Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

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Author: search.filters.author.Yenidünya, Ali Fazıl

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  • Master Thesis
    Genotypic Characterization of Extracellular Enzyme Producing Thermophilic Bacteria in Balçova Geothermal Region
    (Izmir Institute of Technology, 2003) Yavuz, Elif; Yenidünya, Ali Fazıl; Yavuz, Elif; Yenidünya, Ali Fazıl; 04.03. Department of Molecular Biology and Genetics; 01. Izmir Institute of Technology; 04. Faculty of Science
    Thermophiles are the organisms which are adapted to live at high temperatures. The enzymes from thermophiles find a number of commercial applications because of their thermostability and thermoactivity. Therefore, the isolation of thermophilic bacteria from natural sources and their identification are very important in terms of discovering new industrial enzymes.In keeping with this view, Balçova Geothermal Region could serve as a good source for new thermophilic microorganisms with novel industrially important properties.The aim of this research was therefore the isolation of industrially important extracellular enzyme producing thermophilic bacteria from Balçova Geothermal Region and their identification by genetical means. 16S-ITS rDNA RFLP, plasmid profiling and pulsed field gel electrophoresis studies were performed for this purpose.112 thermophilic strains were isolated from various environmental samples collected within Balçova Geothermal Region. These strains were screened for the existence of 6 extracellular enzyme activities. These were, lipases, amylases, proteases, xylanases, cellulases and pectinases. In total, 110 lipase (tween 20 as substrate), 106 amylase, 55 protease, 28 xylanase, 10 cellulase and 3 pectinase activities were detected.Some other phenotypic tests were also performed for these isolated strains. Since all the isolated strains were Gram (+), endospore forming rods, they were identified as Bacillus sp.16S-ITS rDNA RFLP and plasmid RFLP profiles were produced by using two restriction endonucleases Taq I and Hae III . The isolated strains were clustered into eleven groups by Taq I restriction profiles of 16S-ITS rDNA while nine groups were obtained by Hae III digestion profiles. When these groups were compared, it was concluded that 17 genotypically different strains existed in total 112 isolates. Two of the isolated strains yielded similar RFLP profiles to those of Bacillus stearothermophilus (CECT 43) reference strain.Plasmid profiling was also performed. It was found that 23 of the isolated strains contained plasmid DNA. Hae III restriction profiles indicated the existence of three different types of plasmids.PFGE optimization studies by Sma I restriction endonuclease for thermophilic Bacilli were also performed. A new method for preparation of agarose plugs was developed.
  • Master Thesis
    Screening for Industrially Important Extracellular Enzymes From Alkalophilic Bacillus Genus
    (Izmir Institute of Technology, 2003) Akbalık, Güney; Yenidünya, Ali Fazıl; Yenidünya, Ali Fazıl; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Alkalophilic Bacillus include industrially important species since they can produce many extracellular enzymes which are active and stable at high pH values.These alkaline enzymes (proteases, amylases, xylanases, cellulases, lipases and pectinases) find use in various field of industry such as leather, detergent, paper industries and waste water treatment.Isolation of diverse bacteria plays an important role in finding novel enzymes with improved characteristics. The aim of this study was therefore to screen for alkaline extracellular enzymes of alkalophilic Bacillus isolated from soil, horse feces and leather processing and to characterize these strains by phenotypic tests and by 16S-ITS rDNA based RFLP.At the end of the study, rod-shaped, endospore forming and Gram positive 116 strains were identified as Bacillus. Ten of the 116 strains were found to be obligate alkalophilic. 91 protease, 77 amylase, 18 xylanase, 3 cellulase, 74 pectinolytic enzyme (71 polygalacturonic acid degrading and 72 pectin degrading) and 55 lipase (41 Tween 20 hydrolyzing and 14 Tween 80 hydrolyzing) producing strains were obtained. Isolated and reference strains were classified into 18 groups in respect of the enzymes they produced.Two enzymes, Taq I and Hae III were used for 16S-ITS rDNA based RFLPanalysis. Both of the enzymes were found to be necessary for the discrimination of the strains. Reference strains were clustered into different groups by both Taq I and Hae III.Taq I digestion revealed 16 genotypic groups while Hae III revealed 15 different groups. And comparative analysis of the RFLP profiles of 116 isolates and 5 reference strains resulted in 26 genotypic groups.
  • Master Thesis
    Isolation and Molecular Characterization of Lactic Acid Bacteria From Raw Milk
    (Izmir Institute of Technology, 2002) Çetin, Ali Emrah; Yenidünya, Ali Fazıl; Yenidünya, Ali Fazıl; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Lactic acid bacteria are industrially important because they are used as starter cultures in food production, they produce antimicrobial compounds and they are used in the formulation of probiotic products. Several dairy products such as raw milk, traditionally fermented cheese (produced without the use of commercial starter cultures), and kefir which are produced in country are good sources of novel lactic acid bacterial strains. These lactic acid bacterial strains may have potential for the production of new fermented dairy products with characteristic aroma and flavour. Therefore, the isolation of lactic acid bacteria from natural products and their identification are important. For many years, several phenotypic methods have been used to identify lactic acid bacteria, but they are not often capable of effectively differentiating subspecies and strains within a genus. New methods based on the genotypic properties have been developed and used for the proper classification of bacteria The aim of this research was the isolation of lactic acid bacteria from raw milk and the identification of the lactic acid bacterial isolates by biochemical tests, polymerase chain reaction (PCR)-based methods and pulsed field gel electrophoresis (PFGE). Lactic acid bacteria were isolated from cow.s raw milk and identified by biochemical reactions. Two PCR based methods, ITS-PCR (Internal Transcribed Spacer-PCR) and PCR-RFLP (PCR- Restriction Fragment Length Polymorphism) were then used for the differentiation of reference strains of lactic acid bacteria. PCR-RFLP method, based on the amplification and restriction digestion of 16S rRNA gene, was found to be useful for the identification. Thirteen raw milk isolates were identified as Lactococcus lactis, 24 as Enterococcus spp., and 2 as Lactococcus lactis subsp. cremoris by PCR-RFLP method. Pulsed field gel electrophoresis was also optimized for the identification of reference strains. Restriction profiles obtained by digesting the genomic DNA with Sma I enabled differentiation of the reference strains of Lactococcus, Enterococcus, and Streptococus thermophilus.
  • Master Thesis
    Isolation and Molecular Characterization of Lactic Acid Bacteria From Cheese
    (Izmir Institute of Technology, 2003) Bulut, Çisem; Yenidünya, Ali Fazıl; Yenidünya, Ali Fazıl; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Specially selected starter cultures are required for the industrial production of cheese. These starter cultures are mainly composed of lactic acid bacteria (LAB). StarterLAB have many functions in cheese production. They produce lactic acid during the fermentation process and provide formation of the curd. Futhermore, they show proteolytic activity and also they play a role in the production of aroma compounds and antimicrobial substances. In order to prevent loss of LAB biodiversity and loss of traditional cheese diversity, it is important to identify novel LAB from traditional cheese.The aim of this project was to isolate and identify natural LAB flora involved in traditional "Çömlek Peyniri" fermentation. In order to achive this goal, LAB were isolated and characterized by using phenotypic ( cell morphology, Gram staining, physiological and biochemical tests ) and genotypic methods (PCR- Restriction Fragment Length Polymorphism). Moreover, technological characterization was performed by monitoring the acid production profiles of the isolates.At the end of the study, a total of 113 coccal and 21 mesophilic lactobacilli were obtained and maintained for future use. It was found that cocci shaped isolates included 54 lactococci and 59 enterecocci. Further identification at the species level indicated that all of the lactococci isolates were L. lactis ssp. lactis. Thirty of the enterecocci were E. faecium, 8 of them were E. faecalis , 3 of them were E. avium, 2 of them were E. durans and 16 of them were other Enterococcus ssp. Lactobacilli isolates were identified as Lb. paracasei ssp. paracasei (3 isolate), Lb. casei ( 3 isolate ) and other Lactobacillus spp ( 15 isolate) . PCR-RFLP method which is based on the amplification of 16S rRNA- ITS genes and restriction digestion with HaeIII and TaqI endonucleases was found to be useful for further identification. Finally, acid production profiles of isolates indicated that 35 of the isolates could lower the pH of UHT skim milk below 5.3 for 6 h incubation at 30 °C and these isolates were therefore the best starter candidates for industrial applications.