Guidelines for model adaptation: A study of the transferability of a general seagrass ecosystem Dynamic Bayesian Networks model

In general, it is not feasible to collect enough empirical data to capture the entire range of processes that define a complex system, either intrinsically or when viewing the system from a different geographical or temporal perspective. In this context, an alternative approach is to consider model transferability, which is the act of translating a model built for one environment to another less well‐known situation. Model transferability and adaptability may be extremely beneficial—approaches that aid in the reuse and adaption of models, particularly for sites with limited data, would benefit from widespread model uptake. Besides the reduced effort required to develop a model, data collection can be simplified when transferring a model to a different application context. The research presented in this paper focused on a case study to identify and implement guidelines for model adaptation. Our study adapted a general Dynamic Bayesian Networks (DBN) of a seagrass ecosystem to a new location where nodes were similar, but the conditional probability tables varied. We focused on two species of seagrass (Zostera noltei and Zostera marina) located in Arcachon Bay, France. Expert knowledge was used to complement peer‐reviewed literature to identify which components needed adjustment including parameterization and quantification of the model and desired outcomes. We adopted both linguistic labels and scenario‐based elicitation to elicit from experts the conditional probabilities used to quantify the DBN. Following the proposed guidelines, the model structure of the general DBN was retained, but the conditional probability tables were adapted for nodes that characterized the growth dynamics in Zostera spp. population located in Arcachon Bay, as well as the seasonal variation on their reproduction. Particular attention was paid to the light variable as it is a crucial driver of growth and physiology for seagrasses. Our guidelines provide a way to adapt a general DBN to specific ecosystems to maximize model reuse and minimize re‐development effort. Especially important from a transferability perspective are guidelines for ecosystems with limited data, and how simulation and prior predictive approaches can be used in these contexts.     

核不均一核糖核蛋白R基因沉默抑制非小细胞肺癌细胞恶性转化

核不均一核糖核蛋白R(hnRNPR)是一种与mRNA生物学功能密切相关的RNA结合蛋白质,与多种肿瘤细胞的恶性转化相关。然而,在非小细胞肺癌(NSCLC)中的作用机制尚不清楚。本研究通过检索公共数据库发现,hnRNPR蛋白主要在肺癌细胞核中表达,hnRNPR mRNA在非小细胞肺癌组织中高表达,并且与肺腺癌患者的生存率呈负相关;hnRNPR的表达与非小细胞肺癌患者的性别、T分期显著相关(P<0.05)。构建hnRNPR基因沉默的非小细胞肺癌稳定细胞株,检测细胞功能变化,结果显示,hnRNPR基因沉默抑制了细胞增殖、迁移和侵袭能力以及上皮-间质转化(EMT),并将细胞周期阻滞在G₁期(P<0.01)。生物信息学分析显示,非小细胞肺癌中hnRNPR基因与9 310个基因的表达正相关(皮尔逊相关系数>0,P<0.05),与10 680个基因的表达负相关(皮尔逊相关系数<0,P<0.05)。综上所述,hnRNPR在非小细胞肺癌中高表达,可能作为剪接体的组分,通过调节相关基因的表达,促进了NSCLC细胞的恶性转化。     

Cryo-EM structure of the fatty acid reductase LuxC–LuxE complex provides insights into bacterial bioluminescence

The discovery of reduced flavin mononucleotide and fatty aldehydes as essential factors of light emission facilitated study of bacterial luminescence. Although the molecular mechanisms underlying bacterial luminescence have been studied for more than 60 years, the structure of the bacterial fatty acid reductase complex remains unclear. Here, we report the cryo-EM structure of the Photobacterium phosphoreum fatty acid reductase complex LuxC–LuxE to a resolution of 2.79 Å. We show that the active site Lys238/Arg355 pair of LuxE is >30 Å from the active site Cys296 of LuxC, implying that catalysis relies on a large conformational change. Furthermore, mutagenesis and biochemical experiments support that the L-shaped cleft inside LuxC plays an important role in substrate binding and reaction. We obtained a series of mutants with significantly improved activity as measured by in vitro bioluminescence assays and demonstrated that the double mutant W111A/F483K displayed the highest activity (370% of the WT). Our results indicated that the activity of LuxC significantly affects the bacterial bioluminescence reaction. Finally, we expressed this mutated lux operon in Escherichia coli but observed that the in vivo concentrations of ATP and NADPH limited the enzyme activity; thus, we conclude that the luminous intensity mainly depends on the level of metabolic energy.     

生态复杂性研究——综述与展望

简要介绍了生态复杂性研究的最新进展与动态,生态复杂性研究的背景及若干重要的概念与方法,生态复杂性指生态系统内不同层次上的结构与功能的多样性,自组织及有序性,生态复杂性研究的显著特征是：它应用复杂的理论,方法和观点来研究生态与进化问题,其研究方法主要有元胞机法和遗传算法,认为生态系统是一个适应复杂系统,处于混沌的边缘或临界态,内部作用是生态系统复杂化,有序化及自组织的主要推动力。     

Characterizing the Interaction between Root-knot Nematodes and Soil-borne Fungi which are Pathogenic to Passion Fruit (Passiflora Edulis)

For decades there have been anecdotal claims of synergistic interactions between plant-parasitic nematodes and soil-borne fungi causing decline of productivity of passion fruit (Passiflora edulis) orchards. An empirical confirmation of these disease complexes would impact disease management and plant breeding for resistance. To test those claims, we subjected passion fruit plants to single or concomitant parasitism by Meloidogyne javanica or M. incognita and Fusarium nirenbergiae or Neocosmospora sp. under controlled conditions. Non-inoculated plants served as control for the assays. The severity of shoot symptoms and variables related to plant growth, the extent of fungal lesions, and nematode reproduction were assessed to characterize the interactions. The shoot symptoms and effect on plant growth induced by the pathogens varied, but no synergy between the pathogens was observed. Moreover, the volume of tissue lesioned by the fungi was not affected by co-parasitism of the nematodes. Conversely, plant resistance to the nematodes was not affected by co-parasitism of the fungi. The interactions M. incognita-F. nirenbergiae, M. incognita-Neocosmospora sp., M. javanica-F. nirenbergiae, and M. javanica-Neocosmospora sp. were not synergistic as previously claimed, but instead neutral.     

The Nup2 meiotic-autonomous region relieves inhibition of Nup60 to promote progression of meiosis and sporulation in Saccharomyces cerevisiae

During meiosis, chromosomes undergo dramatic changes in structural organization, nuclear positioning, and motion. Although the nuclear pore complex has been shown to affect genome organization and function in vegetative cells, its role in meiotic chromosome dynamics has remained largely unexplored. Recent work in the budding yeast Saccharomyces cerevisiae demonstrated that the mobile nucleoporin Nup2 is required for normal progression through meiosis I prophase and sporulation in strains where telomere-led chromosome movement has been compromised. The meiotic-autonomous region, a short fragment of Nup2 responsible for its role in meiosis, was shown to localize to the nuclear envelope via Nup60 and to bind to meiotic chromosomes. To understand the relative contribution these 2 activities have on meiotic-autonomous region function, we first carried out a screen for meiotic-autonomous region mutants defective in sporulation and found that all the mutations disrupt interaction with both Nup60 and meiotic chromosomes. Moreover, nup60 mutants phenocopy nup2 mutants, exhibiting similar nuclear division kinetics, sporulation efficiencies, and genetic interactions with mutations that affect the telomere bouquet. Although full-length Nup60 requires Nup2 for function, removal of Nup60’s C-terminus allows Nup60 to bind meiotic chromosomes and promotes sporulation without Nup2. In contrast, binding of the meiotic-autonomous region to meiotic chromosomes is completely dependent on Nup60. Our findings uncover an inhibitory function for the Nup60 C-terminus and suggest that Nup60 mediates recruitment of meiotic chromosomes to the nuclear envelope, while Nup2 plays a secondary role counteracting the inhibitory function in Nup60’s C-terminus.     

北京城市土地复合生态服务功效演变特征

城市的发展依赖于土地复合生态系统提供各项的生态服务功能,其产出是生态服务功效,可分为正向和负向的服务功效。快速的城市化导致的土地利用变化影响了土地的生态服务功效。在GIS平台的支持下,基于遥感影像和城市社会经济发展数据,以特大城市北京为案例城市,建立了基于正向和负向生态功效的空间指标体系,采用划分单元空间网格评价方法,评估了上一版城市总体规划实施以来土地复合生态服务功效的变化特征。研究表明由于城市化的快速发展影响了土地的复合生态功效,2003—2011年城市土地复合生态功效评价结果显示,土地的生态服务负功效在增长,而正功效在不断减少,2003年土地正负服务功效空间分别为57.7%和42.3%,2011年则分别为51.3%和48.7%。2003年的生态服务负功效空间以中心城为核心,成放射状向新城辐射;而2011年生态服务负功效空间以中心城为核心向外呈饼状蔓延;外延式的城市发展空间发展模式是导致负功效增长的主要因素。为建设良好的城市生态环境,需要在未来的城市规划和管理中,重视非建设用地的生态功能管理,引导外部生态空间渗入城市,强化土地生态服务功能;同时优化城乡结合部的用地结构,保育郊区的生态环境。     

内质网膜复合亚基3调控内质网应激影响人畸胎瘤细胞的存活

内质网膜蛋白复合物(endoplasmic reticulum membrane complex,EMC)在跨膜蛋白质的生物发生和膜整合中发挥重要作用.内质网膜复合亚基3 (endoplasmic reticulum membrane complex 3,EMC3)是EMC的重要组成部分,但其在生殖细胞中发挥的作用未见...     

中国不同规模城市可持续发展综合评价

城市是一类社会-经济-自然复合生态系统,城市的可持续发展指标体系和评价方法是衡量城市经济、社会、环境状况及可持续发展能力的重要手段。采用全排列多边形综合图示法,以中国277个地级及地级以上城市为研究对象,建立了不同规模城市的可持续发展指标体系,包括经济发展、社会进步、生态环境3类24项指标,对其2000—2010年的可持续发展能力进行了综合评价。研究结果表明:从不同城市规模类型间横向对比分析来看,随着城市规模的增大,经济发展、社会进步和可持续发展综合指数相应提高,生态环境指数却随之下降。从不同规模城市类型内的时间序列分析对比来看,2000—2010年不同规模城市的经济发展、社会进步、生态环境指数各个方面均有显著提高,可持续发展综合指数也伴随着提升。并且,巨大特大型城市在生态环境保护方面提高幅度最大;大型城市在社会进步方面提高幅度最大;中小型城市在经济发展和可持续发展综合能力方面提高幅度最大。但截止到2010年,不同规模城市的可持续发展综合指数均为Ⅲ级,可持续发展能力仅处于一般水平。探究了中国不同规模的城市可持续发展过程中面临的诸多问题,然后提出相应的对策建议,为今后的新型城市化建设提供参考。     

Binding of the erlin1/2 complex to the third intralumenal loop of IP3R1 triggers its ubiquitin-proteasomal degradation

Long-term activation of inositol 1,4,5-trisphosphate receptors (IP₃Rs) leads to their degradation by the ubiquitin–proteasome pathway. The first and rate-limiting step in this process is thought to be the association of conformationally active IP₃Rs with the erlin1/2 complex, an endoplasmic reticulum–located oligomer of erlin1 and erlin2 that recruits the E3 ubiquitin ligase RNF170, but the molecular determinants of this interaction remain unknown. Here, through mutation of IP₃R1, we show that the erlin1/2 complex interacts with the IP₃R1 intralumenal loop 3 (IL3), the loop between transmembrane (TM) helices 5 and 6, and in particular, with a region close to TM5, since mutation of amino acids D-2471 and R-2472 can specifically block erlin1/2 complex association. Surprisingly, we found that additional mutations in IL3 immediately adjacent to TM5 (e.g., D2465N) almost completely abolish IP₃R1 Ca²⁺ channel activity, indicating that the integrity of this region is critical to IP₃R1 function. Finally, we demonstrate that inhibition of the ubiquitin-activating enzyme UBE1 by the small-molecule inhibitor TAK-243 completely blocked IP₃R1 ubiquitination and degradation without altering erlin1/2 complex association, confirming that association of the erlin1/2 complex is the primary event that initiates IP₃R1 processing and that IP₃R1 ubiquitination mediates IP₃R1 degradation. Overall, these data localize the erlin1/2 complex–binding site on IP₃R1 to IL3 and show that the region immediately adjacent to TM5 is key to the events that facilitate channel opening.