Biology subjects

Blanco, S.

Publications and source records attributed to Blanco, S..

11 recordsLinked to original sources

bioRxiv2026

Particle-Only gECM Wafers Enable Cohesive, ECM-Rich Scaffolds Without Secondary Polymers

Granular extracellular matrix (gECM)-based biomaterials commonly contain polymer components to improve scaffold cohesion and handling during fabrication and use. However, these polymer hydrogel components may dilute ECM content and increase fabrication and regulatory complexity. This study evaluated whether particle-only gECM wafers could serve as a simplified alternative to hydrogel-based gECM scaffolds while maintaining structural, mechanical, and biological performance. Decellularized human cartilage and skin tissues were processed and fabricated into three scaffold formats: gECM hydrogels, freeze-dried gECM hydrogel wafers, and freeze-dried particle-only gECM wafers. Across fabrication methods, scaffold swelling, volume fraction, and stiffness were strongly influenced by both tissue type and fabrication approach. gECM hydrogels exhibited the greatest swelling and lowest stiffness, while gECM wafers displayed higher volume fractions and greater mechanical stiffness. Notably, gECM particle-only wafers achieved performance comparable to gECM hydrogel wafers despite the absence of a secondary polymer network. Particle-only wafers also maintained swelling behavior and structural properties over 3 months of dry storage at room temperature, with only modest decreases in stiffness. In vitro studies showed sustained cell viability over 14 days on particle-only wafers, with chondrocytes infiltrating cartilage wafers and fibroblasts remaining primarily surface-localized on skin wafers. In addition, particle-only wafers remained cohesive during implantation into a bovine cartilage defect model. These findings demonstrate that particle-only gECM wafers can achieve structural integrity, mechanical performance, and cytocompatibility without the need for an additional polymer network, highlighting a simplified and ECM-rich biomaterial platform. By eliminating polymer carriers and enabling dry storage with preserved function, this approach supports the development of off-the-shelf, translationally accessible gECM particle-only wafers for tissue engineering applications.

bioengineering↗

bioRxiv2026

Human Osteochondral Granular Extracellular Matrix (gECM) Hydrogels Drive Tissue-Specific Composition and Mechanics

Osteochondral defects remain a major clinical challenge due to the limited regenerative capacity of cartilage and the complexity of the osteochondral interface. Here, we present a human-derived granular extracellular matrix (gECM) hydrogel platform designed for translational osteochondral repair. Using otherwise discarded human donor tissues, we developed cartilage and bone gECM hydrogels under current good manufacturing practice workflows. These materials are shear-thinning, immediately hold their form, and crosslink under physiological conditions to form stable constructs. Proteomic analysis confirmed that cartilage and bone gECM retain distinct tissue-specific biochemical signatures, while mechanical characterization demonstrated tissue-relevant stiffness, with bone gECM hydrogels exhibiting greater stiffness than cartilage gECM hydrogel. Particle packing density primarily governed viscosity, whereas tissue type contributed strongly to bulk stiffness. Together, these findings establish a scalable, human-derived gECM platform that integrates tissue-specific structural and mechanical cues, and advances a clinically translatable strategy for osteochondral repair.

bioengineering↗

bioRxiv2026

Granular Extracellular Matrix (gECM) Hydrogel Wafers as Shelf-Stable 2.5D Substrates for Microphysiological Modeling

Understanding disease pathology and evaluating emerging therapeutics require in vitro models that accurately recapitulate human tissue environments. However, existing microphysiological systems often compromise either biomimicry or ease-of-use, limiting widespread adoption and scalability. Here, we present lyophilized granular extracellular matrix (gECM) hydrogel wafers as shelf-stable, humanized 2.5D substrates that enable physiologically relevant modeling while simplifying integration into experimental workflows. Derived from decellularized human cartilage and bone, gECM hydrogel wafers retain tissue-specific architecture while introducing microporosity and surface topography through lyophilization. These wafers maintain swelling behavior, structural integrity, and mechanical properties over three months of room-temperature storage, allowing pre-fabrication and on-demand use without loss of function. gECM hydrogel wafers support direct cell seeding without encapsulation and sustain viability and proliferation of human adipose-derived mesenchymal stromal cells over 21 days, with gene expression trends comparable to 3D gECM hydrogels. Furthermore, wafers can be readily integrated into microfluidic systems with in situ hydration and transport of large biomolecules. Together, this platform bridges the gap between conventional 2D culture ease-of-use and 3D biomaterial biomimicry, providing a scalable and physiologically relevant in vitro model approach for high-throughput disease studies and therapeutic screening.

bioengineering↗

bioRxiv2026

Granular Extracellular Matrix (gECM) Hydrogels Enable Distinct Composition and Mechanics Across Tissue Types for Translation

Biomaterials-based tissue engineering aims to recapitulate native tissue architecture and function for both clinical repair and advanced in vitro models. While improvements in biomaterials have been made, including granular hydrogels and ECM-derived scaffolds, current biomaterials lack intentional design choices for effective translation, including regulatory considerations, practical extrusion delivery, and biomimetic characteristics. Here, we develop and characterize a library of granular ECM (gECM) biomaterials for five key tissues (cartilage, bone, skin, liver, and kidney), in which ECM particles are densely packed within a hyaluronic acid hydrogel. We optimize tissue processing methods that preserve proteomic content and structure while also aligning with scale-up manufacturing and regulatory guidelines. We show that gECM hydrogels can be molded, extruded, and 3D-printed while retaining their shape, and they stabilize at physiological temperature and pH. Lastly, we demonstrate that bulk gECM mechanics are driven by tissue type, and gECM hydrogels support viability, proliferation, and tissue-specific cellular activity. Together, these findings establish gECM hydrogels as a translational and biomimetic platform for clinical tissue repair and complex in vitro models.

bioengineering↗

bioRxiv2026

Flowable Grafts Made from Granular Extracellular Matrix (gECM) Hydrogels Promote Integrative Repair of Articular Cartilage in a Large-Animal Model

Focal injuries to articular cartilage in load-bearing joints fail to heal and often progress to degeneration, underscoring the need for repair strategies that result in restored cartilage structure and function rather than fibrocartilage formation. Granular extracellular matrix (gECM) hydrogels, flowable grafts composed of densely-packed matrix particles, offer a promising approach but lack long-term functional validation in large-animal models. Here, we developed a flowable gECM hydrogel composed of decellularized cartilage microparticles incorporated within a thiol-functionalized hyaluronan matrix. Proteomic analysis confirmed enrichment of cartilage-specific gECM matrisome components. When implanted into critical-sized femoral condyle defects in a goat model and evaluated 12 months post-implantation, both gECM hydrogel and microdrilling (surgical controls) achieved >80% defect filling. However, in contrast to microdrilling, gECM repair tissue exhibited surface tribological (friction, adhesion) and compressive mechanical properties comparable to native cartilage, with a similar proteoglycan-to-collagen ratio, enrichment of type II collagen, minimal type I collagen (typical of a fibrous scar), improved quantitative MRI metrics, and evidence of lateral cartilage integration and subchondral bone remodeling. Together, these findings demonstrate that a flowable gECM hydrogel supports integrative, cartilage-like repair in a load-bearing joint, supporting advancement of this approach toward clinical translation. One Sentence SummaryA granular ECM hydrogel implanted in a goat condyle provided a robust repair, filling the defect tissue with integrated, hyaline-like cartilage at 12 months.

bioengineering↗

bioRxiv2025

Frequency-dependent diffusion tensor distribution imaging in the evaluation of ischemic stroke

Non-invasive MRI is widely used to assess and monitor ischemic stroke, yet conventional approaches often lack sensitivity to subtle microstructural changes and struggle to evaluate tissue viability across lesion, penumbra, and distal regions. In this study, frequency dependent diffusion tensor distribution imaging ({omega}DTD) was combined with clustering of diffusion tensor distributions D({omega}) and multivariate regression modeling to characterize ischemic tissue alterations in a whole brain section. Ex vivo {omega}DTD and histology were performed in rats subjected to middle cerebral artery occlusion (MCAO) or sham surgery (P = 17) 24 hours after reperfusion. Lesions showed cell loss and an increased presence of smaller, likely glial, cells. A random forest (RF) model was used to explain and predict histological parameters from diffusion tensor imaging (DTI), manually bin resolved {omega}DTD features, and cluster resolved {omega}DTD parameters. Model performance was evaluated using leave one animal out cross validation (LOO CV). {omega}DTD features better represented cell number than DTI metrics ({omega}DTD R2 = 0.73 vs. DTI R2 = 0.49), with similar advantages for nuclear area and circularity ({omega}DTD R2 = 0.64 and 0.61 vs. DTI R2 = 0.40 and 0.35). The RF model further proved beneficial in capturing complex, nonlinear relationships between MRI parameters and tissue characteristics. Overall, these results indicate that {omega}DTD provides richer microstructural information than standard DTI, and that combining {omega}DTD with advanced machine learning methods enhances interpretation of ischemic tissue damage.

neuroscience↗

bioRxiv2025

Sensitivity analysis enlightens effects of connectivity in a Neural Mass Model under Control-Target mode

Biophysical models of human brain represent the latter as a graph of inter-connected neural regions. Building from the model by Naskar et al. [1], our motivation was to understand how these brain regions can be connected at neural level to implement some inhibitory control, which calls for inhibitory connectivity rarely considered in such models. In this model, regions are made of inter-connected excitatory and inhibitory pools of neurons, but are long-range connected only via excitatory pools (mutual excitation). We thus extend this model by generalizing connectivity, and we analyse how connectivity affects the behaviour of this model. Focusing on the simplest paradigm made of a Control area and a Target area, we explore four typical kinds of connectivity: mutual excitation, Target inhibition by Control, Control inhibition by Target, and mutual inhibition. For this, we build an analytical sensitivity framework, nesting up sensitivities of isolated pools, of isolated regions, and of the full system. We show that inhibitory control can emerge only in Target inhibition by Control and mutual inhibition connectivities. We next offer an analysis of how the model sensitivities depends on connectivity structure, depending on a parameter controling the strength of the self-inhibition within Target region. Finally, we illustrate the effect of connectivity structure upon control effectivity in response to an external forcing in the Control area. Beyond the case explored here, our methodology to build analytical sensitivities by nesting up levels (pool, region, system) lays the groundwork for expressing nested sensitivities for more complex network configurations, either for this model or any other one.

neuroscience↗

bioRxiv2024

Comprehensive Proteomic, Ultrastructural and Functional Analysis of Cryopreservation Effects on Marine Mussel Oocytes

Cryopreservation is a valuable tool for preserving marine genetic diversity and supporting selective breeding in aquaculture. The blue mussel (Mytilus galloprovincialis) is an important species for the aquaculture industry and a useful model for studying cryopreservation in marine invertebrates. Declining mussel seed availability over the past decade, combined with the growing demand for year-round hatchery production, has increased interest in developing effective cryopreservation methods for gametes and embryos. However, cryopreservation remains challenging, particularly for marine invertebrate oocytes, as it requires balancing cryoprotectant cytotoxicity with sufficient cell protection during freezing and thawing. Moreover, the molecular, structural, and functional changes associated with oocyte cryopreservation in invertebrates are still poorly understood. This study examines the effects of two commonly used cryoprotectants, dimethyl sulfoxide (DMSO) and ethylene glycol (EG), on M. galloprovincialis oocytes under a monitored slow freezing (MSF) protocol. Using an integrative analytical approach combining proteomics, functional assessments, and ultrastructural analyses, we provide a comprehensive understanding of cryoprotectant-induced changes. Our findings reveal that cryoprotectants cause significant proteomic alterations, with DMSO having more pronounced effects. These alterations are associated with increased oxidative stress, an insufficient antioxidant response, and disruptions in meiosis restart mechanisms, ultimately delaying larval development. Cryoprotectant-induced oxidative stress may also weaken the oocyte membrane, leading to rupture during the MSF protocol and subsequent fertilisation failure post-thawing. These results provide evidence that EG is less cytotoxic than DMSO and suggest that supplementing cryoprotectants with antioxidants and membrane stabilizers could enhance success rates in the cryopreservation of oocytes from mussels and other marine invertebrate species.

developmental biology↗

bioRxiv2018

Metal-induced abnormalities in diatom girdle bands

There have been a number of studies that described a serial of type of teratology occurring in different diatom taxa and that highlight the relation between metal concentration and diatom deformities, but this subject still remain not deeply understood. The present study refers to the effect of metal pollution on the diatom Achnanthidium minutissimum s.l. by describing a new form of teratology. The samples were collected in a mine area, Rosia Montana, from Romania. We observed that, exposed to environmental stress, the frustule of diatom cells appeared altered in several ways, with abnormal forms occurring in different diatom species that presented deformed valve outlines, modifications of the raphe canal system, irregular striation or mixed teratologies. In a particular sampling location where A. minutissimum s.l. was identified as the dominant species, 20.53% of the individuals presented an unreported type of deformity. This kind of teratology affects the cingulum, the valvocopula more exactly, by becoming markedly undulate.

ecology↗

bioRxiv2018

Pervasive contaminations in sequencing experiments are a major source of false genetic variability: a Mycobacterium tuberculosis meta-analysis

Contaminant DNA is a well-known confounding factor in molecular biology and in genomic repositories. Strikingly, analysis workflows for whole-genome sequencing (WGS) data usually neglect the errors introduced by potential contaminations. We performed a comprehensive evaluation of the extent and impact of contaminant DNA in WGS by analyzing more than 4,000 bacterial samples from 20 different studies. We found that contaminations are pervasive and can introduce large biases in variant analysis. We showed that these biases can translate in hundreds of false positive and negative SNPs, even for samples with slight contaminations. Studies investigating complex biological traits from sequencing data can be completely biased if contaminations are neglected during the bioinformatic analysis. We used both real and simulated data to evaluate and implement reliable, contamination-aware analysis pipelines. Our results urge for the implementation of such pipelines as sequencing technologies consolidate as a precision tool in the research and clinical context.

genomics↗

bioRxiv2018

Mathematical modeling supports fate restriction in neurogenic progenitors of the embryonic ventral spinal cord

In the developing neural tube in chicken and mammals, neural stem cells proliferate and differentiate according to a stereotyped spatio-temporal pattern. Several actors have been identified in the control of this process, from tissue-scale morphogens patterning (Shh, BMP) to intrinsic determinants in neural progenitor cells. In a previous study (Bonnet et al. eLife 7, 2018), we have shown that the CDC25B phosphatase promotes the transition from proliferation to differentiation in a cell-cycle independent fashion. In this study, we set up a mathematical model linking progenitor modes of division to the dynamics of progenitors and differentiated populations. Here, we build on this previous model to propose a complete dynamical picture of this process. We start from the standard model in which progenitors are homogeneous and can perform any type of divisions (proliferative division yielding two progenitors, asymmetric neurogenic divisions yielding one progenitor and one neuron, and terminal symmetric divisions yielding two neurons). We constraint this model using published data about mode of divisions and population dynamics of progenitors/neurons at different developmental stages (Saade et al. Cell Reports 4, 2013), and check the effect of CDC25B gain of function in this context. Next, we explore the scenarios in which progenitors population is actually split into two different pools, one of which composed of cells that have lost the capacity to perform proliferative divisions (fate restriction). We show that one such scenario appears relevant and calls for further identification of the alternative role of CDC25B in such a fate restriction.

developmental biology↗