Long-term repeatability and interlaboratory reproducibility of high-precision ID-TIMS U-Pb geochronology

Age determination of minerals using the U-Pb technique is widely used to quantify time in Earth’s history. A number of geochronology laboratories produce the highest precision U-Pb dates employing the...

Galleria mellonella as an infection model: an in-depth look at why it works and practical considerations for successful application

ABSTRACT The larva of the greater wax moth Galleria mellonella is an increasingly popular model for assessing the virulence of bacterial pathogens and the effectiveness of antimicrobial agents. In this review, we discuss details of the components of the G. mellonella larval immune system that underpin its use as an alternative infection model, and provide an updated overview of the state of the art of research with G. mellonella infection models to study bacterial virulence, and in the evaluation of antimicrobial efficacy. Emphasis is given to virulence studies with relevant human and veterinary pathogens, especially Escherichia coli and bacteria of the ESKAPE group. In addition, we make practical recommendations for larval rearing and testing, and overcoming potential limitations of the use of the model, which facilitate intra- and interlaboratory reproducibility.

Analytical validation of the Immunoscore and its associated prognostic value in patients with colon cancer

BackgroundNew and fully validated tests need to be brought into clinical practice to improve the estimation of recurrence risk in patients with colon cancer. The aim of this study was to assess the analytical performances of the Immunoscore (IS) and show its contribution to prognosis prediction.MethodsImmunohistochemical staining of CD3+ and CD8+ T cells on adjacent sections of colon cancer tissues were quantified in the core of the tumor and its invasive margin with dedicated IS modules integrated into digital pathology software. Staining intensity across samples collected between 1989 and 2016 (n=595) was measured. The accuracy of the IS workflow was established by comparing optical and automatic counts. Analytical precision of the IS was evaluated within individual tumor block on distant sections and between eligible blocks. The IS interlaboratory reproducibility (n=100) and overall assay precision were assessed (n=3). Contribution of the IS to prediction of recurrence based on clinical and molecular parameters was determined (n=538).ResultsOptical and automatic counts for CD3+ or CD8+ were strongly correlated (r=0.94, p<0.001 and r=0.92, p<0.001, respectively). CD3 and CD8 staining intensities were not altered by the age of the tumor block over a period of 30 years. Neither the position of tested tissue sections within a tumor block nor the selection of the tissue blocks affected the IS. Reproducibility of the IS was not affected by multiple variables (eg, antibody lots, DAB revelation kits, immunohistochemistry automates and operators). Interassay repeatability of the IS was 100% and interlaboratory reproducibility between two testing centers was 93%. Finally, in a case series of patients with stage II–III colon cancer, the relative proportion of variance for time to recurrence was greatest for the IS (53% of prognostic variability) in a model that included IS, T-stage, microsatellite instability status and total number of lymph nodes.ConclusionIS is a robust and validated clinical assay leveraging immune scoring to predict recurrence risk of patient with localized colon cancer. The strong and independent prognostic value of IS should pave the way for it use in clinical practice.

The ABRF Metabolomics Research Group 2016 Exploratory Study: Investigation of Data Analysis Methods for Untargeted Metabolomics

Lack of standardized applications of bioinformatics and statistical approaches for pre- and postprocessing of global metabolomic profiling data sets collected using high-resolution mass spectrometry platforms remains an inadequately addressed issue in the field. Several publications now recognize that data analysis outcome variability is caused by different data treatment approaches. Yet, there is a lack of interlaboratory reproducibility studies that have looked at the contribution of data analysis techniques toward variability/overlap of results. The goal of our study was to identify the contribution of data pre- and postprocessing methods on metabolomics analysis results. We performed urinary metabolomics from samples obtained from mice exposed to 5 Gray of external beam gamma rays and those exposed to sham irradiation (control group). The data files were made available to study participants for comparative analysis using commonly used bioinformatics and/or biostatistics approaches in their laboratories. The participants were asked to report back the top 50 metabolites/features contributing significantly to the group differences. Herein we describe the outcome of this study which suggests that data preprocessing is critical in defining the outcome of untargeted metabolomic studies.

Analytical Method of Multi-Mycotoxins in Table-Ready Foods for a Total Diet Study Using Stable Isotope Dilution Liquid Chromatography–Tandem Mass Spectrometry

Background: Determining the multi-mycotoxins present in table-ready foods is necessary for a total diet study. However, so far, most methods of analyzing multi-mycotoxins apply to raw foods. Therefore, a reliable method for analyzing multi-mycotoxins in table-ready foods is needed. Objective: We developed and validated methods of multi-mycotoxin analysis that employed stable isotope dilution with LC–tandem MS (LC–MS/MS) using two representative matrices. Methods: Samples were fortified with [13C]-labeled mycotoxins as internal standards and extracted with 50% acetonitrile in water for high-carbohydrate foods and 3% formic acid in acetonitrile for high-protein and/or high-fat foods, cleaned up with n-hexane and the quick, easy, cheap, effective, rugged, and safe (QuEChERS) method, and followed up by LC–MS/MS. Results: Validation of the methods was performed, and the results were as follows: the correlation coefficient, R2, was 0.99; method detection limit, 0.01–2.4 μg/kg; recoveries, 83.6–114%; precision, 0.8–10 (intraday) and 3.1–22% (interday); interlaboratory reproducibility, ≤15%; and uncertainty, 3.5–19%error. The applicability of the methods was evaluated by analyzing table-ready foods spiked with standards. Conclusions: These methods were successfully evaluated and deemed appropriate for determining the multi-mycotoxins in table-ready foods. Highlights: This work demonstrates that stable isotope dilution with LC–MS/MS can be effectively used to analyze multi-mycotoxins simultaneously in a total diet study.

Analytical Method of Multi-Mycotoxins in Table-Ready Foods for a Total Diet Study Using Stable Isotope Dilution Liquid Chromatography–Tandem Mass Spectrometry

Background: Determining the multi-mycotoxins present in table-ready foods is necessary for a total diet study. However, so far, most methods of analyzing multi-mycotoxins apply to raw foods. Therefore, a reliable method for analyzing multi-mycotoxins in table-ready foods is needed. Objective: We developed and validated methods of multi-mycotoxin analysis that employed stable isotope dilution with LC–tandem MS (LC–MS/MS) using two representative matrices. Methods: Samples were fortified with [13C]-labeled mycotoxins as internal standards and extracted with 50% acetonitrile in water for high-carbohydrate foods and 3% formic acid in acetonitrile for high-protein and/or high-fat foods, cleaned up with n-hexane and the quick, easy, cheap, effective, rugged, and safe (QuEChERS) method, and followed up by LC–MS/MS. Results: Validation of the methods was performed, and the results were as follows: the correlation coefficient, R2, was 0.99; method detection limit, 0.01–2.4 μg/kg; recoveries, 83.6–114%; precision, 0.8–10 (intraday) and 3.1–22% (interday); interlaboratory reproducibility, ≤15%; and uncertainty, 3.5–19%error. The applicability of the methods was evaluated by analyzing table-ready foods spiked with standards. Conclusions: These methods were successfully evaluated and deemed appropriate for determining the multi-mycotoxins in table-ready foods. Highlights: This work demonstrates that stable isotope dilution with LC–MS/MS can be effectively used to analyze multi-mycotoxins simultaneously in a total diet study.