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Journal articleBagchi D, Majumdar A, 2026,
Dual advantage of <i>Klebsiella oxytoca</i> layered biofilm in fixing aerial nitrogen to rice plant roots, arresting soil arsenic availability and translocation
, Environmental Pollutants and Bioavailability, Vol: 38, ISSN: 2639-5932 -
Journal articleMaia RA, Oki Y, Medina I, et al., 2026,
Atlantic forest tree enhances photoprotective and thermotolerance in soils contaminated by mining tailings
, Theoretical and Experimental Plant Physiology, Vol: 38Large-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.
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Journal articleHui T-Y, Epopa PS, Millogo AA, et al., 2026,
Variance partitioning reveals contrasting random effect contributions to the density and species composition of malaria-transmitting mosquitoes in Western Burkina Faso
, Parasites and Vectors, Vol: 19, ISSN: 1756-3305Background 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
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Journal articleDe Lorm TA, Heon SP, Bernard H, et al., 2026,
Bird and mammal communities transform without collapsing in response to oil palm replanting
, Forest Ecology and Management, Vol: 619, ISSN: 0378-1127Replanting 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.
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Journal articleDi Domenico F, Kucharczyk MW, Patel R, et al., 2026,
Perioperative pregabalin does not alter behavioural or diffuse noxious inhibitory control responses in 2 rat models of chronic pain
, PAIN Reports, Vol: 11<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Introduction:</jats:title> <jats:p>Multiple mechanisms contribute to the experience of pain where the use of model organisms to dissect mechanistically sensory regulatory circuitry is a vital component of discovering underlying causes of persistent pain in disease states. Such disease states can be modelled in animals using surgical procedures that, ethically, should involve administration of analgesia. However, since basic pain researchers often wish to measure pain-related events, animals may be denied perioperative analgesia to avoid adversely influencing experimental outcomes.</jats:p> </jats:sec> <jats:sec> <jats:title>Methods:</jats:title> <jats:p>We conducted a structured review of perioperative analgesia usage in rat spinal nerve ligation (SNL) and cancer-induced bone pain (CIBP) models. Using a combination of behavioural testing and in vivo electrophysiology in the dorsal horn of the spinal cord, we assessed the impact of perioperative pregabalin on nociceptive behaviours in the acute recovery phase, and behavioural and electrophysiological experimental outcomes in the established phase, of rat SNL and CIBP models.</jats:p> </jats:sec> <jats:sec> <jats:title>Results:</jats:title> <jats:p>A literature search revealed that, for studies using rat models of SNL or CIBP, only 5.37% and 12.69%, respectively, reported the use of perioperative analgesia. We then demonstrated that the use of pregabalin as a perioperative analgesic reduced mechanical hypersensitivity in the acute period after SNL surgery, with no impact on behavioural, electrophysiological, or neuropharmacological outcomes in the established p
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Journal articleOh J, Jiménez JI, Kim J, 2026,
Safe and resource-aware microbial design for food production
, Current Opinion in Biotechnology, Vol: 100, ISSN: 0958-1669Precision fermentation is redefining microbial food manufacturing by enabling programmable biosynthesis of nutrients and functional ingredients. Despite this progress, industrial-scale deployment is limited by metabolic burden, growth-production trade-offs, biosafety concerns, and the costs of downstream processing. Conventional intracellular systems inherently generate host-derived impurities and endotoxins, challenging food-grade standards. Here, we review platform-level advances that decouple biosynthesis from cellular constraints and streamline process design, with a focus on approaches aligned to food industry requirements. We highlight cell-free systems and non-replicative minicells as intrinsically contained production chassis, detail advances in secretion and efflux engineering for efficient extracellular product recovery, and discuss division-of-labor microbial consortia to address resource allocation limits. Together, these innovations integrate biosafety and process efficiency, providing a safe-by-design framework for next-generation microbial food systems that meet both regulatory and industrial needs.
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Journal articleBose A, Bopanna Y, Shetty P, et al., 2026,
Therapeutic zinc targets dysregulated GC-C signaling and restores ileal defects in a preclinical model of familial diarrheal disease.
, Am J Physiol Gastrointest Liver Physiol, Vol: 331, Pages: G125-G139Hyperactivating mutations in guanylyl cyclase C (GC-C) are monogenic causes of early-onset inflammatory bowel disease, familial diarrheal syndrome, and congenital secretory diarrhea. The mechanisms linking elevated cGMP levels to immune imbalance remain poorly defined. Here, using a preclinical model of a disease-associated GC-C mutation, we observe pleiotropic alterations in the small intestinal epithelium. Transcriptomic and functional analyses revealed impaired Paneth and goblet cell differentiation, compromised barrier integrity, heightened epithelial permeability, and increased proinflammatory cytokine levels. Intestinal organoids from mutant mice exhibited amplified cGMP responses to GC-C ligands and defects in secretory lineage specification, confirming cell-autonomous mechanisms. Strikingly, oral zinc administration suppressed aberrant GC-C activity, normalized cGMP levels, and restored barrier function. These findings highlight the central role of epithelial cGMP signaling in coordinating barrier integrity and immune-epithelial interactions and identify zinc as a tractable therapeutic strategy for GC-C-mediated intestinal disorders.NEW & NOTEWORTHY Activating mutations in GUCY2C, which encodes the receptor guanylyl cyclase C (GC-C), cause early-onset diarrheal disease and gastrointestinal inflammation. Knock-in mice carrying a familial diarrheal syndrome mutation exhibited impaired gut barrier function. Mutant organoids showed defective secretory lineage specification associated with reduced Wnt3 expression. Zinc administration, which lowers epithelial cGMP levels by inhibiting GC-C, reversed most pathological changes in both mice and organoids.
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Journal articleSchlenker P, Lamberton J, Lan N, et al., 2026,
Ancestral iconicity: the dance language of bees revisited.
, Biol Rev Camb Philos Soc, Vol: 101, Pages: 2033-2052The waggle dance of bees has given rise to some of the most striking and detailed studies of animal communication. But because of its gradient character, the waggle dance has widely been taken to have properties that are wholly distinct from those of human language. We argue that this is mistaken, and that the waggle dance represents the oldest instantiation of an iconic system also found in human language, notably in sign language. The waggle dance helps bees locate a food source through four properties: (1) food distance is conveyed through the duration of the waggling phase; and (2) food direction is conveyed through the orientation of the waggle run. In addition, (3) while in bees that dance horizontally, the waggle run points towards the food source, in bees that dance vertically the information involves transposition: the angle of the dance relative to 'upwards' is interpreted as the angle of the food direction relative to the sun. Finally, (4) the number of waggle runs increases with food quality. We show that properties 1 and 2 are instantiated in sign language classifier predicates, highly iconic constructions that produce visual animations of the orientation and movement of an entity. Furthermore, classifier movement (property 3) can be interpreted either directly or with 'viewpoint shift', a more flexible version of transposition. Property 4 seems to be instantiated more generally in the pragmatics of human and animal communication, as repetition can convey intensification and/or excitement (e.g. Go, go, go!). We further show experimentally that properties 1-3 are instantiated in some gestures understood by non-signers. Thus the waggle dance is a primitive form of a semantic system also found (through convergent evolution) in human language. It is remarkably ancient, at least 20 million years old according to phylogenetic reconstructions. While the horizontal dance (without transposition) is usually thought to be ancestral, a closer look at extant phyloge
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Journal articleMajumdar A, Upadhyay MK, Ghosh A, et al., 2026,
Revolutionising Agricultural Sustainability: New 'Furrow Tillage' can Mitigate Short-Term Soil-to-Atmosphere CO2 Flux and Promote Soil-Plant-Microbe Health.
, Adv Sci (Weinh)Global agricultural carbon loss demands refined tillage practices. This study evaluates a hybrid furrow tillage field (FTF) approach that combines the bed geometry of conservation tillage with controlled, localised disturbance of conventional tillage. Distinct from strip-tillage and permanent-bed planting, FTF is designed for puddled, lowland rice systems, featuring a continuously water-filled furrow and an alternately wet-dry mid-bed. A two-year, twelve-site field trial across the Gangetic deltaic plain of West Bengal, India, assessed FTF through agronomy, geochemistry, crop physiology, and molecular microbiology, and presented all CO2-flux and labile-carbon results as short-term responses. FTF produced CO2 efflux comparable to no-tillage (3.94-4.38 vs. 2.43-2.84 g C m- 2 d- 1) while sustaining nutrient bioavailability close to conventional deep tillage (6.29-7.11 g C m- 2 d- 1), demonstrating that hybrid bed-and-furrow geometry can decouple short-term CO2 flux from nutrient-mineralisation benefits. Microbial diversity and gene-ontology profiles indicate active microbial interactions with reduced soil-to-atmosphere CO2 transfer. Molecular modelling identifies AmtB and HypC-HypD as candidate CO2-handling routes; mid-bed physical properties independently contribute to flux reduction. Long-term SOC stability requires multi-year, multi-soil-order validation with isotopic partitioning. The study integrates CO2 flux chambers, Kriging interpolation, elemental bioavailability analysis, plant ultrastructural observation, metagenomics, and molecular modelling.
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Journal articlePai H, Sakai T, Posbeyikian A, et al., 2026,
Contrasting evolutionary patterns of helper and sensor NRC NLRs in lettuce reflect functional divergence following subfunctionalization.
, PLoS Genet, Vol: 22Nucleotide-binding domain and leucine-rich repeat immune receptors (NLRs) are known for their rapid evolution, even at the intraspecific level, yet the rates of evolution differ significantly across NLRs. However, the degree to which evolutionary patterns reflect functional divergence remains poorly understood, notably in important crop species. Within the NRC (NLR Required for Cell Death) network in Asterids, sensor NLRs detect pathogen presence but require NRC helpers for signaling and to confer immunity. We conducted a comparative analysis of NLRs across 40 Solanales and 29 Asterales genomes to explore NRC network expansion and diversification within the less-studied Asterales order. Our findings reveal that the NRC network has expanded less in Asterales compared to Solanales. We functionally validated an Asterales NRC network with 2 helpers and 9 sensors in common lettuce (Lactuca sativa). Through selection analysis and structural modeling of NRC gene family in the Lactuca genus, we found distinct evolutionary trajectories between NRC helpers and sensors. Sensors reliant on the phylogenetically conserved helper NRC0 experience limited diversification, whereas sensors dependent on other NRC helpers show higher rates of positive selection and gene duplication. Our results highlight the lineage- and function-specific evolution of the NRC network, offering insights into the evolutionary pressures shaping plant immune receptor networks.
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Journal articleNematbakhsh M, Koufopanou V, Cass A, et al., 2026,
Genomic characterisation and diversity of dsRNA viruses and their killer satellites in a natural population of the yeast <i>Saccharomyces paradoxus</i>
, Virus Evolution<jats:title>Abstract</jats:title> <jats:p>Killer yeasts secrete protein toxins that inhibit other yeast strains, a trait often encoded by M satellites of L-A dsRNA viruses. These systems serve as important molecular models, yet their adaptive significance in natural settings remains unclear. This study surveyed 60 strains from a natural Saccharomyces paradoxus population in the UK to characterise dsRNA viral genomic diversity. Our survey revealed 27% of strains showed killer activity mediated by dsRNA viruses. Additionally, five of 18 non-killer strains also contained dsRNA viruses. Deep sequencing of pooled dsRNAs from 17 strains identified six distinct M satellite types, including three novel lineages, with single nucleotide and structural polymorphisms creating multiple variant sequences within types. Predicted preprotoxin proteins generally contained post-translational modification sites necessary for toxin maturation, although with variable numbers among different types, potentially affecting processing and expression. Eight L-A virus sequences were also assembled. These were all closely related to each other and clustered phylogenetically with viruses from other European S. paradoxus strains. Extended 5′ sequence analysis revealed novel structural features in both L-As and their M satellites, including a pair of inverted repeats ending in a pair of inverted conserved motifs (GA5–6 and corresponding U5–6C in Ms and GAAUA and corresponding UAUUC in L-As) which is in turn flanked by a pair of direct repeats. The pair of conserved motifs also exists in all described Saccharomyces cerevisiae M satellites. The observed diversity of dsRNA satellites within a single yeast population is a challenge to explain, with many evolutionary forces potentially contributing.</jats:p>
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Journal articleMajumdar A, Bagchi D, Kotta-Loizou I, et al., 2026,
The One Health resistome: Integrating environmental, microbial, and human antimicrobial resistance surveillance and risk analysis in the digital age.
, J Hazard Mater, Vol: 513Antimicrobial resistance (AMR) and antibiotic resistance (ABR) represent one of the most pressing global health threats, driven by the complex interplay between human, animal, and environmental factors. The One Health resistome framework recognises that resistance genes circulate continuously across clinical, agricultural, and environmental compartments through horizontal gene transfer, co-selection mechanisms, and anthropogenic contamination. This comprehensive review synthesises current evidence on integrated AMR surveillance, examining how digital technologies are transforming our capacity to monitor, predict, and respond to resistance emergence. Key advances include whole-genome sequencing enabling high-resolution pathogen tracking, metagenomics revealing environmental resistome diversity, machine learning algorithms predicting resistance phenotypes with > 85% accuracy, and point-of-care diagnostics extending sophisticated testing to resource-limited settings. Geographic information systems facilitate spatial hotspot identification, while wastewater-based surveillance provides early warning capabilities, detecting resistance genes before clinical manifestation. Despite technological progress, substantial challenges persist: fragmented data streams across sectors, lack of standardised environmental monitoring methods, limited laboratory capacity in low- and middle-income countries, and chronic underfunding. Emerging technologies, portable nanopore sequencing, CRISPR-based diagnostics, artificial intelligence, and blockchain-enabled data governance promise to address these gaps. Realising comprehensive One Health resistome surveillance requires sustained investment in interoperable digital infrastructure, international standardisation, capacity building, and political commitment to cross-sectoral coordination, prioritising equitable global implementation.
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Journal articleGodson A, Eddie L, Schuster M, et al., 2026,
NbRD21 protease controls receptor kinase homeostasis in Nicotiana benthamiana.
, New PhytolRD21-like proteases are papain-like cysteine proteases with a C-terminal granulin domain that are abundant and ubiquitous in angiosperms and have often been implicated in immunity. We previously found that the activity of RD21 in Nicotiana benthamiana (NbRD21) is suppressed during infection with Pseudomonas syringae. Here, we studied the role of NbRD21 in immunity and proteome processing. NbRD21 was disrupted by genome editing and rd21 mutants were subjected to disease assays and shotgun proteomics. Dipeptide substrate zLR-AMC was used in protease assays and agroinfiltration was used to transiently express NbRD21 and candidate substrates. Genome-edited lines lacking NbRD21 develop normally but have drastically reduced zLRase activity and are significantly more susceptible to P. syringae. Shotgun proteomics revealed an increased accumulation of c. 20 diverse receptor-like kinases (RLKs) in untreated rd21 knockout lines, but their transcript levels are unaltered when compared to wild-type plants. 35S-driven GFP-tagged RLKs accumulate more upon transient expression in rd21 plants than in wild-type plants. These data indicate that NbRD21 post-translationally controls RLK homeostasis, either by directly degrading RLKs or indirectly by regulating endocytic RLK recycling.
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Journal articleLau R, Giblin S, Sugar A, et al., 2026,
SpyCEP dismantles neutrophil immunity via disorder-drivenchemokine remodeling and GAG targeting
, Proceedings of the National Academy of Sciences of the United States of America, ISSN: 0027-8424Streptococcus pyogenes (Group A Streptococcus; GAS) employs sophisticated virulence strategies to evade human immunity, including secretion of the cell envelope protease SpyCEP, which cleaves and inactivates key neutrophil‑attracting chemokines such as CXCL8. Here, we integrate cryo‑electron microscopy (cryo‑EM), nuclear magnetic resonance (NMR) spectroscopy, and native mass spectrometry (MS) to investigate how SpyCEP disrupts CXCL8 function. We demonstrate that a disordered aromatic and acidic region within the cleaved autocatalytic maturation loop (CAML) of SpyCEP mimics receptor N-domains and binds an allosteric site on CXCL8. The resulting interaction forms a dynamic fuzzy complex and is coupled to dimer dissociation, consistent with enhanced access to the cleavage site. This disorder‑mediated substrate engagement differs from classical protease mechanisms that rely on rigid recognition interfaces. Additionally, glycan microarray and NMR analyses show that the CAML region mediates glycosaminoglycan (GAG) binding, suggesting a means to recruit SpyCEP and maximize encounters with GAG‑enriched CXCL8 reservoirs. Together, these findings provide a structural and biophysical framework for understanding how SpyCEP combines substrate engagement with GAG targeting to dismantle chemokine gradients and inhibit neutrophil recruitment. More broadly, this work highlights the role of intrinsic disorder in protease recognition and suggests new avenues for anti‑virulence therapies and vaccine strategies targeting SpyCEP.
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Journal articleGhosh M, Goodman D, 2026,
Partial recurrence can enable robust and efficient computation
, Communications AI and computing, ISSN: 3091-292X -
Journal articleAguirre-Gutiérrez J, Cortes I, Nunes MH, et al., 2026,
Remote sensing delivers tropical forest resilience monitoring for the Global Biodiversity Framework
, Nature Reviews Biodiversity -
Journal articleEndres R, 2026,
The unreasonable likelihood of being: origin of life, terraforming, and AI
, npj Systems Biology and Applications, ISSN: 2056-7189The origin of life on Earth via the spontaneous emergence of a protocell prior to Darwinian evolution remains a fundamental open question in physics and chemistry. Here, we develop a conceptual framework based on information theory and algorithmic complexity. Using estimates grounded in modern computational models, we evaluate the difficulty of assembling structured biological information under plausible prebiotic conditions. Our results highlight the formidable entropic and informational barriers to forming a viable protocell within the available window of Earth’s early history. While the idea of Earth being terraformed by advanced extraterrestrials might violate Occam’s razor from within mainstream science, directed panspermia—originally proposed by Francis Crick and Leslie Orgel—remains a speculative but logically open alternative. Ultimately, uncovering physical principles for life’s spontaneous emergence remains a grand challenge for biological physics.
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Journal articleStegemann A, Liu S, Retana Romero OA, et al., 2026,
Author Correction: Prefrontal engrams of long-term fear memory perpetuate pain perception.
, Nat Neurosci -
Journal articleEneli AA, Siu PC, Perez MF, et al., 2026,
On the use of generative models for demographic inference in malaria vectors from genomic data.
, G3 (Bethesda), Vol: 16Malaria in sub-Saharan Africa is transmitted by mosquitoes from the Anopheles genus. Efforts to control the spread of malaria have often focused on these vectors, but little is known about the demographic history of populations and species of Anopheles mosquitoes. Here, we adapt and apply an innovative generative deep learning algorithm to infer the joint evolutionary history of Anopheles gambiae populations sampled in Guinea and Burkina Faso. We further develop a model selection approach and discover that an evolutionary model with migration fits this pair of populations better than a model without post-split migration. For the migration model, we find that our method accurately captures population genetic differentiation. These findings demonstrate that machine learning and generative models are a valuable direction for future understanding of the evolution of malaria vectors, including the joint inference of demography and natural selection. Understanding changes in population size, migration patterns, and adaptation in hosts, vectors, and pathogens will assist malaria control interventions, with the ultimate goal of predicting nuanced outcomes from insecticide resistance to population collapse.
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Journal articleGao C, Meng X, Chen X, et al., 2026,
Surface immune signaling unlocks NLR activation through mRNA alternative splicing.
, Science, Vol: 393, Pages: 65-70Plants activate pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) to combat pathogens. However, how these systems coordinate immune activation while preventing autoimmunity remains poorly understood. In this study, we uncovered a regulatory mechanism in which surface immune signaling unlocks nucleotide-binding leucine-rich repeat (NLR) immune receptor activation through mRNA splicing. We identified an N-terminal prodomain in the potato late blight resistance protein Rpi-vnt1.1 that inhibits resistosome formation, preventing potential autoactivation of this NLR. Upon pathogen perception, PTI signaling induced alternative splicing of Rpi-vnt1.1 mRNA, removing this inhibitory element. This primed Rpi-vnt1.1 for activation by the Phytophthora infestans effector AVRvnt1, enabling resistosome assembly and immune signaling. The widespread conservation of N-terminal extensions in coiled coil-type NLRs points to a common regulatory mechanism in preventing potential autoactivation while preserving pathogen sensitivity.
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Journal articleBanks AM, Abdulmutalib U, Wain B, et al., 2026,
Engineering environmental bacteria for whole-cell PET hydrolysis and assimilation
, Trends in Biotechnology, ISSN: 0167-7799Poly(ethylene terephthalate) (PET) is one of the most widely used plastics in food and textile applications, yet post-consumer PET waste persists and accumulates in the environment as macro- and microplastics with adverse health and ecological impacts. Although PET-hydrolysing enzymes have been extensively studied in vitro, whole-cell microbial systems capable of using PET as a growth substrate remain limited, particularly for difficult-to-collect waste. Here, we engineer an environmental bacterium to directly assimilate PET. A strain of Pseudomonas umsongensis capable of metabolising the PET monomer terephthalic acid was isolated and engineered to secrete the high-activity PET hydrolase polyester hydrolase Leipzig 7 via a recombinant twin-arginine translocation motif signal peptide. PET bioavailability was further enhanced through solvent-based pretreatment to generate an amorphous, macroporous substrate. The engineered strain demonstrated direct PET utilisation and hydrolysis, supporting self-sustaining microbial growth. Additionally, in non-sterile wastewater the strain survived and hydrolysed PET microplastics, highlighting its potential for bioremediation and sustainable upcycling applications.
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Journal articleMajumdar A, Kotta-Loizou I, Buck M, et al., 2026,
Temperature-dependent biofilm and sublancin production arrest soil arsenic and antibiotic resistance gene mobility.
, J Hazard Mater, Vol: 512Climate change-induced warming and arsenic soil contamination synergistically threaten agricultural sustainability by restructuring microbial communities and accelerating antimicrobial resistance dissemination. Here, through integrated greenhouse and field trials, we demonstrate that Bacillus subtilis 168-derived biofilm and sublancin, a glycosylated antimicrobial peptide, simultaneously immobilise rhizospheric arsenic and suppress horizontal transfer of antibiotic resistance genes (ARGs). Temperature-dependent biofilm formation (25-35°C) enhanced arsenic sequestration within the extracellular polymeric substance matrix, with SEM-EDX revealing a 74% increase in arsenic weight percentage at 35°C and ToF-SIMS confirming ∼14-fold and ∼9-fold increases in root-associated arsenic on biofilm-colonised surfaces in greenhouse and field trials, respectively. Sublancin production peaked at 30°C (129.72 mg L⁻¹), selectively suppressing all 12 tested pathogenic Gram-positive species by 74-86% while preserving Gram-negative communities. Bio-amendment reduced horizontal gene transfer frequency by 74.7% (p < 0.001) across all temperature regimes. Transcriptomic profiling revealed coordinated upregulation of exopolysaccharide biosynthesis (FDR ∼1.0 × 10⁻²⁷) and sublancin machinery (sunA: +3.5 log₂), alongside downregulation of conventional ARGs (vanA, blaTEM: -2.5 to -4.0 log₂). These findings establish sublancin as a dual-function, climate-adaptive soil bio-amendment simultaneously addressing arsenic bioaccumulation and antibiotic resistance gene dissemination under warming scenarios.
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Journal articleGottweis J, Weng W-H, Daryin A, et al., 2026,
Accelerating scientific discovery with Co-Scientist
, Nature, ISSN: 0028-0836Scientific discovery is driven by scientists generating hypotheses for complex problems that undergo rigorous experimental validation. To augment this process, we introduce Co-Scientist, a multi-agent artificial intelligence (AI) system built on Gemini for structured scientific thinking and hypothesis generation. Co-Scientist aims to help scientists discover new original knowledge. Conditioned on their research objectives and previous scientific evidence, it formulates demonstrably novel research hypotheses for experimental verification. The system’s design involves agents continuously generating, critiquing and refining hypotheses accelerated by scaling test-time compute. Key contributions include (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling, and (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute scaling, improving hypothesis quality over time. Although this is a general-purpose system, we focus the validation in three biomedical applications: drug repurposing; novel-target discovery1; and explaining mechanisms of antimicrobial resistance2. Specifically, Co-Scientist helped to identify new drug-repurposing candidates and synergistic combination therapies for acute myeloid leukaemia that were validated through in vitro experiments. These real-world validations demonstrate the potential of Co-Scientist to accelerate scientific discovery and usher in an era of AI-empowered scientists.
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Journal articleGider Yaman G, Bozkurt O, Akgun E, et al., 2026,
Neonatal Intestinal Perforations Due to IL10RB Deficiency.
, Indian J Pediatr, Vol: 93 -
Journal articleDas A, Majumdar A, Thakur BK, et al., 2026,
Integrated Groundwater Management and Arsenic Mitigation in the Indo-Gangetic Plain: Aligning Strategies with Global Sustainability Goals
, Water, Air, & Soil Pollution, Vol: 237, ISSN: 0049-6979 -
Journal articleNozawa LCC, BanksLeite C, Lima MR, et al., 2026,
Contrasting Forest Trajectories Drive Changes in Bird Functional Traits
, Journal of Biogeography, Vol: 53, ISSN: 0305-0270<jats:title>ABSTRACT</jats:title> <jats:sec> <jats:title>Aim</jats:title> <jats:p>We investigated how bird functional diversity varies across forest habitat types with distinct successional trajectories, namely (1) natural succession forests, with naturally regenerating forests established on former grasslands; (2) secondary forest remnants resulting from deforestation; and (3) conserved forests.</jats:p> </jats:sec> <jats:sec> <jats:title>Location</jats:title> <jats:p>Araucaria forests in southern Brazil.</jats:p> </jats:sec> <jats:sec> <jats:title>Time Period</jats:title> <jats:p>1991 to 2015.</jats:p> </jats:sec> <jats:sec> <jats:title>Taxon</jats:title> <jats:p>Birds.</jats:p> </jats:sec> <jats:sec> <jats:title>Methods</jats:title> <jats:p>We compiled functional trait data for bird communities from 47 sites of Araucaria forests under three distinct successional trajectories. We calculated standardised effect sizes for functional richness (SESFRic) and functional dispersion (SESFDis), and generalised linear models were initially fitted. To account for spatial autocorrelation, we fitted spatial models (spaMM) to assess whether forest habitat type, forest cover, and patch size help explain functional variation in bird assemblages. In addition, we performed canonical correspondence analysis to evaluate differences in trait composition among forest habitat types.</jats:p> </jats:sec> <jats:sec>
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Journal articleBrook T, Piponi K, Collins T, et al., 2026,
Genomic architecture and breeding trade-offs of coconut drought tolerance
, Plants, People, Planet, ISSN: 2572-2611Climate change threatens coconut palms (Cocos nucifera), a vital tropical crop supporting millions, with yields projected to drop nearly 50%. We assessed drought tolerance in over four thousand trees from the world’s largest coconut collection in Côte d'Ivoire, using 30 years of yield and climate data. Our reaction norm modelling approach revealed substantial variation in drought tolerance and a potential trade-off with yield. Using a quantitative genomic approach, we identified a substantial heritable component, highlighting the potential for genomic selection approaches in breeding climate-resilient coconuts.
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Journal articleSanchez-Garrido J, David S, Rattle J, et al., 2026,
Type 3 fimbrial regulation underpins anti-MrkA immunotherapeutic efficacy in experimental Klebsiella pneumoniae infection.
, J Infect DisBACKGROUND: Klebsiella pneumoniae (KP) is a critical-priority organism due to prevalent last-line antibiotic resistance. Alternative treatments, including vaccines and monoclonal antibodies (mAb), depend on antigen (Ag) expression at infection sites for immunotherapeutic activity. However, the relationship between genome-encoded Ag presence and Ag expression is often overlooked. Here, we use the KP type 3 fimbrial (T3F) subunit MrkA as a prototype to build a generalisable framework to assess Ag expression and its correlation with in vivo immunotherapeutic efficacy. METHODS: We perform genomic analysis of 1649 KP genomes for T3F genes, including structural and regulatory components. We generate isogenic mutants with absent, normal or overexpressed MrkA and profile MrkA expression at single-cell level from murine pneumonia and bacteraemia models. We compare anti-MrkA mAb efficacy in vivo against strains with normal and enhanced MrkA expression. RESULTS: T3F structural and regulatory genes are highly conserved, however, regulatory gene disruption (mrkH) is more common than structural gene disruption and, in both cases, MrkA Ag is not expressed. In vivo Ag profiling revealed site-specific differences in MrkA expression, with ∼20% of KP cells expressing MrkA in the lung versus ∼5% in the bloodstream. Anti-MrkA mAb activity was dependent on MrkA abundance, with significantly enhanced efficacy following infection with MrkA-overexpressing KP. CONCLUSIONS: Regulatory genes are as important to characterise as structural gene presence when evaluating antigen candidates in clinical isolates, and Ag expression can vary by anatomical context. For MrkA, Ag abundance determines anti-MrkA mAb activity, suggesting infections with high MrkA expression will respond better to therapy.
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Journal articleEttema TW, Inaba-Inoue S, Thangaratnarajah C, et al., 2026,
Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters
, Nature Communications, Vol: 17, ISSN: 2041-1723SbmA is a membrane transporter from Escherichia coli that imports antimicrobial peptides. SbmA belongs to the SbmA-like peptide transporter (SLiPT) family. Although the protein is a secondary active transporter that is energized by the proton gradient, it is structurally related to the transmembrane domain (TMD) of ATP-binding cassette (ABC) transporters. SbmA therefore bridges the structural divide between primary and 61 secondary transporters. However, it remains unclear, if SbmA also shares the mechanism of alternating access with ABC transporters, because only a single (outward-open) state is resolved. Here, we show by sequence analysis that SbmA is likely evolved from the TMD of an early ancestor of the ABC transporter YddA. We determine the cryogenic electron microscopy structures of SbmA in occluded and inward-facing states. These conformations closely resemble equivalent states found in ABC trans- porters, indicating a shared structural mechanism of transport. In contrast to ABC transporters, where nucleotide binding, hydrolysis and release steer conformational changes necessary for substrate translocation, electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations reveal how pH changes induce conformational transitions in SbmA, consistent with a mechanism of substrate internalization that utilizes the transmembrane proton gradient.
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Journal articleHobbs B, Limmer N, Clenshaw GL, et al., 2026,
Accurate interdomain contacts in a mixed folded protein from NMR-guided coarse-grained simulations.
, Phys Chem Chem PhysIntrinsically disordered, low-complexity regions frequently cooperate with folded domains to mediate protein-protein interactions, yet accurately describing these mixed folded-disordered systems remains challenging. To visualize these mixed folded proteins, experimentally guided coarse-grained (CG) molecular dynamics simulations are often employed to extend the timescales required to capture the complex dynamics in play. However, the minimalistic nature of these approaches often compromises structural accuracy and can lead to inaccurate inter-domain interactions. Here we introduce backbone dihedral terms directly derived from NMR chemical shift data in CG-simulations to characterize the open state of a mixed-folded construct of the anti-aggregation chaperone DNAJB6 that contains a folded J-domain and a disordered GF linker. By tuning residue-specific backbone dihedral parameters to match NMR-derived secondary-structure propensities of the linker in CG-simulations, we generate conformational ensembles that yield accurate interdomain contact maps. In agreement with analysis of NMR relaxation data, the resulting ensembles show that even in the nominally open state the linker experiences motions that resemble those of the closed state driven by hydrophobic residues in GF. More generally, we show that by expanding CG-simulations to allow them to capture both local and global structural properties, physically relevant interdomain contacts can be retrieved.
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