Genome evolution of endosymbiotic bacteria in blood-sucking insects
ŘÍHOVÁ, Jana
2023 - English The research on insect-bacteria symbiosis is experiencing a rapid burst leading to the identification of much higher complexity and dynamics of the insect-bacteria associations than ever before envisaged. The generally accepted concept of obligate bacterial symbionts as providers of essential compounds (vitamins, aminoacids) has been further developed into the framework of microbiomes, i.e. communities of microorganisms associated with the host. The majority of the knowledge has been derived from plant sap-feeders, while data on blood-feeding insects remain fragmented and even inconsistent. In this thesis, we employ amplicon, genomic and in-vivo approaches to investigate several symbiotic systems of obligate blood-feeders and address the following questions: What is the diversity of symbiotic bacteria in our studied systems? What are the metabolic capacities of these symbionts? What is the role of symbionts in the biology of their hosts? What are the possible sources of bacteria prone to establish symbiosis with obligate blood-feeders? Where these symbionts reside in the host´s body? What is the coevolutionary pattern of these bacteria with their hosts? As an answer to these questions, I present the results detailed in the course of this thesis, which are preceded by a comprehensive introduction to the studied topics and wraps up with a summary of the main results. Keywords: symbiotic bacteria; obligate blood-feeders; microbiome; amplicon sequencing; whole-genome sequencing; metaboic capacities Available in the Digital Repository of University of South Bohemia. Genome evolution of endosymbiotic bacteria in blood-sucking insects

The research on insect-bacteria symbiosis is experiencing a rapid burst leading to the identification of much higher complexity and dynamics of the insect-bacteria associations than ever before ...

ŘÍHOVÁ, Jana
Jihočeská univerzita v Českých Budějovicích, 2023

Biomolecular simulations in non-aqueous media
FADAEI, Fatemeh
2023 - English Available in the Digital Repository of University of South Bohemia. Biomolecular simulations in non-aqueous media

FADAEI, Fatemeh
Jihočeská univerzita v Českých Budějovicích, 2023

Dung beetles of Central Europe: Diversity and conservation
AMBROŽOVÁ, Lucie
2023 - English Tato disertační práce se skládá ze tří ochranářsky orientovaných studií, které se zabývají zejména faktory určujícími diverzitu koprofágních brouků ve střední Evropě. První studie hodnotila vliv rutinního odčervování hospodářských zvířat ivermektinem na druhovou diverzitu a funkční výkonnost společenstva koprofágních brouků. Druhá studie zkoumala vliv alternativních lesních managementů pařazení a odstranění svrchní vrstvy půdy na druhovou a funkční diverzitu lesních koprofágních brouků a drabčíků. Poslední studie se zabývala environmentálními a managementovými faktory, které určují -diverzitu koprofágních brouků, s cílem identifikovat prioritní oblasti druhové ochrany středoevropských Koprofágů. The thesis consists of three conservation-oriented studies, mainly focusing on the factors determining dung beetle diversity in Central Europe. We assessed the role of routine ivermectin treatment on diversity and functional performance of dung beetle community. Alternative forest managements of coppicing and additional topsoil removal were evaluated in terms of their suitability for increasing diversity of dung-inhabiting dung and rove beetles. Further, we examined environmental and management-related factors driving dung beetle beta-diversity to facilitate conservation prioritization of Central European dung beetles. Keywords: ivermektin; beta-diverzita; ochrana přírody; chráněné druhy; koprofágní brouci; Scarabaeidae; Geotrupidae; pastevní management Available in the Digital Repository of University of South Bohemia. Dung beetles of Central Europe: Diversity and conservation

Tato disertační práce se skládá ze tří ochranářsky orientovaných studií, které se zabývají zejména faktory určujícími diverzitu koprofágních brouků ve střední Evropě. První studie hodnotila vliv ...

AMBROŽOVÁ, Lucie
Jihočeská univerzita v Českých Budějovicích, 2023

Isolation and characterisation of extracellular vesicles of parasitic helminths
MAZANEC, Hynek
2023 - English Exkrečně sekreční produkty (ESP) slouží jako důležití mediátoři mezibuněčných a mezidruhových komunikací. Původně se předpokládalo, že jsou vylučovány hlavně v rozpustné formě, ale nedávné objevy naznačují i jejich vylučování za pomoci extracelulárních vezikul (EV). Tyto membránové částice poskytují svému obsahu ochranu před degradací a zároveň i cílený transport skrz specifických receptorů na svém povrchu. Díky tomu jsou studovány jako silné imunomodulátory vztahů mezi hostitelem a patogenem. S ohledem na parazitické helminty, EV jsou studovány jako prostředky pro diagnostiku, vakcinaci či terapii. Nicméně jejich obecná biologie, zejména pak jejich biogeneze, je stále špatně prostudována v porovnání s jejich potenciální funkců. Cílem této práce je tedy podrobněji prozkoumat sekreční aktivitu EV u různých zástupců tasemnic a jejich životních stádií. Životní cyklus tasemnice Schistocephalus solidus byl založen v laboratorních podmínkách za účelem studia sekrece EV napříč jednotlivými stádii. Zároveň jsme prozkoumali hlavní cesty biogeneze EV u tasemnice Hymenolepis diminuta za pomoci ultrastrukturních a proteomických analýz. Oba směry zároveň umožnily porovnání tvorby EV u tasemnic s různými typy hostitelů. Excretory-secretory products (ESP) serve as important mediators of intercellular and inter-species communication. They were originally thought to be secreted mainly in a soluble form, but recent discoveries indicate their delivery through extracellular vesicles (EVs). These membraneous particles provide protection from degradation for some of their components, as well as targeted delivery through various receptors on their surface. As such they have been studied as potent immunomodulators in host-pathogen relationships. With respect to parasitic helminths, EVs are being studied as agents for diagnosis, vaccination or therapeutics. However, their general biology, especially their biogenesis patterns, is still poorly understood compared to their functional role.Therefore, the goal of this thesis is to investigate in more detail the secretion activity of EVs in different tapeworms and their life-cycle stages. Under laboratory conditions, the life cycle of Schistocephalus solidus, a tapeworm with an aquatic life cycle, was established to explore EVs secretion at different developmental stages. Moreover, we used proteomic analyses and ultrastructural observations to identify the main biogenesis pathways behind EVs secretion in a terrestrial tapeworm Hymenolepis diminuta. This also allowed for the comparison of EVs generation in tapeworms with different host types. Keywords: Extracelulární vezikuly; parazit; tasemnice; Schistocephalus solidus; Hymenolepis diminuta; elektronová mikroskopie; proteomika Available in the Digital Repository of University of South Bohemia. Isolation and characterisation of extracellular vesicles of parasitic helminths

Exkrečně sekreční produkty (ESP) slouží jako důležití mediátoři mezibuněčných a mezidruhových komunikací. Původně se předpokládalo, že jsou vylučovány hlavně v rozpustné formě, ale nedávné objevy ...

MAZANEC, Hynek
Jihočeská univerzita v Českých Budějovicích, 2023

Microbial and Viral Genomic Diversity in Freshwater Environments
SILVA KAVAGUTTI, Vinicius
2022 - English Most abundant microbes from natural environments remain uncultured as traditional culture approaches fail to sufficiently simulate native conditions. Moreover, the efforts to obtain axenic cultures are also hampered due to inter-microbial dependencies. The absence of cultured representatives has several downstream effects, e.g., little chance of experimentation and creating genetic models or hypothesis testing, phage isolation, or even producing complete, closed reference genomes. Lack of all these maintains severe gaps in our abilities to understand microbes in appropriate phylogenetic and ecological contexts and also their habitat at large. This thesis tries to circumvent these issues through a meticulous investigation of freshwater microbes and their viruses using a metagenomic approach in the Římov reservoir. Most abundant microbes from natural environments remain uncultured as traditional culture approaches fail to sufficiently simulate native conditions. Moreover, the efforts to obtain axenic cultures are also hampered due to inter-microbial dependencies. The absence of cultured representatives has several downstream effects, e.g., little chance of experimentation and creating genetic models or hypothesis testing, phage isolation, or even producing complete, closed reference genomes. Lack of all these maintains severe gaps in our abilities to understand microbes in appropriate phylogenetic and ecological contexts and also their habitat at large. This thesis tries to circumvent these issues through a meticulous investigation of freshwater microbes and their viruses using a metagenomic approach in the Římov reservoir. Available in the Digital Repository of University of South Bohemia. Microbial and Viral Genomic Diversity in Freshwater Environments

Most abundant microbes from natural environments remain uncultured as traditional culture approaches fail to sufficiently simulate native conditions. Moreover, the efforts to obtain axenic cultures ...

SILVA KAVAGUTTI, Vinicius
Jihočeská univerzita v Českých Budějovicích, 2022

W chromosomes in Lepidoptera: evolution, diversity and molecular features
HEJNÍČKOVÁ, Martina
2022 - English Sex chromosome evolution is a fascinating and very dynamic process, which is best to be studied on diverse groups of organisms. Moths and butterflies (Lepidoptera) are known for their species diversity and female heterogamety, which makes them an ideal research model. Most species of Lepidoptera have a WZ/ZZ (female/male) system, although some species lack the W chromosome. The first part of this thesis discusses possible mechanisms and points of its origin in terms of phylogeny. Specifically, it focuses on the lack of W chromosome in the group of bagworms (Psychidae), supporting recent theory about the independent origin of W chromosomes in Lepidoptera. The second part of the thesis provides valuable information about the W chromosome variability and molecular content within the group of loopers (Geometridae). Finally, the third part describes the accumulation of retrotransposons on the W chromosome in Peribatodes rhomboidaria and emphasizes their importance in the process of sex chromosome differentiation. Keywords: W chromosome; sex chromosomes; Lepidoptera; moths and butterflies; sex chromosome evolution; sex determination; retrotransposons; Geometridae; Psychidae; sex chromatin; repetitive DNA Available in the Digital Repository of University of South Bohemia. W chromosomes in Lepidoptera: evolution, diversity and molecular features

Sex chromosome evolution is a fascinating and very dynamic process, which is best to be studied on diverse groups of organisms. Moths and butterflies (Lepidoptera) are known for their species ...

HEJNÍČKOVÁ, Martina
Jihočeská univerzita v Českých Budějovicích, 2022

Conservation genetics of Galápagos mockingbirds: from immune genes to genomes
VLČEK, Jakub
2022 - English In this thesis I have dealt with the population genetic processes of mockingbirds in the Galápagos Islands ( Mimus ) in relation to the limited island area, from the perspective of two types of immune genes and the genome-wide approach. The thesis starts with an introduction to population genetic concepts relevant to conservation genetics followed by description of immune genes: the major histocompatibility complex (MHC) and the Toll-like receptors (TLR). In the final part of the introduction, I address how genetic drift, selection and inbreeding shape genome-wide genetic patterns in small populations. The introduction is followed by four chapters, beginning with an examination of MHCII polymorphism in populations of mockingbirds in the Galápagos Islands. The study of the relationship between MHCII and the abundance of ectoparasites is the content of the second chapter. The third chapter shows how polymorphism of TLRs is shaped by interaction of genetic drift and natural selection. The last chapter deals with the effects of limited island size on inbreeding and genetic load, supported by inferences of the past demography of mockingbirds. The thesis concludes with a summary of the results and their potential implications in the field of conservation genetics. In this thesis I have dealt with the population genetic processes of mockingbirds in the Galápagos Islands ( Mimus ) in relation to the limited island area, from the perspective of two types of immune genes and the genome-wide approach. The thesis starts with an introduction to population genetic concepts relevant to conservation genetics followed by description of immune genes: the major histocompatibility complex (MHC) and the Toll-like receptors (TLR). In the final part of the introduction, I address how genetic drift, selection and inbreeding shape genome-wide genetic patterns in small populations. The introduction is followed by four chapters, beginning with an examination of MHCII polymorphism in populations of mockingbirds in the Galápagos Islands. The study of the relationship between MHCII and the abundance of ectoparasites is the content of the second chapter. The third chapter shows how polymorphism of TLRs is shaped by interaction of genetic drift and natural selection. The last chapter deals with the effects of limited island size on inbreeding and genetic load, supported by inferences of the past demography of mockingbirds. The thesis concludes with a summary of the results and their potential implications in the field of conservation genetics. Keywords: population genetics; birds; inbreeding; genetic drift; immunogenetics; conservation; MHC; TLR; major histocompatibility complex; Toll-like receptors; genome; genetic load; extinction; effective population size; island size Available in the Digital Repository of University of South Bohemia. Conservation genetics of Galápagos mockingbirds: from immune genes to genomes

In this thesis I have dealt with the population genetic processes of mockingbirds in the Galápagos Islands ( Mimus ) in relation to the limited island area, from the perspective of two types of ...

VLČEK, Jakub
Jihočeská univerzita v Českých Budějovicích, 2022

Drivers of karyotype evolution in Lepidoptera
PROVAZNÍKOVÁ, Irena
2022 - English Research of lepidopteran karyotypes and their evolution has been challenging for decades due to their many peculiar characteristics. However, this field has advanced thanks to modern cytogenetic techniques and sequencing technologies. We combined explored possibilities how to detect chromosomal rearrangements, and cytogenetic and genomic approaches to explore evolutionary forces shaping karyotypes of non-model Lepidoptera including representatives of early diverging species. Results obtained in the present thesis point to a possible role of satellite DNA and sexual antagonistic selection in mobilisation of rDNA and sex chromosome turnover, respectively. Keywords: Lepidoptera; karyotype evolution; sex chromosomes; repetitive sequences; chromosomal rearrangements; gene families; FISH Available in the Digital Repository of University of South Bohemia. Drivers of karyotype evolution in Lepidoptera

Research of lepidopteran karyotypes and their evolution has been challenging for decades due to their many peculiar characteristics. However, this field has advanced thanks to modern cytogenetic ...

PROVAZNÍKOVÁ, Irena
Jihočeská univerzita v Českých Budějovicích, 2022

Role of adenosine pathway on cell growth and stress response in Drosophila
MAAROUFI, Houda Ouns
2022 - English The thesis surveyed the effects of the adenosine pathway on cell growth and stress response. We described the effects of mutation of the concentrative nucleoside transporter cnt1 on male fertility, particularly spermatogenesis, using a Drosophila melanogaster model. We also described the effects of the adenosine pathway on the cytotoxicity of mHTT. The thesis surveyed the effects of the adenosine pathway on cell growth and stress response. We described the effects of mutation of the concentrative nucleoside transporter cnt1 on male fertility, particularly spermatogenesis, using a Drosophila melanogaster model. We also described the effects of the adenosine pathway on the cytotoxicity of mHTT. Keywords: cell growth; stress response; cnt1; adenosine pathway; metabolism; mHTT Available in the Digital Repository of University of South Bohemia. Role of adenosine pathway on cell growth and stress response in Drosophila

The thesis surveyed the effects of the adenosine pathway on cell growth and stress response. We described the effects of mutation of the concentrative nucleoside transporter cnt1 on male fertility, ...

MAAROUFI, Houda Ouns
Jihočeská univerzita v Českých Budějovicích, 2022

Ecology of alpine plants at their uppermost limit in the Himalayas
CHLUMSKÁ, Zuzana
2022 - English This dissertation studies the key abiotic factors and plant characteristics that influence the performance of the highest growing herbaceous alpine plants in Ladakh, Western Himalayas, and examines vegetation changes likely associated with climate change. The study site, located in the Rupshu region of eastern Ladakh, hosts some of the world´s highest-growing angiosperm plant species that occur above 6000 m a.s.l. The gentle slopes characteristic for the region, resulting in long elevational gradients, are particularly suitable for studying plant adaptations to the harsh dry and cold environment typical of whole Ladakh. The study presents novel insights into the causes of plant elevation limits and the direction of the vegetation shifts related to climate change at the very edge of the existence of angiosperms. Keywords: alpine plants; herbaceous plants; Western Himalayas; high elevation; elevational distribution limits; climate change; nonstructural carbohydrates Available in the Digital Repository of University of South Bohemia. Ecology of alpine plants at their uppermost limit in the Himalayas

This dissertation studies the key abiotic factors and plant characteristics that influence the performance of the highest growing herbaceous alpine plants in Ladakh, Western Himalayas, and examines ...

CHLUMSKÁ, Zuzana
Jihočeská univerzita v Českých Budějovicích, 2022