土壤原生动物研究方法

原生动物是土壤中形态和功能多样性高且占绝对优势的微型真核生物,在维持土壤生产力和生态系统功能上起着重要作用。随着研究方法的不断改进和创新,对土壤原生动物生态功能的认识已逐步加深。但缺乏统一且有效的定量分析方法仍是土壤原生动物生态学研究中的主要问题。本文综述相关的定量、定性以及群落结构与功能的研究方法,并着重介绍新技术方法,包括土壤定量蛋白银法、分子指纹图谱分析、同位素示踪技术,以及环境宏基因组学技术等。     

Methodological issues in the biological monitoring of urinary benzene and S-phenylmercapturic acid at low exposure levels

Biological monitoring of low level exposure to pollutants is a very challenging analytical activity, and the quality of results is difficult to assess, especially when a certified reference material is unavailable. The aim of this work was to evaluate the reliability of the assays used to measure urinary benzene (Benz-U) and S-phenylmercapturic acid (SPMA), by applying an internal quality control protocol. Urine spot samples from 705 subjects who were either members of the general urban population, gasoline station attendants, or refinery plant workers were assayed for Benz-U and SPMA, using GC/MS and LC/MS/MS, with quantification limits of 15 ng/L and 0.10 μg/L. The median Benz-U concentration was 263 ng/L (60-2789 ng/L, 5th-95th percentile), and the median SPMA concentration was 0.19 μg/L (<0.1-2.5 μg/L, 5th-95th percentile). Linearity of both assays was good, but a less-than-proportional response was found for SPMA concentrations below 1 μg/L. Between-run precision and accuracy for Benz-U concentration determination were assessed using quality controls at 120 ng/L and 1000 ng/L and were 10.3% and 4.8%, and 104.8% and 98.9%, respectively; while the precision and accuracy for SPMA concentration determination at 0.3 μg/L, 2.5 μg/L, and 20 μg/L were 40.3%, 6.2%, and 6.2%, and 48.3%, 96.3%, and 98.8%, respectively. Precision, estimated using duplicates of unknown samples, was 13.4% for Benz-U and 26.5% for SPMA analyses. Control charts for the means of the slope of the linear calibration curve of Benz-U showed good stability of the means over a five-year period. For SPMA, a two-laboratory comparison revealed acceptable agreement between ln-transformed data pairs, with a slope of the linear regression of 0.863 (confidence interval 0.774-0.952), null intercept, and a Pearson's r value of 0.844. Reliable results were obtained for Benz-U analyses over the entire concentration range, and for high and medium SPMA levels. However, the determination of SPMA concentrations at levels close to the limit of quantification was less reliable.     

Methodological issues in alpha biofeedback training

Current controversies concerning outcomes of EEG alpha feedback training are at least in part due to methodological differences among different studies. The aim of this paper is to provide future and present researchers in this field with an analysis of methods used in most of the studies published from 1968 to 1976, and to comment on those methodological issues we think most important. These include alpha assessment, training schedules, and uni- versus bidirectional training. This analysis is accomplished in part by a series of tables listing 45 studies and the detailed methodologies used. It is believed that the probabilities of successful feedback enhancement of alpha can be substantially improved by incorporating the following suggestions: (a) employing at least four training sessions, (b) the use of continuous rather than dichotomous feedback, supplemented by periodic quantitative scores of progress, and (c) using training trials of at least 10 minutes' duration.     

Methodological issues unsaid in medical research

Methodology consitutes the study of methods considered as < manners of leading its thought, of establishing or of showing truths according to certain principles and with a certain order >. We will see that medical < truths >, knowledge, could be of an extremely different nature: factual knowledge is a simple observation, often with operational vocation\; theoretical knowledge belongs to a coherent whole, it fascines and facilitates our representations of pathologies\; the causal knowledge is often the subject of extreme interrogations in medical practice\; it is of primarily metaphysical nature. These distinctions are not without consequence in methodological terms. Theories are useful because they facilitate the choice of the assumptions to be tested, the variables to be measured and the interpretation of the results of experiments. The risk however exists to be unable to think apart from their framework, and thus to neglect any source of knowledge which they could not integrate. The cause is inaccessible to science\; it will be necessary, in practice, to be limited to the search for variables of upstream on which action of prevention or cure could be undertaken. To establish, to show this medical knowledge, it is necessary to resort to the scientific method by formulating refutable assumptions by reproducible experiments, and that this process involves a belief in the found results. It appears thus that for the same experimental plan, the level of belief and thus the level of proof of the results is a function of the type of measurement carried out (commonplace measurement or of high technicality), of the medical discipline and the media character or not of studied pathology, even of stakes of being able. The medical reproducibility of experiments is problematic since results of these experiments are in general random. This results from the considerable number of variables entering in the determination of human pathologies, and that the majority of these variables are either unknown, or impossible to control. Randomisation makes it possible to give a probabilistic character to this risk: it is then possible to resort to mathematics to carry out statistical tests, to calculate confidence intervals and to profit from a possibility of making inferences with a known margin of error. In the absence of randomisation, it is possible to resort to models\; they imply however the knowledge of statistical methods, reserve, experience and a great intellectual honesty during the interpretation of the results, finally a replication of the experiments is here, more than elsewhere, essential.     

Methodological issues in pooled analysis of biomarker studies

The number of epidemiological studies involving biological markers has dramatically increased in the last years. These studies are generally small sized and this feature has called attention to the need to summarize the individual results, while waiting for the completion of larger studies, designed to answer questions that have been raised by preliminary studies. We describe here some of the methodological issues related to pooling data of biomarker studies, taking advantage of the experience accumulated by conducting two pooled analyses, one of studies of metabolic gene polymorphisms and cancer, the other on cytogenetic damage. Topics that are considered are: data standardization, population selection and bias, statistical analysis, ethical issues.Pooled analysis seems to provide a relevant improvement over meta-analysis in molecular epidemiology studies, though more research on methodology is needed.     

Autism genetics: Methodological issues and experimental design

Autism is a complex neuropsychiatric disorder of developmental origin, where multiple genetic and environmental factors likely interact resulting in a clinical continuum between affected and unaffected individuals in the general population. During the last two decades, relevant progress has been made in identifying chromosomal regions and genes in linkage or association with autism, but no single gene has emerged as a major cause of disease in a large number of patients. The purpose of this paper is to discuss specific methodological issues and experimental strategies in autism genetic research, based on fourteen years of experience in patient recruitment and association studies of autism spectrum disorder in Italy.     

基于生态位理论研究群落构建的方法进展

理解群落构建过程可以解释生物多样性格局的形成和维持,对于生物多样性保护起到关键作用。生态位理论是群落构建研究的核心框架之一。该理论认为群落构建是生物作用和非生物作用将区域物种库中的物种选入局域群落的确定过程。近年来,随着该领域受到的关注越来越多,研究者不但从物种、谱系或功能等生物多样性维度来研究群落构建,所使用的多样性指数、零模型算法和物种库界定方式等也多种多样。本文回顾了从生物多样性不同维度研究群落构建的优势与局限,总结了群落构建过程中构建零模型和界定物种库时需要注意的一些问题,介绍了部分群落构建研究的最新方法学进展和研究成果。最后,结合近年来的研究案例提出了对未来群落构建研究的一些建议。     

Recent advances in biological imaging

Recent innovations in microscopy and digital image processing have greatly enhanced the power of biological imaging. Basic principles of several new methods in light and electron microscopy will be discussed, and examples presented of their application to cell and molecular biology.     

Methodological advances in the discovery of protein and peptide disease markers

The quest for biomarkers has seen a renaissance due to the application of newly developed separation methodologies and advances in biomolecular mass spectrometry. It can be argued that each disease influences the physiology of an organism and that these changes should be measurable. Many diagnostic and therapeutic decisions are supported by measurable biochemical or cellular changes in plasma, serum or urine but it is unquestionable that there is a great lack in better markers for early disease detection and prevention. In this review we cover recent developments in the areas of separation science, sample preparation and mass spectrometry as applied to biomarker discovery. We focus, in particular, on the use of LC-MS and SELDI-TOF-MS as two approaches that have seen an upswing in recent years. While validation of newly discovered biomarkers or biomarker patterns and their introduction into diagnostic practice will be a long process, it is our believe that many future diagnostic tests will be based on markers discovered through novel profiling technologies as those outlined in this article.     

植物内生菌研究进展及其存在的问题

植物内生菌是一个多样性十分丰富的微生物类群 ,分布于没有外在感染症状的健康植物组织内 ,并与宿主植物协同进化 ,其存在和作用长期以来一直为人们所忽视。随着研究领域的不断拓宽和研究方法的不断深入 ,植物内生菌的生态和生理作用及其作为潜在的生防资源和外源基因载体 ,在农业和医药领域中的巨大应用潜力 ,已逐渐成为国内外研究的热点。本文综述了近 10年来国内外植物内生菌研究的概况和最新进展 ,并对该研究领域中存在的若干问题进行了探讨。     

Methodological issues with the interpolated twitch technique.

A number of methodological issues in the use of the interpolated twitch technique were investigated for their effect on true maximum force (TMF) and activation (ACT): timing of control (pre- vs post-contraction) and superimposed twitches (first vs second); type of twitch stimulus (primarily magnitude); and the type of extrapolation utilised. On three occasions subjects performed a series of maximal and sub-maximal contractions of the knee extensors, with electrically evoked twitches delivered before, during and after each contraction. The twitch-voluntary force relationship was concave for all types of twitch stimuli, and extrapolation using this relationship typically calculated TMF 39N (7%) higher, and ACT 7% lower than linear extrapolation. The timing of the control (2-4%) and superimposed twitches (approximately 4%) both influenced TMF and ACT. Despite the different twitch stimuli being a range of magnitudes (13-32% maximum voluntary force) they did not affect TMF and ACT. A novel finding was that prior potentiation changed the shape of the twitch-voluntary force relationship. For precise measurement of TMF and ACT it is recommended that: extrapolation is based on the twitch-voluntary force relationship of the experimental model; and post-contraction potentiated twitches be used, as the superimposed twitch on a high level contraction appears to be potentiated.     

Methodological issues related to thickness-based muscle size evaluation

The purpose of this study was to highlight the issues related to thickness-based muscle size evaluation that is commonly done in field studies. The cross-sectional area, thickness (the vertical distance from the upper end of the elbow flexors to that of the humerus) and width (the horizontal distance from the left to the right end of the elbow flexors) of the elbow flexors at levels from the reference site (60% of the upper arm length from the acromial process of the scapula to the lateral epicondyle of the humerus) to 5 cm distal to it were determined in 11 young men using magnetic resonance imaging, both at rest and during isometric elbow flexion at 30% of maximal voluntary contraction. During 30% of maximal voluntary contraction, the thickness increased but the width decreased at each measurement site compared with those at rest. This was possibly due to difference in muscle slackness between both conditions. The correlation coefficients between the thickness and cross-sectional area for the elbow flexors were significantly lower at rest (r=0.551-0.856) than during 30% of maximal voluntary contraction (r=0.711-0.922). The present findings indicate that the thickness-based muscle size measurement at rest includes errors owing to the slackness of the resting muscles.     

Methodological approaches and insights on protein aggregation in biological systems

Introduction: The proper folding of native proteins is critical and dynamic, but inherently unstable. Therefore, proteins eventually end up adopting misfolded conformations which compromise their function and may even trigger aggregation. Risk factors for neurodegenerative, metabolic and heart diseases compromise cellular protein quality-control systems, promoting protein aggregation. Multiple protein post-translational modifications dynamically regulate protein aggregation and disaggregation in a very complex, intricate and delicate balance.

Areas covered: Herein, we overview the more promising techniques and approaches for the elucidation of the biological implications of protein aggregation. The particular insights provided by different techniques were discriminated and several examples of post-translational modifications together with their targets were pooled and critically discussed, representing promising future therapeutic targets.

Expert commentary: In the years to come, differences between physiological and pathological protein aggregation will certainly become easier to determine. Techniques such as hydrogen/deuterium exchange, circular dichroism spectroscopy and novel mass spectrometry-based approaches are being optimized and are expected to introduce inhibitors of protein aggregation into the clinic. However, protein aggregation is not an isolated phenomenon, but rather influenced by multiple cellular components which complete knowledge is still far.     

生物保护廊道研究进展

生物保护廊道是景观生态廊道的一种应用类型。本文介绍了有关生物保护廊道的基本概念、理论基础、结构和作用、质量与功能、有效性验证、建设与管理等研究进展;其基本现状是生物保护廊道的理论探讨较多而具体实践较少、社区参与的重要性成为共识却缺乏实际研究;深入剖析西双版纳生物保护廊道规划与建设的实例,发现社区参与成为生物保护廊道建设成败的关键。因此认为,社区参与的共管模式将成为生物保护廊道规划和建设的重要方向。     

Recent advances in biological production of erythritol

Erythritol is a natural sweetener commonly used in the food and pharmaceutical industries. Produced by microorganisms as an osmoprotectant, it is an ideal sucrose substitute for diabetics or overweight persons due to its almost zero calorie content. Currently, erythritol is produced on an industrial scale through the fermentation of sugars by some yeasts, such as Moniliella sp. However, the popularity of erythritol as a sweetener is still small because of its high retail price. This creates an opportunity for further process improvement. Recent years have brought the rapid development of erythritol biosynthesis methods from the low-cost substrates, and a better understanding of the metabolic pathways leading to erythritol synthesis. The yeast Yarrowia lipolytica emerges as an organism effectively producing erythritol from pure or crude glycerol. Moreover, novel erythritol producing organisms and substrates may be taken into considerations due to metabolic engineering. This review focuses on the modification of erythritol production to use low-cost substrates and metabolic engineering of the microorganisms in order to improve yield and productivity.     

Methodological issues and inconsistencies in the field of omega-3 fatty acids research

There is growing interest into researching omega-3 fatty acids; however, there are considerable variations in the methodologies employed. Many studies add oils to animal feed and under ambient conditions omega-3 fatty acids are particularly unstable and prone to autoxidation and peroxidative damage. It is therefore important to take specific precautions with the stock preparations and when preparing the experimental diets. There is a need for clarity in the reporting of methodologies employed, such as how oil preparations are stored and handled, how experimental diets are prepared, the potential effects of adding additional antioxidants, whether there is a clear rationale for the selection of control/placebo diets, which may be situation dependent, and consistency in expressing the experimental doses. The purpose of this article is to highlight some of these issues in the hope of promoting discussion, and potentially developing guidelines as to what represents best practice.     

Special issues on advances in quantitative genetics: introduction

Adaptation is commonly a multidimensional problem, with changes in multiple traits required to match a complex environment. This is epitomized by balanced polymorphisms in which multiple phenotypes co-exist and are maintained in a population by a balance of selective forces. Consideration of such polymorphisms led to the concept of the supergene, where alternative phenotypes in a balanced polymorphism segregate as if controlled by a single genetic locus, resulting from tight genetic linkage between multiple functional loci. Recently, the molecular basis for several supergenes has been resolved. Thus, major chromosomal inversions have been shown to be associated with polymorphisms in butterflies, ants and birds, offering a mechanism for localised reduction in recombination. In several examples of plant self-incompatibility, the functional role of multiple elements within the supergene architecture has been demonstrated, conclusively showing that balanced polymorphism can be maintained at multiple coadapted and tightly linked elements. Despite recent criticism, we argue that the supergene concept remains relevant and is more testable than ever with modern molecular methods.