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ACS Nano

American Chemical Society (ACS)

Preprints posted in the last 30 days, ranked by how well they match ACS Nano's content profile, based on 113 papers previously published here. The average preprint has a 0.09% match score for this journal, so anything above that is already an above-average fit.

1
Lipid nanoparticle protein coronas arise through lipoprotein fusion rather than shell-like adsorption

Grumelot, S.; Mohammed, N.; Yerima, G.; Colonrosado, J.; Sadeghi, S. A.; Fang, F.; Hilsen, K.; Shango, B.; Saei, A. A.; Murray, A. M.; Mitchell, M. J.; Borhan, B.; Sun, L.; Vali, H.; Mofrad, M.; Whitehead, K.; Mahmoudi, M.

2026-06-23 bioengineering 10.64898/2025.12.21.695162 medRxiv
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The protein corona influences the in vivo biodistribution of ionizable lipid nanoparticles (LNPs) in nucleic acid delivery, yet its structural architecture remains poorly defined. Using cryo-transmission electron microscopy, we visualized LNP-protein interactions in their native state. We show that, unlike the discrete "fuzzy" shells observed on hard nanoparticles, LNPs displayed no peripheral protein shell. Instead, controlled incubation and competitive "dual-particle" assays, supported by molecular dynamics simulations, indicate that LNP membranes undergo localized thickening and electron-dense remodeling consistent with lipoprotein integration rather than surface adsorption. Similar features were observed in extracellular vesicles, suggesting this behavior is shared among lipid-based carriers, and proteomic analysis identified apolipoproteins as the dominant associated proteins. Together, these findings support a model in which the biological identity of LNPs arises through membrane remodeling rather than shell-like adsorption, and provide a framework for the rational design of targeted nanomedicines. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/695162v2_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@5275d3org.highwire.dtl.DTLVardef@1b59ae4org.highwire.dtl.DTLVardef@1cc290eorg.highwire.dtl.DTLVardef@9b7bfb_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Clinically derived micro- and nanoplastics uptake drives spatiotemporally confined metabolic stress revealed by bond-selective imaging

Li, J.; Liu, N.; Zhang, D.; Lee, H. J.

2026-07-07 biophysics 10.64898/2026.07.02.735952 medRxiv
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Although microplastics and nanoplastics (MP/NP) are pervasive environmental contaminants, our understanding of cellular toxicity remains incomplete, as adverse effects are often attributed to long-term intracellular accumulation, while the spatiotemporal onset of cellular damage remains poorly defined. Here, we employ chemical-bond-selective stimulated Raman scattering (SRS) microscopy and cell models that decouple continuous exposure from intracellular retention to directly visualize clinically derived MP/NP-cell interactions. Cellular stress occurs primarily during MP/NP exposure, accompanied by alterations in lipid droplet (LD) composition. In contrast, following extracellular removal, intracellularly retained MP/NP become largely inert, with recovery of lipid metabolism and cellular functions. Lipidomics identifies arachidonic acid (AA) as a key dysregulated metabolite, and SRS imaging further reveals transient, spatially confined AA enrichment in MP/NP-proximal LDs during uptake. Importantly, phospholipid coating of MP/NP attenuates LD alterations and cytotoxicity while preserving particle internalization, establishing uptake-driven metabolic stress, rather than long-term intracellular retention, as primary source of MP/NP-induced damage.

3
Scalable Plasmonic Metasurface-Enabled Physics-Guided Self-Supervised Cellular Imaging

Zhang, C.; choudhury, s.; jansen, k.; balkenhol, j.; Heinze, K.

2026-06-25 biophysics 10.64898/2026.06.21.733589 medRxiv
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High-quality cellular imaging, especially in live cells, remains constrained by the trade-off among signal-to-noise ratio, phototoxicity, and instrumentation complexity. Here, we report a scalable plasmonic metasurface that generates a spatially ordered array of fluorescence-enhancing near-field hotspots and enables self-supervised denoised, cellular imaging with improved feature readability on a conventional wide-field microscope. The registered hotspot lattice serves as a physics-derived functional prior that identifies where fluorescence amplification is physically grounded and steers neural-network training accordingly, reducing reliance on paired ground truth, large external pretrained models, or extensive supervised datasets. We demonstrate two labeling-density-dependent operating regimes: dense labeling for cytoskeleton structural imaging and sparse labeling for multiplexed sensing of plasma-membrane-associated dynamics across the hotspot array. Our work unites scalable nanophotonic hardware and self-supervised computational imaging into a practical platform for structural bioimaging and on-chip live-cell biosensing under simple wide-field imaging conditions.

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Origin of Fe ions in ROS production induced in magnetic hyperthermia anti-cancer nanotherapy: release from iron oxide nanoparticles or not?

Journaux-Duclos, J.; Bejko, M.; Clerc, P.; Al Yaman, Y.; Abdelhamid, A. G. A.; Ballon, G.; Bousquet, C.; Carrey, J.; Mornet, S.; Sandre, O.; Gigoux, V.

2026-07-08 cancer biology 10.64898/2026.07.06.736751 medRxiv
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The first and critical reaction in magnetic hyperthermia to induce the death of cancer cells is the production of ROS (reactive oxygen species). We previously showed that it is possible to specifically deliver iron oxide magnetic nanoparticles (IONPs) in the lysosomes of cancer cells and eradicate them by targeted magnetic intra-lysosomal hyperthermia (MILH) via the application of a high frequency alternating magnetic field (AMF) without macroscopic temperature elevation. The mechanism involves a local temperature elevation at the IONPs surface which enhances the ROS production through the Fenton reaction; ROS then peroxide the proteins and lipids of the lysosomal membrane, inducing its permeabilization and leading to lysosomal enzymes release and cell death. Fe ions, critical to produce ROS in MILH, were assumed to be released by IONPs. We thus developed PEGylated multi-cores IONPs called NanoFlowers (NF@PEG) presenting or not a SiO2 shell (NF@SiO2@PEG), the later preventing the Fe3+ release from IONPs. NF@PEG released Fe ions and produced ROS production in vitro, in acidic medium mimicking lysosome upon AMF exposure, whereas NF@SiO2@PEG did not. Surprisingly, both nanoparticles increased the ROS production in cells, induced lysosome permeabilization and cell death, and slowed down the proliferation of cancer cells with the same efficacy, upon AMF application, indicating that MILH was efficient in absence of Fe3+ release from IONPs. In contrast, Ferristatin-II, an iron uptake inhibitor, prevented the ROS production and cell death in MILH induced by both IONPs, elucidating the role of endogenous iron cations responsible for the ROS production ROS in MILH to kill cancer cells.

5
A generalizable codesigned platform for solid-state nanopore sensing beyond the capacitive-noise constraints

Cai, N.; Guo, W.; Teng, Y.; Lou, Y.; Wong, S.-H.; Naidu, A. S.; Cona, F.; Thei, F.; Chen, T.-H.; Bastings, M.; Radenovic, A.

2026-07-09 biophysics 10.64898/2026.07.06.731876 medRxiv
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Solid-state nanopores offer label-free, real-time single-molecule sensing. However, resolving fast biomolecular transport requires high-bandwidth data acquisition while the intrinsic high-frequency noise limits recovery of informative events. Here we present a hardware-software co-designed nanopore sensing platform that combines wafer-scale low-noise device engineering with deep learning-based signal reconstruction. A low-dielectric SU8 coating on silicon nitride nanopores reduces device capacitance to the pF range and suppresses high-frequency noise by up to 5-fold while maintaining facile, controllable and reproducible fabrication. This extends usable acquisition to 40 MHz and enables capture of fast molecular features. Coupled with a reconstruction model trained on synthetic translocation events embedded in experimentally measured noise, the platform recovers transient sublevels while preserving blockage edges and temporal fidelity. Using engineered DNA molecules carrying dumbbell-like barcodes, we resolve nanometer-scale structural spacings on sub-microsecond timescales, and experimentally quantify translocation dynamics within the sub-10 nanometer regime. Dual-channel measurement on a single nanopore device further demonstrates transferability of the platform by showing robust cross-channel signal reconstruction across distinct baseline noise levels. Our approach provides a general route for reliable recovery of fast event features and may enable more information-rich single-molecule sensing across diverse biomolecular targets.

6
Anisotropic Thermal Conductivity in Topologically Networked Protein-MXene Composites

Demirel, M.; Hopkins, P.; Vural, M.; Jung, H.; Tomko, J.

2026-07-13 bioengineering 10.64898/2026.07.10.737764 medRxiv
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Governing thermal transport in engineered materials creates opportunities to redirect and recover the excess heat generated in electronic and energy-conversion devices. Materials that pair low cross-plane thermal conductivity with high in-plane thermal conductivity are particularly valuable because they confine heat and channel it away from sensitive regions, preventing localized device failure. Two-dimensional crystals are efficient building blocks for such anisotropic thermal conductors, but they are brittle, and the polymer composites used to toughen them usually forfeit much of the intrinsic anisotropy: in conventional percolation-based design, filler fraction is the only handle available, and it governs both in-plane and cross-plane conduction. Here we report a composite of Ti3C2Tx (MXene) nanosheets and squid ring teeth (SRT) inspired recombinant tandem-repeat (TR) proteins in which the protein serves as a molecular template and bridge, setting the spacing between nanosheets with angstrom-level precision through the number of tandem-repeat units and independently of the filler fraction. This structural handle provides a second, independent design parameter. At a fixed MXene loading, the number of repeats tunes the cross-plane conductivity (0.30 to 0.93 W/mK) and, with it, the thermal anisotropy ratio over a wide range (from about 70 down to 17), while the in-plane conductivity stays high (16 to 21 W/mK). We rationalize these trends with a Gaussian Network Model (GNM) of the protein embedded in a two-phase layered medium, which reproduces the measured directional conductivities from a single structural parameter and identifies the protein gallery as the cross-plane bottleneck. Extending the model to a mechanically loaded five-period stack, we find that the anisotropy is robust to reversible compression and twist, changing by only a few percent, so the number of tandem repeats, not the applied strain, is the dominant design handle. Because anisotropy is tuned structurally rather than volumetrically, these protein-MXene composites decouple thermal anisotropy from filler content, pointing toward flexible thermal materials that are not bound by the rules of mixture and percolation.

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In Vitro Detection of Breast Cancer Cell Types Using Machine Learning-Assisted Spectral Fingerprinting of SWCNTs

Rahmani, M.; Van Gorden, K.; Peyton, S. R.; Roxbury, D.

2026-07-01 bioengineering 10.64898/2026.06.30.735651 medRxiv
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The early detection of breast cancer currently relies on expensive mammography, followed by pathology that uses biopsied, fixed, and immunohistochemically stained tissues. A live-cell detection approach could be highly beneficial as a supportive diagnostic and research tool to better understand and resolve the dynamic nature of breast cancer cells and their response to treatment in real time. Here, we present a single-walled carbon nanotube (SWCNT) near-infrared fluorescence spectral fingerprinting approach combined with machine learning to precisely detect the heterogeneity of breast cancer cells in live culture. We introduced DNA-functionalized SWCNTs to MCF-10A (a non-tumorigenic healthy control) and cancer cell lines spanning known extrinsic disease subtypes: MCF-7 (luminal A), HCC1954 (HER2+), MDA-MB-231, and MDA-MB-468 (both triple-negative). The NIR fluorescence spectra of DNA-SWCNTs across 600 individual cells within each type showed significant differences in emission peak intensities, center wavelengths, and peak intensity ratios, attributable to variations in cellular uptake and biomolecular interactions. These spectral changes likely arise from complex SWCNT cellular interaction fingerprint that includes redox-mediated modulation of the local nanotube environment, rather than from a single biomarker response. The extracted spectral features were used to train an ensemble machine learning model. The model achieved 98% classification accuracy for breast cancer detection and 95% classification accuracy for breast cancer cell subtyping. Moreover, Raman microscopy further showed that MDA-MB-468 cells exhibited the highest SWCNT uptake, whereas MCF-10A cells showed greater SWCNT aggregation, consistent with their lower broadband NIR fluorescence intensity. These results demonstrate that SWCNT NIR fluorescence fingerprints can capture cell line-specific optical signatures. This platform provides a foundation for nanomaterial-enabled biosensing strategies aimed at real-time monitoring of cancer-associated cellular states.

8
High-Density Wild-Type IL-2 Nanoparticles Preferentially Enhance CD8⁺ T-Cell Expansion and Reprogram the Tumor Microenvironment

Wang, R.; Kumar, P.; Crumrine, N. A.; Watcharawittayakul, T.; Wallstrum, A.; Reda, M.; Mills, G. B.; Ngamcherdtrakul, W.; Yantasee, W.

2026-07-15 bioengineering 10.64898/2026.07.14.738558 medRxiv
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Low response rates to immune checkpoint inhibitors (ICIs) in solid tumors are often driven by insufficient tumor-infiltrating CD8 T cells and immunosuppressive tumor microenvironment (TME). Although interleukin-2 (IL-2) potently expands and activates CD8 T cells, its clinical use is limited by rapid clearance, dose-limiting toxicity, and regulatory T cell (Treg) stimulation. Engineered IL-2 variants have not yet achieved meaningful clinical efficacy. Here, polymer-modified mesoporous silica nanoparticles displaying dense, unmodified wild-type IL-2 on their surface (IL2-NP) are developed, conferring proteolytic stability and tumor retention. IL2-NP enables avidity-mediated CD8 T cell binding and enhances proliferation and effector function without increased Treg binding or proliferation. Intratumoral IL2-NP expands CD8 T cells, increases CD8/Treg ratios, and reprograms TME through dendritic cell activation and M1-like macrophage polarization. IL2-NP induces regression of both treated and untreated distant colorectal tumors in a CD8 T cell-dependent manner. IL2-NP synergizes with ICIs and leads to complete tumor regression and immunological memory that protect against rechallenge. Treatment is well tolerated, with strong efficacy also observed in triple-negative breast and metastatic ovarian cancer models. Overall, intratumoral IL2-NP elicits robust systemic antitumor immunity, offering a promising strategy to enhance ICIs, cancer vaccines, and adoptive T-cell therapies. Graphical abstractThis work introduces a nanoparticle platform that overcomes major shortcomings of IL-2 immunotherapy by presenting wild-type IL-2 at high density on the nanoparticle surface, thereby increasing binding avidity to effector T cells. The resulting IL-2 nanoparticles enhance cytotoxic T cell expansion, reprogram the tumor microenvironment, and augment responses to immune checkpoint blockade to achieve robust ant-tumor immune response in mouse tumor models. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/738558v1_ufig1.gif" ALT="Figure 1"> View larger version (82K): org.highwire.dtl.DTLVardef@12f8c8corg.highwire.dtl.DTLVardef@b46b1forg.highwire.dtl.DTLVardef@e4efc5org.highwire.dtl.DTLVardef@3993e6_HPS_FORMAT_FIGEXP M_FIG C_FIG

9
Dynamically actuated reconfigurable topographical surface enables active control of implant-associated infections

Asadi Tokmedash, M.; Lee, J.; VanEpps, J. S.; Nam, S.; Min, J.

2026-07-01 bioengineering 10.64898/2026.06.29.735318 medRxiv
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Implant-associated infections are driven by bacterial biofilm formation and remain difficult to eradicate using conventional antibiotic-based strategies. Here, we present a dynamically actuated reconfigurable topographical surface (DARTS) that integrates intrinsically bactericidal nanoscale surface topography with programmable mechanical actuation to achieve durable, antibiotic-free infection control. Using a scalable bottom-up nanofabrication strategy, we generate tunable wrinkled MXene topographies that exhibit contact-mediated bactericidal activity against both Gram-positive and Gram-negative bacteria without chemical leaching. Integration with a soft robotic actuator enables reversible modulation of surface geometry, which synergistically enhances bacterial removal and killing, resulting in near-complete disruption of mature biofilms. Dynamic actuation further sensitizes released bacteria to antibiotic treatment. In a mouse subcutaneous implant infection model, DARTS with actuation achieves sustained suppression of bacterial burden and markedly improves host tissue outcomes. Remote, noninvasive actuation using near-infrared laser stimulation further highlights the translational potential of this platform for implantable antibacterial applications.

10
Extracellular injection system combined with peptides for intracellular Staphylococcus aureus treatment

Feng, L.; Qiao, Y.; Xu, H.; Wang, G.; Ren, S.; Ouyang, X.; Song, N.; Zhao, X.; Feng, X.

2026-07-10 synthetic biology 10.64898/2026.07.06.736670 medRxiv
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The inaccessibility of intracellular bacteria has long rendered the treatment of Staphylococcus aureus infections an challenge. Studies have demonstrated that the extracellular injection system PVC can accurately deliver proteins into cells, which would not need small molecules, and enables effective intracellular delivery of antimicrobial peptides for treatment. Accordingly, we selected antimicrobial peptides including Cecropin, LL37 and Indolicidin that possess potent bactericidal activity, and established the Directed Antimicrobial Assault platform (DAAT) by leveraging the intracellular delivery capacity of PVC. DAAT Cecropin, DAAT LL37 and DAAT Indolicidin inhibited intracellular bacteria in a dose-dependent manner, with DAAT LL37 reaching 86.76% inhibition; after 72 h of treatment, viable-cell numbers reduse to 66--82-fold those of the control. Tail-fibre retargeting enabled direct extracellular S. aureus killing, while combined DAAT therapy promoted wound healing in mice. These findings expand the utility of PVC-derived nanosyringes and establish DAAT as a modular platform for intracellular antimicrobial peptide therapy.

11
DNA: A Nanoscale Archimedes Screw

Mleziva, X.; Maffeo, C.; Aksimentiev, A.

2026-06-30 biophysics 10.64898/2026.06.25.734429 medRxiv
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Rotating helices have been utilized for many purposes, including the transport of solid material and fluids within man-made machines, for a little over two millennia. Here, we show that the rotation of a biological helical molecule--a DNA duplex--can move water and ions through a nanoscale pore. While the rotation-induced flow of water is generated by the steric shape of the DNA molecule, an even faster transport of cations is caused by electrostatic interactions. The rotation-induced ion flux is found to depend on the cation type, offering potential utility for ion separation. Finally, we show that the torque-driven duplex can move ions against a concentration gradient, realizing the Archimedes screw principle at the nanoscale.

12
Emergence of large-scale polar microtubule swarms for dense molecular transport

Zaferani, M.; Wingreen, N. S.; Stone, H. A.; Petry, S.

2026-07-08 biophysics 10.64898/2026.07.06.736790 medRxiv
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Microtubules (MTs) and their motor proteins collectively harness chemical energy to generate mechanical work, driving some of the most coordinated self-organized dynamics in living cells. The unique properties of these molecules also make them versatile building blocks of cytoskeletal active matter and biomimetic nanomachines that recapitulate cellular motility, emergent pattern formation, and motor-driven transport. However, these canonical systems use MTs of fixed length and do not incorporate the natural ability of MTs to grow and regenerate. Here, we go beyond these limits by using dynamic self-amplifying branched MT networks. Driven by kinesin-1 and cytoplasmic dynein activity, surface-gliding branched MT bundles undergo swarming that yields large-scale collective MT architectures with several sought-after features. They are polar and orientationally aligned, dense, span millimeter scales, and persist over hours. We then show that these features enable molecular transport along the swarm at unprecedented capacities, with up to six million motor complexes walking in parallel across millimeter-scale distances over hours. Our results introduce a new regime in cytoskeletal active matter in which the interplay between motor-driven activity and filament generation via branching leads to emergent polar order in proliferating swarms. Such emergent polarity makes these swarms suitable for engineering scalable transport nanotechnologies and programmable soft materials.

13
Long-term single-particle tracking by NIR imaging using Au42 (gold) quantum needles

Yagi, S.; Takano, S.; Nishiyama, R.; Oketani, R.; Tsukuda, T.; Hiramatsu, K.

2026-06-30 biophysics 10.64898/2026.06.24.734378 medRxiv
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Single-particle tracking (SPT) over time enables direct observation of molecular transport and interactions in living cells. Fluorescence-based SPT has provided insights into intracellular processes such as endocytosis, receptor signaling, and drug delivery. Extending the observation window to several hours and beyond is critical for capturing slow intracellular dynamics, including the full course of endosomal trafficking, the long-term accumulation of particles within subcellular compartments, and transitions between transport modes that occur on hour-scale timescales. However, long-term intracellular SPT under visible-wavelength excitation remains challenging because fluorescence probes generally suffer from photobleaching and phototoxicity. While near-infrared (NIR) excitation can simultaneously mitigate these issues, generally weak emission of NIR-emitting dyes has hindered its wide application in long-term SPT. Here, we demonstrate long-term NIR SPT using atomically precise gold quantum needles, Au42(PET)32 (PET = 2-phenylethanethiolate). Continuous tracking of intracellular particles in living HEK293 cells was achieved for up to 12 h. Trajectory analysis revealed temporal transitions between directional and diffusive transport, as well as the accumulation of multiple particles within localized intracellular domains over several-hour timescales. The high photostability of Au42, combined with low phototoxicity of NIR excitation, enables visualization of intracellular transport dynamics over timescales difficult to access using conventional visible fluorescent probes. These results establish Au42-based NIR imaging as a platform for long-term, low-phototoxicity intracellular SPT and provide a framework for investigating slow intracellular dynamics in living systems.

14
A Bottom-Up Platform for Quantitative Single-Molecule Tracking Through Bacterial Biofilm Mimics

Shepherd, J. W.; Howard, J. A. L.

2026-07-04 biophysics 10.64898/2026.07.02.736016 medRxiv
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Chronic infections persist in large part thanks to protection that biofilms afford their bacterial creators. The extracellular polymeric substance of biofilms is a hydrated matrix of DNA, polysaccharides, and structural proteins, amongst other components, through which nutrients, signalling molecules, and antimicrobial agents must diffuse to reach the bacteria within. Quantitative measurement of transport on the nanoscale within in vivo biofilms remains challenging due to optical heterogeneity, autofluorescence, active remodelling of biofilms and the ambiguity in trajectory reconstruction during single-particle tracking (SPT). Here, we present a methodological framework for measuring molecular transport in defined minimal extracellular matrix models using quantum dots as fluorescent nanoscale probes imaged with high-speed SlimVar microscopy. To establish conditions in which high-diffusivity particle trajectories can be reliably reconstructed, upper limits to quantum dot concentrations were estimated from Brownian motion. The 99th-percentile inter-frame jump distance was estimated from the three-dimensional Brownian jump distance distribution and used to define a target average nearest neighbour distance, and therefore a per-particle volume, used for calculating a concentration which minimises the probability of trajectory collision during data acquisition. Quantum dot movement was imaged at sub-millisecond frame rates and diffusion coefficients were calculated in a 20% glycerol control and in DNA nanostar hydrogels modelling minimal extracellular matrix scaffolds assembled at 250 M and 500 M. Median diffusion coefficients decreased from 94.9 m2*s-1 in glycerol to 15.9 m2*s-1 and 8.3 m2*s-1 in the 250 M and 500 M hydrogels, respectively. More broadly, this work establishes a workflow for quantitative SPT in minimal biofilm models. Rather than attempting to reproduce the full biological complexity of native biofilms, this approach provides the basis of a modular experimental framework in which individual extracellular matrix components can be incorporated sequentially and their effects on molecular transport quantified.

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Transcription-induced coacervation accelerates and sensitizes cell-free biosensing

Feng, S.; Rasmussen, R.; Garcia, A.; Clark, L.; Srivastava, S.; Lucks, J. B.

2026-07-10 synthetic biology 10.64898/2026.07.02.736143 medRxiv
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Cell-free biosensors leverage in vitro gene expression reactions to detect chemicals. While inexpensive, modular, and distributable, these platforms are constrained by slow readouts at ambient temperatures, precluding practical field operation. In cells, phase separation accelerates biochemical reactions; however, recapitulating these gains in vitro has remained challenging for complex biochemistries. Here, we report the first self-assembling coacervate system that accelerates in vitro transcription. Prepared by simple mixing, coacervation with spermine and polyacrylic acid occurs dynamically in response to NTP consumption and co-localizes DNA templates and RNA polymerase to accelerate transcription, mimicking intracellular phenomena. We exploit this discovery to accelerate the cell-free biosensing of six ligands, demonstrating that coacervation can preserve platform modularity, improve sensitivity, retain lyophilization compatibility, function in field matrices, and reduce ambient-temperature time-to-signal by hours. This work contributes to a growing understanding of phase separation in biology and advances the use of membrane-less organization for real-world applications.

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Chronic Polystyrene Nanoplastics Exposure Reprograms Gene Expression, Alternative Splicing, and Disrupts Host Microbiome Metabolic Networks to Promote Atherosclerosis in LDLr- Knockout Mice

Khan, A.; Cardenas Vasquez, D. E.; Si, Y.; S. Vidar, W.; Wu, K.; Chiu, N.; Jia, Z.

2026-07-10 molecular biology 10.64898/2026.07.09.736446 medRxiv
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Although micro- and nanoplastics have been detected in human atherosclerotic plaques, their mechanistic contribution to disease pathogenesis remains poorly defined. Most experimental studies have used microplastics (particles > 1 micrometer) in non-atherosclerotic animal models or the ApoE KO; mouse, relying on short-term exposure or single-pathway analyses, whereas the chronic cardiovascular effects of nanoplastics (< 100 nm) remain exceedingly scarce, despite their higher biological reactivity and greater tissue penetrance. To address this gap, this study employs a multi-omics approach to investigate the chronic (12-week) oral exposure to 80 nm polystyrene nanoplastics in LDLr KO; mice. We uniquely integrate aortic plaque quantification, hepatic transcriptomics with global alternative splicing profiling, gut microbiome 16S sequencing, and liver untargeted metabolomics to construct a unified host-microbiome-metabolite network. Nanoplastics exposure significantly exacerbates aortic lipid deposition, suppresses hepatic detoxification and anti-atherogenic lipid pathways primarily through transcriptional and post-transcriptional level changes driven by alternative splicing events (e.g., intron retention and isoform switching), and induces gut dysbiosis marked by a reduction in SCFA-producing commensals and enrichment of pro-atherogenic pathobionts-perturbations that correlate with specific hepatic functional modules. Metabolomic changes, including decreased levels of the glutathione precursor gamma-glutamylcysteine and the choline-derived metabolite neurine, implicate oxidative stress and TMAO-related pathways. Cross-species validation using human atherosclerotic transcriptomic and metagenomic datasets supports the clinical translatability. By integrating multi-level biological responses, this work establishes nanoplastics as an environmental cardiovascular risk factor and uncovers novel regulatory mechanisms involving splicing-associated transcriptional reprogramming and gut-liver crosstalk, offering potential early-warning biomarkers and therapeutic targets for nanoplastics-associated cardiovascular disease.

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Modular split-trigger based cooperative activation platform for Cas13-12 tandem biosensing system

Sang, R.;Goldys, E.;Deng, F.

2026-06-27 Molecular Biology 10.64898/2026.06.26.734747 medRxiv
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Achieving precise control of CRISPR/Cas trans-cleavage depends on understanding how nucleic acid activators engage Cas effectors, yet the fundamental principles of split-trigger activation of Cas12a remain unclear. Here, we uncover the mechanistic determinants that enable fragmented nucleic acids to collectively initiate Cas12a activity. We show that split triggers bearing external extensions fully support the R-loop formation, whereas internal extensions which disrupt the spacer complementarity abolish Csa12a activation. We further demonstrate that covalent linkage of split-trigger fragments prevents R-loop propagation, revealing that Cas12as activation strictly requires two physically independent split fragments. Together, these findings establish a synergistic split-trigger activation mechanism in which cooperative hybridization of two individually fragments nucleates and extends the Cas12a R-loop with high efficiency. Conceptually, this mechanism enables a cascade architecture that transforms CRISPR diagnostics from a one-target one-Cas ribonucleoprotein (RNP) paradigm into a highly amplifying process in which a single target molecule activates numerous downstream Cas RNPs. Building on this principle, we show that the cleavage of a rationally designed linear DNA-RNA-DNA mediator by LbuCas13a generates optimally configured split triggers for Cas12a activation, thereby coupling RNA recognition to large-scale Cas12a activation without enzymatic preamplification. The resulting Split Trigger Activated Cas13-Cas12 Cascade System (STACS) achieves amplification-free detection down to 1 copy/{micro}L within 15 minutes and maintains robust performance in complex biological (serum, saliva) and environmental (mud) matrices. This work establishes a generalizable strategy for engineering programmable CRISPR cascades with high Cas RNP activation multiplicity for ultrasensitive molecular diagnostics. Graphic abstract.Mechanism and detection workflow of the Split Trigger Activated Cas13-12 Cascade System (STACS). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/734747v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1407364org.highwire.dtl.DTLVardef@57d5f5org.highwire.dtl.DTLVardef@a00693org.highwire.dtl.DTLVardef@fab93_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Nanoarchaeosome-mediated epirubicin delivery induces sustained intracellular stress and suppresses adaptive glioblastoma phentoypes

Gopalakrishnan, A. S.; Ariraman, S.; Ganguli, S.; Hitesh, A.; Mohammad, S.; B, M.; Sudhakar, S.; Chavali, P. L.

2026-07-10 cancer biology 10.64898/2026.07.06.736470 medRxiv
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Although anthracyclines such as epirubicin are potent DNA-damaging agents, their application in glioblastoma (GBM) is limited by poor intracellular penetration, lack of durable responses and rapid emergence of adaptive tumor phenotypes. Here, we demonstrate that nanoarchaeosome-mediated delivery of epirubicin (NanoEpi) enables functional reprogramming of GBM survival under therapeutic stress. Nanoarchaeosomes composed of archaeal ether lipids exhibited high encapsulation efficiency ([~]96%) and nanoscale stability. Although both Epi and NanoEpi showed similar bulk uptake, both in established (U251-MG) and patient-derived (Gli5) glioblastoma models, NanoEpi induced significantly greater cytotoxicity than free epirubicin, indicating enhanced intracellular drug engagement. NanoEpi induced enhanced DNA damage, elevated reactive oxygen species, and mitochondrial depolarisation, leading to cytoskeletal collapse. In 3D gliomasphere systems, NanoEpi showed improved penetration and sustained retention, resulting in suppression of core viability and invasion. This correlates with its increased uptake by the lysosomes. Notably, even a transient exposure led to depletion of sphere-initiating capacity and complete loss of clonogenic recovery, indicating targeting of the stem-like compartment. This was accompanied by attenuation of MMP-2/9 activity and reduced angiogenic signalling in a chorioallantoic membrane model. These findings establish nanoarchaeosomes as a robust lysosome-directed delivery platform that extends beyond passive drug transport to sustain intracellular stress and suppress invasive adaptation and limit recurrence in GBM.

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A Protease-Cleavable iNOS-Inhibitor Polymeric Prodrug Designed for Controlled Modulation of Nitric Oxide

Alimoradi, H.; Panahpour, A.; Fallah, A.; Delporte, C.

2026-06-29 pharmacology and toxicology 10.64898/2026.06.23.733308 medRxiv
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Inducible nitric oxide synthase (iNOS) is frequently overexpressed in inflammatory disorders and solid tumors, where sustained nitric oxide (NO) production promotes angiogenesis, tumor progression, and resistance to therapy. Despite promising preclinical results, the clinical translation of iNOS inhibitors remains limited by poor tumor selectivity, rapid systemic clearance, and off-target toxicities. To address these challenges, we developed a protease-responsive polymeric iNOS-inhibiting prodrug (ProCIP) designed for localized activation within protease-rich pathological microenvironments. ProCIP was synthesized from poly(ethylene glycol)-poly(L-glutamate) and functionalized with amidine-based iNOS inhibitory moieties. The resulting cationic polymer readily formed nanoscale polyionic complexes with anionic polymers or molecules. In cell-free assays, enzymatic activation of ProCIP resulted in a significant reduction in iNOS activity, whereas non-activated nanoparticles showed minimal inhibition. Cellular studies confirmed efficient nanoparticle uptake by RAW264.7 macrophages and revealed a significant reduction in intracellular NO levels in lipopolysaccharide-stimulated cells. These findings demonstrate that ProCIP enables protease-triggered iNOS inhibition and localized NO regulation, offering a promising strategy for improving the safety and efficacy of iNOS-targeted therapies in cancer and other inflammatory diseases.

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Critical reassessment of lipophilic dye labeling reveals negligible incorporation into small extracellular vesicles derived form serum-free cultured cells

Ji, Y.; Ji, Q.; Ji, J.; Shentu, Y.; Zhou, l.; Wu, J.; Shao, Q.; Xu, W.; Zhang, C.; Shen, M.; Xie, Q.

2026-07-08 bioengineering 10.64898/2026.07.04.722344 medRxiv
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Lipophilic dyes are widely used to track extracellular vesicles (EVs), yet their labeling efficiency toward bona fide small EVs (sEVs) remains poorly defined. Here, we critically reassess this efficiency using a serum-free HEK293F system that generates endogenously fluorescent protein-tagged sEVs (sEVs-FPT) as an unambiguous positive reference, thereby minimizing interference from co-isolated, dye-labelable non-vesicular extracellular particles (NVEPs). Two orthogonal methods, nanoflow cytometry and fluorescence microscopy, were employed for cross-validation. We found that PKH26, PKH67, and DiD labeled <0.5% of sEVs-FPT, regardless of vesicle heterogeneity. In vivo tracking confirmed that dye-derived signals were far weaker than FPT signals and strikingly failed to colocalize with them. Preliminary mechanistic evidence indicates that this failure is due to an inability of sEVs to actively internalize dye aggregates. Our findings raise serious concerns about the validity of lipophilic dye-based EV tracking and call for a critical reevaluation of the relevant literature.