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Dissertations / Theses on the topic 'Artificial Yeast Chromosomes'

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Published: 4 June 2021
Last updated: 16 February 2022

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1

Morroll, Shaun Michael. "Mapping of yeast artificial chromosomes from Arabidopsis chromosome 5." Thesis, University of Nottingham, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308922.

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2

Meaney, Paul James. "Mapping the Plasmodium falciparum genome with yeast artificial chromosomes." Thesis, University of Edinburgh, 1995. http://hdl.handle.net/1842/12640.

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Yeast Artificial Chromosome cloning vectors, with their capacity to maintain up to 1 Mb of cloned DNA in a stable form, have proved extremely useful in mapping the genomes of higher eukaryotes. These vectors possess features which can circumvent some of the problems associated with classical molecular manipulation in Plasmodium falciparum. The research presented in this thesis is aimed at contributing to genome mapping in P. falciparum. The primary objective is the construction of a complete, detailed YAC- based physical map of chromosome 6, with a resolution of 10 Kb. To accomplish this, an 1100 YAC library of the P. falciparum isolate HB3 was constructed. The library contains clones with an average insert size of 100 Kb. Insert DNA is stable when cultured over 100 generations and the library is predicted to have a 4/5 fold genome redundancy, corresponding to 90% of the genome. Chromosome 6 specific YAC's have been isolated and three contigs initiated. Overlapping YAC's have been identified by using Sequence Tagged Site markers obtained from the 5 and 3 ends of each YAC by Inverse PCR. A total of 700 Kb of P. falciparum DNA has been cloned and this has been extensively mapped with seven restriction enzyme. Maps for all available YAC's will be presented. In addition, an attempt has been made to evaluate the degree of stage specific gene expression of cloned DNA within each YAC. The implications of these findings for genome mapping in P. falciparum will be discussed in the thesis.
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3

Francis, Michael J. "Physical mapping around the SMA gene using yeast artificial chromosomes (YACs)." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259879.

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4

Davies, Nicholas Paul. "Modification, transfer and expression of yeast artificial chromosomes carrying human immunoglobulin genes." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318326.

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5

Meyer, Knut. "Positional cloning of the ABI1 locus of Arabidopsis thaliana using yeast artificial chromosomes /." [S.l.] : [s.n.], 1994. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=10974.

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6

White, Jacqueline Katie. "Analysis of human NRAMP, IL8R and V1L1 genes (2q35) using yeast artificial chromosomes." Thesis, University of Cambridge, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.339595.

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7

Van, Brabant Anja Josifa. "Characterizing YAC replication : identification and deletion of replication origins within a human DNA insert /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/10274.

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8

McGuigan, Amanda Jane. "Functional analysis of DNA cloned in yeast artificial chromosomes for replication and centromere function in mammalian cells." Thesis, Imperial College London, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299885.

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9

Mathrubutham, Umamaheshwar. "An investigation into the use of yeast artificial chromosomes for the identification of origins of replication in human DNA." Thesis, University of Southampton, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296259.

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10

Buchanan, Christina Diane. "Identification and characterization of a checkpoint triggered by delayed replication in S. cerevisiae /." Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/10253.

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11

Wood, Lynn. "High resolution physical mapping of an 840KB region at the 5' end of the dystrophin gene by construction of ordered phage lambda sublibraries from yeast artificial chromosomes." Thesis, University of Southampton, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242219.

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12

Hughes, Amanda L. "Dissecting cis and trans Determinants of Nucleosome Positioning: A Dissertation." eScholarship@UMMS, 2011. http://escholarship.umassmed.edu/gsbs_diss/743.

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Eukaryotic DNA is packaged in chromatin, whose repeating subunit, the nucleosome, consists of an octamer of histone proteins wrapped by about 147bp of DNA. This packaging affects the accessibility of DNA and hence any process that occurs on DNA, such as replication, repair, and transcription. An early observation from genome-wide nucleosome mapping in yeast was that genes had a surprisingly characteristic structure, which has motivated studies to understand what determines this architecture. Both sequence and trans acting factors are known to influence chromatin packaging, but the relative contributions of cis and trans determinants of nucleosome positioning is debated. Here we present data using genetic approaches to examine the contributions of cis and trans acting factors on nucleosome positioning in budding yeast. We developed the use of yeast artificial chromosomes to exploit quantitative differences in the chromatin structures of different yeast species. This allows us to place approximately 150kb of sequence from any species into the S.cerevisiae cellular environment and compare the nucleosome positions on this same sequence in different environments to discover what features are variant and hence regulated by trans acting factors. This method allowed us to conclusively show that the great preponderance of nucleosomes are positioned by trans acting factors. We observe the maintenance of nucleosome depletion over some promoter sequences, but partial fill-in of NDRs in some of the YAC v promoters indicates that even this feature is regulated to varying extents by trans acting factors. We are able to extend our use of evolutionary divergence in order to search for specific trans regulators whose effects vary between the species. We find that a subset of transcription factors can compete with histones to help generate some NDRs, with clear effects documented in a cbf1 deletion mutant. In addition, we find that Chd1p acts as a potential “molecular ruler” involved in defining the nucleosome repeat length differences between S.cerevisiae and K.lactis. The mechanism of this measurement is unclear as the alteration in activity is partially attributable to the N-terminal portion of the protein, for which there is no structural data. Our observations of a specialized chromatin structure at de novo transcriptional units along with results from nucleosome mapping in the absence of active transcription indicate that transcription plays a role in engineering genic nucleosome architecture. This work strongly supports the role of trans acting factors in setting up a dynamic, regulated chromatin structure that allows for robustness and fine-tuning of gene expression.
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13

Hughes, Amanda L. "Dissecting cis and trans Determinants of Nucleosome Positioning: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/743.

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Eukaryotic DNA is packaged in chromatin, whose repeating subunit, the nucleosome, consists of an octamer of histone proteins wrapped by about 147bp of DNA. This packaging affects the accessibility of DNA and hence any process that occurs on DNA, such as replication, repair, and transcription. An early observation from genome-wide nucleosome mapping in yeast was that genes had a surprisingly characteristic structure, which has motivated studies to understand what determines this architecture. Both sequence and trans acting factors are known to influence chromatin packaging, but the relative contributions of cis and trans determinants of nucleosome positioning is debated. Here we present data using genetic approaches to examine the contributions of cis and trans acting factors on nucleosome positioning in budding yeast. We developed the use of yeast artificial chromosomes to exploit quantitative differences in the chromatin structures of different yeast species. This allows us to place approximately 150kb of sequence from any species into the S.cerevisiae cellular environment and compare the nucleosome positions on this same sequence in different environments to discover what features are variant and hence regulated by trans acting factors. This method allowed us to conclusively show that the great preponderance of nucleosomes are positioned by trans acting factors. We observe the maintenance of nucleosome depletion over some promoter sequences, but partial fill-in of NDRs in some of the YAC v promoters indicates that even this feature is regulated to varying extents by trans acting factors. We are able to extend our use of evolutionary divergence in order to search for specific trans regulators whose effects vary between the species. We find that a subset of transcription factors can compete with histones to help generate some NDRs, with clear effects documented in a cbf1 deletion mutant. In addition, we find that Chd1p acts as a potential “molecular ruler” involved in defining the nucleosome repeat length differences between S.cerevisiae and K.lactis. The mechanism of this measurement is unclear as the alteration in activity is partially attributable to the N-terminal portion of the protein, for which there is no structural data. Our observations of a specialized chromatin structure at de novo transcriptional units along with results from nucleosome mapping in the absence of active transcription indicate that transcription plays a role in engineering genic nucleosome architecture. This work strongly supports the role of trans acting factors in setting up a dynamic, regulated chromatin structure that allows for robustness and fine-tuning of gene expression.
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14

Hassock, Sheila Ruth. "Physical and transcriptional mapping in the distal Xq28 region of the human X chromosome." Thesis, King's College London (University of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312021.

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15

Chew, Joyce Siew Khim. "Isolation and characterization of Oreochromis niloticus DNA yeast artifical chromosome clones." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ36348.pdf.

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16

Tanaka, Karo. "Characterisation of the murine homologue of the CIC-5 gene : a voltage-gated chloride channel implicated in human X-linked hereditary nephrolithiasis." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302335.

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17

Coffey, Alison Jane. "Physical mapping on the human X chromosome and its application to the positional cloning of the XLP gene." Thesis, King's College London (University of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.327181.

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18

Everson, Ted. "A construct of overlapping yeast artificial chromosomes spanning a seven centimorgan region of human chromosome 8p22." Thesis, 1997. http://hdl.handle.net/2429/6316.

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An important goal of the Human Genome Project is the physical mapping of the human genome. This thesis describes the preparation of a set of overlapping yeast artificial chromosomes (YACs), spanning approximately a 7 centiMorgan (cM) region of chromosome 8p22, delimited distally by D8S550 and proximally by D8S552. This set of overlapping YACs, or YAC contig, is a useful contribution to the human genome physical map. It will have valuable applications for the identification of sequence ready clones and for the detection of disease genes that may be mapped to 8p22. To construct the YAC contig, the Whitehead Institute/ Massachussetts Institute of Technology (MIT) Center for Genome Research genomic database was searched for YACs containing markers that were previously localized to the region of interest. A singly-linked contig, WC8»1, was found, which identifies a set of 62 overlapping YACs within this region. Database information for these YACs was examined in order to exclude from analysis any YACs for which significant evidence of chimaerism was available. A subset of YACs was chosen for further analysis; these included eight YACs with no evidence for chimaerism, and two YACs with relatively weak evidence for chimaerism. DNA sequence from the insert ends (terminal sequence) of a number of these YACs was isolated by a modified bubble PCR protocol (Riley et al.,1990), a procedure that amplifies terminal sequences. These sequences were then used to develop new markers for the region. PCR was performed, using selected markers from WC8«1 and the new markers designed from terminal sequences. PCR amplification of markers in the set of ten YACs resulted in the identification of overlapping YACs, forming a contig that completely spanned the region of interest. In addition, terminal sequences from YAC 729el2 were found to be highly similar to the murine guanine nucleotide release factor 2 (GRF2) gene; a marker designed from this sequence was amplified in a human chromosome 5 somatic cell hybrid, localizing this putative human gene to chromosome 5.
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19

Mu, Yi. "Cloning, disruption cytochrome c gene and construction of yeast artificial chromosome library of Kluyveromyces marxianus." 2004. http://catalog.hathitrust.org/api/volumes/oclc/56204766.html.

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20

Jacques, Samuel. "Generation and screening of natural product-like compounds for antibiotic discovery." Thesis, 2016. http://hdl.handle.net/1866/16243.

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Avec l’apparition de plus en plus de souches de bactérie résistante aux antibiotiques, le développement de nouveaux antibiotiques est devenu une important problématique pour les agences de santé. C’est pour cela que la création de nouvelles plateformes pour accélérer la découverte de médicaments est devenu un besoin urgent. Dans les dernières décennies, la recherche était principalement orientée sur la modification de molécules préexistantes, la méta-analyse d’organismes produisant des molécules activent et l’analyse de librairies moléculaires pour trouver des molécules synthétiques activent, ce qui s’est avéré relativement inefficace. Notre but était donc de développer de nouvelles molécules avec des effets thérapeutiques de façon plus efficace à une fraction du prix et du temps comparé à ce qui se fait actuellement. Comme structure de base, nous avons utilisé des métabolites secondaires qui pouvaient altérer le fonctionnement des protéines ou l’interaction entre deux protéines. Pour générer ces molécules, j’ai concentré mes efforts sur les terpènes, une classe de métabolites secondaires qui possède un large éventail d’activités biologiques incluant des activités antibactériennes. Nous avons développé un système de chromosome artificiel de levure (YAC) qui permet à la fois l’assemblage directionnel et combinatoire de gènes qui permet la création de voies de biosynthèse artificielles. Comme preuve de concept, j’ai développé des YACs qui contiennent les gènes pour l’expression des enzymes impliquées dans la biosynthèse de la -carotène et de l’albaflavenone et produit ces molécules avec un haut rendement. Finalement, Des YACs produits à partir de librairies de gènes ont permis de créer une grande diversité de molécules.
With the appearance of more and more antibiotic resistant strains of bacteria, the development of new antibiotics becomes an issue of utmost importance for society. It is for that reason that new platforms and methodologies to accelerate the discovery of novel antibiotics are urgently needed. For the last decades, research was mainly oriented on modifying existing antibiotics, mining natural producers or screening for synthetic molecules from giant chemical libraries but these approaches did not manage to keep the pipelines filled with a sufficient number of novel antibiotics. Therefore, our goal was to develop a way to create and screen new molecules more efficiently at a fraction of the cost when compared to traditional approaches and within a short time frame. As chemical scaffolds we use natural product-like compounds that modulate the function of individual proteins or of protein-protein interactions. To generate these compounds, I focused first on the terpene scaffold class, a class containing molecules with a wide range of biological activities and includes compounds with antibacterial activities. We developed a yeast artificial chromosome (YAC) platform that allows both directional and combinatorial assembly of biosynthetic genes that can be used to create artificial biosynthetic pathways. As a proof of principle, YACs were successfully assembled containing genes coding for enzymes involved in the biosynthesis of both B-carotene and albaflavenone, and that allowed high yield production of these compounds. Finally, YACs encoding terpene gene libraries were also created and which produced a diversity of terpenoid molecules.
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