Plant–soil feedback during biological invasions: effect of litter decomposition from an invasive plant (Sphagneticola trilobata) on its native congener (S. calendulacea)

生物入侵过程中的植物-土壤反馈：一种入侵植物的凋落物分解对其本地近缘植物的影响 植物入侵可通过正或负的植物-土壤反馈效应改变土壤的生物和非生物性质,从而影响入侵栖息地的土壤理化性质。许多入侵物种的凋落物分解可增加土壤养分,降低本地植物多样性,并导致进一步的植物入侵。关于入侵植物凋落物在不同土壤类型及深度分解及反馈效应的研究依然很少。本研究旨在明确入侵植物南美蟛蜞菊(Sphagneticola trilobata)凋落物在不同土壤类型和不同土壤深度条件下的分解情 况及其对本地近缘植物蟛蜞菊(S. calendulacea)生理生长的影响。将装有南美蟛蜞菊凋落物的尼龙袋加入到不同深度(即0、2、4 和6 cm)的砂土、营养土和粘土中,经6个月的分解后,回收凋落物袋并计算分解速率,随后在凋落物分解处理后的土壤中种植本地蟛蜞菊,并在生长期结束时测量其生理生态指标。研究结果表明,所有处理土壤类型中,凋落物在土壤深度为2和4 cm处分解后显著增加了土壤养分,而对本 地蟛蜞菊的叶片叶绿素、叶氮含量等生长指标表现为负效应。因此,入侵植物南美蟛蜞菊凋落物分解对土壤养分表现为正的反馈效应,而对本地植物蟛蜞菊的生长表现为负效应。我们的研究结果还表明,入侵植物的凋落物分解对土壤和本地物种的影响还因凋落物分解所在的土壤深度而显著不同。未来的研究应侧重于入侵栖息地中更多本地和入侵物种的植物-土壤反馈效应,以及更多土壤类型和土壤深度的入侵植物凋落物效应。     

Analysis of Protein Three-Dimension Structure Using Amino Acids Depths

The issue of amino acid depth in proteins gives important insights to our understanding of protein’s three-dimensional structure. There has already been much research done in mathematical and statistical sciences regarding the general definitions, properties and algorithms describing the particle depth of spatially extended systems. We constructed a method of calculating the amino acids depths and applied it to a set of 527 protein structures. We propose the introduction of amino acid depth tendency factors for three-dimensional structures of proteins. The depth tendency factors relate not only to the hydrophobicity indices but also to the electrostatic charge. We found a relationship between the protein size and the number of residues using the distance between the deepest residue and surface residues. We made a prediction regarding the number of residues on the surface of a protein, the deepest amino acid, and the average depth, all of which are fitted well to a linear functional relationship with the length of the protein. Finally, we have predicted the depths of multiple peptides in protein’s three-dimension structure. Electronic supplementary material The online version of this article () contains supplementary material, which is available to authorized users.     

青菜/油菜茬口下水稻栽植方式对温光资源利用和产量的影响

轻简化栽培和优质稻是当前我国水稻生产的主要方向,气象因子是对水稻生长发育和产量形成影响最大的环境因素,但在不同轻简化栽植方式下水稻产量与其田间小气候的关系鲜有研究。为探究西南地区不同前作下杂交稻各生育阶段温、光和水等气候因子与水稻产量形成的关系,在2019—2020年,以杂交籼稻‘宜香优2115'为试验材料,采用两因素裂区设计,主区为青菜和油菜2种前作,副区为机直播、毯苗机插和人工移栽3种栽植方式,研究杂交稻产量对气候因子的响应及水稻植株对温光资源的利用。结果表明: 与油菜-水稻模式相比,青菜-水稻模式下杂交稻积温生产效率和降水生产效率显著提高,进而提高了有效穗数、结实率和千粒重,2年产量分别提高了12.7%和8.3%。与人工移栽相比,机插稻提高了单位面积有效穗数、全生育期光能生产效率、积温生产效率、籽粒光能利用效率和降水生产效率,2年平均产量提高了4.6%;而机直播全生育期降水生产效率、光能生产效率、积温生产效率、籽粒光能利用效率、每穗粒数和千粒重都显著降低,导致2年平均产量下降了8.7%。与2019年相比,2020年机插稻和人工移栽稻在同一茬口下提前一个月播种造成花后生育期缩短、气温降低和降雨量增多,导致有效积温和光辐射量大幅减少,积温生产效率、光能生产效率、降水生产效率和籽粒光能利用效率以及每穗粒数、结实率和千粒重均大幅降低,进而导致产量严重降低。用偏最小二乘法回归分析建立的气象因子产量预报方程标准化回归系数显示,水稻产量与阶段生育期或全生育期内有效积温和总辐射量呈正相关关系,与全生育期内降水量呈显著负相关关系。综上,青菜-水稻模式下机插秧与西南地区稻季光温资源匹配度最高,更有利于温光资源的充分利用和获得高产,但不宜过早播种或移栽。     

街谷绿化消减机动车排放污染物的研究方法与进展

随着街道两侧建筑群向高密度、高层化发展,传统“树越多越好”的绿化模式在应对城市街谷空气污染时是否适用受到广泛关注。明晰街谷绿化植物特征及其种植设计模式对机动车排放污染物消减的调控机理是发挥其提升街谷空气品质的重要前提。本文通过对近年国内外相关文献的梳理,比较分析了现场观测、风洞试验和数值模拟3种研究方法的适用性及局限性,详细剖析了行道树、绿篱两类绿化模式对街谷空气污染物扩散与沉降的影响机制,提出了一套面向空气质量提升的街谷绿化适应性设计工作框架。最后,分别从典型街谷绿化设计图示语言研制、街谷空气污染暴露评估技术指南编制、计算机流体力学模型中街谷绿化效应物理过程参数化方案优化等方面进行探讨,以期为后续研究提供思路和借鉴。     

商代前期中原地区多品种农作物种植制度的初探：以河南新郑望京楼遗址为例

农业经济的发展是华夏文明形成的最重要的前提条件之一,郑洛地区作为夏商王朝建都和统治的核心区域,其农业经济发展状况一直是学术界研究的重点问题。相关研究表明,多品种农作物种植制度在龙山时期中原地区的出现,在华夏文明的形成过程中可能起到了至关重要的作用。为了探索这一种植制度在商代前期中原地区的具体实践情况,本文选取河南新郑望京楼遗址夏商时期（二里头文化和二里岗文化时期）29例先民肢骨和23例先民肋骨进行C、N稳定同位素分析。结果表明,先民骨胶原的δ¹³C值变化范围为-18.1‰~7.0‰,平均值为-9.5‰±2.1‰（n=52）,δ¹⁵N值变化范围为7.3‰~10.5‰,平均值为8.9‰±0.7‰（n=52）,先民仍以C₄类食物（粟黍）为主,但是也包含少量C₃类（水稻、小麦或大豆）食物,证明中原地区自龙山时代出现的多品种农作物种植制度,在商代得以延续,但是粟作农业的主导地位,始终未发生明显变化,这可能与中原地区长期以来的旱作农业经济模式习惯有关。     

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project

The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed “consensus calling,” to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.     

Mechanical understanding of hunting waves generated by killer whales

The wave wash hunting employed by Orcinus orca, also known as killer whales, is unique in that the prey is hunted outside of the water by generating waves. To quantitatively analyze the specific mechanism of the wave wash, data were obtained using computational fluid dynamics (CFD), and wave theory was introduced as the theoretical background to clarify the mechanism. The relationships between the swimming characteristics and wave parameters are defined in this paper. The results obtained by numerical investigation revealed that the wavelength increased with the swimming speed. Additionally, the wave height increased as the swimming speed increased and the swimming depth became shallower, and subsequently converged to a maximum of 2.42 m. The success of hunting is determined by two wave parameters, which indicate the intensity of the wave wash: the wave height and force exerted on the prey. The metabolic rate and the drag force are considered to evaluate the efficiency of the locomotion, which varied according to the swimming speed (V) and swimming depth (d) of the whales. To generate hunting waves efficiently, the optimal ranges of V and d were estimated to be 3 ~ 5 m/s and 0.5 m ~ 1.1 m respectively.     

An Introduction to a Special Issue on Large‐Scale Submerged Aquatic Vegetation Restoration Research in the Chesapeake Bay: 2003–2008

The Chesapeake Bay is one of the world's largest estuaries. Dramatic declines in the abundance and distribution of submerged aquatic vegetation (SAV) in the Chesapeake Bay over the last few decades led to a series of management decisions aimed at protecting and restoring SAV populations throughout the bay. In 2003, the Chesapeake Bay Program established a goal of planting 405 ha of SAV by 2008. Realizing that such an ambitious goal would require the development of large‐scale approaches to SAV restoration, a comprehensive research effort was organized, involving federal and state agencies, academia, and the private sector. This effort differs from most other SAV restoration programs due to a strong emphasis on the use of seeds rather than plants as planting stock, a decision based on the relatively low labor requirements of seeding. Much of the research has focused on the development of tools and techniques for using seeds in large‐scale SAV restoration. Since this research initiative began, an average of 13.4 ha/year of SAV has been planted in the Chesapeake Bay, compared to an average rate of 3.6 ha/year during the previous 21 years (1983–2003). The costs of conducting these plantings are on a downward trend as the understanding of the limiting factors increases and as new advances are made in applied research and technology development. Although this effort was focused in the Chesapeake Bay region, the tools and techniques developed as part of this research should be widely applicable to SAV restoration efforts in other areas.