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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.
1

Functional Characterization of the NSF1 (YPL230W) Gene using Correlation Clustering and Genetic Analysis in Saccharomyces Cerevisiae

Bessonov, Kyrylo 09 January 2012 (has links)
High throughput technologies such as microarrays and modern genome sequencers produce enormous amounts of data that require novel data processing. This thesis proposes a method called Interdependent Correlation Cluster (ICC) to analyze the relations between genes represented by microarray data that are conditioned on a specific target gene. Based on Correlation Clustering, the proposed method analyzes a large set of correlation values related to the gene expression profiles extracted from given microarray datasets. The proposed method works on any size microarray datasets and could be applied to any target gene. In this study the selected target gene, NSF1 /USV1 / YPL230W, encodes a poorly characterized C2H2 zinc finger transcription factor (TF) involved in stress responses in yeast. The method is successful in the identification of novel NSF1 functional roles during fermentation stress conditions in the M2 industrial yeast strain. The new identified functions include regulation of energy and sulfur metabolism, protein synthesis, ribosomal assembly and protein trafficking as well as other processes. NSF1 involvement in sulfur metabolism was experimentally confirmed using biological laboratory techniques. Importantly, implication of NSF1 in sulfur metabolism regulation has highly relevant implications to wine and beer production industries concerned with production of compounds having sulfur-like off odour (SLO) and toxic properties. The correlation clustering also provides a means of understanding complex interactions existing between genes. / The pdf file contains numerous hyperlinks and bookmarks to facilitate navigation. This thesis will be of interest to those working with topics such as data mining of microarray data, novel gene function discovery and prediction, and genome-wide responses to fermentation stresses. / Ministry of Training, Colleges and Universities of Ontario (Ontario Graduate Scholarship and Ontario Graduate Scholarships in Science and Technology); The Natural Sciences and Engineering Research Council of Canada (NSERC)
2

Brain Aging: Uncovering Cortical Characteristics of Healthy Aging in Young Adults

Bajaj, Sahil, Alkozei, Anna, Dailey, Natalie S., Killgore, William D. S. 11 December 2017 (has links)
Despite extensive research in the field of aging neuroscience, it still remains unclear whether age related cortical changes can be detected in different functional networks of younger adults and whether these networks respond identically to healthy aging. We collected high-resolution brain anatomical data from 56 young healthy adults (mean age = 30.8 +/- 8.1 years, 29 males). We performed whole brain parcellation into seven functional networks, including visual, somatomotor, dorsal attention, ventral attention, limbic, frontoparietal and default mode networks. We estimated intracranial volume (ICV) and averaged cortical thickness (CT), cortical surface area (CSA) and cortical volume (CV) over each hemisphere as well as for each network. Averaged cortical measures over each hemisphere, especially CT and CV, were significantly lower in older individuals compared to younger ones (one-way ANOVA, p < 0.05, corrected for multiple comparisons). There were negative correlations between age and averaged CT and CV over each hemisphere (p < 0.05, corrected for multiple comparisons) as well as between age and ICV (p = 0.05). Network level analysis showed that age was negatively correlated with CT for all functional networks (p < 0.05, corrected for multiple comparisons), apart from the limbic network. While age was unrelated to CSA, it was negatively correlated with CV across several functional networks (p < 0.05, corrected for multiple comparisons). We also showed positive associations between CV and CT and between CV and CSA for all networks (p < 0.05, corrected for multiple comparisons). We interpret the lack of association between age and CT of the limbic network as evidence that the limbic system may be particularly resistant to age-related declines during this period of life, whereas the significant age-related declines in averaged CT over each hemisphere as well as in all other six networks suggests that CT may serve as a reliable biomarker to capture the effect of normal aging. Due to the simultaneous dependence of CV on CT and CSA, CV was unable to identify such effects of normal aging consistently for the other six networks, but there were negative associations observed between age and averaged CV over each hemisphere as well as between age and ICV. Our findings suggest that the identification of early cortical changes within various functional networks during normal aging might be useful for predicting the effect of aging on the efficiency of functional performance even during early adulthood.
3

Network Models for Capturing Molecular Feature and Predicting Drug Target for Various Cancers

Liu, Enze 12 1900 (has links)
Indiana University-Purdue University Indianapolis (IUPUI) / Network-based modeling and analysis have been widely used for capturing molecular trajectories of cellular processes. For complex diseases like cancers, if we can utilize network models to capture adequate features, we can gain a better insight of the mechanism of cancers, which will further facilitate the identification of molecular vulnerabilities and the development targeted therapy. Based on this rationale, we conducted the following four studies: A novel algorithm ‘FFBN’ is developed for reconstructing directional regulatory networks (DEGs) from tissue expression data to identify molecular features. ‘FFBN’ shows unique capability of fast and accurately reconstructing genome-wide DEGs compared to existing methods. FFBN is further used to capture molecular features among liver metastasis, primary liver cancers and primary colon cancers. Comparisons among these features lead to new understandings of how liver metastasis is similar to its primary and distant cancers. ‘SCN’ is a novel algorithm that incorporates multiple types of omics data to reconstruct functional networks for not only revealing molecular vulnerabilities but also predicting drug targets on top of that. The molecular vulnerabilities are discovered via tissue-specific networks and drug targets are predicted via cell-line specific networks. SCN is tested on primary pancreatic cancers and the predictions coincide with current treatment plans. ‘SCN website’ is a web application of ‘SCN’ algorithm. It allows users to easily submit their own data and get predictions online. Meanwhile the predictions are displayed along with network graphs and survival curves. ‘DSCN’ is a novel algorithm derived from ‘SCN’. Instead of predicting single targets like ‘SCN’, ‘DSCN’ applies a novel approach for predicting target combinations using multiple omics data and network models. In conclusion, our studies revealed how genes regulate each other in the form of networks and how these networks can be used for unveiling cancer-related biological processes. Our algorithms and website facilitate capturing molecular features for cancers and predicting novel drug targets.
4

Functional network macroscopes for probing past and present Earth system dynamics

Donges, Jonathan Friedemann 14 January 2013 (has links)
Vom Standpunkt des Physikers aus gesehen, ist die Erde ein dynamisches System von großer Komplexität. Funktionale Netzwerke werden aus Beobachtungs-, und Modelldaten abgeleitet oder aufgrund theoretischer Überlegungen konstruiert. Indem sie statistische Zusammenhänge oder kausale Wirkbeziehungen zwischen der Dynamik gewisser Objekte, z.B. verschiedenen Sphären des Erdsystems, Prozessen oder lokalen Feldvariablen darstellen, bieten funktionale Netzwerke einen natürlichen Ansatz zur Bearbeitung fundamentaler Probleme der Erdsystemanalyse. Dazu gehören Fragen nach dominanten, dynamischen Mustern, Telekonnektionen und Rückkopplungsschleifen in der planetaren Maschinerie, sowie nach kritischen Elementen wie Schwellwerten, sogn. Flaschenhälsen und Schaltern im Erdsystem. Der erste Teil dieser Dissertation behandelt die Theorie komplexer Netzwerke und die netzwerkbasierte Zeitreihenanalyse. Die Beiträge zur Theorie komplexer Netzwerke beinhalten Maße und Modelle zur Analyse der Topologie (i) von Netzwerken wechselwirkender Netzwerke und (ii) Netzwerken mit ungleichen Knotengewichten, sowie (iii) eine analytische Theorie zur Beschreibung von räumlichen Netzwerken. Zur Zeitreihenanalyse werden (i) Rekurrenznetzwerke als eine theoretisch gut begründete, nichtlineare Methode zum Studium multivariater Zeitreihen vorgestellt. (ii) Gekoppelte Klimanetzwerke werden als ein exploratives Werkzeug der Datenanalyse zur quantitativen Charakterisierung der komplexen statistischen Interdependenzstruktur innerhalb und zwischen distinkten Feldern von Zeitreihen eingeführt. Im zweiten Teil der Arbeit werden Anwendungen zur Detektion von dynamischen Übergängen (Kipppunkten) in Zeitreihen, sowie zum Studium von Flaschenhälsen in der atmosphärischen Zirkulationsstruktur vorgestellt. Die Analyse von Paläoklimadaten deutet auf mögliche Zusammenhänge zwischen großskaligen Veränderungen der afrikanischen Klimadynamik während des Plio-Pleistozäns und Ereignissen in der Menschheitsevolution hin. / The Earth, as viewed from a physicist''s perspective, is a dynamical system of great complexity. Functional complex networks are inferred from observational data and model runs or constructed on the basis of theoretical considerations. Representing statistical interdependencies or causal interactions between objects (e.g., Earth system subdomains, processes, or local field variables), functional complex networks are conceptually well-suited for naturally addressing some of the fundamental questions of Earth system analysis concerning, among others, major dynamical patterns, teleconnections, and feedback loops in the planetary machinery, as well as critical elements such as thresholds, bottlenecks, and switches. The first part of this thesis concerns complex network theory and network-based time series analysis. Regarding complex network theory, the novel contributions include consistent frameworks for analyzing the topology of (i) general networks of interacting networks and (ii) networks with vertices of heterogeneously distributed weights, as well as (iii) an analytical theory for describing spatial networks. In the realm of time series analysis, (i) recurrence network analysis is put forward as a theoretically founded, nonlinear technique for the study of single, but possibly multivariate time series. (ii) Coupled climate networks are introduced as an exploratory tool of data analysis for quantitatively characterizing the intricate statistical interdependency structure within and between several fields of time series. The second part presents applications for detecting dynamical transitions (tipping points) in time series and studying bottlenecks in the atmosphere''s general circulation structure. The analysis of paleoclimate data reveals a possible influence of large-scale shifts in Plio-Pleistocene African climate variability on events in human evolution.
5

Evolutionary genetics of malaria: genetic susceptibility and natural selection

Sikora, Martin 04 June 2010 (has links)
Una de les forces selectives més fortes que han afectat a les poblacions humanes en la història més recent és el paràsit de la malària: Plasmodium falciparum, que és la causa de varis exemples d'adaptació induïda per patògens en els éssers humans. Una forma especial de malària és l'associada a l'embaràs, que es caracteritza per l'acumulació d'eritròcits infectats en la placenta, i que pot arribar a causar fins a 200.000 morts maternoinfantils cada any. L'objectiu d'aquest treball és descriure com aquesta forma peculiar de malària ha afectat la variació genètica humana. Amb aquesta finalitat, hem utilitzat mètodes tant de la genètica evolutiva com de l'epidemiologia molecular, resultant en la primera investigació a gran escala de la base genètica de la malària placentària. Els resultats ofereixen una nova visió sobre els gens que modulen el risc d'infecció, ,així com de la selecció natural actuant sobre les vies cel·lulars implicades en la patogènesi de la malaltia. Finalment, també aportem noves dades sobre l'estructura genètica de les poblacions sub-saharianes analitzades. / One of the strongest selective forces affecting human populations in recent history is the malaria parasite Plasmodium falciparum, which is the cause of a variety of well-established examples of pathogen-induced adaptation in humans. A special form of malaria is pregnancy-associated malaria, which is characterised by the accumulation of infected erythrocytes in the placenta, and causes up to 200,000 maternal and infant deaths every year. The aim of this work is to characterise how this particular form of malaria has shaped human genetic variation. To that end we use methods of both evolutionary genetics and molecular epidemiology, reporting the first large-scale investigation of the genetic basis of placental infection. Our results provide new insights into genes modulating the risk of infection, as well as natural selection acting on cellular pathways involved in the pathogenesis of the disease. Finally, we also provide new data on the genetic structure of affected populations in Sub-Saharan Africa.

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