高黎贡山不同土地利用方式对土壤 微生物数量和多样性的影响

测定了高黎贡山不同利用方式土壤中微生物的数量、小型真菌的多样性和属的分布,分析了上述指标在不同利用方式土壤中的分布与人为干扰和环境因素之间的相互关系。结果表明微生物数量和真菌的多样性在不同利用方式土壤中的分布是,原生林(次生林(幼杉木纯林;耕作通常使条件更有利于土壤微生物生长繁殖,成熟人工纯林和旱地的土壤微生物数量及真菌多样性均较高;在五类利用方式中,土壤微生物数量及真菌多样性以原生林最高,荒地最低。     

塔克拉玛干沙漠腹地人工植被下土壤微生物的初步研究

在极端干旱的塔克拉玛干沙漠腹地利用矿化度为4～5 g/L的地下咸水灌溉,在风沙土上建立了人工绿地。对流沙和人工绿地中微生物三大类群（细菌、真菌和放线菌）进行了数量测定,结果显示：流沙上微生物数量很少,人工绿地的微生物数量显著增加;种植时间相同而植被类型不同的样地中的微生物数量有差异;微生物的组成中,细菌占绝大多数,达微生物总数的90%以上,其次是放线菌,真菌数量最少;表层微生物数量明显高于下层。人工绿地微生物数量的变化,说明风沙土已逐步向具有一定肥力水平的土壤方向演变。     

甘孜州炉霍县不同植被土壤微生物特性初步研究

研究了四川省甘孜州炉霍县不同植被条件下土壤微生物群落的分布状况及两种土壤酶活情况。结果表明,不同植被条件下,土壤微生物类群数量存在差异,草甸土壤微生物群落比森林覆盖土壤的微生物群落多。在同一土壤中,细菌、真菌、放线菌数量随土层深度的增加而降低,0~20cm土层微生物数量高于20~40cm的土层。土壤酶活在土壤剖面中的分布随深度增加而降低。     

荒漠草原区土壤粒径组成对柠条根际土壤微生物数量及酶活性的影响

柠条(Caragana korshinskii)是荒漠草原区主要的造林绿化树种,研究其根际土壤微生物和酶活性与不同土壤类型土壤粒径组成的关系有重要意义,然而土壤粒径对荒漠草原柠条根际土壤微生物数量和酶活性的影响知之甚少,探讨土壤颗粒组分与微生物数量、土壤酶活性之间的关系,以及土壤颗粒组成对荒漠草原区固沙灌木植物柠条根际土壤微生物数量及酶活性的影响,可为揭示荒漠草原土壤退化及生态修复提供参考。以宁夏荒漠草原区土壤粒径组成差异显著的灰钙土、红黏土、风沙土环境下栽植的柠条为研究对象,研究不同土壤颗粒组成对根际土壤微生物数量及酶活性的相互关系与影响。结果表明:土壤微生物的数量表现为细菌放线菌真菌。根际土壤中的细菌、真菌数量显著高于非根际,且在3种不同类型的土壤中随着细砂粒的增多,真菌和放线菌数量逐渐降低,而细菌数量呈先增大后减小的趋势;根际与非根际土壤的蔗糖酶、碱性磷酸酶及过氧化氢酶活性均呈现出灰钙土红黏土风沙土的趋势,红黏土根际土壤中的脲酶活性显著高于灰钙土与风沙土;除过氧化氢酶外,土壤酶活性表现为根际高于非根际,在3种不同类型的土壤中随着细砂含量的增加,土壤酶活性均呈递减趋势。土壤颗粒组成与微生物数量之间没有明显的相关性,而与土壤酶活性之间显著相关,土壤酶活性与黏粒、粉粒呈正相关,与细砂、中砂呈负相关关系,根际土壤中酶活性更高,能够为植物及微生物提供更多的营养。     

不同植被恢复模式对铁尾矿微生物和酶活性的影响

对河北省迂安市马兰庄镇铁尾矿不同恢复模式土壤微生物和酶活性进行了分析。结果表明：不同铁尾矿中主要微生物数量存在显著差异,在总体数量上,细菌最多,放线菌次之,真菌较少;在表层0～20cm,土壤微生物数量和土壤酶活性均表现为人工林〉自然恢复〉新尾矿;土壤微生物数量和土壤酶活性随采样深度的增加而显著降低;尾矿土壤微生物和土壤酶之间均呈正相关,但相关程度有所不同。自然恢复和人工林恢复均能够增加尾矿库的微生物数量和土壤酶活性,人工林的恢复效果高于自然恢复。     

近三年微生物多样性研究进展（英文）

综述了近三年来微生物多样性研究领域的研究进展,对不同年份相关文章的数量、不同数据库中相关文章的数量以及作者倾向于选择的不同微生物多样性研究对象的相关文章的数量进行了统计。文中针对微生物多样性研究领域作者选择的不同研究重点进行了分类和归纳,并且对其研究结果进行了简要介绍。为研究者提供了近年来微生物多样性研究的大致框架,为研究对象的选择和研究重点的设定提供依据。     

桂林会仙喀斯特湿地芦苇群落土壤微生物数量动态分析

以广西桂林会仙喀斯特湿地典型芦苇植物群落为研究对象,于春、夏、秋、冬四个季节分别采集0~10cm,10~20 cm和20~30 cm不同层次的土壤样品,分析根际微生物与非根际微生物的数量特征及季节动态变化特点,探讨微生物数量对水热季节变化的响应规律。结果表明:不同季节的根际微生物与非根际微生物组成,均以细菌占绝对优势;微生物数量分布大小顺序为细菌放线菌真菌,细菌最高比例为96.62%,放线菌最高比例为35.38%,真菌的比例较低,最高仅为0.30%。细菌,真菌和放线菌的垂直变化明显,均随着土层的增加而呈现递减的趋势。不同土壤层次根际微生物与非根际微生物的季节变化一致,细菌数量表现为夏季秋季春季冬季,真菌数量表现为秋季夏季春季冬季,放线菌数量表现为秋季春季夏季冬季;细菌、放线菌、真菌的最大值分别为2.70×10~7、1.92×10~6、3.35×10~4cfu·g~-1,土壤微生物数量与土壤有机碳、全氮、全磷、全钾、速效氮、速效磷、速效钾等呈显著正相关。芦苇植物群落根际土壤微生物呈现出一定的根际效应,并与微生物数量、土壤深度、月平均降雨量和月平均气温变化等有关,而在冬季的根际效应则表现不显著。土壤养分含量是调节会仙喀斯特湿地土壤微生物数量变化的一个主要因素。     

短期放牧对草甸草原土壤微生物与土壤酶活性的影响

【目的】为呼伦贝尔草甸草原生态系统的保护、恢复及重建提供微生物学基础数据。了解草原土壤微生物和酶活性对放牧强度的响应。【方法】分别采集六个不同放牧强度的土壤样品,测定土壤微生物数量、土壤微生物量和土壤酶活性,分析短时期不同放牧强度土壤微生物数量、土壤微生物量和土壤酶活性的变化特征及其相互关系。【结果】不同放牧强度下,菌群数量分布为细菌>放线菌>真菌;土壤微生物数量、微生物量均表现为放牧区高于对照区;在土壤表层(0 10 cm),土壤过氧化氢酶、转化酶和蛋白酶活性表现出随放牧强度的增加先上升后略降的趋势,且放牧区均高于对照区,与土壤表层比较,在较深层(10 cm 20 cm),土壤细菌、真菌的数量和微生物量碳、氮下降幅度随放牧强度的增大而增大。土壤微生物数量、微生物量及土壤酶活性的垂直分布为0 10 cm>10 cm 20 cm。相关分析结果表明:放牧干扰条件下,土壤微生物数量与微生物量之间均存在显著或极显著的相关性。土壤酶活性与微生物数量、微生物量密切相关,过氧化氢酶、转化酶与细菌、放线菌极显著相关(P<0.01)、与微生物量碳显著相关(P<0.05);蛋白酶与真菌及微生物量碳、氮极显著相关(P<0.01),与细菌显著相关(P<0.05)。【结论】适度放牧可使土壤微生物数量、微生物量和土壤酶活性增加。土壤微生物数量、微生物量与土壤酶活性之间具有密切关系。     

东天山地区庙儿沟雪坑中微生物多样性、群落结构与环境关系研究

通过荧光计数、恢复培养和变形梯度凝胶电泳(DGGE),分析了东天山地区庙儿沟不同深度积雪中的可培养细菌数量、多样性及其群落结构。结果表明,东天山地区冰雪微生物数量和多样性指数与气候环境替代指标钙离子、镁离子、氯离子等具有相关性。该地区雪坑中细菌隶属于4个不同系统发育群:proteobacteria(α-,β-,γ-),CFB,HGC和LGC,其中CFB类和proteobacteria类为主要类群。与青藏高原、南北极冰雪中微生物的比较分析发现Paracoccu和Aquasalina属是该地区的特殊微生物类群。直接培养和DGGE分析发现不同深度雪坑中微生物数量和群落结构都有明显的变化。结果表明,由于东天山地区的特殊地理位置,该地区冰雪微生物具有其特殊性。     

冰川微生物菌群分布的研究概况及其前景

冰川中以耐冷的生物为主,形成一个以微生物为主要生命形式的相对简单的生态系统.冰川中的微生物包括病毒、细菌、放线菌、丝状真菌、酵母菌和藻类.其中一些病毒对人类健康具有潜在的危害性.着重论述了不同区域和不同海拔高度的冰川微生物类群和数量分布特征以及冰芯（深冰川）细菌菌群分布与气候环境的关系.综述结果表明：一些微生物类群广泛存在于各地的冰川上,具有全球分布特性;另一些类群只出现在个别冰川上,为一些地方性冰川微生物.随着海拔高度的增加,冰川上呈现出冰、雪冰和雪环境明显不同的生态条件;微生物类群分布也具有明显的差异性,与冰川上的生态条件和盛行的风向有关.优势类群对冰、雪冰和雪环境具有一定的指示意义.冰川微生物数量分布不仅受到冰川上的水热、光照和营养状况的影响,还与降雪的沉积作用有关.冰芯中的细菌数量与矿物微粒含量具有密切的对应关系.最后指出了冰川微生物研究在基因多样性、气候环境变化、生物地球化学循环、微生物对环境变化的响应机制和星际生命探索中的重要性及其生态学和社会经济意义.     

高粱和苏丹草酯酶同工酶分析

采用聚丙烯酰胺凝胶电（PAGE）分析了6个高粱和4个苏丹草的酯酶同工酶差异,并通过聚类分析方法对10个品种的种质关系进行分层聚类。结果表明酯酶同工酶谱可以作为鉴别苏丹草和高粱的有效生化标记。     

Proteomic analysis of formalin-fixed, paraffin-embedded lung neuroendocrine tumor samples from hospital archives

Hospital tissue repositories host an invaluable supply of diseased samples with matched retrospective clinical information. In this work, a recently optimized method for extracting full-length proteins from formalin-fixed, paraffin-embedded (FFPE) tissues was evaluated on lung neuroendocrine tumor (LNET) samples collected from hospital repositories. LNETs comprise a heterogeneous spectrum of diseases, for which subtype-specific diagnostic markers are lacking. Six archival samples diagnosed as typical carcinoid (TC) or small cell lung carcinoma (SCLC) were subjected to a full-length protein extraction followed by a GeLC-MS/MS analysis, enabling the identification of over 300 distinct proteins per tumor subtype. All identified proteins were categorized through DAVID software, revealing a differential distribution of functional classes, such as those involved in RNA processing, response to oxidative stress and ion homeostasis. Moreover, using spectral counting for protein abundance estimation and beta-binomial test as statistical filter, a list of 28 differentially expressed proteins was generated and submitted to pathway analysis by means of Ingenuity Pathway Analysis software. Differential expression of chromogranin-A (more expressed in TCs) and stathmin (more expressed in SCLCs) was consistently confirmed by immunohistochemistry. Therefore, FFPE hospital archival samples can be successfully subjected to proteomic investigations aimed to biomarker discovery following a GeLC-MS/MS label-free approach.     

Public proteomic MS repositories and pipelines: available tools and biological applications

As proteomic MS has increased in throughput, so has the demand to catalogue the increasing number of peptides and proteins observed by the community using this technique. As in other 'omics' fields, this brings obvious scientific benefits such as sharing of results and prevention of unnecessary repetition, but also provides technical insights, such as the ability to compare proteome coverage between different laboratories, or between different proteomic platforms. Journals are also moving towards mandating that proteomics data be submitted to public repositories upon publication. In response to these demands, several web-based repositories have been established to store protein and peptide identifications derived from MS data, and a similar number of peptide identification software pipelines have emerged to deliver identifications to these repositories. This paper reviews the latest developments in public domain peptide and protein identification databases and describes the analysis pipelines that feed them. Recent applications of the tools to pertinent biological problems are examined, and through comparing and contrasting the capabilities of each system, the issues facing research users of web-based repositories are explored. Future developments and mechanisms to enhance system functionality and user-interfacing opportunities are also suggested.     

Application of 2-D DIGE to formalin-fixed, paraffin-embedded tissues

The ability to investigate the proteome of formalin-fixed, paraffin-embedded (FFPE) tissues can be considered a major recent achievement in the field of clinical proteomics. However, gel-based approaches to the investigation of FFPE tissue proteomes have lagged behind, mainly because of insufficient quality of full-length protein extracts. Here, the 2-D DIGE technology was investigated for applicability to FFPE proteins, for internal reproducibility among replicate FFPE extracts, and for comparability between FFPE and fresh-frozen tissue profiles. The 2-D DIGE patterns obtained upon labeling and electrophoresis of replicate FFPE tissue extracts were highly reproducible, with satisfactory resolution and complexity. Moreover, the implementation of DIGE enabled to highlight and characterize the consistent differences found in the FFPE profiles compared with fresh-frozen profiles, represented by an acidic shift, directly correlated to the protein pI value, and by a reduction in spot signal intensity, directly correlated to molecular weight and percentage of lysine residues. Being constantly and reproducibly present in all FFPE tissue extract replicates at similar extents, these modifications do not appear to hinder the comparative analysis of FFPE tissue extracts by 2-D DIGE, opening the way to its application for the differential proteomic investigation of archival tissue repositories.     

Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens

The use of next-generation sequencing technologies to produce genomic copy number data has recently been described. Most approaches, however, reply on optimal starting DNA, and are therefore unsuitable for the analysis of formalin-fixed paraffin-embedded (FFPE) samples, which largely precludes the analysis of many tumour series. We have sought to challenge the limits of this technique with regards to quality and quantity of starting material and the depth of sequencing required. We confirm that the technique can be used to interrogate DNA from cell lines, fresh frozen material and FFPE samples to assess copy number variation. We show that as little as 5 ng of DNA is needed to generate a copy number karyogram, and follow this up with data from a series of FFPE biopsies and surgical samples. We have used various levels of sample multiplexing to demonstrate the adjustable resolution of the methodology, depending on the number of samples and available resources. We also demonstrate reproducibility by use of replicate samples and comparison with microarray-based comparative genomic hybridization (aCGH) and digital PCR. This technique can be valuable in both the analysis of routine diagnostic samples and in examining large repositories of fixed archival material.     

A comparative evaluation of technical solutions for long-term data repositories in integrative biodiversity research

The current study investigates existing infrastructure, its technical solutions and implemented standards for data repositories related to integrative biodiversity research. The storage and reuse of complex biodiversity data in central databases are becoming increasingly important, particularly in attempts to cope with the impacts of environmental change on biodiversity and ecosystems. From the data side, the main challenge of biodiversity repositories is to deal with the highly interdisciplinary and heterogeneous character of standardized and unstandardized data and metadata covering information from genes to ecosystems. Furthermore, the technical improvements in data acquisition techniques produce ever larger data volumes, which represent a challenge for database structure and proper data exchange.The current study is based on comprehensive in-depth interviews and an online survey addressing IT specialists involved in database development and operation. The results show that metadata are already well established, but that non-meta data still is largely unstandardized across various scientific communities. For example, only a third of all repositories in our investigation use internationally unified semantic standard checklists for taxonomy. The study also showed that database developers are mostly occupied with the implementation of state of the art technology and solving operational problems, leaving no time to implement user's requirements. One of the main reasons for this dissatisfying situation is the undersized and unreliable funding situation of most repositories, as reflected by the marginally small number of permanent IT staff members. We conclude that a sustainable data management system that fosters the future use and reuse of these valuable data resources requires the development of fewer, but more permanent data repositories using commonly accepted standards for their long-term data. This can only be accomplished through the consolidation of hitherto widely scattered small and non-permanent repositories.     

Centralized mouse repositories

Because the mouse is used so widely for biomedical research and the number of mouse models being generated is increasing rapidly, centralized repositories are essential if the valuable mouse strains and models that have been developed are to be securely preserved and fully exploited. Ensuring the ongoing availability of these mouse strains preserves the investment made in creating and characterizing them and creates a global resource of enormous value. The establishment of centralized mouse repositories around the world for distributing and archiving these resources has provided critical access to and preservation of these strains. This article describes the common and specialized activities provided by major mouse repositories around the world.     

Flow cytometric DNA ploidy analysis of soft tissue sarcomas. A comparative study of preoperative fine needle aspirates and postoperative fresh tissues and archival material

Flow cytometric (FCM) DNA ploidy measurements on frozen fresh samples of soft tissue sarcomas were compared with the corresponding analyses on preoperative fine needle aspirates and postoperative formalin-fixed archival tissues from the same tumors. A concordance in ploidy status (diploid versus non-diploid) was obtained for 63% of the fresh tissue-fine needle aspiration (FNA) sample comparisons and for 85% of the fresh tissue-archival material comparisons. The majority of discordances in the fresh tissue-FNA sample comparisons could be explained by FNA sampling errors. In the remaining discordant cases (3 of 27 FNA sample comparisons and 6 of 40 archival material comparisons), sampling errors could not explain the differences in ploidy status. The discordant cases were evenly distributed among the different sampling methods. Method reproducibility was not responsible for the differences in ploidy determinations; tumor heterogeneity may be an explanation for the discrepancies. This study showed that archival soft tissue sarcoma samples are as well suited for DNA ploidy analysis as are fresh frozen tissues.     

The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine

Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system‐wide observations, and cross‐species observational studies, but pigs have so far been underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within the veterinary proteomics domain, and this article demonstrates how the expression of isoform‐unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM assays, which are equally important for progress in research that supports farm animal production and veterinary health, as for developing pig models with relevance to human health research.