Coenzyme Reorientations in the Active Sites of Aspartate Aminotransferase Isoenzymes Studied by Linear Dichroism Method

Abstract

Cytosolic and mitochondrial pig heart aspartate aminotransferases (cAspAT and mAspAT) and chicken heart cAspAT have been oriented in a compressed slab of polyacrylamide gel and their linear dichroism LD spectra have been recorded. The coenzyme's tilt angles in the active sites of chicken cAspAT and pig mAspAT and their quasisubstrate complexes imitating catalytic intermediates have been computed. The computations are based on reduced linear dichroism values (ΔA/A), the known directions of the transition dipole moments in the coenzyme ring and atomic coordinates of the coenzyme obtained by X-ray crystallography. It has been found that formation of the enzyme complex with glutarate and protonation of the internal pyridoxal-lysine aldimine induce reorientations of the coenzyme. As a result of protonation, the coenzyme ring tilts by 27° in cAspAT and 13° in mAspAT. Formation of the external aldimine with 2-mehtylaspartate is accompanied by tilting of the coenzyme ring by 44° in cAspAT and 39° in mAspAT. For the quinonoid complex with erythro-3-hydroxyaspartate, the tilt angles were found to be 63° in cAspAT and 53° in mAspAT. It is inferred that the basic features of the active site dynamics are similar in the three AspATs studied. The diiferences in the coenzyme tilt angles between cAspAT and mAspAT may be linked to catalytic and structural peculiarities of the isoenzymes.     

基于多源遥感数据的生态保护修复项目区监测方法评述

回顾了山水林田湖草生态保护修复项目的实施背景,针对生态保护修复项目监测监管范围广、技术难等问题,强调了基于多源遥感数据开展项目遥感监测的重要性与必要性。从监测指标拟定、遥感地物信息提取、多源遥感数据融合、动态变化检测等方面评述了基于多源遥感数据的生态保护修复项目区监测方法,包括基于中高空间分辨率遥感数据的地物信息提取、融合机器学习的非线性混合像元分析、基于混合像元分析的时空融合等。在总结技术和工作推进方面的优势、局限基础上,提出要结合实际工作,持续优化国土空间生态保护修复监测指标;充分挖掘遥感数据解析的相关算法潜力,提升地物信息提取和混合像元分析的精度;加强时空融合算法与变化检测方法的研究探索,加强相关方法的实践应用;以“山水林田湖草生态保护修复工程试点”项目为平台,建立稳定的国土空间生态保护修复遥感监测运行机制,加强科技创新,形成技术标准,指导工作开展。     

天山森林生态系统树生地衣植物群落数量分类及其物种多样性的研究

地衣是由低等植物中的藻类与菌类中的真菌和兰细菌共生而成的一群特殊的植物。由于耐寒耐旱对生活中的养分要求不高,在养纷贫瘠、环境恶劣的高山寒漠、平原、戈壁和沙漠中地衣都能生长,因而广泛地分布和生长在不同的生态环境中。有关新疆地衣方面的研究报道集中在物种分类水平上,对于地衣群落结构方面的研究比较少。因此,我们应用多元分析中的主分量分析及聚类分析方法对分布在天山森林生态系统中树生地衣植物群落进行数量分类并对群落结构物种多样性、相似性和均匀度等群落参数进行了比较系统的研究。结果表明, 在西部天山不同森林生态系统中树生地衣群落的分布与海拔高度和树种有密切的关系, 不同海拔的不同类型的森林生态系统中分布着不同种类的树生地衣植物。 根据多元分析结果和生境的综合特征,该地区的树生地衣可划分为4种类型: 1) 茎口果粉衣+金黄茶衣群丛Chaenotheca stemonea+Candellaria aurella Association; 2)叉小孢衣+裸扁枝衣+粉唇蜈蚣衣群丛Bryoria furcellata+Evernia esorediosa+Physcia tribacoides Association; 3)亚广开梅衣+槽梅衣+疑小梅衣群丛Parmelia fertilis+Parmelia sulcata+Parmeliopsis ambigua Association; 4)睫毛黑蜈蚣衣+黑蜈蚣衣群丛Phaeophyscia ciliata+Phaeophyscia nigricans Association。其群落多样性指数以亚广开梅衣+槽梅衣+疑小梅衣群丛为最高 (1.920), 叉小孢衣+裸扁枝衣+粉唇蜈蚣衣群丛为最低 (1.562)。     

基于生态系统服务供需匹配的深圳市生态安全格局构建

构建基于生态系统服务供需匹配的生态安全格局对于深圳市实现中国特色社会主义先行示范区中的可持续发展先锋和民生幸福标杆的战略定位具有重要意义。选取水源供给、碳固持和游憩服务,通过InVEST模型、生态供需比、手机信令数据分析以及电路理论等方法,识别深圳市生态系统服务综合供需状态,构建耦合生态系统服务供需的生态安全格局,并探讨了不同划定界限对生态源地面积和个数的影响。结果表明: 深圳市综合生态供需比大体呈现东部充裕、西部不足的分布状态,其中,水源供给服务在数量和空间分布上均基本满足需求,碳固持服务则相反,而游憩服务虽然数量上可以满足需求,但空间分布极度不均;识别出总面积为347.62 km²的25块生态源地以及总长度为346.06 km的34条生态廊道,其中,生态源地面积呈现东多西少的分布状态,廊道长度呈现相反的分布趋势;不同的划定界限对生态源地面积和个数的影响不同,一级、二级和三级生态源地面积分别为347.62、520.84和557.58 km²,呈逐步增加趋势,源地个数分别为25、35和32个,呈现出先增后减的变化趋势;深圳市存在未纳入生态管控的重要生态斑块且生态控制线内部分斑块生态可持续性较差,可据此制定针对性的保护和管理政策。研究结果可以为深圳市生态管控单元的划定提供空间指引。     

我国生态环境大数据建设方案实施及其公开效果评估

生态环境大数据建设是新一代环境管理手段,也是我国建设"数据强国"的基本要求。在《生态环境大数据建设总体方案》实施2年后,针对31个省级、27个省会城市、6个大数据建设试点城市的环境保护厅/局落实生态环境大数据的建设进行调查分析,通过文献分析和资料调查,全面评估我国生态环境大数据建设的总体状况,以期为生态环境大数据建设的下一步工作提供建议。结果表明,尽管生态环境大数据建设在数据资源整合方面取得了较大进步,但在地区发展、机构建设、数据共享开放和大数据应用等方面还存在着许多问题,针对这些不足,提出了未来几年我国生态环境大数据建设的发展方向,包括扩充环境信息中心相关职能、推进大数据整合与共享、加强国际交流和提升大数据在重点领域的应用范围。     

Association Tests for a Censored Quantitative Trait and Candidate Genes in Structured Populations with Multilevel Genetic Relatedness

Summary Several statistical methods for detecting associations between quantitative traits and candidate genes in structured populations have been developed for fully observed phenotypes. However, many experiments are concerned with failure‐time phenotypes, which are usually subject to censoring. In this article, we propose statistical methods for detecting associations between a censored quantitative trait and candidate genes in structured populations with complex multiple levels of genetic relatedness among sampled individuals. The proposed methods correct for continuous population stratification using both population structure variables as covariates and the frailty terms attributable to kinship. The relationship between the time‐at‐onset data and genotypic scores at a candidate marker is modeled via a parametric Weibull frailty accelerated failure time (AFT) model as well as a semiparametric frailty AFT model, where the baseline survival function is flexibly modeled as a mixture of Polya trees centered around a family of Weibull distributions. For both parametric and semiparametric models, the frailties are modeled via an intrinsic Gaussian conditional autoregressive prior distribution with the kinship matrix being the adjacency matrix connecting subjects. Simulation studies and applications to the Arabidopsis thaliana line flowering time data sets demonstrated the advantage of the new proposals over existing approaches.     

Trends and uncertainties in Siberian indicators of 20th century warming

Estimates of past climate and future forest biomass dynamics are constrained by uncertainties in the relationships between growth and climatic variability and uncertainties in the instrumental data themselves. Of particular interest in this regard is the boreal-forest zone, where radial growth has historically been closely connected with temperature variability, but various lines of evidence have indicated a decoupling since about the 1960s. We here address this growth-vs.-temperature divergence by analyzing tree-ring width and density data from across Siberia, and comparing 20th century proxy trends with those derived from instrumental stations. We test the influence of approaches considered in the recent literature on the divergence phenomenon (DP), including effects of tree-ring standardization and calibration period, and explore instrumental uncertainties by employing both adjusted and nonadjusted temperature data to assess growth-climate agreement. Results indicate that common methodological and data usage decisions alter 20th century growth and temperature trends in a way that can easily explain the post-1960 DP. We show that (i) Siberian station temperature adjustments were up to 1.3 °C for decadal means before 1940, (ii) tree-ring detrending effects in the order of 0.6–0.8 °C, and (iii) calibration uncertainties up to about 0.4 °C over the past 110 years. Despite these large uncertainties, instrumental and tree growth estimates for the entire 20th century warming interval match each other, to a degree previously not recognized, when care is taken to preserve long-term trends in the tree-ring data. We further show that careful examination of early temperature data and calibration of proxy timeseries over the full period of overlap with instrumental data are both necessary to properly estimate 20th century long-term changes and to avoid erroneous detection of post-1960 divergence.     

A goodness-of-fit test for the marginal Cox model for correlated interval-censored failure time data

The marginal Cox model approach is perhaps the most commonly used method in the analysis of correlated failure time data (Cai, 1999; Cai and Prentice, 1995; Lin, 1994; Wei, Lin and Weissfeld, 1989). It assumes that the marginal distributions for the correlated failure times can be described by the Cox model and leaves the dependence structure completely unspecified. This paper discusses the assessment of the marginal Cox model for correlated interval-censored data and a goodness-of-fit test is presented for the problem. The method is applied to a set of correlated interval-censored data arising from an AIDS clinical trial.     

A workbench for multiple alignment construction and analysis

Multiple sequence alignment can be a useful technique for studying molecular evolution, as well as for analyzing relationships between structure or function and primary sequence. We have developed for this purpose an interactive program, MACAW (Multiple Alignment Construction and Analysis Workbench), that allows the user to construct multiple alignments by locating, analyzing, editing, and combining "blocks" of aligned sequence segments. MACAW incorporates several novel features. (1) Regions of local similarity are located by a new search algorithm that avoids many of the limitations of previous techniques. (2) The statistical significance of blocks of similarity is evaluated using a recently developed mathematical theory. (3) Candidate blocks may be evaluated for potential inclusion in a multiple alignment using a variety of visualization tools. (4) A user interface permits each block to be edited by moving its boundaries or by eliminating particular segments, and blocks may be linked to form a composite multiple alignment. No completely automatic program is likely to deal effectively with all the complexities of the multiple alignment problem; by combining a powerful similarity search algorithm with flexible editing, analysis and display tools, MACAW allows the alignment strategy to be tailored to the problem at hand.