Applying the science of measurement to biology: Why bother?

Multicenter evaluation of light transmission platelet aggregation reagents: communication from the ISTH SSC Subcommittee on Platelet Physiology

BACKGROUND

Light transmission aggregation (LTA) is used widely by the clinical and research communities. Although it is a gold standard, there is a lack of interlaboratory harmonization.

OBJECTIVES

The primary objective was to assess whether sources of activators (mainly adenosine diphosphate [ADP], collagen, arachidonic acid, epinephrine, and thrombin receptor activating peptide6) and ristocetin contribute to poor LTA reproducibility. The secondary objective was to evaluate interindividual variability of results to appreciate the distribution of normal values and consequently better interpret pathologic results.

METHODS

An international multicenter study involving 28 laboratories in which we compared LTA results obtained with center-specific activators and a comparator that we supplied.

RESULTS

We report variability in the potency (P) of activators in comparison with the comparator. Thrombin receptor activating peptide 6 (P, 1.32-2.68), arachidonic acid (P, 0.87-1.43), and epinephrine (P, 0.97-1.34) showed the greatest variability. ADP (P, 1.04-1.20) and ristocetin (P, 0.98-1.07) were the most consistent. The data highlighted clear interindividual variability, notably for ADP and epinephrine. Four profiles of responses were observed with ADP from high-responders, intermediate-responders, and low-responders. A fifth profile corresponding to nonresponders (5% of the individuals) was observed with epinephrine.

CONCLUSION

Based on these data, the establishment and adoption of simple standardization principles should mitigate variability due to activator sources. The observation of huge interindividual variability for certain concentrations of activators should lead to a cautious interpretation before reporting a result as abnormal. Confidence can be taken from the fact that difference between sources is not exacerbated in patients treated with antiplatelet agents.

Unboxing the black box-one step forward to understand the soil microbiome: A systematic review

Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.

Impact of Formulation Choices on the Freeze-Drying of an Interleukin-6 Reference Material

Formulation is critical to successful delivery of lyophilized biologics. We have compared the impact of buffer choice and the addition of sodium chloride (a formulant often viewed as unfavorable for freeze-drying applications) on the outcome of trial lyophilization of an interleukin-6 reference material. While phosphate buffer was a preferred choice and yielded well-formed cakes associated with fair recovery of biological activity, the resultant residual moisture content was high (2–4% w/w). By inclusion of isotonic levels of NaCl, the freeze-dried appearance and process were not impaired, but the residual moisture delivered was considerably reduced to levels <1% w/w. We postulate that this is due to the presence of a more open-cake structure and support this with evidence from thermal analysis and scanning electron microscopy. This work illustrates the importance of wide ranging empirical investigation of formulation options in order to optimize freeze-drying outcomes for biologics.

Assessing the Variability of Cell-Associated HIV DNA Quantification through a Multicenter Collaborative Study

Reliable and accurate quantification of cell-associated HIV DNA (CA HIV DNA) is critical for early infant diagnosis, clinical management of patients under therapy, and to inform new therapeutics efficacy. The present study assessed the variability of CA HIV DNA quantification obtained from various assays and the value of using reference materials to help harmonize the measurements. Using a common set of reagents, our multicenter collaborative study highlights significant variability of CA HIV DNA quantification and lower limit of quantification across assays. The quantification of CA HIV DNA from a panel of infected PBMCs can be harmonized through cross-subtype normalization but assay calibration with the commonly used 8E5 cell line failed to reduce quantification variability between assays, demonstrating the requirement to thoroughly evaluate reference material candidates to help improve the comparability of CA HIV DNA diagnostic assay performance. IMPORTANCE Despite a global effort, HIV remains a major public health burden with an estimated 1.5 million new infections occurring in 2020. HIV DNA is an important viral marker, and its monitoring plays a critical role in the fight against HIV: supporting diagnosis in infants and underpinning clinical management of patients under therapy. Our study demonstrates that HIV DNA measurement of the same samples can vary significantly from one laboratory to another, due to heterogeneity in the assay, protocol, and reagents used. We show that when carefully selected, reference materials can reduce measurement variability and harmonize HIV DNA quantification across laboratories, which will help contribute to improved diagnosis and clinical management of patients living with HIV.

The importance of metrological tools to implementation of alternative method OECD TG 428

Usually, if percutaneous absorption tests are conducted in accordance with OECD Guideline 428, in vitro determination is accepted by mainly regulatory agencies. In this paper, we focus on the lack of comparability of the results regarding the permeation parameter/flow rate, although it is widely discussed in the literature. This work sought to evaluate the absorption of caffeine using Franz-type diffusion cell with porcine ear skin samples, varying the storage duration and the way to handle them. Metrological tools were used for caffeine quantification such as certified reference material candidate, calibrated instruments, and validated methodology. Our results corroborate with the recommendation that membranes should be freshly prepared or frozen for short periods. Samples frozen for approximately one year should not be used because they present high cutaneous absorption. The results obtained for the absorption rate (J) are comparable to the results obtained by previous studies using similar experimental conditions. The evidence of the barrier characteristic promoted by the stratum corneum and the effect promoted by the storage time is shown through J = 6.25 ± 0.48 μg/cm²/h. We demonstrated the importance of metrological tools to guarantee reproducibility and comparability of the results between different laboratories.

Essential signals in publication trends and collaboration patterns in global Research Integrity and Research Ethics (RIRE)

Amid an increasingly demanding research environment, there has been a growing interest in studies concerning Research Integrity and Research Ethics (RIRE). Between 1990 and 2020, over 9700 publications were published to address problematic research conduct such as falsification, plagiarism, and related protocols and standards. In this work, country-level trends and collaborative structures are examined with respect to economic group. Our results showed that RIRE publications are predominantly led by the West, with North America and Western Europe contributing the most. While there is interest within growing economies such as China, the pace is not comparable to its overall publications. However, international collaborations on RIRE grew to account for nearly 30% of all publications on the subject in 2020. Although there is a stronger preference for high income countries to collaborate with other high income countries, we observe a rise in partnerships between high-/middle-income and middle-/lower-income co-authorship pairs in the last decade. These trends point to a maturing global community with distributed knowledge transfer, towards more unified international standards for research ethics and integrity.

An SI-traceable reference material for virus-like particles

A reference material for virus-like particles traceable to the International System of Units (Système International d'Unités – the SI) is reported. The material addresses the need for developing reference standards to benchmark virus-like gene delivery systems and help harmonize measurement approaches for characterization and testing. The material is a major component of synthetic polypeptide virus-like particles produced by the state-of-the-art synthetic and analytical chemistry methods used to generate gene delivery systems. The purity profile of the material is evaluated to the highest metrological order demonstrating traceability to the SI. The material adds to the emerging toolkit of reference standards for quantitative biology.

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A reference material for virus-like particles with traceability to the SI

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The material is a major component of virus-like particles capable of gene delivery

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Purity profile of the material is evaluated to the highest metrological order

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The material allows comparability of physicochemical properties of virus-like systems

Measuring Fibrinolysis

Physiological fibrinolysis under normal conditions progresses slowly, in contrast to coagulation which is triggered rapidly to stop bleeding and defend against microbial invasion. Methods to detect fibrinolysis abnormalities are less simple and poorly standardized compared with common coagulation tests. Fibrinolysis can be accelerated by preparing euglobulin from plasma to reduce endogenous inhibitors, or by adding plasminogen activators to normal plasma. However, these manipulations complicate interpretation of results and diagnosis of a "fibrinolysis deficit." Many observational studies on antigen levels of fibrinolysis inhibitors, plasminogen activator inhibitor 1 or thrombin-activatable fibrinolysis inhibitor, zymogen or active enzyme have been published. However, conclusions are mixed and there are clear problems with harmonization of results. Viscoelastic methods have the advantage of being rapid and are used as point-of-care tests. They also work with whole blood, allowing the contribution of platelets to be explored. However, there are no agreed protocols for applying viscoelastic methods in acute care for the diagnosis of hyperfibrinolysis or to direct therapy. The emergence of SARS-CoV-2 and the dangers of associated coagulopathy provide new challenges. A common finding in hospitalized patients is high levels of D-dimer fibrin breakdown products, indicative of ongoing fibrinolysis. Well-established problems with D-dimer testing standardization signal that we should be cautious in using results from such tests as prognostic indicators or to target therapies.

Bioavailability and bioaccessibility of food bioactive compounds; overview and assessment by in vitro methods

Oral bioavailability is the key to the bioefficiency of food bioactive ingredients; it evaluates the relationship between foods and their health benefits. The analysis of the main factors limiting the oral bioavailability (bioaccessibility, absorption, and transformation) has led to the proposal of classification systems for pharmaceuticals and nutraceuticals (Biopharmaceuticals Classification System and Nutraceutical Bioavailability Classification Scheme). Based on the relevant studies published in the last decade, this review presents the essential aspects regarding the factors limiting the oral bioavailability of the biocomponents and different in vitro methods used to investigate the mechanisms involved in the digestion, absorption, and metabolism of biocomponents, particularly encapsulated bioactive compounds. Oral bioavailability investigated by in vitro studies provides the food and drug manufacturers with information to formulate delivery systems more efficiently and to determine the dosage of biocomponents for increase the health benefits and avoid or reduce the risk of toxicity.

Establishment of a WHO Reference Reagent for anti-Mullerian hormone

BACKGROUND

There is a need for a reference material to support the development and ensure the quality of immunoassays for human AMH. A batch of ampoules, coded 16/190, containing lyophilised recombinant AMH was evaluated in a WHO Collaborative Study. The aims of the study were to determine the AMH content in terms of the calibration of each immunoassay method, to predict long-term stability and to assess the suitability of the preparation to calibrate AMH immunoassays.

METHODS

Study participants were asked to report the AMH content of specific dilutions of coded ampoules of 16/190 and a comparator preparation containing approximately half the AMH content. In each assay, participants also reported the AMH content of 22 patient samples to assess commutability. A robust all-laboratory geometric mean of the content estimates was determined using the laboratory geometric mean estimates. Commutability was assessed using a difference in bias approach. Stability was predicted by the measurement of thermally accelerated degradation samples.

RESULTS

Seven laboratories performed twenty-one immunoassay method-platform combinations, sixteen of which provided data which met the validity criteria, giving a consensus geometric mean estimate of AMH content of 511 ng/ampoule (95% CI, 426-612, n = 16, GCV 42%) and a robust geometric mean of 489 ng/ampoule. By contrast, the GCV% for the all-laboratory geometric mean of the relative content estimates for the comparator sample to 16/190 was 12%. Commutability was assessed using 20 of the 22 representative patient samples. Of the valid assays, 16/190 was within the limits of acceptable commutability for 6 methods, partially commutable for a further 3 methods and non-commutable when measured by 7 methods. The preparation was predicted to be highly stable when stored at - 20 °C.

CONCLUSION

The majority of methods met the validity criteria. Content estimates showed a high between-method variability, yet assays exhibited a similar proportionality of response as demonstrated using the comparator sample. 16/190 was commutable in some but not all methods. On the basis of these results, it was agreed by the WHO Expert Committee on Biological Standardization to establish 16/190 as a WHO Reference Reagent for AMH with a content defined by consensus immunoassay of 489 ng/ampoule.

Developing standards for the microbiome field

BACKGROUND

Effective standardisation of methodologies to analyse the microbiome is essential to the entire microbiome community. Despite the microbiome field being established for over a decade, there are no accredited or certified reference materials available to the wider community. In this study, we describe the development of the first reference reagents produced by the National Institute for Biological Standards and Control (NIBSC) for microbiome analysis by next-generation sequencing. These can act as global working standards and will be evaluated as candidate World Health Organization International Reference Reagents.

RESULTS

We developed the NIBSC DNA reference reagents Gut-Mix-RR and Gut-HiLo-RR and a four-measure framework for evaluation of bioinformatics tool and pipeline bias. Using these reagents and reporting system, we performed an independent evaluation of a variety of bioinformatics tools by analysing shotgun sequencing and 16S rRNA sequencing data generated from the Gut-Mix-RR and Gut-HiLo-RR. We demonstrate that key measures of microbiome health, such as diversity estimates, are largely inflated by the majority of bioinformatics tools. Across all tested tools, biases were present, with a clear trade-off occurring between sensitivity and the relative abundance of false positives in the final dataset. Using commercially available mock communities, we investigated how the composition of reference reagents may impact benchmarking studies. Reporting measures consistently changed when the same bioinformatics tools were used on different community compositions. This was influenced by both community complexity and taxonomy of species present. Both NIBSC reference reagents, which consisted of gut commensal species, proved to be the most challenging for the majority of bioinformatics tools tested. Going forward, we recommend the field uses site-specific reagents of a high complexity to ensure pipeline benchmarking is fit for purpose.

CONCLUSIONS

If a consensus of acceptable levels of error can be agreed on, widespread adoption of these reference reagents will standardise downstream gut microbiome analyses. We propose to do this through a large open-invite collaborative study for multiple laboratories in 2020. Video Abstract.

Growing a circular economy with fungal biotechnology: a white paper

Fungi have the ability to transform organic materials into a rich and diverse set of useful products and provide distinct opportunities for tackling the urgent challenges before all humans. Fungal biotechnology can advance the transition from our petroleum-based economy into a bio-based circular economy and has the ability to sustainably produce resilient sources of food, feed, chemicals, fuels, textiles, and materials for construction, automotive and transportation industries, for furniture and beyond. Fungal biotechnology offers solutions for securing, stabilizing and enhancing the food supply for a growing human population, while simultaneously lowering greenhouse gas emissions. Fungal biotechnology has, thus, the potential to make a significant contribution to climate change mitigation and meeting the United Nation’s sustainable development goals through the rational improvement of new and established fungal cell factories. The White Paper presented here is the result of the 2nd Think Tank meeting held by the EUROFUNG consortium in Berlin in October 2019. This paper highlights discussions on current opportunities and research challenges in fungal biotechnology and aims to inform scientists, educators, the general public, industrial stakeholders and policymakers about the current fungal biotech revolution.

Collaborative study for the calibration of the replacement International Standard for pertussis toxin for use in histamine sensitisation and CHO cell clustering assays

Pertussis toxin (PT) in its detoxified form is one of the major protective antigens in vaccines against Bordetella pertussis (whooping cough). Reference preparations of native PT are required for the quality control of pertussis vaccines. Stocks of the first WHO International Standard (IS) for PT (JNIH-5) were low and a replacement was required. One candidate material was donated by a vaccine manufacturer to NIBSC. It was formulated, lyophilised into sealed glass ampoules and coded 15/126. An international collaborative study assessed the suitability of this material to replace JNIH-5. Fourteen laboratories from 12 countries took part in the study. Eleven laboratories performed lethal murine histamine sensitisation assay (HIST), 14 performed Chinese Hamster Ovary (CHO) cell clustering assay. International Units (IU) were assigned to the material using these assays as they were used to assign units to JNIH-5. It was found that, unlike JNIH-5, the activities of 15/126 in HIST and CHO cell assays did not agree and therefore different unitage for each assay was assigned. The preparation 15/126 was established as the Second WHO IS for PT for HIST and CHO cell assays. It was assigned a unitage of 1,881 IU/ampoule in HIST and 680 IU/ampoule in the CHO cell clustering assay.

The Role of Reference Materials in the Research and Development of Diagnostic Tools and Treatments for Haemorrhagic Fever Viruses

Following the Ebola outbreak in Western Africa in 2013-16, a global effort has taken place for preparedness for future outbreaks. As part of this response, the development of vaccines, treatments and diagnostic tools has been accelerated, especially towards pathogens listed as likely to cause an epidemic and for which there are no current treatments. Several of the priority pathogens identified by the World Health Organisation are haemorrhagic fever viruses. This review provides information on the role of reference materials as an enabling tool for the development and evaluation of assays, and ultimately vaccines and treatments. The types of standards available are described, along with how they can be applied for assay harmonisation through calibration as a relative potency to a common arbitrary unitage system (WHO International Unit). This assures that assay metrology is accurate and robust. We describe reference materials that have been or are being developed for haemorrhagic fever viruses and consider the issues surrounding their production, particularly that of biosafety where the viruses require specialised containment facilities. Finally, we advocate the use of reference materials at early stages, including research and development, as this helps produce reliable assays and can smooth the path to regulatory approval.