Person: AKBAŞ, FAHRİ
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Publication Metadata only Molecular cloning and characterization of NAD(+) dependent isocitrate dehydrogenase enzyme from Shewanella putrefaciens(2021-10-01T00:00:00Z) Fahri, Akbas; Metin, Demirel; Ahmet, Ozaydin; Sahabettin, ŞAHBETTİN; AKBAŞ, FAHRİ; DEMİREL, METİN; SELEK, ŞAHABETTİNIsocitrate dehydrogenase (IDH) is a fundamental enzyme for carbon metabolism in the Krebs cycle. This enzyme is required for oxidation-reduction reactions in both eukaryotic and prokaryotic cells and plays a critical role in their growth and pathogenesis. In this study, we cloned the gene encoding NAD(+) dependent isocitrate dehydrogenase from Shewanella putrefaciens. The expression of recombinant protein was induced with 0.5 mM of IPTG. His-tagged IDH overexpressed in E. coli was purified and characterized. The expressed IDH enzyme was purified in an active soluble form. The molecular weight of the enzyme was confirmed with Western blotting. High sequence homology was observed with IDH sequences of other Shewanella strains and remarkable sequence homology was found with other bacteria reported in the database.Publication Metadata only Lucilia sericata Larval Secretions Stimulating Wound Healing Effects on Rat Dermal Fibroblast Cells(2020-09-01T00:00:00Z) AKBAŞ, FAHRİ; Ozaydin, Ahmet; Polat, Erdal; Onaran, Ilhan; AKBAŞ, FAHRİThe extract from larval Lucilia sericata is used clinically to promote wound healing and tissue regeneration. However, its effect and underlying mechanisms on fibroblast cells, which are involved in the wound healing process, are still poorly understood. This study aimed to examine the effects of larval secretions on dermal fibroblast activity and gene expression and to evaluate the wound healing potential of their major components. Primary rat fibroblasts were cultured and treated with larval secretions. Following the treatment, the cells were used to extract RNA for gene profiling. In addition, migration to the injury site was studied with the scratch healing assay. Our results showed that larval secretion accelerated the migration of the fibroblasts compared to the control cells and that several mRNAs were differentially expressed during a period of 72 h incubation. Additionally, we analyzed the chemical composition of larval secretions and showed that fumaric acid, ferulic acid, and p-coumaric acid, which were selected and identified for their major components, enhanced the migration of the fibroblasts. Therefore, these results indicate that L. sericata larval secretions could modulate the mRNA expression of some wound healing-related genes of the fibroblasts and contain the effective components for wound healing.Publication Metadata only Cloning, expression and characterization of recombinant CagA protein of Helicobacter pylori using monoclonal antibodies: Its potential in diagnostics.(2020-09-14T00:00:00Z) Salih, BA; Karakus, C; Ulupinar, Z; Akbas, FAHRİ; Uslu, M; Yazici, D; Bolek, BK; Bayyurt, N; Turkay, C; AKBAŞ, FAHRİPublication Metadata only Iron alters Ca<sup>2+</sup> homeostasis in doxorubicin-resistant K562 cells.(2020-03-05T00:00:00Z) Yalcintepe, L; Erdag, D; Akbas, FAHRİ; Kucukkaya, B; AKBAŞ, FAHRİPublication Metadata only The Effects of Transcranial Focused Ultrasound Stimulation of Nucleus Accumbens on Neuronal Gene Expression and Brain Tissue in High Alcohol-Preferring Rats(2022-11-01) Deveci E.; Akbaş F.; Ergun A. Ş.; Kurtulmuş A.; Koçak A. B.; Boyraz R. K.; Tok O. E.; Aydın M. Ş.; Kılıç Ö.; Bozkurt A.; et al.; AKBAŞ, FAHRİ; KILIÇ, ÖZGE; EŞREFOĞLU, MUKADDES; KOÇYİĞİT, ABDÜRRAHİM; KIRPINAR, İSMETWe investigated the effect of low-intensity focused ultrasound (LIFU) on gene expression related to alcohol dependence and histological effects on brain tissue. We also aimed at determining the miRNA-mRNA relationship and their pathways in alcohol dependence-induced expression changes after focused ultrasound therapy. We designed a case-control study for 100 days of observation to investigate differences in gene expression in the short-term stimulation group (STS) and long-term stimulation group (LTS) compared with the control sham group (SG). The study was performed in our Experimental Research Laboratory. 24 male high alcohol-preferring rats 63 to 79 days old, weighing 270 to 300 g, were included in the experiment. LTS received 50-day LIFU and STS received 10-day LIFU and 40-day sham stimulation, while the SG received 50-day sham stimulation. In miRNA expression analysis, it was found that LIFU caused gene expression differences in NAc. Significant differences were found between the groups for gene expression. Compared to the SG, the expression of 454 genes in the NAc region was changed in the STS while the expression of 382 genes was changed in the LTS. In the LTS, the expression of 32 genes was changed in total compared to STS. Our data suggest that LIFU targeted on NAc may assist in the treatment of alcohol dependence, especially in the long term possibly through altering gene expression. Our immunohistochemical studies verified that LIFU does not cause any tissue damage. These findings may lead to new studies in investigating the efficacy of LIFU for the treatment of alcohol dependence and also for other psychiatric disorders.Publication Metadata only Downregulatory effect of miR-342-3p on epileptogenesis in the PTZ-kindling model.(2022-10-22T00:00:00Z) Pala, Mukaddes; Meral, İSMAİL; Pala Acikgoz, Nilgun; Gorucu Yilmaz, Senay; Okur, Semra Karaca; Acar, Seyma; Polat, Yalcin; Akbas, Fahri; MERAL, İSMAİL; AKBAŞ, FAHRİPublication Metadata only Pentylenetetrazole-induced kindling rat model: miR-182 and miR-27b-3p mediated neuroprotective effect of thymoquinone in the hippocampus(2022-03-01T00:00:00Z) Pala, Mukaddes; MERAL, İSMAİL; Acikgoz, Nilgun Pala; GÖRÜCÜ YILMAZ, ŞENAY; TAŞLIDERE, ELİF; Okur, Sema Karaca; Acar, Seyma; AKBAŞ, FAHRİ; MERAL, İSMAİL; AKBAŞ, FAHRİObjectives: Epilepsy is a neurological disease that pathologically affects brain functions. The epileptic hippocampus has modified microRNA(miRNA) levels. Therefore, we aimed to evaluate the neuroprotective effect of thymoquinone (TQ) in PTZ-induced epilepsy and to demonstrate the overlap between miRNA and mRNA expression profiles. Methods: Male adult Wistar albino rats (200-230 g, n = 20) were divided into three groups as control (n = 6), PTZ (n = 7), and TQ + PTZ (n = 7). The PTZ kindling model was created by injecting PTZ in sub convulsive doses to rats on days 1, 3, 5, 8, 10, 12, 15, 17, 19, 22, and 24 of the study into animals. Clonic and tonic seizures were induced by injecting a convulsive dose of PTZ on day 26 of the study. Rats in the TQ+PTZ group were treated by oral gavage with a 20 mg/kg TQ 2 h before each PTZ injection. The rats in the control group were treated with 0.5 ml saline. Seizure severity was evaluated with the Racine scale. The genes and signaling pathways targeted by miRNAs were determined by bioinformatics analysis. Results: In the rat hippocampus, mature 728 miRNAs were analyzed by microarray and the nine miRNA were verified by quantitative Real-Time PCR. rno-miR-182 and rno-miR-27b-3p were up-regulated in the PTZ group and down-regulated in the TQ + PTZ group. Discussion: In the PTZ kindling epilepsy model, the expression of these two miRNAs was regulated by TQ and exerted a neuroprotective effect by controlling the activities of target genes.Publication Metadata only The effect of lucilia sericata larvae secretions on healing of osteochondral defects in a rat model(2021-07-29) BOTANLIOĞLU H.; KARAİSMAİLOĞLU B.; AYDINGÖZ Ö.; ÖZŞAHİN M. K.; YETİŞMİŞ S. C.; POLAT E.; ONARAN İ.; RAMADAN S.; TANRIVERDİ G.; DAĞISTANLI F.; et al.; AKBAŞ, FAHRİPublication Metadata only Effects of Methylprednisolone in the Treatment of Spinal Cord Injuries by Evaluation of microRNA-21: An Experimental Study.(2022-04-19T00:00:00Z) Abdallah, Anas; Tekin, Abdurrahim; Oztanir, Mustafa Namik; Süsgün, Seda; Yabacı, AYŞEGÜL; Çınar, İrfan; Can, Engin; Tokar, Sadık; Akbaş, Fahri; Seyithanoğlu, Mehmet Hakan; SÜSGÜN, SEDA; YABACI TAK, AYŞEGÜL; AKBAŞ, FAHRİ; SEYİTHANOĞLU, MEHMET HAKANPublication Metadata only Engineering of siRNA loaded PLGA Nano-Particles for highly efficient silencing of GPR87 gene as a target for pancreatic cancer treatment.(2020-04-01T00:00:00Z) Ceylan, S; Akbas, FAHRİ; BAHADORİ, FATEMEH; AKBAŞ, FAHRİ