Person: TURAN, KADİR
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TURAN
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KADİR
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Publication Metadata only Chitosan-DNA nanoparticles: The effect of cell type and hydrolysis of chitosan on in vitro DNA transfection(TAYLOR & FRANCIS INC, 2006) TURAN, KADİR; Turan, Kadir; Nagata, KyosukeCommercial chitosan (Ch) with low (LMWCh) and medium molecular weight (MMWCh) were hydrolyzed in diluted hydrochloric acid by heating at different temperatures. The viscosity average molecular weight of Chs was gradually decreased from 450 to 14 kDa as a function of temperature. Ch fractions were used for formation of Ch-DNA nanoparticles and tested for the ability to introduce DNA into HEK293, Swiss3T3, HeLa, and MDCK cells in vitro. The average diameter of nanoparticles was 200-220 nm. The surface charge of nanoparticles varied depending on the Ch/DNA ratio. The cell lines different response to DNA transection with Ch fractions depended on molecular weight. HEK293 cells were efficiently transfected by nanoparticles prepared with Chs having a wide range of molecular weight (similar to 14-195 kDa). Swiss3T3 cells were efficiently transfected by Ch polymers with about <17 kDa. In contrast, HeLa and MDCK cells were highly resistant to DNA transfection with Ch polymers. These results strongly suggest that Ch polymers may be widely used for DNA trasnfection of the mammalian cells under optimized conditions.Publication Metadata only Dermatologic Findings in Renal Transplant Recipients: Possible Effects of Immunosuppression Regimen and p53 Mutations(ELSEVIER SCIENCE INC, 2010) TURAN, KADİR; Serdar, Z. A.; Eren, P. A.; Canbakan, M.; Turan, K.; Tellioglu, G.; Gulle, S.; Ozgezer, T.; Kara, M.; Berber, I.; Titiz, M. I.Objective. To analyze the dermatologic lesions and possible effects of immunosuppression treatment and p53 gene mutations on dermatologic findings in renal transplant recipients. Materials and Methods. The study included 163 renal transplant recipients. After dermatologic examination, cultures, and histopathologic and genetic analyses were performed. A single-strand conformation polymorphism technique was used to analyze p53 gene mutations. Patients were categorized into 3 groups according to time since the transplantation procedure. Results were analyzed using the chi(2) test, using a software program (SPSS version 13.0; SPSS, Inc, Chicago, Illinois). Results. Mean (SD) age of the 163 transplant recipients (65 women and 98 men) was 40 (11) years, and posttransplantation follow-up was 65 (55) months. The most frequently observed drug-related lesion was hypertrichosis, in 46 of 150 patients. Of 115 lesions, the most commonly observed were verruca vulgaris (n = 34) from viruses, and pityriasis versicolor (n = 21) from superficial fungal infections. Of the total group, 20 patients (12.2%) were mutation carriers. Compared with the entire cohort, the group with premalignant lesions demonstrated more p53 mutations (11% vs 50%; P = .004). Patients given cyclosporine therapy exhibited more premalignant or malignant cutaneous lesions compared with patients who received other agents (P = .03). Conclusion. Patients carrying p53 mutations developed a malignant lesion in the late posttransplantation period, which suggests the importance of prediction of risk.Publication Metadata only The Human MTCH2 Protein Has a Negative Effect On the Influenza a Virus Replication(2021-12-26) TURAN, KADİR; Ulupınar P., Çağlayan E., Turan K.Influenza A viruses have a segmented genome consists of eight single-stranded RNA molecules. Viral replication and transcription are carried out by viral RNA polymerase (RdRP), which consists of PB2, PB2 and PA subunits. During viral infection, RdRP and other viral proteins interact with several host proteins to perform their functions. In this work, mitochondrial carrier homolog 2 (MTCH2) protein, which was found to be associated with viral PA protein by yeast two-hybrid assay, was investigated its importance in terms of viral replication. In order to detect the effects of MTCH2 on virus replication in HeLa and HEK293 cells, the protein level was artificially changed. RNA interference and CRISPR/Cas9 techniques were used for down-regulation of the MTCH2. To increase the MTCH2, the HEK293 cells were transfected with pCHA-MTCH2 plasmid. The cells with altered MTCH2 transcript/protein level were infected with influenza A/WSN and A/DkPen viruses, and the viral replication was evaluated by detection of viral RNA/proteins with qPCR/Western blot techniques and plaque assays. In addition, the RdRP activities in these cells were determined by mini-replicon tests. A significant increase of viral mRNA/protein was observed in knockdown HeLa. It was shown that avian influenza A/DkPen replication was affected more. The over-expression of MTCH2 in HEK293 cells had a negative effect on the viral RdRP. These results showed that the MTCH2 is a negative cellular factor for influenza A virus. Although deletion of MTCH2 genes was detected in HEK293 cells knocked out by CRISPR/Cas9 technique, no negative effect on viral replication was observed. This situation is thought to be caused by heterozygosity or some other factors. From these results, it was concluded that the MTCH2 protein functions as a negative regulation factor for influenza A viruses. This work was supported by a grant of the Scientific and Technological Research Council of Turkey (SBAG-112S518).Keywords: Influenza a Viruses, MTCH2 Protein, Viral Rna Polymerase, PA ProteinPublication Metadata only Interaction of influenza A virus NS2/NEP protein with the amino-terminal part of Nup214(TUBITAK SCIENTIFIC & TECHNICAL RESEARCH COUNCIL TURKEY, 2020) TURAN, KADİR; Senbas Akyazi, Burcak; Pirincal, Aysegul; Kawaguchi, Atsushi; Nagata, Kyosuke; Turan, KadirInfluenza A viruses have a single-stranded RNA genome consisting of 8 segments. Each RNA segment associates with the nucleoprotein (NP) and viral RNA polymerase to and from a viral ribonucleoprotein (vRNP) particle. The viral mRNA synthesis is dependent on a capped pruner derived from nascent host RNA transcripts. For these processes to take place, vRNPs must pass through the cell nuclear pore complex (NPC) to the nucleus. The influenza A virus NS2 protein, also called the nuclear export protein (NES), has an important role in the nucleocytoplasmic transport of vRNPs. This protein interacts with the host cellular nucleoporins during the nuclear export of vRNPs. In this study, the human nucleoporin 214 (Nup214) was identified as an NS2-binding protein by using a yeast two-hybrid assay. The interaction between NS2 and human Nup214 was confirmed in both yeast and mammalian cells. It has been shown that the NS2 protein interacts with the amino terminal FG domain of the Nup214 protein. The influenza viral replication was suppressed in knockdown cells for the Nup214 protein. It was concluded that the FG domains of nucleoporins have an important role in the interaction of the influenza NS2 protein with host NPC for vRNA export.Publication Open Access Nuclear MxA proteins form a complex with influenza virus NP and inhibit the transcription of the engineered influenza virus genome(OXFORD UNIV PRESS, 2004-01-21) TURAN, KADİR; Turan, K; Mibayashi, M; Sugiyama, K; Saito, S; Numajiri, A; Nagata, KMx proteins belong to the dynamin superfamily of high molecular weight GTPases and interfere with multiplication of a wide variety of viruses. Earlier studies show that nuclear mouse Mx1 and human MxA designed to be localized in the nucleus inhibit the transcription step of the influenza virus genome. Here we set a transient influenza virus transcription system using luciferase as a reporter gene and cells expressing the three RNA polymerase subunits, PB1, PB2 and PA, and NP. We used this reporter assay system and nuclear-localized MxA proteins to get clues for elucidating the anti-influenza virus activity of MxA. Nuclear-localized VP16-MxA and MxA-TAg NLS strongly interfered with the influenza virus transcription. Over-expression of PB2 led to a slight resumption of the transcription inhibition by nuclear MxA, whereas over-expression of PB1 and PA did not affect the MxA activity. Of interest is that the inhibitory activity of the nuclear MxA was markedly neutralized by over-expression of NP. An NP devoid of its C-terminal region, but containing the N-terminal RNA binding domain, also neutralized the VP16-MxA activity in a dose-dependent manner, whereas an NP lacking the N-terminal region did not affect the VP16-MxA activity. Further, not only VP16-MxA but also the wild-type MxA was found to interact with NP in influenza virus-infected cells. This indicates that the nuclear MxA suppresses the influenza virus transcription by interacting with not only PB2 but also NP.Publication Open Access Heterologous expression and initial in silico characterization of a novel snakin-Z peptide(2023-08-01) TURAN, KADİR; Teker T., Albayrak G., Turan K.Heterologous expression of the plant-derived snakin-Z (SNK-Z) peptide was carried out inEscherichia coliBL21 and Mach 1 strains using the pET14b, and pGEX-6P-1 vectors, and its tertiary structure was determined. The most efficient production of the recombinant fusion peptide (GST/SNK-Z) in both strains was achieved by induction with 0.1 mM isopropyl β-D-1-thiogalactopyranoside at 32°C. GST/SNK-Z with 30.14kDa which yielded 6.5mg/L protein, was purified by affinity chromatography followed by dialysis. The GST tags were removed using PreScission protease. The IC50of GST/SNK-Z was calculated as 12.07 µM forStaphylococcus aureus(ATCC 25923) using nonlinear regression analysis. The secondary structure of recombinant SNK-Z consisted of α-helix and coil sites. It’s 3-D model was generated with a confidence score of -0.20 and a template modeling score of 0.69 ± 0.12. The predicted solvent accessibility and B-factor profile were detected.This is the first report of heterologous expression of SNK-Z inE. coli. Our study provides fundamental data for the large-scale production of SNK-Z, which has a high potential for use in the pharmaceutical industry because of its previously reported antimicrobial effects.Publication Open Access Human sorting nexin 2 protein interacts with Influenza A virus PA protein and has a negative regulatory effect on the virus replication(SPRINGER, 2022-01) TURAN, KADİR; Kocmar, Tugba; Caglayan, Elif; Rayaman, Erkan; Nagata, Kyosuke; Turan, KadirBackground Replication of the influenza A viruses occurs in the cells through the viral RdRP consisting of PB1, PB2, and PA. Several cellular proteins are involved in these processes. This study aims to reveal the interaction between human SNX2 protein and the PA protein and the effects of the SNX2 on the virus replication. Results To identify potential host interacting proteins to the PA, yeast two-hybrid assay was carried out with HEK293 cell cDNA library and the PA as a bait. We focused on SNX2 protein, which interacts with the PA in the yeast cells. By using the co-immunoprecipitation assays, it has been demonstrated that the amino-terminal part of the PA was important for binding to the SNX2. Immunolocalization of the proteins in HeLa cells supported this interaction. Knockdown of the SNX2 with siRNA in the cells resulted in a significant increase in both viral transcripts and virus growth. However, the increase of SNX2 in transfected cells didn't cause a significant change in the viral RdRP activity in minireplicon assay. This may suggest that the negative effect of SNX2 on the virus replication could be saturated with its authentic intra-cellular amount. Conclusions This study revealed that the SNX2 and PA protein interact with each other in both yeast and HEK293 cells, and the SNX2 has a negative regulatory function on the virus replication. However, more knowledge is required to elucidate the action mechanism of the SNX2 on the influenza A virus replication at the molecular level.Publication Open Access Effects of intra- and extracellular factors on anti-aging klotho gene expression(FUNPEC-EDITORA, 2011) TURAN, KADİR; Turan, K.; Ata, P.Inactivation of the klotho gene in mice causes serious systemic disorders, resembling human aging. However, at the molecular level, its action mechanisms are not well understood. The stimulatory or inhibitory effects of cis- and trans-regulatory factors on the klotho gene expression are also still unclear. We studied the effects of intra- and extracellular factors on human klotho gene expression. For this purpose, pHKP-Luc and pHKP-GFP reporter vectors were constructed with the 2.1-kbp upstream region of human klotho, covering its promoter region, using luciferase and GFP genes as the reporter. A series of vectors that have deletions in the upstream region of the klotho gene were constructed to assay cis-acting factors. Deletion of some parts of the klotho gene upstream region significantly affected reporter gene expression in HEK293 cells. p16 and p53 proteins inhibited reporter luciferase expression under the control of human klotho promoter in a dose-dependent manner. Calcium and phosphate ions stimulated klotho expression. p21, PTH, IGF-1, and angiotensin-II had no significant effect on klotho expression in HEK293 cells.Publication Open Access An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast-two-hybrid screening data(2023-06-02) TURAN, KADİR; Çağlayan E., Turan K.The human C14orf166 protein, also known as RNA transcription, translation, and transport factor, shows positive modulatory activity on the cellular RNA polymerase II enzyme. This protein is a component of the tRNA-splicing ligase complex and is involved in RNA metabolism. It also functions in the nucleo-cytoplasmic transport of RNA molecules. The C14orf166 protein has been reported to be associated with some types of cancer. It has been shown that the C14orf166 protein binds to the influenza A virus RNA polymerase PA subunit and has a stimulating effect on viral replication. In this study, candidate interactor proteins for influenza A virus PA protein were screened with a Y2H assay using HEK293 Matchmaker cDNA. The C14orf166 protein fragments in different sizes were found to interact with the PA. The three-dimensional structures of the viral PA and C14orf166 proteins interacting with the PA were generated using the I-TASSER algorithm. The interaction models between these proteins were predicted with the ClusPro protein docking algorithm and analyzed with PyMol software. The results revealed that the carboxy-terminal end of the C14orf166 protein is involved in this interaction, and it is highly possible that it binds to the carboxyterminal of the PA protein. Although amino acid residues in the interaction area of the PA protein with the C14orf166 showed distribution from 450th to 700th position, the intense interaction region was revealed to be at amino acid positions 610–630.Publication Metadata only TÜSEB destekli COVID-19 aşı projeleri(2021-09-09) TURAN, KADİR; Turan K.