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Molecular typisation of lactic acid bacteria
Jelínek, Zdeněk ; Ing. Špano Miroslav,PhD. (referee) ; Rittich, Bohuslav (advisor)
Lactic acid bacteria play important role both in food industry and health care. They are part of many fermented dairy products and gastrointestinal microflora. There is a whole variety of methods for bacteria identification, but we will focus on Rep-PCR and RAPD only. The aim of this work will be to discuss the impact of different correlation coefficients and cluster analysis algorithms on the results of taxonomic analysis.
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Molecular characterization of selected clostridial strains isolated from cheeses
Chroboková, Maria ; Kvasničková, Eva (referee) ; Rittich, Bohuslav (advisor)
The study was focused on molecular characterization of 42 clostridial strains. DNA was isolated by fenol-chloroform extraction procedure and precipitated with ethanol. After DNA isolation, PCR amplifications with specific primer sets were used for genus and species identification. Finally 19 strains were clasified as Clostridium tyrobutyricum and 3 strains were clasified as Clostridium butyricum. Presence of hydrogenase gene hydA was tested by PCR amplification using specific primer set HGf and HGr. Presence of hydrogenase gene was detected within 21 strains. (GTG)5 primer (rep-PCR) and Pr1 and Pr6 primers (RAPD) were used for differentiation of clostridial strains. Next, the cultivation of Clostridium tyrobutyricum S5 was studied under different conditions. The cultivation was carried out in liquid Reinforced Clostridial Medium (RCM) with lactose and cheese whey instead of glucose under anaerobe conditions. Growth was observed at laboratory temperature (20 to 23 °C) and at 37 °C, pH values ranging from 4.0 to 8.0 with 0.5 unit.
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Identification and characterization of selected species of lactic acid bacteria
Trojánek, Zdeněk ; Špano,, Miroslav (referee) ; Rittich, Bohuslav (advisor)
Among the important representative of lactic acid bacteria are gram-positive bacteria of the genus Bifidobacterium. They are constituent part of ordinary intestinal flora, which help keep the balance and prevent colonization of intestinal by pathogens. Bifidobacteria are used in various dairy products for their prebiotic effect. Molecular biological methods are used for rapid and accurate identification of bacteria of genus Bifidobacterium. In our case, we have focused on DNA isolation and application of the polymerase chain reaction (PCR) for identification of bacteria of genus Bifidobacterium. Statistical evaluation of fingerprints obtained by rep-PCR with (GTG)5 primer was carrid out.
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Automatic genotyping of bacteria by rep-PCR
Pelikánová, Veronika ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
This thesis deals with automatic bacteria genotyping by rep-PCR method. Its theoretical part presents various methods of DNA typing, basic information on electrophoresis and modern electrophoretic approaches, including their problems, misleading data distortion. In order to automate typing, there has been introduced a program for phylogenetic sample classification from rep-PCR, also applicable for data from chip capillary electrophoresis. The program consists of three main parts: digitization, bandmatching and clustering apparatus to bacterial type classification. The result of the algorithm is a phylogenetic tree, which indicates the cluster of sapmles according to bacterial type. The program has a graphical user interface for possible use in the Children's Hospital. Finally, the program is tested with data from the Children´s Hospital.
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Automatic Genotyping Of Bacteria By Rep-Pcr
Pelikánová, Veronika
This paper deals with automatic genotyping of bacteria by rep-PCR. The main goal is to create a program to analyze bacterial type in the samples. The result of the algorithm is phylogenetic tree, which indicates the cluster of samples according to bacterial type. This program consists of two main parts, a transformation function to reduce distortion of data and a clustering apparatus to bacterial type classification.
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Automatic genotyping of bacteria by rep-PCR
Pelikánová, Veronika ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
This thesis deals with automatic bacteria genotyping by rep-PCR method. Its theoretical part presents various methods of DNA typing, basic information on electrophoresis and modern electrophoretic approaches, including their problems, misleading data distortion. In order to automate typing, there has been introduced a program for phylogenetic sample classification from rep-PCR, also applicable for data from chip capillary electrophoresis. The program consists of three main parts: digitization, bandmatching and clustering apparatus to bacterial type classification. The result of the algorithm is a phylogenetic tree, which indicates the cluster of sapmles according to bacterial type. The program has a graphical user interface for possible use in the Children's Hospital. Finally, the program is tested with data from the Children´s Hospital.
|
|
|
Molecular characterization of selected clostridial strains isolated from cheeses
Chroboková, Maria ; Kvasničková, Eva (referee) ; Rittich, Bohuslav (advisor)
The study was focused on molecular characterization of 42 clostridial strains. DNA was isolated by fenol-chloroform extraction procedure and precipitated with ethanol. After DNA isolation, PCR amplifications with specific primer sets were used for genus and species identification. Finally 19 strains were clasified as Clostridium tyrobutyricum and 3 strains were clasified as Clostridium butyricum. Presence of hydrogenase gene hydA was tested by PCR amplification using specific primer set HGf and HGr. Presence of hydrogenase gene was detected within 21 strains. (GTG)5 primer (rep-PCR) and Pr1 and Pr6 primers (RAPD) were used for differentiation of clostridial strains. Next, the cultivation of Clostridium tyrobutyricum S5 was studied under different conditions. The cultivation was carried out in liquid Reinforced Clostridial Medium (RCM) with lactose and cheese whey instead of glucose under anaerobe conditions. Growth was observed at laboratory temperature (20 to 23 °C) and at 37 °C, pH values ranging from 4.0 to 8.0 with 0.5 unit.
|
|
|
Identification and characterization of selected species of lactic acid bacteria
Trojánek, Zdeněk ; Špano,, Miroslav (referee) ; Rittich, Bohuslav (advisor)
Among the important representative of lactic acid bacteria are gram-positive bacteria of the genus Bifidobacterium. They are constituent part of ordinary intestinal flora, which help keep the balance and prevent colonization of intestinal by pathogens. Bifidobacteria are used in various dairy products for their prebiotic effect. Molecular biological methods are used for rapid and accurate identification of bacteria of genus Bifidobacterium. In our case, we have focused on DNA isolation and application of the polymerase chain reaction (PCR) for identification of bacteria of genus Bifidobacterium. Statistical evaluation of fingerprints obtained by rep-PCR with (GTG)5 primer was carrid out.
|
|
|
Molecular typisation of lactic acid bacteria
Jelínek, Zdeněk ; Ing. Špano Miroslav,PhD. (referee) ; Rittich, Bohuslav (advisor)
Lactic acid bacteria play important role both in food industry and health care. They are part of many fermented dairy products and gastrointestinal microflora. There is a whole variety of methods for bacteria identification, but we will focus on Rep-PCR and RAPD only. The aim of this work will be to discuss the impact of different correlation coefficients and cluster analysis algorithms on the results of taxonomic analysis.
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