Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Determination of the Effects of Biomaterials on Human Peripheral Blood Mononuclear Cells (pbmc)(IOS Press, 2002) Sudağıdan, Mert; Güneş, Hatice; Harsa, ŞebnemArticle Citation - WoS: 16Citation - Scopus: 14Identification of Staphylococci by 16s Internal Transcribed Spacer Rrna Gene Restriction Fragment Length Polymorphism(Microbiology Society, 2005) Sudağıdan, Mert; Yenidünya, Ali Fazıl; Güneş, HaticeThe capacity of 16S internal transcribed spacer (16S-ITS) rRNA gene RFLP to differentiate 16 type strains and nine clinical isolates of staphylococci was evaluated. The 16S rRNA gene was amplified together with the ITS region and the amplification products were digested with TaqI restriction enzyme. Analysis of the 16S-ITS rRNA gene RFLP profiles differentiated each of the 16 type strains into distinct RFLP haplotypes.Article Citation - WoS: 40Citation - Scopus: 38Homofermentative Lactic Acid Bacteria of a Traditional Cheese, Comlek Peyniri From Cappadocia Region(Cambridge University Press, 2005) Bulut, Çisem; Güneş, Hatice; Okuklu, Burcu; Harsa, Hayriye Şebnem; Kılıç, Sevda; Çoban, Hatice S.; Yenidünya, Ali FazılComlek peyniri is a typical artisanal cheese in Central Anatolia. This type of cheese was made by using the indigenous lactic acid bacteria (LAB) flora of cow or ewes' milk. Majority of the samples were taken from fresh cheese because the aim was to isolate homofermentative LAB. Initially 661 microbial isolates were obtained from 17 cheese samples. Only 107 were found to be homofermentative LAB. These isolates were selected and identified by using both phenotypic and molecular methods. Phenotypic identification included curd formation from skim milk, catalase test, Gram staining and light microscopy, growth at different temperatures and salt concentrations, arginine hydrolysis, gas production from glucose, and carbohydrate fermentation. Molecular identification was based on the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the 16S rRNA gene-ITS (internally transcribed spacer) region. By combining the phenotypic and molecular identification results, isolates belonging to each of the following genera were determined at species or subspecies level: 54 Lactococcus lactis subsp. lactis, 21 Enterococcus faecium, 3 Ec. faecalis, 2 Ec. durans, 10 Ec. sp., 15 Lactobacillus paracasei subsp. paracasei, and 2 Lb. casei strains. Technological characterisation was also performed by culturing each of the strains in UHT skim milk, and by monitoring pH change and lactic acid production at certain time intervals through the 24 h incubation. Results of the technological characterisation indicated that 33% of the isolates (35 strains) were capable of lowering the pH of UHT milk below 5.3 after 6 h incubation at 30°C. Thirty four of these strains were Lc. lactis subsp. lactis, and only one was an Ec. faecium strain.Article Citation - WoS: 21Citation - Scopus: 24Isolation and Characterization of Bacillus Thuringiensis Strains From Different Grain Habitats in Turkey(Springer Verlag, 2005) Apaydın, Özgür; Yenidünya, Ali Fazıl; Harsa, Hayriye Şebnem; Güneş, HaticeBacillus thuringiensis (Bt) is a gram-positive, spore-forming bacterium and it produces insecticidal crystal (cry) proteins during sporulation. Because the genetic diversity and toxic potential of Bt strains differ from region to region, strains have been collected and characterized all over the world. The aim of this study is to isolate Bt strains in grain-related habitats in Turkey and to characterize them on the basis of crystal morphology, cry gene content, and chromosomal and plasmid DNA profiles. Four approaches were taken analysis with phase contrast (PC) microscopy, polymerase chain reaction (PCR), pulsed field gel electrophoresis (PFGE) and plasmid isolation. Ninety-six samples were collected from Central Anatolia and the Aegean region. Bt was isolated from 61 of 96 samples (63.5) and 500 Bt-like colonies were obtained. One hundred and sixty three of the colonies were identified as Bt based on cry protein formation using PC microscopy. Among the examined colonies, the overall proportion identified (as Bt index) was 0.33. We found that 103 isolates were positive for the five different cry genes (cry1, cry2, cry3, cry4 and cry9) examined with PCR. In addition, plasmid profiling of 37 cry gene-positive isolates indicated that the 15 kb plasmid band was present in all isolates; however, 11 of 37 isolates had more than one plasmid band at different sizes. Finally, chromosomal DNA profiling by PFGE gave rise to different DNA patterns for isolates containing the same cry gene which suggests a high level of diversity among the Bt strains isolated.Article Citation - WoS: 7Citation - Scopus: 8Identification of Extracellular Enzyme Producing Alkalophilic Bacilli From Izmir Province by 16s-Its Rdna Rflp(John Wiley and Sons Inc., 2004) Akbalık, Güney; Güneş, Hatice; Yavuz, Elif; Yaşa, İhsan; Harsa, Hayriye Şebnem; Elmacı, Zehra Seda; Yenidünya, Ali FazılAims: To screen industrially important extracellular enzymes from the newly isolated alkalophilic bacilli and to characterize them by phenotypic and 16S-internal transcribed spacer (ITS) rDNA restriction pattern analysis. Methods and Results: Three different environmental samples, soil, leather and horse faeces, were collected within the province of Izmir. Isolates grown on Horikoshi-I medium for 24 h at 37°C were screened for extracellular enzyme activity by using eight different substrates: birchwood xylan, carboxymethylcellulose, casein, citrus pectin, polygalacturonic acid, soluble starch, and Tween 20 and 80. In total, 115 extracellular enzyme-producing bacilli were obtained. Casein was hydrolysed by 78%, soluble starch by 67%, citrus pectin by 63%, polygalacturonic acid by 62%, Tween 20 by 34%, birchwood xylan by 16%, Tween 80 by 12%, and carboxymethylcellulose by 3% of the isolates. The isolates were differentiated into 19 distinct homology groups by the 16S-ITS rDNA restriction pattern analysis. Conclusions: Eight different extracellular enzyme activities were determined in 115 endospore forming bacilli. The largest 16S-ITS rDNA homology group (HT1) included 36% of the isolates, 98% of which degraded casein, polygalacturonic acid, pectin and starch. Significance and Impact of the Study: This study is the first report on the characterization of the industrial enzyme-producing alkalophilic bacilli by 16S-ITS rDNA restriction fragment length polymorphism (RFLP). Restriction profiles of 64% of the isolates were found to be different from those of five reference strains used.Article Citation - WoS: 24Citation - Scopus: 25Identification of Extracellular Enzyme Producing Thermophilic Bacilli From Balcova (agamemnon) Geothermal Site by Its Rdna Rflp(John Wiley and Sons Inc., 2004) Yavuz, Elif; Güneş, Hatice; Harsa, Hayriye Şebnem; Yenidünya, Ali FazılAims: Molecular characterization of extracellular enzyme producing thermophilic bacilli from Balcova geothermal site. Methods and Results: Three types of geothermal samples were collected: mud, re-injection water, and samples from uncontrolled hydrothermal vents. Isolates grown at 55°C in culture media prepared in sterilized re-injection water, were screened for extracellular enzyme activity by using eight different substrates: casein, carboxymethyl-cellulose, pectin, polygalacturonic acid (PGA), soluble starch, Tween 20 and 80, and xylan. In total, 109 thermoaerophilic isolates were selected. All of the isolates could hydrolyse Tween 20 (100%) but not Tween 80. Soluble starch was hydrolysed by 96%, casein by 55%, xylan and carboxymethylcellulose by 9%, and pectin and PGA by 2% of the isolates. The isolates were grouped into 14 different homology groups by the restriction pattern analysis of 16S-internal transcribed spacer (ITS) rDNA RFLP. Each of the RFLP groups was also studied by 16S rRNA gene partial sequence analysis. Plasmid DNA profiles revealed that 15 of the isolated strains contained small plasmid DNA molecules ranging in size from 12 000 to 35 000 bp. Conclusions: Combined analysis of 16S-ITS rDNA RFLP and 16S rRNA gene partial sequence results indicated the presence of novel or existing species of Anoxybacillus (nine species) and Geobacillus (three species). Significance and Impact of the Study: In this study 16S-ITS rDNA RFLP was applied for the first time to differentiate thermophilic bacilli. It was also the first study on thermophilic bacilli of Balcova geothermal site.Article Citation - WoS: 17Citation - Scopus: 20Rflp of 16s-Its Rdna Region To Differentiate Lactobacilli at Species Level(Springer Verlag, 2004) Yavuz, Elif; Güneş, Hatice; Bulut, Çisem; Harsa, Hayriye Şebnem; Yenidünya, Ali FazılThe 16S-ITS (internal transcribed spacer) region of the rrn operon was amplified by polymerase chain reaction (PCR). The amplification products were analysed by restriction fragment length polymorphism (RFLP) using a set of restriction enzymes, AluI, HaeIII, and TaqI. Restriction pattern analyses revealed that TaqI restriction enzyme could clearly differentiate the nine reference strains of Lactobacillus used in the study.Article Citation - WoS: 3Citation - Scopus: 3Optimization of Pulsed Field Gel Electrophoresis (pfge) Conditions for Thermophilic Bacilli(Springer Verlag, 2004) Yavuz, Elif; Güneş, Hatice; Harsa, Hayriye Şebnem; Bulut, Çisem; Yenidünya, Ali FazılAlthough thermophilic members of the genus Bacillus are known to tolerate extreme environmental conditions, they appeared to be readily damaged upon mechanical manipulations. This fact was evidenced in genotyping of some strains of thermophilic Bacillus by pulsed field gel electrophoresis (PFGE). Consequently, a new procedure for the preparation of agarose plugs was developed. The procedure produced interpretable genomic DNA restriction profiles.Article Citation - WoS: 1Citation - Scopus: 1Identification of Differentially Expressed Genes in Isogenic Highly Metastatic and Poorly Metastatic Cell Lines of R3230ac Rat Mammary Adenocarcinoma(John Wiley and Sons Inc., 2003) Güneş, Hatice; Carlsen, S. A.Tumour metastasis occurs as a result of a cascade of events including alterations in the expression of various genes. The identification of such genes is essential to understanding formation of metastasis. In a previous study, highly metastatic (LN4.D6) and poorly metastatic (CAb.D5) cell lines were obtained from the rat mammary adenocarcinoma cell line R3230AC. Subtractive hybridization was used to identify differentially expressed genes between these two cell lines. We identified eight cDNA clones in CAb.D5 and six cDNA clones in LN4.D6 that were differentially expressed. One of the cDNA clones in each cell line had no homology with known sequences. Expression patterns of these differentially expressed genes were examined in a pair of rat mammary and prostate adenocarcinoma cell lines. Compared with cell lines examined, cDNA FF-10 was only expressed in CAb.D5; however, cDNA RB-8, RE-1, RF-5 were only expressed in the highly metastatic LN4.D6. No correlation was observed between expression patterns of the differentially expressed genes and metastatic potential of these cells. However, differential expression of genes, especially cytokeratins (CK8 and CK5) and collagens (III and IV) between highly metastatic and low metastatic rat mammary adenocarcinoma cell lines might initiate further investigation of these genes in metastatic process.Article Citation - WoS: 5Citation - Scopus: 4Prolactin Receptor Expression by Splenocytes From Rats in Various Hormonal States(John Wiley and Sons Inc., 1997) Güneş, Hatice; Zawilla, S.; Mastro, Andrea M.Prolactin (PRL) is mitogenic for lymphocytes in vitro, but the responsiveness of lymphocytes depends on the in vivo hormonal status of the rats from which the cells were obtained. Lymphocytes from ovariectomized (OVX) rats, but not from rats in oestrus or from male rats, respond to prolactin; administration of oestradiol to OVX rats diminishes the response. In order to determine if a correlation exists between lymphocyte responsiveness to prolactin and levels of cell surface prolactin receptors (PRL-R) expression, the percentage of splenocytes and each splenocyte subpopulation expressing surface PRL-R from rats of various hormonal states (OVX, oestradiol-injected OVX, oestrus and male) was analysed by single-colour and dual-colour flow cytometric analysis. We found that approximately 20% of splenocytes expressed surface PRL-R regardless of hormonal states (n = 16). The majority (85%) of PRL-R positive splenocytes were B lymphocytes whereas 11.1% and 4.8% of splenocytes expressing the PRL-R were CD4 positive T-helper (TH) and CD8 positive T-cytotoxic (TC) lymphocytes, respectively. B lymphocytes also stained more brightly than T lymphocytes. This distribution of PRL-R expression did not show significant alterations on total splenocytes or TH and TC lymphocytes during various hormonal stages. However, the percentage of PRL-R-positive B lymphocytes increased markedly in OVX rats (twofold), compared to rats at oestrus. In summary, no correlation was found between the responsiveness to prolactin as a mitogen and levels of PRL-R expression by lymphocytes from rats at different hormonal states. This result suggests that sex steroid hormones may control prolactin responsiveness of lymphocytes by affecting the signal transduction pathway through PRL-R rather than by altering the level of the cell surface receptor expression.