Lichens of Trubínský vrch hill near Beroun (central Bohemia) and a study of Aspicilia dominiana Veronika Lenzová Abstract This diploma thesis is divided into two separate parts. The goal of the first part was to carry out a complete lichenofloristic research of Trubín hill near Beroun. There are diabasic outcrops on the south side of the hill. Due to wide spectrum of the lichen species this substrate is very interesting for the lichenologists. In total I have found 125 lichen species there. 105 lichen species grow on diabasic rocks. A considerable amount of recorded lichens is among endangered species for example Aspicilia dominiana, Caloplaca conversa, Lichinella stipatula, Phaeophyscia constipata. The second part is focused on the taxonomic study of the Aspicilia dominiana and related species. A. domininana is recently known only from a few diabasic localities in the Czech Republic. After revision of the herbarium material based on microscopic and chemical characteristics I have found out that the taxon A. dominiana is similar with the A. intermutans. Compliance of these taxa have been confirmed with the molecular data from the sequencing of the two genes nrITS and mTSS too. Therefore I propose to synonymize these two taxa. According to the phylogenetic tree the lichen A. intermutans is not closely...

The principal goal of my study was to find if ecologically and chemically different populations of lichens in the Physconia muscigena (Ach.) Poelt group belong to several species or a single one. This study focused on the molecular and chemical investigations of mostly European and Canadian populations. I use sequence data from three genes (ITS rDNA, mtSSU rDNA and TEF1) for the reconstruction of phylogenetic trees. I investigate phylogenetic relationships among the closely related species P. muscigena, P. bayeri, P. rossica, and P. isidiomuscigena. Also, I wanted to detect any possible geographical or ecological trends among chemotypes and haplotypes. As an additional goal I checked the recent localities of P. muscigena in the Czech Republic for valorising its conservation status. Results show that: (1) sequenced data of ITS rDNA and TEF1 show high intraspecific variability in P. muscigena samples. This genetic variability does not correlate neither with geographical distribution nor thallus chemistry; (2) P. bayeri is synonymous with P. muscigena; (3) some samples P. muscigena contain new undetermined secondary metabolite, (4) Physconia muscigena has only three recent localities in Czech Republic. Key words: Physconia muscigena, Physconia bayeri, infraspecific variability, taxonomy, TEF1, ITS...

This thesis deals with the phylogeny of the lichen genus Usnea (Parmeliaceae, Ascomycetes). The relationships and the morphological variation among Usnea species has been studied, as well as the relationship of Usnea to allied genera. Two species, U. florida and U. subfloridana, which earlier were regarded to form two separate species have been synonymized. In an analysis based on sequence data these two taxa formed a monophyletic group of intermixed specimens. Usnea florida and U. subfloridana have earlier been regarded to form a species pair, but the species pairs concept cannot be applied in this case. The morphological characters traditionally used for species recognition of a number of European Usnea species have been analyzed regarding their reliability. The evolution and distribution of the morphological characters was studied in relation to a phylogeny based on sequence data. Most characters proved to be homoplastic in relation to the phylogeny. Few characters were consistent in a clade, and the same character could be inconsistent in another clade. Therefore a combination of several characters is recommended for species recognition. The relationship of Neuropogon to Usnea was investigated based on sequence data. Neuropogon showed to be closely related to Usnea subg. Usnea. The subgenera Eumitria and Dolichousnea formed the sister group to the clade comprising subg. Usnea and Neuropogon. Usnea is paraphyletic in this investigation. Eumitria is treated as a genus and the subgenus Dolichousnea is elevated to generic rank. The position of Usnea, Neuropogon, Eumitria, and Dolichousnea in the family Parmeliaceae was investigated based on a phylogeny obtained by sequence data. Protousnea probably forms the sister group to the clade of Usnea, Neuropogon, Eumitria, and Dolichousnea. Several monophyletic groups in the family Parmeliaceae were identified.

As doenças respiratórias constituem um sério problema em sistemas intensivos de criação de suínos, causando enormes prejuízos à industria suína no Brasil e no mundo. Estes prejuízos estão freqüentemente relacionados à redução de peso, mortalidade, maior predisposição a doenças entéricas, gastos com vacinas e medicamentos. Os distúrbios respiratórios em suínos são manifestados através de um complexo de doenças, com envolvimento de agentes virais, bacterianos e fúngicos. Dentre estes, a presença do circovírus (PCV2) e o Pneumocystis sp. começa a ser gradativamente caracterizada como uma associação entre um agente causador de imunossupressão e um organismo de ação oportunista. O trabalho objetivou diagnosticar Pneumocystis sp. através das técnicas de imunohistoquímica, Grocott e nested-PCR, em suínos abatidos nos Estados do Rio Grande do Sul (RS) e Mato Grosso (MT), diagnosticar a ocorrência de PCV2 na mesma população de suínos, verificar a associação entre Pneumocystis sp. e PCV2, e determinar as relações filogenéticas entre as amostras de Pneumocystis sp. O estudo avaliou um total de 591 pulmões, 297 com alterações macroscópicas (pneumonia) e 294 normais obtidos em frigoríficos. Foram analisados 292 pulmões procedentes do RS e 299 pulmões do MT Para diagnóstico do Pneumocystis sp. as amostras foram analisadas através das técnicas de Grocott, Imunohistoquímica e nested-PCR (mtLSU e mtSSU rRNA). Do total das amostras, 36,9% foram positivas para Pneumocystis. O índice de positividade para o vírus PCV2 foi de 32,7% na amostra total. Os resultados revelaram uma alta prevalência do vírus (PCV2) em pulmões sem lesões macroscópicas. A co-infecção (PCV2 e Pneumocystis sp.), foi detectada em 28,0% em 564 pulmões examinados. As análises das seqüências dos nucleotídeos dos produtos de PCR dos genes mtLSU e mtSSU do rRNA do Pneumocystis sp. nos pulmões analisados, sugerem a presença até o presente momento de 2 espécies diferentes de Pneumocystis no Brasil. Este estudo evidencia a ocorrência da co-infecção de dois agentes (Pneumocystis sp. e PCV2) em animais hígidos, fato que, indica a necessidade de planejamento e implementação de medidas de controle para melhorar a produtividade na suinocultura. / Respiratory diseases are a major problem in intensive systems of swine husbandry. They are a cause for high losses in the swine industry in Brazil and in the world. These losses are often related to weight reduction, mortality, higher vulnerability to enteric diseases, and expenses with vaccines and drugs. Respiratory diseases in swine appear through a complex of diseases, caused by virus, bacteria and fungi; among these, the porcine circovirus 2 (PCV2) and Pneumocystis sp., the former an agent which causes immunosupression and the latter an oportunistic microorganism. Both are being recognized as capable of being associated. The objectives of this study were to: identify Pneumocystis sp. through immunohystochemistry techniques, Grocott and nested-PCR in swine slaughtered in the States of Rio Grande do Sul and Mato Grosso (MT); investigate PCV2 in the same swine population; investigate the association between Pneumocystis sp. and PCV2, and establish a filogenetic relationship between isolated of Pneumocystis sp. The study was carried out with a total of 591 lungs, 297 with macroscopic alterations characteristic of pneumonia, and 294 normal lungs from the industry. 292 lungs came from RS and 299 lungs came from MT. In order, to diagnose Pneumocystis infection, samples were analysed through Grocott technique, immunohystochemistry and nested-PCR (mtLSU and mtSSU rRNA). Among all samples 36,9% were positive for Pneumocystis sp.. PCV2 virus was found in 37,2% of the samples. Results revealed a high prevalence of the PCV2 virus in lungs without macroscopic lesions. Co-infection (PCV2 and Pneumocystis sp.) was found in 28,0% of 564 lungs examined. So far, the analyses of the sequences of nucleotides from the products of PCR from the genes mtlSU rRNA and mtSSU rRNA from Pneumocystis obtained from the examined lungs suggest that, it is possible the existence of two different species of Pneumocystis in Brazil. This study shows co-infection by two agents (Pneumocysts sp. and PCV2) in apparently healthy animals. This fact points out the necessity planning and implementation of control measures in order to improve productiviy in swine husbandry and industry.

As doenças respiratórias constituem um sério problema em sistemas intensivos de criação de suínos, causando enormes prejuízos à industria suína no Brasil e no mundo. Estes prejuízos estão freqüentemente relacionados à redução de peso, mortalidade, maior predisposição a doenças entéricas, gastos com vacinas e medicamentos. Os distúrbios respiratórios em suínos são manifestados através de um complexo de doenças, com envolvimento de agentes virais, bacterianos e fúngicos. Dentre estes, a presença do circovírus (PCV2) e o Pneumocystis sp. começa a ser gradativamente caracterizada como uma associação entre um agente causador de imunossupressão e um organismo de ação oportunista. O trabalho objetivou diagnosticar Pneumocystis sp. através das técnicas de imunohistoquímica, Grocott e nested-PCR, em suínos abatidos nos Estados do Rio Grande do Sul (RS) e Mato Grosso (MT), diagnosticar a ocorrência de PCV2 na mesma população de suínos, verificar a associação entre Pneumocystis sp. e PCV2, e determinar as relações filogenéticas entre as amostras de Pneumocystis sp. O estudo avaliou um total de 591 pulmões, 297 com alterações macroscópicas (pneumonia) e 294 normais obtidos em frigoríficos. Foram analisados 292 pulmões procedentes do RS e 299 pulmões do MT Para diagnóstico do Pneumocystis sp. as amostras foram analisadas através das técnicas de Grocott, Imunohistoquímica e nested-PCR (mtLSU e mtSSU rRNA). Do total das amostras, 36,9% foram positivas para Pneumocystis. O índice de positividade para o vírus PCV2 foi de 32,7% na amostra total. Os resultados revelaram uma alta prevalência do vírus (PCV2) em pulmões sem lesões macroscópicas. A co-infecção (PCV2 e Pneumocystis sp.), foi detectada em 28,0% em 564 pulmões examinados. As análises das seqüências dos nucleotídeos dos produtos de PCR dos genes mtLSU e mtSSU do rRNA do Pneumocystis sp. nos pulmões analisados, sugerem a presença até o presente momento de 2 espécies diferentes de Pneumocystis no Brasil. Este estudo evidencia a ocorrência da co-infecção de dois agentes (Pneumocystis sp. e PCV2) em animais hígidos, fato que, indica a necessidade de planejamento e implementação de medidas de controle para melhorar a produtividade na suinocultura. / Respiratory diseases are a major problem in intensive systems of swine husbandry. They are a cause for high losses in the swine industry in Brazil and in the world. These losses are often related to weight reduction, mortality, higher vulnerability to enteric diseases, and expenses with vaccines and drugs. Respiratory diseases in swine appear through a complex of diseases, caused by virus, bacteria and fungi; among these, the porcine circovirus 2 (PCV2) and Pneumocystis sp., the former an agent which causes immunosupression and the latter an oportunistic microorganism. Both are being recognized as capable of being associated. The objectives of this study were to: identify Pneumocystis sp. through immunohystochemistry techniques, Grocott and nested-PCR in swine slaughtered in the States of Rio Grande do Sul and Mato Grosso (MT); investigate PCV2 in the same swine population; investigate the association between Pneumocystis sp. and PCV2, and establish a filogenetic relationship between isolated of Pneumocystis sp. The study was carried out with a total of 591 lungs, 297 with macroscopic alterations characteristic of pneumonia, and 294 normal lungs from the industry. 292 lungs came from RS and 299 lungs came from MT. In order, to diagnose Pneumocystis infection, samples were analysed through Grocott technique, immunohystochemistry and nested-PCR (mtLSU and mtSSU rRNA). Among all samples 36,9% were positive for Pneumocystis sp.. PCV2 virus was found in 37,2% of the samples. Results revealed a high prevalence of the PCV2 virus in lungs without macroscopic lesions. Co-infection (PCV2 and Pneumocystis sp.) was found in 28,0% of 564 lungs examined. So far, the analyses of the sequences of nucleotides from the products of PCR from the genes mtlSU rRNA and mtSSU rRNA from Pneumocystis obtained from the examined lungs suggest that, it is possible the existence of two different species of Pneumocystis in Brazil. This study shows co-infection by two agents (Pneumocysts sp. and PCV2) in apparently healthy animals. This fact points out the necessity planning and implementation of control measures in order to improve productiviy in swine husbandry and industry.

As doenças respiratórias constituem um sério problema em sistemas intensivos de criação de suínos, causando enormes prejuízos à industria suína no Brasil e no mundo. Estes prejuízos estão freqüentemente relacionados à redução de peso, mortalidade, maior predisposição a doenças entéricas, gastos com vacinas e medicamentos. Os distúrbios respiratórios em suínos são manifestados através de um complexo de doenças, com envolvimento de agentes virais, bacterianos e fúngicos. Dentre estes, a presença do circovírus (PCV2) e o Pneumocystis sp. começa a ser gradativamente caracterizada como uma associação entre um agente causador de imunossupressão e um organismo de ação oportunista. O trabalho objetivou diagnosticar Pneumocystis sp. através das técnicas de imunohistoquímica, Grocott e nested-PCR, em suínos abatidos nos Estados do Rio Grande do Sul (RS) e Mato Grosso (MT), diagnosticar a ocorrência de PCV2 na mesma população de suínos, verificar a associação entre Pneumocystis sp. e PCV2, e determinar as relações filogenéticas entre as amostras de Pneumocystis sp. O estudo avaliou um total de 591 pulmões, 297 com alterações macroscópicas (pneumonia) e 294 normais obtidos em frigoríficos. Foram analisados 292 pulmões procedentes do RS e 299 pulmões do MT Para diagnóstico do Pneumocystis sp. as amostras foram analisadas através das técnicas de Grocott, Imunohistoquímica e nested-PCR (mtLSU e mtSSU rRNA). Do total das amostras, 36,9% foram positivas para Pneumocystis. O índice de positividade para o vírus PCV2 foi de 32,7% na amostra total. Os resultados revelaram uma alta prevalência do vírus (PCV2) em pulmões sem lesões macroscópicas. A co-infecção (PCV2 e Pneumocystis sp.), foi detectada em 28,0% em 564 pulmões examinados. As análises das seqüências dos nucleotídeos dos produtos de PCR dos genes mtLSU e mtSSU do rRNA do Pneumocystis sp. nos pulmões analisados, sugerem a presença até o presente momento de 2 espécies diferentes de Pneumocystis no Brasil. Este estudo evidencia a ocorrência da co-infecção de dois agentes (Pneumocystis sp. e PCV2) em animais hígidos, fato que, indica a necessidade de planejamento e implementação de medidas de controle para melhorar a produtividade na suinocultura. / Respiratory diseases are a major problem in intensive systems of swine husbandry. They are a cause for high losses in the swine industry in Brazil and in the world. These losses are often related to weight reduction, mortality, higher vulnerability to enteric diseases, and expenses with vaccines and drugs. Respiratory diseases in swine appear through a complex of diseases, caused by virus, bacteria and fungi; among these, the porcine circovirus 2 (PCV2) and Pneumocystis sp., the former an agent which causes immunosupression and the latter an oportunistic microorganism. Both are being recognized as capable of being associated. The objectives of this study were to: identify Pneumocystis sp. through immunohystochemistry techniques, Grocott and nested-PCR in swine slaughtered in the States of Rio Grande do Sul and Mato Grosso (MT); investigate PCV2 in the same swine population; investigate the association between Pneumocystis sp. and PCV2, and establish a filogenetic relationship between isolated of Pneumocystis sp. The study was carried out with a total of 591 lungs, 297 with macroscopic alterations characteristic of pneumonia, and 294 normal lungs from the industry. 292 lungs came from RS and 299 lungs came from MT. In order, to diagnose Pneumocystis infection, samples were analysed through Grocott technique, immunohystochemistry and nested-PCR (mtLSU and mtSSU rRNA). Among all samples 36,9% were positive for Pneumocystis sp.. PCV2 virus was found in 37,2% of the samples. Results revealed a high prevalence of the PCV2 virus in lungs without macroscopic lesions. Co-infection (PCV2 and Pneumocystis sp.) was found in 28,0% of 564 lungs examined. So far, the analyses of the sequences of nucleotides from the products of PCR from the genes mtlSU rRNA and mtSSU rRNA from Pneumocystis obtained from the examined lungs suggest that, it is possible the existence of two different species of Pneumocystis in Brazil. This study shows co-infection by two agents (Pneumocysts sp. and PCV2) in apparently healthy animals. This fact points out the necessity planning and implementation of control measures in order to improve productiviy in swine husbandry and industry.