From a mouse: systematic analysis reveals limitations of experiments testing interventions in Alzheimer’s disease mouse models. Systematic review and meta-analysis are powerful tools to assess the validity and robustness of data published in a certain research field. In this article, Egan et al. used a systematic review approach to analyze the prevalence and impact of quality factors known to influence the risk of bias (e.g. reporting of random allocation to group, blinded assessment of outcome, sample size calculation, compliance with animal welfare legislation and a statement declaring a possible conflict of interest) in the literature describing Alzheimer’s disease models. The authors found that only a few studies report fundamental aspects of study quality items (e.g. blinding, randomization) and that the risk of bias does indeed impact the observed efficacy. In summary, this article demonstrates the need to develop more precise standards and guidelines on how to decrease the risk of overstating efficacy from experiments conducted in animal models and how to build confidence in data obtained from preclinical animal studies.
Origin of the U87MG glioma cell line: Good news and bad news. The use of in vitro-cultured cells within the biomedical life sciences is an indispensable tool for a variety of fundamental assays. However, examples of using incorrect cell lines in research have been reported for a variety of tumor types. A database maintained by the International Cell Line Authentication Committee (ICLAC) lists over 350 cell lines that have been misidentified or cross-contaminated and publications based on these cell lines. Although many of these have been contaminated by the HeLa cell line, the problem is even more pervasive. In this report, published in Science Translational Medicine, Allen et al. asked two key questions: 1. Have the identity of the donor and the actual tumor origin of the cell line been accurately determined? 2. To what extent does the cell line reflect the phenotype of the tumor type of origin? The authors showed, based on genotyping of short tandem repeat (STR) markers, that the commonly used cell line U87MG, which was established around 1960 in Uppsala, Sweden, does not originate from the patient it is claimed to stem from. Importantly, Nature research journals, AACR publications, and other scientific journals initiated a crucial step forward in quality assurance by requiring cell line authentication using DNA analysis. Nevertheless, the new findings published by Allen et al., demonstrate that it is not suffice to establish the identity of a cell line if the alleged origin of the reference line is unknown or even false, as shown in the case of U87MG. This is an essential point if scientists want to claim that the cells, and thereby the research results, are true representatives of the original tumor.
Analysis and Implementation of an Electronic Laboratory Notebook in a Biomedical Research Institute. Scientists use lab notebooks (LNs) to document their hypotheses, experiments and initial analysis or interpretation of experiments. While complexity of science has changed dramatically over the last century, LNs have remained essentially unchanged since pre-modern science. However, in the past few years, the number of electronic LNs (ELNs) has increased considerably from open-source software solutions to commercial ones. In this article, Guerrero et al. performed a technical comparison of six ELNs and conducted two survey-based studies to compare two of them with each other (PerkinElmer Elements and Microsoft OneNote). In addition, use of tablet-based devices and wearable technology as parts of ELNs were tested. Finally, this publication defines essential features of ELNs that could be used to improve ELN implementation and software development in a scientific laboratory environment.
Mouse microbes may make scientific studies harder to replicate.“Microbiome” is a term used to refer to gut bacteria but also to other inhabitants of the gut, like viruses, fungi, and protozoa. In this article, K. Servick discussed the impact of the microbiome on varying experimental data. The microbes that reside in mice can make it difficult to replicate scientific studies. While mice in the same cage tend to have the same microbes, differences exist between groups, cages, and even individual mice based on a variety of factors (e.g. change in diet, a new stress level, or where and how mice were kept by vendors) that cannot be easily standardized or regulated in an experimental setting.
However, although the microbiome issue can have an effect on in-between-lab reproducibility, it should not be an issue for evaluating the impact of a treatment for humans. Here, potential drugs and new applications are expected to produce strong and robust effects in humans, which represent many different genotypes with different microbiological states. Mice showing those differences due to the microbiome may therefore be beneficial for immunological studies and could help explain some of the differing biological responses to treatment experienced in humans.
Empirical assessment of published effect sizes and power in the recent cognitive neuroscience and psychology literature. In this article, published in ‘bioRxiv’, a free online platform for unpublished preprints, Denes Szucs and John PA Ioannidis have analyzed the distribution of effect sizes and estimated power in recent cognitive neuroscience and psychology papers published during the past 5 years. They found that a combination of low power, selective reporting and other biases and errors leads to a “false report probability” that is expected to exceed 50% of the whole literature. Since low power, selection bias, questionable research practices and errors apparently favor the publication of statistically significant results and have been proposed as major contributing factors to the reproducibility crisis, the results published by Szucs and Ioannidis emphasize that efforts to increase sample size and reduce bias are likely to be beneficial for the credibility of the scientific literature.
A STAR Is Born – Cell Press transforms the methods section of articles to improved transparency and accessibility. As one of the steps to improve scientific reproducibility, the biomedical journal Cell will introduce a redesigned methods section to help authors to communicate more clearly how experiments are conducted. As stated by Cell, ‘the Structured, Transparent, Accessible Reporting (STAR) Methods promote rigor and robustness with an intuitive, consistent framework that integrates seamlessly into the scientific information flow – making reporting easier for authors and replication easier for readers. The focus is on the “Key Resources Table,” which offers an overview of the key reagents and resources (e.g. antibodies, animal models or software) used to produce the results in the paper.’ This initiative highlights the importance of the methods section in the scientific literature and will help to support robust and rigorous reporting.
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