The Bio3D packages for structural bioinformatics

Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/ .     

草莓种苗壮苗指数模型的构建与质量评价

随着我国草莓栽培面积逐年增加,草莓种苗需求量越来越大,为了确保种苗育苗质量,亟需开展壮苗评价的研究。本研究以生长40 d的‘红颜’穴盘苗为对象,在测定地上部和地下部生长、鲜重、干重等16项指标的基础上,分别构建单项指标隶属函数,使用加权模糊评判法计算种苗综合评价指数;利用主成分分析筛选的关键指标组成多个壮苗指数模型,与种苗综合评价指数进行相关性分析后,确定最佳草莓壮苗指数模型并进行验证。结果表明: 随机选取的320株草莓种苗16项指标存在显著差异,综合评价指数为0.165～0.817,可作为壮苗指数模型构建和种苗质量评价的依据。主成分分析将16项指标划分为地上部相关指标、地下部相关指标和色素指标3个主成分,累计贡献率达到79.7%;从每个主成分中选择贡献值最大的3个指标随机组成27种壮苗指数模型,通过相关性分析筛选出与综合评价指数相关性最大的5个壮苗指数模型,其中“地上干重×根系表面积×叶绿素a”的相关性最高,用‘红颜’、‘香野’和‘甜查理’种苗验证相关系数均最大,分别为0.879、0.924和0.975,确定可作为草莓壮苗指数计算模型。以综合评价指数为种苗质量分级依据,可将种苗健壮程度分为3个等级:等级Ⅰ(综合评价指数≥0.5,壮苗指数≥4.0)为优质苗,等级Ⅱ(综合评价指数0.3～0.5,壮苗指数0.5～4.0)为合格苗,等级Ⅲ(综合评价指数≤0.3,壮苗指数≤0.5)为弱苗。研究结果可为草莓或其他种苗壮苗指数计算和种苗健壮程度评价提供理论依据与科学方法。     

黄山松土壤可溶性有机质对氮添加的响应及其与细菌群落的关联

为探究黄山松土壤可溶性有机质(DOM)数量和质量对短期氮(N)添加的响应及其与细菌群落的关联,在福建戴云山自然保护区设置不同N添加水平(0、40和80 kg N·hm^-2·a^-1)试验,采用三维荧光与平行因子联用法,并结合高通量测序手段分别对土壤DOM和细菌群落进行分析。结果表明: 与对照相比,N添加整体降低了0～10和10～20 cm土层可溶性有机碳(DOC)含量和DOM腐殖化指数(HIX),其中,高氮(80 kg N·hm^-2·a^-1)添加下均显著降低。平行因子分析法进一步表明N添加下DOM中类腐殖质组分(C1、C2)的相对含量降低。此外,N添加减少了富营养细菌(变形菌门、酸微菌纲)的相对丰度,而增加了贫营养细菌(斯巴达杆菌纲)的相对丰度。富营养细菌的相对丰度与HIX、C1、C2呈显著正相关,与相对易分解的类富里酸组分(C3)呈显著负相关;而贫营养细菌的情况则相反。说明N添加下不同生活策略的细菌类群对DOM中难分解和易分解组分存在明显的偏好性。我们推测N沉降加剧背景下土壤微生物生活策略的转变可能有助于DOM组分的塑造。     

兰州兴隆山土壤微生物的分布及其相关特性分析

目的以兰州兴隆山不同区域的土壤微生物为研究对象,分析比较土壤微生物数量与土壤酶活性之间的相关性。方法利用不同方法测定土壤理化性质、微生物数量以及土壤相关酶活特性;采用三区划线法进行土壤微生物的分离与纯化,通过16S rDNA和ITS方法进行优势菌株鉴定。结果兰州兴隆山土壤中微生物菌群数量由多到少依次为细菌、放线菌、真菌。通过分离纯化后,对其中的2株优势菌进行了鉴定,初步推断X2为萎缩芽胞杆菌属(Bacillus atrophaeus)细菌,Z2为栎生青霉属(Penicillium glandicola)真菌。从酶活特性可知,阳面的土壤过氧化氢酶活性比阴面高;随着海拔高度的增加,过氧化氢酶活性呈现增加趋势;阳面的土壤脱氢酶活性总体比阴面高,并且随着海拔梯度的升高,土壤脱氢酶活性也在不断升高。从相关性分析可知,不同海拔土样间微生物数量与酶活性之间表现出明显的相关性。结论兰州兴隆山土壤微生物数量丰富,且细菌数量居多;不同阴、阳面土壤微生物的层次分布以及活性也各有不同。以上研究可为兰州兴隆山土壤生态系统演替等提供参考依据,并为土壤生态环境的治理做铺垫。     

Redundancy or heterogeneity in the electric activity of the biceps brachii muscle? Added value of PCA-processed multi-channel EMG muscle activation estimates in a parallel-fibered muscle

Conventional bipolar EMG provides imprecise muscle activation estimates due to possibly heterogeneous activity within muscles and due to improper alignment of the electrodes with the muscle fibers. Principal component analysis (PCA), applied on multi-channel monopolar EMG yielded substantial improvements in muscle activation estimates in pennate muscles. We investigated the degree of heterogeneity in muscle activity and the contribution of PCA to muscle activation estimates in biceps brachii (BB), which has a relatively simply parallel-fibered architecture. EMG-based muscle activation estimates were assessed by comparison to elbow flexion forces in isometric, two-state isotonic contractions in eleven healthy male subjects. Monopolar EMG was collected over the entire surface of the BB with about 63 electrodes. Estimation quality of different combinations of EMG channels showed that heterogeneous activation was found mainly in medio-lateral direction, whereas adding channels in the longitudinal direction added largely redundant information. Multi-channel bipolar EMG amplitude improved muscle activation estimates by 5–14% as compared to a single bipolar. PCA-processed monopolar EMG amplitude yielded a further improvement of (12–22%). Thus multi-channel EMG, processed with PCA, substantially improves the quality of muscle activation estimates compared conventional bipolar EMG in BB.     

基于主成分分析法探讨人体测量学参数与青少年血糖关系的研究

目的:调查分析人体测量学参数包括体重指数(BMI)、腰围(WC)、臀围(HC)、腰围/臀围比(WHR)及腰围/身高比(WHtR)对南昌地区青少年空腹血糖的影响。方法:在南昌地区进行随机抽样检查731例12-18岁之间的青少年,测量身高、体重、BMI、WC、HC、WHR、WHtR和空腹血糖,用SAS软件进行统计分析。结果:男女性的五项人体测量学指标和空腹血糖间均呈显著正相关,相关系数为0.14-0.38;通过主成分分析得到四个主成分,多重回归分析结果表明联合四个主成分比单独使用其中任何一个更能解释空腹血糖的变异。结论:BMI、WC、HC、WHR、WHtR与男性和女性空腹血糖都有一定相关性,并且联合这五项测量学指标比单独使用其中任何一个能更精确预测空腹血糖。     

Objective classification of scapular kinematics in participants with movement faults of the scapula on clinical assessment

The aim of this study was to assess the potential of employing a classification tool to objectively classify participants with clinically assessed movement faults (MFs) of the scapula. Six participants with a history of shoulder pain with MFs of the scapula and 12 healthy participants with no movement faults (NMFs) performed a flexion movement control test of the scapula, while scapular kinematic data were collected. Principal component scores and discrete kinematic variables were used as input into a classifier. Five out of the six participants with a history of pain were successfully classified as having scapular MFs with an accuracy of 72%. Variables related to the upward rotation of the scapula had the most influence on the classification. The results of the study demonstrate the potential of adopting a multivariate approach in objective classification of participants with altered scapular kinematics in pathological groups.     

Developmental stability and morphological differences in Plantago major L. leaves under contrasting environmental conditions

Abstract

In the present study, an additional combination of end‐points was applied on the natural populations of the common plantain, previously estimated using morphometric assays. Here, besides measuring developmental instability (DI), by determining the level of fluctuating asymmetry (FA) and the total amount of phenotypic variability (PV), we tried to distinguish the three natural populations under contrasting environmental conditions using the morphological data. Results obtained using both FA indices were the same; higher asymmetry levels in the reference than in the polluted environments were detected for leaf width, vein distances within a leaf and lobe length. The one‐way analysis of variance results revealed that there were significant differences in PV values among populations analysed for each character. When all leaf traits were considered together, the PV median value was significantly higher in Crni Lug leaves compared with leaves from other sites. The multivariate analysis of variance results revealed the significant effect of environment on both FA₄ and PV values. The component scores of first factor (PC1) were significantly different between the Karaburma and Crni Lug populations. Besides, component scores of both PC1 and PC2 were significantly different between the Zemun and Crni Lug samples. The stepwise discriminant functional analysis results allowed us to identify a set of four variables, with a sufficient discriminating ability (75%).     

Comparison of allometric relationships and morphological differences in Tilia cordata Mill. outer leaves exposed to different environmental conditions

The study is based on four leaf parameters: leaf width (LW), lobe length (LL), leaf size (LS) and leaf shape which is calculated as LW to leaf length (LW/LL) ratio. Under different environmental conditions, LL is an isometric character, LW shows positive allometry, whereas LW/LL shows negative allometry. Regression analysis results indicated that there is no significant difference either in slopes or in regression coefficients between investigated sites. Thus, in this study, we found that allometric relationships between leaf parameters and LS are character specific and that they tended not to differ significantly between Tilia cordata Mill. outer leaves exposed to different environmental conditions. Also, there are no significant interpopulation differences for both principal component PC1 and PC2 scores. The stepwise discriminant functional analysis results allowed us to identify a set of two leaf parameters (LS and LL) with a moderate discriminating ability (59.8%). T. cordata outer leaves are significantly larger and broader in the reference area (R-leaves) than leaves from polluted (P-leaves) site. The data also indicated that there is a relatively larger petiole size in R-leaves than in P-leaves. We found that in P-leaves, LW increased faster with increasing LS than in R-leaves.     

Variability in the Essential‐Oil Composition of Sideritis scardica Griseb. from Native Bulgarian Populations

The essential‐oil composition of six native populations of Sideritis scardica from Bulgaria was studied by GC‐FID and GC/MS analyses. Altogether, 37 components, representing 73.1 to 79.2% of the total oil content were identified. Among them, α‐pinene (4.4–25.1%), β‐pinene (2.8–18.0%), oct‐1‐en‐3‐ol (2.3–8.0%), phenylacetaldehyde (0.5–9.5%), β‐bisabolene (1.3–11.0%), benzyl benzoate (1.1–14.3%), and m‐camphorene ( 1 ; 0.3–12.4%) were the main compounds. All samples were characterized by low contents of oxygenated mono‐ and sesquiterpenes (≤1.6 and 2.3%, resp.). Principal component analysis (PCA) and cluster analysis (CA) showed a significant variability in the chemical composition of the studied samples as well as a correlation between the oil profiles and the ecological conditions of the natural habitats of S. scardica.