Biology subjects

Ozturk, E.

Publications and source records attributed to Ozturk, E..

4 recordsLinked to original sources

bioRxiv2024

Species delimitation analysis indicates cryptic speciation for Terpios gelatinosus (Porifera, Demospongiae) from coastal regions of the northeastern Mediterranean Sea

Sponges, comprising over 9000 recorded species, represent one of the most primitive groups of metazoans. Given the importance of species distribution records and the identification of new species in scientific research, these endeavors play a crucial role in enhancing ecological insights, conserving biodiversity, facilitating a better understanding of the relationships between various groups of organisms, advancing our knowledge of evolution, and potentially expanding biomedical implications. In this study, we used basic morphological data, mitochondrial Cytochrome Oxidase I (COI) gene, and Internal Transcribed Spacer two (ITS2) regions to evaluate the Terpios samples collected from four coastal sites along the northeastern Mediterranean Sea, covering a distance of approximately 450 km. For this purpose, 81 COI and 11 ITS2 records of the order Suberitida were mined from GenBank, and species delimitation analysis was performed using both the Automatic Barcode Gap Discovery method and the Poisson Tree Process (PTP), along with 11 samples from the present study. While we observed slight differences in spicule sizes, the overall morphology of all samples from our study was similar. Within the scope of this research, we report the first-ever presence record of T. gelatinosus in the northeastern Mediterranean Sea. Furthermore, we document evidence pointing to the potential existence of cryptic speciation in the region.

evolutionary biology↗

bioRxiv2023

Extracellular matrix sulfation in the tumor microenvironment stimulates cancer stemness and invasiveness

Tumor extracellular matrices (ECM) exhibit aberrant changes in composition and mechanics compared to normal tissues. Proteoglycans (PG) are vital regulators of cellular signaling in the ECM with ability to modulate receptor tyrosine kinase (RTK) activation via their sulfated glycosaminoglycan (sGAG) side chains. However, their role on tumor cell behavior is controversial. Here, we demonstrate that PGs are heavily expressed in lung adenocarcinoma patients in correlation with invasive phenotype and poor prognosis. We developed a bioengineered human lung tumor model which recapitulates the increase of sGAGs in tumors in an organotypic matrix with independent control of stiffness, viscoelasticity, ligand density and porosity. Our model reveals that increased sulfation stimulates extensive proliferation, epithelial-mesenchymal transition and stemness in cancer cells. We identified the FAK-PI3K-mTOR signaling axis as a mediator of sulfation-induced molecular changes in cells upon activation of a distinct set of RTKs within tumor-mimetic hydrogels. We demonstrate that the transcriptomic landscape of tumor cells in response to increased sulfation resembles native PG-rich patient tumors through employing integrative omics and network modeling approaches.

bioengineering↗

bioRxiv2023

Species delimitation of eight ascidian (Tunicata) species from the North Eastern Mediterranean

Members of the tunicates, a subphylum of marine filter-feeder chordates, inhabit all marine and oceanic habitats from the subtidal to the abyssal. Considered as the closest relatives to the vertebrates, the tunicates are widely used as model organisms for evo-devo, allorecognition, senescence, and whole-body regeneration studies. Yet, species boundaries are poorly understood due to high morphological and genetic plasticity that characterize many tunicates taxa. Here we study taxonomy and the distribution of eight tunicate species (Botrylloides niger Herdman, 1886/ aff. leachii, Botrylloides israeliense Brunetti, 2009, Botrylloides sp., Botrylloides anceps (Herdman, 1891), Botryllus schlosseri (Pallas, 1766), Didemnum perlucidum Monniot F., 1983, Symplegma brakenhielmi (Michaelsen, 1904) and Polyclinum constellatum Savigny, 1816) sampled from six Turkish North Eastern Mediterranean Sea sites and employed the mitochondrial barcoding marker (COI) for evaluating the relationships among geographically restricted and widely spread ascidian species. Species delimitation analysis was conducted using NCBI and the present study sequences. Morphological examinations were first done in the field and then, styelide colonies were cultured in the laboratory and studied using stereo and light microscopes. A putative new Botrylloides species (Botrylloides sp.) from the Antalya region was revealed, with 99% matching on the COI gene from Saudi Arabia, further awaiting for detailed traditional taxonomy.

genetics↗

bioRxiv2022

Human anelloviruses produced by recombinant expression of synthetic genomes.

Human anelloviruses are acquired universally in infancy, highly prevalent, abundant in blood, and extremely diverse. Their apparent lack of pathogenicity indicates that they are a major component of the commensal human virome. Despite their being extensively intertwined with human biology, these viruses are poorly understood. A major impediment in studying anelloviruses is the lack of an in vitro system for their production and/ or propagation. Here we show that the T cell-derived human cell line MOLT-4 can be transfected with plasmids comprising tandem anellovirus genomes to produce viral particles visualized by electron microscopy. We found that a previously described human anellovirus of the Betatorquevirus genus (LY2), as well as a second Betatorquevirus detected by sequencing DNA extracted from a human retinal pigmental epithelium (nrVL4619), can be synthesized and produced by these means, enabling further molecular virology studies. Southern blot was used to demonstrate replication, and site-directed mutagenesis of the viral genome was performed to show that the production of anellovirus in this cell line is dependent on the expression of certain viral proteins. Finally, experiments performed in mice using purified nrVL4619 particles produced in MOLT-4 cells demonstrated infectivity in vivo in the tissue of origin. These results indicate that anelloviruses can be produced in vitro and manipulated to improve our understanding of this viral family which is ubiquitous in humans and many other mammals. Applications of this work to gene therapy and other therapeutic modalities are currently under investigation. IMPORTANCEAnelloviruses are a major component of the human virome. However, their biology is not well understood mainly due to the lack of an in vitro system for anellovirus production and/or propagation. In this study, we used multiple orthogonal measures to show that two different anelloviruses belonging to the Betatorquevirus genus can be produced in a T-cell-derived human cell line, MOLT-4, via recombinant expression of synthetic genomes. Additionally, we show that anellovirus particles generated in this in vitro system demonstrate infectivity in vivo. Our findings enable new molecular virology studies of this highly prevalent, non-pathogenic, and weakly immunogenic family of viruses, potentially leading to therapeutic applications.

microbiology↗