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.     

广东西樵山细石叶石核的开发策略

长期以来,细石叶技术的发展和传播是更新世末期到全新世初期文化传播、人群迁徙和生态适应研究领域探讨的重要课题。20世纪50年代,发现于广东西樵山石器制造场的大批细石叶技术产品,突破了传统意义上对细石叶技术流行、传播范围的认识。早期研究中不少学者就西樵山细石叶制品的形态特征、分布情况进行了介绍,随后鲜见后续研究,缺乏对技术内涵、石核开发策略的深入解析,亦未开展对其所指示的文化传播与人口迁徙问题的探讨。本文选取收藏于中山大学人类学博物馆的343件细石叶石核,通过对石料、毛坯类型、台面类型和数量、剥片面等多方位观察以及对相关技术数值的测量统计,建构西樵山细石叶石核开发策略的模式。这项工作总结了西樵山细石叶技术的特点,并与其他区域的细石叶技术进行对比,加深了对出现在亚热带地区的细石叶技术的认识,为尝试进一步讨论其可能的技术源流和指示人口迁徙与文化传播提供了基础。     

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.     

Microbial cycling of iron and sulfur in sediments of acidic and pH-neutral mining lakes in Lusatia (Brandenburg, Germany)

A vast number of lakes developed in the abandoned opencast lignite mines of Lusatia (East Germany) contain acidic waters (mmolSm^–2a^–). Potential Fe(III) reduction measured by the accumulation of Fe(II) during anoxic incubation yielded similar rates in both types of sediments, however, the responses towards the supplementation of Fe(III) and organic carbon were different. Sulfate reduction rates estimated with ³⁵S-radiotracer were much lower in the slightly acidic sediment than in the pH-neutral sediment (156 v.s. 738mmolSO₄ ^2–m^–2a^–1). However, sulfate reduction rates were increased by the addition of organic carbon. Severe limitation of sulfate-reducing bacteria under acidic conditions was also reflected by low most probable numbers (MPN). High MPN of acidophilic iron- and sulfur-oxidizing bacteria in acidic sediments indicated a high reoxidation potential. The results show that potentials for reductive processes are present in acidic sediments and that these are determined mainly by the availability of oxidants and organic matter.     

Immigration and emigration of Burkholderia cepacia and Pseudomonas aeruginosa between and within mixed biofilm communities

AIMS: To investigate the dynamics of binary culture biofilm formation through use of both the Sorbarod model of biofilm growth and the constant depth film fermenter (CDFF). METHODS AND RESULTS: Pseudo steady-state biofilm cultures of laboratory and clinical strains of Pseudomonas aeruginosa, selected on the basis of their ability to produce a Burkholderia cepacia growth-inhibitory substance, were established on Sorbarod filters and challenged with corresponding planktonic grown cultures of B. cepacia. Reverse challenges were also conducted. Both B. cepacia and P. aeruginosa were able to form steady-state monoculture biofilms after 48 h growth. When steady-state biofilms of B. cepacia NTCT 10661 were challenged with planktonically grown P. aeruginosa PAO1 known to produce a B. cepacia growth-inhibitory substance, the immigrant population was rapidly and almost completely bound to the biofilm, displacing B. cepacia. By contrast, established biofilms of P. aeruginosa PAO1 resisted immigration of B. cepacia 10661. Similar experiments conducted with a nongrowth inhibitory substance producing clinical pairing of P. aeruginosa 313113 and B. cepacia 313113 led to the formation of stable, mixed biofilm populations in both instances. Moreover, co-inoculation with these clinical isolates resulted in a stable, mixed steady-state biofilm. Similar observations were made for biofilms generated in CDFFs. In such instances following pan-swapping between two monoculture CDFFs, B. cepacia 313113 was able to integrate into an established P. aeruginosa 313113 biofilm to form a stable binary biofilm. CONCLUSIONS: Establishment of a mixed species community follows a specific sequence of inoculation that may either be due to some degree of match between co-colonizers or that P. aeruginosa predisposes uncolonized sections of the surface to permit B. cepacia colonization. SIGNIFICANCE AND IMPACT OF THE STUDY: Colonization of a surface with one bacterial species confers colonization resistance towards other species. Disinfection of a surface might well increase the probability of pathogen harbourage.     

春玉米根系生育特征与冠层关系的研究

以农田实际观测资料为依据,分析了春玉米根系生育特征及其与冠层生长的关系,并提出了定量描述方程;较详细地阐述了水分条件对根系生长的影响,指出利用根系伸展深度确定灌溉计划湿润深度和进行根冠调控,以指导农田优化灌溉的可行性。