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Journal articleYoun T, Ehsan M, Hariharan P, et al., 2025,
Tailoring butane-1,2,3,4-tetraol-based maltosides (BTMs) via group-swapping and detergent unsymmetry: new detergent design strategies for membrane protein studies
, Journal of Materials Chemistry B, Vol: 13, Pages: 12569-12578, ISSN: 2050-750XMembrane proteins are essential bio-macromolecules involved in numerous critical biological processes and serve as therapeutic targets for a wide range of modern pharmaceuticals. Small amphipathic molecules, called detergents or surfactants, are widely used for the isolation and structural characterization of these proteins. A key requirement for such studies is their ability to maintain membrane protein stability in aqueous solution, a task where conventional detergents often fall short. While many new detergents have been developed based on novel molecular scaffolds, comparatively little effort has been made to enhance detergent performance through rational modification of existing structures, largely due to the limited availability of guiding design principles and strategies. In this study, we refined previously developed butane-1,2,3,4-tetraol based maltosides (BTMs), using two structural modification strategies, head/tail group-swapping and the introduction of hydrophobic unsymmetry. The resulting group-swapped (GS)-BTMs exhibited distinctive physical properties compared to the original BTM, including differences in water-solubility (∼7 to >10 wt%), critical aggregation concentration (5 to 15 μM), and self-assembly size (7.6 to 34.2 nm). When evaluated using model membrane proteins, including the human adrenergic receptor (β2AR), symmetric GS-BTMs (e.g., GS-BTM-C11 and GS-BTM-C12) showed superior performance relative to the original BTM-C11 and benchmark detergents (DDM and LMNG). The unsymmetric variants, such as GS-BTM-C14,10 and GS-BTM-C15,9, further improved protein stability. These findings highlight group-swapping and hydrophobic unsymmetry as effective strategies for enhancing detergent performance. This work demonstrates how minimal structural modifications can impact detergent properties and efficacy, providing valuable insights for the development of improved detergents from existing molecular frameworks.
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Journal articleVarga T, Woods R, Pitsillides F, et al., 2025,
Whole genome sequencing of historical specimens from the world's largest fungal collection yields high-quality assemblies
, NEW PHYTOLOGIST, ISSN: 0028-646X -
Journal articleCambron TW, Fisher JB, Hungate B, et al., 2025,
Plant nutrient acquisition under elevated CO2 and implications for the land carbon sink
, Nature Climate Change, ISSN: 1758-678XTerrestrial ecosystems currently sequester around a third of anthropogenic carbon emitted each year, slowing the pace of climate change. However, the future of this sink under rising atmospheric CO2 concentrations remains uncertain, in part due to the impact that nutrient limitation may have on plant biomass. Here, we review plant nutrient acquisition strategies and evidence of the enhanced utilization of these strategies under experimental and real-world elevated CO2 (eCO2). Many of the strategies that are key to nutrient limitation alleviation under eCO2 are not yet well represented in Earth System Models (ESMs). A simple, data-driven analysis implies that ESMs without nutrient acquisition strategies could underestimate the land sink.
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Journal articleClaramunt S, Sheard C, Brown JW, et al., 2025,
A new time tree of birds reveals the interplay between dispersal, geographic range size, and diversification
, Current Biology, Vol: 35, Pages: 3883-3895.e4, ISSN: 0960-9822The spatial and temporal dynamics of biodiversity are shaped by complex interactions among species characteristics and geographic processes. A key example is the effect of dispersal on geographical range expansion and gene flow, both of which may determine speciation rates. In this study, we constructed a time-calibrated phylogeny of over 9,000 bird species and leveraged extensive data on avian traits and spatial occurrence to explore the connections between dispersal, biogeography, and speciation. Phylogenetic path analyses and trait-dependent diversification models reveal that geographic range size is strongly associated with the hand-wing index, a proxy for wing aspect ratio related to flight efficiency and dispersal ability. By contrast, we found mixed evidence for the effect of dispersal on diversification rates: dispersive lineages show either slightly higher speciation rates or higher extinction rates. Our results therefore suggest that high dispersal ability increases range expansion and turnover, perhaps because dispersive lineages expand into islands or other geographically restricted environments and have lower population sizes. Our results highlight the nuanced and interconnected roles of dispersal and range size in shaping global patterns of avian diversification and biogeography and provide a richly sampled phylogenetic template for exploring a wide array of research questions in macroecology and macroevolution.
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Journal articleDonini R, Blundell P, Pleass RJ, et al., 2025,
Genetic Divergence and Antibody Expression Influence the N-Glycomes of CHO-K1 and CHO-S Cells
, BIOTECHNOLOGY AND BIOENGINEERING, ISSN: 0006-3592 -
Journal articleVerma A, Khadke L, Budakoti S, 2025,
Understanding the dynamics of 2024 extreme heat event in India: spatial variability, hydrometeorological impacts, and model evaluation
, Atmospheric Research, Vol: 322, ISSN: 0169-8095Heatwaves are becoming more intense, frequent, and prolonged due to global warming, posing significant risks to ecosystems and human societies. Despite their profound impact, detailed regional assessments of extreme heat events remain limited, particularly in India. This study addresses the gap by systematically investigating the 2024 extreme heat event in India. We evaluated the performance of various land surface schemes in simulating heat extremes using the Weather Research and Forecasting model and also assessed the accuracy of Global Forecast System (GFS) forecasts. Our analysis reveals a strong co-occurrence of drought and heat stress during the extreme heat event. This combination results in increased fire risk and negative impacts on vegetation productivity in regions affected by both drought and heat stress highlighting the severe consequences of this compound event. We compare different land surface models (RUC, Noah, Noah-MP, Noah-MP with dynamic vegetation, CLM) against India Meteorological Department (IMD) observations. We observe that Noah is optimal for reducing bias and RMSE, while Noah-MP with dynamic vegetation is most accurate for simulating extreme heat, with the highest hit rate and threat score for the 90th percentile threshold. Additionally, GFS maximum temperature forecasts for 1–3 day lead times perform well at short lead times, especially in Southern India but overestimate temperatures in heatwave-prone regions like the Indo-Gangetic Plains. Our findings highlight the importance of enhancing land surface models and forecasting systems to better predict extreme heat events, which is crucial for localized hazard and risk assessments and improving disaster management efficiency.
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Journal articleMadsen CD, Barbensi A, Zhang SY, et al., 2025,
The topological properties of the protein universe
, NATURE COMMUNICATIONS, Vol: 16 -
Journal articleMadge Pimentel I, Albini D, Beermann AJ, et al., 2025,
Hypothesis-Driven Research on Multiple Stressors: An Analytical Framework for Stressor Interactions
, ECOLOGY AND EVOLUTION, Vol: 15, ISSN: 2045-7758 -
Journal articleKontopoulos D-G, Patmanidis I, Barraclough TG, et al., 2025,
Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases
, EVOLUTION LETTERS -
Journal articleTobias JA, Bullock JM, Dicks LV, et al., 2025,
Biodiversity conservation requires integration of species-centric and process-based strategies
, Proceedings of the National Academy of Sciences, Vol: 122, ISSN: 0027-8424Conservation science and policy are geared primarily toward the preservation of species and habitats, with priority often given to the rarest, most vulnerable or most charismatic forms. This pattern-based approach has broad appeal and offers a pragmatic short-cut for targeting conservation action. However, the long-term efficacy of species and landscape conservation programs remains highly uncertain, amid growing evidence that sustainable conservation action requires an increased emphasis on preserving ecological and evolutionary processes. This reframing of conservation goals was first proposed 50 y ago, but the concept has struggled to gain traction, particularly in terms of translation into policy. Nonetheless, recent events have shifted the narrative, with multiple interlinked global challenges—including biological invasions, food security, disease, and climate change—putting ecological processes firmly back on the agenda. Concurrently, conservation finance is changing rapidly, driven in part by the 2022 Kunming-Montreal Global Biodiversity Framework, which prioritized actions to enhance and restore ecosystem stability, connectivity, and resilience. These ecosystem properties are fundamentally process-driven and appear to create an operational gulf between current conservation practice and the targets of international agreements. We describe how new approaches can be used to close this gap by redirecting conservation attention toward processes at the heart of ecosystem function, including adaptation, gene flow, dispersal, and trophic interactions. Wider adoption of these approaches is urgently needed to forge a deeper connection between conservation practice and policy targets, thereby ensuring that ongoing investment in biodiversity conservation goes beyond damage limitation and instead leaves a lasting legacy of resilient ecosystems.
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Journal articleMoon Y, Lee Y, Lee HJ, et al., 2025,
Unsymmetric or hybrid detergents for membrane protein structural study
, Current Opinion in Structural Biology, Vol: 93, ISSN: 0959-440XDetergent micelles are widely used as a membrane-mimetic system for membrane protein extraction, isolation and structural study. Many recently developed detergents feature multiple tail and head groups, with architectures that are symmetric (i.e. the same alkyl chain) and non-hybrid (single head group type). Further diversification has involved incorporating structural differences in the tail groups (unsymmetric), head groups (hybrid), or both head and tail groups (unsymmetric hybrid). In this mini-review, we introduce these novel detergents, focusing on the relationships between their structural features, physical properties and performance in membrane protein applications. The detergent design strategy utilizing unsymmetric/hybrid structures expands the detergent repertoire and the detergent structure–property-efficacy relationships presented offer valuable design guidelines, collectively advancing membrane protein research.
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Journal articleNikov GI, Pretorius D, Murray JW, 2025,
SOLeNNoID: a deep learning pipeline for solenoid residue detection in protein structures
, Bioinformatics, Vol: 41, ISSN: 1367-4811Motivation: Solenoid proteins, a subset of tandem repeat proteins, have structurally distinct, modular, and elongated architectures that differentiate them from globular proteins. These proteins play essential roles in diverse biological processes, including protein binding, enzymatic catalysis, ice binding, and nucleic acid interactions. Despite their biological significance and increasing commercial applications–such as in therapeutic engineered variants like DARPins and designed PPR proteins–accurate identification and annotation of solenoid structures remain challenging. Given that solenoid structures are more conserved than their sequences, recent advances in protein structure prediction suggest that structure-based solenoid detection methods are preferable to sequence-based ones.Results: We introduce SOLeNNoID, a deep-learning-based pipeline for predicting solenoid residues in protein structures. Our method employs a convolutional neural network architecture to analyse protein distance matrices, enabling accurate identification of solenoid-containing regions. SOLeNNoID covers all three solenoid subclasses: α-, α/β-, and β-solenoids. Comparative evaluation against existing structure-based methods demonstrates the superior performance of our approach. Applying SOLeNNoID to the entire Protein Data Bank led to a 71% increase in detected solenoid-containing entries compared to the gold-standard RepeatsDB database, significantly expanding the known solenoid protein repertoire.Availability and implementation: SOLeNNoID is implemented in Python and available on github at https://github.com/gnik2018/SOLeNNoID. The source code and pre-trained models are accessible under a free-software license. Training data are available on Zenodo at https://zenodo. org/records/14927497
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Journal articlePowell HR, Islam SA, David A, et al., 2025,
Phyre2.2: a community resource for template-based protein structure prediction
, Journal of Molecular Biology, Vol: 437, ISSN: 0022-2836Template-based modelling, also known as homology modelling, is a powerful approach to predict the structure of a protein from its amino acid sequence. The approach requires one to identify a sequence similarity between the query sequence and that of a known structure as they will adopt a similar conformation, and the known structure can be used as the template for modelling the query sequence. Recently several approaches, most notably AlphaFold, have employed enhanced machine learning and have yielded accurate models irrespective of whether there is an identifiable template. Here we report Phyre2.2 which incorporates several enhancements to our widely-used template modelling portal Phyre2. The main development is facilitating a user to submit their sequence and then Phyre2.2 identifies the most suitable AlphaFold model to be used as a template. In Phyre2.2 the user searches a template library of known structures. We have now included in our library a representative structure for every protein sequence in the protein databank (PDB). In addition, there are representatives for an apo and a holo structure if they are in the PDB. The ranking of hits has been modified to highlight to the user if there are different domains spanning the sequence. Phyre2.2 continues to support batch processing where a user can submit up to 100 sequences facilitating processing of proteomes. Phyre2.2 is freely available to all users, including commercial users, at https://www.sbg.bio.ic.ac.uk/phyre2/.
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Journal articleDeng X, Carvajal DE, Urrutia-Jalabert R, et al., 2025,
Quantifying the functional composition and potential resilience hotspots across a large latitudinal and environmental gradient in South American forests
, International Journal of Applied Earth Observation and Geoinformation, Vol: 142, ISSN: 1569-8432Accurately inferring plant functional trait composition, diversity, and redundancy across space and time is pivotal for understanding environmental change impacts on forests’ biodiversity and functioning. Here, we tested the capabilities of combining in-situ and remote sensing approaches to deliver accurate estimates of functional trait composition, diversity, and redundancy of temperate forest vegetation in South America (30°S to 53°S) considering leaf and stem morphological, nutrient, hydraulic, and photosynthetic traits. We identified hydrological stress, soil properties, and topography as key drivers of plant functional trait distribution and variation. Further, hydrological stress and soil properties were key determinants of functional diversity and redundancy across a large latitudinal gradient. Functional diversity peaked across Mediterranean forests, occupying between 30°S to 35°S. Functional diversity and redundancy were both high at latitudes between 35°S and 42°S, coinciding with Valdivian rainforests. Conversely, functional redundancy peaked between 42°S and 48°S, corresponding to Austral forests. Towards the southernmost extent of the study area, functional diversity and redundancy were both low between 48°S and 53°S, corresponding to the Magellanic subpolar forests. Our results highlight areas in South American temperate forests where both plant functional diversity and redundancy were maximal, hence potentially pointing towards areas more resilient to environmental change.
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Journal articleMathews DH, Casadio R, Sternberg MJE, 2025,
Computational Resources for Molecular Biology 2025
, JOURNAL OF MOLECULAR BIOLOGY, Vol: 437, ISSN: 0022-2836 -
Journal articleNishikawa M, Tang W, Kostrzewa M, et al., 2025,
Discrimination of Klebsiella pneumoniae and Klebsiella quasipneumoniae by MALDI-TOF mass spectrometry coupled with machine learning
, MicrobiologyOpen, Vol: 14, ISSN: 2045-8827Klebsiella species, including Klebsiella pneumoniae and Klebsiella quasipneumoniae, present significant challenges in clinical microbiology due to their genetic similarity, which complicates accurate species identification using established methods, including matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) on the protein/peptide level. Although the treatment choice for infections caused by these pathogens is often similar, precise species characterization enhances our epidemiological understanding. While whole-genome sequencing can accurately distinguish Klebsiella species accurately, those analyses are time-consuming, requiring specialized expertise, and are not currently used in routine clinical laboratories. Therefore, developing a timely and accurate pathogen characterization method is essential for effective treatment, management, and infection control measures. This study combined MALDI-TOF MS in negative ion mode with machine learning techniques to identify potential lipid biomarkers as a novel method to distinguish between K. pneumoniae and K. quasipneumoniae. Using this method, we identified discriminative features between the species, with peaks at m/z 2157, m/z 1931, m/z 1964, m/z 2042, and m/z 1407 highlighted as potential biomarkers for species identification. Our findings suggest that the lipid profiles of the species obtained from MALDI-TOF MS can serve as effective biomarkers for distinguishing Klebsiella species. Further research should focus on the structural identification of these biomarkers and expand the data set to include more isolates for each of the species. This approach holds promise for developing more cost-effective and rapid diagnostic tools in clinical microbiology, ultimately improving patient outcomes and infection control.
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Journal articleStewart K, Venditti C, Carmona CP, et al., 2025,
Threat reduction must be coupled with targeted recovery programmes to conserve global bird diversity
, Nature Ecology & Evolution, Vol: 9, Pages: 1499-1511, ISSN: 2397-334XAmbitious international commitments have been made to preserve biodiversity, with the goal of preventing extinctions and maintaining ecosystem resilience, yet the efficacy of large-scale protection for preventing near-term extinctions remains unclear. Here, we used a trait-based approach to show that global actions—such as the immediate abatement of all threats across at least half of species ranges for ~10,000 bird species—will only prevent half of the projected species extinctions and functional diversity loss attributable to current and future threats in the next 100 years. Nonetheless, targeted recovery programmes prioritizing the protection of the 100 most functionally unique threatened birds could avoid 68% of projected functional diversity loss. Actions targeting ‘habitat loss and degradation’ will prevent the greatest number of species extinctions and proportion of functional diversity loss relative to other drivers of extinction, whereas control of ‘hunting and collection’ and ‘disturbance and accidental mortality’ would save fewer species but disproportionately boost functional richness. These findings show that conservation of avian diversity requires action partitioned across all drivers of decline and highlight the importance of understanding and mitigating the ecological impacts of species extinctions that are predicted to occur even under optimistic levels of conservation action.
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Journal articleMathews DH, Casadio R, Sternberg MJE, 2025,
Computational Resources for Molecular Biology 2025.
, J Mol Biol, Vol: 437 -
Journal articleDrobnic T, Cohen EJ, Calcraft T, et al., 2025,
In situ structure of a bacterial flagellar motor at subnanometre resolution reveals adaptations for increased torque (vol 10, pg 1723, 2025)
, NATURE MICROBIOLOGY, Vol: 10, Pages: 2092-2092, ISSN: 2058-5276 -
Journal articlede Campos GY, Guimaraes JG, Machado MP, et al., 2025,
Mannan-targeting chimeric antigen receptor redirected antifungal activity of NK-92 cells against<i> Candida</i><i> albicans</i>
, CYTOTHERAPY, Vol: 27, Pages: 917-932, ISSN: 1465-3249 -
Journal articleFoster JC, Pham B, Pham R, et al., 2025,
Barrel expansion of outer membrane protein G nanopore through β-hairpin duplication
, PROTEIN SCIENCE, Vol: 34, ISSN: 0961-8368 -
Journal articleGao F, Ye F, Jovanovic M, et al., 2025,
Subunit specialization in AAA+ proteins and substrate unfolding during transcription complex remodeling (vol 122, e2425868122, 2025)
, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 122, ISSN: 0027-8424 -
Journal articleRidelfi M, Vezzani G, Roscioli E, et al., 2025,
A multifunctional anti-O-Antigen human monoclonal antibody protects against<i> Shigella</i><i> sonnei</i> infection in vivo
, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 122, ISSN: 0027-8424 -
Journal articleContini C, 2025,
From light to life-like protocells
, Nature Synthesis, ISSN: 2731-0582 -
Journal articleSant DG, Smith TP, Wong ELY, et al., 2025,
Eco-evolutionary robustness of wild bacterial communities to experimental perturbation
, The ISME Journal, ISSN: 1751-7362Most knowledge about bacterial evolution and ecological interactions comes from laboratory studies. One difference between the wild and most laboratory experiments is the diversity of bacterial taxa present. Understanding how wild bacteria respond to perturbation therefore requires consideration of how ecological sorting, colonization, and genetic changes of constituent species interact. Ecological sorting of species might reduce evolutionary rates and make communities robust to disturbance, or it could amplify selection pressures and lead to unstable co-evolutionary cascades. Even estimates of basic rates of ecological sorting, dispersal, and genetic change are rare. Here, we addressed these knowledge gaps by liming wild decomposer communities living in beech tree holes and tracking ecological and evolutionary responses for 12 weeks. Overall, tree hole communities were extremely robust to liming involving short-term pulses up to 4 pH units and long-term increases up to 2 pH units. Species diversity and composition displayed significant but small changes in treatment tree holes compared to control ones. New bacterial taxa colonized at a low rate that did not vary with liming. Genetic changes in the frequency of single nucleotide polymorphisms in metagenome assembled genomes occurred at rates that were both comparable to and correlated with ecological changes in the same metagenome assembled genomes, but the rate of genetic changes did not vary between limed and control tree holes. Analysis of rates of genetic change estimated low effective population size (~104) and generation times of roughly 1 day. Our study provides estimates of rates of ecological and evolutionary processes in wild bacterial communities, which displayed remarkable robustness to our experimental perturbation.
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Journal articleOdom KJ, Araya-Salas M, Benedict L, et al., 2025,
Global incidence of female birdsong is predicted by territoriality and biparental care in songbirds
, Nature Communications, Vol: 16, ISSN: 2041-1723Pronounced sexual dimorphism is generally assumed to evolve through sexual selection for elaborate male traits. However, there is increasing evidence that sexual dimorphism in traits such as birdsong may also evolve through loss of elaboration in females, but the evolutionary drivers underlying this process are obscure. Here we analyse ecological and natural history traits for over 1300 songbird species and show that increased female song incidence and elaboration are most directly associated with year-round territoriality, biparental care, and large body size. Phylogenetic path analysis indicates that mating system and breeding latitude primarily have indirect effects on female song evolution. Stable, tropical life histories and mating systems with biparental care promote female song, whereas evolutionary transitions to migration, reduced territoriality, and loss of male care led to losses or reductions of female song incidence. Our analyses provide a comprehensive framework for studying the drivers of sex differences and similarities in birdsong and reveal novel interactions among natural history and sexual selection pressures that have been hypothesized to independently shape elaborate traits.
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Journal articleCrilly A, Malivert A, Jørgensen ACS, et al., 2025,
Ten simple rules for navigating AI in science
, PLoS Computational Biology, Vol: 21, ISSN: 1553-734X -
Journal articleShmool TA, Martin LK, Jirkas A, et al., 2025,
Design principles for engineering ionic liquid-gold nanoparticles for therapeutic delivery to the brain
, ACS Nano, Vol: 19, Pages: 24806-24816, ISSN: 1936-0851Ionic liquid (IL) nanotechnology holds significant promise for designing nanoscale materials with tunable viscosity, polarity, and thermal stability for advanced therapeutic applications. However, the field currently lacks comprehensive guidelines for integrating ILs into complex therapeutic formulations. Herein, we propose the key design considerations for engineering immunoglobulin G (IgG) conjugated to gold nanoparticles (AuNPs) in the presence of choline-based ILs. By judicious IL cation and anion selection, we fine-tune the supramolecular assemblies and leverage the unique physicochemical properties of ILs to impart AuNPs with advantageous characteristics including enhanced structural, thermal, and thermodynamic stabilities, highly tunable morphologies, and markedly reduced aggregation propensities. Through systematic circular dichroism measurements, the thermodynamic parameters of the complex formulations were determined, offering insight into the IgG conformational changes and design parameters for systems of enhanced IgG conjugation to AuNP surfaces. In demonstrating the power of our design approach, the complex formulation of IgG-choline chloride-AuNPs, also including trehalose, histidine, and arginine, was delivered via focused ultrasound and microbubbles across the blood–brain barrier and showed a 7.6-fold increase in delivery in vivo compared to the traditional formulation. We demonstrate that IgG-IL-AuNPs can be easily and precisely manipulated at the nanometer scale, enabling the formation of versatile structural configurations. Holistically, we believe the rational design approach developed will advance the engineering of tailored IL-nanocarriers for targeted therapeutic delivery and broaden the scope of IL applications in biomedicine.
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Journal articleAumann RA, Gouvi G, Gregoriou M-E, et al., 2025,
Decoding and engineering temperature-sensitive lethality in<i> Ceratitis</i><i> capitata</i> for pest control
, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 122, ISSN: 0027-8424 -
Journal articleOToole N, Allen ME, Contini C, et al., 2025,
Microfluidic generation of bacterial biohybrids for magnetic guidance and content release
, Chemical Communications, ISSN: 1359-7345Bacterial biohybrids use bacterial and synthetic components for biotechnological applications. Here, we outline an adaptable and high-throughput microfluidic platform to create microscale biocontained bacterial biohybrids enclosed in a hydrogel with magnetotactic and biosensing properties. The biohybrids are capable of magnetically driven motility, biochemical sensing and controlled cargo release. This approach enables the scalable fabrication of biocontained multifunctional biohybrids for potential industrial and biomedical applications.
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