Shapes and Dimensions of Blood Clots Affect the Rate and Extent of Platelet-Driven Clot Contraction and Will Determine the Outcomes of Thrombosis

Khismatullin, R. R.; Khabirova, A. I.; Saliakhutdinova, S. M.; Litvinov, R. I.; Weisel, J. W.

doi:10.1101/2025.03.30.646236

Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.03.30.646236

Shapes and Dimensions of Blood Clots Affect the Rate and Extent of Platelet-Driven Clot Contraction and Will Determine the Outcomes of Thrombosis

Khismatullin, R. R.·Khabirova, A. I.·Saliakhutdinova, S. M.·Litvinov, R. I.·Weisel, J. W.

View original source ↗Export metadata ↓

Abstract

BackgroundContraction (retraction, shrinkage) of hemostatic blood clots and obstructive thrombi is an important pathophysiological process. To mimic thrombi of various locations, we sought to determine whether the initial shape and dimensions of blood clots affect the rate and extent of clot contraction. MethodsThrombin-induced clots were formed in 0.3-5.7 ml samples of citrated human blood or platelet-rich plasma in a cylinder, cuboid, or flat chamber. The clots were allowed to contract at 37{degrees}C for 60 minutes with shrinkage tracked photographically. Following complete contraction, the physiologically most relevant cylindrical clots of various initial volumes (0.5 ml or 1.5 ml) were analyzed with scanning electron microscopy for composition and spatial non-uniformity with the emphasis on compressed polyhedral erythrocytes (polyhedrocytes). ResultsWith the same volumes studied, the rates and final extents of contraction of whole blood clots were shape-dependent in the following order: flat > cuboid = cylindrical. Irrespective of the shape, the initially smaller clots always contracted to a larger extent. Unlike clots in whole blood, the platelet-rich plasma clots contracted almost independently of the clot volumes and shapes studied, indicating a key role of erythrocytes. The smaller blood clots with a higher extent of contraction contained more relative volume fraction of erythrocytes, especially compressed polyhedrocytes, due to tight packing and a decrease in the intercellular space. Unlike the smaller clots, the larger clots were not clearly segregated into distinct layers, reflecting incomplete spatial redistribution of blood clot components typical for contraction. ConclusionsContraction of blood clots depends on their shape and size. The smaller and larger clots have distinct size-dependent rates and extents of contraction as well as degrees of structural non-uniformity, reflecting different spatial gradients of compressive stresses. The physiological relevance of these findings is related to the variable geometry and size of intravascular blood clots and thrombi.

Source connections

Published article ↗

Explore related subjects

cell biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Khismatullin, R. R., Khabirova, A. I., Saliakhutdinova, S. M., Litvinov, R. I., Weisel, J. W.. 2025-04-01. Shapes and Dimensions of Blood Clots Affect the Rate and Extent of Platelet-Driven Clot Contraction and Will Determine the Outcomes of Thrombosis. https://doi.org/10.1101/2025.03.30.646236

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Differential requirement for the Ire1 luminal domain in Candida albicans drug susceptibility and pathogenicity

The opportunistic human pathogen Candida albicans depends on the unfolded protein response (UPR) for cell wall integrity, antifungal tolerance, filamentous growth, and virulence. The UPR is driven by the conserved transmembrane sensor Ire1, which is activated either by misfolded proteins through its luminal domain or by lipid bilayer stress (LBS) through its transmembrane domain. In budding yeast, these two activation modes deploy divergent transcriptional programs. Whether the requirement for these two input domains is separable in C. albicans, where the cell membrane and cell wall are themselves the targets of major antifungal drug classes, remains unknown. Here, we engineered a C. albicans strain expressing Ire1 lacking an intact luminal domain (ire1{Delta}LD), which no longer detects proteotoxic stress. The ire1{Delta}LD strain grew in the presence of the azole antifungals fluconazole and miconazole but was highly sensitive to heat shock, cell wall stress, and the echinocandin caspofungin. It was also unable to sustain filamentous growth and showed reduced virulence in a Caenorhabditis elegans infection model. RNA sequencing revealed only modest changes to the steady-state transcriptome of ire1{Delta}LD cells. Together, these findings define a differential requirement for the input domains of C. albicans Ire1, uncoupling growth under azole-induced membrane stress from the cell wall, thermal, and virulence-associated outputs that depend on proteotoxic sensing, a distinction that could inform antifungal strategies targeting the UPR.

cell biology↗

bioRxiv2026

Nucleosome Core Allostery Governs Chromatin Recognition and Cell Fate

Nucleosomes regulate chromatin folding, accessibility, and factor recruitment. Current models primarily attribute these functions to histone tail modifications, while the core is largely viewed as a structural scaffold. Yet subtle changes within the nucleosome core can produce profound functional consequences, and the mechanisms underlying these effects remain unclear. Here, we describe nucleosome core allostery as a fundamental principle of chromatin regulation that amplifies the impact of minimal nucleosome variations. Leveraging natural differences between H2A.Z variants, we show that the nucleosome core encodes distinct conformational dynamics that propagate allosterically, thereby controlling nucleosome accessibility and recognition by chromatin factors. As a result, a single buried amino acid substitution alone is sufficient to reprogram nucleosome dynamics and bias cell identity. Our findings establish the nucleosome core as an allosteric regulatory module and provide a generalizable framework for how subtle variation within nucleosomes is amplified into diverse biological outcomes in development and disease.

cell biology↗

bioRxiv2026

A Novel Open-Source CellProfiler Pipeline for Automated, User-Friendly Hierarchical and K-Means Clustering of Microglial Morphology

Microglia represent a highly dynamic and heterogeneous cell type that is critically implicated in states of health and pathology. Microglial morphological subgroups have been identified that correspond to functional characteristics determining health-related outcomes. The identification of states based on morphological characteristics will therefore provide invaluable insights into the microglia-specific functional mechanisms driving treatment effects. The application of clustering analyses enables the detection of groupings within samples reflecting differences in morphological features. Here we propose the application of three custom-created modules to be used within the open-source software CellProfiler. These modules enable the automated detection of clusters present within the sample of microglia, as well as the assessment of the abundance of these clusters across conditions. The application of the analysis is conducted in a highly user-friendly manner, with a user interface integrated into the pipeline, enabling the performance of the analysis with only minimal user input. The workflow thereby includes the conduction of an outlier assessment, followed by hierarchical clustering and k-means clustering and the generation of interactive graphs to determine the number of microglia states present in the sample. Bar plots displaying the abundance of the microglia states across conditions included in the sample will be created. This approach will facilitate faster and more comparable detection of microglial morphological clusters across studies.

cell biology↗