Biology subjects

Eroglu, E.

Publications and source records attributed to Eroglu, E..

11 recordsLinked to original sources

bioRxiv2026

Insulin fails to mitigate amyloid pathology but modulates intestinal morphology in the 5xFAD model revealed by synchrotron-based XPCT

Intranasal insulin has been investigated as a metabolic intervention in Alzheimers disease (AD), but its effects across the brain-gut axis remain unclear. We combined multiscale synchrotron X-ray phase-contrast tomography (XPCT), amyloid-{beta} immunofluorescence, and fecal metaproteomics to examine structural and molecular responses in 5xFAD mice. Twenty-four mice representing wild-type and 5xFAD genotypes, saline and insulin conditions, and terminal ages of 2 and 6 months received insulin at 1 U/mouse/day for 5 weeks. Micro-XPCT visualized plaque-like deposits, nanoXPCT revealed their heterogeneous internal organization, and MOAB-2 labeling provided qualitative support for amyloid pathology. Detectable plaque burden was not lower after treatment: deposits occurred in two of three treated versus none of three untreated 5xFAD mice at 2 months, and treated animals had higher descriptive regional means at 6 months. In the ileum, insulin was associated with lower villus length and crypt depth in 6-month-old 5xFAD mice, whereas no significant differences were detected at 2 months. Fecal profiles retained broad taxonomic overlap but differed in functional annotations, with hydrolase-associated fractions of 81%, 92%, 96%, and 93% across untreated wild-type, treated wild-type, untreated 5xFAD, and treated 5xFAD conditions, respectively, within the selected peptide subset. Thus, lower ileal dimensions coexisted with non-reduced detectable brain plaque burden and a fecal protein profile distinct from untreated wild type. Together, these findings reveal contrasting central and peripheral patterns following intranasal insulin treatment in 5xFAD mice: no detectable reduction in cerebral plaque burden, alongside attenuation of selected ileal structural alterations and distinct fecal metaproteomic profiles. Although exploratory, the findings raise the possibility that intranasal insulin alters amyloid compartmentalization or plaque detectability rather than promoting amyloid clearance, while producing distinct peripheral remodeling.

biophysics↗

bioRxiv2026

Claudin-dependent clonal expansion couples epicardial activation to regenerative fate acquisition

Epicardial activation is a conserved response to injury across vertebrates, yet only in regenerative species do epicardium-derived cells (EPDCs) acquire the capacity to invade the injury site and contribute to cardiac regeneration. How regenerative competence is established in epicardial cells downstream of activation remains poorly understood. Using multicolour lineage tracing we find that epicardial cells of the salamander species Pleurodeles waltl undergo a transient phase of clonal expansion that precedes EPDC accumulation at the injury site. Depletion of cCpE-sensitive Claudins from otherwise intact tight junctions alters the organisation and the mechanical state of the epicardium, impairs clonal expansion and reduces the capacity of epicardial cells to delaminate. Consequently, EPDCs fail to activate a regenerative transcriptional programme and complete their transition into injury-induced migratory EPDCs that are required to sculpt a Tenascin-C-rich matrix supporting cardiomyocyte protrusion at the injury site. Together, our findings demonstrate that epicardial activation alone is insufficient for regeneration and identify Claudin-dependent clonal expansion as a mechanism that couples epicardial activation to the acquisition of a regenerative EPDC state.

cell biology↗

bioRxiv2026

Chemogenetic Hydrogen Sulfide Rescues Vascular Senescence in Ageing

Vascular senescence is a central driver of whole-body ageing, yet rescue strategies remain limited. Here we show that hydrogen sulfide (H2S) bioavailability declines in ageing and atherosclerosis and is associated with endothelial senescence. Developing a novel remote-control, endothelial-specific, mitochondria-targeted chemogenetic system, we spatiotemporally controlled H2S generation and thereby mitigated endothelial senescence-driven programs and reversed vascular remodeling in aged mice.

cell biology↗

bioRxiv2026

Adaptive immunity is dispensable for salamander appendage regeneration

Complex multi-tissue regeneration capacity varies across vertebrates. Mammals are amongst the least regenerative species, while salamanders can regenerate complex tissues such as limbs and tails throughout life. Previous studies have shown that innate and adaptive immune cells are present during salamander limb regeneration. While innate immune cells have been shown to promote limb regeneration, it is unknown whether adaptive immunity is responsive to amputation or plays a role in appendage regeneration. Here we show that during limb regeneration in axolotls, the immune response is characterized by a coordinated immunoregulatory signature including the downregulation of antigen presentation, cytokine secretion, and T cell activation. We corroborate this transcriptomic data in vivo using skin allografts in newts and define the blastema as an immunosuppressed niche. To test the role of adaptive immune cells in regeneration, we generated Recombination activating gene 1 deficient (Rag1-/-) newts. Rag1-/- newts lack antigen receptor recombination and show a marked reduction of adaptive immune cells. We find that Rag1-/- newts do not reject allografts, confirming their functional immunodeficiency. Finally, we demonstrate that both larval and adult newts regenerate appendages in the absence of adaptive immunity. Our work demonstrates that the adaptive arm of the immune system is not required for appendage regeneration and establishes an important model for novel experimental approaches in comparative immunology and regenerative biology.

immunology↗

bioRxiv2025

Angiotensin 1-7 Modulates the Dynamics and Activation of the Proto-oncogene Mas Receptor

The proto-oncogene Mas receptor (MasR, UniProt ID: P04201) is a class-A (orphan-type) G protein-coupled receptor (GPCR) that mediates the protective effects of Angiotensin 1-7 (Ang 1-7) within the renin-angiotensin system (RAS). Despite its therapeutic relevance, the molecular mechanisms underlying MasR activation by Ang 1-7 remain elusive due to the lack of experimental structural data. In this study, we performed 1-microsecond all-atom molecular dynamics (MD) simulations of AlphaFold-modeled active and inactive MasR conformations, with and without Ang 1-7, to characterize ligand-induced conformational dynamics. Ang 1-7 binding led to increased interaction stability in the active state, reflected by higher occupancy of hydrogen bonds, salt bridges, and hydrophobic contacts. Structural analyses revealed reduced RMSD/RMSF values and stabilization of key transmembrane (TM) helices and the NPxxY micro-switch. TM distance and dihedral analyses indicated partial TM6 displacement and time-dependent NPxxY reorganization. Network-based metrics including betweenness centrality and shortest path length highlighted the emergence of state-specific communication hubs, while PCA, correlation and communication propensity analyses revealed enhanced conformational diversity and selective inter-residue signaling in the ligand-bound state. Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations showed favorable binding energetics in the active state ({Delta}GBind = -13.99 kcal/mol). These results demonstrate that Ang 1-7 acts as a partial agonist of MasR by stabilizing the inactive conformation while inducing limited activation features in the active state through non-canonical micro-switch dynamics. This work advances structural insights into MasR regulation and provides a foundation for therapeutic targeting of the ACE2/Ang 1-7/MasR axis.

biophysics↗

bioRxiv2025

Switching ON Hydrogen Sulfide: A Chemogenetic Toolkit for Spatially Resolved H2S Manipulation

Hydrogen sulfide (H2S) is emerging as a multifaceted signalling molecule that shapes energy metabolism, vascular tone, cancer biology and neurodegeneration. Although fluorescent and genetically encoded sensors now allow real-time H2S imaging, tools for selective control of intracellular H2S remain scarce. Here we benchmark two substrate-based chemogenetic enzymes--the yeast D-amino-acid oxidase (mDAAO) and the Salmonella typhimurium D-cysteine desulfhydrase (stDCyD)--for controlled H2S production. Both enzymes catalyse the conversion of D-cysteine to H2S, yet only mDAAO concomitantly generates hydrogen peroxide, introducing an unwanted oxidative signal. In contrast, stDCyD produces exclusively H2S, thereby offering a clean and efficient means to elevate intracellular H2S in vitro. Our data position stDCyD as the superior chemogenetic actuator for dissecting H2S biology without confounding redox artefacts.

biochemistry↗

bioRxiv2025

Development of a Genetically Encoded Live-Cell Iron Mapping System

Any disturbances in cellular iron regulation can lead to dysfunctions and various diseases. However, our current understanding of iron dynamics in living cells is hampered by the lack of high-resolution iron reporter systems capable of monitoring the iron status of individual cells dynamically. To address this challenge, we have developed the Live-Cell Iron Mapping System (LIMS), which consists of two distinct genetically encoded fluorescent iron reporter systems: the rFeRepS and IronFist. The rFeRepS (ratiometric Iron Reporter Systems) code for two genetically encoded constructs that translate the iron status of individual cells into a ratiometric fluorescent signal. The ratio signal reflects the cellular iron status, based on endogenous iron-responsive proteins. A high rFeRepS ratio indicates ferritin-based cellular iron storage, while a low ratio implies transferrin receptor (TfR)-based active cellular iron uptake. The IronFist (Iron Fluorescent Indicators based on Stability and Translation) is derived from the hemerythrin-like domain (Hr) of the F-box and leucine-rich protein 5 (FXBL5), which undergoes a structural rearrangement upon binding to ferrous iron, preventing its ubiquitination and subsequent degradation. In the IronFist design, we fused either the blue or green fluorescent protein (FP) variant, mTagBFP2 or mNeonGreen, to the C-terminus of Hr and co-expressed mCherry via a ribosomal skipping sequence as a reference protein for normalization. Thus, IronFist dynamically translates fluctuations of the labile iron pool into a ratiometric fluorescent signal. We demonstrated the functionality of both iron reporter systems by treating cells with different iron formulations including iron carbohydrate nanoparticles. Our results show clear cell-to-cell variations in the response to high iron treatments.

biochemistry↗

bioRxiv2023

Visualizing H2O2 and NO in endothelial cells: strategies and pitfalls

The relationship between hydrogen peroxide (H2O2) and nitric oxide (NO) in the vasculature is multifaceted and remains controversial because the dynamic detection of these reactive molecules is challenging. Genetically encoded biosensors (GEBs) allow visualizing real-time dynamics in living cells and permit multiparametric detection of several analytes. Although robust, GEBs utility depends on several parameters that need fine-tuning for proper imaging and correct data analysis: i.e., camera binning, temperature, and the resolution power of the imaging instruments are some critical parameters that require optimization. We have generated a new double-stable transgenic endothelial cell line stably expressing the biosensors HyPer7 and O-geNOp and systematically tested different imaging modes and their impact on the performance of each biosensor. Ambient temperature and the type of imaging mode did not influence the results, while camera resolution settings significantly affected readouts of HyPer probes but not O-geNOp. Changing a single parameter in a co-imaging mode significantly altered the biosensors dynamic measurements, potentially causing misinterpretation. This study provides a general guide and the pitfalls of employing GEBs in a multispectral imaging mode.

cell biology↗

bioRxiv2022

Neurons protect themselves by active shrinkage upon axonal transection

Trauma, vascular events, or neurodegenerative processes can lead to axonal injury and eventual transection (axotomy). Neurons can survive axotomy, yet the underlying mechanisms are not fully understood. Excessive water entry into injured neurons poses a particular risk due to swelling and subsequent death. Using in vitro and in vivo neurotrauma model systems based on laser transection, we demonstrated that axotomy triggers actomyosin contraction coupled with calpain activity. As a consequence, neurons shrink acutely to force water out through aquaporin channels preventing swelling and bursting. Inhibiting shrinkage increased the probability of neuronal cell death by about three-fold. These studies reveal a previously unrecognized cytoprotective response mechanism to neurotrauma and offer a fresh perspective on pathophysiological processes in the nervous system. One-Sentence SummaryWhen the axon of a neuron is cut, its soma shrinks to pump out water to avoid deadly swelling.

neuroscience↗

bioRxiv2019

Dynamics of activating and repressive histone modifications in Drosophila neural stem cell lineages and brain tumors

During central nervous system (CNS) development, spatiotemporal gene expression programs mediate specific lineage decisions to generate neuronal and glial cell types from neural stem cells (NSCs). However, little is known about the epigenetic landscape underlying these highly complex developmental events. Here, we perform ChIP-seq on distinct subtypes of Drosophila FACS-purified neural stem cells (NSCs) and their differentiated progeny to dissect the epigenetic changes accompanying the major lineage decisions in vivo. By analyzing active and repressive histone modifications, we show that stem cell identity genes are silenced during differentiation by loss of their activating marks and not via repressive histone modifications. Our analysis also uncovers a new set of genes specifically required for altering lineage patterns in type II neuroblasts, one of the two main Drosophila NSC identities. Finally, we demonstrate that this subtype specification in NBs, unlike NSC differentiation, requires Polycomb-group (PcG)-mediated repression.\n\nSummary statementDynamic epigenetic landscape of Drosophila neural stem cell lineages.

developmental biology↗

bioRxiv2019

The transcription factor Odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop

Neural progenitors undergo temporal patterning to generate diverse neurons in a chronological order. This process is well-studied in the developing Drosophila brain and conserved in mammals. During larval stages, intermediate neural progenitors (INPs) serially express Dichaete (D), grainyhead (Grh) and eyeless (Ey/Pax6), but how the transitions are regulated is not precisely understood. Here, we developed a method to isolate transcriptomes of INPs in their distinct temporal states to identify a complete set of temporal patterning factors. Our analysis identifies odd-paired (opa), as a key regulator of temporal patterning. Temporal patterning is initiated when the SWI/SNF complex component Osa induces D and its repressor Opa at the same time but with distinct kinetics. Then, high Opa levels repress D to allow Grh transcription and progress to the next temporal state. We propose that Osa and its target genes opa and D form an incoherent feedforward loop (FFL) and a new mechanism allowing the successive expression of temporal identities.

developmental biology↗