Examination of reproducibility in microbiological degradation experiments

Experimental data indicate that certain microbiological degradation experiments have a limited reproducibility. Nine identical batch experiments were carried out on 3 different days to examine reproducibility. A pure culture, isolated from soil, grew with toluene as the only carbon and energy source. Toluene was degraded under aerobic conditions at a constant temperature of 28 °C. The experiments were modelled by a Monod model – extended to meet the air/liquid system, and the parameter values were estimated using a statistical nonlinear estimation procedure. Model reduction analysis resulted in a simpler model without the biomass decay term. In order to test for model reduction and reproducibility of parameter estimates, a likelihood ratio test was employed. The limited reproducibility for these experiments implied that all 9 batch experiments could not be described by the same set of parameter values. However, experiments carried out the same day (within the same run) were more uniform than experiments carried out on different days (between runs), and a common set of parameter estimates could be accepted for experiments within runs, but not for experiments from different runs. The limited reproducibility may be caused by variability in the preculture, or more precisely, variations in the physiological state of the bacteria in the precultures just before used as inoculum.     

本科生“分子生物学实验”课程设计的改革与探索

"分子生物学实验"是分子生物学理论课配套的实验课。掌握分子生物学基本实验技术是生命科学对新时代人才发展的基本需求。上海科技大学通过整合教学资源与实验室资源,对传统本科生"分子生物学实验"的教学内容和体系进行调整,建立了一套基础实验与前沿实验相结合、验证性实验和自主设计性实验相结合的教学体系,为提高本科生"分子生物学实验"课程教学质量和培养综合型人才奠定了基础。     

Comparison of methods for quantitative determinations of airborne bacteria and evaluation of total viable counts.

Three different methods of estimating airborne bacteria were compared. An Anderson sampler, a slit sampler, an impinger, and filter samplers with gelatine filters or membrane filters were tested for collection efficiency. The comparisons were made in laboratory experiments with an aerosol of Staphylococcus epidermidis or Serratia marcescens, in field experiments in two different industries, i.e., cotton mill and sewage plant, and in experiments with skin fragment sampling. Experiments were also performed estimating the total number of viable microorganisms on the airborne particles. The Andersen sampler gave the highest bacterial counts in all environments tested. The slit sampler gave statistically lower counts only in the aerosol experiments and cotton mill experiments, where the size of the majority of the particles carrying visible bacteria was 2 to 6 micrometers or smaller. In the sewage plant and skin fragment experiments, where the particles were mainly 5 micrometers or larger, the difference was not significant. The filters were efficient in sampling in skin fragment experiments only. With the agar impingement method, the total viable cell count showed a rising index value with increasing particle size. A mean of 13 bacteria was found per particle in the cotton mill, a mean of 24 in the sewage plant, and a mean of 147 in skin fragment experiments.     

Combining Information from Similar Experiments: II. Quantifying Qualitative Results

Suppose that independent experiments each indicate general qualitative results, such as higher than normal incidence rates of tumors for exposed populations. This paper suggests methods for amalgamating the qualitative results from several such experiments into a more quantitative form, such as a dose-response relationship. The methods are designed to be robust both to systematic bias in one of the experiments and also to procedural variability across experiments. Data from four rodent experiments with tolazamide are used to illustrate the methods.     

Molecular weights of nitrogenase components from Azotobacter vinelandii.

Meniscus depletion sedimentation equilibrium ultracentrifuge experiments were performed on purified MoFe and Fe proteins of $\text{Azotobacter vinelandii}$. The MoFe protein was found to have a molecular weight of 245,000, using an experimentally confirmed partial specific volume of 0.73. The MoFe protein formed one band on sodium dodecyl sulfate gel electrophoresis and had a subunit molecular weight of 56,000. The subunit molecular weight from ultracentrifuge experiments in 8 M urea was 61,000. The molecular weight of the Fe protein was calculated to be 60,500 in meniscus depletion experiments. Similar experiments in 8 M urea solvent indicated a subunit molecular weight of 30,000. A subunit molecular weight of 33,000 was obtained from sodium dodecyl sulfate gel electrophoresis experiments.     

Complex plasmas: III. Experiments on strong coupling and long-range correlations

This paper continues a series of review papers devoted to the physics of complex plasmas, in which one of the components (dust) is in a crystalline or liquid state, while the others (electron, ions, and neutral atoms) are in a gaseous state. This review is devoted to the experimental investigations of new phenomena incomplex plasmas. The experiments are explained using estimates based on the theory of elementary processes in complex plasmas, including the new phenomena considered in the previous parts of the review. The paper describes (i) the experiments on multilayer plasma crystals, including the study of their structure and phase transitions; (ii) the experiments on dust monolayer crystals; (iii) the experiments on plasma clusters formed by small number of dust grains; (iv) the experiments on dust ion-sound waves, dust acoustic waves, dust lattice waves, and dust shear waves; (v) the experiments on shock waves; (vi) the experiments on the ionization instabilities and the creation of dust voids and dust clumps; and (vii) the experiments on Mach cones excited either by fast grains or laser radiation.     

Glasshouse vs field experiments: do they yield ecologically similar results for assessing N impacts on peat mosses?

? Peat bogs have accumulated more atmospheric carbon (C) than any other terrestrial ecosystem today. Most of this C is associated with peat moss (Sphagnum) litter. Atmospheric nitrogen (N) deposition can decrease Sphagnum production, compromising the C sequestration capacity of peat bogs. The mechanisms underlying the reduced production are uncertain, necessitating multifactorial experiments. ? We investigated whether glasshouse experiments are reliable proxies for field experiments for assessing interactions between N deposition and environment as controls on Sphagnum N concentration and production. We performed a meta-analysis over 115 glasshouse experiments and 107 field experiments. ? We found that glasshouse and field experiments gave similar qualitative and quantitative estimates of changes in Sphagnum N concentration in response to N application. However, glasshouse-based estimates of changes in production--even qualitative assessments-- diverged from field experiments owing to a stronger N effect on production response in absence of vascular plants in the glasshouse, and a weaker N effect on production response in presence of vascular plants compared to field experiments. ? Thus, although we need glasshouse experiments to study how interacting environmental factors affect the response of Sphagnum to increased N deposition, we need field experiments to properly quantify these effects.     

Combining Information from Similar Experiments: I. Statistical Issues

A general method for combining information from similar experiments is illustrated in the case where two independent experiments are designed to estimate a dose-response curve. By accounting for variability across experiments, the proposed method avoids inferential pitfalls such as extended forms of Simpson's paradox. The validity of the method is supported by seven fundamental assumptions about data from replicated experiments. In contrast, an example indicates that failing to reject a preliminary test of equal distributions is inadequate justification for pooling data from two experiments. Methods that account for the variability across experiments in terms of known covariates are also discussed.     

The use of water and some inorganic salt solutions to advance sugar beet seed. II. Experiments under controlled and field conditions

The effect of seed advancement on the early growth of sugar beet was determined in two experiments made under controlled conditions and eight field experiments made between 1974 and 1978. The experiments in the growth room suggested that seed advancement increased the rate of emergence and seedling dry weight over a wide range of soil moisture contents but seedling numbers were only greater under sub-optimal moisture conditions. Similarly, in most field experiments, seed advancement resulted in more rapid emergence and larger seedlings. In four field experiments, seed advancement gave up to 16% more plants, and in three experiments a significant increase in final sugar yield of up to 0–7 t h^-1 was detected. The plants were hand-singled to a uniform stand and had the crops been drilled to a stand, some yield responses would have been larger. Seed advancement did not decrease the plant stand or final yield in any experiments. Results in 1977 and 1978 provided some evidence that seed advancement may help reduce the damage caused by field mice and the number of plants which bolt and, by making emergence more rapid, be particularly beneficial on soils prone to slumping or capping. There might, however, be a slightly increased risk of frost injury if advanced seed is used for early sowings.     

陆地生态系统环境控制实验的研究方法及技术体系

生物及生态系统与环境变化间的反馈关系及其过程机制是生态学研究的重要内容。不同类型的生物环境因素控制实验以及大尺度的联网野外控制实验被认为是认识生态系统响应和适应环境变化过程机制、精细定量表达的有效手段及认知过程的加速器。近年来发展了大型野外物理模拟实验装置网络(如ECOTRON)、生态系统分析与实验平台(AnaEE)、国际干旱实验研究网络(Drought Network)、氮沉降联合实验网络(Nutrient Network),以及基于各区域性生态观测实验站的联网控制实验(如USA-ILTER)。发展大陆尺度联网实验研究平台事业正日益受到学术界的重视,将会在认知生态系统环境响应过程机制方面发挥更重要的作用。基于以上背景,本文综述了生态系统环境控制实验的研究方法和实验体系的发展,明确指出各种类型的生物环境控制实验需要形成联合协作体系,共同解决生态系统对环境变化的响应及适应的基本科学问题。目前的控制实验包括: 1) 实验室封闭装置内的生物生理生态学控制实验;2) 野外实验场的半开放部分环境要素控制实验;3) 近自然状态的野外环境控制实验;以及4) 基于野外生态站的联网控制实验。进而,本文还深入讨论了陆地生态系统的环境响应及适应过程机制实验系统设计的发展趋势,分析了基于大尺度自然环境梯度实验及生态站尺度的要素控制实验的优势,提出了整合两种实验技术、发展新一代的野外联网实验体系的科学设想,讨论了基于野外联网控制实验的研究体系,论证了研究生态系统对环境变化短期响应和长期适应的规律和机制、生态系统环境响应定量表达的技术途径。若本文提出的控制实验体系设计方案能够得以实施,必将大大促进我国乃至全球生态系统和环境变化科学的研究水平,对我国应对气候变化和生态环境建设具有重要的科学意义。     

Kinetics of alpha-amylase secretion in Aspergillus oryzae.

Pulse and pulse-chase experiments have been performed to study L-[(35)S] methionine incorporation and protein secretion kinetics in Aspergillus oryzae. Pulse experiments confirmed the mechanism of methionine uptake reported previously for Penicillium chrysogenum (Benko et al., 1967). Pulse-chase experiments were carried out to investigate the alpha-amylase secretion kinetics in A. oryzae. No unglycosylated alpha-amylase was detected neither intracellularly nor extracellularly demonstrating that glycosylation was not the rate controlling step in the secretory pathway. The pulse chase experiments indicated that there are two pools of intracellular alpha-amylase: a fast secreted and a slow secreted. The secretion of those two pools were described with a kinetic model, which was fitted to the pulse chase experiments.     

Designing fermentation media: A comparison of neural networks to factorial design

Summary Neural networks were compared to factorial experiments as techniques for designing fermentation media. The production of intracellular oil byRhodotorula gracilis (Rhodosporidium toruloides) was used as a model system. Investigating three factors, the molasses, ammonium nitrate and yeast extract concentrations, each at three concentrations, 27 experiments were required for a complete factorial expriment. In contrast, neural networks could be trained on 10 experiments and predict the test experiments with reasonable accuracy. This represents a 63% saving in the number of experiments that need to be conducted. Thus neural networks are a useful tool in developing fermentation medium.     

The Role of a Green Alga in the Precipitation of Calcite and the Coprecipitation of Phosphate in Freshwater

The precipitation of calcite from a calcium bicarbonate solution, similar in ionic strength to natural hardwaters, was observed in a series of experiments utilizing an automated culture apparatus. Seeded growth experiments, using calcite seed crystals, were performed at a range of phosphate concentrations to observe inhibitory effects. These experiments demonstrated a linear relationship of increasing inhibition with increasing initial phosphate concentration. A further series of experiments was performed in which an actively photosynthesizing culture of a unicellular green alga (Chlorococcum sp.) was added to the culture vessel in order to initiate precipitation. Experiments to observe spontaneous precipitation, occurring in the absence of both seed and alga additions, were carried out to compare with precipitation rates in the algal experiments. A control experiment was also performed to investigate whether precipitation occurrred in algal cultures maintained in darkness. The carbonate site mechanistic model, developed for calcite precipitation in abiotic conditions, was used to analyse the results of the algal experiments and found to be applicable.     

Soil movement in long-term field experiments

Summary Soil movement from plot to plot in long-term field experiments caused by tillage, soil fauna, wind, and water leads to experimental errors. The paper attempts to quantify the total movement in current long-term field experiments.A soil movement model was fitted to soil-phosphorus (P) recordings of two 90-year-old field experiments. The model fitted well and indicated why the soil P concentration of the unmanured plots had increased for many years. The removal of P by crops from the unmanured plots had simply been more than compensated for by the soil exchange between the unmanured plots and the adjacent P-fertilized ones.Furthermore, the model was used for simulating soil movement in 21 of the worlds more than 50-year-old field experiments assuming the same rate of soil transport as estimated before. The simulations showed that on average of these experiments only 28% of the plough-layer soil present in their net-plots (the central quarter of each plot) to day should originate from the plough-layer soil that was inside the plots when the experiments started.The work indicates that the movement of soil is a serious general problem in long-term field experiments, a problem with implications for our understanding of long-term processes in agro-ecosystems.     

Chi-square and Mendel's experiments: where's the bias?

Mendel has been accused of "cooking" his data to meet a particular hypothesis. The earliest time he could have formulated an hypothesis in the course of his experiments was at the end of the second year of experiments 1 and 2. If he knew what to expect as the result of his first two pea-seed experiments, one might expect the chi-square values of subsequent experiments to exhibit a trend toward smaller values. However, when the individual experiments are, each in turn, subjected to a chi-square test, there is no evidence of the expected trend. With few exceptions, the data show no systematic variation in a particular direction. In our view, the suggestion of bias is not supported.     

Proton homonuclear correlated spectroscopy as an assignment tool for hyperfine-shifted resonances in medium-sized paramagnetic proteins: cyanide-ligated yeast cytochrome c peroxidase as an example.

Two types of homonuclear proton COSY experiments are shown to be useful in making resonance assignments in cyanide-ligated cytochrome c peroxidase, a 34 kDa paramagnetic heme protein. Both magnitude COSY and phase-sensitive COSY experiments provide spectra useful for making proton assignments to resonances of strongly relaxed hyperfine-shifted protons. This initial investigation demonstrates that COSY experiments combined with NOESY experiments are feasible for hyperfine-shifted protons of paramagnetic proteins larger than metmyoglobins and ferricytochromes c, for which the nuclear spin-lattice relaxation times are in the range 70-300 ms. Taken together, COSY and NOESY experiments, although not yet widely applied to paramagnetic metalloproteins, provide a reliable protocol for accurately assigning hyperfine-shifted resonances that are part of a metalloenzyme's active site. Specific examples of expected proton homonuclear COSY connectivities that were not observed in these experiments are presented, and utilization of COSY with respect to the proton resonance line widths and apparent nuclear relaxation times is discussed. The COSY experiments presented here provide valuable verification of previously proposed hyperfine resonance assignments for cyanide-ligated cytochrome c peroxidase, which were made by using NOESY experiments alone, and in several instances expand these assignments to additional protons in particular amino acid spin systems.     

A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions

Differing arresting agents and protocols can be used to synchronize cells in cultures to specific phases of the cell when studying cell-cycle gene expressions. Often, data derived from individual experiments are analyzed separately, since no appropriate statistical methodology is available at the moment to analyze the data from all such experiments simultaneously. The focus of this paper is to determine the association and coherence of the relative activation times of cell-cycling genes under different experimental conditions. Using a circular-circular regression model, we define two parameters, a rotation parameter for the angular difference between cells' arresting times (phases) in two cell-cycle experiments, and an association parameter to describe the correspondence between the cycle times of maximal expression (phase angles) for a set of genes studied in two experiments. Further, we propose a procedure to assess coherence across multiple experiments, i.e. to what extent the circular ordering of the phase angles of genes is maintained across multiple experiments. Coherence of genes across experiments suggests that functionally these genes tend to respond in a stereotypically sequenced way under different experimental conditions. Our proposed methodology is illustrated by applying it to a HeLa cell-cycle gene-expression data.     

Precision of herbivore tolerance experiments with imposed and natural damage

Tiffin and Inouye (2000) discussed the use of natural and imposed (controlled) damage in experiments of herbivore tolerance. They constructed a statistical model of the effect of herbivory on plant fitness, including damage level and an environmental factor as the independent factors, in which tolerance is defined as a slope of the regression line when damage level is regressed with plant fitness. They claim that while experiments with imposed damage are more accurate (i.e., they give a more correct estimate of tolerance), experiments with natural damage are more precise under a wide range of parameter values (i.e., tolerance estimates explain a larger part of variation in fitness). I show, however, that experiments with imposed damage are less precise only when an experimenter uses an experimental design that has weaker statistical power than in experiments with natural herbivory. The experimenter can nevertheless control the damage levels to optimize the experimental designs. For instance, when half of the experimental plants are left undamaged and the other half treated with maximal relevant damage level, experiments with imposed damage are almost always much more precise than experiments with natural damage.     

Application of a model of scale dependence to quantify scale domains in open predation experiments

We use a model of open predation experiments to define scale domains that differ in terms of the controlling processes and scale dependence of predator impacts. For experimental arenas that are small compared to the movements of the prey (small scale domain) the model predicts that predator impacts are scale independent and controlled by prey movements. For arenas of intermediate scale we predict that predator impacts are scale dependent and controlled by both prey movements and direct predation, and for the largest scale domain we predict weak scale dependence and predation control.
We propose that the scale‐domain concept is useful when designing and interpreting field experiments. As an illustration we apply the concept to experiments examining predator effects on the stream benthos. First, we test two key assumptions of the underlying model: that area‐specific prey migration rates decrease with increasing size of experimental arenas and that predation rates are independent of arena size. For this purpose we used published estimates of prey emigration and predator consumption rates for nine studies examining the effects of stream predators on benthic prey. We found that prey per capita emigration rates but not predation rates decreased with increasing arena length.
Second, we demonstrate a method for identifying the scale domain of real experiments. The model of predation experiments was parameterized using experimental data and the expected spatial and temporal scale dependence of predator impacts on prey in these experiments was simulated. The simulations suggest that the studies conducted in the largest arenas (length 15–35 m) should be classified as large‐scale, consumption‐controlled experiments, whereas the experiments conducted in smaller arenas (length 1.5–6 m) should be classified as small or intermediate‐scale. We also attempted to determine the scale domain of the experiments in a large data set, including results from most published stream predation experiments. The majority of arenas used in these experiments (73%) were smaller than 1 m in length. Our data on the scale dependence of predation and prey migration rate suggest that experiments in this scale range (<1 m) should be classified as small‐scale, movement‐controlled experiments for most prey taxa.