Biology subjects

Gul, S.

Publications and source records attributed to Gul, S..

14 recordsLinked to original sources

bioRxiv2026

Phosphorylation-dependent Remodeling of the CLOCK/BMAL1/nucleosome Complex

Phosphorylation of the CLOCK/BMAL1 complex is a reversible post-translational modification that plays a central role in regulating circadian oscillations; however, its underlying mechanistic basis remains poorly understood. Although biochemical studies have shown that phosphorylation modulates CLOCK/BMAL1 binding to DNA, yet it remains unclear whether these effects are confined to local perturbation or also propagate through allosteric effects. Moreover, the influence of phosphorylation on histone dynamics and transcription factor-nucleosome interactions has not been systematically investigated. Here, we address these questions using atomistic trajectories obtained through backmapping of coarse-grained molecular dynamics simulations based on the recently resolved cryo-EM structure of the CLOCK/BMAL1 and nucleosome complex. We investigated three experimentally identified phosphorylation states: CLOCK bHLHS38/42, BMAL1 bHLHS78, and simultaneous phosphorylation of both proteins. Our results demonstrate that phosphorylation regulates CLOCK and BMAL1 asymmetrically. Whereas phosphorylation weakens the interaction of the modified bHLH domain with the E-box, BMAL1 phosphorylation simultaneously enhances DNA engagement by the CLOCK bHLH domain, an effect that persists in the doubly phosphorylated complex and identifies BMAL1 phosphorylation as the dominant regulatory event. Steered pulling simulations further demonstrate that phosphorylation equalizes the mechanical stability of CLOCK and BMAL1 interactions with DNA. Beyond modulating DNA binding, phosphorylation remodels protein-histone interactions by altering contacts between the CLOCK PASB domain and histone H3 and between the BMAL1 PASA domain and the H2A/H2B acidic patch, while simultaneously rewiring residue-correlation and allosteric communication networks throughout the heterodimer. Importantly, phosphorylation increases the separation between the CLOCK HI loop and the H3 1-L1 elbow, supporting a structural model in which phosphorylation acts as a priming event that provides a more permissive environment for CRY1 recruitment to the chromatin-bound CLOCK-BMAL1 complex, thereby facilitating transcriptional repression. Collectively, our findings reveal that phosphorylation regulates the CLOCK-BMAL1 complex through coordinated remodeling of DNA binding, nucleosome interactions, and long-range allosteric communication, providing a mechanistic framework for circadian transcriptional repression and a foundation for the rational design of therapeutics targeting the molecular circadian clock.

biophysics↗

bioRxiv2025

Assessment of Genetic Resources to Major Tomato Diseases: Insights from wild germplasm and public S. lycopersicum collections

Tomato (Solanum lycopersicum L.) production is severely impacted by biotic stresses, leading to significant yield losses. Developing genetically resistant cultivars presents a sustainable alternative to chemical control, which is often costly and ineffective against evolving pathogens. This study utilized molecular markers to assess genetic resistance to key tomato diseases, including Fusarium wilt, late blight, bacterial wilt, root-knot nematode, Tomato Mosaic Virus (ToMV), and Tomato Yellow Leaf Curl Virus (TYLCV), across 964 tomato accessions comprising both wild germplasm and cultivated varieties. Wild germplasm exhibited the highest frequencies, with S. peruvianum identified as a rich reservoir of resistance loci. Markers associated with TYLCV (Ty-1/3, Ty2) and Fusarium wilt (I2(OH)) were particularly prevalent in wild species. The potential for gene pyramiding potential was evident, with some wild accessions carrying up to six resistance loci. In contrast, resistance loci were limited in Solanum lycopersicum. Two S. lycopersicum germplasm collections were screened: a geographically representative collection from four Southeast Asian national genebanks and a genetically representative core collection from global public genebanks. The highest resistance frequencies in S. lycopersicum were observed for bacterial wilt-associated markers SLM12-2 and SLM12-10. However, the overall scarcity of resistance alleles in S. lycopersicum emphasizes the need for further introgression of resistance genes from wild relatives. This study provides valuable genetic insights into tomato germplasm for combating biotic stress, forming a foundation for sustainable breeding strategies to enhance disease resistance and safeguard global tomato production.

plant biology↗

bioRxiv2025

Amphetamine in Adolescence Induces a Sex-Specific Mesolimbic Dopamine Phenotype in the Adult Prefrontal Cortex

Drugs of abuse in adolescence impact brain maturation and increase psychiatric risk, with differences in sensitivity between males and females. Amphetamine in adolescent male, but not female mice, causes dopamine axons intended to innervate the nucleus accumbens and to grow ectopically to the prefrontal cortex (PFC). This is mediated by drug-induced downregulation of the Netrin-1 receptor DCC. How off-target dopamine axons function in the adult PFC remains to be determined. Here we report that males and females show place preference for amphetamine in adolescence. However, only in males, amphetamine increases PFC dopamine transporter expression in adulthood: leading to aberrant baseline dopamine transients, faster dopamine release, and exaggerated responses to acute methylphenidate. Upregulation of DCC in adolescence, using CRISPRa, prevents all these changes. Mesolimbic dopamine axons rerouted to the PFC in adolescence retain anatomical and functional phenotypes of their intended target, rendering males enduringly vulnerable to the harmful effects of drugs of abuse.

neuroscience↗

bioRxiv2024

Jasmonic acid signalling is targeted by a smut fungal Tin2-fold effector

In plants, jasmonate signaling is a hub integrating environmental cues with growth and development. Due to its role in balancing defense responses against pathogens, it is a target of effector proteins from various pathogens. Here, we characterized the fungal effector protein Tue1 from the Brassicaceae smut fungus Thecaphora thlaspeos. T. thlaspeos naturally infects Arabis hirsuta but can also colonize the non-host Arabidopsis thaliana. In planta, the fungal protein Tue1 hijacks the plant importin- dependent nuclear transporter to reach the plant nucleus. It interacts with jasmonate ZIM domain 10 (JAZ10) proteins of both A. thaliana and Ar. hirsuta. Structure-guided analysis of Tue1 suggests that it binds the Jas motif of JAZ10 indicating a role in stabilization or binding competition with proteins like MYC3 and COI1. A subset of jasmonate-responsive genes is differentially regulated during T. thlaspeos infection, proposing a link of the Tue1 function to infection. Tue1 share structural similarity to the Tin2-fold family recently described in the corn smut Ustilago maydis. Our study therefore suggests that this structural effector family is expanded across fungal pathogens, although future studies have to reveal whether targeting JAZ-repressors is a conserved mechanism or specifically acquired as an adaptation to its perennial host.

biochemistry↗

bioRxiv2023

Testicular mosaicism in non-mosaic postpubertal Klinefelter patients with focal spermatogenesis and in non-mosaic prepubertal Klinefelter boys

The aim of the study is to investigate testicular mosaicism in non-mosaic postpubertal Klinefelter Syndrome patients and in non-mosaic prepubertal Klinefelter boys Testes of the males with non-mosaic Klinefelter Syndrome at different developmental stages were used. Immunohistochemical and fluorescent in situ hybridization analyses were applied for X chromosome ploidy in testis-specific cells in testicular biopsy samples from non-mosaic Klinefelter Syndrome patients. According to our findings, all analyzed spermatogonia in both postpubertal and prepubertal non-mosaic Klinefelter Syndrome patients have a 46,XY karyotype. However, while the Sertoli cells surrounding spermatogonia in postpubertal samples also have a 46,XY karyotype, the Sertoli cells surrounding spermatogonia in prepubertal samples have a 47,XXY karyotype. Peritubular myoid cells and Leydig cells may also have mosaicism in both postpubertal patients and prepubertal boys. In conclusion, we confirmed in situ using cell-specific markers that testicular mosaicism exists in non-mosaic Klinefelter Syndrome patients. Therefore, we hypothesize that focal spermatogenesis seen in some postpubertal Klinefelter Syndrome patients originates from euploid spermatogonia and Sertoli cells. Additionally, our findings suggest that only spermatogonia that have lost their X chromosome can survive. Furthermore, our data suggest that spermatogonia lose the extra X chromosome during fetal or neonatal life, while Sertoli cells lose it around puberty. These findings will lay the groundwork for new studies on exactly when and by which mechanism an extra X chromosome is lost in spermatogonia and Sertoli cells.

genetics↗

bioRxiv2023

Impact Evaluation of Significant Feature Set in Cross Project for Defect Prediction through Hybrid Feature Selection in Multiclass

AbstractCross-project defect prediction (CPDP) is a significant way of defect identification in the project. In cross-project defect prediction, we extract knowledge from the source project and apply that learned knowledge to predict labels for the target project. However, the model performance can be affected by features that are insignificant and irrelevant. Hybrid feature selection (HFS) can play a significant role in achieving high prediction accuracy by selecting significant and only relevant features. Our aim is to explore effect of significant feature selection through a hybrid approach upon cross-project (CP) defect prediction for datasets which are multi-class in nature. We leveraged the strengths of Random Forest (RF) and Recursive Feature Elimination Cross Validation (RFECV) which can constructively select few features which are significant. The design of our controlled experiment is 1 Factor 2 Treatments (1F2T). Exploratory Data Analysis (EDA) proves that all versions of PROMISE repository are multi class and have duplicated rows in data, distribution gap among values, and imbalance classes. Hence after removing duplicated rows, reducing the gap present in distribution of data, and balancing classes, we selected significant feature set through Hybrid approach i.e. Random Forest (RF) and Recursive Feature Elimination Cross Validation (RFECV). We used Convolutional Neural Network (CNN) as a classifier to predict Cross project defects along with SoftMax as the last layer. Our experimental setup resulted in the average 78% prediction accuracy measure of all 14 versions in terms of AUC. Our experimental result showed that there is significant impact of HFS on defect prediction accuracy for different datasets in the CP.

scientific communication and education↗

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↗

bioRxiv2023

The novel coronary artery disease risk factor ADAMTS-7 modulates atherosclerotic plaque formation by degradation of TIMP-1

BackgroundThe ADAMTS7 locus was genome-wide significantly associated with coronary artery disease (CAD). Lack of the extracellular matrix (ECM) protease ADAMTS-7 was shown to reduce atherosclerotic plaque formation. ObjectiveTo identify molecular mechanisms and downstream targets of ADAMTS-7 mediating risk of atherosclerosis. MethodsTargets of ADAMTS-7 were identified by high-resolution mass spectrometry of atherosclerotic plaques from Apoe-/- and Apoe-/-Adamts7-/- mice. ECM proteins were identified using solubility profiling. Putative targets were validated using immunofluorescence, in vitro degradation assays, co-immunoprecipitation, and Forster resonance energy transfer (FRET)-based protein-protein interaction assays. ADAMTS7 expression was measured in fibrous caps of human carotid artery plaques. ResultsIn humans, ADAMTS7 expression was higher in caps of unstable as compared to stable carotid plaques. Compared to Apoe-/- mice, atherosclerotic aortas of Apoe-/- mice lacking Adamts-7 (Apoe-/-Adamts7-/-) contained higher protein levels of tissue inhibitor of metalloproteases 1 (Timp-1). In co-immunoprecipitation experiments, the catalytic domain of ADAMTS-7 bound to TIMP-1, which was degraded in the presence of ADAMTS-7 in vitro. ADAMTS-7 reduced the inhibitory capacity of TIMP-1 at its canonical target matrix metalloprotease 9 (MMP-9) As a downstream mechanism, we investigated collagen content in plaques of Apoe-/- and Apoe-/-Adamts7-/- mice after Western diet. Picrosirius red staining of the aortic root revealed less collagen as a readout of higher MMP-9 activity in Apoe-/- as compared to Apoe-/- Adamts7-/- mice. In order to facilitate high-throughput screening for ADAMTS-7 inhibitors with the aim to decrease TIMP-1 degradation, we designed a FRET-based assay targeting the ADAMTS-7 catalytic site. ConclusionADAMTS-7, which is induced in unstable atherosclerotic plaques, decreases TIMP-1 stability reducing its inhibitory effect on MMP-9, which is known to promote collagen degradation and is likewise genome-wide significantly associated with CAD. Disrupting the interaction of ADAMTS-7 and TIMP-1 might be a strategy to increase collagen content and plaque stability for reduction of atherosclerosis-related events.

molecular biology↗

bioRxiv2022

MultiGML: Multimodal Graph Machine Learning for Prediction of Adverse Drug Events

Adverse drug events constitute a major challenge for the success of clinical trials. Several computational strategies have been suggested to estimate the risk of adverse drug events in preclinical drug development. While these approaches have demonstrated high utility in practice, they are at the same time limited to specific information sources and thus neglect a wealth of information that is uncovered by fusion of different data sources, including biological protein function, gene expression, chemical compound structure, cell-based imaging, etc. In this work we propose an integrative and explainable Graph Machine Learning approach (MultiGML), which fuses knowledge graphs with multiple further data modalities to predict drug related adverse events. MultiGML demonstrates excellent prediction performance compared to alternative algorithms, including various knowledge graph embedding techniques. MultiGML distinguishes itself from alternative techniques by providing in-depth explanations of model predictions, which point towards biological mechanisms associated with predictions of an adverse drug event. MotivationAdverse drug events are a major risk for failure of late-stage clinical trials. Attempts to prevent adverse drug events in preclinical drug development include experimental procedures for measuring liver-toxicity, cardio-toxicity, etc. Yet these procedures are costly and cannot fully guarantee success in later clinical studies, specifically in situations without a reliable animal model. Computational approaches developed for adverse event prediction have shown to be valuable, but are mostly limited to single data sources. Our approach successfully integrates various data sources on protein functions, gene expression, chemical compound structures and more, into the prediction of adverse events. A main distinguishing characteristic is the explainability of our model predictions which allow further insight into biological mechanisms.

bioinformatics↗

bioRxiv2022

Redox-controlled structural reorganization and flavin strain within the ribonucleotide reductase R2b-NrdI complex monitored by serial femtosecond crystallography

Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b-NrdI complex, a di-metal carboxylate- flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free-electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. We show that the flavin in the hydroquinone state is under steric strain in the R2b-NrdI protein complex, presumably tuning its redox potential to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O2-interacton site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b- NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed.

biochemistry↗

bioRxiv2021

Intravenous whole blood transfusion results in faster recovery of vascular integrity and increased survival in experimental cerebral malaria

Transfusion of 10 mg/kg of whole blood via intraperitoneal route to mice with late-stage experimental cerebral malaria (ECM) along with artemether has been shown to result in markedly increased survival (75%) compared to artemether alone (51%). Intraperitoneal route was used to overcome the restrictions imposed by injection of large volumes of viscous fluid in small and deranged blood vessels of mice with ECM. In the present study, a method of intravenous transfusion was implemented by injecting 200L of whole blood through the right jugular vein in mice with late-stage ECM, together with artemether given intraperitoneally, leading to a remarkable increase in survival, from 54% to 90%. On the contrary, mice receiving artemether plus plasma transfusion showed a worse outcome, with only 18% survival. Compared to the intraperitoneal route, intravascular transfusion led to faster and more pronounced recoveries of hematocrit, platelet counts, angiopoietins levels (ANG-1, ANG-2 and ANG-2/ANG-1) and blood brain barrier integrity. These findings indicate that whole blood transfusion when given intravenously show more efficacy over intraperitoneal transfusion, reinforcing evidence for benefit as an adjuvant therapy for cerebral malaria.

microbiology↗

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

The Janus-faced role of KDM5B heterogeneity in melanoma: differentiation as a situational driver of both growth arrest and drug-resistance

Melanoma is a highly plastic tumor characterized by dynamic interconversion of different cell identities depending on the biological context. For example, melanoma cells with high expression of the H3K4 demethylase KDM5B (JARID1B) rest in a slow-cycling, yet reversible persister state. Over time, KDM5Bhigh cells can promote rapid tumor repopulation with equilibrated KDM5B expression heterogeneity. The cellular identity of KDM5Bhigh persister cells has not been studied so far, missing an important cell state-directed treatment opportunity in melanoma. Here, we have established a doxycycline-titratable system for genetic induction of permanent intratumor expression of KDM5B and screened for chemical agents that phenocopy this effect. Transcriptional profiling and cell functional assays confirmed that the dihydropyridine phenoxyethyl 4-(2-fluorophenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxylate (termed Cpd1) supports high KDM5B expression and directs melanoma cells towards differentiation along the melanocytic lineage and to cell cycle-arrest. The high KDM5B state additionally prevents cell proliferation through negative regulation of cytokinetic abscission. Moreover, treatment with Cpd1 promoted the expression of the melanocyte-specific tyrosinase gene specifically sensitizing melanoma cells for the tyrosinase-processed antifolate prodrug 3-O-(3,4,5-trimethoxybenzoyl)-(-)-epicatechin (TMECG). In summary, our study provides proof-of-concept for a new dual hit strategy in melanoma, in which persister state-directed transitioning limits tumor growth and plasticity and primes melanoma cells towards lineage-specific elimination.

cancer biology↗

bioRxiv2018

Differential requirement for centriolar satellites in cilium formation among different vertebrate cells

Centriolar satellites are ubiquitous in vertebrate cells. They have recently emerged as key regulators of centrosome/cilium biogenesis, and their mutations are linked to ciliopathies. However, their precise functions and mechanisms of action, which potentially differ between cell types, remain poorly understood. Here, we generated retinal pigmental and kidney epithelial cells lacking satellites by genetically ablating PCM1 to investigate their functions. While satellites were essential for cilium assembly in retinal epithelial cells, kidney epithelial cells lacking satellites still formed full-length cilia but at significantly lower levels, with reduced centrosomal levels of key ciliogenesis factors. Using these cells, we identified the first satellite-specific functions at cilia, specifically in regulating ciliary content, Hedgehog signalling, and epithelial cell organization. However, other satellite-linked functions, namely proliferation, cell cycle progression and centriole duplication, were unaffected in these cells. Quantitative transcriptomic and proteomic profiling revealed that loss of satellites scarcely affects transcription, but significantly alters the proteome, particularly actin cytoskeleton pathways and neuronal functions. Together, our findings identify cell type-specific roles for satellites and provide insight into the phenotypic heterogeneity of ciliopathies.

cell biology↗