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Identification of Organisms Based on Analysis of Nucleotide Density Vectors
Maděránková, Denisa ; Babula, Petr (referee) ; Schwarz, Daniel (referee) ; Provazník, Ivo (advisor)
Most methods for analysis of genomic data work with symbolic sequences. Numerically represented genomic sequences can be analyzed by signal processing methods. A new method of numerical representation of DNA sequences, nucleotide density vectors, is proposed in this thesis. Usability of this method for purposes of molecular species identification is tested on DNA barcoding sequences. DNA barcoding is modern and popular methodology based on comparison of short mitochondrial DNA sequences. Beside species identification by proposed method based on nucleotide density vectors, higher taxa rank identification (e.g. families) was also tested. Furthermore, dendrograms were constructed from standardly used evolutionary distances and distances between nucleotide density vectors and the dendrograms were compared.
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Analysis of animal mitochondrial genes for DNA barcoding
Brabencová, Klára ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The aim of this work is a literature review on the topic of the mitochondrial genome and DNA barcoding, building a dataset of mitochondrial sequences from GenBank database and creatione of a software function for extraction of individual genes that are present in the mitochondrial genome. This function was developed in Matlab. DNA barcoding is a method that uses short DNA sequence of mitochondrial genome for identification of species. There is no comprehensive work examining the appropriateness of different mitochondrial genes. This aim investigates the potential of other mitochondrial genes and evaluate their effectiveness for DNA barcoding and calculation of intra-and interspecific variability.
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Molecular taxonomy of sand flies (Diptera: Psychodidae) in Europe
Grešová, Markéta ; Dvořák, Vít (advisor) ; Brzoňová, Jana (referee)
Phlebotomine sand flies (Diptera, Psychodidae) are small blood sucking insects which are only proven vectors of neglected tropical disease called leishmaniasis. Sand flies of the genus Phlebotomus act as vectors in the Old World and those of genus Lutzomyia are vectors in the New World. However, not all of them are capable of transmitting the disease. It is therefore crutial to conclusively determinate the species and have up-to-date knowledge of their natural occurence. Routine identification based on morphological characters is challenging due to intraspecific variability of these or their possible damage during the capture and preparation. In adition, correct assessment of distinctive cahracters, especially for females, is difficult and requires certain expertise. Thus, approaches of molecular taxonomy have been recently increasingly used for sand flies species determination. This thesis presents usage of DNA sequencing and MALDI-TOF protein profiling for routine determination of sand flies caught in southeastern Europe and adjacent regions, where we have lack of information of present sand flies species. Another part of this thesis focus on closer examination of relations between selected closely related species within species complexes. Key words: Phlebotomus, molacular identification, DNA...
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Highschool students' practical knowledge of nature subjects
Moravcová, Kamila Štěpánka ; Novotný, Petr (advisor) ; Pavlasová, Lenka (referee)
TITLE: Highschool students practical knowledge of nature subjects AUTHOR: Bc. Kamila Štěpánka Moravcová DEPARTMENT: Biology and Environmental Studies Department SUPERVISOR: PhDr. Petr Novotný, Ph.D. Abstract This text is aiming to species identification. Main target is how good or bad are students of secondary education (junior high school) in species identification. Theoretical part: Definition of basic terminilogy and detailed research and comparison (outcomes and methodics) of previous testings and questionaires of pre-school childern, primary, secondary and college students. Practical part: 1) Pre-research: Making lists of species, which would be used to test students. These lists were based on what contained students notes and what contained biology education itself. 2) Research: I was testing students and I compared outcomes with previous testings. Result is, that species identification is part of biology education, which still needs developing, because students aren't good at all in species identification. Key words: species knowledge, species identification, product of nature
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Molecular phylogeny of the genus Geosmithia
Korittová, Celie ; Kolařík, Miroslav (advisor) ; Tomšovský, Michal (referee)
The genus Geosmithia contains 11 described and several tens of undescribed species of fungi living nearly exclusively in galleries of subcorticolous insects, especially bark beetles. In this work, a phylogenetic analysis of the genus was made using DNA sequences of four protein-coding genes, namely TEF-1, RPB2, Mcm7 and Tsr1. The analysis has confirmed that ecological strategies of these fungi (such as association with conifers or broad leaved trees or symbiosis with ambrosia beetles) have evolved several times in this genus. 51 species are recognized based on the obtained phylogenetic tree according to Genealogical Concordance Phylogenetic Species Recognition. I have also tested utility of the above mentioned genes to serve as "barcode" for identification of closely related Geosmithia species.
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Identification of Organisms Based on Analysis of Nucleotide Density Vectors
Maděránková, Denisa ; Babula, Petr (referee) ; Schwarz, Daniel (referee) ; Provazník, Ivo (advisor)
Most methods for analysis of genomic data work with symbolic sequences. Numerically represented genomic sequences can be analyzed by signal processing methods. A new method of numerical representation of DNA sequences, nucleotide density vectors, is proposed in this thesis. Usability of this method for purposes of molecular species identification is tested on DNA barcoding sequences. DNA barcoding is modern and popular methodology based on comparison of short mitochondrial DNA sequences. Beside species identification by proposed method based on nucleotide density vectors, higher taxa rank identification (e.g. families) was also tested. Furthermore, dendrograms were constructed from standardly used evolutionary distances and distances between nucleotide density vectors and the dendrograms were compared.
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Analysis of animal mitochondrial genes for DNA barcoding
Brabencová, Klára ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The aim of this work is a literature review on the topic of the mitochondrial genome and DNA barcoding, building a dataset of mitochondrial sequences from GenBank database and creatione of a software function for extraction of individual genes that are present in the mitochondrial genome. This function was developed in Matlab. DNA barcoding is a method that uses short DNA sequence of mitochondrial genome for identification of species. There is no comprehensive work examining the appropriateness of different mitochondrial genes. This aim investigates the potential of other mitochondrial genes and evaluate their effectiveness for DNA barcoding and calculation of intra-and interspecific variability.
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Identification of species within \kur{Adelgidae} by molecular markers
VĚCHTOVÁ, Pavlína
Four molecular markers (nuclear ITS, EF1 alpha and mitochondrial AT-Rich and COI) were tested for use in species identification of Adelgidae family. Markers EF1 alpha and COI were successfuly amplified and sequenced. Aligned sequences of those two markers were used for reconstruction of dendrogram by Minimum Evolution method with Kimura 2-Parameter model. Comparison of dendrogram with assumptions based on morfology and biology of Adelgids confirmed suitability of chosen molecular markers for reliable resolution of taxonomic relationship within Adelgidae, although further testing and markers will be required to delineate sister species with higher precision.
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