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Dissertations / Theses on the topic 'Repetitive element'

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Published: 14 March 2023

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1

Albarazi, Rayan. "Evaluation of Roadway Embankment Under Repetitive Axial Loading Using Finite Element Analysis." Thesis, Luleå tekniska universitet, Institutionen för samhällsbyggnad och naturresurser, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-81916.

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2

Razavi, Borghei Seyyed Moein. "The Modeling of Partial Discharge under Fast, Repetitive Voltage Pulses Using Finite-Element Analysis." Thesis, Virginia Tech, 2020. http://hdl.handle.net/10919/98001.

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By 2030, it is expected that 80% of all electric power will flow through power electronics systems. Wide bandgap power modules that can tolerate higher voltages and currents than silicon-based modules are the most promising solution to reducing the size and weight of power electronics systems. These wide-bandgap power modules constitute powerful building blocks for power electronics systems, and wide bandgap-based converter/power electronics building blocks are envisaged to be widely used in power grids in low- and medium-voltage applications and possibly in high-voltage applications for high-voltage direct current and flexible alternating current transmission systems. One of the merits of wide bandgap devices is that their slew rates and switching frequencies are much higher than silicon-based devices. However, from the insulation side, frequency and slew rate are two of the most critical factors of a voltage pulse, influencing the level of degradation of the insulation systems that are exposed to such voltage pulses. The shorter the rise time, the shorter the lifetime. Furthermore, lifetime dramatically decreases with increasing frequency. Thus, although wide bandgap devices are revolutionizing power electronics, electrical insulating systems are not prepared for such a revolution; without addressing insulation issues, the electronic power revolution will fail due to dramatically increased failure rates of electrification components. In this regard, internal partial discharges (PDs) have the most effect on insulation degradation. Internal PDs which occur in air-filled cavities or voids are localized electrical discharges that only partially bridge the insulation between conductors. Voids in solid or gel dielectrics are challenging to eliminate entirely and may result simply during manufacturing process. The objective of this study is to develop a Finite-Element Analysis (FEA) PD model under fast, repetitive voltage pulses, which has been done for the first time. The model is coded and implemented in COMSOL Multiphysics linked with MATLAB, and its simulation results are validated with experimental tests. Using the model, the influence of different parameters including void shape, void size, and void air pressure on PD parameters are studied.
M.S.
To decarbonize and reduce energy consumption for commercial aviation, the development of lightweight and ultra-efficient all-electric powertrain including electric motors, drives, and associated thermal management systems has been targeted. Using wide bandgap (WBG) power modules that can tolerate high voltages and currents can reduce the size and weight of the drive. However, the operation of WBG-based power converter can endanger the reliability of the electrified systems, most importantly, the insulation system. In this study, it is attempted to model the impact of such threats to the insulation system using numerical models.
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3

Yoshimoto, Hideki. "Pulse and rhythm : exploring the value of repetitive motion as an element of design." Thesis, Royal College of Art, 2015. http://researchonline.rca.ac.uk/1708/.

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With this thesis I want to share my exploration of pulse and rhythm as elements of design. I locate my research on the meeting point of two different contexts: one is the expansion of kinetic art into design projects, resulting in aesthetic use of motion playing wider roles in design, and the other is the expansion, in relation to technological development, of the value of pulse as a design element. My hypothesis is that the value of pulse as an element of design can be heightened by acquiring the aesthetic use of repetitive motion seen in kinetic art, forging emotional communication with viewers/users. The mission of this research is to demonstrate this argument through practice, collecting working ideas and methods. I propose a model of pulse which can be used as a tool to reflect on projects from a new perspective. To forge a workable focus for the research, I articulate a definition of Japanese aesthetics and deploy related criteria of design. My exploration covers three topics - single pulse, pulse synchronisation, and pulse interference. Several ideas and methods were tested across eight projects in total, related to theories from various fields including biology, physiology, psychology, philosophy, mathematics and physics, and inspired by art and design practice. The insights gained from the projects allowed me to expand the scope of the exploration from pulse to rhythm, and I also reflect on my work from this perspective, distinguishing rhythm from pulse. Furthermore, I conducted an interview-based study to look into rhythm inferred from non-pulsing motions, and the insights from the interviews are presented in the thesis with an additional discussion. The output of the research takes two forms: recommendations, as a simpliflied and generalised summary of my findings, and case studies (projects), as a concrete source of inspiration for the reader's own creations. By thus interweaving the practical and theoretical knowledge gained in the research, I believe this work provides a useful contribution to the field of design.
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4

Bryden, Louis J. "ROn-1 SINES, a short interspersed repetitive element from the genome of oreochromis niloticus and its species distribution in cichlid fishes." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/mq24809.pdf.

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5

Glugoski, Larissa. "Análise de marcadores cromossômicos em Rineloricaria (Siluriformes: Loricariidae) com ênfase na diversidade cariotípica." UNIVERSIDADE ESTADUAL DE PONTA GROSSA, 2017. http://tede2.uepg.br/jspui/handle/prefix/940.

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The Loricariidae family is the largest in the Siluriformes order, being comprised of eight subfamilies. One of these, the Loricariinae subfamily, shows great diversity in respect to the number of chromosomes and karyotype formula, varying in the diploid number (2n) from 36 to 74 chromosomes. This diverse range originated mainly from Robertsonian(Rb) rearrangements. Rineloricaria is the largest genre in the Loricariinae subfamily, its species ranging from 2n = 36 to 70 chromosomes. In spite of this, little is known about which kinds of repetitive DNA gave rise to the events of chromosome fusion or fission. Previous studies have revealed the presence of multiple 5S rDNA sites in specimens of Rineloricaria from the Paraná River Basin, associated to the Robertsonian fission/fusion events. The aim of this work was the molecular characterization of the fragile sites associated to the 5S rDNA, besides localizing in situ marker chromosomes in Rineloricaria latirostris from the Das Pedras River and R. latirostris from the Piumhi River (first described in this work), seeking to understand the 2n diversification in this group. Rineloricaria latirostris from the Pedras River exhibited 2n = 46 chromosomes, while those from the Piumhi River presented 2n = 48 chromosomes, and both had a fundamental number (FN) of 60. Fluorescence in situ hybridization (FISH) assays in R. latirostris from the Piumhi River revealed 2 chromosome pairs with 5S rDNA sites, pair 7 with 18S rDNA, and only terminal staining when subjected to a telomeric probe (TTAGGGn). The population of the Pedras river exhibited 5 pairs with 5S rDNA sites, the metacentric (m) pair 2 marked with 18S rDNA, TTAGGGn markers in the terminal regions of the chromosomes, and the presence of interstitial telomeric sites (ITS) in pairs m 1 and m 3. The latter, in synteny with 5S rDNA, is indicative of Robertsonian fusion events. The isolation, cloning and sequencing of the 5S rDNA revealed clones with high sequence identity to 5S rDNA from other species, in addition to the necessary regions for recognition and transcription by RNA polymerase III. One clone of ~700 bp exhibited a degenerated fragment of hAT transposon in its sequence. It was named degenerated 5S rDNA. The fluorescence in situ hybridization assay highlighted chromosomes with co-localized staining for 5S rDNA/hAT, 5S rDNA/degenerated 5S rDNA, and 5S rDNA/ITS (m 3 pair) in R. latirostris from das Pedras River. In R. latirostris from Piumhi River, there was no detection of degenerated 5S rDNA sites. These results allow us to infer the role of the hAT transposon in the dispersion of 5S rDNA sites in the population, since some studies have indicated a relation between 5S rDNA dispersion and transposons in fish. In conclusion, data obtained by this study indicate a possible association between the hAT and the dispersion of 5S rDNA sites and Robertsonian events in the studied population of R. latirostris. The presence of the 5S rDNA/degenerated 5S rDNA/ITS generates hotspots for chromosomal breakage, contributing to the large karyotype diversity found in Loricariidae.
A família Loricariidae é a mais numerosa dentro da ordem Siluriformes e abrange oito subfamílias. A subfamília Loricarinae apresenta uma grande diversidade no que diz respeito ao número de cromossomos e a fórmula cariotípica, com variação do número diploide (2n) de 36 a 74 cromossomos, sendo os rearranjos Robertsonianos (Rb) considerados os principais mecanismos para explicar esta variação cromossômica. Rineloricaria é o gênero mais numeroso de Loricariinae, com espécies apresentando 2n = 36 - 70 cromossomos. Contudo, pouco ainda se sabe sobre quais os tipos de DNAs repetitivos originaram os eventos de fissão e fusão cromossômica. Estudos anteriores revelaram a presença de sítios múltiplos de rDNA 5S em exemplares de Rineloricaria da bacia do Rio Paraná, associados aos eventos de fissão/fusão Robertsonianos. O objetivo deste trabalho foi a caracterização molecular de sítios frágeis associados ao rDNA 5S, além da localização in situ de marcadores cromossômicos em Rineloricaria latirostris do rio das Pedras e R. latirostris do rio Piumhi (pela primeira vez descrito neste trabalho), visando a compreensão da diversificação do 2n neste grupo. Rineloricaria latirostris do rio das Pedras apresentou 2n = 46 cromossomos, enquanto R. latirostris do rio Piumhi apresentou 2n = 48 cromossomos, ambos com número fundamental (NF) de 60. Ensaios de hibridação in situ fluorescente em R. latirostris do rio Piumhi revelaram 2 pares cromossômicos marcados com rDNA 5S, o par 7 marcado com rDNA 18S, além de apenas marcações terminais utilizando-se a sonda telomérica (TTAGGGn). A população do rio das Pedras apresentou 5 pares portadores de sítios de rDNA 5S, o par metacêntrico (m) 2 marcado com rDNA 18S, marcações de TTAGGGn nas regiões terminais dos cromossomos, além da presença de vestígios de sítios teloméricos intersticiais (interstitial telomeric sites - ITS) nos pares m 1 e m 3, sendo este último em sintenia com o rDNA 5S, indicativo de eventos de fusão Robertsoniana. O isolamento, clonagem e sequenciamento de fragmentos de rDNA 5S, revelaram clones apresentando alta identidade ao rDNA 5S de outras espécies, além das regiões necessárias para o reconhecimento e transcrição pela RNA polimerase III. Um dos clones de ~700 pb apresentou um fragmento do transposon hAT em sua sequência, já em intensa degeneração molecular, sendo denominado de rDNA 5S degenerado. A hibridação in situ fluorescente evidenciou cromossomos com marcações co-localizadas de rDNA 5S/hAT, rDNA 5S/rDNA 5S degenerado e rDNA 5S/ITS (no par m 3) em R. latirostris do rio da Pedras. Em R. latirostris do rio Piumhi, não foram detectados sítios com rDNA 5S degenerado. Estes resultados nos permitem inferir o papel do TE hAT na dispersão dos sítios de rDNA 5S na população estudada, visto que alguns estudos indicam haver uma relação entre a dispersão do rDNA 5S pelo genoma e TEs em peixes. Em conclusão, os dados obtidos neste estudo indicam uma possível associação entre o elemento hAT e a dispersão de sítios de rDNA 5S e eventos Robertsonianos presentes na população de R. latirostris estudada. A presença de rDNA 5S/rDNA 5S degenerado/ITS geram hotspots para as quebras cromossômicas, contribuindo assim para a ampla diversidade cariotípica encontrada em Loricariidae.
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6

Motta, V. "DIFFERENTIAL SUSCEPTIBILITY OF REPETITIVE ELEMENTS TO AIRBORNE POLLUTANTS." Doctoral thesis, Università degli Studi di Milano, 2013. http://hdl.handle.net/2434/216407.

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Background. Repetitive elements take up >40% of the human genome and can change distribution through transposition, thus generating subfamilies. Repetitive element DNA methylation has been associated with several diseases and environmental exposures, including exposure to airborne pollutants. No systematic analysis has yet been conducted to examine the effects of exposures across different repetitive element subfamilies. Objective. To evaluate sensitivity of DNA methylation and expression in differentially‐evoluted LINE, Alu, and HERV subfamilies to different types of airborne pollutants. Methods. We sampled a total of 120 male participants from three studies (20 high-, 20 low-exposure in each study) of steel workers exposed to metal-rich particulate matter (measured as PM10) (Study 1); gas-station attendants exposed to air benzene (Study 2); and truck drivers exposed to traffic-derived elemental carbon (Study 3). We measured methylation by bisulfite-PCR-pyrosequencing in 10 differentially‐evoluted repetitive element subfamilies. We evaluate sensitivity of DNA methylation of the same 10 subfamilies and the expression of the most representative and well studied subfamilies AluSx and L1HS in a more wide population of 120 individuals (Beijing Truck Driver Air Pollution Study, BTDAS) with a well characterized personal exposure levels of PM2.5 and ambient PM10. Results. In the three studies, high-exposure groups exhibited subfamily-specific methylation differences compared to low-exposure groups: L1PA2 showed lower DNA methylation in steel workers (P=0.04) and gas station attendants (P=0.03); L1Ta showed lower DNA methylation in steel workers (P=0.02); AluYb8 showed higher DNA methylation in truck drivers (P=0.05). Within each study, dose-response analyses showed subfamily-specific correlations of methylation with exposure levels. Interaction models showed that the effects of the exposures on DNA methylation were dependent on the subfamily evolutionary age, with stronger effects on older LINEs from PM10 (p‐interaction=0.003) and benzene (p‐interaction=0.04), and on younger Alus from PM10 (p-interaction=0.02). In the BTDA Study the group analysis showed a significantly lower DNA methylation in the truck drivers group in AluSx (P=0.02) and MLT1d (P=0.01). The dose response analysis confirmed a lower AluSx methylation in relation to PM10 8-day mean (P=0.047) and a lower MLT1d methylation in relation to exposure to PM2.5 (P=0.002), EC (P=0.008), ambient PM10 study day mean (P=0.005) and ambient PM10 8-day mean (P=0.018). Conclusions. The evolutionary age of repetitive element subfamilies determines differential susceptibility of DNA methylation and expression to airborne pollutants.
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7

Ward, Michelle Claire. "The regulatory potential of repetitive elements in mammalian genomes." Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648276.

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8

Hypský, Jan. "Rekonstrukce repetitivních elementů DNA." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2018. http://www.nusl.cz/ntk/nusl-385940.

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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 of repetitive DNA and represents an implementation of a novel de novo assembler focusing on searching and constructing LTR retrotransposons and satellite DNA. Assembler accepts on his input short reads (single or pair-end), obtained from next-generation sequencing machines (NGS). This assembler is based on Overlap Layout Consensus approach.
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9

Casas, Masnou Eduard. "A role for heterochromatin and repetitive elements in epigenetic inheritance." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/668338.

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Gene regulation mechanisms control the level of transcription of each gene into RNA and the combination of expressed genes determines cell identity. Gene regulation is maintained by epigenetic mechanisms including DNA methylation, histone modifications and non-coding RNAs. These same mechanisms are responsible for silencing of transposable elements and heterochromatin formation. Interestingly, epigenetic mechanisms can transmit the transcriptional state of a gene to the next generation. Epigenetic inheritance differs from conventional genetics: it does not follow the law of segregation and importantly, can transmit acquired traits. The advent of next generation sequencing (NGS) allows for gene expression quantification and epigenome profiling, opening the door to genome wide screenings of epigenetic factors and phenotypes linked to epigenetic inheritance. Here, I study the role of heterochromatin and transposable elements in epigenetic inheritance. In the first chapter I present how an IAP insertion in the Nocturnin gene triggers the birth of new piRNA cluster in mouse. We hypothesize that many piRNA producing loci have evolved from ERV insertions into germline expressed genes. Last, we identify NXF1 as a key factor in piRNA biogenesis of IAP-derived piRNA loci. In the second chapter I test whether the IAP insertion in Nocturnin, and therefore piRNAs produced from this gene in the male germline, affect expression of the gene in the embryo. I find that the piRNA-producing allele of Nocturnin is more highly expressed from the paternal that the maternal allele in early embryo. Thus, the IAP insertion in Nocturnin leads to transmission of an altered epigenetic expression state from parents to progeny, potentially via the production of piRNAs in the male germline. In the third chapter of this thesis I describe a model of intergenerational epigenetic inheritance in flies. My work describes genome wide changes in gene expression that are direct consequences of epigenetic inheritance and I identify chromatin factors related to the transmission and maintenance of the phenotype in the next generation. In the fourth chapter of my thesis I use worms exposed to high temperature to identify endogenous genes that are able to maintain memory of expression for many generations. Interestingly, I find that transposable elements that are upregulated by temperature and repressed by heterochromatin can transmit epigenetic information to the progeny. In the fifth chapter of this thesis I study heritable expression of acquired expression states after epigenetic information loss linked to impaired DNA replication. My work describes how the loss of repressive marks during impaired replication in embryos leads to heritable changes in gene expression of loci regulated by heterochromatin and polycomb means.
Els mecanismes de regulació gènica controlen el nivell de transcripció de cada gen I l’estabilitat dels ARNs produïts. El perfil d’expressió gènica determina la identitat d’una cèl·lula, permetent que es formin teixits diferenciats partint d’exactament el mateix ADN. L’epigenètica és el conjunt de factors que asseguren que es mantingui el patró d’expressió gènica durant les divisions cel·lulars i el temps, i inclouen mecanismes com la metilació de l’ADN i la cromatina. També són responsables del silenciament d’elements repetitius i exògens presents al genoma. En aquesta tesi estudio el rol de l’epigenètica en transmetre informació d’expressió gènica no lligada a la seqüència d’ADN a les següents generacions. En concret, em centro en el paper que juguen l’heterocromatina i els elements repetitius en mantenir i transmetre canvis d’expressió a les següents generacions.
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10

Carter, Andrew T. "VL30 : a mouse retrovirus-like family of repetitive DNA elements." Thesis, University of Warwick, 1985. http://wrap.warwick.ac.uk/67115/.

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Mouse and rat cells encode an abundant 30S RNA which shares many structural properties with retroviral genomic RNA. This VL30 RNA can be efficiently packaged into retrovirus particles. Mouse cells recently infected with a MuLV (VL30) pseudotype were shown to contain full length, reverse-transcribed DNA copies of both RNA species. VL30 DNA could also be synthesized in quantity using the endogenous reverse transcriptase activity of detergent-disrupted MuLV (VL30) particles. This DNA was found to be identical to that produced in vivo. Several 4.6-4.9kbp molecular clones (NVL clones) of VL30 cDNA were obtained. The retrovirus-like LTRs of each clone displayed a moderate restriction enzyme site heterogeneity, but NVL unique sequence was identical in each case. Southern blotting experiments using NVL probes showed that (a) most of the 100-200 NIH-3T3 DNA mouse VL30 elements were organized into provirus-like structures with a high degree of sequence conservation, and (b) the majority of these elements were hypermethylated and transcriptionally inactlve, whereas an expressed NVL-like sub-class could account for no more than 5% of mouse VL30 genes. NVL-related sequences in rodent DNAs other than the mouse were markedly less abundant and showed a greater sequence divergence. This was in contrast to MuLV-related sequences whose copy number and homology to a cloned MuLV probe decreased more gradually with phylogenetic distance from the mouse. Sub-genomic NVL probes showed that two rodent species had each conserved a different block of NVL-like sequence. These data indicate that each family has exhibited a different rate of sequence divergence during rodent evolution. Finally, a MuLV (VL30)-infected rat fibroblast line was shown to have received 1-2 copies per cell of a transcriptionally active NVL-like element. This suggests the possibility that evolution of each rodent VL30 family has been influenced by retrovirus-mediated transmission across the species barrier.
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11

Beitel, Lenore K. (Lenore Katherine). "Characterization of HSAG elements : a middle repetitive family of genetic elements which stimulate gene amplification." Thesis, McGill University, 1990. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=70164.

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Members of the HSAG family of genetic elements stimulate amplification of the pSV$ sb2$DHFR vector in cis, such that HSAG-pSV$ sb2$DHFR transfected cell populations generate methotrexate resistant cells at a higher frequency than pSV$ sb2$DHFR transfectants. Repetitive DNA sequences such as Alu elements were found in HSAG-1, HSAG-2, and HSAG-5; HSAG-1 and HSAG-2 also contain poly purine-pyrimidine tracts. Analysis of subfragments of HSAG-1, HSAG-2, and HSAG-5 demonstrated that the interaction of multiple positive-acting elements was necessary for maximum amplification stimulatory activity. Proposed positive-acting elements include Alu-like sequences, poly purine-pyrimidine tracts, A/T rich regions and potential stem-loop structures. For HSAG-1, the native configuration of these elements gives optimal activity; transcriptional activation has also been implicated. Both transcriptional activity and the aforementioned elements have been shown to promote recombination in other systems; it is therefore suggested that the HSAG elements stimulate gene amplification by increasing recombination.
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12

Taquary, Adriana Maria Antunes. "Tamanho, montagem de novo e anotação do genoma de Dipteryx alata (Leguminosae)." Universidade Federal de Goiás, 2017. http://repositorio.bc.ufg.br/tede/handle/tede/7297.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG
Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq
In recent years there has been a rapid increase in the availability and quality of sequencing data and with this an explosion of projects of sequencing of the genomes of plants occurred. In this scenario, genomic analyzes have been characterized as efficient to generate genetic information on a large scale, including for non-model species. Dipteryx alata is a non-model tree species endemic to the Cerrado biome belonging to the Leguminosae family. The objectives of this work were to estimate the number of chromosomes and the size of the genome of D. alata, and also assemble and annotate sequences of the genomes organelles and nuclear of the species using Illumina sequencing data. The size of the genome of D. alata was estimated as 1C = 0.825 pg, which corresponds to a haploid genome of 807.2 MB with 2n = 16 chromosomes. Were assembled 275,709 nuclear genomic sequences with N50 equal to 1598, which corresponds to 355MB and 44% of the whole genome. In the nuclear sequences, 21,981 microsatellite regions were annotated, of which 49.3% had dinucleotide motifs, 42.7% trinucleotide motifs and 4% tetranucleotide motifs. Transposable elements (TEs) were found in 39.29% of the sequences analyzed, corresponding to 421,701 TEs. LTR retrotransposons (gypsy and copy) were the most abundant TEs in nuclear sequences. Were annotated 1,431 RNA genes non-translated into proteins, being 176 rRNAs, 189 tRNAs, 477 snRNAs, 8 snoRNAs, 466 miRNAs and 115 lncRNAs. Were annotated also 62,200 protein coding genes with an average size of 1,156 bp. The estimated number of mRNAs transcribed by the set of annotated nuclear genes was 160,450, of which 131,228 showed significant similarity with known sequences and 84,793 were classified functionally in the Gene Ontology terms. A total of 736,787 SNPs and 90,803 InDels were discovered in the nuclear sequences. A mean of 1 SNP was identified for each 189 bp of the genome and the ratio between the transition (Ts) and transversion (Tv) mutations was 1.58. A percentage of 46.5% of the SNPs occurs in the genic context and the effects of the SNPs were annotated mainly in exons and intergenic regions. Were assembled 110 KB of chloroplastid sequences with N50 of 2,384 bp and 327 KB of mitochondrial sequences with N50 of 1,784 bp. Were annotated genes of 3 rRNA, 13 tRNA, 6 miRNA and 20 lncRNA for the chloroplast and genes of 4 rRNA, 26 tRNA, 7 miRNA and 54 lncRNA for the mitochondria. For the chloroplast were predicted 20 protein coding genes with a mean size of 2,374 bp and for mitochondria were predicted 176 genes with a mean size of 1,279 bp. The estimated number of mRNAs transcribed by this gene set was 63 and 525 for chloroplast and mitochondria respectively. Were annotated 39 microsatellite regions and 4 TEs in the chloroplastid sequences and 158 microsatellite regions and 26 TEs in the mitochondrial sequences. This work, which can be considered one of the first genomic studies for Cerrado species, represents a great advance in the knowledge on the structure and organization of the D. alata genome. The obtained results open the way for further genetic and genomic investigation for the species.
Nos últimos anos houve um rápido aumento na disponibilidade e qualidade dos dados de sequenciamento e com isso ocorreu uma explosão de projetos de sequenciamento dos genomas de plantas. Nesse cenário, as análises genômicas vêm sendo caracterizadas como eficientes para gerar informações genéticas em larga escala, inclusive para espécies não modelos. Dipteryx alata é uma espécie de árvore não modelo endêmica do bioma Cerrado pertencente à família Leguminosae. Os objetivos deste trabalho foram estimar o número de cromossomos e o tamanho do genoma de D. alata, e também montar e anotar sequências dos genomas organelares e nuclear da espécie usando dados de sequenciamento Illumina. O tamanho do genoma de D. alata foi estimado como 1C = 0.825 pg, o que corresponde a um genoma haplóide de 807.2 MB com 2n=16 cromossomos. Foram montadas 275.709 sequências genômicas nucleares com N50 igual a 1598, o que corresponde a 355MB e 44% do genoma inteiro. Nas sequências nucleares foram anotados 21.981 regiões microssatélites, das quais 49,3% possuem motivos dinucleotídeos, 42,7% trinucleotídeo e 4% tetranucleotídeo. Elementos transponíveis (TEs) foram encontrados em 39,29% das sequências analisadas, o que corresponde a 421.701 TEs. Os retrotransposons LTR (gypsy e copia) foram os TEs mais abundantes nas sequências nucleares. Foram anotados 1.431 genes de RNAs não traduzidos em proteínas, sendo 176 rRNAs, 189 tRNAs, 477 snRNAs, 8 snoRNAs, 466 miRNAs e 115 lncRNAs. Foram anotados também 62.200 genes codificadores de proteínas com tamanho médio de 1.156 pb. O número estimado de mRNAs transcritos pelo conjunto de genes nucleares anotados foi igual a 160.450, dos quais 131.228 apresentaram similaridade significativa com sequências já conhecidas e 84.793 foram classificadas funcionalmente nos termos do Gene Ontology. Um total de 736.787 SNPs e 90.803 InDels foram descobertos nas sequências nucleares. Foi identificada uma média de 1 SNP a cada 189 pb do genoma e a razão entre as mutações de transição (Ts) e transversão (Tv) foi de 1,58. Uma porcentagem de 46,5% dos SNPs ocorreu em contexto gênico e os efeitos dos SNPs foram anotados principalmente em éxons e regiões intergênicas. Foram montados 110 KB de sequências cloroplastidiais com N50 de 2.384 pb e 327 KB de sequências mitocondriais com N50 de 1.784 pb. Foram anotados genes de 3 rRNA, 13 tRNA, 6 miRNA e 20 lncRNA para o cloroplasto e genes de 4 rRNA, 26 tRNA, 7 miRNA e 54 lncRNA para a mitocôndria. Para o cloroplasto foram preditos 20 genes codificantes de proteínas com tamanho médio de 2.374 pb e para a mitocôndria foram preditos 176 genes com tamanho médio de 1.279 pb. O número estimado de mRNAs transcritos por esse conjunto de genes foi igual a 63 e 525 para cloroplasto e mitocôndria, respectivamente. Foram anotados também 39 regiões microssatélites e 4 TEs nas sequências cloroplastidiais e 158 regiões microssatélites e 26 TEs nas sequências mitocondriais. Este trabalho, que pode ser considerado um dos primeiros estudos genômicos para espécies do Cerrado, representa um grande avanço nos conhecimentos sobre a estrutura e a organização do genoma de D. alata. Os resultados obtidos abrem caminho para novas investigações genéticas e genômicas para a espécie.
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13

Docherty, Louise E. "Identification and characterisation of novel small RNAs from repetitive elements in mammals." Thesis, University of Glasgow, 2007. http://theses.gla.ac.uk/16/.

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Transposable elements account for the almost half of the sequence encoded by mammalian genomes, which become silenced during early embryonic development. This thesis sought to explore the hypothesis of the involvement of the RNAi pathway in the silencing of transposable elements in mammals, predominantly through the identification of transposon-associated RNA of -20-25nt using a gel blotting technique. Initially cell lines of embryonic and tumour origin were analysed. This lead to the identification of several previously unreported transposon-associated RNA ranging from 70-90nt. However, it was not until a more detailed analysis of the embryonic cell lines, with the induction of differentiation in cell culture that several discrete RNA of -20nt were detected for the mouse transposons L1 and B2. The differentiation of embryonic cell lines in culture also serendipitously lead to the detection of several short 55 rRNA of -22-26nt, these were also later detected in several human cell lines of breast cancer origin and healthy breast tissue. Intriguingly the -20-26nt repeat-associated identified were predominantly observed after two-days of differentiation in cell culture in several cell lines and often coincided with an ethidium bromide stainable band of -19nt. The latter may indicate a large proportion of these RNAs. Further analysis of the B2 and 55 rRNA repeat-associated short RNA revealed both to have reduce accumulation in Dicer-null embryonic stem cells, implicating a possible association with a known component of the RNAi pathway. Dicer was also observed to process the longer -50-80nt 55rRNA to -20-26nt in vitro. BLAST was also used to identify possible mRNA targets for the short B2 and 55 rRNA. One of these, the mRNA encoding sialic acid acetylesterase (SIAE) was consistently observed to be reduced with the accumulation of the short RNA using end-point RT-PCR, consistent with targeting through the RNAi or a similar pathway. However, no further links with the RNAi pathway were established, with no targeting detected for the short B2 or 55 rRNA using dual luciferase sensor assays. The repeat-associated RNA identified in this thesis are among the first of their type and further work will be required to establish what relevance they have to the RNAi pathway and transposon regulation.
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14

Migeon, Pierre. "Comparative genomics of repetitive elements between maize inbred lines B73 and Mo17." Thesis, Kansas State University, 2017. http://hdl.handle.net/2097/35377.

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Master of Science
Genetics Interdepartmental Program
Sanzhen Liu
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, revealing differences in organization of highly repetitive sequences between the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.
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15

Gao, Guangping. "Transcriptional Analysis of Bm-1 Repetitive Elements in the genome of Bombvx mori." FIU Digital Commons, 1991. http://digitalcommons.fiu.edu/etd/3616.

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Bm-1 repetitive element family represents a group of sequences in the genome of the silkmoth, Bombyx mori. and is found to be transcribed. There are about 3X more Bm-1 cytoplasmic transcripts as compared to their nuclear counterparts. The size range of Bm-1 nuclear transcripts is greater than that of their cytoplasmic species. Alpha- amanitin inhibition and nuclear ”run-on” experiments demonstrated that 80-85% of the Bm-1 transcripts are produced by RNA polymerase II; the other 15-20% may be transcribed by polymerase I and/or III. Sharply contrasting with most of the transcribed SINE families, the Bm-1 transcripts are dramatically enriched in both poly A+ and polysomal RNA fractions. Compared to Bm-1 transcripts in total RNA there are 2-4X more Bm-1 transcripts in the poly A+ RNA population and up to 22X more in the polysomal RNA fractions. This strongly suggests that the transcripts of the Bm-1 family may be involved in translation. To express exogenous Bm-1 elements in vivo and explore their effect(s) on transcriptional actitivity in Bombyx mori cells in culture and their possible function in gene regulation, two members of the Bm-1 family, clone 1 and clone 10, have been subcloned into a selectable and inducible plasmid vector and were named as pG/1 and pG/10, respectively. Subsequently, they were introduced into the BmN and Bm-5 Bombyx mori cell lines by electro-transfection. A G418 (Geneticin) resistant Bombyx mori cell population has been selected out, following transfection.
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16

Mazzuchelli, Juliana [UNESP]. "Identificação e caracterização de sequências repetidas de DNA no genoma do ciclídeo Astronotus ocellatus." Universidade Estadual Paulista (UNESP), 2008. http://hdl.handle.net/11449/102712.

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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Universidade Estadual Paulista (UNESP)
Uma grande porção do genoma da maioria dos organismos é composta por seqüências repetidas de DNA que foram considerados, por muitos anos, como DNA “egoísta” ou como DNA “lixo”. Pouca atenção tem sido dada a estes segmentos de DNA uma vez que eles não são transcritos em produtos codificantes ou funcionais. Atualmente diversos trabalhos têm sugerido o envolvimento destas seqüências na regulação e reparo de alguns genes, na diferenciação de cromossomos sexuais e na organização estrutural e funcional do genoma. Os estudos citogenético-moleculares, como o mapeamento físico cromossômico, têm demonstrado que as seqüências de DNA repetidas podem ser muito úteis como ferramentas para definir a estrutura e revelar a organização e evolução do genoma das espécies. No presente trabalho, vários elementos repetidos (AoHinfI-4, AoHaeIII-6, AoHaeIII-15) foram isolados, através de restrição enzimática, do genoma do ciclídeo sul-americano Astronotus ocellatus, popularmente conhecido como “Oscar” ou “Apaiari”. Estes elementos foram seqüenciados e utilizados como sondas para hibridação cromossômica para o estudo de seu padrão de distribuição no cariótipo. As seqüências dos elementos repetidos isolados por restrição enzimática apresentaram alta similaridade com outros DNAs repetidos de outras espécies de peixes já depositadas em banco de dados. Os resultados da hibridação in situ de todos os elementos utilizados mostraram um acúmulo de marcações preferencialmente centromérica em todos os cromossomos do complemento. Essas marcações também são coincidentes com a localização da heterocromatina evidenciada através do bandamento C, reforçando a idéia do acúmulo de DNA repetitivo em regiões heterocromáticas. Essa distribuição preferencialmente centromérica dos elementos repetidos isolados sugere que tais seqüências devam desempenhar...
In most organisms a great portion of the genome is composed of repetitive DNA sequences. However little attention has been given to these segments of DNA, which were considered by many years as selfish or “junk” DNA. On the other hand, several works have suggested the involvement of these sequences in the regulation and repair of some genes, in the differentiation of sex chromosomes and in the structural and functional organization of the genome. The cytogenetics and molecular studies, as the physical chromosome mapping, has been demonstrating that repetitive sequences can be very useful as tools to define the structure and to reveal the organization and evolution of the genome of the species. In the present work several repetitive elements (retrotransposons Rex1, Rex3 and Rex6; transposon Tc1; the elements AoHinfI-4, AoHaeIII-6, AoHaeIII-15) were isolated using PCR and enzymatic restriction digestion of the genome of the cichlid Astronotus ocellatus, popularly known as Oscar or Apaiari. These elements were sequenced and their genomic distribution determined by chromosomal in situ hybridization. The nucleotide sequences of the isolated elements showed high similarity to repetitive DNAs of other fish species available in public databases. The results of in situ hybridization showed an accumulation of all obtained elements preferentially in centromeres of all chromosomes of the complement. The chromosomal signals were also coincident with the location of the heterocromatins evidenced through the C banding, reinforcing the idea of the accumulation of repetitive DNA in heterocromatic areas. These preferential distribution in the centromeres, suggests that such sequences should play an important role in the functional organizational and structure of the centromeres and, thus in the genome of this species. The great majority of the studies using the physical chromosome mapping... (Complete abstract click electronic access below)
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17

Primo, Cleberson Cezario. "Estudo cromossômico em espécies de Rineloricaria (ACTINOPTERYGII: SILURIFORMES: LORICARIIDAE): diversidade cariotípica e DNAs repetitivos." UNIVERSIDADE ESTADUAL DE PONTA GROSSA, 2015. http://tede2.uepg.br/jspui/handle/prefix/933.

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The Loricariidae family (Actinopterygii: Siluriformes) is morphologically diverse, has a number close to 900 valid species, distributed in seven subfamilies (Lithogeneinae, Delturinae, Neoplecostominae, Hypoptopomatinae, Loricariinae, Ancistrinae and Hypostominae). However, cytogenetic studies in species of the family show evolutionary trends of karyotype diversification well defined for each of the subfamilies and the diploid number (2n) of 54 chromosomes is considered basal. Among the representatives of the subfamily Loricariinae, the variation of 2n is 36 to 74 chromosomes. Given these data, the Robertsonian rearrangements are the main mechanisms to explain the chromosome number variation in the subfamily. Rineloricaria is the most specious genus of Loricariinae, porting species with 2n = 36 to 2n = 70 chromosomes. However, little is known about what types of repetitive DNAs originate fission and fusion chromosome events. In this study, species of Rineloricaria from different rivers of the Paraná drainage were studied: Rineloricaria latirostris (Laranjinha river, Cinzas basin and Barra Grande river, Ivaí basin); Rineloricaria pentamaculata (Barra Grande and Juruba rivers, Tibagi basin); and, Rineloricaria stellata and Rineloricaria capitonia (Upper Uruguai river). The aim of this study was to characterize the karyotypes of populations/species of Rineloricaria and to check what types of repetitive DNAs may be related to Robertsonian events in the genus. In R. latirostris was detected 2n = 46 chromosomes for both populations, as well as for a triploid specimen from Laranjinha river. Rineloricaria pentamaculata had 2n = 56 chromosomes to populations from Barra Grande and Juruba rivers and a karyomorph in Barra Grande river with 2n = 54 chromosomes. Rineloricaria stellata had 2n = 54 chromosomes, while R. capitonia presented 2n = 64 chromosomes, both from the Uruguai river. The results using the chromosomal markers of 18S rDNA, 5S rDNA and TTAGGGn telomeric probe showed that these repetitive DNAs participated in end to end fusions of the st/a chromosomes in the karyotype diversification of R. latirostris. Vestiges of interstitial telomeric sites (ITS) were also detected in R. pentamaculata, karyomorph of 54 chromosomes from the Barra Grande river, suggesting chromosomal fusion to the diversification of this karyotype. The wide range of 2n between R. stellata and R. capitonia is compatible to the reproductive isolation of syntopic species and the diversification of R. capitonia can be explained by centric fusions. In addition to Robertsonian rearrangements, the pericentric inversions also assisted in the diversification of karyotypic formulas among the species/populations. In situ localization analysis using the transposable element Tc1-Mariner Like probe showed no evidence of the participation of transposon in chromosomal rearrangements and dispersion of multiple sites of 5S rDNA in Rineloricaria. Furthermore, analyzes of the Tc1-Mariner Like sequences showed intense molecular degeneration, especially in transposase domains. These results indicate the absence of activity of these sequences, which must be inert or serve to other genomic functions in the genus. Thus, this study discusses the telomeric instability, repetitive DNAs and the participation of rDNA gene families in karyotype diversification events in Rineloricaria.
A família Loricariidae (Actinopterygii: Siluriformes) é extremamente diversificada morfologicamente, conta com um número próximo a 900 espécies válidas, distribuídas em sete subfamílias (Lithogeneinae, Delturinae, Neoplecostominae, Hypoptopomatinae, Loricariinae, Ancistrinae e Hypostominae). Não obstante, os estudos citogenéticos em representantes da família mostram tendências evolutivas da diversificação cariotípica bem definidas para cada uma das subfamílias, sendo considerado basal o número diploide (2n) de 54 cromossomos. Entre os representantes da subfamília Loricariinae a variação do 2n é de 36 a 74 cromossomos. Diante destes dados, os rearranjos Robertsonianos são os principais mecanismos para explicar a variação cromossômica numérica na subfamília. Rineloricaria é o gênero mais especioso de Loricariinae, com espécies apresentando 2n = 36 até 2n = 70 cromossomos. Contudo, pouco se sabe sobre quais os tipos de DNAs repetitivos originam os eventos de fissão e fusão cromossômica. Neste estudo, foram avaliadas espécies de Rineloricaria de diferentes rios do sistema hidrográfico do Paraná: Rineloricaria latirostris (rio Laranjinha, bacia do rio das Cinzas e rio Barra Grande, bacia do rio Ivaí); Rineloricaria pentamaculata (rio Barra Grande e rio Juruba, bacia do rio Tibagi); e, Rineloricaria stellata e Rineloricaria capitonia (Alto Rio Uruguai). O objetivo foi de caracterizar cariotipicamente as populações/espécies de Rineloricaria estudadas, além de verificar quais os tipos de DNAs repetitivos podem estar relacionados aos eventos Robertsonianos no gênero. Em R. latirostris foi detectado 2n = 46 cromossomos para ambas populações, além de um exemplar triploide para o rio Laranjinha. Rineloricaria pentamaculata apresentou 2n = 56 cromossomos para as populações dos rios Barra Grande e Juruba e um cariomorfo 2n = 54 cromossomos no rio Barra Grande. Rineloricaria stellata apresentou 2n = 54 cromossomos, enquanto R. capitonia detém 2n = 64 cromossomos, ambas do rio Uruguai. Os resultados com marcadores cromossômicos de rDNA 18S, rDNA 5S e sonda TTAGGGn evidenciaram que estes DNAs repetitivos participaram dos eventos de fusão terminal para terminal (end to end fusions) de cromossomos st/a na diversificação cariotípica de R. latirostris. Vestígios de sítios teloméricos intersticiais (ITS) foram evidenciados também em R. pentamaculata, cariomorfo de 54 cromossomos do rio Barra Grande, sugerindo fusão cromossômica para a diversificação deste cariótipo. A ampla variação de 2n entre R. stellata e R. capitonia é compatível para o isolamento reprodutivo das espécies sintópicas e pode ser explicado por fissões cêntricas na diversificação de R. capitonia. Além dos rearranjos Robertsonianos, as inversões pericêntricas também auxiliaram na diversificação de fórmulas cariotípicas entre as espécies/populações. A análise de localização in situ do elemento transponível Tc1-Mariner Like não mostrou evidências da participação deste transposon nos rearranjos cromossômicos e na dispersão dos sítios múltiplos de rDNA 5S em Rineloricaria. Ainda, as análises das sequências Tc1-Mariner Like evidenciaram intensa degeneração molecular, principalmente nos domínios transposase. Estes resultados indicam a ausência de atividade destas sequências, as quais devem ser inertes ou servir para outras funções genômicas no gênero. Desta forma, este estudo discute a instabilidade telomérica, DNAs repetitivos e a participação das famílias gênicas de rDNA nos eventos de diversificação cariotípica em Rineloricaria.
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18

Barbosa, Patrícia. "ELEMENTOS GENÔMICOS REPETITIVOS NO COMPLEXO Astyanax scabripinnis (TELEOSTEI, CHARACIDAE)." UNIVERSIDADE ESTADUAL DE PONTA GROSSA, 2013. http://tede2.uepg.br/jspui/handle/prefix/982.

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The most part of the eukaryote genomes is constituted for repetitive DNA or multiple copies DNA, which has already been considered as “junk”, may be associated to the heterochromatin. In this study three Astyanax scabripinnis populations from Pindamonhangaba and Guaratinguetá (SP, Brazil) rivers and stream and one population from Maringá (PR, Brazil) were analyzed about the nucleolar organizing region (NORs), As51 satellite DNA, 18S and 5S rDNA location. Moreover, repetitive sequences were isolated and mapped through Cot-1 technique, which showed homology with UnaL2, a LINE type retrotransposon. The fluorescent in situ hybridization (FISH), with the isolated built retrotransposon probe, evidenced disperse labeled and stronger in centromeric and telomeric chromosomes regions, co-located and interspersed with the 18S DNAr and As51, proven by the fiber-FISH technique. The B chromosome of those populations showed very conspicuous labeled with the LINE probe, also co-located with the As51 sequences. The NORs were actives in a single site of a homologue pair in all three populations, with no evidence that the transposable elements and repetitive DNA have influence in its regulation at the performed analyzes level.
A maior parte do genoma dos eucariotos é constituída por DNA repetitivo ou DNA de múltiplas cópias, o qual já foi considerado “lixo”, podendo estar associado à heterocromatina. Neste estudo foram analisadas três populações de Astyanax scabripinnis provenientes de rios e córregos de Pindamonhangaba e Guaratinguetá (SP, Brasil) e uma população da cidade de Maringá (PR, Brasil) quanto a localização das regiões organizadoras de nucléolo (RONs), DNA satélite As51, DNA ribossomal (DNAr) 18S e DNAr 5S. Ainda, foram isoladas e mapeadas sequências repetitivas por meio da técnica de Cot-1, que mostrou homologia com UnaL2, retrotransposon do tipo LINE. A hibridação in situ fluorescente (FISH), com sonda construída para o retrotransposon isolado, evidenciou marcações dispersas e mais concentradas em regiões centroméricas e teloméricas dos cromossomos, co-localizadas e interespaçadas com DNAr 18S e As51, comprovada pela técnica de fiber-FISH. O cromossomo B das populações mostrou marcações bastante conspícuas com a sonda LINE, também co-localizada com sequências As51. As RONs apresentaram-se ativas em sítios únicos de um par homólogo nas três populações, não havendo indícios de que elementos transponíveis e DNA repetitivo tenham influência na sua regulação ao nível das análises realizadas.
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19

Silva, Carlos Eduardo Faresin e. "Mapeamento físico cromossômico de elementos repetitivos em marsupiais Amazônicos." Instituto Nacional de Pesquisas da Amazônia, 2016. http://bdtd.inpa.gov.br/handle/tede/2219.

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Fundação de Amparo à Pesquisa do Estado do Amazonas - FAPEAM
Currently, marsupials are the second largest mammals living family. The groups evolutionary history is linked to the geological history of the continent and in South America, they are represented mainly by Didelphidae family. This family is the only present in the Amazon and in the rest of Brazil. Marsupial cytogenetic characterization shows a conservation of diploid numbers ranging from 10 to 32 chromosomes, and in didelphids are known karyotypes 14, 18 and 22 chromosomes. In this context, molecular cytogenetic allows for new inferences about the chromosomal evolution, supplying additional characters to analyze, for example, mapping repetitive regions of the genome. In this paper we map repetitive elements in species didelphids collected in 13 new locations in the Amazon in unexplored regions, seeking to understand evolutionary patterns of karyotypes. In all were analyzed 194 individuals of 16 species featured in conventional staining, band C, Ag-RON and FISH with probes DNAr18S, telomeric and transposable element LINE-1. We observed variation on the X chromosome, the distribution of heterochromatin and mapping sequences of 18S ribosomal DNA and telomeric sequences. The main variation found in the position of the centromere was the X chromosome of C. lanatus and Marmosa murina. Geographically, the different types of X, both species showed a segregation between eastern and western Brazil, with contact in the central Amazon. For species Marmosops spp. two patterns of X were evidenced by the C-band technique, but less obvious geographical distribution. The nucleolar organizer regions were confirmed by 18S rRNA gene probe in all species except the marking of the Y chromosome Monodelphis brevicaudata. The distribution of this marker showed only variable in Marmosa genre. Considering RON simple as a character plesiomorphic conclude that the species of the genus Didelphis and Marmosa evolved independently for multiple system. Marsupials are considered chromosomally conservative, however, given the current state of knowledge to this group, inter variations and intraspecific are observed and this is due to the expansion of the sample and the application of more accurate techniques, suggesting the presence of chromosomal rearrangements in evolution this animal group. Regarding the telomeric sequences, 11 species were analyzed and compared the presence of interstitial telomeric sequences (ITSs) with the distribution of the C band and found that STIs are coincident with heterochromatin blocks. Of the 11 species examined, only 5 had STIs, all within the centromeric heterochromatin region. The presence of STIs was constant on the X chromosome of Marmosa individuals and murine variable in the other species. We believe that the variable presence of STIs is a particular characteristic of each lineage. Our results support the inference that such sequences can not always be interpreted as a consequence of chromosomal rearrangement. Finally, we map the LINE-1 retroelement to five species of copies: Caluromys philander, Gracilinanus emiliae, Marmosa murina, Marmosa demerarae and Didelphis marsupialis. The markings are shown scattered all chromosomes, with no preference for specific chromosome regions, or even the X chromosome, as reported in the literature for other marsupials. The most informative variations were in the morphology of the X chromosome, which verified the existence of geographic patterns and are possibly related to different species, showing that chromosomal variation has relation to the diversification of species. Markers of repetitive sequences (18S, telomere and L1) showed variations possibly be related to more recent events of speciation.
Os marsupiais sulamericanos estão representados principalmente pela família Didelphidae considerada conservada cariotipicamente. No presente trabalho mapeamos elementos repetitivos em 194 indivíduos, representando 16 espécies de didelfídeos, coletadas em 13 localidades ainda não exploradas, do ponto de vista científico, na Amazônia, para verificar possíveis padrões de evolução cariotípica. Para isso foram utilizados métodos citogenéticos clássicos e moleculares. Variações no cromossomo X, na distribuição da heterocromatina e no mapeamento de sequências de DNA ribossomal 18S e sequências teloméricas foram registradas. A principal variação foi na posição do centrômero do cromossomo X de Caluromys lanatus e de Marmosa murina. Os diferentes tipos de cromossomos X, de ambas espécies, mostraram uma separação em termos geográficos entre leste e oeste do Brasil, com contato na Amazônia central. Para as espécies de Marmosops spp., dois padrões de X foram evidenciados pelo método de banda C, porém não foram separados geográficamente. As regiões organizadoras de nucléolo foram confirmadas pelas sondas de DNAr 18S em todas as espécies, exceto a marcação do cromossomo Y de Monodelphis brevicaudata. A distribuição desse marcador se mostrou variável apenas no gênero Marmosa. Considerando a RON simples como um caráter plesiomórfico sugerimos que as espécies do gênero Marmosa e Didelphis marsupialis evoluíram independentemente para o sistema múltiplo. Em relação às sequências teloméricas, 11 espécies foram analisadas e cinco apresentaram ITSs, todas dentro da região de heterocromatina centromérica. A presença de ITS foi constante no cromossomo X de indivíduos de Marmosa murina e variável nas demais espécies. Acreditamos que a presença variável das ITSs seja uma característica particular de cada linhagem. O retroelemento LINE-1 foi mapeado em exemplares de cinco espécies: Caluromys philander, Gracilinanus emiliae, Marmosa murina, Marmosa demerarae e Didelphis marsupialis. As marcações se mostraram dispersas por todos os cromossomos, não havendo preferência por regiões específicas do cromossomo, nem mesmo pelo cromossomo X. A variação do cromossomo X e os padrões de distribuição dos elementos repetitivos podem ser reflexo dos eventos de especiação ocorridos nos didelfídeos.
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20

Cattani, Amanda Malvessi. "Elementos repetitivos na regulação da transcrição de Mycoplasma hyopneumoniae." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2016. http://hdl.handle.net/10183/143890.

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Mycoplasma hyopneumoniae é uma bactéria de tamanho diminuto, caracterizada por um genoma pequeno, com baixo conteúdo GC. Está associada com doenças respiratórias de suínos, resultando em prejuízos produtivos e econômicos na indústria animal. A presença de sequências de DNA repetitivas, que ocorrem em grandes quantidades em células eucarióticas, vem sendo cada vez mais identificadas em genomas de procariotos, sendo também associadas a um potencial papel regulador. Uma vez que a regulação da transcrição nesses organismos ainda é pouco entendida, o objetivo do presente estudo foi realizar uma busca in silico por elementos repetitivos nas regiões intergênicas do genoma de M. hyopneumoniae linhagem 7448. Dois tipos de repetições foram selecionados para a busca inicial: tandem e palindromes. Regiões intergênicas de até 500 pb a montante do sítio de início da tradução de todas as CDSs do genoma de M. hyopneumoniae linhagem 7448 foram utilizadas para a predição. Para cada tipo de elemento dois programas computacionais independentes foram utilizados. As predições in silico resultaram em 144 repetições em tandem e 1.171 palindromes. O DNA repetitivo se encontra distribuído a montante de 86% das unidades transcricionais de M. hyopneumoniae linhagem 7448. Análises comparativas entre genomas de micoplasmas demonstraram diferentes níveis de conservação dos elementos repetitivos entre linhagens patogênicas e não-patogênicas. Linhagens patogênicas revelaram uma conservação de 59%, enquanto que a não patogênica, somente de 46%. Através de ensaios de amplificação quantitativa de DNA, foi observado diferentes níveis de expressão em genes codificantes para importantes proteínas, como glicina hidroximetiltransferase, lipoproteína, adesinas e proteína ligadora de GTP. Os genes codificantes para essas proteínas divergiam no número de repetições palindromes e tandens na sua respectiva região intergênica. Além disso, repetições encontradas em 206 genes já descritos como regulados em diferentes condições em M. hyopneumoniae linhagem 232 mostraram aproximadamente 80% de conservação em relação à linhagem M. hyopneumoniae linhagem 7448. Todos esses resultados sugerem um potencial papel regulador das repetições de DNA em tandem e palindromes em Mycoplasma.
Mycoplasma hyopneumoniae is a diminutive bacterium, characterized by a small genome with a low GC content. It is commonly associated with swine respiratory diseases, resulting in productivity and economic losses in the animal industry. Repetitive DNA, which occurs in large quantities in eukaryotic cells, has been increasingly identified in prokaryotic genomes, and has been associated with a potential regulatory function. Once transcription regulation in these organisms is still poorly understood, the aim of the current study was to perform an in silico search of repeat elements in the genomic intergenic regions of M. hyopneumoniae strain 7448. Two types of repeats were selected for initial search: Tandem and Palindromic. Intergenic regions up to 500 bp upstream from start codon of M. hyopneumoniae strain 7448 CDSs were used as input for the software’s prediction. For each type of repeat sequence, two independent software packages were used. Computational analysis results in 144 tandem repeats and 1,171 palindrome elements. The repeats were distributed in the upstream region of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct mycoplasmas, demonstrate different indices of repeat conservation among pathogenic and non-pathogenic strains. Pathogenic strains revealed 59% conservation, while non-pathogenic only 46%. Through assays of quantitative amplification of DNA, different levels of expression in genes coding important proteins have been demonstrated, as glycine hydroxymethyltransferase, lipoprotein, adhesins and GTP-binding protein. These protein coding genes differ in number of palindromes or tandem repeats in respective upstream regions. In addition, repeats found in 206 genes already described to be regulated in different grow conditions in M. hyopneumoniae strain 232 showed almost 80% of conservation in relation to M. hyopneumoniae strain 7448. All these findings, suggests a potential regulatory role of tandem and palindrome DNA repeats.
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21

Grady, Patrick James Robert. "Epigenome control by chromatin modifiers: roles for histone H3 lysine modifiers in the regulation of repetitive elements." Thesis, Boston College, 2015. http://hdl.handle.net/2345/bc-ir:104931.

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Thesis advisor: Hugh P. Cam
Chromatin is the site of numerous structural features that contribute to the regulation of the genome. Although numerous posttranslational modifications to the histone proteins that make up chromatin have been identified, it remains unclear whether and to what extent these modifications might regulate transposons and other repetitive sequences. One such modification is methylation of histone H3 lysine 4 (H3K4me), which is catalyzed by Set1 and its associated complex Set1C/COMPASS. Although H3K4me is associated with actively transcribed regions in euchromatin, an emerging body of evidence suggests that Set1-mediated transcriptional control is often repressive. This thesis work describes expanded functions for Set1C/COMPASS as a regulatory module with roles throughout the genome. We identify novel locus-dependent repressive functions for Set1 at repetitive genomic regions. Interestingly, Set1 has multiple repressive modes that are dependent and independent of H3K4me. Additionally, we show that Set1 controls the nuclear organization of Tf2 retrotransposons by antagonizing H3K4 acetylation. We describe how the roles of Set1 in the nuclear organization and transcriptional repression of Tf2 cooperate to restrict Tf2 transposition. Finally, we identify an H3K4-dependent role in countering the reduced dosage of histone H3 genes to help maintain genome stability and silencing of Tf2s and pericentromeric heterochromatin. Our study considerably expands the regulatory repertoire of an important histone modifier and highlights the multifaceted function by a highly conserved chromatin-modifying complex with diverse roles in genome control
Thesis (PhD) — Boston College, 2015
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
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22

Mazzuchelli, Juliana. "Identificação e caracterização de sequências repetidas de DNA no genoma do ciclídeo Astronotus ocellatus /." Botucatu : [s.n.], 2008. http://hdl.handle.net/11449/102712.

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Orientador: Cesar Martins
Banca: André Luís Laforga Vanzela
Banca: Luiz Antônio Carlos Bertollo
Resumo: Uma grande porção do genoma da maioria dos organismos é composta por seqüências repetidas de DNA que foram considerados, por muitos anos, como DNA "egoísta" ou como DNA "lixo". Pouca atenção tem sido dada a estes segmentos de DNA uma vez que eles não são transcritos em produtos codificantes ou funcionais. Atualmente diversos trabalhos têm sugerido o envolvimento destas seqüências na regulação e reparo de alguns genes, na diferenciação de cromossomos sexuais e na organização estrutural e funcional do genoma. Os estudos citogenético-moleculares, como o mapeamento físico cromossômico, têm demonstrado que as seqüências de DNA repetidas podem ser muito úteis como ferramentas para definir a estrutura e revelar a organização e evolução do genoma das espécies. No presente trabalho, vários elementos repetidos (AoHinfI-4, AoHaeIII-6, AoHaeIII-15) foram isolados, através de restrição enzimática, do genoma do ciclídeo sul-americano Astronotus ocellatus, popularmente conhecido como "Oscar" ou "Apaiari". Estes elementos foram seqüenciados e utilizados como sondas para hibridação cromossômica para o estudo de seu padrão de distribuição no cariótipo. As seqüências dos elementos repetidos isolados por restrição enzimática apresentaram alta similaridade com outros DNAs repetidos de outras espécies de peixes já depositadas em banco de dados. Os resultados da hibridação in situ de todos os elementos utilizados mostraram um acúmulo de marcações preferencialmente centromérica em todos os cromossomos do complemento. Essas marcações também são coincidentes com a localização da heterocromatina evidenciada através do bandamento C, reforçando a idéia do acúmulo de DNA repetitivo em regiões heterocromáticas. Essa distribuição preferencialmente centromérica dos elementos repetidos isolados sugere que tais seqüências devam desempenhar... (Resumo completo clicar acesso eletrônico abaixo)
Abstract: In most organisms a great portion of the genome is composed of repetitive DNA sequences. However little attention has been given to these segments of DNA, which were considered by many years as "selfish" or "junk" DNA. On the other hand, several works have suggested the involvement of these sequences in the regulation and repair of some genes, in the differentiation of sex chromosomes and in the structural and functional organization of the genome. The cytogenetics and molecular studies, as the physical chromosome mapping, has been demonstrating that repetitive sequences can be very useful as tools to define the structure and to reveal the organization and evolution of the genome of the species. In the present work several repetitive elements (retrotransposons Rex1, Rex3 and Rex6; transposon Tc1; the elements AoHinfI-4, AoHaeIII-6, AoHaeIII-15) were isolated using PCR and enzymatic restriction digestion of the genome of the cichlid Astronotus ocellatus, popularly known as "Oscar" or "Apaiari". These elements were sequenced and their genomic distribution determined by chromosomal in situ hybridization. The nucleotide sequences of the isolated elements showed high similarity to repetitive DNAs of other fish species available in public databases. The results of in situ hybridization showed an accumulation of all obtained elements preferentially in centromeres of all chromosomes of the complement. The chromosomal signals were also coincident with the location of the heterocromatins evidenced through the C banding, reinforcing the idea of the accumulation of repetitive DNA in heterocromatic areas. These preferential distribution in the centromeres, suggests that such sequences should play an important role in the functional organizational and structure of the centromeres and, thus in the genome of this species. The great majority of the studies using the physical chromosome mapping... (Complete abstract click electronic access below)
Mestre
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23

Souza, Renata Torres [UNIFESP]. "Identificação de um novo elemento repetitivo de Trypanosoma cruzi que apresenta inserção sítio-específica no genoma." Universidade Federal de São Paulo (UNIFESP), 2007. http://repositorio.unifesp.br/handle/11600/39421.

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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Agência Internacional de Energia Atômica (IAEA)
Nós identificamos em T. cruzi uma nova família de retroelementos sítioespecífico chamada TcTREZO (Trypanosoma cruzi Tandem Repetitive Element ZO). O elemento TcTREZO é uma repetição de natureza composta sendo constituído por seqüências presentes em outras localidades do genoma não associadas ao elemento. Análise da distribuição do TcTREZO no genoma indica claramente que o elemento está inserido em sítios específicos do genoma. A maioria dos elementos TcTREZO é flanqueada por seqüências conservadas. A região 5´ do elemento é flanqueada por uma seqüência conservada de 68-pb e a região 3´ por um domínio de aproximadamente 500 pb cujas extremidades não são muito bem definidas. Análises de hibridação em “northern blot” e amplificação por RT-PCR indicam a presença de transcritos TcTREZO poliadenilados cujo tamanho (1,6 kb) corresponde ao tamanho do elemento completo. Também foram detectados transcritos de ~ 0,2 kb derivados de uma pequena região do elemento TcTREZO. O número de cópias do elemento foi estimado como sendo de ~ 1800 cópias por genoma haplóide. TcTREZO parece ter sido formado por inserção de seqüências em um elemento progenitor. Uma vez associadas entre si, essas foram amplificadas com sucesso gerando um novo elemento que representa ~ 5 % do genoma de T. cruzi. TcTREZO poderia ter sido originado por um único evento de inserção após o qual o aumento do número de cópias teria ocorrido por “crossing-over” desigual ou conversão gênica. O fato de TcTREZO ser encontrado apenas em T. cruzi sugere que ele possa ter tido algum papel na especiação deste parasita por amplificação e distribuição no genoma. TcTREZO insere-se em sítios específicos, sugerindo que uma endonuclease específica pode ser a responsável por sua inserção em sítios únicos do genoma.
A new family of site-specific retroelements identified in Trypanosoma cruzi, which we named TcTREZO, is described here. TcTREZO appears to be a composite repeated element, since three subregions may be defined within it on the basis of sequence similarities with other T. cruzi sequences. Analysis of the distribution of TcTREZO in the genome clearly indicates that it displays site specificity for insertion. Most TcTREZO elements are flanked by conserved sequences. There is a highly conserved 68-bp sequence at the 5’ end of the element and a sequence domain of ~500 bp without a well-defined borderline at the 3’ end. Northern blot hybridization and RT-PCR analyses showed that TcTREZO transcripts are expressed as oligo (A)-terminated transcripts whose length corresponds to the unit size of the element (1.6 kb). Transcripts of ~0.2 kb derived from a small part of TcTREZO are also detected in steady-state RNA. The copy number of TcTREZO sequences was estimated to be ~ 1800 copies per haploid genome. TcTREZO appears to have been assembled by insertions of sequences into a progenitor element. Once associated with each other, these subunits were amplified as a new transposable element with such remarkable success that TcTREZO comprises ~ 5 % of the T. cruzi genome. TcTREZO could presumably have originated from a single insertion event after which its copy number increased, possibly through unequal sister-chromatid exchange or gene conversion. As it is only present in T. cruzi, TcTREZO could have played a role in the speciation of this parasite by amplification and genome-wide dispersion. TcTREZO shows site specificity for insertion, suggesting that a sequence-specific endonuclease could be responsible for its insertion at a unique site.
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24

Dockter, Rhyan B. "Genome Snapshot and Molecular Marker Development in Penstemon (Plantaginaceae)." BYU ScholarsArchive, 2011. https://scholarsarchive.byu.edu/etd/2512.

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Penstemon Mitchell (Plantaginaceae) is one of the largest, most diverse plant genera in North America. Their unique diversity, paired with their drought-tolerance and overall hardiness, give Penstemon a vast amount of potential in the landscaping industry—especially in the more arid western United States where they naturally thrive. In order to develop Penstemon lines for more widespread commercial and private landscaping use, we must improve our understanding of the vast genetic diversity of the genus on a molecular level. In this study we utilize genome reduction and barcoding to optimize 454-pyrosequencing in four target species of Penstemon (P. cyananthus, P. davidsonii, P. dissectus and P. fruticosus). Sequencing and assembly produced contigs representing an average of 0.5% of the Penstemon species. From the sequence, SNP information and microsatellite markers were extracted. One hundred and thirty-three interspecific microsatellite markers were discovered, of which 50 met desired primer parameters, and were of high quality with readable bands on 3% Metaphor gels. Of the microsatellite markers, 82% were polymorphic with an average heterozygosity value of 0.51. An average of one SNP in 2,890 bp per species was found within the individual species assemblies and one SNP in 97 bp were found between any two supposed homologous sequences of the four species. An average of 21.5% of the assembled contigs were associated with putative genes involved in cellular components, biological processes, and molecular functions. On average 19.7% of the assembled contigs were identified as repetitive elements of which LTRs, DNA transposons and other unclassified repeats, were discovered. Our study demonstrates the effectiveness of using the GR-RSC technique to selectively reduce the genome size to putative homologous sequence in different species of Penstemon. It has also enabled us the ability to gain greater insights into microsatellite, SNP, putative gene and repetitive element content in the Penstemon genome which provide essential tools for further genetic work including plant breeding and phylogenetics.
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25

Bikár, Robert. "Rekonstrukce opakujících se segmentů DNA." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2016. http://www.nusl.cz/ntk/nusl-255392.

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Hlavní motivací diplomové práce bylo najít vhodný algoritmus, který by vytvořil grafovou reprezentaci NGS sekvenačních dat v lineárním čase. Zvolenou metodou pro reprezentaci je de Bruijnův graf. V další části práce byl navrhnut nástroj, který je schopen transformovat graf do přijatelné podoby pro vykreslování, a dále je schopen odstraňovat chyby, které vznikají při konstrukci grafu. Cílem práce je vytvořit nástroj, který rekonstruuje repetitivní segmenty v DNA. Implementovaný nástroj byl otestován a je schopen identifikovat opakující se segmenty, určit jejich typy, vizualizovat je a sestavit jejich sekvenci na jednodušších genomech s velkou přesnotí. Při použití složitějších genomů, nástroj nalezne pouze fragmenty repetitivních segmentů.
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26

MARCO, C. DE. "SELF-REPRESENTING PARABLES:THE AUTOBIOGRAPHICAL ELEMENT IN PER OLOV ENQUIST'S WORKS." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/529848.

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Questa tesi si propone di analizzare l’opera di Per Olov Enquist alla luce di una prospettiva autobiografica. Dopo aver pubblicato numeri romanzi e opere teatrali di grande successo, in cui spesso compaiono elementi e dettagli autobiografici, nel 2008 l’autore svedese ha dato alle stampe un’autobiografia, la cui lettura rafforza l’impressione che le sue esperienze personali abbiano costituito una fondamentale fonte di ispirazione per le opere di finzione. Per inquadrare gli scritti di Enquist in un’ottica autobiografica vengono utilizzate alcune chiavi di lettura offerte dagli stessi testi presi in analisi. Si tratta in primo luogo di due metafore che rappresentano il bisogno di ordinare e di trovare un significato all’esperienza del mondo e della propria identità, attività che parte della critica identifica come motore stesso della scrittura autobiografica: l’assemblare puzzle e il disegnare mappe. In secondo luogo, anche l’uso quasi ossessivo della ripetizione di episodi, immagini ed espressioni viene interpretato come portatore di una valenza autobiografica. A ricorrere sono una serie di «punti dolenti» (smärtpunkterna in originale) che da un lato non vengono mai raccontati fino in fondo, dall’altro si ripresentano da un libro all’altro proprio in virtù della loro carica emotiva inespressa. Questo porta a identificare le due forze contrarie all’opera contemporaneamente nella scrittura di Enquist: da un lato l’impulso a nascondere, a negare, dall’altro quello a mostrare, a rivelare. Alla luce di queste chiavi di lettura, vengono prese in esame gran parte delle opere di Enquist, dagli esordi nel 1961 al libro più recente del 2013. Questa analisi evidenzia un’evoluzione nelle strategie di auto-rappresentazione utilizzate. In una prima fase (Kristallögat, Färdvägen, Hess, Legionärerna), gli elementi autobiografici sono isolati e spesso attribuiti a personaggi di finzione. In un secondo gruppo di opere (Sekonden, Musikanternas uttåg, Nedstörtad ängel, I lodjurets timma), assistiamo a un aumento del livello di autobiograficità, pur mantenendo un contesto finzionale. Infine, nell’ultima fase la dimensione autobiografica diventa centrale, sebbene con modalità diverse nei vari testi presi in considerazione: declinata sotto forma di saggio in Kartritarna, l’auto-rappresentazione assume forma metaforica in Kapten Nemos bibliotek, dichiaratamente autobiografica in Ett annat liv, per poi tornare a una forma ibrida ma a forte componente memorialistica in Liknelseboken. Da questa analisi delle opere di Per Olov Enquist emerge la conclusione che la costante presenza di elementi autobiografici nella sua scrittura è indice di un’esigenza di creare un ordine e trovare un senso al sé e al mondo. Tuttavia, la forma tipicamente autobiografica (cronologica, analitica) non sembra essere la più adatta a soddisfare questa esigenza, a cui risponde meglio una rappresentazione basata sulla metafora.
This dissertation aims at analysing Per Olov Enquist’s work in the light of an autobiographical perspective. After giving to print a number of acclaimed novels and dramas, often strewn with autobiographical elements and details, in 2008 he also published an autobiography, which reinforced the impression that his personal experience had been a fundamental inspiration for his fictional works. The keys that allow to read Enquist’s writings in an autobiographical light are taken from his own works: in particular, I have identified two metaphors that represent the need for ordering and finding a meaning in the world and himself, i.e. assembling puzzles and drawing maps, as well as an obsessive use of repetition, seen as the other side of the coin of the silence under which sensitive subjects (or smärtpunkterna, as the author calls them) are passed. In Enquist’s works in fact the opposing forces of negation and revelation are always at work at the same time: although disturbing experiences are often disguised or passed under silence, their intrinsic force makes sure that they are mentioned again and again, from one book to another. Enquist’s works have then been grouped into three sets with different self-representing strategies: from inserting isolated personal elements in the plot, often attributed to fictional characters, as in the first group (Kristallögat, Färdvägen, Hess and Legionärerna), to a more marked presence of the autobiographical elements, albeit still in a fictionalised frame, in the second group (Sekonden, Musikanternas uttåg, Nedstörtad ängel and I lodjurets timma), to a clear self-representative purpose in the third group, although with deeply different methods: oneiric and symbolical in Kapten Nemos bibliotek, essaistic in Kartritarna, straightforwardly autobiographical in Ett annat liv, pensively memoiristic in Liknelseboken. The conclusions I have drawn from this survey of Per Olov Enquist’s production is that the persistent recurrence of autobiographical elements in his writing is connected to the need to find a meaning and a unity, both in himself and in the world. However, straightforward autobiography is not necessarily the most adequate way to satisfy that need: in Enquist’s case, metaphor seems to offer a more effective solution.
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27

KEE, SOONBOK. "Elements of Continuity in Alexander Scriabin's Musical Language: An Analysis of Selected Piano Preludes." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1204677896.

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28

Matocha, Petr. "Efektivní hledání překryvů u NGS dat." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2017. http://www.nusl.cz/ntk/nusl-363811.

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The main theme of this work is the detection of overlaps in NGS data. The work contains an overview of NGS sequencing technologies that are the source of NGS data. In the thesis, the problem of overlapping detection is generally defined. Next, an overview of the available algorithms and approaches for detecting overlaps in NGS data is created. Principles of these algorithms are described herein. In the second part of this work a suitable tool for detecting approximate overlaps in NGS data is designed and its implementation is described herein. In conclusion, the experiments performed with this tool and the conclusions that follow are summarized and described.
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29

Cabral-de-Mello, Diogo Cavalcanti [UNESP]. "Organização cromossômica de elementos repetitivos de DNA em representantes da sufamília Scarabaeinae (Coleoptera: Scarabaeidae)." Universidade Estadual Paulista (UNESP), 2011. http://hdl.handle.net/11449/102679.

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O mapeamento cromossômico de seqüências repetitivas de DNA tem se mostrado uma eficiente ferramenta nos estudos comparativos e evolutivos em diversos organismos. Estudos cromossômicos com besouros da subfamília Scarabaeinae têm revelado ampla variabilidade, entretanto a análise da organização cromossômica de DNAs repetitivos neste grupo é escassa e direcionada unicamente ao mapeamento do DNA ribossomal (DNAr) 18S. O presente trabalho teve como objetivo caracterizar cromossomicamente DNAs repetitivos em espécies de Scarabaeinae, utilizando bandeamentos cromossômicos e mapeamento físico cromossômico de seqüências repetitivas, incluindo famílias multigênicas de RNAr 18S, RNAr 5S e histona H3 e a fração de DNA C0t-1. Ampla variabilidade foi observada relacionada ao número/localização dos sítios de DNAr 18S, aparentemente associada a diversificação da heterocromatina. Por outro lado, os genes de RNAr 5S e histona H3, mostraram-se amplamente conservados e co-localizados em um par cromossômico, com aparente intercalação. Análises em representantes de Dichotomius revelaram conservação dos blocos de heterocromatina, entretanto com aparente compartimentalização dos mesmos. O uso da fração DNA C0t-1 confirmou o enriquecimento em DNAs repetitivos da heterocromatina, que se apresentou diversificada entre as espécies, utilizando como referência D. geminatus. Por outro lado, regiões terminais dos cromossomos apresentaram-se amplamente conservadas entre as seis espécies. Além disso, a análise da fração de DNAs repetitivos em D. geminatus indicou origem intraespecífica do cromossomo B desta espécie que possivelmente pode estar sofrendo homogeneização com seqüências encontradas no complemento A. Os resultados indicam distintos padrões de diversificação para o DNA repetitivo nos representantes de Scarabaeinae, sugerindo extensiva reorganizaçãomicrogenômica ao longo
The chromosomal mapping of repeated DNAs has been used as an efficient tool in comparative and evolutionary studies in some organism. The chromosomal studies in beetles belonging to the subfamily Scarabaeinae have revealed wide variability, although the analysis of chromosomal organization of repeated DNAs in this group is scarce and directed solely for 18S rDNA mapping. The present study aimed in chromosomal characterization of repeated DNAs in Scarabaeinae species using chromosomal banding and physical chromosome mapping of repeated sequences, including the multigene families for 18S and 5S rRNAs and H3 histone genes and the C0t-1 DNA fraction. Wide variability was observed concerning the number and location of 18S rDNA sites, apparently associated to the heterochromatin diversification. On the other hand, the 5S rRNA and H3 histone genes were widely conserved and co-located in one chromosomal pair, showing apparently interspersion. Analysis in Dichotomius representatives revealed conservation for heterochromatic blocks, although an apparent compartmentalization was observed. The use of C0t-1 DNA fraction confirmed the heterochromatin repeated DNAs enrichment, which is diversified among the species, using as reference D. geminatus. On the other hand, the terminal regions of the chromosomes were highly conserved among the six species. Moreover, the analysis of repeated DNA fraction from D. geminatus indicated intraspecific origin of a B chromosome in this species that possibly could be suffering homogenization with A complement sequences. The results indicate distinct diversification patterns for repeated DNAs in Scarabaeinae representatives, suggesting extensive microgenomic reorganization along the cladogenesis of the group
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30

Cabral-de-Mello, Diogo Cavalcanti. "Organização cromossômica de elementos repetitivos de DNA em representantes da sufamília Scarabaeinae (Coleoptera: Scarabaeidae) /." Botucatu : [s.n.], 2011. http://hdl.handle.net/11449/102679.

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Resumo: O mapeamento cromossômico de seqüências repetitivas de DNA tem se mostrado uma eficiente ferramenta nos estudos comparativos e evolutivos em diversos organismos. Estudos cromossômicos com besouros da subfamília Scarabaeinae têm revelado ampla variabilidade, entretanto a análise da organização cromossômica de DNAs repetitivos neste grupo é escassa e direcionada unicamente ao mapeamento do DNA ribossomal (DNAr) 18S. O presente trabalho teve como objetivo caracterizar cromossomicamente DNAs repetitivos em espécies de Scarabaeinae, utilizando bandeamentos cromossômicos e mapeamento físico cromossômico de seqüências repetitivas, incluindo famílias multigênicas de RNAr 18S, RNAr 5S e histona H3 e a fração de DNA C0t-1. Ampla variabilidade foi observada relacionada ao número/localização dos sítios de DNAr 18S, aparentemente associada a diversificação da heterocromatina. Por outro lado, os genes de RNAr 5S e histona H3, mostraram-se amplamente conservados e co-localizados em um par cromossômico, com aparente intercalação. Análises em representantes de Dichotomius revelaram conservação dos blocos de heterocromatina, entretanto com aparente compartimentalização dos mesmos. O uso da fração DNA C0t-1 confirmou o enriquecimento em DNAs repetitivos da heterocromatina, que se apresentou diversificada entre as espécies, utilizando como referência D. geminatus. Por outro lado, regiões terminais dos cromossomos apresentaram-se amplamente conservadas entre as seis espécies. Além disso, a análise da fração de DNAs repetitivos em D. geminatus indicou origem intraespecífica do cromossomo B desta espécie que possivelmente pode estar sofrendo homogeneização com seqüências encontradas no complemento A. Os resultados indicam distintos padrões de diversificação para o DNA repetitivo nos representantes de Scarabaeinae, sugerindo extensiva reorganizaçãomicrogenômica ao longo
Abstract: The chromosomal mapping of repeated DNAs has been used as an efficient tool in comparative and evolutionary studies in some organism. The chromosomal studies in beetles belonging to the subfamily Scarabaeinae have revealed wide variability, although the analysis of chromosomal organization of repeated DNAs in this group is scarce and directed solely for 18S rDNA mapping. The present study aimed in chromosomal characterization of repeated DNAs in Scarabaeinae species using chromosomal banding and physical chromosome mapping of repeated sequences, including the multigene families for 18S and 5S rRNAs and H3 histone genes and the C0t-1 DNA fraction. Wide variability was observed concerning the number and location of 18S rDNA sites, apparently associated to the heterochromatin diversification. On the other hand, the 5S rRNA and H3 histone genes were widely conserved and co-located in one chromosomal pair, showing apparently interspersion. Analysis in Dichotomius representatives revealed conservation for heterochromatic blocks, although an apparent compartmentalization was observed. The use of C0t-1 DNA fraction confirmed the heterochromatin repeated DNAs enrichment, which is diversified among the species, using as reference D. geminatus. On the other hand, the terminal regions of the chromosomes were highly conserved among the six species. Moreover, the analysis of repeated DNA fraction from D. geminatus indicated intraspecific origin of a B chromosome in this species that possibly could be suffering homogenization with A complement sequences. The results indicate distinct diversification patterns for repeated DNAs in Scarabaeinae representatives, suggesting extensive microgenomic reorganization along the cladogenesis of the group
Orientador: Cesar Martins
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31

Lougou, Komla Gaboutou. "Méthodes multi-échelles pour la modélisation des vibrations de structures à matériaux composites viscoélastiques." Thesis, Université de Lorraine, 2015. http://www.theses.fr/2015LORR0044/document.

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Dans cette thèse, des techniques d’homogénéisation multi-échelles sont proposées pour l’analyse des vibrations des matériaux composites viscoélastiques. Dans la première partie, la Méthode Asymptotique à Deux Echelles (MADE) est proposée pour la modélisation des vibrations des longues structures sandwichs viscoélastiques répétitives. Pour ce type de structures les pulsations amorties correspondant aux modes propres de vibration sont regroupées en paquets bien distincts. La MADE décompose le problème initial de grande taille en deux problèmes de petites tailles. Le premier est défini sur quelques cellules de base et le second est une équation différentielle d’amplitude à coefficients complexes. La résolution de ces problèmes permet de déterminer les propriétés amortissantes correspondant aux modes de début et de fin de paquet de la structure tout en évitant la discrétisation de toute la structure. Pour les structures dont les coeurs ont un module d’Young dépendant de la fréquence, le problème non linéaire formulé sur les cellules de bases est résolu par l’approche diamant. Les modèles ADF et à dérivées fractionnaires ont été considérés dans les tests numériques. En utilisant la MADE, on évite la discrétisation de toute la structure, ce qui permet donc de réduire considérablement le temps de calcul ainsi que l’espace mémoire CPU nécessaires. L’approche proposée a été validée en comparant les résultats à ceux de la simulation éléments finis basée sur la discrétisation de toute la structure, et utilisant l’approche diamant. Dans la seconde partie de cette thèse, la méthode des éléments finis multi-échelles (EF2) a été développée pour le calcul des propriétés modales des structures à matériaux hétérogènes viscoélastiques en terme de fréquences amorties et amortissements modaux. Dans le principe de l’approche EF2, le problème de vibration est formulé à deux échelles : l’échelle de la structure globale (échelle macroscopique) et l’échelle d’un VER minutieusement choisi (échelle microscopique). Le problème à résoudre à l’échelle microscopique est un problème non linéaire alors que le problème à résoudre à l’échelle macroscopique est un problème linéaire. La non linéarité à l’échelle microscopique est introduite par la dépendance en fréquence du module d’Young des matériaux des phases viscoélastiques. Le problème non linéaire ainsi généré à l’échelle microscopique est résolu grâce à la MAN et ses outils de différentiation automatique réalisés sous Matlab, Fortran et C++. Un outil numérique, générique, robuste, peu coûteux en temps de calcul et espace mémoire CPU, de résolution des problèmes de vibrations non amorties des structures composites viscoélastique est ainsi mis en place. Le modèle viscoélastique à module constant ainsi que des modèles à modules dépendant de la fréquence notamment le modèle ADF et le modèle à dérivées fractionnaires ont été considérés pour les tests numériques de validation. Les comparaisons avec les résultats ABAQUS ont confirmé l’efficacité du code propos é. Le modèle est ensuite utilisé pour le calcul des propriétés amortissantes des structures sandwichs viscoélastiques à coeur composite. Les capacités de la nouvelle approche à concevoir des structures sandwichs viscoélastiques à coeur composite et à haut pouvoir amortissant ont été testées avec succès à travers l’étude de l’influence des différents paramètres des inclusions sur les propriétés amortissantes d’une structure sandwich viscoélastique à coeur composite
In this thesis, multiscale homogenization techniques are proposed for vibration analysis of structures with viscoelastic composite materials. In the first part, the Double Scale Asymptotic Method is proposed for vibration modeling of large repetitive viscoelastic sandwich structures. For this kind of structures, la eigenfrequencies are closely located in well separated packets. The DSAM splits the initial problem of large size into two problems of relatively small sizes. The first problem is posed on few basic cells, and the second one is an amplitude equation with complex coefficients. The resolution of these equations permits to compute the damping properties that correspond to the beginning and the end of every packets of eigenmodes. In case of structure with frequency dependent Young modulus in the core, the diamant approach is used to solve the nonlinear problem posed on basic cells. The ADF and fractional derivative models are considered in numerical tests. By using the DSAM, one avoid the discretization of the whole structure, and the computation time and needed CPU memory are thus reduced. The proposed method is validated by comparing its results with those of the direct finite element method using the diamant approach. In the second part of this thesis, the multiscale finite element method (FE2) is proposed for computation of modal properties (resonant frequency and modal loss factors) of structures with composite materials. In the principle of the (FE2) method, the vibration problem is formulated at two scales: the scale of the whole structure (macroscopic scale) and the scale of a Representative Volume Element (RVE) considered as the microscopic scale. The microscopic problem is a nonlinear one and the macroscopic problem is linear. The nonlinearity at the microscopic scale is introduced by the frequency dependence of the Young modulus of the viscoelastic phases. This nonlinear problem is solved by the Asymptotic Numerical Method and its automatic differentiation tools realizable in Matlab, Fortran or C++. From this approach, numerical tool that is generic, flexible, robust and inexpensive in term of CPU time and memory is proposed for vibration analysis of viscoelastic structures. The constant Young modulus and frequency dependent Young modulus are considered in validation tests. The results of numerical simulation with ABAQUS are used are reference. The model is then used to compute the modal properties of sandwich structure with viscoelastic composite core. To test the capacities of the proposed approach to design sandwich viscoelastic structure with high damping properties, the influence of parameters of the inclusions are studied
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32

Wang, Suyue. "Characterization of a Human 28S Ribosomal RNA Retropseudogene and Other Repetitive DNA Sequence Elements Isolated from a Human X Chromosome-Specific Library." Thesis, University of North Texas, 1994. https://digital.library.unt.edu/ark:/67531/metadc278083/.

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Three genomic clones encompassing human DNA segments (designated LhX-3, LhX-4, and LhX5) were isolated from an X chromosome-specific library and subjected to analysis by physical mapping and DNA sequencing. It was found that these three clones are very rich in repetitive DNA sequence elements and retropseudogenes.
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33

Victoria, Filipe de Carvalho. "Análise evolutiva de genes de homeostase de ferro e de elementos repetitivos em espécies modelo." Universidade Federal de Pelotas, 2011. http://guaiaca.ufpel.edu.br/handle/123456789/1290.

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Iron is an essential element for plant development, involved in metabolic processes, such respiration and photosynthesis. However, data regarding the genotype by environment interaction are lacking. Comparative analysis with lower plant groups and crop plants can increase the understanding about these processes. The use of bryophytes as model plants rise as a promising strategy since they present simpler patterns of development. The present work aimed to identify the occurrence patterns of molecular markers in model plant species, as well as to infer about the phylogenetical relationships of gene families related with iron homoestasis in plants, allowing the development of tranfer strategies of genomic data across model and orphan species. Using bioinformatics tools, a survey analysis was performed to detect repetitive elements in EST banks of eleven plant species. To validate the SSR markers found, 100 primer pairs were developed on the microsatelite sequences obtained for Physcomitrella patens Brid. and tested against genomic DNA of Polytrichum juniperinum Hedw. Phylogenetic and divergence time analysis was performed for the gene families Iron Regulated Transporter (IRT), Ferric Redectase Oxidase (FRO), Nicotinamide synthase (NAS), Yellow Stripe-Like (YSL) and Natural Resistance-Associated Macrophage Protein (NRAMP), related to the iron homoestasis, with help of the Bayesian inference and using the rice, Arabidopsis and P. patens genes for the Blast search in distinct land plants species. Also, primers for transposable elements recognizably related to Ysl genes were developed and applied jointly with the SSR primers by the IRAP/REMAP technic searching to find microsatellite markers associated to copies of this gene family. A total of 13,133 SSR markers were discovered in non- redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. Thirty percent of EST-SSE were successfully transferred with a relative polimorphism information across Physcomitrella patens Brid. and P. juniperinum, being promising for mapping and comparative genome analyses in plants. A total of 243 iron uptake gene sequences for 30 plant species were found using rice and Arabidopsis thaliana (L.) Heynh. homologues as queries. The evolutionary fingerprinting analyses suggested a positive selective pressure on iron uptake genes for most of the plant homologues analyzed, enabling an optimization and maintenance of gene function. The divergence time analysis indicates IRT as the most ancient gene family and FRO as the most recent. NRAMP and YSL genes appear as a close branch in the evolution of iron uptake gene families. No recent duplication in grasses were found based in the bayesian inference, and paralogue copies were only observed for dicot species. The Nramp cis-acting homology search indicated an ancestral duplication hypothesis for this gene family in grasses. Using IRAP/REMAP techniques, it was observed that YSL homologues in Physcomitrella are surrounded by copia-like retrotransposons as occurs in the maize ZmYSL1 copy. Also Polytrchum juniperinum Hedw. in vitro cultures were estabilished using spores as explants. Protonemal and gametophyte development were obtained using a growth regulator free culture medium.
O ferro é um elemento essencial para o crescimento e desenvolvimento das plantas, envolvido em processos metabólicos essenciais, como fotossíntese e respiração. Porém, são poucos os dados relacionando a interação entre diferentes genótipos e ambientes. Análises comparativas entre plantas inferiores e plantas cultivadas podem possibilitar o melhor entendimento destes processos. O uso de briófitas como modelo para estudos de processos biológicos em plantas surge como uma estratégia promissora devido ao padrão relativamente simples de desenvolvimento destas plantas. O presente trabalho objetivou identificar padrões de ocorrência de marcadores moleculares em plantas modelo, bem como inferir acerca da filogenia das famílias gênicas envolvidas na homoestase do ferro em plantas, possibilitando a criação de estratégias de transferência de informação genômica entre espécies modelo e espécies órfãs. Utilizando ferramentas de bioinformática foram realizadas análises exploratórias para detectar as ocorrências de elementos repetitivos em bancos de ESTs de onze espécies de plantas. Para a validação destes marcadores moleculares foram desenvolvidos 100 conjuntos de iniciadores a partir das sequências contendo microssatélites obtidas para Physcomitrella patens Brid. e testadas contra o DNA genômico de Polytrichum juniperinum Hedw. Foram realizadas análises filogenéticas e de divergência das famílias gênicas Iron Regulated Transporter (IRT), Ferric Redectase Oxidase (FRO), Nicotinamide synthase (NAS), Yellow Stripe-Like (YSL) e Natural Resistance-Associated Macrophage Protein (NRAMP), envolvidas na homoestase de ferro por meio de inferência bayesiana, utilizando genes de arroz, Arabidopsis e Physcomitrella patens Brid. na busca de homólogos em diferentes espécies de plantas terrestres, com o auxílio da ferramenta Blast (NCBI). Também foram desenvolvidos iniciadores para elementos transponíveis reconhecidamente associados a genes Ysl de milho e utilizados conjuntamente com os iniciadores EST-SSR por meio da técnica IRAP/REMAP buscando encontrar marcadores microssatélites associados a cópias desta familia gênica. Como resultados foram identificados 13.133 marcadores microssatélites em bancos de dados não redundantes de regiões expressas (EST) de onze espécies de plantas. Os motivos dinucleotídeos foram mais frequentes em espécies basais, enquanto os motivos trinucleotídeos foram mais frequentes em espécies derivadas. Em 30% dos conjuntos de iniciadores EST SSR testados contra o DNA de P. juniperinum, foi obtido bandas polimórficas promissoras para estudos de mapeamento comparativo e de diversidade genética. Foram encontrados 243 homólogos de genes relacionados as famílias gênicas envolvidas com a homoestase de ferro em trinta espécies de plantas. A análise de fingerprinting realizada sugere que a maioria destes genes estão submetidos a seleção positiva, indicando acúmulo de mutações adaptativas, essencial para a manutenção e otimização da resposta gênica. A análise de tempo de divergência indica que os genes IRT são mais basais e os genes FRO os mais recentes entre as familias gênicas estudadas. As famílias NRAMP e YSL são evolutivamente próximas. A análise bayesiana das sequências e de regiões promotoras dos genes NRAMP não indica duplicações recentes em gramíneas, sendo as duplicações provenientes de divergência ancestral a origem do grupo. Parálogos foram identificados somente em dicotiledôneas. Por meio da transferência de marcadores IRAP/REMAP é observado que genes YSL de P. patens estão cercados por retroelementos do tipo cópia, a exemplo do que ocorre com o gene ZmYSL1 em milho. Também foi estabelecido o cultivo, em condições axênicas, de Polytrichum juniperinum Hedw. utilizando esporos como explantes, onde foi observado que protonemas são obtidos utilizando meio de cultura livre de fitorreguladores, regenerando gametófitos em cultivo in vitro.
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34

Fabris, S. "GENOMIC AND EPIGENETIC APPROACHES IN THE CLINICAL AND PROGNOSTIC STRATIFICATION OF CHRONIC LYMPHOCYTIC LEUKEMIA." Doctoral thesis, Università degli Studi di Milano, 2011. http://hdl.handle.net/2434/150561.

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Chronic lymphocytic leukemia (CLL) is characterized by highly clinical heterogeneity; the identification of factors that could predict the clinical course of early-stage CLL represents a crucial objective in this malignancy. The aim of the study is to identify novel biological markers that may be clinically relevant to envisage specific risk subgroups of CLL patients using both genomic (integrated FISH and microarray technology) and an epigenetic approach in highly purified B-cell populations obtained from early-stage CLLs (Binet stage A). The availability of information concerning the follow-up of the analyzed patients allowed the investigation of a potential prognostic significance associated with the biological markers identified. Genome-wide DNA profiling and FISH were used to perform a deletion-mapping analysis of 17p in a subset of 18 CLLs with TP53 deletion and in all the investigated cases, the breakpoints were scattered along the 17p10–p11.2 region. Additionally, gene expression profile (GEP) analysis revealed specific transcriptional patterns and altered molecular pathways associated with 17p aberrations. SNP-array technology and gene expression profiling data were also applied to investigate the 13q14 deletion occurring in a panel of 100 CLLs representative of the major genetics, molecular and biological features of the disease. Based on SNP-array, our study shows the presence of two different molecular groups of patients with del(13)(q14) based on the deletion size and the presence of biallelic deletions. Notably, global gene expression profiling identified a significant transcriptional deregulation specifically associated with the two groups. The genomic complexity detected by SNP-array approach indicates that a relatively high degree of genomic alterations is associated with early-stage CLLs. As regards the genomic changes, the most important and novel finding is the occurrence of 2p gain in a recurrent fraction of early-stage CLLs, which appears to represent an independent prognostic factor for treatment occurrence. An epigenetic approach was used to investigate global DNA hypomethylation affecting repeated sequences, such as long interspersed nuclear elements-1 (LINE-1), Alu and satellite α DNA (SAT-α DNA), reported to be associated with chromosomal instability. Our analysis was performed in a panel of 77 CLLs and 7 healthy donors using robust quantitative Pyrosequencing methodology to detect the methylation status of the three repetitive elements. For the first time, we reported a significant association between Alu, LINE-1 and SAT-α hypomethylation and the occurrence of the 17p13 deletion; our data also indicate that SAT-α hypomethylation may represent an independent negative prognostic marker significantly correlated with the need of starting treatment. Overall, our data further support: i) the use of microarray technology to characterize well-known lesions for a better prognostic stratification of the disease as well as to investigate genomic changes in CLL, allowing the definition of novel aberrations with pathogenetic and prognostic implications; ii) the use of an epigenetic approach to identify the potential clinical relevance of specific repetitive elements hypomethylation, which may be used as a novel prognostic indicator of unfavorable disease progression.
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35

Coan, Rafael Luiz Buogo. "Análise genômica em larga escala de elementos repetitivos com foco em cromossomos B do ciclídeo Astatotilapia latifasciata." Botucatu, 2016. http://hdl.handle.net/11449/144542.

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Orientador: Cesar Martins
Resumo: Cromossomos B são elementos supranumerários presentes em diversos grupos taxonômicos. Sua composição heterocromática está ligada a grande quantidade de sequências repetitivas que possuem. Sua origem está relacionada ao conjunto cromossômico A, sendo um mosaico de sequências deste. O primeiro relato de cromossomos B em ciclídeos africanos foi na espécie Astatotilapia latifasciata, que pode carregar 0, 1 ou 2 cromossomos B. Estudos citogenéticos clássicos encontraram alta carga de elementos repetitivos no cromossomo B da espécie. Portanto, o estudo dos elementos repetitivos presentes no cromossomo B de A. latifasciata pode elucidar sua origem e manutenção no genoma. Os resultados utilizando dados de sequenciamento de nova geração, mapeamento por hibridização fluorescente in situ (FISH) e PCR em tempo real mostraram vários elementos com maior número de cópias no cromossomo B de A. latifasciata. Transposons de DNA, como Tc1-Mariner, e retrotransposons, como os membros da família Bel/Pao e Gypsy, foram encontrados expandidos no cromossomo B. Com o sequenciamento em larga escala de RNA (RNA-seq), foi avaliada a transcrição diferencial entre indivíduos sem cromossomos B (B-) e com esses (B+). Mesmo alguns elementos apresentando expressão diferencial entre os grupos, elementos expandidos no B permanecem com expressão constante. A presença de sequências repetitivas expandidas no cromossomo B e seu perfil transcricional traz informações sobre sua composição e dinâmica.
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36

Silva, Marcelo João da. "Estudo da organização estrutural de elementos repetitivos isolados do genoma de espécies de Proceratophrys (Amphibia, Anura, Odontophrynidae) /." Rio Claro, 2019. http://hdl.handle.net/11449/180991.

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Orientador: Patricia Pasquali Parise-Maltempi
Coorientador: Thiago Gazoni
Banca: Vanessa Bellini Bardella
Banca: Cintia Pelegrineti Targueta de Azevedo Brito
Resumo: Dados citogenéticos de Proceratophrys ainda são escassos na literatura quando comparados a alguns outros grupos de anuros, e são restritos atualmente às espécies P. boiei, P. appendiculata e P. renalis, que possuem um número diploide de 2n = 22 cromossomos e Região Organizadora de Nucléolo (RON) localizada no par 8, além de um padrão incomum de distribuição da heterocromatina constitutiva nos cromossomos de P. boiei, que apresentam grandes blocos heterocromáticos, além de um sistema de cromossomos sexuais do tipo ZZ:ZW. A maioria dos genomas eucarióticos são compostos por grandes porções de sequências de DNAs repetitivos que estão localizadas principalmente na heterocromatina altamente compactada, e em muitos casos, é um dos componentes mais abundantes dos cromossomos sexuais. Nesse sentido, o grupo dos Proceratophrys torna-se interessante alvo para análises citogenéticas juntamente com a aplicação de ferramentas moleculares e genômicas, as quais podem contribuir no entendimento da evolução e diversidade de DNAs repetitivos, e com isso explorar discussões em relação a diferenciação de cromossomos sexuais. Portanto, o objetivo deste estudo foi analisar citogeneticamente a espécie P. boiei, sob o ponto de vista clássico e genômico, em busca de sequências repetitivas, avaliar a presença dessas sequências e buscar entender a sua organização no genoma dessa espécie. Ainda, o trabalho teve como objetivo descrever citogeneticamente outras espécies de Proceratophrys, aumentando a amo... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Cytogenetic data from Proceratophrys are still scarce in the literature when compared to some other groups of anurans, and are currently restricted to the species P. boiei, P. appendiculata and P. renalis, which have a diploid number of 2n = 22 chromosomes and the Nuclear Organizing Region (NOR) located in pair 8, in addition to an unusual pattern of distribution of constitutive heterochromatin in the P. boiei chromosomes, which present large heterochromatic blocks, as well as a system of ZZ:ZW sex chromosomes. Most eukaryotic genomes are composed of large portions of repetitive DNA sequences that are located primarily in highly compacted heterochromatin, and in many cases, is one of the most abundant components of sex chromosomes. In this sense, the Proceratophrys group becomes an interesting target for cytogenetic analysis along with the application of molecular and genomic tools, which may contribute to the understanding of the evolution and diversity of repetitive DNAs, and thereby explore discussions regarding the differentiation of sex chromosomes. Therefore, the objective of this study was to analyze the P. boiei species, from a classical and genomic point of view, in a search for repetitive sequences, evaluating the presence of these sequences and seeking to understand their organization in the genome of this species. In addition, the objective of this work was to describe cytogenetically other species of Proceratophrys, increasing the karyotype sample described in th... (Complete abstract click electronic access below)
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37

Herai, Roberto Hirochi. "Metodologias de bioinformatica para detecção e estudo de sequencias repetitivas em loci genicos de transcritos quimericos." [s.n.], 2010. http://repositorio.unicamp.br/jspui/handle/REPOSIP/317152.

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Orientador: Michel Eduardo Beleza Yamagishi
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A grande quantidade de dados biológicos gerados recentemente permitiu verificar que os genomas são repletos de seqüências repetitivas (SR), como microsatélites e elementos genéticos móveis, altamente improváveis de ocorrer estatisticamente se os genomas fossem gerados a partir de uma distribuição aleatória de nucleotídeos. Tal comprovação motivou a classificação de tais seqüências e também a construção de diversas ferramentas de bioinformática, além de mecanismos de armazenamento baseados em sistemas de gerenciamento de bancos de dados (SGBD) para permitir localizá-las e armazená-las para posterior estudo. Entretanto, foi com a comprovação biológica da importância das SR, como no mecanismo de interferência por RNAi (SR reversa complementar), que as SR despertaram maior interesse por parte da comunidade científica. Atualmente, já há fortes evidências que associam as SR com fenômenos biológicos bastante interessantes, como o processamento de RNA por cis-splicing e a formação de transcritos quiméricos, freqüentes em organismos inferiores e muito raro em organismos superiores. Tais tipos de transcritos podem ser gerados a partir de trans-splicing ou, como conjecturamos nesse trabalho, pela transposição de elementos genéticos móveis (como por exemplo transposons ou retrotransposons). Em virtude disso, este projeto propõe a construção de metodologias de Bioinformática, disponibilizadas na WEB, para detectar transcritos quiméricos em genomas de organismos, tanto em versões draft ou em alta qualidade, e também estudar as SR que ocorrem no locus gênico dos transcritos envolvidos na formação de uma seqüência quimérica. As ferramentas propostas permitiram identificar, a partir de bibliotecas de transcritos de full-length cDNA, tanto de humanos quanto de bovinos, novos transcritos quiméricos provenientes de células de tecidos normais, e que não seguem splice-sites canônicos na região de fusão dos transcritos envolvidos. Além disso, as seqüências encontradas apresentam uma elevada taxa de concentração de pares de SR do tipo reverso complementar no locus gênico dos dois transcritos que formam a seqüência quimérica. As ferramentas propostas podem ser utilizadas para outros organismos e direcionar trabalhos experimentais para tentar comprovar em bancada novos transcritos quiméricos, tanto em organismos inferiores quanto em superiores
Abstract: The recent availability of a huge amount of biological data allowed to know about the high concentration of repetitive sequences (SR) like microsatellites and genetic mobile elements in different genomes. Repetitive sequences are improbable to occur statistically if genome data were generated by a random distribution of nucleotides. Such observation motivated the classification of repetitive sequences, and the construction of several bioinformatics tools. Furthermore, several mechanisms to store repetitive sequences, which are based on data base management systems (DBMS) were proposed and created. They can be used to search for specific sequences to make a posteriori study. However, it was with the biological confirmation of the importance of repetitive sequences, like by the RNA interference (reverse complement, or inverted repeat) mechanism, that the scientific community gained more interest by such sequences. Actually, there is strong evidence that associates the repetitive sequences with some interesting biological phenomena, like in RNA processing by cis-splicing, and in chimeric transcript formation mechanism. This last one is very frequently in inferior organism, but rare in superior organisms. Such types of transcripts can be generated by trans-splicing, or like conjectured in this work, by the retrotransposition of mobile genetic elements (like transposons or retrotransposons). In this way, this work proposed the construction of several Bioinformatics methodologies, available in the WEB, to detect new evidences of chimeric transcripts in genomes of different organisms, both in draft genome and in high quality genome assemblage. We also studied repetitive sequences in gene loci of the involved transcripts in a chimeric sequence formation. The proposed tools allowed us to identify, using a full-length cDNA databank, new chimeric transcript candidates in human and in bovine genome. They are from cells of normal tissues, and do not follow canonical splice-sites in the fusion region of the involved transcripts. Moreover, it was possible to show that the detected sequences have high concentration pairs of reverse complement type of repetitive sequences in gene loci of the two involved transcripts, which originated a new chimeric transcript candidate. The created bioinformatics tools can be used in other organisms in addition to the one used in this work, leading to the proposition of new experimental work to try to prove in vivo new chimeric transcripts, both in superior organism and in inferior organism
Doutorado
Bioinformatica
Doutor em Genetica e Biologia Molecular
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38

Silva, Edson Lourenço da [UNESP]. "Estudo da organização estrutural de elementos repetitivos isolados do genoma de Leporinus elongatus em diferentes espécies da família Anostomidae (Teleostei, Characiformes)." Universidade Estadual Paulista (UNESP), 2012. http://hdl.handle.net/11449/100526.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
A família Anostomidae compreende um grupo com 12 gêneros que apresenta ampla distribuição pela América do Sul e Central. Estudos citogenéticos de várias espécies da família mostram uma estrutura cariotípica bastante conservada, com o número diplóide igual a 54 cromossomos, dos tipos meta e submetacêntricos e apenas um par de cromossomos portador de regiões organizadoras de nucléolos (NOR) localizadas em posições e pares distintos nas diferentes espécies do grupo. Através de estudos envolvendo técnicas de citogenética molecular têm se conseguido uma caracterização mais resolutiva dos cromossomos de algumas espécies da família. Estas metodologias forneceram evidências de polimorfismos de NOR, diferentes padrões de distribuição da heterocromatina constitutiva, presença de seqüências repetitivas sexo-específicas e novos sistemas de cromossomos sexuais heteromórficos do tipo ZZ/ZW bem como a diferenciação de híbridos interespecíficos. Dessa forma, o presente trabalho teve como objetivo acrescentar novos dados que auxiliem no estabelecimento de padrões para esclarecer a história evolutiva dos cromossomos sexuais em espécies de Anostomidae, baseado no estudo da organização de seqüências repetitivas isoladas do genoma de Leporinus elongatus em diferentes espécies de Anostomidae. Para tanto, novos elementos repetitivos do genoma de Leporinus elongatus foram isolados através de restrição enzimática e usados em experimentos de hibridação fluorescente in situ (FISH) tanto em L. elongatus quanto nas espécies L. macrocephalus, L. obtusidens, L. friderici, L. lacustris, L. striatus, Schizodon borellii, S. isognathus e Abramites hypselonotus. Além disso, sondas de cromossomos inteiros obtidos por microdissecção também foram usadas nesses experimentos, a fim de buscar identificar...
The Anostomidae family comprises a group with 12 genera widely distributed throughout Central and South American Rivers. Cytogenetic studies carried out in several anostomids shows a karyotypic structure very conserved, with a diploid number equals to 54 chromosomes, metacentric and submetacentric, and only one chromosome pair carrier of nucleolar organizing regions (NOR), localized at distinct chromosome positions in the species of the family. The studies using molecular cytogenetic techniques have been providing a more accurate characterization of some species. These methods highlighted NOR polymorphisms, differential pattern of heterochromatin distribution, the presence of sex specific repetitive sequences, as well as new heteromorphic sex chromosomes and interspecific hybrids differentiation. Thus, the present study aimed to add new data to assist in to establish patterns to clarify the evolutionary history of sex chromosomes in Anostomidae species, based on the study of the organization of repetitive sequences isolated from Leporinus elongatus genome in different species of Anostomidae. For this, new repetitive elements were isolated from L. elongatus and used in Fluorescent in situ hybridisations experiments (FISH) in L. elongatus as well in the species L. macrocephalus, L. obtusidens, L. friderici, L. lacustris, L. striatus, Schizodon borellii, S. isognathus e Abramites hypselonotus. Indeed, probes of whole sex chromosomes obtained through microdissection were also used in order to identify similarities among the anostomids chromosomes and the presence of sex chromosomes in differentiation stages. The LeSmaI repetitive element has 378 bp and is exclusive to L. elongatus individuals. This is a satellite DNA localized near to the NOR in a highly heterochromatic region. The presence of this satellite DNA reinforces... (Complete abstract click electronic access below)
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39

Silva, Edson Lourenço da. "Estudo da organização estrutural de elementos repetitivos isolados do genoma de Leporinus elongatus em diferentes espécies da família Anostomidae (Teleostei, Characiformes) /." Rio Claro : [s.n.], 2012. http://hdl.handle.net/11449/100526.

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Orientador: Patrícia Pasquali Parise Maltempi
Banca: Luciana Bolsoni Lourenço
Banca: Daniela Cristina Ferreira
Banca: Vladimir Trifonov
Banca: Liano Centofante
Resumo: A família Anostomidae compreende um grupo com 12 gêneros que apresenta ampla distribuição pela América do Sul e Central. Estudos citogenéticos de várias espécies da família mostram uma estrutura cariotípica bastante conservada, com o número diplóide igual a 54 cromossomos, dos tipos meta e submetacêntricos e apenas um par de cromossomos portador de regiões organizadoras de nucléolos (NOR) localizadas em posições e pares distintos nas diferentes espécies do grupo. Através de estudos envolvendo técnicas de citogenética molecular têm se conseguido uma caracterização mais resolutiva dos cromossomos de algumas espécies da família. Estas metodologias forneceram evidências de polimorfismos de NOR, diferentes padrões de distribuição da heterocromatina constitutiva, presença de seqüências repetitivas sexo-específicas e novos sistemas de cromossomos sexuais heteromórficos do tipo ZZ/ZW bem como a diferenciação de híbridos interespecíficos. Dessa forma, o presente trabalho teve como objetivo acrescentar novos dados que auxiliem no estabelecimento de padrões para esclarecer a história evolutiva dos cromossomos sexuais em espécies de Anostomidae, baseado no estudo da organização de seqüências repetitivas isoladas do genoma de Leporinus elongatus em diferentes espécies de Anostomidae. Para tanto, novos elementos repetitivos do genoma de Leporinus elongatus foram isolados através de restrição enzimática e usados em experimentos de hibridação fluorescente in situ (FISH) tanto em L. elongatus quanto nas espécies L. macrocephalus, L. obtusidens, L. friderici, L. lacustris, L. striatus, Schizodon borellii, S. isognathus e Abramites hypselonotus. Além disso, sondas de cromossomos inteiros obtidos por microdissecção também foram usadas nesses experimentos, a fim de buscar identificar... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The Anostomidae family comprises a group with 12 genera widely distributed throughout Central and South American Rivers. Cytogenetic studies carried out in several anostomids shows a karyotypic structure very conserved, with a diploid number equals to 54 chromosomes, metacentric and submetacentric, and only one chromosome pair carrier of nucleolar organizing regions (NOR), localized at distinct chromosome positions in the species of the family. The studies using molecular cytogenetic techniques have been providing a more accurate characterization of some species. These methods highlighted NOR polymorphisms, differential pattern of heterochromatin distribution, the presence of sex specific repetitive sequences, as well as new heteromorphic sex chromosomes and interspecific hybrids differentiation. Thus, the present study aimed to add new data to assist in to establish patterns to clarify the evolutionary history of sex chromosomes in Anostomidae species, based on the study of the organization of repetitive sequences isolated from Leporinus elongatus genome in different species of Anostomidae. For this, new repetitive elements were isolated from L. elongatus and used in Fluorescent in situ hybridisations experiments (FISH) in L. elongatus as well in the species L. macrocephalus, L. obtusidens, L. friderici, L. lacustris, L. striatus, Schizodon borellii, S. isognathus e Abramites hypselonotus. Indeed, probes of whole sex chromosomes obtained through microdissection were also used in order to identify similarities among the anostomids chromosomes and the presence of sex chromosomes in differentiation stages. The LeSmaI repetitive element has 378 bp and is exclusive to L. elongatus individuals. This is a satellite DNA localized near to the NOR in a highly heterochromatic region. The presence of this satellite DNA reinforces... (Complete abstract click electronic access below)
Doutor
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40

PETY, Ananda Marques. "Novas abordagens evolutivas em peixes da Amazônia: mapeamento de elementos repetitivos como marcadores para estudos em espécies do clado Peckoltia (Siluriformes, Loricariidae)." Universidade Federal do Pará, 2018. http://repositorio.ufpa.br/jspui/handle/2011/9992.

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CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico
Os dados citogenéticos fornecem informações importantes sobre a diversidade de Loricariidae, pois eles corroboram as análises de classificação das espécies não descritas e ajudam na compreensão da diversidade inter-intraespecífica. No entanto, entre as espécies do clado Peckoltia, somente a determinação do número de cromossomos não resolve essas questões, porque a maioria das espécies exibe um número diplóide (2n) estável. Assim, o uso de outros marcadores cromossômicos, são necessários para esclarecer a organização genômica dessas espécies e entender sua diversidade. O mapeamento físico de DNAs repetitivos tem sido amplamente utilizado como uma ferramenta importante no estudo de problemas taxonômicos e evolutivos em peixes, bem como para entender os processos de organização genômica e diversificação. O objetivo do presente trabalho foi mapear sítios ribossômicos (rDNA) 5S e 18S em Ancistomus feldbergae e cinco espécies de Peckoltia: P. cavatica; P. multispinis; P. oligospila; P. sabaji e P.vittata, e discutir os mecanismos de organização e diversificação dessas sequências. Os resultados do presente estudo demonstram que todas as seis espécies analisadas possuem cariótipo constituído de 52 cromossomos, mas possuem fórmula cariotípica divergente. Regiões Organizadoras de Nucléolo (NOR) do tipo simples foram observadas em Ancistomus feldbergae, P. cavatica, P. multispinis e P.vittata, enquanto NOR múltiplas foram encontradas em P. oligospila e P. sabaji. Foram observadas variações extensas no número e localização dos sítios de rDNA 5S e 18S entre as espécies. Esses dados indicam que as inversões não são os únicos eventos mais importantes na evolução do cariótipo neste grupo e devem ser úteis na identificação das espécies estudadas aqui. Além das inversões, as transposições são importantes eventos evolutivos envolvidos, pelo menos, em clusters de rDNA que se espalham em Peckoltia e provavelmente em outras espécies de Hypostominae.
Cytogenetic data provide important information on the diversity of Loricariidae, as they corroborate the classification analyzes of the species not described and help in the understanding of inter-intraspecific diversity. However, among the species of the Peckoltia clade, the determination of the number of chromosomes alone does not resolve these questions, since most species exhibit a stable diploid (2n) number. Thus, the use of other chromosomal markers is necessary to clarify the genomic organization of these species and to understand their diversity. The physical mapping of repetitive DNA has been widely used as an important tool in the study of taxonomic and evolutionary problems in fish, as well as to understand the processes of genomic organization and diversification. The objective of the present work was to map ribosomal sites (rDNA) 5S and 18S in Ancistomus feldbergae and five species of Peckoltia: P. cavatica; P. multispinis; P. oligospila; P. sabaji and P.vittata, and discuss the mechanisms of organization and diversification of these sequences. The results of the present study demonstrate that all six species analyzed have a karyotype composed of 52 chromosomes but have divergent karyotype formulas. Nucleolus Organizing Regions (NOR) of the single type were observed in Ancistomus feldbergae, P. cavatica, P. multispinis and P.vittata, while multiple NORs were found in P. oligospila and P. sabaji. Extensive variations in the number and location of 5S and 18S rDNA sites among species were observed. These data indicate that inversions are not the only most important events in karyotype evolution in this group and should be useful in identifying the species studied here. In addition to inversions, transpositions are important evolutionary events involved, at least in rDNA clusters that spread in Peckoltia and probably in other species of Hypostominae.
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41

Barros, Lucas Caetano de. "Isolamento, caracterização e mapeamento cromossômico de elementos repetitivos em espécies da família Anostomidae (Ostariophysi – Characiformes): análise comparativa em diferentes tipos de águas amazônicas." Instituto Nacional de Pesquisas da Amazônia, 2017. http://bdtd.inpa.gov.br/handle/tede/2325.

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Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq
The Anostomidae are a fish family composed about 145 species distributed in 13 genera. The family is known in the North of Brazil as aracus and in other regions as piaus. In the present work 90 specimens of this family were analyzed, representing the species Megaleporinus trifasciatus (former Leporinus trifasciatus), Leporinus fasciatus, L. friderici, L. agassizi, Laemolyta taeniata, Anostomoides laticeps, Rhytiodus microlepis and Shizodon fasciatus. The samples were collected in five different locations in the Amazon region with the objective of identifying how chromosomal / genomic modifications can be related to different environmental conditions, such as the different types of water found in this region. For this, classical (Giemsa, Ag-RON, Bandeamento C) and molecular (fluorescence in situ hybridization - FISH, cross-FISH and microdissection of the W chromosome of M. trifasciatus) cytogenetics techniques were used. Overall, the results did not reveal patterns associated with the different biotopes, both in intraspecific and interspecific analysis. Regarding the karyotype structure, all species are conservative in relation to several conventional chromosome markers, however, significant differences were found in the distribution of the heterochromatin and the carrier pair of the nucleolus organizer region. 18S rDNA showed multiple sites, evidenced in several chromosome pairs in some species, whereas 5S rDNA was located in a single chromosome pair in all species. Cross-hybridization with M. trifasciatus (WMt), M. elongatus (WMe) and M. macrocephalus (WMm) probes (species already analyzed) revealed that the genomes of M. trifasciatus, M. macrocephalus (With ZZ / ZW system) and M. elongatus (species with system Z1Z1Z2Z2 / Z1W1Z2W2) present a high degree of similarity both in the structure and in the location of the hybridization sites. However, crosshybridization of this probe in the genome of species of the genus Leporinus, which do not present a differentiated sex chromosome system, showed low similarity. This information is of great importance, since the accumulation of repetitive sequences in the gene rich regions may reflect the differentiation between proto-sexual, in contrast with the heteromorphic pair ZW. The results obtained in this study show that the repetitive sequences actually play an active role in the anostomide carioevolution, especially in the evolution of the sex chromosome system in M. trifasciatus, M. elongatus and M. macrocephalus and in the origin of the multiple sites of 18S ribosomal DNA in Rhytiodus microlepis, Laemolyta taeniata, Schizodon fasciatus and Megaleporinus trifasciatus.
Anostomidae abriga cerca de 145 espécies, distribuidas em 13 gêneros, conhecidas, na região Norte, como aracus e nas demais regiões do Brasil, como piaus. No presente trabalho foram analisados 90 espécimes desta família, representando as espécies Megaleporinus trifasciatus (antigo Leporinus trifasciatus), Leporinus fasciatus, L. friderici, L. agassizi, Laemolyta taeniata, Anostomoides laticeps, Rhytiodus microlepis e Shizodon fasciatus, coletadas em cinco locais na Amazônia, com o objetivo de identificar como as modificações cromossômicas/genômicas podem estar relacionadas com diferentes condições ambientais, como os diferentes tipos de água que são encontrados nesta região. Para isso foram utilizadas técnicas da citogenética clássica (Giemsa, Ag-RON, Bandeamento C), citogenética molecular (Hibridização in situ fluorescente - FISH, cross-FISH e microdissecção do cromossomo W de M. trifasciatus). No geral, os resultados não revelaram padrões associados aos diferentes biótopos, tanto na análise intra-específica quanto interespecífica. Com relação à estrutura cariotípica, todas as espécies são conservativas em relação a vários marcadores cromossômicos convencionais, porém, diferenças significativas foram encontradas na distribuição da heterocromatina e do par portador da região organizadora de nucléolo. O DNAr 18S apresentou sítios múltiplos, evidenciados em vários pares cromossômicos em algumas espécies, enquanto o DNAr 5S foi localizado em um único par cromossômico em todas as espécies. A hibridização cruzada (crossFISH) com sondas de M. trifasciatus (WMt), M. elongatus (WMe) e M. macrocephalus (WMm)(espécies já analisadas) revelou que os genomas de M. trifasciatus, M. macrocephalus (espécies com sistema ZZ/ZW) e M. elongatus (espécie com sistema Z1Z1Z2Z2/Z1W1Z2W2) apresentam alto grau de similaridade, tanto na estrutura quanto na localização dos sítios de hibridização. Entretanto, a hibridização cruzada desta sonda, no genoma de espécies do gênero Leporinus, que não apresentam sistema de cromossomo sexual diferenciado, mostrou baixa similaridade. Esta informação é de grande importância, uma vez que o acúmulo de sequências repetitivas nas regiões ricas em genes pode refletir a diferenciação entre proto-sexuais, em diferenciação para o par heteromórfico ZW. Os resultados obtidos neste estudo mostram que as sequências repetitivas realmente possuem papel atuante na carioevolução dos anostomídeos, principalmente na evolução do sistema de cromossomos sexuais em M. trifasciatus, M. elongatus e M. macrocephalus e na origem dos múltiplos sítios de DNA ribossomal 18S em Rhytiodus microlepis, Laemolyta taeniata, Schizodon fasciatus e Megaleporinus trifasciatus.
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42

Salem, Hatem. "Role de DAXX et de CAF-1 dans le ciblage de l'histone H3.3 au chromosome X et aux elements répétés." Thesis, Strasbourg, 2019. http://www.theses.fr/2019STRAJ105.

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La chaperone d'histones DAXX cible H3.3 à l'hétérochromatine péricentrique et télomérique d'une manière indépendante de la réplication. Le mécanisme qui assure le recrutement de DAXX dans les régions hétérochromatiques est largement inconnu. En utilisant des approches protéomiques et biochimiques, nous montrons qu'en plus du complexe bien connu ATRX/H3/3, DAXX forme un complexe alternatif avec CAF-1, ADNP, HP1 et Trim28. DAXX interagit physiquement avec la partie C-terminal de la sous-unité CAF1-p150 via son domaine N-terminal. Le domaine SIM de DAXX est essentiel à son ciblage aux corps PML et pour le recrutement de CAF-1 au chromosome X et aux éléments répétés. L'inactivation de DAXX entraîne une déplétion importante de CAF-1 des éléments répétés SINEs et LINEs du chromosome X. Nos données révèlent une nouvelle fonction de DAXX et de CAF-1 dans le ciblage de H3.3 au chromosome X
The histone chaperone DAXX targets H3.3 to pericentric and telomeric heterochromatin in a replication independent manner. The mechanism that ensures appropriate recruitement of DAXX to heterochromatic region is largely unknown. Using proteomic and buochemical approaches, we show that in addition to the well-known ATRX/H3.3 complex, DAXX forms an alternative complex with CAF-1, ADNP, HP1 and trim28. DAXX physically interact with the C-terminus of CAF1-p150 subunit through its N-terminal domain. The DAXX SIM domain was found to be essential for targeting DAXX to PML-NBs, for the recruitment of CAF-1 to heterochromatin. Our genomic date further revealed that DAXX targets CAF-1 to X-chromosome and repetitive elements. Inactivation of DAXX results in major depletion of CAF-1 from X-chromosome SINEs and LINEs. Our data point to a novel function of DAXX and CAF-1 in targeting H3.3 to X-chromosome
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43

Noordhuis-Fairfax, Sarina. "Field | Guide: John Berger and the diagrammatic exploration of place." Phd thesis, Canberra, ACT : The Australian National University, 2018. http://hdl.handle.net/1885/154278.

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Positioned between writing and drawing, the diagram is proposed by John Berger as an alternative strategy for articulating encounters with landscape. A diagrammatic approach offers a schematic vocabulary that can compress time and offer a spatial reading of information. Situated within the contemporary field of direct data visualisation, my practice-led research interprets Berger’s ‘Field’ essay as a guide to producing four field | studies within a suburban park in Canberra. My seasonal investigations demonstrate how applying the conventions of the pictorial list, dot-distribution map, routing diagram and colour-wheel reveals subtle ecological and biographical narratives.
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44

Liang, Kai-Chiang, and 梁凱強. "Construct a gene-based repetitive element database." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/47446099187090227150.

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碩士
國立成功大學
生物資訊研究所
97
More than 50% of human genome is constituted by repetitive elements. Recent studies implied that the complexity of living organisms is not just a direct outcome of the number of coding sequence; there should be harbored regulatory information in other genome parts where repetitive elements may play a role in it. Most genes can be regulated by their sequences flanking the coding region, such as 5’ untranslated region (5’ UTR), 3’ untranslated region (3’ UTR), and promoter regions. Nowadays, we know repetitive elements in these regions may play a role in gene expression. However there is no systematical survey the distribution of type and location of these elements. This study aims to thoroughly examine the repetitive elements in the human genome that may be involved in gene regulation by computational approaches. We downloaded the sequences flanking all human genes from internet resources and identified repetitive elements by cross-matching sequences against RepeatMasker database. Interestingly, we found that the tandem repetitive elements preferentially locate close to genes and interspersed repetitive elements showed a tendency to be accumulated distantly from genes. The annotation and distribution of distinct classes of repetitive elements associated with individual gene were then used to construct a gene-based repetitive element database (GBRED). Furthermore, we designed a user-friendly web interface to provide searching function for repetitive elements associated with any particular gene(s). To further characterize the role of these repetitive elements in gene regulation, programs for pathway analysis were used to analyze genes from various repeat groups. Our data suggested that genes containing tandem repetitive elements in their UTRs and upstream 1000-bp region may be involved in development processes, whereas the genes with interspersed repetitive elements in 3’ UTR and upstream 1000-bp region are related to metabolic processes. Finally, our data indicate that distinct classes of repetitive elements display different distribution in human genome and might imply associations with specific biological processes that might provide a hint to predict the unknown gene functions and the biological processes they involving in. All information mentioned above could be acquired from the GBRED.
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45

Braet, S., K. Vandelannoote, Conor J. Meehan, Fontes A. N. Brum, E. Hasker, P. S. Rosa, R. N. Lucena-Silva, L. Rigouts, P. N. Suffys, and Jong B. C. de. "The Repetitive Element RLEP Is a Highly Specific Target for Detection of Mycobacterium leprae." 2018. http://hdl.handle.net/10454/17260.

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46

Galvao, Bezerra dos Santos Karla. "Isolation, molecular characterisation and chromosomal location of repetitive DNA sequences in Brassica." Doctoral thesis, 2004. http://hdl.handle.net/11858/00-1735-0000-0006-AB64-B.

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47

Heitkam, Tony. "The retrotransposon landscape of the Beta vulgaris genome: Evolutionary conservation and diversity." Doctoral thesis, 2011. https://tud.qucosa.de/id/qucosa%3A33484.

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Retrotransposons are major components of plant genomes influencing their genome size, organization and evolution. In the frame of this work, retrotransposons of the Beta vulgaris genome have been identified by molecular methods and whole genome bioinformatics approaches. Neither belonging to the rosids nor asterids, B. vulgaris (cultivated beet including sugar beet, beet root and mangold) is taxonomically placed at a key position at the root of the core eudicots, and considerably different from traditional plant model species such as thale cress or rice. Its genome has been sequenced, and annotation is under way. In order to compare different evolutionary lineages of B. vulgaris retrotransposons, long terminal repeat (LTR) and non-LTR retrotransposon family have been analyzed in detail. Full-length members have been isolated and characterized by bioinformatics, Southern and fluorescent in situ hybridization. Hallmarks of the LTR retrotransposon family Cotzilla are an additional env-like open reading frame (ORF), homogeneity of the members and the very high abundance. Most family members are evolutionarily young, and have most likely been created during recent bursts of amplification during species radiation. In contrast, the non-LTR retrotransposon family BNR has fewer copies and is much more diverged. Although the BNR ORF2 resembles previously analyzed long interspersed nuclear elements (LINEs) of the L1 clade, its ORF1 sequence differs strongly. It lacks the zinc finger domain described for plant LINEs, but contains instead an RNA recognition motif (RRM) likely to have an RNA-binding function. Database searches revealed the presence of similar LINE families in higher plant genomes such as poplar, lotus and soybean. Comparing their reverse transcriptase regions with other retrotransposons, these BNR-like LINEs form a separate group of L1 LINEs designated as BNR subclade. Availability of the B. vulgaris genome sequence allowed retrotransposon analyses on a genome-wide scale. A Hidden Markov Model-based detection algorithm has been developed in order to retrieve retrotransposon information directly from the database. Nearly 6000 B. vulgaris reverse transcriptase sequences have been isolated and classified into LTR retrotransposons of the Ty3-gypsy and Ty1-copia type, and non-LTR retrotransposons of the LINE type. As a result, a comprehensive overview of the retrotransposon spectrum of the B. vulgaris genome has been generated. Since plant LINEs have been only rarely investigated, the B. vulgaris LINE composition was studied in detail. Out of 28 described LINE clades, only members of the L1 and RTE clades have been identified. Based on a minimal shared sequence identity of 60 %, they form at least 17 L1 families and one RTE family. Full-length members of all investigated L1 families have been analyzed regarding their sequence, structure and diversity. In order to transfer the algorithm tested in B. vulgaris to other angiosperm genomes, twelve additional plant genomes have been queried for LINE reverse transcriptases. Key finding is the presence of only two LINE clades (L1 and RTE) in the analyzed genomes of higher plants. Whereas plant L1 LINEs are highly diverse and form at least seven subclades with members across species borders, RTE LINEs are extremely homogenized and constitute most likely only a single family per genome. In summary, this work’s results help to gain an understanding of the different strategies of retrotransposon evolution in plants, whereas the generated data directly contributes to the B. vulgaris genome annotation project.
Retrotransposons sind eine wesentliche Komponente von Pflanzengenomen, die sowohl die Größe und Organisation als auch die Evolution dieser Genome wesentlich beeinflussen können. Im Rahmen dieser Arbeit wurden verschiedene Gruppen von Retrotransposons des Beta vulgaris Genoms mittels molekularer und bioinformatischer Methoden identifiziert. Innerhalb der dikotyledonen Blütenpflanzen gehört B. vulgaris (kultivierte Rübe einschließlich Zuckerrübe, Roter Beete und Mangold) weder zu den Rosiden noch zu den Asteriden, sondern nimmt eine Schlüsselposition innerhalb der Kerneudikotyledonen ein. Somit zeigt das Rübengenom wesentliche Unterschiede zu traditionellen Modellpflanzen wie Arabidopsis thaliana oder Oryza sativa. Das Genom ist bereits sequenziert, die Annotation jedoch noch nicht abgeschlossen. Um verschiedene evolutionäre Linien von B. vulgaris Retrotransposons vergleichend zu untersuchen wurden insbesondere Long Terminal Repeat (LTR)- und Non-LTR-Retrotransposon-Familien detailliert analysiert. Vollständige Mitglieder wurden isoliert und mittels bioinformatischer Methoden, Southern- und Fluoreszenz-in situ-Hybridisierung untersucht. Die LTR-Retrotransposon-Familie Cotzilla ist durch einen zusätzlichen env-ähnlichen offenen Leserahmen (ORF), Homogenität ihrer Mitglieder und eine hohe Abundanz gekennzeichnet. Die meisten Cotzilla-Kopien sind evolutionär jung und wurden wahrscheinlich innerhalb eines kurzen Zeitraumes während der Artentstehung stark amplifiziert. Im Gegensatz zur Cotzilla-Familie besitzt die Non-LTR-Retrotransposon-Familie BNR weniger Kopien und ist wesentlich divergierter. Während der BNR-spezifische ORF2 starke Ähnlichkeiten zu anderen pflanzlichen Long Interspersed Nuclear Elements (LINEs) der L1-Klade aufweist, unterscheidet sich der BNR ORF1 von diesen sehr stark. Im Gegensatz zu bereits beschrieben pflanzlichen LINEs kodiert er kein Zinkfingermotiv, sondern substituiert dieses durch ein RNA-Erkennungsmotiv (RRM). Durch Datenbanksuche konnten BNR-ähnliche LINEs in den Genomen höherer Pflanzen wie Soja, Lotus und Pappel identifiziert werden. Ein Vergleich der entsprechenden Reversen Transkriptasen (RT) mit den RTs anderer Retrotransposons zeigt, dass die BNR-ähnlichen LINEs eine separate Gruppe innerhalb der L1 LINEs bilden. Diese wurde daher als BNR-Subklade definiert. Die Untersuchung von Retrotransposons auf Genomebene wurde durch die B. vulgaris Genomsequenz ermöglicht. Um Retrotransposon-Informationen direkt aus dem Genom zu extrahieren, wurde ein Hidden Markov Modell (HMM)-basierter Detektions-algorithmus entwickelt. Annähernd 6000 B. vulgaris Reverse Transkriptase-Sequenzen konnten identifiziert und in LTR-Retrotransposons des Ty3-gypsy- beziehungsweise des Ty1-copia-Typs und in Non-LTR-Retrotransposons des LINE-Typs klassifiziert werden. Somit wurde ein umfassender Überblick über die Bandbreite der B. vulgaris Retrotransposons arhalten. Da pflanzliche LINEs bisher nur wenig erforscht sind, wurde die B. vulgaris LINE Zusammensetzung genauer untersucht. Von 28 beschriebenen LINE-Kladen konnten nur Mitglieder der L1- und der RTE-Klade identifiziert werden. Basierend auf einer Identität von mindestens 60 % bilden die Sequenzen 17 L1 Familien und eine RTE Familie. Vollständige Mitglieder aller L1 Familien wurden hinsichtlich ihrer Sequenz, Struktur und Diversität analysiert. Um den in B. vulgaris getesteten HMM-basierten Algorithmus auf andere Angiospermengenome zu übertragen, wurden zwölf weitere Pflanzengenome auf das Vorhandensein von LINE-spezifischen Reversen Transkriptasen untersucht. Wesentlichstes Ergebnis ist der Nachweis von nur zwei LINE-Kladen (L1 und RTE) in höheren Pflanzen. Während pflanzliche L1 LINEs hochgradig divers sind und über Artgrenzen hinaus mindestens sieben Subkladen mit Vertretern verschiedener Pflanzen bilden, sind RTE LINEs extrem homogenisiert und stellen höchstwahrscheinlich nur eine einzelne Familie pro Genom einer Art dar. Zusammenfassend ermöglichen die Ergebnisse dieser Arbeit eine Erweiterung des Verständnisses der unterschiedlichen Evolutionsstrategien von Retrotransposons in Pflanzen. Zusätzlich tragen die gewonnen Daten zur Annotation des B. vulgaris Genoms bei.
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48

Kögler, Anja. "Diversity and Evolution of Short Interspersed Nuclear Elements (SINEs) in Angiosperm and Gymnosperm Species and their Application as molecular Markers for Genotyping." 2019. https://tud.qucosa.de/id/qucosa%3A72118.

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Short interspersed nuclear elements (SINEs) are small non-autonomous and heterogeneous retrotransposons, widespread in animals and plants and usually differentially propagated in related species resulting in genome-specific copy numbers. Within the monocots, the Poaceae (sweet grasses) is the largest and economically most important plant family. The distribution of 24 Poaceae SINE (PoaS) families, five of which showing a subfamily structure, was analyzed in five important cereals (Oryza sativa, Triticum aestivum, Hordeum vulgare, Sorghum bicolor, Zea mays), the energy crop Panicum virgatum and the model grass Brachypodium distachyon. The comparative investigation of SINE abundance and sequence diversity within Poaceae species provides insights into their species‐specific diversification and amplification. The PoaS families and subfamilies fall into two length and structural categories: simple SINEs of up to 180 bp and dimeric SINEs larger than 240 bp. Of 24 PoaS families, 20 are structurally related across species, in particular either in their 5′ or 3′ regions. Hence, reshuffling between SINEs, likely caused by nested insertions of full-lengh and truncated copies, is an important evolutionary mechanism of SINE formation. Most striking, the recently evolved homodimeric SINE family PoaS‐XIV occurs exclusively in wheat (T. aestivum) and consists of two tandemly arranged PoaS‐X.1 copies. Exemplary for deciduous tree species, the evolutionary history of SINE populations was examined in six Salicaceae genomes (Populus deltoides, Populus euphratica, Populus tremula, Populus tremuloides, Populus trichocarpa, Salix purpurea). Four of eleven Salicaceae SINE (SaliS) families exhibit a subfamily organization. The SaliS families consist of two groups, differing in their phylogenetic distribution pattern, sequence similarity and 3’ end structure. These groups probably emerged at different evolutionary periods of time: during the ‘salicoid duplication’ (~ 65 million years ago) in the Salix-Populus progenitor, and during the separation of the genus Salix (~ 45 - 65 million years ago), respectively. Similar to the PoaS families, the majority of the 20 SaliS families and subfamilies share regions of sequence similarity, providing evidence for SINE emergence by reshuffling. Furthermore, they also contain an evolutionarily young dimeric SINE family (SaliS-V), amplified only in two poplar genomes. The special feature of the Salicaceae SINEs is the contrast of the conservation of 5’ start motifs across species and SINE families compared to the high variability of 3’ ends within the SINE families, differing in sequence and length, presumably resulting from mutations in the poly(A) tail as a possible route for SINE elongation. Periods of increased transpositional activity promote the dissemination of novel 3’ ends. Thereby, evolutionarily older motifs are displaced leading to various 3’ end subpopulations within the SaliS families. Opposed to the PoaS families with a largely equal ratio of poly(A) to poly(T) tail SINEs, the SaliS families are exclusively terminated by adenine stretches. Among retrotransposon-based markers, SINEs are highly suitable for the development of molecular markers due to their unidirectional insertion and random distribution mainly in euchromatic genome regions, together with an easy and fast detection of the heterogeneous SINE families. As a prerequisite for the development of SINE-derived inter-SINE amplified polymorphism (ISAP) markers, 13 novel Theaceae SINE families (TheaS-I - TheaS-VII, TheaS-VIII.1 and TheaS-VIII.2, TheaS-IX - TheaS-XIII) were identified in the angiosperm tree species Camellia japonica. Moreover, six Pinaceae SINE families (PinS-I.1 and PinS-I.2, PinS-II – PinS-VI) were detected in the gymnosperm species Larix decidua. Compared to the SaliS and PoaS families, structural relationships are less frequent within the TheaS families and absent in the PinS families. The ISAP analysis revealed the genetic identity of Europe’s oldest historical camellia (C. japonica) trees indicating their vegetative propagation from the same ancestor specimen, which was probably the first living camellia on European ground introduced to England within the 18th century. Historical sources locate the native origin of this ancestral camellia specimen either in the Chinese province Yunnan or at the Japanese Gotō Islands. Comparative ISAPs showed no accordance to the Gotō camellia sample pool and appropriate Chinese reference samples were not available. However, the initial experiments demonstrated the potential of ISAP to resolve variations among natural populations. The ISAP application on angiosperm trees also concerned fast growing Populus clones grown in short rotation coppice plantations for energy production. The species-specific P. tremula ISAP primers might also be applied for the discrimination of hybrid poplar clones involving P. tremuloides genome portions, since SINEs of these two species are highly related. However, due to lineage-specific SINE evolution during speciation, cross-species applications are generally only successful to limited extent. The analysis of poplar hybrids composed of P. maximowiczii with either P. trichocarpa or P. nigra based on P. tremula ISAP primers showed a strongly reduced resolution. In forestry, hybrid larch (e.g. Larix × eurolepis) genotypes have to be selected from the offspring of Japanese (Larix kaempferi) and European larch (Larix decidua) crosses, as they exhibit superior growth rates compared to the parental species. Initial ISAP-based examinations of European larch genotypes provided less polymorphic banding patterns, probably resulting from general high levels of synteny and collinearities reported for gymnosperm species. Hence, the ISAP was combined with the AFLP technique to the novel marker system inter-SINE-restriction site amplified polymorphism (ISRAP). The amplicons originating from genomic regions between SINEs and EcoRI cleavage sites were visualized with the sensitive capillary gel electrophoresis. The ISRAP assays, based on EcoRI adapter primers combined with two different SINE-derived primers, resulted in a sufficient number of polymorphic peaks to distinguish the L. decidua genotypes investigated. Compared to ISAPs, the ISRAP approach provides the required resolution to differentiate highly similar larch genotypes.
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49

Fried, Claudia, Sonja J. Prohaska, and Peter F. Stadler. "Exclusion of repetitive DNA elements from gnathostome Hox clusters." 2004. https://ul.qucosa.de/id/qucosa%3A32631.

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Despite their homology and analogous function, the Hox gene clusters of vertebrates and invertebrates are subject to different constraints on their structural organization. This is demonstrated by a drastically different distribution of repetitive DNA elements in the Hox cluster regions. While gnathostomes have a strong tendency to exclude repetitive DNA elements from the inside of their Hox clusters, no such trend can be detected in the Hox gene clusters of protostomes. Repeats “invade” the gnathostome Hox clusters from the 5′ and 3′ ends while the core of the clusters remains virtually free of repetitive DNA. This invasion appears to be correlated with relaxed constraints associated with gene loss after cluster duplications.
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50

Le, Brese Christopher. "Robust matching of images containing perspective projection and repetitive elements." Thesis, 2014. http://handle.uws.edu.au:8081/1959.7/uws:30148.

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Image matching is an important stage of many computer vision tasks including image registration, object tracking, 3-dimensional reconstruction, augmented reality, and photogrammetry to name a few. It can be defined as the process of establishing reliable correspondence between interest points that have been found in two or more images. Current state-of-the-art methods use processes such as normalisation and simulation to match scenes that may have undergone geometric or photometric transformation. However, none have been shown to effectively handle all types of transformations. Although many simulation methods such as Affine-SIFT (ASIFT) do well when presented with large viewpoint changes, the large number of simulations required may make the method inefficient. When matching images that contain repetitive elements, many methods fail to remove erroneous matches due to ambiguity between detected features. Some methods have tried to avoid ambiguity by providing local context, global context, or combined neighbouring features. Filtering methods attempt to remove erroneous matches using geometric models or spatial relationships. However, some errors may go undetected. The aim of this thesis is to successfully match images containing affine or perspective viewpoint change, and scenes containing repetitive elements more accurately and efficiently than current state-of-the-art methods. This thesis proposes a new affine invariant method that utilises tentatively matched features to approximate the transform between views through normalisation and whitening. The calculated orientation is then used to simulate potential view transforms. An advantage of the proposed approach is that fewer simulations of the scene are required than state-of-the-art methods. Two novel methods of match filtering are proposed in an attempt to solve the ambiguity caused by repetitive patterns. The first is an enhancement of ASIFT to allow it to match scenes that contain repetitive elements. The second is the proposed Hierarchical Match Filtering (HMF) algorithm. HMF segments feature points into local cliques which are checked for spatial consistency by validating the area encapsulated by the clique; then neighbouring cliques are compared and collapsed into stronger ones if they are spatially consistent. An advantage of the proposed approach is that the accuracy of the filtered matches is better than current methods. Results for the affine invariant method show that scenes containing perspective projection of up to 80 degrees can be matched with an average accuracy of 97%, and an average residual error of 3.46 pixels, which is comparable to current methods. However, the method is more efficient than previous methods. Results have shown that HMF can match planar and 3D scenes containing repetitive elements with an accuracy of 98.66% and a residual error of 1.92 pixels. Current methods are only able to achieve 92% accuracy and a minimum error of 10.76 pixels. The algorithms have also been applied to the field of photogrammetry. Results have shown that the matches found by the proposed methods are able to be used to automate the detection of retro reflective markers (non-coded targets) and average proportional accuracies of the photogrammetry network are similar to those produced by the coded variety, 1:52000 compared to 1:57100 by current methods. The methods proposed in this thesis achieve the aim of accurately and robustly matching both perspectively warped scenes and images containing repetitive elements. Thus, the methods introduced may be used in fields such as 3D urban reconstruction, image registration, and augmented reality where both perspective projection and repetitive elements are commonly found.
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