Quantitative, Systems & Engineering Biology Publications

Niamh E. Harrington​, Freya Allen​, Ramón Garcia Maset and Freya Harrison

The opportunistic pathogen Pseudomonas aeruginosa forms biofilm infections in the lungs of people with the genetic condition cystic fibrosis (CF) that can persist for decades. There are numerous P. aeruginosa lifestyle changes associated with chronic biofilm infection that are cued by the CF lung environment. These include a loss of virulence, metabolic changes and increased antimicrobial tolerance. We have investigated P. aeruginosa PA14 biofilm infection over 7 days in an ex vivo pig lung (EVPL) model for CF, previously shown to facilitate formation of a clinically relevant P. aeruginosa biofilm structure with expression of key genes comparable to human infection. We have compared P. aeruginosa gene expression between sequential time points: 24 h, 48 h and 7 days post-infection, and investigated tolerance to polymyxins. Our results demonstrate that the EVPL model can maintain a P. aeruginosa biofilm population, which exhibits increased antibiotic tolerance, for at least 7 days. Differential expression of antimicrobial resistance-associated genes was not observed; however, there was significant upregulation of sulphur metabolism and maintenance of a structured biofilm. Our findings demonstrate that 7 days is a viable time point for studying established, chronic biofilm infection in the EVPL model and provide insight into the accompanying gene expression changes.

Microbiology, March 2026

Wanqing Jiang, Cecilia Skoug, Ian Rodrigues, Ernesto Ciabatti, Fiona M. Gribble, Frank Reimann, Daniel I. Brierley, Marie K. Holt, Stefan Trapp

Glucagon-like peptide-1 receptor (GLP-1R) activation in the brain strongly reduces appetite, but most brain GLP-1Rs are not accessible for systemically administered GLP-1R agonists. Acute activation of nucleus tractus solitarius (NTS) GLP-1 neurons, known as preproglucagon (PPG) neurons, strongly suppresses food intake separate from GLP-1R agonists. However, it is unknown if chronic stimulation of PPG neurons is a viable strategy for appetite suppression, or if obesity disrupts their function. Here we demonstrate that PPG neurons in the NTS and intermediate reticular nucleus (IRT) determine meal size, and that their total number is inversely correlated with bodyweight gain. We report that PPGNTS and PPGIRT neurons receive distinct monosynaptic inputs, but have convergent efferent projection targets throughout the brain, and that combined ablation of both populations delays the onset of physiological satiation to a degree sufficient to promote weight gain under ad libitum chow fed conditions. Crucially, chronic daily chemogenetic activation of PPGNTS+IRT neurons drives robust and sustained hypophagia and weight loss in obese mice without notable adverse effects, demonstrating their value as targets for obesity pharmacotherapy.

Molecular Metabolism, May 2026

Daniela M Riley, Randa Elsayed, Mark D Walsh, Simaran Johal, Ying Lin, Harry Walton, Till Bretschneider, Sascha Ott, Andrew C Nelson

Although vertebrate species are superficially diverse, they share key commonalities in terms of overall morphology, as well as organ configuration and function. Maintenance of these traits during evolution is partially explained by the conservation of critical genes governing embryonic development. However, for conserved genes to deliver consistent developmental outcomes between species, similar gene regulatory programs and gene expression patterns must also be maintained. The endoderm germ layer makes major contributions to the respiratory and gastrointestinal tracts and to associated organs including the liver and pancreas. We used functional genomic approaches to identify highly conserved endodermal cis-regulatory modules (CRMs) functioning across the 400 million years of evolution separating zebrafish and humans. Our analyses suggest that there are few endoderm-specific CRMs, with many CRMs governing pancreas development also likely acting within the nervous system. Furthermore, these highly conserved CRMs are strongly enriched for binding sites of “neuro-pancreatic” transcription factors governing both pancreas and nervous system development, potentially suggesting function across these distinct organ systems. Additionally, we identify highly conserved CRMs potentially participating in endodermal patterning of adjacent craniofacial structures and sensory tissues. The highly conserved CRMs we identify are characterized by conserved patterns of transcription factor binding site co-occurrence. However, rigid arrangement of binding sites is not a common characteristic of the identified CRMs, suggesting more complex or individual grammatical rules. Overall, our analyses provide key insights into critical gene regulatory control during vertebrate endoderm organogenesis and define a compendium of highly conserved CRMs that should be prioritized for analysis of neuro-pancreatic gene transcriptional control and of anterior embryonic patterning.

Genome Research, March 2026

Vasthi Alonso Chávez, Nathan Brown, Stephen Parnell, Matt Coombes, Alison Dyke, Clare Hall, Berglind Karlsdóttir, Mariella Marzano, Joanne Morris, Liz O'Brien, David Williams, Alice E. Milne

• Across the world, emerging pests and diseases are increasing in number, range and co-occurring with other invasive biotic factors. Ash trees (Fraxinus excelsior L.; Oleaceae) in Great Britain face the potential invasion of the emerald ash borer (EAB; Agrilus planipennis Fairmaire; Coleoptera: Buprestidae) and the ongoing impact of ash dieback (ADB; Hymenoscyphus fraxineus T. Kowalski (Helotiales: Helotiaceae)). Surveillance and management strategies accounting for land manager behaviour are crucial for improved control.
• We developed a spatially explicit model that integrates (i) the estimated prevalence of ADB, (ii) the dynamics of EAB arrival and spread and (iii) a socio-dynamics model, based on a values-driven theory that simulates land manager decision-making in relation to surveillance and tree management. In the model, if EAB is detected, contingency measures—including tree felling and intensified monitoring—are enacted, with the potential to eradicate or slow its spread. We used the model to assess whether targeting high-risk sites with traps, using routine tree inspections by land managers, or encouraging volunteer surveillance (with or without subsidised trapping) could significantly slow EAB spread.
• Interviews (n=45), a survey (n=368), and three workshops (n=27) informed the socio-dynamics model's structure and parameterisation. The interaction between EAB and ADB is complex, with potential positive effects (e.g. increased perceived value of ash) and negative effects (e.g. belief that ash cannot be saved, misidentification of decline causes).
• Results showed that if land managers are made aware of EAB, health and safety inspections have a substantial role to play in slowing the spread but are unlikely to lead to eradication due to the pest's cryptic larval phase. Official trapping at a limited number of locations is similarly unlikely to succeed in early detection and eradication unless entry pathways are well-defined, and ash connectivity is low. Volunteer trapping is important for early detection and if this is subsidised, EAB eradication becomes more likely.
• Synthesis and applications. Tree-health policies must balance identifying likely entry points and deployment of traps, targeted information campaigns and surveillance subsidies for land managers. Our unique, cross-disciplinary approach can be applied to other pest/pathogen systems to inform tree-health plans and how to balance resources.

Journal of Applied Ecology, March 2026

Christopher James O’Grady, Sally Hilton, Emma Picot, Sebastien Raguideau 2, Christopher Quince, Christopher J. van der Gast, Hendrik Schaefer, Gary D. Bending

Biological soil crusts (BSCs) are formed by phototrophic organisms at the soil surface and play a key role in structuring microbial communities and biogeochemical processes in dryland ecosystems. Similar surface associated communities occur in temperate agricultural soils, but their development, assembly dynamics and functional significance remain poorly understood. We investigated the temporal development of the soil surface microbiome following tillage and during subsequent growth of a winter wheat crop, integrating multi-kingdom amplicon sequencing with metagenomic analysis to track phototrophic, bacterial, fungal and protist communities, together with co-amplified macroscopic phototrophs. Distinct surface communities of phototrophs, bacteria and protists established rapidly, within 4 weeks of tillage, and underwent marked succession from early dominance by yellow-green algae (Xanthophyceae) to cyanobacteria, charophytes and ultimately mosses. Across all taxonomic groups, community assembly at the soil surface increasingly shifted towards dispersal limitation over time, whereas bulk soil communities were predominantly shaped by ecological drift. By the end of the growing season, the soil surface had developed a functional profile distinct from bulk soil, characterised by a greater representation of photosynthetic processes, largely due to eukaryotic algal carbon fixation, alongside increased genetic potential for heterotrophic carbon, nitrogen, phosphorus and sulphur cycling. These functional shifts were associated with enrichment of Actinobacteria, Bacteroidetes and Proteobacteria. Our results demonstrate that the soil surface of temperate agricultural systems represents a dynamic and functionally differentiated microbial habitat, which shares key biological features with dryland BSCs while exhibiting distinct functional and successional trajectories, revealing an overlooked component of managed temperate ecosystems.

Soil Biology and Biochemistry, June 2026

Roisin Murphy, Julia A. Fairbairn, Becca W.A. Baileeves, Phillip J. Stansfeld, Timothy D.H. Bugg

A series of 4-aryl-2-imidazoles containing an ortho-substituted benzyl substituent were designed as a new peptidomimetic scaffold for an Arg-Trp-x-x-Trp motif used by lysis protein E from bacteriophage ϕX174 to target translocase MraY on the peptidoglycan biosynthesis pathway. The analogues showed antimicrobial activity against a panel of ESKAPE pathogens, with compound 9c (substituent CF3) showing effective antimicrobial activity against antibiotic-resistant Acinetobacter baumannii 19606 (MIC 8 μg/mL) and Staphylococcus aureus MRSA USA300 (MIC 8 μg/mL). The analogues showed 33–47% inhibition of particulate E. coli MraY at 200 μM concentration, with highest enzyme inhibition shown by compound 9b (substituent F, IC50 210 μM). Docking against the structure of E. coli MraY revealed a possible binding site in the “elbow” of bent helix 9, close to Phe-288. This work identifies the MraY-protein E interaction site as a possible target for the antimicrobial activity of bromoageliferin, and establishes a new skeleton for design of non-nucleoside MraY inhibitors.

Bioorganic & Medicinal Chemistry Letters, July 2026

Gwendolyn V. Davis, Jan J. Pavlou, Patrick Li, Marija Smokvarska, Richard S. Smith, Emmanuelle Bayer, George W. Bassel

Cell-to-cell communication underpins pattern formation and organ function in multicellular organisms. Plant cells can communicate directly through cytoplasmic channels called plasmodesmata. The distribution, abundance, and density of plasmodesmata on plant cell interfaces impact the flow of molecules between plant cells; yet the extent to which these properties are genetically and dynamically regulated remains poorly understood at an organ scale. We developed a quantitative approach to map plasmodesmata pit fields across roots in 3D at cell type and cell interface-specific resolution. Multiple parameters are captured simultaneously, including plasmodesmata pit field abundance, density, and spatial distribution, enabling parallel multiscale analyses at cellular resolution across this organ. During root maturation, plasmodesmata abundance increases, with the greatest biogenesis occurring within the inner cell layers. This is coupled with changes in the degree of clustering of the pit fields on these inner cell layers: becoming more dispersed on specific cell interface types and more clustered on others. Significant differences in plasmodesmata pit field spatial patterning were detected at cell type-specific resolution in the BRASSINOSTEROID INSENSITIVE1 mutant, demonstrating a role for this hormone pathway in channel patterning. The ability to quantify pit field abundance and patterning at cell type-specific resolution provides novel insight into the developmental and hormonal regulation of potential symplastic connectivity across plant organs, while providing a powerful tool toward the investigation of quantitative systems-level plasmodesmata distribution and macro-communication between cells in a complex multicellular system.

The Plant Journal, February 2026

Boltze J., Fisher M

Recanalization therapies for ischemic stroke, in particular endovascular thrombectomy, have revolutionized acute stroke management. Cytoprotective approaches were unsuccessfully tested in the pre-recanalization era but have seen a renaissance in translational research and early clinical trials as a potential intervention to augment the impact of recanalization therapies. The new clinical trial approaches in which cytoprotective therapies are now being applied require refinement of cytoprotective application strategies. This has a profound impact on both preclinical translational and clinical research. This review summarizes current cytoprotection concepts and explains their rationale based on ischemic stroke pathophysiology and provides an overview of cytoprotection approaches currently under clinical assessment. Preclinical assessment of novel cytoprotective paradigms will require advanced in vivo testing in models resembling human stroke patients as much as possible. The review therefore also describes ways to improve preclinical and translational research with respect to comorbidities and other aspects impacting stroke pathophysiology. Moreover, the role of modern brain imaging approaches is discussed including their use as potential biomarkers or patient selection tools. The review further provides detailed considerations of novel clinical trial design features for cytoprotection trials in the context of recanalization therapies and provides an outlook on potential future research approaches.

Advanced Science, February 2026

Ziyue Zeng, John W. Mansfield, Andrea Vadillo-Dieguez, John Connell, James Irvine, Michelle T. Hulin, Fernando Duarte Frutos, Mojgan Rabiey, Nastasiya F. Grinberg, Richard J. Harrison, Xiangming Xu, Robert W. Jackson

Plant surfaces host diverse microbial communities acting as reservoirs for pathogenic lineages, yet the ecological dynamics and evolutionary consequences of such reservoirs remain underexplored. We conducted landscape-scale genomic surveillance of Pseudomonas syringae on symptomless leaves of cultivated cherry in orchards and wild plant species in adjacent woodlands across the UK, aiming to understand how phyllosphere populations contribute to the emergence of bacterial canker. Whole genome sequencing of 540 isolates collected over two years and across four regions revealed 10 diverse P. syringae phylogroups (PGs) on symptomless leaves. Both orchard and woodland environments harboured a similar range of PGs, but recovery frequency was very different. PG2d strains dominated cherry orchards, whereas PGs 2b and 13a were prevalent in woodlands. Certain PG2d subclades, recovered from both environments, caused disease on cultivated and wild cherry leaves. Additional strains were found to be pathogenic to Phaseolus bean pods. The pathogens of cherry were characterised by the presence of genes encoding the synthesis of the pathotoxin syringolin A and a subset of effector proteins including HopAW1, AvrRpm1 and HopAR1. Resolution of subclades within PG2d provided insights into the emergence of virulent epiphytic strains that have not yet reached the mostly northerly sampling sites but are threats to both cultivated and environmental Prunus spp. Fine-scale analysis of subclade PG2d-3 revealed potential divergence between orchard and woodland populations, with 49 genes exclusive to a woodland lineage. Thirty-eight of these genes were found within prophages, indicating the potential role of bacteriophage-mediated horizontal gene transfer in adaptation to non-agricultural reservoirs.

Molecular Plant Pathology, February 2026

Andreas Ensslin, Adelaide Clemente, Udayangani Liu, Elke Zippel, Carla Pinto-Cruz, Carolina Sanchez Romero, Simone Schneider, Agustí Agut Escrig, Charlotte Allender, Külli Annamaa, Marina Antic, Bertille Asset, Gianluigi Bacchetta, Oz Baranzani, Anamaria Barata, Philippe Bardin, Joze Bavcon, Anabela D. F. Belo, Marina Belovarska, Karim Benkhelifa, Christian Berg, Karl-Georg Bernhardt, Marcin Beza, Kristina Bjureke, Sina Bohm, Peter Borgmann, Josep Borrell, Stéphane Buord, Jocelyne Cambecedes, Francesca Carruggio, Angelino Carta, Pedro Casimiro, Ted Chapman, Iveta Cicova, Regis Crisnaire, Antonia Cristaudo, Lucia De la Rosa, Maîte Delmas, Gergana Desheva, Valter Di Cecco, Luciano Di Martino, Katia Diadema, Lara Dixon, Denise Dostatny, Marie Duval, Roland K. Eberwein, Mikel Etxeberria-Okariz, Caroline Favier, Nick Fenby, Mariana P. Fernandes, Inmaculada Ferrando-Pardo, Pablo Ferrer, Noémie Fort, Luigi Forte, Catia F. Freitas, Agnese Gailite, Katarzyna Galej-Ciwis, Rosa Maria Garcia, Ana Irene García-del Bao, Catherine Gautier, Bronislovas Gelvonauskis, Gian Petro Giusso del Galdo, Miguel Angel González Pérez, Johan Gourvil, Luisa Gouveia, Thierry Helminger, Brais Hermosilla Lorenzo, Laetitia Hugot, Marko Hyvärinen, Ignac Janžekovič, Andreas König, Nikos Krigas, Emilio Laguna, Ludivine Lapébie, Denis Larpin, Maja Lazarević, Dikla Lifshitz, Vincent Lipa, Carlos Lobo, Ulrike Lohwasser, Sandrine Loriot, Sara Magrini, Francesca Mantino, Mauro Mariotti, Evi Matiatou, Lubomir Mendel, Marine Millet, Mari Miranto, Andrea Mondoni, Santiago Moreno Vázquez, Valeria Negri, Peter Nick, Maciej Niemczyk, Humberto Nobrega, Pawel Olejniczak, Małgorzata Pałucka, Katerina Papanastasi, Ioanna Papanikolaou, Miguel A. A. Pinheiro de Carvalho, Marco Porceddu, Sotirios Porevis, Peter Poschlod, Lorenzo Raggi, Sarmite Rancane, Leonid Rasran, Blanka Ravnjak, Stéphane Rivière, Axelle Roumier, Anna Rucińska, Felix Schlatti, Marco Schmidt, Guy-Xavier Seznec, Manuela Sim-Sim, Ana Luisa Soares, Nora Stoeckl, Silvia Strajeru, Gitana Stukeniene, Andrej Šušek, Andreas Titze, Sarah Trinder, Zlatina Tsvetanova, Theo Van Hintum, Nils Van Rooijen, Magdalena Vicens Fornés, Mariacristina Villani, Silvia Villegas, Fiona J. White, Sabine Zachago, Elena Zappa, Vince Zsigmond, Sandrine Godefroid

Ambitious targets have been set to backup seeds of threatened plants by the global strategy for plant conservation (GSPC), but it is unclear in how far these targets have been met and how seed collection should be organized to meet future challenges. Here, we provide an overview of the status of 44 countries in achieving seed conservation targets. We show that progress varies strongly across countries, but in general, targets of the 2011–2020 GSCP have not been reached. By a regional example, we illustrate how seed collection could be organized to safeguard our threatened flora.

Plants People Planet, March 2026

Minghui Ren, Yangmu Huang, Christopher Dowson, Ming Xu, Lewis Husain

Global health faces unprecedented strain and challenges to its legitimacy. The health-related Sustainable Development Goals and progress towards universal health coverage are off track, and multilateral cooperation is suffering due to geopolitical tensions. The future of global health is likely to be less aid-based and more reliant on domestic financing in low-income and middle-income countries (LMICs), more equitable markets for access to health technologies and digitally mediated treatment guidelines, and strengthened country capabilities.1 Progress will be piecemeal and experimental, and will require new forms of cooperation.

A 2025 conference on strengthening UK–China research cooperation for global health during times of crisis, jointly organised by the Institute of Development Studies, Peking University, China, and the Howard Dalton Centre, University of Warwick, UK, explored what a new kind of cooperation might look like. This cooperation would build on earlier collaboration on China's domestic health challenges and on the work done in the 2010s when the two countries sought a new, post-aid relationship.

The Lancet, February 2026

Wei Ma, Yuanming Liu, Xiaochun Wei, Xiaomeng Zhang, Xiaonan Li, Zhaokun Liu, Lingyun Yuan, Guangguang Li, Shu Zhang, Qihang Yang, Xiaocong Chang, Zizhuo Han, Hao Liang, Zhaoshui Luan, Qianyun Wang, Yujie Gu, Xinlong Wang, Xianlei Zhao, Qing Liu, Xiaoxue Sun, Mengyang Liu, Daling Feng, Yin Lu, Shuangxia Luo, Lei Yang, Mengyuan Li, Robin Allaby, Kai Wang, Tianzhen Zhang, Shuxing Shen, Yves Van de Peer, Yiguo Hong, Yuxiang Yuan, Jianjun Zhao

Brassica rapa (Br) encompasses many morphotypes and subspecies, so it is a good model with which to investigate plant diversification and subspeciation. Here, we resequenced the genomes of 1720 Br accessions and de novo assembled 11 representative telomere-to-telomere gapless genomes for seven elite subspecies that underwent intensive morphotypification and developed distinct agronomic traits valued to agriculture. We identified 6992 unknown genes, 110 complete (peri)centromeres, and five new satellites associated with Br morphotypes and subspecies and Brassica species evolution. The pangenome, built on 11 gapless and 20 published genomes, reveals structural variations and gene diversities among Br subspecies. Pangenome-wide association studies uncovered that the gene BrLH1 controls leaf-head formation. We show that structural changes have occurred in satellites, (peri)centromeres, and genes, contributing to fast subspeciation and morphotypification during the short history of Br cultivation, providing invaluable resources for Brassica breeding.

Science, February 2026

Tatjana Popović Milovanović, Shannon F. Greer, Renata Iličić, Aleksandra Jelušić, Daisy Bown, Murray Grant, Joana G. Vicente, David J. Studholme

This Technical Resource presents genome sequence data for three strains of the bacterial pathogen Xanthomonas euvesicatoria pv. euvesicatoria (Xeu) collected in Serbia. We isolated these strains from pepper crops showing bacterial spot symptoms in 2016 at the municipality of Irig, in the Srem district. The presented data comprise raw sequencing reads and annotated, contig-level genome assemblies. We checked for the presence of sequences of known type-3 secretion system (T3SS) effector genes and plasmid-like sequences. Phylogenomic reconstruction revealed that the three strains fell in the same clade within Xeu. Strain X13 is most closely related to strain 66b, collected in Bulgaria in 2012. Strains X22 and X31 are most closely related to Tu-10 collected in the Southeastern Anatolia region of Türkiye in 2020. In common with other members of the clade, all three strains share a 75 kb plasmid that carries T3SS effector genes avrBs3, xopBA, xopAQ and xopE. Additionally, strain X13 shares extensive sequence similarity to the pXCV183 plasmid, including T3SS effector gene xopAX, and shares extensive sequence similarity with plasmid pXap41, including T3SS effector gene xopE3. This difference in plasmid content might contribute to the observed difference in virulence among the Serbian Xeu strains. The three Serbian strains lack a 31 kb plasmid, pLMG730.4, that is seen in several Vietnamese and Canadian strains within this clade of Xeu. The data presented will be a useful resource for future molecular epidemiology and genomic surveillance of this pathogen in the Balkan region, augmenting the previously available draft genome sequences of Xeu strains 66b (Bulgaria) and 83M (North Macedonia).

Access Microbiology, February 2026

Vid Kavaš, Carlos Contreras-Martel, Stane Pajk, Damijan Knez, Alexandre Martins, Thomas A. Gould, David I. Roper, Irena Zdovc, Andréa Dessen, Martina Hrast Rambaher, Stanislav Gobec

Monobactams, a subclass of β-lactam antibiotics with a monocyclic scaffold, are uniquely resistant to hydrolysis by metallo-β-lactamases, providing a distinct therapeutic advantage. Here, we report an in silico-based structure–activity relationship (SAR) investigation of aztreonam-related monobactams. A focused library of monobactam derivatives was synthesized and evaluated for inhibition of penicillin-binding proteins (PBPs) and antibacterial activity. Ten compounds, including aztreonam, were crystallized with truncated PBP1b from Streptococcus pneumoniae, used as a model PBP. Potent PBP1b inhibitors were developed, although high enzymatic potency was not always reflected in strong antibacterial activity. Certain derivatives showed activity against Staphylococcus aureus, which is typically resistant to monobactams. 2D similarity search identified potent inhibitors active against Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii. Crystal structures revealed previously unrecognized binding interactions, including a halogen bond with a conserved threonine residue, underscoring the potential of these interactions to support the development of more potent PBP inhibitors.

Journal of Medicinal Chemistry, February 2026

Jessica Chadwick, Jingyi Shi, Megan L. Purchase, Peng Zhang, Iseult Lynch, Sami Ullah, Deying Wang, Ryan M. Mushinski

Reactive nitrogen losses from agriculture contribute substantially to greenhouse gas emissions, water pollution and ecosystem degradation. Controlled-release fertiliser technologies offer potential solutions, yet few comprehensively evaluate performance across multiple nitrogen loss pathways and soil types. This study evaluated the environmental performance and agronomic efficacy of urea-doped amorphous calcium phosphate (U-ACP) nanoparticles compared to conventional urea across three contrasting soil types (sandy, sandy loam, clay loam) using lettuce (Lactuca sativa) as a model crop. U-ACP nanoparticles (20–100 nm) were synthesised and characterised for dissolution kinetics in simulated soil environments. Controlled glasshouse experiments (8 weeks, 100 kg N ha − 1 application rate) quantified gaseous emissions (ammonia, nitrous oxide, nitric oxide), aqueous leaching losses, soil biochemical properties, plant nitrogen uptake and functional gene abundances for nitrogen cycling processes. U-ACP demonstrated significantly reduced reactive nitrogen losses across all pathways and soil types. Cumulative ammonia volatilisation decreased by 53%–57% in sandy and sandy loam soils compared to conventional urea (p < 0.001), whilst nitrous oxide emissions declined by 19%–27% across all soil types (p < 0.001). Total nitrogen leaching concentrations were 44% lower in sandy soils where losses are typically highest (p < 0.001), with ammonium leaching reduced by 71%–85% across soil types. Cumulative gaseous nitrogen losses decreased by 20%–48% depending on soil type. Despite these substantial reductions in nitrogen losses, U-ACP maintained comparable plant biomass whilst achieving 52%–89% higher nitrogen uptake index across soil types (p < 0.001). U-ACP also supported enhanced soil microbial functionality, with significantly elevated complete ammonia oxidiser (comammox) and alkaline phosphatase (phoD) gene abundances (p < 0.05). Calcium phosphate-based nanocomposite fertilisers offer a viable pathway towards sustainable intensification of agriculture by simultaneously reducing environmental nitrogen pollution whilst maintaining or improving crop productivity across diverse soil conditions.

Journal of Sustainable Agriculture and Environment, March 2026

Ling Cai, Yan Li, Chong Wang, Tim Magnus, Chengye Yao, Xiaoming Hu, Ann M. Stowe, Anna Rosell, Sunghee Cho, Stuart M. Allan, Jieqing Wan, Yulong Ma, Yang Liu, Daniel I. Sessler, Johannes Boltze, Tianlong Wang, Weifeng Yu, Yueman Zhang, Peiying Li,

Ischemic stroke is a major global health burden, leading to considerable mortality and long-term disability. Endovascular thrombectomy and mechanical recanalization have revolutionized acute stroke care. Nonetheless, many patients experience poor long-term neurological outcomes, which are often attributed to the no-reflow phenomenon and activation of inflammatory cascades. The perioperative period of endovascular thrombectomy, managed under either general anesthesia or conscious sedation, represents a critical window where anesthetic strategies may influence recovery through hemodynamic control and possibly immune modulation. This consensus review was generated by an international multidisciplinary expert group and synthesizes preclinical and clinical evidence to evaluate the promise of various immunomodulatory strategies for improving functional outcomes in patients with ischemic stroke following endovascular thrombectomy. Our goal is to provide a foundational reference for future research and development of novel perioperative immune therapies for patients with endovascular thrombectomy.

Stroke, February 2026

Jennifer Byrne, Lael Walsh, Robert Lillywhite, Henry Creissen, Antonia dos Santos, Fiona Thorne

An extended Technology Acceptance Model (TAM) was used to explore the pathway between the perception of Integrated Pest Management (IPM) by growers and its practical uptake. IPM is an established framework for the management of crop health based on a range of strategic and tactical horticultural techniques. In this research, IPM adoption is quantified through the application of a novel IPM metric. Policy makers need to understand the perception to practice pathway for IPM in order to increase adoption in line with regulatory frameworks. The TAM examines perceived usefulness (PU) and perceived ease of use (PEOU) on the attitude and subsequent acceptance of a technology; extended TAM frameworks incorporate additional antecedent variables. In this study, we include the additional latent variables of business features and innovativeness to examine their capacity to predict the adoption of IPM at the farm business level for growers of horticultural crops (n = 100) in the Republic of Ireland, surveyed in 2023. Findings verify the correlation between PU, PEOU and attitude and the effect of PEOU on PU. PU has a stronger association with attitude than PEOU. Neither business features nor innovativeness were significantly related to PU or PEOU, respectively. The hypothetical correlation between attitude and IPM adoption was rejected, demonstrating a divide in the perception to practice trajectory and adding to the literature on the attitude to adoption gap. The findings demonstrate the value of empirical assessment of behavioural data. An implication for IPM policy direction is that grower perception does not always infer future grower adoption. Therefore, a cautionary reliance on perception data during the ex-ante stages of IPM incentivisation development is recommended.

Crop Protection, February 2026

Freya Harrison, Oluwatosin Q. Orababa

The modern antibiotic era began in the early twentieth century, but humans have long used materials from the natural world to attempt to treat the symptoms of infection. In this primer, we will discuss the rationale for attempting to reconstruct historical infection remedies in order to assess their antimicrobial activity and how this approach could aid the discovery of molecular cocktails with potential for development into novel treatments for infection.

Microbiology Society, January 2026

Charlotte Dykes, Jonathan Pearson, Gary Bending, Soroush Abolfathi

Microplastics (MPs) are emerging contaminants, with wastewater treatment plants (WWTPs) as principal hotspots for their release into downstream systems, including constructed wetlands (CWs), a nature-based solution for water treatment. While non-buoyant MPs readily settle, buoyant MPs risk bypassing CWs and entering aquatic environments. Biofilm formation could influence MP transport by altering buoyancy, promoting sinking, and enhancing MP retention, yet its role in CWs remains unknown. This study, for the first time, quantifies the effects of MP polymer type, particle characteristics, exposure time, and seasonality on biofilm colonisation and its impact on terminal rising velocities of initially buoyant MPs in a UK-based CW receiving partially treated wastewater. Polypropylene (PP), expanded polystyrene (PS), and low-density polyethylene (LDPE) particles (3–5 mm) in spherical, beaded, and film shapes were incubated in situ over 12 months. Sampling followed two approaches: (1) a rolling bi-monthly schedule to capture seasonal variation, and (2) a long-term deployment with subsets retrieved every two months. Biofilm biomass was quantified by crystal violet staining, surface characteristics were captured by scanning electron microscopy (SEM), and terminal rising velocity experiments measured buoyancy changes. Biofilm growth showed strong seasonality, with peak biomass in late spring showing up to a 1972 % increase compared to winter. Despite widespread colonisation, changes in terminal rising velocity were minimal and largely non-significant (p < 0.05), indicating that biofilm formation alone is insufficient to retain initially buoyant MPs in CWs. These findings are crucial for deriving MP transport models and challenge assumptions that biofilm-induced density changes drive MP retention in CWs.

Journal of Hazardous Materials, February 2026

Megan L. Purchase, Richard P. Phillips, Jonathan D. Raff, Amy I. Phelps, Elizabeth Huenupi, Ryan M. Mushinski

The emergence of periodical cicadas from soil every 13 or 17 years is a unique ecological phenomenon with the potential to affect soil biogeochemistry in forests, with increased emissions of climate-relevant gases as a consequence. While it's well-known that cicada carcasses create resource pulses of carbon and nitrogen (N) in soil when they die in mass, the processes underlying these effects, as well as the consequences of these effects for N losses, are poorly known. We investigated how the emergence of Brood X cicadas (Magicicada spp.) in 2021 affected soil microbial communities – particularly N cycling taxa - in forests of the United States. We found that decaying carcasses led to emissions of nitrous oxide (N2O) and ammonia (NH3) gas at around 0.53 mg-N m−2 h−1, estimated to be a ∼ 35-fold increase over ∼21 days from the annual average emissions from US forest soils (0.015 mg-N m−2 h−1), with the greatest effects occurring at the interface between carcasses and soil surface. Using amplicon sequencing and qPCR, we determined the potential microbial mechanisms behind N2O and NH3 production, including correlations between taxa capable of carrying out less well studied processes DNRA and nitrifier denitrification, and increased emissions of N2O and NH3. Although distinguishing the relative contributions of DNRA, denitrification, and nitrifier denitrification requires direct rate measurements, our results suggest these processes working together contribute to previously unrecognised greenhouse gas emissions following insect emergence events. Collectively, our results indicate that cicadas significantly affect nutrient cycling in forests with the potential to alter soil microbial communities in ways that may enhance ecosystem N emissions.

Applied Soil Ecology, March 2026

Sebastian Raubach, Miriam Schreiber, Ruth Hamilton, Gaynor McKenzie, Susan McCallum, Benjamin Kilian, Alan Humphries, Loi Huu Nguyen, Tin Huynh Quang, Akanksha Singh, Shivali Sharma, Sarah Trinder, Manuel Feser, Paul D. Shaw

Accurate acquisition of phenotypic data is critical for cataloguing and utilising genetic variation in cultivated crops, landraces, and their wild relatives. The collection of phenotypic data using handwritten notes often introduces errors which can and should be avoided. Electronic data collection is crucial for ensuring error prevention and data standardisation and thus ensuring high-quality, reliable data.

This paper describes the development of GridScore NEXT, a new plant phenotyping application that significantly advances the state of the art for collecting field trial data in plant genetics, pre-breeding and crop improvement research. Building on its predecessor, GridScore, the development of GridScore NEXT was driven by real life, in the field interactions with expert user groups across a number of crops. This iterative design methodology allowed the development and testing of new features. Collaborators from the 'Biodiversity for Opportunities, Livelihoods and Development' (BOLD) project, focusing on crops including rice, grasspea, and alfalfa, along with barley, potato, vegetable and blueberry teams, provided invaluable insights through training sessions and interviews and in the field use of the application.

Key improvements to GridScore NEXT include enhanced data collection tools, supporting individual plant phenotyping within plots and enabling new data types such as GPS coordinates and image traits. GridScore NEXT provides customisable user defined validation rules to help prevent errors and incorporates barcode scanning for accurate, efficient data capture. The application offers an increased toolbox of data visualizations over its predecessor including heatmaps and statistical box plots, which aid in identifying potential data issues and understanding trial performance in the field. GridScore NEXT is cross-platform and can operate without an internet connection, making it ideal for field use in remote areas. Its adoption has led to standardisation of methods, significant error reduction, and the timely sharing of data, enabling quicker decision-making in pre-breeding and characterisation experiments. GridScore NEXT is available under an open-source (Apache 2.0) licence and freely available to all with no restrictions. It offers self-hosting options for enhanced data security and privacy. GridScore NEXT shows broad applicability across a diverse range of not only plant phenotyping experiments, but any experiment that requires the collection of accurate data.

BMC Bioinformatics, January 2026

Adam Evans, Bethan Kelly, Pooja Sridhar, Alice J. Rothnie, Naomi L. Pollock, Philip M. Ireland, David I. Roper, Tim R. Dafforn

Extraction and purification of membrane proteins has for a long time represented a significant challenge. Polymer-based extraction methods, like those using styrene maleic acid co-polymers have provided a fertile approach to generate samples that include the local lipid environment surrounding the protein. However, the wide variety of different polymers now available provides a challenge to identify the optimal solution. In this study we develop and demonstrate a novel high-throughput screening approach for rapid optimization of polymer solubilization agents and chromatography resins for membrane protein purification. Using this approach, we explore whether there are standard conditions that perform well for a range of membrane protein morphologies, sources and functions. These data show that no such standard conditions exist for either polymer solubilization agent or chromatography resin and that some combinations are rarely suitable for membrane protein purifications under these conditions, such as the use of TALON resin at a pH of 7.5 or SMALP300 in the Synthetic Nanodisc Screening Kit MINI kit. Instead, the use of the screening approach developed in this work is the best route to an optimal membrane protein preparation protocol.

Protein Science, January 2026

Joshua Williams, Ioannis P Nezis, Antonia P Sagona

The rising incidence of antimicrobial resistance (AMR) in bacterial infections has strongly necessitated the development and deployment of alternative therapeutics. Bacteriophages (phages) are one such alternative, discovered in the early twentieth century. While a key tool in landmark molecular biology studies throughout the twentieth century, their popularity as an antimicrobial in clinical contexts was largely overshadowed by the development and use of antibiotics. The global threat of AMR has since reignited interest in utilizing phages as therapeutics. A key advantage of phages is their genetic tractability, allowing for the generation of a cornucopia of derivatives armed with numerous exogenous functions depending on the end use. A nascent yet growing interest in this field is the arming of phages for direct and selective human tissue entry to eradicate intracellular bacterial infections, where many bacterial species exert their pathogenesis. Engineering phages in such a way also opens opportunities to study the complex, multilayered cellular mechanisms behind phage–eukaryote interactions. In this review, we discuss the progress of phage genetic engineering with an emphasis on phage–eukaryote interactions and how knowledge of the underlying molecular mechanisms may serve further development of this prospective enhancement of engineered phages.

Current Opinion in Microbiology, February 2026

Matthew J Padgett , Nela Fucelova , Johannes Boltze, Timothy J England , Tuuli Hietamies , Karen Horsburgh , Terence J Quinn , Emily S Sena , Lorraine M Work, Marietta Zille, Rebecca C Trueman, Tracy D Farr

Hypoperfusion via bilateral carotid artery stenosis is the most common mouse model of vascular cognitive impairment, but the literature varies surrounding which behavioural tests are most appropriate to detect cognitive deficits in this model. We aimed to address this via a systematic review and meta-analysis. We also aimed to provide a recommendation that also considers how the tests cover the different cognitive domains. We identified 1714 publications and extracted data from 56. Interestingly, only six cognitive behavioural tests were employed across the literature with the most common being the Morris water and radial arm mazes, followed by the Y maze, novel object recognition, open field, and the Barnes maze. While all examined tests were able to detect cognitive impairments in hypoperfused mice, there was a high degree of heterogeneity across the publications, highlighting that not all research groups consistently observed cognitive deficits in the model. There was also evidence of publication bias, and occasionally some publications with extremely high effect sizes were influential. We recommend all tests, but ideally experiments should be complemented with additional approaches that examine a greater range of cognitive functions.

Journal of Cerebral Blood Flow & Metabolism, January 2026

Agnieszka Mierek-Adamska, Jose Gutierrez-Marcos, Claudia A. Blindauer

Zinc and cadmium share similar chemical properties; however, while zinc is an indispensable microelement involved in several physiological processes, cadmium is highly toxic. Cadmium toxicity results at least to some extent from replacing zinc (and other metals) from their active sites in enzymes and other proteins. This highlights why the correct population of metalloproteins with metals is crucial for proper cellular metabolism. In the face of growing demand for food, both in terms of quantity and quality, a rapid development of crop cultivars containing a higher amount of bioavailable zinc in the edible parts of plants, crucially without the simultaneous accumulation of cadmium, is imperative. Type 4 plant metallothioneins (pMT4s) are seed-specific proteins for which a potential role as a zinc specificity filter has been proposed. It was suggested that two conserved histidine residues are key for discrimination between zinc and cadmium. In this study, we analysed the metal-binding properties of Sorghum bicolor pMT4 (SbMT4) wild-type and mutant proteins with histidine/s replaced by tyrosine/s (H32Y, H40Y, and H32Y/H40Y) using mass spectrometry, elemental analysis, and NMR spectroscopy. SbMT4 is a Zn-thionein, but unexpectedly, it was also fully folded in the presence of cadmium – owing to a zinc ion remaining in the mononuclear Cys2His2 site in domain II. All three mutant proteins were misfolded in the presence of either zinc or cadmium, but increased Cd-to-protein stoichiometry was observed. The presence of histidines impacted SbMT4 metal selectivity when expressed in bacterial cells, but did not affect Zn/Cd accumulation in transgenic Arabidopsis thaliana plants.

Journal of Inorganic Biochemistry, January 2026

Gbeminiyi J. Oyedele, Ankit Shanker, Michael J. Tildesley, Ivo Vlaev

Adherence to self-isolation was a central measure for controlling the spread of COVID-19; however, compliance varied widely. Understanding the behavioural determinants that drive adherence is critical for informing future public health intervention. This study applied the COM-B model to examine the associations between capability, opportunity, motivation, and self-isolation behaviour during the COVID-19 pandemic in the United Kingdom. A retrospective analysis was conducted using secondary data from the UK Office for National Statistics 2019 Opinions and Lifestyle Survey, which was not originally designed to measure COM-B constructs. Structural equation modelling (SEM) was used to examine the relationships between capability, opportunity, motivation, and self-isolation behaviour. Opportunity and motivation were significantly associated with self-isolation, while capability was linked to behaviour indirectly through its association with motivation, reflecting a possible pathway suggested by the structural model. Although some measurement indicators demonstrated lower reliability owing to the use of secondary data, the overall model fit was good (RMSEA = 0.049, CFI = 0.966, TLI = 0.944, SRMR = 0.040). These findings highlight the dominant influence of social and motivational factors in shaping adherence. This study demonstrates the utility of the COM-B model for understanding self-isolation behaviour despite the constraints of secondary data. The findings highlight opportunity and motivation as key levers for promoting adherence and offer actionable insights for policymakers to design interventions that enhance motivation, strengthen social support, and sustain compliance during future public health emergencies.

Scientific Reports, January 2026

Shashank K. Pandey, Tatiana S. Moraes, Aswin Nair, Bibek Aryal, Abdul Azeez, Pal Miskolczi, Guillaume Maucort, Fabrice P. Cordelières, Lysiane Brocard, Gwendolyn V. Davis, Hannah Dromiack, Swanand Khanapurkar, Sara I. Walker, George W. Bassel, Emmanuelle M. Bayer, Rishikesh P. Bhalerao

Dormancy is a key mechanism in perennial plants in boreal and temperate regions, protecting buds from winter damage by repressing precocious bud break before spring onset. How plants robustly time dormancy release under fluctuating environments remains unknown. Here, we show that, rather than simply sensing cold duration, buds leverage warm spikes to sense winter progression and time dormancy release. This timing mechanism is mediated by previously unrecognized regulation of plasmodesmata by warm spikes acting through tree ortholog of FLOWERING LOCUS T (FT1) and the gibberellic acid pathway. Our results reveal FT1 as a previously unrecognized, suppressor of callose levels and show that warm spikes repress cold induction of FT1 and GA pathway to suppress PD opening and dormancy release. Importantly, buds exhibit heterogeneity in bud break. This heterogeneity in bud break crucial for bet hedging is amplified under temperature fluctuations and is associated with the thermal responsiveness of plasmodesmata. Altogether, our work reveals dynamic plasmodesmata regulation as a crucial tissue-level mediator of variable temperature processing by buds, enabling robust adaptation of trees to seasonal changes.

Nature Communications, January 2026

Steven Xingyu Wu, Christopher N. Davis,Mark Arnold, Michael J. Tildesley

Previous research efforts on highly pathogenic H5N1 avian influenza (HPAI) suggest that different avian species exhibit a varied severity of clinical signs after infection. Waterfowl, such as ducks or geese, can be asymptomatic and act as silent carriers of H5N1, making detection harder and increasing the risk of further transmission, potentially leading to significant economic losses. For backyard hobby farmers, passive reporting is a common HPAI detection strategy. We aim to develop a computational, mechanistic model to quantify the effectiveness of this strategy by simulating the spread of H5N1 in a mixed-species, small-population backyard flock. Quantities such as detection time and undetected burden of infection in various scenarios are compared. Our results indicate that the presence of ducks can lead to a higher risk of an outbreak and a higher burden of infection. If most ducks within a flock are resistant to H5N1, detection can be significantly delayed. We find that within-flock infection dynamics can heavily depend on the species composition in backyard farms. Ducks, in particular, can pose a higher risk of transmission within a flock or between flocks. Our findings can help inform surveillance and intervention strategies at the flock and local levels.

PLOS Computational Biology, January 2026

Amol Mohan Bhandare, Adwoa Boaten, Dylan Dunkwu, Jade Hill, Biborka Balazs, Nicholas Dale

Impaired CO₂ responsiveness in epilepsy can result in hypoventilation and hypercapnia and these respiratory disturbances are key contributors to Sudden Unexpected Death in Epilepsy (SUDEP). While mild to moderate inflammation is known to modulate respiratory function, its specific role in regulating respiratory responses in the context of epilepsy remains unclear. We studied the effects of lipopolysaccharide (LPS)-induced inflammation and microglial inhibition via minocycline during the acute and chronic phases of epilepsy on hypercapnic ventilatory responses (HCVR) in the intrahippocampal kainic acid model of temporal lobe epilepsy in male C57BL/6 mice. LPS treatment during acute seizures and minocycline during spontaneous seizures in the chronic phase of epilepsy restored the impaired HCVR in mice. Notably, LPS treatment during acute seizures also reduced the frequency of spontaneous seizures. In contrast, minocycline given during acute seizures and LPS administered during chronic epilepsy further exacerbated HCVR impairment. Immunohistochemical analysis of chemosensitive retrotrapezoid nucleus (RTN) revealed varied effects of different treatments in epileptic mice on microglia density, morphology and their expression of triggering receptor expressed on myeloid cells 2 (TREM2), P2Y12 receptor, and astrocytic adenosine 2A receptor (A2AR). Overall, the inflammation during epileptogenic or acute phase preserves HCVR and reduces spontaneous seizure frequency in chronic epilepsy, whereas in chronic phase it worsens HCVR. Although not yet fully validated, changes in microglial and astrocytic receptor expression could contribute to this HCVR impairment and may represent a mechanistic target for preserving HCVR in epilepsy; a dysfunction that could potentially lead to SUDEP.

Journal of Neuroinflammation, January 2026

Trupti Gaikwad, Susan Breen, Emily Breeze, Erin Stroud, Rana Hussain, Satish Kulasekaran, Nestoras Kargios, Fay Bennett, Marta de Torres-Zabala, David Horsell, Lorenzo Frigerio, Pradeep Kachroo, Murray Grant

Successful recognition of pathogen effectors by plant disease resistance proteins, or effector-triggered immunity (ETI), contains the invading pathogen through localized hypersensitive cell death. ETI also activates long-range signalling to establish broad-spectrum systemic acquired resistance (SAR). Here we describe a sensitive luciferase (LUC) reporter that captures the spatial–temporal dynamics of SAR signal generation, propagation and establishment in systemic responding leaves following ETI. JASMONATE-INDUCED SYSTEMIC SIGNAL 1 (JISS1) encodes an endoplasmic-reticulum-localized protein of unknown function. JISS1::LUC captured very early ETI-elicited SAR signalling, which surprisingly was not affected by classical SAR mutants but was dependent on calcium and was also wound responsive. Both jasmonate biosynthesis and perception mutants abolished JISS1::LUC signalling and SAR to Pseudomonas syringae. Furthermore, we discovered that ETI initiated jasmonate-dependent systemic surface electrical potentials. These surface potentials were dependent on both glutamate receptors and JISS1, despite neither JISS1 loss-of-function nor glutamate receptor mutants altering SAR to Pseudomonas syringae. We thus demonstrate that jasmonate signalling, usually associated with antagonism of defence against biotrophs, is crucial to the rapid initiation and establishment of SAR systemic defence responses (including the activation of systemic surface potentials) and that JISS1::LUC serves as a reporter to further dissect these pathways.

Nature Plants, January 2026

Christopher N. Davis, Edward M. Hill, Chris P. Jewell, Kristyna Rysava, Robin N. Thompson, Michael J. Tildesley

Since 2020, large-scale outbreaks of highly pathogenic avian influenza (HPAI) H5N1 in Great Britain have resulted in substantial poultry mortality and economic losses. Alongside the costs, the risk of circulation leading to a viral reassortment that causes zoonotic spillover raises additional concerns. However, the precise mechanisms driving transmission between poultry premises and the impact of potential control measures in Great Britain, such as vaccination, are not fully understood. We have developed a spatial transmission model for the spread of HPAI in poultry premises calibrated to infected premises data for the 2022–23 season using Markov chain Monte Carlo. Our results indicate that reducing the susceptibility of the premises surrounding an identified infected premises (for example, through enhanced biosecurity measures and/or vaccination) can substantially reduce the overall number of infected premises. Our findings highlight that enhanced control measures could limit the future impact of HPAI on the poultry industry and reduce the risk of broader health threats.

PLOS Computational Biology, January 2026

Nikhil Bhalla, Mojgan Rabiey, Prachi Bendale, Katie Lawther, Janice Spencer, Alberto Longo, Lucky Lucky, Vishal Chaudhary, Paul McCormack, Saikat Jana, Patrick S. M. Dunlop, Linda Oyama

Antimicrobial resistance (AMR) is a silent pandemic that presents a global challenge, urging researchers to develop innovative and transdisciplinary solutions. Our initiative aims to promote collaboration across science, engineering, economics, social sciences, and the arts to address the complex dimensions of AMR. We highlight the unique role of early-career researchers (ECRs) in advancing such cross-cutting approaches and conclude that empowering ECRs through equitable support and recognition is essential to sustaining innovation and mobilising communities against AMR.

Nature Communications, January 2026

E. Burton, S.P. Borriello, P.J. Gregory, J. Healing, C. Nicholson, T.H. Oliver, S. Pearson, R. Smith, M. Tildesley, J. Wastling, J. O'Brien

Establishing research priorities to support evidence-based regulatory goals requires cross disciplinary collective expert input. This paper reviews the application of expert elicitation to identify and prioritize research questions in food safety regulation, which approach offers regulators and research funders a rapid, reliable, and cost-effective method for assessing evidence gaps in an expanding scientific landscape. While similar methodologies have been applied in ecology and other fields, this is, to our knowledge, the first use in food safety research. Recommendations are provided to strengthen the process.

A facilitated workshop shortlisted 51 questions, grouped into 12 themes, from a long list of 262 submissions, which spanned broad topics, including understanding the origins of emerging hazards and their health impacts. Environmental and sustainability themes address unintended consequences of decarbonization, food waste reduction, and risks from recycled plastics and food byproducts. Dietary change raises questions on emerging allergens, nutritional adequacy of alternative proteins, low fibre intake, and microbiome-related health impacts. Technology-driven changes, such as new production systems, kitchen devices, and secondary food economies, intersect with these dietary shifts.

Scientific advances provide opportunities to improve understanding of the dietary exposome through better intake data. Exposure to dietary chemicals occurs alongside complex mixtures of other agents, requiring structured approaches to risk assessment. The evolving science of chemical mixtures and rapid innovation in food systems underscore the need for robust, prioritized research compatible with good regulatory practice.

Trends in Food Science & Technology, January 2026

Xuming Zhang, Mitali Malhotra

Mutual interaction between the nervous and immune systems underpins many pathophysiological processes. Transient Receptor Potential Melastatin 2 (TRPM2) channels are abundantly expressed in both systems, acting as a critical interface of neuroimmune interaction. TRPM2 channels in immune cells participate in innate immunity and immune inflammation by acting as an oxidative stress and metabolic sensor. TRPM2 in neurons functions not only as an oxidative sensor but also a temperature sensor and a pain transducer critical to neuronal death, temperature sensing, thermoregulation, and chronic pain. Cooperation between immune and neuronal TRPM2 influences the outcome of neuroimmune interaction and many diseases such as infection, inflammation, ischemic stroke, pain, and neurodegenerative diseases. Improved understanding of neuronal and immune TRPM2 interaction is essential for therapeutic interventions for the treatment of diseases mediated by TRPM2 channels.

Cells, 2026

Piotr Walczak, Shen Li, Xunming Ji, Johannes Boltze

Most conditions of the central nervous system (CNS) and the peripheral nervous system are not stand-alone disorders but are modulated and influenced by other pathobiological processes. For instance, the impact of frequent comorbidities such as hypertension or dyslipidemia as factors contributing to and aggravating CNS diseases has been much better understood in recent years. Another prominent disease-modifying factor is the gut microbiome which can exert both protective and detrimental effects on the nervous system in health and disease. An even better understanding of these factors will contribute to the development of individualized treatment approaches, a major research objective in the era of precision medicine. The current issue of Neuroprotection presents articles focusing on disease-modifying factors or novel treatment approaches for a broad spectrum of conditions. This provides a wide perspective but also novel insights into disease mechanisms and targeted treatment approaches. Priority has been given to articles reporting, reviewing or meta-analyzing clinical data as well as articles providing results of translationally relevant preclinical work.

Neuroprotection, December 2025

Irnia Nurika, Eka Nur Shabrina, Nurul Azizah, Sri Suhartini, Guy C. Barker, Timothy D.H. Bugg

This study assesses the facultative anaerobe Comamonas testosteroni as a mild, chemical-free pre-treatment for valorising oil palm empty fruit bunches (OPEFB) into biomethane and lignin-derived aromatics. Incubation with 2 % (v/v) C. testosteroni for 7 days at 30 °C, reduced lignin to 15.67 % (33.42 % removal), while retaining high cellulose (53.48–56.19 %) and hemicellulose (up to 16.21 %). Pre-treated OPEFB showed 20 % weight loss (vs 8 % in controls) and a 51 % rise in total soluble phenols, evidencing active lignin depolymerisation. GC–MS of liquor and solids qualitatively confirmed lignin breakdown and identified representative low-molecular-weight products (e.g., phenol, betulin, acetic acid and benzoxazole), supporting co-product potential. In biochemical methane potential tests, the pre-treated residue achieved a specific methane potential of 0.173 m³ CH4 kg⁻¹ VS, an 85 % increase over the abiotic residue and higher than non-treated OPEFB. Kinetic fitting with Transference, Modified Gompertz and Logistic models yielded good agreement (R2 up to 0.92), with Modified Gompertz best capturing cumulative methane production and the shortest lag phases. A simple energy check indicates a favourable margin: the incremental methane (ΔSMP ≈ 0.08 m³ CH₄ kg⁻¹ VS) equates ∼0.8 kWh kg⁻¹ VS, whereas estimated mixing for pre-treatment is ∼0.017–0.034 kWh kg⁻¹ VS. Overall C. testosteroni pre-treatment enables dual valorisation (biomethane plus aromatics) under mesophilic conditions, offering a practical route for integrated OPEFB biorefineries.

Biochemical Enigneering Journal, March 2026

Hugo Millat, Cassandra Falcou, Cassandra Lenoir, Nicholas S. Briggs, Jack Stone, Pierre Simon Garcia, Sylvie Manuse, Caroline Cluzel, André Zapun, Cécile Morlot, David I. Roper, Adrien Ducret, Christophe Grangeasse

Class A penicillin-binding proteins (aPBPs) are involved in the biosynthesis and remodelling of peptidoglycan (PG). The human bacterial pathogen Streptococcus pneumoniae produces three aPBPs, which are regulated to maintain the bacterium’s ovoid shape. Evidence suggests that PBP1a and PBP2a activities are closely coordinated; however, their precise functions remain unclear. Here we characterized the pneumococcal S protein, which contains a LysM-PG-binding domain and a GpsB-interacting domain. Using S protein fusion constructs or mutant bacterial strains, we show that S protein localizes to the division ring and is required to prevent premature cell lysis and minicell formation due to aberrant division site placement. S protein interacts with PBP1a and activates its PG synthesis activity. Co-immunoprecipitation experiments combined with biochemical, genetic, structural prediction and microscopy analyses suggest that S protein is part of a larger multiprotein complex containing aPBPs and PG-modifying enzymes, and coordinated by the scaffolding protein GpsB. Together, these findings suggest that a GpsB-associated complex orchestrates PG biosynthesis and remodelling in S. pneumoniae.

Nature Microbiology, January 2026

Emma L. Fairbanks, Matthew Baylis, Janet M. Daly, Michael J. Tildesley

Vector-borne disease transmission involves complex interactions between vectors, reservoir hosts and dead-end hosts. We present a mathematical model for the vectorial capacity that incorporates multiple host types and their interactions, focusing specifically on West Nile virus transmission by Culex pipiens mosquitoes. Our model integrates climate-dependent parameters affecting vector biology with vector control interventions to predict transmission potential under various scenarios. We demonstrate how vector control interventions targeting one host type can significantly impact transmission dynamics across all host populations. By examining the effects of different vector control tool modes of action (repellency, preprandial killing, disarming and postprandial killing), we develop target product profiles that minimise unintended consequences of vector control. Notably, we identify the optimal intervention characteristics needed to prevent repellency on dead-end hosts from inadvertently increasing transmission among reservoir hosts. This research provides valuable insights for public health officials designing targeted vector control strategies and offers a flexible modelling framework that can be adapted to other vector-borne diseases with complex host dynamics.

PLOS Computational Biology, December 2025

Matthew Adeoye, Xavier Didelot, Simon E.F. Spencer

The Bayesian analysis of infectious disease surveillance data from multiple locations typically involves building and fitting a spatio-temporal model of how the disease spreads in the structured population. Here we present new generally applicable methodology to perform this task. We introduce a parsimonious representation of seasonality and a biologically informed specification of the outbreak component to avoid parameter identifiability issues. We develop a computationally efficient Bayesian inference methodology for the proposed models, including techniques to detect outbreaks by computing marginal posterior probabilities at each spatial location and time point. We show that it is possible to efficiently integrate out the discrete parameters associated with outbreak states, enabling the use of dynamic Hamiltonian Monte Carlo (HMC) as a complementary alternative to a hybrid Markov chain Monte Carlo (MCMC) algorithm. Furthermore, we introduce a robust Bayesian model comparison framework based on importance sampling to approximate model evidence in high-dimensional space. The performance of our methodology is validated through systematic simulation studies, where simulated outbreaks were successfully detected, and our model comparison strategy demonstrates strong reliability. We also apply our new methodology to monthly incidence data on invasive meningococcal disease from 28 European countries. The results highlight outbreaks across multiple countries and months, with model comparison analysis showing that the new specification outperforms previous approaches.

Epidemics, December 2025

Shuya Wang, Tong Li, Matthew Naish, Russell Chuang, Evan K. Lin, Christian Fonkalsrud, Yan He, Suhua Feng, Ian R. Henderson, Steven E. Jacobsen

DNA methylation is a conserved epigenetic modification essential for maintaining genome stability. However, how methyltransferases maintain CG methylation within compact chromatin, including centromeres, remains unclear. In humans, CDCA7 is necessary for the inheritance of DNA methylation at juxta-centromeres. Mutations that impair its ability to bind chromatin result in Immunodeficiency, Centromeric Instability, and Facial Anomalies (ICF) syndrome, characterized by centromeric instability. To investigate whether CDCA7 function is conserved, we identified two Arabidopsis thaliana orthologs, CDCA7α and CDCA7β. The loss of both copies results in CG hypomethylation at pericentromeric regions and centromeric satellite repeat arrays. Machine learning analysis suggested that heterochromatic nucleosomes, with enrichment of H1, H2A.W, and H3K9me2, depend heavily on CDCA7 proteins for CG methylation maintenance of the associated DNA. Loss of H1 restores heterochromatic DNA methylation in cdca7α cdca7β mutants, indicating that CDCA7α and CDCA7β mainly remodel H1-containing nucleosomes for methyltransferases to access DNA. Notably, in h1.1 h1.2 mutants, CG methylation shows a significant increase in centromeres, which reveals a new inhibitory role of H1 in DNA methylation maintenance within satellite repeat arrays. Centromeric DNA hypermethylation is lost in h1.1 h1.2 cdca7α cdca7β quadruple mutants, demonstrating that CDCA7α and CDCA7β can act independently of H1 to enhance MET1 activity at nucleosomes. Overall, these findings establish CDCA7α and CDCA7β as conserved regulators of DNA methylation within heterochromatin and centromeric satellite repeat arrays.

PNAS, December 2025

Emma Short, Ramzi Ajjan, Thomas M Barber, Sunil Bhandari, Paul Chazot, Jennifer L. Garrison, Anushka Goyal, Robert Huckstepp, Noordin Jamal, Venkateswarlu Kanamarlapudi, Alpar Lazar, Thomas Lee, Adriana A. S. Tavares, Jeremy J Tree, Jack Wellington, Stuart RG Calimport, Barry Bentley

An ageing-related pathology has recently been described as one that develops and/or progresses with increasing chronological age, that is associated with, or contributes to, functional decline and that is evidenced by studies in humans. The pineal gland is a photo-neuroendocrine organ whose primary function is to produce and secrete melatonin in response to light-dark cycle environmental cues. The gland may undergo ageing-related structural and morphological changes, including calcification, gliosis, cyst formation, and reduced density of β-adrenergic receptors, which are hypothesised to reduce melatonin secretion. Pineal gland senescence describes the ageing-related decline in neuroendocrine function, with reduced secretion of melatonin, which may contribute to ageing-related sleep disorders and disruption of other circadian-driven physiological functions and may have secondary effects such as contributing to cognitive and mood disorders related to sleep disturbance.

Hormones, December 2025

Kathryn A. Lord, Greger Larson, Robin G. Allaby, Elinor K. Karlsson

We recently provided a new definition for domestication as “the process in which nonhuman populations adapt to an environment created through human activity” (1). It brings domestication fully into an evolutionary framework, obviates the need for assumptions about how domestication occurred, and can be applied equally to plants, animals, and microbes.

In response, Kohl (2) argues that our definition does not recognize domestication as a “special case of evolution.” However, as we describe in our article, extensive literature demonstrates that under modern evolutionary theory, domestication is not a special case of evolution, contrary to views held by many scientists in the 19th and early 20th centuries. Our observation that a population can change its relationship to the anthropogenic niche as a result of environmental shifts is fully consistent with this framework. As R. A. Fisher noted in The Genetical Theory of Natural Selection (3), “fitness may be increased or decreased by changes in the environment.” Because evolution by natural selection proceeds through changes in fitness, alterations in the environment, like genetic change, are integral components of the evolutionary process.

Kohl states that the terms “self-sustaining” and “human-created” are arbitrary. Self-sustaining is a key concept in population biology (4) that is also fundamental to the definition of obligate synanthropes. If a population is not self-sustaining, then it is a sink population that requires immigration to persist and by definition maladapted (5). Populations that are adapted to a human-created niche therefore must be self-sustaining, which makes the concept a critical component for the identification of such populations. Similarly, our definition specifies "an environment created through human activity" as distinct from the human body itself, since organisms adapted to live on or in the human body are not necessarily domestic and the evolutionary processes required to thrive in anthropogenic environments differ from those required to survive on the human body.

PNAS, December 2025

Fatima Ulhuq, Amy K. Tooke, Chriselle Mendonca​, Guillermina Casabona​, Johann Habersetzer​, Yaping Yang​, Margarida C. Gomes, Felicity Alcock​, Serge Mostowy​, Tracy Palmer

The Staphylococcus aureus type VIIb secretion system (T7SSb) is a multiprotein secretion system that secretes toxins with antibacterial activity, but which is also required for full virulence in animal models of infection. S. aureus strains carry one of four T7SSb locus types, named essC1 to essC4, each of which encodes a characteristic LXG-family substrate at the T7SS locus. In essC2 strains, this LXG-domain protein is EsxX, which has a glycine zipper sequence in its C-terminus and has potent antibacterial, membrane-depolarizing activity. In this work, we recognize conserved features of the essC2 and essC3 systems, identifying the LXG protein SAR0287 as structurally and functionally similar to EsxX. Using a zebrafish larval hindbrain ventricle infection model, we demonstrate that the T7SSb of essC2 and essC3 representative strains contributes to bacterial replication and zebrafish mortality. However, there is no significant loss of virulence in the model system if EsxX or SAR0287 is absent. These findings indicate that there is no discernible role for either toxin in this virulence model.

Microbiology, December 2025

Annabelle R de Vries , Lochlan Chadwick , Mark Carine , Robin G Allaby

Adhesives have been integral to the production of herbaria for paper making, securing plant material to paper, and, in the case of bound volumes, for bookbinding. The adhesives used may be of plant, animal, or synthetic origin. Here we investigated herbarium specimens from the Natural History Museum London (NHM), collected between 1698 and 1970, to determine whether information on the adhesives used in the preparation of herbarium specimens can be established using ancient DNA analysis of the mounted plant material. Ancient DNA was obtained from leaf tissue of 14 herbarium specimens of Trochetiopsis and sequenced using Illumina MiSeq. Non-Trochetiopsis DNA was identified using metagenome analysis software (MEGAN). Reads identified as animal were further analysed using the metagenomics pipeline Phylogenetic Intersection Analysis (PIA). Two specimens showed distinct animal reads. One specimen from 1698, which had glue residue observable on the leaf material, showed evidence for Pecora and Bovidae, specifically Bos, and with lower read counts also for both Leporidae and Ovis. The bones of cattle, rabbits, and sheep are all likely to have been used in the preparation of glue in this period, and consequently the animal DNA retrieved is probably from the glue used for mounting. The second sample was from 1970 and showed reads of Pecora, Bovidae, and Bos. Latex adhesives were used at the NHM during the 1970s with synthetic adhesives used thereafter. We infer that the animal DNA retrieved is probably from gelatine used for paper sizing. The results of this study demonstrate that the genetic analysis of plant material can also provide insights into the process of making herbaria.

Botanical Journal of the Linnean Society, December 2025

Bertil B. Fredholm, Lauren May, Christa E. Müller, Joel Linden, Karl-Norbert Klotz, Kenneth A. Jacobson, Adriaan P. IJzerman, Rebecca Hills, Bruno G. Frenguelli, Gary L. Stiles

Adenosine receptors (nomenclature as agreed by the NC-IUPHAR Subcommittee on Adenosine Receptors [114]) are activated by the endogenous ligand adenosine (potentially inosine also at A3 receptors). Crystal and cryo-EM structures for all four adenosine receptors have been solved, occupied by either agonists (sometimes in the presence of an allosteric modulator) or antagonists. Many of these structures were incorporated in a recent review [155]. More recently, structures for the A2B receptor [58, 48] and the A3 receptor [279, 47] were elucidated. The A2A receptor is used as a workhorse in GPCR structure elucidation: almost 100 structures are available in the Protein Data Bank (www.rcsb.org). istradefylline, a selective A2A receptor antagonist, is on the market for the treatment of Parkinson's disease, while caffeine's mechanism of action is largely due to its antagonism of at least three of the four adenosine receptor subtypes. Allosteric modulators, particular PAMs of A1 and A3 receptors, have been explored chemically and structurally.

IUPHAR/BPS Guide to Pharmacology CITE, December 2025

Ning Wang, Linda M. Westermann, Mingyu Li, Chun-Yang Li, Andrew R. J. Murphy, Zengtian Gu, Eleonora Silvano, Claudia A. Blindauer, Ian D. E. A., Yu-Zhong Zhang, David J. Scanlan, Yin Chen

All cells use lipid membranes to maintain cellular integrity and function, though Archaea utilize lipids composed of glycerol-1-phosphate (G1P), while Bacteria and Eukaryotes use glycerol-3-phosphate (G3P). Given that Archaea contribute significantly to global marine biomass, accounting for 0.3 gigatonnes (Gt) of carbon in the oceans, we aimed to uncover how archaeal G1P is recycled by marine microorganisms. Through a multidisciplinary approach combining microbiology, biochemistry, and structural biology, we identified a G1P transporter in marine bacteria, which we named GpxB. Phylogenetic analysis revealed that GpxB belongs to the organic phosphonate transporter (PhnT) family and is widely distributed in the marine microbiome, found in approximately 5 to 10% of microbial cells in surface marine waters. Strikingly, we also identified a second G1P transporter, UgpB, that is known to transport G3P and belongs to the carbohydrate uptake transporter-1 (CUT1) family, in the model bacterium Phaeobacter sp. MED193. To explore the evolutionary pathways that led to the formation of G1P binding sites in both the PhnT and CUT1 families, we determined the structures of GpxB and UgpB bound to G1P and G3P. Using structure-guided mutagenesis and a comparative analysis of the binding pockets within the PhnT and CUT1 families, we traced their evolutionary trajectories, highlighting the distinct strategies through which G1P-binding sites developed in these two protein families.

PNAS, December 2025

Nicola Gorringe , Stephanie Topp , Robin Burns , Sota Yamaguchi , Fernando ARabanal , Joiselle B Fernandes , Detlef Weigel , Tetsuji Kakutani , Matthew Naish , Ian R Henderson

Eukaryotic centromeres mediate chromosome segregation during cell division. Plant centromeres are loaded with CENH3-variant nucleosomes, which direct kinetochore formation and spindle-microtubule interaction. Centromeres are frequently composed of megabase-scale satellite repeat arrays, or retrotransposon nests. In monocentric genomes, such as the model plant Arabidopsis thaliana, pericentromeric heterochromatin surrounds the CENH3-occupied satellite arrays. A zone of suppressed meiotic crossover recombination contains the centromere and extends into the pericentromeres. Here, we explore how natural variation in Arabidopsis influences centromere-proximal crossover frequency and segregation distortion when centromeres are heterozygous. We used fluorescent crossover reporters to quantify the effect of genetic variation on centromere-proximal recombination in 12 F1 hybrids between the reference strain Col-0 and nonreference accessions that captured Eurasian and relict diversity, and in total, we measured 3,037,802 meioses. The majority of the F1 hybrids (49 of 60) had significantly higher or lower centromere-proximal crossover frequency than inbreds. We relate hybrid crossover frequencies to patterns of nucleotide diversity and centromeric structural variation, and in a subset of 7 accessions, to epigenetic patterns of CENH3 enrichment and DNA methylation. Using linear modeling, we observed that chromosome and accession, and their interaction, together explained 85% of variation in crossover frequency, consistent with cis- and trans-acting modifying effects. The fluorescent reporters also allow segregation distortion through meiosis to be quantified between hybrids and inbreds. We observed a minority of hybrids (18 of 60) with distorted segregation through meiosis compared to inbreds, which occurred with or without a simultaneous change to centromere-proximal crossover frequency. Linear modeling revealed that 56% of variation in segregation distortion is explained by chromosome and accession, but with a stronger effect of accession compared to crossover frequency. We discuss how Arabidopsis centromeric structural heterozygosity may modify recombination and cause segregation distortion through meiosis.

Genetics, December 2025

Yayoi Sugita, Amanda J. Dowson, Ichiro Kajisa, Katsuaki Takechi, Yilan E, Jingzhi Zhao, Jiaqi Wang, Xiaofei Lin, Laura Diaz-Saez, Adrian J. Lloyd, Christopher G. Dowson, Hiroyoshi Takano

It is understood that a cyanobacterium was the progenitor of plastids and that the biosynthesis of cell wall peptidoglycan was lost during chloroplast evolution. However, accumulated data, especially from the moss Physcomitrium patens, suggest that peptidoglycan remains essential for plastid division in some land plants. A fundamental set of peptidoglycan biosynthesis (Mur) genes has been identified in the genomes of these land plants, while many angiosperms no longer encode some core Mur genes, including a bifunctional penicillin-binding protein (PBP). Ten incomplete Mur genes were previously identified in the genome of the gymnosperm Picea abies but these could be pseudogenes or encode proteins that have been repurposed. For instance, mutant albino maize and Arabidopsis seedlings possess a defective UDP-N-acetylmuramoyl-l-alanyl-d-glutamate--2,6-diaminopimelate ligase (MurE), an intact MurE ligase being essential for peptidoglycan synthesis. In this study, we isolated a full set of cDNAs for peptidoglycan biosynthesis from P. abies. GFP fusion proteins with either P. abies (Pa)MurE or PaPBP were detected in chloroplasts. Cross-species complementation assays with PaMurE in Arabidopsis albino MurE mutants and Physcomitrium MurE chloroplast division mutants showed that the gymnosperm MurE completely rescued both mutant phenotypes. Enzymatic assay of recombinant PaMurE proteins revealed they catalyze the same reaction performed by their bacterial MurE homologs. Moreover, the expression of the PaPbp cDNA partially rescued the giant chloroplast phenotype in the moss Pbp knockout line. These results are consistent with the operation of a functional Mur gene set in the Norway spruce genome.

The plant Journal, December 2025

European Food Safety Authority (EFSA), Elena Lázaro, Stephen Parnell, Antonio Vicent Civera, Martijn Schenk, Jose Cortiñas Abrahantes, Juan Navas-Cortes, Hans-Hermann Thulke, Francesco Pecori, Joshua Koh, Jan Schans, Marc Aerts, Gabriele Zancanaro, Sybren Vos, Tomasz Kaluski

At the request of the European Commission, EFSA prepared the general guidelines for surveys of plant pests, describing the legal, international and scientific context in which the surveys are designed, the basic principles implemented for surveillance of quarantine pests and introducing the concepts needed for the design of statistically sound and risk-based surveys. Three types of specific surveys are addressed: detection surveys for substantiation of pest freedom, delimiting surveys to determine the boundaries of a potential infested zone, and monitoring surveys for prevalence estimation when measuring the effectiveness of eradication measures or for the confirmation of a low pest prevalence area. For each type of survey, the survey parameters are introduced and their interactions analysed showing the importance of the assumptions that are taken for each one of them:

1) The aims of the survey are defined as achieving a certain level of confidence of detecting a given pest prevalence (design prevalence), this reflects the trade-off between the acceptable level of the risk and availability of resources that determine the strength of the evidence to support the conclusion of the survey;

2) The target population is described by its structure and size, including the risk factors; and

3) The method sensitivity is defined as the combination of the sampling effectiveness and the diagnostic sensitivity for each inspection unit. EFSA's RiPEST and RiBESS+ tools1 are introduced for calculating the sample size using the survey parameters as input values for a statistically sound and risk-based survey design. The mathematical principles behind the tools are in line with the International Standards for Phytosanitary Measures. The survey design is flexible and can be tailored to each pest and specific situation in the Member States. Once the survey is implemented following this approach, the conclusions allow surveys to be compared across time and space, contributing to the harmonisation of surveillance activities across the EU Member States.

EFSA Supporting Publications, December 2025

Alicia Gill, Jere Koskela, Xavier Didelot, Richard G Everitt

Inference of the reproduction number through time is of vital importance during an epidemic outbreak. Typically, epidemiologists tackle this using observed prevalence or incidence data. However, prevalence and incidence data alone are often noisy or partial. Models can also have identifiability issues with determining whether a large amount of a small epidemic or a small amount of a large epidemic has been observed. Sequencing data however are becoming more abundant, so approaches which can incorporate genetic data are an active area of research. We propose using particle MCMC methods to infer the time-varying reproduction number from a combination of prevalence data reported at a set of discrete times and a dated phylogeny reconstructed from sequences. We validate our approach on simulated epidemics with a variety of scenarios. We then apply the method to real datasets of HIV-1 in North Carolina, USA and tuberculosis in Buenos Aires, Argentina. The models and algorithms are implemented in an open source R package called EpiSky which is available at https://github.com/alicia-gill/EpiSkyLink opens in a new window.

Journal of the Royal Statistical Society Series C (Applied Statistics), December 2025