Biology subjects

Sahin, A. T.

Publications and source records attributed to Sahin, A. T..

6 recordsLinked to original sources

bioRxiv2026

Real-time Four-dimensional Imaging and Flow Dynamics Analysis of Cilia-driven Transport in Mammalian Tissues

Quantifying cilia-driven transport in mammalian tissues requires resolving rapid ciliary dynamics while preserving native three-dimensional geometry. Here we combine real-time four-dimensional light-field microscopy with tomographic particle tracking and physics-informed volumetric flow reconstruction to simultaneously image ciliary activity and reconstruct three-dimensional velocity fields in minimally dissected tissues. Applied across brain, respiratory, and reproductive epithelia, the workflow reveals conserved flow structures across individual and enables quantitative analysis of flow-tissue coupling.

biophysics↗

bioRxiv2025

High-throughput Mucus Microrheology for Phenotyping and Disease Modeling

Mucus mechanics regulate barrier, clearance, and transport functions across epithelial tissues, yet quantitative rheology remains difficult to scale because available assays require large volumes, specialized equipment, or extensive manual analysis. Here, a high-throughput microrheology workflow based on Differential Dynamic Microscopy is established for frequency-dependent measurements from 3-10 uL mucus samples and intact mucosal surfaces using standard epifluorescence microscopy. The workflow combines preloaded tracer chambers, controlled sample handling, short video acquisition, and automated analysis to reduce operator intervention while preserving sensitivity to mucus relaxation on 1--20 s time scales. Validation against shear rheometry and particle tracking in reconstituted mucin gels shows robust recovery of viscoelastic trends across mucus-like material states. Applications in human airway epithelial air--liquid interface cultures resolve culture-medium, age, donor, COPD, cigarette-smoke, cystic-fibrosis treatment, and IL-13-associated differences, including spatial heterogeneity in situ. Measurements of clinical cervical mucus further demonstrate parallel testing of scarce specimens and sensitivity to osmotic swelling. This platform provides a scalable route to quantitative mucus phenotyping for disease modeling, therapeutic testing, and future precision-medicine studies.

bioengineering↗

bioRxiv2024

A widely-occurring family of pore-forming effectors broadens the impact of the Serratia Type VI secretion system

The ability to compete with diverse competitors is essential for bacteria to succeed in microbial communities. A widespread strategy for inter-bacterial competition is the delivery of antibacterial toxins, or effector proteins, directly into rival cells using the Type VI secretion system (T6SS). Whilst a large number of broad-spectrum enzymatic T6SS effectors have been described, relatively few which form pores in target cell membranes have been reported. Here, we describe a widely-occurring new family of T6SS-dependent pore-forming effectors, exemplified by Ssp4 of Serratia marcescens Db10. We show in vitro that Ssp4 forms regulated pores that have higher selectivity for cations and use molecular dynamics simulations to support a high resolution structural model of a tetrameric membrane pore formed by Ssp4. Notably, Ssp4 displays a distinct ion selectivity, phylogenetic distribution and impact on intoxicated cells compared with Ssp6, the other cation-selective pore-forming toxin delivered by the same T6SS. Ssp4 is also active against a wider range of target species than Ssp6, highlighting that T6SS effectors are not always broad-spectrum. Finally, use of Tn-seq to identify Ssp4-resistant mutants reveals that a mucA mutant of Pseudomonas fluorescens, which overproduces extracellular polysaccharide, provides resistance to T6SS attacks. We conclude that possession of two distinct T6SS-dependent pore-forming toxins may be a common strategy to ensure effective de-energisation of closely- and distantly-related competitors.

microbiology↗

bioRxiv2023

Structure-function relationships of mucociliary clearance in the human airways

Mucociliary clearance is a vital defense mechanism of the human airways, protecting against harmful particles and infections. When this process fails, it contributes to respiratory diseases like chronic obstructive pulmonary disease (COPD) and asthma. While advances in single-cell transcriptomics have revealed the complexity of airway composition, much of what we know about how airway structure impacts clearance relies on animal studies. This limits our ability to create accurate human-based models of airway diseases. Here we show that the airways in female rats and in humans exhibit species-specific differences in the distribution of ciliated and secretory cells as well as in ciliary beat, resulting in significantly higher clearance effectiveness in humans. We further reveal that standard lab-grown cultures exhibit lower clearance effectiveness compared to human airways, and we identify the underlying structural differences. By combining diverse experiments and physics-based modeling, we establish universal benchmarks to assess human airway function, interpret preclinical models, and better understand disease-specific impairments in mucociliary clearance.

biophysics↗

bioRxiv2023

Characterisation of ligand gating, ion conduction and the ion selectivity mechanism in the endo-lysosomal ion channel hTPC2

Two pore channels (TPCs) are two-fold symmetric endo-lysosomal cation channels forming important drug targets especially for antiviral drugs. They are activated by calcium, ligand binding, and membrane voltage, and to date, are the only ion channels shown to alter their ion selectivity depending on the type of bound ligand. However, despite their importance in the field, ligand activation of TPCs and the molecular mechanisms underlying their ion selectivity are still poorly understood. Here, we set out to elucidate the mechanistic basis for the ion selectivity of human TPC2 (hTPC2) and the molecular mechanism of ligand-induced channel activation by the lipid PI(3,5)P2. We performed all-atom in silico electrophysiology simulations to study Na+ and Ca2+ permeation across hTPC2 in real-time and to investigate the conformational changes induced by the presence or absence of bound PI(3,5)P2. Our findings reveal that hTPC2 adopts distinct structures depending on the presence of PI(3,5)P2 and elucidate the conformational transition pathways between these structures. Additionally, we examined the permeation mechanism, solvation states, and binding sites of ions during ion permeation through the pore. Our simulations reproduce the experimental observation that hTPC2 is more selective for Na+ over Ca2+ ions in the presence of PI(3,5)P2 and explain the mechanism of this ion selectivity. They highlight the importance of specific ion binding sites at the luminal channel entrance, the selectivity filter, and the central channel cavity for ion conduction, enabling a distant knock-on mechanism for efficient permeation of Na+ ions.

biophysics↗

bioRxiv2021

Quantitative proteomics identifies secreted diagnostic biomarkers as well as tumor-dependent prognostic targets for clear cell Renal Cell Carcinoma

Clear cell Renal Cell Carcinoma (ccRCC) is the third most common and most malignant urological cancer, with a 5-year survival rate of 10% for patients with advanced tumors. Here, we identified 10,160 unique proteins by in-depth quantitative proteomics, of which 955 proteins were significantly regulated between tumor and normal adjacent tissues. We verified 4 putatively secreted biomarker candidates, namely PLOD2, FERMT3, SPARC and SIRP, as highly expressed proteins that are not affected by intra- and inter-tumor heterogeneity. Moreover, SPARC displayed a significant increase in urine samples of ccRCC patients, making it a promising marker for clinical screening assays. Furthermore, based on molecular expression profiles, we propose a biomarker panel for the robust classification of ccRCC tumors into two main clusters, which significantly differed in patient outcome with an almost three times higher risk of death for cluster 1 tumors compared to cluster 2 tumors. Moreover, among the most significant clustering proteins, 13 were targets of repurposed inhibitory FDA-approved drugs. Our rigorous proteomics approach identified promising diagnostic and tumor-discriminative biomarker candidates which can serve as therapeutic targets for the treatment of ccRCC.

cancer biology↗