The breeding and foraging ecology of the House Sparrow in rural and urban environments
HAVLÍČEK, Jan
2021 - English This study describes the effect of farming practices, farmland utilization, and habitat composition in farmland settlements on the distribution and population density of the House Sparrow. Another goal of this study was to describe food availability for offspring and habitat use in rural and urban settlements. The results imply the importance of farms, their surroundings, small-scale farming, and the presence of natural habitats (shrubs, trees, ruderal vegetation) for the local House Sparrow populations. Increased home range size and flight distance were found in urban breeding pairs, implying the absence or lower availability of critical food sources in the urban environment. Future perspectives, threats, and management recommendations to prevent negative factors affecting House Sparrows and the entire bird community inhabiting similar habitats are discussed in this study. This study describes the effect of farming practices, farmland utilization, and habitat composition in farmland settlements on the distribution and population density of the House Sparrow. Another goal of this study was to describe food availability for offspring and habitat use in rural and urban settlements. The results imply the importance of farms, their surroundings, small-scale farming, and the presence of natural habitats (shrubs, trees, ruderal vegetation) for the local House Sparrow populations. Increased home range size and flight distance were found in urban breeding pairs, implying the absence or lower availability of critical food sources in the urban environment. Future perspectives, threats, and management recommendations to prevent negative factors affecting House Sparrows and the entire bird community inhabiting similar habitats are discussed in this study. Available in the Digital Repository of University of South Bohemia. The breeding and foraging ecology of the House Sparrow in rural and urban environments

This study describes the effect of farming practices, farmland utilization, and habitat composition in farmland settlements on the distribution and population density of the House Sparrow. Another ...

HAVLÍČEK, Jan
Jihočeská univerzita v Českých Budějovicích, 2021

Bioenergetic studies in the parasitic protist Trypanosoma brucei: functional characterisation of the mitochondrial FoF1-ATP synthase/ATPase complex
HIERRO YAP, Carolina
2021 - English This Ph.D. thesis focuses on the functional characterisation of the mitochondrial FoF1-ATP synthase/ATPase complex in the parasitic protist Trypanosoma brucei, a eukaryotic system that enables the study of both operation modes of the complex in physiological settings. The results presented in this thesis are divided in four topics: (i) bioenergetics consequences of mitochondrial FoF1-ATP synthase deficiency in two life cycle stages of the parasite, with emphasis on the roles of subunits ATPaseTb1 and OSCP, (ii) changes in energy metabolism of bloodstream form parasites depleted of cardiolipin, (iii) role of the FoF1-ATP synthase dimerisation in mitochondrial biogenesis and bioenergetics, with focus on the functional characterisation of the dimer-specific subunit g in the insect stage of the parasite, and (iv) role of subunit OSCP in the structural and functional integrity of the FoF1-ATPase in trypanosomes lacking mitochondrial DNA (akinetoplastic). This Ph.D. thesis focuses on the functional characterisation of the mitochondrial FoF1-ATP synthase/ATPase complex in the parasitic protist Trypanosoma brucei, a eukaryotic system that enables the study of both operation modes of the complex in physiological settings. The results presented in this thesis are divided in four topics: (i) bioenergetics consequences of mitochondrial FoF1-ATP synthase deficiency in two life cycle stages of the parasite, with emphasis on the roles of subunits ATPaseTb1 and OSCP, (ii) changes in energy metabolism of bloodstream form parasites depleted of cardiolipin, (iii) role of the FoF1-ATP synthase dimerisation in mitochondrial biogenesis and bioenergetics, with focus on the functional characterisation of the dimer-specific subunit g in the insect stage of the parasite, and (iv) role of subunit OSCP in the structural and functional integrity of the FoF1-ATPase in trypanosomes lacking mitochondrial DNA (akinetoplastic). Keywords: Trypanosoma brucei; mitochondria; FoF1-ATP synthase/ATPase; bioenergetics. Available in the Digital Repository of University of South Bohemia. Bioenergetic studies in the parasitic protist Trypanosoma brucei: functional characterisation of the mitochondrial FoF1-ATP synthase/ATPase complex

This Ph.D. thesis focuses on the functional characterisation of the mitochondrial FoF1-ATP synthase/ATPase complex in the parasitic protist Trypanosoma brucei, a eukaryotic system that enables the ...

HIERRO YAP, Carolina
Jihočeská univerzita v Českých Budějovicích, 2021

Diversity and Ecological Role of Cyanobacterial Lipopeptides
GALICA, Tomáš
2021 - English The presented study focuses on the biosynthesis and distribution of lipopeptides in the context of evolutionary history and life strategies of cyanobacteria. Cyanobacteria are ancient organisms often naturally exposed to situations in which other bacteria, such as Bacillus or Pseudomonas, were shown to employ lipopeptides to facilitate colony expansion or iron acquisition. The study explores these analogies and maps the distribution and diversity of lipopeptides across cyanobacteria with various lifestyles. Furthermore, the study provides evidence that widespread cyanobacterial lipopeptides containing a particular structural motif with two -hydroxy aspartate residues are a part of iron stress response and likely facilitate iron acquisition. The gathered information aims to integrate and deepen our knowledge of the ecophysiological roles of cyanobacterial lipopeptides. Keywords: Cyanobacteria; Lipopeptides; Siderophores Available in the Digital Repository of University of South Bohemia. Diversity and Ecological Role of Cyanobacterial Lipopeptides

The presented study focuses on the biosynthesis and distribution of lipopeptides in the context of evolutionary history and life strategies of cyanobacteria. Cyanobacteria are ancient organisms ...

GALICA, Tomáš
Jihočeská univerzita v Českých Budějovicích, 2021

Borrelia - host interactions: zoom in on the big picture.
STRNAD, Martin
2021 - English The thesis was written with the intention to bring together cutting-edge imaging methods and applications in order to illustrate how imaging can answer pathogenesis-related questions in Lyme disease at various resolution scale. Correlative light and electron microscopy, atomic force microscopy-based single-molecule force spectroscopy and solution nuclear magnetic resonance have been used to shed light on the underlying mechanisms associated with Lyme disease Borrelia infection. Specifically, the key molecular players and interactions responsible for the variance in the pathogenicity and disease outcome of Borrelia species have been studied. The rationale behind such studies was highlighted by review articles, which are part of the thesis. The thesis was written with the intention to bring together cutting-edge imaging methods and applications in order to illustrate how imaging can answer pathogenesis-related questions in Lyme disease at various resolution scale. Correlative light and electron microscopy, atomic force microscopy-based single-molecule force spectroscopy and solution nuclear magnetic resonance have been used to shed light on the underlying mechanisms associated with Lyme disease Borrelia infection. Specifically, the key molecular players and interactions responsible for the variance in the pathogenicity and disease outcome of Borrelia species have been studied. The rationale behind such studies was highlighted by review articles, which are part of the thesis. Keywords: microscopy; borrelia; diversity; lyme disease; adhesins Available in the Digital Repository of University of South Bohemia. Borrelia - host interactions: zoom in on the big picture.

The thesis was written with the intention to bring together cutting-edge imaging methods and applications in order to illustrate how imaging can answer pathogenesis-related questions in Lyme disease ...

STRNAD, Martin
Jihočeská univerzita v Českých Budějovicích, 2021

Mechanisms structuring host-parasitoid communities in a global warming perspective
THIERRY, Mélanie Jeanne
2021 - English Ecological communities are composed of a multitude of interacting species, and the outcome of pairwise interactions depends on other co-occurring species within the community. With current global environmental changes, both abiotic and biotic environment are changing, affecting the structure and dynamics of communities. I used a series of laboratory experiments on a set of Drosophila species and their parasitic wasps to investigate the effects of biotic and abiotic factors on interactions and communities. I first compared the outcome of host-parasitoid interactions across community modules commonly found in host-parasitoid communities (i.e., pairwise interaction, exploitative competition, apparent competition, and both exploitative and apparent competition). I found generally higher host suppression with multiple parasitoid species, but species-specific effects for parasitoid performance. I then observed that warming impacts host communities through direct effects on species performance rather than altered competitive interactions and parasitism. Finally, I found that temperature strongly influences the effects of multiple parasitoids on host suppression across different parasitoid assemblages, suggesting a general pattern for the environmental dependence of trophic and non-trophic interactions. My thesis emphasizes the importance of considering environmental factors and different interaction types to better predict community dynamics in a rapidly changing world. Ecological communities are composed of a multitude of interacting species, and the outcome of pairwise interactions depends on other co-occurring species within the community. With current global environmental changes, both abiotic and biotic environment are changing, affecting the structure and dynamics of communities. I used a series of laboratory experiments on a set of Drosophila species and their parasitic wasps to investigate the effects of biotic and abiotic factors on interactions and communities. I first compared the outcome of host-parasitoid interactions across community modules commonly found in host-parasitoid communities (i.e., pairwise interaction, exploitative competition, apparent competition, and both exploitative and apparent competition). I found generally higher host suppression with multiple parasitoid species, but species-specific effects for parasitoid performance. I then observed that warming impacts host communities through direct effects on species performance rather than altered competitive interactions and parasitism. Finally, I found that temperature strongly influences the effects of multiple parasitoids on host suppression across different parasitoid assemblages, suggesting a general pattern for the environmental dependence of trophic and non-trophic interactions. My thesis emphasizes the importance of considering environmental factors and different interaction types to better predict community dynamics in a rapidly changing world. Keywords: Climate change; temperature; host-parasite networks; multiple predator effects; interactions; Drosophila Available in the Digital Repository of University of South Bohemia. Mechanisms structuring host-parasitoid communities in a global warming perspective

Ecological communities are composed of a multitude of interacting species, and the outcome of pairwise interactions depends on other co-occurring species within the community. With current global ...

THIERRY, Mélanie Jeanne
Jihočeská univerzita v Českých Budějovicích, 2021

Function of the Type IV pili proteins in the cyanobacterium Synechocystis sp. PCC 6803.
LINHARTOVÁ, Markéta
2021 - English The thesis is focused on the function of the Type IV pili machinery in the cyanobacterium Synechocystis sp. PCC. 6803. In my work, I provided evidence that in phototrophs, some pilin proteins have acquired a novel function related to metal transport and assembly of photosynthetic complexes. The tight connection between the synthesis of the major pilin PilA1 and the biogenesis of photosynthetic complexes has been demonstrated in the pilD mutant lacking prepilins peptidase. I isolated and characterized pilD suppressor strains, which revealed the important role of the minor pilin PilA2 in the glycosylation of PilA1 and the restricted mobility of PilA1 prepilin in the membrane. My unpublished data indicate that the retraction mode of pili, driven by the PilT1 molecular motor, facilitates manganese uptake and the activity of this machine is critically important during the regulation from the exponential to the linear growth phase. The thesis is focused on the function of the Type IV pili machinery in the cyanobacterium Synechocystis sp. PCC. 6803. In my work, I provided evidence that in phototrophs, some pilin proteins have acquired a novel function related to metal transport and assembly of photosynthetic complexes. The tight connection between the synthesis of the major pilin PilA1 and the biogenesis of photosynthetic complexes has been demonstrated in the pilD mutant lacking prepilins peptidase. I isolated and characterized pilD suppressor strains, which revealed the important role of the minor pilin PilA2 in the glycosylation of PilA1 and the restricted mobility of PilA1 prepilin in the membrane. My unpublished data indicate that the retraction mode of pili, driven by the PilT1 molecular motor, facilitates manganese uptake and the activity of this machine is critically important during the regulation from the exponential to the linear growth phase. Keywords: type IV pili; Synechocystis; photosystem II; PilD peptidase; major pilin; prepilin toxicity; photoautotrophy; metal transport Available in the Digital Repository of University of South Bohemia. Function of the Type IV pili proteins in the cyanobacterium Synechocystis sp. PCC 6803.

The thesis is focused on the function of the Type IV pili machinery in the cyanobacterium Synechocystis sp. PCC. 6803. In my work, I provided evidence that in phototrophs, some pilin proteins have ...

LINHARTOVÁ, Markéta
Jihočeská univerzita v Českých Budějovicích, 2021

Contribution to the taxonomic revision of the order Oscillatoriales
HAUEROVÁ, Radka
2021 - English With the increased use of molecular data, especially the 16S rRNA gene and the following 16S-23S ITS region, many new species and genera have been described in recent years. At the same time, numerous traditional taxa have been recognized as polyphyletic and subsequently subjected to the revisionary process leading to their smaller size and narrower definition. However, there are many species and genera for which no molecular data are available as they were described long before the invent of the sequencing techniques. Thus, it is difficult to allocate their position in the modern phylogenies and move forward with their revisions. This thesis focuses on several simple filamentous cyanobacteria currently classified in the order Oscillatoriales and on the detail study of their type species. The connection of traditional descriptions with corresponding organism results in possibility to obtain reliable molecular data and study the taxa's relationship with other cyanobacteria. Thus, the reference phylogenetic points were established in this thesis for the traditional genera Arthrospira and Oscillatoria, and subsequently two new genera Limnospira and Tenebriella were introduced together with their reference strains. Clarification of the phylogenetic position of the type species of Oscillatoria, O. princeps, means first step towards resolving the polyphyletic nature of the whole order Oscillatoriales and its taxonomic revision. With the increased use of molecular data, especially the 16S rRNA gene and the following 16S-23S ITS region, many new species and genera have been described in recent years. At the same time, numerous traditional taxa have been recognized as polyphyletic and subsequently subjected to the revisionary process leading to their smaller size and narrower definition. However, there are many species and genera for which no molecular data are available as they were described long before the invent of the sequencing techniques. Thus, it is difficult to allocate their position in the modern phylogenies and move forward with their revisions. This thesis focuses on several simple filamentous cyanobacteria currently classified in the order Oscillatoriales and on the detail study of their type species. The connection of traditional descriptions with corresponding organism results in possibility to obtain reliable molecular data and study the taxa's relationship with other cyanobacteria. Thus, the reference phylogenetic points were established in this thesis for the traditional genera Arthrospira and Oscillatoria, and subsequently two new genera Limnospira and Tenebriella were introduced together with their reference strains. Clarification of the phylogenetic position of the type species of Oscillatoria, O. princeps, means first step towards resolving the polyphyletic nature of the whole order Oscillatoriales and its taxonomic revision. Available in the Digital Repository of University of South Bohemia. Contribution to the taxonomic revision of the order Oscillatoriales

With the increased use of molecular data, especially the 16S rRNA gene and the following 16S-23S ITS region, many new species and genera have been described in recent years. At the same time, ...

HAUEROVÁ, Radka
Jihočeská univerzita v Českých Budějovicích, 2021

The role of p38-MAPKs in mouse preimplantation embryonic development: Regulating translation towards blastocyst maturation and lineage specification.
BORA, Pablo
2021 - English Preimplantation embryonic development in mammals is the period from fertilisation of the gametes to implantation of the blastocyst embryo in to the uterine walls, poised for post-implantation foetal development. This is a 5-day long process in mouse, and encompasses signalling and gene regulatory mechanisms, metabolic, cellular and organellar structural transformations, resulting in progressively reduced cellular potency and three distinct lineages. The outer and inner cells around the 16-32-cell stage are designated as the trophectoderm (TE) and the inner cell mass (ICM), respectively. 32-cell stage onwards, the ICM further differentiates to the pluripotent epiblast (EPI) and epithelial, multi-potent primitive endoderm (PrE). TE and PrE generates the extra-embryonic tissues, placenta and yolk sac, respectively, and EPI forms the embryo proper. Typical generation of extra-embryonic cells and tissues is indispensable for normal embryonic development. p38-MAPKs, a family of four stress-activated kinases, play crucial roles throughout early development, though mechanistic understanding is limited. Studies within this thesis, building upon previous work, reports on the requirement of functional p38-MAPKs towards a translational landscape conducive for developmental cell fate specification and blastocyst maturation (E3.5 to E4.5). Phosphoproteomics, transcriptomics and experimental analysis revealed possible complications in ribosome biogenesis and an attenuated translational landscape upon inhibition of p38-MAPK activity, likely due to impaired function and localisation of downstream effectors. Some of the effectors identified, such as DDX21, MYBBP1A, and GNL3, are involved in rRNA transcription and processing, with null mutants demonstrating lethality prior to implantation. Similar to p38-MAPK inhibition, loss-of-function analysis of the effectors also resulted in fewer cells, particularly of GATA4 expressing PrE lineage. Experiments to identify the position of p38-MAPK in cell fate specifying signalling cascade revealed it as independent of the quintessential FGF4-FGFR-MEK/ERK pathway, but upstream of mTOR and potentially functional in the recently described FGFR2/PDGFRa-PI3K-mTOR pathway mediating PrE survival. p38-MAPK was also found to be functional in ameliorating amino acid deprivation induced oxidative stress during blastocyst maturation, by facilitating gene expression of anti-oxidant enzymes. Available in the Digital Repository of University of South Bohemia. The role of p38-MAPKs in mouse preimplantation embryonic development: Regulating translation towards blastocyst maturation and lineage specification.

Preimplantation embryonic development in mammals is the period from fertilisation of the gametes to implantation of the blastocyst embryo in to the uterine walls, poised for post-implantation foetal ...

BORA, Pablo
Jihočeská univerzita v Českých Budějovicích, 2021

Fungi, Herbivores and Predators as Determinants of Secondary Succession in Tropical Rainforest
SZEFER, Piotr
2021 - English Available in the Digital Repository of University of South Bohemia. Fungi, Herbivores and Predators as Determinants of Secondary Succession in Tropical Rainforest

SZEFER, Piotr
Jihočeská univerzita v Českých Budějovicích, 2021

Community structure of caterpillar parasitoids from tropical rain forest
LIBRA, Martin
2021 - English The aim of this dissertation is to investigate the community structure of parasitoids and their interactions with their hosts - caterpillars in the rainforest of Papua New Guinea, focusing on beta diversity and altitudinal trends. We show that parasitoid beta diversity is higher than the beta diversity of their hosts, which was also projected in their interactions. The altitude plays important role in the diversity of parasitoids, where we show that Ichneumonidae are more diverse at high elevation than at low elevation, which was not observed for other large insect families. Further, we performed a manipulative experiment, exposing live caterpillars in different elevations of tropical rainforest. Caterpillars faced similar mortality from parasitoids between elevations, but higher mortality from predation at low elevation. In the last chapter, we point out how important is correct species identification because wrong identification can misinterpret observed interactions. The aim of this dissertation is to investigate the community structure of parasitoids and their interactions with their hosts - caterpillars in the rainforest of Papua New Guinea, focusing on beta diversity and altitudinal trends. We show that parasitoid beta diversity is higher than the beta diversity of their hosts, which was also projected in their interactions. The altitude plays important role in the diversity of parasitoids, where we show that Ichneumonidae are more diverse at high elevation than at low elevation, which was not observed for other large insect families. Further, we performed a manipulative experiment, exposing live caterpillars in different elevations of tropical rainforest. Caterpillars faced similar mortality from parasitoids between elevations, but higher mortality from predation at low elevation. In the last chapter, we point out how important is correct species identification because wrong identification can misinterpret observed interactions. Keywords: parasitoid; diversity; beta diversity; altitudinal gradient; taxonomy; Ichneumonidae; Braconidae; Tachinidae; food-web interactions Available in the Digital Repository of University of South Bohemia. Community structure of caterpillar parasitoids from tropical rain forest

The aim of this dissertation is to investigate the community structure of parasitoids and their interactions with their hosts - caterpillars in the rainforest of Papua New Guinea, focusing on beta ...

LIBRA, Martin
Jihočeská univerzita v Českých Budějovicích, 2021