Biology subjects

Uribe, D.

Publications and source records attributed to Uribe, D..

3 recordsLinked to original sources

bioRxiv2026

A Micro-Patterned, hiPSC-Derived Vascular Graft with Enhanced Endothelialization via Shear Redistribution

Small-diameter vascular grafts that can grow with pediatric patients and resist thrombosis remain an unmet need, primarily due to slow and unstable endothelialization. Here, we engineer a tri-layer, human induced pluripotent stem cell (hiPSC)-derived vascular graft featuring a soft, patterned lumen. We introduce a scalable soft-lithography method to imprint longitudinal micro-grooves directly into the lumen of compliant hydrogel tubes, a key advance for cell-laden constructs. Computational fluid dynamics reveals that these grooves redistribute wall shear stress into protective low-shear valleys and aligning high-shear ridges without increasing the mean load. This engineered shear landscape, combined with a bioactive elastin-like recombinamer (ELR) hydrogel matrix, synergistically enhances hiPSC-endothelial cell (hiPSC-EC) capture and retention under perfusion. Patterned grafts accelerate the formation of confluent, axially aligned endothelial monolayers with mature VE-cadherin junctions, outperforming non-patterned controls. Concurrently, smooth muscle cells within the graft wall deposit extracellular matrix, driving time-dependent mechanical maturation. This platform provides a physiologically relevant model for vascular disease and a promising strategy for engineering growth-competent pediatric grafts.

bioengineering↗

bioRxiv2026

Patterned ELR-Gelatin Hydrogels Enable Rapid Endothelial Monolayer Formation via Bioactive Matrix Chemistry and Surface Topography

The endothelialization of organ-on-chip platforms and vascular implants is often limited by slow cell attachment and unstable monolayer formation. This work presents a scalable workflow that imprints micro- and nano-gratings into elastin-like recombinamer (ELR)-based hydrogels, enabling rapid endothelial cell capture and accelerating monolayer formation within 14 days. Three gelatin-ELR formulations are engineered, with {superscript 1}H-NMR confirming incorporation of sequences designed to modulate bioactivity (ELR1: inert; ELR2: uPA-responsive; ELR3: RGD-adhesive). ELR incorporation generates fibrillar microstructures and enhances mechanical performance, yielding elastic-dominant networks suitable for high-fidelity pattern transfer and stable culture. Using this library, the combined effects of ELR bioactivity and groove geometry on human iPSC-derived endothelial cells (iPSC-ECs) are systematically evaluated. In a 15-minute attachment assay, patterned ELR composites markedly improve cell retention compared to gelatin, with ELR2 on [~]350 nm and [~]4 {micro}m grooves performing best, consistent with controlled, cell-mediated interfacial remodeling. This early advantage persists, as ELR2 and ELR3 hydrogels support rapid alignment and reach confluence by day 14, whereas gelatin remains sub-confluent. Cytoskeletal analysis confirms F-actin alignment. By combining enhanced early capture with protease-regulated remodeling, ELR2 identifies a favorable design window. These results establish a materials design framework linking programmable ELR chemistry with surface topography to engineer endothelial interfaces, providing a versatile platform for vascular biomaterials and microphysiological systems.

bioengineering↗

bioRxiv2025

Genome-Resolved Metagenomics Analysis of Rice Straw Degradation Experiments Unveils MAGs with High Potential to Decompose Lignocellulosic Residues

BackgroundRice is one of the top three crops that contribute 60% of the calories consumed by humans worldwide. Nonetheless, extensive rice harvesting yields more than 800 million tons of rice straw (RS) per year globally, generating a byproduct that is often difficult for farmers to manage efficiently without burning it. As a result, millions of tons of carbon dioxide and greenhouse gases are released, causing issues such as respiratory problems, soil degradation, and global warming. In this work, we explore the biological decomposition of RS through the application of microbial consortia from a metagenomics perspective. ResultsWe applied different treatments to RS placed in a mulching setup during experiments carried out in Colombian rice fields, using various combinations of a Trichoderma-based commercial product, the bacterial strain Bacillus altitudinis IBUN2717, inorganic nitrogen, and a mixture of potassium-reducing organic acids. Before inoculation and after 30 days of treatment, we characterized the microbial community on the RS surface and from the bulk soil by performing a reference-based compositional analysis, and reconstructing and functionally annotating Metagenome-Assembled Genomes (MAGs). High-quality MAGs with great potential to decompose RS, represented by the extensive number of carbohydrate-active enzymes, were recovered. Soil MAGs taxonomic classification indicates that they may represent potential novel microbial taxa. At the same time, the main part of the RS MAGs with superior lignocellulose-degrading capacity were affiliated under Actinomycetota and Bacteroidota phyla. Moreover, {beta}-glucosidase activity measurements indicated an increased RS degradation after the application of the treatment that included inorganic nitrogen. ConclusionsThis contribution underscores the possibility of promoting RS degradation through the application of biological strategies. Further, the newly unveiled MAGs with high RS-degrading potential provide a valuable resource for exploring the functional potential of previously uncharacterized microbial diversity in Colombian agricultural ecosystems, including microorganisms that have not been previously reported as remarkable lignocellulose decomposers. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/642948v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@bc3c35org.highwire.dtl.DTLVardef@14ce6aorg.highwire.dtl.DTLVardef@1fbb30aorg.highwire.dtl.DTLVardef@1a788ce_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗