bioRxiv Preprints

{
  "doi": "10.64898/2026.07.24.740621",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740621v1",
  "title": "Predictive Feature Engineering for Stress Detection using Physiological Signals, A Comparative Study",
  "source": "biorxiv",
  "authors": "Gonzalez Nunez, J. G.; Sabri, S.; Kebria, P.; Crook, J.; Brattain, L.",
  "version": "1",
  "abstract": "This paper presents a two-stage pipeline for implicit feature engineering in time series-based physiological stress detection using electrodermal activity (EDA) signals. In the first stage, we forecast three descriptive statistics of future EDA signals over short horizons (3, 5, and 10 seconds) based on a 60-second context window. In the second stage, a lightweight linear classifier detects stress from these predicted statistics. We evaluate three forecasting architectures spanning the domain expertise spectrum: a domain-specific bidirectional long short-term memory (BiLSTM) recurrent neural network, zero-shot and fine-tuned variants of Amazon Chronos T5 time series foundation model, and the Tabular Prior-data Fitted Network (TabPFN) applied to engineered physiological features. Experiments on the publicly available Wearable Stress and Affect Detection (WESAD) dataset, comprising chest-worn multimodal physiological signals from 15 subjects under baseline and stress conditions, demonstrate that the domain-specific BiLSTM achieves the highest classification performance, with area under the receiver operating characteristic curve (AUC) values ranging from 0.913 to 0.962. TabPFN follow",
  "category": "bioengineering",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Jose Gabriel Gonzalez Nunez",
  "journal_published_doi": null,
  "corresponding_institution": "University of Central Florida"
}

{
  "doi": "10.64898/2026.07.24.740575",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740575v1",
  "title": "Total Synthesis of Self-Assembling Semi-Synthetic Proteins Utilizing a Dendritic Solubility Tag",
  "source": "biorxiv",
  "authors": "Hati, K. C.; Sandanaraj, B.",
  "version": "1",
  "abstract": "The chemical synthesis of well-defined, self-assembling semi-synthetic proteins (SSPs) has attracted growing interest in recent years. Approaches such as micelle-assisted protein-labeling technology (MAPLabTech) and supramolecule-assisted protein-labeling technology (SAPLabTech) have been used to generate a wide range of SSPs. The central challenge in synthesizing SSPs is solubilizing a hydrophobic chemical probe in aqueous medium prior to bioconjugation. Both MAPLabTech and SAPLabTech rely on non-covalent interactions to solubilize hydrophobic probes and present certain limitations. The present study introduces a complementary chemical strategy in which a hydrophobic chemical probe is covalently tagged with a cleavable, water-soluble dendritic domain. This covalent tagging renders the probe fully water-soluble, enabling quantitative bioconjugation to yield monomeric semi-synthetic proteins. Subsequent, selective removal of the solubility tag converts the hydrophilic semi-synthetic proteins into facially amphiphilic, semi-synthetic proteins.",
  "category": "bioengineering",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Britto Sandanaraj",
  "journal_published_doi": null,
  "corresponding_institution": "Indian Institute of Science Education and Research Pune"
}

{
  "doi": "10.64898/2026.07.24.740597",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740597v1",
  "title": "Cryoaerosolization Enables Scalable Vitrification-Based Cell Cryopreservation",
  "source": "biorxiv",
  "authors": "Kangas, J. R.; Ojha, A.; Jiang, M.; Shameem, M.; Singh, B. N.; Bischof, J. C.; Hogan, C. J.",
  "version": "1",
  "abstract": "Cell therapies hold transformative potential for treating cancer, neurologic disorders, organ failure, diabetes, and other conditions, but their widespread clinical deployment is constrained by the lack of scalable cryopreservation methods that maintain high post-thaw viability. Current standard practice using slow freezing can lead to cell death and impaired cell function. Vitrification offers an alternative by cooling samples rapidly enough to bypass ice formation entirely, better preserving cell structure and function. The high cooling and warming rates required for vitrification have previously been achieved by quenching microliter-scale samples directly into convective cooling and warming baths. Here, we present a cryopreservation platform that overcomes the throughput limitations of existing systems by combining a vibrating orifice aerosol generator with an impinging conical nozzle to generate and confine micrometer-scale droplets mid-flight in liquid nitrogen. This approach mitigates cooling losses due to the inverse Leidenfrost effect, increasing cooling and warming rates by nearly an order of magnitude compared to conventional droplet vitrification, while improving through",
  "category": "bioengineering",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Joseph R Kangas",
  "journal_published_doi": null,
  "corresponding_institution": "University of Minnesota"
}

{
  "doi": "10.64898/2026.07.24.740618",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740618v1",
  "title": "Surface-stabilized sub-micron condensates for compartmentalizing synthetic cells and enhanced enzyme kinetics",
  "source": "biorxiv",
  "authors": "Ghosh, U.; van der Velde, E.; Hussain, Z.; te Brake, D. W.; Chen, C.; Zheng, C.; van der Gucht, J.; de Vries, R.; Deshpande, S.",
  "version": "1",
  "abstract": "Living cells harbor numerous membraneless organelles (MOs), which are dynamic protein/nucleic acid assemblies responding to specific physicochemical triggers. Liquid-liquid phase separation (LLPS) plays a crucial role in their formation and activity. Inspired by the natural MOs that maintain their individual identities, this work presents a bioengineering strategy to generate LLPS-driven, isochemical MO populations using surfactant-like peptides that stabilize the MO interface. The result is highly stable, monodispersed, sub-{micro}m-sized MO populations, which are not only capable of compartmentalizing synthetic cells but also provide superior environments for enzymatic reactions. This is achieved using pH-responsive elastin-like polypeptides (PREs) as MOs and formulating an amphiphilic PRE-based peptide to stabilize the MO interface. Relative abundance of the surface-active peptide, as well as the rate of pH change, allows direct control over the MO size. Encapsulating these components within synthetic vesicles using a microfluidic platform leads to on-demand multi-compartmentalization via an external pH trigger. Lastly, a functional consequence of the acute size control is shown",
  "category": "bioengineering",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Siddharth Deshpande",
  "journal_published_doi": null,
  "corresponding_institution": "Wageningen University"
}

{
  "doi": "10.64898/2026.07.24.740565",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740565v1",
  "title": "Cerclage Wire as an Affordable Alternative for Internal Fixation in Murine Critical Sized Defect Models",
  "source": "biorxiv",
  "authors": "Cimney, K.; Sawant, S.; Sprangel, K.; Osborn-King, Z.; Diop, K.; Marshall, J.; Smith, A.; Kling, A.; Medved, D.; Sterling, C.; Wolf, K.; Brune, R.; Busel, G. A.; Collins, A. C.; Nicolaou, D.; Walter, B. A.; McBride-Gagyi, S.",
  "version": "1",
  "abstract": "Critical sized defects (CSDs) are a serious challenge in orthopedics that require the development of more robust and effective treatments to improve quality of life for patients. Current CSD research is limited by the applicable and affordable animal models available. Mice would be the preferred species as they are cheaply housed and have many transgenic variations readily available; however, their small size makes CSD surgeries difficult and expensive. We propose the use of cerclage wires to achieve internal plate fixation. PEEK plates were secured to the right femur of 26 C57BL/6 mice using four cerclage wires to achieve modified double-loop fixation implemented through bicortical holes and defects were created. 10 received 3mm defects and 6 received 4mm defects that were left empty and were taken out to 20 weeks (Group E3, E4). Another 10 received 3mm defects that were filled with a morselized bone graft and were taken out to 8 weeks (Group G3). Blinded longitudinal x-ray grading by orthopedic surgeons was conducted on the empty defects for plate stability and wire fixation. All samples received microCT analysis at their endpoints. There were no significant differences in plate ",
  "category": "bioengineering",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Sara McBride-Gagyi",
  "journal_published_doi": null,
  "corresponding_institution": "The Ohio State University"
}

{
  "doi": "10.64898/2026.07.24.740064",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740064v1",
  "title": "MeFluHyA: a novel fluorescent screening tool for high-throughput identification of HDAC6-selective inhibitors",
  "source": "biorxiv",
  "authors": "Klingl, Y. E.; Goethals, J.; Sicart, A.; Borgarelli, C.; Van Lindt, J.; Prior, R.; Ismalaj, E.; De Borggraeve, W.; Van Damme, P.; Hooker, J. M.; Curcio, M.; Verhelst, S.; Schönberger, M.; Van Den Bosch, L.",
  "version": "1",
  "abstract": "The cytosolic histone deacetylase 6 (HDAC6) plays a key role not only in cancer but also in neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) peripheral neuropathies. Pharmacological inhibition as well as genetic silencing of HDAC6 is able to rescue several defects. Therefore, developing pharmacological compounds targeting this enzyme is of crucial interest. Here, we report the design, synthesis, and characterization of Methyl Fluorescent Hydroxamic Acid (MeFluHyA), a novel fluorescent HDAC6-selective probe designed for cell imaging. By integrating a Cy5 fluorophore into a phenyl hydroxamic acid scaffold, MeFluHyA shows binding to the catalytically active CD2 domain of HDAC6 without significantly inhibiting its deacetylating function in the sub-micromolar range. Biochemical enzymatic activity assays confirmed its selectivity over other HDAC isoforms. Fluorescent imaging studies in HeLa cells demonstrated strong colocalization with HDAC6-eGFP and a commercial HDAC6 antibody. Competitive binding assays revealed that MeFluHyA effectively identifies known HDAC6 inhibitors, with reduced probe-binding serving as a readout for successful target engagement. MeFluHyA",
  "category": "biochemistry",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Yvonne Eileen Klingl",
  "journal_published_doi": null,
  "corresponding_institution": "VIB-KU Leuven"
}

{
  "doi": "10.64898/2026.07.24.740493",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740493v1",
  "title": "The FKBP42, TWISTED DWARF1, prioritizes auxin over brassinosteroidtransport by peptidyl-prolyl cis-trans isomerization of ABCB1",
  "source": "biorxiv",
  "authors": "Tsering, T.; Iacobini, F. R.; Sapia, J.; di Donato, M.; Bailly, A.; Hunyadi, P.; Xia, X.; Wei, H.; Hegedus, T.; Geisler, M.",
  "version": "1",
  "abstract": "The ATP-binding cassette (ABC) transporter ABCB1 transports both auxins and the brassinosteroid brassinolide (BL). ABCB1-mediated auxin (IAA) transport depends on interaction with the FKBP42 protein TWISTED DWARF1 (TWD1), yet the mechanism underlying substrate selectivity remains unclear. Here, we confirm dual IAA and BL transport by ABCB1 and show that the two substrates compete for ABCB1-mediated transport. We demonstrate that a conserved proline residue (P1008) is required for IAA, but not BL, transport. Furthermore, we identify TWD1 as a calmodulin-activated peptidyl-prolyl cis-trans isomerase (PPIase) that selectively enhances IAA, but not BL, transport through isomerization of the E1007-P1008 peptide bond. Loss of TWD1 PPIase activity abolishes ABCB1-mediated IAA export without affecting BL transport, revealing a regulatory mechanism that prioritizes auxin over brassinosteroid transport. Cryo-EM, molecular docking, and molecular dynamics simulations of wild-type ABCB1 and the ABCB1P1008G variant suggest that the P1008 loop mediates long-range communication between the nucleotide-binding domain surface and the substrate-binding pocket, thereby providing a structural mechanism ",
  "category": "biochemistry",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Markus Geisler",
  "journal_published_doi": null,
  "corresponding_institution": "University of Fribourg"
}

{
  "doi": "10.64898/2026.07.24.740637",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740637v1",
  "title": "Dynamic structural changes and inhibition of insect delta and epsilon glutathione S-transferases by ethacrynic acid and permethrin",
  "source": "biorxiv",
  "authors": "Sharma, M.; Qin, S.; Thibodeaux, C. J.; Dastmalchi, M.",
  "version": "1",
  "abstract": "Insect glutathione S-transferases (GSTs) play critical roles in xenobiotic detoxification and insecticide resistance, making them promising targets for selective pest-control strategies. Here, we performed a comparative analysis of GSTs representing multiple classes from beneficial insects, agricultural pests, and disease vectors. We found significant isozyme-specific variations in catalytic activity, stability, and conformational dynamics, notably, in relation to inhibition by the commercial chemical agents, ethacrynic acid (ECA) and permethrin (PER). Sequence similarity network analysis revealed distinct clustering of major GST classes and further highlighted the relatively recent evolutionary divergence of the insect-specific delta and epsilon classes. Structural modeling revealed highly conserved glutathione-binding sites (G-site), but substantial variation in the hydrophobic substrate-binding regions (H-site). Further, epsilon-class GSTs exhibited 4 helices oriented approximately 10{degrees} closer to the glutathione-binding site than delta enzymes, suggesting differences in active-site architecture. Steady-state kinetic analyses using 1-chloro-2,4-dinitrobenzene (CDNB) demons",
  "category": "biochemistry",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Mehran Dastmalchi",
  "journal_published_doi": null,
  "corresponding_institution": "University of Toronto"
}

{
  "doi": "10.64898/2026.07.24.740502",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740502v1",
  "title": "Comparative epigenomics across the barley pangenome links structural variation to regulatory genome function",
  "source": "biorxiv",
  "authors": "Zhu, Z.; Chen, E.; Navratilova, P.; Schreiber, M.; Padmarasu, S.; Koenig, P.; Himmelbach, A.; Macaulay, M.; Waugh, R.; Mascher, M.; Stein, N.",
  "version": "1",
  "abstract": "Structural variants (SVs) are abundant in plant genomes and influence agronomic traits, yet their regulatory interpretation remains challenging. Here, we combine pangenome-wide profiling of DNA methylation and chromatin accessibility across 20 barley genotypes, complemented by histone modification and chromatin interaction data in a subset of 10 genotypes. Comparative analysis of genotype-specific epigenomes reveals a globally conserved DNA methylation landscape across the barley pangenome alongside extensive regulatory variability at orthologous genes. We show that SVs do not broadly remodel global chromatin landscapes but instead act through context-dependent rewiring of local regulatory interactions. Despite this epigenomic stability, SVs may contribute to gene expression changes via chromatin contacts. Tissue-specific chromatin accessibility demonstrates that SV effects depend on developmental context. Integrating chromatin state variation with SVs at key vernalization genes explains epigenetic contributions to growth habit diversity. Together, these results provide a framework for interpreting the regulatory consequences of structural variation in crop genomes.",
  "category": "plant biology",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Nils Stein",
  "journal_published_doi": null,
  "corresponding_institution": "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)"
}

{
  "doi": "10.64898/2026.07.24.740384",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740384v1",
  "title": "Paralog diversification masks conserved diel regulatory programs during cold acclimation in Brassica rapa",
  "source": "biorxiv",
  "authors": "Ricono, A. M.; Myers, Z. A.; Schoenecker, D.; Menon, A.; Such, D.; Hazen, A.; Wise, A.; Bruna, T.; Jenkins, J.; Plott, C.; Webber, J.; Boston, L.; Shu, S.; Qiu, Y.; Barry, K.; Nwakama, C. K.; Grimwood, J.; Schmutz, J.; Lovell, J. T.; Greenham, K. M.",
  "version": "1",
  "abstract": "Plant stress responses occur within daily cycles of physiology, metabolism, and growth, making timing a critical dimension of acclimation. In Arabidopsis, circadian and diel regulation influence responses to abiotic stress, including cold, but how this temporal regulation is conserved, diversified, or expanded in crop genomes remains unclear. This question is especially challenging in Brassica rapa, which underwent a genome triplication after diverging from Arabidopsis, resulting in multiple retained paralogs that can be grouped by Arabidopsis orthology and ancient homeologous relationships. Here, we generated a B. rapa pangenome spanning six morphotypes and used it to profile diel (24 h) cold acclimation responses across diverse accessions differing in freeze tolerances. Cold altered peak expression time for thousands of genes, which we grouped into distinct phase-change groups. Circadian leaf movement assays revealed accession-specific differences in clock period and temperature compensation under cold, suggesting that altered clock behavior may contribute in part to the diel transcriptome retiming. At the individual gene level, inferred gene regulatory networks (GRNs) were highl",
  "category": "plant biology",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Kathleen M Greenham",
  "journal_published_doi": null,
  "corresponding_institution": "University of Minnesota"
}