Search bioRxiv⌕ Search

Biology subjects

Biddle, M.

Publications and source records attributed to Biddle, M..

4 recordsLinked to original sources

Addressing antibody validation failures: a multi-stakeholder Delphi consensus study on actionable solutions

The experimental use of antibodies that have not been validated for context-specific use frequently misdirects biomedical research. Experimental results that derive from the use of inadequately validated antibodies are estimated to waste over $1 billion annually in the United States alone and to consume millions of animal and human biological samples in experiments whose conclusions may be unreliable. Community validation frameworks, reporting standards, and independent characterisation initiatives have made important progress, and multi-stakeholder coordination efforts are emerging. However, the research community lacks a formally developed, consensus-based action plan that specifies what each stakeholder group should do, by when, and with what priority. We conducted a modified Delphi study with international experts representing academic researchers, scientific publishers, research funders, antibody manufacturers, and institutional research leaders to develop actionable recommendations for improving antibody validation, selection, and reporting practices. Thirty-two participants rated 33 proposed actions on effectiveness and feasibility using 9-point scales, with consensus assessed using the RAND/UCLA Appropriateness Method. Over two rounds, the panel achieved consensus on 15 items as both effective and feasible for implementation by 2030. These spanned institutional actions (training in antibody validation, integration into research integrity frameworks, support for local expertise networks), funder actions (dedicated validation budgets, grant application requirements, endorsement of community reporting standards), publisher actions (complete antibody reporting packages, clear validation standards), manufacturer actions (assignment of unique identifiers at source), and cross-stakeholder coordination (a shared roadmap for improvement). An additional 15 items were rated as effective but with uncertain feasibility, reflecting a consistent pattern in which the panel agreed on the value of proposed interventions but expressed reservations about realistic implementation timelines. One item was rejected by the panel with concerns around effectiveness and feasibility. Participants described four interconnected barriers to progress: diffuse ownership of the problem across stakeholders; market dynamics that inadequately reward antibody quality; difficulty justifying investment when returns are distributed across the research system; and coordination challenges among actors with different incentive structures. These barriers are addressable through coordinated action, and the findings complement existing technical and data-sharing initiatives by providing the structured, stakeholder-endorsed policy framework needed to translate awareness of the problem into concrete practice and policy changes.

scientific communication and education↗

Drivers and ethical impacts of insufficient validation of antibodies in research

Lack of antibody validation by researchers frequently misdirects biomedical research, yet the ethical consequences -- particularly avoidable use of animal and human biological materials -- remain unquantified. Using focus groups (n=12), surveys (n=107), and systematic analysis of 785 publications, we examined how researchers select and validate antibodies, and quantified the downstream ethical costs. Antibody selection is substantially influenced by social factors such as previous laboratory use and peer recommendations, while systematic evaluation of performance characteristics remains limited. From a dataset of 614 antibodies subjected to rigorous characterisation using knockout controls, 97 (15.8%) failed across all tested applications; we systematically searched for publications linked to these antibodies. Within the 760 publications (those where validation status could be confirmed), only 120 (15.8%) presented any validation evidence -- despite 72.0% of surveyed researchers reporting having used at least one recommended validation method. The remaining 640 papers reported a minimum of 8,064 animal samples and 4,424 human tissue samples used with antibodies of demonstrated poor performance and without evidence of fitness for the specific experimental purpose; we describe these as samples at risk of waste. Reserving the term waste for samples used with reagents since withdrawn from sale, and therefore irreproducible, conservative extrapolation gives lower-bound, order-of-magnitude estimates of millions of animal and human tissue samples consumed globally. Researchers identified time, cost, and lack of supervisor support as primary barriers, whilst strongly supporting open data sharing, dedicated validation funding, and publisher requirements as solutions. These findings provide a first quantification of the ethical costs of inadequate antibody validation and highlight the need for coordinated stakeholder interventions to reduce avoidable biological sample waste in biomedical research.

cell biology↗

Atomistic TCR-ligand interactions instruct memory T-cell differentiation

Memory CD8 T cells provide durable protection against recurrent infection and cancer, but how distinct memory fates are specified remains unclear. Here, we define the functional landscape of 242 murine CD8 TCR{beta} clonotypes specific for influenza NP366-374/H-2D ligand (pMHC) by integrating single-cell transcriptomics and TCR sequencing with force-dependent biophysics, structural analysis, and in vivo investigation of memory development. Fate essentially tracks with TCR mechanotransduction: TCM-associated clonotypes preferentially engage pMHC through TCR{beta}, whereas TEM-associated clonotypes preferentially engage through TCR. Clonotypes with balanced, bipolar signaling generate both memory subsets, optimize expansion, and display broad heterosubtypic crossreactivity but with exhaustion susceptibility. In contrast, diverse TCM clonotypes are largely clonal singlets with considerable mutant-epitope recognition in aggregate and stemness preservation, revealing complementary strategies for immunodefense coverage. Atomistically, subtle pMHC contact differences and load transmission through the TCR holoreceptor appear to tune phosphorylation, memory differentiation, and functional durability, features applicable to adoptive T-cell immunotherapies.

immunology↗

Big Data, Sound Science, Lasting Impact: a framework for passive acoustic monitoring

Marine passive acoustic monitoring (PAM) has produced petabytes of data that are used by researchers, resource managers, industry, and regulators to understand how marine animals use sound and the impacts of anthropogenic noise on species and ecosystems throughout the global ocean. These big data provide unprecedented opportunities to study underwater soundscapes and marine ecology but also enormous challenges to efficiently extract information. To address these challenges, a U.S. federally funded and led Sound Cooperative (SoundCoop) project built community-focused cyberinfrastructure to promote improved, scalable and sustainable processing and access of marine PAM data for management, science, industry and military applications. Driven by cross-institutional participation representing a diversity of data collection methods and conditions, the SoundCoop project established guidance for standardized processing of ocean sound level metrics using freeware software toolkits and developed core tools and processes that support open science. Four examples of comparative analyses that connect disparate PAM monitoring efforts, and integrate non-acoustic data illustrate how comparable, interoperable sound level metrics support a more coherent and synoptic perspective on global ocean soundscapes using methods that current and future PAM projects can leverage. Such a framework around PAM big data offers the opportunity to revolutionize large-scale marine ecology and oceanography in similar ways to other transformative approaches for understanding environmental or ecological patterns and processes at global scales.

ecology↗