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Öğe Acinetobacter baumannii’nin colistin dirençli ve duyarlı suşlarının metabolomik profil karşılaştırması(Sivas Cumhuriyet Üniversitesi, 2022) Atron, Bydaa; Hasbek, MürşitAcinetobacter baumannii kritik bir hastane patojenidir. Solunum yolu enfeksiyonu, sepsis, idrar yolu ve yara enfeksiyonları gibi birçok ciddi enfeksiyondan sorumludur. Kolistin (CST) dahil olmak üzere mevcut tüm antimikrobiyallere direnç geliştirme yeteneği nedeniyle terapötik seçenekler son derece azdır. Metabolomik yöntem, ilaca dirençli bakteriler hakkında ek bilgi veren düşük moleküler ağırlıklı bileşiklerin ve bunlarla ilgili biyokimyasal yolların gözlemlenmesine yardımcı olabilir. Bu çalışmanın amacı, A. baumannii'nin kolistine duyarlı ve dirençli klinik suşları arasındaki metabolitlerin farklılıkların ekspresyonunu karşılaştırmaktır. Toplam 18 izolat (9 duyarlı suş ve 9 dirençli suş) analiz edildi. Metabolik profil oluşturma, Q-TOF LC/MS kütle spektrometresi (UPLC Q-TOF/MS) kullanılarak gerçekleştirilmiştir. Veri toplama, sınıflandırma ve tanımlama LC-MS/MS verilerinin elde edilmesi için Agilent MassHunter yazılımı kullanıldı. Veri ön işleme, normalleştirme, görselleştirme ve tepe hizalama, XCMS ve Mass profiler Proffesional yazılımı kullanılarak gerçekleştirildi. Tanımlanan metabolitlerin açıklaması, MetaboAnalyst 5.0 yazılımı KEGG aracılığıyla yapıldı. Metabolik yol analizi için çevrimiçi yazılımlar ve veritabanları kullanılmıştır. Bunlar şunları içerir: PubChem, MetaCyc, ChEBI. Küresel metabolomik profillememiz, test edilen suşlar arasında önemli bir fark gösterdi. Bu çalışma, ilaç direncini anlamak ve/veya A. baumanni'ye karşı yeni tedavilerin keşfi hakkında tamamlayıcı araştırmalar için değerli bir bilgi kaynağı olabilir.Öğe Antifungal and Antibiofilm Activities of Some Essential Oils Against Candida spp(2022) Atron, Bydaa; Ahamada, Hanaou; Kafa, Ayşe Hümeyra Taşkın; Çelik, Cem; Hasbek, MürşitCandida species are commonly encountered strains associated with a wide range of infections. Unlike bacterial pathogens, fungal pathogens treatment is difficult and the development of resistance has been increasing at an alarming rate. In this study, the antifungal and antibiofilm effect of thyme oil, rosemary oil, mint oil, citronella oil, was tested on Candida albicans, Candida tropicalis, Candida kefyr, Candida glabrata, Candida parapsilosis isolated from clinical samples. The agar disc diffusion method was employed to determine the antifungal effect of the essential oils, and the inhibition of biofilm formation was assessed using microtiter biofilm inhibition assay. The results indicated that all the essential oils inhibited Candida strains and their biofilm in varying degrees. The highest antifungal activity in all isolates was observed in the thyme oil (>50mm), while rosemary oil showed the highest antibiofilm effect (>77%) in all tested strains. These findings led us to assume that the active components found in essential oils might be potential antifungal agents, adding to the repertoire of therapeutic options for the treatment of candidiasis.Öğe Identification and characterization of potential druggable targets among Essential Hypothetical Proteins of A. baumannii(International Society of Academicians, 2022) Atron, BydaaAcinetobacter baumannii, a gram negative bacteria, has emerged as a critical pathogen responsible for nosocomial and other infections. A. baumannii exhibits resistance to a variety of antibiotic classes, emphasizing that new therapeutic targets are urgently needed. In A. baumannii, ATCC 179778, 458 genes have been identified as essential genes, indispensable for growth and survival of the pathogen. The functions of 47 proteins encoded by A.baumannii essential genes were found to be hypothetical and thus referred as essential hypothetical proteins (EHPs). The present study aims to carry out functional characterization of EHPs using bioinformatics tools/databases. Evaluation of physicochemical parameters, homology search against known proteins, domain analysis, subcellular localization analysis, 3D structure prediction and virulence prediction assisted us to characterize EHPs. They belong to different functional classes like enzymes, binding proteins, helicases, transporters, miscellaneous proteins and virulence factors. Around 47% of EHPs were enzymes. A group of EHPs (17.6%) were predicted as virulence factors. Proteins present in the pathogen but absent in the host were identified using host non-homology analysis. Further druggability analysis examined the druggable property of the proteins. Of 34, 27 essential pathogen-specific proteins which could serve as potential novel drug and vaccine targets. Druggability analysis was performed to examined the druggable property of the proteins. One target was found to be druggable and others were novel targets. The study's findings might assist in the development of new drugs for the treatment of Acinetobacter baumannii infections.Öğe Relationship between STOX1 gene variations and preeclampsia in Turkish population(Elsevier, 2023) Bildirici, Aslihan Esra; Akin, Seyda; Atron, Bydaa; Pinarbasi, Ergun; Cekin, Nilgun; Kucukyildiz, IremPreeclampsia (PE) is a common pregnancy disease that occurs in the second trimester of pregnancy and is characterized by high blood pressure and proteinuria. Recent studies have shown that the STOX1 gene, which is associated with the FOX multigene family and expressed in the early placenta, can directly affect the PE phenotype. STOX1 is a transcription factor that affects the high prevalence of human gestational disease by targeting genes in the pathways that affect cell proliferation and migration. In this study, the effects of STOX1 gene variations Y153H and -922 T > C polymorphisms, previously associated with PE by our team, were evaluated on each other and the disease phenotype. In the study, the results obtained from our previous polymorphism studies were used. As a result of statistical analysis, it was observed that STOX1 Y153H and -922 T > C variations were effective together in the development of early-onset Preeclampsia (EOPE). Our in-silico analysis revealed the deleterious impact of the mutation on the structure and function of the protein. Although PE is a disease that occurs with pregnancy and shows its effects mostly during this period, it has been stated that women and children with a history of PE are more prone to various disorders, especially cardiovascular disease in the following years. Therefore, understanding the pathogenesis of the disease is important for both prevention and treatment process. The variations on STOX1 gene appear to be important in terms of disease risk.Öğe Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium spp: An in silico Approach(DergiPark, 2024) Kafa, Ayşe Hümeyra TAŞKIN; Aslan, Rukiye; Ahamada, Hanaou; Atron, BydaaBiofilm-associated infections are characterized by chronicity, recurrence, and the requirement of a prolonged administration of multiple drugs. Several non-pathogenic and pathogenic species of microorganisms including Mycobacteria spp. compose biofilm. Mycobacterial biofilms present a unique composition. Instead of exopolysaccharides in other bacteria, proteins are essential compounds of the biofilm matrix in mycobacteria. To tackle Mycobacterial infections, a detailed understanding of the biofilm-forming mechanisms is crucial. In this present study, all available mycobacterial proteins involved in the biofilm were selected. Their sequences were retrieved and characterized through the determination of their physicochemical properties, secondary structure, 3D structure, subcellular localization, conserved domain, ubiquitination sites, and virulence potentiality. Furthermore, druggability testing was undertaken after excluding proteins with homology to human proteins for identify possible drug targets. The results showed that they possess functionally important domains and families. All of the selected hypothetical proteins were stable. Six of them were classified as soluble and the remaining as transmembrane proteins. A sole protein was found to lack ubiquitination sites. Additionally, three of these were discovered to be virulent. Moreover, host non-homology results indicated eight pathogen-specific proteins that might be potential therapeutic targets. Among them, D-alanyl-D-alanine carboxypeptidase is a druggable target that is inhibited by beta-lactam antibiotics. The remainder of the proteins were categorized as new targets. In conclusion, this study may increase our knowledge of pathogenesis and host adaptation, drug resistance, and identification of drug and vaccine targets against infections caused by Mycobacteria sp. It can also guide new research. © (2024), (DergiPark). All rights reserved.
