中国土壤环境功能区划方案

针对我国土壤环境功能分类分区管理的重大需求,本文讨论了土壤环境功能的广义与狭义概念及其对应属性.基于土壤环境质量对功能的约束分析,阐明了其与土壤环境质量区划关系.在比较不同土壤环境功能区划方法与指标基础上,以土壤环境质量适宜性和土壤环境功能分类为依据,构建了土壤环境功能区划指标体系.提出了全国土壤环境功能区划方案,具体归纳了4个一级功能类型,10个二级功能类型,划分为75个土壤环境功能区.根据不同区域的功能分区现状,提出了相应的管理对策,为我国土壤污染防治规划与区域风险管控提供科学依据.     

京津冀地区县域耕地景观多功能性评价

随着城镇化发展和农业产业化升级,耕地景观功能由单一的生产功能向经济功能、生态功能、文化功能拓展,耕地景观多功能性成为新的学术热点。已有研究往往侧重于探讨耕地功能的多指数耦合,缺乏耕地景观多重功能空间定量化与相互关联的分析。以京津冀地区为研究区,对耕地景观的粮食供给功能、生境维持功能、景观连通功能、土壤保持功能、景观美学功能和人口承载功能六项功能及其冷热点聚集区分别空间定量化,评价县域尺度耕地景观多功能性,并识别耕地景观多种功能的空间关联。研究结果表明,京津冀中部平原地区粮食供给功能显著,南部平原地区景观连通功能突出,燕山与太行山山脉土壤保持功能、维持生境功能最高,山前平原地带人口承载功能相对重要。2010年京津冀地区耕地景观功能总体呈现南高北低的分布格局,但功能高低值分布规律差异明显,各功能全部处于高值或低值的样本极少;耕地景观不同功能间的权衡与协同关系数量相当,景观连通功能与粮食供给功能呈现明显协同关系,而与土壤保持功能呈现较强权衡关联。     

2000-2020年京津冀地区国土空间多功能权衡强度时空演变及影响机制

厘清国土空间多功能相互关系及影响因素,对实现国土空间可持续利用与保护具有重要意义。以京津冀地区为例,揭示了其国土空间多功能时空变化特征,利用Spearman相关性分析、均方根误差和地理探测器诊断了多功能之间相互关系与权衡强度,并探析了多功能权衡强度影响机制。结果表明,生产功能和生活功能主要集中在东南部平原区,生态功能主要集中在西北山区,2000-2020年生产功能和生活功能提升而生态功能呈退化态势。国土空间多功能权衡强度均值表现为"生活功能-生态功能"＞"生产功能-生态功能"＞"生产功能-生活功能"。2000-2020年生产与生活功能间的权衡强度增强,从0.038上升至0.060;而生产与生态功能间权衡强度减弱,从0.190下降至0.180;生活与生态功能间的权衡强度轻微减弱,从0.206下降至0.205。京津冀西北区是生产与生态功能以及生活与生态功能权衡强度高值区,集中在承德、秦皇岛和北京市。东南部平原区是生产与生活功能权衡强度高值区,尤其是衡水、邯郸和邢台等地权衡明显加剧。国土空间多功能权衡强度空间分异受土地利用、自然因素和社会经济因素共同影响,其中土地利用强度是最主要影响因子,各影响因素在不同年份影响程度略有不同。研究结果可以帮助决策者将国土空间多功能权衡理念纳入国土空间规划与管理。     

市县级限制开发区环境功能区划研究——以河北省张家口市为例

限制开发地区是我国主体功能区划中划定的提供重要生态功能和农产品的地区,对其进行环境功能区划对于推动环境功能区划制度落地与实施,以及限制开发区的保护与发展有着重要意义。当前国家及省级的环境功能区划研究已经相对成熟,而市县尺度的限制开发地区环境功能区划相关研究较少。在总结现有环境功能区划研究方法的基础上,以河北省张家口市为例,探讨了市县级限制开发地区环境功能区划体系设计和技术方法,提出了以公里格网作为分析单元,结合县域行政边界,基于环境功能综合评价的结果,从自然生态安全、维护人群健康和区域环境支撑能力等3个方面,开展环境功能区划。基于该方法,将张家口市分为自然生态保留区、生态功能保持区、生态功能恢复区、农产品安全保障区、环境开发准入区、聚居发展维护区6类环境功能区,并根据各环境功能区的主要功能及生态环境特点提出相应的发展建议,以期为该区域管理提供可行的操作手段。本文提出的方法也可为其他限制开发地区的环境功能区划提供参考。     

Ratings of overall olfactory function

The aim of this study was to investigate the accuracy of self-reported ratings of olfactory function in 83 healthy subjects. Such ratings were compared with quantitative measures of olfactory function, as well as with ratings of nasal patency. In experiment 1 subjects rated olfactory function and nasal patency before olfactory testing, whereas in experiment 2 the reverse was the case. No feedback regarding test results were provided until after completion of the testing. The principal findings were: (i) when ratings preceded measurements of olfactory function, there was no significant correlation between the two parameters. However, ratings of olfactory function correlated significantly with ratings of nasal airway patency. (ii) In contrast, when measurements of olfactory function preceded the ratings, this constellation switched. Now ratings of olfactory function correlated significantly with measured olfactory function, whereas there was no significant correlation between ratings of nasal airway patency and ratings of olfactory function. In conclusion, these data suggest that ratings of olfactory function are unreliable in healthy, untrained subjects. The ratings seem to reflect changes of nasal airway patency to a larger degree than measurable olfactory function. The results further indicate that this is mainly due to the limited attention the sense of smell receives in daily life.     

新疆阿勒泰地区草地资源可持续管理分析

通过分析新疆阿勒泰地区草地资源的利用现状,草地类型的生产性能、生态服务价值和在区域发展中的主导功能,指出分类经营是该区草地资源可持续管理的有效途径。研究表明,阿勒泰地区的草地资源在空间上可划分为生态功能区(高寒草甸和草原、沼泽、山地荒漠草原、山地草原化荒漠和部分平原荒漠),经济功能区(山地草甸,低地草甸和草甸草原)和混合功能区(山地草原、平原荒漠草原和大部分平原荒漠),在时间上可采取不同的经营策略。生态功能区经营策略是禁牧和封育,经济功能区的经营策略是通过施肥、灌溉等手段,集约化管理,提高单位面积产值I混合功能区的经营策略是以草定畜,合理轮牧。     

New paradigm in protein function prediction for large scale omics analysis

Biological interpretation of large scale omics data, such as protein-protein interaction data and microarray gene expression data, requires that the function of many genes in a data set is annotated or predicted. Here the predicted function for a gene does not necessarily have to be a detailed biochemical function; a broad class of function, or low-resolution function, may be sufficient to understand why a set of genes shows the observed expression pattern or interaction pattern. In this Highlight, we focus on two recent approaches for function prediction which aim to provide large coverage in function prediction, namely omics data driven approaches and a thorough data mining approach on homology search results.     

我国自然保护区功能分区研究进展

自然保护区功能分区是保护区规划和科学管理的重要环节。我国自然保护区功能区划主要采用国际"人与生物圈"计划的"三区"划分模式,即核心区、缓冲区和实验区。介绍了我国自然保护区的分区依据,在总结自然保护区功能分区方法研究进展上,分析了目前我国自然保护区功能区划中存在的难点与问题,并对其进行了展望,以期为我国自然保护区功能区的科学划分与完善提供依据。     

Long-term sexual allocation in herbivore resistant and susceptible pinyon pine (Pinus edulis)

Chronic herbivory by the stem-boring moth (Dioryctria albovittella) alters the sexual expression of a monoecious tree, pinyon pine (Pinus edulis) by reducing female function and increasing male function. Observations and long-term moth removal experiments show that 55% of susceptible trees can lose all female function. Moth herbivory has little effect on male function in young trees, but has an important effect on older trees, where moth-susceptible trees produced 1.5 times more pollen than moth-resistant trees. Susceptible trees were 6.5 times more likely to exhibit male-only function than either resistant trees or susceptible trees that have had their moths experimentally removed. This herbivore-induced sex change is caused primarily by differential moth attack and the resulting mortality of the shoots that bear female reproductive structures. Moth attack rates were positively correlated with individual stem biomass (female stems >non-reproductive stems >male stems). Moth attack also increased conelet abortion on unattacked shoots, indicating that moths indirectly reduce female function. Moth-induced altering of sexual function is also expressed at the population level. Male function is relatively greater in stands with high moth densities on stressful soils than in stands with few moths. Under certain conditions, sexual selection theory suggests that the negative effects on female function could be overcome with greater investment in male function. Because susceptible trees produce large amounts of pollen and are more abundant than moth-resistant trees, frequency-dependent selection may counteract selection against susceptible genotypes. Plant-herbivore interaction studies typically examine negative impacts of herbivory on female function, but not positive effects on male function. Here we demonstrate that herbivory may have important effects on the evolutionary ecology of pinyon by both promoting male function and depressing female function.     

稻纵卷叶螟卷叶有虫率与化蛹率关系的研究

探索利用稻纵卷叶螟 Cnaphalocrocis medinalis（Guenée）卷叶有虫率估测化蛹率的方法和途径。本文基于稻纵卷叶螟化蛹进度的田间调查数据,用化蛹率（y）和卷叶有虫率（x）分别拟合直线函数、一元二次函数、一元三次函数、对数函数、指数函数和幂函数6种不同模型。结果表明,以一元三次函数方法估计精度最高,误差最小,应用效果最好,并根据最优数学模型建立化蛹率（y）与卷叶有虫率（x）的关系速查表。生产中可以应用拟合的 最优数学模型对田间稻纵卷叶螟化蛹进度进行监测。     

Stability and the evolvability of function in a model protein

Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to evolve the function of binding to a ligand. Although our model contains no built-in tradeoff between stability and function, proteins evolved function more efficiently when the stability requirement was relaxed. Proteins with both high stability and high function evolved more efficiently when the stability requirement was gradually increased than when there was constant selection for high stability. These results show that in our model, the evolution of function is enhanced by allowing proteins to explore sequences corresponding to marginally stable structures, and that it is easier to improve stability while maintaining high function than to improve function while maintaining high stability. Our model also demonstrates that even in the absence of a fundamental biophysical tradeoff between stability and function, the speed with which function can evolve is limited by the stability requirement imposed on the protein.     

Local function conservation in sequence and structure space

We assess the variability of protein function in protein sequence and structure space. Various regions in this space exhibit considerable difference in the local conservation of molecular function. We analyze and capture local function conservation by means of logistic curves. Based on this analysis, we propose a method for predicting molecular function of a query protein with known structure but unknown function. The prediction method is rigorously assessed and compared with a previously published function predictor. Furthermore, we apply the method to 500 functionally unannotated PDB structures and discuss selected examples. The proposed approach provides a simple yet consistent statistical model for the complex relations between protein sequence, structure, and function. The GOdot method is available online (http://godot.bioinf.mpi-inf.mpg.de).     

A Statistical Model of Protein Sequence Similarity and Function Similarity Reveals Overly-Specific Function Predictions

Background

Predicting protein function from primary sequence is an important open problem in modern biology. Not only are there many thousands of proteins of unknown function, current approaches for predicting function must be improved upon. One problem in particular is overly-specific function predictions which we address here with a new statistical model of the relationship between protein sequence similarity and protein function similarity.

Methodology

Our statistical model is based on sets of proteins with experimentally validated functions and numeric measures of function specificity and function similarity derived from the Gene Ontology. The model predicts the similarity of function between two proteins given their amino acid sequence similarity measured by statistics from the BLAST sequence alignment algorithm. A novel aspect of our model is that it predicts the degree of function similarity shared between two proteins over a continuous range of sequence similarity, facilitating prediction of function with an appropriate level of specificity.

Significance

Our model shows nearly exact function similarity for proteins with high sequence similarity (bit score >244.7, e-value >1e⁻⁶², non-redundant NCBI protein database (NRDB)) and only small likelihood of specific function match for proteins with low sequence similarity (bit score <54.6, e-value <1e⁻⁰⁵, NRDB). For sequence similarity ranges in between our annotation model shows an increasing relationship between function similarity and sequence similarity, but with considerable variability. We applied the model to a large set of proteins of unknown function, and predicted functions for thousands of these proteins ranging from general to very specific. We also applied the model to a data set of proteins with previously assigned, specific functions that were electronically based. We show that, on average, these prior function predictions are more specific (quite possibly overly-specific) compared to predictions from our model that is based on proteins with experimentally determined function.     

A continued role for signaling functions in the early evolution of feathers

Persons and Currie (2015) argued against either flight, thermoregulation, or signaling as a functional benefit driving the earliest evolution of feathers; rather, they favored simple feathers having an initial tactile sensory function, which changed to a thermoregulatory function as density increased. Here, we explore the relative merits of early simple feathers that may have originated as tactile sensors progressing instead toward a signaling, rather than (or in addition to) a thermoregulatory function. We suggest that signaling could act in concert with a sensory function more naturally than could thermoregulation. As such, the dismissal of a possible signaling function and the presumption that an initial sensory function led directly to a thermoregulatory function (implicit in the title “bristles before down”) are premature.     

KIDNEY FUNCTION TESTS IN CHILDREN

Total renal function is best determined by urinalysis and serum creatinine determination. This may be supplemented, under controlled conditions, by fractional urinary phenosulfonphthalein clearance. The excretory urogram, while invaluable as a diagnostic test, lacks quantitative value as a function test.Until recently, individual renal function determinations depended upon the difficult and tedious cystoscopy and bilateral ureteral catheterization and skilled laboratory techniques. Frequently the necessity of anesthesia artificially depressed kidney function.Since 1956, the radioisotope kidney function test has offered an external, innocuous means of assessing individual renal blood flow, function and drainage plus evaluation of vesico-ureteral reflux. The method has distinct advantages for evaluation of pediatric urological problems.     

Bacteriophage Mu-induced modification of DNA is dependent upon a host function.

The DNA of bacteriophage Mu, extracted from induced lysates, is partially resistant to digestion by the endonuclease BalI. This modification of DNA is controlled by the Mu modification function (mom), which acts in conjunction with the dam (DNA-adenine methylation) function of Escherichia coli. Since the BalI recognition site is apparently different from the dam recognition site, these results imply that either the specificity of the dam function is changed by the mom function or the mom function requires the dam function for its activity.     

点格局研究过程中K-函数的累积效应

植物种群空间格局是生态学研究的基本问题之一, 点格局分析已成为植物种群空间格局研究的重要方法之一, 其中, Ripley's K函数是点格局常用分析方法。然而, 由于Ripley's K函数具有累积效应, 这种累积效应可能会导致特定的格局特征。为了探讨Ripley's K函数的累积效应如何影响种群格局研究结果, 以大针茅种群数据为基础, 通过R软件模拟聚集分布、随机分布和均匀分布3种格局类型, 对比使用具有累积效应的Ripley's K函数和不具有累积效应的成对相关函数进行分析。结果表明: 对于聚集分布和均匀分布, Ripley's K函数的累积效应表现在2个方面: 一方面增加了聚集分布(或均匀分布)的尺度, 另一方面能够检测到聚块或负相互作用范围在取样空间的分布差异而表现出不同的格局特征。而对于随机分布, Ripley's K函数没有累积效应。因此, 在种群格局研究过程中, 通过重复取样且Ripley's K 函数与成对相关函数相结合的方法探讨种群格局, 更能揭示空间格局的本质特征。     

Improved protein-ligand docking using GOLD

The Chemscore function was implemented as a scoring function for the protein-ligand docking program GOLD, and its performance compared to the original Goldscore function and two consensus docking protocols, "Goldscore-CS" and "Chemscore-GS," in terms of docking accuracy, prediction of binding affinities, and speed. In the "Goldscore-CS" protocol, dockings produced with the Goldscore function are scored and ranked with the Chemscore function; in the "Chemscore-GS" protocol, dockings produced with the Chemscore function are scored and ranked with the Goldscore function. Comparisons were made for a "clean" set of 224 protein-ligand complexes, and for two subsets of this set, one for which the ligands are "drug-like," the other for which they are "fragment-like." For "drug-like" and "fragment-like" ligands, the docking accuracies obtained with Chemscore and Goldscore functions are similar. For larger ligands, Goldscore gives superior results. Docking with the Chemscore function is up to three times faster than docking with the Goldscore function. Both combined docking protocols give significant improvements in docking accuracy over the use of the Goldscore or Chemscore function alone. "Goldscore-CS" gives success rates of up to 81% (top-ranked GOLD solution within 2.0 A of the experimental binding mode) for the "clean list," but at the cost of long search times. For most virtual screening applications, "Chemscore-GS" seems optimal; search settings that give docking speeds of around 0.25-1.3 min/compound have success rates of about 78% for "drug-like" compounds and 85% for "fragment-like" compounds. In terms of producing binding energy estimates, the Goldscore function appears to perform better than the Chemscore function and the two consensus protocols, particularly for faster search settings. Even at docking speeds of around 1-2 min/compound, the Goldscore function predicts binding energies with a standard deviation of approximately 10.5 kJ/mol.     

Proinflammatory cytokines disrupt epithelial barrier function by apoptosis-independent mechanisms

It is well known that inflammatory conditions of the intestinal mucosa result in compromised barrier function. Inflammation is characterized by an influx into the mucosa of immune cells that influence epithelial function by releasing proinflammatory cytokines such as IFN-gamma and TNF-alpha. Mucosal barrier function is regulated by the epithelial apical junctional complex (AJC) consisting of the tight junction and the adherens junction. Since the AJC regulates barrier function, we analyzed the influence of IFN-gamma and TNF-alpha on its structure/function and determined the contribution of apoptosis to this process using a model intestinal epithelial cell line, T84, and IFN-gamma and TNF-alpha. AJC structure/function was analyzed by confocal microscopy, biochemical analysis, and physiologic measurement of epithelial gate/fence function. Apoptosis was monitored by determining cytokeratin 18 cleavage and caspase-3 activation. IFN-gamma induced time-dependent disruptions in epithelial gate function that were potentiated by coincubation with TNF-alpha. Tight junction fence function was somewhat disrupted. Cytokine treatment was associated with internalization of AJC transmembrane proteins, junction adhesion molecule 1, occludin, and claudin-1/4 with minimal effects on the cytoplasmic plaque protein zonula occludens 1. Detergent solubility profiles of junction adhesion molecule 1 and E-cadherin and their affiliation with "raft-like" membrane microdomains were modified by these cytokines. Inhibition of cytokine-induced apoptosis did not block induced permeability defects; further emphasizing their primary influence on the epithelial AJC structure and barrier function. Our findings for the first time clearly separate the proapoptotic effects of IFN-gamma and TNF-alpha from their abilities to disrupt barrier function.     

生态系统健康评价方法初探

生态系统是维持人类环境的最基本单元,生态系统功能主要体现在两个方面：一是生态服务功能（service);二是价值功能（goods)这两种功能是人类生态和发展的基础,生态系统健康是保证生态系统功能正常发挥的前提,结构和功能的完整性,具有抵抗干扰和恢复能力（resilience)、稳定和可持续性是生态系统健康的特征,生态系统健康评价需要基于生态系统的结构、功能过程来确定指标,包括生态系统的完整性,适应性和效率,生态系统健康评价主要有两种方法：一是指示物种评价,二是结构功能指标评价,结构功能指标评价包括单指标评价,复合指标评价和指标体系评价,指标体系评价中又包括自然指标体系评价,社会－经济－自然复合生态系统指标体系评价,本文针对生态系统健康的不同评价方法进行了对比研究,同时,针对不同的生态系统类型应选择其健康评价方法方面进行了简要的阐述。