Cross-contamination of CRISPR guides and other unrelated nucleotide sequences among commercial oligonucleotides.

Custom oligonucleotides (oligos) are widely used reagents in biomedical research. Some common applications of oligos include polymerase chain reaction (PCR), sequencing, hybridization, microarray, and library construction. The reliability of oligos in such applications depends on their purity and specificity. Here, we report that commercially available oligos are frequently contaminated with nonspecific sequences (i.e. other unrelated oligonucleotides). Most of the oligos that we designed to amplify clustered regularly interspersed palindromic repeats (CRISPR) guide sequences contained nonspecific CRISPR guides. These contaminants were detected in research-grade oligos procured from eight commercial oligo-suppliers located in three different geographic regions of the world. Deep sequencing of some of the oligos revealed a variety of contaminants. Given the wide range of applications of oligos, the impact of oligo cross-contamination varies greatly depending on the field and the experimental method. Incorporating appropriate control experiments in research design can help ensure that the quality of oligo reagents meets the intended purpose. This can also minimize risk depending on the purposes for which the oligos are used.

From viability to cell death: Claims with insufficient evidence in high-impact cell culture studies.

BACKGROUND: Reliability of preclinical research is of critical concern. Prior studies have demonstrated the low reproducibility of research results and recommend implementing higher standards to improve overall quality and robustness of research. One understudied aspect of this quality issue is the harmony between the research hypotheses and the experimental design in published work. METHODS AND FINDINGS: In this study we focused on highly cited cell culture studies and investigated whether commonly asserted cell culture claims such as viability, cytotoxicity, proliferation rate, cell death and apoptosis are backed with sufficient experimental evidence or not. We created an open access database containing 280 claims asserted by 103 different high-impact articles as well as the results of this study. Our findings revealed that only 64% of all claims were sufficiently supported by evidence and there were concerning misinterpretations such as considering the results of tetrazolium salt reduction assays as indicators of cell death or apoptosis. CONCLUSIONS: Our analysis revealed a discordance between experimental findings and the way they were presented and discussed in the manuscripts. To improve quality of pre-clinical research, we require clear nomenclature by which different cell culture claims are distinctively categorized; materials and methods sections to be written more meticulously; and cell culture methods to be selected and utilized more carefully. In this paper we recommend a nomenclature for selected cell culture claims as well as a methodology for collecting evidence to support those claims.

Development and validation of a multiplex real-time qPCR assay using GMP-grade reagents for leprosy diagnosis.

Leprosy is a chronic dermato-neurological disease caused by Mycobacterium leprae, an obligate intracellular bacterium. Timely detection is a challenge in leprosy diagnosis, relying on clinical examination and trained health professionals. Furthermore, adequate care and transmission control depend on early and reliable pathogen detection. Here, we describe a qPCR test for routine diagnosis of leprosy-suspected patients. The reaction simultaneously amplifies two specific Mycobacterium leprae targets (16S rRNA and RLEP), and the human 18S rRNA gene as internal control. The limit of detection was estimated to be 2.29 copies of the M. leprae genome. Analytical specificity was evaluated using a panel of 20 other skin pathogenic microorganisms and Mycobacteria, showing no cross-reactivity. Intra- and inter-operator Cp variation was evaluated using dilution curves of M. leprae DNA or a synthetic gene, and no significant difference was observed between three operators in two different laboratories. The multiplex assay was evaluated using 97 patient samples with clinical and histopathological leprosy confirmation, displaying high diagnostic sensitivity (91%) and specificity (100%). Validation tests in an independent panel of 50 samples confirmed sensitivity and specificity of 97% and 98%, respectively. Importantly, assay performance remained stable for at least five months. Our results show that the newly developed multiplex qPCR effectively and specifically detects M. leprae DNA in skin samples, contributing to an efficient diagnosis that expedites the appropriate treatment.

Occlusal Indicators Used in Dental Practice: A Survey Study.

INTRODUCTION: The function of the masticatory apparatus is complete when the dentition is intact with contact between the individual teeth and proper occlusion with the antagonists. For years, occlusal contacts have been studied to determine their exact location and describing various materials and methods for their registration such as paper foil, silk, and Shimstock foil. For years, occlusal contacts have been studied to determine their exact location and describe various materials and methods for their registration such as paper foil, silk, shim stock foil, the T-Scan system, and more recently the OccluSense system. The primary aim of the study was at evaluating which of the occlusal indicators is the most commonly used in practice, and the secondary aim was whether dentists are willing to use digital methods to examine occlusion. MATERIALS AND METHODS: The main primary information of the survey was collected by sending electronically anonymous questionnaires to 2014 dentists, randomly selected from all regions of the country. 228 questionnaires were filled in and returned. To achieve the goal of the study, the self-developed questionnaire was created and tested to survey the opinion about the use of occlusal indicators in dental practice. Each questionnaire contains questions about the sociodemographic and professional status of the people in the group and their opinion about the positives and negatives and the effectiveness of occlusal indicators. RESULTS: The obtained results confirm the statement that the most frequently used occlusal indicator in dental practice is the articulation paper. Articulation foil and silk are used less frequently than articulation paper. Of the listed quality indicators, Shimstock foil is rarely used in practice. Of the indicated quantitative indicators, the T-Scan system is more used than the OccluSense system. In the era of rapid technology development, the opinion and desire of dentists to increasingly want to introduce in their clinical practice quantitative methods are the digital diagnosis of occlusion. CONCLUSION: In any dental practice, if technically possible, digital methods would be used, giving more accurate and reliable data on the registered occlusal contacts.

Opinion: Independent third-party entities as a model for validation of commercial antibodies.

A vast array of commercial antibodies covers a large percentage of human gene products, but determining which among them is most appropriate for any given application is challenging. This leads to use of non-specific antibodies that contributes to issues with reproducibility. It is our opinion that the community of scientists who use commercial antibodies in their biomedical research would benefit from third-party antibody characterization entities that use standardized operating procedures to assess and compare antibody performance. Ideally, such entities would follow the principles of open science, such that all antibodies against any given protein target would be tested in parallel, and all data generated released to the public domain without bias. Furthermore, there should be no financial incentive for the entity beyond cost-recovery. Such non-profit organizations, combined with other scientific efforts, could catalyse new discoveries by providing scientists with better validated antibody tools.

Producing molecular biology reagents without purification.

We recently developed 'cellular' reagents-lyophilized bacteria overexpressing proteins of interest-that can replace commercial pure enzymes in typical diagnostic and molecular biology reactions. To make cellular reagent technology widely accessible and amenable to local production with minimal instrumentation, we now report a significantly simplified method for preparing cellular reagents that requires only a common bacterial incubator to grow and subsequently dry enzyme-expressing bacteria at 37°C with the aid of inexpensive chemical desiccants. We demonstrate application of such dried cellular reagents in common molecular and synthetic biology processes, such as PCR, qPCR, reverse transcription, isothermal amplification, and Golden Gate DNA assembly, in building easy-to-use testing kits, and in rapid reagent production for meeting extraordinary diagnostic demands such as those being faced in the ongoing SARS-CoV-2 pandemic. Furthermore, we demonstrate feasibility of local production by successfully implementing this minimized procedure and preparing cellular reagents in several countries, including the United Kingdom, Cameroon, and Ghana. Our results demonstrate possibilities for readily scalable local and distributed reagent production, and further instantiate the opportunities available via synthetic biology in general.

Research and discussion on the evaluation scheme of reagent lot-to-lot differences in 16 chemiluminescence analytes, established by the EP26-A guidelines of the CLSI.

BACKGROUND: Verification of new reagent lots is a part of the crucial tasks in clinical laboratories. The Clinical and Laboratory Standards Institute (CLSI) EP26-A guideline provides laboratories with an evaluation method for reagent verification. The purpose of this study was to compare the performance of EP26-A with our laboratory reagent lot verification protocol and get the final scheme. METHOD: 16 chemiluminescence analytes including estradiol (E2), progesterone (P), ferritin (FER), cortisol (COR),carbohydrate antigen 153 (CA153), and free prostate-specific antigen (FPSA). were prospectively evaluated in two reagent lots. The laboratory's lot verification process included evaluating 5 patient samples with the current and new lots and acceptability according to a predefined criteria. For EP26-A, method imprecision data and critical differences at medical decision points were important factors affecting the sample size requirements and rejection limits. RESULT: The number of samples required for EP26-A was 3 to 12, of which P, CA153, and FPSA had increased by more than 5 samples compared with the current protocol. Of the 16 chemiluminescence analytes, 11 had higher rejection limits when using EP26-A than the current laboratory scheme. Our current protocol and EP26-A were in agreement in 32 of the 32 (100%) paired verifications. CONCLUSION: The EP26-A protocol is an important tool to find the differences between reagent lots, and it makes up for the loopholes in the statistical efficiency, sample concentration and quantity, and the selection of rejection limits in the current protocol.

China NMPA perspective on clinical evaluation of SARS-CoV-2 antibody test reagents in the process of emergency approval.

Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 antibody testing an important supplement to nucleic acid testing. In the process of emergency approval, the Center for Medical Device Evaluation of the China National Medical Products Administration released The Key Points of Technical Review for the Registration of SARS-CoV-2 Antigen/Antibody Detection Reagents. The Clinical Study Requirement section of the Key Point has put forward requirements in terms of reference methods and subject enrolment among others, which can ensure that the test results can meet the clinical needs. This article draws on the experience of the China NMPA in evaluating diagnostic reagents used to supplement the gold standard test method in the early stage of an epidemic of an infectious disease, as well as to serve as reference for clinicians and regulators.

Monoclonal Antibody Reagent Stability and Expiry Recommendation Combining Experimental Data with Mathematical Modeling.

Monoclonal antibodies (mAbs) are widely used as critical reagents in analytical assays. While regulatory guidelines exist for stability monitoring of biopharmaceutical antibodies, they do not apply directly to the stability of mAbs used as assay reagent. We investigated alternative approaches to real-time stability monitoring of assay reagents. We compared functional (ELISA and cell-based) and biochemical (aggregation, deamidation) assay results using temperature-stressed mAb reagents. Data from both assay groups were compared for indications of antibody degradation. Arrhenius model kinetics was used to further extrapolate stability trends. Changes detected by traditionally monitored biochemical changes were not directly predictive of assay function. Instead, monitoring of reportable results was a closer indication of changes in assay performance related to mAb degradation. Using Arrhenius kinetic modeling, we combined forced degradation of individual reagents with reportable assay results to classify reagents into risk groups with associated re-evaluation and monitoring plans. This combined approach mitigates risk by monitoring each mAb reagent individually under stressed conditions while streamlining expiry assignment through simplified Arrhenius kinetics with only limited real-time stability data.

The European Federation for Medicinal Chemistry (EFMC) Best Practice Initiative: Validating Chemical Probes.

As part of an initiative aimed to share best practices in Medicinal Chemistry, the European Federation for Medicinal Chemistry (EFMC) is preparing a series of webinars and slide sets focused on the early phase of drug discovery. This educational material is freely accessible through the EFMC. The main target audiences are students or early career scientists and we also believe it will be valuable for experienced practitioners. The first of the series is focused on the generation and validation of high-quality chemical probes, which are critical for drug discovery and more broadly to further our understanding of human biology and disease.

[Determination of Absolute Purities of Hygroscopic Substances by Quantitative NMR Analysis for the Standardization of Quantitative Reagents in the Japanese Pharmacopoeia (Part 1)].

Quantitative NMR (qNMR) has been developed as an absolute quantitation method to determine the purity or content of organic compounds including marker compounds in crude drugs. The "qNMR test" has been introduced into the crude-drug section of the Japanese Pharmacopoeia (JP) for determining the purity of reagents used for the assay in the JP. In Supplement II to the JP 17th edition published in June 2019, fifteen compounds adopted qNMR test were listed as the reagents for the assay. To establish the "qNMR test" in the crude drug section of the JP, there were several problems to be solved. Previously, we reported that the handling impurity signals from reference substances and targeted marker compounds, chemical shifts of reference substances, and peak unity of signals of targeted marker compounds are important factors to conduct qNMR measurements with intended accuracy. In this study, we investigated that the hygroscopicity of reagents could cause the changes in the compounds' purity depending on increasing their water content. Twenty-one standard products used for the crude-drug test in JP were examined by water sorption-desorption analysis, and ginsenosides and saikosaponins were found to be hygroscopic. To prepare a sample solution of saikosaponin b2 for qNMR analysis, samples need to be maintained for 18 h at 25°C and 76% relative humidity; further, samples need to be weighed at the same humidity for the qNMR analysis.

[Discussion on Management Model of Medical Devices for Clinical Trials].

By analyzing the main problems existing in the current management of medical devices for clinical trials, this study proposes a feasible management model and specific requirements for acceptance, distribution, storage and recovery combining with the characteristics of medical consumable equipment and diagnostic reagent, which provides a favorable guarantee for the authenticity and reliability of clinical trials.

Validation of presumptive tests for non-human blood using Kastle Meyer and Hemastix reagents.

Kastle Meyer and Hemastix reagents are presumptive tests commonly used in forensic casework for the detection of blood, and their suitability has been reviewed in numerous publications. However, studies to date have focused on the validation of these tests on human blood alone, and no published work has looked at the sensitivity, specificity and effect on DNA analysis when using these reagents to presumptively test for animal blood. The aim of this study was to validate the two reagents for use with animal blood, and compare their performance in order to choose the best test based on the circumstances in wildlife crime investigation. The sensitivity, specificity, stability and robustness of the methods were assessed by experiments with dilutions of animal blood (from 1:4 to 1:65536) using direct and indirect (rub) tests, potential interfering substances, blood sources from different species and aged blood. The effects of the two reagents on subsequent DNA analysis were also investigated. During the direct tests, Kastle Meyer showed a higher sensitivity, detecting blood down to a dilution of 1:16,384, one order of magnitude lower than Hemastix. However during the rub test, Hemastix showed a higher sensitivity, detecting blood down to a dilution of 1:64 on porous materials while Kastle Meyer was positive only down to a dilution of 1:16. Moreover, when using the same swab for presumptive testing and DNA extraction, Hemastix testing allowed amplification of a sufficient amount of DNA for species identification at its limit of sensitivity on porous materials (1:64) while Kastle Meyer inhibited most amplification of DNA at its less sensitive limit of 1:16 dilution. On the other hand, Hemastix showed a much lower specificity, producing false positive results when exposed to tomato, potato, rust, avian uric acid, bleach and sink rot, while Kastle Meyer only produced a faint positive reaction from potato. Both tests performed equally well detecting fresh blood of different animal species. The stability test gave comparable results among the tests except for aged fish blood stains, where the Kastle Meyer test performed poorly. Owing to its ease of use, higher sensitivity, and lack of interference with downstream DNA analysis, and despite its reduced specificity compared to Kastle Meyer, the Hemastix method is more appropriate for use in wildlife crime investigations. Positive results would always be confirmed with DNA analysis and the low interference of the reagent will allow the use of a single swab for presumptive testing and DNA sampling.