Profiling of the assembly of RecA nucleofilaments implies a potential target for environmental factors to disturb DNA repair

Double-strand breaks (DSBs), one class of the most harmful DNA damage forms that bring elevated health risks, need to be repaired timely and effectively. However, an increasing number of environmental pollutants have been identified to impair DSB repair from various mechanisms. Our previous work indicated that the formation of unsaturated RecA nucleofilaments plays an essential role in homology recombination (HR) pathway which can accurately repair DSBs. In this study, by developing a benzonase cutting protection assay and combining it with traditional electrophoretic mobility shift assay (EMSA) analysis, we further investigated the assembly patterns of four RecA mutants that display differential DSB repair ability and ATPase activity. We observed that the mutants (G204S and S69G) possessing both ATP hydrolysis and DSB repair activities form unsaturated nucleofilaments similar to that formed by the wild type RecA, whereas the other two ATP hydrolysis-deficient mutants (K72R and E96D) that fail to mediate HR form more compacted nucleofilaments in the presence of ATP. These results establish a coupling of ATPase activity and effective DSB repair ability via the assembly status of RecA nucleofilaments. This linkage provides a potential target for environmental factors to disturb the essential HR pathway for DSB repair by suppressing the ATPase activity and altering the assembly pattern of nucleofilaments.     

Drivers of microbial beta-diversity in wastewater treatment plants in China

As one of the most well-documented biogeographic patterns, the distance-decay relationship provides insights into the underlying mechanisms driving biodiversity distribution. Although wastewater treatment plants (WWTPs) are well-controlled engineered ecosystems, this pattern has been seen among microbial communities in activated sludge (AS). However, little is known about the relative importance of environmental heterogeneity and dispersal limitation in shaping AS microbial community across China; especially they are related to spatial scale and organism types. Here, we assessed the distance-decay relationship based on different spatial scales and microbial phylogenetic groups by analyzing 132 activated sludge (AS) samples across China comprising 3,379,200 16S rRNA sequences. Our results indicated that the drivers of distance-decay pattern in China were scale-dependent. Microbial biogeographic patterns in WWTPs were mainly driven by dispersal limitation at both local and national scales. In contrast, conductivity, SRT, and pH played dominant roles in shaping AS microbial community compositions at the regional scale. Turnover rates and the drivers of beta-diversity also varied with microorganism populations. Moreover, a quantitative relationship between dispersal limitation ratio and AS microbial turnover rate was generated. Collectively, these results highlighted the importance of considering multiple spatial scales and micro-organism types for understanding microbial biogeography in WWTPs and provided new insights into predicting variations in AS community structure in response to environmental disturbance.     

多维微振动模拟平台理论建模与仿真研究

目的模拟空间飞行器上反作用产生的微振动。方法设计一种多维微振动模拟平台,该模拟平台可产生空间六维微振动加速度谱。首先分析各个驱动腿及负载质心处的速度与加速度间的关系,接着结合牛顿-欧拉方法与拉格朗日方程推导得到多维微振动模拟平台的完整动力模型,最后利用多体系统软件ADAMS与MATLAB/Simulink进行联合仿真,以此联合仿真技术来验证理论模型的准确性。结果理论模型与仿真分析之间的最大误差为2.84%。结论该理论模型准确可靠,可以作为动力学控制的理论基础。     

Patterns of plant trait-environment relationships along a forest succession chronosequence

Land-use change due to socioeconomic factors leads to the abandonment of traditional intensive coppice management in large areas of the mountainous landscapes of the Apennines (Italy). In this study we explored the multivariate relationship between plant species traits, stage of forest succession and environmental gradients. We focused on community-level patterns in plant traits of the vegetation of beech forest understory along the regeneration chronosequence initiated after cessation of coppicing. We hypothesized that the correlations between the traits and environmental factors should increase with succession age due to the decreasing role of chance.Landscape-level heterogeneity, i.e. changing elevation, slope, exposition, bedrock and forest stand age was assessed using a stratified random sampling design. Sixty sites were sampled for stand structure and species composition. We focused on 14 plant traits related to persistence, growth and dispersal. The recently developed data-analytical method, Model-Based Recursive Partitioning, was used to disentangle the relationships between patterns of plant traits and environmental gradients.About half (seven) of the studied plant traits showed significant correlations with succession stand age, elevation, inclination, heat index and bedrock. Contrary to the low number of trait-environment correlations in early succession, eight traits showed significant relationships with one or more abiotic factors in older stages of the post-coppice development. Stand age had the highest independent explanatory power, explaining 40% of variance of SLA, more than 17% of variance of short-distance seed dispersal and more than 15% of variance of both long-term connection and extensive perennial root. Among the other abiotic factors, elevation explained 27% of variance of SLA, inclination explained 6-8% of variance of long-term connection, extensive perennial root, thickening and large bud bank.The observed trait-environmental relationship is assumed to be driven by various environmental factors operating at various levels of complexity. While forest succession in relatively homogeneous landscapes might be driven mainly by environmental factors related to forest succession itself and associated abiotic changes (such as changes in light and soil moisture patterns), in heterogeneous landscapes the succession pathways may be structured by landscape-level environmental factors such as inclination. However, in the present study, forest stand age had the highest explanatory power for most of the investigated traits, supporting the assumption of the overall strong impact of succession-driven environmental factors in trait-environment relationships.     

Screening and characterization of extremophiles in spacecraft assembly environment北大核心CSCD

Spacecrafts need to strictly control microorganisms before entering space flight. The Spacecraft Assembly, Integration, and Test Center (AITC) is an important environmental source for spacecrafts to carry microorganisms. The assembly clean room has characteristics of ventilation, dryness, and lack of nutrients that are not conducive to the growth and reproduction of microorganisms, except for extremophiles. In this study, based on the internal air and surface environment of the AITC in China, 13 strains of bacteria were identified by plate culture and 16S sequence analysis, and their extreme environmental tolerance, antibiotic resistance, and film-forming ability were tested. All these bacteria belonged to the Firmicutes and Proteobacteria phyla, and nine strains belonged to the Bacillus genus. All 13 strains of bacteria were salt-tolerant, acid-tolerant, and alkali-tolerant, and 69.2% of the bacteria survived heat shock at 80 ℃. Among these, one strain of Sphingomonas sp. JCM7513 isolated from the surface environment was insensitive to all the tested antibiotics and had strong drug resistance, while the other 12 strains were sensitive to most β-lactam antibiotics but had strong resistance to tetracyclic antibiotics and erythromycin. Most of the isolated bacteria exhibited strong biofilm-forming abilities. The study showed that there are a certain number of extremophiles in the spacecraft assembly environment. To protect spacecrafts from biological corrosion and planetary protection forward pollution, more effective monitoring and elimination methods are needed. © 2022 Science Press. All rights reserved.     

东部平原矿区复垦土壤微生物群落特征及其组装过程

复垦对恢复矿区土壤生产力极为重要,但复垦土壤生产力重建的微生物学机制尚不清晰.为此,采集复垦8 a、复垦11 a、复垦14 a和复垦17 a这4个复垦时长和1个未复垦对照共75个表层土样进行16S rRNA扩增子高通量测序,分析微生物群落组成、潜在功能及其组装机制.结果表明：(1)群落丰富度随复垦时间增加而增加,且高于对照样.但群落多样性和均匀度却随复垦时间增加而降低(P<0.05);(2)复垦土壤中酸杆菌门(Acidobacteria)、绿弯菌门(Chloroflexi)、变形菌门(Proteobacteria)和拟杆菌门(Bacteroidetes)占主导地位,且前两者相对丰度显著高于对照样(P<0.05),后两者则相反(P<0.05);(3)复垦土壤中辅酶转运与代谢、翻译、核糖体结构与生物发生等8种功能呈正向演替,随复垦时长不断增强;(4)平原矿区微生物群落生态网络模块性良好,且关键类群多属酸杆菌门和拟杆菌门.群落组装以确定性过程为主导,同质性选择贡献最大,主要受当地特殊环境操控.这些发现为改善复垦土壤生产力和生态服务提供了理论依据.     

Exploring community assembly through an individual-based model for trophic interactions

Traditionally, the dynamics of community assembly has been analyzed by means of deterministic models of differential equations. Despite the theoretical advances provided by such models, they are restricted to questions about community-wide features. The individual-based modeling offers an opportunity to link bionomic features to patterns at the community scale, allowing us to understand how trait-based assembly rules can arise by dynamical processes. The present paper introduces an individual-based model of community assembly, and discusses some of the major advantages and drawbacks of this approach. The model was framed to deal with predation among size-structured populations, incorporating allometric constraints to energetic requirements, movement, life-history features and interaction relationships among individuals. A protocol of assembly procedure is proposed, in which a period of intense species introductions is followed by a period without introductions. The resultant communities did not present any pattern of trait over-dispersion, meaning that the multivariate distances of bionomic features among co-occurring species were neither larger nor more regular than expected in a random collection of species. It suggests a weak influence of interspecific interactions in the model environment and individualistic rules of coexistence, driven mainly by the spatial structure. This highlights that trait over-dispersion and resource partitioning should not be considered a necessary condition for coexistence, even in communities entirely structured by internal processes like predation and competition.     

生境过滤驱动庞泉沟华北落叶松林土壤真菌群落的构建过程

随机过程和确定过程的权衡作用对群落构建的影响机制是群落生态学研究的中心议题,也是目前群落生态学最具争议的问题.本研究以关帝山庞泉沟自然保护区华北落叶松林土壤真菌群落为研究对象,探讨确定过程和随机过程的权衡作用在局域尺度对土壤真菌群落构建的影响机制.通过土壤理化因子和优势真菌门的相关分析、冗余分析以及结构方程模型分析,表明土壤理化因子和地上植被多样性对真菌群落结构有显著影响,并且林下植被多样性对真菌群落结构的直接影响最大(1.185 8).由此推断确定过程对真菌群落的构建有一定的影响.真菌群落的β多样性表现为距离衰减的生物地理分布格局,由此推断随机过程(扩散限制)对真菌群落的构建有一定的影响作用.通过构建零模型分析,表明确定过程对真菌群落演替的贡献远大于随机过程,是本研究区真菌群落构建的主要驱动因子.并且确定过程的相对重要性随着海拔梯度而动态变化.由于零偏差值在本研究区都为负值,观测值的相似性小于期望值的相似性,由此推断生境过滤是群落构建的驱动因子.综上,确定过程和随机过程的权衡作用驱动了本研究区真菌群落的构建过程,且确定过程起主导作用.     

Distinct community assembly processes underlie significant spatiotemporal dynamics of abundant and rare bacterioplankton in the Yangtze River

• Season and landform influenced spatiotemporal patterns of abundant and rare taxa. • Different stochastic processes dominated abundant and rare subcommunity assembly. • River flow and suspended solids regulated assembly processes of rare taxa. The rare microbial biosphere provides broad ecological services and resilience to various ecosystems. Nevertheless, the biogeographical patterns and assembly processes of rare bacterioplankton communities in large rivers remain uncertain. In this study, we investigated the biogeography and community assembly processes of abundant and rare bacterioplankton taxa in the Yangtze River (China) covering a distance of 4300 km. The results revealed similar spatiotemporal patterns of abundant taxa (AT) and rare taxa (RT) at both taxonomic and phylogenetic levels, and analysis of similarities revealed that RT was significantly influenced by season and landform than AT. Furthermore, RT correlated with more environmental factors than AT, whereas environmental and spatial factors explained a lower proportion of community shifts in RT than in AT. The steeper distance–decay slopes in AT indicated higher spatial turnover rates of abundant subcommunities than rare subcommunities. The null model revealed that both AT and RT were mainly governed by stochastic processes. However, dispersal limitation primarily governed the AT, whereas the undominated process accounted for a higher fraction of stochastic processes in RT. River flow and suspended solids mediated the balance between the stochastic and deterministic processes in RT. The spatiotemporal dynamics and assembly processes of total taxa were more similar as AT than RT. This study provides new insights into both significant spatiotemporal dynamics and inconsistent assembly processes of AT and RT in large rivers.     

全基因合成方法学研究

通过基因全合成实现基因的分子改造和人工组建正成为一种实验室常规手段,因此,建立一种能够在相对低廉和短时间内准确和高效地设计和合成长片段基因的方法十分重要.本研究报道了一种重复性好、错误率低、低成本和简便的基因设计和全合成方法.此方法包含经DNA2.0软件的序列优化,Gene2Oligo软件的寡核苷酸设计,覆盖全长基因双链的寡核苷酸的组合和引物介导下的全基因的合成等步骤.运用此方法,对3个不同长度的基因(分别为653bp,1309bp和1498bp)成功地进行了密码子优化和一步全合成.其中的amyFF在大肠杆菌中表达量提高了12倍.图2参18