Biology subjects

Ozkan, S.

Publications and source records attributed to Ozkan, S..

4 recordsLinked to original sources

bioRxiv2025

Evaluating Labelling Efficiency of Commercial SPIONs in Mesenchymal Stem/Stromal Cells for Magnetic Particle Imaging Applications

Magnetic Particle Imaging (MPI) is a state-of-the-art, highly sensitive modality for non-invasive cell tracking. This study evaluated labelling efficiency, biocompatibility, intracellular localization, and MPI detection sensitivity of four commercial superparamagnetic iron oxide nanoparticles (SPIONs)--ProMag, VivoTrax, SynoMag-D, and Ferumoxytol--in mouse mesenchymal stem/stromal cells. SPION labelling efficiency and cytotoxicity was assessed at varying concentrations and incubation times using Prussian blue staining and ATP-based viability assays, respectively. MPI characterization and transmission electron microscopy (TEM) evaluations were performed for cells labelled for two-hour with ProMag or VivoTrax. For >90% labelling efficiency, ProMag required 20{square}{micro}g Fe/mL across all time points. VivoTrax, however, required [≥]240{square}{micro}g Fe/mL, reducing cell viability by >20% necessitating a reduction to 120 {micro}g/mL for further analyses. Transfection agents improved SynoMag-D and Ferumoxytol labelling but compromised viability. MPI analysis revealed linear dependence of signal intensity on labelled cell numbers for ProMag and VivoTrax (r2=0.99). ProMag yielded higher signal intensity due to greater iron uptake, although VivoTrax exhibited higher signal per unit iron. TEM confirmed intracellular SPION localization, with ProMag present as individual particles and VivoTrax as aggregates within endocytic vesicles. Low-temperature assays confirmed energy-dependent endocytosis as the primary uptake mechanism. Despite ProMags stronger MPI signals and lower detection threshold (12,500 cells), VivoTraxs superior magnetization per iron suggests its potential following further optimization of cell uptake. Overall, ProMag and VivoTrax emerged as optimal candidates for MPI-based stem cell tracking. These findings underscore the importance of optimizing both nanoparticle selection and labelling protocols to maximize MPI performance and inform future in vivo applications.

cell biology↗

bioRxiv2025

Molecular circuit between Aspergillus nidulans transcription factors MsnA and VelB to coordinate fungal stress and developmental responses

Development and secondary metabolism of the filamentous fungus Aspergillus nidulans are tightly controlled by concerted actions of several master regulator transcription factors. The connection between fungal development and cellular stress response programs is often elusive. Here we show that the MsnA zinc finger transcription factor, which controls salt-stress response, is a novel major player in fungal development. A molecular circuit among MsnA and the velvet domain regulator VelB was discovered, which mutually fosters the actions of both regulatory proteins during development. MsnA controls the expression of several genes encoding master transcriptional regulators of asexual as well as sexual development. In addition, MsnA affects directly and indirectly the synthesis of specific secondary metabolites relevant for fungal defense against other organisms and growth, in addition to salt-stress responses. Moreover, the expression of genes encoding the epigenetic regulators VapA and VipC are also directly controlled by MsnA. These subunits of the VapA-VipC-VapB methyltransferase signal transduction complex promote asexual differentiation. MsnA is therefore placed at a novel prominent position of the central regulatory network, which coordinates stress responses with the developmental and metabolic fate of the fungus.

microbiology↗

bioRxiv2024

Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A

Continued advances in variant effect prediction are necessary to demonstrate the ability of machine learning methods to accurately determine the clinical impact of variants of unknown significance (VUS). Towards this goal, the ARSA Critical Assessment of Genome Interpretation (CAGI) challenge was designed to characterize progress by utilizing 219 experimentally assayed missense VUS in the Arylsulfa-tase A (ARSA) gene to assess the performance of community-submitted predictions of variant functional effects. The challenge involved 15 teams, and evaluated additional predictions from established and recently released models. Notably, a model developed by participants of a genetics and coding bootcamp, trained with standard machine-learning tools in Python, demonstrated superior performance among sub-missions. Furthermore, the study observed that state-of-the-art deep learning methods provided small but statistically significant improvement in predictive performance compared to less elaborate techniques. These findings underscore the utility of variant effect prediction, and the potential for models trained with modest resources to accurately classify VUS in genetic and clinical research.

genetics↗

bioRxiv2023

Phospholipid Scramblase-1 is required for efficient neurotransmission and synaptic vesicle retrieval at cerebellar synapses

Structural phospholipids are asymmetrically distributed at the plasma membrane, with phosphatidylethanolamine and phosphatidylserine (PS) virtually absent from the outer leaflet. This asymmetric lipid distribution is transiently altered during specific biological processes including calcium-regulated exocytosis. However, the impact of this transient remodeling of membrane asymmetry on presynaptic function remains unknown. PhosphoLipid SCRamblase 1 (PLSCR1), a protein that randomizes phospholipid distribution between the two leaflets of the plasma membrane in response to calcium activation is an ideal candidate to alter this asymmetry. We therefore set out to determine the role of PLSCR1 in both neurotransmitter release and synaptic vesicle recycling by combining electron microscopy, optical live cell imaging of pHluorin probes and electrophysiology in cerebellar granule cells (GrC) from Plscr1 knock-out mice (Plscr1-/-). We report that PLSCR1 is expressed in GrCs and that PLSCR1-dependent PS egress occurred at synapses in response to neuron stimulation. Furthermore, synaptic transmission is impaired at GrC Plscr1-/- synapses and both PS egress and synaptic vesicle endocytosis are inhibited in Plscr1-/- cultured neurons, demonstrating that PLSCR1 controls phospholipid asymmetry remodeling and synaptic vesicle retrieval following neurotransmitter release. Altogether, our data reveal a key role for PLSCR1 in synaptic vesicle recycling and provide the first evidence that phospholipid scrambling at the plasma membrane is a prerequisite for optimal presynaptic performance.

cell biology↗