New papers on Bioengineering
76 new papers on bioengineering in the last 7 days, within Biology. These are the 50 Pipette rates most worth reading, with the main result in the authors' own words.
The best of the week
Generative Neuromorphic Programming of Mammalian Cells
Here we establish generative programming of mammalian cells through a neuromorphic framework that compiles desired behavior into DNA.
PreprintClaims a big stepAn in-body networking system for communication between wearable and implantable therapeutics
In vivo in rats, we demonstrate coordinated, full-body networks of sensors and neural interfaces that enable wireless dual-limb motor control.
Peer-reviewed journalBold claims, read criticallyClaims a big stepReal-world useOptically addressable and programmable spins in DNA
Here, we show that DNA can serve as a functional nanoscale scaffold for optically addressable spin systems.
PreprintBold claims, read criticallyReal-world useExo-LAMP: A Rapid Extraction-Free Isothermal Assay for Exosomal mRNA Detection
Here, we report Exo-LAMP, an extraction-free isothermal assay for detecting placental exosomal KISS1 mRNA, representing the first isothermal approach for exosomal mRNA detection.
PreprintClaims a big stepReal-world useFiberPro 1.0: Multiagent AI-Guided Design for High-Throughput Production and Conformal Deposition of Functional Protein Micro/Nanofibers
Here, we report FiberPro 1.0, a large language model driven multi agent framework that unites high-throughput spinning with real-time experimental feedback for autonomous design, execution, and optimization.
PreprintBold claims, read criticallyReal-world useCascaded Nano-ring Dialyzer for Continuous Regenerative Peritoneal Dialysis
These results demonstrate that cascaded nano-ring enables continuous dialysate regeneration with scalable throughput, reduced dependence on fresh dialysate, and in vivo control of uremic toxins, providing a technological foundation for portable or wearable regenerative peritoneal dialysis systems.
PreprintBold claims, read criticallyReal-world useSilicon exaptation discovers antimicrobial peptides
We systematically evaluated the antimicrobial potential of these peptides using broth microdilution assays and membrane integrity tests, identifying several candidates with potent and selective antibacterial activity without detectable cytotoxicity toward mammalian cells.
PreprintReal-world useControlling membrane tension by dynamic DNA nanorings
To bridge this technological gap, we present reconfigurable DNA origami rings for dynamically controlling membrane tension of sub-100 nm liposomes.
PreprintReal-world useBreaking Pore Symmetry to Prolong DNA Residence in Solid-State Nanopores
Here we show that breaking pore symmetry through geometric inclination produces exceptionally prolonged DNA residence without surface functionalization or external trapping.
PreprintReal-world useThe hydrocup: a hollow electrospun scaffold for in vivo hydrogel-laden cell delivery
These results demonstrate that the hydrocup is the first, to our knowledge, cell-laden hydrogel delivery scaffold.
PreprintBold claims, read criticallyClaims a big stepReal-world useAI-Guided Multi-Objective Engineering of Glucoamylase Enables Acidification-Free Starch Saccharification
Here, we developed an artificial intelligence-guided strategy to simultaneously improve the thermostability, pH tolerance, and catalytic activity of glucoamylase from Penicillium oxalicum (PoGA).
PreprintReal-world useA phage DUF669 protein mediates post-cleavage DNA repair against host CRISPR immunity
Here, we report a phage-encoded two-protein system, termed Healer, which neutralizes CRISPR immunity via a post-cleavage DNA repair mechanism.
Peer-reviewed journalBold claims, read criticallyReal-world useBRIDGE: A broad-host platform for interkingdom DNA delivery enabling the genetic domestication of phylogenetically diverse yeasts
Here, we present BRIDGE (Bacteria-to-yeast Rapid Interkingdom DNA Gene Exchange), an integrated synthetic biology platform for broad-host interkingdom DNA delivery.
PreprintReal-world useNanobody-Functionalized AAV achieves Promoter-independent Neuronal Targeting in the CNS
Together, these results establish nanobody-functionalized AAV-DJ as a modular, single-component platform for precision CNS gene delivery that circumvents the packaging and expression trade-offs of promoter-based cell-type restriction, with potential for retargeting to additional CNS cell types and disease-relevant receptors.
PreprintReal-world useAcoustically patterned hepatic lobule-like units for vascularized artificial liver
Here, we present an ultrasonic standing wave (USW)-based strategy that concurrently organizes vascular and parenchymal compartments during a single extrusion.
PreprintReal-world useA Dynamically Regulated Designed IL-2 for Tumor-localized Signaling
Here we designed a regulated IL-2 module, OUTSMART designed IL-2 (dIL-2), that functions robustly in solid tumors and reduces systemic activity that could trigger toxicity: we computationally redesigned IL-2 to have a novel topology that increases stability, preserves native IL-2R{beta}{gamma} interfaces, ablates IL-2R binding, and delivers IL-2 signaling to CD8+ immune-effector cells.
PreprintBold claims, read criticallyReal-world useA Rationally Designed Transgene Drives CAR T Functional Persistence and Durable Regression of Solid Tumors
Ultimately, this work demonstrates that intrinsic T cell dysfunction and extrinsic tumor-derived barriers can be simultaneously overcome by integrating synergistic technologies.
PreprintBold claims, read criticallyReal-world useSpecific and efficient translation inhibition–transcription activation resistance module against viruses in plants
Here, we constructed a virus-activated synthetic immune circuit, wherein viral sgRNA production drives host defense responses via a translation inhibition–transcription activation (TI-TA) module.
Peer-reviewed journalBold claims, read criticallyReal-world useDe novo design of protease-activatable cytokine prodrugs
Here we describe a de novo protein design strategy for generating protease-activatable cytokine prodrugs that overcomes these challenges.
PreprintReal-world usePROXINAUT: An Automation Platform for Rapid Hit-to-Degrader Discovery
Here, we report PROXINAUT, an end-to-end workflow integrating self-encoded library-based hit discovery with an automated parallel solid-phase synthesis platform to streamline hit discovery, validation, optimization, and degrader development.
PreprintReal-world useMetabolic engineering of Salmonella enterica for coupled kynurenine sensing and depletion enhances antitumor efficacy
Tumor-targeting Salmonella enterica strains were engineered to deplete the intratumoral immunosuppressive kynurenine, triggering metabolic rewiring and fostering an active antitumor immune microenvironment.
PreprintReal-world useMultimodal Sensitivity Enhancement of Binding-based Diagnostic Assays Using Functional Hydrogels
Here, we present a universal strategy for hydrogel integration into immunoassay platforms for enhanced optical and electronic biosensing.
PreprintBold claims, read criticallyReal-world useCharge-screening dominates signal transduction in electrochemical nucleic acid sensors for aminoglycosides
Here, using a suite of interfacial electrochemical and optical characterization methods, we systematically show that charge-screening, not structure switching, dominates the signaling mechanism in the case of the aminoglycoside EAB sensor.
PreprintGeometry-dependent mRNA delivery with programmable RNA-DNA nanostructures
Here, we develop a modular RNA-DNA hybrid nanoplatform that enables controlled investigation of geometry-dependent mRNA delivery.
PreprintReal-world useModeling lung adenocarcinoma using layer-by-layer nanoparticles mitigates innate immune cell activation
Here, we develop a layer-by-layer (LbL) polyplex platform using poly({beta}-aminoester) (PBAE) polymers layered with poly-L-aspartic acid (PLD) to deliver Cre mRNA to lungs while avoiding immune cell transfection and activation.
PreprintGenomic Engineering of Gene Dosage: A Generalizable Framework for Modeling Haploinsufficiency-Mediated Human Disorders through Splicing Modulation
Here, we present a generalizable framework to modulate gene dosage by alternative splicing via genome editing.
PreprintBold claims, read criticallyBoolean Logic-responsive FRET Biosensors via Genetically Encoded Autonomous Compilation
In this work, we introduce a generalizable strategy to construct genetically encoded protein-based FRET biosensors capable of recognizing multiple inputs following Boolean logic-type (YES/OR/AND) operations.
PreprintBold claims, read criticallyCytosMPS: an automated multimodal pooled screening platform for protein, morphology and transcriptomics
Cytos Multimodal Pooled Screening (CytosMPS) measures CRISPR guide identity, morphology, native 3' transcriptome, and protein abundance and localization in the same fixed cells.
PreprintaaRSID, an engineered pyrrolysyl-tRNA synthetase platform for multi-probe proximity proteomics
Our work establishes aminoacyl-tRNA synthetases as a new PL enzyme class and introduces a versatile chemical platform for developing ncAA-derived probes to map cellular microenvironments, greatly expanding the applications possible of PL technology.
PreprintBold claims, read criticallyLow-Noise Finite-Bandgap FET Biosensors in the Nonlinear Gouy-Chapman-Stern Region: A Universal Calibration Curve
Using a fully nonlinear Gouy-Chapman-Stern (GCS) theory, a universal calibration curve is derived and shown to collapse the low-noise FET signals for miRNA, extracellular vesicles (EV), and protein, captured either directly or through silica and magnetic nanoparticle charge reporters, over eleven decades of analyte concentration.
PreprintBold claims, read criticallyReal-world useMegascale recombination generates millions of catalytically competent PETases
Together, these results demonstrate that large-scale recombination can generate millions of diverse and catalytically competent enzymes while remaining compatible with modern high-throughput screening workflows.
PreprintBold claims, read criticallySpatiotemporal Control of Genetic and Epigenetic Editing through Covalent Tethering of CRISPR Nanoparticles to Zwitterionic Microgels
This work establishes a novel strategy to covalently tether nanoparticles to biomaterial substrates through SnoopTag and SpyTag bioconjugation systems for spatiotemporal control of non-viral CRISPR delivery.
PreprintReal-world useCatamers: Multi-specific therapeutics that concatenate individual warheads on a DNA scaffold via Watson-Crick interactions
We describe the concept for a new modality to create multi-specific therapeutics that utilizes modified nucleic acids as a scaffold to concatenate multiple warheads (hence called 'catamers').
PreprintBold claims, read criticallyReal-world useTwin-prime editing enables endogenous protein visualization and mutant allele tracking
Together, these results establish twin-prime editing as a versatile platform for directly linking precise endogenous genome modification to protein visualization and allele-specific mutation analysis in intact vertebrate tissues.
PreprintStimulatrix: An open-source automated platform for high-throughput functional characterization of engineered contractile tissues
Here we present Stimulatrix, an open-source platform integrating automated video acquisition within a cell culture incubator, synchronized electrical stimulation and deep learning for longitudinal assessment of contractile tissues in multiwell plates.
PreprintReal-world useDevelopment and characterization of a miniaturized focused ultrasound extraction (FUSE) system to enable rapid, point-of-care genetic testing
The feasibility of DNA extraction from piscine and timber tissues was evaluated, and results show that the device can release DNA with quality suitable for PCR-based detection from both tissue types.
PreprintReal-world useATHENA: a dynamic metabolic hub balancing carbon economy and energy supply in microbial synthesis
Ultimately, ATHENA significantly improves yields and titers of five products with differential acetyl-CoA and energy demands.
Peer-reviewed journalBold claims, read criticallyReal-world useEngineering Persistent and Rewritable Genetic Memory in Bacteria through Multiscale Plasmid Competition
Our results establish a framework for engineering persistent and rewritable genetic memory through control of intracellular competition and population-level fitness.
PreprintA step toward synthetic endosymbiosis: introducing Escherichia coli and the trypanosomatid endosymbiont Candidatus Kinetoplastibacterium crithidii into mammalian cells using a polyethylene glycol-based fusion protocol
Here we describe a protocol based on polyethylene glycol (PEG), long used to fuse mammalian cells, that delivers Escherichia coli into HeLa cells without genetic modification of either partner or the use of specialised equipment.
PreprintEntry exclusion enables selective conjugative DNA delivery in synthetic bacterial communities.
These results establish entry exclusion as a recipient-side strategy for selective conjugative DNA delivery and, when combined with selection, for controlling the composition of assembled bacterial communities.
PreprintHeterologous Reconstitution of 4-Amidopentadienoate Biosynthesis Identifies the PKS Machinery Responsible for Warhead Formation
These findings establish the biosynthetic origin of the APD warhead and provide a foundation for incorporating this privileged pharmacophore into engineered peptide scaffolds.
PreprintRandom in vitro Protein single-Loop Engineering (RiPLE) by mRNA display
Together, these results establish RiPLE as a powerful and complementary alternative to peptide-guided lasso-grafting, enabling de novo evolution of functional binding surfaces directly within their final protein scaffold.
PreprintReoviridae-derived short trimerization domain for stabilizing homo-trimerization of vaccine immunogens and therapeutic proteins
These findings highlight rFd1303 as a versatile trimerization platform for vaccine and therapeutic protein development.
Peer-reviewed journalReal-world useidTAG enables programmable and physiologically faithful control of endogenous protein degradation
Here, we develop idTAG, an inducible degron platform that decouples protein expression from protein degradation by integrating Tet-On 3G-mediated transcriptional control with dTAG-mediated degradation.
PreprintWall stiffening is a primary contributor to motility loss in Crohn's disease: an electromechanical modeling study
Within the parameter ranges examined, increased wall stiffness emerged as the dominant contributor to motility loss, followed by impaired smooth-muscle contractility.
PreprintReal-world useDe novo design of functional RNAs through higher-order interactions
Here we present DS3dRNA, an interaction-based framework for de novo RNA sequence design that combines a three-body statistical potential with physics-guided sequence sampling and supports design against multiple conformations.
PreprintA climate-resilient microalga, Desmodesmus ecotolerans sp. nov., for biophotovoltaic applications
Taken together, these findings identify D. ecotolerans as a novel climate-resilient Desmodesmus species with bioelectrochemical properties that support further evaluation for BPV applications.
PreprintReal-world useCORE: Deterministic alignment for bias-free organoid histology
We present Coplanar Organoid Reproducible Embedding (CORE), which aligns heterogeneous specimens on a shared sectioning plane to enable reproducible, bias-free histology.
PreprintBold claims, read criticallyRNA self-association limits the removal of double-stranded RNA by affinity chromatography
Decreasing fLucWT concentrations increased the effectiveness of dsRNA-AC by reducing polydispersity. dsRNA levels were measured with ELISA, dot-blots, immuno-northern blots, and a cell-based interferon release assay, enabling comparison and cross-validation of these analytical methods. dsRNA-AC is a new chromatography modality, and this study identifies sample polydispersity as a key determinant of efficient dsRNA removal.
PreprintA Chemigenetic Fluorescence Lifetime Biosensor for Dopamine Sensing
Here we introduce dHaloLife635, a novel genetically encoded fluorescence-lifetime-based dopamine (DA) sensor that exhibits a fluorescence lifetime change up to -0.20 ns upon dopamine binding. dHaloLife635 consists of a G protein-coupled dopamine receptor (DRD1), a circularly permuted HaloTag (cpHaloTag), and a cell-permeable dye JF635 functionalized with a HaloTag ligand, a reactive chloroalkane linker (JF635-HTL).
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