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.

Uncoupling Molecular Testing for SARS-CoV-2 From International Supply Chains.

The rapid global rise of COVID-19 from late 2019 caught major manufacturers of RT-qPCR reagents by surprise and threw into sharp focus the heavy reliance of molecular diagnostic providers on a handful of reagent suppliers. In addition, lockdown and transport bans, necessarily imposed to contain disease spread, put pressure on global supply lines with freight volumes severely restricted. These issues were acutely felt in New Zealand, an island nation located at the end of most supply lines. This led New Zealand scientists to pose the hypothetical question: in a doomsday scenario where access to COVID-19 RT-qPCR reagents became unavailable, would New Zealand possess the expertise and infrastructure to make its own reagents onshore? In this work we describe a review of New Zealand's COVID-19 test requirements, bring together local experts and resources to make all reagents for the RT-qPCR process, and create a COVID-19 diagnostic assay referred to as HomeBrew (HB) RT-qPCR from onshore synthesized components. This one-step RT-qPCR assay was evaluated using clinical samples and shown to be comparable to a commercial COVID-19 assay. Through this work we show New Zealand has both the expertise and, with sufficient lead time and forward planning, infrastructure capacity to meet reagent supply challenges if they were ever to emerge.

Comparability of laboratory-developed and commercial PD-L1 assays in non-small cell lung carcinoma.

PD-L1 expression in non-small cell lung cancer (NSCLC) is predictive of response to treatment with PD-1 and PD-L1 inhibitors. Different inhibitors have been developed with different PD-L1 assays, which use different PD-1 antibody clones on different immunohistochemistry platforms. Depending on instrument and reagent availability, laboratory-developed tests with cross-platform use of PD-L1 antibodies may have practical benefits over commercial assays. The 22C3 pharmDx Assay (referred to as 22C3 DAKO), the VENTANA PD-L1 SP263 Assay (referred to as SP263 VENTANA) and a lab-developed test using the 22C3 antibody on the VENTANA BenchMark ULTRA IHC/ISH system (referred to as 22C3 VENTANA) were performed on whole sections of 85 NSCLC surgical resections. All sections were independently scored by three pathologists using tumor proportion scores. Correlation coefficients for continuous scores in pairwise comparisons between assays ranged from 0.976 to 0.978. When using a 1% positivity threshold (dichotomous scores), the 22C3 DAKO assay and 22C3 VENTANA assays showed the greatest agreement (93% agreement, κ = 0.86, 95% CI 0.75-0.97), and the 22C3 DAKO and SP263 VENTANA assays tended to show slightly less agreement (84% agreement, κ = 0.66, 95% CI 0.50-0.82). When using a 50% positivity threshold (dichotomous scores), all pairwise comparisons showed similar agreement (96-99% agreement, κ = 0.89-0.97). Overall, there was no significant difference between assays at 1% or 50% thresholds (P = .77). These data are consistent with potential interchangeability of these assays, which may widen the scope of PD-L1 assays available to laboratories and reduce logistical barriers to testing.

Annot: a Django-based sample, reagent, and experiment metadata tracking system.

BACKGROUND: In biological experiments, comprehensive experimental metadata tracking - which comprises experiment, reagent, and protocol annotation with controlled vocabulary from established ontologies - remains a challenge, especially when the experiment involves multiple laboratory scientists who execute different steps of the protocol. Here we describe Annot, a novel web application designed to provide a flexible solution for this task. RESULTS: Annot enforces the use of controlled vocabulary for sample and reagent annotation while enabling robust investigation, study, and protocol tracking. The cornerstone of Annot's implementation is a json syntax-compatible file format, which can capture detailed metadata for all aspects of complex biological experiments. Data stored in this json file format can easily be ported into spreadsheet or data frame files that can be loaded into R ( https://www.r-project.org/ ) or Pandas, Python's data analysis library ( https://pandas.pydata.org/ ). Annot is implemented in Python3 and utilizes the Django web framework, Postgresql, Nginx, and Debian. It is deployed via Docker and supports all major browsers. CONCLUSIONS: Annot offers a robust solution to annotate samples, reagents, and experimental protocols for established assays where multiple laboratory scientists are involved. Further, it provides a framework to store and retrieve metadata for data analysis and integration, and therefore ensures that data generated in different experiments can be integrated and jointly analyzed. This type of solution to metadata tracking can enhance the utility of large-scale datasets, which we demonstrate here with a large-scale microenvironment microarray study.

Addressing potential ethical issues regarding the supply of human-derived products or reagents in in vitro OECD Test Guidelines.

The number and scope of Organisation for Economic Cooperation and Development (OECD) in vitro test guidelines (TGs) are increasing, in an effort to both improve human relevance and replace in vivo animal testing.  In vitro test methods being developed for TG use are increasing the use of human based reagents, in combination with, or replacing animal derived reagents, and demand for human reagents is likely to grow in the near future.  There are a range of issues associated with the ethical use of human reagents, particularly human serum, in the adaptation and development of in vitro TGs, especially to ensure that there is no human exploitation, legal requirements are adhered to, and that the origin of the reagent is assured. To address these concerns, the OECD has instigated a workshop on ethics, sources, availability and traceability of human based reagents for TG purposes, to be held in March, 2019. The focus is to provide guidance on acceptable sources of human serum for use in in vitro TGs, in terms of donor ethics and informed consent regarding commercial use and Quality Control for safety and consistent performance, with a view to providing guidance to support the adaptation and/or development of in vitro TGs using human reagents, and to ensure that in reporting the test results to regulators, clearly defined ethical and traceability aspects are adequately addressed, for the Mutual Acceptance of Data principle to be accepted in all OECD member countries. This thought-starter provides a discussion basis to achieve those objectives.

Distribution and Availability of Essential Tuberculosis Diagnostic Items in Amhara Region, Ethiopia.

Adequate supplies of tuberculosis laboratory reagents and consumables are necessary for tuberculosis diagnosis and monitoring of treatment response. This study assessed the distribution and stock levels of laboratory commodities used in tuberculosis control in health centers of Amhara region, Ethiopia. A cross-sectional study was conducted in 82 health centers, among 801, providing sputum microscopy services. Stock levels were calculated, and distribution of reagents and consumables assessed. Thirty three (40.2%) health centers were under stocked for at least one of the key items for tuberculosis diagnosis at the time of visit. Fifteen (18.3%) health centers had no stocks of at least one of the key items (methylene blue (11%), carbol fuchsin (11%), acid alcohol (8.5%) and sputum cups (3.7%)). Of the 82 health centers, 77 (93.9%) did not fulfill the criteria for effective distribution of tuberculosis laboratory reagents and consumables. There were many health centers that had no or only low stocks of key tuberculosis laboratory reagents and consumables as a result of ineffective distribution system. It is necessary to strengthen supply chain management to ensure uninterrupted TB diagnostic service.

External quality assessment for acid fast bacilli smear microscopy in eastern part of Ethiopia.

BACKGROUND: External quality assessment (EQA) of sputum smear microscopy is essential and indispensable component of any tuberculosis program. This study assessed the EQA of acid fast bacilli (AFB) smear microscopy through onsite evaluation, blinded rechecking and panel test. A one year study was conducted on eight health institution laboratories from December 2011 to December 2012. Onsite evaluation, blinded rechecking and panel tests were used to collect data. Data were analyzed using SPSS version 16. Sensitivity, specificity, predictive values, and proportions of false readings were calculated. The level of agreement was measured using Kappa (κ) value. RESULTS: Problems observed during onsite evaluation include shortages of materials, disinfectant, and poor storage and working condition. A total of 578 slides were collected for blinded rechecking, of which 102 (17.6%) were reported as positive by peripheral laboratories. The panel test revealed an overall error of 17 (25.25%) of which 14 (17.5%) were minor errors [low false negative 6 (7.5%) and low false positive 8 (10%)], and 3 (3.75%) were major errors (high false positive). The sensitivity, specificity, positive predictive values (PPV) and negative predictive values (NPV) of the peripheral laboratories were 83.5, 97.8, 91.7, and 95.7, respectively. The false readings at the peripheral laboratories were 32 (5.5%). Agreement on reading the slides was observed on 546 (94.5%) slides (K = 0.84, SE = 0.054). CONCLUSIONS: Lack of reagents, supplies, favorable working environment and AFB related technical problems were identified in the peripheral laboratories. High false negative error was found to be the predominant major error. A continuous and strong EQA scheme should be implemented to avoid reporting errors and produce quality sputum results.

Ligand binding assay critical reagents and their stability: recommendations and best practices from the Global Bioanalysis Consortium Harmonization Team.

The L4 Global Harmonization Team on reagents and their stability focused on the management of critical reagents for pharmacokinetic, immunogenicity, and biomarker ligand binding assays. Regulatory guidance recognizes that reagents are important for ligand binding assays but do not address numerous aspects of critical reagent life cycle management. Reagents can be obtained from external vendors or developed internally, but regardless of their source, there are numerous considerations for their reliable long-term use. The authors have identified current best practices and provided recommendations for critical reagent lot changes, stability management, and documentation.

[The actual place of molecular analysis for donors and recipients in red blood cell immuno-hematology]. / Place actuelle de la biologie moléculaire en immuno-hématologie donneur et receveur.

Molecular testing in red blood cell immuno-haematology is used extensively since the last 5 past years because of the technical developments and the possibility to use commercial kits. But these analyses have a high cost and rely on dedicated laboratories. Therefore, serology remains a reference technique for many laboratories in France, and in the world. Molecular analyses are used to resolve problems that cannot be resolved by serology. In this review, we will detail the main indications of molecular analysis, in donors and recipients, taking into account the technical tools that we can use, and the knowledge that we have about blood groups and their different variants. In this context, we have to remember that a molecular analysis has to be performed only if there is a benefice for the patient in the transfusion or the obstetrical setting.

[Research of regional medical consumables reagent logistics system in the modern hospital].

OBJECTIVE: To explore the modern hospital and regional medical consumable reagents logistics system management. METHODS: The characteristics of regional logistics, through cooperation between medical institutions within the region, and organize a wide range of special logistics activities, to make reasonable of the regional medical consumable reagents logistics. To set the regional management system, dynamic management systems, supply chain information management system, after-sales service system and assessment system. By the research of existing medical market and medical resources, to establish the regional medical supplies reagents directory and the initial data. The emphasis is centralized dispatch of medical supplies reagents, to introduce qualified logistics company for dispatching, to improve the modern hospital management efficiency, to costs down. RESULTS: Regional medical center and regional community health service centers constitute a regional logistics network, the introduction of medical consumable reagents logistics services, fully embodies integrity level, relevance, purpose, environmental adaptability of characteristics by the medical consumable reagents regional logistics distribution. CONCLUSIONS: Modern logistics distribution systems can increase the area of medical consumables reagent management efficiency and reduce costs.

Synthesis of coumestan derivatives via FeCl3-mediated oxidative ring closure of 4-hydroxy coumarins.

A concise and efficient approach to the syntheses of coumestan analogues has been developed. The underpinning strategy involves a FeCl(3)-mediated direct intramolecular oxidative annellation of 4-hydroxy-3-phenyl-2H-chromen-2-one derivatives. Utilizing this synthetic protocol, a variety of coumestan derivatives were conveniently obtained from readily available reagents.

[Contribution to the establishment of quality assurance in five medical microbiology departments in Togo]. / Contribution à la mise en place d'un système d'assurance qualité dans cinq laboratoires de bactériologie médicale au Togo.

In Togo, as in many other developing countries, there is a lack of data on quality control and assurance of laboratories. The present study aimed to access for the quality management system in five medical bacteriology laboratories in Togo. The study was conducted from May to August 2006. Data were recorded by an audit on the reliability of results and the technical organization of laboratories. The standard ISO 15189:2003, the Togolese guide of good laboratory practices (GBEA-Togo) and the WHO medical bacteriology standards were used as references. The results of the audit showed a lack of culture media in laboratories, inappropriate choice of culture media, partial identification of some microorganisms, variability of identification procedures, a lack of diagnostic reagents and an inability to identify some potentially pathogenic bacteria. Concerning the technical organization of laboratories, compliance average ranging from 25.8 to 54.8 % was recorded. This indicates a limited organization of such laboratories. The issue of this study showed that laboratories must be equipped, their technical organization should be improved and they must establish a program of equipment maintenance.

Advances in preparation of biological extracts for protein purification.

There are a variety of reliable methods for cellular disintegration and extraction of proteins ranging from enzymatic digestion and osmotic shock to ultrasonication, and pressure disruption. Each method has inherent advantages and disadvantages. Generally vigorous mechanical treatments reduce extract viscosity but can result in the inactivation of labile proteins by heat or oxidation, while gentle treatments may not release the target protein from the cells, and resulting extracts are extremely viscous. Depending on the cell type selected as the source for target protein expression, cellular extracts contain large amounts of nucleic acid, ribosomal material, lipids, dispersed cell wall polysaccharide, carbohydrates, chitin, small molecules, and thousands of unwanted proteins. Isolation and recovery of a single protein from this complex mixture of macromolecules presents considerable challenges. The first and possibly most important of these challenges is generation of a cellular extract that can be efficiently manipulated in downstream processes without inactivation or degradation of labile protein targets. Cell disruption techniques must rapidly and efficiently lyse cells to extract proteins with minimal proteolysis or oxidation while reducing extract viscosity caused by cell debris and genomic DNA contamination. Advanced bioprocessing equipment and reagents have been developed over the past twenty years to complement established disruption procedures and accomplish these tasks with even greater success. This chapter will summarize these advances and describe detailed protocols for some of the most popular methods for protein extraction.

Isoelectric focusing and two-dimensional gel electrophoresis.

By far the highest resolution of all separation techniques for intact proteins in a single analytical run continues to be by the combination of isoelectric focusing (IEF) and SDS-PAGE, originally introduced by O'Farrell [(1975). J. Biol. Chem.250, 4007-4021]. This analytical platform has seen a number of significant advances and applications over the past 25years, including reproducibility using immobilized pH gradient (IPG) strips [Bjellqvist et al. (1982). J. Biochem. Biophys. Methods6, 317-339.], resolution in alkaline IEF using hydroxyethyldisulfide (HED) [Olsson et al. (2002). Proteomics2, 1630-1632], and quantification for differential expression proteomics on intact proteins on a global scale [DIGE; Unlu et al. (1997). Electrophoresis18, 2071-2077]. These major improvements will be highlighted in this chapter alongside the principle and theory of 2D gel electrophoresis, as well as detailed methods for general 2D gel electrophoresis best use protocols.