Quantitative, Systems & Engineering Biology Publications

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

Amadeus Plewnia, Brandon D. Hoenig, Stefan Lötters, Christopher Heine, Jesse Erens, Philipp Böning, Gary D. Bending, Henrik Krehenwinkel, Molly Ann Williams

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats—CRISPR-associated nucleases) systems allow researchers to detect, capture, and even alter parts of an organism's genome. However, while the use of CRISPR-Cas has revolutionised many fields in the life sciences, its full potential remains underutilised in ecology and biodiversity research. Here we outline the emerging applications of CRISPR-Cas in ecological contexts, focusing on three main areas: nucleic acid detection, CRISPR-enhanced sequencing, and genome editing. CRISPR-based nucleic acid detection of environmental DNA samples is already reshaping species monitoring, providing highly sensitive and non-invasive tools for both scientists and the public alike, with reduced costs and minimal experience required. Further, CRISPR-enhanced sequencing, including Cas-mediated target enrichment, enables efficient recovery of ecologically relevant loci and supports diverse applications such as amplification-free metagenomics. Finally, while genome editing on wild species remains largely theoretical in ecology, these tools are already being used in controlled settings to study adaptation and resilience in the face of ongoing global stressors. Together, the applications of CRISPR-Cas are paving the way for more affordable, accessible, and impactful applications for species conservation, and promise to improve our ability to tackle the ongoing global biodiversity crisis.

Molecular Ecology Resources, December 2025

Clara Bergis-Ser, Qingyi Wang, Xiaoning He, Maherun Nisa, Vickie Kaise, Christelle Mazubert, Jeannine Drouin-Wahbi, Rim Brik-Chaouche, Layla Chmaiss, Jelle Van Leene, Geert De Jaeger, Jose Gutierrez-Marcos, Catherine Bergounioux, Clara Bourbousse, David Latrasse, Moussa Benhamed, Cécile Raynaud

Genomic integrity is constantly challenged by transcription/replication conflicts, a major source of replication stress and instability across all life forms. While extensive studies have elucidated mechanisms for resolving transcription/replication conflicts in animals, yeast, and prokaryotes, their counterparts in plants remain largely unexplored. Through a forward genetic screen, we identified LUMINIDEPENDENS (LD), previously known for its role in regulating the flowering repressor FLC, as a key factor in mitigating replication stress in plants. Notably, transcriptomic analyses reveal that LD loss results in the upregulation of over half of the Arabidopsis genes, placing LD as a global transcriptional repressor. Consistent with this role, LD directly binds a substantial portion of the Arabidopsis genome and interacts with the MED18 subunit of the Mediator complex to modulate RNA polymerase II phosphorylation. These findings uncover a fundamental function of LD in fine-tuning transcription at a genome-wide scale, with potentially an additional role in suppressing transcription–replication conflicts by locally dampening transcription and promoting replication fork progression. Our work highlights an intriguing genome-protective strategy in plants, that could shed light on mechanisms involved in transcription–replication conflict management in eukaryotic systems.

PNAS, December 2025

Nabil Karah, Nathan Faille​, Nancy Allard, Frédéric Grenier, Antoine Abou-Fayad, Paul G. Higgins, Leena Al-Hassan, Benjamin A. Evans, Laurent Poirel, Rémy A. Bonnin, Anette M. Hammerum, Frank Hansen, Rayane Rafei, Monzer Hamze, Xavier Didelot, Santiago Castillo-Ramírez, Simon Lévesque, Sébastien Rodrigue, Bernt Eric Uhlin, Louis-Patrick Haraoui

Infections caused by carbapenem-resistant Acinetobacter baumannii (CRAB) are of great concern, as mortality is high, and treatment options are very limited. Despite having among the highest rates reported worldwide, scarce genomic data are available on CRAB strains from the Middle East. Here, we report the global emergence of a novel International Clone (IC), designated IC12, based on the epidemiological, phenotypic and genome sequencing data (short reads and long reads) of a set of 60 A. baumannii isolates belonging to multilocus sequence type 158 (Pasteur scheme). IC12, prevailing in the Middle East since 2007, has also been found in Europe, Asia and South America. Alleles OXA-65 and ADC-117, coded by the blaOXA-51-like and blaADC A. baumannii-intrinsic genes, respectively, were hallmarks shared by all the isolates. Plasmid pIC12-2 (80,000 bp), which carries a repAci6 replication initiator (RP-T1) and a type IV conjugative transfer system, played a major role in the antimicrobial resistance profile of 54/60 of the IC12 isolates. This resistance was mediated by three mobile genetic elements, namely Tn2008, MITEAb-IC12 and TnaphA6. All four Peruvian IC12 isolates lacked pIC12-2 and carried a different set of plasmids. Two of the Peruvian isolates carried a chromosomal resistance island of 79,396 bp long (designated IC12-RI) marked by the occurrence of tet(X3). The global spread of IC12 is worrying and calls for further studies on the virulence features and clinical impact of this clone.

Microbial Genomics, November 2025

Chao Yan,Shanwei Tong, Yarong Wu, Yujie Chen,Xinyu Jia,Yan Guo,Mengnan Cui,Guangqian Pei, Zuming Zhang, Hao Zhou, BAdmin , Kai Mu,Xue Ren,Bing Du, Hanqing Zhao,Yanling Feng,Jinghua Cui,Yuyan Xia, MBBS , Zhen Wang, Yu Sun,Prof Linqing Zhao, Prof Chuangli Hao, Zhijie Zhu, Shengqiang Luo, Han Zhang, Yongjun Wang , Prof Lili Zhong, DehuiChen , Prof Yong Yin , Longji Hu, Prof Yuehua Ke, Prof Guanhua Xue, Prof Ling Cao, , Prof Xavier Didelot, Prof Jing Yuan, Prof Yujun Cui,

Background: After a prolonged period of low detection rates, Mycoplasma pneumoniae resurged in China, during September to November, 2023, raising global concern. This study aims to gain a better understanding of the genetic mechanisms underlying the 2023 increase in cases and the evolutionary dynamics of the epidemic populations, which has been previously hampered due to limited genomic data of this pathogen.

Methods: We sequenced 685 M pneumoniae isolates, including 248 isolates from 11 Chinese provinces and municipalities in 2023 and 437 isolates from Beijing (2013–22). By analysing these isolates and 436 publicly global sequences, we reconstructed the pathogen’s evolutionary history using time-calibrated phylogenies and effective population size inference. We investigated potential genomic variations contributing to the 2023 resurgence through genome-wide association study and conducted phylogeographic analysis of the 2023 isolates across China.

Findings: Two macrolide-resistant epidemic clusters (T1-2-EC1 and T2-2-EC2) were responsible for the 2023 resurgence in China. Both clusters, having acquired the 23S ribosomal RNA A2063G mutation conferring macrolide resistance, emerged in approximately 1997 and 2014, respectively, and subsequently outcompeted their predecessor populations. This coincided with China’s large-scale adoption of azithromycin for paediatric community-acquired pneumonia around the early 2000s. Aside from macrolide resistance, T1-2-EC1 independently acquired 17 clade-specific mutations and T2-2-EC2 four clade-specific mutations, which could further explain their increased competitiveness. Whole-genome analysis revealed no resurgence-specific mutations in the 2023 isolates. Phylogeographic analysis showed rapid mixing of T1-2-EC1 isolates between different sampled regions within China.

Interpretation: Our study provides evidence that the 2023 resurgence in China is a continuation of the pre-COVID epidemic, rather than emergence of novel variants. The high prevalence of macrolide resistance and rapid intranational spread emphasise the urgent need for enhanced global surveillance of this pathogen.

The Lancet (Microbe), December 2025

Amelia Longa, Daniel N. Franklin

As global fertility rates decline, improving the success rates of assisted reproductive technologies (ART) becomes ever more important. Many factors impact the success of ART and understanding these is key to enhancing treatment efficacy. We analysed a large UK national dataset from the Human Fertilisation and Embryology Authority to determine which factors predict success of ART. Binary logistic regression identified significant predictors of biochemical pregnancy. Patient age, diagnosed ovulatory disorder, specific ART treatment, PGT-A testing, donor egg, number of embryos transferred, patient ethnicity, and day of embryo transfer were significant predictors of success. These results add detail and evidence to previous studies and the insights can inform clinical practices to enhance ART success rates.

Heliyon, January 2026

Kandas Traore, Damien Seyer, Agnes Mihajlovski, Antonia P Sagona

Antimicrobial resistance represents one of the most serious threats to both public health and economic sustainability. One of the promising approaches to address this problem is phage therapy – treatment of pathogenic bacterial infections using bacteriophages. Bacteriophages have a narrow host spectrum of activity, minimal side effects and self-replication at the infection site, which positions them as promising candidates to complement or replace conventional antibiotics. Moreover, they can be easily genetically modified to enhance their effectiveness and safety. In this At a Glance article, we highlight the timely relevance of engineered phages as an innovative solution in a rapidly evolving healthcare landscape. First, we introduce bacteriophages' life cycle, ecology and therapeutic history, emphasizing their role in One Health strategies. Then, we describe advanced engineering techniques that can be used to expand bacteriophages' functionalities. Finally, we discuss innovative applications of engineered bacteriophages in biotechnological applications and as a potential countermeasure for antimicrobial resistance, including serving as a shuttle for delivering genes and drugs to the targeted bacterial and eukaryotic cells, targeting intracellular bacteria, contributing to vaccine development, facilitating advancements in tissue engineering and improving bacteriophages' antibacterial properties.

Disease Models and Mechanisms, September 2025

Carmen Sánchez-Cañizares , Raphael Ledermann , Joseph McKenna, Thomas J Underwood , Marcela Mendoza-Suárez , Rob Green , Karunakaran Ramakrishnan , Alison K East , Isabel Webb , Charlotte Kirchhelle , Beatriz Jorrín , Gerhard Saalbach , Euan K James , Flavia Moreira-Leite , Jason Terpolilli , Philip S Poole

Within legume root nodules, rhizobia differentiate into bacteroids, which reduce N2 into NH3 for secretion to the plant. Bacteroids may be swollen and terminally differentiated or non-swollen and can regenerate outside nodules. It is unclear why these different endosymbiotic lifestyles exist and whether they differ in symbiotic efficiency. Here, we compared N2 fixing bacteroids of the near isogenic strains Rhizobium leguminosarum bv. phaseoli 4292 (Rlp4292) and R. leguminosarum bv. viciae A34 (RlvA34), nodulating Phaseolus vulgaris (common bean) and Pisum sativum (pea), respectively. The larger bean plants fixed more N2, but peas fixed 1.6-3-fold more per unit nodule mass. Values per unit volume were similar between bean and pea because bean nodules are 2.7-fold denser (i.e., mass per unit volume). Bean nodules have higher numbers of smaller (∼1/5 the volume) bacteroids than peas. Bean bacteroids are denser (i.e., 2.5-fold protein per unit volume) although less closely packed than pea bacteroids (i.e. more space between bean bacteroids). Critically, pea bacteroids, fix N2 at higher rates versus bean per unit bacteroid protein, as protein expression is skewed towards N2 fixation and TCA-cycle enzymes. Pea bacteroids infect 1.6 times the percentage of nodule volume of beans (i.e., 14.2% versus 9.1%). Overall, the increased packing density of pea bacteroids, as well as the bias of their proteome to nitrogenase, associated N2 fixation processes, and dicarboxylate metabolism, contributes to their greater symbiotic efficiency, which is likely driven by plant antimicrobial peptides.

Plant Physiology, December 2025

Matt Combes, Nathan Brown, Robin N. Thompson, Alexander Mastin, Peter Crow, Stephen Parnell

Invasive plant pests and pathogens cause substantial environmental and economic damage. Visual inspection remains a central tenet of plant health surveys, but its sensitivity (probability of correctly identifying the presence of a pest) and specificity (probability of correctly identifying the absence of a pest) are not routinely quantified. As knowing sensitivity and specificity of visual inspection is critical for effective contingency planning and outbreak management, we address this deficiency using empirical data and statistical analyses. Twenty-three citizen scientist surveyors assessed up to 175 labelled oak trees for three symptoms of acute oak decline. The same trees were also assessed by an expert who has monitored these individual trees annually for over a decade. The sensitivity and specificity of surveyors was calculated using the expert data as the ‘gold-standard’ (i.e., assuming perfect sensitivity and specificity). The utility of an approach using Bayesian modelling to estimate the sensitivity and specificity of visual inspection in the absence of a rarely available ‘gold-standard’ dataset was then examined with simulated plant health survey datasets. There was large variation in sensitivity and specificity between surveyors and between different symptoms, although the sensitivity of detecting a symptom was positively related to the frequency of the symptom on a tree. By leveraging surveyor observations of two symptoms from a minimum of 80 trees on two sites, with reliable prior knowledge of sites with a higher (~0.6) and lower (~0.3) true disease prevalence we show that sensitivity and specificity can be estimated without ‘gold-standard’ data using Bayesian modelling. We highlight that sensitivity and specificity will depend on the symptoms of a pest or disease, the individual surveyor, and the survey protocol. This has consequences for how surveys are designed to detect and monitor outbreaks, as well as the interpretation of survey data that is used to inform outbreak management.

PLOS - Computational Biology, November 2025

Sean Savitz, Edgar Samaniego, David Liebeskind, Johannes Boltze

A STAIR XIII workshop was held to discuss aspects of trials likely to have the greatest impact on detecting meaningful treatment effects of cerebroprotection in acute stroke. Intended goals for hyperacute protection should be focused on preserving penumbral tissue and delaying infarct core growth to augment the impact of reperfusion therapies. Infarct volume is a biologically and clinically meaningful surrogate imaging marker to assess the treatment effects of cerebroprotection. Lastly, clinical outcome measures for cerebroprotection should include domain-specific and patient-centered outcomes to detect clinically meaningful changes across multiple functional domains.

Stroke, November 2025

Matt Bawn, Nigel Francis, Liz Alvey, Christopher Hassall, Andre Pires-daSilva, Pedro Barra, Denise Hough, Hannah Campbell, Matt Hardy, Juanvi Canet-Perez

The advent of Generative Artificial Intelligence (GenAI) is already impacting pedagogic strategies and assessment methodologies in higher education, particularly in the biological sciences which have traditionally relied heavily on written assessments. GenAI's rapid and plausible text generation capabilities challenge traditional written assessments and prompt a shift towards more authentic assessment types. This paper explores innovative applications of GenAI in biology education through case studies presented at a recent workshop. These case studies illustrate how GenAI has the potential to enhance academic activities, from developing learning resources to fostering student engagement through active learning strategies. The discussion highlights a shift from product-oriented assessments to process-oriented approaches that prioritize continuous interaction, iteration, and reflection among learners. Despite GenAI's reliance on pre-existing data raising concerns about originality and contextual accuracy, and its limitations in tasks requiring high creativity and deep understanding, it has the potential to enhance educational practices when applied with awareness of its constraints. The paper concludes with a balanced analysis of the transformative impact and inherent challenges of integrating GenAI into biology education, advocating for thoughtful implementation to ensure it augments rather than replaces traditional teaching methods.

Advances in Physiology Education- November 2025

Fernando Baile, Javier Antúnez-Sánchez, Jose Gutierrez-Marcos, Myriam Calonje

Background: PcG complexes are pivotal in orchestrating the transition from embryonic to vegetative development in plants. However, the mechanisms underlying the gene expression reprogramming that takes place during this developmental transition are still not fully understood. Several studies suggest that incorporating PcG modifications into distinct histone variants may play a key role in this process. However, while PRC2-mediated H3K27me3 is essential for gene repression, the timing of PRC2 action on canonical H3.1 or variant H3.3 remains unclear. Furthermore, the exact role of PRC1 in transcriptional regulation is still unresolved, partly owing to limited knowledge of the conditions under which this complex monoubiquitinates canonical H2A or H2A.Z variant.

Results: Here, we demonstrate that H2A.Z undergoes monoubiquitination during the seed-to-seedling transition. H2A.Zub facilitates the recruitment of PRC2 to mediate H3.3 trimethylation, repressing seed-specific genes; however, H2A.Zub also promotes the activation of vegetative-specific genes by preventing H3K27me1 incorporation into H3.1. Notably, the histone demethylase REF6 initiates this process by removing two methyl groups from stably repressed H3.1K27me3-marked genes, enabling the subsequent H2A.Zub incorporation. This result suggests that REF6 activity is a critical early step in PRC1-mediated transcriptional activation.

Conclusions: Our findings reveal the long-sought mechanism by which PRC1 participates in transcriptional activation. We demonstrate that PRC1-mediated H2A.Zub, acting as a “switcher”, plays a pivotal role in reprogramming active and repressed genes during the transition from embryonic to vegetative development. Moreover, our results provide new insights into the intricate relationship between histone modifications and histone variants in reprogramming and maintaining gene expression patterns.

Genome Biology, November 2025