is ready for application in primary care and community hospitals or health care centers, and even patients' own houses in response to the current SARS-CoV-2 epidemic because the assay does not require sophisticated equipment and skilled personnel. Furthermore, it is also ready to be used in fields for screening samples from wild animals and environments to facilitate the identification of potential intermediate hosts that mediate the cross-species transmission of SARS-CoV-2 from bats to humans.