subject:(satellite DNA)

Universidade Estadual de Campinas

1. Vittorazzi, Stenio Eder, 1984-. Caracterização citogenética e molecular do DNAr 5S e sua forma variante de DNA satélite em espécies do grupo de Physalaemus cuvieri (Anura, Leptodactylidae) = Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae): Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae).

Degree: 2014, Universidade Estadual de Campinas

URL: http://repositorio.unicamp.br/jspui/handle/REPOSIP/317964

► Abstract: The genomes of eukaryotic organisms are rich in repetitive DNA sequences, which can be dispersed or arrayed in tandem. The tandem repeat sequences include… (more)

▼ Abstract: The genomes of eukaryotic organisms are rich in repetitive DNA sequences, which can be dispersed or arrayed in tandem. The tandem repeat sequences include the satellite DNA, the ribosomal DNA, and paralogous copies. Satellite DNA is the main component of constitutive heterochromatin, while the ribosomal genes encode the rRNAs that make up the ribosomes; they are divided into two families, the 45S and 5S rRNA. Different types of 5S rDNA have been identified in a single organism, proving that there is diversity in this type of DNA sequence. In the anuran Physalaemus cuvieri, a satellite DNA family called PcP190 has been identified, which is thought to have derived from the 5S rDNA of an ancestor species. In different populations of P. cuvieri that were previously studied with conventional cytogenetic tools, an accentuated interpopulational variation among chromosomes harboring the NOR was observed, while in other species of the P. cuvieri group, interspecific traits were found. However, the karyotypes in these species are very similar. The aim of this thesis was to expand the cytogenetic studies on P. cuvieri species that needed further chromosomal description, such as P. kroyeri and P. cicada. Another objective was to analyze the PcP190 satellite DNA at the chromosomal and molecular level, as well as to study the molecular organization and the diversity of 5S rDNA sequences in the genomes of the Physalaemus species and other species of related genera. We present three chapters as a result of this research: (i) "Long-time evolution and highly dynamic satellite DNA in frogs," which demonstrates that the PcP190 satellite DNA is widely conserved and was recognized in representatives of two anurans families, Leptodactylidae and Hylodidae. Moreover, it also demonstrates that these sequences are highly dynamic within the chromosomes of the P. cuvieri species group. (ii) "5S rDNA in Leiuperinae (Anura): new insights on its evolution." The results show that in the genomes of these anurans there is wider diversity among this multigenic family than previously assumed and that these 5S rDNA sequences have remained conserved since the evolutionary divergence of Actinopterygii and Sarcopterygii. (iii) "Karyotype and repetitive DNA mapping of the Physalaemus kroyeri and P. cicada (Anura Leptodactylidae)," which demonstrates that the 5p chromosomal band of P. kroyeri is a good chromosomal marker for species from the P. cuvieri group, indicating that it is a chromosomal synapomorphy. Conversely, the absence of this 5p band in P. cicada does not provide evidence for the inclusion of this species in the P. cuvieri group or any other species group Advisors/Committee Members: UNIVERSIDADE ESTADUAL DE CAMPINAS (CRUESP), Recco-Pimentel, Shirlei Maria, 1954- (advisor), Pimentel, Shirlei Maria Recco, 1954- (advisor), Lourenço, Luciana Bolsoni, 1972- (coadvisor), Universidade Estadual de Campinas. Instituto de Biologia (institution), Programa de Pós-Graduação em Biologia Celular e Estrutural (nameofprogram), Junior, Odair Aguiar (committee member), Kuhn, Gustavo Campos e Silva (committee member), Mello, Diogo Cavalcanti Cabral de (committee member), Brito, Cíntia Pelegrineti Targueta de Azevedo (committee member).

Subjects/Keywords: DNA satélite; DNA ribossômico; Citogenética; Physalaemus; Anuro; DNA, Satellite; DNA, Ribosomal; Cytogenetics; Physalaemus; Anura

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APA (6^th Edition):

Vittorazzi, Stenio Eder, 1. (2014). Caracterização citogenética e molecular do DNAr 5S e sua forma variante de DNA satélite em espécies do grupo de Physalaemus cuvieri (Anura, Leptodactylidae) = Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae): Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae). (Thesis). Universidade Estadual de Campinas. Retrieved from http://repositorio.unicamp.br/jspui/handle/REPOSIP/317964

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Vittorazzi, Stenio Eder, 1984-. “Caracterização citogenética e molecular do DNAr 5S e sua forma variante de DNA satélite em espécies do grupo de Physalaemus cuvieri (Anura, Leptodactylidae) = Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae): Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae).” 2014. Thesis, Universidade Estadual de Campinas. Accessed March 01, 2021. http://repositorio.unicamp.br/jspui/handle/REPOSIP/317964.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Vittorazzi, Stenio Eder, 1984-. “Caracterização citogenética e molecular do DNAr 5S e sua forma variante de DNA satélite em espécies do grupo de Physalaemus cuvieri (Anura, Leptodactylidae) = Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae): Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae).” 2014. Web. 01 Mar 2021.

Vancouver:

Vittorazzi, Stenio Eder 1. Caracterização citogenética e molecular do DNAr 5S e sua forma variante de DNA satélite em espécies do grupo de Physalaemus cuvieri (Anura, Leptodactylidae) = Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae): Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae). [Internet] [Thesis]. Universidade Estadual de Campinas; 2014. [cited 2021 Mar 01]. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/317964.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Vittorazzi, Stenio Eder 1. Caracterização citogenética e molecular do DNAr 5S e sua forma variante de DNA satélite em espécies do grupo de Physalaemus cuvieri (Anura, Leptodactylidae) = Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae): Cytogenetic and molecular analysis of the 5S rDNA and its variant form of satellite DNA in Physalaemus cuvieri species group (Anura, Leptodactylidae). [Thesis]. Universidade Estadual de Campinas; 2014. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/317964

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

2. McGurk, Michael Peter. Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution.

Degree: PhD, Biochemistry, Molecular and Cell Biology, 2019, Cornell University

URL: http://hdl.handle.net/1813/67819

► Eukaryotic genomes are replete with repeated sequence, in the form of transposable elements (TEs) dispersed throughout genomes and as large stretches of tandem repeats (satellite… (more)

▼ Eukaryotic genomes are replete with repeated sequence, in the form of transposable elements (TEs) dispersed throughout genomes and as large stretches of tandem repeats (satellite arrays). Neutral and selfish evolution likely explain their prevalence, but repeat variation can impact function by altering gene expression, influencing chromosome segregation, and even creating reproductive barriers between species. Yet, while population genomic analyses have illuminated the function and evolution of much of the genome, our understanding of repeat evolution lags behind. Tools that uncover population variation in non-repetitive portions of genomes often fail when applied to repetitive sequence. To extend structural variant discovery to the repetitive component of genomes we developed ConTExt, employing mixture modelling to discover structural variation in repetitive sequence from the short read data that commonly comprises available population genomic data. We first applied ConTExt to investigate how mobile genetic parasites can transform into megabase-sized tandem arrays, as some satellites clearly originated as TEs. Making use of the Global Diversity Lines, a panel of Drosophila melanogaster strains from five populations, this study revealed an unappreciated consequence of transposition: an abundance of TE tandem dimers resulting from TEs inserting multiple times at the same locus. Thus, the defining characteristic of TEs—transposition—regularly generates structures from which new satellite arrays can arise, and we further captured multiple stages in the emergence of satellite arrays ongoing in a single species. We then investigated the complex array of processes which shape TE evolution, focusing on the putatively domesticated HeT-A, TAHRE, and TART (HTT) elements that maintain the telomeres of Drosophila. To provide context, we compared HTT variation to that of other TE families with known properties. Our results suggest that differences between HTT variation and other TE families largely result from the rapid sequence turnover at telomeres. We further suggest that the localization of the HTTs to the telomere reflects a successful evolutionary strategy rather than pure domestication. However, we find evidence that susceptibility to host regulation varies among HTTs and across populations, suggesting that despite constituting the mechanism of telomere maintenance, the HTTs remain in conflict with the genome like any other TE. Advisors/Committee Members: Barbash, Daniel A. (chair), Clark, Andrew (committee member), Soloway, Paul (committee member).

Subjects/Keywords: Repetitive DNA; Satellite DNA; Transposable elements; Evolution & development; Genetics; Bioinformatics

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APA (6^th Edition):

McGurk, M. P. (2019). Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/67819

Chicago Manual of Style (16^th Edition):

McGurk, Michael Peter. “Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution.” 2019. Doctoral Dissertation, Cornell University. Accessed March 01, 2021. http://hdl.handle.net/1813/67819.

MLA Handbook (7^th Edition):

McGurk, Michael Peter. “Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution.” 2019. Web. 01 Mar 2021.

Vancouver:

McGurk MP. Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution. [Internet] [Doctoral dissertation]. Cornell University; 2019. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1813/67819.

Council of Science Editors:

McGurk MP. Uncovering variation in the repetitive portions of genomes to elucidate transposable element and satellite evolution. [Doctoral Dissertation]. Cornell University; 2019. Available from: http://hdl.handle.net/1813/67819

University of Rochester

3. Khost, Danielle Emerson. Structure and dynamics of satellite DNA evolution in drosophila melanogaster and the simulans clade.

Degree: PhD, 2019, University of Rochester

URL: http://hdl.handle.net/1802/35356

► Satellite DNAs (satDNAs) are a class of repetitive elements that exist in large tandem blocks. They typically accumulate in areas of reduced recombination around centromeres… (more)

▼ Satellite DNAs (satDNAs) are a class of repetitive elements that exist in large tandem blocks. They typically accumulate in areas of reduced recombination around centromeres and telomeres. SatDNAs are found in almost all eukaryotic organisms, and can comprise huge portions of a given genome. One explanation for the widespread nature of satDNA is that they are selfish replicators that pass themselves on at the expense of the host genome without serving any adaptive function. Their rate of self-replication exceeds the rate at which selection can remove them, allowing for spread and persistence of satDNAs in genomes. However, in some cases, satDNA can have functional roles within the cell, such as in chromosome pairing during meiosis, proper chromosome disjunction during cell division, and contributing to centromere strength. Despite their abundance we only have a low resolution on the basic features of satDNA organization and evolution due to technical issues in sequencing and assembling the large, highly repetitive regions of genomes. This leaves many open questions about satDNA evolution and biology, such as the detailed structure of satDNA loci, mechanisms of satDNA rearrangement, and the consequences of the rapid turnover between species. In this work, I explore these questions using newly developed sequencing technology to assemble and study the evolution of satDNA loci at a base-pair level resolution. In Chapter 2, I develop methods to optimize the assembly of satDNA loci using single-molecule long-read sequencing and describe the detailed structure of several satDNA loci in Drosophila melanogaster. I show that contiguity of satDNA arrays is improved using a more permissive error rate during assembly, which allowed us to assemble several satDNA loci whose structures we verified using molecular methods. Using these improved assembly methods, in Chapter 3 I work in collaboration with other labs to assemble the genomes of three species in the closely related simulans clade and compare overall changes in repetitive DNA content. Satellite distribution and copy number are highly variable between the species; in addition, satellites are highly overrepresented on the X chromosome euchromatin. Lastly, in Chapter 4, I focus in on these satDNA loci in the euchromatin of the X chromosome, study their detailed evolutionary dynamics, and provide insight into potential mechanisms driving their dynamic evolution between genomes. I find recent expansions of a particular satDNA family in two of the simulans clade species that likely occurred independently. These expanded repeats are non-randomly distributed: different satDNA families are preferentially located adjacent to each other, which is likely facilitated by an acquired sequence homology.

Subjects/Keywords: Satellite DNA; Drosophila; Long read sequencing; Comparative genomics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Khost, D. E. (2019). Structure and dynamics of satellite DNA evolution in drosophila melanogaster and the simulans clade. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/35356

Chicago Manual of Style (16^th Edition):

Khost, Danielle Emerson. “Structure and dynamics of satellite DNA evolution in drosophila melanogaster and the simulans clade.” 2019. Doctoral Dissertation, University of Rochester. Accessed March 01, 2021. http://hdl.handle.net/1802/35356.

MLA Handbook (7^th Edition):

Khost, Danielle Emerson. “Structure and dynamics of satellite DNA evolution in drosophila melanogaster and the simulans clade.” 2019. Web. 01 Mar 2021.

Vancouver:

Khost DE. Structure and dynamics of satellite DNA evolution in drosophila melanogaster and the simulans clade. [Internet] [Doctoral dissertation]. University of Rochester; 2019. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1802/35356.

Council of Science Editors:

Khost DE. Structure and dynamics of satellite DNA evolution in drosophila melanogaster and the simulans clade. [Doctoral Dissertation]. University of Rochester; 2019. Available from: http://hdl.handle.net/1802/35356

University of Alberta

4. Lee, Charles. Identification and characterization of two mammalian centromeric satellite DNA families.

Degree: PhD, Department of Medical Sciences, 1996, University of Alberta

URL: https://era.library.ualberta.ca/files/g732db74g

Subjects/Keywords: Satellite DNA.; Deer – Genetics.

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Lee, C. (1996). Identification and characterization of two mammalian centromeric satellite DNA families. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/g732db74g

Chicago Manual of Style (16^th Edition):

Lee, Charles. “Identification and characterization of two mammalian centromeric satellite DNA families.” 1996. Doctoral Dissertation, University of Alberta. Accessed March 01, 2021. https://era.library.ualberta.ca/files/g732db74g.

MLA Handbook (7^th Edition):

Lee, Charles. “Identification and characterization of two mammalian centromeric satellite DNA families.” 1996. Web. 01 Mar 2021.

Vancouver:

Lee C. Identification and characterization of two mammalian centromeric satellite DNA families. [Internet] [Doctoral dissertation]. University of Alberta; 1996. [cited 2021 Mar 01]. Available from: https://era.library.ualberta.ca/files/g732db74g.

Council of Science Editors:

Lee C. Identification and characterization of two mammalian centromeric satellite DNA families. [Doctoral Dissertation]. University of Alberta; 1996. Available from: https://era.library.ualberta.ca/files/g732db74g

McMaster University

5. Lou, Peter. Satellite DNA in Halobacterium Salinarium: A physical and biochemical study.

Degree: MSc, 1970, McMaster University

URL: http://hdl.handle.net/11375/18786

►

The extremely halophilic bacterium, Halobacterium salinarium, contains a light density satellite DNA component which is 20% of the total DNA. The purpose of this… (more)

Subjects/Keywords: halobacterium; salinarium; satellite DNA; biochemical

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APA (6^th Edition):

Lou, P. (1970). Satellite DNA in Halobacterium Salinarium: A physical and biochemical study. (Masters Thesis). McMaster University. Retrieved from http://hdl.handle.net/11375/18786

Chicago Manual of Style (16^th Edition):

Lou, Peter. “Satellite DNA in Halobacterium Salinarium: A physical and biochemical study.” 1970. Masters Thesis, McMaster University. Accessed March 01, 2021. http://hdl.handle.net/11375/18786.

MLA Handbook (7^th Edition):

Lou, Peter. “Satellite DNA in Halobacterium Salinarium: A physical and biochemical study.” 1970. Web. 01 Mar 2021.

Vancouver:

Lou P. Satellite DNA in Halobacterium Salinarium: A physical and biochemical study. [Internet] [Masters thesis]. McMaster University; 1970. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/11375/18786.

Council of Science Editors:

Lou P. Satellite DNA in Halobacterium Salinarium: A physical and biochemical study. [Masters Thesis]. McMaster University; 1970. Available from: http://hdl.handle.net/11375/18786

Loyola University Chicago

6. Ziccardi, William. Organization and Composition of the α21-II Region of Human Chromosome 21.

Degree: MS, Biology, 2012, Loyola University Chicago

URL: https://ecommons.luc.edu/luc_theses/730

► The purpose of this project was to develop a better map of the alpha 21-II region of human chromosome 21 in regards to size… (more)

Subjects/Keywords: Alpha Satellite DNA; Down Syndrome; Human Chromosome 21; Human Genome; Biology

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APA (6^th Edition):

Ziccardi, W. (2012). Organization and Composition of the α21-II Region of Human Chromosome 21. (Thesis). Loyola University Chicago. Retrieved from https://ecommons.luc.edu/luc_theses/730

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ziccardi, William. “Organization and Composition of the α21-II Region of Human Chromosome 21.” 2012. Thesis, Loyola University Chicago. Accessed March 01, 2021. https://ecommons.luc.edu/luc_theses/730.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ziccardi, William. “Organization and Composition of the α21-II Region of Human Chromosome 21.” 2012. Web. 01 Mar 2021.

Vancouver:

Ziccardi W. Organization and Composition of the α21-II Region of Human Chromosome 21. [Internet] [Thesis]. Loyola University Chicago; 2012. [cited 2021 Mar 01]. Available from: https://ecommons.luc.edu/luc_theses/730.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ziccardi W. Organization and Composition of the α21-II Region of Human Chromosome 21. [Thesis]. Loyola University Chicago; 2012. Available from: https://ecommons.luc.edu/luc_theses/730

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Brno University of Technology

7. Bikár, Robert. Rekonstrukce opakujících se segmentů DNA: Reconstruction of Repetitive DNA Segments.

Degree: 2018, Brno University of Technology

URL: http://hdl.handle.net/11012/61884

► The main motivation for master's thesis is to find suitable algorithm that creates a graph representation of NGS sequencing data in linear time. De Bruijn… (more)

Subjects/Keywords: bioinformatika; DNA; opakující se elementy DNA; transposon; DNA satelit; de Bruijnův graf; bioinformatics; DNA; repetitive elements of DNA; transposon; DNA satellite; de Bruijn graph

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APA (6^th Edition):

Bikár, R. (2018). Rekonstrukce opakujících se segmentů DNA: Reconstruction of Repetitive DNA Segments. (Thesis). Brno University of Technology. Retrieved from http://hdl.handle.net/11012/61884

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Bikár, Robert. “Rekonstrukce opakujících se segmentů DNA: Reconstruction of Repetitive DNA Segments.” 2018. Thesis, Brno University of Technology. Accessed March 01, 2021. http://hdl.handle.net/11012/61884.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Bikár, Robert. “Rekonstrukce opakujících se segmentů DNA: Reconstruction of Repetitive DNA Segments.” 2018. Web. 01 Mar 2021.

Vancouver:

Bikár R. Rekonstrukce opakujících se segmentů DNA: Reconstruction of Repetitive DNA Segments. [Internet] [Thesis]. Brno University of Technology; 2018. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/11012/61884.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Bikár R. Rekonstrukce opakujících se segmentů DNA: Reconstruction of Repetitive DNA Segments. [Thesis]. Brno University of Technology; 2018. Available from: http://hdl.handle.net/11012/61884

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

8. Guizard, Sébastien. Etude de l'organisation du génome de poulet à travers les séquences répétées : Study of the organization of the chicken genome through repeated sequences.

Degree: Docteur es, Sciences de la vie, 2016, Université François-Rabelais de Tours

URL: http://www.theses.fr/2016TOUR4015

►

Les génomes des espèces aviaires ont des caractéristiques particulières comme la structure des chromosomes et le contenu en séquences répétées. En effet, alors que dans… (more)

▼

Les génomes des espèces aviaires ont des caractéristiques particulières comme la structure des chromosomes et le contenu en séquences répétées. En effet, alors que dans les génomes vertébrés, la proportion de répétitions dans le génome varie de 30 à 55 %, dans les espèces aviaires, cette proportion est plus faible et varie de 8 à 10 %. L’annotation du contenu répété est le plus souvent réalisée avec le programme RepeatMasker qui s’appuie généralement sur la banque de séquences répétées Repbase. Ce genre de méthode repose uniquement sur la séquence des éléments transposables connus. De fait, ce programme n’est pas en mesure de détecter de nouvelles séquences répétées, et la qualité de l’annotation sera donc dépendante de la banque de séquences d’éléments transposables utilisée. De plus en plus d’études montrent que les éléments transposables jouent un rôle dans le fonctionnement du génome et peuvent influer sur l’expression des gènes. Il est donc primordial que l’annotation de ces séquences soit la plus complète possible. Au cours de ma thèse a été mise en place une stratégie d’annotation des séquences répétées que nous avons élaborée et appliquée à un génome de grande taille, celui de la poule rouge de jungle. L’annotation ainsi obtenue m’a permis d’étudier l’organisation du génome de cette espèce au travers de ses séquences répétées et éléments transposables.

The genomes of avian species have special features such as the structure of chromosomes or their content in repeated sequences. Indeed, compared to vertebrate genomes in which the amount of repetitions varies from 30 to 55%, it is lower in avian species and varies from 8 to 10%. The annotation of repeated content is most often done with the RepeatMasker program that is generally use the Repbase database of repeated sequences. This kind of approach is based solely on the sequence of already known transposable elements. In fact, this program is not able to detect new repeats and in consequence produced annotations with a quality that depends on the sequences of transposable elements used. More and more studies show that transposable elements play a role in the functioning of the genome and can influence gene expression. It is therefore essential that the annotation of these sequences is as complete as possible. There are many programs using methods for detecting de novo transposable elements, either by searching for characteristic structures, or by comparing the genome against itself. However, no standard strategy of annotation for repeated sequences have been defined yet. My thesis aims to set-up a standard strategy of annotation for repeated sequences that was applied to a large genome, that of the red jungle fowl. The obtained annotation allowed me studying the genome organization in this species through its repeated sequences and transposable elements.

Advisors/Committee Members: Bigot, Yves (thesis director).

Subjects/Keywords: Poulet; ADN satellite; Éléments transposables; Bio-informatique; Benchmarking; Répétitions; Chicken; Satellite DNA; Transposable elements; Bioinformatics; Benchmarking; Repeat

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Guizard, S. (2016). Etude de l'organisation du génome de poulet à travers les séquences répétées : Study of the organization of the chicken genome through repeated sequences. (Doctoral Dissertation). Université François-Rabelais de Tours. Retrieved from http://www.theses.fr/2016TOUR4015

Chicago Manual of Style (16^th Edition):

Guizard, Sébastien. “Etude de l'organisation du génome de poulet à travers les séquences répétées : Study of the organization of the chicken genome through repeated sequences.” 2016. Doctoral Dissertation, Université François-Rabelais de Tours. Accessed March 01, 2021. http://www.theses.fr/2016TOUR4015.

MLA Handbook (7^th Edition):

Guizard, Sébastien. “Etude de l'organisation du génome de poulet à travers les séquences répétées : Study of the organization of the chicken genome through repeated sequences.” 2016. Web. 01 Mar 2021.

Vancouver:

Guizard S. Etude de l'organisation du génome de poulet à travers les séquences répétées : Study of the organization of the chicken genome through repeated sequences. [Internet] [Doctoral dissertation]. Université François-Rabelais de Tours; 2016. [cited 2021 Mar 01]. Available from: http://www.theses.fr/2016TOUR4015.

Council of Science Editors:

Guizard S. Etude de l'organisation du génome de poulet à travers les séquences répétées : Study of the organization of the chicken genome through repeated sequences. [Doctoral Dissertation]. Université François-Rabelais de Tours; 2016. Available from: http://www.theses.fr/2016TOUR4015

9. Cacheux, Lauriane. Diversité et histoire évolutive de l’ADN alpha satellite chez les Cercopithèques : Diversity and evolutionary history of alpha satellite DNA in Cercopithecini.

Degree: Docteur es, Biologie moléculaire - Génomique évolutive, 2016, Paris, Muséum national d'histoire naturelle

URL: http://www.theses.fr/2016MNHN0020

► Les régions centromériques reposent, chez les Primates, sur une famille de séquences répétées en tandem appelée l'ADN alpha satellite. Les monomères de cet ADN (≈170… (more)

▼ Les régions centromériques reposent, chez les Primates, sur une famille de séquences répétées en tandem appelée l'ADN alpha satellite. Les monomères de cet ADN (≈170 pb) se sont diversifiés au cours de l'évolution, formant des familles de séquences aux profils d'organisation et distribution variés. La diversité des alphas satellites chez les primates non-humains reste cependant peu caractérisée, et la compréhension de la dynamique évolutive de cet ADN nécessite son intégration dans de plus larges analyses comparatives. Les Cercopithèques, qui présentent une évolution chromosomique originale par fissions et émergences de nouveaux centromères, apparaissent comme des modèles d'étude prometteurs.Nous avons appliqué une nouvelle technologie de séquençage à des monomères et dimères d'alpha satellites, isolés à partir des génomes de Cercopithecus solatus (2n = 60) et C. pogonias (2n = 72). Ces deux espèces appartiennent à des lignées primaires distinctes au sein des Cercopithèques, et ont divergé l'une de l'autre il y a plusieurs millions d'années. L'analyse computationnelle des séquences collectées a permis la caractérisation de six familles d'alpha satellites, dont quatre sont partagées entre espèces et deux ne sont retrouvées que chez C. pogonias. Au moins trois familles seraient impliquées dans des répétitions d'ordre supérieur, profil d'organisation jusque-là inconnu dans l'ADN alpha satellite des Cercopithèques. L'hybridation in situ en fluorescence des familles identifiées, réalisée grâce à des sondes oligonucléotidiques hautement discriminantes, a permis de visualiser leur distribution sur les chromosomes de C. solatus et C. pogonias. Certaines de ces familles se distribuent différentiellement entre chromosomes, révélant l'existence d'une diversité interchromosomique de l'ADN alpha satellite chez les singes de l'Ancien Monde. Leurs positions sur les régions centromériques vont en faveur de l'hypothèse du gradient d'âge des alphas satellites, selon laquelle les familles se forment aux centromères en déplaçant les familles préexistantes vers les péricentromères. L'extension de cette analyse cytogénétique à quinze espèces et l'interprétation de ses résultats à la lumière d'une phylogénie moléculaire, nouvellement reconstruite, nous ont permis de proposer un scénario évolutif pour l'ADN alpha satellite chez les Cercopithèques. Celui-ci apparaît évoluer de manière concertée avec les chromosomes, se diversifiant et se déplaçant sur les régions centromériques à mesure que ces derniers se fissionnent et voient l'émergence de nouveaux centromères. Ces travaux ont enfin apporté des informations nouvelles quant aux relations de parenté entre Cercopithèques, invitant à une intégration de l'ADN alpha satellite dans l'étude de l'histoire évolutive des Primates. L'approche méthodologique mise au point a permis de caractériser la diversité et de comprendre l'évolution de l'ADN alpha satellite chez les Cercopithèques. Elle pourra être appliquée à l'étude de ces séquences particulières chez d'autres primates, ainsi qu'à l'étude de… Advisors/Committee Members: Escudé, Christophe (thesis director), Denys, Christiane (thesis director).

Subjects/Keywords: ADN alpha satellite; Cercopithèques; Centromère; Evolution des génomes; Alpha satellite DNA; Cercopithecini; Centromere; Genome evolution; 571.6; 572.86; 591.3

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cacheux, L. (2016). Diversité et histoire évolutive de l’ADN alpha satellite chez les Cercopithèques : Diversity and evolutionary history of alpha satellite DNA in Cercopithecini. (Doctoral Dissertation). Paris, Muséum national d'histoire naturelle. Retrieved from http://www.theses.fr/2016MNHN0020

Chicago Manual of Style (16^th Edition):

Cacheux, Lauriane. “Diversité et histoire évolutive de l’ADN alpha satellite chez les Cercopithèques : Diversity and evolutionary history of alpha satellite DNA in Cercopithecini.” 2016. Doctoral Dissertation, Paris, Muséum national d'histoire naturelle. Accessed March 01, 2021. http://www.theses.fr/2016MNHN0020.

MLA Handbook (7^th Edition):

Cacheux, Lauriane. “Diversité et histoire évolutive de l’ADN alpha satellite chez les Cercopithèques : Diversity and evolutionary history of alpha satellite DNA in Cercopithecini.” 2016. Web. 01 Mar 2021.

Vancouver:

Cacheux L. Diversité et histoire évolutive de l’ADN alpha satellite chez les Cercopithèques : Diversity and evolutionary history of alpha satellite DNA in Cercopithecini. [Internet] [Doctoral dissertation]. Paris, Muséum national d'histoire naturelle; 2016. [cited 2021 Mar 01]. Available from: http://www.theses.fr/2016MNHN0020.

Council of Science Editors:

Cacheux L. Diversité et histoire évolutive de l’ADN alpha satellite chez les Cercopithèques : Diversity and evolutionary history of alpha satellite DNA in Cercopithecini. [Doctoral Dissertation]. Paris, Muséum national d'histoire naturelle; 2016. Available from: http://www.theses.fr/2016MNHN0020

10. Conflon, Deborah. Evaluation de la capacité du Tomato yellow leaf curl virus à maintenir des ADNs satellites : Assessing the capability of Tomato yellow leaf curl virus to maintain DNA satellites.

Degree: Docteur es, MP - Microbiologie/Parasitologie, 2015, Montpellier, SupAgro

URL: http://www.theses.fr/2015NSAM0037

► Les virus du genre Begomovirus (famille Geminiviridae) sont fréquemment détectés en association avec des ADN satellites appelées alphasatellite et betasatellite qui font la moitié de… (more)

▼ Les virus du genre Begomovirus (famille Geminiviridae) sont fréquemment détectés en association avec des ADN satellites appelées alphasatellite et betasatellite qui font la moitié de la taille du génome viral. L’alphasatellite est autonome pour sa réplication et dépend du virus pour son mouvement et son encapsidation tandis que le betasatellite est dépendant de ces fonctions virales. L’alphasatellite a rarement été montré comme ayant un impact sur le virus assistant, contrairement au betasatellite qui augmente la virulence de son virus assistant. En dehors des bégomovirus tels que le Cotton leaf curl virus (CLCuV) qui ont besoin d’un betasatellite pour initier une infection symptomatique dans leur hôte naturel, la plupart des bégomovirus peuvent causer des symptômes, même sans les satellites avec lesquels ils sont parfois détectés. Le Tomato yellow leaf curl virus (TYLCV), un des virus les plus dommageables dans le monde a rarement été détecté associé à des ADN satellites. Les souches méditerranéennes qui sont aussi les plus invasives, n’ont jamais été détectées avec des ADN satellites, bien qu’elles soient capables en conditions artificielles de les assister avec pour conséquence une considérable augmentation de la virulence en cas de co-inoculation avec un betasatellite. Le risque potentiel d’association de satellites avec le TYLCV-Mld a été évalué en testant divers facteurs potentiellement impliqués dans le maintien de l’association TYLCV-satellite: (i) l'accumulation relative intra-plante du TYLCV et des satellites, (ii) la fréquence de co-infection au niveau cellulaire du TYLCV et des satellites, et (iii) l'efficacité de transmission des satellites par le vecteur Bemisia tabaci. Trois satellites précédemment isolés sur coton au Burkina Faso ont été montrés comme pouvant être assistés par le TYLCV dans des plantes de tomate: Cotton leaf curl Gezira betasatellite (CLCuGB), Cotton leaf curl Gezira alphasatellite (CLCuGA) et Okra leaf curl Burkina Faso alphasatellite (OLCBFA). La quantification par PCR quantitative des ADN du TYLCV et des trois satellites entre 11 et 150 jours après inoculation (dpi) révèle qu’en général, les satellites ont une accumulation supérieure à celle du virus, et que, contrairement aux alphasatellites qui n’ont aucun impact, le betasatellite affecte l’accumulation du TYLCV-Mld. Bien que le rapport des quantités de virus/satellites varie au cours du temps, les satellites sont maintenus avec le TYLCV-Mld au temps tardif de 150 dpi et sont transmis par B. tabaci à 32 et 150 dpi. Le TYLCV-IL interagit différemment avec le CLCuGB car son accumulation n’est pas affectée dans les plantes coinfectées.L’estimation par la technique FISH à 18 et 32 dpi de la fréquence d’association des molécules au niveau cellulaire montre que plus de la moitié des cellules infectées sont coinfectées par le TYLCV et un satellite. Ce résultat est cohérent avec la fréquence observée d’ADN satellite dans les plantes. Cependant, on observe de manière inattendue un nombre important de cellules ne semblant contenir que le… Advisors/Committee Members: Peterschmitt, Michel (thesis director), Urbino, Cica (thesis director), Gentit, Pascal (thesis director).

Subjects/Keywords: Geminivirus; ADN Satellite; PCR quantitative; Fish; Diagnostic; Pseudorecombinaison; Geminivirus; DNA Satellite; Real time PCR; Fish; Diagnostic; Pseudorecombinaison

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Conflon, D. (2015). Evaluation de la capacité du Tomato yellow leaf curl virus à maintenir des ADNs satellites : Assessing the capability of Tomato yellow leaf curl virus to maintain DNA satellites. (Doctoral Dissertation). Montpellier, SupAgro. Retrieved from http://www.theses.fr/2015NSAM0037

Chicago Manual of Style (16^th Edition):

Conflon, Deborah. “Evaluation de la capacité du Tomato yellow leaf curl virus à maintenir des ADNs satellites : Assessing the capability of Tomato yellow leaf curl virus to maintain DNA satellites.” 2015. Doctoral Dissertation, Montpellier, SupAgro. Accessed March 01, 2021. http://www.theses.fr/2015NSAM0037.

MLA Handbook (7^th Edition):

Conflon, Deborah. “Evaluation de la capacité du Tomato yellow leaf curl virus à maintenir des ADNs satellites : Assessing the capability of Tomato yellow leaf curl virus to maintain DNA satellites.” 2015. Web. 01 Mar 2021.

Vancouver:

Conflon D. Evaluation de la capacité du Tomato yellow leaf curl virus à maintenir des ADNs satellites : Assessing the capability of Tomato yellow leaf curl virus to maintain DNA satellites. [Internet] [Doctoral dissertation]. Montpellier, SupAgro; 2015. [cited 2021 Mar 01]. Available from: http://www.theses.fr/2015NSAM0037.

Council of Science Editors:

Conflon D. Evaluation de la capacité du Tomato yellow leaf curl virus à maintenir des ADNs satellites : Assessing the capability of Tomato yellow leaf curl virus to maintain DNA satellites. [Doctoral Dissertation]. Montpellier, SupAgro; 2015. Available from: http://www.theses.fr/2015NSAM0037

University of Oxford

11. Oakey, Rebecca. The structure of alphoid satellite DNA on normal and abnormal human Y chromosomes.

Degree: PhD, 1989, University of Oxford

URL: http://ora.ox.ac.uk/objects/uuid:162cb1a7-3176-4b56-be8b-353b65fee236 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257155

► The long-range structure of the Y chromosome alphoid satellite DNA has been determined in the cell lines 3E7 and OXEN. Variation in alphoid DNA block… (more)

Subjects/Keywords: 572.8; Y chromosome; Abnormalities; Satellite DNA

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APA (6^th Edition):

Oakey, R. (1989). The structure of alphoid satellite DNA on normal and abnormal human Y chromosomes. (Doctoral Dissertation). University of Oxford. Retrieved from http://ora.ox.ac.uk/objects/uuid:162cb1a7-3176-4b56-be8b-353b65fee236 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257155

Chicago Manual of Style (16^th Edition):

Oakey, Rebecca. “The structure of alphoid satellite DNA on normal and abnormal human Y chromosomes.” 1989. Doctoral Dissertation, University of Oxford. Accessed March 01, 2021. http://ora.ox.ac.uk/objects/uuid:162cb1a7-3176-4b56-be8b-353b65fee236 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257155.

MLA Handbook (7^th Edition):

Oakey, Rebecca. “The structure of alphoid satellite DNA on normal and abnormal human Y chromosomes.” 1989. Web. 01 Mar 2021.

Vancouver:

Oakey R. The structure of alphoid satellite DNA on normal and abnormal human Y chromosomes. [Internet] [Doctoral dissertation]. University of Oxford; 1989. [cited 2021 Mar 01]. Available from: http://ora.ox.ac.uk/objects/uuid:162cb1a7-3176-4b56-be8b-353b65fee236 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257155.

Council of Science Editors:

Oakey R. The structure of alphoid satellite DNA on normal and abnormal human Y chromosomes. [Doctoral Dissertation]. University of Oxford; 1989. Available from: http://ora.ox.ac.uk/objects/uuid:162cb1a7-3176-4b56-be8b-353b65fee236 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257155

University of Washington

12. Kasinathan, Sivakanthan. Characterization and analysis of repetitive centromeres.

Degree: PhD, 2018, University of Washington

URL: http://hdl.handle.net/1773/40937

► Centromeres are specialized regions of eukaryotic chromosomes that ensure faithful transmission of genetic information at each cell division. The molecular architecture of centromeres is defined… (more)

▼ Centromeres are specialized regions of eukaryotic chromosomes that ensure faithful transmission of genetic information at each cell division. The molecular architecture of centromeres is defined by evolutionarily dynamic protein and DNA components, which have been proposed to contribute to the origin of new species, while defects in centromeres have been linked to human disease. Centromeres are embedded in regions composed of large arrays of head-to-tail 'satellite' DNA elements, which are not amenable to many conventional genomic analyses. Here, I describe the development of methods for the analysis of repetitive genomic regions and apply these tools to study primate centromeres, which are composed of ~170-bp alpha-satellite units. Although centromeric DNA is known to be polymorphic in humans, comprehensive cataloguing of variants at centromeres has not been possible. To gain insight into centromeric genetic variation, I developed a method that uses single-molecule sequencing for analyzing characteristic sequence periodicities called higher-order repeats that arise in human centromeres. The application of this approach to catalogue inter-individual, population-scale, and disease-associated structural variation identified extensive polymorphism in centromeres associated with binding sites for CENP-B, a sequence-specific DNA binding protein. This work also defined a set of functionally important alpha-satellite dimeric units that are underrepresented in current centromere models and demonstrated aberrations in centromeric sequence in breast cancer. I suggest a role for CENP-B in the evolution and maintenance of higher-order periodicities in centromeric arrays. Although alpha-satellite is present at the centromeres of most primates, the precise mechanisms of evolution of centromeric DNA and the contribution of genetic sequence to the specification of centromere identity remain unresolved. I examined centromere evolution in primates using a combination of data from different whole-genome sequencing methods. This approach demonstrated the presence of higher-order periodicities in all primates and identified an important role for CENP-B in shaping centromeric repeat organization. Further analysis of alpha-satellite uncovered interspecific variation in the presence of short inverted repeats, which may form hairpin and stem-loop structures. Based on these data, I propose a genetic mechanism for centromere specification that depends on the formation of cruciform or other non-B-form nucleic acid structures. Taken together, this work enables the cataloguing of variation in satellite DNA, defines important evolutionary transitions in primate centromeres, and advances a model for primate centromere evolution and a theory for centromere specification. Advisors/Committee Members: Henikoff, Steven (advisor).

Subjects/Keywords: CENP-A; CENP-B; Centromere; DNA; Satellite; Molecular biology; Genetics; Molecular and cellular biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kasinathan, S. (2018). Characterization and analysis of repetitive centromeres. (Doctoral Dissertation). University of Washington. Retrieved from http://hdl.handle.net/1773/40937

Chicago Manual of Style (16^th Edition):

Kasinathan, Sivakanthan. “Characterization and analysis of repetitive centromeres.” 2018. Doctoral Dissertation, University of Washington. Accessed March 01, 2021. http://hdl.handle.net/1773/40937.

MLA Handbook (7^th Edition):

Kasinathan, Sivakanthan. “Characterization and analysis of repetitive centromeres.” 2018. Web. 01 Mar 2021.

Vancouver:

Kasinathan S. Characterization and analysis of repetitive centromeres. [Internet] [Doctoral dissertation]. University of Washington; 2018. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1773/40937.

Council of Science Editors:

Kasinathan S. Characterization and analysis of repetitive centromeres. [Doctoral Dissertation]. University of Washington; 2018. Available from: http://hdl.handle.net/1773/40937

13. Martins, Camila Augusta de Oliveira. Seqüências ORESTES (open reading frame expressed sequence tags) de trypanosoma cruzi e transcrição de DNA satélite.

Degree: PhD, Bioquímica, 2008, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/46/46131/tde-19052008-135857/ ;

► Nos bancos de dados de T. cruzi há cerca de 3.750 ESTs de amastigotas e tripomastigotas, seqüenciadas a partir das extremidades 5óu 3d́e clones de… (more)

▼ Nos bancos de dados de T. cruzi há cerca de 3.750 ESTs de amastigotas e tripomastigotas, seqüenciadas a partir das extremidades 5óu 3d́e clones de cDNA. A metodologia ORESTES (Open Reading Frame Expressed Sequence Tags) possibilita obter seqüências transcritas parciais derivadas majoritariamente da porção central dos mRNAs, favorecendo a descoberta de novos genes. Neste trabalho, caracterizamos ORESTES de formas infectantes amastigotas e tripomastigotas da cepa humana VL10 (ATVL). A metodologia foi padronizada com formas epimastigotas da cepa CL Brener (ECL), monitorando-se nas preparações de mRNA a contaminação por DNA e a integridade dos transcritos. Populações de cDNA foram obtidas utilizando-se diferentes iniciadores aleatórios. O mesmo iniciador foi empregado nas etapas de RT e PCR, realizada em condições de baixa estringência. Obtivemos 776 e 1522 ORESTES de ECL e ATVL, respectivamente. Após análise com o programa PHRED, aceitaram-se 745 ORESTES de ECL e 1476 de ATVL. As ORESTES apresentaram um tamanho médio de 680 pb e um conteúdo de G+C de 53%. O agrupamento com CAP3 gerou 463 agrupamentos de ECL (360 singletons e 103 contigs) e 454 de ATVL (337 singletons e 117 contigs). A anotação foi feita utilizando-se o programa BLAST contra o banco nr do NCBI. Na biblioteca de ATVL observamos um número elevado de seqüências de RNA ribossômico (27%), amplificadas preferencialmente por dois iniciadores. Para ECL, a contaminação por rRNA foi de 3,6%. Para cerca de 50% das ORESTES de ATVL (n= 729) foi encontrada similaridade em bancos de dados de proteínas. Destas, 316 apresentaram similaridade com proteínas putativas conhecidas e 413 foram anotadas como proteínas hipotéticas e hipotéticas conservadas. Para 87 ORESTES de ATVL (5,9%) não foi observada nenhuma similaridade. 628 ORESTES de ECL (84%) apresentaram similaridade com proteínas depositadas em bancos públicos, ao passo que nenhuma similaridade foi encontrada para 18 cDNAs (2,4%). Ensaios de Southern blot confirmaram a presença de 4 ORESTES no match analisadas nos genomas das duas cepas. Não puderam ser atribuídas a processos biológicos conhecidos 39% e 68% das seqüências dos contigs de ECL e ATVL, respectivamente. Nos processos de Proteólise e Peptidólise, estão incluídas 11% das ORESTES de ECL e 0,3% das ORESTES de ATVL. Outras diferenças funcionais putativas foram observadas. A abundância diferencial dos transcritos de algumas ORESTES foi analisada por northern blot nos estágios evolutivos das cepas. Southern blot do contig ATVL95 originou um padrão de hibridização com múltiplas bandas, característico de seqüências repetitivas. Este contig corresponde ao transcrito do DNA satélite de 195 pb (195 SAT), uma seqüência repetitiva que perfaz cerca de 10% do genoma de T. cruzi e cuja transcrição é controversa na literatura. A transcrição do 195 SAT foi comprovada por experimentos de + northern blot e por RT-PCR. Transcritos de 195 SAT foram detectados nas frações… Advisors/Committee Members: Zingales, Bianca Silvana.

Subjects/Keywords: Amastigota; Amastigote; DNA satélite; ORESTES; ORESTES; Satellite DNA; Transcrição; Transcription; Tripomastigota; Trypanosoma cruzi; Trypanosoma cruzi; Trypomastigote

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Martins, C. A. d. O. (2008). Seqüências ORESTES (open reading frame expressed sequence tags) de trypanosoma cruzi e transcrição de DNA satélite. (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/46/46131/tde-19052008-135857/ ;

Chicago Manual of Style (16^th Edition):

Martins, Camila Augusta de Oliveira. “Seqüências ORESTES (open reading frame expressed sequence tags) de trypanosoma cruzi e transcrição de DNA satélite.” 2008. Doctoral Dissertation, University of São Paulo. Accessed March 01, 2021. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-19052008-135857/ ;.

MLA Handbook (7^th Edition):

Martins, Camila Augusta de Oliveira. “Seqüências ORESTES (open reading frame expressed sequence tags) de trypanosoma cruzi e transcrição de DNA satélite.” 2008. Web. 01 Mar 2021.

Vancouver:

Martins CAdO. Seqüências ORESTES (open reading frame expressed sequence tags) de trypanosoma cruzi e transcrição de DNA satélite. [Internet] [Doctoral dissertation]. University of São Paulo; 2008. [cited 2021 Mar 01]. Available from: http://www.teses.usp.br/teses/disponiveis/46/46131/tde-19052008-135857/ ;.

Council of Science Editors:

Martins CAdO. Seqüências ORESTES (open reading frame expressed sequence tags) de trypanosoma cruzi e transcrição de DNA satélite. [Doctoral Dissertation]. University of São Paulo; 2008. Available from: http://www.teses.usp.br/teses/disponiveis/46/46131/tde-19052008-135857/ ;

Universidade Estadual de Campinas

14. Gatto, Kaleb Pretto, 1987-. Comparative molecular cytogenetics of genus Pseudis (Anura, Hylidae) and genomic analysis of the sex chromosomes of Pseudis tocantins : Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins: Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins.

Degree: 2018, Universidade Estadual de Campinas

URL: http://repositorio.unicamp.br/jspui/handle/REPOSIP/351342

► Abstract: Several studies using mainly mammals and birds have added valuable information on sex chromosome evolution. However, there are only a few works with sex… (more)

▼ Abstract: Several studies using mainly mammals and birds have added valuable information on sex chromosome evolution. However, there are only a few works with sex chromosomes of amphibians, which is a group with different levels of sex chromosome heteromorphism. Pseudis tocantins, an anuran species with female heterogamety (ZZ/ZW), has highly heteromorphic sex chromosomes, with the submetacentric W chromosome being larger than the metacentric Z chromosome. Size difference occurs due to amplification of the interstitial heterochromatin in Wq, which shows accumulation of PcP190 satellite DNA. Pseudis tocantins sex chromosomes also differs in NOR position, with the NOR being interstitial in Zq and pericentromeric in Wq. Based on morphology and NOR location, the chromosomes of pair 7 of other Pseudis species (pair 5 in P. cardosoi) are inferred as homeologues of the sex chromosomes of P. tocantins. However, additional evidence that corroborate with this homeology hypothesis is missing. Furthermore, there are no information about the sex determination system in the other Pseudis species. Therefore, the goal of this study was to analyze the sex chromosome differentiation in Pseudis by investigating the presence of the PcP190 satellite DNA and sex chromosome heteromorphism in P. bolbodactyla, P. cardosoi, P. fusca, P. minuta, P. paradoxa and Pseudis sp. (aff. fusca) in the light of the phylogenetic relationships previously inferred for these species. We also used next-generation sequencing of male and female genomes and microdissected samples of Z and W chromosomes to investigate the molecular composition of the sex chromosomes of P. tocantins. The PcP190 satellite DNA was mapped to the NOR-bearing chromosomes of P. bolbodactyla, P. cardosoi, P. fusca, P. minuta, P. paradoxa and Pseudis sp., corroborating the hypothesis of homeology of these chromosomes with the sex chromosomes of P. tocantins. In P. bolbodactyla and Pseudis sp. there are signals of PcP190 hybridization only in females. Comparative genomic hybridization confirmed that the chromosome that bears the NOR and PCP190 site is the W chromosome in P. bolbodactyla and Pseudis sp. By plotting the cytogenetic data in a species tree three chromosome inversions could be inferred: (a) a paracentric inversion in the common ancestor of P. bolbodactyla + P. fusca + P. paradoxa + Pseudis sp. + P. tocantins, which moved the NORs from a distal region (character state observed in P. cardosoi, P. minuta and almost all Lysapsus species) to a region closer to the centromere; (b) a pericentric inversion in the common ancestor of P. fusca + Pseudis sp. + P. tocantins, that moved the PcP190 site from the short arm (condition observed in P. bolbodactyla, P. cardosoi, P. minuta and P. paradoxa) to the long arm; and (c) a paracentric inversion in the W chromosome of P. tocantins. The paracentric inversion in the W chromosome of P. tocantins could have favored heterochromatin amplification in the long arm of this chromosome, since it may have enlarged the non-recombining region between Z… Advisors/Committee Members: UNIVERSIDADE ESTADUAL DE CAMPINAS (CRUESP), Lourenço, Luciana Bolsoni, 1972- (advisor), Universidade Estadual de Campinas. Instituto de Biologia (institution), Programa de Pós-Graduação em Biologia Celular e Estrutural (nameofprogram), Foresti, Fausto (committee member), Ventura, Karen (committee member), Brasileiro, Cinthia Aguirre (committee member), Lyra, Mariana Lúcio (committee member).

Subjects/Keywords: Cromossomos sexuais; DNA satélite; Microdissecação; Hylidae; Sequenciamento de nova geração; Sex chromosomes; DNA, Satellite; Microdissection; Hylidae; Next-generation sequence

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gatto, Kaleb Pretto, 1. (2018). Comparative molecular cytogenetics of genus Pseudis (Anura, Hylidae) and genomic analysis of the sex chromosomes of Pseudis tocantins : Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins: Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins. (Thesis). Universidade Estadual de Campinas. Retrieved from http://repositorio.unicamp.br/jspui/handle/REPOSIP/351342

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Gatto, Kaleb Pretto, 1987-. “Comparative molecular cytogenetics of genus Pseudis (Anura, Hylidae) and genomic analysis of the sex chromosomes of Pseudis tocantins : Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins: Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins.” 2018. Thesis, Universidade Estadual de Campinas. Accessed March 01, 2021. http://repositorio.unicamp.br/jspui/handle/REPOSIP/351342.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Gatto, Kaleb Pretto, 1987-. “Comparative molecular cytogenetics of genus Pseudis (Anura, Hylidae) and genomic analysis of the sex chromosomes of Pseudis tocantins : Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins: Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins.” 2018. Web. 01 Mar 2021.

Vancouver:

Gatto, Kaleb Pretto 1. Comparative molecular cytogenetics of genus Pseudis (Anura, Hylidae) and genomic analysis of the sex chromosomes of Pseudis tocantins : Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins: Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins. [Internet] [Thesis]. Universidade Estadual de Campinas; 2018. [cited 2021 Mar 01]. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/351342.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Gatto, Kaleb Pretto 1. Comparative molecular cytogenetics of genus Pseudis (Anura, Hylidae) and genomic analysis of the sex chromosomes of Pseudis tocantins : Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins: Citogenética molecular comparativa do gênero Pseudis (Anura, Hylidae) e análise genômica dos cromossomos sexuais de Pseudis tocantins. [Thesis]. Universidade Estadual de Campinas; 2018. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/351342

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

15. SANTOS, Tiago Ribeiro Barros dos. Os cromossomos holocêntricos de rhynchospora vahl (cyperaceae): Evolução cariotípica e diversidade de sequências satélites .

Degree: 2016, Universidade Federal de Pernambuco

URL: https://repositorio.ufpe.br/handle/123456789/17678

► Cromossomos holocêntricos apresentam atividade cinetocórica difusa e essa organização favorece, em teoria, rápidas variações cromossômicas numéricas e o acúmulo de DNA satélite (DNAsat) predominantemente nas… (more)

▼ Cromossomos holocêntricos apresentam atividade cinetocórica difusa e essa organização favorece, em teoria, rápidas variações cromossômicas numéricas e o acúmulo de DNA satélite (DNAsat) predominantemente nas regiões terminais dos cromossomos. O gênero de plantas Rhynchospora (Cyperaceae), um dos diversos grupos com esse tipo cromossômico, apresenta espécies com cariótipos entre 2n = 4 e 2n = 58, cuja variação é atribuída à poliploidia e a eventos de quebra/fusão, levando a disploidias. Quanto à distribuição de DNAsat, o único relato até o momento revelou uma baixa proporção dessas sequências, com o único repeat identificado (Tyba) associado aos holocentrômeros. Com o intuito de entender como a estrutura centromérica difusa interfere na organização de sequências ao longo do cromossomo e na evolução do cariótipo como um todo, foram realizadas uma análise de reconstrução dos números cromossômicos ancestrais de Rhynchospora em um contexto filogenético e a caracterização de DNAsats em três espécies do gênero. O complemento cromossômico 2n = 10 foi indicado como o mais provável para o ancestral do gênero, tendo sido mantido em diferentes taxa. A maioria dos clados mostrou números estáveis e a homoplasia de cariótipos foi observada em uma frequência relativamente baixa. Os genomas de R. ciliata/R. globosa e R. tenuis apresentaram duas e uma família(s) de DNAsat, respectivamente, com um padrão de condensação típico (blocos condensados em intérfase). Uma localização preferencial nos terminais cromossômicos foi observada apenas para os DNAsat de R. globosa. Três tipos de cromatina foram revelados pela distribuição dessas sequências: (1) associadas à heterocromatina e presente na forma de cromocentros em intérfase e blocos nos cromossomos metafásicos (R. ciliata e R. globosa); (2) compactados em interfase mas parcialmente descondensados em metáfase e não diretamente associados à heterocromatina (R. ciliata e R. tenuis); ou (3) associados aos holocentrômeros (R. ciliata e R. tenuis). De forma geral em Rhynchospora, os eventos de fusão e fissão parecem atuar localmente no remodelamento dos cariótipos e as sequências satélites não mostram uma tendência única de distribuição. A estrutura centromérica difusa, portanto, não determina em larga escala a dinâmica evolutiva dos cromossomos do gênero. Advisors/Committee Members: PEDROSA-HARAND, Andrea (advisor), VANZELA, André L. L (advisor).

Subjects/Keywords: conteúdo de DNA, cromossomos holocêntricos, disploidia, DNA ribossomal, DNA satélite, fissão, fusão, poliploidia, reconstrução de número cromossômico; DNA C-value, dysploidy, polyploidy, chromosome number reconstruction, holocentric chromosomes, fusion, fission, ribosomal DNA, satellite DNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

SANTOS, T. R. B. d. (2016). Os cromossomos holocêntricos de rhynchospora vahl (cyperaceae): Evolução cariotípica e diversidade de sequências satélites . (Thesis). Universidade Federal de Pernambuco. Retrieved from https://repositorio.ufpe.br/handle/123456789/17678

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

SANTOS, Tiago Ribeiro Barros dos. “Os cromossomos holocêntricos de rhynchospora vahl (cyperaceae): Evolução cariotípica e diversidade de sequências satélites .” 2016. Thesis, Universidade Federal de Pernambuco. Accessed March 01, 2021. https://repositorio.ufpe.br/handle/123456789/17678.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

SANTOS, Tiago Ribeiro Barros dos. “Os cromossomos holocêntricos de rhynchospora vahl (cyperaceae): Evolução cariotípica e diversidade de sequências satélites .” 2016. Web. 01 Mar 2021.

Vancouver:

SANTOS TRBd. Os cromossomos holocêntricos de rhynchospora vahl (cyperaceae): Evolução cariotípica e diversidade de sequências satélites . [Internet] [Thesis]. Universidade Federal de Pernambuco; 2016. [cited 2021 Mar 01]. Available from: https://repositorio.ufpe.br/handle/123456789/17678.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

SANTOS TRBd. Os cromossomos holocêntricos de rhynchospora vahl (cyperaceae): Evolução cariotípica e diversidade de sequências satélites . [Thesis]. Universidade Federal de Pernambuco; 2016. Available from: https://repositorio.ufpe.br/handle/123456789/17678

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Adelaide

16. Eini Gandomani, Omid. Regulation and functional analysis of a geminiviral DNA β satellite encoded gene.

Degree: 2008, University of Adelaide

URL: http://hdl.handle.net/2440/55293

► Geminiviruses (family Geminiviridae) are characterized structurally by twinned (geminate) morphology of virions (ca. 18-30 nm) and genetically by a genome comprising one or two small… (more)

▼ Geminiviruses (family Geminiviridae) are characterized structurally by twinned (geminate) morphology of virions (ca. 18-30 nm) and genetically by a genome comprising one or two small circular single stranded DNA (ssDNA) molecules and they are responsible for major crop losses worldwide. The genus Begomovirus (type member Bean golden yellow mosaic virus) is the largest genus of the family Geminiviridae. The members of this genus have either monopartite or bipartite genomes. They are transmitted by whiteflies and infect only dicotyledonous plants. DNA β molecules are symptom modulating single-stranded sat-DNA molecules which are associated with certain monopartite begomoviruses. These molecules are around half the size (approximately 1350 nt in length) of their helper viruses and rely on the helper begomovirus for movement in plant tissues, replication and plant-to-plant transmission by the whitefly (Bemisia tabaci). They contribute to production of symptoms and enhance helper virus accumulation in certain hosts. DNA β molecules encode a single gene, called βC1, on the complementary strand which is important for pathogenicity and suppression of post transcriptional gene silencing. In this study the regulation of βC1 gene expression, a host factor interacting with βC1 and its role in the pathogenicity of DNA β are described. Transient expression studies using Nicotiana tabacum plants and GUS as a reporter gene, identified the sequences important for transcription of βC1 from DNA β associated with Cotton leaf curl Multan virus (CLCuMV). A 68 nt fragment (between -139 to -207), which contains a G-box motif was sufficient for DNA β promoter activity. Deletion of this region also led to loss of DNA β replication capacity. Mutation of the G-box, located at 143 nucleotides upstream of the βC1 start codon, resulted in a two to three times reduction in the DNA β promoter activity. This motif was shown to bind specifically to the nuclear factors isolated from tobacco leaf tissues. Histochemical staining of transgenic tobacco plants expressing the gus gene driven by full length DNA β promoter showed phloem specific localisation patterns. It was concluded that a G-box motif is required for binding of host nuclear factors and is necessary for efficient expression of this phloem specific βC1 gene. An ubiquitin-conjugating enzyme, called SlUBC, was retrieved from screening of a tomato cDNA library, using βC1 encoded by DNA β associated with CLCuMV as the bait. The SlUBC was shown to complement yeast deficient in the ubiquitin-conjugating enzyme. It is thought that this enzyme is a key factor in the ubiquitin proteasome pathway, which plays a central role in many eukaryotic cellular processes. The authenticity and specificity of this interaction was confirmed both in vivo, using a bimolecular fluorescence complementation assay, and in vitro. Domain mapping of βC1 showed that a myristoylation-like motif is required for the interaction with SlUBC in the yeast system and induction of DNA β specific symptoms in host plants. Western… Advisors/Committee Members: Randles, John Wesley (advisor), School of Agriculture, Food and Wine : Plant and Food Science (school).

Subjects/Keywords: plant virus; geminivirus; satellite DNA; promoter; protein-protein interaction

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Eini Gandomani, O. (2008). Regulation and functional analysis of a geminiviral DNA β satellite encoded gene. (Thesis). University of Adelaide. Retrieved from http://hdl.handle.net/2440/55293

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Eini Gandomani, Omid. “Regulation and functional analysis of a geminiviral DNA β satellite encoded gene.” 2008. Thesis, University of Adelaide. Accessed March 01, 2021. http://hdl.handle.net/2440/55293.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Eini Gandomani, Omid. “Regulation and functional analysis of a geminiviral DNA β satellite encoded gene.” 2008. Web. 01 Mar 2021.

Vancouver:

Eini Gandomani O. Regulation and functional analysis of a geminiviral DNA β satellite encoded gene. [Internet] [Thesis]. University of Adelaide; 2008. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2440/55293.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Eini Gandomani O. Regulation and functional analysis of a geminiviral DNA β satellite encoded gene. [Thesis]. University of Adelaide; 2008. Available from: http://hdl.handle.net/2440/55293

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Florida

17. Venkatakrishnan, Balasubramania. Endosomal pH Mediated Structural Transitions in Adeno- Associated Viruses.

Degree: PhD, Medical Sciences - Biochemistry and Molecular Biology (IDP), 2012, University of Florida

URL: https://ufdc.ufl.edu/UFE0043993

► Adeno-Associated Viruses (AAVs) are single stranded DNA viruses that belong to the Parvoviridae family. The AAV infective pathway involves the binding of the virus to… (more)

Subjects/Keywords: Capsid; Crystal structure; DNA; Endosomes; Parvovirus; pH; Satellite viruses; Signals; Viral morphology; Viruses; aav – endosome – infection – ph

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Venkatakrishnan, B. (2012). Endosomal pH Mediated Structural Transitions in Adeno- Associated Viruses. (Doctoral Dissertation). University of Florida. Retrieved from https://ufdc.ufl.edu/UFE0043993

Chicago Manual of Style (16^th Edition):

Venkatakrishnan, Balasubramania. “Endosomal pH Mediated Structural Transitions in Adeno- Associated Viruses.” 2012. Doctoral Dissertation, University of Florida. Accessed March 01, 2021. https://ufdc.ufl.edu/UFE0043993.

MLA Handbook (7^th Edition):

Venkatakrishnan, Balasubramania. “Endosomal pH Mediated Structural Transitions in Adeno- Associated Viruses.” 2012. Web. 01 Mar 2021.

Vancouver:

Venkatakrishnan B. Endosomal pH Mediated Structural Transitions in Adeno- Associated Viruses. [Internet] [Doctoral dissertation]. University of Florida; 2012. [cited 2021 Mar 01]. Available from: https://ufdc.ufl.edu/UFE0043993.

Council of Science Editors:

Venkatakrishnan B. Endosomal pH Mediated Structural Transitions in Adeno- Associated Viruses. [Doctoral Dissertation]. University of Florida; 2012. Available from: https://ufdc.ufl.edu/UFE0043993

Queensland University of Technology

18. Tsao, Theresa Tsun-Hui. Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.

Degree: 2008, Queensland University of Technology

URL: https://eprints.qut.edu.au/17031/

► Banana bunchy top virus (BBTV) causes one of the most devastating diseases of banana. Transgenic virus resistance is now considered one of the most promising… (more)

▼ Banana bunchy top virus (BBTV) causes one of the most devastating diseases of banana. Transgenic virus resistance is now considered one of the most promising strategies to control BBTV. Pathogen-derived resistance (PDR) strategies have been applied successfully to generate plants that are resistant to numerous different viruses, primarily against those viruses with RNA genomes. BBTV is a circular, single-stranded (css) DNA virus of the family Nanoviridae, which is closely related to the family Geminiviridae. Although there are some successful examples of PDR against geminiviruses, PDR against the nanoviruses has not been reported. Therefore, the aim of this thesis was to investigate the potential of BBTV genes to interfere with virus replication when used as transgenes for engineering banana plants resistance to BBTV. The replication initiation protein (Rep) of nanoviruses is the only viral protein essential for viral replication and represents an ideal target for PDR. Therefore, this thesis focused on the effect of wild-type or mutated Rep genes from BBTV satellite DNAs or the BBTV integral genome on the replication of BBTV in banana embryogenic cell suspensions. A new Rep-encoding satellite DNA, designated BBTV DNA-S4, was isolated from a Vietnamese BBTV isolate and characterised. When the effect of DNA-S4 on the replication of BBTV was examined, it was found that DNA-S4 enhanced the replication of BBTV. When the replicative capabilities of DNA-S4 and the previously characterised Rep-encoding BBTV satellite, DNA-S1, were compared, it was found that the amount of DNA-S4 accumulated to higher levels than DNA-S1. The interaction between BBTV and DNA-S1 was also examined. It was found that over-expression of the Rep encoded by DNA-S1 using ubi1 maize polyubiquitin promoter enhanced replication of BBTV. However, when the Rep-encoded by DNA-S1 was expressed by the native S1 promoter (in plasmid pBT1.1-S1), it suppressed the replication of BBTV. Based on this result, the use of DNA-S1 as a possible transgene to generate PDR against BBTV was investigated. The roles of the Rep-encoding and U5 genes of BBTV DNA-R, and the effects of over-expression of these two genes on BBTV replication were also investigated. Three mutants of BBTV DNA-R were constructed; plasmid pUbi-RepOnly-nos contained the ubi1 promoter driving Rep expression from DNA-R, plasmid pUbi-IntOnly-nos contained the ubi1 promoter driving expression of the DNA-R internal gene product (U5), while plasmid pUbi-R.ORF-nos contained the ubi1 promoter driving the expression of both Rep and the internal U5 gene product. The replication of BBTV was found to be significantly suppressed by pUbi-RepOnly-nos, weakly suppressed by pUbi-IntOnly-nos, but strongly enhanced by pUbi-R.ORF-nos. The effect of mutations in three conserved residues within the BBTV Rep on BBTV replication was also assessed. These mutations were all made in the regions in the ATPase motifs and resulted in changes from hydrophilic to hydrophobic residues (i.e. K187→M, D224→I and N268→L). None of…

Subjects/Keywords: banana bunchy top virus; nanoviruses; replication initiation protein (Rep); pathogen-derived resistance; BBTV DNA-R; BBTV DNA-S1; BBTV DNA-S3; BBTV DNA-S4; satellite DNA; ATPase; post-transcriptional gene silencing; RNA silencing suppressor

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Tsao, T. T. (2008). Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. (Thesis). Queensland University of Technology. Retrieved from https://eprints.qut.edu.au/17031/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Tsao, Theresa Tsun-Hui. “Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.” 2008. Thesis, Queensland University of Technology. Accessed March 01, 2021. https://eprints.qut.edu.au/17031/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Tsao, Theresa Tsun-Hui. “Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.” 2008. Web. 01 Mar 2021.

Vancouver:

Tsao TT. Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. [Internet] [Thesis]. Queensland University of Technology; 2008. [cited 2021 Mar 01]. Available from: https://eprints.qut.edu.au/17031/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tsao TT. Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. [Thesis]. Queensland University of Technology; 2008. Available from: https://eprints.qut.edu.au/17031/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Texas A&M University

19. Moyer, Susan Pavlosky. Isolation and characterization of a highly repeated satellite DNA sequence from the cyprinid fish Notropis lutrensis.

Degree: MS, genetics, 2012, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-1986-THESIS-M938

Subjects/Keywords: genetics.; Major genetics.; DNA replication.; Satellite DNA.; Red shiner - Genetics.

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Moyer, S. P. (2012). Isolation and characterization of a highly repeated satellite DNA sequence from the cyprinid fish Notropis lutrensis. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-1986-THESIS-M938

Chicago Manual of Style (16^th Edition):

Moyer, Susan Pavlosky. “Isolation and characterization of a highly repeated satellite DNA sequence from the cyprinid fish Notropis lutrensis.” 2012. Masters Thesis, Texas A&M University. Accessed March 01, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-1986-THESIS-M938.

MLA Handbook (7^th Edition):

Moyer, Susan Pavlosky. “Isolation and characterization of a highly repeated satellite DNA sequence from the cyprinid fish Notropis lutrensis.” 2012. Web. 01 Mar 2021.

Vancouver:

Moyer SP. Isolation and characterization of a highly repeated satellite DNA sequence from the cyprinid fish Notropis lutrensis. [Internet] [Masters thesis]. Texas A&M University; 2012. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1986-THESIS-M938.

Council of Science Editors:

Moyer SP. Isolation and characterization of a highly repeated satellite DNA sequence from the cyprinid fish Notropis lutrensis. [Masters Thesis]. Texas A&M University; 2012. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1986-THESIS-M938

Brno University of Technology

20. Jenčo, Michal. Bioinformatický nástroj pro anotaci transposonů: Bioinformatics Tool for Transposons Annotation.

Degree: 2019, Brno University of Technology

URL: http://hdl.handle.net/11012/69517

► This thesis provides theoretical resources for the design of a new bioinformatics tool for transposon annotation with focus on their additional structural elements. There is… (more)

Subjects/Keywords: transpozóny; satelitná DNA; bioinformatika; anotácia; extra ORF; tandemové repetície; LTR retrotranspozóny; transposons; satellite DNA; bioinformatics; annotation; extra ORF; tandem repeats; LTR retrotransposons

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Jenčo, M. (2019). Bioinformatický nástroj pro anotaci transposonů: Bioinformatics Tool for Transposons Annotation. (Thesis). Brno University of Technology. Retrieved from http://hdl.handle.net/11012/69517

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Jenčo, Michal. “Bioinformatický nástroj pro anotaci transposonů: Bioinformatics Tool for Transposons Annotation.” 2019. Thesis, Brno University of Technology. Accessed March 01, 2021. http://hdl.handle.net/11012/69517.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Jenčo, Michal. “Bioinformatický nástroj pro anotaci transposonů: Bioinformatics Tool for Transposons Annotation.” 2019. Web. 01 Mar 2021.

Vancouver:

Jenčo M. Bioinformatický nástroj pro anotaci transposonů: Bioinformatics Tool for Transposons Annotation. [Internet] [Thesis]. Brno University of Technology; 2019. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/11012/69517.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Jenčo M. Bioinformatický nástroj pro anotaci transposonů: Bioinformatics Tool for Transposons Annotation. [Thesis]. Brno University of Technology; 2019. Available from: http://hdl.handle.net/11012/69517

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

21. Figueiredo, Luís Gustavo Girardi. Efeito da proporção de DNA de origem Bos taurus em características ligadas a precocidade sexual e de acabamento na raça Nelore.

Degree: PhD, Qualidade e Produtividade Animal, 2005, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/74/74131/tde-30112007-142217/ ;

►

O presente trabalho teve como objetivos estimar os efeitos da inclusão de linha materna e do DNA mitocondrial (mtDNA) nos modelos de avaliação genética, avaliar… (more)

▼

O presente trabalho teve como objetivos estimar os efeitos da inclusão de linha materna e do DNA mitocondrial (mtDNA) nos modelos de avaliação genética, avaliar o efeito do DNA satélite em características de desenvolvimento ponderal, bem como estimar parâmetros genéticos para características de carcaça e idade ao primeiro parto. Análises do mtDNA foram realizadas a partir de sangue coletado de 457 animais da raça Nelore, linhagem Lemgruber. Para as características de desenvolvimento ponderal foram analisados 14.432 registros de produção relacionados com 16.561 animais no pedigree. Para característica reprodutiva e as de carcaça foram analisados 4.621 registros de idade ao primeiro parto e 951 registros de área de olho de lombo e espessura de gordura subcutânea, relacionados com 7.135 registros de pedigree. As estimativas dos efeitos de linha materna e DNA mitocondrial foram analisadas sob 5 modelos diferentes. Os componentes de (co)variância para idade ao primeiro parto e características carcaça foram estimados em análises uni e bicaracterísticas. Não foram encontrados efeitos significativos de linhagem materna ou de DNA mitocondrial sobre as características de produção. Entretanto, foi verificado que animais com mitocôndria de origem Bos taurus, apresentam uma pequena superioridade na média de seus valores genéticos para as características de desenvolvimento ponderal. Animais com padrão de DNA satélite B tiveram suas médias ligeiramente superiores aos outros padrões. Os efeitos da precocidade de acabamento sobre a precocidade sexual devem ser avaliados utilizando-se estruturas de dados mais adequadas.

The aim of this research was to estimate the effect of the maternal lineage and mitochondrial DNA inclusion in the genetic evaluation model for growth traits, to evaluate the satellite DNA effect in these traits and to estimate genetic parameters for carcass traits and age at first calving. Blood samples were collected to mtDNA analysis from 457 Nellore cattle. Growth traits were analyzed from 14,432 production data and 16,561 pedigree data. Reproductive and carcass traits were analyzed from 4,621 age at first calving data and 951 loin-eye area and subcutaneous fat thickness data related to 7,135 pedigree data. Maternal lineage and mitochondrial DNA estimative were analyzed under 5 different models, (co)variance components for age at first calving and carcass traits were estimated in single and multiple-trait. There were no significant effects of maternal lineage or mitochondrial DNA related to production traits, but animals harboring Bos taurus mtDNA showed a low superiority on breeding values average for growth traits and animals harboring satellite DNA B pattern also showed a low superiority related to the other patterns. Further studies are suggested to evaluate the backfat thickness precocity effect related to sexual precocity.

Advisors/Committee Members: Eler, Joanir Pereira.

Subjects/Keywords: Beef cattle; Bovino de corte; DNA mitocondrial; DNA satélite; Linha materna; Maternal lineage; Mitochondrial DNA; Nellore breed; Raça Nelore; Satellite DNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Figueiredo, L. G. G. (2005). Efeito da proporção de DNA de origem Bos taurus em características ligadas a precocidade sexual e de acabamento na raça Nelore. (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/74/74131/tde-30112007-142217/ ;

Chicago Manual of Style (16^th Edition):

Figueiredo, Luís Gustavo Girardi. “Efeito da proporção de DNA de origem Bos taurus em características ligadas a precocidade sexual e de acabamento na raça Nelore.” 2005. Doctoral Dissertation, University of São Paulo. Accessed March 01, 2021. http://www.teses.usp.br/teses/disponiveis/74/74131/tde-30112007-142217/ ;.

MLA Handbook (7^th Edition):

Figueiredo, Luís Gustavo Girardi. “Efeito da proporção de DNA de origem Bos taurus em características ligadas a precocidade sexual e de acabamento na raça Nelore.” 2005. Web. 01 Mar 2021.

Vancouver:

Figueiredo LGG. Efeito da proporção de DNA de origem Bos taurus em características ligadas a precocidade sexual e de acabamento na raça Nelore. [Internet] [Doctoral dissertation]. University of São Paulo; 2005. [cited 2021 Mar 01]. Available from: http://www.teses.usp.br/teses/disponiveis/74/74131/tde-30112007-142217/ ;.

Council of Science Editors:

Figueiredo LGG. Efeito da proporção de DNA de origem Bos taurus em características ligadas a precocidade sexual e de acabamento na raça Nelore. [Doctoral Dissertation]. University of São Paulo; 2005. Available from: http://www.teses.usp.br/teses/disponiveis/74/74131/tde-30112007-142217/ ;

Brno University of Technology

22. Hypský, Jan. Rekonstrukce repetitivních elementů DNA: Reconstruction of Repetitive Elements in DNA.

Degree: 2018, Brno University of Technology

URL: http://hdl.handle.net/11012/84923

► Eukaryotic genomes contain a large number of repetitive structures. Their detection and assembly today are the main challenges of bioinformatics. This work includes a classification… (more)

Subjects/Keywords: repetitivní DNA; sestavení repetic; de novo assembler; LTR retrotranspozony; satelitní DNA; krátké ready; Overlap Layout Consensus; repetitive DNA; repeats assembly; de novo assembler; LTR retrotransposons; satellite DNA; short reads; Overlap Layout Consensus

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hypský, J. (2018). Rekonstrukce repetitivních elementů DNA: Reconstruction of Repetitive Elements in DNA. (Thesis). Brno University of Technology. Retrieved from http://hdl.handle.net/11012/84923

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Hypský, Jan. “Rekonstrukce repetitivních elementů DNA: Reconstruction of Repetitive Elements in DNA.” 2018. Thesis, Brno University of Technology. Accessed March 01, 2021. http://hdl.handle.net/11012/84923.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Hypský, Jan. “Rekonstrukce repetitivních elementů DNA: Reconstruction of Repetitive Elements in DNA.” 2018. Web. 01 Mar 2021.

Vancouver:

Hypský J. Rekonstrukce repetitivních elementů DNA: Reconstruction of Repetitive Elements in DNA. [Internet] [Thesis]. Brno University of Technology; 2018. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/11012/84923.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Hypský J. Rekonstrukce repetitivních elementů DNA: Reconstruction of Repetitive Elements in DNA. [Thesis]. Brno University of Technology; 2018. Available from: http://hdl.handle.net/11012/84923

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

23. Swanson, Eric C. Higher-Order Unfolding of Peri/Centric Satellite Heterochromatin is an Early and Consistent Event in Cell Senescence: A Dissertation.

Degree: Cell Biology, NeuroNexus Neuroscience Institute, 2014, U of Massachusetts : Med

URL: http://escholarship.umassmed.edu/gsbs_diss/765

► Cellular senescence is thought to play an essential role in many biological functions including tumor suppression and organismal aging. Senescent cells, which are permanently… (more)

▼ Cellular senescence is thought to play an essential role in many biological functions including tumor suppression and organismal aging. Senescent cells, which are permanently removed from the cell cycle, can be found both in vivo in many different tissue types and in vitro within cultures of non-immortalized cells. Despite their inability to proliferate, these cells persist and remain metabolically active for indefinite periods of time. This physiologic process occurs in response to a variety of cellular insults including oxidative stress, shortened telomeres, constitutive oncogene expression, and DNA damage, and can be initiated by upregulation of one of the two known senescent pathways, involving p16/Rb or p53/p21. The senescent cell phenotype is also characterized by changes to cell and nuclear morphology and to the secretory profile of the cell. Related to changes in nuclear morphology, epigenetic modifications to the packaging of DNA are thought to be key to the initiation and maintenance of the senescence program. While a large number of earlier studies focused on the findings that senescent cells gain regions of condensed heterochromatin, often in the form of Senescent Associated Heterochromatin Foci (SAHF), this thesis work shows that there is a marked loss of heterochromatin in the peri/centromeric regions of the genome. In fact, both α-satellite and satellite II sequences across the genome distend in a striking and unanticipated fashion; this can be readily visualized by fluorescence in situ hybridization (FISH) as their structure changes from a condensed spot to highly elongated and fine thread-like signals. We have termed this exceptional decondensation of constitutive heterochromatin Senescence Associated Distension of Satellites (SADS). Importantly, a series of experiments shows that SADS is both a consistent and an early event in the cell senescence process, which occurs as a result of every senescence induction method examined. We also observed that this distension was characteristic of both human and murine cells and in vivo in human benign Prostatic Intraepithelial Neoplasia (PIN) tissue. Furthermore, unlike SAHF formation, SADS can occur due to the activation of either of the two senescence pathways, p16/Rb or p53/p21. Additionally, the cytological dimensions of the thread-like satellite signals indicates that SADS represents “unraveling” of DNA on an unprecedented scale. Thus, it was surprising that this event was not facilitated by changes to several canonical histone modifications associated with condensed heterochromatin, namely H3K9Me3, H3K27Me3, or H3K4Me3, nor is it caused by loss of DNA methylation. Consequently, we believe that this marked distension of satellite DNA is due to changes in higher-order folding of the chromatin fiber. This is important for understanding fundamental events in the cell senescence process, but also provides a unique system for study of chromatin packaging that may provide new insights into the organization of DNA well beyond nucleosome packaging… Advisors/Committee Members: Jeanne B. Lawrence, PhD.

Subjects/Keywords: Cell Aging; Chromatin; Heterochromatin; Satellite DNA; Down Syndrome; Genetic Epigenesis; Protein Unfolding; Cell and Developmental Biology; Cell Biology; Cellular and Molecular Physiology; Genetics and Genomics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Swanson, E. C. (2014). Higher-Order Unfolding of Peri/Centric Satellite Heterochromatin is an Early and Consistent Event in Cell Senescence: A Dissertation. (Doctoral Dissertation). U of Massachusetts : Med. Retrieved from http://escholarship.umassmed.edu/gsbs_diss/765

Chicago Manual of Style (16^th Edition):

Swanson, Eric C. “Higher-Order Unfolding of Peri/Centric Satellite Heterochromatin is an Early and Consistent Event in Cell Senescence: A Dissertation.” 2014. Doctoral Dissertation, U of Massachusetts : Med. Accessed March 01, 2021. http://escholarship.umassmed.edu/gsbs_diss/765.

MLA Handbook (7^th Edition):

Swanson, Eric C. “Higher-Order Unfolding of Peri/Centric Satellite Heterochromatin is an Early and Consistent Event in Cell Senescence: A Dissertation.” 2014. Web. 01 Mar 2021.

Vancouver:

Swanson EC. Higher-Order Unfolding of Peri/Centric Satellite Heterochromatin is an Early and Consistent Event in Cell Senescence: A Dissertation. [Internet] [Doctoral dissertation]. U of Massachusetts : Med; 2014. [cited 2021 Mar 01]. Available from: http://escholarship.umassmed.edu/gsbs_diss/765.

Council of Science Editors:

Swanson EC. Higher-Order Unfolding of Peri/Centric Satellite Heterochromatin is an Early and Consistent Event in Cell Senescence: A Dissertation. [Doctoral Dissertation]. U of Massachusetts : Med; 2014. Available from: http://escholarship.umassmed.edu/gsbs_diss/765

University of Florida

24. Ng, Robert. Structural Characterization of Adeno-Associated Virus Serotypes 1 and 6 Glycan Interactions.

Degree: PhD, Medical Sciences - Biochemistry and Molecular Biology (IDP), 2012, University of Florida

URL: https://ufdc.ufl.edu/UFE0044403

► Adeno-Associated Viruses (AAVs) are small ssDNA viruses with the ability to package non-genomic DNA for therapeutic gene delivery. Due to their non-pathogenicity and ability to… (more)

▼ Adeno-Associated Viruses (AAVs) are small ssDNA viruses with the ability to package non-genomic DNA for therapeutic gene delivery. Due to their non-pathogenicity and ability to transduce non-dividing and dividing cells, these viruses have generated significant interest in their development as therapeutic vectors. These properties dictate the tissue of choice for a particular gene delivery application. Towards understanding the capsid determinant(s) of these functions, we have employed AAV1 and AAV6, which differ by just 6 of 736 VP residues yet exhibit tissue and transduction differences, as models for receptor attachment site characterization. AAV1 binds sialic acid (SIA), while AAV6 binds both SIA and heparan sulfate (HS). The crystal structures of AAV1 and AAV6 at 2.5Å and 3.0Å resolution showed 5 of 6 differing AAV1/AAV6 amino acids within the ordered VP structure localized proximal to the icosahedral three-fold axis and identified this capsid region as dictating important functions during infection. A series of reciprocal single residue mutations (AAV1 to AAV6 and AAV6 to AAV1) were thus generated to interrogate the role of the interior and exterior residues in dictating transduction efficiency. Quantitative comparisons of virus titers using ELISA, qPCR, and a HEK293 GFP infectivity assay show no significant differences in capsid assembly, genome packaging, and cellular transduction, respectively, among recombinant wild-type AAV1 and AAV6 and their mutations. In addition, to structurally characterizing the glycan receptor interaction of AAV1 with SIA,X-ray crystallography was used to map it’s binding site on the AAV1 capsid to a region conserved in AAV6, suggesting that these two viruses utilize the same capsid region for this interaction. Site-directed mutagenesis and biochemical studies are underway to confirm this finding. With respect to HS binding, the docking algorithm DOCK6 was used as to localize a potential binding site to a region on the AAV6 capsid that contains an AAV1/AAV6 E531K residue difference consistent with previous mutagenesis and biochemical data. Data arising from these studies will aid the targeting of the AAV capsid to specific tissues or receptor populations for improved targeted gene delivery through recombinant DNA engineering. ( en ) Advisors/Committee Members: Agbandje-Mckenna, Mavis (committee chair), Snyder, Richard O (committee member), Srivastava, Arun (committee member), Flanegan, James B (committee member), Muzyczka, Nicholas (committee member).

Subjects/Keywords: Amino acids; Capsid; Crystal structure; DNA; Gene therapy; Genomes; Receptors; Satellite viruses; Viral morphology; Viruses; aav – capsid – cryo-em – glycan – interaction – parvovirus – receptor – resolution – serotype – structure – therapy – virus – x-ray

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ng, R. (2012). Structural Characterization of Adeno-Associated Virus Serotypes 1 and 6 Glycan Interactions. (Doctoral Dissertation). University of Florida. Retrieved from https://ufdc.ufl.edu/UFE0044403

Chicago Manual of Style (16^th Edition):

Ng, Robert. “Structural Characterization of Adeno-Associated Virus Serotypes 1 and 6 Glycan Interactions.” 2012. Doctoral Dissertation, University of Florida. Accessed March 01, 2021. https://ufdc.ufl.edu/UFE0044403.

MLA Handbook (7^th Edition):

Ng, Robert. “Structural Characterization of Adeno-Associated Virus Serotypes 1 and 6 Glycan Interactions.” 2012. Web. 01 Mar 2021.

Vancouver:

Ng R. Structural Characterization of Adeno-Associated Virus Serotypes 1 and 6 Glycan Interactions. [Internet] [Doctoral dissertation]. University of Florida; 2012. [cited 2021 Mar 01]. Available from: https://ufdc.ufl.edu/UFE0044403.

Council of Science Editors:

Ng R. Structural Characterization of Adeno-Associated Virus Serotypes 1 and 6 Glycan Interactions. [Doctoral Dissertation]. University of Florida; 2012. Available from: https://ufdc.ufl.edu/UFE0044403

25. Giraud, Delphine. Dynamique des éléments transposables et évolution du génome des spartines polyploïdes : Transposable elements dynamics and evolution of polyploid Spartina genome.

Degree: Docteur es, Génétique, génomique et bioinformatique, 2019, Rennes 1

URL: http://www.theses.fr/2019REN1B057

►

Les conséquences de la spéciation divergente ou réticulée (par hybridation) ont été explorées au cours de la diversification des spartines depuis 6-10MA à travers l’analyse… (more)

▼

Les conséquences de la spéciation divergente ou réticulée (par hybridation) ont été explorées au cours de la diversification des spartines depuis 6-10MA à travers l’analyse des séquences répétées, de leur expression et régulation. Nous avons montré une corrélation entre éléments transposables, tailles de génome, et relations phylogénétiques, tout en mettant en évidence une dynamique variable des catégories d’éléments transposables ou de séquences satellites selon les lignées, et l’ancienneté des évènements de spéciation. L’abondance des éléments transposables a été mise en relation avec leur niveau d’expression et le rôle des petits ARN dans leur contrôle. Cette régulation se met rapidement en place suite à l’hybridation interspécifique et explique la « quiescence génomique » (absence de prolifération d’éléments transposables) détectée chez l’allododécaploïde récent S. anglica. Les annotations d’éléments transposables et de petits ARNs, les nouveaux transcriptomes de références réalisés chez différentes espèces au cours de ce travail représentent des ressources additionnelles qui permettront d’explorer de manière plus exhaustive la dynamique des génomes de spartines et de comprendre les mécanismes génomiques impliqués dans l’adaptation et l’écologie de ces espèces ingénieurs d’écosystèmes.

We explored the consequences of divergent speciation or reticulate evolution (resulting from hybridization) during diversification of the Spartina genus in the last 6-10 MY, based on the analysis of repeated sequences, their expression and regulation. Transposable element amounts, genome size, and phylogenetic relationships were found correlated, although differential dynamics of specific transposable element families or satellite sequences were encountered according to lineages, and to divergence times following the speciation events. The abundance of transposable elements appears related to their level of expression and the role of small RNAs in their control. This regulation is rapidly established following interspecific hybridization and explains the "genomic quiescence" (absence of transposable element “burst”) detected in the recent allododecaploid S. anglica. Annotations of transposable elements and small RNAs, new reference transcriptomes generated for different species during this work represent additional resources that will allow a more comprehensive exploration of the Spartina genome history and dynamics for a better understanding of the genomic mechanisms involved in the adaptation and ecology of these “ecosystem engineers” species.

Advisors/Committee Members: Ainouche, Malika (thesis director), Salmon, Armel (thesis director).

Subjects/Keywords: Génomique comparative; Évolution; Polyploïdie; Hybridation; Génome; Séquençage à haut débit; Éléments transposables; ADNs satellites; Spartines; Comparative genomic; Evolution; Polyploidy; Hybridization; Genome; Next generation sequencing; Transposable elements; Satellite DNA; Spartina

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Giraud, D. (2019). Dynamique des éléments transposables et évolution du génome des spartines polyploïdes : Transposable elements dynamics and evolution of polyploid Spartina genome. (Doctoral Dissertation). Rennes 1. Retrieved from http://www.theses.fr/2019REN1B057

Chicago Manual of Style (16^th Edition):

Giraud, Delphine. “Dynamique des éléments transposables et évolution du génome des spartines polyploïdes : Transposable elements dynamics and evolution of polyploid Spartina genome.” 2019. Doctoral Dissertation, Rennes 1. Accessed March 01, 2021. http://www.theses.fr/2019REN1B057.

MLA Handbook (7^th Edition):

Giraud, Delphine. “Dynamique des éléments transposables et évolution du génome des spartines polyploïdes : Transposable elements dynamics and evolution of polyploid Spartina genome.” 2019. Web. 01 Mar 2021.

Vancouver:

Giraud D. Dynamique des éléments transposables et évolution du génome des spartines polyploïdes : Transposable elements dynamics and evolution of polyploid Spartina genome. [Internet] [Doctoral dissertation]. Rennes 1; 2019. [cited 2021 Mar 01]. Available from: http://www.theses.fr/2019REN1B057.

Council of Science Editors:

Giraud D. Dynamique des éléments transposables et évolution du génome des spartines polyploïdes : Transposable elements dynamics and evolution of polyploid Spartina genome. [Doctoral Dissertation]. Rennes 1; 2019. Available from: http://www.theses.fr/2019REN1B057

26. Aldrich, John C. The Origins and Phenotypic Consequences of Repetitive Sequence Variation in Drosophila melanogaster.

Degree: PhD, Biology, 2015, Texas A&M University

URL: http://hdl.handle.net/1969.1/156363

► Environmental stimuli can have a significant impact on gene expression patterns and this impact is not always confined to a single cell cycle, but can… (more)

▼ Environmental stimuli can have a significant impact on gene expression patterns and this impact is not always confined to a single cell cycle, but can sometimes persist through multiple divisions or even transgenerationally. Such phenomena are often classified as epigenetic because genetic mutations are not thought to behave in such a directed, nonrandom manner. Studies concerning epigenetics often overlook unstable variation in repetitive heterochromatic sequences as a potential mode of transgenerational inheritance. Although they constitute a large fraction of most eukaryotic genomes, technological limitations have greatly hindered our understanding of the functional importance of such sequences. Copy number variation in the unstable ribosomal RNA gene array (rDNA) -a specific class of repetitive sequence- modulates heterochromatin formation and influences the expression of a large fraction of the Drosophila genome. The primary aim of this study was to identify an environmental source of rDNA instability and to characterize the phenotypic consequences of the variation generated by that instability. Using genetic, cytological, and molecular assays, I discovered that increased dietary yeast concentration results in rDNA instability and copy number reduction in the soma and germline. Modulation of Insulin/TOR signaling produces similar results, indicating a role for known nutrient sensing signaling pathways in this process. Previous studies suggest that rDNA deletions influence the regulation of a number of metabolically important genes. Supporting this, I found that variation in rDNA modulates the Drosophila starvation response and affects lipid metabolism. This effect is potentially mediated by differential rDNA transcription, suggesting a link between the cause of instability and its phenotypic outcome. Instability is not just thought to be a property of rDNA, but seems to occur via similar mechanisms in other repetitive sequences. I developed a novel polymerase chain reaction (PCR) technique to quantify simple pentameric sequence repeats and used it to discover previously uncharacterized natural and mutationally-induced variation on the heterochromatic Y chromosome. Taken together, these findings suggest a non-epigenetic mechanism through which the environment can influence gene expression patterns in a manner that is specific, heritable, and consequential. Advisors/Committee Members: Maggert, Keith (advisor), Hu, James (committee member), Hardin, Paul (committee member), Ryan, Kathryn (committee member).

Subjects/Keywords: Drosophila melanogaster; Chromatin; epigenetics; ribosomal DNA; nucleolus; satellite sequences

…4.4 Quantification of satellite copy number in X/Y and X/Y/Y males ........ 82 4.5 RT-PCR… …term exposure to the Su(var)205 mutation induces satellite copy number variation… …discovery of non-coding DNA has largely resolved the C-value paradox, the evolutionary… …In a typical C0T experiment, genomic DNA is sheared into small fragments and then heated to… …stranded DNA is monitored via spectrophotometry. Low complexity (i.e. repetitive)…

11 more images…

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Aldrich, J. C. (2015). The Origins and Phenotypic Consequences of Repetitive Sequence Variation in Drosophila melanogaster. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/156363

Chicago Manual of Style (16^th Edition):

Aldrich, John C. “The Origins and Phenotypic Consequences of Repetitive Sequence Variation in Drosophila melanogaster.” 2015. Doctoral Dissertation, Texas A&M University. Accessed March 01, 2021. http://hdl.handle.net/1969.1/156363.

MLA Handbook (7^th Edition):

Aldrich, John C. “The Origins and Phenotypic Consequences of Repetitive Sequence Variation in Drosophila melanogaster.” 2015. Web. 01 Mar 2021.

Vancouver:

Aldrich JC. The Origins and Phenotypic Consequences of Repetitive Sequence Variation in Drosophila melanogaster. [Internet] [Doctoral dissertation]. Texas A&M University; 2015. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1969.1/156363.

Council of Science Editors:

Aldrich JC. The Origins and Phenotypic Consequences of Repetitive Sequence Variation in Drosophila melanogaster. [Doctoral Dissertation]. Texas A&M University; 2015. Available from: http://hdl.handle.net/1969.1/156363

York University

27. Ghotra, Gurbrinder. Optimizing the Toehold-Mediated Strand Displacement Reaction on the Nanoparticle Surface by Altering the Surface DNA Density for the Design of a microRNA NanoOptical Sensor.

Degree: MSc -MS, Chemistry, 2020, York University

URL: http://hdl.handle.net/10315/37851

► We present a method for modulating the kinetics and thermodynamic properties of aggregation and disassembly processes of DNA-functionalized nanoparticles. Specifically, we examine factors influencing the… (more)

Subjects/Keywords: Materials Science; Localized surface plasmon resonance; Plasmonic nanoparticles; Biosensor; miRNA detection; Attinebility; DNA functionalized Gold nanoparticle; Oligonucleotide; DNA surface density; Toehold-mediated strand displacement reaction; FRET; Aggregation; Disassembly; Darkfield microscopy; Cooperativity; Avidity; Label-free; Low cost; Miniaturized; Biosensing; Core-satellite nanoassemblies; Affinity; DNA hybridization; Plasmonic coupling; Calorimetric assay; DNA crowding; Point-of-care; Hypoxia; Normoxia; Direct detection

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ghotra, G. (2020). Optimizing the Toehold-Mediated Strand Displacement Reaction on the Nanoparticle Surface by Altering the Surface DNA Density for the Design of a microRNA NanoOptical Sensor. (Masters Thesis). York University. Retrieved from http://hdl.handle.net/10315/37851

Chicago Manual of Style (16^th Edition):

Ghotra, Gurbrinder. “Optimizing the Toehold-Mediated Strand Displacement Reaction on the Nanoparticle Surface by Altering the Surface DNA Density for the Design of a microRNA NanoOptical Sensor.” 2020. Masters Thesis, York University. Accessed March 01, 2021. http://hdl.handle.net/10315/37851.

MLA Handbook (7^th Edition):

Ghotra, Gurbrinder. “Optimizing the Toehold-Mediated Strand Displacement Reaction on the Nanoparticle Surface by Altering the Surface DNA Density for the Design of a microRNA NanoOptical Sensor.” 2020. Web. 01 Mar 2021.

Vancouver:

Ghotra G. Optimizing the Toehold-Mediated Strand Displacement Reaction on the Nanoparticle Surface by Altering the Surface DNA Density for the Design of a microRNA NanoOptical Sensor. [Internet] [Masters thesis]. York University; 2020. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/10315/37851.

Council of Science Editors:

Ghotra G. Optimizing the Toehold-Mediated Strand Displacement Reaction on the Nanoparticle Surface by Altering the Surface DNA Density for the Design of a microRNA NanoOptical Sensor. [Masters Thesis]. York University; 2020. Available from: http://hdl.handle.net/10315/37851

28. Ripamonte, Paula. Estimativa da participação do genoma de Bos taurus no rebanho Nelore.

Degree: Mestrado, Qualidade e Produtividade Animal, 2002, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/74/74131/tde-03072002-154349/ ;

►

A espécie Bos indicus, particularmente a raça Nelore, é grande maioria no rebanho bovino da região acima do trópico no Brasil. Embora a habilidade desses… (more)

▼

A espécie Bos indicus, particularmente a raça Nelore, é grande maioria no rebanho bovino da região acima do trópico no Brasil. Embora a habilidade desses animais em resistir às doenças parasitárias, condições climáticas e pastagens de baixa qualidade enalteçam a utilização em larga escala desta raça, estes animais não são considerados bons conversores de alimento e, conseqüentemente, precoces em comparação aos seus homólogos Bos taurus. Durante a formação das raças zebuínas brasileiras, houve uma participação das linhas maternas de Bos taurus, que pode ser demonstrada pela contribuição majoritária do genoma mitocondrial desta subespécie. Embora em escala muito menor, estima-se que exista também uma participação destas linhas maternas no genoma nuclear. O objetivo deste trabalho foi iniciar os estudos para estimar esta participação. Para os estudos foram utilizados 104 animais da raça Nelore e 8 animais de diferentes raças européias. Cinco regiões do DNA que produzem fragmentos microssatélites taurus/indicus específicos (HEL1, HEL9, ETH225, ILSTS005 e INRA063) foram amplificadas com a utilização de primers marcados com sondas fluorescentes. Os fragmentos foram submetidos à eletroforese em gel de poliacrilamida desnaturante 6% e visualizados após excitação com laser. No total foram encontrados 23 alelos para os microssatélites analisados o que representa uma média de 4,6±1,82 alelos por locus. Amplificou-se também uma região do DNA satélite 1711b que posteriormente foi digerida com a enzima de restrição Msp I. Verificou-se a existência de três possíveis genótipos entre os animais Nelore mtDNA Bos taurus e mtDNA Bos indicus. Os animais europeus analisados apresentaram sempre o mesmo padrão de restrição. A comparação dos componentes de variância do tamanho dos alelos intra e inter população usando os fragmentos microssatélites permitem a separação dos animais Bos taurus dos animais Nelore, mas não dos Nelore de origem materna distinta. No entanto, a freqüência de alelos indicus específicos nos microssatélites e de padrões de digestão do DNA satélite também indicus específicos sugerem uma participação da ordem de aproximadamente 6% do genoma taurus na população de gado Nelore.

Bos indicus specie, especially Nellore breed is responsible for the majority of Brazilian tropical herd. These animals are notably capable to endure parasite infection as well as hot weather and low quality feed. In one hand this qualities suggest the large scale application of this breed, but in other hand this same breed is well characterized as bad food converter and consequently far from having good precocity status compared with its Bos taurus homologues. It has been reported a matrilineal European participation in Zebu cattle since its introduction in American lands. This hybridization is confirmed by the majority contribution of Bos taurus mtDNA in these animals. Although in a much lower frequency, we hypothesize a Bos taurus cow participation in nuclei genome. The main aim of this work was to give the firsts steps towards the estimation…

Advisors/Committee Members: Meirelles, Flavio Vieira.

Subjects/Keywords: bos indicus; bos taurus; bovinos; microsatellites; microssatélites; mitochondrial DNA; mtDNA; satélite 1711b; satellite DNA 1711b

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ripamonte, P. (2002). Estimativa da participação do genoma de Bos taurus no rebanho Nelore. (Masters Thesis). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/74/74131/tde-03072002-154349/ ;

Chicago Manual of Style (16^th Edition):

Ripamonte, Paula. “Estimativa da participação do genoma de Bos taurus no rebanho Nelore.” 2002. Masters Thesis, University of São Paulo. Accessed March 01, 2021. http://www.teses.usp.br/teses/disponiveis/74/74131/tde-03072002-154349/ ;.

MLA Handbook (7^th Edition):

Ripamonte, Paula. “Estimativa da participação do genoma de Bos taurus no rebanho Nelore.” 2002. Web. 01 Mar 2021.

Vancouver:

Ripamonte P. Estimativa da participação do genoma de Bos taurus no rebanho Nelore. [Internet] [Masters thesis]. University of São Paulo; 2002. [cited 2021 Mar 01]. Available from: http://www.teses.usp.br/teses/disponiveis/74/74131/tde-03072002-154349/ ;.

Council of Science Editors:

Ripamonte P. Estimativa da participação do genoma de Bos taurus no rebanho Nelore. [Masters Thesis]. University of São Paulo; 2002. Available from: http://www.teses.usp.br/teses/disponiveis/74/74131/tde-03072002-154349/ ;

Swedish University of Agricultural Sciences

29. Leke, Walter Nkeabeng. Molecular epidemiology of begomoviruses that infect vegetable crops in southwestern Cameroon.

Degree: 2010, Swedish University of Agricultural Sciences

URL: http://pub.epsilon.slu.se/2338/

► Begomoviruses are plant-infecting viruses, which are transmitted by the whitefly vector Bemisia tabaci. They have a genome of single-stranded DNA that consists of either a… (more)

▼ Begomoviruses are plant-infecting viruses, which are transmitted by the whitefly vector Bemisia tabaci. They have a genome of single-stranded DNA that consists of either a single (monopartite) or two components (bipartite) with a component size of approximately 2.8 kb. Many monopartite begomoviruses in the Old World have been found to be associated with betasatellite and alphasatellite molecules, which are about half the size of their helper begomovirus genome. Betasatellites have been shown to be necessary for inducing severe disease symptoms. In Cameroon, B. tabaci has been associated with suspected begomovirus infections in many crop and weed species. Despite their growing importance, only begomoviruses infecting cassava have been studied in Cameroon in any detail. Thus, there was a need for additional information on diversity and distribution of begomoviruses and satellites in vegetable crops and dictyledonous weeds, which likely serve as virus reservoirs. In field studies carried out in this study, a high incidence of okra leaf curl disease was found in Cameroon. Sequencing of viral genomes showed that the okra plants were infected by viruses of two previously known begomovirus species (Cotton leaf curl Gezira virus and Okra yellow crinkle virus) as well as a new recombinant begomovirus species (Okra leaf curl Cameroon virus). In addition, a betasatellite (Cotton leaf curl Gezira betasatellite) and two alphasatellites (Okra leaf curl Mali alphasatellite and Okra yellow crinkle Cameroon alphasatellite) were identified. Tomato plants with leaf curling were shown to contain isolates of a new begomovirus, Tomato leaf curl Cameroon virus, and an alphasatellite, Tomato leaf curl Cameroon alphasatellite (ToLCCMA). To study the potential begomovirus complexes infecting weeds, begomoviruses and satellites in plants of the weed Ageratum conyzoides with leaf curl symptoms were characterized. Sequence analyses showed that they were infected by isolates of a new begomovirus (Ageratum leaf curl Cameroon virus), two new betasatellites (Ageratum leaf curl Cameroon betasatellite and Ageratum leaf curl Buea betasatellite), an alphasatellite (ToLCCMA) and two types of defective recombinants between a begomovirus and ToLCCMA. Putative recombinations were detected in begomovirus genomes for all three plant species studied, indicating that recombination is an important mechanism for their evolution. A close relationship between the begomoviruses infecting tomato and A. conyzoides, and the detection of the same alphasatellite in them support the idea that weeds are important reservoirs for begomoviruses and their satellites. This study has revealed a huge complexity of begomoviruses and DNA satellites previously largely unknown in West Africa and Central Africa. With this high diversity, recombination potential and transmission by B. tabaci, begomoviruses and their associated DNA satellites pose a serious threat to crop production in the region.

Subjects/Keywords: lycopersicon esculentum; abelmoschus esculentus; ageratum conyzoides; indigenous organisms; plant diseases; infectious diseases; plant viruses; genetic variation; genomes; dna; plant disease; mixed infection; Abelmoschus esculentus; Ageratum conyziodes; satellite DNAs; begomovirus diversity; native species; Solanum lycopersium

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Leke, W. N. (2010). Molecular epidemiology of begomoviruses that infect vegetable crops in southwestern Cameroon. (Doctoral Dissertation). Swedish University of Agricultural Sciences. Retrieved from http://pub.epsilon.slu.se/2338/

Chicago Manual of Style (16^th Edition):

Leke, Walter Nkeabeng. “Molecular epidemiology of begomoviruses that infect vegetable crops in southwestern Cameroon.” 2010. Doctoral Dissertation, Swedish University of Agricultural Sciences. Accessed March 01, 2021. http://pub.epsilon.slu.se/2338/.

MLA Handbook (7^th Edition):

Leke, Walter Nkeabeng. “Molecular epidemiology of begomoviruses that infect vegetable crops in southwestern Cameroon.” 2010. Web. 01 Mar 2021.

Vancouver:

Leke WN. Molecular epidemiology of begomoviruses that infect vegetable crops in southwestern Cameroon. [Internet] [Doctoral dissertation]. Swedish University of Agricultural Sciences; 2010. [cited 2021 Mar 01]. Available from: http://pub.epsilon.slu.se/2338/.

Council of Science Editors:

Leke WN. Molecular epidemiology of begomoviruses that infect vegetable crops in southwestern Cameroon. [Doctoral Dissertation]. Swedish University of Agricultural Sciences; 2010. Available from: http://pub.epsilon.slu.se/2338/

University of Ottawa

30. Levesque, Steve. DNA Methylation, Cellular Stress Response and Expression of Inner Nuclear Membrane Proteins .

Degree: 2011, University of Ottawa

URL: http://hdl.handle.net/10393/19949

► Hutchinson-Gilford Progeria Syndrome is described as a series of mutations within the lamin A gene leading to the accumulation of progerin in the nucleus, contributing… (more)

Subjects/Keywords: Epigenetics; DNA methylation; Nuclear stress bodies; Inner nuclear membrane (INM); Lamin A; Lamin B; Emerin; Satellite III (Sat III); Stress response; Heat shock (HS); 2H12; Lamina associated polypeptide 2 (Lap2); Fibrillarin; Laminopathies; Hutchinson Gilford Progeria Syndrome (HGPS)

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Levesque, S. (2011). DNA Methylation, Cellular Stress Response and Expression of Inner Nuclear Membrane Proteins . (Thesis). University of Ottawa. Retrieved from http://hdl.handle.net/10393/19949

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Levesque, Steve. “DNA Methylation, Cellular Stress Response and Expression of Inner Nuclear Membrane Proteins .” 2011. Thesis, University of Ottawa. Accessed March 01, 2021. http://hdl.handle.net/10393/19949.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Levesque, Steve. “DNA Methylation, Cellular Stress Response and Expression of Inner Nuclear Membrane Proteins .” 2011. Web. 01 Mar 2021.

Vancouver:

Levesque S. DNA Methylation, Cellular Stress Response and Expression of Inner Nuclear Membrane Proteins . [Internet] [Thesis]. University of Ottawa; 2011. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/10393/19949.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Levesque S. DNA Methylation, Cellular Stress Response and Expression of Inner Nuclear Membrane Proteins . [Thesis]. University of Ottawa; 2011. Available from: http://hdl.handle.net/10393/19949

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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