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Dissertations / Theses on the topic 'Vertebrate DNA'

Author: Grafiati

Published: 10 December 2022

Last updated: 19 July 2025

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1

Elango, Navin. "Evolutionary impacts of DNA methylation on vertebrate genomes." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26691.

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Thesis (Ph.D)--Biology, Georgia Institute of Technology, 2009.<br>Committee Chair: Dr. Soojin Yi; Committee Member: Dr. Eric Vigoda; Committee Member: Dr. James Thomas; Committee Member: Dr. John McDonald; Committee Member: Dr. Kirill Lobachev; Committee Member: Dr. Michael Goodisman. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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2

Schofield, Julian Paul. "Studies on the structure of vertebrate genes." Thesis, University of Cambridge, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386858.

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3

Long, Hannah Katherine. "Evolutionary usage and developmental roles of vertebrate non-methylated DNA." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:78b14c1d-1fa3-46f1-815f-a8ba55579c43.

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Vertebrate genomes exhibit global methylation of cytosine residues where they occur in a cytosine-guanine dinucleotide (CpG) context and this epigenetic mark is generally thought to be repressive to transcription. Punctuating this pervasive DNA methylation landscape are short, contiguous regions of non-methylated DNA which are found at two thirds of mammalian gene promoters. These non-methylated regions exhibit CpG content close to expected levels as they escape the depletion of CpGs observed across the methylated fraction of the genome. The unique nucleotide properties of these CpG island (CGI) regions enable their identification by computational prediction in mammalian genomes. Owing to a lack of high-resolution genome-wide DNA methylation profiles in non-mammalian species, these CGI predictions have often been used as a proxy for non-methylated DNA in these organisms. In contrast to mammals, CGI predictions in cold-blooded vertebrates rarely coincide with gene promoters, leading to the belief that CGls are significantly divergent between vertebrate species, and that unique promoter-associated features may have been acquired during warmblooded vertebrate evolution. This thesis is primarily concerned with the location, establishment and biological function of non-methylated islands of DNA in vertebrate genomes. To experimentally determine genome-wide profiles of non-methylated DNA, a novel biochemical technique was established called biotinylated ZF-CxxC affinity purification (Bio-CAP), and development of this method is discussed in Chapter 3. Experimental analysis of non-methylated DNA profiles in this thesis initially addresses two main questions: (1) 'How does the non-methylated DNA landscape compare genome-wide for seven vertebrates considering distinct tissue types and developmental stages?' (2) 'How are vertebrate non-methylated regions of DNA defined and interpreted in the nuclear environment?' To address the first question, non-methylated DNA was profiled by Bio-CAP sequencing across the genomes of seven diverse vertebrate species, representing all major branch points of vertebrate evolution, and the results are discussed in Chapters 4 and S. Contrary to previously held dogma, experimentally determined nonmethylated islands of DNA (NMls) constitute an ancient epigenetic feature of vertebrate gene regulatory elements. However, despite having numerous high-resolution maps of vertebrate non-methylated DNA, the means by which NMls are identified and maintained in the nuclear environment remains poorly understood. To address the second question and identify features which determine the methylation state of DNA, exogenous DNA sequences were introduced into mouse embryonic stem (ES) c~.II~. Non-methylated DNA was profiled by Bio-CAP sequencing to investigate how different features, such as sequence-specific binding motifs, chromatin architecture and nucleotide composition of a given DNA sequence impact local DNA methylation patterns. Interestingly, the majority of exogenous promoters were appropriately non-methylated in mouse ES cells, germline and somatic cells suggesting that gene promoters have retained strong signals for the nonmethylated state across millions of years of evolution (discussed in Chapter 6). During mouse embryogenesis, genome-scale DNA demethylation and remethylation events occur to remodel the epigenetic landscape and loss of DNA methylation during this time leads to embryonic lethality. To investigate the biological function of non-methylated DNA, the third question addressed in this thesis is (3) 'What is the developmental importance of non-methylated islands of DNA during vertebrate embryogenesis?' To investigate this, members of the ZF-CxxC domain-containing family of chromatin modifiers were ablated in zebrafish embryos to perturb the chromatin landscape at NMls, and therefore interfere with their function during early development (Chapter 7). Early embryonic development and patterning was disrupted in knockdown embryos, suggesting that interpretation of non-methylated DNA and placement of chromatin modifications at NMls is essential for normal zebrafish embryogenesis. Together this work sheds light on the evolutionary origins of NMls, the mechanisms involved in the recognition and establishment of nonmethylated loci and provides an insight into the function of non-methylated DNA during early embryonic development.

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4

Chua, Shijia Joy. "Establishing the role of RNF4 in the vertebrate DNA damage response." Thesis, University of Dundee, 2012. https://discovery.dundee.ac.uk/en/studentTheses/20679582-0300-40ac-8d30-e733210c76b4.

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RNF4 belongs to the family of SUMO-targeted ubiquitin E3 ligases (STUbLs). The role of STUbLs in maintaining genomic stability was first discovered in yeast. Theyeast STUbL mutants displayed genomic instability, elevated mutation rates, sensitivity to DNA damaging agents and also demonstrated synthetic lethality with other DNA repair genes. Although the role of vertebrate RNF4 in the DNA damage response was not yet established, it could rescue the Schizosaccaromyces pombe STUbL mutant phenotypes, showing that RNF4 is a functional homologue of the yeast STUbL proteins,and that it might be implicated in the vertebrate DNA damage response.A homozygous knockout of RNF4 in the DT40 chicken lymphocyte cell line was generated to investigate the involvement of vertebrate RNF4 in protecting cells against DNA damage. Although the complete loss of RNF4 did not affect cell proliferation or cell cycle distribution, the RNF4 -/- cells exhibited a selective hypersensitivity to some S-phase specific DNA damaging agents. This hypersensitivity could be rescued by introducing an ortholog of RNF4 from another vertebrate species, and this was dependent on a functional ubiquitin E3 ligase activity of RNF4.To explore the physiological function of RNF4 in the context of a wholeorganism, Danio rerio was chosen as an in vivo model. Danio rerio RNF4 sharedsimilar in vitro biochemical characteristics as RNF4 from other vertebrates – it was able to autoubiquitylate itself and also ubiquitylate SUMO2 chains. In Danio rerio, RNF4 is a maternally provided gene and is highly expressed in the adult gonads. In the ovaries, RNF4 expression was restricted to the early stage oocytes, suggesting a possible role in oocyte development. Loss-of-function studies in Danio rerio were performed using morpholino knockdown and zinc-finger knockout technologies, and the depletion of RNF4 in zebrafish did not affect early embryonic development or viability of the animal.The results presented in this thesis suggests that while vertebrate RNF4 is notlikely to be an essential gene in some vertebrates, it plays a role in the DNA damage response and might be implicated in gonad development in Danio rerio. The zinc-finger knockout model has just been established and a more in-depth analysis is necessary to shed more light on the in vivo functions of RNF4.

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5

Barr, Alexis. "Characterising the function of CDK5RAP2 in the vertebrate centrosome." Thesis, University of Cambridge, 2010. https://www.repository.cam.ac.uk/handle/1810/228639.

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The centrosome is the major microtubule organising centre in vertebrate cells. CDK5RAP2 is a human protein that localises to the centrosome. At the start of this thesis work, the function of CDK5RAP2 was uncharacterised. Significantly, cdk5rap2 is one of several centrosomal genes that are mutated in the developmental disorder Primary Microcephaly, where affected individuals have smaller brains than expected for the age- and sex-adjusted mean. Orthologues of CDK5RAP2 in the fruit fly (Centrosomin/Cnn) and in fission yeast (Mod20p) have been well characterised and are known to have important roles in maintaining centrosome structure and in regulating microtubule nucleation. CDK5RAP2 shares two evolutionarily conserved domains with Cnn, known as CNN motif 1 and 2. Using the chicken B-cell line, DT40, I have used gene-targeting methods to disrupt both of these domains in CDK5RAP2. This revealed a function for CDK5RAP2 in attaching centrosomes to mitotic spindle poles. Centrosome attachment to spindle poles is mediated by a binding partner of CDK5RAP2, AKAP450. AKAP450 also localises to centrosomes and provides anchorage sites for spindle poles in the centrosome. Disruption of the CNN1 and CNN2 domains of CDK5RAP2 causes mislocalisation of AKAP450 from the centrosome and detachment of centrosomes from spindle poles. My studies in DT40 and in human cell lines revealed that CDK5RAP2 and AKAP450 also cooperate during interphase to maintain the two centrioles in the centrosome as a pair. In addition to a structural role in the centrosome, I also find that CNN motif 1 of CDK5RAP2 plays a role in the cellular response to DNA damage. In the absence of CNN motif 1, cells no longer efficiently arrest the cell cycle in response to damage. Centrosome-mediated mitotic spindle alignment and the DNA damage response have both been implicated in microcephaly. Therefore, defects in these functions of CDK5RAP2 may explain how mutations in cdk5rap2 may lead to microcephaly.

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6

Veeman, Michael Terrence. "Zebrafish prickle : non-canonical Wnt/PCP functions in vertebrate gastrulation /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/4999.

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7

Gohm, Birgit [Verfasser]. "The Role of DNA Repair in the Evolution of Vertebrate Longevity / Birgit Gohm." Konstanz : Bibliothek der Universität Konstanz, 2016. http://d-nb.info/1171131860/34.

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8

Yoshimura, Michio. "Vertebrate POLQ and POLβ cooperate in base excision repair of oxidative DNA damage". Kyoto University, 2007. http://hdl.handle.net/2433/135652.

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9

KOLINJIVADI, CHANDRA MOULI ARUM KUMAR. "DISSECTING THE ROLE OF BRCA2, RAD51 AND SMARCAL1 IN VERTEBRATE CHROMOSOMAL DNA REPLICATION." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/470900.

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DNA replication is a fundamental macromolecular event that is essential for cell division. During each cell cycle the entire genome has to be precisely duplicated to ensure genome integrity and stability. In the process of DNA replication, replication forks encounter endogenous and exogenous lesions and these lesions have to be rectified to transfer stable genetic material to daughter cells. Emerging evidences connected a role for Homologous Recombination (HR) proteins to replication fork protection during unperturbed DNA replication. Since HR protein, BRCA2 and Rad51 are essential for cell survival we used Xenopus laevis cell-free extract to dissect the function of BRCA2 and Rad51 during chromosomal DNA replication. Using Electron Microscopy (EM) we show that BRCA2 and Rad51 function together to prevent single-stranded DNA (ssDNA) accumulation at and behind the forks during unperturbed DNA replication. We further discovered that BRCA2 mediates interaction between Rad51, Polymerase alpha (α) and Polymerase delta (δ) and this interaction likely promote efficient re-priming and polymerising activity at stalled replication forks to prevent ssDNA accumulation. Moreover we show that inhibition of replicative polymerases in the absence of Rad51 results in increased frequency of replication fork reversal activity. We further found that replication fork reversal is predominantly induced by an annealing helicase SMARCAL1 in the absence of Rad51. Collectively our findings indicate that, to prevent ssDNA accumulation and aberrant replication fork architecture, timely re-priming of Polymerase alpha mediated by Rad51 is essential. Hence, loss of Rad51 impact replication fork architecture, eventually resulting in chromosomal abnormalities.

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10

Parker, Hugo. "The role of highly conserved non-coding DNA sequences in vertebrate development and evolution." Thesis, Queen Mary, University of London, 2010. http://qmro.qmul.ac.uk/xmlui/handle/123456789/1267.

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Comparisons between vertebrate genome sequences, from mammals to fishes, have revealed thousands of conserved non-coding elements (CNEs) that are associated with developmental genes. Interestingly, the vast majority of these CNEs cannot be found in invertebrate genomes by sequence homology. As many CNEs have been demonstrated to act as enhancers in-vivo, it has been postulated that CNEs represent gene regulatory elements with crucial roles in aspects of development that are shared between vertebrates. To trace the evolution of CNE sequences in vertebrates, a preliminary search for CNEs in the lamprey genome was conducted using the draft lamprey genome sequence. This thesis documents how the CNEs identified in lamprey have been used as a guide to ask questions about the function and evolution of CNEs in the vertebrate lineage. Through the combined use of comparative genomics and developmental biology techniques, including a newly developed reporter assay for sea lamprey embryos, crucial first steps have been taken toward systematically de-coding these ancient gene regulatory elements. Special attention is paid toward utilising the low sequence identity of lamprey CNEs for „phylogenetic footprinting‟, an approach which uncovers striking enrichment of CNEs for a set of motifs that are characteristic of Hox-regulated elements. These findings help to establish CNEs within a developmental and evolutionary context.

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11

Bednar, Theresa [Verfasser], George [Akademischer Betreuer] Iliakis, and Jürgen [Akademischer Betreuer] Thomale. "Efficient support of DNA replication functions by DNA ligase 3 in vertebrate cells / Theresa Bednar. Gutachter: Jürgen Thomale. Betreuer: George Iliakis." Duisburg, 2013. http://d-nb.info/1042373493/34.

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12

ROSSI, FRANCESCO. "ROLES OF THE SMC5/6 COMPLEX IN DNA REPAIR AND CHROMOSOME INTEGRITY IN VERTEBRATE CELLS." Doctoral thesis, Università degli Studi di Milano, 2018. http://hdl.handle.net/2434/559145.

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DNA damage response (DDR) mechanisms are crucial in all organisms to detect DNA damage and integrate its repair with cell cycle control, chromatin structure, and other adaptive changes in cell physiology. The highly conserved structural maintenance of chromosomes (SMC) complex, SMC5/6, contains both SUMO and ubiquitin ligase activities in its composition and is crucial for processing recombination structures arising during replication. Differently from related SMC complexes such as Cohesin and Condensin, the function of SMC5/6 in genome maintenance and its mode of action remain to date hardly understood. Moreover, a lack of cellular models for SMC5/6, especially in human cell lines, has hampered progress in understanding its roles in DDR in model systems most relevant for human disease. Here, we established vertebrate and human cellular models of SMC5/6 knockouts and characterized the associated phenotypes in a battery of assays. Specifically, I established (conditional) SMC5 knockout (KO) in chicken (DT40) and human (TK6) B cell lines. We generated a conditional SMC5 KO in TK6 human cell lines, and uncovered that SMC5 depletion caused apoptosis-mediated lethality, associated with increased DSBs and cohesion defects. In chicken DT40 cell lines, SMC5 KO causes a slow growth phenotype depending on the temperature condition. Second, we investigated the roles of SMC5/6 in intra- and inter-strand crosslink (ICL) repair. SMC5 shows epistasis with FA core mutations, as well as with DDX11 and RAD17, without affecting FANCD2-I ubiquitination and CHK1 phosphorylation. We propose that SMC5 is working downstream of FA and RAD17/DDX11-mediated pathways, likely in resolving the emerging recombination intermediates. Third, we are attempting to identify the principles underlying SMC5/6 roles in the establishment/maintenance of chromatin structure/cohesion and integrity of specific genomic loci such as replicating fragile sites and centromeric/peri-centromeric regions. To these ends, we have used BLISS, a genomic approach to map DSBs, and plan to employ ChIP-seq of endogenously tagged SMC5/6.

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13

Roach, Jared C. "Random subcloning, pairwise end sequencing, and the molecular evolution of the vertebrate trypsinogens /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/8331.

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14

Bianchi, Julie. "Investigating the role of a novel primase-polymerase, PrimPol, in DNA damage tolerance in vertebrate cells." Thesis, University of Sussex, 2013. http://sro.sussex.ac.uk/id/eprint/45544/.

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Genome duplication is an essential task our cells have to achieve prior to cell division, and requires a highly specialized replication machinery to ensure it is performed in an accurate and complete manner. DNA primase and polymerases are essential components of the replisome. Primases initiate DNA replication by synthesising short RNA primers that are then elongated by faithful and processive replicative DNA polymerases. However, both exogenous and endogenous agents can damage DNA and hinder progression of the replicative machinery. Translesion synthesis DNA polymerases assist in bypassing these DNA lesions in a process called DNA damage tolerance that enables chromosomal replication to proceed in in spite of damaged templates. This thesis details the characterisation of a novel eukaryotic DNA primase, coiled-coil domain containing protein (CCDC111), a member of the Archaeo Eukaryotic Primase (AEP) superfamily. Preliminary in vitro characterisation of CCDC111 demonstrated that the recombinant protein is capable of both DNA-dependant priming and polymerase activities, which is unprecedented for a eukaryotic polymerase, and it was therefore renamed Primase-polymerase (PrimPol). The aim of this thesis was to provide one of the first cellular characterisations of PrimPol by generating a knockout of the gene in avian DT40 cells and also depleting the protein in human cells using RNAi. In vivo evidence supports the involvement of this novel polymerase in replication fork progression following replicative stress, such as exposure to UV light, but also during unperturbed DNA replication. Work in this thesis also indicates a role for PrimPol in mitochondrial DNA maintenance. Together, the data presented here establish a role for PrimPol in DNA damage tolerance in avian and human cells.

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15

Nakamura, Kyoko. "Genetic dissection of vertebrate 53BP1 : a major role in non-homologous end joining of DNA double strand breaks." Kyoto University, 2008. http://hdl.handle.net/2433/135861.

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16

Kohzaki, Masaoki. "Cooperative roles of vertebrate Fbh1 and Blm DNA helicases in avoidance of crossovers during recombination initiated by replication fork collapse." Kyoto University, 2007. http://hdl.handle.net/2433/135695.

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17

Sangrithi, Mahesh Nataraj. "Insights into the functions of a novel vertebrate RecQ helicase in chromosomal DNA replication and in the response to stalled replication forks." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.616261.

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18

Whiteman, Erin Tuxford. "The development of a real-time PCR multiplex TaqMan™ assay for vertebrate class in non-human DNA samples for forensic science." Thesis, Whiteman, Erin Tuxford (2021) The development of a real-time PCR multiplex TaqMan™ assay for vertebrate class in non-human DNA samples for forensic science. Masters by Research thesis, Murdoch University, 2021. https://researchrepository.murdoch.edu.au/id/eprint/64836/.

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Non-human DNA (e.g. animal DNA) has become an increasingly useful tool to forensic science, aiding in linking suspects, victims, and crime scenes (24). However, due to many complexities (eg. the potential for non-human DNA to be from any species and the challenges of distinguishing DNA mixtures) and limited resources, this kind of DNA often remains unanalysed in investigations. Presumptive identification of blood is not always human specific and current DNA testing usually stops when DNA samples fail human DNA testing protocols. An efficient way to routinely detect and confirm the presence of animal DNA within samples is therefore needed. This research outlines the framework and development of a universal Vertebrate Class assay for the detection of Mammalian (mammal), Aves (bird), Fish, and Reptilia (reptile) DNA. The assay functions as a real-time PCR TaqMan multiplex assay, with an internal positive control. Primers and probes have been designed with Geneious Prime, targeting the mitochondrial genome, specifically regions of the cytochrome b gene (Cyt b) and cytochrome c oxidise subunit 1 gene (COX1) (4, 25-29). Multistage testing was conducted (eg. primer and probe screening and selection, SYBR green testing and TaqMan multiplex testing). Varied success was reported for the identification of Mammalian, Aves and Fish DNA samples across all multistage laboratory testing processes. The Reptilia probe was not able to be tested at this time due to unforeseen delays. With necessary further testing and validation, this will be the first Vertebrate Class assay design with potential capabilities of detecting Mammalian, Aves, Fish, and Reptilia classes simultaneously, providing both universal and specific detection in one convenient and rapid assay.

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19

Su, Xinyi. "A vertebrate N-end rule conditional protein degradation system and its use in temporal dissection of DNA transactions in a single cell cycle." Thesis, University of Cambridge, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612541.

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20

Khare, Dheeraj. "Crystallographic and functional study on DNA binding proteins: repressor and partitioning protein KorB from RP4 plasmid and the transposase "Sleeping Beauty" of vertebrate origin." [S.l. : s.n.], 2004. http://www.diss.fu-berlin.de/2004/155/index.html.

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21

Katragadda, Chakravarthy. "Survey of Ehrlichia and Anaplasma species in white tailed deer and in ticks by real-time RT-PCR/PCR and DNA sequencing analysis." Thesis, Kansas State University, 2011. http://hdl.handle.net/2097/9158.

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Master of Science<br>Department of Diagnostic Medicine/Pathobiology<br>Roman Reddy R. Ganta<br>Ehrlichia and Anaplasma species are rickettsial organisms which infect a variety of mammalian species. The organisms are transmitted from ticks and are maintained in reservoir hosts. Several pathogens have been identified in recent years as the causative agents for emerging infections in people. One of the primary reservoir hosts for the pathogens is the white tailed deer. In this study, 147 deer blood samples and 37 ticks were evaluated for the prevalence of Ehrlichia/Anaplasma species by TaqMan-based real time amplification assay and DNA sequence analysis. One hundred and thirteen (74%) samples tested positive with the Ehrlichia/Anaplasma genera-specific probe. Further analysis of the samples with the probes specific for human ehrlichiosis agents, E. chaffeensis and E. ewingii identified 4 (2.7%) and 7 (4.7%) positives, respectively. Test positives from 24 randomly selected samples were further evaluated by sequence analysis targeting to a 450 bp segment of 16S rRNA gene. All 24 samples were confirmed as positive for the Ehrlichia GA isolate # 4 (GenBank #U27104.1). DNAs from 37 pools of ticks collected from the white tailed deer were also evaluated. The TaqMan-based real time PCR assay with Anaplasma/Ehrlichia common probe identified 29 (78%) tick pools as positives whereas E. chaffeensis- and E. ewingii-specific probes identified three (8%) and one (3%) positives, respectively. The PCR and sequence analysis of tick samples identified Gram-negative bacteria species which included one endosymbiont of Rickettsia species (one tick pool), one Alcaligenes faecalis strain (three tick pools), five different Pseudomonas species (9 tick pools) and five different uncultured bacteria organisms (7 tick pools). Although the pathogenic potential of the white-tailed deer isolates of Anaplasma and Ehrlichia agents remains to be established, their high prevalence and the presence of human ehrlichiosis pathogens in white-tailed deer is similar to earlier findings. The high prevalence of the deer isolates of Anaplasma and Ehrlichia species demonstrates the need for further assessment of the pathogenic potential of these organisms to people and domestic animals.

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22

Ryan, James L. "Multiscale landscape genetics analysis of feral pigs in the Herbert region of far-north Queensland." Thesis, Queensland University of Technology, 2022. https://eprints.qut.edu.au/227325/1/James_Ryan_Thesis.pdf.

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Management of invasive species is notoriously difficult and often expensive. The aim of this study was to inform feral pig management practises in far-north Queensland by utilising molecular markers and geographic information systems to evaluate the affect of landscape features on feral pig population structure. This thesis evaluated landscape features at multiple spatial scales to identify landscape features that are a barrier or facilitator of feral pig movement and makes recommendations for future management strategies.

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23

Meng, Anming. "DNA fingerprinting and minisatellite variation of swans." Thesis, University of Nottingham, 1990. http://eprints.nottingham.ac.uk/13889/.

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Genetic variation in natural populations of four species of swans (Cygnus bewickii, Cygnus olor, Cygnus buccinator and Cygnus cygnus) has been investigated by examining minisatellite loci using human DNA fingerprinting probes pSPT19.6 and pSPT18.15. It has been found that swan minisatellites are highly variable. However, the degree of variation depends on the population structure and species. Bewick's Swans at Slimbridge have the highest degree of minisatellite variation, Whooper Swans at Caerlaverock come second, and then Mute Swans, and Trumpeter Swans in Montana. Comparative study of DNA fingerprints among populations and among species suggested that swan minisatellites are subject to specific as well as population differentiation, although the function of minisatellites remains an unsolved mystery. Hypervariable minisatellites of swans that are detected by DNA fingerprinting are stably inherited as codominant markers. DNA fingerprinting has been used to study mating behaviour of Mute and Whooper Swans in the wild The results showed that the Whooper swans were almost strictly monogamous and Mute Swans exhibited an adaptable reproductive system. A genomic library from Cygnus olor was constructed and dozens of minisatellites were isolated. Most of the cloned swan minisatellites were variable, some showed specific variation, and one (pcoMS6.1) detected RFLPs in PstI digests of Trumpeter Swans.

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Lau, Tze Chin. "In vitro and in vivo analyses of the impact of Mab21l2 and its targets on neural patterning and differentiation in vertebrates /." View abstract or full-text, 2010. http://library.ust.hk/cgi/db/thesis.pl?BIOL%202010%20LAU.

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Petruti-Mot, Anca. "Genetic and functional analysis of topoisomerase II in vertebrates." Thesis, University of Edinburgh, 2000. http://hdl.handle.net/1842/8985.

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The degree of DNA supercoiling in the cell is carefully controlled by DNA topoisomerases. These enzymes catalyze the passage of individual DNA strands (Type I DNA topoisomerases), or double helices (Type II DNA topoisomerases) through one another. The purpose of the present study is to conduct a detailed analysis of the topo llα and β mRNAs expressed in several vertebrate cell lines. The final aim of this project is to analyze the relative roles of topo llα in chromatin condensation and chromosome segregation during mitosis, by performing topo llα gene targeting experiments in the DT 40 chicken lymphoblastoid cell line. The knock-out strategy was based on the observation of a high rate of homologous recombination versus random integration in the DT40 cell line. The topo llα gene was shown to be located on the chicken chromosome 2 (APM unpublished), for which the DT40 cell line is trisomic. The targeting vector completely replaced the 32 kb topo IIα genomic locus, generating a topo llα (-/+/+)cell line, which showed an increased resistance to topo II inhibitors. Paradoxically, 150 uM etoposide or 100 uM mitoxanthrone induced apoptosis within 5 hours in the topo llα (-1+1+) cell line, more rapidly as compared to the normal DT 40 cells. A topo IIα (-I-I+) cell line has also been generated. This study revealed the presence of evolutionarily conserved alternatively spliced forms of both topo llα and β isoforms between birds and humans. Hybridization screening of two chicken cDNA libraries, MSB-1 and DU249, revealed the presence of two distinct forms of both topo llα and β cDNAs. One form of topo llα, designated topo llα-1, encodes the chicken topo llα amino acid sequence previously reported (dbjiAB007445) in the database (unpublished). The second form, designated topo llα-2, encodes a protein containing an additional 35 amino acids inserted after Lysine-322 of chicken topo IIα-1 protein sequence. In the case of topo 11(3 mANA, one form, designated topo IIβ-1, encodes the protein already described (dbjiAB007446). The second form, tapa IIβ-2, would encode a protein missing the next 86 amino acids after Valine-25 in tapa II β-1 protein sequence. The tapa 11β variant is positioned similarly to one previously described in human (Hela) cells. The 5 amino acid insertion in the human tapa 11β-2 variant follows v23. In chicken cells, a longer insertion of 86 amino acids sequence follows v25, the homologous position in the tapa 11β protein. In human cells, the situation with tapa llα is more complex, as revealed by RT-PCR experiments (APM, unpublished) which generated several bands. One of these amplified species was found to contain a 36 amino acids insertion, positioned after residue K321 in the human tapa IIα cDNA, similarly to chicken tapa IIα-2 variant. The second human tapa llα spliced form cDNA was shown to contain a 26 amino acids insertion after residue A401 in the canonical human tapa llα protein sequence. The third cDNA variant isolated from human cells was described to encode a 81 amino acids insertion after residue Q355 positioned within the known human tapa IIα protein. It appears possible that the posttranslational modifications of the a-2 and β-2 isoforms may differ substantially from those of the canonical a-1 and β-1 isoforms. Such variant proteins could fulfil specialized functions, which might be tissue or cell-type specific. In summary, two novel forms of tapa llα and β cDNAs have been identified in three chicken cell lines. These spliced versions of both tapa llα and 13 isoforms seem to be evolutionary conserved, with similar forms occurring in their human counterparts. Future functional analysis of vertebrate tapa IIα and β will have to account for the existence of these novel isoforms, which might encode proteins that may exhibit different regulation of their subcellular localization, interaction with other proteins, or catalytic activity.

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26

Yant, Stephen Russell. "Sleeping beauty : a DNA transposon system for therapeutic gene transfer in vertebrates /." Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/5068.

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MARSICH, ELEONORA. "CARATTERIZZAZIONE DI PROTEINE NUCLEARI INTERAGENTI CON IL DNA RIPETITIVO TELOMERICO DEI VERTEBRATI." Doctoral thesis, Università degli studi di Trieste, 2000. http://thesis2.sba.units.it/store/handle/item/12644.

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28

Haynes, Susan. "The history of wild and domesticated vertebrates deduced from modern and ancient DNA sequences." Thesis, University of York, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325669.

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29

Cordonnier, Agnès. "Etude des mecanismes moleculaires de la replication de l'adn mitochondrial de xenopus laevis." Paris 6, 1987. http://www.theses.fr/1987PA066156.

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30

Milinkovitch, Michel. "Phylogenetic analyses of molecular data in vertebrates with special emphasis on the implications of mitochondrial DNA sequences for reevaluating morphological and behavioral evolution in cetaceans." Doctoral thesis, Universite Libre de Bruxelles, 1994. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/212689.

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31

Orfanoudakis, Georges. "Diadenosine tetraphosphate : implication dans l'activite mitotique, la replication et la reparation du dna." Université Louis Pasteur (Strasbourg) (1971-2008), 1988. http://www.theses.fr/1988STR13121.

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Le diadenosine tetraphosphate (ap**(4)a) est le principal produit de la reaction d'aminoacylation catalysee par certaines aminoacyl-trna synthetases. L'ap**(4)a est une molecule "signal" s'accumulant a l'interphase g1/5 du cycle cellulaire des cellules eucarydes declenchant ainsi la synthese du dna precedant la division cellulaire. Quantification du contenu cellulaire en ap**(4)a et en atp apres synchronisation des cellules (hepertome de rat, fibroblaste de souris) en culture par l'aphidicoline agent bloquant les cellules en phase s et par privation de serum qui arrete la croissance en mi-phase g. Mise au point d'un modele de reparation, dans les ovocytes ou les oeufs non fecondes de xenopus laevis, du plasmute pbr322 modifie par l'acetylaminofluorene. L'effet de l'ap**(4)a sur la reparation est etudie

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32

Tratner, Isabelle. "Etude de la methylation des genes codant pour l'albumine et l'alphafoetoproteine dans differents tissus au cours du developpement et dans des cellules d'hepatomes chez le rat : correlation avec l'expression genique." Paris 6, 1987. http://www.theses.fr/1987PA066651.

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33

Bonne-Andrea, Catherine. "Contribution à l'étude des propriétés et du rôle biologique de la protéine non-histone HMG1." Paris 6, 1986. http://www.theses.fr/1986PA066451.

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34

Dunon-Bluteau, Dominique. "Etude de la region origine de replication de l'adn mitochondrial de xenopus laevis." Paris 7, 1987. http://www.theses.fr/1987PA077049.

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Chez les vertebres, l'adn mitochondrial est dna bicatenaire (15 kb). Un intermediaire de replication possedant dune boucle de deplacement (boucle d) contient un brin h neosynthetise de taille fixe et est trouve en proportion variable dans les mitochondries. Le quart du genome mitochondrial de xenopus laevis a ete sequence: la region boucle d, 4 genes d'arn de transfert, le gene de l'apocytochrome b et celui de l'arn 125. La sequence nucleotique indique que l'organisation genetique de cette region est identique a celles des mammiferes. La cartographie au nucleotide pres du brin h de la boucle d a mis en evidence 2 familles de brin h ayant une extremite 3' commune, des structures secondaires sont potentiellement inapliquees dans la terminaison des brins h de la boucle d. Une proteine de 21,5 k da a ete isolee, se fixe a l'adn dans la region origine de replication et semble jouer un role regulateur dans la replication ou l'expression de l'adn mitochondrial. La replication du brin h peut etre observee dans un systeme de synthese d'adn "in vitro" (adn polymerase indispensable)

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35

Wion, Didier. "Etude de la regulation du nerve growth factor (ngf) : clonage du gene ngf de poulet et d'un cdna codant pour la chaine lourde des neurofilaments." Paris 7, 1988. http://www.theses.fr/1988PA077168.

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La regulation de l'expression du gene ngf a ete etudiee dans la lignee de fibroblastes nurins l-929 a l'aide d'une sonde de cdna permettant de quantifier le rna messager ngf. L'abondance du ngf transcript est dependante des conditions de culture: serum, hormones thyroidiennes et acide retinoique stimulent le taux de transcription du gene ngf alors que la dexamethasone la diminue. Le gene ngf du poulet et le dna complementaire de la chaine lourde des neurofilaments ont ete clones et sequences. Les sondes moleculaires rendent possibles l'etude de la coexpression au cours de l'embryogenese des genes codant pour des facteurs trophiques (ngf) et des marqueurs neuronaux (neurofilament)

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36

Blanchetot, Alain. "Organisation, structure et comparaison du gène de la myoglobine (mb) chez les mammifères." Paris 6, 1986. http://www.theses.fr/1986PA066602.

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37

GILSON, GEORGES. "Le diadenosine tetraphosphate : etudes immunochimiques et analyse de son role dans les mecanismes de reponse au stress et de reparation du dna." Université Louis Pasteur (Strasbourg) (1971-2008), 1988. http://www.theses.fr/1988STR13110.

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38

Sari, Marie-Agnès. "Syntheses de porphyrines cationiques solubles dans l'eau et etude de leurs interactions avec l'adn de thymus de veau." Paris 6, 1988. http://www.theses.fr/1988PA066528.

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Preparation et caracterisation de porphyrines cationiques dont le nombre et la position des charges varient. Cytotoxicite vis-a-vis des cellules l1210 et de bacteries sensibles aux intercalants et deficients ou non dans leurs systemes de reparation de l'adn

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39

Smedley, Marie A. "Nutritional and environmental effects on triploid Atlantic salmon skeletal deformity, growth and smoltification." Thesis, University of Stirling, 2016. http://hdl.handle.net/1893/23342.

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The Atlantic salmon (Salmo salar) is an iconic species that dominates the global finfish production sector with increasing market demand. The Scottish industry and government alone aspires for expansion of the sector to 210,000 t by 2020 with 154, 000 t produced in 2013. As such, there are pressures to improve sustainable development in particular to minimise the genetic impact of escapees on wild populations and reduce sea lice infection which are required for the granting of “green licenses” in Norway. The use of triploidy has been tested in the 1980’s with little success owing to suboptimal rearing conditions leading to elevated mortalities, poorer growth and a higher prevalence of deformities, in particular of the skeleton. Collectively: recent success of triploid trout farming, expansion to the salmon production sector and potential resulting pressure on wild stocks through escapee increases have reinstated interest to implement artificially induced triploid Atlantic salmon in commercial production. As diploid Atlantic salmon have undertaken extensive domestication to achieve the high quality production and welfare standards observed to date, triploid conspecifics too require husbandry optimisation to realise potential. In particular, industrialisation requires that higher observations of deformities and inconsistent growth trajectories during seawater ongrowing be resolved through optimisation of rearing regimes and subsequent standardization of husbandry protocols. Triploids possess additional genomic material and increased cell size yet reduced frequency that reflects known differences in physiology and supports that, in effect, triploids should be considered as a new species relative to diploid conspecifics. Therefore, this doctoral thesis aimed to study nutrition and temperature effects on triploid Atlantic salmon traits throughout the production cycle from ‘egg to plate’. Nutrition trials aimed to improve growth potential and mitigate skeletal deformities both in freshwater (FW) and saltwater (SW) whilst attempts were made to define a window of smoltification to ensure optimal ongrowing performance. Finally, impacts of embryonic temperature regimes that are known to impact long term performance and deformity development in triploids, were examined in relation to DNA regulation and yolk composition in an attempt to underpin potential mechanisms for the environmental impact of temperature on developmental phenotype. One of the main restrictions to triploid Atlantic salmon implementation is the increased prevalence and severity of skeletal deformities, particularly after the maring phase. The work performed in this thesis first demonstrated that protein and/or phosphorous (P) supplementation throughout SW ongrowing not only reduced the level of severely deformed (≥ 10 deformed vertebrae observable by x-radiography) individuals by 30 % but also sustained 6.8 % faster growth and improved harvest grade compared to triploids fed a standard grower diet (chapter 2). Comparison of x-radiography and severely deformed individuals between harvest and sea transfer highlighted that protein and P supplementation arrested deformity development whereas prevalence increased in triploids fed a standard grower diet. This implied that severe deformities were of FW origin and strongly suggest requirement for improved nutrition in FW to optimise SW performance. Therefore investigation of higher dietary P inclusion in FW was investigated and results showed significantly reduced number of deformed vertebrae and no severely deformed individuals in those fed 19.7 g total P Kg-1 compared with those fed 13.0 & 16.7 g total P Kg-1 (chapter 3). Most deformities were localised in the central (vertebrae 27 – 31) and caudal (vertebrae 52 – 57) regions for all treatments. However, triploids fed lower dietary P displayed a particular increase in prevalence within the tail region (vertebrae 32- 47) which is consistent with SW ongrowing reports and results from chapter 2, further highlighting FW origin of higher vertebral deformities reported in SW ongrowing in triploids. Higher P supplementation in FW also significantly improved growth in triploid parr compared to diploids and lower supplementation. However, this effect did not transpire in later FW smolt stages where weights were significantly higher in triploids fed lower compared to higher P supplementation. Expression of target genes involved in osteogenesis and bone P homeostasis in vertebrates were then analysed and a ploidy effect of osteogenic genes alp, igf1r and opn as well as a dietary effect on P homeostasis gene fgf23 was apparent in the parr stages but not smolt. In addition, stronger ploidy-diet effects were also observed in parr stages for whole body mineral concentrations. Collectively, growth, gene expression and whole body mineral content results indicate these earlier parr life stages may be more sensitive to P supplementation. This pronounced effect may be a consequence of seasonal accelerated growth associated with this period, where higher temperatures were also observed. The potential for shorter P supplementation windows in commercial production was addressed in chapter 4 with hope to cut economic cost to raw mineral inclusion in feed and also mitigate potential anthropogenic eutrophication on the environment that may be induced by P leached through uneaten feed and faeces. Triploids were fed higher dietary P (17.4 g total P Kg-1) until either early (5 g) or later (20 g) parr stages, or smolt (83 g) and monitored for performance throughout freshwater (FW) development. During later parr development (30 g), x-radiography assessment demonstrated that increased dietary P reduced the number of deformities and severely deformed individuals with no indication that feeding P for shorter windows improved skeletal integrity. Hence, P supplementation may be required throughout FW development for optimal skeletal performance. In addition, no differences in deformities were observed between triploid treatments at smolt. An effect of dietary P supplementation on whole body mineral concentration was observed in the early and later parr stages that was not as pronounced as smolt, which is consistent with results in chapter 3. Together, these results indicate that skeletal assessment during early developmental stages may not reflect smolt performance most likely as a consequence of seasonal effects of improved linear growth in the cooler winter temperatures prior to smolt where reversible deformities observed at parr may also be alleviated. In the same study (chapter 4), the inclusion of the probiotic Pediococcus acidilactici (Bactocell™) was also tested as a means to enhance gut assimilation as suggested in previous studies and therefore reduce the levels of P supplementation. Results clearly indicate superior skeletal performance in parr (30 g) as well as significantly less deformed vertebrae and no severely deformed individuals. However, at smolt (~83g), no effects of the dietary probiotic treatment were observed which may also be attributed to seasonal effects. Overall, nutritional research clearly indicate triploids require higher dietary P for optimal growth and skeletal development, which although is not consistent between life stages, is ultimately required throughout FW for optimal skeletal development at smolt. The use of probiotics offer a promising avenue for reduced P requirement in FW feed and further research should verify results and assess long-term performance. Timing of SW transfer according to correct parr-smolt transformation (PST) is essential for survival and growth performance in ongrowing where feeding and growth rate accelerate post-transfer. So far, SW transfer regimes and in particular the smoltification ‘window’ remains loosely defined in triploid Atlantic salmon and it is crucial that this be addressed to ensure optimal ongrowing survival and performance.

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40

Moris, Gilbert. "Le diadenosine tetraphosphate : roles dans la regulation de la croissance et du cycle cellulaires et dans la reponse cellulaire a un stress a l'ethanol." Université Louis Pasteur (Strasbourg) (1971-2008), 1988. http://www.theses.fr/1988STR13118.

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41

Farache, Gabriel. "Etudes des regions genomiques delimitant les domaines des genes globine chez le poulet." Paris 7, 1987. http://www.theses.fr/1987PA077009.

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Cette etude concerne les regions d'adn delimitant le domaine des genes alpha globine du poulet. Dans les cellules de lignee erythroide, ce domaine est limite de part et d'autre par des regions en interaction permanente avec la matrice nucleaire. Les regions internes au domaine sont associees a la matrice pendant la transcription des genes. Les segments delimitant ce domaine se localisent a l'interieur ou a proximite de regions riches en aet t, comprenant aussi des sequences repetees. Une sequence riche en at contenant 4 sites homologues au consensus definis pour la topoisomerase ii, et un element repetifif appartenant a la famille cr1 a ete identifie dans la sequence du segment delimitant le domaine du cote 3'. Un element cr1 a l'interieur du gene epsilon globine de poulet a ete caracterise, cette structure permet d'envisager l'existence d'au moins deux mecanismes moleculaires alternatifs de dispersion de cette famille de sequence dans le genome du poulet. La sequence cr1 contient un site d'interaction pour un facteur nucleaire present dans les cellules erythroides

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42

Kaushik, Azad Kumar. "Etude idiotypique, structurale et analyse du repertoire des autoanticorps dans deux modeles d'autoimmunite naturelle chez la souris : autoanticorps reagissant avec les globules rouges de souris bromelises, autoanticorps reagissant avec l'adn et les." Paris 7, 1987. http://www.theses.fr/1987PA077074.

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43

HEILIG, ROLAND. "Identification du gene de la myopathie de duchenne : caracterisation du messager chez le poulet : etude de la dystrophine." Université Louis Pasteur (Strasbourg) (1971-2008), 1989. http://www.theses.fr/1989STR13011.

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La myopathie de duchenne (dmd), maladie hereditaire grave liee au chromosome y. Isolement d'un point d'acces au locus dmd, par une marche genomique, les auteurs ont isole une region de 230 kb de ce gene gigantesque. Une etude structurale comparative entre deux especes eloignees (homme et poulet) a permis d'identifier une region de la proteine soumise a tres forte pression selective. Chez la souris, le mutant "max" pourrait correspondre a l'homologue de la mutation dmd et constituer a ce titre un modele animal de choix pour l'etude de certains aspects de la pathologie humaine

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44

Walter, Philippe. "Le recepteur de l'oestradiol humain : isolement, sequence et expression de l'adnc et homologie avec l'oncogene erb-a." Université Louis Pasteur (Strasbourg) (1971-2008), 1986. http://www.theses.fr/1986STR13003.

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45

Sobczak, Joëlle. "Etude de l'expression genetique dans le foie de rat en hypertrophie compensatrice." Paris 6, 1988. http://www.theses.fr/1988PA066543.

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46

Labidi, Brahim. "Etude de la transcription dans des noyaux contenant un seul chromosome." Grenoble 2 : ANRT, 1987. http://catalogue.bnf.fr/ark:/12148/cb37606769q.

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47

Ronquist, Göran. "Some Characteristics of Human Prostasomes and Their Relationship to Prostate Cancer." Doctoral thesis, Uppsala universitet, Klinisk kemi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-100799.

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Background: The secretory epithelial cells of the prostate gland use sophisticated vehicles named prostasomes to relay important information to sperm cells in semen. This prostasome-forming and secretory ability of the epithelial cells is also preserved in poorly differentiated prostate cancer cells. Aim: The aim of this thesis was to examine different characteristics of prostasomes, especially those derived from malignant prostate cells, linked to their potential role in diagnosis and prognostication of prostate cancer. Results: Serum samples of prostate cancer patients contained autoantibodies against seminal prostasomes in a higher concentration than did control sera. These autoantibodies were most frequently directed against 25 prostasome-associated proteins, but no one was prostate specific. Clusterin was one of the most frequently occurring prostasomal proteins. Elevated titers were however seen in both patients´ and control sera. Clusterin turned out to be a major antigen of seminal prostasomes. No prostate specific or prostate cancer specific protein was discovered upon proteomic analysis of prostasomes deriving from malignant cells of vertebral metastases of prostate cancer patients. Human chromosomal DNA was identified in both seminal prostasomes and PC-3 cell prostasomes and strong evidence existed that the DNA was localized inside the prostasomes. Four out of 13 DNA clones of seminal prostasomes featured gene sequences (31%). The corresponding figures for PC-3 cell prostasomes were 4 out of 16 clones (25%). Conclusions: Prostasomes are immunogenic and give rise to serum autoantibodies. The most frequently occurring autoantibodies were directed against 25 prostasomal proteins but none of these was exclusively prostate specific. Thirty different proteins were identified in prostate cancer metastasis-derived prostasomes but none of these proteins was prostate cancer specific. Human chromosomal DNA was identified in prostasomes of both normal and malignant cell origin.

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48

Giraudat, Jérôme. "Etude de l'organisation fonctionnelle des chaines polypeptidiques du récepteur nicotinique de l'acétylcholine." Paris 6, 1986. http://www.theses.fr/1986PA066403.

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49

Legrand, Alain. "Liposomes cibles et vecteurs retroviraux pour le transfert et l'expression du gene de la preproinsuline i de rat dans des cellules eucaryotes." Orléans, 1987. http://www.theses.fr/1987ORLE2011.

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Encapsulation d'adn dans des liposomes contenant du lactosylceramide dont le sucre terminal est reconnu specifiquement par des recepteurs presents sur la membrane plasmique des cellules visees, c. A. D. , les hepatocytes et les cellules endotheliales du foie et egalement les lymphocytes de la rate. Injection par voie intraveineuse des liposomes. Role de l'endocytose, dans leur internalisation. Modele genetique constitue du gene de la preproinsuline i de rat insere dans des vecteurs retroviraux permettant l'expression du gene dans des celules non insulogenes

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50

Delmas, Véronique. "Structure et proprietes biologiques du papovavirus de hamster." Paris 6, 1986. http://www.theses.fr/1986PA066550.

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Le papovavirus de hamster (hapv) possede un tropisme restreint in vivo vis a vis des keratinocytes et des lymphocytes. Il se replique dans les tumeurs cutanes qui apparaissent chez des hamsters syriens, et induit egalement des lymphomes chez le hamster. L'organisation genetique du hapv deduite de sa sequence a montre qu'il appartient a la famille des polyomavirus. Le hapv est present dans les lymphomes sous forme de multiples copies libres possedant toujours une deletion localisee dans la meme region du genome. Les signaux de transcription precoce du hapv semblent etre actives par la region precoce de ce virus

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