Provenance selection and site conditions determine growth performance of pedunculate oak

Forests of the future need to cope with adverse climatic conditions, in particular drought, to ensure forest stability and productivity. Given the usually long rotation period of forests, forest managers need to select appropriate, i.e. productive and climate-change resilient tree species and/or provenances, to lower tree-mortality risks and sustain current wood production rates at the end of the 21^st century. A frequent means of assessing which provenances of a given species are adapted to anticipated climate conditions is common garden experiments, where trees from different provenances are planted under similar climate conditions. However, in this context soil conditions also play an important role, since they govern how climate translates into plant-available water and hence plant’s ability to cope with extreme drought events. Here, we examine the effects of soil conditions on pedunculate oak (Quercus robur L.), by studying 10 different Dutch oak provenances that were planted in three provenance trials on different soil types in 1988 in the Netherlands. Using dendroecological methods, we quantified provenance-specific productivity and assessed provenance- and site-specific growth patterns. Our results indicated clear differences in productivity among provenances as well as soil-type specific growth patterns. Consequently, our study highlights the importance of incorporating soil characteristics when evaluating the growth performance of provenances within common garden experiments.     

Artificial radiofrequency driven life-table parameters of perilla seed bugs (Nysius sp.) (Heteroptera: Lygaeidae)

The genus Nysius (Hemiptera: Lygaeidae) are polyphagous pests of various plants that damage seeds, foliage, and flowers. Here, we studied the life-table parameters and adult performances of Nysius plebeius Distant and Nysius hidakai Nakatani after exposure to five radiofrequencies: 0 (control), 5, 10, 20, and 30 kHz in infested perilla seeds. In addition, we measured the follow on effects of treatment for four generations (Parent, F1-, F2-, and F3-generation), for both Nysius species. Radiofrequency application significantly affected the life-table parameters of both Nysius species. Radiofrequency exposures affected bug oviposition, developmental period, adult weight, and longevity. Exposure also negatively affected the fecundity of subsequent generations; total developmental period from egg to adult emergence was longer while adult longevity was shorter in the radiofrequency treatments than in the untreated control. Low radiofrequency levels had the greatest effect on the life-table parameters of Nysius species, with the lowest rate of adult emergence and the shortest adult longevity at 5 kHz. The potential of using Nysius bug susceptibilities to radiofrequency as an alternative to chemical treatment is discussed.     

Muscle endurance time estimation during isometric training using electromyogram and supervised learning

Constant-force isometric muscle training is useful for increasing the maximal strength , rehabilitation and work-fatigue assessment. Earlier studies have shown that muscle fatigue characteristics can be used for evaluating muscle endurance limit. Study Objective: To predict muscle endurance time during isometric task using frequency spectrum characteristics of surface electromyography signals along with analysis of frequency spectrum shape and scale during fatigue accumulation. Method: Thirteen subjects performed isometric lateral raise at 60% MVC of deltoid (lateral) till endurance limit. Time windowed sEMG frequency spectrum was modelled using 2-parameter distributions namely Gamma and Weibull for spectrum analysis and endurance prediction. Results: Gamma distribution provided better spectrum fitting (P < 0.001) than Weibull distribution. Spectrum Distribution demonstrated no change in shape but shifted towards lower frequency with increase of magnitude at characteristic mode frequency. Support Vector Regression based algorithm was developed for endurance time estimation using features derived from fitted frequency spectrum. Time taken till endurance limit for acquired dataset 38.53 ± 17.33 s (Mean ± Standard Deviation) was predicted with error of 0.029 ± 4.19 s . R-square: 0.956, training and test sets RMSE was calculated as 3.96 and 4.29 s respectively. The application of the algorithm suggested that model required 70% of sEMG signal from maximum time of endurance for high prediction accuracy. Conclusion: Endurance Limit prediction algorithm was developed for quantification of endurance time for optimizing isometric training and rehabilitation. Our method could help personalize and change conventional training method of same weight and duration for all subjects with optimized training parameters, based upon individual sEMG activity.     

UV-B辐射诱导芒果叶片抗氧化响应研究

为了解增强UV-B辐射诱导芒果叶片抗氧化响应的机制,以?台农1号?芒果(Mangifera indica?Tainong No. 1?)成年树为材料,以自然光为对照(CK),设置24和96 kJ/(m~2·d)两个增强UV-B辐射处理水平,观测叶片生理生化指标的动态变化。结果表明,24k J/(m~2·d)处理的芒果叶片MDA含量、相对电导率、净光合速率、抗氧化酶活性、多酚、Vc和芒果苷含量均与对照没有显著差异,而类黄酮和还原型GSH含量显著高于对照;而96 kJ/(m~2·d)处理的芒果叶片MDA含量、相对电导率、抗氧化酶活性及多酚、类黄酮、还原型GSH、芒果苷等还原型保护成分的含量均显著高于对照,而净光合速率和Vc含量均显著低于对照。因此,24 kJ/(m~2·d) UV-B辐射未引起?台农1号?芒果成年树损伤,可能是通过提高类黄酮和还原型GSH的含量来清除活性氧自由基;96 kJ/(m~2·d)处理则引起叶片活性氧损伤,但仍可能以两种机制减轻损伤,一是通过增强抗氧化酶活性和提高还原性成分含量来清除活性氧自由基,二是利用芒果苷、类黄酮和还原型GSH等成分吸收UV-B辐射。     

优良单株家系辣木叶的表型性状分析

为挖掘辣木(Moranga oleifera)优良种质资源,对30个优良单株家系的叶片表型性状进行研究。结果表明,除叶形外,辣木不同家系间的叶柄和叶片颜色、复叶数、复叶柄长度和直径、复叶间距、叶长、叶宽均存在不同程度的差异。复叶数与复叶柄长度和直径、复叶间距、叶长、叶宽呈极显著正相关;主成分分析表明,叶长、叶宽、复叶柄长度和直径、复叶间距、叶柄和叶片颜色是区分辣木不同家系最主要的叶片性状指标。聚类分析结果表明,30个辣木家系可分为3大类,叶片表型性状存在显著差异的家系的遗传距离较远。因此,叶柄和叶片颜色、复叶数、复叶柄长度和直径、复叶间距、叶长、叶宽将为直观区分辣木家系提供参考。     

Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish

Gene flow has tremendous importance for local adaptation, by influencing the fate of de novo mutations, maintaining standing genetic variation and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of the evolutionary mechanisms impending or favouring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (Mallotus villosus). We first assembled a 490‐Mbp draft genome of M. villosus to map our RAD sequence reads. Then, we used a large data set of genome‐wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they probably diverged from 3.8 to 1.8 million years ago and experienced secondary contacts. Within each lineage, our analyses provided evidence for large N_e and high gene flow among spawning sites. Within the Northwest Atlantic lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype–environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that both shared polymorphisms among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.     

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。