No description available.

Background. Aspects of genetics/genomics are increasingly being incorporated into medicine. Nurses are crucial in helping transform healthcare through genomic nursing (Loud, 2010). However the integration of genetics/genomics into nursing education has been sporadic (Dodson and Lewallen, 2011). Influencing its uptake into practice may be via nurses who are already utilising genetics/genomics in their practice (adopters) and nurses who may lead the way and encourage others (opinion leaders) to do likewise. Identifying the characteristics of such adopters and opinion leaders within nursing may provide useful information for more wide-scale detection of these individuals to support a strategy for the inclusion of genetics/genomics into nursing practice. Methods. Five change behaviour theories were used to inform the study including the Theory of Planned Behaviour and the Diffusion of Innovations. A mixed methods approach was taken over two phases. In Phase 1 experts in the field of genetics/genomics and nursing were contacted to gain a consensus on four potential genetic indicators of adoption (GIAs), which would identify a nurse who had adopted genetics/genomics. In Phase 2, oncology nurses and practice nurses completed a questionnaire to identify the characteristics and demographic indicators of nurse genetic adopters and opinion leaders. Results. A consensus (>75%) was achieved for all four GIAs to be included as indicators of adoption of genetics/genomics within nursing practice (Phase 1). Individuals identified (in Phase 2) were subcategorised into six different groups, including genetic adopters and opinion leaders. There were 18 identifying features that defined an adopter, with some of the main features being Openness to Experience (p<0.001), seeing the relevance of genetics/genomics to their patient group (p<0.001) and talking to colleagues about genetics/genomics (p<0.001). There were six features that identified an opinion leader, including academic achievement (p=0.007), level of perceived influence over others (p<0.001) and being high on the opinion leadership scale (p<0.001). Two of the biggest barriers to incorporation by nurses were lack of time for adopters and a lack of local study sessions for opinion leaders. Conclusion. It has been identified that nurses can be categorised in terms of their relationship to genetics/genomics, through a number of distinguishing characteristics. It will be important to further identify and clarify these and other characteristics through the development of additional tools. These data can inform approaches to promote a greater integration of genetics/genomics into nursing practice, ultimately improving patient healthcare.

Made available in DSpace on 2015-03-03T11:52:35Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-02-28Bitstream added on 2015-03-03T12:06:25Z : No. of bitstreams: 1 000807323_20160228.pdf: 863780 bytes, checksum: f9edab5c1d353f33385731e8fc06aa46 (MD5) Bitstreams deleted on 2016-02-29T12:16:26Z: 000807323_20160228.pdf,. Added 1 bitstream(s) on 2016-02-29T12:17:25Z : No. of bitstreams: 1 000807323.pdf: 3263368 bytes, checksum: e50d8228791f0d071b3e2c640b0eefa9 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Os retrotransposons com LTR (long terminal repeats) (LTR-RTEs) são os componentes mais abundantes nos genomas vegetais. Eles são divididos em duas superfamílias, Copia e Gypsy, de acordo com a ordem dos domínios internos e com a similaridade das sequências. São conhecidos pela sua natureza ubíqua e plasticidade, o que os leva a serem explorados como ferramentas para o desenvolvimento de marcadores moleculares, utilizando-se assim o padrão de inserção dos LTR-RTEs para geraçã o de polimorfismos. As famílias de LTR-RTEs apresentam número de cópias variável dentro de um mesmo genoma, mas a amplificação de poucas famílias pode contribuir com grandes diferenças de tamanho entre genomas próximos. Em plantas do gênero Eucalyptus existem poucos estudos relacionados aos LTR-RTEs, que geralmente limitam-se a análises em bancos de dados privados. Este trabalho tem como objetivo a caracterização de LTR-RTEs transcricionalmente ativos pertencentes as superfamílias Copia e Gypsy, encontrados no genoma de eucalipto. A partir de análises preliminares de bioinformática, um total de nove famílias de LTR-RTEs foram identificadas; os elementos da superfamília Copia foram classificadas em cinco linhagens e elementos da superfamília Gypsy foram divididos em três linhagens. As análises in silico no genoma draft de Eucalyptus grandis identificaram que as famílias caracterizadas possuem entre 38 e 290 cópias. Os LTR-RTEs foram utilizados para o desenvolvimento de marcadores moleculares IRAP, REMAP e RBIP, que foram avaliados em cinco espécies de eucalipto. Dezesseis primers IRAP foram avaliados e um total de 1521 fragmentos foram gerados, com 321 fragmentos polimórficos, em um intervalo de 250 a 2500 bp e uma média de 19,01 fragmentos amplificados por primer. Vinte e oito combinações de primers REMAP foram avaliadas e geraram 1910 fragmentos, dos quais 492 são polimórficos, em um intervalo de 200 a 1250 bp, com uma média de ... / Long Terminal Repeat Retrotransposons (LTR-RTEs) are the most abundant component of plant genomes. They are divided into two superfamilies, Copia and Gypsy, based on coding domain order and sequence similarity. As dynamic and ubiquitous entities in plant genomes, marker systems based in LTR-RTEs were developed to exploit LTR-RTEs insertion pattern polymorphism. In most angiosperm genomes, LTR-RTEs families have a wide range of copy number, but the amplification of a few families individually contribute to a large fraction of the genome. LTR-RTEs were scarcely studied in the Eucalyptus genus, with most findings derived from global analyses of private genomic databases. The aim of this work is to characterize transcriptionally active Copia and Gypsy LTR-RTEs in Eucalyptus sp genomes. After preliminary bioinformatics analyses, a total of 9 full-length LTR-RTEs families were classified into five Copia and three Gypsy lineages. BLAT analysis in Eucalyptus grandis draft genome identified that these elements have between 38 and 290 copies. These LTR-RTEs were used to develop IRAP, REMAP and RBIP markers, which were evaluated in five Eucalyptus species (Eucalyptus brassiana, E. grandis, Eucalyptus saligna, Eucalyptus tereticornis and Eucalyptus urophylla). Sixteen IRAP primers produced 321 polymorphic fragments from a total of 1521 bands, ranging from 250 to 2500 bp, with an average of 19.01 bands amplified per IRAP primer. Twenty-eight REMAP primer combinations produced 1910 bands. 492 of them were polymorphic, ranging from 200 to 1250 bp. An average of 13.64 REMAP bands was scored per primer. Our results showed that the genetic similarity assessed by both IRAP and REMAP markers did not reflect molecular phylogenetic analysis. Nonetheless, these markers are useful for the assessment of genetic diversity the individual level and population analysis. We developed RBIP markers for three site-specific ...

As sequências genômicas carregam uma ampla gama de informações sobre os organismos que a compõem. Obviamente, devido à grande semelhança destas informações e funções, espera-se que uma determinada sequência possa pertencer a muitos organismos, com probabilidades semelhantes. Entretanto, cada genoma carrega dentro de si certas peculiaridades que podem ser extraídas utilizando as ferramentas adequadas. Neste contexto, este trabalho propõe um processo de análise de sequências genômicas de bactérias, utilizando algumas medidas que são particularmente importantes: a entropia de triples (Sn), a quantificação da periodicidade 3 (P3) em uma sequência, o coeficiente de clusterização (D) e o percentual de GC. O processo aqui proposto nos permite inferir a qual organismo uma determinada sequência genômica pode pertencer, mostrando-se viável a sua utilização em metagenômica. Os resultados neste trabalho demonstram a eficácia deste método. Foram identificados 100% dos organismos presentes nas amostras estudadas (VP). Por outro lado, foi encontrado um grande número de organismos não pertencentes às amostras (FP), o que indica a grande similaridade de determinadas sequências, corroborando com alguns estudos que indicam que o genoma carrega consigo sequências órtologas, comuns a inúmeros organismos. / Submitted by Ana Guimarães Pereira (agpereir@ucs.br) on 2015-11-17T13:29:43Z No. of bitstreams: 1 Tese Ricardo Augusto Manfredini.pdf: 3422485 bytes, checksum: f6111d39384f0d874a1c4820a7faf475 (MD5) / Made available in DSpace on 2015-11-17T13:29:43Z (GMT). No. of bitstreams: 1 Tese Ricardo Augusto Manfredini.pdf: 3422485 bytes, checksum: f6111d39384f0d874a1c4820a7faf475 (MD5) / Genomic sequences carry a wide range of information on organism that compose it. Obviously, by reason that great similarity of this information and functions, it is expected that each sequence can belong to many organisms with a similar probability. However, each genome carries within itself certain peculiarities that can be extracted using appropriate tools. In this context , this paper proposes a methodology for the analysis of genomic sequences of bacteria , using some measures that are particularly important : The entropy of triples ( Sn ) , the quantification of frequency 3 (P3) in a sequence , the clustering coefficient ( D ) and the percentage of GC . The method proposed here allows us to infer which a particular organism genome sequence may belong, being feasible for use in Metagenomics. The results of this study demonstrate the effectiveness of this method, 100 % of the organisms were identified in the samples studied (VP). On the other hand, a large number of bodies which did not belong samples were found (FP), which indicates the high similarity of certain sequences, corroborating some studies indicate that the genome carries ortholog sequences, common to countless organisms.

As sequências genômicas carregam uma ampla gama de informações sobre os organismos que a compõem. Obviamente, devido à grande semelhança destas informações e funções, espera-se que uma determinada sequência possa pertencer a muitos organismos, com probabilidades semelhantes. Entretanto, cada genoma carrega dentro de si certas peculiaridades que podem ser extraídas utilizando as ferramentas adequadas. Neste contexto, este trabalho propõe um processo de análise de sequências genômicas de bactérias, utilizando algumas medidas que são particularmente importantes: a entropia de triples (Sn), a quantificação da periodicidade 3 (P3) em uma sequência, o coeficiente de clusterização (D) e o percentual de GC. O processo aqui proposto nos permite inferir a qual organismo uma determinada sequência genômica pode pertencer, mostrando-se viável a sua utilização em metagenômica. Os resultados neste trabalho demonstram a eficácia deste método. Foram identificados 100% dos organismos presentes nas amostras estudadas (VP). Por outro lado, foi encontrado um grande número de organismos não pertencentes às amostras (FP), o que indica a grande similaridade de determinadas sequências, corroborando com alguns estudos que indicam que o genoma carrega consigo sequências órtologas, comuns a inúmeros organismos. / Genomic sequences carry a wide range of information on organism that compose it. Obviously, by reason that great similarity of this information and functions, it is expected that each sequence can belong to many organisms with a similar probability. However, each genome carries within itself certain peculiarities that can be extracted using appropriate tools. In this context , this paper proposes a methodology for the analysis of genomic sequences of bacteria , using some measures that are particularly important : The entropy of triples ( Sn ) , the quantification of frequency 3 (P3) in a sequence , the clustering coefficient ( D ) and the percentage of GC . The method proposed here allows us to infer which a particular organism genome sequence may belong, being feasible for use in Metagenomics. The results of this study demonstrate the effectiveness of this method, 100 % of the organisms were identified in the samples studied (VP). On the other hand, a large number of bodies which did not belong samples were found (FP), which indicates the high similarity of certain sequences, corroborating some studies indicate that the genome carries ortholog sequences, common to countless organisms.

Philosophiae Doctor - PhD / Despite the fact that the sequence of the human genome is now complete it has become clear that the elucidation of the transcriptome is more complicated than previously expected. There is mounting evidence for unexpected and previously underestimated phenomena such as alternative splicing in the transcriptome. As a result, the identification of novel transcripts arising from the genome continues. Furthermore, as the volume of transcript data grows it is becoming increasingly difficult to integrate expression information which is from different sources, is stored in disparate locations, and is described using differing terminologies. Determining the function of translated transcripts also remains a complex task. Information about the expression profile – the location and timing of transcript expression – provides evidence that can be used in understanding the role of the expressed transcript in the organ or tissue under study, or in developmental pathways or disease phenotype observed. In this dissertation I present novel computational approaches with direct biological applications to two distinct but increasingly important areas of research in gene expression research. The first addresses detection and characterisation of alternatively spliced transcripts. The second is the construction of an hierarchical controlled vocabulary for gene expression data and the annotation of expression libraries with controlled terms from the hierarchies. In the final chapter the biological questions that can be approached, and the discoveries that can be made using these systems are illustrated with a view to demonstrating how the application of informatics can both enable and accelerate biological insight into the human transcriptome. / South Africa

Magister Scientiae - MSc (Biochemistry) / Alternative RNA splicing is one of the leading mechanisms contributing towards transcript and protein diversity. Several alternative splicing surveys have confirmed the frequent occurrence of exon skipping in human genes. However, the occurrence of exon skipping in mouse genes has not yet been extensively examined. Recent improvements in mouse genome sequencing have permitted the current study to explore the occurrence of exon skipping in mouse genes orthologous to human genes on chromosome 22. A low number (5/72 multi-exon genes) of mouse exon-skipped genes were captured through alignments of mouse ESTs to mouse genomic contigs. Exon-skipping events in two mouse exon-skipped genes (GNB1L, SMARCB1) appear to affect biological processes such as electron and protein transport. All mouse, skipped exons were observed to have ubiquitous tissue expression. Comparison of our mouse exon-skipping events to previously detected human exon-skipping events on chromosome 22 by Hide et al.2001, has revealed that mouse and human exon-skipping events were never observed together within an orthologous gene-pair. Although the transcript identity between mouse and human orthologous transcripts were high (greater than 80% sequence identity), the exon order in these gene-pairs may be different between mouse and human orthologous genes. Main factors contributing towards the low detection of mouse exon-skipping events include the lack of mouse transcripts matching to mouse genomic sequences and the under-prediction of mouse exons. These factors resulted in a large number (112/269) of mouse transcripts lacking matches to mouse genomic contigs and nearly half (12/25) of the mouse multi-exon genes, which have matching Ensembl transcript identifiers, have under-predicted exons. The low frequency of mouse exon skipping on chromosome 22 cannot be extrapolated to represent a genome-wide estimate due to the small number of observed mouse exon-skipping events. However, when compared to a higher estimate (52/347) of exon skipping in human genes for chromosome 22 produced under similar conditions by Hide et al.2001, it is possible that our mouse exon-skipping frequency may be lower than the human frequency. Our hypothesis contradicts with a previous study by Brett et al.2002, in which the authors claim that mouse and human alternative splicing is comparable. Our conclusion that the mouse exon-skipping frequency may be lower than the human estimate remains to be tested with a larger mouse multi-exon gene set. However, the mouse exon-skipping frequency may represent the highest estimate that can be obtained given that the current number (87) of mouse genes orthologous to chromosome 22 in Ensembl (v1 30th Jan. 2002) does not deviate significantly from our total number (72) of mouse multi-exon genes. The quality of the current mouse genomic data is higher than the one utilized in this study. The capture of mouse exon-skipping events may increase as the quality and quantity of mouse genomic and transcript sequences improves. / South Africa

No description available.

The expression of a mammalian ras gene analog was previously found by Reymond et al. to be developmentally regulated in Dictyostelium discoideum using Northern analysis of strain AX-3 RNA (1984, Cell 39;141) and by Pawson et al. using specific immunoprecipitation of in vivo synthesized proteins from strain V12M2 (1985, Mol. Cell Biol. 5;33). Due to differences in the results of the two studies, it was decided to further examine ras expression by applying both protein and RNA techniques to a single strain of D.discoideum, V12M2. RNA samples from strain V12M2 cells at different stages of development were analyzed using Northern blotting. The same RNAs were translated in vitro, and the ras proteins synthesized were immunoprecipitated and analysed by polyacrylamide gel electrophoresis. In agreement with the findings of Reymond et al. (1984, Cell 39;141), Northern analysis with the cDNA ras probe revealed that the highest levels of the 1.2 and 0.9 kb ras mRNAs were present in the total RNA of V12M2 cells at the pseudoplasmodial stage of development, and very little ras mRNA was present in early developing cells. In contrast to the Northern analysis the greatest amount of ras protein was in vitro translated from the RNA of vegetative and 2 hour cells. Hence this work confirms in a single strain of Dictyostelium that the greatest amount of ras protein is synthesized at those developmental stages that contained the lowest levels of mRNA detectable by the cDNA probe. Possible reasons for this phenomena are discussed. In vitro RNA translation was also used to study the relationship between the two ras proteins of 23 and 24 kd. The proteins did not appear to be derived from one another by degradation or by post-translational modification. This result suggested that the two ras proteins of strain V12M2 must be derived from two different mRNAs. High stringency Southern blots of AX-3 DNA showed the expected restriction fragments detected by Reymond et al. (1984, Cell 39;141) . Low stringency blots showed three faint additional restriction fragments in Eco RI digests of AX-3 DNA. No additional restriction fragments were generated by an Eco RI-Bg1 II digest, but two of the three faint bands were smaller. This suggested that at least two of the Eco RI ras fragments are non-contiguous, and hence two to three ras genes may be present in addition to the one characterized by Reymond et al. (1984, Cell 39;141). All Northern and Southern bolts were probed with antisense RNA probes in order to gain greater sensitivity of detection as described by Cox et al. (1984, Dev. Biol. 101;485). / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

O trabalho descreve um método para isolamento de núcleos morfologicamente intacto e fisiologicamente ativos, além da caracterização parcial do DNA de Acanthamoeba castellanii (linhagem Neff). O DNA celular total de trofozoitos contém quatro famílias com diferentes velocidades de renaturação. A fração com renaturação mais lenta (DNA \"único\"), corresponde ao DNA nuclear (86% do genoma) e apresenta características cinéticas compatíveis com uma complexidade de sequência igual a 1,46x1011 daltons. O DNA reiterado (14% do genoma), compreende três famílias de sequências de nucleotídeos, denominadas \"rápidas\", \"intermediária\" e \"lenta\", com complexidade cinética respectivamente igual a 1,5x106; 2,1x10<SUP.7 e 2,6x108 daltons, presentes em aproximadamente 3x103, 3x102 e 50 cópias. As famílias de DNA reiterado têm localização predominantemente citoplasmática, sendo que as famílias \"intermediárias\" e \"lentas\" fazem parte do genoma mitocondrial. O comportamento cinético heterogêneo do DNA mitocondrial e sua complexidade assemelham-se aos dados existentes para outros microrganismos eucariotos. A constatação de uma espécie de DNA extramitocondrial pode ser relacionada com a descrição anterior de corpúsculos citoplasmáticos contendo DNA ou com a extrusão de cromatina para o citoplasma, verificada no início do encistamento. O DNA de trofozoitos também foi caracterizado quanto ao padrão de sedimentação em gradientes de densidade, desnaturação térmica e composição de bases. O DNA celular total apresenta dois componentes em gradientes de CsCl, caracterizados por densidade de flutuação iguais a 1,717 g/cm3 (Componente maior) e 1,692 g/cm3 (componente menor). O perfil de fusão do DNA mitocondrial sugere heterogeneidade de composição de bases. / Abstract not available.