Browsing by Author "Arslan, Mevlut"

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Antitumor Activity of Urtica Dioica Seed Extract on Diethylnitrosamine-Induced Liver Carcinogenesis in Rats
(Natl inst Science Communication-niscair, 2024) Keles, Omer Faruk; Huyut, Zubeyir; Arslan, Mevlut; Yildizhan, Kenan; Yener, Zabit
Hepatocellular carcinoma (HCC) is a significant health problem for human life; therefore, new therapeutic approaches are essential. In vitro studies have shown that the extract of Urtica dioica seed extract (UDSE) may be a crucial protective agent to prevent HCC. Therefore, this study aimed to investigate the antitumor efficacy of UDSE in the process of carcinogenesis induced by diethylnitrosamine (DENA). The antitumor efficacy was evaluated by examining liver tissue histopathology and expression of Hep par-1, alpha-fetoprotein (AFP), caspase-3, and inducible nitric oxide synthase (iNOS) in the liver tissue and activities/levels of aspartate transaminase (AST), alanine transaminase (ALT), lactate dehydrogenase (LDH), carbohydrate antigen (CA) 15-3, CA 19-9, CA 125-II in the serum, and also total oxidative stress (TOS), malondialdehyde (MDA), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT), total antioxidant status (TAS) in the serum and liver. In addition, real-time PCR was used to evaluate the levels of tumor necrosis factor-alpha (TNF-alpha), interleukin (IL-1 beta, IL-6), and proliferating cell nuclear antigen (PCNA) in liver tissue. It was observed that DENA application increased liver function tests, cancer markers, apoptosis, and proinflammatory cytokine levels, but UDSE application and DENA suppressed these increases. The findings and histopathological data demonstrated that the UDSE has a very significant antitumor efficacy on the process of DENA-induced hepatocellular carcinogenesis, which appears to be attributable to its antioxidant, anti-apoptotic, and anti-proliferative activity.
Effects of Centrifugation and Washing of Freeze-Thawed Blood on Isolated Dna Characteristics
(Tubitak Scientific & Technological Research Council Turkey, 2022) Arslan, Mevlut
DNA isolations from the whole blood are commonly performed to obtain DNA for molecular research and diagnostics. Generally, blood samples are taken into anticoagulant tubes and stored in deep freezers until DNA isolation. In fresh blood, pretreatments or leukocytes preparations can be performed and suggested for advanced DNA isolation. However, similar applications in freeze-thawed blood (FTB) have not been shown yet. In the study, centrifugation and washing of FTB were applied as pretreatment before DNA isolations, and their effects on isolated DNA characteristics including DNA integrity, quality, quantity, mitochondrial (mt), and nuclear (n) DNA levels were investigated. Microscopic and flow cytometric analyses were used to check leukocyte integrity in FTB. Spectrophotometric analysis was carried out to determine DNA quality and quantity in the isolated DNA samples. Real-time PCR analyses were used to check mtDNA/nDNA ratio and DNA integrity at the quantitative level. Cell integrity analyses showed that most of the leukocytes were intact in FTB. Therefore, centrifugation enabled intact leukocytes and nuclear pellets in FTB to be harvested and washed and could be applied as pretreatment before DNA isolations. PBS and water washing of FTB led to obtaining high-quality DNA without changing the nDNA/mtDNA ratio and DNA integrity. TE washing of FTB increased DNA quality and enriched nDNA level about 2-fold without changing DNA integrity. Centrifugation and harvesting of a higher volume of FTB increased isolated DNA yield and quality but decreased DNA integrity and nDNA level. To conclude, the pretreatments of FTB had the advantage to obtain DNA with high-quality and high-quantity and can be used before DNA isolation, but they may affect mtDNA/nDNA ratios and DNA integrity levels. The relevant pre-treatment used in the present study can be used and improved for desired DNA isolation from FTB samples.
Genomic, Transcriptomic and Physiological Analyses of Silver-Resistantsaccharomyces Cerevisiaeobtained by Evolutionary Engineering
(Wiley, 2020) Terzioglu, Ergi; Alkim, Ceren; Arslan, Mevlut; Balaban, Berrak Gulcin; Holyavkin, Can; Kisakesen, Halil Ibrahim; Cakar, Zeynep Petek
Silver is a non-essential metal used in medical applications as an antimicrobial agent, but it is also toxic for biological systems. To investigate the molecular basis of silver resistance in yeast, we employed evolutionary engineering using successive batch cultures at gradually increased silver stress levels up to 0.25-mM AgNO(3)in 29 populations and obtained highly silver-resistant and genetically stableSaccharomyces cerevisiaestrains. Cross-resistance analysis results indicated that the silver-resistant mutants also gained resistance against copper and oxidative stress. Growth physiological analysis results revealed that the highly silver-resistant evolved strain 2E was not significantly inhibited by silver stress, unlike the reference strain. Genomic and transcriptomic analysis results revealed that there were mutations and/or significant changes in the expression levels of the genes involved in cell wall integrity, cellular respiration, oxidative metabolism, copper homeostasis, endocytosis and vesicular transport activities. Particularly the missense mutation in theRLM1gene encoding a transcription factor involved in the maintenance of cell wall integrity and with 707 potential gene targets might have a key role in the high silver resistance of 2E, along with its improved cell wall integrity, as confirmed by the lyticase sensitivity assay results. In conclusion, the comparative physiological, transcriptomic and genomic analysis results of the silver-resistantS. cerevisiaestrain revealed potential key factors that will help understand the complex molecular mechanisms of silver resistance in yeast.
Genomic, Transcriptomic, and Metabolic Characterization of 2-Phenylethanol Saccharomyces Cerevisiae Obtained by Evolutionary Engineering
(Frontiers Media Sa, 2023) Holyavkin, Can; Turanli-Yildiz, Burcu; Yilmaz, Ulku; Alkim, Ceren; Arslan, Mevlut; Topaloglu, Alican; Cakar, Z. Petek
2-Phenylethanol is an aromatic compound commonly used in the food, cosmetic, and pharmaceutical industries. Due to increasing demand for natural products by consumers, the production of this flavor by microbial fermentation is gaining interest, as a sustainable alternative to chemical synthesis or expensive plant extraction, both processes relying on the use of fossil resources. However, the drawback of the fermentation process is the high toxicity of 2-phenylethanol to the producing microorganism. The aim of this study was to obtain a 2-phenylethanol-resistant Saccharomyces cerevisiae strain by in vivo evolutionary engineering and characterize the adapted yeast at the genomic, transcriptomic and metabolic levels. For this purpose, the tolerance to 2-phenylethanol was developed by gradually increasing the concentration of this flavor compound through successive batch cultivations, leading to an adapted strain that could tolerate 3.4 g/L of 2-phenylethanol, which was about 3-times better than the reference strain. Genome sequencing of the adapted strain identified point mutations in several genes, notably in HOG1 that encodes the Mitogen-Activated Kinase of the high-osmolarity signaling pathway. As this mutation is localized in the phosphorylation lip of this protein, it likely resulted in a hyperactive protein kinase. Transcriptomic analysis of the adapted strain supported this suggestion by revealing a large set of upregulated stress-responsive genes that could be explained in great part by HOG1-dependent activation of the Msn2/Msn4 transcription factor. Another relevant mutation was found in PDE2 encoding the low affinity cAMP phosphodiesterase, the missense mutation of which may lead to hyperactivation of this enzyme and thereby enhance the stressful state of the 2-phenylethanol adapted strain. In addition, the mutation in CRH1 that encodes a chitin transglycosylase implicated in cell wall remodeling could account for the increased resistance of the adapted strain to the cell wall-degrading enzyme lyticase. Finally, the potent upregulation of ALD3 and ALD4 encoding NAD(+) -dependent aldehyde dehydrogenase together with the observed phenylacetate resistance of the evolved strain suggest a resistance mechanism involving conversion of 2-phenylethanol into phenylacetaldehyde and phenylacetate implicating these dehydrogenases.
Microbial Silver Resistance Mechanisms: Recent Developments
(Springer, 2022) Terzioglu, Ergi; Arslan, Mevlut; Balaban, Berrak Gulcin; cakar, Zeynep Petek
In this mini-review, after a brief introduction into the widespread antimicrobial use of silver ions and nanoparticles against bacteria, fungi and viruses, the toxicity of silver compounds and the molecular mechanisms of microbial silver resistance are discussed, including recent studies on bacteria and fungi. The similarities and differences between silver ions and silver nanoparticles as antimicrobial agents are also mentioned. Regarding bacterial ionic silver resistance, the roles of the sil operon, silver cation efflux proteins, and copper-silver efflux systems are explained. The importance of bacterially produced exopolysaccharides as a physiological (biofilm) defense mechanism against silver nanoparticles is also emphasized. Regarding fungal silver resistance, the roles of metallothioneins, copper-transporting P-type ATPases and cell wall are discussed. Recent evolutionary engineering (adaptive laboratory evolution) studies are also discussed which revealed that silver resistance can evolve rapidly in bacteria and fungi. The cross-resistance observed between silver resistance and resistance to other heavy metals and antibiotics in bacteria and fungi is also explained as a clinically and environmentally important issue. The use of silver against bacterial and fungal biofilm formation is also discussed. Finally, the antiviral effects of silver and the use of silver nanoparticles against SARS-CoV-2 and other viruses are mentioned. To conclude, silver compounds are becoming increasingly important as antimicrobial agents, and their widespread use necessitates detailed understanding of microbial silver response and resistance mechanisms, as well as the ecological effects of silver compounds. [GRAPHICS] .
Physiological and Transcriptomic Analysis of a Chronologically Long-Lived Saccharomyces Cerevisiae Strain Obtained by Evolutionary Engineering
(Springernature, 2018) Arslan, Mevlut; Holyavkin, Can; Kisakesen, Halil Ibrahim; Topaloglu, Alican; Surmeli, Yusuf; Cakar, Zeynep Petek
High-throughput aging studies with yeast as a model organism involve transposon-mutagenesis and yeast knockout collection, which have been pivotal strategies for understanding the complex cellular aging process. In this study, a chronologically long-lived Saccharomyces cerevisiae mutant was successfully obtained by using another high-throughput approach, evolutionary engineering, based on systematic selection in successive batch cultures under gradually increasing levels of caloric restriction. Detailed comparative physiological and transcriptomic analyses of the chronologically long-lived mutant and the reference strain revealed enhanced levels of respiratory metabolism, upregulation of genes related to carbohydrate metabolic processes, glycogen-trehalose pathways, stress response, and repression of protein synthesis-related genes in the long-lived mutant SRM11, already in the absence of caloric restriction. Interestingly, SRM11 had also significantly higher resistance to copper stress, and higher resistance to silver, ethanol, and 2-phenylethanol stresses than the reference strain. It also had lower ethanol production levels and an enhanced ethanol catabolism. To conclude, evolutionary engineering is another powerful high-throughput method for aging research, in addition to its widespread use in industrial strain development. Additionally, the interesting results revealed by this study about the potential relationship between longevity and various cellular properties are yet to be investigated further at molecular level.
Whole-Genome Sequencing and Genomic Analysis of Norduz Goat (Capra Hircus)
(Springer, 2023) Arslan, Mevlut
Artificial and natural selective breeding of goats has resulted in many different goat breeds all around the world. Norduz goat is one of these breeds, and it is a local goat breed of Turkey. The goats are favorable due to pre-weaning viability and reproduction values compared to the regional breeds. Development in sequencing technologies has let to understand huge genomic structures and complex phenotypes. Until now, such a comprehensive study has not been carried out to understand the genomic structure of the Norduz goats, yet. In the study, the next-generation sequencing was carried out to understand the genomic structure of Norduz goat. Real-time PCR was used to evaluate prominent CNVs in the Norduz goat individuals. Whole genome of the goat was constructed with an average of 33.1X coverage level. In the stringent filtering condition, 9,757,980 SNPs, 1,536,715 InDels, and 290 CNVs were detected in the Norduz goat genome. Functional analysis of high-impact SNP variations showed that the classical complement activation biological process was affected significantly in the goat. CNVs in the goat genome were found in genes related to defense against viruses, immune response, and cell membrane transporters. It was shown that GBP2, GBP5, and mammalian ortholog GBP1, which are INF-stimulated GTPases, were found to be high copy numbers in the goats. To conclude, genetic variations mainly in immunological response processes suggest that Norduz goat is an immunologically improved goat breed and natural selection could take an important role in the genetical improvements of the goats.