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Journal articleRostøl JT, Chmielowska C, Marina A, et al., 2026,
Revisiting the life cycle of temperate phages.
, Nat Rev MicrobiolTemperate bacteriophages (phages) are ubiquitous viruses that co-evolve with their bacterial hosts. They are defined by their ability to undergo two distinct life cycles: the lytic cycle, in which the phage produces more viral copies and kills the host, and the lysogenic cycle, in which the temperate phage exists as a prophage in the host. Temperate phages have long served as fundamental models in microbiology, genetics and evolutionary biology research, and their life cycles are among the most thoroughly characterized in virology. Historically, the phage life cycle was viewed primarily through the lens of how excision, replication and packaging drive the formation of infective particles. Although it captures the central processes of the phage life cycle, this narrow perspective overlooks the full range of interactions with the host and with other mobile genetic elements. In this Review, we re-examine the temperate phage life cycle in light of emerging insights that expand on this framework with unanticipated complexities. We argue that many properties of (pro)phages should be viewed as integral parts of their life cycle instead of being discussed separately. This holistic view is important to fully appreciate the intricacies of the temperate phage life cycle and the key roles of these viruses in microbiology and biotechnological applications.
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Journal articlePallett MA, Tocci R, Majstorovic A, et al., 2026,
MAP4Ks drive cell death in response to Salmonella SpvB-induced actin depolymerisation
, mBio, Vol: 17, ISSN: 2161-2129Many pathogens target the host actin cytoskeleton through the delivery of actin depolymerizing toxins, including mono-ADP-ribosyltransferases (mART), ultimately triggering host cell death. Despite the importance of mARTs in pathogen virulence, it remains unclear whether actin ribosylation is required for mART-dependent cell death, and how actin depolymerization leads to cell death. Using the non-typhoidal Salmonella enterica Typhimurium-encoded mART, SpvB, we report that cell death is induced exclusively through ribosylation of actin. We found cell death to be morphologically and mechanistically distinct from apoptosis as well as any previously reported mode of cell death. Instead, our data identify the Hippo signaling MAP4Ks as the essential host cell sensors of actin depolymerization signaling through JNK to facilitate vacuolization and host cell death. Cell death following treatment of cells with the actin depolymerizing agent latrunculin A followed the same pathway, identifying a conserved mechanism of cell death. Therefore, we identify MAP4K family members as key regulators of an atypical caspase-independent cell death induced by actin depolymerization, building on our understanding of host-cell death signaling and mechanisms of bacterial virulence.
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Conference paperChen J, Leung VCH, Wang R, et al., 2026,
Masked Projection Modelling for Sparse-view cryo-EM Reconstruction
, ICASSP 2026 - 2026 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Publisher: IEEE, Pages: 11567-11571 -
Journal articleNoone DP, Bubeck D, 2026,
Advances in cryo-EM that have shaped mechanistic models of membrane attack complex assembly and regulation
, IUCrJ, Vol: 13, Pages: 221-227, ISSN: 2052-2525The complement system is a blood-based immune network that plays a crucial role in fighting infection and maintaining immune homeostasis. The membrane attack complex (MAC) is a pore assembled from complement proteins that creates holes in cells when the immune system is activated. Over the last 10 years, advances in cryo electron microscopy (cryo-EM) have enabled key molecular insights into how MAC assembles, remodels membranes, and is regulated. These new tools revealed the inherent flexibility of complement complexes. By adapting computational approaches that disentangle diverse conformations, these studies have provided detailed mechanisms for MAC activity that could underpin novel complement-targeted therapeutics. Now accelerated by AI-driven image analysis and advances in structural cell biology, the next revolution in cryo-EM o ers new opportunities to understand the cellular consequences of immune activation.
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Journal articleMurray JW, 2026,
Recent advances in the structural biology of photosystem II
, The Plant Journal, Vol: 126, ISSN: 0960-7412Photosystem II (PSII) is the membrane protein-pigment complex responsible for the light-driven oxidation of water to molecular oxygen, a reaction that enables the aerobic biosphere and powers biological carbon fixation. Over the past two decades, structural biology has transformed our understanding of PSII from low-resolution outlines of its protein chains and cofactors to near-atomic resolution models. Early X-ray crystallographic structures from thermophilic cyanobacteria established the architecture of the reaction centre and the Mn4CaO5 oxygen-evolving complex (OEC), defining the protein ligands and cofactor network that support charge separation and water oxidation. The advent of high-resolution single-particle cryo-EM microscopy has expanded structural coverage across taxa, assembly and repair intermediates, and PSII–antenna supercomplexes that are beyond crystallisation. CryoEM now routinely achieves sub-2.5 Å resolution. In situ cryo-EM tomography further bridges atomic models to the native thylakoid membrane environment, exposing the supramolecular organisation of PSII in cells. X-ray free electron laser (XFEL) pump–probe experiments provide time-resolved snapshots of the Kok S-state cycle, revealing substrate water insertion, metal–oxo rearrangements and approaches O–O bond formation. Despite these advances, key challenges remain, including unambiguous assignment of manganese oxidation states, direct localisation of hydrogen atoms and complete structural characterisation of transient S-state intermediates. Integration of structural methods with spectroscopy, computation and emerging protein design approaches promises not only deeper mechanistic insight into biological water oxidation, but also guidance for the development of robust, earth-abundant catalysts.
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Journal articleGovada L, Wang B, Li Y, et al., 2026,
Investigating the effects of nanogels in promoting protein crystallization
, International Journal of Molecular Sciences, Vol: 27, ISSN: 1661-6596X-ray crystallography is still the most widely used and versatile method for structural studies of biological macromolecules. This study concerns the application of nanogels to facilitate protein crystallization, a prerequisite for X-ray crystallography. Nanogels (NGs) are nano-sized, highly crosslinked polymeric particles that have been extensively studied for chemical catalysis and drug delivery but not for protein crystal nucleation. The efficacy of six types of nanogels (three N-isopropylacrylamide-based and three acrylamide-based) was tested, with promising results. They were subsequently functionalised with active hydroxyl groups for further testing. Both functionalised and non-functionalised nanogels were tested on model (trypsin, thaumatin, proteinase K, ferritin and catalase) and target proteins (glulisine, α-crustacyanin and acriflavine resistance protein subunit AcrB) using both manual and automated techniques. All nanogels were found to be effective in promoting protein crystallization in both screening and optimization trials, giving crystal 'hits' that would have otherwise been missed. Overall, the functionalised nanogels were more effective. Nanogel effects are proposed to be due to a combination of surface porosity and surface chemistry.
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Journal articleHe S, David S, Rattle J, et al., 2026,
TraN variants mediate conjugation species specificity of IncA/C, IncH and Acinetobacter baumannii plasmids
, Journal of Bacteriology, Vol: 208, ISSN: 0021-9193IncA/C and IncH plasmids commonly carry antimicrobial resistance genes, notably blaNDM-1. Although these plasmids disseminate among Gram-negative pathogens via conjugation, the mechanisms underlying mating pair stabilisation (MPS) and conjugation species specificity remain poorly understood. In IncF plasmids, MPS is mediated by interactions between outer membrane proteins (OMP) encoded by the plasmids in the donor (TraN) and by the chromosome in the recipient. Using the Plascad database, we extracted 1,436 TraN sequences from 1517 plasmids: 62.5% (898/1,436), mainly in IncF plasmids, are 550–660aa (we renamed TraN short, TraNS); 15% (216/1,436), in IncA/C plasmids, are 880–950aa (TraN medium, TraNM); and 11% (160/1,436), in IncH plasmids, are 1,050–1,070aa (TraN long, TraNL). One TraN, found in six plasmids from Acinetobacter baumannii (891aa), was designated TraN V-shaped (TraNV). Like TraNS, TraNM and TraNL contain a base and one distal tip domain essential for conjugation, whereas TraNV has a base and two distinct tip domains forming a V-shaped structure. TraNM, TraNL and TraNV determine conjugation species specificity, with TraNL cooperating with OmpA. Tip swapping reverses conjugation specificity, revealing how TraNM and TraNL diversity influence plasmid host range and AMR dissemination. Our new data reveal the molecular basis of plasmid host specificity and broaden our understanding of how conjugation drives the dissemination of antimicrobial resistance genes among clinically relevant bacteria.
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Journal articleKadeřábková N, Furniss RCD, Maslova E, et al., 2026,
Antibiotic potentiation and inhibition of cross-resistance in pathogens associated with cystic fibrosis.
, Elife, Vol: 12Critical Gram-negative pathogens, like Pseudomonas, Stenotrophomonas, and Burkholderia, are now resistant to most antibiotics. Complex resistance profiles, together with synergistic interactions between these organisms, increase the likelihood of treatment failure in distinct infection settings, for example in the lungs of cystic fibrosis (CF) patients. Here, we discover that cell envelope protein homeostasis pathways underpin both antibiotic resistance and cross-protection in CF-associated bacteria. We find that inhibition of oxidative protein folding inactivates multiple species-specific resistance proteins. Using this strategy, we sensitize multidrug-resistant Pseudomonas aeruginosa to β-lactam antibiotics and demonstrate promise of new treatment avenues for the recalcitrant emerging pathogen Stenotrophomonas maltophilia. The same approach also inhibits cross-protection between resistant S. maltophilia and susceptible P. aeruginosa, allowing eradication of both commonly co-occurring CF-associated organisms. Our results provide the basis for the development of next-generation strategies that target antibiotic resistance, while also impairing specific interbacterial interactions that enhance the severity of polymicrobial infections.
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Journal articleAlShaer D, Al Musaimi O, Williams DR, 2026,
Application of the OBIMAP (One-Bead Interchain Multipeptide Assembly Platform) to long peptide synthesis: liraglutide as a case study
, ACS Omega, Vol: 11, Pages: 21369-21381, ISSN: 2470-1343This paper reports the application of the recently described OBIMAP (one-bead interchain multipeptide assembly platform) to the synthesis of liraglutide, a representative long peptide (>30 residues), achieving improved yield and purity compared with conventional sequential synthesis. Two synthesis strategies were tested: resin-stapled elongation (RSE) and parallel chain ligation (PCL). RSE, in which two peptide fragments are covalently “stitched” on-resin via orthogonal protection, delivered superior results, up to ∼50% crude purity and 76% recovery versus ∼25% crude purity and 37% recovery for conventional SPPS, while maintained same solvent use as in sequential SPPS. The improved overall purity suggested a reduction in aggregation behavior resulting from the midchain “stitching” step. A current limitation of the process is the extended synthesis time, approximately three times longer than conventional sequential methods, with fragment stitching (linking) representing the most time-consuming step (9–16 h at room temperature). Integration of microwave-assisted fragment linking and automation of three out of nine steps has reduced overall synthesis time to half, while automation of the remaining steps is currently under validation and investigation. The primary challenge for full automation lies in ensuring the compatibility of automated synthesizers with the remaining synthesis steps. Subsequent studies are focused on extending the results obtained at the 0.1 mmol scale to larger production scales (1, 10, and 50 mmol). If successfully implemented at larger scales this strategy, OBIMAP-RSE, could reduce manufacturing costs, enhance accessibility, and accelerate the development of next-generation peptide therapeutics.
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Journal articleMitchell HM, Nocek B, Guinn EJ, et al., 2026,
Crystallization and 1.6 Å resolution crystal structure of an acylated GLP-1/GIP analogue peptide
, Acta Crystallographica Section F:Structural Biology Communications, Vol: 82, Pages: 114-124, ISSN: 2053-230XWith the meteoric rise in interest in GLP-1 and GIP analogue peptides in recent years, there is a drive for the use of alternative purification techniques to alleviate processing bottlenecks and reduce the cost of peptide manufacturing. However, a lack of reported crystal structures for this class of peptides has hindered molecular-scale understanding of GLP-1/GIP analogue peptide crystallization, particularly related to acylated peptides. This paper therefore reports what is believed to be the first crystal structure of a GLP-1 and GIP analogue lipopeptide. Crystals obtained using a microseed matrix-screening protocol diffracted to ≤1.6 Å resolution in space group P43, with unit-cell parameters a = b = 64.66, c = 11.42 Å. Model building and the resultant structural analysis reveals that the predominantly helical peptide forms a uniquely porous spiral crystal structure composed of clockwise-ascending monomers in a square pattern, with aromatic C⋯H—π interactions around Phe22 forming the primary crystal contact between neighbouring square motifs.
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Journal articleFigueroa W, Sabnis A, Ibarra-Chavex R, et al., 2026,
Immune-deficient bacteria serve as gateways to genetic exchange and microbial evolution
, Nature Communications, Vol: 17, ISSN: 2041-1723Horizontal gene transfer plays a key role in bacterial evolution, yet its efficiency under natural conditions, especially between genetically distinct strains, remains unclear. Using Staphylococcus aureus as a model, we found that gene transfer via various mechanisms is significantly restricted between strains from different clonal complexes (CCs), with the notable exception of lateral transduction, which occurs at high frequency. Interestingly, some strains exhibited a promiscuous ability to accept diverse mobile genetic elements. These strains were defective in the key immune defences, specifically the Type I restriction-modification systems that normally protect against foreign DNA. A broader analysis revealed that such immune deficient mutants are widespread within S. aureus populations. Our study uncovered a tradeoff that may account for their persistence in nature: although these mutants are more susceptible to phage attack, they gain an evolutionary advantage by acquiring new genes - such as those conferring antibiotic resistance - which would enhance survival under selective pressure. These immune-deficient cells act as gateways for foreign DNA, which, once integrated and advantageous, can spread within the same CC. Our findings highlight the role for immune-deficient bacteria in facilitating the emergence of novel virulence factors and antibiotic resistance, emphasising their importance in shaping bacterial evolution.
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Journal articleCullen M, Biancaniello C, Taškova K, et al., 2026,
Integrating NMR Restraints into Coarse-Grained Simulations: Toward Accurate Conformational Ensembles of Complex Protein Systems.
, J Am Chem Soc, Vol: 148, Pages: 13160-13173Structural dynamics play critical roles for the biological activity of protein molecules. Characterizing the inherent conformational landscapes of these macromolecules remains a major experimental and computational challenge, particularly for heterogeneous and transient systems such as intrinsically disordered proteins, membrane-associated assemblies and disordered fuzzy coats of amyloid aggregates. In this context, coarse-grained (CG) molecular dynamics simulations have enabled accessing to extended time scales and large system sizes, however, their reduced resolution and simplified interaction potentials often limit the structural accuracy. Here, we introduce Martini3-NMR, an integrative framework that incorporates nuclear magnetic resonance (NMR) observables directly into CG protein force fields. Using artificial neural networks to model NMR chemical shifts at the CG level, and integrating these data with NOE restraints, we define an approach to significantly enhance the accuracy of CG simulations while maintaining their elevated sampling efficiency, thereby resulting in a substantially improved description of protein conformational ensembles. We demonstrate the broad applicability of Martini3-NMR by generating CG ensembles for a range of systems involved in diverse biological processes such as protein folding, oligomer disassembly within lipid bilayers and conformational transitions of disordered fuzzy regions decorating amyloid fibril surfaces, which were found to display condensate-like properties. By enabling an experimentally driven and computationally efficient exploration of protein conformational landscapes, Martini3-NMR provides a novel general framework for investigating dynamic, heterogeneous and multiscale biomolecular processes. This approach opens to significant new opportunities for extending CG simulations toward a more quantitative understanding of the relationship between molecular structure, dynamics and biological function.
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Journal articleHerrera M, El Saghir A, Mansueto S, et al., 2026,
Aggregation and membrane activity of mutant A30P alpha-synuclein on mitochondrial membranes.
, Int J Biol Macromol, Vol: 355The A30P point mutation in the α-synuclein (α-syn) protein is linked to a familial form of Parkinson's disease (PD), the most common motor neurodegenerative disorder. The association of α-syn with lipids in cellular membranes plays a key role in modulating the aggregation behavior of the protein, as well as its toxicity. Here, we studied the impact of the A30P mutation on the interaction of α-syn with mitochondrial membranes, since the interplay between α-syn aggregation and mitochondrial dysfunction is central for the pathogenic process in PD, but still not completely understood. Experiments using model vesicles with membranes enriched in the mitochondrial signature phospholipid cardiolipin (CL) demonstrated that these membranes markedly accelerate and promote the aggregation of A30P α-syn, with respect to the wild-type protein. In turn, A30P caused enhanced changes in membrane fluidity and permeabilization of CL-containing membranes. Moreover, utilizing single-channel planar bilayer measurements, A30P α-syn was shown to increase the membrane conductance in mito-mimetic bilayers, possibly by membrane thinning and incorporation of ion-conducting pores. The incubation of A30P α-syn with isolated mitochondria caused mitochondrial swelling, efflux of cytochrome c and lowered the mitochondrial membrane potential, all key indicators of mitochondrial membrane damage. Collectively, our results demonstrate that the A30P mutation aggravates the deleterious liaison between α-syn and CL-rich membranes, providing a mechanistic basis for mitochondrial dysfunction associated with this α-syn variant.
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Journal articleLi Z, Chawla H, Di Vagno L, et al., 2026,
Xylosyltransferase engineering to manipulate proteoglycans in mammalian cells.
, Nat Chem Biol, Vol: 22, Pages: 612-621Mammalian cells receive signaling instructions through interactions on their surfaces. Proteoglycans are critical to these interactions, carrying long glycosaminoglycans that recruit signaling molecules. Biosynthetic redundancy in the first glycosylation step by two xylosyltransferases XT1/2 complicates annotation of proteoglycans. Here we develop a chemical genetic strategy that manipulates the glycan attachment site of cellular proteoglycans. Through a bump-and-hole tactic, we engineer the two isoenzymes XT1 and XT2 to specifically transfer the chemically tagged xylose analog 6AzGlc to target proteins. The tag contains a bioorthogonal functionality, allowing to visualize and profile target proteins in mammalian cells. Unlike xylose analogs, 6AzGlc is amenable to cellular nucleotide-sugar biosynthesis, establishing the XT1/2 bump-and-hole tactic in cells. The approach allows pinpointing glycosylation sites by mass spectrometry and exploiting the chemical handle to manufacture proteoglycans with defined glycosaminoglycan chains for cellular applications. Engineered XT enzymes permit an orthogonal view into proteoglycan biology through conventional techniques in biochemistry.
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Journal articleHe S, Ishimoto N, Wong J, et al., 2026,
H pilin cyclisation and pilus biogenesis are promiscuous but electrostatic perturbations impair conjugation efficiency
, Nature Communications, Vol: 17, ISSN: 2041-1723During conjugation, plasmid DNA is transferred from donor to recipient bacteria via the plasmid-encoded mating pilus, formed as thin helical assemblies of polymerised pilin subunits. In the IncHI1 R27 plasmid-encoded pilus, the TrhA pilin undergoes cyclisation (via a peptide bond between Gly1 and Asp69), essential for conjugation. Gly1 and Asp69 are exposed on the pilus surface and conserved in all TrhA pilins in the Plascad database. Substituting Asp69 with Asn, Ala, Gly, or Arg does not prevent cyclisation or pilus formation, which remains structurally indistinguishable from the wild type. Conjugation efficiency of the Asp69 substitutions across multiple recipient species correlates with side chain size, in the order Asp69Asn > Asp69Ala > Asp69Gly. However, Asp69Arg, as well as Asp69Lys and Gly1Lys substitutions abolish conjugation, likely due to the positively charged pilus surface (opposite to the wild-type negative charge) forming unfavourable electrostatic interactions with the recipient outer membrane’s inner leaflet, composed solely of zwitterionic phosphatidylethanolamine (PE). Consistently, conjugation is rescued in recipients lacking PE. These findings indicate strong selective pressure to maintain Gly1 and Asp69, as efficient DNA transfer depends on precise electrostatic and steric constraints of the pilus surface.
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Journal articleXu V, McInnes A, Wake M, et al., 2026,
Structural basis for Rep-mediated adeno-associated virus packaging
, Cell Reports, Vol: 45, ISSN: 2211-1247Adeno-associated viruses (AAVs) are parvoviruses utilized as gene therapy vectors. However, the AAV packaging mechanism is unresolved at the molecular level, creating a bottleneck for vector manufacturing, safety, and efficacy. Here, cryo-EM structures of the Rep helicase packaging motor in complex with the packaging marker DNA (ITR) and the Rep-AAV8 capsid complex are presented. Rep-ITR complexes reveal dynamic oligomeric states on the DNA, elucidating the strand separation mechanism coupled to its ATPase cycle. We observe Rep preferentially bound to empty capsids, with a binding interface likely conserved across the virus family. This complex also unveils a cryptic capsid ATP-binding site which, alongside Rep binding, triggers structural rearrangements priming the capsid for packaging. Collectively, these findings advance the understanding of Rep-mediated packaging, with significant implications for parvovirus virology and viral vector design.
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Journal articleNanev C, Saridakis E, Chayen N, 2026,
Flow as a control strategy for the nucleation and growth of biomolecular crystals
, Advances in Biochemical Engineering/Biotechnology, ISSN: 0724-6145The main aim of this chapter is to provide an (at least semi-quantitative) explanation of biomolecular crystallization (nucleation and growth) experimental results in solution flow, in order to further assist with optimization of the process. An overview will be provided of biomolecular crystal nucleation and growth in forced solution flows, but also in the presence and in the absence of natural (buoyancy-driven) convective flows. The chapter will focus first on the theoretical analysis of the different mass transfer modalities, diffusion- versus convection-dominated (both of crystal building blocks and of impurities), leading to biomolecule-depleted and to self-purifying (i.e. impurity-depleted) zones. The same topics will then be addressed, describing the experimentally investigated influence of forced flows, artificially created through air pressure, peristaltic pumping, oscillatory mixing, stirring, shearing, and other methods, both in small-scale laboratory and in large-scale industrial settings. In addition to forced flows, work on the influence of gravity-induced naturally occurring solution convection and crystal sedimentation will be reviewed, as well as the effects of its absence when crystallization trials are carried out under microgravity environments. By developing the principle of the separation of the nucleation and growth stages of crystallization (‘double-pulse technique’) not only in time but also in space, the reported results have shown that at solution flow velocities larger than those of buoyancy-driven convection, most crystals nucleated heterogeneously, while bulk-nucleated crystals predominated at lower flow velocities. Lastly, fluid flow also allowed the investigation of the important role of impurities of biological origin on the kind of crystal nucleation, homogeneous or heterogeneous. In view of the diverse needs for protein crystals (structure determination by conventional X-ray crystallography or by XFEL, industrial produc
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Journal articleRoumelioti G, Montoya A, Fisher GLM, et al., 2026,
High-throughput proteomics sample preparation using a 96-channel pipettor and magnetic pin device
, Journal of Proteome Research, Vol: 25, Pages: 1647-1661, ISSN: 1535-3893High-throughput proteomics requires efficient and highly reproducible sample processing, yet workflows─particularly for PTM profiling─remain complex and costly to fully automate. Here, we present a practical intermediate solution using manually operated 96-channel devices: the Gilson Platemaster P220 pipettor and VP Scientific 96-well magnetic pin device. Using this setup, we achieved robust and reproducible phosphoproteomics in a 96-well format, completing protein aggregation capture (PAC/SP3) digestion, desalting, phosphopeptide enrichment, and a second desalting step within 2 days while minimizing operator workload and variability. Several innovations enable this workflow. First, we describe a cost-efficient method to generate 96-well solid-phase extraction plates by directly packing the Oasis HLB sorbent into tapered filter plates. We extensively characterize these plates in terms of loading capacity, lipid removal efficiency, and suitability for high-pH fractionation. Second, we demonstrate that efficient PAC digestion does not require continuous bead suspension; instead, digestion can be achieved by briefly aspirating beads in protease solution, eliminating the need for orbital shaking and simplifying automation. The presented workflow familiarizes users with 96-channel devices and hence serves as a good step toward full automation.
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Journal articlePessina D, Tian T, Watson O, et al., 2026,
Transfer learning of data-driven crystallisation processes via constrained neural ordinary differential equations
, Digital Chemical Engineering, Vol: 18, ISSN: 2772-5081Modelling complex crystallisation processes remains challenging due to limited ex perimental datasets, high measurement noise, and the need for generalisability across varying operating conditions. Neural Ordinary Differential Equations (NODEs) and transfer learning (TL) offer promising tools to overcome these limitations by provid ing data-efficient, flexible, and transferable modelling frameworks. This work investigates the use of NODEs to model protein crystallisation dynamics under data-scarce conditions. A NODE trained on a data-rich source system successfully captures solute consumption and particle size dynamics, but when applied to data-sparse target sys tems, scratch-trained NODEs exhibit limited generalisation and unphysical behaviours. To address this, several TL strategies are evaluated, including layer freezing, parame ter deviation penalisation, and system-embedding within the neural architecture. Results show that layer freezing and deviation penalty consistently improve knowledge transfer, while system-embedding offers robustness in noisy or undersampled datasets. In addition, physics-informed NODEs, constrained to enforce monotonic concentra tion decay and crystal growth, demonstrate greater stability under high noise andsparse measurement regimes, ensuring physically consistent predictions. Overall, the combination of constrained NODEs with appropriate TL strategies provides a robust framework for accurate, transferable modelling of crystallisation systems in low-dataregimes.
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Journal articleGorzynski J, Harling-Lee JD, Figueroa W, et al., 2026,
Bacterial defense systems and host ecology drive the evolution of intra-species lineages.
, Cell Rep, Vol: 45Horizontal gene transfer (HGT) is a major driver of diversity in bacterial populations. However, our understanding of its impact on the evolution of intra-species lineages is limited. The multi-host bacterial pathogen Staphylococcus aureus is differentiated into genetic lineages known as clonal complexes (CC) with variable host and disease tropisms. Here, we demonstrate that CCs exhibit extensive variation in pangenome size, structure, and gene flow, influenced by both genetic and ecological barriers to HGT. Examination of pangenome openness for each CC revealed remarkable variation that correlated strongly with host-species promiscuity. Notably, CCs were defined by horizontally acquired defense systems, and genetic subpopulations have diverged by changes to their type I restriction-modification (R-M) system repertoire, suggesting a role in lineage emergence. Overall, our data indicate a key role of HGT of defense systems in promoting the differentiation of S. aureus into lineages, with host ecology as a major driver of accessory genome variation.
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Journal articleAl Musaimi O, Williams DR, 2026,
OBIMAP (One-Bead Interchain Multipeptide Assembly Platform)
, ACS Bio & Med Chem Au, Vol: 6, Pages: 90-100, ISSN: 2694-2437A significant advancement in Merrifield’s classic solid-phase peptide synthesis (SPPS) that greatly expands the scope of accessible peptide structures is reported here. Building upon the one-bead, one-compound (OBOC) concept, this approach enables the simultaneous synthesis of multiple peptides on a single bead, followed by a novel solid-phase interchain assembly reaction to produce the final peptide product. This method, the one-bead interchain multipeptide assembly platform (OBIMAP), successfully generates diverse peptide architectures, including linear, cyclic, and bicyclic structures─ranging from minimal cyclic dipeptides to small proteins─many of which are inaccessible through conventional SPPS. OBIMAP demonstrates superior efficiency in both time and product purity compared to traditional methods. Crucially, it eliminates the need for solution-phase fragment condensation, a common but cumbersome step commonly used in synthesizing therapeutic peptides (30–60 amino acids). In addition to enhancing conventional SPPS methodologies, the OBIMAP enables access to novel classes of peptide architectures, including highly constrained peptides that were previously considered synthetically inaccessible.
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Journal articleArnold MFF, Sankari S, Deutsch M, et al., 2026,
BacA(SbmA) importer of legume symbiotic NCR peptides: Protein architecture, function, and evolutionary implications.
, Proc Natl Acad Sci U S A, Vol: 123Some legumes encode families of NCR (Nodule-Cysteine-Rich) peptides that cause their rhizobial partners to terminally differentiate during the development of a nitrogen-fixing symbiosis. Sinorhizobium meliloti, whose plant hosts Medicago truncatula and Medicago sativa express ca. 600 NCR peptides during root nodule development, possesses a symbiotically essential BacASm protein that imports certain NCR peptides into the cytoplasm. This import permits proteolytic degradation of the NCR peptides, thereby protecting the endocytosed bacteria from their antimicrobial peptide-like lethality, while also allowing certain NCR peptides to undergo their symbiotically critical interactions with cytoplasmic components, for example heme-sequestration in the case of NCR247. Our study employed 54 S. meliloti bacASm missense mutants (35 to cysteine and 19 to glycine) that we tested for protein production, ability to establish a nitrogen-fixing symbiosis, and their susceptibility to killing by higher levels of the NCR247 and the Bac7(1-35) peptides. We also used the Single Cysteine Accessibility Method to make topological inferences. Our detailed genetic, biochemical, structural, and physiological analyses have revealed that BacASm and SbmAhomodimers function as finely tuned transporters, whose structures can be relatively easily disrupted by single amino acid changes. Our finding that several mutations that differentially separate nitrogen-fixation, NCR247 import, and Bac7(1-35) import map to the lining of the peptide-binding cavity suggests a molecular explanation underlying the paradoxical observation that SbmA/BacAs from pathogens can fully replace BacASm, whereas BacAs from other rhizobia cannot.
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Journal articleGarmendia-Antoñana N, Dorado-Morales P, Gil C, et al., 2026,
Targeted elimination of Staphylococcus aureus mastitis infections with synthetic phage-based CRISPR-Cas delivery systems.
, NPJ Biofilms Microbiomes, Vol: 12Treatment options for Staphylococcus aureus infections are increasingly limited, particularly in livestock, where S. aureus causes mastitis requiring prolonged antibiotic therapy. This study engineered Phage Inducible Chromosomal Islands (ePICIs) to deliver CRISPR-Cas9 modules targeting small RNA genes. ePICIs exhibit bactericidal activity without chromosomal integration, an expanded host range compared to their parental phages, and biofilm-dependent efficacy influenced by the extracellular matrix composition. Biofilms mediated by the Bap protein strongly protect bacteria from ePICIs, whereas PIA/PNAG-based biofilms do not. Despite Bap-mediated protection in vitro, ePICIs achieved bactericidal effects comparable to vancomycin in a mouse mastitis model caused by Bap-producing strains. These findings reveal key factors affecting phage-delivered CRISPR-Cas efficacy and highlight that antibiofilm therapies should not be dismissed based solely on in vitro performance. Non-replicative ePICIs thus represent a promising alternative for treating localized infections such as mastitis.
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Journal articleChmielowska C, Zamora-Caballero S, Mancheño-Bonillo J, et al., 2026,
A DNA recognition-mimicry switch governs induction in arbitrium phages.
, Cell Host Microbe, Vol: 34, Pages: 291-303.e10Temperate phages integrate multiple information sources to regulate lysis-lysogeny transitions. SPbeta-like phages use arbitrium signaling and DNA damage to control repressor activity during lytic induction, but how the repressor functions and is inactivated by the SOS response remains unclear. Here, we show that SroF, the SPbeta-like phage repressor, binds DNA via a mechanism involving its integrase-like fold, enabling stable prophage repression. Upon DNA damage, the host SOS response triggers derepression of an antirepressor, Sar. Sar binds SroF by mimicking the DNA structure recognized by the repressor, thereby inactivating its function and inducing phage. This mechanism is conserved across SPbeta-like phages, which encode multiple, specific SroF-Sar pairs. Surprisingly, repressor inactivation alone is insufficient for efficient induction when arbitrium levels are high. Our results uncover the mechanism underlying a double layer of control that ensures phage induction occurs only under SOS conditions and in the absence of neighboring prophages.
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Journal articlePeters A, Shareefdeen H, Sanchez Garrido J, et al., 2026,
Stable coexistence of Citrobacter rodentium with a lytic bacteriophage during in vivo murine infection
, mBio, Vol: 17, ISSN: 2161-2129Bacteriophages are ubiquitously present in bacterial communities, yet phage-bacteria interactions in complex environments like the gut remain poorly understood. While antibiotic resistance is driving a renewed interest in phage therapy, most studies have been conducted in in vitro systems, offering limited insight into the complexity of such dynamics in physiological contexts. Here, we use Citrobacter rodentium (CR), a natural mouse-restricted enteric pathogen and well-established model for human enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC and EHEC) infections, to investigate phage-pathogen interactions in vivo. We isolate and characterise Eifel2, a novel lytic phage infecting CR, and generate anti-phage specific antibodies that enable the visualisation of phage infections in vitro. In a murine model of CR infection, oral administration of Eifel2 led to robust phage replication in the gut without reducing the bacterial burden or infection-associated inflammation, confirming the establishment of a stable coexistence in the gut. Despite the emergence of a sub-population of phage-resistant CR mutants in vivo, they did not undergo clonal expansion, indicating that additional selective pressures impaired their widespread dissemination in the gut. Together, our findings demonstrate that imaging approaches can capture key infection stages in vitro, while in vivo models are essential for capturing the complexity of phage-bacteria interactions. This work highlights the importance of studying phage therapy in host-pathogen contexts that include a normal microbiota and a suitable host environment, where dynamic co-existence rather than eradication may define therapeutic outcomes.
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Journal articleSpreng TL, Danaci D, Ram PD, et al., 2026,
Amine-Appended Hyper-Crosslinked Polymers for Direct Air Capture of CO2.
, ACS Sustain Chem Eng, Vol: 14, Pages: 1834-1846, ISSN: 2168-0485Capturing CO2 from the ambient atmosphere is a promising method to reduce the impact of climate change. Fast deployment and scale-up of adsorption-based direct air capture (DAC) technologies are needed to meet the IPCC target and rely, in part, on the development of efficient and scalable low-cost adsorbents. While a benchmark DAC adsorbent, the polymeric resin Lewatit VP OC 1065, has been established, the reasons behind its performance and the potential for further optimization remain largely unknown. Indeed, a fundamental understanding of the relationship between adsorbent pore structure, chemistry, and DAC performance, both equilibrium and kinetics, has yet to be formulated. Here, we have built on the chemistry of Lewatit and synthesized a hyper-crosslinked polymer (HCP) by grafting a microporous chlorine-functionalized support with diethylenetriamine. We produced four different adsorbents by varying the polymerization duration between 10 min and 19 h to assess the impact of pore structure on CO2 uptake at 400 ppm. Reduced degrees of polymerization (i.e., shorter polymerization durations) resulted in higher accessible micropore volume and consequentially increased CO2 uptake and amine efficiency. The best sample achieved an equilibrium uptake of 0.43 mmol/g (400 ppm of CO2, 298 K), which is about half that of the benchmark adsorbent Lewatit VP OC 1065. We have then assessed the CO2 sorption kinetics of this sample (grain size of 24-74 μm) at 400 ppm and 303 K using a gravimetric technique and have compared the results to those of other amine-grafted polymeric adsorbents. We measured a lower bound linear driving force constant (k LDF) of 0.0120 ± 0.0004 s-1. This value is 5.5 times faster than that of the benchmark adsorbent Lewatit VP OC 1065 with the same grain size of 24-74 μm, highlighting the importance of macropore diffusion in addition to the CO2 reaction kinetics. This study shows how synthesis operating conditions alter the pore structures an
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Journal articlevan Thor J, 2026,
Coherent two dimensional electronic-X-ray spectroscopy
, Journal of Chemical Physics, Vol: 164, ISSN: 0021-9606Ultrafast pump–probe time resolved x-ray spectroscopy carries information on the valence-core dynamics of molecular systems. Here, a coherent two-dimensional nonlinear electronic-x-ray spectroscopy (2DEX) application is proposed in order to reveal the frequency–frequency correlations for the valence and the core transition excitations. 2DEX is in the class of extreme-cross peak correlation spectroscopy and is experimentally straightforward to measure as an adaptation of the conventional optical pump–x-ray probe technique by creating a phase-locked pulse pair of the ultrafast laser for the valence excitation. Theoretical evaluation of the coherences and populations for several applications of ultrafast valence-core spectroscopy experiments is shown. Using a response function approach, 2DEX, four wave signals are calculated and evaluated with respect to frequency separation in the electronic and x-ray ranges as well as the line shape characteristics. It is shown that stationary and oscillatory contributions to the rephasing, non-rephasing, and absorptive signals can be resolved depending on pulse shaping and phase cycling, phase matching, x-ray spectrometer, and material response parameters. Calculations are shown for examples that include the valence-core coherences for a vibrational monomer and for Frenkel and charge transfer electronic exciton states, which in the x-ray absorption near-edge structure spectral region has the potential to resolve the population and coherence contributions in the atomic localized basis.
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Journal articleBade I, Etit D, Heng JYY, 2026,
The effect of solvents on crystal regeneration
, CrystEngComm, Vol: 28, Pages: 357-370, ISSN: 1466-8033Solvents play a pivotal role in crystallisation, affecting crystal growth and properties. This study investigates the regeneration behaviour of paracetamol crystals in ethanol, tetrahydrofuran, and acetone using both evaporative and isothermal crystallisation setups, coupled with a custom MATLAB-based edge detection algorithm for facet-specific growth rate measurements. Regeneration was observed in all solvents, with the fastest rate observed in ethanol (0.07 mm h−1), followed by THF (0.03 mm h−1), and acetone (0.02 mm h−1) at a supersaturation ratio of 1.10. In all cases, regeneration was driven by rapid growth of the (0 1 0) facet, restoring crystals to their original shapes. Crystal shape influenced the regeneration time, with a rapid initial phase comprising 8–15% of total regeneration time. Molecular dynamics simulations were utilised to quantify solvent–crystal interactions, showing that not only do the inherent solvent properties play a role but also the solubility of paracetamol significantly affects crystal regeneration.
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Journal articleMishra V, Kozik Z, Biswas P, et al., 2026,
Rehydration rescues Il22-/- mice from lethal Citrobacter rodentium infection
, Nature Communications, Vol: 17, ISSN: 2041-1723Interleukin-22 (IL-22) is considered indispensable for host defence against Citrobacter rodentium, with 100% mortality of Il22 -/- mice. While IL-22 promotes epithelial barrier integrity and production of antimicrobial peptides, the precise mechanism underlying lethality remains unclear. Here, we show that following C. rodentium infection Il22-/- mice succumb due to dehydration, rather than failure to control bacterial burden or regenerate damaged intestinal epithelium. Proteomic and gene expression analysis reveal greater enterocyte depletion in C. rodentium-infected Il22-/- mice, resulting in significant reductions in ion transporter abundances. We show that while not reducing bacterial load, improving the gut barrier integrity, or affecting immune responses, fluid therapy (FT) fully rescues Il22-/- mice by correcting systemic dehydration. Survival is associated with locally increased Reg3b, IL-17F and IL-10 levels, suggesting activation of compensatory pathways that potentially support recovery in the absence of IL-22. Recovered Il22-/- mice exhibit epithelial cell regeneration and tissue physiology similarly to C. rodentium-infected Il22+/+ mice. These findings suggest that dehydration is the primary cause of mortality in Il22-/- mice and reveal that IL-22 prevent this outcome by preserving epithelial integrity and fluid-ion absorption. Importantly, this study underscores the necessity of incorporating supportive therapies into preclinical infection models to better reflect physiological settings and improve their relevance in modelling human disease.
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Journal articleZhang C, Li J, He F, et al., 2026,
Superflexible Fluorescent π-Conjugated Organic Crystals: Synergistic Mechanical-Optical Properties and Molecular Engineering Insights
, Crystal Growth and Design, Vol: 26, Pages: 219-228, ISSN: 1528-7483Molecular crystals exhibit broad application prospects in the field of flexible functional materials due to their unique elastic behavior. This study designed and synthesized four structurally similar flexible molecular crystals with fluorescence properties. Among them, three crystals contain −C═N–NH– groups (named Bhn, Chn, Pthn), while the fourth incorporates −N═N– group (termed Modn). The mechanical response characteristics of these crystals were systematically explored through a comprehensive series of analyses. Experimental results demonstrate that, under external force stimulation, the four crystals exhibit differentiated bending performance, among which Pthn and Modn crystals can achieve complete 180° bending, showcasing excellent flexibility. Through three-point bending tests and nanoindentation techniques, the mechanical properties of these two large-sized single crystals were quantitatively characterized. It was found that they can withstand ultralarge strains of 80% and 120% respectively under extremely low stress conditions before fracturing, while also possessing low elastic moduli (E<inf>Pthn</inf> = 3.17 ± 0.11 GPa, E<inf>Modn</inf> = 3.75 ± 0.13 GPa) and hardness values (H<inf>Pthn</inf> = 0.13 ± 0.02 GPa, H<inf>Modn</inf> = 0.23 ± 0.01 GPa), confirming their outstanding mechanical flexibility and ductility. Furthermore, under ultraviolet excitation, all four crystals emit orange-red fluorescence (λ > 600 nm), but with significant differences in fluorescence intensity. This synergistic regulation effect of mechanical-optical properties provides an important theoretical foundation for developing novel intelligent flexible optoelectronic materials. Further optimization of crystal packing modes through molecular engineering strategies is expected to achieve precise control of force-light coupling characteristics, which holds significan
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