基于GIS的广州市中心城区城市森林可达性分析

城市森林是城市中主要的生态功能景观,已经成为城市生态环境建设的主体。基于居民方便获取城市森林服务的要求,根据大型城市森林斑块、道路网和街区单元数据,利用ArcGIS9.2的Network Analyst工具,分析了广州市中心城区在2km步行距离内街区单元到达城市森林斑块的可达性以及城市森林斑块的承载力,并结合航片解译的树冠覆盖数据对具有不同可达性的街区单元进行了分析。分析结果表明：广州中心城区的外环高速以内的区域范围,分别有73%、46%和18%的的街区单元在步行2km、1km和0.5km距离内能够到达大型城市森林绿地斑块。从街区单元的行政归属看,以越秀区的街区可达性最好,而海珠区和原芳村区的街区可达性较差。研究范围内,0.5km内不能到达大型城市森林斑块且树冠覆盖超过30%的街区类型中,以公共管理单位类型为主,单位绿化对于树冠覆盖的贡献率大;而绝大多数以住宅类型为主的街区单元的树冠覆盖率低于10%,其中64%的街区树冠覆盖率低于5%。以街区单元为基本对象进行可达性度量,分析城市森林斑块现状分布和服务状况,并结合其树冠覆盖特征,可以明确需要重点关注区域的空间分布,可为广州市在较小尺度上的城市森林空间布局优化提供参考。     

蓝藻伪空胞的特性及浮力调节机制

伪空胞为蓝藻在水体中提供浮力,使其获得适宜的生长条件,最终导致蓝藻水华暴发,了解伪空胞的特征对控制蓝藻水华暴发有重要意义。文章简要回顾了蓝藻伪空胞自1865年被Klebahn发现到1965年被正式命名的研究历程,目前已发现150多种原核生物中含有伪空胞;伪空胞是两末端呈圆锥状的中空圆柱体,伪空胞半径与临界压强遵循方程:Pc=275(r/nm)-1.67MPa;伪空胞气体含量可根据不同原理,利用Walsby伪空胞测定装置、压力浊度计和细胞流式仪测得。总结了伪空胞组成的化学特性,评述了伪空胞gvp基因丛结构功能和GvpA、GvpC的蛋白空间结构。GvpA是伪空胞合成的主要成分,gvpA在伪空胞内存在多个拷贝,其功能仍不清楚;GvpC由33个氨基酸重复单位组成,重复单位越多,伪空胞越不易破裂;概述了伪空胞3种浮力调节机制:镇重物的改变、伪空胞的合成、伪空胞的破裂;归纳了环境因子(光照、温度、氮、磷、钾)参与伪空胞浮力网络调控的途径。提出了目前伪空胞研究面临的困难和问题,对伪空胞的未来研究方向提出探索性的建议。     

Rhizosphere soil bacterial communities and nitrogen cycling affected by deciduous and evergreen tree species

Deciduous and evergreen trees differ in their responses to drought and nitrogen (N) demand. Whether or not these functional types affect the role of the bacterial community in the N cycle during drought remains uncertain. Two deciduous tree species (Alnus cremastogyne, an N₂‐fixing species, and Liquidambar formosana) and two evergreen trees (Cunninghamia lanceolata and Pinus massoniana) were used to assess factors in controlling rhizosphere soil bacterial community and N cycling functions. Photosynthetic rates and biomass production of plants, 16S rRNA sequencing and N‐cycling‐related genes of rhizosphere soil were measured. The relative abundance of the phyla Actinobacteria and Firmicutes was higher, and that of Proteobacteria, Acidobacteria, and Gemmatimondaetes was lower in rhizosphere soil of deciduous trees than that of evergreen. Beta‐diversity of bacterial community also significantly differed between the two types of trees. Deciduous trees showed significantly higher net photosynthetic rates and biomass production than evergreen species both at well water condition and short‐term drought. Root biomass was the most important factor in driving soil bacterial community and N‐cycling functions than total biomass and aboveground biomass. Furthermore, 44 bacteria genera with a decreasing response and 46 taxa showed an increased response along the root biomass gradient. Regarding N‐cycle‐related functional genes, copy numbers of ammonia‐oxidizing bacteria (AOB) and autotrophic ammonia‐oxidizing archaea (AOA), N₂ fixation gene (nifH), and denitrification genes (nirK, nirS) were significantly higher in the soil of deciduous trees than in that of the evergreen. Structural equation models explained 50.2%, 47.6%, 48.6%, 49.4%, and 37.3% of the variability in copy numbers of nifH, AOB, AOA, nirK, and nirS, respectively, and revealed that root biomass had significant positive effects on copy numbers of all N‐cycle functional genes. In conclusion, root biomass played key roles in affecting bacterial community structure and soil N cycling. Our findings have important implications for our understanding of plants control over bacterial community and N‐cycling function in artificial forest ecosystems.     

Effect of steady-state response versus excitatory/inhibitory balance on spiking synchronization in neural networks with log-normal synaptic weight distribution

Synchronization of neural activity, especially at the gamma band, contributes to perceptual functions. In several psychiatric disorders, deficits of perceptual functions are reflected in synchronization abnormalities. Plausible cause of this impairment is an alteration in the balance between excitation and inhibition (E/I balance); a disruption in the E/I balance leads to abnormal neural interactions reminiscent of pathological states. Moreover, the local lateral excitatory-excitatory synaptic connections in the cortex exhibit excitatory postsynaptic potentials (EPSPs) that follow a log-normal amplitude distribution. This long-tailed distribution is considered an important factor for the emergence of spatiotemporal neural activity. In this context, we hypothesized that manipulating the EPSP distribution under abnormal E/I balance conditions would provide insights into psychiatric disorders characterized by deficits in perceptual functions, potentially revealing the mechanisms underlying pathological neural behaviors. In this study, we evaluated the synchronization of neural activity with external periodic stimuli in spiking neural networks in cases of both E/I balance and imbalance with or without a long-tailed EPSP amplitude distribution. The results showed that external stimuli of a high frequency lead to a decrease in the degree of synchronization with an increasing ratio of excitatory to inhibitory neurons in the presence, but not in the absence, of high-amplitude EPSPs. This monotonic reduction can be interpreted as an autonomous, strong-EPSP-dependent spiking activity selectively interfering with the responses to external stimuli. This observation is consistent with pathological findings. Thus, our modeling approach has potential to improve the understanding of the steady-state response in both healthy and pathological states.     

植物中参与活性氧调控的基因网络

植物体内活性氧（reactive oxygen species,ROS）是氧化还原反应的必然副产物,具极高的活性和毒性,从而对细胞产生毒害。同时,活性氧作为信号分子对很多生理过程诸如植物生长发育、细胞程序化死亡及生物和非生物胁迫应答起调控作用。植物中ROS双重作用的协调机制目前尚不明确,确定的是细胞中ROS维持于稳定水平需要精细的调节。拟南芥中至少包括152个基因组成的网络参与ROS的调控,该网络具高度的灵活性和互补性。本文综述了ROS网络中鉴定的一些关键基因及细胞学定位和协同作用,ROS信号转导,尤其是叶绿体中ROS信号的调控。     

基于网络特征的道路生态干扰——以澜沧江流域为例

道路网络对区域景观的生态格局和过程产生较大的影响,作为干扰因子,区域道路网络的特征和所产生的生态干扰水平存在一定的相关性.利用GIS和网络分析法,以澜沧江流域县域为基本单元,分析了研究区各县的道路网络特征指数,在揭示了区域道路网络不同特征之间的规律性的基础上,进一步对区域网络特点和生态干扰之间相关性进行了内在关系的探讨.结果表明,澜沧江流域道路网络结构的空间差异很大,流域内各县的道路网络节点数、连接线数目、α环度、β线点率、γ连接度指数等网络特征因子也存在较大差异;道路密度和道路总长度与区域海拔高度呈现较明显的负相关关系;道路密度和区域道路的廊道密度呈现正相关关系,和区域道路的α指数、β指数和γ指数关系可以用倒数模型来拟合.缓冲区分析表明,耕地比例和道路密度线性相关关系显著,而其他类型相关性较差,但区域综合的人工干扰指数(Hd)(1980,2000)和道路网络的特征指数相关显著,而且不同时期的区域景观的斑块密度、平均斑块面积和区域道路网络特征之间也存在较强的相关性,即网络扩展使得区域生态系统受干扰强度增加,破碎化严重,但较短时期内的生态系统变化和道路网络特征之间相关性不显著.     

CircR2Disease v2.0: An Updated Web Server for Experimentally Validated circ RNA–disease Associations and Its Application

With accumulating dysregulated circular RNAs(circRNAs) in pathological processes,the regulatory functions of circRNAs, especially circRNAs as microRNA(miRNA) sponges and their interactions with RNA-binding proteins(RBPs), have been widely validated. However, the collected information on experimentally validated circRNA–disease associations is only preliminary.Therefore, an updated CircR2Disease database providing a comprehensive resource and web tool to clarify the relationships between circRNAs...     

DLGCN:基于图卷积网络的药物-lncRNA[]关联预测

为实现高通量识别新的药物-长链非编码RNA(Long non-coding RNA, lncRNA)关联,本文提出了一种基于图卷积网络模型来识别潜在药物-lncRNA关联的方法DLGCN(Drug-LncRNA graph convolution network)。首先,基于药物的结构信息和lncRNA的序列信息分别构建了药物-药物和lncRNA-lncRNA相似性网络,并整合实验证实的药物-lncRNA关联构建了药物-lncRNA异质性网络。然后,将注意力机制和图卷积运算应用于该网络中,学习药物和lncRNA的低维特征,基于整合的低维特征预测新的药物-lncRNA关联。通过效能评估,DLGCN的受试者工作特性曲线下面积(Area under receiver operating characteristic, AUROC)达到0.843 1,优于经典的机器学习方法和常见的深度学习方法。此外,DLGCN预测到姜黄素能够调控lncRNA MALAT1的表达,已被最近的研究证实。DLGCN能够有效预测药物-lncRNA关联,为肿瘤治疗新靶点的识别和抗癌药物的筛选提供了重要参考。     

抑郁症易感基因和抗抑郁药物靶点相关[]神经细胞类型及相互作用网络分析

基于抑郁症的全基因组关联分析研究(GWAS),对于获得的单核苷酸多态性位点(SNP)使用Haploreg软件进行基因注释,得到SNP注释的102个易感基因.。使用MAGMA软件对GWAS的汇总统计数据做基因水平的分析,获得了270个校正之后显著的基因,两者合并共得到320个抑郁症易感基因。通过药物数据库Drugbank获取133个抗抑郁药物靶点基因。使用EWCE包对抑郁症易感基因和抗抑郁药物靶点在三套脑组织单细胞测序数据中,分别进行神经细胞类型富集分析。结果发现大脑皮质的GABA神经元(抑制性神经元)和谷氨酸能神经元(兴奋性神经元)是抑郁症易感基因和抗抑郁药物靶点共同的神经元。这两种类型的神经细胞可能是抗抑郁药物与抑郁症易感基因相互作用的神经细胞,另外少突胶质前体细胞可能是抑郁症特有的易感神经细胞。使用Network Calculator软件构建网络并进行进行网络拓扑学参数分析。结果表明抑郁症易感基因与抗抑郁药物靶点组成了一个具有显著的相互连接的网络。本研究从单细胞层面揭示抑郁症的遗传机制,在网络层面为寻找新的抗抑郁药物靶点提供了一定的启示。