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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 ...
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
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 ...
Ecology of ants along elevational rainforest gradients in the tropics
MOSES, Jimmy
2021 - English
The thesis investigates the community ecology and species diversity of tropical ants on tropical mountains. The primary focus is on the changes in the ground-dwelling ant communities along elevational rainforest gradients, and how their elevational patterns are influenced by various biotic and abiotic factors. First, we investigated how elevation, leaf litter depth and their interaction affect the abundance, species richness and composition of ground-dwelling ants on Mt. Wilhelm (Papua New Guinea). Next, we investigated how ant communities change with forest succession in time along an extensive tropical elevational gradient in Southern Papua New Guinea. The aim was to assess both spatial and temporal trends in the ant communities and whether these changes could serve as indicators towards ecological recovery after human-induced forest disturbance. Finally, we assessed the relationships of ant species richness and activity, and their relative use of six nutrients, with elevation and season in three different tropical mountain regions (New Guinea,Tanzania and Ecuador). The thesis investigates the community ecology and species diversity of tropical ants on tropical mountains. The primary focus is on the changes in the ground-dwelling ant communities along elevational rainforest gradients, and how their elevational patterns are influenced by various biotic and abiotic factors. First, we investigated how elevation, leaf litter depth and their interaction affect the abundance, species richness and composition of ground-dwelling ants on Mt. Wilhelm (Papua New Guinea). Next, we investigated how ant communities change with forest succession in time along an extensive tropical elevational gradient in Southern Papua New Guinea. The aim was to assess both spatial and temporal trends in the ant communities and whether these changes could serve as indicators towards ecological recovery after human-induced forest disturbance. Finally, we assessed the relationships of ant species richness and activity, and their relative use of six nutrients, with elevation and season in three different tropical mountain regions (New Guinea,Tanzania and Ecuador).
Keywords:
ants; elevational gradients; altitude; tropical forests; nutrient use; leaf-litter; succession; abiotic factors; biotic factors; community ecology; species richness.
Available in the Digital Repository of University of South Bohemia.
Ecology of ants along elevational rainforest gradients in the tropics
The thesis investigates the community ecology and species diversity of tropical ants on tropical mountains. The primary focus is on the changes in the ground-dwelling ant communities along elevational ...
Evolutionary dynamics of satellite DNA in plant genomes
ÁVILA ROBLEDILLO, Laura
2021 - English
Satellite DNA (satDNA) belongs to the highly repetitive fraction of eukaryotic genomes. It is best characterized by the formation of long arrays of almost identical sequences that are tandemly repeated. These repeats are widely distributed in plant species where they can make up a substantial proportion of their genomes. Despite the long history of satDNA research, the classic methodology did not allow for its comprehensive characterization. Consequently, the fragmentary information gathered during the last 60 years does not answer the many questions surrounding the evolution of these elements. The development of new techniques in sequencing, together with the availability of new bioinformatics tools for analyzing different genome fractions, has presented an opportunity to advance studies of tandem repeats. This thesis describes the landscape characterization of satDNA in the genome of Fabeae species by exploring the diversity of satDNA within a genome, the association of these elements with functional centromeres, as well as their genome-wide organization. We employed new computational pipelines specifically designed for the analysis of tandem repeats from next generation sequencing data, and combined their results with molecular and cytogenetic methods to achieve comprehensive characterization of the satellite repeats. Satellite DNA (satDNA) belongs to the highly repetitive fraction of eukaryotic genomes. It is best characterized by the formation of long arrays of almost identical sequences that are tandemly repeated. These repeats are widely distributed in plant species where they can make up a substantial proportion of their genomes. Despite the long history of satDNA research, the classic methodology did not allow for its comprehensive characterization. Consequently, the fragmentary information gathered during the last 60 years does not answer the many questions surrounding the evolution of these elements. The development of new techniques in sequencing, together with the availability of new bioinformatics tools for analyzing different genome fractions, has presented an opportunity to advance studies of tandem repeats. This thesis describes the landscape characterization of satDNA in the genome of Fabeae species by exploring the diversity of satDNA within a genome, the association of these elements with functional centromeres, as well as their genome-wide organization. We employed new computational pipelines specifically designed for the analysis of tandem repeats from next generation sequencing data, and combined their results with molecular and cytogenetic methods to achieve comprehensive characterization of the satellite repeats.
Keywords:
Satellite DNA; cytogenetics; centromere evolution; plant chromosomes; CENH3; ChIP-seq; fluorescence in situ hybridization; Next Generation Sequencing; nanopore sequencing; Fabeae
Available in the Digital Repository of University of South Bohemia.
Evolutionary dynamics of satellite DNA in plant genomes
Satellite DNA (satDNA) belongs to the highly repetitive fraction of eukaryotic genomes. It is best characterized by the formation of long arrays of almost identical sequences that are tandemly ...
Contribution to the taxonomy and biodiversity of crustose lichens from the family Teloschistaceae
FROLOV, Ivan Valerievich
2021 - English
The PhD thesis is composed of five published papers and one manuscript accepted for publication. The main research goal was the investigation of the taxonomy and diversity of crustose Teloschistaceae in Europe and Northern Asia with special emphasis on the genus Pyrenodesmia. The first paper investigated the delimitation of the genus Pyrenodesmia and its relationships with the closely related Caloplaca haematites and C. xerica groups and some other species. The second paper proposed standardized methods for the measurement of the morphological characters of the crustose Teloschistaceae and suggested a phenotype evaluation process for the delimitation of species that are difficult to phenotypically distinguish. The method was practically employed in the third paper for the separation of three seemingly cryptic species from the genus Pyrenodesmia, which were formally described in the paper. Another new Pyrenodesmia species was described in the fourth paper. Investigations presented in the fifth paper substantially extended the known geographical distribution of several species of crustose Teloschistaceae in Europe and Northern Asia. The accepted manuscripts proposes the description of the new species of crustose Teloschistaceae in Siberia and the Russian Far East. Our studies provide a basis for future summarizing papers on the taxonomy and diversity of the genus Pyrenodesmia in the Holarctic and the family Teloschistaceae in Russia.
Available in the Digital Repository of University of South Bohemia.
Contribution to the taxonomy and biodiversity of crustose lichens from the family Teloschistaceae
The PhD thesis is composed of five published papers and one manuscript accepted for publication. The main research goal was the investigation of the taxonomy and diversity of crustose ...
Research on the agronomic and quality characteristics of modern wheat cultivars in organic farming
TRAN, Dang Khoa
2021 - English
Available in the Digital Repository of University of South Bohemia.
Research on the agronomic and quality characteristics of modern wheat cultivars in organic farming
\kur{Apodemus} vs. \kur{Eimeria}: Evolutionary factors of speciation and genomic diversification in host-parasite system
MÁCOVÁ, Anna
2021 - English
This thesis discusses and explains phylogenetic patterns observed in two different organisms: Eimeria, an unicellular parasite, and Apodemus, a rodent that often serves as a host for this parasitic species. The situation in rodents is intuitive, clearly reflecting their biogeographic history. Phylogenetic pattern in A. agrarius corresponds with its spread from the core locality of its distribution eastward. The lack of the genetic variability in European populations hints the recent origin of this population with the low number of founders. The phylogeny of A. flavicollis, a rodent inhabiting almost the whole Europe, reflects the situation during the last glacial maximum (i.e. speciation in several subpopulations that did not interbreed, but retained their independent nature). The situation in Eimeria is more complex. Parasites always fight in "arm races", trying to accommodate to their hosts as best they can, and to avoid their defense. This results in coevolutionary events such as cospeciation, host switches, duplications, and other events that form the genetic variability in parasites. The study of evolutionary relationships in Eimeria may be difficult due to lack or morphological and/or relevant molecular data. This thesis adds more information to this view. Several other studies were also included in this thesis to provide a broader picture of the complexity of host-parasite systems. This thesis discusses and explains phylogenetic patterns observed in two different organisms: Eimeria, an unicellular parasite, and Apodemus, a rodent that often serves as a host for this parasitic species. The situation in rodents is intuitive, clearly reflecting their biogeographic history. Phylogenetic pattern in A. agrarius corresponds with its spread from the core locality of its distribution eastward. The lack of the genetic variability in European populations hints the recent origin of this population with the low number of founders. The phylogeny of A. flavicollis, a rodent inhabiting almost the whole Europe, reflects the situation during the last glacial maximum (i.e. speciation in several subpopulations that did not interbreed, but retained their independent nature). The situation in Eimeria is more complex. Parasites always fight in "arm races", trying to accommodate to their hosts as best they can, and to avoid their defense. This results in coevolutionary events such as cospeciation, host switches, duplications, and other events that form the genetic variability in parasites. The study of evolutionary relationships in Eimeria may be difficult due to lack or morphological and/or relevant molecular data. This thesis adds more information to this view. Several other studies were also included in this thesis to provide a broader picture of the complexity of host-parasite systems.
Keywords:
rodents; parasites; coevolution; host-parasite system; coccidia; evolution
Available in the Digital Repository of University of South Bohemia.
\kur{Apodemus} vs. \kur{Eimeria}: Evolutionary factors of speciation and genomic diversification in host-parasite system
This thesis discusses and explains phylogenetic patterns observed in two different organisms: Eimeria, an unicellular parasite, and Apodemus, a rodent that often serves as a host for this parasitic ...
Aquatic insect assemblages in littoral zones of ponds and other man-made habitats
KOLÁŘ, Vojtěch
2021 - English
This thesis focuses on aquatic insect and newt assemblages in fishponds and other man-made standing waters. It reviews the effects of fishpond management and restoration of post-mining sites on main aquatic taxa, with main focus on aquatic insects in the littoral zone. The next five chapters deal with long-term changes of the littoral habitats in fishponds and with various aspects of the importance of littoral habitats for aquatic organisms, mainly predatory insects and newts. The results are used to recommend management approaches aimed to increase biodiversity and conservation value of fishponds and other man-made habitats.
Keywords:
Fish ponds; man-made habitats; aquatic insect; newts; littoral vegetation
Available in the Digital Repository of University of South Bohemia.
Aquatic insect assemblages in littoral zones of ponds and other man-made habitats
This thesis focuses on aquatic insect and newt assemblages in fishponds and other man-made standing waters. It reviews the effects of fishpond management and restoration of post-mining sites on main ...
Prostorová analýza ekonomických ukazatelů podniku
BERKOVÁ, Ilona
2021 - English
Výběr dobrého umístění pro firmu je jedním z nejdůležitějších dlouhodobých rozhodnutí vlastníků firmy, protože toto rozhodnutí nelze změnit a zajišťuje její budoucí úspěšný rozvoj. Proto je umístění podnikových aktivit po mnoho let součástí ekonomiky. Tato práce se zabývá touto problematikou. Cílem disertační práce je rozpoznání prostorových vztahů sídel společností. Nejprve jsou pozorovány prostorové vztahy mezi jednotlivými společnostmi v rámci jednotlivých sektorů. Následně jsou zodpovězeny otázky, zda zdraví společnosti následuje stejný osud jako ostatní blízké společnosti nebo je zcela nezávislé na jiných společnostech a zda se společnosti daří lépe v klastru nebo ne. Dalším cílem je navrhnout nový ekonometrický model pro rozpoznávání prostorové interakce společností podle jejich zdraví v nehomogenním případě. V analýze byl použit soubor sídel malých a středních podniků umístěných ve třech krajích nacházejících se v České republice, tj. V Jihočeském, Plzeňském a kraji Vysočina. Soubor dat byl shromážděn v roce 2015 a obsahuje 10 201 společností a se svými úplnými adresami. Společnosti jsou rozdělené do 13 sektorů. Metodika je založena na teorii bodového procesu. Vzhledem k tomu, že společnosti vybírají svá místa podle mnoha faktorů, byly pro modelování nehomogenity použity principy lokálního škálování. Výsledky byly získány aplikací Ripleyovy K-funkce a její odvozené Besagovy L-funkce. Nakonec byla nově zavedena funkce Locally Scaled Mark weighted K-function, pro zjištění závislosti zdraví firmy na její poloze. Tato funkce nebyla nikdy předtím použita. Zdraví společnosti bylo určeno pomocí klasifikačního modelu manželů Neumeierových IN05. Analýzy této práce odhalily, že společnosti ve všech odvětvích mají tendenci k silnému shlukování. Podařilo se nám prokázat, že geografická koncentrace společností je silnější než populace, protože pomáhá zesílit výhody výroby a inovací, konkrétně snížit transakční náklady, zvýšit tok informací, zlepšit specializované potřeby a být silnější v konkurenčním prostředí. Jelikož nebylo možné prokázat, že populace plně vysvětlí shlukování firem, byla populace v analýzách nahrazena hustotou bodového procesu společností. Hlavním cílem této disertační práce však bylo odpovědět na otázku, zda je zdraví firmy ovlivněno zdravím jiných blízkých společností a zda jsou společnosti zdravější, když se nacházejí v klastrech nebo ne. V těchto analýzách se podařilo v rámci sektorů odhalit určité zákonitosti, které mohou vysvětlovat trend umístění sídla společnosti. Tyto pravidelnosti jsou podrobně popsány v práci. Analýzy této práce by mohly být použity jako klíč, který může pomoci s výběrem vhodné lokality pro založení nové společnosti. Avšak neexistuje žádná přímá odpověď na to, kde by se měla společnost nacházet. Je třeba vzít v úvahu, že lokalizační teorie mají omezené použití kvůli své obecnosti. Do zpřesnění modelu by bylo nutné přidat další proměnné, například dostupnost technologií a kapitálu, osobní preference, geografickou vzdálenost od konkurence, blízkost dodavatelů, průmyslový areál, suroviny, komunitu, nedokonalá konkurence, externality atd. To choose a good location for a company is one of the most important long-term decision of the company's owners because this decision cannot be changed and ensures the future successful development of a company. That's why the location of corporate activities has been a part of economics for many years. This work also deals with this issue. The purpose of the thesis is the recognition of spatial relationships of the headquarters of companies. Firstly, there are observed spatial relationships between individual companies within individual sectors. Secondly, there are answered the questions if the health of the company follows the same fate as other near companies or is absolutely independent and if the company is doing better in a cluster or not. In particular, whether the company should think of a location close to another successful company or vice versa, a company that is not successful and is threatened by bankruptcy. Lastly, a new econometric model for recognition of spatial interaction of companies according to their health in the inhomogeneous case is proposed. In the analysis, the set of headquarters of small and medium companies in three regions located in the Czech Republic, i.e. Jihočeský, Plzeňský and Vysočina regions were used. The data set was collected in 2015 and contains 10 201 companies and their full addresses divided into 13 sectors. The methodology is based on a point process theory. Since the companies choose their locations according to plenty of factors, thus the local scaling principals were used for modelling the inhomogeneity. The results were obtained by application of Ripley's K-function and its derived Besag's L function that is used for the determination of the distribution of the companies in our research. Lastly, the locally scaled mark-weighted K function was newly introduced to determine the dependence of the firm health and its location. This function has never been used before. As a mark of the company, i.e. the health of the company, the Neumeier classification model IN05 was taken into account. The analyses of this work revealed that companies in all industries tend to strong clustering. We managed to prove that the geographic concentration of companies is stronger than population because it helps to amplify production and innovation benefits, specifically to reduce transaction costs, increase information flow, improve specialized needs and be stronger in a competitive environment. As it was not possible to prove that the population would fully explain the clustering of firms, thus population was replaced with the density of the point process of companies in the analyses. However, the main aim of the thesis was to ask if the health of the firm is influenced by the health of other companies surrounded by and if the companies are healthier when they are located in clusters or not. The analyses succeeded in revealing certain regularities through sectors that may explain the trend of the location of company headquarters in individual sectors. The regularities are described in detail in the thesis. Analyses of this thesis could be used as a key that can help with choosing a suitable locality for starting a new company. However, there is no straightforward answer to where a company should be located. It must be noted that location theories are of limited application since the generality. There is predominantly assumed only a few variables that are not sufficient in the real world. It would be necessary to add more variables to the model, for example, availability of technologies and capital, personal preferences, a geographical distance of competition, the proximity of suppliers, industrial site, raw materials, community, imperfect competition, externalities, etc. to understand the distribution of headquarters of companies.
Keywords:
Lokalizační teorie; shlukování; zdraví firem; lokální škálování; Locally Scaled Mark weighted K-function; Global envelope test
Available in the Digital Repository of University of South Bohemia.
Prostorová analýza ekonomických ukazatelů podniku
Výběr dobrého umístění pro firmu je jedním z nejdůležitějších dlouhodobých rozhodnutí vlastníků firmy, protože toto rozhodnutí nelze změnit a zajišťuje její budoucí úspěšný rozvoj. Proto je umístění ...
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