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1
Garcia, Michael R. "Identification of novel nuclear markers for use in phylogenetic analysis." Tallahassee, Fla. : Florida State University, 2010. http://purl.fcla.edu/fsu/lib/digcoll/undergraduate/honors-theses/2181925.
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Thesis (Honors paper)--Florida State University, 2010.Advisor: Dr. Gavin J.P. Naylor, Florida State University, College of Arts and Sciences, Dept. of Biology. Includes bibliographical references.
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Ribeiro, Maria Margarida. "Genetics of Pinus pinaster Aiton with cytoplasmic and nuclear markers /." Umeå : Swedish Univ. of Agricultural Sciences (Sveriges lantbruksuniv.), 2001. http://epsilon.slu.se/avh/2001/91-576-6061-1.pdf.
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Jeyapalan, Jennie Niroshinie. "Comparison of nuclear and mitochondrial DNA markers for meat authentication." Thesis, University of Nottingham, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.401575.
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Silva, E. P. da. "Population genetic studies of the mussel Mytilus using nuclear DNA markers." Thesis, Swansea University, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.639035.
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The genetics of the mussel Mytilus is one of the most extensively studied among the marine invertebrates. This work is concerned with the use of nuclear DNA polymorphisms to study aspects of Mytilus population genetics. Sixteen populations of three species, M. edulis, M. galloprovincialis and M. trossulus were studied for 6 nDNA markers. SSCP analysis was used to enhance the variability in the N118 anonymous scnDNA region, a PCR fragment which previously showed little RFLP variation, and in a second PCR product from a nrDNA internal transcribed spacer region. In the first case, the number of alleles increased from 4 to 7 and the FST estimate from 0.0072 to 0.0096. In the second case, four alleles were resolved and a statistically significant FST value of 0.08 was revealed. Also, primers for an intron of myosin heavy chain was developed and fifteen alleles were resolved. Three of the alleles are M. trossulus specific, but the others show significant frequency differences among different species and even among populations in the same species. Analysis of the nuclear DNA population structure in M. edulis showed statistical significant levels of geographic variation, and when compared with allozymes revealed significant differences between the two sets of markers. This result is consistent with the operation of balancing selection on allozymes. Moreover, the use of the Ewens-Watterson homozygosity test revealed for the nDNA polymorphism a departure from a strictly neutral model, indicating that assumptions about the neutrality of a DNA polymorphisms could also be under suspicion. Evolutionary relationships between the three mussel species using nDNA markers are in line with morphological and allozymes studies, which show M. edulis as more closely related to M. galloprovincialis than to M. trossulus. However, a much higher level of differentiation than previously reported was found between the three taxa.
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López, Pablo Carlos. "Development of a new automated method for the quantification of nuclear immunohistochemical markers." Doctoral thesis, Universitat Rovira i Virgili, 2010. http://hdl.handle.net/10803/8893.
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Antecedentes: La evaluación de marcadores inmunohistoquímicos se realiza con fines diagnósticos, terapéuticos e investigadores de forma manual. La utilización del análisis informatizado de imágenes digitales para evaluar estos marcadores aún no es suficientemente eficaz. Objetivos: Diseñar un nuevo procedimiento informatizado para cuantificar marcadores inmunohistoquímicos nucleares y evaluar los efectos de la compresión de imágenes.
Métodos: El procedimiento desarrollado consta de diferentes etapas, donde se evalúan diferentes marcadores immunohistoquímicos utilizados en cáncer de mama y en linfoma.
Resultados: El análisis estadístico demostró una gran validez del método automatizado. La redondez fue el único parámetro morfológico afectado por la compresión. Unos factores correctores fueron desarrollados para corregir esta afectación y la variabilidad en la cuantificación producida por esta afectación.
Conclusiones: Este nuevo procedimiento automatizado es un método objetivo, más rápido y reproducible que tiene un excelente nivel de precisión, incluso con imágenes digitales de elevada complejidad y también en imágenes comprimidas.
Background: The evaluation of immunohistochemical markers is carried out manually for diagnostic, therapeutic and research purposes. The use of a computerized digital image analysis to evaluate these markers is not sufficiently effective yet.
Objectives: To design a new computerized procedure to quantify nuclear immunohistochemical markers and evaluate the effects of image compression.
Methods: The procedure developed consists of several stages which evaluate different immunohistochemical markers used in breast cancer and lymphoma.
Results: Statistical analysis demonstrated a high validity of the automated method. The roundness was the only morphological parameter affected by compression. Some correction factors were developed to correct this disorder and the variability in the measurement caused by this disorder.
Conclusions: This new automated process is objective, faster and it has also an excellent level of accuracy, even with highly complex digital images and compressed images.
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Gostel, Morgan. "Evolutionary relationships in Afro-Malagasy Schefflera (Araliaceae) based on nuclear and plastid markers." VCU Scholars Compass, 2010. http://scholarscompass.vcu.edu/etd/122.
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The genus Schefflera is the largest in Araliaceae, with approximately 900 species. Recent studies have shown that Schefflera is polyphyletic and represents no fewer than five distinct clades, each corresponding to a specific geographic region including Asia, continental Africa and Madagascar, Melanesia, the Neotropics, and a small clade distributed throughout several islands in the insular Pacific Ocean. The Afro-Malagasy clade contains nearly 50 species distributed throughout tropical, sub-Saharan Africa, Madagascar, the Comoros, and the Seychelles islands. Previous studies have suggested that this group is monophyletic, identifying two smaller subclades within Afro-Malagasy Schefflera corresponding roughly to informal groups identified as “Meiopanax” and “Sciodaphyllum” on the basis of morphology. Using sequence data from nuclear rDNA spacers and plastid markers derived from 32 of the 48 currently circumscribed species of Afro-Malagasy Schefflera, this study tested the monophyly of Afro-Malagasy Schefflera and of each of its two proposed subclades. Trees based on this molecular data were used to examine patterns of morphological evolution and biogeography among species in the clade. Results support the monophyly of Afro-Malagasy Schefflera and both subclades, which correspond closely to “Meiopanax” and “Sciodaphyllum” which are herein referred to as Neocussonia and Astropanax, respectively. Additional interspecific relationships were examined, which provides evidence for hybridization among several species. Schefflera myriantha, the most widely distributed species of Afro-Malagasy Schefflera, is paraphyletic with respect to two other species, S. humblotiana and S. monophylla. Many morphological features historically used to distinguish species of Afro-Malagasy Schefflera appear to be evolutionarily labile, with a history of gains and losses (e.g., reduction in leaflet number, which occurs independently in both subclades). Biogeographic analyses suggest an African ancestry for the entire Afro-Malagasy Schefflera clade, and for both subclades, with two independent divergence events to Madagascar.
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Reichow, Denise. "Microsatellites as nuclear markers for population studies in the squid Loligo opalescens (Berry, 1911)." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0009/NQ52713.pdf.
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Valdman, Alexander. "Molecular genetic markers of prostate cancer development /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-618-9/.
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Oh, Sun Yeong. "Phylogenetic Relationships of Cottids (Pisces: Cottidae) in Upper Snake River Basin of Western North America." BYU ScholarsArchive, 2016. https://scholarsarchive.byu.edu/etd/6228.
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Freshwater sculpins (Cottus) are common throughout temperate regions of the Northern Hemisphere. Their broad distribution in the Western North America makes them a good model for understanding phylogeographic relationships among western fishes. Within much of the interior west three lineages, C. bairdii, C. confusus, and the C. beldingii complex, are most prevalent. The distribution of these three overlap in the Snake River Basin. All occur below Shoshone Falls on the Snake River. However, only two currently reside in the Upper Snake River above the falls. An exception are the Lost River streams of central Idaho. While these streams are technically part of the Upper Snake River Basin, they do not directly connect with the Snake River. Preliminary studies with a single mitochondrial DNA (mtDNA) gene suggested multiple pathways for Cottus introduction into the Lost River stream complex. Here, three mitochondrial and five nuclear genes were examined to investigate the phylogenetic relationships of these three lineages. Sequences were obtained from 71 different populations in the Lost River streams and surrounding basins. Maximum Likelihood (ML) phylogenies were constructed using these data. Our data indicate that relationships among populations within these species are complex and that no single invasion into the Lost River streams and surrounding regions can account for the phylogenetic signals detected. Instead, it appears that multiple invasions in an evolving landscape played a significant role in the modern distribution of species in this region.
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Irons, Sarah L. "Production, characterisation and use of fluorescent markers in the study of plant nuclear envelope dynamics." Thesis, Oxford Brookes University, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.400355.
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Soto-Calderon, Ivan D. "Evolution of Nuclear Integrations of the Mitochondrial Genome in Great Apes and their Potential as Molecular Markers." ScholarWorks@UNO, 2012. http://scholarworks.uno.edu/td/1510.
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The mitochondrial control region (MCR) has played an important role as a population genetic marker in many taxa but sequencing of complete eukaryotic genomes has revealed that nuclear integrations of mitochondrial DNA (numts) are abundant and widespread across many taxa. If left undetected, numts can inflate mitochondrial diversity and mislead interpretation of phylogenetic relationships. Comparative analyses of complete genomes in humans, orangutans and chimpanzees, and preliminary studies in gorillas have revealed high numt prevalence in great apes, but rigorous comparative analyses across taxa have been lacking.
The present study aimed to systematically compare the evolutionary dynamics of MCR numts in great apes. Firstly, an inventory numts derived from the region containing the MCR subdomains was carried out by genomic BLAST searches. Secondly, presence/absence of each candidate numt was determined in great ape taxa to estimate numt insertion rate. Thirdly, alternative mechanisms of numt insertion, either through direct mitochondrial integration or post-insertional duplications, were also assessed. Fourthly, the effect of nuclear and mitochondrial environment on patterns of nucleotide composition and substitution was assessed through sequence comparisons of nuclear and mitochondrial paralogous sequences. Finally, numts in the gorilla genome were identified through two experimental methods and their use as polymorphic genetic markers was then evaluated in a sample of captive gorillas from U.S. zoos.
A deficit of MCR numts covering two particular mitochondrial subdomains was detected in all three apes examined, and is largely attributed to rapid loss of mitochondrial and nuclear sequence identity in the mitochondrial genome. Insertion rates have varied during the great ape evolution and exhibit substantial differences even between related taxa. The most likely mechanism of numt insertion is direct mitochondrial integration through Non-Homologous-End-Joining Repair. Transition/transversion ratios differed significantly between both mitochondrial and nuclear sequences and between numts from coding and non-coding mitochondrial regions. A previously documented upward bias in the GC content of the primate mitochondrial genome was confirmed and the extent of this bias relative to the corresponding numt sequences increased with numt age. Five gorilla-specific numts were isolated, including three exhibiting insertional polymorphisms that will be used in future population genetic studies in free-range gorilla.
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Okumura, Leah M. "Germ cell nuclear factor is not required for the down-regulation of pluripotency markers in fetal ovarian germ cells." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/77781.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2012.Cataloged from PDF version of thesis.
Includes bibliographical references.
In mouse, germ cells retain expression of the pluripotency markers Oct4 and Nanog longer than any other cells in the body. While somatic cells repress these markers during gastrulation, female germ cells continue to express them until around the time of meiotic initiation. It is not yet clear why pluripotency markers are downregulated with this particular timing, nor is it understood what factors are involved in their repression. I have examined in fetal ovarian germ cells the expression and function of Gcnf (germ cell nuclear factor), an orphan nuclear receptor known to regulate both Oct4 and Nanog in gastrulating embryos. I have found that Gcnf is expressed in a female germ-cell-specific manner at the time when Oct4 and Nanog are down-regulated there. Gcnf mutants in which the ligand binding domain is disrupted display defects after gastrulation comparable to those observed in Gcnf-null mutants and those lacking the DNA binding domain. In contrast, the germ cells Gcnfligand binding domain mutants show no failure in repression of pluripotency markers, and other aspects of female germ cell development appear normal as well. Thus, it appears that the ligand binding domain of GCNF is not required for fetal ovarian germ cell development.
by Leah M. Okumura.
Ph.D.
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Gonzalez, Malinda Wallentine. "Phylogenetic relationships of forest spiny pocket mice (Genus Heteromys) inferred from mitochondrial and nuclear markers with implications for species boundaries /." Diss., CLICK HERE for online access, 2005. http://contentdm.lib.byu.edu/ETD/image/etd777.pdf.
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Gonzalez, Malinda Wallentine. "Phylogenetic relationship of forest spiny pocket mice (Genus Heteromys) inferred from mitochondrial and nuclear markers with implications for species boundaries." BYU ScholarsArchive, 2005. https://scholarsarchive.byu.edu/etd/263.
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I constructed a best estimate phylogeny based on congruence of multiple data sources. In recent years molecular data has been used both to construct phylogenies of taxonomic groups and to aid in the delimitation of new species. I generated and analyzed sequence data for forest spiny pocket mice (Genus Heteromys) for the mitochondrial gene cyt b (1143 bp) and two nuclear gene segments MYH2 (252 bp) and EN2 (189 bp). I used maximum parsimony and Bayesian analyses to infer relationships among species and to provide a framework for using a species delimitation method to investigate the possibility of multiple species within the widespread Heteromys desmarestianus. I found several well-supported lineages within the H.desmarestianus complex, including H. goldmani and H. oresterus. Incorporating karyotype and allozyme data from earlier studies, I found sufficient supporting evidence to justify maintaining H. goldmani and H. oresterus as species as well as identifying four lineages as candidate species. I present a revised taxonomic arrangement within the genus; the subgenus Heteromys should be divided into three species groups: anomalus (H. anomalus and H. australis), gaumeri (H. gaumeri), and desmarestianus (H. desmarestianus, H. goldmani, H. oresterus, and the four candidate species).
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Ingram, Colleen Marie. "The evolution of nuclear microsatellite DNA markers and their flanking regions using reciprocal comparisons within the African mole-rats (Rodentia: Bathyergidae)." Texas A&M University, 2005. http://hdl.handle.net/1969.1/4370.
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Microsatellites are repetitive DNA characterized by tandem repeats of short
motifs (2 â 5 bp). High mutation rates make them ideal for population level studies.
Microsatellite allele genesis is generally attributed to strand slippage, and it is assumed
that alleles are caused only by changes in repeat number. Most analyses are limited to
alleles (electromorphs) scored by mobility only, and models of evolution rarely account
for homoplasy in allele length. Additionally, insertion/deletion events (indels) in the
flanking region or interruptions in the repeat can obfuscate the accuracy of genotyping.
Many investigators use microsatellites, designed for a focal species, to screen for
genetic variation in non-focal species. Comparative studies have shown different
mutation rates of microsatellites in different species, and even individuals. Recent
studies have used reciprocal comparisons to assess the level of polymorphism of
microsatellites between pairs of taxa.
In this study, I investigated the evolution of microsatellites within a phylogenetic
context, using comparisons within the rodent family Bathyergidae. Bathyergidae
represents a monophyletic group endemic to sub-Saharan Africa and relationships are well supported by morphological and molecular data. Using mitochondrial and nuclear
DNA, a robust phylogeny was generated for the Bathyergidae. From my results, I
proposed the new genus, Coetomys.
I designed species-specific genotyping and microsatellite flanking sequence
(MFS) primers for each genus. Sequencing of the MFS provided direct evidence of the
evolutionary dynamics of the repeat motifs and their flanking sequence, including
rampant electromorphic homoplasy, null alleles, and indels. This adds to the growing
body of evidence regarding problems with genotype scores from fragment analysis. A
number of the loci isolated were linked with repetitive elements (LTRs and SINEs),
characterized as robust phylogenetic characters. Results suggest that cryptic variation in
microsatellite loci are not trivial and should be assessed in all studies.
The phylogenetic utility of the nucleotide variation of the MFS was compared to
the well-resolved relationships of this family based on the 12S/TTR phylogeny.
Variation observed in MFS generated robust phylogenies, congruent with results from
12S/TTR. Finally, a number of the indels within the MFS provided a suite of suitable
phylogenetic characters.
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Laitakari, J. (Jaakko). "Computer-assisted quantitative image analysis of cell proliferation, angiogenesis and stromal markers in experimental and laryngeal tumor development." Doctoral thesis, University of Oulu, 2003. http://urn.fi/urn:isbn:9514269497.
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Abstract
Automated quantitative computer-assisted morphometric analysis of immunohistochemical expression of markers of neoplastic development and progression in experimentally induced and in human neoplasms showed very high sensitivity and reproducibility, allowing analysis of large numbers of cell and tissue components. Totals of 26 million pixels, 25,000 cells and 1500 vessels were examined, with a sensitivity exceeding 99% and reproducibility exceeding 99%.
The total expression of proliferating cell nuclear antigen (PCNA) and p53 increased consistently during 7H-dibenz[c, g] carbazole (DBC)-induced formation of dysplasias and squamous cell carcinomas (SCC:s) in hamster lung. In dysplasia, nuclear size and PCNA staining intensity increased; in SCC:s nuclear size decreased. In a retrospective study on archival material of human laryngeal squamous cell carcinomas, the occurrence and location of PCNA-positive cells were specifically related to the degree of differentiation. In SCC:s nuclear size decreased, while shape alterations and PCNA staining intensity increased in relation to degree of malignancy.
In DBC-induced respiratory carcinogenesis increased collagen matrix synthesis occurred prior to neoplasm development. Among squamous cell carcinomas, in well-differentiated tumors, collagen deposition increased, as did fiber size, in moderately differentiated tumors collagen synthesis and the deposition of new collagen decreased. The increase in transforming growth factor beta expression in differentiated cells and in the matrix was isoform-specific.
Increased angiogenesis in laryngeal tumor development occurred in preneoplastic states and in SCC: s, inversely related to the degree of differentiation. In well-differentiated neoplasms the vessels were lying in the direction of the BM, in moderately differentiated neoplasms vessels were lying in the direction of tumor invasion and in poorly differentiated neoplasms irregular, partly abnormal vessels intermixed with tumor cells. Small regular vessels predominated in benign conditions and large, irregular vessels in malignant conditions.
Experimental models provided the advantage of examining homogenous, well-characterized neoplasm progression without interfering with the process. Morphometric methods provided detailed information on large numbers of cells, useful for studies of tumor behavior and with potential clinical applications.
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Sepulveda, Villet Osvaldo Jhonatan. "Population Genetic Structure and Biogeographic Patterns in the Yellow Perch Perca flavescens: An Analysis of Mitochondrial and Nuclear DNA Markers." University of Toledo / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1321458463.
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Hallow, Karen Melissa. "Relationships between Mechanical Stress and Markers of Inflammation in Diseased Human Coronary Arteries." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/16211.
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Rupture of atherosclerotic plaque is one of the primary causes of death due to cardiovascular disease. The factors directing plaque progression to instability are poorly understood. It is well-known that arteries respond to changes in mechanical stress by remodeling, and that remodeling is mediated by the inflammatory response. Studies have shown that both mechanical stress and markers of inflammation are increased in the fibrous cap and shoulder regions of plaque, where rupture most often occurs. In this study we hypothesized that there are spatial relationships between the local mechanical environment and expression of markers of inflammation in atherosclerosis, and that these relationships are plaque-progression dependent. To test these hypotheses, we analyzed cross-sections at intervals along the length of human coronary atherosclerotic arteries. For each cross-section, a heterogeneous finite element model was developed to determine the spatial distribution of stress. In addition, novel techniques for quantifying inflammatory markers at high spatial resolution were used to determine the distributions of inflammatory markers. The distributions of stress and five markers of inflammation activated NF-kB, macrophages, MMP-1, nitrotyrosine, and microvessels - were then compared to determine whether spatial relationships exists.
We demonstrated that the probability of activated NF-kB expression increases monotonically with increasing stress in all stages of plaque progression. This indicates that the relationship between mechanical stress and NF-kB activation is a player throughout the disease process. We found that the relationship between mechanical stress and macrophages is highly dependent on the state of plaque progression. In intermediate stages of progression macrophages increase with moderate stress but drop off again at very high stresses, while in the advanced stage macrophages continue to increase monotonically with stress. We found that MMP1 increases with stress in stages of progression where active remodeling is occurring, but decreases with stress in mature stable plaque. We found no relationship between mechanical stress and nitrotyrosine expression or microvessels. Taken together, these results support the role of mechanical stress in instigating and maintaining the inflammatory response, and help explain how mechanical input is able to direct the complex biological changes involved in remodeling.
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Crosara, Alessia. "Inference of Raja miraletus population structure using mitochondrial and nuclear DNA: comparing the resolution power of molecular markers in exploring species and population boundaries." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amslaurea.unibo.it/9764/.
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This study focused on the role of oceanographic discontinuities and the presence of transitional areas in shaping the population structure and the phylogeography of the Raja miraletus species complex, coupled with the test of the effective occurrence of past speciation events.
The comparisons between the Atlantic African and the North-Eastern Atlantic-Mediterranean geographic populations were unravelled using both Cytochrome Oxidase I and eight microsatellite loci.
This approach guaranteed a robust dataset for the identification of a speciation event between the Atlantic African clade, corresponding to the ex Raja ocellifera nominal species, and the NE Atlantic-Mediterranean R. miraletus clade. As a matter of fact, the origin of the Atlantic Africa and the NE Atlantic-Mediterranean deep split dated about 11.74MYA and was likely due to the synergic influence currents and two upwelling areas crossing the Western African Waters.
Within the Mediterranean Sea, particular attention was also paid to the transitional area represented by Adventura and Maltese Bank, that might have contributed in sustaining the connectivity of the Western and the Eastern Mediterranean geographical populations.
Furthermore, the geology of the easternmost part of Sicily and the geo-morphological depression of the Calabrian Arc could have driven the differentiation of the Eastern Mediterranean Sea. Although bathymetric and oceanographic discontinuity could represent barriers to dispersal and migration between Eastern and Western Mediterranean samples, a clear and complete genetic separation among them was not detected. Results produced by this work identified a speciation event defining Raja ocellifera and R. miraletus as two different species, and describing the R. miraletus species complex as the most ancient cryptic speciation event in the family Rajidae, representing another example of how strictly connected the environment, the behavioural habits and the evolutionary and ecologic drivers are.
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Montemagno, Christopher. "Développement de radiotraceurs pour l'imagerie phénotypique des cancers du sein métastatiques." Thesis, Université Grenoble Alpes (ComUE), 2018. http://www.theses.fr/2018GREAS039/document.
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Le cancer du sein est la première cause de cancer chez la femme. Au moment du diagnostic, 30 % des patientes présente une maladie métastatique avec atteinte ganglionnaire loco-régionale ou d’organes à distance. De plus, 20 % des femmes diagnostiquées sans métastases récidiveront dans les 5 ans. Les métastases sont traitées par chimiothérapie ou thérapie ciblée, en fonction des résultats histologiques du site primitif. Cependant, 20 à 45 % des métastases ont un phénotype différent de celui du site primitif. Pouvoir phénotyper les différentes métastases permettrait de traiter les patientes plus efficacement, en accord avec les caractéristiques moléculaires de ces lésions. Toutes les métastases n’étant pas accessibles à la biopsie, un phénotypage en imagerie moléculaire serait donc d’un grand intérêt. La médecine nucléaire est, à ce jour, la seule technique d’imagerie moléculaire disponible en pratique clinique. Dans le cadre de cette thèse, l’objectif a été de réaliser l’imagerie phénotypique des tumeurs métastatiques du sein en ciblant la mésothéline et VCAM-1 dans des modèles pré-cliniques de cancer du sein. La première partie de ce travail a été consacrée à l’évaluation pré-clinique de nanobodies ciblant la mésothéline, une glycoprotéine à ancre GPI très faiblement exprimée à l’état physiologique mais surexprimée dans de nombreux cancers dont le cancer du sein. De nombreuses thérapies ciblant la mésothéline sont actuellement en cours d’essais cliniques. Un agent d’imagerie ciblant cette protéine permettrait d’identifier les patientes susceptibles d’en bénéficier. Au cours de ces travaux de thèse, le nanobody 99mTc-A1 a été entièrement validé pour l’imagerie des tumeurs exprimant la mésothéline. La seconde partie de ces travaux de thèse a été consacrée à l’imagerie phénotypique des tumeurs du sein exprimant VCAM-1, protéine impliquée dans la dissémination métastatique pulmonaire et osseuse. Un agent d’imagerie ciblant VCAM-1 pourrait servir d’outil pour la caractérisation de l’agressivité de la maladie métastatique. Au cours de ces travaux, l’utilisation d’un nanobody, 99mTc-cAbVCAM1-5, a été validée pour l’imagerie des tumeurs du sein exprimant VCAM-1Breast cancer is the leading cause of cancer among women. At the time of diagnosis, 30 % of patients have developed a metastatic disease either with regional lymph node colonization or distant organs colonization. Metastatic breast cancers are treated by chemotherapy or targeted therapy, according to histological results of primary site. However, 20 to 45 % of metastases have a different phenotype from the primary tumor. Getting access to metastases phenotype would therefore allow treating patients more accurately, in accordance with molecular characteristics of these lesions. Because metastases are not always accessible to biopsy, the use of molecular imaging could be of great interest. Nuclear medicine is the only molecular imaging technic available in clinical practice. The objective of this thesis was to perform the phenotypic imaging of metastatic breast cancer by targeting mesothelin and VCAM-1. The first part of this work was dedicated to the preclinical evaluation of mesothelin-targeting nanobodies. Mesothelin is a GPI-anchored membran protein. While its expression is restricted to a mesothelial cells in normal conditions, mesothelin is overexpressed in several cancers, including breast cancer. Several mesothelin-targeting therapies are currently ongoing clinical transfer. Identifying mesothelin-expressing metastases would allow to select patients who could benefit from those therapies. During this thesis, the nanobody-derived radiotracer 99mTc-A1 has been fully validated for the imaging of mesothelin expressing tumors. The second part of this work was dedicated to the nuclear imaging of VCAM-1 expressing breast cancer lesions. VCAM-1 is a membrane-associated protein involved in the metastatic spread of breast tumor cells. An imaging agent targeting at VCAM-1 could be a suitable tool to evaluate the role of VCAM-1 as a marker of tumor aggressiveness. In the present study, the nanobody 99mTc-cAbVCAM1-5 has been validated for the imaging of VCAM-1 expression in breast cancer
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Lopes, Estela Gallucci. "Atributos diagnósticos da reação em cadeia pela polimerase com oligonucleotídeos iniciadores direcionados a genoma de cinetoplasto e nuclear de Leishmania spp." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-06122011-103958/.
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A técnica de PCR pode ser empregada para a detecção e identificação de agentes patogênicos e, tem por isso grande aplicabilidade em estudos de epidemiologia molecular. Particularmente no que se refere às infecções por Leishmania spp., a detecção do seu agente é de suma importância em animais sorologicamente positivos, no caso de inquéritos para a detecção direta em vetores e em animais de vida livre, cujo anti-soro para provas sorodiagnósticas, não são disponíveis. A PCR ainda pode oferecer o recurso de identificação molecular do agente em pesquisa, quando marcadores filogeneticamente informativos são amplificados e seqüenciados. Neste sentido, foi realizado o presente trabalho, cujo objetivo foi avaliar o desempenho analítico e diagnóstico de PCRs baseadas em primers direcionados a marcadores universais para diagnosticar Leishmania spp. localizados em dois genomas da célula parasitária, a saber, kDNA (maxicírculo e minicírculo) e DNA nuclear. Foram avaliadas PCRs baseadas em primers direcionados ao (i) DNA de kinetoplasto (kDNA) minicirculo, ao gene codificador de Citocromo B e Citocromo C Oxidase subunidade II presentes no (ii) kDNA maxicírculo, e ao gene codificador Citicromo C, presente no (iii) DNA nuclear. Pelos resultados infere-se que a PCR direcionada ao kDNA de minicírculo apresentou uma sensibilidade analítica muito superior às PCRs direcionadas ao DNA maxicirculo e nuclear. Pelo menos uma combinação dos primers de cada marcador foi capaz de detectar DNA de todas as espécies da Coleção de Leishmania do Instituto Oswaldo Cruz (CLIOC), tornando-os uma ferramenta útil para identificação de espécies de Leishmania spp. A PCR direcionada ao kDNA de minicírculo apresentou uma sensibilidade diagnóstica também muito superior às PCRs direcionadas ao DNA maxicirculo e nuclear. Amostras de baço e medula óssea produzem informações complementares para diagnóstico post-mortem de Leishmania spp. em cães soropositivos. Finalmente, as amostras de aspirado de medula óssea demonstraram ser uma alternativa confirmatória para o diagnóstico laboratorial do agente em animais soropositivos assintomáticos.The PCR technique can be employed for the detection and identification of pathogens, and therefore has wide application in molecular epidemiology studies. Particularly in relation to infection by Leishmania spp., the detection of its agent is important in seropositive animals, in the case of surveys for direct detection in vectors and in free-living animals, whose anti-serum for serodiagnosis test are not available. PCR can also offer the molecular identification of the agent, when phylogenetically informative markers are amplified and sequenced. In this sense, we performed the present study, whose aim was to evaluate the analytical and diagnostic performance of PCR based on universal primers that target markers to diagnose Leishmania spp located in two distinct genomes of the parasite cell, namely, kDNA (maxicírcle and minicircle) and nuclear DNA. PCRs were evaluated based on primers targeted to the kinetoplastids (i) DNA (kDNA) minicircles, the cytochrome B and cytochrome C oxidase subunit II genes present in the (ii) kDNA maxicircle and the gene encoding Citicromo C, present in (iii) nuclear DNA. Based on the results, the PCR directed to the kDNA minicircle showed an analytical sensitivity much higher than the PCR targeting the kDNA maxicircle and nuclear DNA. At least one combination of primers of each marker was able to detect DNA from all CLIOC - Leishmania collection of Oswald Cruz institute species, which qualifies a useful tool for species identification of Leishmania spp. The PCR targeted to minicircle kDNA also showed to have a diagnostic sensitivity much higher than PCRs directed to kDNA maxicircle and nuclear DNA. Spleen and bone marrow samples produces additional information post-mortem diagnosis of Leishmania spp. on seropositive dogs. Finally, samples of bone marrow aspirate are an alternative for confirmatory laboratory diagnosis of the agent in asymptomatic seropositive animals.
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Fazenda, Pedro Miguel Jesus. "Identificação de marcadores SSR e de SNPs em medronheiro (Arbutus unedo L.) por sequenciação massiva paralela." Master's thesis, ISA, 2013. http://hdl.handle.net/10400.5/6487.
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Mestrado em Engenharia Agronómica - Instituto Superior de AgronomiaThe strawberry tree (Arbutus unedo L.) is native to the Mediterranean region. The use of molecular markers in this species has been limited to the use of RAPDs, ISSRs as well to the cross-amplification of SSRs from other Ericaceae. In this work, we developed a protocol for extracting nuclear DNA from the strawberry tree and performed partial next-generation sequencing of the Arbutus unedo L. genome using the "Ion Torrent" (Life Technologies) platform. The next-generation sequencing resulted in 198,856 sequences ("raw data") with an average size of 123 bp, which were uploaded to the NCBI database "Sequence Read Archive" (SRA) with the accession number: SRX341237. Data analysis led to the identification of 1085 microsatellite-containing sequences, which were also uploaded with accession numbers: from KF023636 to KF024720 to the NCBI databases. Primers were designed for 18 microsatellite loci of which only three have proved to be polymorphic in a panel of 16 samples. Based on identified 25 SNPs one CAPS marker was developed, which despite being heterozygous revealed to be monomorphic among the 16 analyzed samples.
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Dickens, Alex. "Biofluid analysis to differentiate brain disease." Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.572775.
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It has been demonstrated that by using 1H NMR spectroscopy in combination with multivariate statistical modelling (PLS) it is possible, using urine samples obtained from rats, to distinguish between different types of CNS lesions. Against this background this thesis will explore whether the combination of 1H NMR and PLS modelling on biofluids can be used q-1eientify biomarkers in .. - different neurological diseases and in clinically relevant animal models of neurologic disease. The results in this thesis demonstrate that it is possible to separate sets of animals at different stages of disease in models of multiple sclerosis and to identify the presence of early brain metastasis. The same methodology was also applied to human biofluids. In MS patient cohorts (RR- MS, PP-MS and SP-MS) it was also possible to differentiate between RR-MS and SP-MS as well between MS and healthy controls. Therapy for these two stages of MS are very different and therefore a rapid test to determine a patient's stage of MS would be hugely beneficial in the clinic. Further investigation revealed that it is possible to separate MS patients from individuals with Alzheimer's disease. Metabolomics was then combined with other eo- variants in a study of cerebrospinal fluid obtained from patients with HIV associated dementia (HAD) to discover whether disease progression could be followed in this manner. The results show that it is possible to detect neurocognitive changes in patients with HAD. Indeed, the results demonstrate. that metabolomics is a far more sensitive tool for the following progression than other non-PLS biomarker techniques and should provide a useful method for early diagnosis of CNS disease and the evaluation of therapy in prospective studies.
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BUENO, Luíce Gomes. "Caracterização agronômica e molecular da coleção nuclear de arroz da Embrapa." Universidade Federal de Goiás, 2010. http://repositorio.bc.ufg.br/tede/handle/tde/432.
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Previous issue date: 2010-08-31The plant genetic resources stored ex situ are considered as a genetic repository, and are raw material for the development of the world agriculture. In rice, despite its high genetic variability, the lack of information of accessions to compose a databank prevents its use to help the choice of genitors for the breeding programs. The Embrapa Rice Core Collection (ERiCC) was developed from 10,000 accessions from Embrapa GeneBank, and it was set up by 550 accessions, divided in three subsets: 1) 94 lines and cultivars from Brazil (LCB); 2) 148 lines and cultivars from abroad (LCI); and 3) 308 traditional varieties (VT), obtained from germplasm collection expeditions in Brazil. This work aimed: 1) to evaluate the extension of genetic variability of 550 accessions from ERiCC by means of agronomic traits characterization using mixed models and multivariate statistics; 2) to perform a comparative analysis of the genetic divergence considering the agronomical and SSR markers characterizations; and 3) to identify the genotypes with higher genetic diversity and with the best agronomic performances, aiming to promote the most efficient use of such germplasm in breeding programs. The agronomic characterization of 550 accessions was performed in nine field experiments, evaluating 18 phenological-agronomic traits. The data were analyzed using the mixed linear and AMMI models. There was wide variation range of genotypical values for most evaluated traits. In different environments, it was observed VT accessions among the high-yielding materials, demonstrating the potential of this group of germplasm, particularly important due to its high genetic variability, to contribute to the development of cultivars regionally adapted. The AMMI approach allowed a good discrimination of ERiCC rice genotypes in relation to the adaptive performance, identifying the accessions CA880078, CA990001, CA870071 (subset VT), and CNA0009113 (LCI) as having good yield and broad adaptation to distinct environments. The comparative analysis of genetic diversity between agronomic and molecular data was performed using the 242 lines and cultivars accessions from ERiCC, which were characterized by 86 fluorescent SSR markers, and five agronomic traits with genotypic values predicted (values without from the effects of interaction genotypes x environment, from a joint analysis of nine experiments. The genetic divergence among accessions was estimated by the average Euclidian distance for phenotypical data, and by the Rogers modified by Wright (RW) genetic distance. The datasets were jointly analyzed by descriptive and multivariate statistics, using correlation analyses from hierarchical grouping of Ward and UPGMA methods. The phenotypical and molecular data showed a broad distribution of dissimilarity indexes, despite they showed different patterns of variation between them. Low molecular distances were associated to low phenotypical distances, however to high molecular distances, occurred a high broad range of phenotypical variation. The correlation between genetical and phenotypical dissimilarities was significant for both lowland and upland accessions, despite with different values (r=0.156 and r=0.409, respectively). Due to the low relation between phenotypical and molecular data, the analysis of genotypes to be used in breeding programs must include both evaluations to a better accession characterization. Considering the high yielding accessions, the higher molecular distances were identified among the accessions from lowland system of cultivation, among which BR IRGA 413 and CNA0005014, BR IRGA 413 and CNA0005853, and CNA0004552 and CNA0005014. Considering the upland accessions, maximum genetic distances were identified in CNA0000482 and CNA0006422, CNA0001006 and CNA0006422, and CNA0001006 and CNA0003490. The molecular analysis was able to identify accessions with reduced genetic relationship, that if used as genitors, will result in a progeny with a high probability to find new allelic combinations. On the other hand, the phenotypical characterization is important to identify accessions not just genetically divergent, but with superior agronomic trait performances for breeding programs. The results of this work will permit to increase the activities related to the characterization of accessions from rice Genebank, giving support of breeding programs to choose the best accessions to obtain new cultivars, with favorable traits, and broad genetic basis. In addition, a continuous program of phenotypical and molecular characterization of germplasm will be able to identify accessions to increase the genetic variability of ERiCC.
Os recursos genéticos vegetais armazenados ex situ são considerados reservatórios de genes e funcionam como matéria-prima para o desenvolvimento da agricultura mundial. Na cultura do arroz, apesar da extensa variabilidade genética existente, a deficiência de informações que integrem dados que possam efetivamente auxiliar na escolha de genótipos importantes para os programas de melhoramento constitui o principal fator que limita a utilização mais ampla dos acessos armazenados nos bancos de germoplasma. A Coleção Nuclear de Arroz da Embrapa (CNAE) representa a variabilidade genética de mais de 10 mil acessos constituintes do Banco Ativo de Germoplasma (BAG) da Embrapa Arroz e Feijão, e é composta por 550 acessos subdivididos em três estratos: 1) 94 Linhagens e Cultivares Brasileiras (LCB), provenientes de programas de melhoramento de instituições brasileiras; 2) 148 Linhagens e Cultivares Introduzidas (LCI), provenientes de programas de melhoramento de outros países; e 3) 308 Variedades Tradicionais (VT), que reúne acessos obtidos por expedições de coleta de germoplasma realizadas em vários estados do Brasil. Este trabalho teve como principais objetivos: 1) avaliar a extensão da variabilidade genética dos 550 acessos pertencentes à CNAE por meio da caracterização agronômica via metodologias de modelos mistos e estatísticas multivariadas; 2) realizar a análise comparativa da divergência genética entre acessos, determinada pela avaliação de caracteres agronômicos e marcadores moleculares SSR; e 3) identificar os genótipos com maior diversidade genética e com melhores atributos agronômicos, a fim de indicar uma melhor utilização destes recursos genéticos em programas de melhoramento. Na caracterização agronômica foram avaliados 550 acessos em experimentos conduzidos em nove locais no Brasil, envolvendo um total de 18 caracteres fenológico-agronômicos. Os dados foram analisados empregando-se a abordagem de modelos lineares mistos e modelo AMMI de análise. Verificou-se grande amplitude de variação dos valores genotípicos para a maioria dos caracteres avaliados. Nos diferentes ambientes, houve ocorrência de genótipos do estrato VT entre os mais produtivos, o que demonstra o potencial deste grupo de germoplasma, particularmente importante por sua grande variabilidade genética, em contribuir para o desenvolvimento de cultivares regionalmente adaptadas. A abordagem AMMI permitiu uma boa discriminação dos genótipos de arroz da CNAE quanto ao seu comportamento adaptativo, identificando os acessos CA880078, CA990001, CA870071 (do estrato VT), e CNA0009113 (LCI) com estabilidade, produtividade satisfatória e ampla adaptação à diferentes ambientes. Para a análise comparativa da diversidade genética entre dados agronômicos e moleculares foram considerados 242 acessos da CNAE, os quais foram caracterizados utilizando-se 86 marcadores SSR fluorescentes, sendo que para os dados agronômicos, foram realizadas análises conjuntas dos experimentos e considerados os valores genotípicos preditos de cinco caracteres (valores livres dos efeitos de interação genótipos x ambientes). A divergência genética entre os acessos foi estimada pelo procedimento de distância Euclidiana média para os dados fenotípicos, e por meio da distância de Rogers modificada por Wright (RW) para os dados moleculares, analisando-se os conjuntos de dados por meio de estatísticas descritivas e multivariadas, empregando-se análises de correlação entre matrizes de dissimilaridade e análises de agrupamento hierárquico de Ward e UPGMA. Os dados fenotípicos e moleculares apresentaram uma ampla distribuição dos índices de dissimilaridade, embora tenham apresentado diferentes padrões dessa variação. Baixas distâncias moleculares estiveram associadas a baixas distâncias baseada nos valores genotípicos, no entanto para elevadas distâncias moleculares houve ocorrência de ampla escala de variação fenotípica. A correlação entre as dissimilaridades genéticas e valores genotípicos foi significativa tanto no conjunto de acessos irrigados quanto no de sequeiro, porém, com diferentes magnitudes (r=0,156 e r=0,409, respectivamente). Devido esta baixa relação entre os dados fenotípicos e moleculares, o estudo de genótipos para fins de uso no melhoramento genético deve incluir ambas avaliações para a melhor caracterização dos acessos. Entre os materiais mais produtivos, as maiores distâncias moleculares foram identificadas entre os genótipos do sistema de cultivo irrigado, dentre eles BR IRGA 413 e CNA0005014, BR IRGA 413 e CNA0005853, e CNA0004552 e CNA0005014. Entre os materiais de sequeiro, máximas distâncias genéticas foram identificadas entre os acessos CNA0000482 e CNA0006422, CNA0001006 e CNA0006422, e CNA0001006 e CNA0003490. A análise molecular permitiu que fossem identificados genótipos de vínculo genético reduzido, que quando utilizados como parentais em cruzamentos, possibilitarão que as progênies obtidas apresentem maiores chances de combinações alélicas inéditas. Por sua vez, a caracterização fenotípica tem papel fundamental na identificação de materiais que além de divergentes, apresentem desempenho agronômico superior para os programas de melhoramento. Os resultados deste trabalho permitirão aumentar eficazmente as atividades relacionadas à caracterização de acessos do Banco Ativo de Germoplasma de arroz, subsidiando os programas de melhoramento na escolha de genótipos a serem utilizados para a obtenção de novas cultivares, com características favoráveis, de ampla base genética. Em adição, um programa contínuo de caracterização fenotípica e molecular de germoplasma permitirá ainda a escolha de acessos para a ampliação da variabilidade genética da CNAE.
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Nylander, Ruta. "Magnetic resonance imaging markers of cerebral small vessel disease in an elderly population – association with cardiovascular disease and cognitive function." Doctoral thesis, Uppsala universitet, Radiologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-319766.
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Cerebral small vessel disease (SVD) is identifiable by clinical, neuroimaging, neuropathological and cognitive findings. The aim of this thesis was to assess SVD and cerebral perfusion on magnetic resonance imaging (MRI) in a 75-year-old population and compare the findings with scars of myocardial infarctions, cardiovascular risk markers and cognitive function. In addition, the evolution of SVD over 5 years was studied. The study population included subjects from the Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) study. The subjects had been chosen in a randomized manner from the register of the municipality. MRI of the brain and the heart, cognitive tests and blood tests for cardiovascular risk factors were performed in 406 subjects at age 75 years and 250 of them were re-examined 5 years later at the age of 80. Paper 1 showed that unrecognized myocardial infarctions (UMIs) were found in 120 subjects (30%) and recognized myocardial infarctions (RMIs) in 21 (5%). Men with RMIs displayed an increased prevalence of cortical and lacunar cerebral infarctions, whereas women with UMIs more frequently had cortical cerebral infarctions. Paper 2 showed that one or more brain infarcts were seen in 23% of the subjects (20% had only lacunar infarcts, 1% had only cortical infarcts and 2% had both). Hypertension and obesity were significantly associated with an increased risk of infarction. The newer risk markers investigated were not significantly associated with brain infarcts. Paper 3 showed that MRI manifestations of SVD progressed over 5 years. Relative cerebral blood flow (rCBF) was not associated with WMH volume or progression of WMH volume. Paper 4 showed that moderate to severe WMHs and incident lacunar infarcts on brain MRI were associated with a mild impairment of executive function. In conclusion, this longitudinal population based study compares MRI manifestations of SVD with clinical data, providing knowledge that may be used in further investigations of preventive interventions and for identification of disease in early stages.
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Kögler, Anja [Verfasser], Stefan [Gutachter] Wanke, and Michael [Gutachter] Göttfert. "Diversity and Evolution of Short Interspersed Nuclear Elements (SINEs) in Angiosperm and Gymnosperm Species and their Application as molecular Markers for Genotyping / Anja Kögler ; Gutachter: Stefan Wanke, Michael Göttfert." Dresden : Technische Universität Dresden, 2020. http://d-nb.info/1227201877/34.
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Nicolè, S. "BIODIVERSITY ANALYSIS TROUGH DNA BARCODING Applications in agrifood and seafood products." Doctoral thesis, Università degli studi di Padova, 2010. http://hdl.handle.net/11577/3426881.
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The research activity, the results of which are the subject of doctoral dissertation, focused on the potentials of DNA barcoding, a genomic approach that exploits a short DNA sequence, a barcode, from a standardized region of the plastid genome, mitochondrial and chloroplast, as a universal and unique identification marker for animal and plant species. The main goal was to test a new accurate and automatable method for the genetic traceability of agri-food products, both of animal (fish, crustaceans and molluscs) and plant origin (bean and grapevine).
First of all, we chose the specimens for the analysis: we selected pure lines of bean (Phaseolus vulgaris L.), clones of grapevine (Vitis vinifera L.) and samples of fish, crustaceans and molluscs purchased in famous GDO or local market in Chioggia e Sottomarina. Regarding the selection of seafood samples to analyze, we proceeded with the collection of the marine species most commonly involved in fraudulent substitutions. The experimental procedure adopted were the genomic DNA isolation from 37 specimens followed by the amplification of three target regions, cox1 (cytochrome oxydase subunit I), cob (apo-cytochrome b) and 16S-rDNA (ribosomal RNA small subunit) genes. Once obtained these data, we proceeded with a sequence similarity search using BOLD and GenBank as reference databases and each of the sequences as query. Overall, the phenetic approach proved to be an efficient tool to ensure the correct detection of seafood composition and thus to control the label information. In fact, for most of the samples it was possible to confirm the origin of the meat declared on the label, except in five situations where it was impossible to establish with no doubt the origin of the samples flagging them as likely falsification cases, voluntary or by accident. Cox1 gene proved to be a valid target for traceability aims, except in three genera, Thunnus, Macruronus and Gadus, where the identification was more problematic. Finally, even if GenBank database still remains the best web tool for forensic purposes, BOLD database proved to be enough rich to allow the correct recognition of almost all the specimens.
Regarding plant DNA barcoding, the goal was to test DNA barcoding strategy as a tool to assess the distinctiveness of species and varieties of pure lines and clones. In the case of bean, we selected 54 pure lines of Phaseolus vulgaris species, 24 Italian pure lines, 18 Mesoamerican landraces and 12 Andean landraces, along with a few P. coccineus, P. lunatus and Vigna unguiculata accessions adopted as reference standards and out-types. These samples were characterized by means of the amplification of 7 chloroplast and two nuclear regions followed by the application of a phenetic approach. The procedure confirmed to be a powerful technique to correctly separate different species, whereas at the varietal level it revealed to be scarcely informative to discriminate gene pools and to identify varieties within P. vulgaris. Thus a second approach, the character-based system, was tested and it allowed to detect within P. vulgaris species a total of 16 haplotypes corresponding to as many subgroups, each one made up by Mesoamerican or Andean accessions along with Italian accessions that clustered with one or the other gene pool.
Finally, a third case study is represented by V. vinifera and the potentials of DNA barcoding approach to distinguish grapevine cultivars used in the production of wines. We proceeded with the selection of 123 grapevine cultivars along with other 5 species of Vitis (V. rupestris, V. riparia, V. labrusca, V. cinerea e V. berlandieri) adopted as reference standards and out-types. After a preliminary analysis of the chloroplast DNA that resulted to be monomorphic, we decided to shift to the nuclear genome amplifying four ESTs and the GAI1 (gibberellins insensitive-like) gene. The analysis is still ongoing, but the preliminary results lead to think that a few haplotypes exist within V. vinifera and they could be use to resolve frequent cases of synonymies and homonymies in grapevine. Furthermore, an economically valuable application may be the exploitation of these haplotypes cultivar-specific for the genetic traceability of wines to avoid cases of falsification.L’attività di ricerca, i cui risultati sono oggetto della dissertazione di dottorato, ha riguardato lo studio delle potenzialità applicative del DNA barcoding, una tecnica molecolare volta all’identificazione degli organismi sulla base dei polimorfismi di specifiche sequenze nucleotidiche localizzate nei genomi plastidiale, mitocondriale e cloroplastico. Il progetto di ricerca ha previsto l’impiego di questo approccio per il riconoscimento di specie ai fini della tracciabilità genetico-molecolare di prodotti agro-alimentari, sia di origine animale (pesci, molluschi e crostacei) che vegetale (fagiolo e vite). Inizialmente si è proceduto all’individuazione degli organismi su cui condurre l’analisi: si sono collezionate linee pure di fagiolo (Phaseolus vulgaris L.), cloni di vite (Vitis vinifera L.) e campioni di pesci, crostacei e molluschi acquistati presso famose GDO o ai mercati locali di Chioggia e Sottomarina. In particolare, per quanto concerne la scelta delle specie ittiche su cui condurre l’analisi, si è svolta un’estesa indagine di mercato con l’intento di individuare le specie maggiormente coinvolte in falsificazioni alimentari, cioè sostituzione di specie pregiate con altre di valore inferiore. Si è successivamente proceduto alla purificazione di 37 campioni di DNA genomico e alla loro caratterizzazione dal punto di vista molecolare mediante amplificazione e sequenziamento di specifici geni mitocondriali, quali cox1 (Cytochrome oxydase subunit I), 16S-rDNA (16S small ribosomal subunit RNA) e cob (cytochrome b). Una volta acquisiti questi dati, l’interrogazione di due banche dati disponibili on line, BOLD per il gene cox1 e GenBank per tutti e tre i geni, ha consentito di identificare l’origine dei campioni confermando nella maggioranza dei casi quanto dichiarato nell’etichetta di accompagnamento del prodotto alimentare. In cinque situazioni non è stato possibile stabilire con certezza l’origine del campione e questo potrebbe indicare possibili casi di sostituzione, fraudolenta o accidentale. Il DNA barcoding pertanto è risultato utile ai fini dell’identificazione di specie in tutti e tre i taxa studiati, pesci, molluschi e crostacei, e il gene cox1 si è dimostrato un ottimo target per questi scopi eccetto che in tre casi particolari, i generi Thunnus, Macruronus e Gadus. Inoltre è risultato evidente che nonostante GenBank persista come la banca dati più ricca in termini di numero di sequenze depositate, il BOLD sta rapidamente incrementando la quantità di informazioni contenute al suo interno lasciando presupporre che in breve tempo diventerà la banca dati di riferimento per studi di genetica forense e di tracciabilità genetica. Per quanto riguarda le specie vegetali, l’obiettivo era l’identificazione univoca di specie, e soprattutto delle loro varietà quando fondate su un solo genotipo (linee pure, ibridi e cloni). Nel caso di fagiolo, si sono isolati i DNA genomici da 54 varietà di Phaseolus vulgaris, 18 provenienti dal Centro America, 12 dal Sud America e 24 line pure coltivate e commercializzate in Italia, insieme con alti 6 campioni usati come fuori gruppo (Phaseolus coccineus, Phaseolus lunatus e Vigna unguiculata). Sono risultate indispensabili indagini preliminari di polimorfismi di singoli geni al fine di determinare la variabilità genetica tra le varietà e la tracciabilità genetica di singole varietà. La caratterizzazione, tramite l’amplificazione di 7 differenti regioni cloroplastiche e due nucleari seguita da un approccio fenetico, ha confermato le potenzialità della tecnica come strumento efficace per la distinzione delle specie, mentre è risultata scarsamente informativa per il riconoscimento di singole varietà. Da qui si è rivelata necessaria l’adozione di un approccio alternativo, basato sulla determinazione della composizione nucleotidica e del polimorfismo a carico di ciascun gene esaminato, che ha permesso di definire 16 aplotipi corrispondenti ad altrettanti sottogruppi varietali, ciascuno costituito da accessioni Mesoamericane o Andine insieme con le varietà Italiane. Infine l’applicazione del DNA barcoding per la distinzione di cultivar di vite ha richiesto l’abbandono dello studio del genoma cloroplastico, troppo poco variabile, a favore di quello nucleare. Si sono isolati i DNA genomici da 123 cultivar di Vitis vinifera e da altre 5 specie (V. rupestris, V. riparia, V. labrusca, V. cinerea e V. berlandieri) e si sono amplificati 4 EST ed il gene GAI1 (gibberellins insensitive-like). L’analisi bioinformatica è ancora in corso, ma risultati preliminari fanno ipotizzare l’esistenza di aplotipi cultivar-specifici che potrebbero venir impiegati in futuro per risolvere i frequenti casi di sinonimie ed omonimie diffusi all’interno di questa specie. Infine un’altra interessante applicazione da un punto di vista economico potrebbe essere l’impiego di questi aplotipi cultivar-specifici per la tracciabilità genetica dei vini e la tutela delle denominazioni controllate da casi di falsificazione e concorrenza sleale.
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Oikawa, Fernando Teiichi Costa. "Liberação de marcadores de necrose miocárdica após revascularização cirúrgica com circulação extracorpórea. Um estudo com ressonância nuclear magnética." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/5/5131/tde-10112017-123424/.
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Introdução: O diagnóstico infarto do miocárdio (IAM) Tipo 5 é bastante complexo, especialmente após o surgimento de ensaios com a troponina de alta sensibilidade. Objetivo: Mensurar a liberação de biomarcadores de necrose miocárdica após cirurgia de revascularização (RM) utilizando a circulação extracorpórea (CEC) na ausência de novo realce tardio pelo gadolínio (RTG). Métodos: Neste estudo, avaliamos pacientes com doença arterial coronária estável, multiarterial, função do ventrículo esquerdo preservada, biomarcadores cardíacos basais normais e indicação formal para a cirurgia de revascularização eletiva com CEC. Eletrocardiograma, coleta de amostras de sangue para a mensuração de troponina e CKMB, e ressonância magnética cardíaca (RMC) com realce tardio pelo gadolíneo (RTG) foram efetuadas antes e após o procedimento. O diagnóstico de IM foi definido como acima de 10 vezes o percentil 99 URL, para troponina e CK-MB, respectivamente, e novo RTG pela RMC. Resultados: De 75 pacientes selecionados para RM com CEC, 69 foram analisados; destes, 54 não apresentaram RTG (IAM tipo 5 na RMC). 39 pacientes eram do sexo masculino (72,2%), com idade média de 61,3 (±8,3) anos. A pontuação média do SYNTAX Score foi de 28 (±10). Após a cirurgia, 54 (100%) pacientes tiveram um pico de troponina acima do percentil 99; destes, em 52 (96%) este pico foi maior do que 10 vezes o percentil 99. Por outro lado, 54 (100%) pacientes alcançaram pico de CK-MB acima do limite do percentil 99 e em apenas 13 (24%) foi maior do que 10 vezes o percentil 99. A troponina apresentou mediana do pico de 3,15 (2,0 - 4,9) ng/mL, 78,75x superior ao percentil 99. Conclusão: Nesta amostra estudada, a CKMB, diferentemente da troponina, teve níveis de liberação dentro dos padrões recomendados pelas diretrizes e coincidiu com ausência de realce na RMC. Estes dados permitem sugerir um maior ponto de corte de troponina para o diagnóstico do IAM relacionado ao procedimentoBackground: The diagnosis of periprocedural myocardial infarction is complex, especially after the emergence of high-sensitive markers of myocardial necrosis. Methods: In this prospective study, patients with stable multivessel coronary disease, preserved left ventricular function, normal baseline cardiac biomarkers, and formal indication for elective on-pump coronary bypass surgery (ONCAB) were evaluated. Electrocardiograms, cardiac biomarkers CKMB and troponin I (cTnI), and cardiac magnetic resonance imaging (CMR) with late gadolinium enhancement were performed before and after procedures. Myocardial infarction (MI) was defined as more than ten times the upper reference limit of the 99th percentile for cTnI and for CKMB and by the findings of new late gadolinium enhancement on CMR. We assessed the release of cardiac biomarkers in patients with no evidence of myocardial infarction on CMR. Results: From 75 patients referred to ONCAB, 69 were analyzed in this study. From these, 54 patients did not have evidence of MI on CMR. This group had 39 men (72.2%), mean age of 61.3 (± 8.3) years and a mean SYNTAX Score of 28 (± 10). After CABG, all 54 (100%) patients had a peak cTnI above the 99th percentile, and 52 (96%) had an elevation 10 times higher than the 99th percentile. Regarding CKMB, 54 (100%) patients had a peak CKMB above the 99th percentile limit, and only 13 (24%) had an elevation greater than 10 times the 99th percentile. The median value of cTnI peak was 3.15 (2.0 to 4.9) ng/mL. This represented 78.75 times the 99th percentile. Conclusion: In this sample, CKMB, unlike cTnI, had levels of release within the standards recommended by the guidelines and coincided with lack of enhancement in CMR. These data suggest a higher troponin cutoff point for the diagnosis of MI related to the procedure
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Colom, Sanmartí Glòria. "A Multiplexed diagnostic approach for cardiovascular disease biomarkers." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/396304.
Full textAbstract:
In the course of this thesis, the optimal epitopes for the subsequent polyclonal rabbit antibody production for cTnI and NT-proBNP have been studied and chosen. cTnI and NT-proBNP are the most relevant cardio-specific biomarkers for the diagnosis of cardiovascular diseases. With these antibodies, a sandwich ELISA for the detection of cTnI has been developed together with a competitive ELISA for the detection of NT-proBNP, both in a microplate format.
It has been observed that cTnI has an extraordinary tendency to non-specifically adsorb itself onto surfaces and other biomolecules. This, with the inability to achieve the required detectability for this biomarker, have been the main problems to face with. Regarding the non-specific adsorption, different additives in the analyte or sample buffer have been evaluated. Thus, 0.15% casein in PBST combined with the use of low adsorption microplates (ImmulonTM 2HB) helps considerably to solve this problem. However, the sensitivity obtained for this assay in aqueous buffer is much lower than that required corresponding to the basal levels of cTnI in the blood.
For the NT-proBNP ELISA development, the required limit of detection was achieved after studying various parameters related to heterology and other physicochemical parameters. Moreover, a good accuracy with NT-proBNP fortified plasma samples was obtained.
It has been possible to develop a multiplexed microarray for the simultaneous detection of 5 biomarkers (cTnI, NT-proBNP, very important in the process of developing cardiovascular diseases, CRP, Cys C and H-FABP). Once the microarray is biofunctionalized using a spatial encoding with the corresponding bioconjugates or capture antibodies, immunoreagents and other biomarkers can be used in a cocktail. Neither cooperativity phenomena (union of immunoreagents that are in solution in sites where there are other biomarkers immobilized) nor cross-reactivity (recognition of different biomarkers from those for which immunoreagents have been developed) have been observed in any case. Only Lp(a) immunoreagents produced such interferences and therefore they were discarded.
It has been highlighted the fact that the biomarkers present in different concentration ranges remains one of the main challenges for the multiplexed diagnosis when simultaneous measurements are desired. In this research, it was impossible to quantify the CRP and Cys C in the same microarray than H-FABP, cTnI and NT-proBNP employing direct samples. Fortunately, the fact of using glass surfaces in which 24 microarrays can be printed, has allowed making these measurements in a simultaneous and parallel way.
With the multiplexed microarray, it has been possible to measure samples from patients with different pathologies. The results show that the efficiency of this microarray is much higher than that of analyzers currently used in clinical laboratories, regarding the ability to measure multiple biomarkers in a large number of samples in a short time and the coherence of the results. Thus, the microarray developed in this PhD thesis has been able to measure all the biomarkers from all patient samples, while analyzers only analyzed some of them,
depending on the pathology, due to the cost (financial and time). The microarray was then able to detect high levels of CRP from patient samples that were not analyzed in clinical laboratory. Additionally, the microarray results are coherent with those obtained with analyzers for those cases in which measures had been made, and the disease had been diagnosed. The results have been satisfactory even in the case of NT-proBNP, which had not reached the detectability baseline even though it was very close. Unfortunately, it was not possible to measure cTnI levels with the microarray as it was expected according to previous studies done with the same immunoreagents. Thus, we can consider this multiplexed microarray as a semi-quantitative method useful for improving the diagnosis of cardiovascular disease for patients who are at different stages of the disease.
Finally, preliminary studies have been realized to implement the multiplexed immunochemical system in a fluorescent optical sensor based on the evanescent wave. This was done with the aim to achieve a POC (point-of-care) device suitable to be used outside hospital premises, adapted to non-specialist users, and facilitate the diagnosis of cardiovascular diseases. Unfortunately, the results obtained point to the need to make greater efforts to increase the detectability of the system, since the LOD values obtained are worse than those achieved with the ELISA or the microarray, far from the basal levels in the case of NT-proBNP.
The main problem in this thesis has been to reach the detection limits required by some biomarkers. Although in the literature and in the market there are assays that have achieved it, this fact mainly lies in the signal acquisition method as well as in the intrinsic sensitivity of the instrument addressed to do so.En el transcurs d'aquesta tesi s'han escollit els epítops òptims per a la conseqüent producció d'anticossos policlonals de conill per a cTnl i NT-proBNP, dos dels biomarcadors més cardio-específics i rellevants pel diagnòstic de malalties cardiovasculars. Amb aquests anticossos s'ha desenvolupat un ELISA sandvitx per a la detecció de cTnl i un ELISA competitiu per a la detecció de NT-proBNP, tots dos en format de microplaca. S'ha observat que la cTnl te una extraordinària tendència a adsorbir-se de forma inespecífica a superfícies i també a altres biomolècules. Pel que fa a l'adsorció inespecífica s'han avaluat diferents additius en el tampó de la mostra o analit veient-se que la caseïna al 0,15% en PBST combinat amb l'ús de microplaques de baixa adsorció (ImmulonTM 2HB) ajuda considerablement a solucionar aquest problema. Tot i això, la sensibilitat obtinguda per aquest assaig en tampó aquós és molt inferior a la requerida corresponent als nivells basals d'aquest analit a la sang. En el desenvolupament de l'ELISA per NT-proBNP, després d'estudiar diferents paràmetres relacionats amb l'heterologia i altres paràmetres físico-químics, s'ha aconseguit assolir el límit de detecció necessari obtenint una bona exactitud amb mostres de plasma fortificades amb l'analit en qüestió. Ha estat possible desenvolupar un microarray multiplexat per a la detecció de 5 biomarcardors (cTnl, NT-proBNP, CRP, Cys C i H-FABP). Un cop biofuncionalitzat el microarray amb els corresponents bioconjugats o anticossos de captura, la resta d'immunoreactius i biomarcadors poden ser utilitzats en forma de còctel sense que en cap cas s'hagin observat fenòmens de cooperativitat ni de reactivitat creuada. Tant sols els immunoreactius de Lp(a) van produir aquestes interferències i per aquest motiu es van descartar. En aquest treball de recerca va ser impossible quantificar la CRP i Cys C en el mateix microarray que la H-FABP, cTnl i NT-proBNP de mostres directes. Afortunadament, el fet d'utilitzar superfícies de vidre en les quals es podien imprimir fins a 24 microarrays ha permès poder fer aquestes mesures de forma simultània i paral•ela. Amb el microarray multiplexat ha estat possible mesurar mostres de pacients amb diferents patologies. Malauradament, no va ser possible mesurar els nivells de cTnl amb aquest microarray, tal com era de preveure d'acord amb els estudis previs fets amb els immunoreactius utilitzats. Així doncs, podem considerar aquest microarray com un mètode semi-quantitatiu multiplexat útil per a la millora del diagnòstic de malalties cardiovasculars. Finalment, s'han realitzat estudis preliminars per implementar el sistema immunoquímic multiplexat en un sensor òptic fluorescent d'ona evanescent amb l'objectiu d'aconseguir un dispositiu POC (point-of-care). Malauradament, els resultats obtingut apunten a que és necessari fer un major esforç per a incrementar la detectabilitat d'aquest sistema, donat que els valors de LOD assolits són pitjors que els aconseguits amb l'ELISA o el microarray i, per casos com l'NT-proBNP, es troben molt allunyats dels valors basals.
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Madrid, Gambín Francisco Javier. "Estudio de perfiles metabolómicos asociados al consumo de Legumbres y Café. Aplicación de una Aproximación Metabolómica por Resonancia Magnética Nuclear en Estudios de Intervención Nutricional y Observacionales." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/404909.
Full textAbstract:
Los biomarcadores nutricionales proporcionan una medida precisa y objetiva de la exposición dietética (biomarcadores de ingesta) y de su impacto en el individuo (biomarcadores de efecto), que unidos a las medidas tradicionales de consumo de alimentos pueden mejorar la medida de la exposición dietética y permitir la formulación de nuevas hipótesis sobre el impacto de la dieta en la salud. Esta Tesis Doctoral se enmarca dentro del consorcio “Food Biomarker Alliance” (FOODBALL), el cual propone llevar a cabo el estudio profundo de biomarcadores nutricionales.
La presente Tesis Doctoral tiene como objetivo principal contribuir en el descubrimiento de biomarcadores nutricionales a través del análisis del perfil metabolómico asociado al consumo de legumbres y de café en muestras de orina y/o suero/plasma mediante Resonancia Magnética Nuclear (RMN), en estudios nutricionales con diferentes diseños.
Para la evaluación del metaboloma asociado a la ingesta de legumbres (concretamente lentejas, garbanzos y alubias) se realizaron dos estudios: uno de intervención y uno observacional. En el estudio de intervención con individuos sanos, el perfil metabolómico urinario se caracterizó por estar asociado a metabolitos provenientes del “food metabolome” (trigonelina, dimetilglicina, 3-metilhistidina, trimetilamina, y lisina); y a metabolitos endógenos (mayores niveles de aminoácidos ramificados, glutamina, y ácido xanturénico; y menores niveles de glucosa). El análisis del metaboloma sérico reveló una menor cantidad de metabolitos significativos, mayormente endógenos (asparagina, histidina, dimetilglicina, lisina, 3-hidroxiisovalerato, 2-hidroxibutirato y glucosa). Los principales candidatos a biomarcadores urinarios fueron adicionalmente explorados a través de muestras biológicas recogidas hasta 48 h tras la ingesta de los alimentos.
Para el estudio observacional de la huella metabolómica urinaria asociada con el consumo de legumbres, se estratificaron los sujetos según el consumo reportado mediante un cuestionario de frecuencia de consumo de alimentos. La exposición a legumbres se asoció con metabolitos provenientes del metabolismo de la colina, de compuestos relacionados con el metabolismo de los aminoácidos, y con el metabolismo energético. Con el objetivo de mejorar la capacidad predictiva del consumo de legumbres, se diseñó un modelo combinado de exposición que incluyó glutamina, dimetilamina y 3-metilhistidina. El modelo fue evaluado por una curva característica de funcionamiento del receptor (ROC) exhibiendo mayor área bajo la curva (>90%) en comparación con los modelos individuales (<90% en todos los casos). Los metabolitos provenientes del estudio de intervención replicados en el estudio observacional fueron dimetilglicina, 3-metilhistidina y trimetilamina como precursor de trimetilamina-N-óxido (metabolitos del “food metabolome”); y glutamina, aminoácidos ramificados, y una menor glucosa como metabolitos endógenos. Por lo tanto, estos metabolitos podrían ser los candidatos más robustos a biomarcadores nutricionales de legumbres.
En el caso del estudio de café, el análisis del metaboloma urinario tras el consumo agudo un café con alto contenido en compuestos bioactivos indicó una alta excreción de 2-furoilglicina; y compuestos endógenos tales como ácidos succínico, cítrico, 3-metil-2-oxovalérico y isobutírico. El consumo sostenido del café exhibió un aumento de compuestos derivados de la acción microbiana como los ácidos hipúrico, 3-(3-hidroxifenil)-3-hidroxipropiónico y 3-hidroxihipúrico. Así mismo, la trigonelina se encontró en la orina tras el consumo tanto agudo como sostenido del café.
En ambos estudios de intervención (con legumbres y café) se estudió el perfil metabolómico de los propios alimentos. En el caso de las legumbres se observaron trigonelina, histidina, lisina, y aminas cuaternarias, que posteriormente fueron excretados. Asimismo, en el caso del café se identificaron compuestos furanos y trigonelina que dieron como resultado la 2-furoilglicina y la trigonelina propiamente.
Esta Tesis Doctoral presenta diferentes aproximaciones a través de estudios de intervención nutricional y observacionales para el descubrimiento de biomarcadores nutricionales asociados al consumo de legumbres y café mediante la aplicación de una estrategia metabolómica no dirigida usando la RMN.Nutritional biomarkers provide a more accurate and objective measure of dietary exposure (biomarkers of intake) and their impact on the metabolism (biomarkers of effect) than traditional measures of food consumption. The main aim of this PhD is to contribute to the discovery of nutritional biomarkers by analyzing the metabolomic fingerprint associated with the consumption of pulses and coffee using Nuclear Magnetic Resonance (NMR) through nutritional studies with different designs. To investigate the metabolomic fingerprint associated with the dietary pulses intake (specifically lentils, chickpeas and beans), an intervention study was carried out in healthy individuals. The main candidates for urinary biomarkers (trigonelline, dimethylglycine, 3-methylhistidine, trimethylamine, and lysine) were further explored up to 48 h after food intake. In an observational study, a free-living population was stratified according to the reported consumption of pulses by a food frequency questionnaire. The exposure to pulses was associated with metabolites derived from the metabolism of choline and amino acids, as well as with energy metabolism. A multi-metabolite biomarker model was designed including glutamine, dimethylamine and 3-methylhistidine and positively evaluated by a receiver operating characteristic curve (ROC). The metabolites from the intervention study replicated in the observational study were dimethylglycine, 3-methylhistidine and trimethylamine as a precursor of trimethylamine-N-oxide (food metabolome); and glutamine, branched-chain amino acids, and lower glucose (endogenous metabolites). Therefore, these metabolites could be good candidates for nutritional biomarkers of pulses. Concerning the metabolomic study after the intake of a coffee with high content of bioactive compounds, the acute consumption indicated a higher urinary excretion of 2-furoylglycine and compounds of Krebs cycle. Sustained consumption of coffee exhibited an increase in compounds derived from microbial activity such as hippuric, 3-(3-hydroxyphenyl)-3-hydroxypropionic and 3-hydroxyhippuric acids. Trigonelline was found in the urine after both acute and sustained consumption of coffee. In both intervention studies (with legumes and coffee) the metabolic profile of the food was studied indicating certain precursors of compounds from the food metabolome. This Thesis presents different approaches through intervention and observational studies for the discovery of nutritional biomarkers of pulses and coffee through an untargeted metabolomic strategy using NMR.
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Melo, Rodrigo Morel Vieira de. "Liberação de biomarcadores de necrose miocárdica após angioplastia coronária percutânea em ausência de infarto do miocárdio manifesto: estudo com ressonância nuclear magnética." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/5/5131/tde-02052016-094529/.
Full textAbstract:
Introdução: A liberação de biomarcadores de necrose miocárdica após a intervenção coronária percutânea (ICP) ocorre frequentemente. No entanto, a correlação entre a liberação dos biomarcadores e o diagnóstico do infarto agudo do miocárdio (IAM) tipo 4a tem gerado controvérsia, especialmente com o aumento da sensibilidade nos ensaios de troponina (Tn). Neste estudo, objetivamos quantificar a liberação dos biomarcadores cardíacos em pacientes submetidos à ICP eletiva sem o surgimento de novo realce tardio pelo gadolínio (RTG) na ressonância magnética cardíaca (RMC) após o procedimento. Métodos: Foram incluídos pacientes consecutivos com doença arterial coronária estável e função ventricular preservada, com indicação eletiva para ICP em pelo menos duas artérias epicárdicas. RMC com RTG foi realizada em todos os pacientes antes e depois das intervenções. Medidas seriadas de Tn e creatinoquinase fração MB (CK-MB) foram realizadas imediatamente antes do procedimento até 48 horas após. Pacientes com novo RTG na RMC após o procedimento foram excluídos. Resultados: 71 pacientes foram referenciados para a realização eletiva da ICP sendo que 15 (21,1%) foram excluídos, 10 (14,1%) por causa do surgimento de um novo RTG na RMC após a ICP. Nos 56 pacientes sem a evidência de IAM tipo 4a pela RMC predominava o gênero masculino 37 (66,1%) com idade média de 61,7 (± 8,4) anos e escore de SYNTAX médio de 16,6 (± 7,7). Após a ICP, 48 (85,1%) pacientes apresentaram um pico de elevação de Tn acima do percentil 99 sendo que em 32 (57,1%) a elevação foi superior a 5 vezes esse limite, enquanto que apenas 2 (3,6%) apresentaram um pico de CK-MB maior do que 5 vezes o percentil 99. A mediana do pico de liberação da Tn foi de 0,290 (0,061 - 1,09) ng/mL, valor 7,25 vezes superior ao percentil 99. Conclusão: Diferentemente da CK-MB, a liberação da troponina I ocorre com frequência após procedimento de ICP mesmo na ausência de realce tardio pelo gadolínio na ressonância magnética cardíacaBackground: The release of myocardial necrosis biomarkers after percutaneous coronary intervention (PCI) frequently occurs. However, the correlation between biomarker release and the diagnosis of procedurerelated myocardial infarction (MI) (type 4a) has been controversial. This study aims to evaluate the amount and pattern of cardiac biomarker release after elective PCI in patients without the image of a new MI after the procedure assessed by cardiac magnetic resonance (CMR) with late gadolinium enhancement (LGE). Methods: Patients with normal baseline cardiac biomarkers referred for elective PCI were prospectively included. CMR with LGE was performed in all of the patients before and after the interventions. Measurements of troponin I (TnI) and creatinekinase MB fraction (CK-MB) were systematically performed before and after the procedure. Patients with a new LGE on the post-procedure CMR were excluded. Results: Of the 56 patients without the evidence of a procedure-related MI assessed by the CMR after PCI, 48 (85.1%) exhibited a TnI elevation peak above the 99th percentile. In 32 (57.1%), the peak was greater than 5 times this limit. On the other hand, 17 (30.4%) had a CK-MB peak above the limit of the 99th percentile, and this peak was greater than 5 times the 99th percentile in only 2 patients (3.6%). The median peak release of TnI was 0.290 (0.061 to 1.09) ng/ml, which is 7.25-fold higher than the 99th percentile. Conclusions: In contrast to CK-MB, TnI release often occurs after an elective PCI procedure, despite the absence of a new LGE on CMR
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Almanza, Aguilera Enrique. "Efecto de un patrón de alimentación mediterránea sobre los perfiles metabolómicos asociados a salud metabólica y microbiota intestinal. Estudios de biomarcadores mediante una aproximación metabolómica no dirigida por resonancia magnética nuclear." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/457627.
Full textAbstract:
Cambios en el estilo de vida como la dieta y la actividad física proporcionan beneficios a nivel metabólico frente a factores de riesgo cardiovascular como la obesidad y la diabetes. La aplicación de la metabolómica en estudios de estilo de vida saludable permite profundizar en el conocimiento de los mecanismos moleculares subyacentes, así como en la identificación de biomarcadores que describan estos mecanismos asociados. El objetivo principal de la presente tesis doctoral fue identificar biomarcadores relacionados con factores de riesgo cardiovascular y el estudio de los perfiles metabolómicos asociados a un patrón de alimentación mediterránea mediante el empleo de una aproximación metabolómica no dirigida basada en resonancia magnética nuclear. Para la identificación de biomarcadores y perfiles metabólicos relacionados con un factor de riesgo cardiovascular se caracterizó primero la huella metabólica asociada a la diabetes mellitus tipo 2 (DM2) mediante la comparación del metaboloma urinario de individuos diabéticos y no diabéticos dentro del estudio PREDIMED. A partir de esta huella se calculó un biomarcador de prevalencia de DM2, el cual estuvo compuesto por altos niveles de ácido metilsuccínico, alanina, dimetilglicina y ácido guanidinoacético, y bajos niveles de glutamina, metilguanidina, y ácidos 3-hidroximandelico e hipúrico. Este biomarcador mostró una alta capacidad para discriminar la DM2, con una elevada sensibilidad y especificidad, siendo incluso superior a la observada por la glucosa. Adicionalmente, se observaron dos fenotipos metabólicos (metabotipos) relacionados con la DM2. Entre estos, el metabotipo con los niveles más altos en orina de fenilalanina, ácido acetoacético, fenilacetilglutamina y p-cresol se caracterizó también por tener los niveles de glucosa plasmática más altos. Referente a los perfiles metabolómicos asociados a un patrón de alimentación mediterránea, se han realizado dos aproximaciones. En la primera aproximación se determinó la huella metabólica y un biomarcador multimetabolito asociados a la alta adherencia a la dieta Mediterránea (DietMed) en individuos del estudio PREDIMED. La huella metabólica asociada a la DietMed estuvo compuesta por 34 metabolitos, incluyendo niveles urinarios bajos de algunos metabolitos de origen endógeno (p.e., glucosa) y niveles altos de otros metabolitos de origen exógeno (food metabolome, p.e., prolina betaína). Mientras tanto, el biomarcador que permitió discriminar entre alta y baja adherencia a la DietMed, con una elevada sensibilidad y especificidad, estuvo compuesto por niveles altos de tres metabolitos de origen microbiano: p-cresol, fenilacetilglutamina y ácido 4-hidroxifenilacético. Este biomarcador mostró además correlaciones significativas con la ingesta de frutas, verduras, legumbres, pescado y fibra dietaria. En cuanto a la segunda aproximación, se determinó el efecto de una intervención en el estilo de vida basada en una DietMed hipocalórica y actividad física sobre el metaboloma plasmático de mujeres obesas metabólicamente sanas y la posterior asociación de los cambios producidos en el metaboloma con la pérdida de peso. Después de 3 meses de estudio, tanto la intervención como la pérdida de peso producida se asociaron con cambios en la composición del metaboloma, incluyendo niveles más altos de fosfocreatina, y ácido fórmico, y niveles más bajos de trimetilamina y fragmentos de colesterol LDL/VLDL. Los resultados derivados de los presentes estudios que componen esta Tesis Doctoral refuerzan la importancia de la metabolómica para la identificación y desarrollo de biomarcadores metabólicos que permitan profundizar en los mecanismos moleculares subyacentes a enfermedades crónicas y estilos de vida saludable, así como en la relación de estos biomarcadores con la prevención, prevalencia y mejora de estas enfermedades.The main objective of this doctoral thesis was to identify biomarkers related to cardiovascular risk factors and to study the metabolic profiles associated with a Mediterranean dietary pattern through the use of an untargeted metabolomic approach based on nuclear magnetic resonance. For the identification of biomarkers and metabolic profiles related to a cardiovascular risk factor, the metabolic profile associated with type 2 diabetes mellitus (DM2) was first characterized by comparing the urinary metabolome of diabetic and non-diabetic subjects. From this profile, a biomarker of DM2 prevalence was calculated, showing a high capacity to discriminate DM2, even higher than urinary glucose. In addition, one metabolic phenotype related to DM2, characterized by the highest urine levels of phenylalanine, acetoacetic acid, phenylacetylglutamine and p-cresol, and the highest plasma glucose levels, was also observed. Regarding the metabolic profiles associated to a Mediterranean feeding pattern, two approaches have been carried out. First, the metabolic profile and a multimetabolite biomarker associated with high adherence to the Mediterranean diet (DietMed) in individuals at high cardiovascular risk. The metabolic profile associated with DietMed included metabolites from endogenous and exogenous (e.g. food metabolome) origin. Meanwhile, the biomarker of high adherence to DietMed, with high sensitivity and specificity, was composed of high levels of three metabolites of microbial origin: p-cresol, phenylacetylglutamine and 4-hydroxyphenylacetic acid. This biomarker showed significant correlations with the intake of fruits, vegetables, legumes, fish and dietary fiber. In the second approach, the effect of an intervention based on a hypocaloric DietMed diet and physical activity on the plasma metabolome of metabolically healthy obese women, and the further association between the changes produced in the metabolome and the produced weight loss were determined. After 3 months, both the intervention and the weight loss were associated with higher levels of phosphocreatine and formic acid, and lower levels of trimethylamine and LDL/VLDL cholesterol. The current findings reinforce the importance of metabolomics in the identification and development of biomarkers that allow to deepen in the molecular mechanisms underlying chronic diseases and healthy lifestyles, as well as to relate of these biomarkers with the prevention, prevalence and improvement of these diseases.
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Coser, Sara Morra. "Diversidade em Psidium guajava L. por caracteres morfológicos, moleculares e citogenéticos." Universidade Federal do Espírito Santo, 2012. http://repositorio.ufes.br/handle/10/6635.
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Previous issue date: 2012-07-12A goiabeira (Psidium guajava L.) é uma das fruteiras de maior importância econômica da família Myrtaceae. O Brasil é um dos maiores produtores de goiaba do mundo, sendo esta uma cultura potencial em expansão e rentabilidade. A polinização cruzada da espécie e a existência de pomares heterogêneos de propagação seminal resultam em variabilidade, permitindo a seleção de genótipos para o melhoramento da cultura. O objetivo deste trabalho foi estudar a diversidade genética em genótipos de P. guajava selecionados em pomar de origem seminal e cultivares por características morfológicas e químicas de qualidade de fruto, também associar dados de conteúdo de DNA nuclear (2C), cariótipo, morfológicos e de marcadores moleculares microssatélites. Verificou-se a existência de divergência entre as Cortibel com relação às características de fruto, com genótipos apresentando performance superior e genótipos com desempenho semelhante à cultivares, potenciais para uso em hibridações ou como cultivares. As análises cariotípica e de conteúdo de DNA nuclear (2C) mostraram que os genótipos possuem um genoma estável, pequeno e diplóide e características cariotípicas relacionadas a grupos ancestrais de angiospermas. O dendrograma UPGMA baseado em dados morfológicos e SSR evidenciaram diversidade entre os genótipos, com melhor discriminação pelos dados de SSR. Como a maioria dos genótipos mostraram similaridade morfológica para as características de frutos, aliada a dissimilaridade molecular, estes se mostraram interessantes para o uso em hibridações em programas de melhoramento. O conjunto de dados gerados contribuiu para expandir o conhecimento sobre o genoma e a diversidade genética em P. guajava. Também é importante na estruturação de programas de melhoramento para a cultura, além de contribuir para estudos evolutivos
Guava (Psidium guajava L.) is one of the most economically important fruit crop from Myrtaceae family. Brazil is one of the largest producers of guava in the world, which is a potential crop in growth and profitability. Cross-pollination of the species and the existence of heterogeneous seminal propagation orchards result in variability, allowing the selection of genotypes for crop improvement. The aim of this study was to evaluate genetic diversity between P. guajava L genotypes selected from seminal origin orchard and cultivars, by morphological and fruit quality chemical characteristics, also associate data from nuclear 2C-value, karyotypic, morphological and simple sequence repeat (SSR) marker. There were divergences between Cortibel selections by fruit characteristics, with genotypes showing superior and similar performance when compared with cultivated genotypes, potential for use in hibridation and as cultivars. Karyotype and nuclear 2C-value analyses showed that all genotypes have a stable and very small diploid genome (2n = 2X = 22; 2C = 0.95 pg), and karyotypic characteristics related to ancestral angiosperm groups. UPGMA dendrogram based on morphological and SSR data evidenced diversity among the genotypes, with better discrimination by SSR data. Since most genotypes showed morphological similarity for fruit characteristics, combined with molecular dissimilarity, the use of these genotypes in hybridation breeding programs could be of interest. The obtained data set contributed to expand the knowledge about genome and genetic diversity of P. guajava. Also are important to structure crop improvement programs and contribute to evolutionary approaches
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Johnson, Erik Andrew. "Survivin expression after traumatic brain injury potential roles in neuroprotection /." [Gainesville, Fla.] : University of Florida, 2004. http://purl.fcla.edu/fcla/etd/UFE0008337.
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Thesis (Ph.D.)--University of Florida, 2004.Typescript. Title from title page of source document. Document formatted into pages; contains 87 pages. Includes Vita. Includes bibliographical references.
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Amiri, Neda. "Molecular Phylogeny of Poa L. sensu lato (Poaceae) with a Focus on West Asian Species." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35018.
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Poa L., is known as a highly diverse cosmopolitan genus with taxonomic difficulties that includes unknown species and species with uncertain affinities mainly in West Asia and North Africa. Poa also exhibits a close relationship with two West Asian genera, Eremopoa Roshev. and Oreopoa H. Scholz & Parolly. This study was conducted to: 1) fill the gap of information on the affinities between Poa species with an emphasis on West Asian Poa; 2) revise and evaluate the accuracy of traditional infrageneric classification of West Asian Poa; and 3) clarify the relationship between Poa and two allied genera of Poaceae Barnhart, Eremopoa and Oreopoa. DNA molecular evidence from present phylogenetic analyses of West Asian species of Poa, Eremopoa and Oreopoa, resulted in some great findings as follow: I) Poa caucasica Trin., which is currently assigned to subsection Nivicolae of section Poa from subgenus Poa resolved as a unique new distinct lineage within Poa. II), New treatments are suggested for Poa densa Troitsky, Poa masenderana Freyn & Sint., Poa cenisia All., Poa psychrophila Boiss. & Heldr. and Poa lipskyi. III) Three unclassified species of Poa pseudobulbosa, Poa diversifolia and Poa aitchisonii are assigned here to subgenus Poa and supersection Poa. IV), The present molecular evidence supports inclusion of Eremopoa in Poa and confirms reduction of Eremopoa to a level of subgenus of Poa. V) Present phylogenetic analyses also indicate that monotypic genus Oreopoa H. Scholz & Parolly is part of Poa. These findings require an urgent modification in subgeneric and sectional classification of the genus Poa.
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Choi, Bokyung. "Taxonomic status of Melaleuca argentea "Ashburton biotype" and identification and evaluation of exon capture loci for Myrtaceae." Phd thesis, Canberra, ACT : The Australian National University, 2017. http://hdl.handle.net/1885/142211.
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Melaleuca sensu lato is the second biggest genus (ca. 380 spp.) that is mainly distributed in Australia, but some species are found in Southeast Asia, Papua New Guinea and New Caledonia. Melaleuca occupy a range of habitats and are found in all biomes, which makes this hyper-diverse genus an excellent group to carry out evolutionary studies.
The taxonomy of Melaleuca sensu lato (tribe Melaleuceae) has been controversial. The tribe originally included eight other genera: Beaufortia, Calothamnus, Conothamnus, Eremaea, Lamarchea, Petraeomyrtus, Phymatocarpus, and Regelia. However, with taxonomic changes all of the genera in the tribe were transferred to Melaleuca. To date, the phylogenetic studies based on molecular data have shown that Melaleuca is paraphyletic with respect to the other genera in the tribe. However, the taxonomic boundary of Melaleuca is still debated. Existing molecular phylogenies of Melelauceae have used only a few genetic markers, and the relationships within the genus remain unresolved with large polytomies.
Taxonomy of eucalypts has been problematic. Eucalypts include the
following seven genera (Eucalyptus, Corymbia, Angophora,
Arillastrum, Allosyncarpia, Stockwellia, Eucalyptosis). They are
mainly Australian but some genera/species extend outside
Australia. The taxonomic relationship of Corymbia, and Angophora
is still debated. Some molecular phylogenies have shown monophyly
of Corymbia and Angophora while Corymbia was paraphyletic with
respect to Angophora in other studies.
In Chapter 2, the genetic diversity of Melaleuca argentea (M.
leucadendra complex) was explored. Previous research suggested
that populations in the Pilbara region of Western Australia had
some genetic distinctions. The Pilbara populations were recorded
as M. argentea “Ashburton biotype” (AB) in older literature,
but no further information was available. Morphological
characters and molecular data to assess the taxonomic status of
the Pilbara population were used. We found that AB is more
similar and closely related to M. leucadendra than to M.
argentea. The results did not have conclusive evidence to support
that AB is a distinct species from M. leucadendra. In order to
test the taxonomic status, presence of gene flow between AB and
M. leucadendra need to be further tested.
With the ultimate aim of estimating a comprephensive phylogeny of
Melaleuca and eucalypts using more samples and many more loci
compared to previous studies, we developed genetic markers for
exon capture in Chapter 3. A workflow to locate orthologous and
low copy number nuclear loci is introduced along with the method
that was employed to identify the chloroplast markers. 209
chloroplast and nuclear loci that might be useful for Myrtaceae
were identified by and 43 Myrtaceae taxa were successfully
sequenced.
In Chapter 4, a gene tree approach for each individual locus was
undertaken to remove potentially paralogous loci. We have found
144 loci that might be useful for Melaleuca and 174 loci for
eucalypts. The present study contributes towards more robust
estimations of phylogenetic relationships in the genus Melaleuca,
eucalypts as well as other genera in Myrtaceae. Further work is
required to verify the markers and to study phylogenetic
relationships of the taxa at different taxonomic levels using the
loci.
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Bean, Malcolm (Malcolm K. ). "The portfolio diversification value of nuclear power in liberalized electricity markets." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/76959.
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Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Nuclear Science and Engineering, 2012.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 46-47).
The key difference between a regulated and a liberalized electricity market is the establishment of a competitive generation marketplace via spot markets, day-ahead auctions, and over-the-counter trading activity. In a liberalized market, power plants are no longer guaranteed a fixed return on capital investments or the ability to pass on increases in fuel prices to customers directly. Therefore, power generators have had to modify their capital allocation and marketing strategies to resemble that of a typical competitive market participant more closely, balancing expected returns with portfolio risk. Advanced Combined Cycle Gas Turbine (CCGT) power plants are currently viewed as the most attractive generation investment option, offering low capital costs, short construction lead-times and financial optionlike qualities. In contrast, a nuclear power plant's levelized cost is dominated by large fixed costs and capital expenditures. Even the perception of nuclear power as being a hedge against volatile natural gas markets has been called into question by power market Monte Carlo simulations. These simulations indicate that CCGT power plants are actually the generation option with the least exposure to natural gas and electricity price uncertainty because of the intrinsic hedge created by the historically high correlation of natural gas and electricity prices[1, 2]. Nevertheless our simulations, heavily focused on modeling the non-linearity of the power supply curve, indicate that the portfolio diversification value of nuclear power is dependent on the generation composition of the power market. In markets primarily composed of natural gas fired capacity, an investment in nuclear power offers no portfolio diversification value, with all three baseload generation types are effectively long positions in natural gas. Conversely, in markets with a large amount of coal capacity there is a competition for market share between major marginal fuel types, coal and natural gas, which creates less favorable market dynamics for the CCGT. While we still observe a high natural gas-electricity correlation, the intrinsic hedge no longer stabilizes the CCGT profits. Our simulations indicate that in a bi-marginal fuel market a CCGT power plant is short natural gas, with cheaper natural gas helping to boost capacity factors, reduce operational heat rates, and displace coal power plants. Similarly, as currently observed in Northeastern power markets, cheap natural gas has not only shrunk coal power profit margins but also negatively impacted plant capacity factors. Therefore, the portfolio diversification value of nuclear comes from it being insulated from fossil fuel price uncertainty, but not because this attribute equates to a more stable levelized cost. Rather, nuclear power's low cost and low volatility fuel insures that an unfavorable shift in fossil fuel prices will not result in a large decrease in capacity factor and subsequent increase in profit volatility.
by Malcolm Bean.
S.M.
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Burrows, Kimberley. "Molecular genetic epidemiology studies of quantitative nucleic acid markers." Thesis, University of Bristol, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.761240.
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Petoussis, Andreas G. "Supply function equilibrium analysis for electricity markets." Thesis, University of Warwick, 2009. http://wrap.warwick.ac.uk/1054/.
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The research presented in this Thesis investigates the strategic behaviour of generating firms in bid-based electricity pool markets and the effects of control methods and network features on the electricity market outcome by utilising the AC network model to represent the electric grid. A market equilibrium algorithm has been implemented to represent the bi-level market problem for social welfare maximization from the system operator and utility assets optimisation from the strategic market participants, based on the primal-dual interior point method. The strategic interactions in the market are modelled using supply function equilibrium theory and the optimum strategies are determined by parameterization of the marginal cost functions of the generating units. The AC power network model explicitly represents the active and reactive power flows and various network components and control functions. The market analysis examines the relation between market power and AC networks, while the different parameterization methods for the supply function bids are also investigated. The first part of the market analysis focuses on the effects of particular characteristics of the AC network on the interactions between the strategic generating firms, which directly affect the electricity market outcome. In particular, the examined topics include the impact of transformer tap-ratio control, reactive power control, different locations for a new entry’s generating unit in the system, and introduction of photovoltaic solar power production in the pool market by considering its dependencyon the applied solar irradiance. The observations on the numerical results have shown that their impact on the market is significant and the employment of AC network representation is required for reliable market outcome predictions and for a better understanding of the strategic behaviour as it depends on the topology of the system. The analysis that examines the supply function parameterizations has shown that the resulting market solutions from the different parameterization methods can be very similar or differ substantially, depending on the presence and level of network congestion and on the size and complexity of the examined system. Furthermore, the convergence performance of the implemented market algorithm has been examined and proven to exhibit superior computational efficiency, being able to provide market solutions for large complex AC systems with multiple asymmetric firms, providing the opportunity for applications on practical electricity markets.
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Olsson, Magnus. "Nuclear pore membrane glycoprotein 210 as a new marker for epithelial cells." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3265.
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Epithelial cell polarisation is a prerequisite for the branching morphogenesis in several organs. Differential screening techniques were used to identify genes, which are upregulated during induction of epithelium in early kidney development. This investigation revealed two separate genes, Nuclear localising protein 1 (Nulp1), a previously undescribed gene with sequence characteristics of the basic helix-loop-helix transcription factor family, and glycoprotein 210 (gp210, POM210), an integral membrane protein constituent of the nuclear pore complex (NPC). Of these, gp210 was found to be upreglated during conversion of mesenchyme to epithelium.
The nuclear envelope, which demarcates the nuclear region in the eukaryotic cell, consists of an inner and an outer membrane that are fused at the locations for NPCs. These large macromolecular assemblages are tube like structures connecting the cytoplasmic and nuclear compartments of the cell. NPCs serve as the only conduits for exchange of molecular information between these cellular rooms. Electron microscopy techniques have revealed detailed information about the NPC architecture. A number of proteins (nucleoporins) have been characterised and embodied as components of the NPC structure. Active, energy dependent nucleocytoplasmic transport of RNAs and proteins is mediated by a group of soluble receptor proteins, collectively termed karyopherins.
Gp210 has been suggested to be important for nuclear pore formation. Nevertheless, our analyses showed a limited expression pattern of gp210, with its mRNA and protein largely confined to epithelial cells in the mouse embryo. Furthermore, in several cell lines, gp210 was undetectable. The expression pattern of gp210 was not synchronised with some other nucleoporins, indicating NPC heterogeneity. Characterisation of the structure of the human gp210 gene, including its promoter region, gave insight about possible cell-type specific gene regulatory mechanisms.
Regulation of molecular traffic between the nucleus and the cytoplasm leads to transcriptional control. Cell specific configuration of the NPC structure, due to diffential expression of gp210, could be involved in this control. Gp210 could be of importance for the development of epithelial cell polarisation.
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Olsson, Magnus. "Nuclear pore membrane glycoprotein 210 as a new marker for epithelial cells /." Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3265.
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Rush, Lucas Thorley. "Critical assessment of techniques, markets and overall economics of Generation III+ and IV reactors." Thesis, Massachusetts Institute of Technology, 2018. https://hdl.handle.net/1721.1/121823.
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Thesis: S.M., Massachusetts Institute of Technology, Department of Nuclear Science and Engineering, 2018Cataloged from PDF version of thesis.
Includes bibliographical references (pages 127-132).
This thesis performs a high-level assessment of the economic potential of Generation III+ and IV reactors. It examines both a market and product-based approach for the cost of new nuclear installations. It is the contention of this author that the support of the economic benefits for Generation IV reactors is unwarranted. Based on the uncertainties and lack of detailed design engineering completed, there is not sufficient evidence to suggest that Generation IV reactors, solely by virtue of their different design, will have higher economic potential than current LWRs. A market-based approach was initially taken to determine the upper bound for the cost of nuclear power. In every case, except when the Generation IV reactors had a low operating cost, their capital cost had to be lower than that of a LWR, due to their higher enrichment requirements. It was found that a change of ~0.1 c/kWh in the operation cost corresponded to a cost differential of ~200 $/kW in the capital cost.
Due to the high capital costs and relatively low revenue streams of new nuclear plants it was found that their commercial success was highly sensitive to the capital cost with even mild increases in cost having a significant effect over the entire project. This lead to the conclusion that the ability to guarantee returns on an investment potentially limits nuclear projects to regulated markets. A product-based approach was then used to assess the real and estimated costs of Generation III+ and IV reactors. It was found that the cost breakdown of each Generation III+ reactor was similar, however, the overall cost varied significantly by region. The installation costs where the most significant portion of the costs, ranging from 40-50%, with the nuclear and turbine island equipment costs only represented between 17-25% of the total overnight cost.
The estimated costs for the different Generation IV designs from modern estimates were all localized around 4,750 $/kW, while earlier estimates place the cost much lower, around 1,750 $/kW. The uncertainty in cost estimation, both its effects and its sources, was examined. It was found that when cost information over five years old was used, then the uncertainty in cost escalation was significant. A major factor that was found to have an effect on the reliability of cost estimates was also the design maturity. Novel projects with lower design maturity projects systematically under-predict the final cost resulting in cost escalation with time. A common proposition for Generation IV reactors is that they are used for process heat applications. A study of all industrial sites in the United States, and extended to the world, found that the number of potential sites are lower than expected due to two major reasons.
Firstly, the consumption of by-product streams for heat generation in major energy users, i.e. refineries, form a major component of their heat supply. Secondly, the commercial development of technologies that can actually utilize the process heat for high temperature products, such as hydrogen, have not been completed. A major potential strength would be the requirement of CO₂ free heat for the transportation sector. This would also require the development of other significant technologies, such as biofuels, to be feasible. Should a transition to hydrogen and/or synthetic fuels occur in the transportation sector, the economic opportunity to use nuclear reactors to generate those fuels would be substantial.
by Lucas Thorley Rush.
S.M.
S.M. Massachusetts Institute of Technology, Department of Nuclear Science and Engineering
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Khan, Tanzeer S. "Viability of an expanded United States nuclear power program and its effects on energy markets." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/44831.
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Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Nuclear Science and Engineering, 2006.Includes bibliographical references (p. 51-52).
The four biggest energy sources in the United States are coal, crude oil, natural gas, and nuclear power. While coal and nuclear power are produced domestically, more than 70% of crude oil and 20% of natural gas is imported. This places an unhealthy dependence on foreign products for our economy. Just as importantly, all of these energy sources, with the exception of nuclear power, produce large amounts of polluting emissions in the form of greenhouse gases which are responsible for environmental degradation. For these two reasons, we explore possible government policies to shift the US energy economy towards domestically-produced, environmentally-clean alternative energy sources, the most prevalent of which is nuclear power. Different forms of government support for investment in nuclear power is discussed, such as investment tax credits and production tax credits. As an instrument of public policy to affect energy imports and environmental impact, the possibility of a carbon tax (on the order of $150/tC) is considered. The effects of this carbon tax on the energy sector in the medium-term future (in the year 2020) are analyzed. Under the constraint of maintaining current natural gas demand the results show that there will be an increase in the use of nuclear power while lowering the dependence on crude oil and coal. To accomplish this, the use of natural gas is shifted from the power sector to the residential, commercial and industrial sectors due to the economic incentives to do so. From an environmental perspective, this carbon tax lowers emissions by a predicted 30% of its 2020 business-as-usual rates. Economically, the carbon tax lowers crude oil import levels by 20% and reduces the US balance of payments by over $170 billion in the year 2020.
by Tanzeer S. Khan.
S.B.
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Ward, Jeanine. "MicroRNA Markers of Acetaminophen Toxicity: A Master's Thesis." eScholarship@UMMS, 2012. https://escholarship.umassmed.edu/gsbs_diss/625.
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Background To investigate plasma microRNA (miRNA) profiles indicative of hepatotoxicity in the setting of lethal acetaminophen (APAP) toxicity in mice.
Methods Using plasma from APAP poisoned mice, either lethally (500 mg/kg) or sublethally (150 mg/kg) dosed, we screened commercially available murine microRNA libraries (SABiosciences, Qiagen Sciences, MD) to evaluate for unique miRNA profiles between these two dosing parameters.
Results We distinguished numerous, unique plasma miRNAs both up- and down-regulated in lethally compared to sublethally dosed mice. Of note, many of the greatest up- and down-regulated miRNAs, included, but were not limited to, 574-5p, 466g, 466f-3p, 375, 29c, and 148a. There was a statistically significant increase in alanine aminotransferase levels in the lethal compared to sublethal APAP dosing groups at the 12 h time point ( P < 0.001). There was 90% mortality in the lethally compared to sublethally dosed mice at the 48 h time point ( P = 0.011).
Conclusion We identified unique plasma miRNAs both up- and down-regulated in lethally dosed APAP poisoned mice.
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Yan, Weida. "A Study on Augmented Reality for Supporting Decommissioning Work of Nuclear Power Plants." Kyoto University, 2013. http://hdl.handle.net/2433/179338.
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Stella, Alessandra. "Strategies for applying marker assisted selection in nucleus breeding schemes in dairy cattle." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ56295.pdf.
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Liu, Jiarong. "Phylogeny and biogeography or watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] based on chloropast, nuclear sequence and AFLP molecular marker data." Auburn, Ala., 2005. http://repo.lib.auburn.edu/2005%20Fall/Thesis/LIU_JIARONG_35.pdf.
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Lasn, Helen. "The principal inferior olivary nucleus in aging and Alzheimer's disease /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-970-X/.
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Oetting, Liliana Lotufo. ""Avaliação de diferentes marcadores para a determinação da digestibilidade e taxa de passagem do alimento em suínos"." Universidade de São Paulo, 2002. http://www.teses.usp.br/teses/disponiveis/64/64132/tde-12072002-100432/.
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O objetivo do trabalho foi (1) avaliar a utilização do óxido crômico, lantânio e itérbio como marcadores dietéticos para a determinação da digestibilidade, (2) determinar a taxa de passagem através desses três marcadores, e (3) comparar duas técnicas analíticas (ICP-OES e ED-XRF) na análise dos marcadores. No ensaio de digestibilidade foram utilizadas 12 fêmeas suínas com idade inicial e final de 133 e 153 dias, respectivamente, sendo que os sete tratamentos envolvidos representam a combinação das duas técnicas analíticas (ICP-OES e ED-XRF) com os três marcadores utilizados na coleta parcial de fezes (Cr, La, Yb), e um tratamento padrão (coleta total de fezes). Na taxa de passagem foram utilizados quatro animais em cada ensaio e as coletas tiveram início após o fornecimento de uma dose única (Taxa de Passagem I) ou a interrupção do fornecimento constante dos marcadores na dieta (Taxa de Passagem II). Os seis tratamentos avaliados corresponderam à combinação dos três marcadores com as duas técnicas analíticas. Para a comparação das curvas obtidas foi feita uma análise de regressão para cada tratamento e os valores de inclinação das retas (b) obtidas por equações de regressão linear foram então comparados pelo teste de Tukey. Os coeficientes de digestibilidade obtidos com os marcadores (coleta parcial de fezes) foram significativamente inferiores (P<0,01) aos resultados obtidos pelo método da coleta total de fezes (tratamento padrão), pelo teste de Dunnett. Ostratamentos que mais se aproximaram do resultado esperado foram o Cromo + ICP-OES e La + ED-XRF, com uma diferença de aproximadamente 3 % em relação ao tratamento padrão. Em relação à taxa de passagem, não houve diferença significativa (P>0,01) entre os dois métodos de determinação (Taxa de Passagem I e II). Entretanto, a taxa de passagem do cromo foi superior à do lantânio e itérbio, provavelmente em decorrência da menor taxa de passagem do milho em relação à ração. Outros estudos precisam ser realizados para obter mais informações a respeito da taxa de passagem do alimento em suínos e dos marcadores mais adequados a serem utilizados em sua determinação. Diversos fatores podem influenciar os resultados de digestibilidade aparente obtidos pelo método da coleta parcial de fezes, tais como marcador utilizado, técnica analítica, concentração do marcador na ração, período de adaptação do marcador no trato digestivo dos animais e porcentagem de recuperação dos marcadores nas fezes. Tais fatores necessitam ser melhor investigados, a fim de propor adequações na metodologia de determinação da digestibilidade aparente pelo método da coleta parcial de fezes.The aim of this work was (1) to evaluate the use of chromic oxide, lanthanum and ytterbium as indigestible markers for the measurement of apparent digestibility in finishing pigs, (2) to determine the rate of passage of feed and (3) to compare two analytical techniques (ICP-OES and ED-XRF). In the digestibility assay, 12 finishing gilts was used. The treatments represent the combination of the two analytical techniques (ICP-OES and ED-XRF) with the three markers used in the grab collection (Cr2O3, La, Yb), and a standard treatment (total collection). Four animals had been used to compare the single dose and withdrawal methods for measuring the rate of passage. Three markers (chromic oxide, lanthanum and ytterbium) with two analytical techniques were used. The rate of marker disappearance, or the slopes of the equations of the linear regression equations (b), was used to compare the rate of passage within treatments. Comparing the marker method to the classical method (total collection), lower digestibility coefficients (P<0,01) were obtained, ranging from 3 percents for Chromium + ICP-OES and Lanthanum + ED-XRF until 6 to 10 percents from the other treatments.The rate of markers passage, determined using rate constants (b), was similar for the withdrawal and single dose methods. However, the rate of passage of chromic oxide was higher than lanthanum and ytterbium, indicating that feed, probably, had a faster rate of passage than maize. Future research is necessary to draw a more accurately comparison of the three markers used in this study, and also, to consider adaptations to the methodology of grab collection, mainly regarding the inclusion of markers in the diet and adaptation period of the markers in the digestive tract of the animals.
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Hochschartner, Gerald. "Revealing the past : the potential of a novel small nucleolar RNA (snoRNA) marker system for studying plant evolution." Thesis, University of St Andrews, 2011. http://hdl.handle.net/10023/1695.
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Despite the existence of various molecular marker systems there are still limitations in distinguishing between closely related species based on molecular divergence, especially when hybridization events have occurred in the past. The characterisation of plant small nucleolar RNA (snoRNA) genes and their organisation into multigene clusters provides a potential nuclear marker system which could help in resolving the phylogenetic history of plants and might be applicable in DNA barcoding. Using closely and distantly related Senecio species, I investigated a combination of fragment length and sequence variation of snoRNA genes/snoRNA gene clusters to assess the utility of this marker system for barcoding and resolving species relationships. SnoRNA gene and gene cluster sequences identified in Arabidopsis thaliana were used to find homologues in other species and subsequently used for the design of universal primers. Most of the universal primer pairs designed were successful in amplifying snoRNA fragments in most Senecio species and fragment length variation between and within species could be detected. Furthermore, the combination of some fragment length datasets produced by different primer pairs enabled the separation of species and the detection of reticulate evolution indicating a high potential of snoRNA gene/gene cluster fragment length polymorphisms (SRFLPs) for phylogenetic reconstructions in Senecio and other plant genera. Most of the examined gene clusters showed a similar gene order in Senecio and Arabidopsis. However, the majority of these clusters appeared to exhibit more copies in Senecio, some of which were distinguishable by a combined sequencing/fragment profiling approach, and shown to be putative single copy regions with the potential to be used as co-dominant markers. However, a high number of paralogues and possible differences in copy number between species excludes these regions from being used in DNA barcoding. This is because specific primers would have to be developed for specific copies which would preclude development of a universal application for barcoding. None of the regions showed enough sequence variation to delimit distinctly closely related Senecio species and were therefore also considered to be unsuitable for DNA barcoding. Although most snoRNA genes and gene clusters might be inapplicable for DNA barcoding, they are likely to be valuable for phylogenetic studies of species groups, genera and families. On this scale, specific primers might act universally and the number of paralogous copies is likely to be equal across the species group of interest.