Cell-type action specificity of auxin on Arabidopsis root growth

The plant hormone auxin plays a critical role in root growth and development; however, the contributions or specific roles of cell-type auxin signals in root growth and development are not well understood. Here, we mapped tissue and cell types that are important for auxin-mediated root growth and development by manipulating the local response and synthesis of auxin. Repressing auxin signaling in the epidermis, cortex, endodermis, pericycle or stele strongly inhibited root growth, with the largest effect observed in the endodermis. Enhancing auxin signaling in the epidermis, cortex, endodermis, pericycle or stele also caused reduced root growth, albeit to a lesser extent. Moreover, we established that root growth was inhibited by enhancement of auxin synthesis in specific cell types of the epidermis, cortex and endodermis, whereas increased auxin synthesis in the pericycle and stele had only minor effects on root growth. Our study thus establishes an association between cellular identity and cell type-specific auxin signaling that guides root growth and development.     

SETD2 epidermal deficiency promotes cutaneous wound healing via activation of AKT/mTOR Signalling

ObjectivesCutaneous wound healing is one of the major medical problems worldwide. Epigenetic modifiers have been identified as important players in skin development, homeostasis and wound repair. SET domain–containing 2 (SETD2) is the only known histone H3K36 tri‐methylase; however, its role in skin wound healing remains unclear.Materials and MethodsTo elucidate the biological role of SETD2 in wound healing, conditional gene targeting was used to generate epidermis‐specific Setd2‐deficient mice. Wound‐healing experiments were performed on the backs of mice, and injured skin tissues were collected and analysed by haematoxylin and eosin (H&E) and immunohistochemical staining. In vitro, CCK8 and scratch wound‐healing assays were performed on Setd2‐knockdown and Setd2‐overexpression human immortalized keratinocyte cell line (HaCaT). In addition, RNA‐seq and H3K36me3 ChIP‐seq analyses were performed to identify the dysregulated genes modulated by SETD2. Finally, the results were validated in functional rescue experiments using AKT and mTOR inhibitors (MK2206 and rapamycin).ResultsEpidermis‐specific Setd2‐deficient mice were successfully established, and SETD2 deficiency resulted in accelerated re‐epithelialization during cutaneous wound healing by promoting keratinocyte proliferation and migration. Furthermore, the loss of SETD2 enhanced the scratch closure and proliferation of keratinocytes in vitro. Mechanistically, the deletion of Setd2 resulted in the activation of AKT/mTOR signalling pathway, while the pharmacological inhibition of AKT and mTOR with MK2206 and rapamycin, respectively, delayed wound closure.ConclusionsOur results showed that SETD2 loss promoted cutaneous wound healing via the activation of AKT/mTOR signalling.     

Application of plant metabarcoding to identify diverse honeybee pollen forage along an urban–agricultural gradient

Understanding animal foraging ecology requires large sample sizes spanning broad environmental and temporal gradients. For pollinators, this has been hampered by the laborious nature of morphologically identifying pollen. Identifying pollen from urban environments is particularly difficult due to the presence of diverse ornamental species associated with consumer horticulture. Metagenetic pollen analysis represents a potential solution to this issue. Building upon prior laboratory and bioinformatic methods, we applied quantitative multilocus metabarcoding to characterize the foraging ecology of honeybee colonies situated in urban, suburban, mixed suburban–agricultural and rural agricultural sites in central Ohio, USA. In cross‐validating a subset of our metabarcoding results using microscopic palynology, we find strong concordance between the molecular and microscopic methods. Our results suggest that forage from the agricultural site exhibited decreased taxonomic diversity and temporal turnover relative to the urban and suburban sites, though the generalization of this observation will require replication across additional sites and cities. Our work demonstrates the power of honeybees as environmental samplers of floral community composition at large spatial scales, aiding in the distinction of taxa characteristically associated with urban or agricultural land use from those distributed ubiquitously across the sampled landscapes. Observed patterns of high forage diversity and compositional turnover in our more urban sites are likely reflective of the fine‐grain heterogeneity and high beta diversity of urban floral landscapes at the scale of honeybee foraging. This provides guidance for future studies investigating how relationships between urbanization and measures of pollinator health are mediated by variation in floral resource dynamics across landscapes.     

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/ .     

Cytological and morphology characteristics of natural microsporogenesis within Camellia oleifera

Camellia oleifera is believed to exhibit a complex intraspecific polyploidy phenomenon. Abnormal microsporogenesis can promote the formation of unreduced gametes in plants and lead to sexual polyploidy, so it is hypothesized that improper meiosis probably results in the formation of natural polyploidy in Camellia oleifera. In this study, based on the cytological observation of meiosis in pollen mother cells (PMCs), we found natural 2n pollen for the first time in Camellia oleifera, which may lead to the formation of natural polyploids by sexual polyploidization. Additionally, abnormal cytological behaviour during meiosis, including univalent chromosomes, extraequatorial chromosomes, early segregation, laggard chromosomes, chromosome stickiness, asynchronous meiosis and deviant cytokinesis (monad, dyads, triads), was observed, which could be the cause of 2n pollen formation. Moreover, we confirmed a relationship among the length–width ratio of flower buds, stylet length and microsporogenesis. This result suggested that we can immediately determine the microsporogenesis stages by phenotypic characteristics, which may be applicable to breeding advanced germplasm in Camellia oleifera.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01002-5.     

广州市主城区城市地形类型与风环境评价

对城市地形组合类型及其地形对风场影响的研究,有助于城市风场机理的认识与生态环境的优化。以高层建筑密集的广州市主城区为例,在确定城市宏观地形类型的基础上,基于最小成本路径（LCP）辨识了风道,并对风环境质量进行评价。主要结论有：（1）将城市地形简要概括划分为4个一级地形、11个二级地形类型。（2）以LCP路径与盛行风交角不超过22.5°的标准,筛选确定通风路径作为风道。根据LCP格网的密度与频次,结合不同风向下风速与风频,评价分析了风环境类型与空间分布。（3）根据自然与城市地形的配置,北风风环境质量远高于西北风和东风;东风由于风频与风速最低,因此通风条件较差。（4）珠江航道在三种风向下都是尺度最宽贯穿城市最好的风道;区域性的风道与风环境较好的地段集中在与主风向平行的主干道上,但以近似南北走向的居多;由于广州城市地形高度以珠江新城峰林为中心向外递减,以低地地形为主的主城区外围通风优于中心区域,特别是珠江新城峰林与网络状台地为主的老城区,通风环境较差。基于LCP的评价结果需要同其他方法相互验证,才能使其不断完善优化。     

高阶相互作用对宿主-寄生群落动态的影响

物种间相互作用是影响生物群落稳定性和多样性的重要因素。基于Lotka-Volterra竞争模型,通过构建多宿主种群的种内和种间高阶相互作用模型,研究宿主种群的间接竞争效应对寄生群落动态的影响机制。为有效地揭示高阶作用对种群动态的影响,通过对比宿主-寄生群落的现象模型以及机制模型,利用机制模型产生的合理数据集对现象模型中高阶项的参数进行拟合,进而探讨了高阶相互作用在群落动态中的作用。结果显示,完整的高阶相互作用模型在描述多宿主-寄生系统的群落动态中表现最优,而直接相互作用模型对群落动态的描述相对较差,即同时考虑种间和种内的高阶相互作用模型更加符合机制模型所描述的群落动态。此外,种内高阶作用和种间高阶作用产生不对称效应,宿主间的种间高阶作用对群落产生的影响较种内高阶作用更为显著。该研究结果在一定意义上丰富了宿主-寄生生物群落的稳定性研究,为理解物种间相互作用的多样性研究提供了依据。     

基于景感生态学理念的乡村社会-生态系统供给服务研究

乡村社会-生态系统的稳定和可持续发展为农业农村现代化的实现奠定着基础,在稳定社会经济发展、提高城乡居民福祉方面发挥着重要作用。服务性公共设施作为乡村社会-生态系统供给服务的重要组成部分,代表了乡村的发展水平与该地区居民生活质量水平。研究公共服务设施的空间分布特征和综合评价其供给服务可改善乡村社会-生态系统结构,为城乡居民提供高质量的社会生态系统服务。以厦门市岛外城市化乡村为研究对象,通过厦门市岛外POI数据和乡村社会经济统计数据,以公共服务设施为景感载体,分析其空间分布和测度其供给服务水平,采用核密度分析方法与熵值分析法,分析厦门市乡村社会-生态系统供给服务空间分布特征,结合人口、经济、距岛内核心区距离等指标对各村庄社会-生态系统供给服务能力进行皮尔逊相关性分析。研究发现厦门乡村公共设施供给服务能力表现为集美区 > 海沧区 > 同安区 > 翔安区;各村庄公共设施供给服务能力水平影响因素是多元且具有多样性的;提出从城乡居民的认知心理与物质需求出发对公共设施进行景感生态营造以提高村庄社会-生态系统供给服务能力,更好满足人们的需求。本文对公共服务设施的空间优化提出对策建议,研究结果可为乡村社会-生态系统供给服务提升和乡村可持续发展提供理论研究依据。     

河西走廊植被净初级生产力时空变化及其影响因子研究

干旱半干旱区植被NPP变化对全球碳循环有重要影响,该区域NPP对气候变化的响应表现出较大的时空异质性,其驱动机制并不十分清楚。选择中国河西走廊,利用随机森林算法估算了2002-2018年的NPP,基于偏导数法计算了气候与人类活动对NPP的影响。结果表明：（1）随机森林算法能较好的适用于干旱半干旱区NPP估算。（2）2002-2018年间河西走廊年NPP的平均值为153.32 gC m^-2 a^-1,总量为37.468 Tg C/a,呈东南向西北递减的分布特征,研究期间NPP呈2.37 gC m^-2 a^-1（P=0.09）增长趋势。（3）河西走廊NPP变化52.51%由气候因子贡献,47.49%由人类活动贡献。（4）在气候变化对NPP的影响中,降水主导了该区72.21%的区域,温度对NPP变化量的贡献占73.71%,前者影响着NPP变化格局,后者主导NPP变化数量。升温和增湿均有利于该区NPP增加,随着西北地区气候暖湿化,河西走廊植被会持续改善,该研究有助于理解干旱半干旱区NPP对气候变化的响应机制,为适应气候变化政策制定提供理论依据。