Güneş, Hatice
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Gunes, H
Gunes, H.
Günes, H.
Güneş, H
Güneş, H.
Gunes, Hatice
Günes, Hatice
Gunes, H.
Günes, H.
Güneş, H
Güneş, H.
Gunes, Hatice
Günes, Hatice
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04.03. Department of Molecular Biology and Genetics
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Former Staff
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1NO POVERTY
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2ZERO HUNGER
3
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3GOOD HEALTH AND WELL-BEING
3
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4QUALITY EDUCATION
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5GENDER EQUALITY
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6CLEAN WATER AND SANITATION
3
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7AFFORDABLE AND CLEAN ENERGY
2
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8DECENT WORK AND ECONOMIC GROWTH
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9INDUSTRY, INNOVATION AND INFRASTRUCTURE
8
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10REDUCED INEQUALITIES
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11SUSTAINABLE CITIES AND COMMUNITIES
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12RESPONSIBLE CONSUMPTION AND PRODUCTION
2
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13CLIMATE ACTION
3
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14LIFE BELOW WATER
2
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15LIFE ON LAND
2
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16PEACE, JUSTICE AND STRONG INSTITUTIONS
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17PARTNERSHIPS FOR THE GOALS
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Documents
30
Citations
377
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14
This researcher does not have a WoS ID.
Scholarly Output
23
Articles
15
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24394/13162
Supervised MSc Theses
8
Supervised PhD Theses
0
WoS Citation Count
199
Scopus Citation Count
203
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0
Projects
1
WoS Citations per Publication
8.65
Scopus Citations per Publication
8.83
Open Access Source
23
Supervised Theses
8
| Journal | Count |
|---|---|
| Journal of Applied Microbiology | 3 |
| Cell Proliferation | 3 |
| World Journal of Microbiology and Biotechnology | 3 |
| Molecular and Cellular Endocrinology | 1 |
| Technology and Health Care | 1 |
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23 results
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Now showing 1 - 10 of 23
Master Thesis Expression Profiles of Differentially Expressed Genes of Rat Mammary Adenocarcinoma in Various Tumor Cell Lines and Effects of Some Antioxidants(Izmir Institute of Technology, 2005) Certel, Seçil; Güneş, Hatice; Güneş, HaticeCancer is the most frequent reason of death in humans after heart disease. Most of the cancers are caused by mutations in tumor suppressor genes that play distinct roles in tumor formations. If a tumor suppressor gene is mutated, it loses its function to control cell division which may lead to overgrowth of cells that leads to tumor formation. It is important to identify the genes involved in tumor formation and metastasis to develop new cancer prevention and treatment methods. In a previous study, differentially expressed genes were identified between poorly metastatic and highly metastatic cell lines of rat mammary adenocarcinoma R3230AC. Eight cDNA clones from poorly metastatic CAb.D5 cell line and six cDNA clones from highly metastatic LN4.D6 cell line were identified (Gunes and Carlsen, 2003). The aim of this study was to investigate expression profiles of these differentially expressed genes in a set of different adenocarcinoma cell lines to find if they have any relation with metastasis. Cell culture and stocks of sixteen different cell lines were prepared and RNA from these cells were isolated. After synthesizing cDNA, RT-PCR analysis was carried out using primers specific for each cDNA clone. It was found that the gene clones FF-10 and SG-1 were expressed in non-metastatic cells but not in metastatic cells suggesting that they may have a tumor suppressive potential. Antioxidants are chemicals that prevents oxidation and free radical damages on cells. Because there is some evidence that antioxidants may prevent tumor formation, effects of antioxidants such as green tea catechins, beta carotene, lycopene as well as zeolite were examined on cancer cell growth and expression profiles of the differentially expressed genes. The cells were treated with different amounts of antioxidants and the cell growth was determined by MTT assay. The effects of antioxidants in gene expression were identified by RT-PCR analysis. At 100µM and higher concentrations, epigallocatechingallate (EGCG), epigallocatechin (EGC) and beta carotene significantly inhibited cell growth. Lycopene affected the cell growth at 3µM concentration. FH-2 expression decreased by 1.8-fold with lycopene treatment. In addition, EGCG increased the SG-1 expression by 1.14-fold. No effects of antioxidants as well as zeolite on the expression of other differentially expressed genes were observed. For further studies, investigation of expression profiles of differentially expressed genes in primary and secondary tumors of human will give more definitive results for the metastatic relevance of these genes.Article Citation - WoS: 22Citation - Scopus: 24Prolactin Receptor Gene Expression in Rat Splenocytes and Thymocytes From Birth To Adulthood(Elsevier Ltd., 1996) Güneş, Hatice; Mastro, Andrea M.In vivo and in vitro studies have indicated that the anterior pituitary hormone prolactin (PRL) is an immunoregulator and functions in the development of the neonatal immune system. In this study, prolactin receptor (PRL-R) expression from birth to adulthood as well as the effect of milk ingestion on the PRL-R expression were examined in splenocytes and thymocytes of neonatal rats. Three approaches were taken to measure PRL-R expression: (i) polymerase chain reaction (RT-PCR); (ii) antibody to PRL-R and Western blotting; (iii) antibody to PRL-R and flow cytometry. RT-PCR analysis revealed the short and long form of PRL-R mRNA in both spleen and thymus at every age tested. However, the long form of PRL-R mRNA was always more abundant than that of the short form. In addition, antipeptide antibody against the long form of PRL-R recognized 84 and 42 kD proteins in the spleen, but only the 84 kD protein in the thymus. A monoclonal antibody U6 recognized 38 and 40 kD proteins in both the spleen and thymus. Although the mRNA level of PRL-R was relatively low at birth and increased with age in both the spleen and thymus, the levels of protein bands detected with both antibodies correlated with development in the spleen; whereas the levels remained steady in the thymus. Therefore, we concluded that the expression of PRL-R at the protein level is developmentally regulated in the spleen but not in the thymus. Finally, milk ingestion in the first seven hours decreased the percentage of cells expressing cell surface PRL-R, suggesting that milk-borne PRL may have a direct effect on lymphocytes.Article Citation - WoS: 12Citation - Scopus: 14Identification and Bioactivity of Native Strains of Bacillus Thuringiensis From Grain-Related Habitats in Turkey(Elsevier Ltd., 2008) Apaydın, Özgür; Çınar, Çelenk; Turanlı, Ferit; Harsa, Hayriye Şebnem; Güneş, HaticeA native collection of Bacillus thuringiensis (Bt) strains originated from grain-related habitats in Turkey was characterized according to serotype, cry1 gene content, and bioactivity against Ephestia kuehniella (Lepidoptera: Phycitidae) and Spodoptera littoralis (Lepidoptera: Noctuidae). Twenty-three different serotypes as well as 24 unknown serotypes were obtained from 56 positively agglutinated strains with previously characterized antisera. Most common serovars were sotto, kim, and tochigiensis with the percentages of 14, 14, and 13, respectively. Among the cry1 gene-positive 36 strains, cry1E (100%), cry1Aa (94%), cry1Ac (92%), and cry1D (83%) genes were the most abundant. Bioactivity tests with 56 Bt strains carrying cry1, cry2, and/or cry9 genes indicated that all of them resulted in growth retardation or inhibition of larvae of both E. kuehniella and S. littoralis; however, only one strain, 85PPb (serovar morrisoni), caused high mortality in both insects (84% and 100%, respectively). Different crystal morphology was observed for the strain 85PPb and the standard strain B. thuringiensis subsp. morrisoni. Finally, no correlation was found among serotype, cry gene content and biotoxicity of Bt strains in the collection.Master Thesis Isolation of Bacillus Thuringiensis and Investigation of Crystal Protein Genes(Izmir Institute of Technology, 2002) Çetinkaya, Fatoş Tuba; Güneş, HaticeBacillus thuringiensis is a ubiquitous, gram-positive and spore-forming bacterium. During sporulation, it produces intracellular crystal proteins (cry proteins), which are toxic to insects. Because of its insecticidal activity, it has been used for nearly fifty years to control certain insect species among the orders Lepidoptera, Coloeptera, and Diptera. However, it is still necessary to search for more toxins to control other insect orders and to provide alternatives for coping with the problem of insect resistance. The genetic diversity of B. thuringiensis strains shows differences according to the regions where they were isolated. Thus, each habitat may contain novel B. thuringiensis strains, which have some toxic effects on target spectra of insects. The aim of this study was to isolate B. thuringiensis strains from different environments and to identify the crystalline protein gene content of the isolates. Sixty five samples including soil, stored product dust, insect cadavers, and dry leaf residues were collected from Akhisar/Manisa, İzmir, and Ereğli/Konya. Three approaches were applied for the isolation of B. thuringiensis: sodium acetate selection, heat treatment, and endospore staining. Polymerase Chain Reaction (PCR) method was used for the characterization of cry gene content of B. thuringiensis strains. The universal primers specific to cry 1, cry2, cry 3, and cry 9 genes were used to detect the type of cry gene carried by each environmental isolate of B. thuringiensis strains. In addition, 16S rRNA based PCR-restriction fragment length polymorphism (RFLP) was carried out to confirm B. thuringiensis strains. Finally, SDS-PAGE analysis was optimized to detect protein profiles of crystal proteins obtained from B. thuringiensis isolates. It was found that, 136 of 359 isolates showed B. thuringiensis-like colony morphology and subterminal endospore position. One hundred isolates were screened by PCR and 18 of them were found to contain cry genes (5 cry 1, 3 cry3, and 10 cry 9). However, the cry 2 gene was not detected from any isolates. 16S rRNA based PCR-RFLPfor 18 isolates gave the same restriction pattern as positive controls, indicating that all 18 isolates were B. thuringiensis. SDS-PAGE studies for Cry 9 proteins of the isolates exhibited different protein profile from positive control of B thuringiensis strain.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: 16Citation - Scopus: 14Isolation and Characterization of Bacillus Thuringiensis Strains From Olive-Related Habitats in Turkey(John Wiley and Sons Inc., 2008) Çınar, Çelenk; Apaydın, Özgür; Yenidünya, Ali Fazıl; Harsa, Hayriye Şebnem; Güneş, HaticeAims: To isolate Bacillus thuringiensis strains from different olive-related habitats (olive groves and olive oil factories) in Turkey and to characterize these strains by molecular methods. Methods and Results: A total of 150 samples, consisting of olive grove soil, green olive leaves, olive leaf residues, animal faeces, olive pomace and dust, were examined for the presence of B. thuringiensis. One hundred B. thuringiensis strains were isolated from 54 environmental samples (36%) and characterized in terms of crystal morphology, cry and cyt gene content by polymerase chain reaction, plasmid profiles and 16S-internal transcribed spacer ribosomal DNA restriction fragment length polymorphism (16S-ITS rDNA RFLP). The highest percentage of samples containing B. thuringiensis was found in 38 out of 54 total soil samples (70%). Of the 100 B. thuringiensis isolates, the most frequent crystal shapes were irregularly shaped (24%), spherical-irregular pointed (19%), cuboidal (17%) and spherical (16%). The cry1 plus cry4 genotype was the most abundant genotype in our collection (21%). RFLP analysis of the amplified 16S-ITS rDNA revealed 11 distinct patterns for the isolates and 10 reference strains. Conclusions: Bacillus thuringiensis isolates showed a great genetic diversity and crystal shape heterogeneity. Significance and Impact of the Study: This is the first study on the isolation and characterization of B. thuringiensis from olive-related habitats in Turkey. No correlation was observed between the cry genotypes and insecticidal crystal shapes of the isolates. Restriction profiles of 23% of the isolates were found to be different from those of the 10 reference strains used.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: 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: 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.Master Thesis Test of Biomaterials in Biological Systems(Izmir Institute of Technology, 2001) Sudağıdan, Mert; Güneş, HaticeCeramic, metallic, polymeric and composite materials are generally used as biomaterials in order to improve human health. In addition to desired mechanical properties of biomaterials, biocompatibility is important in the treatment or replacement of body parts. Prior to the introduction of new biomaterials to the market, detailed biological tests are carried out to prevent any undesired side effects in the body. Both in vitro and in vivo tests are applied initially which is followed by the evaluation with clinical trials of the biological safety and performance.The aim of this study was to examine some biomaterials in biological systems.For this purpose, the effects of ceramic, metallic, polymeric and ceramic composite materials with different chemical and surface properties on the viability of peripheral blood mononuclear cells (PBMC) by trypan blue exclusion method, on the proliferation of PBMC by incorporation of bromodeoxyuridine to DNA in the proliferating cells and the activation of PBMC by MTT test were investigated. Furthermore, the effects of biomaterials on the secretion of proinflammatory cytokines (IL-1. and IL-6) from PBMC were examined by using ELISA kits. The alteration of conductivity and pH in different solutions were determined to elucidate dissolution properties of ceramic pellets. In addition, AMES test (Salmonella typhimurium reverse mutation test) for the determination of mutagenic potentials and the agar diffusion method for examination of anti-bacterial effects of biomaterials were applied. Adhesion of pathogenic bacteria to the surface of biomaterials was investigated by staining bacteria and examining under the optical microscope.Except for HA 800 C pellets, all samples showed positive results for biocompatibility compared to the controls without biomaterials. The dissolution of HA 800 °C pellets in the culture medium changed the ionic environment that led to a decrease in the viability, proliferation and activation of PBMC. However, BSA-coated HA 800 °C pellets increased the cell viability with respect to uncoated HA 800 °C pellets. Polished metallic samples and other metallic and polymeric samples showed high percent cell viabilities during 48 hours. After 72 hours, most probably because of released ions and particles to the environment, a decline in the viabilities of PBMC was determined. A negative correlation between increasing extract concentration and the cell viability was observed for all ceramic samples especially after 48 and 72 hours treatments.Cytokine secretion analysis after treatment of PBMC with biomaterials indicated that HA 800 °C, HA-Alumina 1250 °C and HA-Zirconia 1250 °C pellets led to a decrease in IL-1. secretion and BSAcoated HA 800 °C pellets in the presence of LPS. Stainless steel, titanium alloy and cirulene pellets caused low levels of IL-1. secretion. In addition, BSA-coated HA 800 °C pellets increased IL-6 secretion compared to uncoated pellets. In metallic samples, low IL-6 levels were obtained with and without LPS stimulation.Moreover, the proliferation and activation of PBMC in the presence of biomaterials were evaluated. HA 800 °C, HA-Alumina 1250 °C and HA-Zirconia 1250 °C samples had inhibitory effects on the proliferation of PBMC in the presence of Con A. In the activation of PBMC, HA 800 °C and HA 900 °C samples showed the lowest values at all incubation periods. Moreover, other ceramic samples showed lower cell activation than the control cultures after 48 and 72 hours treatments. In addition, the cell activation was observed at 24 hours after treatment with the ceramic extracts at low concentrations.Furthermore, investigation of dissolution properties of ceramic samples indicated that only HA 800 °C pellets led to significant increases in the conductivity of cell culture medium and deionized water. Moreover, a slight increase in the pH levels of solutions was obtained in the presence of HA 800 °C samples, but not in the other samples.Finally, none of the extracts of biomaterials in PBS had mutagenic effect on Salmonella typhimurium TA100 strain when they were compared to the mutagenic material (sodium azide) and the negative controls. In addition, all tested ceramic powders, ceramic pellets, metallic and polymeric materials had no anti-bacterial effects on both gram-negative strains (E. coli, P. aeruginosa, K. pneumonia, Proteus spp.) and gram-positive strains (S. aureus and S. pyogenes). In bacterial adhesion studies, it was found that surface roughness and other surface properties play important roles for attachment, adhesion and formation of biofilm by bacteria on the surface of material.As a result, although the ceramic samples sintered at low temperatures resulted in a decrease in the viability of PBMC, all tested biomaterials showed positive results for in vitro biocompatibility evaluation.
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