Master Degree / Yüksek Lisans Tezleri

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

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  • Master Thesis
    Isolation, Phenotypic and Genotypic Charecterization of Yoghurt Starter Bacteris
    (Izmir Institute of Technology, 2007) Erkuş, Oylum; Harsa, Şebnem
    Specific bacteria cultures, known as starters, are used for manufacturing of fermented milk products. Yoghurt is made from milk by the protocooperative action of well known starters, namely Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus. They lead to coagulation of milk by lactic acid fermentation and other products give the characteristic properties, such as acidity, aroma, and consistency. Traditional method, using part of a previous batch to inoculate a new batch, have been used for centuries. Such cultures lead to variable performance, however industrial production needs consistency. The method of choice is the use of bacterial strains with known physiological, biochemical and genotypic characters. The isolation and identification of natural starters is a need not only for the dairy industry, which still import starters abroad, but also for the preservation of natural lactic acid bacteria diversity of Anatolia. With this perspective, the aim of our study was the isolation of starters from artisanal yoghurts, and their biochemical and molecular characterization. At the end of the study, 66 cocci and 71 bacilli were isolated. According to biochemical identification, all the bacilli isolates were found to be L. delbrueckii ssp. bulgaricus, however cocci isolates showed highly variable sugar fermentation results and only 7 of them were characterized as S. thermophilus. The molecular characterization was based on the amplification and restriction fragment length polymorphism (RFLP) of 16S ribosomal DNA (rDNA) and internal transcribed spacer (ITS) region. Species-specific PCR amplification and 16S sequencing were also used for justification. All of the isolates were well identified with the help of molecular techniques.
  • Master Thesis
    Genotypic Characterization of Extracellular Enzyme Producing Thermophilic Bacteria in Balçova Geothermal Region
    (Izmir Institute of Technology, 2003) Yavuz, Elif; Yenidünya, Ali Fazıl
    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
    Isolation and Molecular Characterization of Lactic Acid Bacteria From Raw Milk
    (Izmir Institute of Technology, 2002) Çetin, Ali Emrah; Yenidünya, Ali Fazıl
    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
    Production and Isolation of Fungal Chitosan by Submerged Fermentation
    (Izmir Institute of Technology, 2003) Alper, Seda; Harsa, Hayriye Şebnem
    Chitosan is the N-deacetylated derivative of chitin which is the supporting material of crustaceans and insects. Chitosan together with chitin are recommended as suitable functional materials because of their excellent biocompatibility, biodegradability, non-toxicity and adsorption properties and can be used in agriculture, biotechnology and food industry. Although chitosan is produced by chemical deacetylation of chitin molecule, it is also a natural component of cell walls of fungi belonging to Zygomycetes and can be produced by extraction from fungus cell walls. Fungi are thus the promising alternative sources of chitosan. Fungi can be manipulated to give chitosan of more consistent and desired physico-chemical properties compared to chitosan obtained from crustacean sources. In this study, Absidia spp, Aspergillus niger, Rhizopus arrhizus, Cunnighamella elegans, and Mucor rouxii were examined for biomass growth. At first, all five species were grown on synthetic medium at 28 C, 180 rpm in shake-flask incubator. Mucorrouxii which gave the maximum biomass concentration was also grown on molasses. The maximum biomass concentration of Mucor rouxii was found to be higher than that of synthetic medium. The best growth conditions obtained were 4% sucrose, 0.2% yeast extract, 1% peptone and 106 spores in 40 ml. The mycelia harvested at late exponential phase was treated with alkali to remove proteins and chitosan was extracted from cell wall by using acetic acid. The yield of extractable chitosan obtained from cell wall of Mucor rouxii was 2500 mg / l and it is almost 20 % of biomass and approximately 35 % of alkali insoluble fraction.
  • Master Thesis
    Isolation of Bacillus Thuringiensis and Investigation of Crystal Protein Genes
    (Izmir Institute of Technology, 2002) Çetinkaya, Fatoş Tuba; Güneş, Hatice
    Bacillus 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.