Results
- Showing results for:
- Reset all filters
Search results
-
Journal articleBruno F, Langhorne J, Lo Celso C, 2026, , STAR Protocols, Vol: 7, ISSN: 2666-1667
In malaria-endemic regions, individuals experience repeated malaria infection throughout life. Here, we present a protocol to investigate the immunological mechanisms triggered by repeated exposure using a murine model of sequential infections with the rodent parasite Plasmodium chabaudi chabaudi. We provide a detailed and standardized series of steps covering primary infection, natural recovery without treatment, and subsequent secondary infection. This approach offers a robust framework to investigate the effects and long-term consequences of repeated malaria infections on the host.
-
Journal articledos Anjos L, Farneda FZ, Medeiros HR, et al., 2026, , Biological Conservation, Vol: 324, ISSN: 0006-3207
While fragmentation is known to affect species diversity, the degree to which functional structure is retained relative to primary forests and the factors driving this retention remain poorly understood. Here, we applied the concept of ecological resilience to forest fragmentation by examining the extent to which bird communities in 20 forest fragments (27-926 ha) retain the functional trait space observed in a large, protected area of primary forest used as a reference, Iguaçu National Park (INP), within the Seasonal Semideciduous Atlantic Forest of southern Brazil. We used retention of the functional trait space of the reference forest as an indicator of potential ecological resilience and, consequently, conservation value. Functional trait spaces were estimated using kernel hypervolumes, and three metrics were calculated: (1) the percentage overlap between the trait spaces of INP and each fragment; (2) the fraction of trait space unique to INP; and (3) the fraction unique to each fragment. Functional overlap ranged from 63 to 77%, the fraction unique to INP ranged from 5 to 29%, and the fraction unique to fragments ranged from 14 to 24%. Although observed functional overlap was substantial, it did not differ significantly from null expectations based on species richness and abundance structure. Landscape diversity is associated with a higher percentage of trait space unique to fragments, whereas larger fragment area was associated with greater overlap in trait space between INP and fragments. Assessing trait space overlap between continuous forest and fragments provides a novel perspective on functional responses to fragmentation and can help identify patterns potentially relevant to ecosystem functioning.
-
Journal articleYuen ELH, 2026, , Phytopathology Research, Vol: 8, ISSN: 2096-5362
Plant immunity operates through two interconnected layers. Pattern-triggered immunity (PTI) is initiated by cell-surface pattern-recognition receptors, whereas effector-triggered immunity (ETI) is executed by intracellular nucleotide-binding leucine-rich repeat (NLR) receptors. The two layers are known to potentiate one another, yet how a signal perceived at the plasma membrane is relayed to prime an intracellular NLR has remained unclear. In a recent study, Gao et al. (2026) show that the potato late blight resistance protein Rpi-vnt1.1 carries a self-imposed restraint, an autoinhibitory N-terminal extension encoded by an intron-retained mRNA isoform. Pathogen perception, acting through PTI, shifts the balance of alternative splicing towards an isoform that lacks this extension, producing a resistosome-competent receptor that the Phytophthora infestans effector AVRvnt1 can then activate. This work defines pre-mRNA alternative splicing as a checkpoint that couples surface and intracellular immunity, and points to a broadly conserved and engineerable mode of NLR control.
-
Journal articleMaia RA, Oki Y, Medina I, et al., 2026, , Theoretical and Experimental Plant Physiology, Vol: 38
Large-scale mining disasters in tropical regions impose long-term pressures on ecosystems by degrading soil fertility and exposing native vegetation to chemical and physical disturbances. This study investigates whether Eugenia florida, a native tree species found in both tailings-impacted and reference areas of the Rio Doce Basin in Brazil, exhibits physiological adjustments that confer resilience to combined edaphic and thermal constraints. We assessed soil properties and 16 physiological traits related to nutrient status, photosynthetic efficiency, photoprotection, and thermal tolerance. Soils in the impacted area exhibited markedly lower organic matter, cation exchange capacity, and nutrient concentrations, along with increased iron concentration. Despite a 10% reduction in nitrogen balance index, plants in the impacted area exhibited 10% more chlorophyll and 19% more flavonoids, indicating compensatory pigment production and enhanced antioxidant capacity. Photosynthetic performance remained stable across environments, but individuals in the impacted area displayed elevated regulated energy dissipation and reduced unregulated energy loss, suggesting efficient photoprotective adjustments. Transient fluorescence analyses revealed intensified excitation fluxes and greater heat dissipation per reaction centre. Thermal thresholds, defined as temperatures causing 15% and 50% reductions in photosynthetic efficiency, were significantly higher in impacted individuals. Multivariate analyses identified excitation flux traits as key predictors of thermal resilience. Physiological function in E. florida is sustained through integrated plastic responses under long-term soil degradation and thermal constraints. Its ability to modulate energy fluxes and antioxidant defences highlights its potential as a candidate species for ecological restoration in tropical regions increasingly affected by human disturbance and climate extremes.
-
Journal articleHui T-Y, Epopa PS, Millogo AA, et al., 2026, , Parasites and Vectors, Vol: 19, ISSN: 1756-3305
Background Spatial-temporal variation exists in the density and species composition of malaria-carrying mosquitoes, which will in turn influence the transmission of the disease. While there has been extensive research on seasonality and other main drivers of the vector populations, the heterogeneity partitioned as random effects at various spatial-temporal scales is just as important but has not attracted the same attention. Methods To investigate the relative contributions of the between-house, between-village, and between year variations, as well as other house-level covariates such as inhabitant number and bed net usage on vector density and species composition, intensive Pyrethroid Spray Catches (PSC) sampling was conducted across a 60-month period between 2012-2019 from four villages in the Sudano-Sahelian region of Burkina Faso. Results For density, measured by female Anopheles gambiae s.l. counts, our modelling showed that the between-house variation was the largest variance component, followed by the between year then between-village variation, after accounting for seasonality and other covariates. Density increased with the number of inhabitants within a household but was uncorrelated with bed net presence. A subset of female mosquitoes was genotyped for species identification, and the composition of An. coluzzii and An. gambiae, the two dominant vectors in the region, varied markedly across villages without an overall trend. The between-village variance contributed up to 76% of the total random variation in species composition, followed by the between-year variance. The between-house variation was statistically insignificant. Neither household size nor bed net usage had any impact on species composition. Conclusions Interestingly, the between-house component of variation was the largest contributor when measuring mosquito density, but it was the least important for species composition. For between-village variation the converse was found. Together with
-
Journal articleWan Y, Wong JLC, Sanchez-Garrido J, et al., 2026, , BMC Genomic Data, Vol: 27, ISSN: 2730-6844
Background Resistance to carbapenems and third-generation cephalosporins is increasing in Klebsiella pneumoniae globally, restricting therapeutic options. The β-lactam/β-lactamase inhibitor combinations are widely used to circumvent β-lactamase-mediated resistance. In 2021, an unusual K. pneumoniae clinical isolate, KpMVR1, was recovered from a hospitalised patient in England, exhibiting resistance to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam. To investigate this phenomenon, we characterised the genome and antimicrobial susceptibility of KpMVR1 alongside two clonally related isolates susceptible to all three β-lactam/β-lactamase inhibitor combinations: KpMVS1, collected from the same patient 42 days earlier, and KpMVS2, from another patient in the same hospital. Methods Illumina and MinION whole-genome sequencing were conducted for these three isolates, followed by hybrid genome assembly. Annotated genome assemblies were compared to identify genetic variation. Mutagenesis experiments were performed to verify predicted functional alterations. Results All isolates belonged to clone ST8134 and carried blaKPC-2 alleles (KpMVR1: blaKPC-157; KpMVS1 and KpMVS2: blaKPC-2) in plasmids predicted to be conjugative. Insertion sequence ISEc68 caused a frameshift mutation in KpMVR1’s ompK36 gene, reducing susceptibility to meropenem-vaborbactam and imipenem-relebactam. KPC-157 demonstrated decreased hydrolysis of imipenem and ceftazidime when compared with KPC-2. KpMVR1 also encoded a disrupted transcriptional repressor MarR and a destabilising mutation in AcrB, a component of the AcrAB-TolC multidrug efflux pump. An intact, iron-transporting fec operon was identified on a novel IncFII(pKP91)/IncFIB(K) plasmid unique to KpMVS2, possibly accounting for the cefiderocol resistance observed in this isolate. ConclusionsKpMVR1 carried multiple resistance-associated genetic alterations and likely developed its resistance profile
-
Journal articlePashley SL, Hair M, Ukegbu CV, et al., 2026, , Life Sci Alliance, Vol: 9
Plasmodium parasites rely on diverse protein kinases to regulate critical processes, yet many remain uncharacterised. Protein kinase 2 (PK2) is required for asexual blood-stage proliferation and merozoite invasion, but its role in sexual stages and transmission is unknown. Here, using live-cell and super-resolution imaging, ultrastructural analysis, functional phenotyping, and quantitative phosphoproteomics, we define the role of PK2 in Plasmodium berghei transmission. PK2 was expressed in merozoites, ookinetes, and sporozoites: the three invasive forms of the parasite. Conditional depletion of PK2 impaired ookinete motility, disrupted apical microneme positioning, abolished oocyst formation, and prevented mosquito-to-host transmission. Direct haemocoel injection of mutant ookinetes failed to restore sporozoite production, demonstrating an additional requirement for PK2 downstream of midgut traversal. Although global protein abundance was largely preserved, phosphoproteomic profiling identified altered phosphorylation of proteins associated with cytoskeletal organisation, host-cell interaction, midgut invasion, and gene regulation. These findings highlight PK2's critical role across multiple invasive stages, advancing understanding of malaria parasite transmission and identifying putative PK2-regulated pathways as potential targets for transmission-blocking interventions.
-
Journal articleNery ET, Cardona T, Avignone-Rossa C, et al., 2026, , FEMS Microbiology Letters, ISSN: 0378-1097
<jats:title>Abstract</jats:title> <jats:p>Purple non-sulfur bacteria (PNSB) are metabolically versatile microorganisms that inhabit diverse environments taking advantage of a remarkably efficient photosynthetic machinery. In this work, we describe the creation of a workflow for experimental studies aiming to compare the light absorption properties of structural variants of the light-harvesting complex 2 (LH2) of PNSB. Through the creation of a library of LH2 variants using site-directed mutagenesis, we engineered proteins with different spectral properties to be expressed in a LH2-defficient mutant of the model PNSB Rhodobacter sphaeroides. We validated this approach by reproducing a previously described mutant with a blue-shift in the B850 absorption peak, in addition to identifying a novel mutant exhibiting a red-shift of this peak. We characterised the fluorescence lifetime of the purified LH2 spectral variants in vitro. Our results suggest that directed evolution approaches can be used to systematically explore the landscape of light absorption in LH2s variants.</jats:p>
-
Journal articleSchroeder J, 2026, , Arctic Science, ISSN: 2368-7460
-
Journal articleArnell M, Suggitt AJ, Antão LH, et al., 2026, , Global Ecology and Biogeography, Vol: 35, ISSN: 1466-822X
Problem: Climate and land-use change are two key drivers of biodiversity change. Their widespread effects on species and communities have prompted fears that interactions between the two drivers could cause severe biodiversity loss. As the literature on this subject expands rapidly, variation in methodological choices and the terminology used to describe results, combined with context-dependent or individualistic responses across taxa and systems, hinders our ability to systematically evaluate how species and communities are affected by the interacting effects of climate and land-use change. Clarification: We provide guidance for investigating climate-land-use interactions, following clear definitions and including recent examples from natural and semi-natural systems. We highlight how variation in methodologies, language inconsistencies, data limitations, and the inherent variation among populations and species can affect the analysis of climate-land-use interactions. Importantly, we demonstrate how failing to consider interactive effects can negatively impact the outcomes of conservation interventions designed to protect biodiversity. Communicating Climate-Land-Use Interactions: We provide a roadmap to guide future work, highlighting important considerations for understanding and communicating climate-land-use interactions relevant for both policy and conservation. Outlining how different factors can complicate our understanding of interactive effects is a key step towards the accurate detection, interpretation and communication of the effects of climate and land-use change on biodiversity in a rapidly-changing world.
-
Journal articleIkhwanuddin R, Le Penru NP, Sethi SS, et al., 2026, , The Journal of the Acoustical Society of America, Vol: 160, Pages: 3754-3769
<jats:p>Automated ecoacoustic monitoring supports biodiversity conservation but struggles with signal degradation in noisy forests. Microphone-array recorders enable beamforming to focus on target directions and reduce background noise, yet their effectiveness in autonomous settings remains underexplored. This study evaluates filter-and-sum beamforming using measured impulse responses (IRs) to enhance bird-call classification. It compares lab-generic IRs from a semi-anechoic chamber with site-specific IRs measured in a forest. Playback experiments were conducted with a multichannel autonomous recorder using Eurasian blue tit calls in a real forest (1 to 64 m) and a 31-speaker virtual soundscape (signal-to-noise ratios from +30 to –30 dB). BirdNET performed classification, with metrics including detection count and confidence improvements versus the omnidirectional baseline. Both beamforming methods outperformed the baseline. Site-specific IR beamforming excelled at intermediate and long ranges. Both significantly raised confidence scores (p &lt; 0.001), with site-specific IRs showing a modest advantage (mean Δ confidence 0.15 vs 0.11; p = 0.00001). These results confirm the value of beamforming for passive acoustic monitoring: site-specific IRs perform best, while lab-generic IRs provide a robust alternative for large-scale use.</jats:p>
-
Journal articleDe Lorm TA, Heon SP, Bernard H, et al., 2026, , Forest Ecology and Management, Vol: 619, ISSN: 0378-1127
Replanting a tree plantation - that is, clearing old trees and replacing these with young plants - drastically alters its habitat structure and microclimate, leading to changes in its biodiversity. Nevertheless, we lack an understanding of how the replanting of oil palm plantations - the most prominent oil crop globally - affects mammals and birds, while the amount of area replanted will increase exponentially over the next decades. We therefore studied how the bird and mammal community of an oil palm plantation in Malaysian Borneo changed in response to replanting. Using camera traps for mammals, and acoustic recordings and BirdNET for birds, we show that both communities are transformed. Mammal species richness slightly dropped, because of the absence from replanted plantations of long- and pig-tailed macaques (Macaca fascicularis and M. nemestrina), both endangered primate species. Bird species richness did not significantly differ between replanted and mature plantations. However, the detection frequency of most species changed, as the bird community shifted from forest and woodland species towards open-habitat species. The detection frequency and species richness of different trophic niches stayed largely constant, indicating that birds will still be able to perform similar high-level ecological functions in replanted plantations. Overall, our results show that replanting reshaped mammal and bird communities, but that their diversity and abundance does not collapse. These findings stress the importance of staggered replanting, as opposed to replanting large stretches of plantation in one go, to bolster landscape level biodiversity, and underscore that tree plantations are temporally dynamic habitats.
-
Journal articleGan W, Garen J, Michaletz S, et al., 2026,
Thermal acclimation as an emergent property ofeconomically optimal photosynthesis
, New Phytologist, ISSN: 0028-646XLeaf-level photosynthesis acclimates to growth conditions over days to weeks, resulting in the instantaneous optimal temperature for photosynthesis (Topt) increasing with growth temperature (Tgrowth). This widely observed behaviour is reproduced as an emergent property of the P model, a generic model of primary production based on eco-evolutionary optimality hypotheses. We show, through comparisons with an experimental data set on the photosynthetic characteristics of three herbaceous plant species grown at different temperatures, that the P model yields a realistic linear increase in Topt with Tgrowth and a realistic peaked relationship between the photosynthetic rate at Topt (Aopt) and Tgrowth. These responses emerge primarily from thermal acclimation of a stomatal sensitivity parameter ;@= that determines the ratio of internal to ambient CO2 (ci:ca) and its sensitivity to vapour pressure deficit, without requiring any change in enzyme kinetics. Furthermore, the decline in Aopt at high growth temperatures, often attributed to heat stress, can be explained by the narrowing gap between Topt and Tgrowth as Tgrowth increases, a direct consequence of the @> ) Topt shift having a slope < 1. The P model as implemented here provides a mechanistic explanation for observed trends in Topt and Aopt with growth temperature, and additionally provides a scalable approach for improving representation of biochemical and stomatal acclimation in land surface models.Keywords: Eco-evolutionary optimality; P model; temperature acclimation; photosynthetic parameters; electron transport; carboxylation; vapour pressure deficit
-
Journal articleBourne A, Amatiello FG, Elger K, et al., 2026, , J Invertebr Pathol, Vol: 219
Honey bees (Apis mellifera) experience variable colony losses across regions and years, with infectious diseases representing a key component of colony health challenges. Among the most prevalent pathogens are the microsporidian parasites Nosema apis and Nosema ceranae, whose impacts on host survival and transmission vary widely depending on context. While nutritional supplementation is commonly used to support honey bee health, its effects on Nosema infection outcomes remain unclear. Here, we experimentally tested whether dietary enrichment alters survival and infection intensity following exposure to a mixed Nosema inoculum. Newly emerged worker bees were challenged with Nosema spores and maintained on either a basic sucrose diet or the same diet supplemented with a commercial pollen substitute. Dietary enrichment significantly increased both mortality risk and infection intensity in Nosema-infected bees, while having no detectable effect on survival in uninfected controls. These results indicate that supplementation can, counter intuitively, exacerbate nosemosis by promoting parasite replication rather than enhancing host resistance. Our findings highlight the importance of distinguishing nutritional effects on host tolerance versus resistance, and caution that interventions intended to improve bee nutrition may inadvertently increase pathogen production and transmission potential under certain conditions.
-
Journal articleLombardi P, Ramon-Gil E, Raja RQ, et al., 2026, , J Hepatol, Vol: 85, Pages: 899-911
BACKGROUND & AIMS: Despite improved outcomes with atezolizumab plus bevacizumab (A+B) in hepatocellular carcinoma, primary refractoriness (PRef), characterised by early progression or short-lived disease stabilisation following treatment, remains a significant challenge. METHODS: We analysed 1,296 patients with hepatocellular carcinoma treated with frontline A+B (AB-real) and validated findings in 645 trial participants recruited to IMbrave150 and GO30140. PRef was defined by SITC (Society for the Immunotherapy of Cancer) criteria. We performed a multi-parametric analysis of pre-treatment tumour tissue, including machine learning-based quantification of tumour-infiltrating lymphocytes, imaging mass cytometry and RNA sequencing (RNA-seq) to evaluate differences in the tumour microenvironment (TME) of patients with PRef vs. responders. Two independent cohorts were further used to refine the TME characterisation through single-cell RNA-seq (n = 20) and imaging mass cytometry (n = 16). We employed conditional inference tree analyses to provide a hierarchical organisation of PRef determinants. RESULTS: Among 677 AB-real patients and 378 trial participants evaluable by SITC criteria, PRef was associated with inferior median overall survival compared to response (AB-real: 7.3 vs. 31.5 months, p <0.001; Trials: 10.8 vs. not reached, p <0.001). Patients with PRef exhibited higher baseline systemic inflammation (neutrophil-to-lymphocyte ratio [NLR] ≥3), a distinctly immunosuppressive TME enriched in CD163+ tumour-associated macrophages and vascular cancer-associated fibroblasts, a higher Treg/Teff cell ratio, and pro-tumour supportive cellular interactions. RNA-seq of tumour tissue confirmed lower intrinsic immunogenicity in PRef samples with elevated myeloid infiltration. Conditional inference tree analysis identified IFN-γ signature downregulation combined with NLR ≥3 as the strongest contributor of PRef. CONCLUSIONS: PRef to A+B identifies a distinct
-
Journal articleJames LS, Oudyk K, Pescaru MI, et al., 2026, , Science, Vol: 394, Pages: 556-561
Bird songs are often described as analogs to human speech and songs, but expansive comparisons are necessary to determine analogy and mechanistic substrates. By analyzing global corpora consisting of 367 bird species (>74,500 vocal elements from ~5900 songs) within two clades of vocal learners (oscines and hummingbirds) and related nonlearners (suboscines and nightjars) and 52 human languages (>15,000 elements in >800 speech or song phrases), we revealed common patterns in bird songs that resemble prevalent patterns in human speech and song with variation in resemblance to speech or song. Vocal learning did not systematically affect acoustic patterning or similarity to human vocalizations. These data underscore the deep analogies between bird and human vocalizations and convergent motor mechanisms shaping communication.
-
Journal articleZhou B, Prentice CI, 2026,
Optimal biomass allocation to leaves across global terrestrial ecosystems
, Global Change Biology, ISSN: 1354-1013Leaves influence global climate and water resources by regulating the flows of COâ‚‚, energy, and water between the atmosphere and land. Here we developed a theoretical framework that predicts the optimal annual fraction of biomass production allocated to the production of new leaves (ηf) as the product of the optimal leaf area index(LAI) and the optimal ratio of leaf mass–per–area to the leaf life cycle (LMA/LC), divided by annual total biomass production (BP). All quantities depend on local environmental variables, with different solutions (embedding a climatic aridity effect on optimal LMA/LC) for evergreen and deciduous plants. Using a global compilation of ηf data, we show that this theory predicts the emergent responses of ηf to growing–season temperature and aridity. These responses arise from the trade–offs among the environmental sensitivities of LMA/LC, LAI, and BP. It is predicted that the rising COâ‚‚ is steadily reducing the fraction of biomass production allocated to leaves.
-
Journal articleBalducci MG, Duffy KJ, 2026, , Ann Bot, Vol: 138, Pages: 1917-1928
BACKGROUND AND AIMS: Disentangling the relative influence of abiotic and biotic factors on plant population differentiation remains a major challenge in evolutionary ecology yet is essential for understanding the drivers of local adaptation. Orchids are suitable for addressing this question since they often occur in patchily distributed populations, and all orchids depend on orchid mycorrhizal (OrM) fungi for seed germination and establishment. Hence, local abiotic conditions together with OrM fungi may influence population differentiation and adaptation. METHODS: Based on 316 952 polymorphic single nucleotide polymorphisms (SNPs) sampled from 21 populations across the central Mediterranean range of Orchis italica, we performed a suite of analyses to test how population differentiation and potential adaptation are influenced by the interplay between abiotic factors and OrM fungi. Outlier detection and functional annotation were performed on a subset of SNPs aligned to the Ophrys sphegodes reference genome. RESULTS: We found strong differentiation at the regional level, while loci under selection were associated with temperature, precipitation regime, soil texture and the abundance of specific OrM fungal taxa. Functional annotation revealed that outlier SNPs were enriched for genes involved in transcription and RNA processing, signal transduction, stress response and metabolic processes, including in the presence of OrM fungi. CONCLUSIONS: Abiotic conditions and OrM fungi jointly determine differentiation in O. italica. Identifying the selective pressures underlying differentiation and adaptive variation is critical for understanding plant responses to ongoing environmental change.
-
Journal articleGainer DJ, Coyle KM, Rätsep MT, et al., 2026, , Circ Res
BACKGROUND: Bronchopulmonary dysplasia (BPD) is a disease of neonatal lung development that is linked to impaired pulmonary vascularization, dysregulated TGF-β (transforming growth factor-β) signaling, and the accumulation of senescent cells. Despite the established role of TGF-β signaling in promoting vascular remodeling and suppressing the senolytic activity of natural killer (NK) cells, the contribution of NK cell TGF-β signaling to postnatal lung patterning and the pathogenesis of BPD remains unclear. METHODS: Mice bearing an NK cell-selective deletion of the type-II TGF-β receptor (Tgfbr2NK-/-) were analyzed for vascular and alveolar structure, lung NK cell infiltration, senescence markers, and lung function testing across neonatal and adult time points. Lung tissue from both neonatal mice and human infants with BPD was assessed by single-cell RNA sequencing. The effects of enhanced NK cell activity in a hyperoxia-induced model of BPD were examined in Tgfbr2NK-/- neonates, as well as pharmacologically, using the TGF-β ligand trap/IL-15 superagonist, HCW9218. RESULTS: Neonatal Tgfbr2NK-/- mice exhibited a baseline reduction in distal arteriolar density, impaired alveolarization, and sex-specific deficits in long-term lung function. Single-cell RNA sequencing identified excessive clearance of senescent endothelial cells by TGF-β-insensitive NK cells in the lungs of Tgfbr2NK-/- neonates. This enhanced NK cell activity promoted a BPD-like phenotype in naïve Tgfbr2NK-/- mice but protected these animals from impaired lung development under hyperoxia. Sequencing of lung tissue from human infants with BPD confirmed excessive TGF-β signaling and cytotoxic impairment in NK cells. Treatment with HCW9218 prevented senescent cell accumulation and rescued lung development in the hyperoxia mouse model. CONCLUSIONS: TGF-β is a tunable regulator of NK cell senolytic activity that is essential for normal postnatal lung developmen
-
Journal articleBrook TS, ODonovan M, Hutton IJ, et al., 2026, , Seed Science Research, Pages: 1-15, ISSN: 0960-2585
<jats:title>Abstract</jats:title> <jats:p> Seed banking can be an efficient approach to conserve plant species <jats:italic>ex situ</jats:italic> . Research into the suitability of long-term seed banking for (sub)tropical species is limited and urgent, especially for taxa with limited distributions such as those endemic to oceanic islands. Here, we combine a stepwise experimental methodology with non-parametric and survival analyses to assess the germination requirements and desiccation tolerance of three species of Currant Bush <jats:italic>Coprosma</jats:italic> (Rubiaceae) from Lord Howe Island, a remote island in the South Pacific. All species germinated best under temperatures equivalent to submontane spring/autumn conditions, consistent with temperatures during ripe fruit dispersal. Although warmer temperatures inhibited germination in all species, the species with the broadest elevational range was the least affected. Consistent with the wider literature, we found a negative relationship between seed size and drying tolerance, with the larger seeds of <jats:italic>Coprosma huttoniana</jats:italic> and <jats:italic>C. ptotopetra</jats:italic> sensitive to the drying required for conventional seed banking, while the smaller seeds of <jats:italic>C. lanceolaris</jats:italic> were tolerant and potentially bankable for long-term conservation. </jats:p>
-
Journal articleIvars J, Gurung J, Gispert I, et al., 2026,
Decorating bacteria with electrostatically bound liposomes as programmable extracellular functional compartments
, ISSN: 2198-3844Living cells are powerful programmable systems, yet efforts to engineer them are limited by the constraints of genetic modification, including metabolic burden, restricted chemical diversity of biomolecular systems, and slow, gene expression–driven responses. Complementary approaches augmenting cells without altering their genome offer an attractive route to expand their functionality. Here, we establish a strategy for equipping bacteria with synthetic extracellular organelle-like compartments by electrostatically assembling liposomes onto the surface of Escherichia coli. This approach yields stable, multi-compartment, high-density coatings without genetic or covalent modification, while preserving bacterial growth, gene expression, and motility. We show that these surface-bound liposomes can function as modular ompartments that operate alongside the cell, enabling capabilities that are difficult to realize genetically, including thermoresponsive cargo release and abiotic catalytic activity. Together, this work shows that bacteria–liposome biohybrids can be engineered with appended, tunable synthetic compartments to expand the functional repertoire of living cells.
-
Journal articleKowal J, Buckley S, Upham R, et al., 2026, , Mycorrhiza, Vol: 36
Root colonisation by endomycorrhizal fungi has long been a widely used metric in mycorrhizal studies. However, due to the significant time required to assess colonisation using traditional microscopy techniques, studies of colonisation at large scales are impractical. Machine-learning-based approaches may increase output and facilitate ecosystem assessments. We trained a machine-learning-based tool (MycorrhizaFinder) on 42 field roots (132 unique 1 cm sections, with > 100,000 tiles) and validated on a further 37 sections from grasslands and heathlands hosting common Northern European plants with arbuscular (AM) and ericoid mycorrhizal (ErM) fungal structures, and dark septate endophytes (DSE), also common in field-sourced roots. We incorporated a user-customized confidence threshold to encourage engagement with morphological ambiguities, in e.g. ErM and DSE. A Macro F1 statistic was used to assess the tool's development performance. We provide a sample workflow from root processing and microscope slide scanning to semi-automated model training and performance evaluation. Our model performance combining all classes, the Macro F1, is conservatively 66% for arbuscular and 57% for ericoid mycorrhizal colonisation assessment. MycorrhizaFinder is user-friendly, requires no programming skills and offers flexibility for advanced agronomists or ecologists to train the tool using their own labelled mycorrhizal root datasets, including images acquired from different instruments or staining protocols. This adaptability allows users to customize the model for specific ecosystems or experimental designs. Leveraged with molecular identification and/or functional traits of fungi (e.g. arbuscules), MycorrhizaFinder supports scalable and repeatable nursery experiments and monitoring across ecosystems to assess mycorrhizal status and track land-use changes over time.
-
Journal articleDrickamer K, Jegouzo S, Feinberg H, et al., 2026, , Journal of Biological Chemistry, ISSN: 0021-9258
The primary role of the multidomain endocytic receptor designated Endo180 or uPARAP (urokinase-plasminogen activator receptor associated protein) is to facilitate internalization of collagen for lysosomal degradation during matrix remodeling in tissues. However, Endo180 interacts both with collagen and sugars and the relationship between these activities is not fully defined. While collagen-binding activity is associated with a fibronectin type 2 domain and an adjacent C-type lectin-like domain 1 (CTLD1), sugar-binding activity resides in CTLD2. Potential interactions of CTLD2 with various glycans have been examined by glycan array screening, solid phase binding assays, x-ray crystallography, and molecular modeling. Glycan array screening suggests potential interactions with exposed GlcNAc residues on truncated core 2 and core 4 O-linked glycans, but such structures are rare. Binding competition assays demonstrate that the disaccharide Glcα1-2Gal, found attached to hydroxylysine residues in collagens, is an alternative ligand. X-ray crystallography analysis of a complex of α-methyl fucoside with CTLD2 provides a basis for modeling how the Glcα1-2Gal disaccharide attached to hydroxylysine can be accommodated in the binding site with both sugar residues making favorable interactions with the protein. In direct binding studies, types IV and V collagen, but not type I collagen, bind to CTLD2 through the sugar-binding site. These results provide direct evidence that sugar-binding activity of CTLD2 contributes to binding of heavily glycosylated collagens. Although other endogenous mammalian glycan targets for CTLD2 are rare, CTLD2 can additionally interact with pathogen glycans such as poly-N-acetylglucosamine, contributing to the general role of Endo180 as a scavenger receptor.
-
Journal articleMaretvadakethope S, Aor I, Fischer MM, et al., 2026, , Cell Syst, Vol: 17
Gene regulatory networks (GRNs) govern many cell processes. While multistability and oscillations are common GRN dynamics, they are typically studied and engineered in isolation. Here, we challenge this separation using the AC-DC circuit, a minimal three-gene network that merges the classical toggle switch and repressilator. Using a thermodynamic formalism and Bayesian inference, we show that a single-inducer version of the circuit displays diverse multifunctional dynamics, including coexistence of oscillations and multistability. We explore robustness, classify emergent behaviors, and analyze critical slowing down. Remarkably, the AC-DC circuit can produce more than thirty topologically distinct bifurcation diagrams, results that challenge the classical view that network topology rigidly constrains dynamical outcomes. This flexibility enables synthetic capabilities coupling hysteresis with oscillations, criticality, and reversibility. By uncovering the potential of minimal genetic circuits and outlining design principles for their implementation, this work opens directions for harnessing emergent complexity using the basic building blocks of life. A record of this paper's transparent peer review process is included in the supplemental information.
-
Journal articleDing R, Nobrega R, Collalti A, et al., 2026,
Resolving the multiple controls of biomass productionefficiency in woody plants
, Global Change Biology, ISSN: 1354-1013Plants assimilate carbon through photosynthesis to support biomass production (BP), autotrophic respiration (Ra) and the synthesis of non-structural compounds. Biomass production efficiency (BPE), the fraction of assimilated carbon allocated to BP, is one key factor influencing ecosystems’ potential to store carbon. However there is no consensus on the controls of BPE, and even the sign of its response to growth temperature is unclear. By means of statistical hypothesis testing using the largest observational dataset to date on annual BPE (n = 514 records) from evergreen and deciduous woody plants, we confirm earlier findings that BPE declines with stand age and is greater in deciduous plants. However, we also show that BPE declines towards more organic, sandy, or alkaline soils and increases with climatic aridity, while declining with warmer growing seasons and increasing with warmer winters. Such a dual temperature response is consistent with additional carbon costs due to the need for cold-hardening processes, and reconciles contradictory published reports of both positive and negative effects of temperature on BPE. Notably, our analysis provides novel evidence that BPE is significantly higher in species associated with arbuscular mycorrhizal (AM) fungi than in those associated with ectomycorrhizal (EcM) fungi and mixed EcM–AM associations. Our analysis explains the observed BPE patterns better than dynamic global vegetation models (DGVMs) from the TRENDY (Trends and Drivers of the Regional-Scale Terrestrial Sources and Sinks of Carbon Dioxide) project, which show a weaker correspondence with observations. In particular, our model captures reduced BPE in boreal regions, consistent with the predominance of ectomycorrhizal (EcM) species there. This study advances understanding of the global controls of BPE, and suggests a route towards the improved representation of plant growth in vegetation and land surface models.
-
Journal articleSecchi MA, Mai C, Liu Q, et al., 2026, , Blood
Interactions of hematopoietic stem cells (HSCs) with the bone marrow microenvironment are critical to regulate stem cell function in homeostasis, emergency hematopoiesis and ageing. The dynamic behavior of endogenous HSCs in their niches has been challenging to study due to the complexity of markers required to define pure HSCs. Multiple recently developed reporter strategies advanced our capacity to identify HSCs in situ. Yet, they provide different levels of HSC enrichment and are frequently not stable in situations of perturbed hematopoiesis, leading to contradictory observations of HSC localization and migratory behavior. Here we employed a new double reporter strategy by combining the Hoxb5-mKO2 and Vwf-GFP reporters, that are stably expressed in homeostasis, stress and ageing. Hoxb5+Vwf+ cells represent a subset of highly pure and potent long-term HSCs with a platelet-biased pattern of differentiation, that are included in the populations identified by other reporter strategies. Intravital microscopy revealed Hoxb5+Vwf+ cells to be non-migratory in homeostasis, ageing, or following acute thrombocytopenia when these cells are actively proliferating, indicating that this non-migratory behavior is independent of cell cycle status. We found Hoxb5+Vwf+ HSCs in perivascular niches with a higher coverage by LepR+ mesenchymal cells but not preferentially located closer to megakaryocytes, when compared to Hoxb5+Vwf- cells. Nevertheless, stress-induced megakaryopoiesis following acute thrombocytopenia bring megakaryocytes into closer proximity of Hoxb5+Vwf+ HSCs, revealing previously unrecognized niche dynamics in HSC regulation during regeneration.
-
Journal articleStorer K, Hawthorne S, Lovell C, et al., 2026,
Pesticide-exposed bees fail to thermoregulate leading to cold colonies with consequences for offspring development
, Communications Biology, ISSN: 2399-3642For many organisms, effective thermoregulation is needed to cope with changing environmental temperatures. But if exposure to pesticides in the environment were to impair this homeostatic process, reproduction and population viability could be at risk. Focusing on an important insect pollinator, we conducted three complementary experiments exposing bumblebees to a pesticide under different temperature challenges and measuring the impacts on thermoregulatory ability and brood development. First, we reveal that pesticideexposed individuals (food spiked with a neonicotinoid insecticide) cannot maintain a stable thorax temperature, especially at lower temperatures. Second, that reductions in body temperature are accompanied by behavioural changes with pesticide-exposed colonies failing to maintain the brood temperatures that control bees achieved. Third, that such collective impairment of brood thermoregulation (not the pesticide toxicity to offspring per se) leads to delayed pupal development and reduced adult population growth. Our study provides a plausible mechanistic pathway for why terrestrial insects requiring brood thermoregulation may be vulnerable to decline. With frequent extreme weather events forecasted, our findings have concerning implications for how populations will adequately persist and grow under current pesticide-use regimes with ramifications for pollination services.
-
Journal articlePrakash S, Isalan M, Varela C, 2026,
A genetically encoded local learning rule enables physical learning in engineered bacteria
, Nature Communications, ISSN: 2041-1723 -
Journal articleDollhopf LC, Perrett S, Schatz D, et al., 2026, , Journal ofthe American Chemical Society, ISSN: 0002-7863
<jats:title>Abstract</jats:title> <jats:p>Photopharmacology using photoswitches is a powerful way to reversibly control biological function with light, through the generation of photoswitchable synthetic ligands. While optimization of bioactive small molecules is increasingly driven by iterative experimental protein–ligand structures, structure-guided improvement in photoswitch photopharmacology using experimental structures remains rare. Here we report the development of the first photoswitchable inhibitors of the human enzyme N-myristoyltransferase 1 (HsNMT1), using an arylazopyrazole (AAP) as the switch motif. Through experimental structure-based design, we obtain inhibitors with single-digit nanomolar affinity for NMT, functional activity in cells, and good differential activity between E and Z photoswitch isomers. The availability of our highly potent ligands and protein–ligand structures, coupled with the excellent photoswitch properties of the AAP, allowed us to study the effect of protein binding on the switching events, including characterization of protein-bound Z → E photoisomerization kinetics for the first time. Overall, this study showcases the potential for structure-based design in photoswitch pharmacology, including understanding the dynamic consequences of target binding, paving the way for the development of advanced photopharmaceuticals.</jats:p>
-
Journal articleGuffick C, Rincon Pabon JP, Griffiths D, et al., 2026, , Analytical Chemistry, ISSN: 0003-2700
<jats:title>Abstract</jats:title> <jats:p>The structural study of membrane proteins has traditionally relied on detergent-based extraction from cellular membranes. Although native-like reconstitution approaches have advanced, fully understanding membrane protein dynamics requires examining them within their native membrane environment. Hydrogen−deuterium exchange mass spectrometry (HDX−MS) is a powerful method for probing structural dynamics in reconstituted systems, but the presence of the lipid bilayer introduces considerable complexity, limiting its broader adoption under physiological conditions. Here, we present the first fully automated HDX−MS platform incorporating a two-stage delipidation workflow. We applied this approach to monitor the dynamics of the ABC transporter MsbA in isolated inner membrane vesicles (IIMVs) from Escherichia coli in its apo and inhibited posthydrolytic states. IIMVs revealed distinct dynamic features within the nucleotide binding domains and substrate binding cavity, highlighting physiologically relevant motions not observed with detergent-solubilized MsbA. This platform significantly advances HDX−MS and underscores the importance of studying membrane proteins in native lipid environments.</jats:p>
This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.
Postgraduate research
Interested in studying a PhD at the Department of Life Sciences? Find out more about postgraduate research opportunties.