基因工程微生物生态学研究进展

基因工程微生物(genctically enginccred microorganism,GEM)生态学的研究已成为微生物分子生态学的一项主要研究内容之一．随着分子标记和分子生物学检测手段的引入,传统的微生物生态学研究被注入了新的活力,在分子水平上探讨基因工程微生物与环境及环境中土著生物之间的关系已成为可能．基因工程微生物生态学是一门内容涉及分子生物学、微生物学、生态学等诸多学科的新型交叉边缘学科．本文提出加紧进行转基因生物生态学和转基因生物的风险评价的研究工作,建立适合中国国情的检测手段和评价标准,有助于我国基因工程微生物生态学的健康发展．     

基因工程生物的生态影响及其评价

随着基因工程技术的迅速发展,基因工程产生的生物将被广泛地应用于非受控的自然环境中,这将带来诸多的环境和生态方面的问题。本文概述了基因工程生物在非受控环境下可能产生的生态影响,提出了“基因工程生态学”这一新的应用生态学分支领域,探讨了该分支学科的概念、主要研究内容和目标,以及当前应采取的研究策略,并就发展基因工程生态学的有关问题提出了建议。     

土壤微生物群落构建理论与时空演变特征

土壤微生物作为陆地生态系统的重要组成部分,直接或间接地参与几乎所有的土壤生态过程,在物质循环、能量转换以及污染物降解等过程中都发挥着重要作用。对土壤微生物时空演变规律及其形成机制的研究,不仅是微生物演变和进化的基础科学问题,也是预测微生物及其所介导的生态功能对环境条件变化响应、适应和反馈的理论依据。讨论了土壤微生物群落的定义、测度方法和指标,认为群落是联系动植物宏观生态学与微生物生态学的基础,群落构建机制是宏观和微观生态学都需要研究的核心科学问题;从生态学的群落构建理论出发,阐述了包括生态位理论/中性理论、过程理论和多样性-稳定性理论在土壤微生物时空演变研究中的应用,以及微生物群落在时间和空间上的分布特征及其尺度效应;确立了以微生物群落构建理论为基础、不同时空尺度下土壤微生物群落演变特征为主要内容的微生物演变研究的基本框架。     

试论原子生态学成为一门生态学分支学科的可能性

生态学依其原来的含义 ,是指生物与其所存在的环境条件之间相互关系的科学 ,这属传统生态学 ,即常称的生态学。由于国内的微生物生态学有很大的发展 ,而微生物又多是单细胞性的 ,这就使人们考虑微生物生态学应扩展为包括高等生物作为细胞性生命单元的细胞在内 ,这就使微生物生态学变为包括高等生物细胞在内的细胞水平的生态学了。这里显然出现了生态学的层次性问题 ,那就是宏观群体水平的生态学 ,微观细胞水平的生态学和超微观分子水平的生态 ;现在一般所称的绿色生态 (包括绿化生态和农业生态 )、兰色生态 (海洋生态 )和白色生态(塑料袋生…     

中国微生物生态学的进展——《微生物生态学专刊》序言

2014年10月在北京召开的“2014年中国生态学会微生物生态专业委员会暨国际学术研讨会”标志着我国微生物生态学研究专业学术组织已经走过了30年的历程。经过几代微生物生态学研究者的不懈努力,我国的微生物生态学从无到有,不断开拓和发展,使得我国微生物生态学研究的队伍不断壮大,在若干方向的研究水平处于国际前沿。为了展现我国微生物生态学研究的最新进展,《微生物学通报》针对本次研讨会组织出版了本期“微生物生态学专刊”,以期促进微生物生态学及相关交叉研究领域的发展。     

空间分析方法在微生物生态学研究中的应用

微生物生态正在受到越来越多的关注,对其研究也渐趋深入。然而由于微生物个体微小的特点及研究手段的限制,多数研究还停留在探索阶段,研究方法也在不断完善当中。近年来,较多的研究开始探讨空间因素在微生物多样性和分布中的影响,对空间分布的探讨有助于更好地认识生态过程,是一种有力的研究手段。微生物空间分析方法已经成为微生物生态学领域中重要的研究方向之一,我国空间方法在微生物生态研究中的应用还没有得到普遍的重视。从不同研究角度出发,结合空间统计的作用,对空间统计方法在微生物生态研究中的应用的必要性及现状做了评述。介绍了空间自相关性的检验,方差图,Mantel检验,Kriging插值等方法在微生物生态研究中的应用,并论述了微生物研究中的尺度问题。这一梳理,对丰富微生物生态学研究中的新方法、新手段具有一定价值。     

海洋微生物的化学生态学研究进展

近年来,海洋生物的化学生态学研究已成为国际化学生态学研究的亮点之一.该领域的研究不仅为生物进化研究提供了理论依据,也对海洋生态养殖、海洋生态环境保护以及海洋资源的可持续发展具有重要意义.本文从海洋动物、植物、微生物三方面综述了它们与海洋微生物之间的化学生态学关系.海洋动物与微生物的化学生态学作用主要包括抗菌、抗附着、共生3种关系.以发现具有生态学效应的化学信号物质的分子结构为主线,介绍了海洋植物和微生物方面的研究进展,并对该领域的关键性问题和发展方向进行了展望.     

土壤生态系统微生物多样性-稳定性关系的思考

自20世纪50年代以来,生物多样性与生态系统稳定性的关系一直是生态学中重点讨论的理论问题之一.在当今人类活动对自然生态系统产生重大影响的情况下,全面理解生态系统多样性与稳定性的关系,有助于我们更好地应对环境变化和生物多样性丧失等生态问题.在陆地生态系统中,关注重点多集中在地上植物生态系统;而对地下生态系统,尤其是对微生物多样性与系统稳定性关系的研究尚重视不够.事实上,土壤微生物作为生命元素循环的驱动者,主导和参与地下生态系统中一系列重要生态过程,对土壤能否正常有序地执行各项生态功能至关重要.对土壤微生物多样性的研究,能使我们明确土壤中微生物对各种环境条件(包括自然和人为因素)变化的响应机制,更好地维持土壤生态系统的稳定性及其生态服务功能.本文在介绍土壤微生物多样性概念、研究方法、地下生态系统稳定性的基础上,重点讨论了土壤微生物多样性对土壤生态系统稳定性的影响,对多样性-稳定性关系在土壤微生物生态学中的应用进行了较为深入和全面的思考.作者提出,土壤微生物系统是一个动态变化的自组织系统,通过遗传来维持其组成和结构的相对稳定性,通过变异而适应外界干扰,共同构成土壤微生物系统的抵抗力(resistance)和恢复力(resilience),维护土壤生态系统的稳定性.今后土壤微生物多样性-稳定性关系的研究,需要注重地上与地下生态系统的结合与统一,借鉴宏观生态学理论来构建微生物生态学的理论框架,建立微生物多样性-稳定性关系的机理模型,从定性描述向定量表征方向发展.     

微生物生态学驱动社会与经济“绿色高效发展”

面对物种数量繁多、生态分布广泛、生态功能强大的微生物资源,微生物生态学的任务一方面在于不断发现和认识这类生命"暗物质"及其存在机制,另一方面要充分挖掘和利用这些微生物资源。微生物生态学的应用从最早的混合发酵发展到极端微生物资源利用、微生物生态制剂开发逐渐拓展到合成微生物生态等多个领域。2019年10月在湖南省长沙市举行的"中国生态学学会微生物生态专业委员会学术年会"设立了3个与微生物生态学应用相关的分会场,本期《微生物学通报》也开辟了"人工生态系统微生物"栏目,凸显了我国微生物生态学在资源、能源和环境等应用领域的成果,让我们看到了其成为社会与经济"绿色高效发展"重要驱动力的希望。     

《生态学报》征订启事

《生态学报》是中国生态学学会主办的综合性学术刊物,创刊于1981年。主要报道动物生态、植物生态、微生物生态、农业生态、森林生态、草地生态、土壤生态、海洋生态、淡水生态、景观生态、区域生态、化学生态、污染生态、经济生态、系统生态、城市生态、人类生态等生态学各领域的学术论文;能反映现代生态学发展方向的优秀综述性文章;原创性研究报告和研究简报;生态学新理论、新方法、新技术介绍;新书评介和学术、科研动态及开放实验室介绍等。     

MBR运行初期对基因工程菌的截留特性研究

在膜-生物反应器(MBR)中实施基因工程菌生物强化时,运行初期基因工程菌流失是生态风险评价的重要内容.在一体式微滤膜-生物反应器中,考察了运行初期不同运行条件对基因工程菌流失密度和截留效率的影响,并对截留特性进行了探讨.结果表明,膜-生物反应器运行初期,不同运行条件对基因工程菌的截留效率影响不同:污泥浓度增加,截留效率提高;提高膜通量和曝气量,截留效率降低.基因工程菌接种密度为1.0×1010CFU/mL时,不同运行条件下的流失密度为1.0×102 CFU/mL～2.5×102 CFU/mL,最大截留效率大于8 lg.膜-生物反应器运行初期,膜组件截留、污泥吸附以及对悬浮细胞迁移阻碍是影响截留效率的主要因素,一定条件下其截留效率贡献率分别为82.3%、14.9%和2.8%.膜-生物反应器稳定运行过程中形成凝胶层,可以提高截留效率.一定条件下,膜组件、污泥和凝胶层对基因工程菌的截留贡献率分别为75.3%、10.7%和14.0%.     

MBR运行初期对基因工程菌的截留特性研究

在膜-生物反应器(MBR)中实施基因工程菌生物强化时, 运行初期基因工程菌流失是生态风险评价的重要内容。在一体式微滤膜-生物反应器中, 考察了运行初期不同运行条件对基因工程菌流失密度和截留效率的影响, 并对截留特性进行了探讨。结果表明, 膜-生物反应器运行初期, 不同运行条件对基因工程菌的截留效率影响不同：污泥浓度增加, 截留效率提高; 提高膜通量和曝气量, 截留效率降低。基因工程菌接种密度为1.0×1010 CFU/mL时, 不同运行条件下的流失密度为1.0×102 CFU/mL~2.5×102 CFU/mL, 最大截留效率大于8 lg。膜-生物反应器运行初期, 膜组件截留、污泥吸附以及对悬浮细胞迁移阻碍是影响截留效率的主要因素, 一定条件下其截留效率贡献率分别为82.3%、14.9%和2.8%。膜-生物反应器稳定运行过程中形成凝胶层, 可以提高截留效率。一定条件下, 膜组件、污泥和凝胶层对基因工程菌的截留贡献率分别为75.3%、10.7%和14.0%。     

GEM: a generic ecological model for estuaries and coastal waters

The set-up, application and validation of a generic ecological model (GEM) for estuaries and coastal waters is presented. This model is a comprehensive ecological model of the bottom of the foodweb, consisting of a set of modules, representing specific water quality processes and primary production that can be combined with any transport model to create a dedicated model for a specific ecosystem. GEM links different physical, chemical and ecological model components into one generic and flexible modelling tool that allows for variable sized, curvilinear grids to accomodate both the requirements for local accuracy while maintaining a relatively short model run-time. The GEM model describes the behaviour of nutrients, organic matter and primary producers in estuaries and coastal waters, incorporating dynamic process modules for dissolved oxygen, nutrients and phytoplankton. GEM integrates the best aspects of existing Dutch estuarine models that were mostly dedicated to only one type of ecosystem, geographic area or subset of processes. Particular strengths of GEM include its generic applicability and the integration and interaction of biological, chemical and physical processes into one predictive tool. The model offers flexibility in choosing which processes to include, and the ability to integrate results from different processes modelled simultaneously with different temporal resolutions. The generic applicability of the model is illustrated using a number of representative examples from case studies in which the GEM model was successfully applied. Validation of these examples was carried out using the ‘cost function’ to compare model results with field observations. The validation results demonstrated consistent accuracy of the GEM model for various key parameters in both spatial dimensions (horizontally and vertically) as well as temporal dimensions (seasonally and across years) for a variety of water systems without the need for major reparameterisation.

基因工程菌对阿特拉津的生物转化及其影响因素

研究考察了基因工程菌转化阿特拉津的共代谢碳源、转化动力学和影响因素。结果表明,作为共代谢碳源,葡萄糖优于乙酸盐,碳源浓度对转化影响不大,对工程菌生长影响显著。阿特拉津比转化速率与工程菌初始密度无关,与阿特拉津初始浓度有关,用Monod方程拟合转化动力学,求得方程参数为V_(max)=0．168/h,Ks= 30．49mg/L。降低温度会显著降低阿特拉津比转化速率;偏碱性的条件下,阿特拉津转化率较高,酸性条件严重抑制阿特拉津转化;盐度在一定范围内不影响转化活性;Co~(2 )、Fe~(2 )、Fe~(3 )和Zn~(2 )促进阿特拉津转化,Mn~(2 )、Ni~(2 )和Cu~(2 )抑制阿特拉津转化。菌体细胞对阿特拉津的吸附和转化作用呈正相关关系。     

Synergistic inhibition of pancreatic adenocarcinoma cell growth by trichostatin A and gemcitabine

We investigated the ability of the histone deacetylase (HDAC) inhibitor trichostatin A (TSA) to interact with gemcitabine (GEM) in inducing pancreatic cancer cell death. The combined treatment with TSA and GEM synergistically inhibited growth of four pancreatic adenocarcinoma cell lines and induced apoptosis. This effect was associated with the induction of reactive oxygen species (ROS) by GEM, increased expression of the pro-apoptotic BIM gene by both TSA and GEM and downregulation of the 5'-nucleotidase UMPH type II gene by TSA. The expression of other genes critical for GEM resistance (nucleoside transporters, deoxycytidine kinase, cytidine deaminase, and ribonucleotide reductase genes) was not affected by TSA. The functional role of ROS in cell growth inhibition by GEM was supported by (i) a significantly reduced GEM-associated growth inhibition by the free radical scavenger N-acetyl-L-cysteine, and (ii) a positive correlation between the basal level of ROS and sensitivity to GEM in 10 pancreatic cancer cell lines. The functional role of both Bim and 5'-nucleotidase UMPH type II in cell growth inhibition by TSA and GEM was assessed by RNA interference assays. In vivo studies on xenografts of pancreatic adenocarcinoma cells in nude mice showed that the association of TSA and GEM reduced to 50% the tumour mass and did not cause any apparent form of toxicity, while treatments with TSA or GEM alone were ineffective. In conclusion, the present study demonstrates a potent anti-tumour activity of TSA/GEM combination against pancreatic cancer cells in vitro and in vivo, strongly supporting the use of GEM in combination with an HDAC inhibitor for pancreatic cancer therapy.     

鼠李糖乳杆菌颗粒表面展示系统的构建

为了比较不同锚钩蛋白基序结合活性,构建新型的鼠李糖乳杆菌颗粒表面展示系统。首先,用热酸处理法制备鼠李糖乳杆菌GEM(Gram-positive enhancer matrix,GEM)颗粒,并通过电镜观察、RT-PCR检测和SDS-PAGE检测鉴定其处理效果;同时,利用大肠杆菌表达了锚定蛋白PA3-EGFP和P60-EGFP并将其与GEM颗粒共同孵育结合;最后,使用免疫印迹、电镜观察、荧光显微镜观察和荧光分光光度法评价鼠李糖乳杆菌GEM颗粒与锚定蛋白的结合效率。结果表明,使用10%的TCA处理鼠李糖乳杆菌得到了灭活的肽聚糖骨架(GEM颗粒),经鉴定其大小形态均一,绝大部分无蛋白残留,3.8×10~6个GEM颗粒样品中的DNA拷贝数仅为32;免疫印迹和荧光显微镜观察均可检测到融合蛋白PA3-EGFP和P60-EGFP锚定在GEM颗粒上,且结合在GEM颗粒表面的锚定蛋白呈絮状。荧光分光光度计法检测结果显示锚定蛋白PA3-EGFP结合GEM的效率稍高于P60-EGFP,但差异不显著(P0.05)。以上结果表明由鼠李糖乳杆菌制得的GEM颗粒与锚定蛋白PA3、P60的结合效率良好,可用于构建新型的外源蛋白表面展示系统,进而为后续的细菌样颗粒疫苗的研究与应用奠定基础。     

Dihydroartemisinin increases gemcitabine therapeutic efficacy in ovarian cancer by inducing reactive oxygen species

Ovarian cancer is the major cause of death in women gynecological malignancy and gemcitabine (GEM) is commonly used in related chemotherapy. However, more than 90% GEM is catalyzed into an inactive metabolite 2′-deoxy-2′,2′-difluorouridine by stromal and cellular cytidine deaminase (CDA). Dihydroartemisinin (DHA), which possesses an intramolecular endoperoxide bridge, could be activated by heme or ferrous iron to produce reactive oxygen species (ROS). The excess ROS generation will excite expression of heme oxygenase-1 and suppress CDA expression. Under low CDA expression, the inactivation of GEM is decreased in turn to exert excellent therapeutic efficiency. Herein, we first studied the ROS generation by DHA in vitro with A2780 cells by means of flow cytometry and confocal laser scanning microscopy. Furthermore, cytotoxicity assay in vitro showed that DHA + GEM had synergistic effect, with molar ratio of DHA and GEM at 10. Eventually, in A2780 ovarian cancer xenograft tumor model, DHA + GEM exhibited significant antitumor efficiency with lower blood toxicity than GEM alone. Noteworthy, the combination treatment group completely eliminated the tumors on day 14.     

Glycosylation affects translocation of integrin, Src, and caveolin into or out of GEM

Endogenous GM3 synthesis and full N-glycosylation in membrane receptors occurred in "4-epimerase-less" ldlD (Krieger's CHO mutant) cells cultured in Gal-containing medium, whereby components of detergent-insoluble, low-density, buoyant membrane fraction, termed "glycolipid-enriched microdomain (GEM)," varied significantly by translocation into or out of GEM. Integrins alpha3 and alpha5 were translocated into GEM in the presence of 0.5 or 0.25% Triton X-100, particularly in the absence of Gal, whereby integrins are underglycosylated and GlcCer is the major glycolipid component in GEM. Src family kinase was translocated into and enriched in GEM fractions when prepared in 0.5 or 0.25% Triton X-100 from cells grown in Gal-containing medium, whereby GM3 synthesis is induced. In contrast, caveolin is highly enriched in GEM when GM3 synthesis does not occur, and is translocated into high-density membrane fraction when GM3 synthesis occurs. The results suggest that levels of key molecules controlling cell adhesion and signaling are defined by translocation into or out of GEM, which depends on glycosylation state.     

Rapid oxidation of ring methyl groups is the primary mechanism of biotransformation of gemfibrozil by the fungus <Emphasis Type="Italic">Cunninghamella elegans</Emphasis>

The hypolipidemic agent gemfibrozil (GEM), which has been studied for its metabolism in humans and animals, was investigated to elucidate its primary metabolism by Cunninghamella elegans. The fungus produced ten metabolites (FM1–FM9 and FM6′) from the biotransformation of GEM. Based on LC/MS/MS and NMR analyses, a major metabolite, FM7, was identified as 2′-hydroxymethyl GEM. FM6 was considered to be 5′-hydroxymethyl GEM, after comparison of results LC/MS, LC/MS/MS, and UV absorption spectra to FM7. The combined concentration of FM6 and FM7 was found to increase up to 0.83 mM by day 2, and then decreased gradually with incubation time, followed by a noticeable increase in the biotransformation product, FM1, up to 0.86 mM by day 15. NMR analyses confirmed that FM1 was 2′,5′-dihydroxymethyl GEM. Further minor oxidations of the aromatic ring and carboxylic acid intermediates were also detected. Based upon these findings, the major fungal metabolic pathway for GEM is likely to occur via production of 2′,5′-dihydroxymethyl GEM from 2′-hydroxymethyl GEM. These relatively rapid and diverse biotransformations of GEM by C. elegans suggest that depending upon conditions, it may also follow a similar biodegradation fate when released into the natural environment.     

Cell growth regulation through GM3-enriched microdomain (glycosynapse) in human lung embryonal fibroblast WI38 and its oncogenic transformant VA13

Cell growth control mechanisms were studied based on organization of components in glycosphingolipid-enriched microdomain (GEM) in WI38 cells versus their oncogenic transformant VA13 cells. Levels of fibroblast growth factor receptor (FGFR) and cSrc were 4 times and 2-3 times higher, respectively, in VA13 than in WI38 GEM, whereas the level of tetraspanin CD9/CD81 was 3-5 times higher in WI38 than in VA13 GEM. Csk, the physiological inhibitor of cSrc, was present in WI38 but not in VA13 GEM. Functional association of GEM components in control of cell growth in WI38 is indicated by several lines of evidence. (i) Confluent, growth-inhibited WI38 showed a lower degree of FGF-induced MAPK activation than actively growing cells in sparse culture. (ii) The level of inactive cSrc (with Tyr-527 phosphate) was higher in confluent cells than in actively growing cells. Both processes i and ii were inhibited by GM3 since they were enhanced by GM3 depletion with d-threo-1-phenyl-2-palmitoylamino-3-pyrrolidino-1-propanol (P4). (iii) The high level of inactive cSrc associated with growth-inhibited cells was caused by coexisting Csk in WI38 GEM. (iv) Interaction of GM3 with FGFR was demonstrated by binding of GM3 to FGFR in the GEM fraction, as probed with GM3-coated beads, and by confocal microscopy. In contrast to WI38, both cSrc and MAPK in VA13 were strongly activated regardless of FGF stimulation or GM3 depletion by P4. Continuous, constitutive activation of both cSrc and MAPK was due to (i) a much higher level of cSrc and FGFR in VA13 than in WI38 GEM, (ii) their close association/interaction in VA13 GEM as indicated by clear coimmunoprecipitation between cSrc and FGFR, and (iii) the absence of Csk in VA13 GEM, making GEM incapable of inhibiting cSrc activation.