Interactive control of physiological experiments

Physiological and biological experiments often require the imposition of repeated influences on an organ or organic system. Then the experimental protocol requires many repetitive functions with adjustable interval times and magnitudes, which are prepared or dictated by experimental results. To control such an experimental set-up interactively with a small computer we chose a more or less general approach. A special language syntax has been developed for: (i) experiment definition; (ii) experiment composition in advance; (iii) real-time control during the actual experiment; and (iv) registration of the actual protocol parameters. The interactive control was realized using the special language and an interpreter as one of the parallel processes for the experimental control.     

Hierarchical analysis of large-scale two-dimensional gel electrophoresis experiments

Large-scale two-dimensional gel experiments have the potential to identify proteins that play an important role in elucidating cell mechanisms and in various stages of drug discovery. Such experiments, typically including hundreds or even thousands of related gels, are notoriously difficult to perform, and analysis of the gel images has until recently been virtually impossible. In this paper we describe a scalable computational model that permits the organization and analysis of a large gel collection. The model is implemented in Compugen's Z4000 system. Gels are organized in a hierarchical, multidimensional data structure that allow the user to view a large-scale experiment as a tree of numerous simpler experiments, and carry out the analysis one step at a time. Analyzed sets of gels form processing units that can be combined into higher level units in an iterative framework. The different conditions at the core of the experiment design, termed the dimensions of the experiment, are transformed from a multidimensional structure to a single hierarchy. The higher level comparison is performed with the aid of a synthetic "adaptor" gel image, called a Raw Master Gel (RMG). The RMG allows the inclusion of data from an entire set of gels to be presented as a gel image, thereby enabling the iterative process. Our model includes a flexible experimental design approach that allows the researcher to choose the condition to be analyzed a posteriori. It also enables data reuse, the performing of several different analysis designs on the same experimental data. The stability and reproducibility of a protein can be analyzed by tracking it up or down the hierarchical dimensions of the experiment.     

基于CRISPR/Cas9基因编辑技术的本科教学实验体系的创建与实践

CRISPR/Cas9是新兴的基因编辑技术,在生命科学研究中发挥着重要的作用。将它引入本科生的实验教学,使本科生了解这项前沿科研技术很有意义。我们创建了一个基于CRISPR/ Cas9技术的本科教学实验体系。该实验体系侧重CRISPR/Cas9技术在哺乳动物细胞中的应用,选用一株基因组上被插入mCherry基因的小鼠胚胎成纤维细胞为实验材料,命名为STO-82。首先设计靶向mCherry的sgRNA,构建CRISPR-Cas9/sgRNA共表达质粒。经测序验证无误后,转染到STO-82细胞。采用流式细胞仪分析检测mCherry阴性和阳性两群细胞,分选出阴性单细胞并扩大培养。最后用测序检验单克隆细胞中靶标DNA序列的编辑情况。结果显示,靶位点有插入或缺失突变,说明体系创建成功。该实验体系将sgRNA设计、CRISPR-Cas9/sgRNA共表达质粒的构建、细胞转染、单细胞分选、单克隆细胞培养、测序序列分析等内容融合为一个综合实验,用于高年级本科生的实验教学。根据实际情况,将教学实践内容分解分块教学,也可以做完整性项目教学。本教学实践采用10人左右的小班分块教学,2人一组,经过3个班（共13组）的实践,绝大部分学生都能完成实验,得到预期结果。通过这个实验,学生加深了对CRISPR/Cas9技术的原理和实验流程的理解,锻炼了实验操作能力和严谨的科研思维,也使学生对该技术的医疗应用风险有了一些认识。     

A step-by-step guide to systematically identify all relevant animal studies

Before starting a new animal experiment, thorough analysis of previously performed experiments is essential from a scientific as well as from an ethical point of view. The method that is most suitable to carry out such a thorough analysis of the literature is a systematic review (SR). An essential first step in an SR is to search and find all potentially relevant studies. It is important to include all available evidence in an SR to minimize bias and reduce hampered interpretation of experimental outcomes. Despite the recent development of search filters to find animal studies in PubMed and EMBASE, searching for all available animal studies remains a challenge. Available guidelines from the clinical field cannot be copied directly to the situation within animal research, and although there are plenty of books and courses on searching the literature, there is no compact guide available to search and find relevant animal studies. Therefore, in order to facilitate a structured, thorough and transparent search for animal studies (in both preclinical and fundamental science), an easy-to-use, step-by-step guide was prepared and optimized using feedback from scientists in the field of animal experimentation. The step-by-step guide will assist scientists in performing a comprehensive literature search and, consequently, improve the scientific quality of the resulting review and prevent unnecessary animal use in the future.     

Maximizing signal-to-noise ratio in the random mutation capture assay

The 'Random Mutation Capture' assay allows for the sensitive quantitation of DNA mutations at extremely low mutation frequencies. This method is based on PCR detection of mutations that render the mutated target sequence resistant to restriction enzyme digestion. The original protocol prescribes an end-point dilution to about 0.1 mutant DNA molecules per PCR well, such that the mutation burden can be simply calculated by counting the number of amplified PCR wells. However, the statistical aspects associated with the single molecular nature of this protocol and several other molecular approaches relying on binary (on/off) output can significantly affect the quantification accuracy, and this issue has so far been ignored. The present work proposes a design of experiment (DoE) using statistical modeling and Monte Carlo simulations to obtain a statistically optimal sampling protocol, one that minimizes the coefficient of variance in the measurement estimates. Here, the DoE prescribed a dilution factor at about 1.6 mutant molecules per well. Theoretical results and experimental validation revealed an up to 10-fold improvement in the information obtained per PCR well, i.e. the optimal protocol achieves the same coefficient of variation using one-tenth the number of wells used in the original assay. Additionally, this optimization equally applies to any method that relies on binary detection of a small number of templates.     

THE β-STRATEGY: AN ALTERNATIVE AND POWERFUL COGNITIVE STRATEGY WHEN PERFORMING SENSORY DISCRIMINATION TESTS

For discrimination tests not requiring the nature of the difference to be specified in the instructions, such as the triangle, duo-trio and same-different protocols, it is usually assumed that the decision rule used by the subject in order to generate an answer involves the comparison of the relative sensory distances between the samples. However, there is evidence that an alternative cognitive strategy, the β-strategy, involving the absolute categorization of the sensations could be used by the subject when performing these protocols. This paper introduces the characteristics of this alternative strategy by discussing its statistical power (higher than the traditional strategies) and by describing means of investigating which strategy is used by the subject during an experiment as well as illustrating the experimental conditions that might facilitate the use of this particular decision rule.     

Identification and prevention of a GC content bias in SAGE libraries

Serial Analysis of Gene Expression (SAGE) is becoming a widely used gene expression profiling method for the study of development, cancer and other human diseases. Investigators using SAGE rely heavily on the quantitative aspect of this method for cataloging gene expression and comparing multiple SAGE libraries. We have developed additional computational and statistical tools to assess the quality and reproducibility of a SAGE library. Using these methods, a critical variable in the SAGE protocol was identified that has the potential to bias the Tag distribution relative to the GC content of the 10 bp SAGE Tag DNA sequence. We also detected this bias in a number of publicly available SAGE libraries. It is important to note that the GC content bias went undetected by quality control procedures in the current SAGE protocol and was only identified with the use of these statistical analyses on as few as 750 SAGE Tags. In addition to keeping any solution of free DiTags on ice, an analysis of the GC content should be performed before sequencing large numbers of SAGE Tags to be confident that SAGE libraries are free from experimental bias.     

Role of ancillary variables in the design,analysis, and interpretation of animal experiments

During the course of an experiment using animals, many variables (e.g., age, body weight at several times, food and water consumption, hematology, and clinical biochemistry) and other characteristics are often recorded in addition to the primary response variable(s) specified by the experimenter. These additional variables have an important role in the design and interpretation of the experiment. They may be formally incorporated into the design and/or analysis and thus increase precision and power. However, even if these variables are not incorporated into the primary statistical design or into the formal analysis of the experiment, they may nevertheless be used in an ancillary or exploratory way to provide valuable information about the experiment, as shown by various examples. Used in this way, ancillary variables may improve analysis and interpretation by providing an assessment of the randomization process and an approach to the identification of outliers, lead to the generation of new hypotheses, and increase generality of results or account for differences in results when compared across different experiments. Thus, appropriate use of additional variables may lead to reduction in the number of animals required to achieve the aims of the experiment and may provide additional scientific information as an extra benefit. Unfortunately, this type of information is sometimes effectively discarded because its potential value is not recognized. Guidelines for use of animals include, in addition to the obligation to follow humane procedures, the obligation to use no more animals than necessary. Ethical experimental practice thus requires that all information be properly used and reported.     

Selection of the experimental unit in teratology studies.

In teratology experiments the litter (pregnant female) rather than the fetus is advocated as being the proper experimental unit upon which to base the statistical analysis. It is pointed out that per litter tests, by being based on the average fetal response within a litter, do take the individual fetus into account. Actual experimental data are used to show that when litter effects are present a per fetus analysis is invalid and may seriously exaggerate the significance level. It is also shown that there appears to be little loss in sensitivity in performing per litter tests even in the unlikely event that there are no litter effects. Thus it certainly seems prudent to analyze teratology data with test procedures that treat the litter as the experimental unit.     

Nonadherence to treatment protocol in published randomised controlled trials: a review

ABSTRACT: This review aimed to ascertain the extent to which nonadherence to treatment protocol is reported and addressed in a cohort of published analyses of randomised controlled trials (RCTs). One hundred publications of RCTs, randomly selected from those published in BMJ, New England Journal of Medicine, the Journal of the American Medical Association and The Lancet during 2008, were reviewed to determine the extent and nature of reported nonadherence to treatment protocol, and whether statistical methods were used to examine the effect of such nonadherence on both benefit and harms analyses. We also assessed the quality of trial reporting of treatment protocol nonadherence and the quality of reporting of the statistical analysis methods used to investigate such nonadherence. Nonadherence to treatment protocol was reported in 98 of the 100 trials, but reporting on such nonadherence was often vague or incomplete. Forty-two publications did not state how many participants started their randomised treatment. Reporting of treatment initiation and completeness was judged to be inadequate in 64% of trials with short-term interventions and 89% of trials with long-term interventions. More than half (51) of the 98 trials with treatment protocol nonadherence implemented some statistical method to address this issue, most commonly based on per protocol analysis (46) but often labelled as intention to treat (ITT) or modified ITT (23 analyses in 22 trials). The composition of analysis sets for their benefit outcomes were not explained in 57% of trials, and 62% of trials that presented harms analyses did not define harms analysis populations. The majority of defined harms analysis populations (18 out of 26 trials, 69%) were based on actual treatment received, while the majority of trials with undefined harms analysis populations (31 out of 43 trials, 72%) appeared to analyse harms using the ITT approach. Adherence to randomised intervention is poorly considered in the reporting and analysis of published RCTs. The majority of trials are subject to various forms of nonadherence to treatment protocol, and though trialists deal with this nonadherence using a variety of statistical methods and analysis populations, they rarely consider the potential for bias introduced. There is a need for increased awareness of more appropriate causal methods to adjust for departures from treatment protocol, as well as guidance on the appropriate analysis population to use for harms outcomes in the presence of such nonadherence.     

Sex-specific effects of handling time on an index of immune activity in zebra finches

Recently, there has been considerable interest in the role of the immune system in shaping life-history evolution, sexual selection strategies, and indexes of individual quality. The most frequently used assay of immune function, particularly in avian field studies, is the phytohemagglunitin (PHA) skin test. PHA is injected subcutaneously into the wing web, and the magnitude of the resultant swelling has traditionally been interpreted as an index of an individual's cell-mediated immunocompetence. The test follows one of two protocols: the traditional two-wing injection protocol, with one wing web injected with PHA and the other with phosphate-buffered saline (PBS), or the simplified one-wing protocol that omits the PBS injection. In this technical comment, we alert researchers to the importance of considering handling time when performing the PHA test. We show that zebra finches (Taeniopygia guttata) subjected to the two-wing protocol had a lower wing-web swelling than individuals injected in one wing. In males, handling time explained over 50% of the variation in an individual's skin swelling response; females were relatively unaffected by handling time. We suggest that caution should be exercised when comparing the magnitude of wing-web swelling across studies in which the alternate protocol was followed. In addition, the recording of handling time, and its inclusion in subsequent statistical analyses, may aid in the detection of subtle differences across treatments.     

Design and analysis of multiple choice feeding preference data

Traditional analyses of feeding experiments that test consumer preference for an array of foods suffer from several defects. We have modified the experimental design to incorporate into a multivariate analysis the variance due to autogenic change in control replicates. Our design allows the multiple foods to be physically paired with their control counterparts. This physical proximity of the multiple food choices in control/experimental pairs ensures that the variance attributable to external environmental factors jointly affects all combinations within each replicate. Our variance term, therefore, is not a contrived estimate as is the case for the random pairing strategy proposed by previous studies. The statistical analysis then proceeds using standard multivariate statistical tests. We conducted a multiple choice feeding experiment using our experimental design and utilized a Monte Carlo analysis to compare our results with those obtained from an experimental design that employed the random pairing strategy. Our experimental design allowed detection of moderate differences among feeding means when the random design did not.     

Bias in interspecific allometry: examples from morphological scaling in varanid lizards

The traditional approach to allometric analysis entails the fitting of a straight line to logarithmic transformations of the data, after which parameters in a two-parameter allometric equation are estimated by back-transformation to the original scale. We re-examined published data for dimensions of the limbs in 22 species of varanid lizards to illustrate the biases that can be introduced into allometric analyses by applying the aforementioned protocol. Statistical models fit to the original data by linear and nonlinear regression conformed better with underlying assumptions than did models obtained by back-transformation from logarithms, and the former generally were better than the latter for describing limb dimensions over the full range in body size. Allometric exponents estimated by the traditional method therefore were based on inappropriate and inaccurate statistical models and, consequently, were biased and misleading. Investigators can avoid problems such as these by performing preliminary graphical and statistical analyses on data in their original scale and by validating the fitted model. Logarithmic transformations should be used sparingly and only for cause.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 296–305.