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Gooseberry Anthocyanins Alleviate Insulin Resistance By Regulating Ceramide Metabolism In High Fat Diet Mice, Xian Tang, Jun Gao, Jinpeng Huang, Chenjuan Zhang, Hongwei Liu, Jie Wei
Gooseberry Anthocyanins Alleviate Insulin Resistance By Regulating Ceramide Metabolism In High Fat Diet Mice, Xian Tang, Jun Gao, Jinpeng Huang, Chenjuan Zhang, Hongwei Liu, Jie Wei
Turkish Journal of Biology
Background/aim: Obesity is the fifth largest risk factor of death in the world. The ceramide produced by obesity is closely related to insulin resistance (IR) caused by obesity. At present, the commercially available weight loss products have large side effects and limited therapeutic effects. Therefore, it is particularly important to find effective natural nontoxic products to treat obesity and explore its possible pathways and mechanisms. Materials and methods: In this paper, a high-fat diet (HFD) mice model was established by intragastric administration of high-fat emulsion to investigate the intervention effect of Gooseberry anthocyanins (GA) on IR in HFD mice. We …
Androgen Receptor Contributes To Repairing Dna Damage Induced By Inflammation And Oxidative Stress In Prostate Cancer, Bi̇lge Debeleç Bütüner, Nurşah Ertunç Hasbal, Eli̇f İşel, Dirk Roggenbuck, Kemal Sami̇ Korkmaz
Androgen Receptor Contributes To Repairing Dna Damage Induced By Inflammation And Oxidative Stress In Prostate Cancer, Bi̇lge Debeleç Bütüner, Nurşah Ertunç Hasbal, Eli̇f İşel, Dirk Roggenbuck, Kemal Sami̇ Korkmaz
Turkish Journal of Biology
Background: Androgen deprivation therapy remains the first-line therapy option for prostate cancer, mostly resulting in the transition of the disease to a castration-resistant state. The lack of androgen signaling during therapy affects various cellular processes, which sometimes paradoxically contributes to cancer progression. As androgen receptor (AR) signaling is known to contribute to oxidative stress regulation, loss of AR may also affect DNA damage level and the response mechanism in oxidant and inflammatory conditions of the prostate tumor microenvironment. Therefore, this study aimed to investigate the role of AR and AR-regulated tumor suppressor NKX3.1 upon oxidative stress-induced DNA damage response (DDR) …
Ribosomal Protein L8 Regulates The Expression And Splicing Pattern Of Genes Associated With Cancer-Related Pathways, Leilei Xu, Gui Yang, Bin Song, Dong Chen, Akbar. Yunus, Jiangtao Chen, Xiaogang Yang, Zheng Tian
Ribosomal Protein L8 Regulates The Expression And Splicing Pattern Of Genes Associated With Cancer-Related Pathways, Leilei Xu, Gui Yang, Bin Song, Dong Chen, Akbar. Yunus, Jiangtao Chen, Xiaogang Yang, Zheng Tian
Turkish Journal of Biology
Background/aim: Ribosomal proteins have been shown to perform unique extraribosomal functions in cell apoptosis and other biological processes. Ribosomal protein L8 (RPL8) not only has important nonribosomal regulatory functions but also participates in the oncogenesis and development of tumors. However, the specific biological functions and pathways involved in this process are still unknown. Materials and methods: RPL8 was overexpressed (RPL8-OE) in HeLa cells. MTT assay and flow cytometry were used to detect cell proliferation and apoptosis, respectively. Transcriptome sequencing was performed to analyze the differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs) by RPL8-OE, both of which were …
The Effects Of Anti-Pd-L1 Monoclonal Antibody On The Expression Of Angiogenesis And Invasion-Related Genes, Cansu Babahan, Samira Abdi Abgarmi, Fatma Gi̇zem Sonugür, Müge Öçal Demi̇rtaş, Hakan Akbulut
The Effects Of Anti-Pd-L1 Monoclonal Antibody On The Expression Of Angiogenesis And Invasion-Related Genes, Cansu Babahan, Samira Abdi Abgarmi, Fatma Gi̇zem Sonugür, Müge Öçal Demi̇rtaş, Hakan Akbulut
Turkish Journal of Biology
Background/aim: The role of PD-L1 in regulating the immunosuppressive tumor microenvironment via its binding on PD-1 receptors is extensively studied. The PD-1/PD-L1 axis is a significant way of cancer immune escape, and PD-L1 expression on tumor cells is suggested as a predictive marker for anti-PD-1/PD-L1 monoclonal antibodies (MoAbs). However, the tumor-intrinsic role of PDL1 is not known well. Therefore, we aimed to investigate the effects of anti-PD-L1 antibodies on the expression of angiogenesis and metastasis-related genes in tumor cells. Materials and methods: The experiments were done with prostate cancer and melanoma cells with low PD-L1 expression (<5%) and prostate and breast cancer cells with high PD-L1 expression (>50%). The gene …
Antioxidant Potential Of Nanomaterials, David Gonzalez Flores, Javier Espino, Jose A. Pariente
Antioxidant Potential Of Nanomaterials, David Gonzalez Flores, Javier Espino, Jose A. Pariente
Turkish Journal of Biology
Background/aim: The novel field of nanomaterials allows infinite possibilities in order to create antioxidant therapies. The present review is aimed to describe the state of art concerning on nanomaterials and their effects on reactive oxygen species (ROS) production. A wide range of nanoparticles has been designed for this purpose, and each one possesses some particular characteristics which allow these significant antioxidant results. Several in vivo and in vitro works state the ability of these nanoparticles to mimic the redox systems of the cells, and thus, the potential role of nanoparticles as antioxidant treatment for several diseases. Materials and methods: This …
A Review With Updated Perspectives On In Vitro And In Vivo Wound Healing Models, Murni Nazira Sarian, Nabilah Zulkefli, Shazeli Zain, Sandra Maniam, Sharida Fakurazi
A Review With Updated Perspectives On In Vitro And In Vivo Wound Healing Models, Murni Nazira Sarian, Nabilah Zulkefli, Shazeli Zain, Sandra Maniam, Sharida Fakurazi
Turkish Journal of Biology
A skin wound or perforation triggers a series of homeostatic reactions to safeguard internal organs from invasion by pathogens or other substances that could damage body tissues. An injury may occasionally heal quickly, leading to the closure of the skin's structure. Healing from chronic wounds takes a long time. Although many treatment options are available to manage wound healing, an unmet therapy need remains because of the complexity of the processes and the other factors involved. It is crucial to conduct consistent research on novel therapeutic approaches to find an effective healing agent. Therefore, this work aims to cover various …
Soloxolone Methyl Induces Apoptosis And Oxidative/Er Stress In Breast Cancer Cells And Target Cancer Stem Cell Population, Eli̇f Ertürk, Oğuzhan Akgün, Yaren Yildiz, Pinar Kalkan, Oksana V. Salomatina, Nariman F. Salakhutdinov, Engi̇n Ulukaya, Ferda Ari
Soloxolone Methyl Induces Apoptosis And Oxidative/Er Stress In Breast Cancer Cells And Target Cancer Stem Cell Population, Eli̇f Ertürk, Oğuzhan Akgün, Yaren Yildiz, Pinar Kalkan, Oksana V. Salomatina, Nariman F. Salakhutdinov, Engi̇n Ulukaya, Ferda Ari
Turkish Journal of Biology
One of the most prevalent malignancies in women and one of the leading causes of cancer-related death is breast cancer. There is a need for new treatment approaches and drugs for breast cancer. Many studies show the high potential of triterpene compounds and their semisynthetic derivatives as anticancer agents due to their ability to induce apoptosis and suppress tumorigenesis. The effects of soloxolone methyl (SM), a semisynthetic derivative of 18-H-glycyrrhetinic acid, on the cytotoxicity and apoptosis of human breast cancer cell line (T-47D) and cancer stem cell (CSCs) population (mammospheres; CD44+/CD24-antigen) derived from breast cancer cells, were examined in this …
Antileukemic Potential Of Nile Blue-Mediated Photodynamic Therapy On Hl60 Human Myeloid Leukemia Cells, Serçi̇n Özlem Çalişkan, Aynur Karadağ, Bariş Uzunok, Numan Taşpinar, Berna Akin, Meti̇n Çalişkan, Rahşan Ilikçi Sağkan
Antileukemic Potential Of Nile Blue-Mediated Photodynamic Therapy On Hl60 Human Myeloid Leukemia Cells, Serçi̇n Özlem Çalişkan, Aynur Karadağ, Bariş Uzunok, Numan Taşpinar, Berna Akin, Meti̇n Çalişkan, Rahşan Ilikçi Sağkan
Turkish Journal of Biology
Background/aim: Photodynamic therapy (PDT) has received great attention over the past decade in the treatment of diseases such as leukemia which is a cancer of the blood and bone marrow cells that causes a significant number of deaths worldwide. In this study, it was aimed to investigate the effects of Nile blue-mediated PDT (NB-mediated PDT) on HL60 cells. Materials and methods: The effect of NB-mediated PDT on cell proliferation was evaluated with cell volume analysis using flow cytometry at 24 h. Cell apoptosis, ROS production, mitochondrial membrane potential, and cell cycle analysis were evaluated using annexin V-FITC, H2 DCFDA, JC-1, …
Targeting Of Notch, Il-1, And Leptin Has Therapeutic Potential In Xenograft Colorectal Cancer, Rumeysa Özyurt, Ni̇lüfer Erkasap, Mete Özkurt, Serdar Mustafa Erkasap, Konstanti̇nos Di̇mas, Ayşe Çakir Gündoğdu, Engi̇n Ulukaya
Targeting Of Notch, Il-1, And Leptin Has Therapeutic Potential In Xenograft Colorectal Cancer, Rumeysa Özyurt, Ni̇lüfer Erkasap, Mete Özkurt, Serdar Mustafa Erkasap, Konstanti̇nos Di̇mas, Ayşe Çakir Gündoğdu, Engi̇n Ulukaya
Turkish Journal of Biology
Background/aim: Colorectal cancer (CRC) is a fatal malignancy type and its occurence still needs to be explored mechanistically. Notch, IL-1, and leptin crosstalk is reported to play a role in the proliferation, migration, and expression of proangiogenic molecules. In this study, we aimed to investigate the effect of inhibition of Notch, IL-1, and leptin on CRC. Materials and methods: To generate colorectal cancer tumor xenografts, 1 × 107 cells from exponentially growing cultures of HCT15 cells were injected subcutaneously, at the axillary region of the left and right rear flanks of forty NOD.CB17-Prkdcscid/J (NOD/SCID) female mice. The mice were then …
Vitamin D Receptor Mediates Liver Ischemia And Reperfusion Injury By Autophagy-Regulated M2 Macrophage Polarization, Mingming Fang, Chen Zhong
Vitamin D Receptor Mediates Liver Ischemia And Reperfusion Injury By Autophagy-Regulated M2 Macrophage Polarization, Mingming Fang, Chen Zhong
Turkish Journal of Biology
Liver ischemia and reperfusion (IR) injury is the major complication of liver-related operations. Macrophage polarization has an essential effect on the mechanism of liver IR injury. Vitamin D receptor (VDR) has been found to regulate macrophage polarization and alleviate IR injury. Nevertheless, the correlation between VDR and macrophage polarization in liver IR injury has not been clearly elucidated. VDR knockout mice and wild-type littermates underwent partial liver ischemia for 90 min and reperfusion for 6 h. RAW264.7 cells were also used to verify the influence of VDR on macrophage polarization in vitro. VDR activation could promote M2 macrophage polarization and …
Linc00460 Mediates Hmga2 Expression Through Binding To Mirna-143-5p Competitively In Gastric Carcinoma, Xuqing Zhu, Yanli Xiang, Feifei Mo, Lingling Jin
Linc00460 Mediates Hmga2 Expression Through Binding To Mirna-143-5p Competitively In Gastric Carcinoma, Xuqing Zhu, Yanli Xiang, Feifei Mo, Lingling Jin
Turkish Journal of Biology
Background: Compelling evidence has manifested a strong association between aberrant expression of long noncoding RNAs (lncRNAs) and gastric carcinoma (GC) development. Nonetheless, biological impacts of differentially expressed lncRNAs (DElncRNAs) on GC are not scrutinized. Methods: Bioinformatics methods were employed for differential expression analysis and target gene prediction. MTT, colony formation, and Transwell methods were implemented for GC cell proliferation, migration, and invasion assessment. Western blot was implemented to test the protein level. The binding of genes was tested with dual-luciferase and RNA binding protein immunoprecipitation (RIP) approaches. Results: Noticeably high level of LINC00460 was observed in GC tissues and cells. …
Antiadipogenic And Antiobesogenic Effects Of Pterostilbene In 3t3-L1 Preadipocyte Models, Bi̇rgül Gülnar, İpek Canatar, Si̇bel Özdaş
Antiadipogenic And Antiobesogenic Effects Of Pterostilbene In 3t3-L1 Preadipocyte Models, Bi̇rgül Gülnar, İpek Canatar, Si̇bel Özdaş
Turkish Journal of Biology
Since obesity causes at least 2.8 million death each year and is a major risk factor for many diseases, it is critical to evaluate alternative treatment approaches. In this context, studies on the research of natural product-based therapeutics in the fight against obesity are increasing. In this study, it was aimed to evaluate the antiadipogenic and antiobesogenic efficacy of pterostilbene a natural phenolic compound in 3T3-L1 cells. The mature 3T3-L1 adipocytes were exposed to pterostilbene at different concentrations and half-maximum inhibitory concentrations (IC50) were determined by MTT assay. Oil-Red-O staining was applied to determine lipid accumulation. Phase contrast microscopy, Giemsa, …
A Ph-Responsive Shell-Sheddable Polymeric Nanoparticles As The Photodynamic Drug Carrier: Synthesis, Characterization, And In Vitro Studies, Jing Lu
Turkish Journal of Biology
Shell-sheddable nanoparticles, composed of amphiphilic blockpolymers, have emerged as an attractive vehicle for the site-specific delivery of therapeutic agents. In this study, pH-responsive sheddable copolymers bearing an orthoester linker were synthesized via the ring-opening polymerization between γ-benzyl-L-glutamate N-carboxyanhydride and orthoester-bearing poly (ethylene glycol) macroinitiator (PEG-pH-NH2). The obtained poly (ethylene glycol)-b-poly(γ-benzyl-L-glutamate) (PEG-PBLG) could form stable nanoparticles in aqueous solutions due to the amphiphilic nature of the block copolymers. The PEG-PBLG-based nanoparticle exhibited good stability in physiological conditions (pH 7.4), whereas the nanoparticle was disassembled under acidic conditions (pH 5.0). The nanoparticles could encapsulate a photosensitizer, protophorphyrin IX …
Effects Of Growth Factor Deprivation On Mkn-45 Spheroid Cells, Özlem Türksoy, Gökhan Terzi̇oğlu
Effects Of Growth Factor Deprivation On Mkn-45 Spheroid Cells, Özlem Türksoy, Gökhan Terzi̇oğlu
Turkish Journal of Biology
Background/aim: Serum and growth factor deprivation, a common cellular stressor in solid tumors, arises upon irradiation, chemotherapy, and antiangiogenesis. Spheroid body culture aims to enrich cancer stem cells by using low attachment conditions and some growth factors, such as basic fibroblast growth factor and epidermal growth factor to support the spheroid formation in serum-free spheroid culture. However, spheroid culture without any growth factors can imitate the tumor environment more realistically. In this study, we aimed to identify the effect of growth factor deprivation on the MKN-45 gastric cancer cell line in terms of stemness characteristics. Materials and methods: The spheroids …
Boquila: Ngs Read Simulator To Eliminate Read Nucleotide Bias In Sequence Analysis, Ümi̇t Akköse, Ogün Adebali̇
Boquila: Ngs Read Simulator To Eliminate Read Nucleotide Bias In Sequence Analysis, Ümi̇t Akköse, Ogün Adebali̇
Turkish Journal of Biology
Sequence content is heterogeneous throughout genomes. Therefore, genome-wide next-generation sequencing (NGS) reads biased towards specific nucleotide profiles are affected by the genome-wide heterogeneous nucleotide distribution. Boquila generates sequences that mimic the nucleotide profile of true reads, which can be used to correct the nucleotide-based bias of genome-wide distribution of NGS reads. Boquila can be configured to generate reads from only specified regions of the reference genome. It also allows the use of input DNA sequencing to correct the bias due to the copy number variations in the genome. Boquila uses standard file formats for input and output data, and it …
Emerging Applications Of 3d Engineered Constructs From Plant Seed Extracts, Sedat Odabaş, Bora Gari̇pcan, Rihab Ksouri
Emerging Applications Of 3d Engineered Constructs From Plant Seed Extracts, Sedat Odabaş, Bora Gari̇pcan, Rihab Ksouri
Turkish Journal of Biology
Seeds, by-products derived from various plants such as mango, quince, and apples, are considered waste, though they have emerging commercial potential, and have been used in biological, industrial, and physiological research. Seed-derived natural macromolecules- mainly polysaccharides, mucilage, gums, and cellulose-have physicochemical and structural diversification, giving the potential for forming gels, texturing, thickening, and providing interfacial adsorption. Seed-derived natural macromolecules have been widely used during the last few years in cell research and tissue engineering applications. Their widespread approachability and safety, high rate of biodegradability, biocompatibility, supporting cell proliferation, and extracellular matrix synthesis are the main properties making plant seed derivatives …
Astragaloside Iv Improves Renal Function And Alleviates Renal Damage And Inflammation In Rats With Chronic Glomerulonephritis, Dong Zhang, Zongying Li, Yuan Gao, Hailing Sun
Astragaloside Iv Improves Renal Function And Alleviates Renal Damage And Inflammation In Rats With Chronic Glomerulonephritis, Dong Zhang, Zongying Li, Yuan Gao, Hailing Sun
Turkish Journal of Biology
From Astragalus membranaceus (Fisch.) Bge.var. mongholicus (Bge.) Hsiao, astragaloside IV (AS-IV), a saponin can be purified and is considered traditional Chinese medicine. The purpose of this study was to evaluate the AS-IV-mediated mechanism on chronic glomerulonephritis (CGN). A cationic bovine serum albumin-induced CGN rat model was established and 10, 15, or 20 mg/kg of AS-IV was administered to measure renal function and inflammatory infiltration. Influences of AS-IV on proliferation, cell cycle, and inflammation of LPS-induced rat mesangial cells (RMCs) were determined. The results demonstrated that AS-IV alleviated renal dysfunction, renal lesions, and inflammation in CGN rats. AS-IV prolonged the G0-G1 …
Methionine Restriction And Cancer Treatment: A Systems Biology Study Of Yeast To Investigate The Possible Key Players, Esra Börklü
Methionine Restriction And Cancer Treatment: A Systems Biology Study Of Yeast To Investigate The Possible Key Players, Esra Börklü
Turkish Journal of Biology
Background/aim: Dietary restriction, mainly carbon and/or methionine restriction are among the upcoming supporting interventions along with chemotherapy in various cancers. Although dietary restriction has been proven to be beneficial, the main cellular machineries affected by its administration lacks deeper information considerably, a notable pitfall in its use as a personalized nutritional approach. Materials and methods: In this study, cellular effects of methionine restriction on a yeast model are explored via systems biology approaches. The methionine biosynthesis network, constructed by integrating interaction data with gene ontology terms, was analysed topologically, and proved to be informative about the intertwined relationship of methionine …
Application Of Scanning Acoustic Microscopy For Evaluation Of Mmp Activation In Multiple Cancer Cell Lines With A Smart Probe, Hasan Ozan Otaş, Nasi̇re Uluç, İrem Demi̇rkan, Ayli̇n Alkan, Açelya Yilmazer, Seda Yaşa Ercan, Davod Khalafkhany, Nesri̇n Özören, Mehmet Burçi̇n Ünlü
Application Of Scanning Acoustic Microscopy For Evaluation Of Mmp Activation In Multiple Cancer Cell Lines With A Smart Probe, Hasan Ozan Otaş, Nasi̇re Uluç, İrem Demi̇rkan, Ayli̇n Alkan, Açelya Yilmazer, Seda Yaşa Ercan, Davod Khalafkhany, Nesri̇n Özören, Mehmet Burçi̇n Ünlü
Turkish Journal of Biology
Background/aim: Matrix metalloproteinases (MMPs) play an important role in the evaluation of many cancer types; however, the detection usually presents a challenge. Further assays for a better understanding of the fundamental roles of MMPs in pathophysiology are still needed. We aimed to use an activatable probe in scanning acoustic microscopy (SAM) to evaluate acoustically if the probe can aid the visualization of the effects of in vitro MMP activity. Materials and methods: We applied scanning acoustic impedance microscopy to obtain acoustic impedance maps of the cell line models of HT1080, THP-1, and SK-MEL-28 with and without MMPSense 680 probe incubation. …
Functional Enhancement Of Acute Infracted Heart By Coinjection Of Autologous Adipose-Derived Stem Cells With Matrigel, Baozhu Wang, Mengmeng Wang, Yan Li, Meihua Shao, Dan Zhan, Shiqi Yan, Xiang Ma, Yitong Ma
Functional Enhancement Of Acute Infracted Heart By Coinjection Of Autologous Adipose-Derived Stem Cells With Matrigel, Baozhu Wang, Mengmeng Wang, Yan Li, Meihua Shao, Dan Zhan, Shiqi Yan, Xiang Ma, Yitong Ma
Turkish Journal of Biology
Recent clinical developments in tissue bioengineering have applications in acute cardiac ischemia and infarction and include the use of stem cells that combine injectable scaffold material. This study aimed to evaluate the effects of adipose-derived stem cells (ADSCs) that combine the Matrigel scaffold on cardiac morphology/functions. The autologous ADSCs myocardial infarction (MI) model was induced by the permanent ligation method of the left anterior descending coronary artery (LAD). MI-operated rats were randomly divided into PBS group, Matrigel group, PBS plus ADSCs group (PBS+ADSCs), and Matrigel plus ADSCs group (Matrigel+ADSCs). Matrigel was used as an injectable scaffold. Rats with a 1-week-old …
Tsrna-15797-Modified Bmsc-Derived Exosomes Mediate Lfng To Induce Angiogenesis In Osteonecrosis Of The Femoral Head, Shanhong Fang, Mengqiang You, Jie Wei, Peng Chen
Tsrna-15797-Modified Bmsc-Derived Exosomes Mediate Lfng To Induce Angiogenesis In Osteonecrosis Of The Femoral Head, Shanhong Fang, Mengqiang You, Jie Wei, Peng Chen
Turkish Journal of Biology
Background: Osteonecrosis of the femoral head (ONFH) is an ischemic disease characterized by the impairment of angiogenesis. We have previously elucidated the role of tsRNAs and BMSC exosomes in ONFH, but whether tsRNA-modified BMSC exosomes promote angiogenesis in ONFH remains unclear. Methods: The expression of angiogenesis-related tsRNA in plasma exosomes from ONFH patients was examined by q-PCR. The function of tsRNA in HUVECs was identified by CCK-8 and angiogenesis assay. Exosomes purified from tsRNA-15797 overexpressed BMSCs were cocultured with HUVECs to examine their role in angiogenesis. The molecule mechanism of tsRNA-15797-modified exosomes was explored by RNA sequencing, dual-luciferase assay, and …
Cryogenic X-Ray Crystallographic Studies Of Biomacromolecules At Turkish Light Source "Turkish Delight", Necati̇ Atalay, Enver Kami̇l Akcan, Mehmet Gül, Esra Ayan, Ebru Destan, Fatma Betül Ertem Kuzucu, Nuretti̇n Tokay, Bariş Çakilkaya, Zeli̇ş Nergi̇z, Gözde Karakadioğlu Usta, Abdullah Kepceoğlu, İlki̇n Yapici, Bi̇lge Tosun, Ni̇lüfer Baldir, Günseli̇ Yildirim, J Austin Johnson, Ömür Güven, Alaleh Shafiei, Nazli Eylül Arslan, Merve Yilmaz, Cahi̇ne Kulakman, Seyi̇de Seda Paydos, Seynep Sena Çi̇nal, Kardelen Şabanoğlu, Ayşegül Pazarçevi̇ren, Ayşenur Yilmaz, Başak Canbay, Bengi̇su Aşçi, Esra Kartal, Serra Tavli, Mehmet Çaliseki̇, Günce Göç, Ari̇f Mermer, Gamze Yeşi̇lay, Sevde Altuntaş, Hiroshi Tateishi, Masami Otsuka, Mikako Fujita, Şaban Teki̇n, Hali̇li̇brahi̇m Çi̇ftçi̇, Serdar Durdaği, Gi̇zem Di̇nler Doğanay, Ezgi̇ Karaca, Burcu Kaplan Türköz, Burak Veli̇ Kabasakal, Ahmet Kati, Hasan Demi̇rci̇
Cryogenic X-Ray Crystallographic Studies Of Biomacromolecules At Turkish Light Source "Turkish Delight", Necati̇ Atalay, Enver Kami̇l Akcan, Mehmet Gül, Esra Ayan, Ebru Destan, Fatma Betül Ertem Kuzucu, Nuretti̇n Tokay, Bariş Çakilkaya, Zeli̇ş Nergi̇z, Gözde Karakadioğlu Usta, Abdullah Kepceoğlu, İlki̇n Yapici, Bi̇lge Tosun, Ni̇lüfer Baldir, Günseli̇ Yildirim, J Austin Johnson, Ömür Güven, Alaleh Shafiei, Nazli Eylül Arslan, Merve Yilmaz, Cahi̇ne Kulakman, Seyi̇de Seda Paydos, Seynep Sena Çi̇nal, Kardelen Şabanoğlu, Ayşegül Pazarçevi̇ren, Ayşenur Yilmaz, Başak Canbay, Bengi̇su Aşçi, Esra Kartal, Serra Tavli, Mehmet Çaliseki̇, Günce Göç, Ari̇f Mermer, Gamze Yeşi̇lay, Sevde Altuntaş, Hiroshi Tateishi, Masami Otsuka, Mikako Fujita, Şaban Teki̇n, Hali̇li̇brahi̇m Çi̇ftçi̇, Serdar Durdaği, Gi̇zem Di̇nler Doğanay, Ezgi̇ Karaca, Burcu Kaplan Türköz, Burak Veli̇ Kabasakal, Ahmet Kati, Hasan Demi̇rci̇
Turkish Journal of Biology
X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, İstanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and …
Sdf-1 Induces Directional Chemotaxis Of Endogenous Bmscs At The Intervertebral Fusion Site And Promotes Osteogenic Differentiation By Regulating Wnt/Ss-Catenin In The Bone Marrow Chimera Spinal Intervertebral Fusion Mouse Model, Qiwen Zhang, Ning Liang, Bin He, Siyou Wu, Depeng Wen, Xiaoyong Tang, Xiongcheng Shen
Sdf-1 Induces Directional Chemotaxis Of Endogenous Bmscs At The Intervertebral Fusion Site And Promotes Osteogenic Differentiation By Regulating Wnt/Ss-Catenin In The Bone Marrow Chimera Spinal Intervertebral Fusion Mouse Model, Qiwen Zhang, Ning Liang, Bin He, Siyou Wu, Depeng Wen, Xiaoyong Tang, Xiongcheng Shen
Turkish Journal of Biology
Clinical observations show that the current spinal fusion with internal fixation has a nonfusion rate of 5%-35%; however, methods to promote spinal fusion are limited. This study aimed to investigate the role of SDF-1-induced directional chemotaxis of BMSCs in bone marrow chimera spinal intervertebral fusion mouse model. BMSCs were isolated from bone marrow and identified by detecting CD44/CD34 positive cells. BMSCs (GFP-BMSCs) were labeled with GFP for tracking in vivo. Mice were inoculated with GFP-BMSCs to construct bone marrow chimera spinal intervertebral fusion model, which were divided into BM-SIF model, BM-SIF+SDF-1, BM-SIF+SDF-1-Anta group. The callus area of intervertebral fusion site …
The Protective Impact Of Growth Hormone Against Rotenone-Induced Apoptotic Cell Death Via Acting On Endoplasmic Reticulum Stress And Autophagy Axis, Özge Rencüzoğullari, Selay Tornaci, Yağmur Çeli̇k, Nayat Narot Taş, Pinar Obakan Yerli̇kaya, Eli̇f Damla Arisan, Ajda Çoker Gürkan
The Protective Impact Of Growth Hormone Against Rotenone-Induced Apoptotic Cell Death Via Acting On Endoplasmic Reticulum Stress And Autophagy Axis, Özge Rencüzoğullari, Selay Tornaci, Yağmur Çeli̇k, Nayat Narot Taş, Pinar Obakan Yerli̇kaya, Eli̇f Damla Arisan, Ajda Çoker Gürkan
Turkish Journal of Biology
Human growth hormone (GH) is crucial modulator of cellular metabolisms, including cell proliferation and organ development, by stimulating insulin-like growth factor-1 (IGF-1), which has various functions such as cell proliferation, tissue growth, survival, or neuroprotection. Therefore, GH is implicated as a critical player in the cell and can enhance neurogenesis and provide neuroprotection during the treatment of neurological diseases such as Parkinson's disease (PD). In this study, the neuroprotective role of GH was investigated in rotenone-induced PD models for the first time. Both SH-SY5Y and SK-N-AS neuroblastoma cells were exposed to rotenone to mimic PD pathogenesis as stated in previous …
Hydroquinidine Displays A Significant Anti-Carcinogenic Activity In Breast And Ovarian Cancer Cells Via Inhibiting Cell-Cycle And Stimulating Apoptosis, Mervenur Yavuz, Betül Şahi̇n, Ahmet Tarik Baykal, Turan Demi̇rcan
Hydroquinidine Displays A Significant Anti-Carcinogenic Activity In Breast And Ovarian Cancer Cells Via Inhibiting Cell-Cycle And Stimulating Apoptosis, Mervenur Yavuz, Betül Şahi̇n, Ahmet Tarik Baykal, Turan Demi̇rcan
Turkish Journal of Biology
Breast and ovarian cancers are women's most commonly diagnosed cancers. Seeking an efficient anticarcinogenic compound is still a top priority regarding the aggressiveness of these cancers and the limited benefit of current therapies. Hydroquinidine (HQ) is a natural alkaloid used in arrhythmia and Brugada syndrome. As an ion channel blocker, HQ exhibits its activity by altering ion gradient and membrane potential. Considering the growing evidence of ion channel blockers' antineoplastic potential, we were prompted to test HQ's effect on breast and ovarian cancers. MCF-7 and SKOV-3 cell lines were used to inspect how HQ acts on survival, clonogenicity, migration, tumorigenicity, …
Rpi-1 (Human Dcdc2) Displays Functional Redundancy With Nephronophthisis 4 In Regulating Cilia Biogenesis In C. Elegans, Oktay İsmai̇l Kaplan
Rpi-1 (Human Dcdc2) Displays Functional Redundancy With Nephronophthisis 4 In Regulating Cilia Biogenesis In C. Elegans, Oktay İsmai̇l Kaplan
Turkish Journal of Biology
Projecting from most cell surfaces, cilia serve as important hubs for sensory and signaling processes and have been linked to a variety of human disorders, including Bardet-Biedl Syndrome (BBS), Meckel-Gruber Syndrome (MKS), Nephronophthisis (NPHP), and Joubert Syndrome, and these diseases are collectively known as a ciliopathy. DCDC2 is a ciliopathy protein that localizes to cilia; nevertheless, our understanding of the role of DCDC2 in cilia is still limited. We employed C. elegans to investigate the function of C. elegans RPI-1, a Caenorhabditis elegans ortholog of human DCDC2, in cilia and found that C. elegans RPI-1 localizes to the entire ciliary …
Mir-216b-5p Promotes Late Apoptosis/Necroptosis In Trastuzumab-Resistant Sk-Br-3 Cells, İştar Burcu Dolapçi, Senem Noyan, Ayşegül Yücel Polat, Hakan Gürdal, Bala Gür Dedeoğlu
Mir-216b-5p Promotes Late Apoptosis/Necroptosis In Trastuzumab-Resistant Sk-Br-3 Cells, İştar Burcu Dolapçi, Senem Noyan, Ayşegül Yücel Polat, Hakan Gürdal, Bala Gür Dedeoğlu
Turkish Journal of Biology
Breast cancer is the most common cancer in women. The human epidermal growth factor receptor 2 (HER2) overexpressing subtype is related to poor prognosis with an aggressive phenotype and is reported as one of the most commonly seen subtypes. Trastuzumab is prevalently used as a treatment method for HER2+ breast cancer however, resistance to the drug frequently occurs following the treatment. MicroRNAs (miRNAs) are 19-23 nucleotide long small RNAs, which regulate gene expression at posttranscriptional level and studies show that there are differentially expressed miRNAs between drug sensitive and resistant groups, indicating that they might have some key roles in …
Transcriptomic Profiling Of Mice Brain Under Bex3 Regulation, Zhimin Xu, Noor Bahadar, Yingxin Zhang, Shuang Tan, Zhongze Wang, Bingyi Ren, Shitao Liu, Huanyan Dai, Yaowu Zheng, Bing Han
Transcriptomic Profiling Of Mice Brain Under Bex3 Regulation, Zhimin Xu, Noor Bahadar, Yingxin Zhang, Shuang Tan, Zhongze Wang, Bingyi Ren, Shitao Liu, Huanyan Dai, Yaowu Zheng, Bing Han
Turkish Journal of Biology
BEX family genes are expressed in various tissues and play significant roles in neuronal development. A mouse model of Bex3 gene knock-out was generated in this study, using the CRISPR-Cas9 system. Transcriptomic analysis of the brain was performed to identify genes and pathways under Bex3 regulation. Essential biological functions under the control of Bex3 related to brain development were identified. Ninety-five genes were differentially expressed under Bex3-/- regulation, with 53 down and 42 up. Among down-regulated genes, LOC102633156 is a member of zf-C2H2, Xlr3a is an X-linked lymphocyte regulated gene, LOC101056144 is a hippocampal related gene, 2210418O10Rik and Fam205a3 are …
Noncoding Rnas In Apoptosis: Identification And Function, Özge Tüncel, Merve Kara, Bi̇lge Yaylak, İpek Erdoğan, Bünyami̇n Akgül
Noncoding Rnas In Apoptosis: Identification And Function, Özge Tüncel, Merve Kara, Bi̇lge Yaylak, İpek Erdoğan, Bünyami̇n Akgül
Turkish Journal of Biology
Apoptosis is a vital cellular process that is critical for the maintenance of homeostasis in health and disease. The derailment of apoptotic mechanisms has severe consequences such as abnormal development, cancer, and neurodegenerative diseases. Thus, there exist complex regulatory mechanisms in eukaryotes to preserve the balance between cell growth and cell death. Initially, protein-coding genes were prioritized in the search for such regulatory macromolecules involved in the regulation of apoptosis. However, recent genome annotations and transcriptomics studies have uncovered a plethora of regulatory noncoding RNAs that have the ability to modulate not only apoptosis but also many other biochemical processes …
Modeling Of C-Terminal Tail Of Human Sting And Its Interaction With Tank-Binding Kinase 1, Rahaf Ata Ouda Al-Masri, Hajara Audu-Bida, Şebnem Eşsi̇z
Modeling Of C-Terminal Tail Of Human Sting And Its Interaction With Tank-Binding Kinase 1, Rahaf Ata Ouda Al-Masri, Hajara Audu-Bida, Şebnem Eşsi̇z
Turkish Journal of Biology
Stimulator of interferon genes (STING) plays a significant role in a cell's intracellular defense against pathogens or self-DNA by inducing inflammation or apoptosis through a pathway known as cGAS-cGAMP-STING. STING uses one of its domains, the C-terminal tail (CTT) to recruit the members of the pathway. However, the structure of this domain has not been solved experimentally. STING conformation is open and more flexible when inactive. When STING gets activated by cGAMP, its conformation changes to a closed state covered by 4 beta-sheets over the binding site. This conformational change leads to its binding to Tank-binding kinase 1 (TBK1). TBK1 …