Genome-wide identification of allele-specific effects on gene expression for single and multiple individuals

The analysis of allele-specific gene expression (ASE) is essential for the mapping of genetic variants that affect gene regulation, and for the identification of alleles that modify disease risk. Although RNA sequencing offers the opportunity to measure expression at allele levels, the availability of powerful statistical methods for mapping ASE in single or multiple individuals is limited. We developed a maximum likelihood model to characterize ASE in the human genome. Approximately 17% of genes displayed an allele-specific effect on gene expression in a single individual. Simulations using our model gave a better performance and improved robustness when compared with the binomial test, with different coverage levels, allelic expression fractions and random noise. In addition, our method can identify ASE in multiple individuals, with enhanced performance. This is helpful in understanding the mechanism of genetic regulation leading to expression changes, alternative splicing variants and even disease susceptibility.     

Growth space competition index(GSCI)and application in the individual intraspecies competition of Pinus tabulaeformis and Platycladus orientalis forests

dized-combination;Yield;Grey system;Related degree0玉米科学Journal of Maize Sciences50-52S513D04723D;D047了20多种衡量竞争程度的竞争指数系统,但有关学者研究后认为,这些竞争指数都没有较好地解决了定量分析中树冠变化的问题。论文首次提出生长空间竞争指数(Growthspacecompetitionindex,GSCI),系树冠表面积与胸高断面积之比,由于树冠外围面积代表树冠接受光照最强的部分并且是决定生产效率的重要指标,因此在群体和群落的竞争中作为反映竞争参数,较好地解决了定量分析中树冠变化的问题,为树冠覆盖程度的无量纲度量。本文还在油松(Pinustabulaeformis)、侧柏(Platycladusorientalis)林种内个体竞争中得到应用,与常用的简单竞争指数(Competitionindex,CI)和空间竞争指数(Growthspaceindex,GSI)进行了对比研究。     

北京东灵山地区主要树生地衣调查初报

首次对北京森林生态定位站所在地东灵山小龙门林场主要森林树种上的地衣进行了调查研究,辽东栎,核桃楸,山杨,黄花柳,白腊和春榆等树种上的地衣覆盖度较大,其覆盖度多为３０％￣６０％,最高可达８０％。     

A simple approach to assess water scarcity integrating water quantity and quality

Water scarcity has become widespread all over the world. Current methods for water scarcity assessment are mainly based on water quantity and seldom consider water quality. Here, we develop a simple approach for assessing water scarcity considering both water quantity and quality. In this approach, a new water scarcity index is used to describe the severity of water scarcity in the form of a water scarcity meter, which may help to communicate water scarcity to a wider audience. To illustrate the approach, we analyzed the historical trend of water scarcity for Beijing city in China during 1995–2009. The results show that Beijing made a huge progress in mitigating water scarcity, and that from 1999 to 2009 the blue and grey water scarcity index decreased by 59% and 62%, respectively. These achievements were made through great efforts of water-saving measures and wastewater treatment. Despite this progress, we demonstrate that Beijing is still characterized by serious water scarcity due to both water quantity and quality. The water scarcity index remained at a high value of 3.5 with a blue and grey water scarcity index of 1.2 and 2.3 in 2009 (exceeding the thresholds of 0.4 and 1, respectively). As a result of unsustainable water use and pollution, groundwater levels continue to decline, and water quality shows a continuously deteriorating trend. To curb this trend, future water policies should further decrease water withdrawal from local sources (in particular groundwater) within Beijing, and should limit the grey water footprint below the total amount of water resources.     

北京东灵山地区景观格局及破碎化评价

 人类活动已将北京东灵山地区地带性原生暖温带落叶阔叶林破坏殆尽。本项研究基于植被图,在地理信息系统(GIS)支持下,选择多种景观格局指数,从斑块面积、斑块数、斑块周长、分形维数和多样性的角度进行了格局分析和破碎化评价。结果表明,该区景观类型以次生林和灌丛为主,面积分布极不均衡,且多呈小面积零散分布。各森林类型的分布面积、周长和斑块数一般小于灌丛、草地和农田,且边界密度和斑块密度较高,显示出较高程度的破碎化。各景观类型的平均斑块面积和周长遵从分形规律,分形维数1.30,景观整体的斑块边界的褶皱程度较低。景观多样性的Shannon指数,景观组分的类型面积(2.262)<类型周长(2.435)<类型斑块数(2.675),均小于等概率情形(2.940)。上述结果均显示,该区森林景观破碎化程度较高。     

北京维管植物编目和分布数据集

区域性维管植物编目对于该区域内植物多样性保护及植物资源可持续利用具有重要意义。北京作为中国首都, 尽管编目工作早在20世纪60年代就得以开展, 但近30年来没有进行系统更新。现有数据零散、不系统, 相关编目进展甚至已经落后于周边地区。本文在《北京植物志(1992年修订版)》的基础上, 结合多年实际野外调查, 通过系统检索文献资料对现有编目数据进行查漏补缺(补充新分类群、新记录)、修订名称(基于新分类修订成果)、更新分类系统(采用基于分子数据的新分类系统), 并添加物种等级、分布状态、生长状态、室内/室外、分布区、了解程度及保护状况等相关信息, 最终完成北京维管植物编目和分布数据集(分为本土植物和外来植物两个表单, 其中外来植物主要基于志书和文献记载)。截至2021年12月31日, 该数据集共有数据2,883条(本土1,680条, 外来1,203条), 其中包含北京本土野生维管植物134科611属1,597个类群(1,440种3天然杂交种46亚种97变种11变型), 与《北京植物志(1992年修订版)》相比增加3科26属173种4亚种28变种11变型, 其中列入《国家重点保护野生植物名录(2021)》的有16种(一级仅1种), 列入《北京市重点保护野生植物名录(2008)》的有90种3亚种4变种; 收录外来维管植物137科581属1,184个类群(含992种及其他种下等级), 其中栽培植物854种19杂交种15亚种29变种2变型87栽培品种38栽培群, 逸生植物132种1亚种, 归化植物77种2变种, 入侵植物27种。编目数据显示, 北京本土野生维管植物多样性整体上并不高, 主要以广泛分布的常见种为主, 特有种、狭域种以及珍稀濒危种数量不多; 同时, 北京存在大量的外来植物(许多种类在《北京植物志》各版中已经收录), 这些植物也是北京维管植物多样性的重要组成部分, 但现有数据尚不完整。     

北京城市公园湿地的休憩吸引力评价

以北京地区20个城市公园湿地为研究对象,从公园湿地的景观质量、区位条件、可达性3方面构建了城市公园湿地休憩吸引力评价指标体系,并基于层次分析法赋权的综合指数评价方法,对公园湿地的休憩吸引力进行评价,最后通过实地问卷调查数据对休憩吸引力评价结果进行验证,结果表明:具有高休憩吸引力的公园湿地依次为颐和园、奥林匹克公园、青龙湖公园、北海公园、圆明园、玉渊潭公园、十渡、金海湖风景区、陶然亭公园、野鸭湖湿地,稻香湖湿地和珍珠湖风景区的休憩吸引力最低,其余8个公园湿地休憩吸引力一般.休憩吸引力评价结果与实际调查数据相符,说明所建立的评价指标体系与评价方法是可行的.20个公园湿地按照其休憩吸引力可聚为4类,据此可制定不同的管理对策.通过城市公园湿地休憩吸引力评价,分析城市公园湿地景观在休闲游憩方面所发挥的作用,可以为城市湿地公园的优化与配置、提高人居环境质量、改善城市景观布局提供依据.     

BsmI polymorphisms in vitamin D receptor gene are associated with diabetic nephropathy in type 2 diabetes in the Han Chinese population

We investigated the relationship between BsmI/ApaI polymorphisms in vitamin D receptor gene and diabetic nephropathy in a Han Chinese population. PCR-restriction fragment length polymorphism was used to test the genotype and allele frequency of BsmI and ApaI polymorphisms in 304 patients with type 2 diabetes mellitus (DM group) and 100 control individuals (ND group). The DM group was further divided into DN0 (no diabetic nephropathy), DN1 (diabetes with small amount of albuminuria), DN2 (diabetes with large amount of albuminuria), L/NDN (late-onset DN after 5 years/no DN over the whole follow-up period of 5 years) and EDN (early-onset diabetic nephropathy occurring within first year) subgroup. We found that (1) genotype and allele frequency of BsmI polymorphism had significant difference between DM and ND group; BB+Bb genotype and B allele frequency were significantly higher in DN2 group than in ND and DN0 group; the ApaI polymorphism and allele frequency did not show any difference between DM and ND group; (2) BsmI BB+Bb genotype and B allele frequency were significantly higher in EDN group than in L/NDN group; (3) among patients with nephropathy, albumin excretion rate (AER) in 24-hour urine was significantly higher in those with BB+Bb phenotype than in those with bb phenotype (P<0.01), (4) unconditional logistic regression analysis showed that BsmI BB+Bb genotype was not only correlated with type 2 diabetic nephropathy, but also correlated with early-onset type 2 diabetic nephropathy. We conclude that the allele B (BB or Bb genotype) in vitamin D receptor gene is correlated with large amount albuminuria in the Han Chinese population with type 2 diabetes, and is probably a risk factor for early-onset diabetic nephropathy.     

北京植物园展览温室植物的害虫调查及主要害虫的防治

９３年春,作者调查了北京植物园展览温室植物的害虫种类及危害状况。调查结果显示,该温室植物主要害虫为棉蚜（Ａｐｈｉｓｇｏｓｙｐｉ）、桃蚜（Ｍｙｚｕｓｐｅｒｓｉｃａｅ）;柑桔红蜘蛛（Ｐａｎｏｎｙｃｈｕｓｃｉｔｒｉ）;吹绵蚧（Ｉｃｅｒｙａｐｕｒｃｈａｓｉ）;红蜡蚧（Ｃｅｒｏｐｌａｓｔｅｓｒｕｂｅｎｓ）、桑白蚧（Ｐｓｅｕｄａｕｌａｃａｓｐｉｓｐｅｎｔａｇｏｎａ）等。文章最后就主要害虫蚜虫类、蚧虫类及白粉虱的防治作了论述