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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
51

A Parallel Computing Approach for Identifying Retinitis Pigmentosa Modifiers in Drosophila Using Eye Size and Gene Expression Data

Chawin Metah (15361576) 29 April 2023 (has links)
<p>For many years, researchers have developed ways to diagnose degenerative disease in the retina by utilizing multiple gene analysis techniques. Retinitis pigmentosa (RP) disease can cause either partially or totally blindness in adults. For that reason, it is crucial to find a way to pinpoint the causes in order to develop a proper medication or treatment. One of the common methods is genome-wide analysis (GWA). However, it cannot fully identify the genes that are indirectly related to the changes in eye size. In this research, RNA sequencing (RNA-seq) analysis is used to link the phenotype to genotype, creating a pool of candidate genes that might associate with the RP. This will support future research in finding a therapy or treatment to cure such disease in human adults.</p> <p><br></p> <p>Using the Drosophila Genetic Reference Panel (DGRP) – a gene reference panel of fruit fly – two types of datasets are involved in this analysis: eye-size data and gene expression data with two replicates for each strain. This allows us to create a phenotype-genotype map. In other words, we are trying to trace the genes (genotype) that exhibit the RP disease guided by comparing their eye size (phenotype). The basic idea of the algorithm is to discover the best replicate combination that maximizes the correlation between gene expression and eye-size. Since there are 2N possible replicate combinations, where N is the number of selected strains, the original implementation of sequential algorithm was computationally intensive.</p> <p><br></p> <p>The original idea of finding the best replicate combination was proposed by Nguyen et al. (2022). In this research, however, we restructured the algorithms to distribute the tasks of finding the best replicate combination and run them in parallel. The implementation was done using the R programming language, utilizing doParallel and foreach packages, and able to execute on a multicore machine. The program was tested on both a laptop and a server, and the experimental results showed an outstanding improvement in terms of the execution time. For instance, while using 32 processes, the results reported up to 95% reduction in execution time when compared with the sequential version of the code. Furthermore, with the increment of computational capabilities, we were able to explore and analyze more extreme eye-size lines using three eye-size datasets representing different phenotype models. This further improved the accuracy of the results where the top candidate genes from all cases showed connection to RP.</p>
52

Multimarker Analysis of Circulating Tumor Cells in Peripheral Blood of Metastatic Breast Cancer Patients: A Step Forward in Personalized Medicine

Albuquerque, Andreia de, Kaul, Sepp, Breier, Georg, Krabisch, Petra, Fersis, Nikos 05 March 2014 (has links) (PDF)
Aim: To develop an immunomagnetic assay for the isolation of circulating tumor cells (CTCs) followed by the analysis of a multimarker panel, which will enable the characterization of these malignant cells with high accuracy. Patients and Methods: Peripheral blood (PB) was collected from 32 metastatic breast cancer patients and 42 negative controls. The antibodies BM7 and VU1D9 were used for immunomagnetic tumor cell enrichment. A real-time reverse transcription-polymerase chain reaction (RT-PCR) approach for the markers KRT19, SCGB2A2, MUC1, EPCAM, BIRC5 and ERBB2 was used for CTC detection and characterization. Results: The positivity rates for each marker were as follows: 46.9% for KRT19, 25.0% for SCGB2A2, 28.1% for MUC1, 28.1% for EPCAM, 21.9% for BIRC5, and 15.6% for ERBB2. After the creation of individualized cutoffs, the sensitivity and specificity of the combined marker gene panel increased to 56.3% and 100%, respectively. Interestingly, 27.0% of the HER2-negative tumor patients showed ERBB2 mRNA-positive CTCs. Conclusions: The described technique can be used to measure CTCs with great accuracy. The use of a multimarker panel for the characterization of CTCs may provide real-time information and be of great value in therapy monitoring. / Ziel: Entwicklung eines immunomagnetischen Verfahrens zur Isolierung zirkulierender Tumorzellen (CTCs) in Kombination mit einer molekularen Multimarkeranalyse für die hochspezifische Identifizierung maligner Zellen. Patientinnen und Methoden: Peripheres Blut (PB) von 32 Patientinnen mit metastasiertem Mammakarzinom und von 42 gesunden Kontrollen wurde für die immunomagnetische Tumorzellanreicherung mit den Antikörpern BM7 und VU1D9 genutzt. Eine Real-Time Reverse Transkription Polymerase-Kettenreaktion (RT-PCR)-Methodik mit den Markern KRT19, SCGB2A2, MUC1, EPCAM, BIRC5 und ERBB2 wurde für den CTC-Nachweis und die Tumorzellcharakterisierung entwickelt. Ergebnisse: Für die einzelnen Marker wurden die folgenden Positivitätsraten ermittelt: 46,9% für KRT19, 25,0% für SCGB2A2, 28,1% für MUC1, 28,1% für EPCAM, 21,9% für BIRC5 und 15,6% für ERBB2. Nach der Bestimmung individualisierter Cut-off-Werte ergab sich für den kombinierten Multimarkernachweis eine Sensitivität und Spezifität von 56,3% bzw. 100%. Bemerkenswert war der Befund, dass 27,0% der HER2-tumornegativen Patientinnen ERBB2-mRNA-positive CTCs aufwiesen. Schlussfolgerung: Die hier beschriebene Methodik bestimmt CTCs mit hoher Spezifität. Die molekulare Multimarkeranalyse liefert wertvolle Real-Time-Informationen für personalisierte Behandlungsmodalitäten. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.
53

Die Bedeutung von CD96 für das inflammatorische Potenzial IL-9-produzierender T-Helferzellen

Stanko, Katarina 25 January 2019 (has links)
T-Helfer-9-(Th9-)Zellen produzieren große Mengen Interleukin-(IL-)9 und lösen bei Wurm- und Tumorerkrankungen protektive Immunantworten aus. Sie sind aber auch maßgeblich an der Pathogenese chronisch entzündlicher Darmerkrankungen beteiligt. Im Widerspruch zu diesen entzündungsauslösenden Eigenschaften steht ihre Rolle bei der Erzeugung von Toleranz gegenüber allogenen Transplantaten. Diese gegensätzlichen inflammatorischen Eigenschaften deuten eine bisher nicht untersuchte funktionelle Heterogenität an. In vitro-differenzierte allo-reaktive Th9-Zellen zeigten sich in ihrer Gesamtheit pro-inflammatorisch. Dies äußerte sich nach Transfer in recombination activating gene-defiziente (Rag-/-) Mäuse durch einen akut einsetzenden Gewichtsverlust mit intestinaler Entzündung und durch die Abstoßung allogener Hauttransplantate. Mittels Einzelzell-Genexpressionsanalyse wurden zwei Th9-Subpopulationen identifiziert, die sich vor allem in ihrer CD96-Expression unterschieden (CD96low versus CD96high Th9-Zellen). Die differenzielle Expression von CD96 spiegelte sich auch im inflammatorischen Potenzial der Zellen wider. Während der Transfer von CD96low Th9-Zellen in Rag-/- Mäuse einen Gewichtsverlust mit Darmentzündung sowie die Transplantatzerstörung verursachte, zeigten CD96high-rekonstituierte Tiere kaum Entzündungsanzeichen im Transplantat bzw. im Darm. Dementsprechend verloren sie auch kein Gewicht. Es zeigte sich, dass CD96low Th9-Zellen ein höheres Potenzial zur Produktion von IL-4 und IL-9 sowie zur Expansion besaßen als CD96high Th9-Zellen. Eine Blockade von CD96 in vivo stellte die inflammatorischen Eigenschaften von CD96high Th9-Zellen wieder her, wodurch die funktionelle Relevanz der CD96-Expression unterstrichen wurde. Diese Daten belegen, dass es sich bei Th9-Zellen um eine funktionell heterogene Zellpopulation handelt. Weiterhin zeigen sie, dass CD96 – ein Molekül mit bislang unklarer Funktion in CD4+ T-Zellen – die Aktivität von Th9-Zellen negativ beeinflusst. / T helper 9 (Th9) cells are potent producers of interleukin(IL-)9 driving host immunity against worm infections and tumors. Furthermore, they are predominantly involved in the pathogenesis of chronic inflammatory bowel diseases. However, they also induce tolerance in allogeneic transplantation, which contrasts with their pro-inflammatory properties. These observations indicate a functional heterogeneity of Th9 cells not examined so far. Total in vitro differentiated allo-reactive Th9 cells injected into recombination activating gene-deficient (Rag-/-) mice caused weight loss, intestinal inflammation and rejection of allogenic skin grafts which proofed their inflammatory character. However, using single cell profiling, two subsets of Th9 cells mainly differing in their CD96 expression were identified (CD96low versus CD96high Th9 cells). Transfer of CD96low Th9 cells into Rag-/- mice induced severe weight loss, intestinal inflammation and graft destruction. In contrast, transfer of CD96high Th9 cells did cause neither weight loss nor resulted in graft rejection. Transcriptional profiling revealed a higher IL-9 and IL-4 expression potential as well as an increased expansion capacity in CD96low Th9 cells compared to CD96high Th9 cells. Blockade of CD96 in vivo restored the inflammatory properties of CD96high Th9 cells demonstrating, that expression of CD96 controls effector functions in Th9 cells. Thus, Th9 cells are heterogeneous in function. Moreover, this study suggests an inhibitory role for the co-signaling receptor CD96 – a molecule with so far unknown function in CD4+ T cells – in Th9 cells.
54

Structure, evolution and expression of the duplicated growth hormone genes of common carp (Cyprinus carpio)

Murakaeva, Asiya 01 September 2009 (has links)
Der Karpfen, Cyprinus carpio, ist eine tetraploide Fischart aus der Familie Cyprinidae, die vor 20-50 Mio Jahren entstanden ist. Das Ziel der vorliegenden Arbeit war der Versuch, die funktionelle Rolle der duplizierten GH Gene des Karpfens durch das Studium ihrer Struktur, Evolution und Expression zu verstehen. Die Introns des zweiten GH Gens des Karpfens wurden erstmalig sequenziert und Sequenzvergleiche der kodierenden und nicht-kodierenden Bereiche von Allelen beider GH Gene wurden vorgenommen. Eine phylogenetische Analyse wurde durchgefuhrt, um die Beziehungen der GH Gene des Karpfens zu denen des tetraploiden Goldfischs und anderer diploider Cypriniden zu untersuchen. Zusatzlich wurden weitere duplizierte Gene des Karpfens, von denen einige auch fur das Wachstum von Bedeutung sind, phylogenetisch analysiert. Der Test der relativen Evolutionsrate nach Tajima (1993) zeigte einen statistisch signifikanten Anstieg der Evolutionsrate des GH I Gens beim Karpfen. Es wurden in der vorliegenden Arbeit einige weitere duplizierte Genpaare des Karpfens und Goldfischs gefunden, die ebenfalls eine Lockerung funktioneller Zwange oder sogar Beweise fur positive Darwin?sche Selektion bei einem der beiden Duplikate zeigen. Der Expressionstest hat gezeigt, dass die GH I und GH II Gene auf identischen Niveaus bei Karpfenbrut exprimiert werden, wahrend bei ein Jahr alten Karpfen, drei Jahre alten Mannchen und Weibchen sowie den 10 Monate alten, an kalte Temperaturen (2°C) angepassten Fischen die Expression von GH II statistisch signifikant geringer war als die von GH I. Es wurde eine neue und einfache Methode zur Herstellung von rekombinanten, biologisch aktiven GH-Proteinen ohne Notwendigkeit des Refolding entwickelt. Sie ermoglicht spatere Tests, ob die Aktivitat von unterschiedlichen GH-Varianten des Karpfens gleich oder unterschiedlich ist. / The common carp, Cyprinus carpio, is a tetraploid fish species from the family Cyprinidae that arose about 20-50 Myr ago. The aim of the present work was attempting to understand the functional role of the duplicated common carp GH genes by studying their structure, evolution and expression. The introns of the second GH gene of common carp were sequenced for the first time and sequence comparisons of coding and non-coding regions of alleles of both GH genes were carried out. A phylogenetic analysis was done to examine the relationships of common carp GH genes with GH genes of the tetraploid goldfish and other diploid Cyprinids. In addition, phylogenetic analyses were done with other duplicated genes of common carp, some of which also important for growth. The relative rate test of Tajima (1993) showed a statistically significant increase in the evolution rate of the common carp GH I gene. In addition, some other duplicated gene pairs in common carp and goldfish with relaxation of functional constraints or even evidence of positive Darwinian selection in one of the two gene duplicates were found in the present study. The test of expression rates of the two GH genes has shown that the GH I and GH II genes were expressed at similar levels in carp fry. In contrast, the expression of GH II was statistically significantly lower than that of GH I in one year old carp, three years old males and females as well as in 10 months old fish adapted to cold temperature (2°C). To enable testing the hypothesis if activity of GH diverged between different GH variants of common carp a new and simple method for production of recombinant, biologically active GH proteins without the necessity of refolding was developed.
55

Untersuchungen zur Genexpression und Differenzierung muriner embryonaler Stammzellen in vitro zur Prädiktion eines embryotoxischen Potentials ausgewählter Chemikalien / Investigations for gene expression and differentiation of murine embryonic stem cells in vitro to predict the embryotoxic potential of selected chemicals

Mazurek, Nicole January 2007 (has links)
Der Embryonale Stammzelltest (EST) ist ein validierter In-vitro-Embryotoxizitätstest, der zur Untersuchung embryotoxischer Wirkungen von Chemikalien eingesetzt werden kann. Während des zehntägigen Differenzierungsassays differenzieren sich die pluripotenten murinen embryonalen Stammzellen (ES-Zellen) der Linie D3 in vitro in spontan kontrahierende Herzmuskelzellen. Dabei rekapitulieren sie Prozesse der frühen Embryogenese in vivo. Ein Zytotoxizitätsassay mit D3-Zellen und ausdifferenzierten, adulten 3T3-Maus-Fibroblasten dient der Ermittlung allgemeiner zytotoxischer Effekte und unterschiedlicher Sensitivitäten beider Zelllinien. Somit basiert der EST auf den beiden wichtigsten Mechanismen pränataler Toxizität, der Störung der Differenzierung und der Zytotoxizität. Ziel dieser Arbeit war es, mit Hilfe des EST das embryotoxische Potential der vier Chemikalien Trichostatin A (TSA), Methylazoxymethanolacetat (MAMac), Natriumdodecylsulfat (SDS) und Benzoesäure (BA) abzuschätzen. Dazu wurde mikroskopisch ermittelt, bei welcher Testsubstanzkonzentration in 50 % der während der In-vitro-Differenzierung gebildeten Embryonalkörperchen die Kardiomyozytendifferenzierung inhibiert wird (ID50). Außerdem wurde die halbmaximale Hemmkonzentration des Zellwachstums auf die beiden Zelllinien bestimmt (IC50D3 bzw. IC503T3). Als Erweiterung dieses konventionellen EST wurden mittels quantitativer Real Time-PCR an den Tagen 5, 7 und 10 der Differenzierung zusätzlich Genexpressionsanalysen etablierter herzmuskelspezifischer Markergene (Mesoderm Posterior 1, Tag 5; Myosin light chain 1, Tag 7 und 10) durchgeführt. Deren Expression korreliert in den ES-Zellen mit der embryonalen Herzdifferenzierung in vivo und kann zur Ermittlung der von der Prüfsubstanz hervorgerufenen halbmaximalen Hemmung der Genexpression in den Kardiomyozyten (IC50 Exp) herangezogen werden. Um letztlich embryotoxische Effekte in vivo auf Grundlage der ermittelten In-vitro-Daten abschätzen zu können, wurden die ermittelten Parameter mittels eines für den EST empirisch abgeleiteten mathematischen Prädiktionsmodells (PM) zur Klassifizierung der Testsubstanzen als nicht, schwach oder stark embryotoxisch herangezogen. Für jede der Substanzen waren die ermittelten Halbhemmkonzentrationen in den überwiegenden Fällen vergleichbar und führten unter Verwendung des PMs im konventionellen und im molekularen EST zu deren identischer Klassifizierung. TSA wurde als „stark embryotoxisch“ klassifiziert und beeinflusste insbesondere das Differenzierungspotential der ES-Zellen. Das als „schwach embryotoxisch“ klassifizierte SDS wirkte auf die D3-Zellen stärker differenzierungsinhibierend als zytotoxisch, hemmte jedoch das Wachstum der 3T3-Zellen bereits in deutlich niedrigeren Konzentrationen. MAMac und BA wurden als „nicht embryotoxisch“ klassifiziert. Bei ihnen stand die zytotoxische Wirkung deutlich im Vordergrund. Diese Prädiktionen stimmten mit In-vivo-Befunden überein, was von der Stabilität und der Brauchbarkeit der im konventionellen und molekularen EST ermittelten Parameter zeugte. Einzige Ausnahme war das als Entwicklungsneurotoxin in vivo bekannte MAMac. Da der EST auf mesodermaler Differenzierung basiert, können spezifische Effekte auf neuronale Entwicklungsprozesse offenbar nicht vollständig erfasst werden. Substanzkonzentrationen, die sich als differenzierungsinhibierend auf die morphologische Kardiomyozytendifferenzierung erwiesen haben, führten auch zu einer messbaren Repression der herzmuskelspezifischen Genexpression. Dabei erwies sich die IC50 Exp als ebenso sensitiv wie die konventionellen Parameter und als nutzbringende Ergänzung zu diesen, da sie bereits nach 5 bzw. 7 Tagen der In-vitro-Differenzierung eine mit dem mikroskopischen Parameter übereinstimmende Einschätzung des embryotoxischen Potentials der Chemikalien in vivo ermöglichte. Genexpressionsanalysen weiterer differenzierungsspezifischer Gene können zusätzlich zur Aufklärung zu Grunde liegender Mechanismen der Embryotoxizität von Testsubstanzen dienen. Somit kann der EST durch die Vorteile der Stammzelltechnologie und der Genexpressionsanalyse als neues prädiktives Screening-Instrument zur frühzeitigen Detektion embryotoxischer Substanzeffekte in der pharmazeutischen und chemischen Industrie genutzt werden. / The embryonic stem cell test (EST) represents a validated in vitro embryotoxicity test that can be utilised for investigations of embryotoxic effects of chemical substances. During the 10-day differentiation assay the pluripotent murine embryonic stem cells (ES cells) of the D3 line differentiate in vitro into spontaneously beating cardiac muscle cells that can be observed microscopically. Thereby, ES cells recapitulate processes of early embryogenesis in vivo. A cytotoxicity assay with D3 cells as well as differentiated, adult 3T3 mouse fibroblasts is used to determine general cytotoxic effects and to consider differences in the sensitivity of both cell lines. Hence the EST is based on the two most important mechanisms of prenatal toxicity, such as inhibition of differentiation and cytotoxicity. The aim of the presented work consisted in the evaluation of the embryotoxic potential of the four chemicals trichostatin A (TSA), methylazoxymethanolacetate (MAMac), sodium dodecyl sulfate (SDS) and benzoic acid (BA) by means of the EST. For this purpose the concentration of the test substance that causes an inhibition of cardiomyocyte differentiation in 50 % of the embryoid bodies which are formed during the in vitro differentiation (ID50-value) and the halfmaximal inhibiting concentration of cell proliferation of D3 and 3T3 cell lines (IC50D3 and IC503T3) were determined. As extension of this conventional EST, the effect of test substances was investigated at the molecular level by gene expression analyses of cardiac specific genes (Mesoderm Posterior 1, day 5; Myosin light chain 1, day 7 and 10). Their expression in ES cells correlates with the embryonic heart differentiation in vivo. Quantitative Real Time-PCR gene expression analysis was used to determine the halfmaximal inhibition of the cardiomyocyte gene expression (IC50 Exp) caused by the test compound. To predict embryotoxic effects in vivo from the determined in vitro data, these parameters were used for the classification of the test chemicals as non, weak or strong embryotoxic via a mathematical prediction model (PM). In the majority of cases comparable halfmaximal inhibiting concentrations were calculated in the conventional and molecular EST that resulted in the identical classification of the tested chemicals concerning their embryotoxic potential. TSA was estimated as “strongly embryotoxic” and affected particularly the differentiation potential of the ES cells. SDS was classified as “weakly embryotoxic” and acted by inhibiting the differentiation of D3 cells at concentrations lower than cytotoxic concentrations but already repressed the growth of the 3T3 cells in significantly lower ranges. As to MAMac and BA that were classified as “non-embryotoxic” the cytotoxic effects on both cell lines predominated. These predictions were consistent with in vivo findings that testifies the stability and the usefulness of the parameters used in the conventional and molecular EST. MAMac, which is known as a developmental neurotoxin in vivo, represented the single exception. Its misclassification as compared to in vivo data may originate from the limitations of the model system that is based on mesodermal differentiation. Thus, specific effects on neuronal developmental processes obviously cannot be detected completely. Gene expression analysis showed that test substance concentrations which were proved to be inhibiting on the morphological differentiation of cardiomyocytes caused a repression of cardiac-specific marker gene expression as well. Thereby, IC50 Exp-values proved to be just as sensitive as the conventional parameters and can provide valuable and supportive data. They allowed a prediction of the embryotoxic potential of the chemicals in vivo already at day 5 and day 7 of in vitro differentiation. Moreover, gene expression analysis of appropriate differentiation specific genes could be used to investigate mechanisms that are responsible for embryotoxic properties of the test compounds. Thus, the EST is considered to represent a new, predictive screening test especially in the pharmaceutical industry to detect the embryotoxic potential of chemical compounds early in the process of compound development.
56

Multimarker Analysis of Circulating Tumor Cells in Peripheral Blood of Metastatic Breast Cancer Patients: A Step Forward in Personalized Medicine

Albuquerque, Andreia de, Kaul, Sepp, Breier, Georg, Krabisch, Petra, Fersis, Nikos January 2012 (has links)
Aim: To develop an immunomagnetic assay for the isolation of circulating tumor cells (CTCs) followed by the analysis of a multimarker panel, which will enable the characterization of these malignant cells with high accuracy. Patients and Methods: Peripheral blood (PB) was collected from 32 metastatic breast cancer patients and 42 negative controls. The antibodies BM7 and VU1D9 were used for immunomagnetic tumor cell enrichment. A real-time reverse transcription-polymerase chain reaction (RT-PCR) approach for the markers KRT19, SCGB2A2, MUC1, EPCAM, BIRC5 and ERBB2 was used for CTC detection and characterization. Results: The positivity rates for each marker were as follows: 46.9% for KRT19, 25.0% for SCGB2A2, 28.1% for MUC1, 28.1% for EPCAM, 21.9% for BIRC5, and 15.6% for ERBB2. After the creation of individualized cutoffs, the sensitivity and specificity of the combined marker gene panel increased to 56.3% and 100%, respectively. Interestingly, 27.0% of the HER2-negative tumor patients showed ERBB2 mRNA-positive CTCs. Conclusions: The described technique can be used to measure CTCs with great accuracy. The use of a multimarker panel for the characterization of CTCs may provide real-time information and be of great value in therapy monitoring. / Ziel: Entwicklung eines immunomagnetischen Verfahrens zur Isolierung zirkulierender Tumorzellen (CTCs) in Kombination mit einer molekularen Multimarkeranalyse für die hochspezifische Identifizierung maligner Zellen. Patientinnen und Methoden: Peripheres Blut (PB) von 32 Patientinnen mit metastasiertem Mammakarzinom und von 42 gesunden Kontrollen wurde für die immunomagnetische Tumorzellanreicherung mit den Antikörpern BM7 und VU1D9 genutzt. Eine Real-Time Reverse Transkription Polymerase-Kettenreaktion (RT-PCR)-Methodik mit den Markern KRT19, SCGB2A2, MUC1, EPCAM, BIRC5 und ERBB2 wurde für den CTC-Nachweis und die Tumorzellcharakterisierung entwickelt. Ergebnisse: Für die einzelnen Marker wurden die folgenden Positivitätsraten ermittelt: 46,9% für KRT19, 25,0% für SCGB2A2, 28,1% für MUC1, 28,1% für EPCAM, 21,9% für BIRC5 und 15,6% für ERBB2. Nach der Bestimmung individualisierter Cut-off-Werte ergab sich für den kombinierten Multimarkernachweis eine Sensitivität und Spezifität von 56,3% bzw. 100%. Bemerkenswert war der Befund, dass 27,0% der HER2-tumornegativen Patientinnen ERBB2-mRNA-positive CTCs aufwiesen. Schlussfolgerung: Die hier beschriebene Methodik bestimmt CTCs mit hoher Spezifität. Die molekulare Multimarkeranalyse liefert wertvolle Real-Time-Informationen für personalisierte Behandlungsmodalitäten. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.
57

Analysis of integration sites of transgenic sheep generated by lentiviral vectors using next-generation sequencing technology

Chen, Yu-Hsiang 31 July 2014 (has links)
Indiana University-Purdue University Indianapolis (IUPUI) / The development of new methods to carry out gene transfer has many benefits to several fields, such as gene therapy, agriculture and animal health. The newly established lentiviral vector systems further increase the efficiency of gene transfer dramatically. Some studies have shown that lentiviral vector systems enhance efficiency over 10-fold higher than traditional pronuclear injection. However, the timing for lentiviral vector integration to occur remains unclear. Integrating in different stages of embryogenesis might lead to different integration patterns between tissues. Moreover, in our previous study we found that the vector copy number in transgenic sheep varied, some having one or more copies per cells while other animals having less than one copy per cell suggesting mosaicism. Here I hypothesized that injection of a lentiviral vector into a single cell embryo can lead to integration very early in embryogenesis but can also occur after several cell divisions. In this study, we focus on investigating integration sites in tissues developing from different germ layers as well as extraembryonic tissues to determine when integration occurs. In addition, we are also interested in insertional mutagenesis caused by viral sequence integration in or near gene regions. We utilize linear amplification-mediated polymerase chain reaction (LAM-PCR) and next- generation sequencing (NGS) technology to determine possible integration sites. In this study, we found the evidence based on a series of experiments to support my hypothesis, suggesting that integration event also happens after several cell divisions. For insertional mutagenesis analysis, the closest genes can be found according to integration sites, but they are likely too far away from the integration sites to be influenced. A well-annotated sheep genome database is needed for insertional mutagenesis analysis.
58

Transcription regulation of the class II alcohol dehydrogenase 7 (ADH7)

Jairam, Sowmya January 2014 (has links)
Indiana University-Purdue University Indianapolis (IUPUI) / The class IV alcohol dehydrogenase (ADH7, µ-ADH, σ-ADH) efficiently metabolizes ethanol and retinol. ADH7 is expressed mainly in the upper gastrointestinal tract with no expression in the liver unlike the other ADHs, and is implicated in various diseases including alcoholism, cancer and fetal alcohol syndrome. Genome wide studies have identified significant associations between ADH7 variants and alcoholism and cancer, but the causative variants have not been identified. Due to its association with two important metabolic pathways and various diseases, this dissertation is focused on studying ADH7 regulation and the effects of variants on this regulation using cell systems that replicate endogenous ADH7 expression. We identified elements regulating ADH7 transcription and observed differences in the effects of variants on gene expression. A7P-G and A7P-A, two promoter haplotypes differing in a single nucleotide at rs2851028, had different transcriptional activities and interacted with variants further upstream. A sequence located 12.5 kb upstream (7P10) can function as an enhancer. These complex interactions indicate that the effects of variants in the ADH7 regulatory elements depend on both sequence and cellular context, and should be considered in interpretation of the association of variants with alcoholism and cancer. The mechanisms governing the tissue-specific expression of ADH7 remain unexplained however. We identified an intergenic region (iA1C), located between ADH7 and ADH1C, having enhancer blocking activity in liver-derived HepG2 cells. This enhancer blocking function was cell- and position- dependent with no activity seen in CP-A esophageal cells. iA1C had a similar effect on the ectopic SV40 enhancer. The CCCTC-binding factor (CTCF) bound iA1C in HepG2 cells but not in CP-A cells. Our results suggest that in liver-derived cells, iA1C blocks the effects of downstream ADH enhancers and thereby contributes to the cell specificity of ADH7 expression. Thus, while genetic factors determine level of ADH7 transcriptional activity, iA1C helps determine the cell specificity of transcription.
59

Applications of Persistent Homology and Cycles

Mandal, Sayan 13 November 2020 (has links)
No description available.
60

The effects of various combinations of different classes of anticancer drugs and tyrosine kinase inhibitors on the human MCF-7 breast carcinoma cell line

Abrahams, Beynon January 2014 (has links)
Magister Scientiae (Medical Bioscience) - MSc(MBS) / This study investigated the effects of TKIs on the growth and proliferation of MCF-7 breast carcinoma cells in culture. MCF-7 cells were exposed to different concentrations of TKIs alone and in combination with each other. Inhibition of cell growth by TKIs used individually occurred in a dose- and time-dependent manner. When EGFR Inhibitor I, EGFR Inhibitor II/BIBX1382 and the multi-specific EGFR/ErbB-2/ErB-4 Inhibitor were used in combination with each other at equimolar log dose concentrations, the combined effects on cell growth was significantly different to inhibitors used individually as reflected in a decreased EC50 (IC50) during combination treatments. Generally, for the combinations with DOX, CPL and the TKIs, synergistic as well as antagonistic effects were observed at isoeffective concentrations with resultant decreases in dose reduction indices (DRIs) implying greater efficacies with the respective combinations. In this study, conventional PCR was used to detect and illustrate the presence of the EGFR gene in the samples, while RT-qPCR was used to determine the mRNA expression levels of this gene in MCF-7 breast carcinoma cells

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