Rozprawy doktorskie na temat „Eukaryotes”
Kliknij ten link, aby zobaczyć inne rodzaje publikacji na ten temat: Eukaryotes.
Utwórz poprawne odniesienie w stylach APA, MLA, Chicago, Harvard i wielu innych
Sprawdź 50 najlepszych rozpraw doktorskich naukowych na temat „Eukaryotes”.
Przycisk „Dodaj do bibliografii” jest dostępny obok każdej pracy w bibliografii. Użyj go – a my automatycznie utworzymy odniesienie bibliograficzne do wybranej pracy w stylu cytowania, którego potrzebujesz: APA, MLA, Harvard, Chicago, Vancouver itp.
Możesz również pobrać pełny tekst publikacji naukowej w formacie „.pdf” i przeczytać adnotację do pracy online, jeśli odpowiednie parametry są dostępne w metadanych.
Przeglądaj rozprawy doktorskie z różnych dziedzin i twórz odpowiednie bibliografie.
1
Clark, Francis. "A computational study of gene structure and splicing in model eukaryote organisms /". St. Lucia, Qld, 2003. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe17395.pdf.
Pełny tekst źródła
2
Plass, Pórtulas Mireya 1982. "Comparative analysis of splicing in eukaryotes". Doctoral thesis, Universitat Pompeu Fabra, 2011. http://hdl.handle.net/10803/78124.
Pełny tekst źródłaStreszczenie:
L’splicing és el mecanisme pel qual els introns són eliminats del pre-mRNA per generar un trànscrit madur. Aquest procés és dut a terme per un complex macromolecular anomenat spliceosoma i requereix el reconeixement dels senyals d’splicing al pre-mRNA. Aquests senyals no són sempre identificats correctament, el que permet la producció de trànscrits diferents a partir d’un únic pre-mRNA mitjançant un procés anomenat splicing alternatiu. Aquest procés pot ser regulat mitjançant factors proteics específics o per altres mecanismes que alteren el reconeixement dels senyals d’splicing com l’estructura secundària adoptada pels pre-mRNAs. En aquesta tesi hem investigat els mecanismes de regulació de l’splicing en eucariotes mitjançant tècniques computacionals. També hem estudiat la relació existent entre les proteïnes que intervenen en la regulació de l’splicing i els senyals d’splicing, i com han coevolucionat en diferents espècies. Finalment, i tenint en compte les possibilitats que l’splicing alternatiu ofereix des del punt de vista evolutiu, també hem analitzat l’impacte de l’splicing alternatiu en l’evolució gènica.Splicing is the mechanism by which introns are removed from the pre-mRNA to create a mature transcript. This process is performed by a macromolecular complex, the spliceosome, and involves the recognition of the splicing signals in the premRNA. These signals are not always perfectly recognized, which allows the production of different mature transcripts from a single pre-mRNA through a process called alternative splicing. This process can be regulated by specific protein factors or by other mechanisms that affect the recognition of the splicing signals, such as the secondary structure adopted by the pre-mRNA. In this thesis we have investigated the mechanisms of splicing regulation in eukaryotes using computational approaches. Moreover, we have also studied the relationship that exists between protein factors involved in splicing regulation and splicing signals, and how they have co-evolved across species. Finally, and considering the possibilities that alternative splicing can offer from the evolutionary point of view, he have also analyzed the impact of alternative splicing in gene evolution.
3
van, Weringh Anna. "Exploring Codon-Anticodon Adaptation in Eukaryotes". Thèse, Université d'Ottawa / University of Ottawa, 2011. http://hdl.handle.net/10393/20303.
Pełny tekst źródłaStreszczenie:
tRNA genes have the fundamental role of translating the genetic code during protein synthesis. Beyond solely a passive decoding role, the tRNA pool exerts selection pressures on the codon usage of organisms and the viruses that infect them because processing codons read by rare tRNAs can be slow or even erroneous. To better understand the interactions of codons and anticodons in eukaryotic species, we first investigated whether tRNAs packaged into HIV-1 particles may relate to the poor codon usage of HIV-1 genes. By comparing the codon usage of HIV-1 genes with that of its human host, we found that tRNAs decoding poorly adapted codons are overrepresented in HIV-1 virions. Because the affinity of Gag-Pol for all tRNAs is non-specific, HIV packaging is most likely passive and reflects the tRNA pool at the time of viral particle formation. Moreover, differences that we found in the codon usage between early and late genes suggest alterations in the tRNA pool are induced late in viral infection. Next, we tested whether a reduced tRNA anticodon pattern, which was called into question by predicted tRNA datasets, is maintained across eukaryotes. tRNA prediction methods are prone to falsely identifying tRNA-derived repetitive sequences as functional tRNA genes. Thus, we proposed and tested a novel approach to identify falsely predicted tRNA genes using phylogenetics. Phylogenetic analysis removed nearly all the genes deviating from the anticodon pattern, therefore the anticodon pattern is reaffirmed across eukaryotes.
4
Takamiya, Minako. "Endocrine disrupting chemical impacts on eukaryotes". Thesis, Cranfield University, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.487012.
Pełny tekst źródłaStreszczenie:
Endocrine Disrupting Chemicals (EDCs) are exogenous substances or mixtures that might lead to endocrine disruption in humans and wildlife. Bispheriol (BPA) was chosen as a model EDC and assessed for its toxic impacts on two eukaryotic test systems: (1) A fungal test system - white-rot basidiomycete, Trametes versicolor T. versicolor was tolerant of high concentrations of BPA (up to 300 ppm). The ligninolytic enzymes produced by the fungi were stimulated by 300 ppm of BPA. Of the three ligninolytic enzyme encoding genes examined, lignin peroxidase showed the greatest increase in expression in the presence ofBPA. (2) A mammalian test system - mouse Leydig tumor cell lines (mLTC-l) Time- and dose-responses of the cells stimulated with gonadotrophin to BPA demonstrated the clearest response in the expression of the steroidogenic genes without a marked effect on cell viability. The studies on the response of global gene expression to BPA by microarray analysis of mLTC-l cells showed 24 genes were differentially expressed in the presence of BPA (8 were increased and 16 were decreased). Several of these genes were related to steroid/cholesterol metabolism, transport and cell cycle regulation. In addition a study of male reproductive impairment was carried out to understand the reproductive toxicity of EDCs and likely effects on male infertility - one of the serious effects caused by EDCs. Human testicular tissues from fertile and infertile patients were examined by a microarray and 2642 genes were differentially expressed between the testes of fertile and infertile patients (955 genes were increased and 1687 genes were decreased in infertile patients). These genes are related to steroidogenesis, Leydig cell function, spermatid metamorphosis, cell cycle, and ribosome function. The array data exhibited phenotype-specific gene expression patterns. The most significant gene expression differences between fertile and infertile. patients were observed in spermatocyte- and spermatid- stages. Though further analysis is required, it is thought that BPA has weak modulatory impacts on eukaryotic test systems used in this study, however, its reproductive toxicity may not be negligible.
5
Plass, Pórtulas Mireya. "Comparative analysis of splicing in eukaryotes". Doctoral thesis, Universitat Pompeu Fabra, 2011. http://hdl.handle.net/10803/78124.
Pełny tekst źródłaStreszczenie:
L’splicing és el mecanisme pel qual els introns són eliminats del pre-mRNA per generar un trànscrit madur. Aquest procés és dut a terme per un complex macromolecular anomenat spliceosoma i requereix el reconeixement dels senyals d’splicing al pre-mRNA. Aquests senyals no són sempre identificats correctament, el que permet la producció de trànscrits diferents a partir d’un únic pre-mRNA mitjançant un procés anomenat splicing alternatiu. Aquest procés pot ser regulat mitjançant factors proteics específics o per altres mecanismes que alteren el reconeixement dels senyals d’splicing com l’estructura secundària adoptada pels pre-mRNAs. En aquesta tesi hem investigat els mecanismes de regulació de l’splicing en eucariotes mitjançant tècniques computacionals. També hem estudiat la relació existent entre les proteïnes que intervenen en la regulació de l’splicing i els senyals d’splicing, i com han coevolucionat en diferents espècies. Finalment, i tenint en compte les possibilitats que l’splicing alternatiu ofereix des del punt de vista evolutiu, també hem analitzat l’impacte de l’splicing alternatiu en l’evolució gènica.Splicing is the mechanism by which introns are removed from the pre-mRNA to create a mature transcript. This process is performed by a macromolecular complex, the spliceosome, and involves the recognition of the splicing signals in the premRNA. These signals are not always perfectly recognized, which allows the production of different mature transcripts from a single pre-mRNA through a process called alternative splicing. This process can be regulated by specific protein factors or by other mechanisms that affect the recognition of the splicing signals, such as the secondary structure adopted by the pre-mRNA. In this thesis we have investigated the mechanisms of splicing regulation in eukaryotes using computational approaches. Moreover, we have also studied the relationship that exists between protein factors involved in splicing regulation and splicing signals, and how they have co-evolved across species. Finally, and considering the possibilities that alternative splicing can offer from the evolutionary point of view, he have also analyzed the impact of alternative splicing in gene evolution.
6
Coulombe-Huntington, Jasmin. "Intron loss and gain in Eukaryotes". Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=18747.
Pełny tekst źródłaStreszczenie:
Although introns were first discovered almost 30 years ago, their evolutionary origin and function remains elusive. In this thesis, I describe a referenced-based intron mapping method based on multi-species whole-genome alignments. We applied this method in two distinct studies. First we studied intron loss and gain dynamics in mammals and subsequently in Drosophila. We mapped known human introns onto the mouse, rat and dog genomes, mouse introns onto the human genome and Drosophila melanogaster introns onto 10 other fully sequenced Drosophila genomes. This genome-wide approach allowed us to assess the presence or absence of over 150,000 known human introns across four mammalian species and more than 35,000 D. melanogaster introns across 11 fruit fly species. We inferred 122 intron loss events in mammals and no intron gain events. In flies, we were able to identify 1754 intron loss events and 213 gain events. In both studies we found that lost introns tend to be extremely short and show higher than average similarity between their 5' splice-site sequence and the 3' partner splice-site sequence. We also demonstrate that losses in mammals occur preferentially in highly expressed house-keeping genes, while in Drosophila we show that lost and gained introns are flanked by longer than average exons, display quite distinct phase distributions and losses demonstrate significant clustering within genes. Across flies, it appears introns that have been lost evolve faster than other introns while they occur in slowly evolving genes. Our results in both studies strongly support the cDNA recombination mechanism of intron loss. The results in flies also suggest that selective pressures affect site-specific loss rates and show that intron gain has occurred within the Drosophila lineage, solidifying the “introns-middle” hypothesis and providing some hints about the gain mechanism and origin of introns.Malgré le fait que les introns furent découverts il y a près de 30 ans, leur origine et leur fonction nous échappent encore. Au cours de cette thèse, je décrirais une méthode qui permet de projeter des introns d'une espèce de référence sur d'autres génomes, basée sur des alignements de génomes complets à plusieurs espèces. Nous avons appliqué cette méthode dans le cadre de deux études distinctes. Premièrement, nous avons étudié les pertes et les gains d'introns chez les mammifères et ensuite chez les Drosophiles. Nous avons projeté les introns humains sur le génome de la souris, du rat et du chien, les introns de la souris sur le génome humain et les introns de la Drosophile melanogaster sur les génomes de 10 autres espèces de Drosophiles complètement séquencées. Cette approche d'ordre génomique nous a permis de comparer la présence ou l'absence de plus de 150,000 introns humains dans quatre espèces de mammifères et plus de 35,000 introns de D. melanogaster dans 11 espèces de drosophiles. Nous avons détecté 122 pertes d'introns chez les mammifères mais aucun gain d'intron. Chez les mouches à fruits, nous avons identifié 1754 pertes d'introns et 213 gains d'introns. Dans les deux études, nous démontrons que les introns perdus sont extrêmement courts et démontrent une similarité relativement élevée entre le site d'épissage au début de l'intron et le site d'épissage à la fin de l'intron. Nous démontrons chez les mammifères les pertes d'introns se produisent de préférence dans des gènes hautement exprimés et de fonctions cruciales à la cellule. Chez les drosophiles nous démontrons que les introns perdus ou gagnés sont délimités par des exons plus longs que la moyenne, ont une distribution de phase plutôt distincte et les pertes démontrent une tendance à se retrouver en groupe à l'intérieur des gènes. Chez les mouches à fruits, il semble que les introns perdus évoluent plus rapidement que la moyenne
7
Keeley, Anthony John. "Holliday junction processing enzymes in eukaryotes". Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313658.
Pełny tekst źródła
8
Fudenberg, Geoffrey. "Three-Dimensional Chromosome Organization in Eukaryotes". Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17467516.
Pełny tekst źródłaStreszczenie:
The study of chromosome, and genome, organization is a both an ongoing challenge, and one with a long history. Following the advent of high-throughput sequencing and genomic technologies, much research has focused on the one-dimensional, or sequence-level, organization of genomes, with many successes. Nonetheless, genomes are physically organized as chromosomes in the three-dimensional confines of the cell nucleus, with implications for processes including gene regulation, DNA replication, and cell division.
Recently, chromosome conformation capture (3C) based methods have enabled new high-resolution and genome-wide views (Hi-C) of chromosome organization in three-dimensions. 3C methods convert direct spatial contacts between pairs of genomic loci into molecular products that can be assayed using high-throughput sequencing. The new views of chromosomal organization enabled by 3C techniques have been the principal motivation for my graduate research. In particular, 3C technologies now pose multiple important computational and theoretical challenges, including how to: (1) process and filter large quantities of experimental data; (2) develop computational models of chromosomes that agree with and help the understanding of experimental data; and (3) integrate views from 3C technologies with other genomic datasets, including complementary characterizations of the chromatin fiber. This thesis presents a series of projects addressing these challenges in chronological order of their publication.
The first project relates to the integration of views from Hi-C with other genomic datasets to understand the functional implications of chromosome organization. This project examined the connection between Hi-C chromosome contact maps and the distribution and positions of somatic copy number alterations observed across a variety of cancers. Since the observed alterations are the consequence of both mutational processes and evolutionary pressures on the cancers, we used a population genetics framework to consider how a mutational process governed by polymer physics might manifest in the patterns of alterations observed in cancer genomes.
The second project relates to the processing and filtering of Hi-C data. This project investigated how to correct for various biases that could be introduced at different stages of the experimental protocol, and then how to decompose the resulting contact maps into dominant features of chromosomal organization. We found that we could dramatically compress the complexity of chromosome interaction patterns, and that these compressed patterns are surprisingly conserved between humans and mice. These methods have been used by our lab and others to investigate 3C data across a broad range of organisms.
The third project involved the analysis of Hi-C data through the cell cycle, and the development of polymer models of chromosome organization in metaphase, when cells are prepared for division. Before cell division, chromosomes undergo extensive compaction; after division, they decondense and resume their cell-type-specific gene expression in interphase. We found that while interphase chromosome organization reflects cell-type-specific programs of gene expression, all traces of this organization are wiped clear in metaphase chromosomes. Our models of metaphase chromosomes allowed us to discriminate between two classic biological hypotheses of metaphase chromosome organization. We found that metaphase chromosomes are inconsistent with classic hierarchical models of folding, yet can be described by a two-stage process of compaction.
The fourth project used polymer models to understand how local interactions, or loops, between genomic elements might in turn alter local chromosome organization. This has implications for gene regulation, as the classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. We found that a chromatin loop can either suppress or facilitate enhancer-promoter interactions, depending on the location of the loop relative to the enhancer-promoter pair, and that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactionsBiophysics
9
Akhtar, Mahmood Electrical Engineering & Telecommunications Faculty of Engineering UNSW. "Genomic sequence processing: gene finding in eukaryotes". Publisher:University of New South Wales. Electrical Engineering & Telecommunications, 2008. http://handle.unsw.edu.au/1959.4/40912.
Pełny tekst źródłaStreszczenie:
Of the many existing eukaryotic gene finding software programs, none are able to guarantee accurate identification of genomic protein coding regions and other biological signals central to pathway from DNA to the protein. Eukaryotic gene finding is difficult mainly due to noncontiguous and non-continuous nature of genes. Existing approaches are heavily dependent on the compositional statistics of the sequences they learn from and are not equally suitable for all types of sequences. This thesis firstly develops efficient digital signal processing-based methods for the identification of genomic protein coding regions, and then combines the optimum signal processing-based non-data-driven technique with an existing data-driven statistical method in a novel system demonstrating improved identification of acceptor splice sites. Most existing well-known DNA symbolic-to-numeric representations map the DNA information into three or four numerical sequences, potentially increasing the computational requirement of the sequence analyzer. Proposed mapping schemes, to be used for signal processing-based gene and exon prediction, incorporate DNA structural properties in the representation, in addition to reducing complexity in subsequent processing. A detailed comparison of all DNA representations, in terms of computational complexity and relative accuracy for the gene and exon prediction problem, reveals the newly proposed ?paired numeric? to be the best DNA representation. Existing signal processing-based techniques rely mostly on the period-3 behaviour of exons to obtain one dimensional gene and exon prediction features, and are not well equipped to capture the complementary properties of exonic / intronic regions and deal with the background noise in detection of exons at their nucleotide levels. These issues have been addressed in this thesis, by proposing six one-dimensional and three multi-dimensional signal processing-based gene and exon prediction features. All one-dimensional and multi-dimensional features have been evaluated using standard datasets such as Burset/Guigo1996, HMR195, and the GENSCAN test set. This is the first time that different gene and exon prediction features have been compared using substantial databases and using nucleotide-level metrics. Furthermore, the first investigation of the suitability of different window sizes for period-3 exon detection is performed. Finally, the optimum signal processing-based gene and exon prediction scheme from our evaluations is combined with a data-driven statistical technique for the recognition of acceptor splice sites. The proposed DSP-statistical hybrid is shown to achieve 43% reduction in false positives over WWAM, as used in GENSCAN.
10
Ettwiller, Laurence Michele. "Computational investigations into cis-regulation in eukaryotes". Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613876.
Pełny tekst źródła
11
Moustafa, Ahmed Bhattacharya Debashish. "Evolutionary and functional genomics of photosynthetic eukaryotes". Iowa City : University of Iowa, 2009. http://ir.uiowa.edu/etd/311.
Pełny tekst źródła
12
Moustafa, Ahmed. "Evolutionary and functional genomics of photosynthetic eukaryotes". Diss., University of Iowa, 2009. https://ir.uiowa.edu/etd/311.
Pełny tekst źródłaStreszczenie:
My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes and the design and implementation of computational methods and tools to enable genome-wide studies to investigate these taxa. The work described here is grouped into two major topics, 1) endosymbiosis and genome evolution, and 2) harmful algal blooms. I discuss my work related to endosymbiosis and genome evolution in chapters 2-4. Chapters 5-6 cover the work related to harmful algal blooms. In chapter 1, I introduce the state-of-art of what is known about the history of plastids and evolution of photosynthesis in eukaryotes, an overview of marine harmful algae, and the specific aims of my dissertation.
In chapter 2, I describe the design and implementation of the phylogenetic sorting tool, PhyloSort and the assembly of a high-throughput phylogenomic pipeline. Together, PhyloSort and the pipeline has become a key tool for multiple subsequent studies. chapter 2 also presents a case study using these tools in which we provide an estimate of the number of cyanobacterial genes that have been transferred to the nuclear genome of Plantae through primary endosymbiotic gene transfer; I use the model unicellular green alga Chlamydomonas reinhardtii for this purpose.
In chapter 3, I discuss another case of prokaryotic contribution to the nucleus of photosynthetic eukaryotes. Here, the intriguing relationship of Chlamydiae-like bacteria and plants and algae is examined in a large-scale analysis, in which we scanned all available genomes of the primary photosynthetic organisms for genes of potential Chlamydiae origin. Surprisingly, we identified more than fifty Chlamydiae-derived genes in plants and algae. Here, we propose a model for the role that a Chlamydiae-like symbiont might have played in the establishment of the primary plastid in the common ancestor of Plantae.
In chapter 4, I describe a study in which we explored the complete protein models of two diatom organisms as representative for photosynthetic chromalveolates and looked for genes that might have been acquired through endosymbiotic (secondary) or horizontal transfers from red or green algae. In contradiction of the “chromalveolate hypothesis” which states that photosynthesis in chromalveolates originated via the engulfment of a red alga symbiont, our study shows an unexpected green algal contribution that is fourfold greater than that of the canonical red algal symbiont. Our data suggest that the chromalveolate history includes a previously unrecognized green algal endosymbiont that was captured and lost prior to the more recent establishment of the red alga plastid, which is widespread in extant photosynthetic chromalveolates.
In chapter 5, I discuss the identification of the phylogenetic origin of the genes involved in the biosynthetic pathway of saxitoxin in cyanobacteria. Here, we used a pyrosequencing approach to sequence de novo genomes of two strains of Anabaena circinalis, one of which is saxitoxin-producing and the other is non-toxic. Using comparative and phylogenetic analyses, I show that, within the saxitoxin gene cluster, genes that encode the key and unique enzymes in the pathway are of foreign origin that originated via horizontal transfer from non-cyanobacterial sources. These genes introduced the ability to produce saxitoxin in the ancestor of the toxic cyanobacterial clade.
In chapter 6, I describe a gene expression study in which we used massively parallel signature sequencing (MPSS) to investigate RNA abundance patterns in the toxic dinoflagellate Alexandrium tamarense. This work provides the first clear evidence for the utilization by dinoflagellates of transcriptional to regulation. Moreover, using MPSS, we provide an estimate of the number of the distinct genes in Alexandrium tamarense; i.e., remarkably 40,000 loci. Taken together, our data indicate that dinoflagellates possess a great metabolic flexibility that allows them to efficiently toggle between photoautotrophy and heterotrophy based on the environmental conditions.
13
Ponce, Toledo Rafael Isaac. "Origins and early evolution of photosynthetic eukaryotes". Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS047/document.
Pełny tekst źródłaStreszczenie:
Les plastes primaires proviennent d'une cyanobactérie qui a établi une relationendosymbiotique avec un hôte eucaryote. Cet événement a donné naissance au super-groupeArchaeplastida qui inclut les Viridiplantae (algues vertes et plantes terrestres), les Rhodophyta (alguesrouges) et les Glaucophyta. Suite à l'endosymbiose primaire, les algues rouges et vertes ont étendu lacapacité de photosynthèse à d'autres lignées eucaryotes via des endosymbioses secondaires. Bien quedes progrès considérables aient été réalisés dans la compréhension de l'évolution des eucaryotesphotosynthétiques, d'importantes questions sont restées ouvertes, telles que l’identité de la lignéecyanobactérienne la plus proche des plastes primaires ainsi que le nombre et l'identité des partenairesdans les endosymbioses secondaires.Ma thèse a consisté à étudier l'origine et l'évolution précoce des eucaryotes photosynthétiques enutilisant des approches phylogénétiques et phylogénomiques. Je montre par mon travail que les plastesprimaires ont évolué à partir d'un symbiote phylogénétiquement proche de Gloeomargarita lithophora,une cyanobactérie représentant un clade s’étant diversifié précocement et qui a été détectéeuniquement dans les milieux terrestres. Ce résultat fournit des pistes nouvelles sur le contexteécologique dans lequel l'endosymbiose primaire a probablement eu lieu. En ce qui concerne l'évolutiondes lignées eucaryotes avec des plastes secondaires, je montre que les génomes nucléaires deschlorarachniophytes et des euglénophytes, deux lignées photosynthétiques avec des plastes dérivésd'algues vertes, encodent un grand nombre de gènes acquis par transferts depuis des algues rouges.Enfin, je mets en évidence que SELMA, la machinerie de translocation des protéines à travers laseconde membrane externe des plastes rouges secondaires à quatre membranes, a une histoireétonnamment compliquée aux implications évolutives importantes : les cryptophytes ont recruté unensemble de composants de SELMA différent de ceux des haptophytes, straménopiles et alvéolés.Ainsi, ma thèse a permis d’identifier pour la première fois la lignée cyanobactérienne la plus proche desplastes primaires et apporte de nouvelles pistes pour éclaircir les événements complexes qui ontjalonné l’évolution des eucaryotes photosynthétiques secondairesPrimary plastids derive from a cyanobacterium that entered into an endosymbioticrelationship with a eukaryotic host. This event gave rise to the supergroup Archaeplastida whichcomprises Viridiplantae (green algae and land plants), Rhodophyta (red algae) and Glaucophyta. Afterprimary endosymbiosis, red and green algae spread the ability to photosynthesize to other eukaryoticlineages via secondary endosymbioses. Although considerable progress has been made in theunderstanding of the evolution of photosynthetic eukaryotes, important questions remained debatedsuch as the present-day closest cyanobacterial lineage to primary plastids as well as the number andidentity of partners in secondary endosymbioses.The main objectives of my PhD were to study the origin and evolution of plastid-bearing eukaryotesusing phylogenetic and phylogenomic approaches to shed some light on how primary and secondaryendosymbioses occurred. In this work, I show that primary plastids evolved from a close relative ofGloeomargarita lithophora, a recently sequenced early-branching cyanobacterium that has been onlydetected in terrestrial environments. This result provide interesting hints on the ecological setting whereprimary endosymbiosis likely took place. Regarding the evolution of eukaryotic lineages with secondaryplastids, I show that the nuclear genomes of chlorarachniophytes and euglenids, two photosyntheticlineages with green alga-derived plastids, encode for a large number of genes acquired by transfersfrom red algae. Finally, I highlight that SELMA, the translocation machinery putatively used to importproteins across the second outermost membrane of secondary red plastids with four membranes, has asurprisingly complex history with strong evolutionary implications: cryptophytes have recruited a set ofSELMA components different from those present in haptophytes, stramenopiles and alveolates.In conclusion, during my PhD I identified for the first time the closest living cyanobacterium to primaryplastids and provided new insights on the complex evolution that have undergone secondary plastid-bearing eukaryotes
14
Grünert, Stefan. "Translation initiation in mammalian systems". Thesis, University of Cambridge, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390257.
Pełny tekst źródła
15
Yanow, Stephanie Kim. "Regulation of Cdc18 and Cdt1 restricts S phase to once per cell cycle in the fission yeast Schizosaccharomyces pombe". Thesis, University College London (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251716.
Pełny tekst źródła
16
Mills, Ian Geoffrey. "Effects of phosphatidylinositol 3-phosphate binding proteins on endosomal dynamics". Thesis, University of Liverpool, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367253.
Pełny tekst źródła
17
Brown, Susan. "Molecular systematics of Vahlkampfid amoebae". Thesis, University of Liverpool, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.363946.
Pełny tekst źródła
18
Grisdale, Cameron James. "The evolution of RNA processing in reduced eukaryotes". Thesis, University of British Columbia, 2014. http://hdl.handle.net/2429/50067.
Pełny tekst źródłaStreszczenie:
RNA-processing encompasses several critical steps in the regulation of gene expression. Both transcription and pre-mRNA splicing are important for the formation of mature RNA. Most eukaryotic genes are interrupted by introns, the removal of which is catalyzed by the spliceosome. The spliceosome is a large molecular machine comprised of five small nuclear RNAs (snRNAs) and up to two hundred proteins. In addition to constitutive removal of introns, alternative splicing increases transcriptome complexity, as it allows for the formation of multiple transcript isoforms from a single pre-mRNA. Although these processes are well-studied in model systems, relatively little is known about their evolution in unicellular eukaryotes.
To investigate RNA-processing in reduced systems, I examined the transcriptomes of the microsporidian parasite Encephalitozoon cuniculi, and the red alga Cyanidioschyzon merolae. E. cuniculi and C. merolae harbour reduced genomes of 2.9Mbp and 16.5Mbp, respectively. Both genomes were annotated with fewer than 30 spliceosomal introns, and both have undergone reduction in spliceosomal components, including the loss of the U1 snRNA. Illumina RNAseq was used to sequence the transcriptomes of E. cuniculi at three time-points during its intracellular stage, and C. merolae under light and dark phases of its growth cycle. I found extremely low levels of pre-mRNA splicing for nearly all intron-containing genes in both organisms, under all conditions examined. These levels of splicing appear to be lower than in any other eukaryote examined, suggesting that reduction in unrelated spliceosomes reveals a common evolutionary trend: decreased splicing efficiency.
In addition to intron-retention, I found examples of other types of alternative splicing in these two reduced systems. C. merolae displayed all major types of alternative splicing, and some events occurred at relatively high frequencies. The presence of few or no alternative splicing regulatory protein-coding genes in C. merolae and E. cuniculi, respectively, made this finding especially surprising. Also, I found high levels of antisense transcription in C. merolae, with the potential to play a regulatory role in gene expression.Science, Faculty of
Botany, Department of
Graduate
19
Nesbeth, Darren Nicholas. "Biochemical studies of intracellular trafficking pathways in eukaryotes". Thesis, Imperial College London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313830.
Pełny tekst źródła
20
Kawamura, Akane. "Structural investigations of arylamine N-acetyltransferases from eukaryotes". Thesis, University of Oxford, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.418524.
Pełny tekst źródła
21
Richards, Thomas Adam. "Horizontal gene transfer and the evolution of eukaryotes". Thesis, University of Oxford, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.425896.
Pełny tekst źródła
22
Glebov, Oleg. "Study of clathrin-independent endocytosis in higher eukaryotes". Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613725.
Pełny tekst źródła
23
Agić, Heda. "Palaeobiology and diversification of Proterozoic-Cambrian photosynthetic eukaryotes". Doctoral thesis, Uppsala universitet, Paleobiologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-265229.
Pełny tekst źródłaStreszczenie:
One of the most important events in the history of life is the evolution of the complex, eukaryotic cell. The eukaryotes are complex organisms with membrane-bound intracellular structures, and they include a variety of both single-celled and multicellular organisms: plants, animals, fungi and various protists. The evolutionary origin of this group may be studied by direct evidence of past life: fossils. The oldest traces of eukaryotes have appeared by 2.4 billion years ago (Ga), and have additionally diversified in the period around 1.8 Ga. The Mesoproterozoic Era (1.6-1 Ga) is characterised by the first evidence of the appearance complex unicellular microfossils, as well as innovative morphologies, and the evolution of sexual reproduction and multicellularity. For a better understanding of the early eukaryotic evolution and diversification patterns, a part of this thesis has focused on the microfossil records from various time periods and geographic locations. Examination of microfossil morphology, cell wall microstructure and biochemical properties, reflect their intracellular complexity and function, and allow reconstructions of their life cycle, as well as observing the evolutionary pattern of change from Mesoproterozoic, to Cambrian-Ordovician transition. Several case studies included assemblages deriving from Mesoproterozoic, Neoproterozoic and early Paleozoic time intervals that show disparate morphotypes and innovative features indicative of algal clades. The Mesoproterozoic Ruyang Group in northern China has yielded a diverse microfossil assemblage that provides important clues about the diversification of different eukaryotic groups. Furthermore these microfossils contributed an additional evidence for the emergence of the crown group Eukarya by 1.7-1.4 Ga. In another part of this thesis, examination of wall microstructure and chemical properties via Raman spectroscopy has been used to assess the biological affinities of various Neoproterozoic problematic carbonaceous compression fossils. Studies on the early Phanerozoic (c. 545-485 Ma) assemblages from Estonia reconstructed patterns of the early radiations of phytoplankton and its evolutionary innovations. A continuing theme in this thesis has been using a combination of evidence of microfossils’ fine-scale morphology, ecology and chemical properties to determine their function in life, in addition to their systematic position.Palaeobiology and diversification of Proterozoic-Cambrian photosynthetic eukaryotes
24
Bhardwaj, Shweta. "Interplay between chromatin conformation and transcription in eukaryotes". Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:7395c490-a296-48e8-b8ca-afd785d516b0.
Pełny tekst źródłaStreszczenie:
The three-dimensional organization of the genome is important for various processes such as transcription, replication, and repair. Several studies have shown that the genome is organized into long-range and short-range chromatin loops. Gene loops represent a short-range chromatin loop, synonymous with the juxtaposition of promoter and terminator regions of a gene. In Chapter III, I investigate the mechanism of gene-loop formation in a constitutively expressed gene, mouse serum albumin (Alb). The Alb locus appears to exist in a clover-leaf structure, with the promoter in close physical proximity with an upstream enhancer and downstream genic sequences. Furthermore, Alb forms a promoter-terminator gene loop that is dependent on serine 2 phosphorylation of RNA polymerase C-terminal domain. I also investigate the presence of gene loop conformation at the human Nuclear factor NF-kappa-B (NFκB1) gene. In response to cytokine stimulation, NFκB1 transcription proceeds as a wave, with nascent RNA appearing as RNA polymerase traverses along the gene length. This coincides with formation of transient contacts between NFκB1 promoter and genic regions. The cohesin complex is a key mediator of chromatin loops and sister chromatid cohesion. The association of cohesin with chromatin is dependent on the loading complex, Mis4/Ssl3. In Chapter IV, I provide direct evidence for two functionally different populations of cohesin is Schizosaccharomyces pombe. Cohesin that co-localizes with Mis4 represents "cohesive" cohesin. In contrast, cohesin alone is unable to maintain stable sister chromatid cohesion, therefore, "less-cohesive" cohesin. Cohesive cohesin ensures stable cohesion because it is acetylated by the Eso1 acetyltransferase, which preferentially interacts with Mis4. In contrast, less-cohesive cohesin may function in recombination/repair. In Chapter V, I have identified a novel interplay between cohesin loading and transcription by RNA polymerase II. Inhibition of transcription initiation results in loss of Mis4 and consequently, cohesin binding on chromosomal arms regions. Furthermore, cohesin and Mis4 physically interact with RNA polymerase II. In Chapter VI, I summarize the above findings and propose a model that describes the stepwise loading of cohesin onto chromosomal arms during the fission yeast cell cycle. To conclude, I discuss the importance of understanding cohesin and its functions in health and diseases.
25
Karlsborn, Tony. "Physiological consequences of Elongator complex inactivation in Eukaryotes". Doctoral thesis, Umeå universitet, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet), 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-125667.
Pełny tekst źródłaStreszczenie:
Mutations found in genes encoding human Elongator complex subunits have been linked to neurodevelopmental disorders such as familial dysautonomia (FD), rolandic epilepsy and amyotrophic lateral sclerosis. In addition, loss-of-function mutations in genes encoding Elongator complex subunits cause defects in neurodevelopment and reduced neuronal function in both mice and nematodes. The Elongator complex is a conserved protein complex comprising six subunits (Elp1p-Elp6p) found in eukaryotes. The primary function of this complex in yeast is formation of the 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) side chains found on wobble uridines (U34) in tRNAs. The aim of this thesis is to investigate the physiological consequences of Elongator complex inactivation in humans and in the yeast Saccharomyces cerevisiae. Inactivation of the Elongator complex causes widespread defects in a multitude of different cellular processes in S. cerevisiae. Thus, we investigated metabolic alterations resulting from Elongator complex inactivation. We show that deletion of the S. cerevisiae ELP3 gene leads to widespread metabolic alterations. Moreover, all global metabolic alterations observed in the elp3Δ strain are not restored in the presence of elevated levels of hypomodified tRNAs that normally have the modified nucleoside mcm5s2U. Collectively, we show that modified wobble nucleosides in tRNAs are required for metabolic homeostasis. Elongator mutants display sensitivity to DNA damage agents, but the underlying mechanism explaining this sensitivity remains elusive. We demonstrate that deletion of the S. cerevisiae ELP3 gene results in post-transcriptional reduction of Ixr1p levels. Further, we show that the reduced Ixr1p levels prevent adequate Rnr1p levels upon treatment with DNA damage agents. These findings suggest that reduced Ixr1p levels could in part explain why Elongator mutants are sensitive to DNA damage agents. Depletion of Elongator complex subunits results in loss of wobble uridine modifications in plants, nematodes, mice and yeast. Therefore, we investigated whether patients with the neurodegenerative disease familial dysautonomia (FD), who have lower levels of the ELP1 protein, display reduced amounts of modified wobble uridine nucleosides. We show that tRNA isolated from brain tissue and fibroblast cell lines derived from FD patients have 64–71% of the mcm5s2U nucleoside levels observed in total tRNA from non-FD brain tissue and non-FD fibroblasts. Overall, these results suggest that the cause for the neurodegenerative nature of FD could be translation impairment caused by reduced levels of modified wobble uridine nucleosides in tRNAs. Thus, our results give new insight on the importance of modified wobble uridine nucleosides for neurodevelopment.
26
Bulfoni, Manuel. "Exploring new paradigms of translational control in eukaryotes". Thesis, Sorbonne Paris Cité, 2018. https://theses.md.univ-paris-diderot.fr/Bulfoni_Manuel_2_complete_20181129.pdf.
Pełny tekst źródłaStreszczenie:
La régulation de la synthèse des protéines est une étape clé de la régulation de l'expression des gènes dans de nombreux processus cellulaires, permettant à la cellule de s'adapter rapidement au changement d’environnement en particulier en réponse à des stimuli externes et au stress. La majeure partie de la régulation de la traduction se produit à l'étape d'initiation, lorsque les ribosomes sont recrutés sur les ARNm, en perturbant eIF4F, le complexe fixé à l’extrémité 5' de l’ARNm via eIF4E, ou en réduisant la disponibilité du complexe ternaire lié au facteur d’initiation eIF2 (eIF2-GTP-Met-tARNMet). Au cours de ma thèse, j’ai montré comment ces étapes universelles sont régulées pour moduler spécifiquement les taux de traduction de différents ARNm.Nous avons montré qu'Angel1, une protéine interagissant avec eIF4E, est spécifiquement localisée dans le compartiment périnucléaire où elle régule la traduction d’ARNm spécifiques. Nous avons aussi décrit un nouvel opéron ARN caractérisé par la liaison spécifique de Hek2, une protéine de type hnRNP K de levure, à un sous-ensemble d'ARNm codant pour les pores nucléaires et régulant leur traduction. De plus, nous avons montré que la liaison de Hek2 à l'ARNm est empêchée par SUMOylation, une modification post-traductionnelle qui est contrecarrée par Ulp1, une SUMO protéase. Enfin, nous avons observé que la perturbation de l'intégrité des pores nucléaires suite à des mutations ou à un stress induisait l'accumulation de la forme SUMOylée de Hek2. Hek2-SUMO est incapable de se lier aux ARNm, dont la traduction se trouve ainsi augmentée dans un processus de rétroaction.Dans la dernière partie de ma thèse, nous avons réalisé la toute première étude de traductome d'une lignée de cellules β pancréatiques humaines en réponse à une stimulation par le glucose. Nous avons observé que le glucose stimule la traduction d'un ensemble défini d'ARNm pour lesquels nous avons identifié des caractéristiques spécifiques. Ces avancées sont importantes pour mieux comprendre la régulation de l’expression des gènes par le glucose.L’ensemble de nos résultats nous ont permis d’établir de nouveaux paradigmes de régulation traductionnelleRegulation of protein synthesis is a key regulatory step of gene expression of many cellular processes allowing the cell to quickly adapt to the changing environment including external stimuli and stresses. Most of the translational regulation occurs at the the initiation step when ribosomes are recruited to the mRNAs, by disrupting eIF4F, the complex bound to the 5’ mRNA extremity through eIF4E, or by reducing the availability of the eIF2 ternary complex (eIF2-GTP-Met-tRNAMet). During my thesis I showed how these universal steps are regulated to specifically modulate the translation rates of different mRNAs.We showed that Angel1, an eIF4E interacting protein, is specifically localized to the perinuclear compartment where it regulates mRNA translation of specific mRNAs.We also described a novel RNA operon characterized by the specific binding of Hek2, a yeast hnRNP K-like protein, to a subset of nuclear-pore-encoding mRNAs regulating their translation. Moreover, we showed that Hek2 binding to the mRNA is impeded by the SUMOylation, a post-translational modification which is counteracted by Ulp1, a SUMO-protease. Finally, we reported that perturbation of the nuclear pore integrity by either mutations or stress, induced the accumulation of the SUMOylated form of Hek2. Hek2-SUMO is unable to bind to the mRNAs whose translation is thereby enhanced in a feedback process.In the last part of my thesis, we performed the first ever translatome study of a human pancreatic β cell line in response to glucose stimulation. We report that glucose stimulates translation of a defined set of mRNAs and identified their specific features providing important advances to better understand regulation of gene expression by glucose. Taken together our results allowed us to establish new paradigms of translational regulation
27
Stanke, Mario. "Gene prediction with a Hidden Markov model". Doctoral thesis, [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=970841310.
Pełny tekst źródła
28
Fisher, Richard James. "Amperometric analysis of exocytosis in adrenal chromaffin cells". Thesis, University of Liverpool, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367144.
Pełny tekst źródła
29
Parikesit, Arli Aditya. "Evolutionary Analysis of the Protein Domain Distribution in Eukaryotes". Doctoral thesis, Universitätsbibliothek Leipzig, 2012. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-100869.
Pełny tekst źródłaStreszczenie:
Investigations into the origin and evolution of regulatory mechanisms require quantitative estimates of the abundance and co-occurrence of functional protein domains among distantly related genomes. The metabolic and regulatory capabilities of an organism are implicit in its protein content. Currently available methods suffer for strong ascertainment biases, requiring methods for unbiased approaches to protein domain contents at genome-wide scales. The discussion will be highlighted on large scale patterns of similarities and differences of domain contains between phylum-level or even higher level taxonomic groups. This provides
insights into large-scale evolutionary trends. The complement of recognizable functional protein domains and their combinations convey essentially the same information and at the same time are much more readily accessible, although protein domain models trained for one phylogenetic group frequently fail on distantly related sequences. Transcription factors (TF) typically cooperate to activate or repress the expression of genes. They play a critical role in developmental processes. While Chromatin Regulation (CR) facilitates DNA organization and prevent DNA aggregation and tangling which is important for replication, segregation, and gene expression. To compare the set of TFs and CRs between species, the genome annotation of equal quality was employed. However, the existing annotation suffers from bias in model organism. The similar count of transcripts are expected to be similar in mammals, but model organism such as human has more annotated transcripts than non model such as gorilla. Moreover, closely related species (e.g, dolphin and human) show a dramatically different distribution of TFs and CRs. Within vertebrates, this is unreasonable and contradicts phylogenetic knowledge. To overcome this problem, performing gene prediction followed by the detection of functional domains via HMM-based annotation of SCOP domains were proposed. This methods was demonstrated to lead toward consistent estimates for quantitative comparison. To emphasize the applicability, the protein domain distribution of putative TFs and CRs by quantitative and boolean means were analyzed. In particular, systematic studies of protein domain occurrences and co-occurrences to study avoidance or preferential co-occurrence of certain protein domains within TFs and CRs were utilized. Pooling related domain models based on their GO-annotation in combination with de novo gene prediction methods provides estimates that seem to be less affected by phylogenetic biases. it was shown for 18 diverse representatives from all eukaryotic kingdoms that a pooled analysis of the tendencies for co-occurrence or avoidance of protein domains is indeed feasible. This type of analysis can reveal general large-scale patterns in the domain co-occurrence and helps to identify lineage-specific variations in the evolution of protein domains. Somewhat surprisingly, strong ubiquitous patterns governing the evolutionary behavior of specific functional classes were not found. Instead, there are strong variations between the major
groups of Eukaryotes, pointing at systematic differences in their evolutionary constraints. Species-specific training is required, however, to account for the genomic peculiarities in many lineages. In contrast to earlier studies wide-spread statistically significant avoidance of protein domains associated with distinct functional high-level gene-ontology terms were found.
30
Ehrismann, Dominic. "The biochemical basis of oxygen sensing in higher eukaryotes". Thesis, University of Oxford, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.534193.
Pełny tekst źródła
31
Gossmann, Toni Ingolf. "Investigating genome wide patterns of natural selection in eukaryotes". Thesis, University of Sussex, 2012. http://sro.sussex.ac.uk/id/eprint/43293/.
Pełny tekst źródłaStreszczenie:
Mutations are the ultimate source of new genetic information and they can be neutral, harmful or beneficial. The ultimate fate of all mutations is either to be lost or to eventually become fixed in a population. In this thesis I investigate genome wide traces of natural selection in eukaryotes. I focus on the most common type of mutations, point mutations, in protein coding genes. I investigated whether there is adaptive evolution in 11 plant species comparisons by applying an extension of the McDonald Kreitman (MK) test and found little evidence of adaptive evolution. However, most of the investigated plant species have low effective population sizes (Ne) and the rate of adaptive evolution is thought to be correlated to Ne. I therefore extended my study using additional data from mammals, drosophilids and yeast to investigate the relationship between the rate of adaptive evolution and Ne. I found a highly significant correlation between the rate of adaptive evolution relative to the rate of neutral evolution (!a) and Ne. It has been proposed that evidence of adaptive evolution can be an artifact of fluctuating selection. I simulated a model of fluctuating selection, in which the average strength of selection acting upon mutations is zero. Under this model adaptive evolution is inferred using MK-type tests. However, the mutations which become fixed are on average positively selected. The signal of adaptive evolution is therefore genuine. Ne can not only vary between species but also across genomes. However, how much variation there is, and whether this affects the efficiency of natural selection, is unknown. I analysed 10 species and show that variation in Ne is widespread. However, this variation is limited, amounting to a few fold variation in Ne between most genomic regions. This is never-the-less sufficient to cause variation in the efficiency of selection.
32
Schmidt, Hugo Gerald. "Does transcription activator diffusion drive gene clustering in eukaryotes?" Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648245.
Pełny tekst źródła
33
Bell, Christian H. "Structural studies of chemotaxis in prokaryotes and higher eukaryotes". Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:94441e35-6b9a-4af9-a113-097e2c5da900.
Pełny tekst źródłaStreszczenie:
Chemotaxis, the ability of a cell to change its motility as a response to environmental stimuli, belongs to the most important signal transduction mechanisms in life. Evolution has created a plethora of different molecular mechanisms to enable cells to react appropriately to extracellular changes. In this thesis, chemotactic signal transduction pathways in bacteria, in particular two component signalling in R. sphaeroides, and eukaryotes, in particular human axon guidance, are studied by means of X-ray crystallography complemented with biophysical, biochemical and cellular studies. Two-component signal transduction in bacteria is one of the most abundant signalling pathways in biology. Here the determinants for specificity for a crucial sensor kinase-response regulator interaction are presented and used to design novel, synthetic two-component pairs. The activation mechanism of response regulators has been extensively studied and a model for activation that crucially involves a Thr and a Tyr residue has been widely accepted in the field. In this thesis, two structures of a response regulator from R. sphaeroides are presented and together with biophysical and cellular assays suggest a novel paradigm for response regulator activation. Axon guidance is an essential process in human development and relies crucially on chemotaxis. Two signalling pathways, the plexin-semaphorin and the Rgm-Neogenin pathway are studied extensively in this work. Structures of the intracellular region of Plexin-B1 provide an elegant mechanism explaining how ligand binding events on the extracellular and intracellular side can be integrated into a single signalling output. The study of RgmB in complex with its receptor Neogenin provides the first structural insight into the important family of repulsive guidance molecules and explains their role in the disease juvenile hemachromatosis. In summary, this work provides insights into a plethora of chemotactic pathways and extends our current knowledge of these important mechanisms significantly.
34
Dong, Lin. "Contributions to the Proterozoic and Cambrian Evolution of Eukaryotes". Diss., Virginia Tech, 2007. http://hdl.handle.net/10919/26626.
Pełny tekst źródłaStreszczenie:
This thesis makes several contributions to improve our understanding of
Proterozoic-Cambrian evolution of eukaryote life. Chapter 1 provides, for the first time, a quantitative characterization of the evolutionary trends of Proterozoic macroalgae. The analysis reveals that morphological disparity of Paleoproterozoic macroalgae was low but increased in the Mesoproterozoic and Ediacaran, with a plateau in between. There was also a significant increase in thallus surface/volume ratio and maximum canopy height of the Ediacaran macroalgal communities. The prolonged plateau between the Mesoproterozoic and Ediacaran may be related to either nutrient stress or the absence of animal grazing pressure. The Ediacaran increase in surface/volume ratio and morphological complexity may have been driven by decreasing pCO2 levels and increasing animal grazing pressure.
Chapter 2 presents a systematic re-examination of the carbonaceous compression fossils Protoarenicola baiguashanensis Wang, 1982, Pararenicola huaiyuanensis Wang, 1982, and Sinosabellidites huainanensis Zheng, 1980, from the early Neoproterozoic Liulaobei and Jiuliqiao formations in northern Anhui, North China. These fossils were previously interpreted as worm-like metazoans. Our study reveals new morphological features that weaken the metazoan interpretation. Instead, the new data indicate that these fossils can be alternatively interpreted as erect epibenthic organisms, possibly coenocytic algae.
Chapter 3 examines two important eukaryote fossils: Horodyskia Yochelson and Fedonkin, 2000, and Palaeopascichnus Palij, 1976, from the upper Ediacaran chert of the Liuchapo Formation in central Guizhou, South China. These exceptionally preserved fossils offer us a unique opportunity to investigate their body constructions and affinities. The morphologies of Horodyskia and Palaeopascichnus support a phylogenetic relationship with agglutinated foraminifers, shedding new light on the divergence of bikont eukaryotes, the rise of rhizarians, and the ecological importance of heterotrophic eukaryotes in Proterozoic ecosystems.
Chapter 4 focuses on Cambrian microfossils that represent the primary producersâ cyanobacteria and eukaryotic phytoplankton (acritarchs). Careful investigation of the basal Cambrian Yanjiahe Formation in the Yangtze Gorges area and the Yurtus Formation in the Aksu area revealed abundant acanthomorphic acritarchs, clustered coccoidal microfossils, filamentous cyanobacteria, and tubular microfossils. This study confirms previous stratigraphic correlation between the Yanjiahe and Yurtus formations and suggests that animals and phytoplankton radiated in tandem during the Cambrian explosion.Ph. D.
35
Clever, Beate. "DNA repair in eukaryotes: the Rad54 recombinational repair protein /". [S.l : s.n.], 1996. http://www.ub.unibe.ch/content/bibliotheken_sammlungen/sondersammlungen/dissen_bestellformular/index_ger.html.
Pełny tekst źródła
36
Lange, Anja. "Structural characterization of the interaction of the Stam2's ubiquitin binding domains with ubiquitin chains by NMR : Cooperativity or not, that is the question !" Thesis, Lyon 1, 2010. http://www.theses.fr/2010LYO10308.
Pełny tekst źródłaStreszczenie:
Résumé en anglais uniquementFrom the discovery of ubiquitin and its function as signal for proteasomal degradation over 20 years ago to this days, it became evident that ubiquitin is a universal signal in eukaryotic cells. Ubiquitin in its different forms is involved in many versatile cellular processes. Knowing that the ubiquitin signal is differently translated, depending on its occurrences as mono-ubiquitin or poly-ubiquitin, raises the question: how do cells distinguish between the different occurrences of ubiquitin and translate it into the proper response? Proteins interacting with ubiquitin contain so called ubiquitin binding domains (UBDs), whereas the affinities to ubiquitin vary from a few _M to mM. So far only three (K63, K48 and linear chains) out of the eight possible chain-linkages can be produced in sufficient amounts to characterize their interaction with UBDs. K48- and K63- linked ubiquitin chains regulate different cellular events and need to be recognized by different proteins. Thus, it is of prime importance to characterize the binding of different UBDs to these two kinds of ubiquitin chains, as it can give important clues related to the general mechanism of chain discrimination by ubiquitin adapter proteins. Some isolated UBDs exhibit a preference for one chain linkage type over the other, whereas others do not discriminate between mono-ubiquitin or K63- and K48-linked chains. Interestingly, many ubiquitin adapter proteins harbor more than one UBD. STAM2 is a ubiquitin adapter protein, that is involved in endosomal receptor sorting and supposed to preferentially bind mono-ubiquitin and K63- over K48-linked ubiquitin. STAM2 contains two UBDs (a VHS and UIM domain) that were shown to bind to ubiquitin . The current manuscript shows that STAM2’s SH3 domain binds ubiquitin as well. To understand the function of the sequential arrangement of three UBDs in one protein, first binding of the individual VHS and UIM domains to monoubiquitin as well as K48- and K63-linked di-ubiquitin was investigated. This work shows, that the VHS domain displays a different mode of binding for K63- and K48-linked diubiquitin. In spite of the fact, that the apparent Kd for both chains is the same, only one VHS domain can bind to K48-linked di-ubiquitin chains (with a preference for the distal domain), whereas K63-linked di-ubiquitin can accommodate two VHS domains at a time. Since no conclusion can be drawn with respect to the apparent Kds, the different binding modes might gain more impact in consideration of the ensemble of three UBDs. Results presented in this manuscript, based on a construct containing the VHS and UIM domain, show that binding to K63- but not K48-linked di-ubiquitin is cooperative
37
Haider, Mustafa M. "The intracellular sorting of vacuolar proteins in the yeast Saccharomyces cerevisiae". Thesis, Durham University, 1989. http://etheses.dur.ac.uk/6495/.
Pełny tekst źródłaStreszczenie:
The mechanism of protein sorting to the vacuole in yeast was studied both in vitro and in vivo. A series of experiments were performed to reconstitute transport of carboxypeptidase Y (CPY) from Golgi vesicles to vacuoles. In order to investigate this process, microsomes were purified from sec, pep4-3 mutant strains that accumulate inactive proCPY in the Golgi when incubated at the nonpermissive temperature. These were mixed with purified vacuoles isolated from a mutant lacking CPY activity, but containing active proteinases A and B. Transported proCPY is maturated by these proteinases to active form. Experiments indicate that maturation of CPY is due to the correct transport of proCPY from microsomes to vacuoles because:- Firstly, the reaction is temperature sensitive, requires ATP and is stimulated by the addition of soluble factors (S100). Secondly, the addition of proteinase A and B inhibitors to the reaction mixtures has a negligible effect on the maturation process. Thirdly, disrupting the membranes by the addition of Triton X-100 before addition of the proteinase inhibitors, inhibited the maturation of proCPY. Fourthly, the majority of CPY activity was observed in the sedimented fraction of the reaction mixtures rather than supernatant fractions. Lastly, analysis with western blot shows a clear band of mature CPY only in the sedimented fraction of the reaction mixtures with ATP. This in vitro system will be invaluable in investigating the molecular events of vacuolar biogenesis. For in vivo sorting of proteins to the vacuole, a series of experiments were performed that involved the genetic fusion of the CPY promoter and prepro-sequence of CPY to the bacterial Gus (β-glucuronidase) reporter gene. The Gus gene was expressed in yeast with high efficiency and the results of sub-cellular fractionation indicated that the Gus product was distributed in all cell components. Using a centromeric vector gave similar results but with a lower efficiency of Gus expression. Removal of 90bp from Gus, including Gus initiation codon does not completely inhibit Gus expression either in bacteria or in yeast. Fusion of the shortened Gus with the CPY prepro-fragment and expression in yeast led to the correct sorting of the CPY-Gus hybrid protein to the vacuole. This CPY-Gus fusion is potentially useful in the genetic analysis of mutations defective in vacuolar protein sorting.
38
Day, Deborah Anne. "Regulation of cap-dependent and cap-independent translational initiation in stressed yeast cells". Thesis, University of Kent, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.244341.
Pełny tekst źródła
39
Nuttall, M. E. "A study of polyamine acetylation in mammalian cells in culture". Thesis, University of Aberdeen, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.234143.
Pełny tekst źródłaStreszczenie:
Methylglyoxal bis(guanylhydrazone) (MGBG) was incorporated extensively into baby hamster kidney (BHK-21/C13) cells by a temperature - and Na+, K+ - ATPase linked mechanism. The uptake of the drug was dependent on the growth state of the cells and transformed cells (PyY-cells) incorporated MGBG to a greater extent than normal BHK cells. The uptake of the drug was inhibited by coadministration with spermidine, spermine and N1-acetylspermine and to a lesser extent by putrescine and Mg2+ ions. MGBG and spermine were cytotoxic and both compounds stimulated spermidine acetyltransferase (SAT) activity in BHK cells but not in PyY-cells suggesting that transformation enhanced resistance of the cells.SAT activity was present in both the nuclear and cytosolic compartment of both cell-lines and MGBG stimulation resulted in an increase in both N1- and N8-acetylspermidine production in the nucleus and almost exclusive N1-acetylspermidine production in the cytosol. MGBG stimulated spermine acetyltransferase activity in both nuclear and cytosolic compartments of mammalian cells. Increased intracellular acetylation after MGBG-treatment resulted in enhanced excretion of putrescine and N1-acetylspermidine from both BHK- and PyY-cells implicating acetylation as a means to control intracellular polyamine content. MGBG was itself acetylated in the nucleus of both cell-lines, as was putrescine. However, prior MGBG treatment inhibited the acetylation of MGBG itself and the diamine suggesting that the two compounds are acetylated by a common nuclear acetyltransferase.A cytosolic spermidine acetyltransferase enzyme was purified over 2000-fold from BHK-cells and was found to acetylate putrescine, spermidine, spermine and MGBG. The activity of the enzyme preparation to all these compounds suggests that the enzyme preparation contained nuclear acetyltransferase activity. A model is preposed for the role of acetylation in both the nuclear and cytosolic compartments of mammalian cells.
40
Cammarano, Rosalia. "Compositional heterogeneity and gene distribution in the genomes of eukaryotes". Thesis, Open University, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.548071.
Pełny tekst źródła
41
Yao, Xiaoquan. "Sequence features affecting translation initiation in eukaryotes: A bioinformatic approach". Thesis, University of Ottawa (Canada), 2008. http://hdl.handle.net/10393/27658.
Pełny tekst źródłaStreszczenie:
Sequence features play an important role in the regulation of translation initiation. This thesis focuses on the sequence features affecting eukaryotic initiation. The characteristics of 5' untranslated region in Saccharomyces cerevisiae were explored. It is found that the 40 nucleotides upstream of the start codon is the critical region for translation initiation in yeast. Moreover, this thesis attempted to solve some controversies related to the start codon context. Two key nucleotides in the start codon context are the third nucleotide upstream of the start codon (-3 site) and the nucleotide immediately following the start codon (+4 site). Two hypotheses regarding +4G (G at +4 site) in Kozak consensus, the translation initiation hypothesis and the amino acid constraint hypothesis, were tested. The relationship between the -3 and +4 sites in seven eukaryotic species does not support the translation initiation hypothesis. The amino acid usage at the position after the initiator (P1' position) compared to other positions in the coding sequences of seven eukaryotic species was examined. The result is consistent with the amino acid constraint hypothesis. In addition, this thesis explored the relationship between +4 nucleotide and translation efficiency in yeast. The result shows that +4 nucleotide is not important for translation efficiency, which does not support the translation initiation hypothesis. This work improves our current understanding of eukaryotic translation initiation process.
42
Haghighat, Ashkan. "Studies on the mechanisms ofmRNA binding to ribosomes in eukaryotes". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape11/PQDD_0002/NQ44448.pdf.
Pełny tekst źródła
43
Morita, shigeru. "Improved methods for production of useful recombinant proteins in eukaryotes". Kyoto University, 2001. http://hdl.handle.net/2433/150355.
Pełny tekst źródła
44
Rajagopal, Abbhirami. "Identification and characterization of HRG-1 heme transporters in eukaryotes". College Park, Md.: University of Maryland, 2008. http://hdl.handle.net/1903/8867.
Pełny tekst źródłaStreszczenie:
Thesis (Ph. D.) -- University of Maryland, College Park, 2008.Thesis research directed by: Dept. of Cell Biology and Molecular Genetics . Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
45
Pandya, Siddharth. "Directional Selection on Tyrosine Frequences in Eukaryotes Versus Solvent Accessibility". Thesis, The University of Arizona, 2013. http://hdl.handle.net/10150/297727.
Pełny tekst źródłaStreszczenie:
Amino acids are the building blocks of proteins, and the composition of those proteins plays a major role in cell signaling. Recently, Tan et al. showed that the overall frequency of the amino acid tyrosine is lower in more complex organisms, which have more cell types and more complex signaling networks. Tan et al. hypothesized that this reduction in tyrosine frequency was driven by selection to avoid potentially deleterious phosphorylation by signaling kinases, termed "spurious cross-talk". Because a phosphate moiety is highly negatively charged, (PO₃³⁻), spurious phosphorylation may disrupt protein folding or inappropriately alter protein activity. Our prediction is that if the loss of tyrosine is driven by selection to avoid spurious phosphorylation, then the loss of tyrosine should be more dramatic on the outside of proteins, because these tyrosines are most accessible to kinases. To test this prediction, we characterize tyrosine frequency versus both organismal complexity (measured by number of tyrosine kinases) and solvent accessibility. To measure absolute solvent accessibility (ASA) of individual residues, we ran the entire proteomes of 16 eukaryotic species through a secondary structure predictor, SPINE-X. In addition, we compared orthologous proteins between humans and yeast to determine whether there was a decrease in tyrosine frequency due to selection, and we analyzed SNP data from 1000 Genomes Phase 1 project to see if there was any ongoing selection in humans at the genomic level. Given that our results suggest that tyrosine is being lost independent of ASA and that there is no change in frequency between Human and Yeast orthologous proteins, we can conclude that the decrease in tyrosine frequency as the complexity of signaling networks increases is not due to the Tan et al. hypothesis of spurious phosphorylation.
46
Forget, Anthony L. "Homologous Recombinational DNA Repair: from Prokaryotes to Eukaryotes: a Dissertation". eScholarship@UMMS, 2004. https://escholarship.umassmed.edu/gsbs_diss/68.
Pełny tekst źródłaStreszczenie:
The error free repair of DNA double strand breaks through the homologous recombinational repair pathway is essential for organisms of all types to sustain life. A detailed structural and mechanistic understanding of this pathway has been the target of intense study since the identification of bacterial recA, the gene whose product is responsible for the catalysis of DNA strand exchange, in 1965. The work presented here began with defining residues that are important for the assembly and stability of the RecA filament, and progressed to the identification of residues critical for the transfer of ATP-mediated allosteric information between subunits in the protein's helical filament structure. My work then evolved to investigate similar mechanistic details concerning the role of ATP in the human RecA homolog, Rad51.
Results from non-conservative mutagenesis studies of the N-terminal region of one subunit and the corresponding interacting surface on the neighboring subunit within the RecA protein, led to the identification of residues critical for the formation of the inactive RecA filament but not the active nucleoprotein filament. Through the use of specifically engineered cysteine substitutions we observed an ATP-induced change in the efficiency of cross subunit disulfide bond formation and concluded that the position of residues in this region as defined by the current crystal structure may not accurately reflect the active form of the protein.
These ATP induced changes in positioning led to the further investigation of the allosteric mechanism resulting in the identification of residue Phe217 as the key mediator for ATP-induced information transfer from one subunit to the next.
In transitioning to investigate homologous mechanisms in the human pathway I designed a system whereby we can now analyze mutant human proteins in human cells. This was accomplished through the use of RNA interference, fluorescent transgenes, confocal microscopy and measurements of DNA repair. In the process of establishing the system, I made the first reported observation of the cellular localization of one of the Rad51 paralogs, Xrcc3, before and after DNA damage. In addition we found that a damage induced reorganization of the protein does not require the presence of Rad51 and the localization to DNA breaks occurs within 10 minutes.
In efforts to characterize the role of ATP in human Rad51 mediated homologous repair of double strand breaks we analyzed two mutations in Rad51 specifically affecting ATP hydrolysis, K133A and K133R. Data presented here suggests that, in the case of human cells, ATP hydrolysis and therefore binding, by Rad51 is essential for successful repair of induced damage.
47
Roger, Andrew J. "Studies on the phylogeny and gene structure of early-branching eukaryotes". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/nq24782.pdf.
Pełny tekst źródła
48
Bakaric, Robert [Verfasser]. "Genomics of Gene Gain and Gene Loss in Eukaryotes / Robert Bakaric". Kiel : Universitätsbibliothek Kiel, 2016. http://d-nb.info/1122438567/34.
Pełny tekst źródła
49
Haghighat, Ashkan. "Studies on the mechanisms of mRNA binding to ribosomes in eukaryotes". Thesis, McGill University, 1997. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=34730.
Pełny tekst źródłaStreszczenie:
The binding of eukaryotic ribosomes to mRNA is a complex process that is considered to be rate-limiting in translation initiation, and consequently a key target for translational regulation. Ribosome binding to mRNA is facilitated by the 5' cap structure, m7GpppN (where N is any nucleotide). The initiation factor eIF4F plays a key role in regulating translation rates. eIF4F is a three-subunit complex composed of eIF4E, the cap-binding protein; eIF4A, an RNA helicase; and eIF4G (p220), which bridges eIF4E and eIF4A, and enhances dramatically the interaction of eIF4E with the mRNA 5' cap structure. eIF4F in conjunction with another initiation factor, eIF4B, is thought to unwind the mRNA 5 '-secondary structure to facilitate the binding of mRNA to ribosomes The activity of eIF4F, and the regulation of mRNA binding to ribosomes is tightly correlated with the growth status of the cell. Recently, proteins that interact with eIF4E, termed 4E-BPs, have been identified; these proteins link translation initiation and growth promoting signal transduction pathways. Phosphorylation of 4E-BPs in response to insulin and mitogens decreases their affinity for eIF4E. 4E-BPs compete with eIF4G for binding to eIF4E through binding domains that share common sequence motifs. Consequently, 4E-BPs restrain eIF4E from forming an active cap-binding complex, eIF4F, and prevent subsequent binding of 40S ribosomal subunit to capped mRNAs. Under these conditions, the binding of eIF4E to the mRNA cap structure is extremely inefficient. As a result, cap- and eIF4E-dependent translation is downregulated. Modulation of eIF4F activity is also observed following infection by certain viruses. One of the most dramatic examples of this occurs upon picornaviral infection. As we report here, eIF4G alone is a relatively poor substrate for cleavage by the rhinovirus 2A proteinase (2Apro). However, an eIF4G-eIF4E complex is cleaved efficiently by the 2Apro suggesting that eIF4F is a preferred target for di
50
Pommier, Yves. "Les agents intercalants affectent le fonctionnement des adn topoisomerases deux eukaryotes". Paris 6, 1986. http://www.theses.fr/1986PA066570.
Pełny tekst źródłaStreszczenie:
Parmi les medicaments anticancereux les plus actifs, les agents intercalants de l'adn (anthracyclines, acridines) produisent des lesions sur l'adn de type soit cassure du dna, soit pontage adn-proteine. Ces alterations sont analysees par elution alcaline, sedimentation de nucleotide et sedimentation alcaline. Ces lesions sont reversibles apres suppression des intercalants (culture cellulaire, cellules leuconiques(l1210)). Les dna topoisomerase 2 (enzyme de replication, de transcription, d'organisation de chromatine) sont responsables des lesions provoquees par les agents intercalants du dna, car dans ces conditions, elles forment les ponts proteine-dna. L'utilisation des cellules soit sensibles soit resistantes aux inhibiteurs de dna topoisomerase 2 a permis de mettre en evidence leur role dans la formation de ces alterations au dna