Biology subjects

Eren, M.

Publications and source records attributed to Eren, M..

4 recordsLinked to original sources

bioRxiv2025

AFM-based nanoscale characterization of physical interaction within hematopoietic stem cells niche at single-cell level

Hematopoietic stem cells (HSCs) produce all blood cells throughout the lifespan of the organism. HSC requires a specialized bone marrow microenvironment, known as the niche, for proper differentiation and self-renewal. While several molecular and cellular elements of the niche are described, the precise understanding of the mechanobiology underlying HSC adhesion to the niche remains poorly understood. Here, we aim to characterize physical interactions and adhesion within the hematopoietic niche by combining cell sorting, surface functionalization, and atomic force microscopy. Using this approach, we quantified and compared the adhesion of bone marrow (BM) mesenchymal stromal cells (MSCs) to different extracellular proteins, as well as the adhesion of HSCs to MSCs. We observed that MSCs adhere with the greatest force to fibronectin in an Arg-Gly-As (RGD) motif mediated and actin cytoskeleton-dependent manner. Additionally, we showed that HSCs strongly adhere to MSC within 30 seconds and that the binding is RGD-independent. In conclusion, we demonstrated how to implement atomic force microscopy to measure the physiological interactions within the HSCs niche in a direct, specific, and quantitative way. This approach provides a more comprehensive and precise characterization of the biology of the HSC niche compared to previously used methods. Furthermore, it highlights the complexity of studying extremely small structures and rare cell populations in biophysical experiments.

cell biology↗

bioRxiv2021

Cooperative Allostery and Structural Dynamics of Streptavidin at Cryogenic- and Ambient-temperature

Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 [A] resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 [A] resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.

biophysics↗

bioRxiv2021

Pharmacological inhibition of PAI-1 alleviates cardiopulmonary pathologies induced by exposure to air pollutants PM2.5

OBJECTIVEExposure to air pollutants leads to the development of pulmonary and cardiovascular diseases, and thus air pollution is one of the major global threats to human health. Air pollutant particulate matter 2.5 (PM2.5)-induced cellular dysfunction impairs tissue homeostasis and causes vascular and cardiopulmonary damage. To test a hypothesis that elevated plasminogen activator inhibitor-1 (PAI-1) levels play a pivotal role in air pollutant-induced cardiopulmonary pathologies, we examined the efficacy of a drug-like novel inhibitor of PAI-1, TM5614, in treating PM2.5-induced vascular and cardiopulmonary pathologies. APPROACH AND RESULTSResults from biochemical, histological, and immunohistochemical studies revealed that PM2.5 increases the circulating levels of PAI-1 and thrombin and that TM5614 treatment completely abrogates these effects in plasma. PM2.5 significantly augments levels of pro-inflammatory cytokine IL-6 in bronchoalveolar lavage fluid, and this also can be reversed by TM5614, indicating its efficacy in amelioration of PM2.5-induced increases in inflammatory and pro-thrombotic factors. TM5614 reduces PM2.5-induced increased levels of inflammatory markers Mac3 and pSTAT3, adhesion molecule VCAM1, and apoptotic marker cleaved caspase 3. Longer exposure to PM2.5 induces pulmonary and cardiac thrombosis, but TM5614 significantly ameliorates PM2.5-induced vascular thrombosis. TM5614 also reduces PM2.5-induced increased blood pressure and heart weight. In vitro cell culture studies revealed that PM2.5 induces the levels of PAI-1, type I collagen, fibronectin, and SREBP-1/2, a transcription factor that mediates profibrogenic signaling, in cardiac fibroblasts. TM5614 abrogated that stimulation, indicating that it may block PM2.5-induced PAI-1 and profibrogenic signaling through suppression of SREBP-1. Furthermore, TM5614 blocked PM2.5-mediated suppression of Nrf2, a major antioxidant regulator in cardiac fibroblasts. CONCLUSIONSPharmacological inhibition of PAI-1 with TM5614 is a promising therapeutic approach to control air pollutant PM2.5-induced cardiopulmonary and vascular pathologies. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

pharmacology and toxicology↗

bioRxiv2019

High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategies

Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and often yield biased sampling of taxa due to ecological and evolutionary factors. New strategies are needed to enable ample representation of rare taxa and slow-growers that are outcompeted by fast-growing organisms. We developed a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts droplets based on colony density. We applied our strategy to mouse and human gut microbiomes and used 16S ribosomal RNA gene amplicons to characterize taxonomic composition of cells grown using different media. We found up to 4-fold increase in richness and larger representation of rare taxa among cells grown in droplets compared to conventional culture plates. Automated sorting of droplets for slow-growing colonies further enhanced the relative abundance of rare populations. Our method improves the cultivation and analysis of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.

microbiology↗