PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 33Citation - Scopus: 34Effects of N-Terminal and C-Terminal Polyhistidine Tag on the Stability and Function of the Thermophilic P450 Cyp119(Hindawi Publishing Corporation, 2019) Aslantaş, Yaprak; Sürmeli, Nur Başak; Sürmeli, Nur Başak; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyBiocatalysts are sought-after in synthesis of pharmaceuticals and agrochemicals due to their high regioselectivity and enantioselectivity. Among biocatalysts, heme-containing cytochrome P450 (P450) oxygenases are an attractive target since they catalyze oxidation of "unactivated" carbon-hydrogen bonds with high efficiency. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius, which has the potential to be widely used as a biocatalyst since it shows activity at high temperatures and low pH. Polyhistidine tags (His-tags) are widely used to simplify purification of proteins. However, His-tags can cause changes to protein structure and function. Here, we demonstrate the effects of His-tags on CYP119. To this end, the His-tags were cloned at the N-terminus or C-terminus of the CYP119, and His-tagged proteins were expressed and isolated. The thermostability and peroxidase activity of His-tagged CYP119s were tested and compared to wild type CYP119. Results indicated that while addition of His-tags increased the yield and simplified isolation of CYP119, they also influenced the electronic structure of active site and the activity of the protein. We show that N-terminal His-tagged CYP119 has desirable properties and potential to be used in industrial applications, but mechanistic studies using this protein need careful interpretation since the His-tag affects electronic properties of the active site heme iron.Article Citation - WoS: 14Citation - Scopus: 18Comparison of Antimicrobial Activity of Allium Sativum Cloves From China and Taskopru, Turkey(Hindawi Publishing Corporation, 2018) Yetgin, Ali; Yetgin, Ali; Canlı, Kerem; Altuner, Ergin Murat; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyIn this study, antimicrobial activities of two different samples of Allium sativum L. from Turkey (TR) (Taskopru, Kastamonu, Turkey) and China (CN) were determined. A broad spectrum of Gram-negative and Gram-positive bacteria (17 bacteria) including species of Bacillus, Enterobacter, Enterococcus, Escherichia, Klebsiella, Listeria, Pseudomonas, Salmonella, and Staphylococcus were used for testing antibacterial activity. In addition, antifungal activity against Candida albicans was also investigated. Antimicrobial activity was tested by using 3 different processes (chopping, freezing, and slicing by the disk diffusion method). The results showed that TR garlic presented more antimicrobial activity than CN garlic. Mechanism of activity of CN garlic could be proposed to be different from that of TR garlic.Article Citation - WoS: 22Citation - Scopus: 26In Vitro Antimicrobial Activity Screening of Ethanol Extract of Lavandula Stoechas and Investigation of Its Biochemical Composition(Hindawi Publishing Corporation, 2019) Canlı, Kerem; Yetgin, Ali; Yetgin, Ali; Benek, Atakan; Bozyel, Mustafa Eray; Altuner, Ergin Murat; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThe aim of this study was to test antimicrobial activity of ethanol extract of Lavandula stoechas against 22 bacteria and 1 yeast. Also, biochemical composition of the extract was investigated. A wide range of Gram-positive, Gram-negative microorganisms, and multidrug resistant bacteria were selected to test the antimicrobial activity. As a result, the extract is observed to contain fenchone (bicyclo[2.2.1]heptan-2-one, 1,3,3-trimethyl-, (1R)-) and camphor (+)-2-bornanone) as major components and showed antimicrobial activity against all studied microorganisms except Escherichia coli ATCC 25922 and Klebsiella pneumoniae. The results of the study present that L. stoechas is active against MDR strains too.Article Citation - WoS: 11Citation - Scopus: 11Mice With Catalytically Inactive Cathepsin a Display Neurobehavioral Alterations(Hindawi Publishing Corporation, 2017) Çalhan, Osman Yipkin; Seyrantepe, Volkan; Seyrantepe, Volkan; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyThe lysosomal carboxypeptidase A, Cathepsin A (CathA), is a serine protease with two distinct functions. CathA protects β-galactosidase and sialidase Neu1 against proteolytic degradation by forming a multienzyme complex and activates sialidase Neu1. CathA deficiency causes the lysosomal storage disease, galactosialidosis. These patients present with a broad range of clinical phenotypes, including growth retardation, and neurological deterioration along with the accumulation of the vasoactive peptide, endothelin-1, in the brain. Previous in vitro studies have shown that CathA has specific activity against vasoactive peptides and neuropeptides, including endothelin-1 and oxytocin. A mutant mouse with catalytically inactive CathA enzyme (CathAS190A) shows increased levels of endothelin-1. In the present study, we elucidated the involvement of CathA in learning and long-term memory in 3-, 6-, and 12-month-old mice. Hippocampal endothelin-1 and oxytocin accumulated in CathAS190A mice, which showed learning impairments as well as long-term and spatial memory deficits compared with wild-type littermates, suggesting that CathA plays a significant role in learning and in memory consolidation through its regulatory role in vasoactive peptide processing.Article Citation - Scopus: 19Feature Selection Has a Large Impact on One-Class Classification Accuracy for Micrornas in Plants(Hindawi Publishing Corporation, 2016) Yousef, Malik; Demirci, Müşerref Duygu Saçar; Allmer, Jens; Allmer, Jens; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyMicroRNAs (miRNAs) are short RNA sequences involved in posttranscriptional gene regulation. Their experimental analysis is complicated and, therefore, needs to be supplemented with computational miRNA detection. Currently computational miRNA detection is mainly performed using machine learning and in particular two-class classification. For machine learning, the miRNAs need to be parametrized and more than 700 features have been described. Positive training examples for machine learning are readily available, but negative data is hard to come by. Therefore, it seems prerogative to use one-class classification instead of two-class classification. Previously, we were able to almost reach two-class classification accuracy using one-class classifiers. In this work, we employ feature selection procedures in conjunction with one-class classification and show that there is up to 36% difference in accuracy among these feature selection methods. The best feature set allowed the training of a one-class classifier which achieved an average accuracy of 95.6% thereby outperforming previous two-class-based plant miRNA detection approaches by about 0.5%. We believe that this can be improved upon in the future by rigorous filtering of the positive training examples and by improving current feature clustering algorithms to better target pre-miRNA feature selection.