Proteomics in environmental and technical microbiology

Nowadays, the field of proteomics encompasses various techniques for the analysis of the entirety of proteins in biological samples. Not only 2D electrophoresis as the primary method, but also MS‐based workflows and bioinformatic tools are being increasingly applied. In particular, research in microbiology was significantly influenced by proteomics during the last few decades. Hence, this review presents results of proteomic studies carried out in areas, such as fundamental microbiological research and biotechnology. In addition, the emerging field of metaproteomics is addressed because high‐throughput genome sequencing and high‐performance MS facilitate the access to such complex samples from microbial communities as found in sludge from wastewater treatment plants and biogas plants. Both current technical limitations and new concepts in this growing and important area are discussed. Moreover, it was convincingly shown that future prospective applications of proteomics in technical and environmental microbiology might also be closely connected with other Omics approaches as well as bioinformatics for systems biology studies.     

Optimal experimental design for a nonlinear response in environmental toxicology

A start-stop experiment in environmental toxicology provides a backdrop for this design discussion. The basic problem is to decide when to sample a nonlinear response in order to minimize the generalized variance of the estimated parameters. An easily coded heuristic optimization strategy can be applied to this problem to obtain optimal or nearly optimal designs. The efficiency of the heuristic approach allows a straightforward exploration of the sensitivity of the suggested design with respect to such problem-specific concerns as variance heterogeneity, time-grid resolution, design criteria, and interval specification of planning values for parameters. A second illustration of design optimization is briefly presented in the context of concentration spacing for a reproductive toxicity study.     

纳米孔测序技术在环境微生物研究中的应用

高通量测序技术是研究环境微生物的有效手段,而以纳米孔测序为代表的第三代测序技术以其测序读长长、测序速度快、测序数据实时监控、仪器方便携带、无GC偏好性、无需经过PCR扩增等显著优势有力推动了环境微生物研究的发展.本文对纳米孔测序技术的技术原理和特点进行了简要概述,重点介绍了纳米孔测序技术在环境微生物扩增子测序、宏基因组...     

“环境工程微生物学”实验教学改革初探

"环境工程微生物学"是我国高校环境工程和环境科学专业的一门专业基础必修课,环境工程微生物学实验是本课程的重要组成部分。但目前环境工程微生物学实验教学中存在实验内容滞后、单调,学生的预习甚至实验过程往往流于形式,缺乏有效的考核方法等一系列问题。针对以上问题,作者采取将移动互联网引入环境工程微生物学实验,鼓励学生参与实验的前期准备等措施来改革传统教学模式,通过编写实验教材、精心安排实验内容、将科研带入到实际教学中等途径来优化教学内容,采用将平时成绩纳入最终实验成绩的方法来改革传统考核方式,取得了较好的教学效果,本文对以上教改内容进行详细阐述。     

“质量工程”背景下的环境工程微生物学实验教学改革探索

传统的环境工程微生物学实验在教学内容方面多是一些操作性和验证性的实验,在教学手段上多采用灌输式被动教学,这些教学内容和教学方式极大的抑制了学生的自主创新能力。作者结合自己的教学改革实践,以培养学生的自主创新兴趣和能力为目标,对环境工程微生物学实验进行了一系列教学改革尝试,并取得了良好的结果。在总结教学改革实践的基础上,从优化实验教学内容和改进教学方法两个方面进行系统阐述。     

Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology.

Fluorescent-dye-conjugated oligonucleotides were used to classify 14 Fibrobacter strains by fluorescence microscopy. On the basis of partial 16S rRNA sequences of six Fibrobacter strains, four hybridization probes were designed to discriminate between the species Fibrobacter succinogenes and Fibrobacter intestinalis and to identify F. succinogenes subsp. succinogenes. After in situ hybridization to whole cells of the six sequenced strains, epifluorescence microscopy confirmed probe specificity. The four probes were then used to make presumptive species and subspecies assignments of eight additional Fibrobacter strains not previously characterized by comparative sequencing. These assignments were confirmed by comparative sequencing of the 16S rRNA target regions from the additional organisms. Single-mismatch discrimination between certain probe and nontarget sequences was demonstrated, and fluorescent intensity was shown to be enhanced by hybridization to multiple probes of the same specificity. The direct detection of F. intestinalis in mouse cecum samples demonstrated the application of this technique to the characterization of complex natural samples.     

ELISAs for parasitologists: or lies, damned lies and ELISAs

The introduction in 1971, by Engvoll and Perlmann, of enzyme labels in immunoassays represented a significant technical advance. Their enzyme-linked immunosorbent assay (ELISA) proved to be as sensitive as radioimmunoossoys but safer to use. Since then, ELISAs have been widely used in the assay o f anti-bodies and antigens. In this article, Pradhib Venkateson and Derek Wokelin focus on some o f the problems associated with ELISAs when applied to parasitic infections, which can modify antibody responses, by immunosuppression or polyclonal activation. The article also considers optimization, which is an essential step in the establishment o f on ELISA.     

Scaling up: the next challenge in environmental microbiology

Great strides have recently been made in identifying and characterizing the staggering diversity of microorganisms conducting primary and secondary production, nutrient transformation and mineralization processes that underlie ecosystem and regional biogeochemical, trophodynamic and ecological change. We are now faced with the challenge of assigning and coupling function to structure in highly complex and interactive microbial communities mediating such change. Previous and ongoing ecophysiological work has shown that microbial processes controlled by environmental variables and limiting resources are highly specific in terms of what, when, where and why they are active, not to mention how they impact ecosystem dynamics. As such, it is imperative that we assess the activities and roles of key microbial 'players' along the appropriate environmental scales and gradients catalysing ecological change. Here, we discuss conceptual and technical challenges for some key microbially mediated environmental processes, problems and extremes that require synthesizing our growing knowledge of microbial community structure with emerging knowledge of function in aquatic ecosystems. We emphasize the importance of assessing ecological change over a range of relevant time scales that vary from minutes to millennia and spatial scales that range from microscale aggregates to ocean basins.     

Sometimes the result is not the answer: the truths and the lies that come from using the complementation test

It is standard genetic practice to determine whether or not two independently obtained mutants define the same or different genes by performing the complementation test. While the complementation test is highly effective and accurate in most cases, there are a number of instances in which the complementation test provides misleading answers, either as a result of the failure of two mutations that are located in different genes to complement each other or by exhibiting complementation between two mutations that lie within the same gene. We are primarily concerned here with those cases in which two mutations lie in different genes, but nonetheless fail to complement each other. This phenomenon is often referred to as second-site noncomplementation (SSNC). The discovery of SSNC led to a large number of screens designed to search for genes that encode interacting proteins. However, screens for dominant enhancer mutations of semidominant alleles of a given gene have proved far more effective at identifying interacting genes whose products interact physically or functionally with the initial gene of interest than have SSNC-based screens.