Biology subjects

Kavakli, I. H.

Publications and source records attributed to Kavakli, I. H..

7 recordsLinked to original sources

bioRxiv2026

Functional Human Retinohypothalamic Tract Assembloid Model for Circadian Rhythm Research

The retinohypothalamic tract (RHT) is the primary pathway for circadian photoentrainment. Rodent models exhibit a significant translational gap for human physiology due to their nocturnal nature. To overcome this, we developed a functional human RHT assembloid by fusing human pluripotent stem cell (hPSC) derived retinal and hypothalamus organoids. Characterization revealed mature retinal brush borders and the preservation of melanopsin-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs) integrated via excitatory glutamatergic synapses. Multielectrode array (MEA) analysis confirmed synchronized network activity across the interface. The development of the human RHT assembloid represents a significant leap forward in chronobiology. The "gold standard" for circadian models--self-sustained gene expression oscillations--was demonstrated using a PER2::Luciferase reporter, showing robust 20- 30 hour rhythms. This validates the hypothalamic component as a functional "clock in a dish". This platform provides a readout to screen drugs or test light-pulse effects on circadian phase, directly modeling jet lag or phase-shifting. Overall, this model offers a high-fidelity system for investigating human-specific chronobiological mechanisms in vitro. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/700761v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1327027org.highwire.dtl.DTLVardef@61183corg.highwire.dtl.DTLVardef@7e280eorg.highwire.dtl.DTLVardef@77e7ce_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Microgravity Remodels Longevity Networks in Astronaut PBMCs: Integrated Findings of Telomere Elongation, DNA Repair Responses, and miRNA Suppression

Microgravity provides a unique environment for elucidating the fundamental mechanisms of human aging. In the Microgravity Associated Genetics (MESSAGE) Science Mission--Turkiyes first human space biology experiment--we performed an integrative analysis of telomere dynamics, transcriptomic remodeling, and microRNA regulation in peripheral blood mononuclear cells (PBMCs) collected before launch (L-7day), after suborbital ascent (L+3hrs), and during days 4-10 aboard the International Space Station (ISS). Spaceflight induced a striking early elongation of telomeres, accompanied by transcriptional activation of DNA repair, oxidative stress mitigation, mitochondrial homeostasis, and immune regulatory pathways. Concurrently, microgravity triggered robust suppression of longevity-associated microRNAs, including members of the miR-17-92, miR29, and miR34 families, suggesting coordinated epigenetic reprogramming of genome stability and stress responses. Notably, the adaptor protein gene AP2A1, recently implicated in cellular rejuvenation and mechanotransductive aging processes, emerged as a consistently microgravity-responsive hub, linking cytoskeletal signaling to telomere maintenance and DNA repair networks. Together, these findings reveal that short-duration spaceflight initiates a multi-layered molecular longevity program in human immune cells, characterized by telomere extension, stabilization of genome maintenance pathways, and suppression of aging-associated miRNA regulators. This systems-level view provides foundational insight into how human biology adapts to short-term microgravity exposure and identifies AP2A1-centered networks as promising targets for enhancing astronaut health and performance and ultimately understanding terrestrial aging.

molecular biology↗

bioRxiv2023

TW68, Cryptochromes stabilizer, regulates fasting blood glucose level in ob/ob and fat-induced diabetic mice

Cryptochromes (CRYs), transcriptional repressors of the circadian clock in mammals, inhibit cAMP production when glucagon activates G-protein coupled receptors. Therefore, molecules that modulate CRYs have the potential to regulate gluconeogenesis. In this study, we discovered a new molecule called TW68 that interacts with the primary pockets of mammalian CRY1/2, leading to reduced ubiquitination levels and increased stability. In cell-based circadian rhythm assays using U2OS:Bmal1-dLuc cells, TW68 extended the period length of the circadian rhythm. Additionally, TW68 decreased the transcriptional levels of two genes, Phosphoenolpyruvate carboxykinase 1 (PCK1) and Glucose-6-phosphatase (G6PC), which play crucial roles in glucose biosynthesis during glucagon-induced gluconeogenesis in HepG2 cells. Oral administration of TW68 in mice showed good tolerance, a good pharmacokinetic profile, and remarkable bioavailability. Finally, when administered to fasting ob/ob and fat-induced diabetic animals, TW68 reduced blood glucose levels by enhancing CRY stabilization and subsequently decreasing the transcriptional levels of Pck1 and G6pc. These findings collectively demonstrate the antidiabetic efficacy of TW68 in vivo, suggesting its therapeutic potential for controlling fasting glucose levels in the treatment of type 2 diabetes mellitus.

molecular biology↗

bioRxiv2022

Crystal structure of Vibrio cholerae (6-4) photolyase with DNA binding region

Photolyases (PLs) reverse UV-induced DNA damage using blue light as an energy source. Of these photolyases, (6-4) PLs repair (6-4)-lesioned photoproducts. We recently identified a gene from Vibrio cholerae (Vc) encoding a (6-4) PL, but structural characterization is needed to elucidate specific interactions with the chromophore cofactors. Here, we determined the crystal structure of Vc(6-4) PL at 2.5 [A] resolution. Our high-resolution structure revealed that the two well-known cofactors, flavin adenine dinucleotide (FAD) and the photoantenna 6,7-dimethyl 8-ribityl-lumazin (DMRL), stably interact with an -helical and an /{beta} domain, respectively. Additionally, the structure has a third cofactor with distinct electron clouds corresponding to a [4Fe-4S] cluster. Moreover, we identified that Asp106 makes a hydrogen bond with the water and DMRL, which indicates further stabilization of the photoantenna DMRL within Vc(6-4) PL. Further analysis of the Vc(6-4) PL structure revealed a possible region responsible for DNA binding. The region located between residues 478-484 may bind the lesioned DNA, with Arg483 potentially forming a salt bridge with DNA to stabilize further the interaction of Vc(6-4) PL with its substrate. Our comparative analysis revealed that the DNA lesion could not bind to the Vc(6-4) PL in a similar fashion to the Drosophila melanogaster Dm(6-4) PL without a significant conformational change of the protein. The 23rd helix of the bacterial (6-4) PLs seems to have remarkable plasticity, and conformational changes facilitate DNA binding. In conclusion, our structure provides further insight into DNA repair by a (6-4) PL containing three cofactors.

molecular biology↗

bioRxiv2021

Discovery of a small molecule that selectively destabilizes Cryptochrome 1 and enhances life span in p53 knockout mice

Cryptochromes are negative transcriptional regulators of the circadian clock in mammals. It is not clear how reducing the level of endogenous level of the CRY1 in mammals will affect circadian rhythm and the relation of such a decrease with apoptosis is unknown. Here, we discovered a molecule that destabilizes Cryptochrome 1 (CRY1) both in vitro and in vivo. The small molecule, called M47, selectively enhanced the degradation rate of CRY1 by increasing its ubiquitination and the period of U2OS Bmal1-dLuc cells. In addition, subcellular fractionation studies from mice liver indicated that M47 enhanced degradation rate of the CRY1 level in the nucleus. Furthermore, M47-mediated CRY1 reduction enhanced cisplatin-induced apoptosis in Ras-transformed p53 null fibroblast cells. Finally, systemic repetitive administration of M47 increased the median lifespan of p53-/- mice by ~25%. Collectively our data suggest that M47 is a very promising molecule to treat forms of cancer depending on the p53 mutation.

molecular biology↗

bioRxiv2020

Plasmon-Coupled Photocapacitor Neuromodulators

Efficient transduction of optical energy to bioelectrical stimuli is an important goal for effective communication with biological systems. For that plasmonics has significant potential via boosting the light-matter interactions. However, plasmonics has been primarily used for heat-induced cell stimulation due to membrane capacitance change (i.e., optocapacitance). Instead, here we demonstrate that plasmonic coupling to photocapacitor biointerfaces improves safe and efficacious neuromodulating displacement charges for an average of 185% in the entire visible spectrum while maintaining the Faradaic currents below 1%. Hot-electron injection dominantly leads the enhancement of displacement current at blue spectral window, and nanoantenna effect is mainly responsible for the improvement at red-spectral region. The plasmonic photocapacitor facilitates wireless modulation of single cells at 3-orders of magnitude below the maximum retinal intensity levels corresponding to one of the most sensitive optoelectronic neural interfaces. This study introduces a new way of using plasmonics for safe and effective photostimulation of neurons and paves the way toward ultra-sensitive plasmon-assisted neurostimulation devices.

biophysics↗

bioRxiv2020

CRY1-CBS binding regulates circadian clock function and metabolism

Circadian disruption influences metabolic health. Metabolism modulates circadian function. However, the mechanisms coupling circadian rhythms and metabolism remain poorly understood. Here we report that Cystathionine {beta}-synthase (CBS), a central enzyme in one-carbon metabolism, functionally interacts with the core circadian protein Cryptochrome1 (CRY1). In cells, CBS augments CRY1 mediated repression of the CLOCK/BMAL1 complex and shortens circadian period. Notably, we find that mutant CBS-I278T protein, the most common cause of homocystinuria, does not bind CRY1 or regulate its repressor activity. Transgenic CbsZn/Zn mice, while maintaining circadian locomotor activity period, exhibit reduced circadian power and increased expression of E-BOX outputs. CBS function is reciprocally influenced by CRY1 binding. CRY1 modulates enzymatic activity of the CBS. Liver extracts from Cry1-/- mice show reduced CBS activity that normalizes after the addition of exogenous wild type (WT) CRY1. Metabolomic analysis of WT, CbsZn/Zn, Cry1-/-, and Cry2-/- samples highlights the metabolic importance of endogenous CRY1. We observed temporal variation in one-carbon and transsulfuration pathways attributable to CRY1 induced CBS activation. CBS-CRY1 binding provides a post-translational switch to modulate cellular circadian physiology and metabolic control.

molecular biology↗