Дисертації: "Genomic resources"

1

Voutsina, Nikol. "Elucidating the genomics of nutritional and morphological traits in watercress (Nasturtium officinale R. Br.) : the first genomic resources." Thesis, University of Southampton, 2017. https://eprints.soton.ac.uk/425884/.

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Watercress (Nasturtium officinale R. Br.; Brassicaceae) has a long history of human use for medicine and consumption. In recent years, it has received a large deal of attention as one of the most nutrient-dense foods. Despite this, watercress remains largely underdeveloped with limited breeding resources through which to meet current and future intensifying market demands, such as for a more compact morphology, enhanced nutritional benefits and resource-use efficiency. The aim of this PhD has been to characterize the genetic structure of nutritional and morphological traits in watercress and develop molecular breeding tools that will inform and facilitate future work on this crop. To this end, Chapter 1 provides an overview of pre-existing knowledge on watercress and reviews the opportunities offered by Next Generation Sequencing tools for undeveloped crops. Chapter 2 describes the application of RNASeq towards de novo assembly and functional annotation the watercress transcriptome for the first time. Differential expression analysis resulted in a catalogue of significant genes for antioxidant capacity and glucosinolate content in watercress and identified orthologs to known phenylpropanoid and glucosinolate biosynthetic pathway genes. In Chapter 3, the first genetic linkage map and QTL analysis were completed for this crop, utilizing Genotyping-By-Sequencing for marker discovery. In a novel undertaking to identify QTL for chemopreventive qualities in a plant genome, the toxicity of watercress to human cancer cells was mapped successfully explaining 20 % of variation in this trait. As the development of new cultivars remains central to this work, Chapter 4 reports on the first commercial trials of the new ‘Boldrewood’ accession, aimed at informing its commercialization process. Excitingly, this study also highlighted previously unknown trends in phytonutrient character of the crops across a temporal gradient, which suggests the potential for increasing consumer health benefit by alternations to crop management practices. The sum of this work has resulted in significant advances in the understanding of watercress genetics and genomics and the production of valuable resources for its future preservation and advancement.

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2

Wang, Biao. "Development and Application of Genomic Resources in Non-model Bird Species." Doctoral thesis, Uppsala, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-183645.

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Understanding the genetic basis of biological processes is a fundamental component of modern ecology and evolutionary biology studies. With the recent advent of next generation sequencing (NGS) technologies, it is now possible to perform large genome and transcriptome projects for ecologically important non-model species. In this thesis, I focused on the development and application of genomic resources of two non-model bird species, the black grouse (Tetrao tetrix) and the great snipe (Gallinago media). Using the chicken genome as a reference, I developed a reference guided NGS pipeline to assemble the complete draft genome of black grouse. The draft genome has a good coverage of the main 29 chromosomes of the chicken genome. The genome was used to develop a vast number of genetic markers. Comparing this genome with that of other species, I identified the genomic regions which were important for the lineage specific evolution of black grouse. I also sequenced and characterised the spleen transcriptome of the black grouse. I identified and validated a large number of gene-based microsatellite markers from the transcriptome and identified and confirmed the expression of immune related genes. Using a similar RNA-Seq approach, I also sequenced the blood transcriptomes of 14 great snipe males with different mating success. I identified genes and single nucleotide polymorphisms (SNPs) which might be related to male mating success in this species, both in terms of gene expression levels and genetic variation structure. For the immunologically important major histocompatibility complex (MHC) gene region of black grouse, I constructed a fosmid library and used it to sequence the complete core MHC region of this species. This resource allowed me to perform a comprehensive comparative genomics analysis of the galliform MHC, by which I found that some genes in this region were affected by selective forces. I was also able to develop a single locus genotyping protocol for the duplicated MHC BLB (class IIB) genes and found that the two black grouse BLB loci followed different evolutionary trajectories. This thesis set an example of developing genomic resources in non-model species and applying them in addressing questions relevant to ecology and evolutionary biology.

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3

Ramsey, John, Alex Wilson, Vos Martin de, Qi Sun, Cecilia Tamborindeguy, Agnese Winfield, Gaynor Malloch, et al. "Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design." BioMed Central, 2007. http://hdl.handle.net/10150/610401.

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BACKGROUND:The green peach aphid, Myzus persicae (Sulzer), is a world-wide insect pest capable of infesting more than 40 plant families, including many crop species. However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species.RESULTS:Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). Aphids for library construction were raised on Arabidopsis thaliana, Nicotiana benthamiana, Brassica oleracea, B. napus, and Physalis floridana (with and without Potato leafroll virus infection). The M. persicae cDNA libraries include ones made from sexual and asexual whole aphids, guts, heads, and salivary glands. In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. Furthermore, 2423 genes that are novel to science and potentially aphid-specific were identified. Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. In particular, non-conservative amino acid substitutions in a highly expressed gut protease may be of adaptive significance for M. persicae feeding on different host plants. The Agilent eArray platform was used to design an M. persicae oligonucleotide microarray representing over 10,000 unique genes.CONCLUSION:New genomic resources have been developed for M. persicae, an agriculturally important insect pest. These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. These resources will help elucidate the adaptations that allow M. persicae to develop compatible interactions with its host plants, complementing ongoing work illuminating plant molecular responses to phloem-feeding insects.

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4

章明明 and Ming-ming Cheung. "An examination of the regulation of gene expression using microarray and genomic resources." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2002. http://hub.hku.hk/bib/B31225809.

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5

Cheung, Ming-ming. "An examination of the regulation of gene expression using microarray and genomic resources /." Hong Kong : University of Hong Kong, 2002. http://sunzi.lib.hku.hk/hkuto/record.jsp?B25205717.

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6

Jeffries, Daniel Lee. "Genetic and genomic approaches to the conservation of the threatened crucian carp Carassius carassius (L.) : phylogeography, hybridisation and introgression." Thesis, University of Hull, 2015. http://hydra.hull.ac.uk/resources/hull:13225.

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Biological invasions can have dramatic detrimental impacts on ecosystems, however they also represent rich opportunities to study the evolutionary processes associated with them. Hybridisation and subsequent introgression are two such processes and are common among native and non-native species. The crucian carp, Carassius carassius (L.), is a European freshwater fish that is threatened throughout much of its native range by several factors including hybridisation and introgression with three non-native species, the goldfish, Carassius auratus (L.), the gibel carp, Carassius gibelio (Bloch), and the common carp, Cyprinus carpio (L.). The conservation of C. carassius is hampered by a lack of phylogeographic knowledge for the species and no knowledge of the extent or impact of hybridisation and introgression. Contemporary genomic approaches such as Restriction Site Associated DNA sequencing (RADseq) can offer unprecedented insights into such research areas, however RADseq comes with several sources of potential bias. Exploratory analyses in Chapter 2 show that two sources of bias in particular, null alleles and over merged ohnolog loci, are highly important in this dataset, but can be filtered using population genetics statistics. The filtered dataset is used in phylogeographic analyses in Chapter 3, along with microsatellite and mitochondrial DNA and show that C. carassius exists as two major lineages in Europe, which diverged approximately 2.26 million years ago, and should be treated as separate units for conservation. These lineages result from the C. carassius postglacial recolonisation routes thtough Europe, which are highly distinct from the general patterns seen in other freshwater fish species. These phylogeographic results showed high similarity between C. carassius in England and those in continental Europe, calling into question the presently assumed native status of C. carassius in England, which has been contentious in the past. Empirical tests of this status using microsatellites showed that, in fact, C. carassius is most likely introduced in England around the 15th century, raising interesting discussions pertaining to their conservation in the England. Lastly, in Chapter 5, microsatellite and RADseq approaches show that hybridisation between C. carassius and non-native species is prevalent where they are sympatric, however backcrosses are rare, and there is no evidence of further introgression between the species studied. Taken together, these results suggest that postzygotic mechanisms of isolation limit interspecific gene flow, and conservationists should focus further research on the direct impacts of non-native species and F1 hybrids.

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7

Munoz-Torres, Monica Cecilia. "Comparative genomics and molecular evolution new genomic resources for the Hymenoptera and evolutionary studies on the genes of the Nasonia vitripennis Hox complex /." Connect to this title online, 2009. http://etd.lib.clemson.edu/documents/1246558786/.

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8

Nogueira, Marques João Pedro. "Using genomic tools to understand species differentiation and admixture in hares and mice." Thesis, Université de Montpellier (2022-….), 2022. http://www.theses.fr/2022UMONG010.

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Cette thèse a contribué, en utilisant le séquençage haut débit de génomes, à la compréhension de l’histoire de la divergence conduisant à la spéciation, et des causes et conséquences des échanges génétiques entre espèces.Ce travail a contribué au développement des ressources génomiques pour étudier la génomique des populations de lièvres, en produisant le premier assemblage de novo d’un génome de lièvre (Lepus timidus), et en évaluant son utilité en comparaison au génome de référence du lapin, préalablement disponible. Nous avons aussi produit le premier transcriptome de L. timidus, le plus complet de ceux disponibles pour les lièvres. En combinaison avec des données publiées sur L. europaeus, nous avons trouvé les différences fixées entre les deux espèces, qui peuvent être utilisées pour construire des outils pour étudier les échanges interspécifiques dans les zones d’hybridation.Nous avons contribué à la compréhension de l’introgression massive documentée du génome mitochondrial de L. timidus vers L. granatensis dans la péninsule ibérique, en reconstituant l’évolution démographique post-glaciaire de cette dernière à partir de la variation génétique actuelle. Nous avons démontré que cette introgression s’est faite à la faveur de l’envahissement du territoire de l’espèce donneuse par la receveuse, soulignant l’importance de la démographie et de la biogéographie pour favoriser l’introgression.A partir de séquences de génomes complets, nous avons étudié la différenciation et le re-mélange en Iran, la région d’origine des trois sous-espèces connues de souris domestique (Mus musculus domesticus, musculus et castaneus), source de leur expansion au reste de l’Eurasie, conduisant à leurs distributions parapatriques actuelles. Nous avons découvert au centre de l’Iran une population différenciée de ces trois sous-espèces, et inféré qu’elle résulte d’un mélange passé entre M. m. domesticus (environ 40%) et une population apparentée à M. m. musculus. Les lignées domesticus et musculus se sont donc largement mélangées à proximité de leur région d’origine, mais apparaissent isolées suite à leurs expansions géographiques indépendantes vers l’Europe, où elles forment une zone de tension étroite, un patron évocateur d’une espèce en anneau. Ceci offre un modèle exceptionnel pour étudier l’évolution et les déterminants de l’isolement reproductif entre ces sous-espèces. Nos analyses suggèrent un avantage sélectif du chromosome Y de la lignée musculus dans ce contexte de mélange en Iran central.Nous avons aussi découvert au NW de l’Iran une population d’origine majoritairement domesticus, avec des contributions de ses deux voisins (musculus et Iran central), mais qui a fixé une lignée de chromosome Y de la branche musculus. Nous trouvons que cette introgression massive de Y est accompagnée par la co-introgression de gènes impliqués dans la fertilité mâle, particulièrement sur le chromosome X. Nous avons testé le lien potentiel de cette invasion de Y avec une course aux armements entre le X et le Y qui pourrait biaiser les sex-ratios, et ainsi pu aborder la question du rôle des conflits génétiques comme promoteurs de l’introgression. Entre sous-espèces, nous avons trouvé une corrélation entre les nombres de copies Y et X de familles ampliconiques (gènes Sly/Slx) dont l’interaction est connue pour contrôler le sex-ratio de manière antagoniste en fonction de la dose. Plus de copies dans la lignée musculus suggère des propriétés distortrices plus fortes. Toutefois nous argumentons que ce conflit X-Y n’est pas le moteur de l’invasion du Y, qui résulterait plutôt d’un avantage intrinsèque du Y musculus en situation de mélange entre sous-espèces. La propension du Y musculus à envahir les régions où musculus se mélange avec d’autres sous-espèces semble générale et observée dans d’autres régions géographiques. Le conflit entraînerait la co-introgression ou la coévolution des régions ampliconiques du X dans les zones de mélange
The present thesis has contributed, using high throughput genome sequencing, to understanding the history of divergence leading to speciation, and the causes and consequences of genetic exchanges between species, in hares and mice.First, this work has contributed to the development of the genomic resources available to study hare population genomics, by providing the first de novo assembly of a hare genome (for the mountain hare, Lepus timidus), and assessing its utility as compared to the rabbit assembly, previously available. We have also generated the first mountain hare transcriptome, and the most complete among the currently available Lepus transcriptomes. In combination with published data on the European brown hare (L. europaeus), we pinpointed candidate fixed differences between the two species that can be used to build genotyping tools to monitor gene exchange in contact zones.Second, we have contributed to the understanding of the documented massive introgression of the mitochondrial genome from the mountain hare to the Iberian hare (L. granatensis) in Iberia, by reconstructing the post-glacial demographic dynamics of the latter species using Single Nucleotide Polymorphism data. We demonstrated that this introgression occurred at the favor of the invasive replacement of the donor species by the recipient one during the last deglaciation, thus showing the importance of demographic and biogeographic history in driving introgression.Third, using whole genome sequencing, we studied genetic differentiation and admixture in Iran, the region of origin of the three described house mouse subspecies (M. m. domesticus, musculus and castaneus), source of their expansion to the rest of Eurasia, leading to their present parapatric distributions. We discovered in Central Iran a population that is differentiated from these three subspecies, and inferred that it results from an ancient admixture between M. m. domesticus (about 40%) and a population related to M. m. musculus. The domesticus and musculus lineages thus admixed extensively close to their region of origin, but appear genetically isolated after their independent geographical expansions to Europe, where they form a narrow tension zone, a pattern evocative of a ring species. This offers an exceptional model to further study the evolution and determinants of reproductive isolation between these subspecies. Our analyses also suggest a selective advantage of non-domesticus Y chromosome in this context of admixture in Central Iran.We also discovered in North Western Iran a population that is mostly of domesticus origin, with inferred admixture from its geographical neighbours (musculus and central Iran), but which has fixed a Y chromosome lineage related to that of musculus. We show that this massive Y introgression is accompanied by co-introgression of genes with functions related to male fertility, especially on the X chromosome. We tested the potential link of this Y invasion with an arms-race between the X and Y chromosomes that could bias sex-ratio, and therefore address the question of the potential role of genetic conflicts in promoting introgression. Among subspecies we found a correlation between copy numbers of Y and X ampliconic families (Sly/Slx genes) whose interaction is known to control sex chromosome transmission in a dosage dependent manner. Higher copy numbers in the musculus lineage suggest stronger distortion properties. We however argue that this X-Y conflict is not the cause of massive Y introgression, which would rather reflect an intrinsic advantage of the musculus Y lineage in zones of admixture between the subspecies. The ability of the musculus Y chromosome to invade zones where musculus admixes with other subspecies seems to be a ubiquitous pattern, observed in other geographic regions. The conflict would rather cause co-introgression or co-evolution of the X ampliconic region in admixed populations

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9

Verbruggen, Bas. "Generating genomic resources for two crustacean species and their application to the study of White Spot Disease." Thesis, University of Exeter, 2016. http://hdl.handle.net/10871/25535.

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Over the last decades the crustacean aquaculture sector has been steadily growing, in order to meet global demands for its products. A major hurdle for further growth of the industry is the prevalence of viral disease epidemics that are facilitated by the intense culture conditions. A devastating virus impacting on the sector is the White Spot Syndrome Virus (WSSV), responsible for over US $10 billion in losses in shrimp production and trade. The Pathogenicity of WSSV is high, reaching 100 % mortality within 3-10 days in penaeid shrimps. In contrast, the European shore crab Carcinus maenas has been shown to be relatively resistant to WSSV. Uncovering the basis of this resistance could help inform on the development of strategies to mitigate the WSSV threat. C. maenas has been used widely in studies on ecotoxicology and host-pathogen interactions. However, like most aquatic crustaceans, the genomic resources available for this species are limited, impairing experimentation. Therefore, to facilitate interpretations of the exposure studies, we first produced a C. maenas transcriptome and genome scaffold assembly. We also produced a transcriptome for the European lobster (Homarus gammarus), an ecologically and commercially important crustacean species in United Kingdom waters, for use in comparing WSSV responses in this, a susceptible species, and C. maenas. For the C. maenas transcriptome assembly we isolated and pooled RNA from twelve different tissues and sequenced RNA on an Illumina HiSeq 2500 platform. After de novo assembly a transcriptome encompassing 212,427 transcripts was produced. Similar, the H. gammarus transcriptome was based on RNA from nine tissues and contained 106,498 transcripts. The transcripts were filtered and annotated using a variety of tools (including BLAST, MEGAN and RSEM) and databases (including GenBank, Gene Ontology and KEGG). The annotation rate for transcripts in both transcriptomes was around 20-25 % which appears to be common for aquatic crustacean species, as a result of the lack of well annotated gene sequences for this clade. Since it is likely that the host immune system would play an important role in WSSV infection we characterized the IMD, JAK/STAT, Toll-like receptor and other innate immune system pathways. We found a strong overlap between the immune system pathways in C. maenas and H. gammarus. In addition we investigated the sequence diversity of known WSSV interacting proteins amongst susceptible penaeid shrimp/lobster and the more resistant C. maenas. There were differences in viral receptor sequences, like Rab7, that correlate with a less efficient infection by WSSV. To produce the genome scaffold assembly for C. maenas we isolated DNA from muscle tissue and produced both paired-end and mate pair libraries for processing on the Illumina HiSeq 2500 platform. A de novo draft genome assembly consisting of 338,980 scaffolds and covering 362 Mb (36 % of estimated genome size) was produced, using SOAP-denovo2 coupled with the BESST scaffolding system. The generated assembly was highly fragmented due to the presence of repetitive areas in the C. maenas genome. Using a combination of ab initio predictors, RNA-sequencing data from the transcriptome datasets and curated C. maenas sequences we produced a model encompassing 10,355 genes. The gene model for C. maenas Dscam, a gene potentially involved in (pan)crustacean immune memory, was investigated in greater detail as manual curation can improve on the results of ab initio predictors. The scaffold containing C. maenas Dscam was fragmented, thus only contained the latter exons of the gene. The assembled draft genome and transcriptomes for C. maenas and H. gammarus are valuable molecular resources for studies involving these and other aquatic crustacean species. To uncover the basis of their resistance to WSSV, we infected C. maenas with WSSV and measured mRNA and miRNA expression for 7 time points spread over a period of 28 days, using RNA-Seq and miRNA-Seq. The resistance of C. maenas to WSSV infection was confirmed by the fact that no mortalities occurred. In these animals replicating WSSV was latent and detected only after 7 days, and this occurred in five of out 28 infected crabs only. Differential expression of transcripts and miRNAs were identified for each time point. In the first 12 hours post exposure we observed decreased expression of important regulators in endocytosis. Since it is established that WSSV enters the host cells through endocytosis and that interactions between the viral protein VP28 and Rab7 are important in successful infection, it is likely that changes in this process could impact WSSV infection success. Additionally we observed an increased expression of transcripts involved in RNA interference pathways across many time points, indicating a longer term response to initial viral exposure. miRNA sequencing showed several miRNAs that were differentially expressed. The most striking finding was a novel C. maenas miRNA that we found to be significantly downregulated in every WSSV infected individual, suggesting that it may play an important role in mediating the response of the host to the virus. In silico target prediction pointed to the involvement of this miRNA in endocytosis regulation. Taken together we hypothesize that C. maenas resistance to WSSV involves obstruction of viral entry by endocytosis, a process probably regulated through miRNAs, resulting in inefficient uptake of virions.

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10

Galata, Valentina [Verfasser]. "Resources for the analysis of bacterial and microbial genomic data with a focus on antibiotic resistance / Valentina Galata." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2020. http://d-nb.info/1214240755/34.

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11

Nogueira, Marques João Pedro. "Utilisation des outils génomiques pour comprendre la différenciation et le mélange des espèces chez les lièvres et les souris." Thesis, Montpellier, 2022. http://www.theses.fr/2022MONTG010.

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Cette thèse a contribué, en utilisant le séquençage haut débit de génomes, à la compréhension de l’histoire de la divergence conduisant à la spéciation, et des causes et conséquences des échanges génétiques entre espèces.Ce travail a contribué au développement des ressources génomiques pour étudier la génomique des populations de lièvres, en produisant le premier assemblage de novo d’un génome de lièvre (Lepus timidus), et en évaluant son utilité en comparaison au génome de référence du lapin, préalablement disponible. Nous avons aussi produit le premier transcriptome de L. timidus, le plus complet de ceux disponibles pour les lièvres. En combinaison avec des données publiées sur L. europaeus, nous avons trouvé les différences fixées entre les deux espèces, qui peuvent être utilisées pour construire des outils pour étudier les échanges interspécifiques dans les zones d’hybridation.Nous avons contribué à la compréhension de l’introgression massive documentée du génome mitochondrial de L. timidus vers L. granatensis dans la péninsule ibérique, en reconstituant l’évolution démographique post-glaciaire de cette dernière à partir de la variation génétique actuelle. Nous avons démontré que cette introgression s’est faite à la faveur de l’envahissement du territoire de l’espèce donneuse par la receveuse, soulignant l’importance de la démographie et de la biogéographie pour favoriser l’introgression.A partir de séquences de génomes complets, nous avons étudié la différenciation et le re-mélange en Iran, la région d’origine des trois sous-espèces connues de souris domestique (Mus musculus domesticus, musculus et castaneus), source de leur expansion au reste de l’Eurasie, conduisant à leurs distributions parapatriques actuelles. Nous avons découvert au centre de l’Iran une population différenciée de ces trois sous-espèces, et inféré qu’elle résulte d’un mélange passé entre M. m. domesticus (environ 40%) et une population apparentée à M. m. musculus. Les lignées domesticus et musculus se sont donc largement mélangées à proximité de leur région d’origine, mais apparaissent isolées suite à leurs expansions géographiques indépendantes vers l’Europe, où elles forment une zone de tension étroite, un patron évocateur d’une espèce en anneau. Ceci offre un modèle exceptionnel pour étudier l’évolution et les déterminants de l’isolement reproductif entre ces sous-espèces. Nos analyses suggèrent un avantage sélectif du chromosome Y de la lignée musculus dans ce contexte de mélange en Iran central.Nous avons aussi découvert au NW de l’Iran une population d’origine majoritairement domesticus, avec des contributions de ses deux voisins (musculus et Iran central), mais qui a fixé une lignée de chromosome Y de la branche musculus. Nous trouvons que cette introgression massive de Y est accompagnée par la co-introgression de gènes impliqués dans la fertilité mâle, particulièrement sur le chromosome X. Nous avons testé le lien potentiel de cette invasion de Y avec une course aux armements entre le X et le Y qui pourrait biaiser les sex-ratios, et ainsi pu aborder la question du rôle des conflits génétiques comme promoteurs de l’introgression. Entre sous-espèces, nous avons trouvé une corrélation entre les nombres de copies Y et X de familles ampliconiques (gènes Sly/Slx) dont l’interaction est connue pour contrôler le sex-ratio de manière antagoniste en fonction de la dose. Plus de copies dans la lignée musculus suggère des propriétés distortrices plus fortes. Toutefois nous argumentons que ce conflit X-Y n’est pas le moteur de l’invasion du Y, qui résulterait plutôt d’un avantage intrinsèque du Y musculus en situation de mélange entre sous-espèces. La propension du Y musculus à envahir les régions où musculus se mélange avec d’autres sous-espèces semble générale et observée dans d’autres régions géographiques. Le conflit entraînerait la co-introgression ou la coévolution des régions ampliconiques du X dans les zones de mélange
The present thesis has contributed, using high throughput genome sequencing, to understanding the history of divergence leading to speciation, and the causes and consequences of genetic exchanges between species, in hares and mice.First, this work has contributed to the development of the genomic resources available to study hare population genomics, by providing the first de novo assembly of a hare genome (for the mountain hare, Lepus timidus), and assessing its utility as compared to the rabbit assembly, previously available. We have also generated the first mountain hare transcriptome, and the most complete among the currently available Lepus transcriptomes. In combination with published data on the European brown hare (L. europaeus), we pinpointed candidate fixed differences between the two species that can be used to build genotyping tools to monitor gene exchange in contact zones.Second, we have contributed to the understanding of the documented massive introgression of the mitochondrial genome from the mountain hare to the Iberian hare (L. granatensis) in Iberia, by reconstructing the post-glacial demographic dynamics of the latter species using Single Nucleotide Polymorphism data. We demonstrated that this introgression occurred at the favor of the invasive replacement of the donor species by the recipient one during the last deglaciation, thus showing the importance of demographic and biogeographic history in driving introgression.Third, using whole genome sequencing, we studied genetic differentiation and admixture in Iran, the region of origin of the three described house mouse subspecies (M. m. domesticus, musculus and castaneus), source of their expansion to the rest of Eurasia, leading to their present parapatric distributions. We discovered in Central Iran a population that is differentiated from these three subspecies, and inferred that it results from an ancient admixture between M. m. domesticus (about 40%) and a population related to M. m. musculus. The domesticus and musculus lineages thus admixed extensively close to their region of origin, but appear genetically isolated after their independent geographical expansions to Europe, where they form a narrow tension zone, a pattern evocative of a ring species. This offers an exceptional model to further study the evolution and determinants of reproductive isolation between these subspecies. Our analyses also suggest a selective advantage of non-domesticus Y chromosome in this context of admixture in Central Iran.We also discovered in North Western Iran a population that is mostly of domesticus origin, with inferred admixture from its geographical neighbours (musculus and central Iran), but which has fixed a Y chromosome lineage related to that of musculus. We show that this massive Y introgression is accompanied by co-introgression of genes with functions related to male fertility, especially on the X chromosome. We tested the potential link of this Y invasion with an arms-race between the X and Y chromosomes that could bias sex-ratio, and therefore address the question of the potential role of genetic conflicts in promoting introgression. Among subspecies we found a correlation between copy numbers of Y and X ampliconic families (Sly/Slx genes) whose interaction is known to control sex chromosome transmission in a dosage dependent manner. Higher copy numbers in the musculus lineage suggest stronger distortion properties. We however argue that this X-Y conflict is not the cause of massive Y introgression, which would rather reflect an intrinsic advantage of the musculus Y lineage in zones of admixture between the subspecies. The ability of the musculus Y chromosome to invade zones where musculus admixes with other subspecies seems to be a ubiquitous pattern, observed in other geographic regions. The conflict would rather cause co-introgression or co-evolution of the X ampliconic region in admixed populations

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12

Cailleau, Aurélie. "Evolution de la composition génétique du tissu nourricier de la graine : Double fécondation, polysporie et empreinte parentale." Thesis, Montpellier 2, 2010. http://www.theses.fr/2010MON20242/document.

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Chez les plantes à graine, l'albumen est un tissu nourricier surprenant, puisqu'il résulte de la double fécondation, qui est la fécondation concomitante de l'oosphère d'une part, et de la cellule mère de l'albumen, la cellule centrale, d'autre part. Dans cette thèse, nous étudions les pressions de sélection qui déterminent l'évolution de l'albumen et pourraient expliquer l'évolution (1) de la double fécondation, (2) d'un doublement des contributions maternelles dans la cellule centrale, (3) de la polysporie, qui consiste en la participation de plusieurs produits de méiose à la formation du gamétophyte, et (4) de l'empreinte parentale, l'expression différentielle des allèles maternels et paternels.Ces innovations modifient l'hétérozygotie dans le tissu nourricier et par conséquent, ont le potentiel de changer l'hétérosis de la graine. Dans cette thèse, nous commençons par étudier comment les changements génétiques qui découlent de la double fécondation, du doublement des contributions maternelles, de la polysporie et de l'empreinte parentale modifient l'hétérosis, ce qui peut jouer en faveur ou en défaveur de leurs évolutions. Puis, nous faisons une revue des données disponibles dans la littérature pour tester si ces traits sont le résultat d'un conflit mâle-femelle sur l'allocation des ressources. Enfin, nous étudions de manière expérimentale les patrons de l'allocation des ressources chez le maïs, pour tester si les embryons sont en compétition pour les ressources, ce qui est une des conditions nécessaires pour qu'un conflit sur l'allocation des ressources ait lieu.Nos modèles théoriques nous permettent de décrire un conflit mâle-femelle sur l'exposition des allèles délétères dans les tissus pour lesquels l'expression des gènes est asymétrique. Ce conflit n'avait jamais été décrit auparavant, et ouvre de nouvelles perspectives pour la compréhension de l'évolution de l'expression génétique. L'analyse des données indique que les théories alternatives à la théorie du conflit sur l'allocation des ressources ont parfois un bon pouvoir explicatif, et méritent par conséquent d'être d'avantage explorées. Enfin, notre étude expérimentale sur le maïs montre que la compétition entre embryons est prédominante lors de l'allocation des ressources chez cette espèce, ce qui est concordant avec les prédictions de la théorie du conflit sur l'allocation
In seed plants, the endosperm is a surprising nutritive tissue, because it results from double fertilization, an eccentricity which results from the parallel fertilization of the egg cell on the one hand, and of the mother cell of the endosperm, the central cell, on the other hand. In this thesis, we study the selective pressures which drive the evolution of the endosperm and may explain the evolution of (1) double fertilization, (2) a doubling of maternal contributions in the central cell, (3) polyspory, the participation of several meiotic products to the gametophyte and (4) imprinting, the differential expression of maternal and paternal alleles. These innovations modify heterozygosity in the endosperm and as a consequence, have the potential to change heterosis in the seed. In this thesis, we first investigate how genetic changes that result from double fertilization, doubling of maternal contribution, polyspory and imprinting modify heterosis, which may play in favour or against the evolution of these traits. Second, we review the available data to test whether these traits are the result of a male-female conflict over resource allocation. Finally, we study experimentally patterns of resource allocation in maize to assess whether embryos compete for resources, which is a necessary condition for the conflict over resource allocation to occur. Our theoretical models allow us to describe a male-female conflict over the exposition of deleterious alleles in tissues with asymmetrical gene expression. This conflict had never been described before and opens perspectives for understanding the evolution of gene expression. We conclude from our analysis of data that theories which are alternative to the conflict theory over resource allocation may have a better explanatory power and therefore deserve to be further explored. Finally, our experimental study in maize shows that competition between embryos drives resource allocation in this species, which is consistent with predictions of the conflict over resource allocation theory

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13

Arnaiz, Olivier. "Annotation des génomes de paramécies Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences ParTIES: a toolbox for Paramecium interspersed DNA elimination studies." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL046.

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Les nouvelles technologies de séquençage (NGS) ont révolutionné nos approches de la génomique.De nombreux génomes d'organismes ont été séquencés et assemblés.Le décryptage de l'information qu'ils contiennent (annotation) est plus que jamais une étape cruciale.Dans ce manuscrit, je vais me focaliser sur l’impact qu'ont eu les NGS sur l'annotation des génomes de paramécies, et notamment l'annotation de gènes et d'éléments transposables (ET).La paramécie est un eucaryote unicellulaire possédant deux types de noyaux. Un noyau germinal (MIC) utilisé pour transmettre l'information génétique à la génération sexuelle suivante, et un noyau somatique (MAC) assurant l'expression des gènes.Les caractéristiques particulières des gènes de paramécies m'ont incité à développer une chaîne de procédures dédiée à leur annotation, utilisant des données ARN-seq.A chaque cycle sexuel, le MAC parental est perdu et un nouveau MAC est généré à partir d'un MIC impliquant des réarrangements programmés de génome et notamment de l'élimination d'ADN portant des ET et de petites séquences à copie unique appelées IES (Internal Eliminated Sequence). Nous avons développé le logiciel ParTIES, utilisant des données ADN-seq, pour identifier les ~45 000 IES du génome de Pararamecium tetraurelia et montré que les IES sont des reliques d'ET.Une série de trois duplications globales de génome (WGD) anciennes mais encore visible, pendant l'histoire évolutive de la lignée, nous a permis de décrire la dynamique d'invasion et d'évolution des ET à l'origine des IES
The next generation sequencing technologies (NGS) have revolutionized genomics.Genomes of numerous organisms have been sequenced and assembled.Deciphering the encoded information (annotation) has more than ever become crucial. In this thesis manuscript, I focus on the impact of NGS on the annotation of Paramecium genomes, in particular the annotation of genes and transposable elements (TE).Paramecia is a unicellular eukaryote possesses two types of nuclei. A germline nucleus (MIC) transmits the genetic information to the next sexual generation, and a somatic nucleus (MAC) is responsible for gene expression.Special genes caracteristics of paramecia stimulated me to develop a workflow dedicated to their annotation, using RNA-seq data.At each sexual cycle, the parental MAC is lost and a new MAC develops from a copy of the MIC, through programmed genome rearrangements, notably the elimination of DNA corresponding to TE and short unique copy sequences called IES (Internal Eliminated Sequence).I developed the ParTIES software, using DNA-Seq data, to identify the ~45,000 IESs in the germline genome of Paramecium tetraurelia and to show that the IESs are remnants of TE.A series of three whole genome duplications (WGD) in the evolutionary history of the lineage, ancient but still visible, allow us to describe the dynamics of the invasion and evolution of TE that decay to become IES

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14

DiGuistini, William Scott. "Creating a genomic resource for Grosmannia clavigera." Thesis, University of British Columbia, 2010. http://hdl.handle.net/2429/26644.

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Rapid advances in DNA sequencing have created the possibility for probing deeply into the genomes and transcriptomes of organisms; however, bioinformatic tools for handling these massive quantities of data are changing rapidly. In this thesis I describe the bioinformatic methods and molecular resources developed for studying the ascomycete fungus Grosmannia clavigera (Gc), a lodgepole pine (Pinus contorta) pathogen specifically associated with the Mountain Pine Beetle (MPB), and results from initial analyses using these resources. We have developed genomic resources for Gc including: a) the whole genome sequence, b) expressed sequence tags (ESTs), and c) RNA-seq data. We have annotated the genome using the transcriptome resources (e.g. ESTs and RNA-seq) and computational (gene prediction software) data. In an initial analysis of the Gc genome we focused on aspects important for colonizing the host tree and for tolerance towards conifer defence chemicals. We showed that Gc is heterothallic, and report evidence for repeat-induced point mutation. Gene expression profiling provided insight into mechanisms for Gc’s tolerance towards conifer defence chemicals, specifically oleoresin terpenoids. RNA-seq revealed a substantial antimicrobial stress response of Gc induced by terpenoids, and our data suggests that Gc may reduce the toxicity of these defence chemicals by utilizing them as a carbon source. Terpenoid treatment strongly activated a ~100 kb region of the Gc genome that contains a set of genes that may be important for detoxification of these host defence chemicals. Using a recently developed Gc gene knock-out system, we provide evidence that a PDR-type ABC transporter is important for the successful response of Gc against host terpenoids.

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15

Tesniere, Germain. "Arrangements institutionnels à l’ère de la génomique : une approche comparative des régimes et des instruments de sélection animale dans trois pays européens." Thesis, Paris Sciences et Lettres (ComUE), 2017. http://www.theses.fr/2017PSLEM058/document.

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Depuis les années 2000, le développement de la génomique, permettant une connaissance étendue de l’ADN des êtres vivants, transforme la façon dont ceux-ci sont évalués, sélectionnés (sélection génomique des plantes et animaux) et mis en marché. Couplée à des changements politiques et règlementaires, cette technologie contribue à faire évoluer les arrangements institutionnels dans le champ étudié ici de l’amélioration génétique animale, aussi bien au niveau des dispositifs nationaux que des pratiques des acteurs. La libéralisation en cours questionne notamment la dimension collective de la production du progrès génétique et les droits de propriétés sur les ressources génétiques. Dans une perspective comparative entre la France, l’Irlande et les Pays-Bas, cette thèse a pour objectif d’analyser la pluralité des arrangements institutionnels établis dans le champ de la sélection génomique de la race bovine Holstein. Elle mobilise les évolutions récentes de la théorie néo-institutionnelle s’intéressant à l’hétérogénéité organisationnelle et à la matérialité des institutions. Premièrement, elle met en évidence trois régimes institutionnels qui révèlent des arrangements différents notamment entre organisations publiques et privées. Deuxièmement, cette diversité d’arrangements est précisée par l’analyse des instruments contractuels entre entreprises de sélection et éleveurs via des modèles d’organisation de la production et des échanges de ressources génétiques (sous leurs formes biologiques et informationnelles). Ces modèles illustrent la diversité des formes de propriété dont ces ressources génétiques font l’objet entre éleveurs et entreprises et, montrent que les rôles respectifs de ces acteurs sont redéfinis. Ces résultats permettent de mieux comprendre le développement d’une logique libérale (Pays-Bas) en dualité avec le renforcement (Irlande) ou la fragilisation (France) d’une logique coopérative de production du progrès génétique
Since the early 2000s, the development of genomics, which enables extensive knowledge of the DNA of living entities, has transformed the way in which living entities are evaluated, selected (genomic selection of plants and animals) and marketed. Coupled with political and regulatory changes, this technology contributes to modify the national institutional arrangements in the targeted field of animal genetic improvement, practices of actors. The current liberalization process questions both the collective dimension of genetic progress and the property rights of the genetic resources. In a comparative perspective between France, Ireland and The Netherlands, the objective of this thesis is to analyze the plurality of institutional arrangements pertaining to the Holstein cattle breed’s genomic selection. This thesis is situated within the recent evolutions of the neo-institutional theory focused on organizational heterogeneity and materiality of institutions. Firstly, it highlights three institutional regimes that reveal different arrangements particularly between public and private organizations. Secondly, this diversity of arrangements is completed by an analysis of contractual tools between breeding companies and animal breeders through models of production strategies and exchanges related to genetic resources (both biological and informational forms). These models emphasize a variety of property forms of genetic resources between companies and breeders and also show that actors’ roles in genetic selection activities are redefined. These results provide a better understanding of the development of a liberal logic (The Netherlands) in duality with the reinforcement (Ireland) or weakening (France) of a cooperative logic for the production of improved animal genetics

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16

Dang, Ha X., Barry Pryor, Tobin Peever, and Christopher B. Lawrence. "The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species." BioMed Central Ltd, 2015. http://hdl.handle.net/10150/610283.

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BACKGROUND: Alternaria is considered one of the most common saprophytic fungal genera on the planet. It is comprised of many species that exhibit a necrotrophic phytopathogenic lifestyle. Several species are clinically associated with allergic respiratory disorders although rarely found to cause invasive infections in humans. Finally, Alternaria spp. are among the most well known producers of diverse fungal secondary metabolites, especially toxins. DESCRIPTION: We have recently sequenced and annotated the genomes of 25 Alternaria spp. including but not limited to many necrotrophic plant pathogens such as A. brassicicola (a pathogen of Brassicaceous crops like cabbage and canola) and A. solani (a major pathogen of Solanaceous plants like potato and tomato), and several saprophytes that cause allergy in human such as A. alternata isolates. These genomes were annotated and compared. Multiple genetic differences were found in the context of plant and human pathogenicity, notably the pro-inflammatory potential of A. alternata. The Alternaria genomes database was built to provide a public platform to access the whole genome sequences, genome annotations, and comparative genomics data of these species. Genome annotation and comparison were performed using a pipeline that integrated multiple computational and comparative genomics tools. Alternaria genome sequences together with their annotation and comparison data were ported to Ensembl database schemas using a self-developed tool (EnsImport). Collectively, data are currently hosted using a customized installation of the Ensembl genome browser platform. CONCLUSION: Recent efforts in fungal genome sequencing have facilitated the studies of the molecular basis of fungal pathogenicity as a whole system. The Alternaria genomes database provides a comprehensive resource of genomics and comparative data of an important saprophytic and plant/human pathogenic fungal genus. The database will be updated regularly with new genomes when they become available. The Alternaria genomes database is freely available for non-profit use at http://alternaria.vbi.vt.edu.

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17

Moss, Stephen Paul. "The development of computational methods for large-scale comparisons and analyses of genome evolution." Thesis, University of Hull, 2015. http://hydra.hull.ac.uk/resources/hull:13083.

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The last four decades have seen the development of a number of experimental methods for the deduction of the whole genome sequences of an ever-increasing number of organisms. These sequences have in the first instance, allowed their investigators the opportunity to examine the molecular primary structure of areas of scientific interest, but with the increased sampling of organisms across the phylogenetic tree and the improved quality and coverage of genome sequences and their associated annotations, the opportunity to undertake detailed comparisons both within and between taxonomic groups has presented itself. The work described in this thesis details the application of comparative bioinformatics analyses on inter- and intra-genomic datasets, to elucidate those genomic changes, which may underlie organismal adaptations and contribute to changes in the complexity of genome content and structure over time. The results contained herein demonstrate the power and flexibility of the comparative approach, utilising whole genome data, to elucidate the answers to some of the most pressing questions in the biological sciences today. As the volume of genomic data increases, both as a result of increased sampling of the tree of life and due to an increase in the quality and throughput of the sequencing methods, it has become clear that there is a necessity for computational analyses of these data. Manual analysis of this volume of data, which can extend beyond petabytes of storage space, is now impossible. Automated computational pipelines are therefore required to retrieve, categorise and analyse these data. Chapter two discusses the development of a computational pipeline named the Genome Comparison and Analysis Toolkit (GCAT). The pipeline was developed using the Perl programming language and is tightly integrated with the Ensembl Perl API allowing for the retrieval and analyses of their rich genomic resources. In the first instance the pipeline was tested for its robustness by retrieving and describing various components of genomic architecture across a number of taxonomic groups. Additionally, the need for programmatically independent means of accessing data and in particular the need for Semantic Web based protocols and tools for the sharing of genomics resources is highlighted. This is not just for the requirements of researchers, but for improved communication and sharing between computational infrastructure. A prototype Ensembl REST web service was developed in collaboration with the European Bioinformatics Institute (EBI) to provide a means of accessing Ensembl’s genomic data without having to rely on their Perl API. A comparison of the runtime and memory usage of the Ensembl Perl API and prototype REST API were made relative to baseline raw SQL queries, which highlights the overheads inherent in building wrappers around the SQL queries. Differences in the efficiency of the approaches were highlighted, and the importance of investing in the development of Semantic Web technologies as a tool to improve access to data for the wider scientific community are discussed. Data highlighted in chapter two led to the identification of relative differences in the intron structure of a number of organisms including teleost fish. Chapter three encompasses a published, peer-reviewed study. Inter-genomic comparisons were undertaken utilising the 5 available teleost genome sequences in order to examine and describe their intron content. The number and sizes of introns were compared across these fish and a frequency distribution of intron size was produced that identified a novel expansion in the Zebrafish lineage of introns in the size range of approximately 500-2,000 bp. Further hypothesis driven analyses of the introns across the whole distribution of intron sizes identified that the majority, but not all of the introns were largely comprised of repetitive elements. It was concluded that the introns in the Zebrafish peak were likely the result of an ancient expansion of repetitive elements that had since degraded beyond the ability of computational algorithms to identify them. Additional sampling throughout the teleost fish lineage will allow for more focused phylogenetically driven analyses to be undertaken in the future. In chapter four phylogenetic comparative analyses of gene duplications were undertaken across primate and rodent taxonomic groups with the intention of identifying significantly expanded or contracted gene families. Changes in the size of gene families may indicate adaptive evolution. A larger number of expansions, relative to time since common ancestor, were identified in the branch leading to modern humans than in any other primate species. Due to the unique nature of the human data in terms of quantity and quality of annotation, additional analyses were undertaken to determine whether the expansions were methodological artefacts or real biological changes. Novel approaches were developed to test the validity of the data including comparisons to other highly annotated genomes. No similar expansion was seen in mouse when comparing with rodent data, though, as assemblies and annotations were updated, there were differences in the number of significant changes, which brings into question the reliability of the underlying assembly and annotation data. This emphasises the importance of an understanding that computational predictions, in the absence of supporting evidence, may be unlikely to represent the actual genomic structure, and instead be more an artefact of the software parameter space. In particular, significant shortcomings are highlighted due to the assumptions and parameters of the models used by the CAFE gene family analysis software. We must bear in mind that genome assemblies and annotations are hypotheses that themselves need to be questioned and subjected to robust controls to increase the confidence in any conclusions that can be drawn from them. In addition functional genomics analyses were undertaken to identify the role of significantly changed genes and gene families in primates, testing against a hypothesis that would see the majority of changes involving immune, sensory or reproductive genes. Gene Ontology (GO) annotations were retrieved for these data, which enabled highlighting the broad GO groupings and more specific functional classifications of these data. The results showed that the majority of gene expansions were in families that may have arisen due to adaptation, or were maintained due to their necessary involvement in developmental and metabolic processes. Comparisons were made to previously published studies to determine whether the Ensembl functional annotations were supported by the de-novo analyses undertaken in those studies. The majority were not, with only a small number of previously identified functional annotations being present in the most recent Ensembl releases. The impact of gene family evolution on intron evolution was explored in chapter five, by analysing gene family data and intron characteristics across the genomes of 61 vertebrate species. General descriptive statistics and visualisations were produced, along with tests for correlation between change in gene family size and the number, size and density of their associated introns. There was shown to be very little impact of change in gene family size on the underlying intron evolution. Other, non-family effects were therefore considered. These analyses showed that introns were restricted to euchromatic regions, with heterochromatic regions such as the centromeres and telomeres being largely devoid of any such features. A greater involvement of spatial mechanisms such as recombination, GC-bias across GC-rich isochores and biased gene conversion was thus proposed to play more of a role, though depending largely on population genetic and life history traits of the organisms involved. Additional population level sequencing and comparative analyses across a divergent group of species with available recombination maps and life history data would be a useful future direction in understanding the processes involved.

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18

Li, Weizhong. "An integrated suite of informatics tools and resources to support post genomics investigation." Thesis, University of Liverpool, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.490901.

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The genome sequencing projects have brought about a massive increase in the scale ofbioinformatic analysis. To engage in post-genomic analysis requires the development of techniques for processing these huge datasets automatically, efficiently and effectively, and this requires the discovery of new approaches, the development of new efficient bioinformatics tools and the establishment of high-quality, accessible information resources. This thesis describes the development ofbioinformatic tools and resources, and analytical methods for a major post-genomic project directed at an open transcriptomic screen ofmechanisms involved in the environmental stress adaptation of an important environmental model species, the common carp Cyprill11S carpio L. The project required the identification and characterisation ofcDNA resources through expressed sequence tag (EST) analysis, for which a new user-configurable package, EST-ferret, was developed. The package integrates a suite of open source algorithms connected by PERL scripts that includes options for EST sequence cleaning-up, assembly, BLAST homology search, protein domain searches, and Gene Ontology (GO) annotation. ~13,500 ESTs were processed through EST-ferret and the results have been incorporated into a comprehensively annotated and searchable database, carpBASE 2.1. Thus 9202 high-quality EST sequences were assembled into 6033 non-redundant sequences. Extending the alignment search methods to include protein domains, UTRs and repeat elements annotated an additional 12.6% ofESTs. Finally, a 'GOprofiler' programme was developed and embedded in EST-ferret to assign GO annotations to ESTs. Collectively these tools maximised the identification and functional annotations for cDNA clones. Analysing gene expression profiles from microarrays is fundamental for post-genomic approaches. ExprAlign was developed to cluster and visualise gene expression data. This included CORR, a programme which determines the similarity of gene expressions between genes by computing millions of Pearson correlation coefficients. ExprAlign also implemented the Vxlnsight package to align ESTs into different expression clusters and ordinate and visualise the resulting clusters as a 3D landscape. ExprAlign was used to suggest identities for unidentified ESTs by relating 522 unclassifiable ESTs in carpBASE 2.1 to other BLAST-identified genes, and separating some unique gene and some gene isoforms. GOmatrix, using Fisher's exact test, was developed to determine which non-redundant gene expression clusters were statistically over- or under-represented in GO categories of interest. This has greatly assisted the understanding of biological roles and molecular functions of different gene groups identified from the transcript profile. Comparative, cross-species analysis of sequence data and gene expression data is important to functional genomic investigation. Orthology analysis was processed across carp, zebrafish and human and a tool called FindOrthologs was developed for this purpose. ExprAlign was implemented in the orthology analysis for discovering how conserved the correlated gene expressions of orthologous genes were across carp and human. GOmatrix also indicated the conserved biological processes for the orthologous gene groups. Supplied by The British Library - 'The world's knowledge'

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19

Boardman, Anelda Philine. "Assessment of genome visualization tools relevant to HIV genome research: development of a genome browser prototype." Thesis, University of the Western Cape, 2004. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_3632_1185446929.

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Over the past two decades of HIV research, effective vaccine candidates have been elusive. Traditionally viral research has been characterized by a gene -by-gene approach, but in the light of the availability of complete genome sequences and the tractable size of the HIV genome, a genomic approach may improve insight into the biology and epidemiology of this virus. A genomic approach to finding HIV vaccine candidates can be facilitated by the use of genome sequence visualization. Genome browsers have been used extensively by various groups to shed light on the biology and evolution of several organisms including human, mouse, rat, Drosophila and C.elegans. Application of a genome browser to HIV genomes and related annotations can yield insight into forces that drive evolution, identify highly conserved regions as well as regions that yields a strong immune response in patients, and track mutations that appear over the course of infection. Access to graphical representations of such information is bound to support the search for effective HIV vaccine candidates. This study aimed to answer the question of whether a tool or application exists that can be modified to be used as a platform for development of an HIV visualization application and to assess the viability of such an implementation. Existing applications can only be assessed for their suitability as a basis for development of an HIV genome browser once a well-defined set of assessment criteria has been compiled.

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20

Benjelloun, Badr. "Diversité des génomes et adaptation locale des petits ruminants d’un pays méditerranéen : le Maroc." Thesis, Université Grenoble Alpes (ComUE), 2015. http://www.theses.fr/2015GREAV011/document.

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Les progrès technologiques récents nous permettent d'accéder à la variation des génomes complets ce qui nous ouvre la porte d'une meilleure compréhension de leur diversification via des approches de génomique des populations et de génomique du paysage. Ce travail de thèse se base sur l'analyse des données de génomes complets (WGS) pour caractériser la diversité génétique des petits ruminants (chèvre et moutons) et rechercher les bases génétiques d'adaptations locales.Dans un premier temps, ce travail appréhende un aspect méthodologique et examine la précision et le biais de différentes approches d'échantillonnage des génomes pour caractériser la variabilité génétique, en les comparant aux données WGS. Nous mettons en évidence un fort biais des approches classiques (i.e. puces à ADN, capture de l'exome) ainsi que des séquençages de génomes à faibles taux de couverture (1X et 2X), et nous suggérons des alternatives basées sur un échantillonnage aléatoire de marqueurs dont la densité est variable selon les objectifs d'étude (évaluation de la diversité neutre, déséquilibre de liaison, signatures de sélection). Le jeu de données produit a permis d'évaluer l'état des ressources génétiques de différentes populations domestiques (races locales marocaines, iraniennes, races industrielles) et sauvages (aegagre, mouflon asiatique). Nous relevons une très forte diversité génétique dans les populations indigènes et sauvages qui constituent des réservoirs d'allèles et peuvent jouer un rôle important pour préserver le potentiel adaptatif des petits ruminants domestiques dans un contexte de changement climatique. L'étude plus approfondie des populations de chèvres du Maroc montre une forte diversité génétique faiblement structurée géographiquement, et met en évidence des portions de génome présentant des signaux de sélection. Leur étude montre l'existence de mécanismes adaptatifs potentiellement différents selon les populations (e.g. transpiration/halètement dans l'adaptation probable à la chaleur).Enfin, nous explorons les bases génétiques de l'adaptation locale à l'environnement chez les moutons et chèvres via une approche de génomique de paysage. En scannant les génomes de 160 moutons et 161 chèvres représentant la diversité éco-climatique du Maroc, nous identifions de nombreux variants et gènes candidats qui permettent d'identifier les voies physiologiques potentiellement sous-jacentes à l'adaptation locale. En particulier, il apparait que les mécanismes respiratoires et les processus cardiaques joueraient un rôle clé dans l'adaptation à l'altitude. Les résultats suggèrent que les chèvres et moutons ont probablement développé différents mécanismes adaptatifs pour répondre aux mêmes variations environnementales. Cependant, nous identifions plusieurs cas probables de voies adaptatives communes à plusieurs espèces. Par ailleurs, nous avons caractérisé les patrons de variations du niveau de différenciation de régions chromosomiques sous sélection en fonction de l'altitude. Cela nous permet de visualiser la diversité des réponses adaptatives selon les gènes (par exemple, sélection de variants à faible et/ou haute altitude). Ainsi, ce travail pose les bases de la compréhension de certains mécanismes d'adaptation locale
Recent technological developments allow an unprecedented access to the whole genome variation and would increase our knowledge on genome diversification using population and landscape genomics. This work is based on the analysis of Whole Genome Sequence data (WGS) with the purpose of characterising genetic diversity in small ruminants (sheep and goats) and exploring genetic bases of local adaptation.First, we addressed a methodological aspect by investigating the accuracy and possible bias in the widely used genotyping approaches to characterize genetic variation in comparison with WGS data. We highlighted strong bias in conventional approaches (SNP chips and exome capture) and also in low-coverage whole genome re-sequencing (1X and 2X), and we suggested effective solutions based on sampling panels of random markers over the genome depending the purpose of the study (assessing neutral diversity, linkage disequilibrium, selection signatures). The various datasets produced allowed assessing genetic resources in various domestic (Moroccan and Iranian indigenous breeds and industrials) and wild populations (bezoars and Asiatic mouflons). We identified a very high diversity in indigenous and wild populations. They constitute a reservoir of alleles allowing them to play a possible key role in the preservation of these species in the context of global changes. The deep study of Moroccan goats showed a high diversity that is weakly structured in geography and populations, and highlighted numerous genomic regions showing signatures of selection. These regions identified different putative adaptive mechanisms according to the population (e.g. panting/sweating to adapt to warm/desert environment).Then, we explored genetic bases of local adaptation to the environment in sheep and goats using a landscape genomics framework. We scanned genomes of 160 sheep and 161 goats representing the eco-climatic Moroccan-wide diversity. We identified numerous candidate variants and genes, which allowed for identifying physiological pathways possibly underlying local adaptation. Especially, it seems that respiration and cardiac process have key roles in the adaptation to altitude. Our results suggest dissimilar adaptive mechanisms for the same environment in sheep and goats. However, we highlighted several cases of common metabolic pathways in different species. Moreover, we characterized some patterns for the variation of genetic differentiation in some candidate genomic regions over environmental gradients. This allowed us to visualise different adaptive reaction depending genes. This work points the way towards a better understanding of some mechanisms underlying local adaptation

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Copetti, Dario, Jianwei Zhang, Baidouri Moaine El, Dongying Gao, Jun Wang, Elena Barghini, Rosa M. Cossu, et al. "RiTE database: a resource database for genus-wide rice genomics and evolutionary biology." BioMed Central Ltd, 2015. http://hdl.handle.net/10150/610281.

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BACKGROUND: Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. RESULTS: Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. CONCLUSIONS: This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.

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22

Frost, Michelle B. "Population genomics and spatial planning for the conservation of the endangered common skate species complex." Thesis, University of Aberdeen, 2017. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=235413.

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23

Harnal, Veera Kumari. "Population genetics and sperm physiology associated with genome resource banking in the Eld's deer." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0035/MQ64367.pdf.

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24

Sundell, David. "Novel resources enabling comparative regulomics in forest tree species." Doctoral thesis, Umeå universitet, Umeå Plant Science Centre (UPSC), 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-133984.

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Lignocellulosic plants are the most abundant source of terrestrial biomass and are one of the potential sources of renewable energy that can replace the use of fossil fuels. For a country such as Sweden, where the forest industry accounts for 10% of the total export, there would be large economical benefits associated with increased biomass yield. The availability of research on wood development conducted in conifer tree species, which represent the majority of the forestry in Sweden, is limited and the majority of research has been conducted in model angiosperm species such as Arabidopsis thaliana. However, the large evolutionary distance between angiosperms and gymnosperms limits the possibility to identify orthologous genes and regulatory pathways by comparing sequence similarity alone. At such large evolutionary distances, the identification of gene similarity is, in most cases, not sufficient and additional information is required for functional annotation. In this thesis, two high-spatial resolution datasets profiling wood development were processed; one from the angiosperm tree Populus tremula and the other from the conifer species Picea abies. These datasets were each published together with a web resource including tools for the exploration of gene expression, co-expression and functional enrichment of gene sets. One developed resource allows interactive, comparative co-expression analysis between species to identify conserved and diverged co-expression modules. These tools make it possible to identifying conserved regulatory modules that can focus downstream research and provide biologists with a resource to identify regulatory genes for targeted trait improvement.
Lignocellulosa är den vanligast förekommande källan till markburen biomassa och är en av de förnybara energikällor som potentiellt kan ersätta användningen av fossila bränslen. För ett land som Sverige, där skogsindustrin som står för 10 \% av den totala exporten, skulle därför en ökad produktion av biomassa kunna ge stora ekonomiska fördelar. Forskningen på barrträd, som utgör majoriteten av svensk skog är begränsad och den huvudsakliga forskningen som har bedrivits på växter, har skett i modell organismer tillhörande gruppen gömfröiga växter som till exempel i Arabidopsis thaliana. Det evolutionära avståndet mellan gömfröiga (blommor och träd) och nakenfröiga (gran och tall) begränsar dock möjligheten att identifiera regulatoriska system mellan dessa grupper. Vid sådana stora evolutionära avstånd krävs det mer än att bara identifiera en gen i en modellorganism utan ytterligare information krävs som till exempel genuttrycksdata. I denna avhandling har två högupplösta experiment som profilerar vedens utveckling undersökts; ett från gömfröiga träd Populus tremula och det andra från nakenföriga träd (barrträd) Picea abies. Datat som behandlats har publicerats tillsammans med webbsidor med flera olika verktyg för att bland annat visa genuttryck, se korrelationer av genuttryck och test för anrikning av funktionella gener i en grupp. En resurs som utvecklats tillåter interaktiva jämförelser av korrelationer mellan arter för att kunna identifiera moduler (grupper av gener) som bevaras eller skilts åt mellan arter över tid. Identifieringen av sådana bevarade moduler kan hjälpa att fokusera framtida forskning samt ge biologer en möjlighet att identifiera regulatoriska gener för en riktad förbättring av egenskaper hos träd.

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Abdelrahman, Hisham, Mohamed ElHady, Acacia Alcivar-Warren, Standish Allen, Rafet Al-Tobasei, Lisui Bao, Ben Beck, et al. "Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research." BIOMED CENTRAL LTD, 2017. http://hdl.handle.net/10150/623031.

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Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries. Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.

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Chai, Hui Hui. "Developing new approaches for transcriptomics and genomics : using major resources developed in model species for research in crop species." Thesis, University of Nottingham, 2014. http://eprints.nottingham.ac.uk/14246/.

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With the estimated increase in global demand for food and over-reliance on staple food crops, the exploitation of agricultural biodiversity is important to address food security challenges. The aim of this study is to develop approaches to transfer major informational and physical resources developed in model plant and major crop species to resources poor crop species, using oil palm and Bambara groundnut as two exemplar crops. XSpecies (cross-species) approach, the core approach of the study, is described as the approach which uses microarrays developed for a given species to analyse another related species. The use of the XSpecies approach (here the cross-hybridisation of DNA from oil palm onto heterologous Affymetrix microarrays for Arabidopsis and rice), is the first experiment reported in oil palm and focused on a bulked segregant analysis of different shell-thicknesses for oil palm fruit. Primers design involved screening candidate probe-pairs filtered using PIGEONS software against oil palm transcriptome sequences generated using 454 sequencing technology. The results provided an insight into the effects of sequence divergence between oil palm and the reference species (Arabidopsis and rice) onto the power of detecting single feature polymorphism (SFPs) in oil palm, implying the importance of close association between studied and model plant/crop in XSpecies approach. The XSpecies approach coupled with genetical genomics was also tested within legumes, with Bambara groundnut as the query species compared to soybean as the resource rich species (20 Mya). A mild drought experiment, conducted in a controlled environment glasshouse, used an F5 segregating population derived from a controlled cross between DipC and Tiga Nicuru in Bambara groundnut. The cross-hybridisation of Bambara groundnut leaf RNA to the soybean GeneChip individual oligonucleotide probes resulted in a total of 1,531 of good quality gene expression markers (GEMs) on the basis of the differences in the hybridisation signal strength. The first ‘expression-based’ genetic map (GEM map) was constructed using 165 GEMs spanning 920.3 cM of Bambara groundnut genome. The first high density DNA-marker genetic map of 1,341.3 cM combining dominant DArT and co-dominant SNPs, developed using the DArT Seq approach, with additional pre-existing microarray-based DArT and SSR markers, was also developed in the F3 segregating population. Both maps were combined to form the first integrated map of 1,250.7 cM with 212 markers. Morphological differences and the rapid reduction in stomatal conductance observed within the F5 segregating population in the drought experiment provided trait data for a QTL analysis. The comprehensive QTL analysis in Bambara groundnut detected significant QTLs for morphological traits using GEM map, including internode length, peduncle length, pod number per plant, pod weight per plant, seed number per plant, seed weight per plant, 100-seed weight, shoot dry weight and harvest index across four linkage groups: LG1, LG2B, LG8B and LG11A. The loci controlling internode length and peduncle length were also consistently mapped to single marker on LG1 in DArTseq map using F3 segregating population, suggesting that these two traits are probably controlled by single gene or two closely linked genes. Despite significant genotypes effects on stomatal conductance tested in ANOVA analysis, no major QTLs were detected, suggesting the contributions of a number of small genetic effects to stomatal conductance. A preliminary homology search using the LG1 linkage group markers and associated gene models showed the ability to develop a framework for identification of candidate genes in Bambara groundnut relative to soybean. The present study also developed the resources for an eQTL analysis in a cross-species context. Translation from major and model plant species to underutilised and resource poor crops is critical to be able to develop many crop species with potential for future agriculture. This study examines some of the approaches which might be adopted and replicated in various underutilised crop species.

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27

Moganeradj, Kartykayan. "IS6110 FAFLP PCR, a tool for genomic mapping enabling investigation of evolutionary relationships of Mycobacterium tuberculosis in resource poor settings." Thesis, University College London (University of London), 2018. http://discovery.ucl.ac.uk/10046354/.

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Tuberculosis (TB) is an important communicable disease affecting the human population world-wide. Despite the efforts of the scientific community, national governments and WHO in controlling the disease, TB still remains a major killer in resource poor settings. New rapid assays and techniques that are simple and cost-effective are urgently needed to identify, treat and understand pathogenesis including the geographical distribution of the disease. The aim of the thesis is to develop a novel genomic mapping tool using Insertion Element, IS6110 that could aid in epidemiological studies of Mycobacterium tuberculosis complex (MTBC) in low and middle income countries. IS6110, a bacterial transposon, plays an essential role in changing the physical and biochemical traits of MTBC. Due to their transposition in TB genomes, they are used as epidemiological markers for differentiation of TB organisms and the mapping of these elements could also shed light on the putative altered function of adjacent genes. In the era of Whole Genome Sequencing (WGS) where repeat elements are difficult to sequence with short read technologies, a rapid and simple method of insertion site mapping using IS6110 FAFLP PCR was developed. This work is aimed at developing a rapid, cost-effective and robust genomic tool box exploiting the IS6110 FAFLP PCR assay that can both identify and characterise the TB genotypes / genetic lineages in any geographical location. For the first time using the assay above, TB samples from Nepal were categorised into different genetic lineages. Fifty-five percent of the samples analysed belong to Principal Genetic Group 1 (PGG1), Beijing and Central Asian strains. Also, new primers were designed targeting the Beijing and the T- groups using the FAFLP derived data that gave rise to the development of rapid lineage specific PCR assays. In addition, it was noticed that 3.9% of the Nepalese strains tested in this research work were likely multi-drug resistant (MDR-TB) using PCR targeting the Rifampicin-resistance-determining region (RRDR) of the rpoB region. It is demonstrated here that IS6110 FAFLP methodology could easily characterise the TB samples into different genetic lineages provided they have more than four IS6110 copies. In addition, lineage specific PCR does not need any expensive instruments or reagents except for PCR blocks and gel visualisers, and could be very effective in the rapid identification of different TB genotypes within hours. These data also add to knowledge about the circulating strains of TB in Nepal, currently a poorly characterised region of the world in this regard, and could help in contact tracing studies by epidemiologists. The IS6110 FAFLP technique thus can be employed in any geographical location to map TB genetic lineages where there is little or no information available on the prevailing TB strains.

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Bergdahl, Philip, and William Bodell. "Behålla personal genom utveckling." Thesis, Högskolan i Skövde, Institutionen för handel och företagande, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-13625.

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BakgrundDen svenska arbetsmarknaden genomgår en förändring som pågått under en längre tid. Synen på en anställning har luckrats upp och guldklocksanställningen är och förblir allt mer ovanlig. I dagens Sverige är det vanligaste sättet att avancera inom yrkeslivet att byta arbetsgivare. Det är höga kostnader som är relaterade till att personal väljer att lämna organisationen och det är således viktigt att behålla befintlig personal. Ett preventivt arbete för att minimera risken att personal överväger att lämna företaget kan vara individanpassat utvecklingsarbete. SyfteSyftet med uppsatsen är att undersöka hur attraktiva, enligt Randstad och Universum, arbetsgivare inom en kunskapsintensiv miljö i Göteborgsregionen arbetar med kompetensutveckling, professionell utveckling och karriärmöjligheter för att behålla personal. MetodStudien genomförs ur ett ledningsperspektiv med hjälp av en kvalitativ forskningsansats då forskningsfrågan inte syftar till att mäta och jämföra olika resultat utan snarare handlar om att undersöka hur företag arbetar med frågan. Insamling av empiri sker genom sex stycken semistrukturerade intervjuer på olika företag. Valet av fallföretag har gjorts med hjälp av vinnarlistan i “Randstad Award 2016” och Universums lista “Sveriges bästa arbetsgivare 2016” vilket är sammanställningar av Sveriges mest attraktiva arbetsgivare år 2016. SlutsatsStudien visar att samtliga företag arbetar med individanpassad utveckling för medarbetaren. Detta utvecklingsarbete sker genom justering av arbetsuppgifter, kompetensutveckling genom kurser, seminarier och “workshops” där de i första hand nyttjar intern kunskap samt mentorskap och tillgång till internt och externt nätverk.
BackgroundIn the last couple of years there has been an ongoing change in the Swedish labor marketwhere the view and the occurrence of long term employment is not as common as it oncewas. The most common way of career development is through change of employer. The costof employee turnover can be avoided or reduced by keeping current employees and anindividually shaped development for the employee may result in the employee staying loyalto the company. PurposeThe purpose of this study is to investigate how attractive employers, based on Randstad andUniversum, within a knowledge based environment in the area of Gothenburg providescompetence development, professional development and career opportunities in order toretain their employees. Method The study applies a qualitative research approach since the purpose of the study is to gain understanding in how companies provide development and not to compare different companies’ results to one another. The study is based on six semi-structured interviews held at each of the six companies. The selection of companies is based on the lists “Randstad Award 2016” and “Sveriges bästa arbetsgivare 2016” by Universum which are summaries of Sweden’s most attractive employers of the year 2016. Conclusion The study shows that all of the companies have an individually shaped development plan for the employee. This is managed through adjustment of duties, competence development through courses, seminars and workshops which are based on internal knowledge within the company. Last but not least development is supplied through the use of mentoring and networking, both internal and external.

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Brouillet, Miriam. "Is it justified to patent human genetic resources?" Thesis, McGill University, 2003. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=19699.

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In the past century, the scope of patentable objects has greatly expanded. Patents are now being granted on living organisms, human biological material and genes. What are the consequences of such practices for scientific research and health care? One of the fundamental philosophical questions behind this issue is the following: are we justified in patenting human genetic material? An examination of the traditional philosophical justification of intellectual property will allow us to critically explore whether or not this practice is ethically justifiable. It will be argued that the consequentialist justification of intellectual property requires, in this present case, that we modify the patent regimes in order to maximise social benefits and minimize public burdens.

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Cahoy, John David. "Genomic analysis of highly purified astrocytes reveals in vivo astrocyte gene expression : a new resource for understanding astrocyte development and function /." May be available electronically:, 2007. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.

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31

Cox, Brian James. "EMS Mutagenesis in Quinoa: Developing a Genetic Resource." BYU ScholarsArchive, 2020. https://scholarsarchive.byu.edu/etd/9080.

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Chenopodium quinoa, a South American pseudocereal, has valuable agricultural traits such as salt tolerance and drought tolerance, and it has beneficial nutritional properties such as high protein content and a complete amino acid profile. However, problems including disease susceptibility, low harvest index, lodging, seed shattering, low heat tolerance, and saponin content plague quinoa. Genetic resources for quinoa are needed to fix these problems and make quinoa more available throughout the world. We used ethyl methanesulfonate (EMS) to create a mutant population of QQ74 quinoa (USDA GRIN PI 614886) of 5,030 mutant families. We did whole exome sequencing (WES) on 44 mutant families. Using the recently published quinoa reference genome and MAPS, a mutation detection pipeline, we found a mutation rate of 11.35 mutations/Mb in these families. We also used whole genome sequencing (WGS) to calculate a mutation rate of 21.67 mutations/Mb in an additional nine mutant families. To demonstrate the utility of this population as a genetic resource, we found an EMS-induced nonsense mutation in the betalain synthesis pathway that prevents red betacyanins from accumulating in the hypocotyl of quinoa. With the mutation rates in our population, we calculate that analysis of 300 mutant families will yield 3-7 mutations in any gene of interest, which will facilitate forward and reverse genetic studies in quinoa.

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Wang, Wenming, Milos Tanurdzic, Meizhong Luo, Nicholas Sisneros, Hye Ran Kim, Jing-Ke Weng, Dave Kudrna, et al. "Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics." BioMed Central, 2005. http://hdl.handle.net/10150/610078.

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BACKGROUND:The lycophytes are an ancient lineage of vascular plants that diverged from the seed plant lineage about 400 Myr ago. Although the lycophytes occupy an important phylogenetic position for understanding the evolution of plants and their genomes, no genomic resources exist for this group of plants.RESULTS:Here we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from the lycophyte Selaginella moellendorffii. Based on cell flow cytometry, this species has the smallest genome size among the different lycophytes tested, including Huperzia lucidula, Diphaiastrum digita, Isoetes engelmanii and S. kraussiana. The arrayed BAC library consists of 9126 clones
the average insert size is estimated to be 122 kb. Inserts of chloroplast origin account for 2.3% of the clones. The BAC library contains an estimated ten genome-equivalents based on DNA hybridizations using five single-copy and two duplicated S. moellendorffii genes as probes.CONCLUSION:The S. moellenforffii BAC library, the first to be constructed from a lycophyte, will be useful to the scientific community as a resource for comparative plant genomics and evolution.

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Li, Miaoxin, and 李淼新. "Development of a bioinformatics and statistical framework to integratebiological resources for genome-wide genetic mapping and itsapplications." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43572030.

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Edström, Magnus. "Syre-18-halt hos markvatten extraherat genom centrifugering och destillering av jordprover." Thesis, Uppsala universitet, Institutionen för geovetenskap, 1993. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-392964.

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Vid hydrologiska studier är det ofta nödvändigt att känna till flödesvägar och uppehållstider för markvattnet. Syreisotopen 18O kan användas som ett konservativt hydrologiskt spårämne för att bestämma vattnets rörelse. Vid extrahering av markvatten från jordprover för 18O-analys används ofta en destillationsmetod. En enklare och snabbare metod för att extrahera markvatten är att använda en höghastighetscentrifug. Problemet är att allt markvatten i ett jordprov inte extraheras med denna metod. Det är därför möjligt att vatten extraherat genom centrifugering inte har en 18O-halt som är representativ för markvattnet. I den här undersökningen jämfördes 18O-halterna i vatten extraherat genom centrifugering och destillering. Markvatten extraherades från ostörda jordprover och från torkade jordprover mättade med vatten av känd 18O-halt. Extraktionerna gjordes både genom centrifugering vid olika hastigheter följt av destillation och genom enbart destillation. Samtliga jordprover torkades sedan. Skillnaden i 18O-halt mellan vatten extraherat genom centrifugering vid olika hastigheter var små. 18O-halten för destillaten var, med ett undantag, lägre än för centrifugaten. Torkningen av jordproverna visade dock att allt markvatten inte hade extraherats vid destillationen. Detta kan vara en förklaring till den lägre 18O-halten hos destillaten. På grund av ofullständig destillation kunde inte den här undersökningen avgöra i vilken grad 18O-halterna i centrifugaten var representativa för den del av markvattnet som är hårdast bunden till marken. För att karaktärisera 18O-halten i det rörligaste markvattnet, är dock centrifugering inte bara en snabbare metod, utan också en metod med färre felkällor än destillationsmetoden.
In hydrological studies it is often necessary to know the ﬂow pathways and residence time of soil water. The oxygen isotope 18O can be used as a conservative hydrological tracer to help determine water´s movement. To extract soil water from soil samples for 18O analysis, a distillation method is often used. An easier and faster method for extracting soil water is high speed centrifugation. All soil water, however, is not extracted from a soil sample by this method. It is therefore possible that the water extracted by centrifugation does not have an 18O content that is representative of the soil water. In this study, the 18O values of water extracted by distillation and centrifugation are compared. Soil water was extracted from undisturbed soil samples and from oven-dried soil samples saturated with water of a known 18O content. The extractions were done both by centrifugation at different speeds followed by distillation and by distillation only. All of the samples were then oven-dried. The differences in 18O content between water extracted by centrifugation at different speeds were small. The 18O content in the water extracted by distillation was, with one exception, more depleted in 18O than the water extracted by centrifugation. From the oven-drying it was seen that the distillations did not succeed in extracting all soil water. This might be a reason for the depletion in 18O content of the water extracted by distillation. Due to incomplete distillation, this study was not able to determine how well the 18O content in water extracted by centrifugation represents the water bound most strongly to the soil. For characterizing the 18O content in the least bound soil water, however, centrifugation is not only faster, but also less prone to error than distillation.

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Lindahl, Britta, and Karin Åstrand. "Chefens resa genom ett alkoholärende. : En studie om chefers upplevelser och erfarenheter av att hantera anställda med alkoholproblematik." Thesis, Umeå universitet, Pedagogiska institutionen, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-100076.

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I Sverige ses alkohol som socialt accepterat under såväl vardag som högtid, både jul och konferensresa skålas in med öl och brännvin. Dock går det inte att frångå det faktum att över 300 000 av landets invånare lider av ett alkoholberoende, vilket gör det till en av våra största folkhälsosjukdomar. En sjukdom som ofta inte syns, men förekommer framförallt på våra arbetsplatser. På arbetsplatsen ligger yttersta ansvaret hos cheferna; deras förmåga att upptäcka och agera när tecknen väl syns hos individen. Dessa tecken är inte alltid enkla att se vilket framgick i denna studie. Studiens syfte var att skapa förståelse för chefers upplevelser och erfarenheter av att hantera anställda med alkoholproblematik samt att utröna vad som påverkar chefers agerande när de ställs inför denna situation. För att uppfylla syftet genomfördes en kvalitativ, hermeneutisk intervjustudie. Deltagare i studien var chefer med erfarenhet av alkoholproblematik samt ledande aktörer inom alkoholarbete i näringslivet. Studiens huvudsakliga slutsatser är att alkohol är ett svårhanterligt ämne för chefer, grundat i rädslor och kunskapsbrist. Det framkom även att chefer upplever en svår balansgång mellan medmänsklighet och arbetsgivaransvar samt lagkrav.

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Tollis, Marc, Dale F. DeNardo, John A. Cornelius, Greer A. Dolby, Taylor Edwards, Brian T. Henen, Alice E. Karl, Robert W. Murphy, and Kenro Kusumi. "The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species." PUBLIC LIBRARY SCIENCE, 2017. http://hdl.handle.net/10150/624695.

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Agassiz's desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.

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Fjällman, Elisabeth, and Viktor Rylander. "Kvarvarande grundvattennivåförändringar efter tunnelbygget genom Hallandsås." Thesis, Uppsala universitet, Institutionen för geovetenskaper, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297087.

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Li, Miaoxin. "Development of a bioinformatics and statistical framework to integrate biological resources for genome-wide genetic mapping and its applications." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43572030.

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Bailey, Susan F. "The Effects of Competition and Ecological Opportunity on Adaptation and Diversification." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/26229.

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Ecological processes have the potential to influence evolution through their effects on selection. This thesis explores the effects of two ecological factors - competition and ecological opportunity. Intraspecific (within-species) competition is often expected to drive adaptation and diversification by increasing selection for the use of novel resources, thereby alleviating the detrimental effects of competition. However, this is not always the expected outcome; theory suggests that intraspecific competition can also drive convergent evolution. On the other hand, interspecific (between-species) competition is usually expected to impede adaptation and diversification because competitor species occupy potential available niches, preventing the focal species from diversifying to do so. In this thesis, I review previous experimental studies exploring the effects of competition on adaptive diversification, and then directly test these effects using experimental evolution of the bacterium Pseudomonas fluorescens. I confirm that intraspecific competition drives adaptive diversification, while the effects of interspecific competition are varied. Strong interspecific competition impedes adaptation and diversification, while the presence of weak, non-diversifying interspecific competitors drives diversification through increased resource competition. The presence of ecological opportunity is essential for adaptation and diversification, and so variation in attributes of those opportunities is expected to have important effects on the dynamics of adaptive evolution. In another evolution experiment with P. fluorescens, I tested the effects of variation in ecological opportunity on adaptive evolution and found that the type and arrangement of ecological opportunities drives adaptation but, in this system, not diversification. I also show that ecological opportunity drives differences in the degree of parallel evolution at the phenotypic and genotypic level. Finally, I explore some unexpected genetic changes identified in one of these evolved populations - two synonymous mutations that conferred fitness benefits, and show that the observed fitness improvements are the result of increased gene expression. I have shown that ecological processes can play an important role in shaping the evolutionary trajectories taken by populations. Understanding the interactions between ecological and evolutionary processes is vital for our understanding of evolutionary dynamics as a whole, and the studies laid out in this thesis represent valuable contributions to this field of study.

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Bernacki, Lucas Edward. "The Molecular Evolution of Non-Coding DNA and Population Ecology of the Spiny Softshell Turtle (Apalone spinifera) in Lake Champlain." ScholarWorks @ UVM, 2015. http://scholarworks.uvm.edu/graddis/289.

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ABSTRACT Spiny softshell turtles (Apalone spinifera) occur at the northwest limit of their range in Lake Champlain. This species, although widespread across North America, is listed as threatened in Vermont due to habitat destruction and disturbances of anthropogenic origin. The population of spiny softshell turtles in Lake Champlain is isolated from other North American populations and is considered as an independent management unit. Efforts to obtain information on the biology of spiny softshell turtles in Lake Champlain precede 1936 with conservation measures being initiated in 1987. Methods of studying spiny softshell turtles in Lake Champlain have included direct observation, mark-recapture, nest beach monitoring, winter diving, and radio telemetry. Each of these approaches has provided some information to the sum of what is known about A. spinifera in Lake Champlain. For example major nesting beaches, hibernacula, and home range size have been determined. Currently spiny softshell turtles primarily inhabit two areas within Lake Champlain, Missisquoi Bay and the mouth of the Lamoille River. However, the population structure and gene flow between spiny softshell turtles inhabiting the Lamoille and Missisquoi regions remained unknown. A GIS model was created and tested in order to identify additional nesting beaches used by spiny softshell turtles along the Vermont shores of Lake Champlain. Although some additional small potential nesting beaches were found, no additional major nesting sites were found. The GIS model identified the mouth of the Winooski River (the site of a historical population) as potentially suitable nesting habitat; however, no evidence of spiny softshell turtle nesting was found at this site. A series of methods developed for collecting molecular and population genetic data about spiny softshell turtles in Lake Champlain are described, including techniques for DNA extraction of various tissue types and the design of new primers for PCR amplification and sequencing of the mitochondrial control region (mtD-loop). Techniques for circumventing problems associated with DNA sequence alignment in regions of a variable numbers of tandem repeats (VNTRs) and the presence of heteroplasmy within some individuals are also described. The mtD-loop was found to be a suitable marker to assess the genetic structure of the Lake Champlain population of spiny softshell turtles. No significant genetic sub-structuring was found (FST=0.082, p=0.223) and an indirect estimate of the migration rate between Lamoille and Missisquoi regions of Lake Champlain was high (Nm>5.576). In addition to consideration of A. spinifera in Lake Champlain, the mtD-loop was modeled across 46 species in 14 families of extant turtles. The primary structure was obtained from DNA sequences accessed from GenBank and secondary structures of the mtD-loop were inferred, (from thermal stabilities) using the program Mfold, for each superfamiliy of turtles. Both primary and secondary structures were found to be highly variable across the order of turtles; however, the inclusion of an AT-rich fold (secondary structure) near the 3' terminus of the mtD-loop was common across all turtle families considered. The Cryptodira showed conservation in the primary structure at regular conserved sequence blocks (CSBs), but the Pluerodira displayed little conservation in the primary structure of the mtD-loop. Overall, greater conservation in secondary structure than primary structure was observed in turtle mtD-loop. The AT-rich secondary structural element near the 3' terminus of the mtD-loop may be conserved across turtles due to it serving a functional role during mtDNA transcription.

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Euclide, Peter T. "Genetic And Demographic Consequences Of Lake And River Habitat Fragmentation On Fishes In Vermont." ScholarWorks @ UVM, 2018. https://scholarworks.uvm.edu/graddis/887.

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Globally, habitat fragmentation has had a major impact on the conservation and management of many species and is one of the primary causes of species extinction. Habitat fragmentation is loosely defined as a process in which a continuous habitat is reduced to smaller, disconnected patches as the result of habitat loss, restriction of migration or the construction of barriers to movement. Aquatic systems are particularly vulnerable to habitat fragmentation, and today an estimated 48% of rivers are fragmented worldwide. My dissertation evaluates how habitat fragmentation has influenced the populations of four different species of fish in the Lake Champlain basin. In chapter 1 I summarize the current state of habitat fragmentation research, I broadly describe habitat fragmentation, review how habitat fragmentation pertains to population genetics, and describe the legacy of habitat fragmentation in the Lake Champlain basin. In chapters 2, 3 and 4 I evaluate and discuss the impact of nine lake causeways on the population structure of slimy sculpin (Cottus cognatus), rainbow smelt (Osmerus mordax), and lake whitefish (Coregonus clupeaformis). The genetic effects of causeways are limited. However, causeways appear to have had a significant influence on rainbow smelt demographics, and the genetic structure observed in lake whitefish may be a product of reduced effective population size resulted from commercial harvest in the late 1800s. In chapter 5 I evaluate how the basin-wide population of tessellated darters (Etheostoma olmstedi) is naturally structured throughout Lake Champlain and three different major tributaries and evaluates the effect that different types of habitat fragmentation (dams, causeways, and natural fall lines) have on tessellated darter populations. Tessellated darters appear to be highly structured by river drainage but not by dams, causeways or fall lines. My dissertation highlights how comparative population genetic studies can be used to identify patterns of isolation within large populations. My results stress the value of reporting both the presence and absence of barrier induced population sub-structuring.

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Hinkle, Jameson. "PROOF-OF-CONCEPT OF ENVIRONMENTAL DNA TOOLS FOR ATLANTIC STURGEON MANAGEMENT." VCU Scholars Compass, 2015. http://scholarscompass.vcu.edu/etd/3932.

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Abstract The Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus, Mitchell) is an anadromous species that spawns in tidal freshwater rivers from Canada to Florida. Overfishing, river sedimentation and alteration of the river bottom have decreased Atlantic Sturgeon populations, and NOAA lists the species as endangered. Ecologists sometimes find it difficult to locate individuals of a species that is rare, endangered or invasive. The need for methods less invasive that can create more resolution of cryptic species presence is necessary. Environmental DNA (eDNA) is a non-invasive means of detecting rare, endangered, or invasive species by isolating nuclear or mitochondrial DNA (mtDNA) from the water column. We evaluated the potential of eDNA to document the presence of Atlantic Sturgeon in the James River, Virginia. Genetic primers targeted the mitochondrial Cytochrome Oxydase I gene, and a restriction enzyme assay (DraIII) was developed. Positive control mesocosm and James River samples revealed a nonspecific sequence—mostly bacteria commonly seen in environmental waters. Methods more stringent to a single species was necessary. Novel qPCR primers were derived from a second region of Cytochrome Oxydase II, and subject to quantitative PCR. This technique correctly identified Atlantic Sturgeon DNA and differentiated among other fish taxa commonly occurring in the lower James River, Virginia. Quantitative PCR had a biomass detection limit of 32.3 ug/L and subsequent analysis of catchment of Atlantic Sturgeon from the Lower James River, Virginia from the fall of 2013 provided estimates of 264.2 ug/L Atlantic Sturgeon biomass. Quantitative PCR sensitivity analysis and incorporation of studies of the hydrology of the James River should be done to further define habitat utilization by local Atlantic Sturgeon populations. IACUC: AD20127

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Jacquin, Justine. "Ecotoxicologie microbienne des plastiques en mer : colonisation et biodégradation par la plastisphère." Electronic Thesis or Diss., Sorbonne université, 2020. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2020SORUS104.pdf.

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De nos jours, les déchets plastiques ont envahi l’ensemble des écosystèmes marins du monde en n’épargnant aucune zone. La demande mondiale de plastique ne cesse de croitre d’année en année, malgré l’impact dramatique qu’il provoque sur l’environnement lorsqu’il est laissé dans la nature. On estime que chaque année entre 4.8 et 12.7 millions de tonnes de plastiques finissent dans les océans. Les travaux de cette thèse s’inscrivent dans le cadre de cette urgence environnementale, en permettant de mieux identifier les biofilms bactériens attachés aux différents plastiques (« plastisphère) et de mieux caractériser le phénomène de biodégradation de certains polymères en milieu marin. Dans un premier temps, l’analyse d’échantillons prélevés pendant deux expéditions (l’expédition Tara-Méditerranée et Tara-Pacifique) ont permis de caractériser la biogéographie des biofilms bactériens spécifiques des plastiques. Cette comparaison a permis de mettre en évidence une niche écologique à la surface des plastiques distincte de l’eau environnante, nettement influencé par la géographie, expliqué principalement par la température. L’étude taxonomique a permis de mettre en évidence un « core microbiome », dominé par un genre de cyanobactérie (Rivularia sp.) et des familles connues (Rhodobacteraceae et Flavobacteraceae) comme étant colonisateurs de plastique en milieu marin. Dans un second temps, la colonisation bactérienne sur différents polymères a été étudiée grâce à des aquariums en circuit ouvert sur la baie de Banyuls. Le processus de biodégradation a été étudié en milieu artificiel sans source de carbone que le polymère, imitant l’environnement marin et en suivant plusieurs paramètres expérimentaux. Dans notre étude aucune spécificité des communautés microbiennes liées à la nature des polymères a été observée pendant la phase de croissance du biofilm. Le processus de biodégradation à pu être mis en évidence sur certains polymères tels que le PHBV, Bioplast, Mater-Bi et la cellulose grâce notamment à une activité bactérienne maintenue tout au long de l’incubation. Dans un troisième temps, une souche provenant du biofilm mature du PHBV a pu être isolée pour étudier spécifiquement son processus de biodégradation. L’analyse du génome d’Alteromonas sp., a révélé la présence de 4 dépolymérases dont 3 externes et 1 interne, expliquant sa capacité à dégrader le PHBV. L’étude du génome a aussi permis de mettre en évidence deux voies de synthèse des PHA l’une permettant la synthèse de PHASCL et l’autre de PHAMCL. Enfin, l’étude de la biodégradation du PHBV par un consortium naturel a été approfondi grâce à un marquage isotopique du polymère. Cette nouvelle expérimentation couplée à une analyse métagénomique a permis d’étudier des communautés fonctionnelles pouvant assimiler le carbone du polymère. Les travaux menés durant cette thèse permettent de mieux identifier les biofilms bactériens se développant à la surface de polymères biodégradables et non dégradables, et également d'affiner la caractérisation du processus de biodégradation en milieu marin grâce à l'utilisation de différents paramètres tels que la production bactérienne, la respiration, la perte de poids, le suivi de l’assimilation du carbone marqué ou l’imagerie en microscopie. Ces études sont primordiales pour mieux comprendre le processus de biodégradation des plastiques en mer et ainsi proposer des adaptations aux normes de standardisations régissant l’environnement marin et actuellement peu représentative
Nowadays, plastic waste has invaded all of the world's marine ecosystems, sparing no area. The global demand for plastic continues to grow year after year, despite its dramatic impact on the environment when plastic is left in nature. It is estimated that each year between 4.8 and 12.7 million tonnes of plastics end up in the oceans. This PhD aims and works fall within the framework of this environmental emergency, by making possible to better identify the bacterial biofilms attached to different plastics (the so called "plastisphere) and to better characterize the biodegradation process of certain polymers in the marine environment. The first stage, was to analyse the microbial diversity of samples taken during two expeditions (the Tara-Mediterranean expedition and Tara-Pacific) in order to characterize the biogeography of bacterial biofilms specific to plastics. The comparison between samples from the Pacific and the Mediterranean see allow to highlight an ecological niche on the surface of plastics distinct from the surrounding water. Niche which is clearly influenced by geography, explained mainly by temperature. The taxonomic study revealed a "core microbiome" dominated by a genus affiliated to the cyanobacteria and families (Rhodobacteraceae and flavobacteraceae) known to be colonizers of plastic in the marine environment. Then, the bacterial colonization on different polymers was studied in aquarium using uninterrupted circulation of seawater collected continuously from the Banyuls Bay. The biodegradation process was studied using an artificial environment without any other carbon source than the polymer in order to mimic the marine environment, and by following several experimental parameters (Bacterial production, respiration, loss of mass). In our study we observed during the growth phase of the biofilm no specific microbial communities related to the nature of the polymers. The biodegradation process has been demonstrated on certain polymers such as PHBV, Bioplast, Mater-Bi and cellulose, in particular due to the bacterial activity maintained throughout the incubation. Next, a strain Alteromonas sp., isolated from the mature biofilm of the PHBV allow us to explore its biodegradation capabilities. The analysis of the genome of Alteromonas sp. revealed the presence of 4 depolymerases, with 3 external and 1 internal, explaining its ability to degrade PHBV. The study of the genome also revealed two pathways for the PHA synthesis, one allowing the synthesis of PHASCL and the other of PHAMCL. Finally, the study of the biodegradation of PHBV by a natural consortium was done using isotopic labelling of the polymer. This experiment, coupled with metagenomic analysis, allowed the study of functional communities that can assimilate the carbon of the polymer. Thus, this PhD work enhanced the identification of the bacterial communities inhabiting the biofilms developed on the surface of polymers (biodegradable and non-degradable), and also to refine the characterization of the biodegradation process in the marine environment owing the use of various parameters such as the bacterial production, respiration, weight loss, monitoring of labeled carbon and microscopy. These studies are essential for a better understanding of the biodegradation process of plastics at sea and thus to propose adaptations to the standards methods governing the marine environment and currently not very representative

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Heidt, Hanna [Verfasser]. "Integration of genome wide association and expression profiling for investigating water holding capacity traits in a Duroc × Pietrain resource population / Hanna Heidt." Bonn : Universitäts- und Landesbibliothek Bonn, 2013. http://d-nb.info/1047666618/34.

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Lindblad, Augustin, and Johanna Odelkrantz. "Lära genom att göra? : En intervjustudie om nyutexaminerade personalvetares syn på kunskap och relationen mellan utbildning och arbetsliv." Thesis, Uppsala universitet, Institutionen för pedagogik, didaktik och utbildningsstudier, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-377787.

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Personalvetarprogrammet läses under tre år, studier visar dock att kunskapen som studenter får med sig när de är klara på många sätt är otillräcklig på dagens arbetsmarknad. Syftet med denna studie är att bidra med kunskap kring hur nyutexaminerade personalvetare ser på den kunskap som förvärvats genom utbildningen och i arbetslivet, samt vilken roll deras arbetsgivare spelat i detta. För att finna information om detta genomfördes åtta semi-strukturerade intervjuer med alumner som läst program med inriktning mot personal- och arbetslivsfrågor vid Uppsala universitet. För att generera kunskap om alumnernas upplevelse har vi använt Wengers (1998) teori om lärande, Communities of Practice och vi har kompletterat denna teori med Lundmarks (1998) kompetensblomma samt Olofssons (2012) utbildningskontrakt. Genom en tematisk analys har studiens tre frågeställningar besvarats. Studiens resultat visar att praktiska kurser är det som respondenterna främst tog med sig från universitet. Resultatet visar även att synen på viktig kunskap är relativt intakt, men att betydelsen av det som ansågs som viktig under studietiden, fick en ökad betydelse när de började arbeta efter uttagen examen. Arbetsgivaren spelar en stor roll i att fylla de kunskapsluckor som finns hos nyutexaminerade personalvetare, men upplevelsen skiljer sig beroende om en person har börjat arbeta på sitt nuvarande företag efter examen eller om personen under studietiden arbetade deltid på företaget, för att sedan påbörja en heltidstjänst efter examen.
The Bachelor's degree in Human Resources (HR) is a three-year program. Studies show that the knowledge that students possess when they have completed is insufficient in numerous of ways in today's labor market. The purpose of this research is to gain information about newly graduated Human Resource professionals view regarding the knowledge received at University and at work, and what role their employer played in this. To gain information eight semi-structured interviews were conducted with alumnis from Uppsala University who has studied the program with focus on HR. To gain knowledge about their experience we have used Wenger's (1998) theory about learning, Communities of Practice and we have extended this theory with Lundmark's (1998) competence flower and Olofsson's (2012) education contract. Through thematic analysis the study's three main questions have been answered. The outcomes show that practical courses are what respondents mainly brought with them from the university. The result also shows that the view of important knowledge is relatively intact, but when they started working after graduation they understood the importance about this knowledge. Employers plays a major role in filling the knowledge gaps that exist for newly graduated HR-professionals. The experience differs depending on whether a person started working at its current company after graduation or if the person worked part-time at the company during the study, and began a full-time job after graduation.

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Dahlborg, Josefine, and Johanna Pettersson. "Employee Retention Management genom det psykologiska kontraktet : En komparativ studie om vad lärare i fristående och kommunala skolor värderar högst i sin anställning." Thesis, Högskolan i Skövde, Institutionen för handel och företagande, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19792.

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Bakgrund: Det är av stor vikt för organisationer att arbeta med employee retention management för att maximera sina chanser att behålla sin personal. Att förlora medarbetare leder till höga kostnader för bland annat nyrekrytering och upplärning. Dessutom uppstår en kompetensförlust. Idag råder en stor lärarbrist i Sverige vilken förväntas öka ytterligare de kommande åren. Det är alltså inte enbart kostsamt för skolor att förlora sina lärare; det är också riskfyllt då det riskeras att den kompetens som krävs inte finns att tillgå på arbetsmarknaden.Syfte: Studien avser att förklara vilken faktor i psykologiska kontraktet som anses vara viktigast när lärare väljer att kvarvara i sin anställning samt i vilken ordning de undersökta faktorerna föredras av de medverkande lärarna. Därtill ämnas att studera vilka skillnader och/eller likheter som finns i vad lärare på kommunala respektive fristående skolor värderar.Teoretisk referensram: Denna studie utgår från teorier om employee retention management och studiens huvudteori är det psykologiska kontraktet som har sin grund i social exchange-teorin. De faktorer i det psykologiska kontraktet som studeras är möjligheter till karriärutveckling, stöd från och kommunikation med chefer, lön och finansiella belöningar, möjligheter till lärande och utbildning, social atmosfär och relation till kollegor, balans mellan arbetsliv och privatliv samt arbetsinnehåll.Metod: Studien är genomförd med kvantitativ metod bestående av enkätundersökning. Därtill används en komparativ design för att söka finna eventuella likheter och/eller skillnader mellan vad lärare på fristående och kommunala skolor värderar i sin anställning.Slutsats: Social atmosfär och relation till kollegor är den faktor i det psykologiska kontraktet som av de svarande lärarna anses vara den viktigaste till att de väljer att kvarvara i sin anställning – både vad gäller rangordning av faktorernas medelvärden och vid val av den allra viktigaste faktorn samt för lärare i både fristående och kommunala skolor. På samma sätt är möjligheter till karriärutveckling den faktorn som anses minst viktig i alla dessa avseenden, vilket skulle kunna förklaras av det faktum att läraryrket inte är karriärfokuserat. Den största skillnaden som återfinns i studien är att faktorn stöd från och kommunikation med chefer värderas högre av lärarna på de fristående skolorna än lärarna på de kommunala skolorna.
Background: It is of great importance for organizations to focus on employee retention management in order to maximize their chances to retain their employees. Losing employees results in high costs for recruitment and training etcetera. In addition, there will be a loss of competence. Today there is a shortage of teachers in Sweden which is expected to grow larger in the coming years. Not only is the loss of employees expensive; it is also critical because of the risk of not being able to find the right competence on the labormarket.Purpose: Present study aims to examine which factor in the psychological contract teachers consider being the most important when choosing to stay in their present employment and in which order the examined factors are preferred by the participating teachers. Moreover, the purpose of this study is also to investigate whether there are similarities and/or differences between what teachers in public and private schools value.Theory: This study originates from theories about employee retention management and the main theory is the psychological contract which in turn originates from the social exchange theory. The studied factors in the psychological contract are career opportunities, support from and communication with supervisors, salary and financial rewards, training and development opportunities, social atmosphere and relationship with co-workers, worklife balance, and job content. Method: This study was conducted through a quantitative method using a questionnaire. In addition, a comparative design was used in order to find which similarities and/or differences that exist between what teachers in private and public schools value in their employment.Conclusion: Social atmosphere and relationship with co-workers is the factor in the psychological contract that the teachers in this study consider to be the most important when they choose to remain in their employment – both when ranking the factors’ means and when choosing the single most important factor and also for teachers in both public and private schools. Similarly, the factor career opportunities is the least important factor in all these regards, which could be explained by the fact that the teaching profession is not career focused. The greatest difference between the two sectors is found in the factor support from and communication with supervisors where the teachers in the private schools find this factor more important than the teachers in the public schools do.

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Brogna, Raffaele [Verfasser], Willem Frederik [Akademischer Betreuer] Wolkers, Harald [Akademischer Betreuer] Sieme, Guus F. [Akademischer Betreuer] Rimmelzwaan, Tobias Gutachter] Kerrinnes, and de Figueiredo Constança Sofia [Gutachter] [Ferreira. "Dry storage of bodily fluids for disease diagnostics and genome resource banking / Raffaele Brogna ; Gutachter: Tobias Kerrinnes, Constança Figueiredo ; Willem F. Wolkers, Harald Sieme, Guus F. Rimmelzwaan." Hannover : Stiftung Tierärztliche Hochschule Hannover, 2021. http://d-nb.info/1237685044/34.

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Thurow, Liane Bahr. "Estrutura Genética do Germoplasma de Prunus persica (L.) Batsch no Brasil." Universidade Federal de Pelotas, 2013. http://repositorio.ufpel.edu.br/handle/ri/1145.

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Made available in DSpace on 2014-08-20T13:25:38Z (GMT). No. of bitstreams: 1 dissertacao_liane_thurow.pdf: 690839 bytes, checksum: 6d23772ac7732bb0c45028fd46e4bcf0 (MD5) Previous issue date: 2013-10-18
Based on the advanced knowledge in genomic, marker-assisted selection shows up as a promising strategy especially to accelerate the development of new cultivars in perennial species, such as peach. In this context, this dissertation addressed the current situation and the prospects of using marker-assisted selection in peach breeding programs as well as to characterize the genetic variability and population structure of an association panel representative of peach germplasm available in Brazil through SSR analysis. Based on a literature review, it was seen that a high number of QTL (Quantitative Trait Loci) is identified in genetic maps of peach, but, despite the importance of the characters studied, the use of markerassisted selection has been incipient by breeding programs. By the other side, with the recent completion of the sequencing of the peach genome, the perspective is that the low use of molecular tools by peach breeding program will change in the coming years. In this trend, the genetic variability present in the association panel representative of peach germplasm in Brazil is quite relevant. On the other hand, this germplasm is structured into two subpopulations according to the fruit flesh type, melting or non-melting, with some genotypes being a mixture of both types of fruit flesh. Greater variability is available in the melting flesh group. These results show that the association panel is suitable for association studies given its relevant genetic variability. However, it should be taken into account in the association studies the genetic structure intrinsic to this germplasm to avoid the identification of false markertrait associations.
Com base no avanço do conhecimento de genômica a seleção assistida por marcadores mostra-se como uma estratégia bastante promissora especialmente para acelerar o desenvolvimento de novas cultivares em espécies perenes, como o pessegueiro. Nesse contexto, esta dissertação aborda a situação atual e as perspectivas do uso de seleção assistida por marcadores moleculares no melhoramento genético de pessegueiro, assim como caracteriza a variabilidade genética e a estrutura de população do painel associativo de pessegueiro representativo do germoplasma disponível no Brasil por meio da análise de 10 loci SSR (Simple Sequence Repeats). Com base na literatura, um elevado número de QTLs (Quantitative Trait Loci) está identificado em mapas genéticos de pessegueiro, mas, apesar da importância dos caracteres envolvidos, até o momento o uso de seleção assistida por marcadores tem sido incipiente pelos programas de melhoramento. Por outro lado, com a conclusão recente do sequenciamento do genoma do pessegueiro, a perspectiva é de que essa realidade mude nos próximos anos. Corroborando com essa tendência, o primeiro passo para a seleção assistida por marcadores moleculares é conhecer a variabilidade genética presente no germoplasma de pessegueiro disponível no Brasil. Nesse sentido, os resultados desse trabalho mostram grande variabilidade genética no germoplasma avaliado. Porém, esse germoplasma está estruturado em duas subpopulações bem definidas e agrupadas de acordo com o tipo de polpa, fundente e não-fundente, com alguns acessos apresentando mistura de ambos, entre os quais a maior variabilidade está disponível dentro do subgrupo fundente. Com base nos resultados infere-se que o germoplasma avaliado é adequado para estudos de mapeamento associativo, dada a sua expressiva variabilidade genética, mas deve ser levada em consideração a estrutura genética desse germplasma a fim de evitar a identificação de associações falso-positivas entre marcadores e fenótipos de interesse.

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Johansson, Matilda. "Produktion av bakteriell cellulose genom användning av det symbiotiska förhållandet mellan bakterier och jäst som används vid Kombuchatillverkning." Thesis, Högskolan i Borås, Akademin för textil, teknik och ekonomi, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:hb:diva-23293.

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Different factors such as growing environmental awareness due to the increasing negative impact of persistent plastic wastes, the uncontrollable price variations of the raw material and the rapid depletion of reserves have increased the interest in research regarding polymers derived from renewable sources to replace petroleum-based materials. One of the earth’s most abundant macromolecules is cellulose. The production of cellulose from another resource replaces and reduces the demand from plants, the other resource being cellulose from a bacterial system. Bcaterial cellulose film were produced by fermenting apple waste (apple pomace) from cider production donated by Herrljunga Cider in Herrljunga, Sweden and expired fruit juice, produced by LoveJuice Indonesia, containing a mixture of fruits, mainly apple. As inoculum for the fermentations two different Kombucha cultures were used. To optimize the fermentation conditions, factors such as nitrogen source, sugar content, temperature, pH, surface area, sterilization of the substrate, culture condition and fermentation time was varied to obtain the desired result. The bacterial cellulose films were dried at 50-70 °C in an oven, air-dried or freeze-dried to evaluate the impact of drying technique on the final material. The behavior of the microorganism during fermentation was monitored by sampling and observation. The consumption rate of carbohydrates was analyzed using high performance liquid chromatography (HPLC). The properties of the obtained biofilms were analyzed using thermogravimetric analysis (TGA), tensile testing and determination of cellulose content in the obtained biofilms. Two different sugar concentrations (35 g/l and 70 g/l) and three different caffeine concentrations (0 g/l, 150 g/l and 225 g/l) as nitrogen source were investigated to determine the best condition. A control batch of conventional (black tea and 70 g/l table sugar) Kombucha was used as reference. The highest tensile strength (50 MPa) and thermal stability was observed in the biofilms with the highest yield that had been dried in oven. The biofilms obtained by fermenting apple pomace from the cider industry showed the highest tensile strength and highest thermal stability in comparison to fermenting expired fruit juice. The biofilm obtained by fermenting apple waste(sugar concentration 70 g/l) in combination with sterilizing the substrate without adding any nitrogen source, dried in an oven and purified using 0,1 M NaOH resulted in the highest tensile strength, highest thermal stability and the purest biofilm from a visual aspect. The highest yield was observed in the fermentation of apple pomace (sugar concentration 70 g/l) from the cider industry without sterilization of the initial media with an addition of nitrogen of approximately 450 mg/l). The optimal fermentation period was observed to be 14-15 days, at 25-28 °C under static conditions using a glass vessel with a diameter of 20 cm and an initial pH of 5,5.

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Sjöblom, Arne. "Hälsobokslut! En drivkraft för förändrad verksamhetsstyrning? : En longitudinell studie av tre kommuners försök att minska sjukfrånvaron genom användningen av verksamhetsstyrningsmodeller." Doctoral thesis, Mälardalens högskola, Akademin för hållbar samhälls- och teknikutveckling, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:mdh:diva-10079.

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I början av 2000-talet finansierade regeringen ett projekt, det kommunala hälsobokslutsprojektet, som primärt syftade till att ge erfarenheter och kunskap om olika verksamhetsstyrningsmodellers användbarhet som underlag för det som kallades hälsobokslut. Vidare förväntades projektet ge erfarenheter och kunskap om vilka stödprocesser som var väsentliga för en lyckosam användning av de valda verksamhetsstyrningsmodellerna. Från Näringsdepartementet, som var uppdragsgivare, fanns det även en förväntan att projektet skulle leda till att en gemensam hälsobokslutsmodell skulle kunna användas inom den kommunala sektorn. Underlaget för denna avhandling utgörs av en longitudinell fallstudie där arbetet med hälsobokslutsprojektet har studerats i tre av de kommuner som deltog i projektet. Undersökningen har gjort det möjligt att få fyra forskningsfrågor besvarade: Hur förändrades verksamhetsstyrningen av införandet av hälsobokslut i respektive kommun? Vad initierade denna förändring? Hur genomfördes förändringen av verksamhetsstyrningen? Vad fick förändringen av verksamhetsstyrningen för resultat i de tre kommunerna? Genom att få dessa forskningsfrågor besvarade har det varit möjligt att få kunskap om hur verksamhetsstyrningsmodeller påverkats under en förändringsprocess. Empirin består i huvudsak av fokusgruppsintervjuer vilka har kompletterats med personliga intervjuer och sekundärdata från tre av de kommuner som deltog i hälsobokslutsprojektet. Avhandlingens resultat kan noteras inom fler områden. En organisations syn på sig själv i förhållande till liknande organisationer kan avgöra om ett förändringsarbete kan initieras. Individuella drivkrafter, och speciellt stabiliserande drivkrafter, är viktiga att beakta, och påverka, om ett förändringsarbete ska genomföras. Vidare noteras att institutionella drivkrafter inte enbart kan knytas till existerande strukturer och att individuella drivkrafter inte enbart kan knytas till individers handlingar. Båda typerna av drivkrafter påverkas av och påverka de modaliteter som existerar som förbindelselänk mellan strukturer och handlingar enligt struktureringsteorin. Stödprocesser är viktiga att beakta i anslutning till organisatoriskt lärande och individers handlingar. Särskilt mobiliserande stödprocesser har varit de kommunikations- och motivationsprocesser som synliggjorts med hjälp av de analyser som genomförts.
In the early 2000s the Swedish government financed a health statement project. This project aimed primarily to provide experience and knowledge of the usability of various management control models to function as health statement models. Furthermore, the project was expected to provide experience and knowledge of the supporting processes that was essential for the successful use of the selected management control models. The Ministry of Enterprise, Energy and Communications, which was the principal of the project, expected that the project would lead to the presentation of a common health statement model that could be used within the municipal sector. The basis for this thesis consists of a longitudinal case study in which the health statement project has been studied in three of the municipalities involved in the project. The investigation has made it possible to get four research questions answered: How were the management control systems within the municipalities changed by the introduction of health statements in each municipality? What initiated this change? How was the change in the management control systems achieved? What was the result of the changes of the management control systems within the three municipalities? By answering these research questions it has been possible to gain insight into how management control models have been affected in a change process. The empirical material consists mainly of focus group interviews which have been supplemented by personal interviews and secondary data from three of the municipalities that participated in health statement project. The findings from the research can be observed in several areas. An organization's vision of itself in relation to similar organizations can determine whether a change process can be initiated. Individual forces, and especially stabilizing forces, are important to consider, and influence, if a change program shall be implemented. Institutional forces are linked not only to existing structures and individual drivers are not only linked to individuals' actions. Both types of forces are affected by and affect modalities that exist as interfaces between structures and actions according to the structuring theory. Supporting processes are important to consider in relation to organizational learning and individuals' actions. The communication and motivational processes has been important as mobilizing supporting processes.

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