Fidan, Özkan
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Fidan, Ozkan
Job Title
Dr. Öğr. Üyesi
Email Address
ozkan.fidan@agu.edu.tr
Main Affiliation
04.01. Biyomühendislik
Status
Current Staff
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ORCID ID
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Sustainable Development Goals
2
ZERO HUNGER
1
Research Products
3
GOOD HEALTH AND WELL-BEING
7
Research Products
8
DECENT WORK AND ECONOMIC GROWTH
1
Research Products
9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
1
Research Products
12
RESPONSIBLE CONSUMPTION AND PRODUCTION
1
Research Products
Documents
21
Citations
263
h-index
9
Documents
22
Citations
231
Scholarly Output
17
Articles
13
Views / Downloads
455/578
Supervised MSc Theses
3
Supervised PhD Theses
0
WoS Citation Count
122
Scopus Citation Count
133
WoS h-index
5
Scopus h-index
5
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0
Projects
1
WoS Citations per Publication
7.18
Scopus Citations per Publication
7.82
Open Access Source
14
Supervised Theses
3
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| Journal | Count |
|---|---|
| Bitlis Eren Üniversitesi Fen Bilimleri Dergisi | 2 |
| ACS Omega | 1 |
| Frontiers in Immunology | 1 |
| Frontiers in Microbiology | 1 |
| International Microbiology | 1 |
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Now showing 1 - 10 of 17
Master Thesis Escherichia Coli Konak Organizmada GLP-1 Analoğunun Rekombinant Üretimi(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Çalış, Burak; Fidan, ÖzkanDiabetes is the most serious metabolic disorder correlated with obesity, hypertension and cardiovascular conditions. High prevalence of Type II Diabetes Mellitus (T2DM) indicates the need for new medication development. In developing therapeutics, higher efficiency and fewer adverse effect features are targeted primarily. Recombinant protein-based biotechnological drug molecules have been developed and used for the treatment of T2DM. Especially, GLP-1 analogues are known by their self-limiting mechanism and insulinotropic effect. In this study, a novel GLP-1 analogue with increased stability and efficiency is produced using recombinant E. coli. The expression plasmid was constructed and confirmed by restriction digestion and whole plasmid sequencing. Then, itwas transformed into various E. coli strains followed by optimized lysis, growth and expression conditions to maximize the yield of the GLP-1 analogue. Various parameters such as pre-induction time, induction point, induction IPTG concentration and post-induction temperature were tested for the succesfull expression with maximum yield. Consequently, it was achieved that E. coli BL21(DE3) as strain, 0.2 mM IPTG induction at OD600nm of 0.6 and 18 °C overnight post-induction growth was the most promising conditions. Under these conditions, the GLP-1 analogue was obtained in the insoluble fraction. Following protein analysis and purification, quantification was performed and the highest titer of GLP-1 analogue was measured as 626 µg/ml. As future prospect, using another host organism and changing growth conditions can provide obtaining target protein in the soluble form. Keywords: T2DM, GLP-1 analogue, recombinant DNA technology, protein expression, E. coliMaster Thesis Tarımsal-Endüstri Atıkları Üzerinde Yetiştirilen Trichoderma Harzianum Kullanılarak Bitki Patojenlerine Karşı Sürdürülebilir Bir Biyofungisit Geliştirilmesi(2025) Serin, Didem Bayraktaroğlu; Fidan, ÖzkanTarım uygulamaları, birçok endüstri için özellikle de gıda üretimi için hayati öneme sahiptir. Tarımsal ürünler, yetiştirme sürecinden tüketime kadar olan tedarik zinciri boyunca her yıl %80 ürün kaybıyla sonuçlanabilen çeşitli zorluklarla karşılaşmaktadır. Ürün kaybını en aza indirmek için çeşitli çözüm stratejileri geliştirilmiş olsa da yaygın olarak kullanılan kimyasal ürünler canlılara ve çevreye zarar vermektedir. Kimyasalların yan etkilerini ortadan kaldırmak için biyolojik alternatiflerin kullanımı önemle teşvik edilmektedir. Trichoderma harzianum, mikoparazitizm, besin ve alan için rekabet avantajı ve antimikrobiyal sekonder metabolit üretimi gibi antagonistik aktiviteleri ile bitki gelişimini destekleyici özellikleri sayesinde iyi bilinen bir biyokontrol ajanıdır. Bu çalışmada, T. harzianum'un, Fusarium solani, Rhizoctonia solani, Aspergillus welwitschiae, Colletotrichum coccodes ve Botrytis cinerea olmak üzere beş fitopatojene karşı antifungal aktiviteleri ortaya konulmuştur. Ayrıca, T. harzianum tarafından üretilen uçucu ve uçucu olmayan organik bileşiklerin söz konusu patojenler üzerindeki etkileri değerlendirilmiştir. En güçlü inhibisyon %96,76 ile C. coccodes'e karşı gözlemlenmiştir, benzer şekilde diğer fitopatojenlere karşı da umut verici antagonistik aktivitesi bulunmuştur. Bitki gelişimini teşvik edici özellikleri de incelenmiş ve indol-3-asetik asit ile siderofor üretimi gözlemlenmiştir. Bunun yanı sıra, T. harzianum'un inkübasyonu için sürdürülebilir ve çevre dostu bir yaklaşım olarak, ayrıca tarımsal-endüstri atıklarının değer kazanımına ve döngüsel ekonomiye katkı sağlayan elma posası bazlı bir besiyeri ortamı oluşturulmuştur. Elde edilen bulgular, T. harzianum'un çevre dostu bir biyofungisit ve biyogübre adayı olarak tarımda kullanılabilirliğini desteklemektedir. Anahtar kelimeler: Biyofungisit, T. harzianum, Elma Posası, Fitopatojenler, MikoparazitizmArticle Citation - WoS: 1Citation - Scopus: 2Discovery of a C-S Lyase Inhibitor for the Prevention of Human Body Malodor Formation: Tannic Acid Inhibits the Thioalcohol Production in Staphylococcus Hominis(Springer, 2025) Fidan, Ozkan; Karipcin, Ayse Doga; Kose, Ayse Hamide; Anaz, Ayse; Demirsoy, Beyza Nur; Arslansoy, Nuriye; Mujwar, SomduttHuman body odor is a result of the bacterial biotransformation of odorless precursor molecules secreted by the underarm sweat glands. In the human axilla, Staphylococcus hominis is the predominant bacterial species responsible for the biotransformation process of the odorless precursor molecule into the malodorous 3M3SH by two enzymes, a dipeptidase and a specific C-S lyase. The current solutions for malodor, such as deodorants and antiperspirants are known to block the apocrine glands or disrupt the skin microbiota. Additionally, these chemicals endanger both the environment and human health, and their long-term use can influence the function of sweat glands. Therefore, there is a need for the development of alternative, environmentally friendly, and natural solutions for the prevention of human body malodor. In this study, a library of secondary metabolites from various plants was screened to inhibit the C-S lyase, which metabolizes the odorless precursor sweat molecules, through molecular docking and molecular dynamics (MD) simulation. In silico studies revealed that tannic acid had the strongest affinity towards C-S lyase and was stably maintained in the binding pocket of the enzyme during 100-ns MD simulation. We found in the in vitro biotransformation assays that 1 mM tannic acid not only exhibited a significant reduction in malodor formation but also had quite low growth inhibition in S. hominis, indicating the minimum inhibitory effect of tannic acid on the skin microflora. This study paved the way for the development of a promising natural C-S lyase inhibitor to eliminate human body odor and can be used as a natural deodorizing molecule after further in vivo analysis.Article Investigation of Antiviral Potential of Food Carotenoids and Apocarotenoids Against RNA-Dependent RNA Polymerase of Hepatitis C Virus(2022) Fidan, OzkanHepatitis C disease have been a global health threat and affects a significant portion of world population. Hepatitis C have also been a silent health threat for Turkiye, where there are around half million people infected with Hepatitis C Virus (HCV). Disease burden and mortality are expected to increase gradually in the next 20 years in Turkiye. Unavailability of enough data on the currently-available drugs in routine clinical practice, their side effects and interactions with other drugs, and their efficacies on the less common genotypes indicates the necessity of alternative treatment options. Natural products from herbal and medicinal plants can indeed provide an alternative as being drug-like dietary supplements. In particular, the carotenoids and apocarotenoids are underexplored in their antiviral potential, including anti-HCV activities. Therefore, we focused on the virtual screening of various carotenoids and apocarotenoids against the RNA-dependent RNA polymerase (RdRp) of HCV. Molecular docking experiments showed strong binding affinities of the ligands to both palm and thumb domains of RdRp of HCV. In fact, some of them such as neoxanthin, crocin, canthaxanthin and cryptoflavin bound quite strongly to both domains compared to native ligands and current antiviral drugs. MD simulation for neoxanthin-RdRp complex confirmed the stability of the ligand within the binding cavity of RdRp throughout 100 ns simulation. This clearly indicated the potential of carotenoids, specifically neoxanthin, as RdRp inhibitor in treating HCV. Thus, this study not only discovered anti-HCV drug candidates with the properties of easy-to-access and low cost, but also paved the way for the development of carotenoid or apocarotenoid based dietary supplement candidates for the prevention and treatment of HCV.Article Citation - WoS: 2Citation - Scopus: 2Draft Genome of Carotenoid-Producing Endophytic Pseudomonas Sp. 102515 From Taxus Chinensis(Amer Soc Microbiology, 2024) Fidan, OzkanHere, we report the draft genome sequence of endophytic Pseudomonas sp. 102515 isolated from Taxus chinensis collected from Logan, UT, USA. The genome is composed of 36 contigs and around 4.9 Mbp in size. The GC content is 66% with an N-50 length of 918.9 kbp and L-50 count of 2.Article Citation - WoS: 31Citation - Scopus: 33Discovery of Adapalene and Dihydrotachysterol as Antiviral Agents for the Omicron Variant of SARS-CoV-2 Through Computational Drug Repurposing(Springer, 2023) Fidan, Ozkan; Mujwar, Somdutt; Kciuk, MateuszSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been significantly paralyzing the societies, economies and health care systems around the globe. The mutations on the genome of SARS-CoV-2 led to the emergence of new variants, some of which are classified as "variant of concern" due to their increased transmissibility and better viral fitness. The Omicron variant, as the latest variant of concern, dominated the current COVID-19 cases all around the world. Unlike the previous variants of concern, the Omicron variant has 15 mutations on the receptor-binding domain of spike protein and the changes in the key amino acid residues of S protein can enhance the binding ability of the virus to hACE2, resulting in a significant increase in the infectivity of the Omicron variant. Therefore, there is still an urgent need for treatment and prevention of variants of concern, particularly for the Omicron variant. In this study, an in silico drug repurposing was conducted through the molecular docking of 2890 FDA-approved drugs against the mutant S protein of SARS-CoV-2 for Omicron variant. We discovered promising drug candidates for the inhibition of alarming Omicron variant such as quinestrol, adapalene, tamibarotene, and dihydrotachysterol. The stability of ligands complexed with the mutant S protein was confirmed using MD simulations. The lead compounds were further evaluated for their potential use and side effects based on the current literature. Particularly, adapalene, dihydrotachysterol, levocabastine and bexarotene came into prominence due to their non-interference with the normal physiological processes. Therefore, this study suggests that these approved drugs can be considered as drug candidates for further in vitro and in vivo studies to develop new treatment options for the Omicron variant of SARS-CoV-2. [GRAPHICS] .Article Citation - WoS: 3Citation - Scopus: 4Can Mesenchymal Stem/Stromal Cells and Their Secretomes Combat Bacterial Persisters(Springer, 2023) Bicer, Mesude; Fidan, OzkanThe increasing number of life-threatening infections caused by persister bacteria is associated with various issues, including antimicrobial resistance and biofilm formation. Infections due to persister cells are often difficult to suppress without the use of last-resort antibiotics. Throughout the world, bacterial persistence and resistance create an unmet clinical demand for the exploration of newly introduced therapeutic approaches. Mesenchymal stem / stromal cells (MSCs) have an antimicrobial activity to protect against bacterial infections, including those caused by bacterial persisters. MSCs have substantial potential to secrete antimicrobial peptides (AMPs), including cathelicidin, beta-defensins, lipocalin-2, hepcidin, indoleamine 2,3-dioxygenase (IDO), cysteine proteases, and inducible nitric oxide synthases (iNOS). MSCs possess the potential to contribute to innate immunity by regulating the immune response. Recently, MSCs and their secreted components have been reported to improve antimicrobial activity. Bactericidal activity by MSCs and their secretomes has been shown to be mediated in part by the secretion of AMPs. Even though they were discovered more than 80 years ago, therapeutic options for persisters are restricted, and there is an urgent need for alternative treatment regimens. Hence, this review intends to critically assess the current literature on the effects of MSCs and their secretomes on persister bacteria. MSCs and their secretome-based therapies could be preferred as an up-and-coming approach to reinforce the antimicrobial efficiency in persister infections.Article Citation - WoS: 2Citation - Scopus: 2Biochemical Characterization and Genome Analysis of Pseudomonas Loganensis Sp. Nov., a Novel Endophytic Bacterium(Wiley, 2025) Karaman, Melisa Z.; Yetiman, Ahmet E.; Zhan, Jixun; Fidan, OzkanPseudomonas species are highly adaptable, thriving in diverse environments and exhibiting remarkable genetic and metabolic diversity. While some strains are pathogenic, others have significant ecological and industrial applications. Bioinformatics and biochemical analyses, including antibiotic sensitivity testing, revealed that Pseudomonas loganensis sp. nov. can tolerate NaCl concentrations up to 5% and pH ranges between 5 and 9. Antibiogram results corroborated genome data, demonstrating resistance to vancomycin, ampicillin, methicillin, oxacillin, and penicillin G. Phylogenetic analysis based on 16S rRNA, rpoB, rpoD, and gyrB genes, combined with average nucleotide identity (ANI) comparisons, confirmed P. loganensis sp. nov. as a novel species within the Pseudomonas genus. Genome analysis further revealed the presence of turnerbactin and carotenoid gene clusters. Turnerbactin, known to contribute to nitrogen fixation in plants, highlights the strain's potential as a biofertilizer. Additionally, the carotenoid gene cluster suggests potential applications in industrial carotenoid production. The discovery of a trehalose synthase (treS) gene indicates the capability for one-step conversion of maltose into trehalose, underscoring its potential utility in trehalose production.Editorial Editorial: Microbial Production of Medicinally Important Agents(Frontiers Media S.A., 2023) Zeng, Jia; Zhan, Jixun; Qiao, Xue; Fidan, OzkanArticle Citation - WoS: 8Citation - Scopus: 8Berberine-Containing Natural-Medicine With Boiled Peanut-Oit Induces Sustained Peanut-Tolerance Associated With Distinct Microbiota Signature(Frontiers Media S.A., 2023) Srivastava, Kamal; Cao, Mingzhuo; Fidan, Ozkan; Shi, Yanmei; Yang, Nan; Nowak-Wegrzyn, Anna; Li, Xiu-MinBackgroundGut microbiota influence food allergy. We showed that the natural compound berberine reduces IgE and others reported that BBR alters gut microbiota implying a potential role for microbiota changes in BBR function. ObjectiveWe sought to evaluate an oral Berberine-containing natural medicine with a boiled peanut oral immunotherapy (BNP) regimen as a treatment for food allergy using a murine model and to explore the correlation of treatment-induced changes in gut microbiota with therapeutic outcomes. MethodsPeanut-allergic (PA) mice, orally sensitized with roasted peanut and cholera toxin, received oral BNP or control treatments. PA mice received periodic post-therapy roasted peanut exposures. Anaphylaxis was assessed by visualization of symptoms and measurement of body temperature. Histamine and serum peanut-specific IgE levels were measured by ELISA. Splenic IgE(+)B cells were assessed by flow cytometry. Fecal pellets were used for sequencing of bacterial 16S rDNA by Illumina MiSeq. Sequencing data were analyzed using built-in analysis platforms. ResultsBNP treatment regimen induced long-term tolerance to peanut accompanied by profound and sustained reduction of IgE, symptom scores, plasma histamine, body temperature, and number of IgE(+) B cells (p <0.001 vs Sham for all). Significant differences were observed for Firmicutes/Bacteroidetes ratio across treatment groups. Bacterial genera positively correlated with post-challenge histamine and PN-IgE included Lachnospiraceae, Ruminococcaceae, and Hydrogenanaerobacterium (all Firmicutes) while Verrucromicrobiacea. Caproiciproducens, Enterobacteriaceae, and Bacteroidales were negatively correlated. ConclusionsBNP is a promising regimen for food allergy treatment and its benefits in a murine model are associated with a distinct microbiota signature.
