Analysis of a bac operon-silenced strain suggests pleiotropic effects of bacilysin in Bacillus subtilis

Ozan Ertekin,Meltem Kutnu,Aslı Aras Taşkın,Mustafa Demir,Ayten Yazgan Karataş,Gülay Özcengiz 한국미생물학회 2020 The journal of microbiology Vol.58 No.4

Bacilysin, as the simplest peptide antibiotic made up of only L-alanine and L-anticapsin, is produced and excreted by Bacillus subtilis under the control of quorum sensing. We analyzed bacilysin-nonproducing strain OGU1 which was obtained by bacA-targeted pMutin T3 insertion into the parental strain genome resulting in a genomic organization (bacA ::lacZ::erm::bacABCDEF) to form an IPTG-inducible bac operon. Although IPTG induction provided 3- to 5-fold increment in the transcription of bac operon genes, no bacilysin activity was detectable in bioassays and inability of the OGU1 to form bacilysin was confirmed by UPLC-mass spectrometry analysis. Phenotypic analyses revealed the deficiencies in OGU1 with respect to colony pigmentation, spore coat proteins, spore resistance and germination, which could be rescued by external addition of bacilysin concentrate into its cultures. 2DE MALDI-TOF/MS and nanoLC-MS/MS were used as complementary approaches to compare cytosolic proteomes of OGU1. 2-DE identified 159 differentially expressed proteins corresponding to 121 distinct ORFs. In nanoLCMS/ MS, 76 proteins were differentially expressed in OGU1. Quantitative transcript analyses of selected genes validated the proteomic findings. Overall, the results pointed to the impact of bacilysin on expression of certain proteins of sporulation and morphogenesis; the members of mother cell compartment- specific σE and σK regulons in particular, quorum sensing and two component-global regulatory systems, peptide transport, stress response as well as CodY- and ScoCregulated proteins.

A Plant Metabolomic Approach to Identify the Difference of the Seeds and Flowers Extracts of Carthamus tinctorius L.

Ozan Kaplan,Nagehan Saltan,Arzu Köse,Yavuz Bülent Köse,Mustafa Çelebier 사단법인 한국질량분석학회 2023 Mass spectrometry letters Vol.14 No.2

Carthamus tinctorius L. (known as safflower) is a valuable oil plant whose importance is increasing rapidly in the world due to its high adaptation to arid regions. The seeds of this unique plant are especially used in edible oil, soap, paint, varnish and lacquer production. Its flowers are used in vegetable dye production and medicinal purposes beside its features as a coloring and flavoring in food. After the oil is removed, the remaining pulp and plant parts are used as animal feed, and dry straw residues are used as fuel. Beside all these features, its usage as a herbal medicinal plants for various diseases has gained importance on recent years. In this study, it was designed a plant metabolomic approach which transfers all the recent data processing strategies of untargeted metabolomics in clinical applications to the present study. Q-TOF LC/MS-based analysis of the extracts (70% ethanol, hexane, and chloroform) for both seed and flowers was performed using a C18 column (Agilent Zorbax 1.8 µM, 100 × 2.1 mm). Differences were observed in seed and fruit extracts and these differences were visualized using principal component analysis (PCA) plots. The total number and intersections of the peaks in the extracts were visualized using peak count comparison graph. Based on the experimental results, the number of the detected peaks for seeds was higher than the ones for the flowers for all solvent systems to extract the samples.

Synergistic Effect of Cold Plasma Treatment and RGD Peptide Coating on Cell Proliferation over Titanium Surfaces

Ozan Karaman,Seyfi Kelebek,Emine Afra Demirci,Fatma Ibis,Murat Ulu,Utku Kursat Ercan 한국조직공학과 재생의학회 2018 조직공학과 재생의학 Vol.15 No.1

The aim of this study was to investigate the synergistic effect of cold atmospheric plasma (CAP) treatment and RGD peptide coating for enhancing cellular attachment and proliferation over titanium (Ti) surfaces. The surface structure of CAP-treated and RGD peptide-coated Ti discs were characterized by contact angle goniometer and atomic force microscopy. The effect of such surface modification on human bone marrow derived mesenchymal stem cells (hMSCs) adhesion and proliferation was assessed by cell proliferation and DNA content assays. Besides, hMSCs’ adhesion and morphology on surface modified Ti discs were observed via fluorescent and scanning electron microscopy. RGD peptide coating following CAP treatment significantly enhanced cellular adhesion and proliferation among untreated, CAP-treated and RGD peptide-coated Ti discs. The treatment of Ti surfaces with CAP may contribute to improved RGD peptide coating, which enables increased cellular integrations with the Ti surfaces.

Diagnostic Signifcance of Ultrasonographic Measurements and Median-Ulnar Ratio in Carpal Tunnel Syndrome: Correlation with Nerve Conduction Studies

Ozan Volkan Yurdakul,Nіlgün Mescі,Yilmaz Çetіnkaya,Duygu Geler Külcü 대한신경과학회 2016 Journal of Clinical Neurology Vol.12 No.3

Background and PurposezzWe determined the reliability of ultrasonography (US) measurements for diagnosing carpal tunnel syndrome (CTS) and their correlation with symptom duration and electrophysiology fndings. We determined whether the ratio of the median-to-ulnar cross-sectional areas (CSAs) can support CTS diagnoses. MethodszzTe pisiform CSA (CSApisiform ), swelling ratio (SR), palmar bowing, and CSApisiform / ulnar CSA (CSAulnar ) measurements made in two subgroups of CTS patients (having sensory afection alone or having both sensory and motor afection) were compared with controls. CSAulnar was measured in Guyon’s canal at the level of most-protuberant portion of the pisiform bone. ResultszzTe values of all of the measured US parameters were higher in patients with CTS (n=50) than in controls (n=62). CSApisiform could be used to diagnose CTS of mild severity. All of the parameters were positively correlated with the distal latency of the compound muscle action potential, and all of them except for SR were negatively correlated with the sensory nerve conduction velocity. A CSApisiform /CSAulnar ratio of ≥1.79 had a sensitivity of 70% and a specifcity of 76% for diagnosing CTS. ConclusionszzOnly CSApisiform measurements were reliable for diagnosing early stages of CTS, and CSApisiform /CSAulnar had a lower diagnostic value for diagnosing CTS.

ON ENTIRE RATIONAL MAPS OF REAL SURFACES

Ozan, Yildiray Korean Mathematical Society 2002 대한수학회지 Vol.39 No.1

In this paper, we define for a component $X_{0}$ of a nonsingular compact real algebraic surface X the complex genus of $X_{0}$, denoted by gc($X_{0}$), and use this to prove the nonexistence of nonzero degree entire rational maps f : $X_{0}$ Y provided that gc(Y) > gc($X_{0}$), analogously to the topological category. We construct connected real surfaces of arbitrary topological genus with zero complex genus.

A Numerical Study on the Estimation of Liquefaction-Induced Free-Field Settlements by Using PM4Sand Model

Ozan Subasi,Serdar Koltuk,Recep Iyisan 대한토목학회 2022 KSCE JOURNAL OF CIVIL ENGINEERING Vol.26 No.2

The present paper treats the estimation of liquefaction-induced, free-field settlements using two-dimensional, fully coupled, finite element (FE) analyses. The PM4Sand model is used to simulate the liquefaction behavior of a homogeneous sand layer with three different relative densities of 35%, 55%, 75% under eleven different strong ground motions. The results of FE analyses are compared with those obtained from the well-known, semi-empirical methods in the literature. The numerical analyses show that, in case of a relative density of 35%, in general, the majority of earthquake-induced settlements occur in the period, in which the excess pore water pressure resulting from the strong ground motion begins to dissipate. The liquefaction-induced settlements are influenced by not only the moment magnitude and peak ground acceleration, but also other parameters of the ground motion. Furthermore, it has been shown that the evaluation of the liquefaction potential using finite element and semi-empirical methods gives similar results. However, the semi-empirical methods yield mostly larger settlements than those obtained from the FE analyses.

Evaluation of Recent Data Processing Strategies on Q-TOF LC/MS Based Untargeted Metabolomics

( Ozan Kaplan ),( Mustafa Çelebier ) 한국질량분석학회 2020 Mass spectrometry letters Vol.11 No.1

In this study, some of the recently reported data processing strategies were evaluated and modified based on their capabilities and a brief workflow for data mining was redefined for Q-TOF LC-MS based untargeted metabolomics. Commercial pooled human plasma samples were used for this purpose. An ultrafiltration procedure was applied on sample preparation. Sample set was analyzed through Q-TOF LC/MS. A C18 column (Agilent Zorbax 1.8 μM, 50 × 2.1 mm) was used for chromatographic separation. Raw chromatograms were processed using XCMS - R programming language edition and Isotopologue Parameter Optimization (IPO) was used to optimize XCMS parameters. The raw XCMS table was processed using MS Excel to find reliable and reproducible peaks. Totally 1650 reliable and reproducible potential metabolite peaks were found based on the data processing procedures given in this paper. The redefined dataset was upload into MetaboAnalyst platform and the identified metabolites were matched with 86 metabolic pathways. Thus, two list were obtained and presented in this study as supplement files. The first list is to present the retention times and m/z values of detected metabolite peaks. The second list is the metabolic pathways related with the identified metabolites. The briefly described data processing strategies and dataset presented in this study could be beneficial for the researchers working on untargeted metabolomics for processing their data and validating their results.

Occupational Health and Safety in the Turkish Fisheries and Aquaculture; a Statistical Evaluation on a Neglected Industry

Soykan Ozan 한국산업안전보건공단 산업안전보건연구원 2023 Safety and health at work Vol.14 No.3

Background: Fisheries and aquaculture are statistically acknowledged to be among the most dangerous occupations. Yet, industrial safety and health precautions against occupational accidents within the sector are not sufficiently implemented in many parts of the world. The present study aims to provide a quantified overview of work accident statistics in the Turkish fisheries and aquaculture industry. Methods: This article presents an overview of reported injuries and fatalities in the Turkish fisheries and aquaculture industries from 2006 to 2020. Incident, permanent incapacity, and fatality rates were calculated, and the difference between fisheries and aquaculture was statistically examined. Results: The overall incident, permanent incapacity, and fatality rates were 449.4, 4.7, and 5.7 per 100,000 worker years, respectively, over the 15-year period. With these fatality rates, fisheries and aquaculture are two of the industries with the highest fatality rates among comparable industries in Turkey. Incident rates in fisheries and aquaculture indicated that aquaculture work is more dangerous and risky. The data set includes 25 fatalities and 22 permanent incapacity cases over 15 years and shows an increase in fatality rates and occupational accidents in the last 8 years. Conclusion: present study showed that the quality of data and reporting in the Turkish fisheries and aquaculture industries including occupational illnesses, must be improved in order to be more preventative and to develop efficient safety management in the sector. Incentives for providing thorough data on occupational incidents must be enhanced to improve occupational safety awareness in Turkish fisheries and aquaculture.

Stereological and Morphometric Analysis of MRI Chiari Malformation Type-1

Alkoc, Ozan Alper,Songur, Ahmet,Eser, Olcay,Toktas, Muhsin,Gonul, Yucel,Esi, Ertap,Haktanir, Alpay The Korean Neurosurgical Society 2015 Journal of Korean neurosurgical society Vol.58 No.5

Objective : In this study, we aimed to investigate the underlying ethiological factors in chiari malformation (CM) type-I (CMI) via performing volumetric and morphometric length-angle measurements. Methods : A total of 66 individuals [33 patients (20-65 years) with CMI and 33 control subjects] were included in this study. In sagittal MR images, tonsillar herniation length and concurrent anomalies were evaluated. Supratentorial, infratentorial, and total intracranial volumes were measured using Cavalieri method. Various cranial distances and angles were used to evaluate the platybasia and posterior cranial fossa (PCF) development. Results : Tonsillar herniation length was measured $9.09{\pm}3.39mm$ below foramen magnum in CM group. Tonsillar herniation/concurrent syringomyelia, concavity/defect of clivus, herniation of bulbus and fourth ventricle, basilar invagination and craniovertebral junction abnormality rates were 30.3, 27, 18, 2, 3, and 3 percent, respectively. Absence of cisterna magna was encountered in 87.9% of the patients. Total, IT and ST volumes and distance between Chamberlain line and tip of dens axis, Klaus index, clivus length, distance between internal occipital protuberance and opisthion were significantly decreased in patient group. Also in patient group, it was found that Welcher basal angle/Boogard angle increased and tentorial slope angle decreased. Conclusion : Mean cranial volume and length-angle measurement values significantly decreased and there was a congenital abnormality association in nearly 81.5 percent of the CM cases. As a result, it was concluded that CM ethiology can be attributed to multifactorial causes. Moreover, congenital defects can also give rise to this condition.

Comparison of Cell Lysis Techniques via Q-TOF LC/MS

Kaplan, Ozan,Oncul, Selin,Ercan, Ayse,Celebier, Mustafa Korean Society for Mass Spectrometry 2020 Mass spectrometry letters Vol.11 No.2

Untargeted metabolomics is a useful tool for drug development focusing on novel chemotherapeutic and chemopreventative agents against cancer cells. In recent years, quadrupole time of flight liquid chromatography-mass spectrometry (Q-TOF LC/MS)-based untargeted metabolomic approaches have gained importance to evaluate the effect of these agents at the molecular level. The researchers working on cell culture studies still do not apply standardized methodologies on sample preparation for untargeted metabolomics approaches. In this study, the rough and wet lysis techniques performed on MCF-7 breast cancer cells were compared with each other via the Q-TOF LC/MS-based metabolomic approach. The C18 and hydrophilic interaction liquid chromatography (HILIC) columns were used for the separation of the metabolites in MCF-7 cell lysates. 505 peaks were detected through the HILIC column and 551 peaks were found through the C18 column for the wet lysis technique. This situation supported by the base peak chromatograms showed that the wet lysis technique allowed us to extract higher number of non-polar metabolites. Almost equal number of metabolites was found for the C18 and HILIC columns (697 peaks for the HILIC column and 695 peaks for the C18 column) when the rough lysis technique was used. However, the intensities of polar metabolites were higher for the rough lysis technique on base peak chromatograms for both the HILIC and C18 columns. Although cell lysis technique, which is the first step in the sample preparation for cell culture studies, does not cause dramatic differences in the number of the detected metabolite peaks, it affects the polar and non-polar metabolite ratio significantly. Therefore, it must be considered carefully especially for in vitro drug development studies.