Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

Permanent URI for this collectionhttps://hdl.handle.net/11147/9

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A Carbohydrate sulfotransferase mutant zebrafish shows importance of keratan sulfate proteoglycan in skeletal structure
(Mary Ann Liebert, 2024) Basol, M.; Ersoz, E.; Özaktaş, Helin; Cakan-Akdogan, G.
Citation - Scopus: 3
A Microrna-Regulated Transcriptional State Defines Intratumoral Cd8+t Cells That Respond To Immunotherapy
(Cell Press, 2025) Tang, William W.; Battistone, Ben; Bauer, Kaylyn M.; Weis, Allison M.; Barba, Cindy; Fadlullah, Muhammad Zaki Hidayatullah; O'Connell, Ryan M.
The rising incidence of advanced-stage colorectal cancer (CRC) and poor survival outcomes necessitate new and effective therapies. Immune checkpoint inhibitors (ICIs), specifically anti-PD-1 therapy, show promise, yet clinical determinants of a positive response are suboptimal. Here, we identify microRNA-155 (miR-155) as necessary for CD8+ T cell-infiltrated tumors through an unbiased in vivo CRISPR-Cas9 screen identifying functional tumor antigen-specific CD8+ T cell-expressed microRNAs. T cell miR-155 is required for anti-PD-1 responses and for a vital intratumor CD8+ T cell differentiation cascade by repressing Ship-1, inhibiting Tcf-1 and stemness, and subsequently enhancing Cxcr6 expression, anti-tumor immunity, and effector functions. Based on an underlying miR-155-dependent CD8+ T cell transcriptional profile, we identify a gene signature that predicts ICI responses across 12 diverse cancers. Together, our findings support a model whereby miR155 serves as a central regulator of CD8+ T cell-dependent cancer immunity and ICI responses that may be leveraged for future therapeutics.
Investigation of the role of Wnt/β-catenin signaling in development of Alzheimer's disease in a zebrafish model of mmyloid-β toxicity
(Wiley, 2024) Nazlı, Dilek; Ipekgil, D.; Poyraz, Y. K.; Catak, B.; Sahin, E. Turhanlar; Özhan, Güneş
The Wnt/β-catenin signaling pathway, an evolutionarily conserved and pivotal pathway associated with synapse formation in adulthood, plays a crucial role in Alzheimer's disease (AD). AD, marked by various pathologies, is primarily linked to the accumulation of extracellular beta-amyloid plaques. The interplay between this accumulation and disruptions in the Wnt/β-catenin signaling pathway triggers synaptic degeneration, resulting in synaptic dysfunction and AD progression. In this study, we modeled AD induced by the Aβ42 peptide using adult transgenic (6XTCF) zebrafish. To establish the zebrafish AD model, we employed cerebroventricular microinjection (CVMI) with the Aβ42 peptide. Fish, anesthetized prior to CVMI, were positioned on a stable platform, and the Aβ42 peptide was injected into the telencephalon region of the brain by a capillary needle. Brain samples were collected on 1, 3, 4, 7, and 14 days post-CVMI (dpi) to analyze changes in Aβ42 peptide accumulation, the immune system response, synaptic degeneration, apoptosis, and the expression of genes related to proliferation using qPCR and immunofluorescent staining. To examine the role of the Wnt/β-catenin signaling pathway in the molecular mechanism of AD development, fish exhibiting high levels of regeneration on days 7 and 14 were treated with the IWR-1 drug, which inhibits the Wnt/β-catenin signaling by stabilizing the Axin2 protein, thereby suppressing the regenerative response. Our results revealed that the AD model manifested on 3dpi, with the regenerative response reaching its peak on 7dpi and 14dpi. Treatment with IWR-1 resulted in increased Aβ42 accumulation, accelerated synaptic degeneration, and elevated cell deaths in fish where the Wnt signaling pathway was inhibited. In conclusion, our adult zebrafish AD model is poised to elucidate the molecular mechanisms connecting the Wnt signaling pathway and AD, thereby contributing to the development of alternative therapeutic approaches for AD patients.
Citation - WoS: 1
Citation - Scopus: 1
Association Mapping of Plant Structure and Yield Traits in Faba Bean (vicia Faba L.)
(John Wiley and Sons Inc., 2023) Abuzayed, M.A.; Baytar, A.A.; Yanar, E.G.; Doğanlar, Sami; Frary, Anne
Tens of thousands of faba bean accessions are available in germplasm collections throughout the world. Morphological characterization of these materials can enrich these collections and aid in the selection of genotypes for use in breeding programs. Results: In this study, 26 morphological characters were analyzed for 61 faba bean landraces and 53 cultivars over two seasons in Izmir, Turkey. The genotypes had high diversity for several yield traits including number of pods per plant, dry seed yield, and 100-seed weight. Association mapping was conducted for the morphological characters using 651 alleles from 100 simple sequence repeat (SSR) markers and a general linear model based on the Q matrix. A false discovery rate of 0.20 was used to test the significance of marker–trait associations resulting in 75 loci detected for 20 of the morphological characters (p ≤ 0.001). Conclusion: Overall, 44% of the quantitative trait loci (QTLs) were for seed traits, with 24%, 15%, and 17% of QTL identified for vegetative, inflorescence, and pod traits, respectively. The phenotypic data and marker–trait associations generated by this work can help breeding programs in the selection and improvement of faba bean. © 2023 Society of Chemical Industry.
Citation - WoS: 4
Epitranscriptomics M⁶a Analyses Reveal Distinct M⁶a Marks Under Tumor Necrosis Factor Α (tnf-Α) Apoptotic Conditions in Hela Cells
(Wiley, 2024) Akçaöz Alasar, Azime; Tüncel, Özge; Sağlam, Buket; Gazaloğlu, Yasemin; Atbinek, Melis; Çağıral, Umut; Akgül, Bünyamin
Tumor necrosis factor-alpha (TNF-alpha) is a ligand that induces both intrinsic and extrinsic apoptotic pathways in HeLa cells by modulating complex gene regulatory mechanisms. However, the full spectrum of TNF-alpha-modulated epitranscriptomic m(6)A marks is unknown. We employed a genomewide approach to examine the extent of m(6)A RNA modifications under TNF-alpha-modulated apoptotic conditions in HeLa cells. miCLIP-seq analyses revealed a plethora of m(6)A marks on 632 target mRNAs with an enrichment on 99 mRNAs associated with apoptosis. Interestingly, the m(6)A RNA modification patterns were quite different under cisplatin- and TNF-alpha-mediated apoptotic conditions. We then examined the abundance and translational efficiencies of several mRNAs under METTL3 knockdown and/or TNF-alpha treatment conditions. Our analyses showed changes in the translational efficiency of TP53INP1 mRNA based on the polysome profile analyses. Additionally, TP53INP1 protein amount was modulated by METTL3 knockdown upon TNF-alpha treatment but not CP treatment, suggesting the existence of a pathway-specific METTL3-TP53INP1 axis. Congruently, METLL3 knockdown sensitized HeLa cells to TNF-alpha-mediated apoptosis, which was also validated in a zebrafish larval xenograft model. These results suggest that apoptotic pathway-specific m(6)A methylation marks exist in cells and TNF-alpha-METTL3-TP53INP1 axis modulates TNF-alpha-mediated apoptosis in HeLa cells.
Citation - WoS: 12
Citation - Scopus: 11
Engineering Periodontal Tissue Interfaces Using Multiphasic Scaffolds and Membranes for Guided Bone and Tissue Regeneration
(Elsevier, 2024) Özkendir, Özge; Karaca, İlayda; Çullu, Selin; Yaşar, Hüsniye Nur,; Erdoğan, Oğulcan; Dikici, Serkan; Dikici, Betul Aldemir
Periodontal diseases are one of the greatest healthcare burdens worldwide. The periodontal tissue compartment is an anatomical tissue interface formed from the periodontal ligament, gingiva, cementum, and bone. This multifaceted composition makes tissue engineering strategies challenging to develop due to the interface of hard and soft tissues requiring multiphase scaffolds to recreate the native tissue architecture. Multilayer constructs can better mimic tissue interfaces due to the individually tuneable layers. They have different characteristics in each layer, with modulation of mechanical properties, material type, porosity, pore size, morphology, degradation properties, and drug-releasing profile all possible. The greatest challenge of multilayer constructs is to mechanically integrate consecutive layers to avoid delamination, especially when using multiple manufacturing processes. Here, we review the development of multilayer scaffolds that aim to recapitulate native periodontal tissue interfaces in terms of physical, chemical, and biological characteristics. Important properties of multiphasic biodegradable scaffolds are highlighted and summarised, with design requirements, biomaterials, and fabrication methods, as well as post-treatment and drug/growth factor incorporation discussed.
Citation - WoS: 1
Citation - Scopus: 1
Evaluating Ethanol Concentrations Against Staphylococcus Spp: a Proposal for Improving Nosocomial Bacteria Control
(Elsevier, 2024) Soyer, Ferda; Özdemir, Özgün Öykü; Polat, Bengi; Ekenel, Nil Hazal
Dear Editor, Nosocomial infections originating from commonly encountered pathogenic bacteria, notably Staphylococcus species, persist as a prominent global public health issue. This phenomenon exerts consequential impacts on both the well-being of patients and the healthcare personnel within hospital environments. Hospital-acquired infections from common bacteria like Staphylococcus remain a global public health concern. The European Centre for Disease Prevention and Control reports prevalence rates of 4.5% in the USA and 7.1% in Europe [1]. An estimated 8.9 million healthcare-associated infections occur annually in European hospitals and long-term care facilities [1]. According to the World Health Organization, although 10% of patients get healthcare-associated infections, at least a 30% reduction can be achieved through adequate infection prevention and control [2]. The efficacy of disinfection methodologies employed in healthcare institutions assumes critical significance in mitigating this threat.
Citation - WoS: 4
Citation - Scopus: 4
Epitranscriptomics M6a Analyses Reveal Distinct M6a Marks Under Tumor Necrosis Factor Α (tnf-Α) Apoptotic Conditions in Hela Cells
(Wiley, 2024) Akçaöz Alasar, Azime; Tuncel, Özge; Sağlam, Buket; Gazaloğlu, Yasemin; Atbinek, Melis; Çağıral, Umut; İşcan, Evin; Özhan, Güneş; Akgül, Bünyamin
Tumor necrosis factor-alpha (TNF-alpha) is a ligand that induces both intrinsic and extrinsic apoptotic pathways in HeLa cells by modulating complex gene regulatory mechanisms. However, the full spectrum of TNF-alpha-modulated epitranscriptomic m(6)A marks is unknown. We employed a genomewide approach to examine the extent of m(6)A RNA modifications under TNF-alpha-modulated apoptotic conditions in HeLa cells. miCLIP-seq analyses revealed a plethora of m(6)A marks on 632 target mRNAs with an enrichment on 99 mRNAs associated with apoptosis. Interestingly, the m(6)A RNA modification patterns were quite different under cisplatin- and TNF-alpha-mediated apoptotic conditions. We then examined the abundance and translational efficiencies of several mRNAs under METTL3 knockdown and/or TNF-alpha treatment conditions. Our analyses showed changes in the translational efficiency of TP53INP1 mRNA based on the polysome profile analyses. Additionally, TP53INP1 protein amount was modulated by METTL3 knockdown upon TNF-alpha treatment but not CP treatment, suggesting the existence of a pathway-specific METTL3-TP53INP1 axis. Congruently, METLL3 knockdown sensitized HeLa cells to TNF-alpha-mediated apoptosis, which was also validated in a zebrafish larval xenograft model. These results suggest that apoptotic pathway-specific m(6)A methylation marks exist in cells and TNF-alpha-METTL3-TP53INP1 axis modulates TNF-alpha-mediated apoptosis in HeLa cells.
Blank Frame and Intensity Variation Distortion Detection and Restoration Pipeline for Phase-Contrast Microscopy Time-Lapse Images
(AVES, 2024) Ucar, Mahmut; Iheme, Leonardo O.; Onal, Sevgi; Pesen-Okvur, Devrim; Yalcin-Ozuysal, Ozden; Toreyin, Behcet U.; Unay, Devrim
In this study, we propose a preprocessing pipeline for the detection and correction of distorted frames in time-lapse images obtained from phase-contrast microscopy. The proposed pipeline employs the average intensities of frames as a foundational element for the analysis. In order to evaluate the degree of correction required for intensity variance, a normalization technique is applied to the difference between the average intensity of a specific frame and the median average intensity of all frames within the study. Our restoration method increases the histogram similarity between the distorted and non-distorted frames, preserves trans-passing pixels in regions of interest, and mitigates the development of additional distortions. The efficacy of the proposed method was evaluated using 15 395 time-lapse image frames from 27 experiments using our own dataset and 830 time-lapse images from four different experiments obtained from the cell tracking challenge. The results of the validation demonstrate a high degree of numerical and visual accuracy of the proposed pipeline.
Citation - WoS: 7
Citation - Scopus: 7
Canonical Wnt and Tgf-β/Bmp Signaling Enhance Melanocyte Regeneration but Suppress Invasiveness, Migration, and Proliferation of Melanoma Cells
(Frontiers Media S.A., 2023) Katkat, Esra; Demirci, Yeliz; Heger, Guillaume; Karagülle, Doğa; Papatheodorou, Irene; Brazma, Alvis; Özhan, Güneş
Melanoma is the deadliest form of skin cancer and develops from the melanocytes that are responsible for the pigmentation of the skin. The skin is also a highly regenerative organ, harboring a pool of undifferentiated melanocyte stem cells that proliferate and differentiate into mature melanocytes during regenerative processes in the adult. Melanoma and melanocyte regeneration share remarkable cellular features, including activation of cell proliferation and migration. Yet, melanoma considerably differs from the regenerating melanocytes with respect to abnormal proliferation, invasive growth, and metastasis. Thus, it is likely that at the cellular level, melanoma resembles early stages of melanocyte regeneration with increased proliferation but separates from the later melanocyte regeneration stages due to reduced proliferation and enhanced differentiation. Here, by exploiting the zebrafish melanocytes that can efficiently regenerate and be induced to undergo malignant melanoma, we unravel the transcriptome profiles of the regenerating melanocytes during early and late regeneration and the melanocytic nevi and malignant melanoma. Our global comparison of the gene expression profiles of melanocyte regeneration and nevi/melanoma uncovers the opposite regulation of a substantial number of genes related to Wnt signaling and transforming growth factor beta (TGF-beta)/(bone morphogenetic protein) BMP signaling pathways between regeneration and cancer. Functional activation of canonical Wnt or TGF-beta/BMP pathways during melanocyte regeneration promoted melanocyte regeneration but potently suppressed the invasiveness, migration, and proliferation of human melanoma cells in vitro and in vivo. Therefore, the opposite regulation of signaling mechanisms between melanocyte regeneration and melanoma can be exploited to stop tumor growth and develop new anti-cancer therapies.
Structural Defense of Plants and Pathogenesis
(01. Izmir Institute of Technology, 2023) Ekinci, Berkay; Ekinci, Berkay
The major challenge in today s world is ensuring an adequate food supply for the growing global population. Achieving this goal requires the development of crops by using sustainable agricultural strategies in ecologically suitable areas (Jan et al. 2011; Doğanlar et al. 2023). However, plant diseases, which are caused by various pathogens such as bacteria, fungi, viruses, nematodes, and herbivores, pose a significant threat to crop quality and yield. Fortunately, plants have several preexisting and induced defense and immune mechanisms to protect themselves against biotic and abiotic stresses (Jones et al. 2006; Freeman et al. 2008). This review aims to provide information on phytopathogens, the steps of pathogenesis, plants’ pre-existing structural defense mechanisms against pathogenesis, and more. It is aimed at broadening the reader's knowledge and perspective by providing a wide range of examples, from simple to complex. I hope that this review will be a good start for enlightening and inspiring all curious scientists who, like me, are enthusiastic about this field.
Citation - WoS: 7
Citation - Scopus: 6
Addition of Exogenous Diacylglycerol Enhances Wnt/Β-catenin Signaling Through Stimulation of Macropinocytosis
(Elsevier, 2023) Azbazdar, Yağmur; Tejeda-Munoz, Nydia; Monka, Julia C.; Dayrit, Alex; Binder, Grace; De Robertis, Edward M.; Özhan, Güneş
Activation of Wnt signaling triggers macropinocytosis and drives many tumors. We now report that the exogenous addition of the second messenger lipid sn-1,2 DAG to the culture medium rapidly induces macropinocytosis. This is accompanied by potentiation of the effects of added Wnt3a recombinant protein or the glycogen synthase kinase 3 (GSK3) inhibitor lithium chloride (LiCl, which mimics Wnt signaling) in luciferase transcriptional reporter assays. In a colorectal carcinoma cell line in which mutation of adenomatous polyposis coli (APC) causes constitutive Wnt signaling, DAG addition increased levels of nuclear β-catenin, and this increase was partially inhibited by an inhibitor of macropinocytosis. DAG also expanded multivesicular bodies marked by the tetraspan protein CD63. In an in vivo situation, microinjection of DAG induced Wnt-like twinned body axes when co-injected with small amounts of LiCl into Xenopus embryos. These results suggest that the DAG second messenger plays a role in Wnt-driven cancer progression. © 2023 The Author(s)
Citation - Scopus: 7
Μdacs Platform: a Hybrid Microfluidic Platform Using Magnetic Levitation Technique and Integrating Magnetic, Gravitational, and Drag Forces for Density-Based Rare Cancer Cell Sorting
(Elsevier, 2023) Keçili, Seren; Yılmaz, Esra; Özçelik, Özge Solmaz; Anıl İnevi, Müge; Günyüz, Zehra Elif; Yalçın Özuysal, Özden; Özçivici, Engin; Tekin, Hüseyin Cumhur
Circulating tumor cells (CTCs) are crucial indicators of cancer metastasis. However, their rarity in the bloodstream and the heterogeneity of their surface biomarkers present challenges for their isolation. Here, we developed a hybrid microfluidic platform (microfluidic-based density-associated cell sorting (µDACS) platform) that utilizes density as a biophysical marker to sort cancer cells from the population of white blood cells (WBCs). The platform utilizes the magnetic levitation technique on a microfluidic chip to sort cells based on their specific density ranges, operating under a continuous flow condition. By harnessing magnetic, gravitational, and drag forces, the platform efficiently separates cells. This approach involves a microfluidic chip equipped with a microseparator, which directs cells into top and bottom outlets depending on their levitation heights, which are inversely proportional to their densities. Hence, low-density cancer cells are collected from the top outlet, while high-density WBCs are collected from the bottom outlet. We optimized the sorting efficiency by varying the flow rates, and concentrations of the sorting medium's paramagnetic properties using standard densities of polymeric microspheres. To demonstrate the platform's applicability, we performed hybrid microfluidic sorting on MDA-MB-231 human breast cancer cells and U-937 human monocytes. The results showed efficient sorting of rare cancer cells (≥100 cells/mL) from serum samples, achieving a sorting efficiency of ∼70% at a fast-processing speed of 1 mL h−1. This label-free approach holds promise for rapid and cost-effective CTC sorting, facilitating in-vitro diagnosis and prognosis of cancer. © 2023 The Author(s)
Citation - WoS: 13
Citation - Scopus: 13
Comparative Membrane Lipidomics of Hepatocellular Carcinoma Cells Reveals Diacylglycerol and Ceramide as Key Regulators of Wnt/Β-catenin Signaling and Tumor Growth
(Wiley, 2023) Heger, Guillaume; Azbazdar, Yağmur; Demirci, Yeliz; İpekgil, Doğaç; Karabiçici, Mustafa; Özhan, Güneş
Hepatocellular carcinoma (HCC) is largely associated with aberrant activation of Wnt/beta-catenin signaling. Nevertheless, how membrane lipid composition is altered in HCC cells with abnormal Wnt signaling remains elusive. Here, by exploiting comprehensive lipidome profiling, we unravel the membrane lipid composition of six different HCC cell lines with mutations in components of Wnt/beta-catenin signaling, leading to differences in their endogenous signaling activity. Among the differentially regulated lipids are diacylglycerol (DAG) and ceramide, which were downregulated at the membrane of HCC cells after Wnt3a treatment. DAG and ceramide enhanced Wnt/b-catenin signaling by inducing caveolin-mediated endocytosis of the canonical Wnt-receptor complex, while their depletion suppressed the signaling activity along with a reduction of caveolin-mediated endocytosis in SNU475 and HepG2 cells. Moreover, depletion of DAG and ceramide significantly impeded the proliferation, tumor growth, and in vivo migration capacity of SNU475 and HepG2 cells. This study, by pioneering plasma membrane lipidome profiling in HCC cells, exhibits the remarkable potential of lipids to correct dysregulated signaling pathways in cancer and stop abnormal tumor growth.
Citation - WoS: 1
Citation - Scopus: 2
C-Met Activation Promotes Extravasation of Hepatocellular Carcinoma Cells Into 3d-Cultured Hepatocyte Cells in Lab-On Device
(Elsevier, 2023) Solmaz, Gülhas; Bağcı, Gülsün; Çömez, Dehan; Topel, Hande; Yılmaz, Yeliz; Bağırsakçı, Ezgi; Güneş, Aysim; Batı Ayaz, Gizem; Tahmaz, İsmail; Bilgen, Müge; Pesen Okvur, Devrim
Activation of c-Met signaling is associated with an aggressive phenotype and poor prognosis in hepatocellular carcinoma (HCC); however, its contribution to organ preference in metastasis remains unclear. In this study, using a Lab on a Chip device, we defined the role of aberrant c-Met activation in regulating the extravasation and homing capacity of HCC cells. Our studies showed that (i) c-Met overexpression and activation direct HCC cells preferentially towards the hepatocytes-enriched microenvironment, and (ii) blockage of c-Met phosphorylation by a small molecule inhibitor attenuated extravasation and homing capacity of HCC cells. These results, thus, demonstrate the role of c-Met signaling in regulating the colonization of HCC cells preferentially in the liver. © 2023 Elsevier B.V.
Citation - WoS: 4
Citation - Scopus: 4
Molecular Trojan Horses for Treating Lysosomal Storage Diseases
(Academic Press, 2023) Leal, Andres Felipe; Rintz, Estera; Çelik, Betül; Ago, Yasuhiko; León, Daniel; İnci, Orhan Kerim; Seyrantepe, Volkan
Lysosomal storage diseases (LSDs) are caused by monogenic mutations in genes encoding for proteins related to the lysosomal function. Lysosome plays critical roles in molecule degradation and cell signaling through interplay with many other cell organelles, such as mitochondria, endoplasmic reticulum, and peroxisomes. Even though several strategies (i.e., protein replacement and gene therapy) have been attempted for LSDs with promising results, there are still some challenges when hard-to-treat tissues such as bone (i.e., cartilages, ligaments, meniscus, etc.), the central nervous system (mostly neurons), and the eye (i.e., cornea, retina) are affected. Consistently, searching for novel strategies to reach those tissues remains a priority. Molecular Trojan Horses have been well-recognized as a potential alternative in several pathological scenarios for drug delivery, including LSDs. Even though molecular Trojan Horses refer to genetically engineered proteins to overcome the blood-brain barrier, such strategy can be extended to strategies able to transport and deliver drugs to specific tissues or cells using cell-penetrating peptides, monoclonal antibodies, vesicles, extracellular vesicles, and patient-derived cells. Only some of those platforms have been attempted in LSDs. In this paper, we review the most recent efforts to develop molecular Trojan Horses and discuss how this strategy could be implemented to enhance the current efficacy of strategies such as protein replacement and gene therapy in the context of LSDs. © 2023
Citation - WoS: 3
Citation - Scopus: 3
Mitigation Potential of Zingerone and Rutin on Toxicity Mechanisms of Nickel To Zebrafish Based on Morphological, Dna Damage and Apoptosis Outcome Analysis
(Elsevier, 2023) Köktürk, Mine; Yıldırım, Serkan; Atamanalp, Muhammed; Kılıçoğlu, Metin; Uçar, Arzu; Özhan, Güneş; Alak, Gonca
Although nickel (Ni) is an important cofactor for various enzymes in biological systems, it can cause serious problems when insufficient or excessive in an organism. Therefore, it is very important to investigate Ni in biological systems, especially in cells with its related pathogenic mechanism. This study was carried out to demonstrate the effects of zingerone (ZO) and rutin (RN) administration against nickel chloride (NiCl2) toxicity on neurobehavioral performance and brain oxidative status in zebrafish (Danio rerio) embryos/larvae on histological perspective. The experimental design of the study, which included twenty groups of fish, each containing 10 embryos, was prepared as semi-static and the trial continued for 96 hpf. In the obtained findings, it was determined that ZO and RN had a mitigating effect in this toxicity table where Ni caused oxidative stress in zebrafish larvae, induced DNA damage and apoptosis. A similar picture is valid for malformation processes as well as survival and hatching rates. These results showed that nickel is toxic to developing embryos via acting different mechanisms. In conclusion, we observed that ZO and RN have a greater effect on physiology, DNA damage and apoptosis than gross morphology, with a significant ameliorative effect.
Elimination of the B4galnt1 Gene Normalizes Lifespan and Prevents Pathology in Tay-Sachs Disease Mice
(Elsevier, 2023) Seyrantepe, Volkan
Tay-Sachs disease is a neurodegenerative lysosomal storage disorder caused by mutations in the Hexa gene, which encodes the alpha subunit of lysosomal ß-hexaminidase A (HEXA). HEXA is responsible for the conversion of GM2 to GM3, therefore the deficiency leads to the accumulation of GM2 in the lysosomes, neurodegeneration, and eventual death. Currently, there is no efficient therapy for the disease yet.
Citation - WoS: 2
Citation - Scopus: 2
Gas Phase Fragmentation Behavior of Proline in Macrocyclic B7 Ions
(American Chemical Society, 2023) Taşoğlu, Çağdaş; Arslanoğlu, Alper; Yalçın, Talat
Thefragmentation characteristics of b (7) ionsproduced from proline-containing heptapeptides have been studiedin detail. The study has utilized the following C-terminally amidatedmodel peptides: PA(6), APA(5), A(2)PA(4), A(3)PA(3), A(4)PA(2), A(5)PA, A(6)P, PYAGFLV, PAGFLVY, PGFLVYA, PFLVYAG,PLVYAGF, PVYAGFL, YPAGFLV, YAPGFLV, YAGPFLV, YAGFPLV, YAGFLPV, YAGFLVP,PYAFLVG, PVLFYAG, A(2)PXA(3), and A(2)XPA(3) (where X = C, D, F, G, L, V, and Y, respectively). The resultshave shown that b (7) ions undergo head-to-tailcyclization and form a macrocyclic structure. Under the collision-induceddissociation (CID) condition, it generates nondirect sequence ionsregardless of the position of the proline and the neighboring aminoacid residues. This study highlights the unusual and unique fragmentationbehavior of proline-containing heptapeptides. Following the head-to-tailcyclization, the ring opens up and places the proline residue in theN-terminal position while forming a regular oxazolone form of b (2) ions for all peptide series. Then, the fragmentationreaction pathway is followed by the elimination of proline with itsC-terminal neighbor residue as an oxazolone (e.g., PXoxa) for all proline-containing peptide series.
A review on the removal of viruses by adsorption
(Gazi University, 2023) Eren, Muhammet Şakir Abdullah; Tanaydın, Elif Sila; Arslanoğlu, Hasan; Çiftçi, Harun
The potential dangers of Covid-19 (SARS-CoV-2 Infection), which spread to almost all countries from Wuhan, China's Hubei province in 2020, have been the focus of attention of scientists worldwide Serious impact processes of Covid-19, ranging from pneumonia to severe acute respiratory infections and from kidney failure to death, continue to threaten millions of people. Isolation of pandemic species is of great importance for the development of appropriate treatment protocols in emerging viral infections. For this, it is necessary to develop existing methods as well as new methods. Viruses do not exist in living form in nature and they need other creatures to transfer their genetic material. In this respect, water resources and air appear as the most important means of transmission. Adsorption processes for the transmission means can be applied to prevent the spread of viruses and to inactivate them. In this review, the interactions of viruses with various adsorbents containing carbonaceous, oxidized, porous anf metal organic framework materials were examined. Electrostatic interactions were found to be more effective in target types of adsorbing processes of adsorbents used in water and air purification. Since the virus surface carries various organic functional groups, it is seen that it will interact with different adsorbents electrostatic and in this way they can be removed and both isolated and rendered ineffective. We think that our study will contribute to effective solutions to prevent the spread of other pathogens, including coronaviruses, by adsorption processes to be applied to air and water sources and to disinfect the specified transmission means.

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