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Dissertations / Theses on the topic 'Paraloid'

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Published: 10 March 2023

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1

Santos, Maria Margarida de Sousa dos. "Cerâmica Arqueológica, estudo comparativo da eficácia inicial de dois consolidantes – polímero acrílico e silicato de etilo." Master's thesis, Faculdade de Ciências e Tecnologia, 2011. http://hdl.handle.net/10362/7524.

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Dissertação para obtenção do Grau de Mestre em Conservação e Restauro
É frequente, em peças de cerâmica arqueológica, o aparecimento de fenómenos de desagregação. Para a conservação deste material há a necessidade de aplicação de produtos que aumentem a sua coesão e resistência mecânica. Dado existirem poucos trabalhos científicos sobre o desempenho de consolidantes alternativos, a utilizar em cerâmica arqueológica, sentiu-se a necessidade de desenvolver um trabalho laboratorial sobre essa temática. Assim, efectuou-se o estudo comparativo de avaliação da eficácia inicial de dois produtos comerciais, o Tegovakon V® e o Paraloid B-72®, como consolidantes. Foram utilizados provetes (sãos) em cerâmica vermelha cozida a 980 °C. Os consolidantes foram aplicados por imersão total e por pincelagem. A cerâmica foi caracterizada por DRX e os consolidantes por FTIR. A micro-estrutura da cerâmica foi caracterizada, antes e após a consolidação, por MEV-EDE, PM e μ-CT. A eficácia inicial do processo de consolidação foi avaliada através de uma série de ensaios laboratoriais, nomeadamente: porosidade acessível à água, absorção de água por capilaridade, velocidade de propagação de ondas longitudinais, resistência à compressão pontual, ângulo de contacto, tempo de absorção da micro-gota e caracterização colorimétrica. A consolidação é um procedimento que interfere nas propriedades físicas e comportamentais da cerâmica intervencionada. Essas alterações nas propriedades da cerâmica são função do consolidante e do método de aplicação. Nos provetes consolidados, por imersão, com Tegovakon V® verificou-se a redução de 62% da porosidade e 98% da capilaridade, o aumento de 4,8% da resistência mecânica e a alteração de ΔΕ de aproximadamente 7,7. Nos provetes consolidados, por imersão, com Paraloid B-72® verificou-se a redução de 4,5% da porosidade e 87% da capilaridade e o aumento de 4,5% da resistência mecânica. A alteração de ΔΕ, aproximadamente 12, foi superior nos provetes consolidados por pincelagem. Com base nestes resultados podemos afirmar que o consolidante que apresenta melhor desempenho, no que diz respeito à eficácia inicial, é o Tegovakon V® aplicado por imersão.
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2

Watters, George Murray. "Models of parasitism and hyperparasitism on Paralomis spinosissima /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1997. http://wwwlib.umi.com/cr/ucsd/fullcit?p9823698.

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3

Taylor, M. R. G. "Mechanism of action of Rad51 paralogs." Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1458671/.

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Homologous recombination (HR) is an essential DNA break repair mechanism that remains incompletely understood. HR is a complex multistep process initiated by the loading of RAD-51 recombinase as filaments onto single stranded DNA (ssDNA). This structure directly invades an intact homologous duplex, which serves as a template for repair DNA synthesis. Numerous positive regulators of HR have been described, including the Rad51 paralogs, but the mechanism of action of Rad51 paralogs in promoting HR is unknown. In this study, I have characterized the mechanism of action of a novel Rad51 paralog complex, RFS-1/RIP-1, from C. elegans. RFS-1 is a Rad51 paralog required for RAD-51 focus formation at stalled replication forks, indicating an early positive regulatory role in HR. I demonstrate that RFS-1 interacts with a nematode-specific orphan protein, RIP-1. I identify a cryptic Walker B ATPase-like motif within RIP-1, which is functionally important in establishing the RFS-1/RIP-1 interaction interface. rip-1 and rfs-1 mutant animals phenocopy for essentially all phenotypes analysed. Together these data suggest RFS-1/RIP-1 functions as a constitutive complex. I show recombinant RFS-1/RIP-1 can be purified and specifically binds ssDNA but lacks measurable ATPase activity. RFS-1/RIP-1 also strongly stimulates strand invasion activity by RAD-51, consistent with a pro-recombinogenic function in vivo. I define for the first time the mechanism of action underlying the intrinsic ability of Rad51 paralogs to stimulate HR. Using a combination of biochemical and biophysical approaches, notably electrophoretic mobility shift assays, stopped-flow reaction kinetics and nuclease protection assays, I show RFS-1/RIP-1 dramatically alters the properties of RAD-51-ssDNA filaments such that RAD-51 is more stably associated with ssDNA yet the ssDNA is more sensitive to nuclease degradation. RFS-1/RIP-1 exerts these effects primarily downstream of filament formation, ruling out a major role in RAD-51 loading. I propose RFS-1/RIP-1 remodels RAD-51-ssDNA filaments to a conformation poised for pairing with the template duplex and strand invasion.
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4

Tarabay, Yara. "Functional studies of mouse Tex19 paralogs during spermatogenesis." Thesis, Strasbourg, 2013. http://www.theses.fr/2013STRAJ091.

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La spermatogenèse est le processus par lequel les cellules germinales se différencient pour former les spermatozoides. Elle se déroule à l’intérieur des tubes séminifères. Pendant la période embryonnaire, les précurseurs des cellules germinales adultes constituent un pool de cellules appelées cellules germinales primordiales (Primordial Germ Cells, PGCs), qui vont migrer pour aller coloniser les gonades (Durcova-Hills and Capel, 2008; Surani et al., 2008). Au cours de leur migration, les PGCs vont subir une reprogrammation épigénétique de l’ensemble de leur génome, qui leur sera nécessaire pour passer de l’état somatique à l’état de totipotence (Ohinata et al., 2005). Durant cette reprogrammation, l’ADN est massivement démethylé, entrainant l’activation de plusieurs gènes qui sont importants pour le développement des PGCs, mais également l’activation des éléments transposables (ETs) (Hajkova et al., 2008; Sasaki and Matsui, 2008; Surani and Hajkova, 2010). Ces derniers constituent environ 50% du génome des mammifères. Ils sont subdivisés en deux classes et sont connus par leur capacité à être mobilisés dans le génome (Zamudio and Bourc'his, 2010). Cette mobilisation se fait au hasard et constitue ainsi un risque considérable de mutations, qui peuvent provoquer des tumeurs, des pathologies de développement et une infertilité (Zamudio and Bourc'his, 2010). Pour cela, leur expression doit être contrôlée pour maintenir l’intégrité du génome de la lignée germinale. Pour toutes ces raisons, les PGCs ainsi que les cellules germinales en cours de méiose ont développé des stratégies de défenses pour contrôler la mobilisation et l’expression des ETs basées entre autre sur la voie des piwi-interacting RNA (piRNA) (Chuma and Pillai, 2009; Pillai and Chuma, 2012b). Dans le laboratoire du Pr. Stéphane Viville, mes travaux de thèse se sont concentrés sur l’étude d’un gène nommé Tex19 pour Testis Expressed gene chez la souris. Nous avons démontré que ce gène est spécifique des mammifères et est dupliqué chez le rat et la souris en deux paralogues nommés Tex19.1 et Tex19.2. Deux domaines hautement conservés ont été identifiés par alignement multiple des protéines TEX19 et nommés MCP et VPTEL. Ces domaines ne présentent aucune homologie avec des domaines déjà caractérisés, prévenant ainsi toute prédiction de leurs fonctions (Kuntz et al., 2008). L’étude du profil d’expression de Tex19.1 et Tex19.2 a montré que ces deux gènes sont exprimés dans l’ectoderme et les PGCs. Ils sont aussi co-exprimés dans le testicule de l’âge embryonnaire à l’âge adulte. Néanmoins, seul Tex19.1 est exprimé dans les ovaires et le précurseur du placenta appelé cône ectoplacentaire (Celebi et al., 2012). Le knockout (KO) de Tex19.1 provoque une infertilité masculine chez la souris avec un arrêt de la spermatogenèse au stade pachytène, accompagnée d’une surexpression d’un rétrotransposon, MMERVK10C (Ollinger et al., 2008). Récemment, il a été démontré que Tex19.1 joue aussi un rôle dans le développement du placenta (Reichmann et al., 2013). Au cours de mes trois années de thèse, nous avons approfondie l’étude du KO de Tex19.1dans le testicule, les cellules embryonnaires souches (Embryonic Stem Cells, ESCs) et le placenta (Tarabay et al., 2013). Nous avons également étudié le phénotype observé suite au double KO de Tex19.1 et Tex19.2. [...]
We recently characterized two new mammalian specific genes, Tex19.1 and its paralog Tex19.2. Both genes are expressed in pachytene spermatocytes in adult testes. In addition, Tex19.1 is expressed in pluripotent cells (ES, EG, iPS and PGC cells), the inner cell mass of the blastocysts and the placenta. In order to decipher Tex19 functions, we generate three types of knockout (KO): i) KO of Tex19.1 ii) KO of Tex19.2 iii) double KO (DKO) of both genes. All Tex19.1-/- KO animals are growth-retarded and half of them die just after birth. This phenotype is probably linked to placenta defects. Surviving adults Tex19.1-/- KO males display a variable spermatogenesis phenotype, associated with an up-regulation of one endogenous retrovirus, MMERVK10C. Tex19.2 KO mice exhibit a subtle phenotype. Few seminiferous epitheliums are degenerated while the rest appear normal. DKO show a fully penetrant phenotype similar to the most severe Tex19.1-/- phenotype. DKO males exhibit small testes. Despite the presence of spermatogonia and spermatocytes, spermatogenesis is blocked at the pachytene stage. By RNA deep-sequencing on 10 days old DKO and WT testes, prior to histological phenotype, 114 genes are significantly up-regulated and 320 genes significantly down-regulated in the DKO compared to the WT. Gene ontology analyses show that among of these genes, two essential pathways are altered: meiosis and the piRNA pathway. Consistent with that, GST-pulldown and immunoprecipitation experiments demonstrate that MIWI, MILI, MAEL and MVH are partners of TEX19. Considering PIWI proteins function in the silencing of transposable elements through the piRNA pathway, we checked if TEX19 paralogs bind piRNA. By immunoprecipitation using WT and KO testes, we show that both TEX19.1 and TEX19.2 bind small RNA of 30 nucleotides through their VPTEL domain. This study highlights the pivot role of Tex19 paralogs in three essential functions of mammalian life cycle, i.e. pluripotency, placenta-supported in utero growth and fertility. The functional similarities of both paralogs, through the expression control of one endogenous retrovirus and the binding of piRNAs, lead us to propose that Tex19 paralogs are new members of the piRNA pathway
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5

Buffleben, George M. "Interactions of human and drosophila Rad 51 paralogs." Scholarly Commons, 2010. https://scholarlycommons.pacific.edu/uop_etds/751.

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Damage to DNA from a variety of sources can lead to damaged proteins, genomic instability, aneuploidy, and cancer. It is therefore essential to repair DNA damage, and to do so a variety of DNA repair mechanisms have evolved. One of the repair mechanisms, known as homologous recombination (HR) repair, uses an undamaged sister chromatid as a template to make error free repairs to double-strand (ds) DNA breaks. While many proteins are involved in HR, this work focuses on testing the interactions of a subset of these proteins known as the Rad51 paralogs. The goal of this study is to determine if the putative Rad51 paralogs in Drosophila melanogaster are sufficiently conserved as to function in the same manner as their human counterparts. This research is part of a larger project to determine if Drosophila melanogaster is a good model organism for studying HR in humans (Hs). The D. melanogaster Rad51 gene, and its four paralogs Spn D, Spn B, Rad51D, XRCC2 (the last 2 identified by sequence homology), and human hsRad51D and hsXRCC2, were cloned into Invitrogen's TOPO protein expression vector. When induced with IPTG, the resulting fusion proteins contains either aN-terminal Xpress TM epitope or a C-terminal V5 epitope. The fusion proteins were used in immunoprecipitation assays with antibodies against the epitope tags to test for proteinprotein interactions. While many of the assays were inconclusive and are still being optimized, the interaction of the C-terminally tagged dmXRCC2 with theN-terminally tagged hsRad51D gave a positive result. This single interspecies result suggests that homologous recombination is highly conserved between D. melanogaster and humans.
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Seberg, Hannah Elizabeth. "Transcription factor AP2 paralogs in melanocytes and melanoma." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6278.

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During development, neural crest (NC) cells arise from the neural plate border and are further differentiated into multiple cell types, including melanocytes. Each step of this process is controlled by a gene regulatory network (GRN), and disruption of the GRN governing melanocyte differentiation contributes to the pathogenesis of pigmentation disorders and melanoma. While many of the factors within this network have been well studied, the role of Transcription Factor Activating Enhancer-Binding Protein 2 (TFAP2) paralogs has been unclear. TFAP2A and TFAP2C are required for NC induction. Later, TFAP2A is also expressed in melanocytes, and TFAP2A mutations cause pigmentation phenotypes in humans, mice, and zebrafish. Other paralogs with high homology to TFAP2A, particularly TFAP2B in mouse and Tfap2e in zebrafish, also function redundantly with TFAP2A in the melanocyte lineage. Here, we have used ChIP-seq and expression profiling to identify direct transcriptional targets of TFAP2A in melanocytes, which include genes involved in melanin synthesis and melanosome biology. Furthermore, we show that TFAP2A directly regulates many of the same genes as Microphthalmia-associated Transcription Factor (MITF), the “master regulator” of the melanocyte lineage. MITF activity has been described as a rheostat in melanoma, with high levels promoting differentiation and lower levels promoting invasiveness. The overlap between TFAP2A and MITF transcriptional targets in melanocytes suggests that TFAP2A may influence the MITF rheostat, driving it toward the differentiated state. To study the role of other TFAP2 paralogs in NC and melanocytes, we generated zebrafish lines that are double and triple mutant for tfap2a, tfap2c, and tfap2e and confirm genetic compensation among these paralogs. We also demonstrate that melanocyte-specific inhibition of Tfap2 activity by Kctd15 affects differentiation and that Kctd15 may participate in a negative feedback loop regulating Tfap2 expression. In support of a pro-differentiation role for TFAP2A in melanocytes, we show that overexpression of tfap2a in a zebrafish melanoma model significantly delays tumor formation. Together these results indicate that, in addition to its earlier roles in the NC, TFAP2A acts within the melanocyte GRN to directly regulate differentiation genes in parallel with MITF. This, combined with the tumor-suppressor function of TFAP2A in melanoma, implicates TFAP2A and the factors that regulate it as potential targets for melanoma therapies.
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7

Behera, Jyoti, and Aruna Kilaru. "Comparative in Silico Analysis of WRINKLED1 Paralogs in Angiosperms." Digital Commons @ East Tennessee State University, 2019. https://dc.etsu.edu/etsu-works/7723.

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8

Behera, Jyoti, Shina Bhatia, and Aruna Kilaru. "Comparative in Silico Analysis of WRINKLED1 Paralogs in Angiosperms." Digital Commons @ East Tennessee State University, 2019. https://dc.etsu.edu/etsu-works/7724.

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WRINKLED 1(WRI1), a member of AP2/EREBP class of transcription factors regulates carbon allocation between glycolytic and fatty acid biosynthetic pathway. Additionally, among the four WRI1 paralogs in Arabidopsis, WRI3 and 4 but not WRI2, are also able to increase fatty acid content in different tissues. While the role of WRI1 is well established in seeds, the potential or WRI1 or its paralogs as master regulators in oilrich nonseed tissues is poorly understood. Recent transcriptome studies of avocado (Persea americana) mesocarp revealed that the ortholog of WRI2, along with WRI1 and WRI3 was highly expressed during oil accumulation.Through transient expression assays, wefurther demonstrated thatbothPaWRI1 andPaWRI2 can accumulate oil in tobacco leaves. We conducted a comprehensive and comparative in silico analysis of WRI paralogs from a dicot, monocot and a basal angiosperm to identify distinct features associated with function. These data provide insights into the possible evolutionary changes in WRI1 homologs and allow for identification of new targets to enhance oil biosynthesis in diverse tissues.
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9

Merhi, Rawan. "Functional Characterization of parla and parlb Paralogs in Zebrafish." Thesis, Université d'Ottawa / University of Ottawa, 2021. http://hdl.handle.net/10393/42409.

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Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease, featuring motor signs such as tremors, bradykinesia, and impaired gait that are often preceded by nonmotor symptoms such as anxiety/depression and olfactory dysfunction. Interestingly, significant olfactory loss was found to be manifested in the majority of PD patients and may precede motor symptoms by years, and thus can be used for the risk assessment of developing PD in asymptomatic individuals. The main pathological feature of PD is the progressive and irreversible loss of dopaminergic (DA) neurons in the substantia nigra pars compacta of the midbrain. Although the detailed etiology of PD remains unclear, most PD cases were found to be sporadic and can be associated with environmental factors. Only 5–10% of patients result from familial PD. With considerable effort in the past two decades, a number of genes associated with familial PD have been identified and interestingly, many of these genes are involved in regulating and maintaining mitochondrial function. The presenilin-associated rhomboid-like (PARL) gene was found to contribute to mitochondrial morphology and function and was linked to familial Parkinson’s disease (PD). The PARL gene product is a mitochondrial intramembrane cleaving protease that acts on a number of mitochondrial proteins involved in mitochondrial morphology, apoptosis, and mitophagy. To date, functional and genetic studies of PARL have been mainly performed in mammals. However, little is known about PARL function and its role in dopaminergic (DA) neuron development in vertebrates. The zebrafish genome comprises two PARL paralogs: parla and parlb. Here, we show novel information concerning the role of PARL in zebrafish by establishing a loss-of-function mutation in parla and parlb via CRISPR/Cas9- mediated mutagenesis. We examined DA neuron numbers in the adult brain and expression of genes associated with DA neuron function in larvae and adults. We show that loss of parla function, as well as loss of both parla and parlb function result in loss of DA neurons in the olfactory bulb and telencephalon of adult zebrafish brain. Changes in the levels of tyrosine hydroxylase transcripts supported this neuronal loss. Expression of fis1, a gene involved in mitochondrial fission, was increased in parla mutants and in fish with loss of parla and parlb function. Furthermore, we showed that loss of parla and/or parlb function translates into altered locomotion parameters and that loss of parla but not parlb function results in impaired olfaction. Finally, increased susceptibility to neurotoxin exposure was identified in mutants with loss of both parla and parlb function but not with loss of parla or parlb function. These results suggest an evident role for parla in the development and/or maintenance of DA neuron function in zebrafish and confirm the existence of redundant and non-redundant functions for the two paralogs, parla and parlb.
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Murphy, Lita. "Interaction between the ovine Bst-2 paralogs and sheep Betaretroviruses." Thesis, University of Glasgow, 2012. http://theses.gla.ac.uk/3113/.

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There is a delicate evolutionary balance between viruses and their hosts. The host has evolved the intrinsic, innate and adaptive immunity to fight viral infections. However, viruses have acquired several counteracting measures to evade host defences. Ovine Betaretroviruses, including the exogenous and pathogenic Jaagsiekte sheep retrovirus (JSRV) and the highly related endogenous enJSRVs are a unique model system to investigate virus-host interaction over long evolutionary periods. Sheep have co-opted some defective enJSRV loci to (i) counteract infection by exogenous viruses and likely (ii) to cope with the continuous retroviral invasion of their genome. In addition, various genes of the innate and intrinsic immunity of the host have evolved to block viral replication. The work presented in this thesis focuses on the ovine bone marrow stromal cell antigen 2 (Bst-2)/ tetherin, a recently identified cellular restriction factor with a broad antiviral activity, and its interaction with sheep Betaretroviruses. In sheep, the BST-2 gene is duplicated into two paralogs termed oBST-2A and -2B. Studies presented in this thesis show that oBST-2B possesses several biological properties distinct from the paralog oBST-2A and from all the other BST-2 orthologs. oBST-2A prevents the release of JSRV/enJSRV viral particles by ‘tethering’ them at the cell membrane similarly to what observed by human BST-2. On the other hand, oBST-2B, does not reach the cell membrane but remains within the Golgi stacks and the trans-Golgi network. Several lines of evidence obtained in this thesis suggest that oBST-2B reduces significantly Env incorporation into viral particles. Therefore, oBST-2B possesses a unique antiviral activity that complements the classical tethering restriction provided by oBST-2A.
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Faure, André. "Investigating the effect of paralogs on microarray gene-set analysis." Master's thesis, University of Cape Town, 2008. http://hdl.handle.net/11427/4260.

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In order to interpret the results obtained from a microarray experiment, researchers often shift focus from analysis of individual differentially expressed genes to analyses of sets of genes. These gene-set analysis (GSA) methods use previously accumulated biological knowledge from databases such as the Gene Ontology (GO) or KEGG to group genes into sets based on their annotations. They aim to rank these gene sets in a way that reflects their relative importance in the experimental situation in question. The objective is that this approach reveals sets of genes with subtle but coordinated behaviour implicating specific biological processes or pathways in the response under study. Several GSA methods have been proposed and debates have ensued on the statistical foundations of the different approaches and the various hypothesis tests used. In particular, criticism has been directed at methods that rely on a strict cut-off to determine significant genes and those that assume genes are expressed independently. We show that paralogs, which typically have high sequence identity and similar molecular functions also exhibit high correlation in their expression patterns. This, together with the fact that the calculation of gene-set significance by all GSA methods is influenced by the number of genes in the gene set, means that sets with high numbers of paralogs are ranked in a biased manner that reflects more the redundant and dependent nature of para logs than any biological phenomenon.
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12

Sakhawalkar, Neha. "Hub Proteins, Paralogs, and Unknown Proteins in Bacterial Interaction Networks." VCU Scholars Compass, 2017. http://scholarscompass.vcu.edu/etd/4730.

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Proteins are the functional units of cells. However, a major portion of the proteome does not have a known functional annotation. This dissertation explores protein -protein interactions, involving these uncharacterized or unknown function proteins. Initially, protein – protein interactions were tested and analyzed for paralogous proteins in Escherichia coli. To expand this concept further and to get an overview, protein – protein interactions were analyzed using ‘comparative interactomics’ for four pathogenic bacterial species including Escherichia coli, Yersinia pestis, Vibrio cholerae and Staphylococcus aureus. This approach was used to study unknown function protein pairs as well as to focus on uncharacterized hub proteins. The dissertation aims at using protein – protein interactions along with other research data about proteins as a possible approach to narrow down on functions of proteins.
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behera, Jyoti Ranjan, Shina Bhatia, and Aruna Kilaru. "Comparative in silico analysis of WRINKLED 1 paralogs in angiosperms." Digital Commons @ East Tennessee State University, 2019. https://dc.etsu.edu/asrf/2019/schedule/10.

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WRINKLED 1(WRI1), a member of AP2/EREBP class of transcription factors regulates carbon allocation between glycolytic and fatty acid biosynthetic pathway. Additionally, among the four WRI1 paralogs in arabidopsis, WRI3 and 4 but not WRI2, are also able to increase fatty acid content in different tissues. While the role of WRI1 is well established in seeds, the potential or WRI1 or its paralogs as master regulators in oil-rich nonseed tissues is poorly understood. Recent transcriptome studies of avocado (Persea americana) mesocarp revealed that the ortholog of WRI2, along with WRI1 and WRI3 was highly expressed during oil accumulation. Through transient expression assays, we further demonstrated that both PaWRI1 and PaWRI2 can accumulate oil in tobacco leaves. We conducted a comprehensive and comparative in silico analysis of WRI paralogs from a dicot, monocot and a basal angiosperm to identify distinct features associated with function. These data provide insights into the possible evolutionary changes in WRI1 homologs and allow for identification of new targets to enhance oil biosynthesis in diverse tissues.
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14

Holtom, Benjamin J. "A Paralogy Based Strategy for Identifying Regulatory Elements in Mammalian Genomes." Thesis, University of Oxford, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.487255.

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The massive advancements in genomics over recent years has not only provided scope to examine what is shared between the genomes of multiple species but also a unique opportunity to investigate that which is responsible for the differences between species of interest. By comparing the proteomes of two species, certain genes can be' clustered and defined as 'inparalogs' - duplicated genes which are respectively unique to each of the species in question having arisen at a time-point subsequent to the speciation event that separated the two lineages in question. Here I report on several analyses that make use of inparalogous genes identified in the mouse genome with' reference to its close relative the rat. Firstly I describe the implementation of a novel .. ) investigative procedure that identifies regions of intragenomic conservation within the upstream sequences of inparalogous gene clusters and report upon the level of resolution that this approach offers with respect to identifying regulatory elements in genomic sequences. In addition to this study, I also describe an investigation into the density of interspersed repeat elements observed in the neighbourhood of inparalogous mouse genes which revealed a marked enrichment of long interspersed nuclear elements (LINEs), highlighting a possible role for these sequences in the evolution of gene duplicates in the mouse genome.
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Hadzhiev, Yavor. "Phylogenomic and functional analyses of enhancer evolution of sonic hedgehog paralogs." Karlsruhe : Forschungszentrum Karlsruhe, 2007. http://d-nb.info/986521795/34.

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Seman, Zulkifli Ahmad. "A functional study of the Phytophthora infestans Avr3a alleles and paralogs." Thesis, University of Dundee, 2013. https://discovery.dundee.ac.uk/en/studentTheses/0c222074-15ba-43cd-b558-22d741c9df51.

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Late Blight disease, caused by Phytophthora infestans, is the most significant threat to potato production world-wide. Identifying and deploying more durable host resistance to P. infestans is a promising way forward to sustain the production of potato. To achieve this goal, it is important to seek key pathogen components that are essential for infection and which, upon detection by the host, trigger a resistance response. One such potential key pathogen molecule is the RXLR-containing effector Avr3a. Avr3a is highly up-regulated during infection and is also required for P. infestans pathogenicity. To date, all P. infestans isolates studied contain Avr3a alleles E80M103 and/or K80I103. However, a study of Avr3a diversity in the Toluca Valley, Mexico, has identified additional alleles such as K80I103L139, K80I103H133, E80M103H133 and E80M103G124. Functional studies of these alleles were conducted as part of this thesis, which also include the Avr3a paralogs Pex147-2 and Pex147-3. By examining the amino acid changes in relation to the established protein structure, it was determined that all alterations within the Avr3a variants occur at surface exposed amino acids. The change R124G that leads to Avr3aEMG is located in the a-helix loop 3 and the changes Q133H and M139L (Avr3aKIH, Avr3aEMH and Avr3aKIL) locate to a helix 4. Whereas amino acid substitutions in PEX147-3 only affect surface exposed residues, amino acid changes that occur in PEX147-2 involves a ‘buried’ amino acid that is key to structure and stability. Indeed, with the exception of PEX147-2, all Avr3a variants and PEX147-3 are stable upon transient expression in planta and in yeast cells. In terms of host recognition, the protein products of the Avr3a alleles derived from Avr3aKI are recognised by the cognate host resistance gene product R3a whereas those derived from Avr3aEM evade recognition. Similarly, PEX147-3 is recognised by R3a but PEX147-2 is not. In addition to host recognition, virulence functions of these alleles and paralogs have been elucidated. INF1 and AVR4/CF-4 induced cell death responses, which are dependent on the host defence protein CMPG1, are suppressed by Avr3aKI, Avr3aKIH, Avr3aKIL, Avr3aEM and Avr3aEMG but not by Avr3aEMH. All Avr3a variants interact with and stabilise the host E3 ubiquitin ligase CMPG1 to various degrees in planta and this interaction was found to be weakest for Avr3aEMH. Interestingly, PEX147-3, which did not interact with or stabilise CMPG1, could only suppress INF1 cell death but not CF-4/AVR4 elicited responses. A P. infestans isolate, CS12, which was stably silenced for Avr3aEM expression and subsequently shown to be compromised in virulence on the normally susceptible host Nicotiana benthamiana, was used for in planta complementation studies. As shown previously, upon transient expression in planta prior to infection with C12, Avr3aKI and Avr3aEM successfully restore pathogenicity. Similar levels of virulence re-establishment were only observed for Avr3KI derived alleles Avr3aKIH and Avr3aKIL but not for alleles derived from Avr3aEM. This study concludes that Avr3aEM is currently the only form of the essential effector that is fully functional and evades recognition by the known resistance gene product R3a. This functionality is the likely reason that 70% of all studied isolates in the Toluca Valley are homozygous for Avr3aEM. This form of the effector is therefore a suitable target for identifying more durable resistances.
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17

Picchioni, Daria. "Biological function of SLIMP, a mitochondrial seryl-tRNA synthetase paralog." Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/283974.

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Our research group focuses on protein translation and more specifically on the mechanism of transfer RNA (tRNA) aminoacylation by a family of essential and universal enzymes called aminoacyl-tRNA synthetases (aaRSs). aaRS are essential and universal components of the genetic code and their long evolutionary history explains the growing number of functions being discovered for aaRS and for aaRS homologues, beyond their canonical role in gene translation. During the process of constructing a model for human disorders caused by mitochondrial tRNA aminoacylation deficiencies in Drosophila melanogaster in the laboratory has been identified a previously uncharacterized paralog of a seryl-tRNA synthetase (SerRS) named SLIMP. Given the conservation of SLIMP in all available insect genomes, a characterization of the phenotype upon SLIMP depletion was conducted in Drosophila melanogaster. We analyzed the specific effect of SLIMP knockdown in muscles and glia, and we observed a dramatic reduction of the lifespan in both mutants. Interestingly, SLIMP knockdown in the glia causes neurodegeneration visualized as vacuolization in the brain of mutant flies. The sequence identity that SLIMP shares with SerRS allowed to predict that this protein has an identical fold of a seryl-tRNA synthetase. It was previously shown that SLIMP does not posses tRNA aminoacylation activity, but it retains the property to bind mitochondrial tRNASer isoacceptors as a possible reflection of the evolutionary origin of the protein. We characterized the RNA-and DNA-binding property of SLIMP through in vitro and in vivo methodologies. We found that SLIMP binds in vitro all RNA sequences that are encoded in the mitochondrial genome. We suggest that the composition of these sequences (AT enrichment) and the respective folding energy (low .G) are the main determinants for SLIMP binding to RNA. We performed ribonucleoprotein immunoprecipitation assay (RIP) in cells to study SLIMP-RNA interaction in vivo and we showed that SLIMP interact with almost all mitochondrial transcripts. Pull-down experiments combined to mass spectrometry analysis revealed at least two SLIMP protein interactors: SRS2 and LON protease. We demonstrated that SLIMP and SRS2 are interdependent, as the knockdown or the overexpression of one protein reduced or increase respectively the level of the other. We suggest that SLIMP and SRS2 might form a functional complex that is maintained at a given SLIMP:SRS2 ratio. LON was the other identified SLIMP interactor. Our data shows that LON and SRS2 do not interact, but SRS2 might be a substrate of LON proteolytic activity. We also found OPA1 as a potential interactor of LON. OPA1 is a dynamin-like GTPase that is responsible for inner membrane fusion. Our results indicated that the overexpression of LON protease results in an increase of the smaller OPA1 isoforms that correlates with mitochondrial stress. Given the proposed role of SLIMP in RNA binding, we aimed to determine whether SLIMP has an effect on mitochondrial transcription. The results obtained by Northern blot screening of some mitochondrial mRNAs revealed that knockdown of SLIMP significantly reduced the steady-state levels of COX2 and COX3 mRNA, and 12S and 16S rRNAs whereas tRNA levels were found constant. Our results suggest that the defect in transcription upon SLIMP depletion, might be limited to mature mRNAs and may reveal a specific function for SLIMP in the binding and stabilization of processed mitochondrial mRNAs rather than a role in the control of their transcriptional rate or processing. We showed that knockdown of SLIMP affects also cellular growth and cell cycle progression, in fact, upon SLIMP depletion, we observed a dramatic increase of cells in G2/M phase. This result suggests that the mitochondrial role of SLIMP, or a consequence of its function, may be acting as a crosstalk between mitochondria and nuclear transcription factors that regulate cell proliferation. Collectively, the work described in this thesis has contributed to the characterization of a mitochondrial seryl-tRNA synthetase paralog that has acquired an essential function in insects despite a relatively modest divergence from a canonical SerRS structure.
El nostre grup de recerca es centra en la traducció de proteïnes i més específicament en el mecanisme d’aminoacilació dels àcids ribonucleics (ARNs) de transferència (ARNt) per una família d’enzims essencials i universals anomenats aminoacil-ARNt sintetases (aaRSs). Al laboratori s’han analitzat el paper de les aaRSs en la traducció proteica, les seves funcions no canòniques, la seva evolució, així com la seva implicació en malalties humanes. Les aaRSs són components universals i essencials del codi genètic. La seva llarga historia evolutiva explica el creixent número de funcions que s’estan descobrint, tant per a elles com per a proteïnes paràlogues, més enllà del seu paper canònic en traducció genètica. Al laboratori, durant el procés d’obtenció d’un model a Drosophila melanogaster per a l’estudi de malalties humanes degudes a deficiències en l’aminoacilació d’ARNt, es va identificar un nou gen, paràlog de la seril-ARNt sintetasa (SeRS) mitocondrial, anomenat SLIMP. La proteïna SLIMP representa un nou tipus de proteïna similar a aaRS que ha adquirit una funció essencial a insectes, tot i la relativament baixa divergència respecta a una estructura d’SeRS canònica. Tot i amb això, són necessaris estudis addicionals per a identificar el paper biològic de SLIMP. Per aconseguir aquesta fita, s’ha portat a terme el projecte descrit en aquest manuscrit, el qual consisteix en anàlisis addicionals del fenotip resultant de la depleció de SLIMP in vivo, seguits d’estudis detallats de les interaccions moleculars amb àcids nucleics i proteïnes, per acabar amb un estudi dels efectes de SLIMP en la fisiologia cel•lular. En conjunt, els nostres resultats demostren que SLIMP s’uneix específicament a ARNs mitocondrials in vivo i in vitro. SLIMP interacciona amb SerRS2 i les dues són interdependents a nivell d’estabilitat proteica. La depleció de SLIMP o de SerRS2 redueix els nivells basals d’alguns ARNm mitocondrials, però la transcripció d’ARNt és manté inalterada. Es proposa un rol en la regulació post-transcripcional o en l’estabilitat dels ARNm madurs. Hem observat també que la depleció de SLIMP indueix l’aturada del cicle cel•lular en la transició G2/M. Aquests resultats suggereixen que SLIMP, o una conseqüència de la seva funció, podria tenir un paper d’enllaç entre els mitocondris i els factors de transcripció nuclears que regulen la proliferació cel•lular.
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18

Ucanok, Deniz. "Zebrafish Gfi1 paralogs play redundant roles in primitive and definitive haematopoietic development." Thesis, University of Nottingham, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.718855.

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Haematopoietic stem cells (HSCs) are multipotent progenitors that can self-renew and give rise to cells of all blood lineages. In vertebrates, HSCs are specified during embryogenesis from haemogenic endothelial cells (HECs) in the ventral wall of the dorsal aorta (vDA). Previously, a transposon-based gene trap approach was used in zebrafish to identify a transgenic line called qmc551 that expresses a GFP reporter gene in primitive red blood cell (prRBC) progenitors and in HECs of the vDA. In this line, GFP expression is retained as the cells undergo endothelial to haematopoietic transition and seed sites of larval and adult haematopoiesis. In the adult kidney marrow, GFP expression is found in progenitors, lymphocytes and myelomonocytes. The transposon that encodes qmc551:GFP is located in intron 1 of gfilaa, one of three zebrafish gfil paralogs along with gfilab and gfilb. In this study, it was shown that qmc551 :GFP is expressed from a spliced transcript that carries the GFP reading frame downstream of exon 1 of gfilaa, demonstrating that GFP expression is under the control of the gfilaa promoter. Consequently, GFP recapitulates gfilaa expression in development. The presence of the transposon in intron 1 interferes with normal splicing of the gfilaa transcript leading to a loss of gfilaa mRNA in primitive and definitive haematopoietic cells as shown in WISH and qRT-PCR experiments. Gfilaa depletion is compatible with the normal development of prRBC which retain the expression of the paralogue, Gfilb. Morpholino-mediated depletion of Gfilb in homozygous qmc551 embryos blocked prRBC maturation, leading to a severe reduction in haemoglobinization. This phenotype is rescued by Gfilaa in a dose dependent manner as morphant embryos carrying one or two wt copies of gfilaa have increasingly normal levels of haemoglobin. This shows that Gfilaa and Gfilb play essential redundant roles in prRBC maturation. During the onset of definitive haematopoiesis, gfilaa expression is induced downstream of Vegf and Notch signalling and is parallel to Runxl in HECs of the vDA. Its depletion in qmc551 homozygous embryos does not interfere with HSC specification or maintenance which is likely due to the Runxl dependent upregulation of its paralog, gfilab, in the vDA. Interestingly, the loss of Gfilb in qmc551 homozygous embryos leads to the hyperproliferation of haematopoietic stem and progenitor cells (HSPCs) in the caudal haematopoietic tissue (CHT), suggesting that these genes, like their mammalian counterparts, are involved in the maintenance of HSPC quiescence. Together, results presented here show that, in contrast to previously published morphant data, zebrafish Gfil factors and their mammalian homologs play functionally conserved roles during primitive and definitive haematopoiesis.
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19

Jung, Megan. "Functional Analysis of Zebrafish Paralogs, parla and parlb, by CRISPR-Cas9 Mediated Mutagenesis." Thesis, Université d'Ottawa / University of Ottawa, 2017. http://hdl.handle.net/10393/36478.

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Parkinson’s disease is a highly prevalent multifactorial neurodegenerative disorder caused by a complex cascade of interactions between various genetic and environmental factors. Due to this, the majority of cases are termed idiopathic. However, about 10% of PD cases are due to defined genetic factors. Interestingly, both idiopathic and familial cases of PD share mitochondrial dysfunction as a central component in the pathology of the disease. The mitochondrial protease, presenilin-associated rhomboid-like (PARL), is one such Parkinson's disease-linked gene, and is associated with diverse processes including mitochondrial dynamics, active inhibition of unnecessary apoptosis and mitophagy in Drosophila and yeast. Here, I investigated the role of the two zebrafish parl paralogs, parla and parlb, through stable CRISPR-Cas9 mediated mutagenesis. I injected wild type embryos with sgRNAs targeting parla and parlb loci, successfully producing indel mutations in parlb and multi-exon deletions in parla at mutation efficiencies of 74% and 40%, respectively. Through whole mount in situ hybridization experiments against th1, I saw no change in dopaminergic (DA) neuron development displayed by parlb mutants compared to wild types. Injection of parla splice blocking morpholinos into parlb mutants indicates that proper DA neuron development may depend principally on Parla function and loss of both Parla and Parlb function increases larval mortality. These results suggest a negative epistatic relationship between the parl paralogs as seen by the more severe phenotype observed in the loss of both Parla and Parlb function compared to the individual effects.
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20

Ferreira, Simone Nasser Matos. "Especificação formal e implementação de um protótipo para a linguagem paralog." reponame:Repositório Institucional da UFPR, 2010. http://hdl.handle.net/1884/24721.

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21

Hoggarth, Daniel David. "An ecological and economical assessment of the Falkland Islands inshore crab, Paralomis granulosa." Thesis, Imperial College London, 1991. http://hdl.handle.net/10044/1/46822.

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22

Hadzhiev, Yavor [Verfasser]. "Phylogenomic and functional analyses of enhancer evolution of sonic hedgehog paralogs / Yavor Hadzhiev." Karlsruhe : Forschungszentrum Karlsruhe, 2007. http://d-nb.info/986521795/34.

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23

Lin, Haining. "Insights into the rice and Arabidopsis genomes intron fates, paralogs, and lineage-specific genes /." [Ames, Iowa : Iowa State University], 2009.

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24

Kawashita, Silvia Yukie [UNIFESP]. "Homologia, paralogia e função da DGF-1, uma família gênica específica de Trypanosoma cruzi." Universidade Federal de São Paulo (UNIFESP), 2009. http://repositorio.unifesp.br/handle/11600/9695.

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Made available in DSpace on 2015-07-22T20:50:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-08-26
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Conselho Nacional de Pesquisa e Desenvolvimento (CNPq)
World Health Organization (WHO)
Howard Hughes Medical Institute
Proteinas de adesao celular sao essenciais para a invasao celular do hospedeiro mamifero pelo parasita Trypanosoma cruzi. Neste trabalho, nos mostramos que membros de gDispersed Gene Family-1 h, originalmente descrita como uma familia de sequencias nucleares repetitivas presente em varios cromossomos e compondo a terceira maior familia genica especifica deste parasita, contem caracteristicas de adesinas, incluindo quatro segmentos com similaridade significante a sequencia da subunidade ƒÀ7 de integrina humana. Ensaios de biotinilacao da superficie de parasitas e citometria de fluxo com anticorpos anti-DGF-1 indicaram que os membros dessa familia genica sao expressos na superficie das formas tripomastigotas. A genealogia de DGF-1, inferida por algoritmos de rede a partir de dados do Projeto Genoma da linhagem CL Brener de T. cruzi, sugere que essa familia genica pode ser dividida em pelo menos tres grupos com diferentes padroes de distribuicao de seus dominios funcionais. Analisando o perfil de uso dos codons, observou-se que as copias expressas apresentavam um uso preferencial de codons, favorecendo as bases GC, ao passo que copias nao-expressas, incluindo alguns pseudogenes, apresentavam uma distribuicao homogenea no uso de codons. A entropia informacional de Shannon foi utilizada como uma medida da variabilidade de sequencia e revelou que quatro segmentos de alta entropia coincidem com modulos funcionais putativos das proteinas preditas. Contradizendo a ideia de que alta variabilidade esta associada a selecao positiva, os resultados de dois testes distintos de selecao mostraram que posicoes altamente variaveis nao estao necessariamente sob selecao positiva. Nossa hipotese e de que membros de DGF-1 estao associados com a habilidade do T. cruzi se ligar a proteinas da matriz extracelular, como fibronectina e laminina, e especulamos sobre os mecanismos que gerariam diversidade nessas moleculas na ausencia de selecao.
Surface adhesion proteins are essential for Trypanosoma cruzi invasion of mammalian cells. Here we show that Dispersed Gene Family-1 (DGF-1) members, previously identified as nuclear repeated sequences present in several chromosomes and comprising the third largest T. cruzi-specific gene family, have conserved adhesin motifs including four segments with significant similarity to human beta 7 integrin. Flow cytometry and biotinylation assays with anti-DGF-1 antibodies indicated that, as expected, DGF-1 members are expressed on the trypomastigote surface. The DGF-1 genealogy, inferred using T. cruzi Genome Project data and network phylogeny algorithms, suggests that this gene family is separated in at least three groups with differential distribution of functional domains. To identify which members of this gene family are expressed we used a combined approach of RT-PCR and codon usage profiles, showing that expressed members have a very biased codon usage favoring GC whereas non-expressed members have a homogeneous distribution. Shannon information entropy was used to measure sequence variability and revealed four major high entropy segments in the extracellular domain of DGF-1 overlapping with important putative functional modules of the predicted proteins. Testing for natural selection, however, indicated that these high entropy segments were not under positive selection, which contradicts the notion that positive selection is the cause of high variability in specific domains of a protein relative to other less variable regions in the same molecule. We hypothesize that members of the DGF-1 family are associated with the ability of T. cruzi to bind extracellular matrix proteins, such as fibronectin and laminin, and speculate on mechanisms that would be generating the localized diversity in these molecules in the absence of selection.
FAPESP: 03/05317-0
TEDE
BV UNIFESP: Teses e dissertações
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Zhao, Guang Yu. "Collaborative roles of gammaH2AX and the Rad51 paralog Xrcc3 in homologous recombinational repair." Kyoto University, 2007. http://hdl.handle.net/2433/135726.

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Diaz, Smoje Mariana Andrea [Verfasser], and George [Gutachter] Coupland. "Functional characterization of NSE4 paralogs in Arabidopsis thaliana / Mariana Andrea Diaz Smoje ; Gutachter: George Coupland." Köln : Universitäts- und Stadtbibliothek Köln, 2018. http://d-nb.info/1160379386/34.

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Al, Haj Baddar Nour W. "BIOINFORMATIC AND EXPERIMENTAL ANALYSES OF AXOLOTL REGENERATION." UKnowledge, 2019. https://uknowledge.uky.edu/biology_etds/61.

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Salamanders have an extraordinary ability to regenerate appendages after loss or amputation, irrespective of age. My dissertation research explored the possibility that regenerative ability is associated with the evolution of novel, salamander-specific genes. I utilized transcriptional and genomic databases for the axolotl to discover previously unidentified genes, to the exclusion of other vertebrate taxa. Among the genes identified were multiple mmps (Matrix metalloproteases) and a jnk1/mapk8 (c-jun-N-terminal kinase) paralog. MMPs function in extracellular matrix remodeling (ECM) and tissue histolysis, processes that are essential for successful regeneration. Jjnk1/mapk8 plays a pivotal role in regulating transcription in response to cellular stress stimuli, including ROS (reactive oxygen species). Discovery of these novel genes motivated further bioinformatic studies of mmps and wet-lab experiments to characterize JNK and ROS signaling. The paralogy of the newly discovered mmps and orthology of 15 additional mmps was established by analyses of predicted, protein secondary structures and gene phylogeny. A microarray-analysis identified target genes downstream of JNK signaling that are predicted to function in cell proliferation, cellular stress response, and ROS production. These inferences were validated by additional experiments that showed a requirement for NOX (NADPH oxidase) activity, and thus presumably ROS production for successful tail regeneration. In summary, my dissertation identified novel, salamander-specific genes. The functions of these genes suggest that regenerative ability is associated with a diverse extracellular matrix remodeling and/or tissue histolysis response, and also stress-associated signaling pathways. The bioinformatic findings and functional assays that were developed to quantify ROS, cell proliferation, and mitosis will greatly empower the axolotl embryo model for tail regeneration research.
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Amunugama, Ravindra Bandara. "Insights into Regulation of Human RAD51 Nucleoprotein Filament Activity During Homologous Recombination." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1321984760.

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Lukmanova-Kegelman, Daniya Maratovna. "The examination of four trypanosome 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase paralogs by RNA interference." Click here for download, 2010. http://proquest.umi.com.ps2.villanova.edu/pqdweb?did=2013968801&sid=1&Fmt=2&clientId=3260&RQT=309&VName=PQD.

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30

Davies, Roy Conan. "High resolution sequence stratigraphic analysis of paralic coal seams from the Book Cliffs, Eastern Utah, USA." Thesis, University of Liverpool, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414853.

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31

Goyal, Manu Jain [Verfasser], and Felix T. [Akademischer Betreuer] Wieland. "Paralog specific role of COPI pathway in P19 neuronal differentiation / Manu Jain Goyal ; Betreuer: Felix Wieland." Heidelberg : Universitätsbibliothek Heidelberg, 2019. http://d-nb.info/1192373146/34.

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Goyal, Manu Jain Verfasser], and Felix T. [Akademischer Betreuer] [Wieland. "Paralog specific role of COPI pathway in P19 neuronal differentiation / Manu Jain Goyal ; Betreuer: Felix Wieland." Heidelberg : Universitätsbibliothek Heidelberg, 2019. http://d-nb.info/1192373146/34.

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Jyoti, Behera, Bhatia Shina, Rahman Mahbubur, and Aruna Kilaru. "C-Terminal Region of WRI1 Paralogs in Avocado Is a Potential Target for Oil Enhancement in Nonseed Tissues." Digital Commons @ East Tennessee State University, 2019. https://dc.etsu.edu/etsu-works/7725.

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WRINKLED1 (WRI1), a member of AP2/EREBP class of transcription factors regulates carbon allocation between glycolytic and fatty acid biosynthetic pathway in plants. Additionally, among the four WRI1 paralogs in arabidopsis, WRI3 and 4 but not WRI2, are also able to increase fatty acid content in seed tissue. While the role of WRI1 is well established in seeds, the potential role of WRI1 or its paralogs as master regulators in oil-rich nonseed tissues is poorly understood. One of the basal angiosperm avocado (Persea americana) accumulates high oil content in its mesocarp throughout its fruit development. Recent transcriptome studies of avocado mesocarp revealed that the ortholog of WRI2, along with WRI1 and WRI3 were highly expressed throughout the developmental stages. Through transient expression assays, we further demonstrated that both PaWRI1 and PaWRI2 can accumulate oil in tobacco leaves. We conducted a comprehensive and comparative in silico analysis of WRI1, 2 & 3 orthologs from A. thaliana (dicot), Z. mays (monocot) and P. americana (basal angiosperm) to identify distinct features associated with function. Our data shows a difference in C-terminal intrinsically disordered region (IDR) and potential phosphorylation sites in PamWRI1 & 2, which might suggest their possible role in high oil biosynthesis in mesocarp tissue. Also, enrichment with hydrophobic amino acid and depletion of hydrophilic amino acid leads to high random coil secondary structure with PamWRI1 &2 showing the highest percentage among all. Absence of C- terminal PEST motif in PamWRI1 & 2 might result in their stability in nonseed tissue and thus leads to high oil biosynthesis and accumulation. These data suggest that variable C-terminal region among the WRI1 orthologs is a potential target to enhance oil biosynthesis in nonseed tissues.
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Timsina, Brinda Adhikari. "Evolution and Expression of polyketide synthase gene in the lichen-forming fungal families Cladoniaceae and Ramalinaceae." NRC Research Press, 2012. http://hdl.handle.net/1993/23271.

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Fungal polyketides are synthesized by polyketide synthases (PKS) encoded by PKS genes. The function of many PKS genes is unknown and the number of PKS genes exceeds the number of polyketides in many genomes. The lichen-forming fungi, Cladonia and Ramalina have chemical variants separated by habitat suggesting that environmental conditions may influence polyketide production. The goal of this thesis was to examine evolutionary relationships as a framework to investigate PKS gene function in the lichen-forming fungal families Cladoniaceae and Ramalinaceae. A phylogenetic analysis of the genus Ramalina (Chapter 2) using nuclear and mitochondrial ribosomal DNA sequences showed monophyly for seven species and included three species, which were not examined in phylogenies prior to this study. One monophyletic species, R. dilacerata was chosen for further tests of the effect of growing conditions on PKS gene expression (Chapter 3). Growth media containing yeast extracts produced the largest colony diameters and the fewest number of polyketides. A significant negative relationship occurred between colony diameter and number of secondary metabolites. Expression of two types of PKS genes was correlated with pH-level and media conditions that produced larger numbers of secondary products in R. dilacerata. A PKS gene phylogeny was constructed for 12 paralogs detected in members of the C. chlorophaea complex (Chapter 4) and gene selection was inferred using dN/dS estimations. The gene phylogeny provided evidence for independent origins and purifying and positive selection of PKS paralogs. This research provided insight into the evolution of PKS genes in the C. chlorophaea complex and identified potential genes that produce non-reduced polyketides present in C. chlorophaea. This thesis provided evidence for diversification of both morphological and chemical species and monophyly of previously unstudied Ramalina species. This research also supported theories of secondary metabolite synthesis based on growing conditions of R. dilacerata, and it revealed that PKS genes under selection in the Cladonia chlorophaea group provide the lichen with the adaptive capacity to survive under variable conditions. Knowledge of the ecological function of fungal polyketides can be valuable for conservation management and policy makers; and for understanding the potential pharmaceutical roles of these natural products.
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Keen, Daniel E. Rossi. "Hope in America Lyotard and Rorty, Dobson and Obama, and the struggle to maintain hope in postmodern times /." Ohio : Ohio University, 2008. http://www.ohiolink.edu/etd/view.cgi?ohiou1219434292.

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36

Kalefa, Mohamed. "Diagenesis and Sequence Stratigraphy : Predictive Models for Reservoir Quality Evolution of Fluvial and Glaciogenic and Non-glaciogenic, Paralic Deposits." Doctoral thesis, Uppsala University, Department of Earth Sciences, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6179.

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Development of a predictive model for the distribution of diagenetic alterations and related evolution of reservoir quality of sandstones was achieved by integrating the knowledge of diagenesis to sequence stratigraphy. This approach allows a better elucidation of the distribution of eogenetic alterations within sequence stratigraphy, because changes in the relative sea level induce changes to: (i) pore water chemistry, (ii) residence time of sediments under certain near-surface geochemical conditions, (iii) variations in the detrital composition, and (iv) amounts and type of organic matter.

This thesis revealed that eogenetic alterations, which are linked to sequence stratigraphy and have an impact on reservoir quality evolution, include formation of: (i) pseudomatrix and mechanically infiltrated clays in fluvial sandstones of the lowstand and highstand systems tracts (LST and HST, respectively), (ii) kaolinite in tide-dominated deltaic and foreshore-shoreface sandstones of HST, Gilbert-type deltaic sandstones of LST and fluvial deltaic sandstones of LST, (iii) kaolinite and mechanically infiltrated clays in sandstones lying below sequence boundary, (iv) K-feldspar overgrowths in fluvial deltaic LST, (v) glaucony towards the top of fluvial deltaic LST immediately below and at transgressive surface (TS) and in foreshore and shoreface transgressive systems tracts (TST) below parasequence boundaries (PB) and maximum flooding surface (MFS), (vi) framboidal pyrite and extensive cementation by calcite and dolomite in foreshore and shoreface and tide-dominated deltaic TST, and shoreface and tidal flat HST bioclastic-rich arenites particularly in the vicinity of PB, TS and MFS, (vii) pervasive cementation by iron oxide in shoreface-offshore and shoreface sandstones of TST immediately below the MFS, (viii) zeolites and palygroskite in shoreface sandstones of TST and HST, particularly above PB, and (ix) cementation by siderite in Gilbert-type deltaic sandstones of LST, tide-dominated deltaic and foreshore-shoreface sandstones of HST and in tide-dominated deltaic sandstones of TST, particularly at MFS. Moreover, this thesis revealed that the distribution of eogenetic alterations strongly control, and thus provide information for constraining the distribution patterns of mesogenetic alterations, such as illitization of mechanically infiltrated clays and dickitization of kaolinite, and hence of related reservoir quality evolution of sandstones during progressive burial.

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37

Gebühr, Christina [Verfasser]. "Investigations on the ecology of the marine centric diatom Paralia sulcata at Helgoland Roads, North Sea, Germany / Christina Gebühr." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2012. http://d-nb.info/1037011295/34.

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38

Ward, Jordan David. "Insight into homologous recombination at replication blocking lesions through analysis of the C. elegans RAD-51 paralog, RFS-1." Thesis, University College London (University of London), 2008. http://discovery.ucl.ac.uk/1446191/.

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The ability to sense and repair replication blocking DNA damage is a critical task for a cell, as evidenced by the embryonic lethality or cancer predisposition caused by mutation in any of these processes. Recent work has implicated homologous recombinational repair (HRR) as a key player in promoting genome stability in response to stalled replication forks, in addition to its well documented role of in the error-free repair of DNA double-strand breaks (DSBs). Although the five paralogs of the mammalian recombinase, Rad51, have been suggested to be general mediators of HRR, genetic evidence fails to support this hypothesis and their exact roles have remained elusive. Here it is shown that the single C. elegans RAD-51 paralog, RFS-1, plays a specific role in promoting HRR at replication forks blocked by DNA cross-linking agents or camptothecin, but is dispensable for HRR at both meiotic and ionizing radiation-induced DSBs. Strikingly, RFS-1 is also dispensable for RAD-51 loading at forks collapsed by hydroxyurea or by the absence of the S-phase checkpoint, indicating that these lesions may resemble a conventional HRR substrate, rfs-1 mutations suppress mitotic catastrophe in a him-6 topS(RNAi) mutant background and accelerate polyG/C tract deletion in dog-1 mutants, demonstrating that these genetic backgrounds drive the formation of replication blocking lesions, a notion that had been previously suggested but never validated. These data suggest that RFS-1 is not a general HRR mediator, but instead specifically promotes RAD-51 loading at replication fork barriers (RFBs). Yeast two-hybrid (Y2H) screening identified a novel RFS-1-interacting protein, RIP-1, mutants of which phenocopied rfs-1 mutants with respect to embryonic lethality, elevated apoptosis and the RAD-51 loading defect in response to replication fork blocking lesions. Use of Y2H analysis of RFS-1 fragments, followed by RFS-1 peptide arrays, fine-mapped the interaction with RAD-51 to a single 30mer and interaction with RIP-1 to two distinct 30mers. Substitution peptide array analysis of RIP-1 has further refined the interaction surfaces in the case of the RIP-1 binding peptides, two residues are critical for binding in each 30mer. These interaction studies, combined with promising attempts at purification of RFS-1 and RIP-1, open the possibility of detailed biochemical analysis of the role of these proteins in HRR at RFBs. Preliminary work has explored the potential role of RFS-1 in aging and meiosis. Although the IGF-1 pathway transcriptional factor DAF-16 and the HRR factors HIM-6 and RFS-1 impact on spontaneous mutation rate, the mechanism behind this effect on mutation rate and interrelation between these proteins, is currently unclear, rfs-1 and rip-1 mutants both have an increased percentage of male progeny, indicating an elevation in X chromosome non-disjunction during meiosis. Additionally, loss of rfs-1 suppresses RAD-51 accumulation in mus-81 him-9/xpf-l double mutants and evidence suggests that these recombination intermediates arise from meiotic DSBs as opposed to mitotic lesions. Elucidating how RFS-1, and presumably RIP-1, impact on meiotic recombination and whether this role is mechanistically distinct from a role in promoting HRR at RFBs will be an important avenue of future study.
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39

Haq, Imdadul, and Aruna Kilaru. "An Endocannabinoid Catabolic Enzyme Faah and Its Paralogs in an Early Land Plant Reveal Evolutionary and Functional Relationship With Eukaryotic Orthologs." Digital Commons @ East Tennessee State University, 2020. https://dc.etsu.edu/etsu-works/7719.

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Endocannabinoids were known to exist only among Animalia but recent report of their occurrence in early land plants prompted us to study its function and metabolism. In mammals, anandamide, as an endocannabinoid ligand, mediates several neurological and physiological processes, which are terminated by fatty acid amide hydrolase (FAAH). We identified nine orthologs of FAAH in the moss Physcomitrella patens (PpFAAH1 to PpFAAH9) with amidase signature and catalytic triad. The optimal amidase activity for PpFAAH1 was at 37 °C and pH 8.0, with higher specificity to anandamide. Further, the phylogeny and predicted structural analyses of the nine paralogs revealed that PpFAAH1 to PpFAAH4 were closely related to plant FAAH while PpFAAH6 to PpFAAH9 were to the rat FAAH, categorized based on the membrane binding cap, membrane access channel and substrate binding pocket. We also identified that a true ‘dynamic paddle’ that is responsible for tighter regulation of FAAH is recent in vertebrates and absent or not fully emerged in plants and non-vertebrates. These data reveal evolutionary and functional relationship among eukaryotic FAAH orthologs and features that contribute to versatility and tighter regulation of FAAH. Future studies will utilize FAAH mutants of moss to elucidate the role of anandamide in early land plants.
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40

Ottolenghi, Chris. "Délétions du bras court du chromosome 9 et détermination du sexe chez l'homme : gènes de la famille doublesex-mab-3 et leur évolution." Paris 7, 2001. http://www.theses.fr/2001PA077227.

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41

Hlal, Osama Ahmed. "Diagenesis and Reservoir-Quality Evolution of Paralic, Shallow Marine and Fluvio-lacustrine Deposits : Links to Depositional Facies and Sequence Stratigraphy." Doctoral thesis, Uppsala universitet, Berggrundsgeologi, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8986.

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Linking diagenesis to depositional facies and sequence stratigraphy enables better prediction of spatial and temporal distribution of diagenetic alterations, and thus of evolution of reservoir quality in sandstones. This thesis demonstrates that employing this approach is possible because depositional facies and sequence stratigraphy can provide useful information on parameters controlling the near-surface diagenesis, such as changes in: (i) pore-water chemistry, (ii) residence time of sediments under certain geochemical conditions, (iii) detrital composition and proportion of extra- and intra-basinal grains, and (iv) types and amounts of organic matter. Evidence from four case studies enabled the development of conceptual models for distribution of diagenetic alterations and of their impact on evolution of reservoir quality in sandstones deposited in paralic, shallow marine and fluvio-lacustrine environments. Diagenetic alterations that have been constrained within the context of depositional facies and sequence stratigraphy include: (i) carbonate cement (microcrystalline and equant calcite spars dolomite over poikilotopic calcite), pyrite and glaucony are most abundant in progradational braid-delta fan sequences, particularly along the topsets (i.e. maxiumum flooding surface, MFS) and along parasequences boundaries in the deltaic facies of the early highstand systems tract HST, (ii) cementation by coarse spar calcite, dolomite, and the formation of moldic porosity by the dissolution of framework carbonate grains are most abundant in the aggradational fan deltas sequences, (iii) eogenetic kaolinitization of framework silicates is largely restricted to the fluvial and paralic HST sandstones, whereas telogenetic kaolinite may occur in the transgressive systems tract TST sandstones too, (iv) formation of goethite ooids in the TST sediments, (v) formation of glaucony, siderite spherules, and extensive grain-coatings, grain-replacing and ooidal berthierine, more in the TST than in the HST sediments, particularly below the transgressive surface TS and MFS, (vi) cementation by calcite with (δ18OV-PDB = -11.5‰ to -5.4‰) and Fe-dolomite/ankerite (δ18OV-PDB = -10.8‰ to -9.6‰) occurs in both TST and HST sandstones, (vii) syntaxial quartz overgrowths are most extensive in the HST sandstones owing to the presence of incomplete grain-coating berthierine/chlorite, (viii) greater amounts of micro-porosity in the TST sandstones than in the HST sandstones are related to the greater amounts of berthierine/chlorite in the former sandstones, and (ix) chlorite rims around quartz grains retarded the precipitation of quartz overgrowths, and hence prevented a greater loss of primary intergranular porosity in fluvio-lacustrine sandstones. Therefore, constraining the distribution of diagenetic alterations in the contexts of depositional facies and sequence stratigraphic context is a powerful approach to be used in hydrocarbon exploration.
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42

Guo, Yuan [Verfasser]. "Mutations in FT-, TFL1-, and FRI paralogs of rapeseed (Brassica napus L.) and their effect on flowering time and heterosis / Yuan Guo." Kiel : Universitätsbibliothek Kiel, 2015. http://d-nb.info/1070819239/34.

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43

Van, Laar Tricia A. "The behavior of RAD51D and XRCC2 in response to drug induced DNA damage and a continuing study of the fly RAD51 paralogs." Scholarly Commons, 2011. https://scholarlycommons.pacific.edu/uop_etds/764.

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Repair of DNA damage is one of the most important processes undergone in a dividing cell. This is a two-part study undertaken to better understand some of the proteins involved in the sensing and repair of DNA damage in Drosophila melanogaster. The first portion of this experiment followed two Drosophila Rad51 paralogs, dmRad51D and dmXRRC2, and using constructs tagged with GFP, found that they entered the nucleus in response to drug induced DNA damage. Approximately one hour after the induction of DNA damage via bleomycin, dmRad51D and dmXRCC2 entered the nucleus of the Drosophila culture cells, where they remained for the next three to four hours. Following this period in the nucleus, the cells were visualized moving back into the cytosol. The second portion of this experiment was concerned with the four Drosophila Rad51 paralogs (dmRad51 D, dmXRCC2, Spn B, and Spn D) and two paralogs from Homo sapiens (hsRad51 D and dmRad51 D) and their interactions.
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44

Al-Ramadan, Khalid. "Impact of Diagenetic Alterations on Reservoir Quality and Heterogeneity of Paralic and Shallow Marine Sandstones : Links to Depositional Facies and Sequence Stratigraphy." Doctoral thesis, Uppsala University, Department of Earth Sciences, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6928.

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This thesis constrains the distribution of diagenetic alterations and their impact on reservoir-quality and heterogeneity evolution pathways in relation to depositional environments and sequence stratigraphy (systems tracts and key sequence stratigraphic surfaces) of four selected paralic and shallow marine siliciclastic successions.

Typical eogenetic alterations encountered include the dissolution and kaolinitization of framework silicates, which are closely associated to shoreface facies of forced regressive systems tract (FRWST), lowstand systems tract (LST), upper part of the highstand systems tract (HST), and below the sequence boundary (SB). These alterations are attributed to incursion of meteoric water owing to rapid and considerable fall in the relative sea level. Extensive carbonate cementation is most evident below marine and maximum flooding surfaces (MFS), whereas dissolution of carbonate cement and detrital dolomite occur in LST, HST and below SB. Parameters controlling the patterns and texture (microcrystalline vs. poikilotopic) of calcite cement have been constrained within sequence stratigraphic framework of the sandstones. Coarse crystalline to poikilotopic calcite textures of meteoric water origin are thus closely linked to the FRWST, LST and upper part of the HST sandstones and occur mainly as stratabound concretions, whereas microcrystalline calcite, which was precipitated from marine porewaters, occurs as continuously cemented layers in the transgressive systems tract (TST) and lower part of the HST sandstones.

Eogenetic alterations impose, in turn, profound control on the distribution pattern of mesogenetic alterations, and hence on reservoir quality evolution (destruction vs. preservation) pathways of sandstones. Eogenetic infiltrated clays, which occur in the tidal estuarine TST and HST sandstones, have helped preserving porosity in deeply buried sandstone reservoirs (≈ 5 km) through inhibition of extensive cementation by quartz overgrowths. Other essential findings of this thesis include deciphering the control on the formation of authigenic illite and chlorite by ultra-thin (≤ 1 µm thick), grain-coating clay mineral substrate.

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45

Siegler, Benedikt Hermann [Verfasser]. "Protektive Effekte des Adiponektins und der Adiponektin-Paraloge C1q/tumor necrosis factor-alpha-related protein (CTRP) 1-9 im Herz / Benedikt Hermann Siegler." Gießen : Universitätsbibliothek, 2016. http://d-nb.info/1082202541/34.

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46

BARTHOLOMEW, ALEXANDER. "CORRELATION OF HIGH ORDER CYCLES IN THE MARINE-PARALIC TRANSITION OF THE UPPER MIDDLE DEVONIAN (GIVETIAN) MOSCOW FORMATION, EASTERN NEW YORK STATE." University of Cincinnati / OhioLINK, 2002. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1022593337.

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47

Pinne, Marija. "Porins of Borrelia burgdorferi." Doctoral thesis, Umeå : Department of Molecular Biology, Umeå University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-740.

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48

Chalikakis, Konstantinos. "Application de méthodes géophysiques pour la reconnaissance et la protection de ressources en eau dans les milieux karstiques." Paris 6, 2006. https://tel.archives-ouvertes.fr/tel-00193513.

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Les méthodes d’investigation actuellement proposées concernant la reconnaissance et la protection des aquifères en milieu karstique ne font que rarement appel aux mesures géophysiques. Le but des présents travaux de recherche est de démontrer que la combinaison de diverses méthodes géophysiques (TDEM, FDEM, RMP) permet de tirer du sous-sol l’information nécessaire à caractériser, en partie et à différentes échelles spatiales, la géométrie des réservoirs et la distribution des zones de haute perméabilité dans les milieux karstiques. Trois sites expérimentaux, caractéristiques de régions karstiques observées autour du bassin Méditerranéen, ont été choisis. Le site de Loussoi (nord-est du Péloponnèse – Grèce), le site de Poumeyssen (Lot - France) et le site de Paralia Agios Andreas (est du Péloponnèse – Grèce). Des techniques géophysiques adaptées au contexte géologique et aux questions hydrogéologiques ont été sélectionnées et utilisées. Des résultats nouveaux ont été obtenus dans trois domaines : (1) la connaissance géologique des sites étudiés, (2) des développements spécifiques des techniques géophysiques et (3) la définition d’une approche méthodologique d’application des méthodes géophysiques à l’étude des karsts.
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49

Saini, Siddharth. "Role of XRCC3 in Acquisition and Maintenance of Invasiveness through Extracellular Matrix in Breast Cancer Progression." VCU Scholars Compass, 2010. http://scholarscompass.vcu.edu/etd/131.

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Acquisition of invasiveness through extracellular matrix is a crucial characteristic of transition to malignancy in the breast. It was previously shown that Polo-like kinase 1 (PLK-1), a mitotic kinase and genome stability regulator, is involved in acquisition of invasiveness in a breast cell model (HMT-3522 cell line) of pre-invasive to invasive transition. This and other data led to the suggestion that a new class of genes called GISEM for Genome Instability and Extracellular Matrix Invasiveness may exist. Previous lab data show that XRCC3 is found downregulated in progression from preinvasive to invasive phenotype. This led to the hypothesis that XRCC3 may be a negative regulator of invasion. To support this hypothesis, overexpression of XRCC3 in the invasive T4-2 cells downregulated invasion, but also growth. In order to verify the role of XRCC3 in invasiveness, and determine whether it is independent from any effects on growth, we tested the effect of downregulating XRCC3 on the invasiveness of T4-2 cells. Short-term downregulation of XRCC3 using siRNAs produced a significant increase in invasiveness, suggesting a role for XRCC3 as a negative regulator of invasion. During the invasion assay time course, XRCC3 downregulation had no effect on growth or apoptosis supporting the idea that this is a direct effect on invasion and not an artifact of the assay. XRCC3 is one amongst the five members of the RAD51 paralog family, consisting of accessory proteins or RAD51 cofactors (namely RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3) which interact with each other to form complexes (BCDX2, BC, DX2 and CX3) that collaboratively assist RAD51 in homologous recombinational repair (HRR) of DNA double-strand breaks. To see if these interactions are important in terms of invasion, as they have been demonstrated for DNA repair, we studied the effect of XRCC3 downregulation on the levels of RAD51 paralogs. We found lowered levels of RAD51C, but not RAD51B or RAD51D, when XRCC3 was downregulated. Since XRCC3 forms the CX3 complex with RAD51C, we downregulated RAD51C using siRNAs in T4-2 cells and found this to significantly increase invasiveness. Consistent with previous findings by other groups, downregulating RAD51C also lead to decreased levels of XRCC3 in invasive T4-2 cells. These results suggest that the XRCC3-RAD51C interaction is important for invasion as well as the previously studied DNA repair function. In delineating the mechanism by which XRCC3 acts as a negative regulator of invasion, we further questioned if XRCC3 alters secreted factors that are important for the invasiveness of T4-2 cells and tested the effects of conditioned medium (CM) from XRCC3 altered T4-2 cells on parental T4-2 cells’ ability to invade. Results show a significant increase in invading T4-2 cells when suspended in CM from XRCC3 siRNA transfected T4-2 cells, suggesting a direct effect of XRCC3 siRNAs on the ability of T4-2 CM to induce invasiveness in T4-2 cells. Furthermore, we investigated the effects of XRCC3 inhibition on cell surface integrins and focal adhesion kinase (FAK). Indirect immunofluorescence results show increased formation of focal adhesions containing two phosphorylated FAK residues- autophosphorylated FAK-Y397 and FAK-Y861 (previously implicated in increased migration and invasion of tumor cells) in XRCC3 siRNA transfected T4-2 cells. Overall, these results support a new role of XRCC3 in invasion, in addition to its previously reported role in DNA repair. These findings imply that loss of XRCC3 function in cancer progression would upregulate invasion as well as downregulate DNA repair and genome stability. Therefore, stabilization of XRCC3 function could provide a promising therapeutic against breast cancer progression. The dual role of XRCC3 in invasion and DNA repair also renders it an attractive candidate risk biomarker of breast pre-cancer to invasive cancer progression.
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Kutil, Brandi Lynn. "The evolution of LOL, the secondary metabolite gene cluster for insecticidal loline alkaloids in fungal endophytes of grasses." Thesis, [College Station, Tex. : Texas A&M University, 2006. http://hdl.handle.net/1969.1/ETD-TAMU-1122.

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