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Using Transposable Elements as Tools to Better Understand Evolution at the Genomic LevelPlatt, Roy Nelson, II 17 May 2014 (has links)
Transposable elements (TEs), also known as jumping genes, are DNA sequences capable of mobilizing and replicating within the genome. In mammals, it is not uncommon for 50% of the genome to be derived from TEs, yet they remain an underutilized tool for tracking evolutionary change. With the increasing number of publicly funded genome projects and affordable access to next-generation sequencing platforms, it is important to demonstrate the role TEs may play in helping us understand evolutionary patterns. The research presented herein utilizes TEs to investigate such patterns at the genomic, specific, and generic levels in three distinct ways. First at the genomic level, an analysis of the historical TE activity within the thirteen-lined ground squirrel (Spermophilus tridecemlineatus) shows that non-LTR retrotransposon activity has been declining for the past ~26 million years and appears to have ceased ~5 million years ago. Since most mammals, and all other rodents studied to date, have active TEs the extinction event in S. tridecemlineatus makes it a valuable model for understanding the factors driving TE activity and extinction. Second, we examined TEs as factors impacting genomic and species diversity. We found that DNA transposon insertions in Eptesicus fuscus, appear to have been exapted as miRNAs. When placed within a phylogenetic context a burst of transposon-driven, miRNA origination and the vespertilionid species radiation occurred simultaneously ~30 million years ago. This observation implies that lineage specific TEs could generate lineage specific regulatory pathways, and consequently lineage specific phenotypic differences. Finally, we utilized TEs to investigate their phylogenetic potential at the level of genus. In particular a method was developed that identified, over 670 thousand Ves SINE insertions in seven species of Myotis for use in future phylogenetic studies. Our method was able to accurately identify insertions in taxa for which no reference genome was available and was confirmed using traditional PCR and Sanger sequencing methods. By identifying polymorphic Ves insertions, it may be possible to resolve the phylogeny of one of the largest species radiations in mammals.
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Genetic characterization of gamma-aminobutyrate metabolism in Sinorhizobium melilotiTrottier, Oliver. January 2008 (has links)
No description available.
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Transposon dynamics in self- and cross-fertilizing plant populationsWright, Stephen, 1975- January 2000 (has links)
No description available.
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Transposons and the evolutionary relationships among modern rice speciesTurcotte, Kime. January 2001 (has links)
No description available.
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Transposon-mediated gene diversificationElrouby, Nabil January 2005 (has links)
No description available.
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Detecção de elementos transponíveis e desenvolvimento parcial de um protocolo de inativação gênica mediada pelo transposon impala em fusarium graminearum / Detection of transposable elemento and partial development of aogenic inactivation protocol mediated for Impala transposon in Fusarium graminearumLeão, Ricardo Costa 22 June 2007 (has links)
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Previous issue date: 2007-06-22 / The fungi Fusarium graminearum (teleomorph Gibberella zeae) is the etiological agent of
scab wheat, one of the most important cereal s winter diseases in Brazil. Outbreaks are
generally sporadic but in the last few years is frequently reported an increase in disease
intensity in almost all the wheat producing areas around the world. Some studies demonstrate
a high genetic diversity in F. graminearum from different geographic areas, as well as in
isolates at the same locality. In filamentous fungi, as the F. graminearum, one of the main
mutation s causes is the transposable elements or transposons which are capable to generate
different types of mutations. In some cases, these mutations are involved with the resistance
break, an important phenomenon for the occurrence of epidemics. The objectives of this study
were to detect putative transposable elements sequences in the F. graminearum genome, as
well as to develop and to analyze adequate procedures for co-transformation of brazilin
isolates of this fungi with the vectors pNI160, which carry the transposon impala and pAN7.1,
which code to hygromycin B resistance. To detect putative sequences of transposable
elements in the F. graminearum genome, specifics oligonucleotides were constructed and 14
isolates, originated from the States of Rio Grande do Sul, Paraná and São Paulo were used. A
total of 10 oligonucleotides pairs were constructed (6 oligonucleotides pairs were specific to
transposase, 3 to transcriptase reverse and 1 to gene that code for GAG protein). Considering
these 10 oligonucleotides pairs, the one that would amplify a transcriptase reverse region
similar to a Magnaporthe grisea reverse transcriptase did not amplify any fragment in the
isolates total DNA, and the pair that would amplify a transposase region similar to
Metarhizium anisopliae originated many fragments of different sizes that do not show relation
with 683 bp expected size fragment. Considering the eight oligonucleotides pairs remained,
five of them amplified the expected fragments for transposase (715 bp region similar to F.
oxysporum f. sp. ciceris transposase, 306 bp similar to Aspergillus awamori transposase, 556
bp similar to A. niger tansposase, 339 bp similar to Arabdopsis thaliana transposase and 554
bp similar to Cochliobolus carbonum transposase), two of them amplified the transcriptase
reverse fragments (161 bp similar to A. thaliana reverse transcriptase and the 752 bp similar
to Caenorhabditis elegans reverse transcriptase) and one oligonucleotide pair amplified an
581 bp expected size fragment similar to F. oxysporum gag gene. The amplification occurred,
even for different oligonucleotides pairs, in all 14 analyzed isolates confirming the presence
of transposable elements putative sequences in Brazilian isolates of F. graminearum. This
also shows a diversity of groups of these putative elements, considering that some of the
sequence amplified is characteristic of a transposable element specific group. To develop the
genic inactivation protocol, we select the isolates F02 and F12 which are pathogenic for
BR18-Terena cultivar. To evaluate the better medium for selection of chlorate resistant
mutants, it was analyzed two different medium. This analysis showed that medium describe
by Cove (1979) is more indicate for selected the chlorate resistant mutants. A total of 15
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chorate resistant mutants were obtained, being five identified as nitrate reductase mutants
(niaD), eight specific regulator mutants (nirA) and two permease mutants. Differences related
to the number of mutants obtained and number inoculated plates, number of nitrate reductase
mutants and macroconides production indicate that the choice of the isolate can influence the
isolation of mutants and in protoplast production. Analysis with different hygromycin B
concentrations revealed that doses up to 30 μg.mL-1 were enough to control the fungal
growth. Two nitrate reductase mutants (M01 and M194) were select to protoplastization and
co-transformation, once these two mutants in relation to others produce lower concentration
of residual mycelium. Only one transformant were obtained and it was denominated T3, what
shows that the transformation protocol needs to be modified to increase the number of
transformants. If hybridization experiments confirm the transformation of T3 with only one
copy of the impala element, it will be confirmed the transposition ability of impala in F.
graminearum, and it will be useful in genetic inactivation studies, especially to genes
involved in pathogenicity process / O fungo Fusarium graminearum (teleomorfo Gibberella zeae) é o agente etiológico da
giberela do trigo, atualmente uma das principais doenças de inverno no Brasil. Epidemias
ocorrem esporadicamente, embora nos últimos anos, registraram-se incrementos na
intensidade da doença em quase todas as áreas produtoras de trigo no mundo. Vários estudos
demonstram uma grande diversidade genética em isolados de F. graminearum de diferentes
áreas geográficas, como também em isolados de uma mesma localidade. Em fungos
filamentosos como o F. graminearum, uma das principais fontes de mutações capaz de gerar
alta variabilidade genética são os elementos transponíveis ou transposons. Essas mutações
algumas vezes estão envolvidas com a quebra de resistência, fenômeno importante para o
surgimento de epidemias. Os objetivos deste trabalho foram de detectar putativas seqüências
de elementos transponíveis no genoma deste fungo, bem como, desenvolver e analisar
procedimentos e métodos adequados para a co-transformação de isolados brasileiros deste
fungo com o plasmídio pNI160, o qual carrega o transposon impala, e o plasmídio pAN7.1, no
qual esta inserido o gene de resistência a higromicina B. Para detectar putativas seqüências de
elementos transponíveis no genoma deste patógeno foram construídos oligonucleotídeos
específicos para amplificação, via PCR de seqüências características destes elementos
transponíveis. Foram utilizados 14 isolados de F. graminearum, provenientes dos Estados do
Rio Grande do Sul, Paraná e São Paulo e um total de 10 pares de oligonucleotídeos foram
construídos (6 pares para genes que codificam a enzima transposase, 3 pares para genes que
codificam a enzima transcriptase reversa e 1 par um gene que codifica a proteína GAG). Dos
10 pares de oligonucleotídeos utilizados, o par que amplificaria uma região de transcriptase
reversa similar ao mesmo gene de Magnaporthe grisea não amplificou nenhum fragmento nos
isolados utilizados, e o par que amplificaria uma região de transposase similar ao mesmo gene
de Metarhizium anisopliae originou muitos fragmentos de diferentes tamanhos não
condizentes com o tamanho esperado de 683 pb. Dos oito pares de oligonucleotídeos
restantes, cinco amplificaram as regiões esperadas para a transposase (regiões de 715 pb
similar a uma transposase de F. oxysporum f. sp. ciceris, 306 pb similar a uma transposase de
Aspergillus awamori, 556 pb similar a uma transposase de A. niger, 339 pb similar a uma
transposase de Arabidopsis thaliana e 554 pb similar a uma transposase de Cochliobolus
carbonum), dois amplificaram as regiões de transcriptase reversa (regiões de 161 pb similar a
uma transcriptase reversa de A. thaliana e 752 pb similar a uma transcriptase reversa de
Caenorhabditis elegans) e um amplificou um fragmento de tamanho esperado de 581 pb
similar ao gene gag de F. oxysporum. A amplificação ocorreu, mesmo que para diferentes
pares de oligonucleotídeos, em todos os 14 isolados analisados, confirmando a presença de
seqüências putativas de elementos transponíveis em isolados de F. graminearum provenientes
de diferentes regiões do Brasil, além de demonstrar uma diversidade de classes de putativos
elementos, uma vez que cada seqüência é característica de um determinado grupo de
elementos transponíveis. Para o desenvolvimento do protocolo de inativação gênica foram
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selecionados os solados F02 e F12 patogênicos a cultivar BR18-Terena. Um teste para
avaliação do meio de cultura para seleção dos mutantes resistentes ao clorato demonstrou que
o meio descrito por Cove (1979) é o mais indicado para os isolados selecionados. Um total de
15 isolados mutantes resistentes ao clorato foi obtido, dos quais 5 foram identificados como
mutantes para o gene nitrato redutase (niaD), 8 mutantes para um regulador específico (nirA)
e 2 mutantes para permease. Diferenças quanto ao número de mutantes selecionados pelo
número de placas inoculadas, número de mutantes nitrato redutase e produção de esporos
assexuais, indicam que a escolha do isolado pode influenciar na obtenção de mutantes e na
produção de protoplastos. Testes com diferentes concentrações de higromicina revelaram que
doses acima de 30 μg. mL-1 são suficientes para o controle do crescimento do fungo. Dois
mutantes nitrato redutase (M01 e M194) foram selecionados para a protoplastização e cotransformação,
com base na menor produção de micélio residual em relação aos demais.
Apenas um transformante foi obtido sendo denominado T3, mostrando a viabilidade do
protocolo, mas também, que mais estudos devem ser realizados para se aumentar o número de
transformantes. Se confirmada, através de hibridização, a transformação de T3 com uma única
cópia do elemento impala, este poderá além de confirmar a capacidade de transposição deste
elemento em F. graminearum, também servir em estudos de expressão gênica, principalmente
àqueles genes envolvidos no processo de patogenicidade
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Résistance aux carbapénèmes médiée par les carbapénèmases de type OXA-48 chez les entérobactéries / carbapenems resistance mediated by OXA-48-like carbapenemasesPotron, Anaïs 03 December 2013 (has links)
Les carbapénèmes constituent le traitement de dernier recours des infections associées à des germes multirésistants producteurs de -lactamases à spectre étendu. Les entérobactéries ont cependant développé des mécanismes de résistance à l’encontre de cette classe d’antibiotiques, notamment par la production de carbapénèmases. La carbapénèmase OXA-48 a rapidement disséminé en Europe et dans le pays du pourtour méditerranéen depuis 2010. Les objectifs de ce travail ont englobé, dans une première partie, la caractérisation de trois variants de la carbapénèmase OXA-48, possédant chacun des particularités phénotypiques ou génétiques. Nous nous sommes ensuite intéressés à l’épidémiologie de la carbapénèmase OXA-48 afin de comprendre ses mécanismes de dissémination puis à la variabilité de son environnement génétique. Le dernier objectif était de déterminer les facteurs génétiques à l’origine de la dissémination de la carbapénèmase OXA-48. Nous avons ainsi montré que les carbapénèmases de type OXA-48 bénéficient de tous les éléments moléculaires pour assurer leur succès : mobilisation par un transposon actif pour certains variants, transfert efficace de plasmides et dissémination clonale de souches. / Carbapenems are often the last therapeutic option for treating infections involving multiresistant ESBL-producing bacteria. Nevertheless, enterobacteria have developped resistance mechanisms toward this class of antibiotics, including carbapenemases production. Carbapenemase OXA-48 has rapidly spread throughout Europe and various countries of Mediterranean area since 2010. The aim of this work was first to characterize three variants of the carbapenemase OXA-48, each possessing phenotypic or genetic characteristics. We focused on the epidemiology of carbapenemase OXA-48 in order to understand the mechanisms of its dissemination and on the variability of its genetic environment. The last objective was to determine the genetic factors responsible for the spread of carbapenemase OXA-48. We have shown that the OXA-48-type carbapenemases possess all the molecular elements to ensure its success: mobilization by an active transposon for some variants, efficient transfer of plasmids and clonal spread of strains.
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Desenvolvimento de marcadores microssatélites para Ololygon centralis (Anura: Hylidae) por sequenciamento de segunda geração com baixa cobertura / Development of microsatellite markers for Ololygon centralis (Anura: Hylidae) using second generation sequencing with low coverageCastro, Andrezza Arantes 12 March 2018 (has links)
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Previous issue date: 2018-03-12 / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / The ease access to Next Generation Sequence methodologies has improved the development
of several projects, once it makes possible the de novo assembly of DNA sequences,
creating a great amount of data and giving access to unknown genomes of different
organisms. The anuran species Ololygon centralis belong to Hylidae family. It is considered
as endemic of Cerrado Biome and little is known about its genomics. The aim of this work
was to realize a draft of the genome of O. centralis in order to identify, to characterize, to
quantify repetitive elements and to predict possible genes. Also, we aimed to develop
microsatellite markers for the species. The genome draft assembled in 13989 scaffolds,
which correspond to 4926069 bp with N50 = 336. The repetitive elements found in the O.
centralis genome (1795 transposons, 957, microsatellite, one satellite DNA and 25 small
nuclear RNAs) comprised 531337 bp. Between the retrotransposons, the LINE element
(49,83%) was the most abundant, followed by LTR (48,66%) and SINE (1,56%). It was
possible to identify coding genes for the 5S, 18S and 28S subunits of ribosomes. Also, 18
types of coding regions for tRNA and 26 putative genes were found in the O. centralis
genome. From the microsatellite regions, it was possible to design 87 pairs of primers for
the flanking sites. There were found 47 regions composed of tetranucleotides, 39
dinucleotides and on trinucleotide on the microsatellite sites. From them, 31 pairs of primers
were selected for amplification and 18 showed good results. The annealing temperatures
varied from 50° e 60° C. Seven markers showed polymorphism. From them, only 5 markers
(PCE05, OCE11, PCE20, OCE21, OCE26) were used to characterize the genotype of 30
individuals. The medium number of alleles was 10, the allelic amplitude varied from 148 bp
(OCE20) to 318 bp (OCE21). The Expected Heterozygosity was 0,7 and the observed was
0,5. The probability of parentage exclusion (Q) was 0,993 and the probability of combined
identity (I) was 1,13x10-6. The global value of the fixation index (FST) was significant and
equal to 0,2 (p<0.05). The data obtained from the NGS Illumina platform represent one
important step for the knowledge of genomics of this species and of the anuran in general. / A facilidade para o acesso às metodologias de Sequenciamento de Segunda Geração (Next
Generation Sequence) tem impulsionado o desenvolvimento de diversos projetos, uma vez
que possibilita a montagem de novo de sequências, gerando uma grande quantidade de
dados e permitindo o acesso a genomas de diversos organismos ainda pouco conhecidos. A
espécie de anuro Ololygon centralis (Pombal e Bastos 1996) pertence à família Hylidae,
considerada endêmica do Bioma Cerrado e que ainda não dispõe de nenhuma informação
genômica. O objetivo desse trabalho foi realizar uma montagem parcial do genoma de
Ololygon centralis a fim de identificar, caracterizar, quantificar elementos repetitivos e
predizer genes nas sequências genômicas, além de desenvolver marcadores microssatélites
para a espécie. O genoma parcial montado resultou em 13.989 scaffolds, que correspondem
a 4.926.069 pb com N50 de 336. Os elementos repetitivos encontrados no genoma de O.
centralis (1.795 elementos transponíveis, 957 microssatélites, um DNA satélite e 25
pequenos RNAs nucleares) totalizaram 531.337 pb. Entre os retrotransposons, o elemento
LINE (49,83%) foi o mais abundante, seguido do LTR (48,66%) e SINE (1,56%). Foram
identificados os genes que codificam as subunidades 5S, 18S e 28S de ribossomos, 18 tipos
de tRNAs no genoma e 26 genes. A partir das sequências foi possível desenhar 87 pares de
primers flanqueando regiões microssatélites. Dentre elas, 47 foram regiões compostas de
tetranucleotídeos, 39 dinucleotídeos, e um trinucleotídeo. Deste total, 31 pares de primers
foram selecionados para padronização em gel de poliacrilamida (6%) e 18 deles
apresentaram produto de amplificação adequado. Durante a padronização, as temperaturas
de anelamento variaram entre 50° e 60° C e sete marcadores apresentaram polimorfismo.
Dos sete, apenas cinco marcadores (OCE05, OCE11, OCE20, OCE21, OCE26) foram
padronizados e utilizados para caracterização em 30 indivíduos de O. centralis no analisador
automático ABI3500. O número médio de alelos foi igual a 10, a amplitude alélica variou
entre 148pb (OCE 20) a 318 pb (OCE 21). A Heterozigosidade média esperada foi 0,7 e a
observada igual a 0,5. A probabilidade de exclusão de paternidade (Q) foi igual a 0,993 e a
probabilidade combinada de identidade (I) igual a 1,13x10-6. O valor global para o índice de
fixação (FST) foi significativo e igual a 0,2 (p <0,05). Os dados obtidos a partir do NGS
plataforma Illumina representam um importante passo para o conhecimento genômico dessa
espécie e dos anfíbios em geral, o desenvolvimento de primers contribuirá para o estudos
genéticos-populacionais de Ololygon centralis e espécies correlacionadas por meio da
transferibilidade.
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Development and application of biotechnological tools in the major crop plant, Brassica napusBabwah, Andy Videsh. January 2001 (has links)
No description available.
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Analysis of clostridial MLS resistance determinantsFarrow, Kylie Ann, 1973- January 2001 (has links)
Abstract not available
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