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 Open Access The Effects of Lucilia sericata Larval Secretions on The Expressions of MicroRNAs that are Suggested to be Related with Wound Healing in Experimental Diabetic Rat Wound Model(2020-01-01T00:00:00Z) Kilinc, Oyku; Arkan, Hulya; AKBAŞ, FAHRİ; Polat, Erdal; Tuncdemir, Matem; Onaran, Ilhan; Ozaydin, Ahmet; AKBAŞ, FAHRİObjective: Normal wound healing is achieved by a cascade of many cellular activities. This process is affected by some of the metabolic diseases like Diabetes Mellitus (DM). DM causes bad prognosis and is one of the major contributors to chronic wound healing problems. Recently, Lucilia sericata larvae are used for wound healing as they are very effective agents in wound healing process. It-s still unclear that how the larvae affect the molecular mechanisms and signaling pathways of chronic wound healing. MicroRNAs (miRNAs) can induce gene expression in post-transcriptional mechanisms. In this study, our aim was to determine whether the larvae secretions could change the expression patterns of selected miRNAs on the diabetic microenvironment.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 Open Access The utility of serum microRNA-93 and microRNA-191 levels for determination of injury severity in adults with multiple blunt trauma(2020-12-01T00:00:00Z) Sogut, Ozgur; Metiner, Merve; Kaplan, Onur; Calık, Mustafa; Cakmak, Sumeyye; Umit, Tugba Betul; Ergenc, Huseyin; Akbas, Fahri; Süsgün, Seda; AKBAŞ, FAHRİ; SÜSGÜN, SEDABACKGROUND: Various scoring systems have been developed to determine the trauma severity and prognosis of patients following multiple blunt trauma (MBT). However, these scoring systems do not provide exactly the desired severity assessment. In recent years, serum concentration of many specific miRNAs, especially for head trauma, has been shown to play an important role in determining the diagnosis, severity and prognosis of injury. To date, however, no studies have investigated serum microRNAs in patients with MBT. Thus, this study measured the expression of miRNA-93 and -191 in the serum of adults with MBT and examined the correlations of Injury Severity Score (ISS) and Revised Trauma Score (RTS) values with serum miRNA-93 and -191 levels in these patients with the aim of predicting trauma severity based on the miRNA levels.METHODS: This prospective case–control study enrolled 50 consecutive adults with MBT and age- and sex-matched 60 healthy controls. The patients were divided into ISS >16 (group 1, major or severe trauma) and ISS ≤16 (group 2, minor or mild-moderate trauma) groups. Serum miRNA-93 and -191 levels were assessed using quantitative real-time reverse transcription-PCR. We evaluated whether the miRNAs were differentially expressed in major and minor MBT patients and determined their utility for assessing the severity of injury.RESULTS: The mean serum miRNA-93 and -191 levels were significantly elevated in the patients compared to the controls and were higher in patients with ISS >16 compared to those with ISS ≤16, although the difference was not significant. In the patients with multitrauma, ISS was significantly, negative and weak correlated with serum miRNA-191 level (rho = –0.320, p = 0.023) but not with the serum miRNA-93 level. No optimal cutoff for the serum miRNA-93 level was found with respect to trauma severity (AUC 0.617, [0.455–0.779]). However, an optimal cutoff value for serum miRNA-191 was identified, with values <1.94 indicating severe trauma (AUC 0.668 [0.511–0.826]; 65.6% sensitivity, 77.8% specificity).CONCLUSION: miRNA-191 and -93 levels were significantly upregulated in multitrauma patients compared to controls. The level of miRNA-191 in conjunction with ISS, but not that of miRNA-93, may be a useful biomarker for determining injury severity in patients with multitrauma.Publication 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 Open Access Fibromiyalji Sendromu ile Bağırsak Mikrobiyotası Arasındaki İlişkinin Araştırılması(2021-03-01T00:00:00Z) Albayrak, Büşra; Süsgün, Seda; Küçükakkaş, Okan; Akbaş, Fahri; Yabacı, Ayşegül; Özçelik, Semra; SÜSGÜN, SEDA; KÜÇÜKAKKAŞ, OKAN; AKBAŞ, FAHRİ; YABACI TAK, AYŞEGÜL; ÖZÇELİK, SEMRAFibromiyalji sendromu (FMS), yetişkin popülasyonda bildirilen prevalansı %3-10 olan, kronik yaygın ağrının sık görülen formlarından biridir. Tipik ağrının klinik görünümü ve ilişkili somatik ve psikolojik semptomların varlığı tanıya temel oluşturur. FMS sinir sistemi disfonksiyonu ile ilişkilidir ve nörotransmitterler fibromiyalji için onaylanmış bir dizi ilacın hedefi olarak rol oynamaktadır. Bununla birlikte, FMS’de altta yatan mekanizmalar kesin olarak henüz bilinmemekle birlikte birçok hipotez ortaya konmuştur. Fibromiyalji ve irritabl bağırsak sendromu (IBS) arasındaki ilişki göz önüne alındığında, değişen bağırsak mikrobiyomu fibromiyalji ile ilişkili olabilir. Bu çalışmada, FMS tanılı hastalarda sağlıklı kontrollere göre değişen bağırsak mikrobiyom düzeylerinin araştırılması amaçlanmıştır. Mikrobiyom çalışması için FMS tanılı 54 hastadan ve 36 sağlıklı kişiden oluşan kohorttan fekal örnekler toplanmıştır. Kontrol grubunda herhangi bir mental ve/veya fiziksel hastalığı olanlar çalışma dışında bırakılmıştır. FMS’li hasta grubu, -American College of Rheumatology (ACR)- 2010 tanı kriterlerine bağlı kalınarak belirlenmiştir. Fekal örnekler, kullanılana kadar -80°C’de muhafaza edilmiş ve buz üzerinde çözülmüş; her ekstraksiyon için 0.3 g feçes tartılmıştır. DNA izolasyonu, ticari kit ile üreticinin protokolüne uygun olarak gerçekleştirilmiştir. Örnekler, gerçek zamanlı polimeraz zincir yöntemi ile Bacteroidetes, Firmicutes, Enterobacter, Lactobacillus, Streptococcus ve Bifidobacterium’a özgül primerler ile 16S rRNA gen amplifikasyonu yapılarak karşılaştırılmıştır. Sonuçlara göre, hasta grubunda Bacteroidetes ve Bifidobacterium istatistiksel olarak anlamlı bir şekilde artarken (p< 0.05), Firmicutes’in azaldığı saptanmıştır (p< 0.001). Enterobacter, Streptococcus ve Lactobacillus için istatistiksel olarak anlamlı sonuç bulunamamıştır (p> 0.05). Bakteriler arasındaki ilişki değerlendirildiğinde, Bacteroidetes ile Firmicutes yüzdesi arasında istatistiksel olarak yüksek anlamlı ve negatif korelasyon bulunurken (r= -0.778, p< 0.001), Enterobacter ve Bifidobacterium yüzdesi arasında orta derecede istatistiksel anlamlılık ve pozitif korelasyon gözlenmiştir (r= 0.460, p= 0.005). Sonuçlar, bağırsak mikrobiyotasının fibromiyaljide rol oynayabileceğini göstermektedir. Bağırsaktaki Firmicutes ve Bacteroidetes filumlarının dengesinin bağırsak homeostazı için önemli etkilere sahip olduğu bilinmektedir. Özetle, daha büyük kohortlarda yapılacak büyük ölçekli araştırmaların, bağırsak mikrobiyomu ve FMS arasındaki ilişkiyi anlamada ve olası tedavi seçeneklerini değerlendirmede etkili olacağı açıktır.Publication 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.
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