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.     

提高植物学实验教学质量的一些体会

实验是植物学教学的重要环节.针对植物学传统实验教学中的实际情况,进行了实验方法力求多样化、变部分过程性实验为过程性实验、增加综合性实验和研究性实验等尝试,进而充分发挥教师和学生在实验教学中的作用,培养学生的创造能力.     

提高植物学实验教学质量的一些体会

实验是植物学教学的重要环节。针对植物学传统实验教学中的实际情况, 进行了实验方法力求多样化、变部分过程性实验为过程性实验、增加综合性实验和研究性实验等尝试, 进而充分发挥教师和学生在实验教学中的作用, 培养学生的创造能力。     

城市生态学自然模拟实验研究进展

自然模拟实验,通过适当控制影响因素研究自然状态下生态系统变化,已经越来越受到生态学家的欢迎。新兴的快速发展的城市生态学越来越多的采用自然模拟实验方法。研究从城市生态学的实验设计方法(如人工梯度、自然梯度和城市建设实验)、环境因子(如空气污染、热岛、灯光和地表硬化)生态效应和生态系统(如社区、绿地、绿化屋顶和集水区)响应等方面,分析了国内外大量城市生态学自然模拟实验的研究案例,并总结了城市生态学自然模拟实验的特点,指出了城市生态学模拟实验应该考虑的主要问题,并提出未来主要发展方向：(1)多种环境因子复合影响模拟实验研究,(2)生态系统结构和功能响应模拟实验研究,(3)近自然的长期模拟实验研究,(4)大范围的联网模拟实验研究和(5)面向城市生态恢复和建设的模拟实验研究。希望研究能够为推进我国城市生态学的实验研究起到抛砖引玉作用。     

Coordinated approaches to quantify long‐term ecosystem dynamics in response to global change

Many serious ecosystem consequences of climate change will take decades or even centuries to emerge. Long‐term ecological responses to global change are strongly regulated by slow processes, such as changes in species composition, carbon dynamics in soil and by long‐lived plants, and accumulation of nutrient capitals. Understanding and predicting these processes require experiments on decadal time scales. But decadal experiments by themselves may not be adequate because many of the slow processes have characteristic time scales much longer than experiments can be maintained. This article promotes a coordinated approach that combines long‐term, large‐scale global change experiments with process studies and modeling. Long‐term global change manipulative experiments, especially in high‐priority ecosystems such as tropical forests and high‐latitude regions, are essential to maximize information gain concerning future states of the earth system. The long‐term experiments should be conducted in tandem with complementary process studies, such as those using model ecosystems, species replacements, laboratory incubations, isotope tracers, and greenhouse facilities. Models are essential to assimilate data from long‐term experiments and process studies together with information from long‐term observations, surveys, and space‐for‐time studies along environmental and biological gradients. Future research programs with coordinated long‐term experiments, process studies, and modeling have the potential to be the most effective strategy to gain the best information on long‐term ecosystem dynamics in response to global change.     

On the squid axon membrane's response to sequential voltage and current clamps.

Starzak and Starzak (1978. IEEE Trans. Biomed. Eng. 25:201-204.) proposed that, in cyclic application of current and voltage-clamps, the fidelity of the match of the output current with the original stimulus could be used to measure the spatial uniformity of voltage in a membrane. However, they failed to find such a match in experiments on either squid axons or an electronic model of a membrane patch. Computer simulations of such experiments show that the failure to return the initial pattern may arise from shortcomings of the instruments or instability of membrane characteristics. Logical arguments show that such cyclic experiments are not able to provide information about spatial gradients of membrane voltage.     

Variation in barbiturate sleeping time in mice. 3. Strain X environment interactions

Environmental factors such as diet, bedding material and temperature at the time of testing affected a 'model' pharmacological response--pentobarbitone sleeping time--differentially in a range of inbred strains. These results are probably explained by variations in the responses of the strains to constituents of the diets and bedding materials used in the experiments. Differences in the results between experiments suggest that there are also fluctuations in the composition of the diets and bedding materials over time. Strain X environment interactions such as those found here may explain differences in strain rankings between experiments. They would also account for some of the variability in results found between laboratories and within a laboratory over time.     

An illustrated gardener's guide to transgenic Arabidopsis field experiments

Field studies with transgenic Arabidopsis lines have been performed over 8 yr, to better understand the influence that certain genes have on plant performance. Many (if not most) plant phenotypes cannot be observed under the near constant, low-stress conditions in growth chambers, making field experiments necessary. However, there are challenges in performing such experiments: permission must be obtained and regulations obeyed, the profound influence of uncontrollable biotic and abiotic factors has to be considered, and experimental design has to be strictly controlled. The aim here is to provide inspiration and guidelines for researchers who are not used to setting up such experiments, allowing others to learn from our mistakes. This is believed to be the first example of a 'manual' for field experiments with transgenic Arabidopsis plants. Many of the challenges encountered are common for all field experiments, and many researchers from ecological backgrounds are skilled in such methods. There is huge potential in combining the detailed mechanistic understanding of molecular biologists with ecologists' expertise in examining plant performance under field conditions, and it is suggested that more interdisciplinary collaborations will open up new scientific avenues to aid analyses of the roles of genetic and physiological variation in natural systems.     

Laboratory selection experiments using Drosophila: what do they really tell us?

Laboratory selection experiments using Drosophila, and other organisms, are widely used in experimental biology. In particular, such experiments on D. melanogaster life history and stress-related traits have been instrumental in developing the emerging field of experimental evolution. However, similar selection experiments often produce inconsistent correlated responses to selection. Unfortunately, selection experiments are vulnerable to artifacts that are difficult to control. In spite of these problems, selection experiments are a valuable research tool and can contribute to our understanding of evolution in natural populations.     

Phytochrome control of amino acid synthesis in cotyledons of Sinapis alba

Continuous far red light, acting through phytochrome, stimulates the rate of incorporation of density label into amino acids in the cotyledons of Sinapis alba. It is shown that such stimulation leads to increased incorporation of label into proteins. This has important consequences for experiments in which rates of enzyme synthesis in light treated and dark grown plants are compared by labelling methods. The results of some such experiments are re-evaluated.     

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.     

Abiotic formation of bioorganic compounds in space--preliminary experiments on ground and future exobiology experiments in space.

Simulation experiments on ground have shown that "amino acid precursors", which give amino acids after acid-hydrolysis, can be formed when an ice mixture simulating ice mantles of interstellar dust particles (lSDs) is irradiated with high energy particles or UV light. It is strongly suggested that such bioorganic compounds were delivered by comets for the first biosphere on the Earth. It is of great interest to confirm this hypothesis in actual space conditions, such as in an exposed facility of JEM. Fundamental designs for such exobiology experiments in earth orbit (EEEO) will be discussed.     

Use of factorial designs to optimize animal experiments and reduce animal use

Optimization of experiments, such as those used in drug discovery, can lead to useful savings of scientific resources. Factors such as sex, strain, and age of the animals and protocol-specific factors such as timing and methods of administering treatments can have an important influence on the response of animals to experimental treatments. Factorial experimental designs can be used to explore which factors and what levels of these factors will maximize the difference between a vehicle control and a known positive control treatment. This information can then be used to design more efficient experiments, either by reducing the numbers of animals used or by increasing the sensitivity so that smaller biological effects can be detected. A factorial experimental design approach is more effective and efficient than the older approach of varying one factor at a time. Two examples of real factorial experiments reveal how using this approach can potentially lead to a reduction in animal use and savings in financial and scientific resources without loss of scientific validity.     

Characterization of Electrode Materials for Lithium Ion and Sodium Ion Batteries Using Synchrotron Radiation Techniques

Intercalation compounds such as transition metal oxides or phosphates are the most commonly used electrode materials in Li-ion and Na-ion batteries. During insertion or removal of alkali metal ions, the redox states of transition metals in the compounds change and structural transformations such as phase transitions and/or lattice parameter increases or decreases occur. These behaviors in turn determine important characteristics of the batteries such as the potential profiles, rate capabilities, and cycle lives. The extremely bright and tunable x-rays produced by synchrotron radiation allow rapid acquisition of high-resolution data that provide information about these processes. Transformations in the bulk materials, such as phase transitions, can be directly observed using X-ray diffraction (XRD), while X-ray absorption spectroscopy (XAS) gives information about the local electronic and geometric structures (e.g. changes in redox states and bond lengths). In situ experiments carried out on operating cells are particularly useful because they allow direct correlation between the electrochemical and structural properties of the materials. These experiments are time-consuming and can be challenging to design due to the reactivity and air-sensitivity of the alkali metal anodes used in the half-cell configurations, and/or the possibility of signal interference from other cell components and hardware. For these reasons, it is appropriate to carry out ex situ experiments (e.g. on electrodes harvested from partially charged or cycled cells) in some cases. Here, we present detailed protocols for the preparation of both ex situ and in situ samples for experiments involving synchrotron radiation and demonstrate how these experiments are done.     

Current issues and perspectives in small rodent magnetic resonance imaging using clinical MRI scanners

Small rodents such as mice and rats are frequently used in animal experiments for several reasons. In the past, animal experiments were frequently associated with invasive methods and groups of animals had to be killed to perform longitudinal studies. Today's modern imaging techniques such as magnetic resonance imaging (MRI) allow non-invasive longitudinal monitoring of multiple parameters. Although only a few institutions have access to dedicated small animal MR scanners, most institutions carrying out animal experiments have access to clinical MR scanners. Technological advances and the increasing field strength of clinical scanners make MRI a broadly available and viable technique in preclinical in vivo research. This review provides an overview of current concepts, limitations, and recent studies dealing with small animal imaging using clinical MR scanners.     

GEST: a gene expression search tool based on a novel Bayesian similarity metric

Gene expression array technology has made possible the assay of expression levels of tens of thousands of genes at a time; large databases of such measurements are currently under construction. One important use of such databases is the ability to search for experiments that have similar gene expression levels as a query, potentially identifying previously unsuspected relationships among cellular states. Such searches depend crucially on the metric used to assess the similarity between pairs of experiments. The complex joint distribution of gene expression levels, particularly their correlational structure and non-normality, make simple similarity metrics such as Euclidean distance or correlational similarity scores suboptimal for use in this application. We present a similarity metric for gene expression array experiments that takes into account the complex joint distribution of expression values. We provide a computationally tractable approximation to this measure, and have implemented a database search tool based on it. We discuss implementation issues and efficiency, and we compare our new metric to other standard metrics.     

Time-resolved methods in biophysics. 5. Femtosecond time-resolved and dispersed infrared spectroscopy on proteins.

In this contribution we describe how femtosecond time-resolved infrared spectroscopy provides insight into the function and dynamics of pigment-protein complexes, and what the technical requirements are to perform such experiments. We further discuss a few examples of experiments performed on the photoactive yellow protein and photosynthetic complexes in more detail.