The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor

Muscle contraction is driven by a cycle of conformational changes in the myosin II head. After myosin binds ATP and releases from the actin fibril, myosin prepares for the next power stroke by rotating back the converter domain that carries the lever arm by 60 degrees . This recovery stroke is coupled to the activation of myosin ATPase by a mechanism that is essential for an efficient motor cycle. The mechanics of this coupling have been proposed to occur via two distinct and successive motions of the two helices that hold the converter domain: in a first phase a seesaw motion of the relay helix, followed by a piston-like motion of the SH1 helix in a second phase. To test this model, we have determined the principal motions of these structural elements during equilibrium molecular dynamics simulations of the crystallographic end states of the recovery-stroke by using principal component analysis. This reveals that the only principal motions of these two helices that make a large-amplitude contribution towards the conformational change of the recovery stroke are indeed the predicted seesaw and piston motions. Moreover, the results demonstrate that the seesaw motion of the relay helix dominates in the dynamics of the pre-recovery stroke structure, but not in the dynamics of the post-recovery stroke structure, and vice versa for the piston motion of the SH1 helix. This is consistent with the order of the proposed two-phase model for the coupling mechanism of the recovery stroke. Molecular movies of these principal motions are available at http://www.iwr.uni-heidelberg.de/groups/biocomp/fischer.     

20种山茶科植物的叶表皮微形态研究

为解决一些山茶科(Theaceae)的分类学问题,该研究在光学显微镜下对山茶科2亚科6属共20种植物的13种叶表皮微形态特征进行了观察,并利用聚类分析和主成分分析对这些特征进行分析,为山茶科的科学分类提供参考资料。结果表明:(1)山茶科20种植物的13种叶表皮微形态特征能够区分种间差异和分类等级,显示了比较全面的分类价值。(2)基于微形态特征的聚类分析和主成分分析结果显示,20个种分为2个大类群以及10个分支,很好地区分了山茶亚科(Theoideae)与厚皮香亚科(Ternstroemoideae),并将大部分分类地位相近的物种归类到一起,较好地反映了物种之间的亲缘关系。(3)该研究结果支持将小黄花茶组(Sect.Luteoflora)作为独立的一个组;支持将重庆山茶(Camellia chungkingensis Chang)从瘤果茶组(Sect.Tuberculata Chang Tax.)中分离;支持将山茶亚科与厚皮香亚科划分为两个较大类群,认为将厚皮香亚科并入五列木科(Pentaphylacaceae)的观点还有待更多实验证据的支持。     

Evolutionary control of leaf element composition in plants

Leaf nitrogen (N) and phosphorus (P) concentrations are correlated in plants. Higher-level phylogenetic effects can influence leaf N and P. By contrast, little is known about the phylogenetic variation in the leaf accumulation of most other elements in plant tissues, including elements with quantitatively lesser roles in metabolism than N, and elements that are nonessential for plant growth. Here the leaf composition of 42 elements is reported from a statistically unstructured data set comprising over 2000 leaf samples, representing 670 species and 138 families of terrestrial plants. Over 25% of the total variation in leaf element composition could be assigned to the family level and above for 21 of these elements. The remaining variation corresponded to differences between species within families, to differences between sites which were likely to be caused by soil and climatic factors, and to variation caused by sampling techniques. While the majority of variation in leaf mineral composition is undoubtedly associated with nonevolutionary factors, identifying higher-level phylogenetic variation in leaf elemental composition increases our understanding of terrestrial nutrient cycles and the transfer of toxic elements from soils to living organisms. Identifying mechanisms by which different plant families control their leaf elemental concentration remains a challenge.     

Unraveling evolutionary constraints: A heterogeneous conservation in dynamics of the titin Ig domains

The giant protein titin, which comprises immunoglobulin (Ig) domains, acts as a bidirectional spring in muscle. The unfolding of Ig domains has been extensively studied, but their dynamics under native states have not been well-characterized. We performed molecular dynamics simulation on a single titin Ig domain and multi-domains. Mobile regions displaying concerted motions were identified. The dynamics of Ig domains are constrained by evolutionary pressures, in such a way that global dominant motion is conserved, yet different flexibilities within Ig domains and in linkers connecting neighbouring domains were observed. We explain these heterogeneous conserved dynamics in relation to sequence conservation across species and the sequence diversity among neighbouring Ig domains.     

伞形多孔菌（猪苓）优良菌株的筛选

以10个不同来源的伞形多孔菌（猪苓）菌株为材料,通过ITS序列分析比较菌株间的亲缘关系,基于菌落、菌丝的形态特征、生长速率、菌丝体干重和产糖能力5个方面的14个指标,采用聚类分析方法分析各指标之间、菌株之间的相关性,主成分分析法提取4个主成分进行分析,通过综合分值比较菌株优劣。ITS序列分析表明,10个菌株间的相似性较高。聚类分析结果显示,指标之间胞外多糖、菌丝团、黑色素、菌丝颜色、长势和分泌物的相关性高;菌丝形态、草酸钙方晶、生长速率和无性孢子的相关性高。5#菌株多糖含量和菌丝生长速率最高;2#和9#菌株胞内多糖含量较高;4#、13#和14#菌株多糖含量较低;10#、11#菌株多糖含量及菌丝体干重也较低。主成分分析显示,5#、2#和1#菌株是综合分值最高的3个菌株,其菌丝生长快、长势旺、产量及多糖含量高。综合上述结果,5#、2#和1#菌株是初步筛选出可用于大规模生产及繁殖的优良菌株。     

Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes

Alongside the well-studied membrane spanning helices, alpha-helical transmembrane (TM) proteins contain several functionally and structurally important types of substructures. Here, existing 3D structures of transmembrane proteins have been used to define and study the concept of reentrant regions, i.e. membrane penetrating regions that enter and exit the membrane on the same side. We find that these regions can be divided into three distinct categories based on secondary structure motifs, namely long regions with a helix-coil-helix motif, regions of medium length with the structure helix-coil or coil-helix and regions of short to medium length consisting entirely of irregular secondary structure. The residues situated in reentrant regions are significantly smaller on average compared to other regions and reentrant regions can be detected in the inter-transmembrane loops with an accuracy of approximately 70% based on their amino acid composition. Using TOP-MOD, a novel method for predicting reentrant regions, we have scanned the genomes of Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The results suggest that more than 10% of transmembrane proteins contain reentrant regions and that the occurrence of reentrant regions increases linearly with the number of transmembrane regions. Reentrant regions seem to be most commonly found in channel proteins and least commonly in signal receptors.     

贵州省典型植烟生态区域根际土壤微生物群落多样性

土壤微生物是土壤的重要组成部分,它对土壤肥力的形成和植物营养的转化起着积极的作用。采用16S V4区高通量测序等方法对贵州省不同生态区域典型植烟土壤根际微生物群落进行分析研究,从根际土壤微生物群落特征上诠释不同生态区域典型土壤根际微生物群落的信息差异。结果表明:贵州省不同生态区域弱酸和酸性土壤占70.06%,有机碳平均2.24%,有机碳含量总体偏高,全氮与有机碳含量具有一定相关性;根际土壤微生物的OTUs数量差异明显,呈现总体是西部高于东部,南部高于北部;微生物属水平物种丰度差异显示,土壤类型对微生物群落丰度影响显著,而在土壤功能微生物上黔北区域的变形菌门(Proteobacteria)和放线菌门(Actinobacteria)两个门的微生物相对丰度最高,而在黔中中部区域变形菌门的丰度显著高于放线菌门的丰度。黔西南和黔中中部区域土壤微生物属水平优势种群显著高于其他地区,种群平衡度不高,具有土传病害发生的潜在危险。通过贵州省不同生态区域土壤微生物根际微生物信息分析与研究,为后续土壤生物修复奠定了良好的研究基础。     

Environmental and seasonal impacts on the chemical composition of Satureja horvatii Šilić (Lamiaceae) essential oils

The chemical composition of the essential oils of Satureja horvatii Šilić from two natural habitats (Mt. Orjen and Mt. Lovćen in Montenegro) and from cultivated plants (Belgrade, Serbia) were characterized. For the latter, plants from the locus classicus, i.e., Orjenske Lokve (Mt. Orjen), were transferred to Belgrade and, after three years of cultivation, the chemical composition of their essential oils at different phenological stages was analyzed. The essential oils were obtained from the aerial parts of the plants by hydrodistillation and analyzed by GC and GC/MS. The yields and chemical compositions of the S. horvatii oils showed significant differences between the plants collected in the natural habitats and those from cultivation, as well as between the plants at different phenological stages. In the populations from the natural habitats, growing in Mediterranean conditions, the most abundant oil constituents were the phenols thymol (63.7% in the samples from Mt. Orjen) or carvacrol (68.1% in the samples from Mt. Lovćen), while the oils from the cultivated plants (Belgrade), growing in continental conditions, were dominated by linalool (up to 65.8 and 55.9% in average). The basic characteristics of the essential oil from plants at the early phenological stage (before flowering) were high percentages of linalool (37.4%), thymol (27.3%), and carvacrol (12.2%). At the stage of flowering, the percentage of linalool (56.6–57.5%) increased, while those of thymol (15.5–15.8%) and carvacrol (1.4–1.5%) significantly decreased. The essential oil of plants in the full stage of fruiting was characterized by the domination of linalool (58.4 and 65.8%) and lower percentages of thymol (7.6 and 1.3%) and carvacrol (0.7 and 0.1%). In conclusion, the oil composition of S. horvatii was found to depend on the pedoclimatic conditions of the habitat and the phenological stage of the plants.     

基于主成分分析的随机森林视网膜OCT图像分层算法研究

视网膜是层状结构,临床上可以根据视网膜层厚度改变对一些疾病进行预测和诊断.为了快速且准确地分割出视网膜的不同层带,本论文提出一种基于主成分分析的随机森林视网膜光学相干断层扫描技术(optical coherence tomography,OCT)图像分层算法.该方法使用主成分分析(principal component analysis,PCA)法对随机森林采集到的特征进行重采样,保留重采样后权重大的特征信息维度,从而消除特征维度间的关联性和信息冗余.结果表明,总特征维度在29维的情况下,保留前18维度训练速度提高了23.20%,14维度训练速度提高了42.38%,而对图像分割精度方面影响较小,实验表明该方法有效地提高了算法的效率.     

基于PCA-XGBoost方法的洲际人群生物地理祖源推断模型研究

目的 通过DNA推断个体的生物地理祖源（biogeographical ancestry,BGA）在人类学、法医学等领域广受关注。目前常用方法是使用几十个祖先信息单核苷酸多态性（single nucleotide polymorphism,SNP）位点,通过主成分分析（principal component analysis,PCA）、似然比（likelihood ratio,LR）等方法判断个体的祖源。伴随高通量测序技术的发展,批量获取人群样本的高密度SNP数据集变得容易,同时计算机领域中机器学习等技术的引入,使得BGA研究发展出新的变化。本研究旨在构建适应高密度SNP数据,且具有高准确率和良好泛化能力的BGA推断模型。方法 首先基于307 866个SNP的数据,使用机器学习领域中的监督学习模型XGBoost,构建了基于多维度主成分（principal component,PC）的PCA-XGBoost推断模型,其次基于LR对推断结果进行评估和优化模型,确定了最佳PC数目和模型训练轮数,最后在其他公共数据的测试集上进一步验证模型的表现。结果 基于LR的结果评估方法,模型在参考集中人群预测准确率可以达到95%以上,在测试集中准确率可以达到90%以上,结论 PCA-XGBoost模型具有较高的洲际人群预测准确性,基于LR的结果评估方法有助于对预测结果的可靠性进行进一步评估。该模型具有很好的泛化能力,更换参考集的人群数据后,有望实现更加精细的人群分析。     

Metabolite Profiling of Cheonggukjang,a Fermented Soybean Paste,Inoculated with Various Bacillus Strains during Fermentation

Metabolite profiling of Cheonggukjang inoculated with different Bacillus strains including Bacillus amyloliqueciens CH86-1, Bacillus licheniformis 58, and Bacillus licheniformis 67 during fermentation, was performed using gas chromatography-time of flight-mass spectrometry after derivatization, combined with multivariate statistical analysis. A total of 20 amino acids, 10 sugars, five sugar alcohols, and seven organic acids were identified in three Cheonggukjang samples. With fermentation time, most of the amino acids showed increasing amounts. On the other hand, most of the sugars including sucrose, fructose, and glucose decreasing patterns, and the amounts of organic acids varied. In order to observe differences in metabolites with fermentation time and inoculated Bacillus strains, principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were carried out, respectively. On PCA plots, some sugars and organic acids including sucrose, fructose, glucose, mannose, succinic acid, and malonic acid, as well as most of the amino acids, contributed mainly to differentiation of the Cheonggukjang samples fermentation time. On the other hand, on PLS-DA, mannose, xylose, glutamic acid, and proline were mainly responsible for differentiating the Cheonggukjang among into various inoculated strains.     

Chemical Variability of the Leaf Essential Oil of Xylopia aethiopica (Dunal) A.Rich. from Côte d'Ivoire

The chemical composition of 48 essential‐oil samples isolated from the leaves of Xylopia aethiopica harvested in six Ivoirian forests was investigated by GC‐FID and ¹³C‐NMR analyses. In total, 23 components accounting for 82.5–96.1% of the oil composition were identified. The composition was dominated by the monoterpene hydrocarbons β‐pinene (up to 61.1%) and α‐pinene (up to 18.6%) and the sesquiterpene hydrocarbon germacrene D (up to 28.7%). Hierarchical cluster and principal component analyses allowed the distinction of two groups on the basis of the β‐pinene and germacrene D contents. The chemical composition of the oils of Group I (38 oil samples) was clearly dominated by β‐pinene, while those of Group II (10 samples) were characterized by the association of β‐pinene and germacrene D. The leaves collected in the four inland forests produced β‐pinene‐rich oils (Group I), while the oil samples belonging to Group II were isolated from leaves harvested in forests located near the littoral.