Biology subjects

Kurowski, A.

Publications and source records attributed to Kurowski, A..

6 recordsLinked to original sources

bioRxiv2026

Intrinsic antifungal activity of curli nanofibers expands the design space for programmable antimicrobial biomaterials

The rise of antifungal resistance and limited antifungal drug classes creates an urgent need for biomaterials with localized, programmable activity. Here, we engineered curli nanofibers displaying the antifungal peptide heliomicin and unexpectedly discovered that wild-type CsgA itself exhibits intrinsic antifungal activity against Candida albicans, reducing fungal viability by approximately 2 log units. Heliomicin fusion enhanced this activity to a 3.5-log fungicidal reduction while preserving nanofiber self-assembly, hydrogel formation, mechanical properties, and 3D printability. Mechanistic analyses linked enhanced activity to membrane disruption and expansion of the cationic surface of CsgA. Heliomicin-CsgA hydrogels further reduced fungal burden and suppressed hyphal development in an ex vivo porcine skin infection model. These findings reveal that extracellular protein nanofibers can harbor intrinsic biological activities that can be uncovered and enhanced through protein engineering, establishing a strategy for developing intrinsically bioactive, programmable biomaterials for localized therapeutic applications against fungal pathogens and potentially other microbial infections.

bioengineering↗

bioRxiv2026

Uhrf1 loss disrupts Ctcf-associated chromatin organization during early mouse embryogenesis

UHRF1 is a chromatin-binding protein essential for maintaining DNA methylation and histone modification states, yet its integrated role in vivo remains incompletely understood. To define its function, we generated conditional Uhrf1 knockout embryonic stem cells (ESCs) and embryos. Uhrf1-/- ESCs exhibited near-complete loss of 5mC and 5hmC but maintained pluripotency, whereas Uhrf1-null embryos developed normally until E8.5 and then failed to develop further by E9.5, phenocopying Dnmt1 loss. Single-cell multi-omic (ME-seq) profiling of E8.5 embryos revealed impaired lineage stabilization, widespread hypomethylation, and disrupted chromatin architecture. Uhrf1 loss was associated with altered CTCF-associated chromatin signal, broad remodeling of chromatin contacts, altered cis-regulatory relationships, and reduced predicted BMP-related ligand-receptor communication, particularly within neural crest populations. These findings identify Uhrf1 as a central regulator that tightly couples DNA methylation maintenance to 3D genome organization during gastrulation, thereby, directing early lineage specification and positioning Uhrf1 as a pivotal mediator of epigenetic information transfer during early embryogenesis. HighlightsO_LIUhrf1 knockout ESCs show global loss of 5mC/5hmC but maintain pluripotency. C_LIO_LIUhrf1-null embryos develop normally until E8.5 but die by E9.5 with severe defects. C_LIO_LISingle-cell multi-omics revealed disrupted chromatin, transcription, and lineage stability upon knockout. C_LIO_LILoss of Uhrf1 alters CTCF-associated chromatin signal, predicted BMP-related communication, and cis-regulatory relationships. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/738670v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@15bf31dorg.highwire.dtl.DTLVardef@1b601ecorg.highwire.dtl.DTLVardef@386018org.highwire.dtl.DTLVardef@12ce99f_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2026

Rational Design Reveals Structural Plasticity of the CsgA β-Solenoid Enabling Programmable Autogenic Engineered Living Materials

Microbial functional amyloids play central roles in biofilm formation and serve as foundational building blocks for autogenic engineered living materials (ELM), yet the structural design space governing their assembly and stability remains poorly defined. In Escherichia coli, the {beta}-solenoid protein CsgA functions as a canonical extracellular matrix scaffold, but prior engineering efforts have primarily focused on terminal functionalization rather than modification of the {beta}-solenoid core itself. Here, inspired by the evolutionary diversification of CsgA-like proteins, which expands along the vertical fiber axis, we explore a second orthogonal axis of structural plasticity: the horizontal dimension of the {beta}-solenoid. We rationally designed a library of CsgA variants in which the length of individual {beta}-strands was systematically reduced or extended from the native seven residues to lengths spanning 3-21 residues, while preserving conserved gate residues and loop regions. Integration of AI-based structure prediction using AlphaFold2 with all-atom molecular dynamics simulations reveals that {beta}-solenoid stability arises from a balance among strand length, residue composition, and solvent interactions, thereby defining both lower and optimal bounds for nanofiber assembly. Experimental validation demonstrates that engineered Escherichia coli can secrete and assemble these CsgA variants into extracellular nanofibers through the native curli biogenesis machinery, while preserving the characteristic cross-{beta} architecture. Additionally, the CsgA {beta}-solenoid variant library translates molecular design into macroscopic ELM, with deletion variants showing an inverse relationship between stiffness and extensibility, from highly extensible 3aa to stiff, strong 5aa films. Insertion-based variants largely retain CsgA-like extensibility while enabling tunable stiffness and strength across strand lengths. Together, these findings uncover previously unrecognized structural plasticity in microbial {beta}-solenoid proteins and establish {beta}-strand length as a generalizable design parameter linking molecular architecture to nanofiber stability, with implications spanning microbial functional amyloids and the rational design of autogenic engineered living materials.

bioengineering↗

bioRxiv2026

Early microglial priming in Alzheimer's disease revealed by ME-seq

Epigenetic modifications, particularly DNA methylation, change dynamically with aging and are implicated in Alzheimers Disease (AD), yet how methylation interfaces with transcriptional and chromatin regulation at single-cell resolution remains poorly understood. Progress has been limited by a lack of scalable technologies capable of jointly profiling these regulatory layers. Here, we present ME-seq, a highly scalable technologies capable of simultaneously profiling DNA methylation, gene expression, and chromatin accessibility, while achieving a 100-fold reduction in cost. We generated over 400,000 single-nucleus trimodal profiles from the aging and AD mouse brain across ages, producing the first such atlas of neurodegeneration. We found AD progression triggers pronounced, disease-specific shifts in cellular composition, characterized by accelerated epigenetic aging and the expansion of disease-associated microglia (DAM). Integrative analyses, including aging clocks, revealed that DNA methylation acts as an early priming layer preceding transcriptional activation with IRF1 identified as a methylation-sensitive transcription factor serving as a gatekeeper for DAM activation. Our results establish ME-seq as a transformative tool for large-scale epigenomic dissection, revealing DNA methylation as a primary coordinator of cell-state transitions in the aging brain. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/702946v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@67435dorg.highwire.dtl.DTLVardef@177c22aorg.highwire.dtl.DTLVardef@16c6fd9org.highwire.dtl.DTLVardef@231b92_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2021

insideOutside: an accessible algorithm for classifying interior and exterior points, with applications in embryology

A crucial aspect of embryology is relating the position of individual cells to the broader geometry of the embryo. A classic example of this is the first cell-fate decision of the mouse embryo, where interior cells become inner cell mass and exterior cells become trophectoderm. Fluorescent labelling, imaging, and quantification of tissue-specific proteins have advanced our understanding of this dynamic process. However instances arise where these markers are either not available, or not reliable, and we are left only with the cells spatial locations. Therefore, a simple, robust method for classifying interior and exterior cells of an embryo using spatial information is required. Here, we describe a simple mathematical framework and an unsupervised machine learning approach, termed insideOutside, for classifying interior and exterior points of a three-dimensional point-cloud, a common output from imaged cells within the early mouse embryo. We benchmark our method against other published methods to demonstrate that it yields greater accuracy in classification of nuclei from the pre-implantation mouse embryos and greater accuracy when challenged with local surface concavities. We have made MATLAB and Python implementations of the method freely available. This method should prove useful for embryology, with broader applications to similar data arising in the life sciences.

developmental biology↗

bioRxiv2020

Oct4 regulates embryonic pluripotency via metabolic mechanisms and Stat3 signalling.

OCT4 is a fundamental component of the molecular circuitry governing pluripotency in vivo and in vitro. To determine how OCT4 protects the pluripotent lineage from differentiation into trophoblast, we used single cell transcriptomics and quantitative immunofluorescence on blastocysts and established differentially expressed genes and pathways between control and OCT4 null cells. Activation of most pluripotency-associated transcription factors in the early mouse inner cell mass appears independent of OCT4, whereas JAK/STAT signalling requires OCT4, via activation of IL6ST. Single cell deconvolution, diffusion component and trajectory inference dissected the process of differentiation of OCT4 null cells by activating specific gene-network and transcription factors. Downregulation of glycolytic and oxidative metabolism was observed. CHIPseq analysis suggests OCT4 directly targets rate-limiting glycolytic enzymes. Concomitant with significant disruption of the STAT3 pathway, oxidative respiration is significantly diminished in OCT4 null cells. Upregulation of the lysosomal pathway detected in OCT4 null embryos is likely attributable to aberrant metabolism. Highlights and noveltyO_LIMajor pluripotency-associated transcription factors are activated in OCT4-deficient early mouse ICM cells, coincident with ectopic expression of trophectoderm markers C_LIO_LIJAK/STAT signalling is defective in OCT4 null embryos C_LIO_LIOCT4 promotes expression of KATS enzymes by means of glycolytic production of Acetyl CoA to secure chromatin accessibility for acquisition of epiblast identity C_LIO_LIOCT4 regulates the metabolic and biophysical processes required for establishment of embryonic pluripotency C_LI

developmental biology↗