Systems Biology Commons^™

Classification Of Breast Cancer Patients Using Somatic Mutation Profiles And Machine Learning Approaches, Suleyman Vural

Theses & Dissertations

The high degree of heterogeneity observed in breast cancers makes it very difficult to classify cancer patients into distinct clinical subgroups and consequently limits the ability to devise effective therapeutic strategies. In this study, we explore the use of gene mutation profiles to classify, characterize and predict the subgroups of breast cancers. We analyzed the whole exome sequencing data from 358 ethnically similar breast cancer patients in The Cancer Genome Atlas (TCGA) project. Identified somatic and non-synonymous single nucleotide variants were assigned a quantitative score (C-score) that represents the extent of negative impact on the function of the gene. Using …

Sampling Terrestrial Arthropod Biodiversity: A Case Study In Arkansas, Michael Joseph Skvarla

Graduate Theses and Dissertations

The Interior Highlands is a biodiversity hotspot, with at least 200 known endemic species, but is understudied compared to hotspots, such as the Southern Appalachians. In order to begin to rectify this issue, a nine month study was conducted from mid-March through early December at a 4 ha site at Steel Creek, Buffalo National River, in Newton County, Arkansas. Thirteen collecting methods were employed, including three colors of Lindgren funnel trap, five colors of pan trap, Malaise traps, canopy traps with upper and lower collectors, pitfall traps, and Berlese-Tullgren extraction of leaf litter, which resulted in the collection of 1311 …

Systematics Of Testudacarine Torrent Mites (Parasitengona: Torrenticolidae), Joseph Charles O'Neill

Graduate Theses and Dissertations

Thirteen new species of Testudacarus (Torrenticolidae: Testudacarinae) are described, four species are redescribed, and the status of previously problematic species are addressed. For Testudacarinae this represents the first published: 1) descriptions from multiple specimens (therefore providing ranges); 2) colored photographs; 3) explicit illustrations and discussion of sexual dimorphism within the subfamily; 4) genetic data. A comprehensive literature review is also included.

Ichthyoplankton Distribution And Assemblage Within And Around The Saco River Plume, Tracey Bauer

All Theses And Dissertations

A majority of research has focused on the importance of large river plumes for ichthyoplankton survival and recruitment. However, the impacts of smaller, more ephemeral river plumes, such as those commonly found in the Gulf of Maine, on ichthyoplankton are far less understood. The purpose of the current study was to use a small river plume located in the southern Gulf of Maine as a model system to increase our understanding of their effects on ichthyoplankton distribution and diversity, and determine what biotic and abiotic factors may be influencing any differences observed. Plankton tow sampling revealed that although ichthyoplankton abundance …

Functional Analysis Of Synthetic Gene Circuits Controlling A Protein Pump In Yeast, Junchen Diao

Dissertations & Theses (Open Access)

Synthetic biology aims to build biological devices to understand living systems and explore new applications. Synthetic gene circuits such as genetic switches, oscillators and logic gates are at the core of many synthetic biology applications. These gene circuits often include a sensor/regulator protein capable to detect small molecules and then transduce them into a regulatory signal to generate measurable output. Similar signal transduction networks are also abundant in nature. However, in many natural and engineered scenarios, the output also affects the regulator/sensor protein. How such interactions between the regulator/sensor and the output affect synthetic gene circuit function has not been …

The Greenhouse Effect: Decomposition Rates In Human Remains Wrapped In Plastic, Barbara R. Forman

Masters Theses

Determining an accurate estimation of the postmortem interval (PMI) of human remains is important for several reasons. First, it is used to determine whether the individual is recently deceased, and therefore of medicolegal concern. If so, the estimated PMI is used in narrowing the possible identities of the deceased. PMI can also be used in excluding, or convicting, a murder suspect.

Though deviations may occur, it has been found that PMI can be calculated from the decomposition stages with reasonable accuracy (Galloway 1989, Megyesi 2001, Megyesi et al. 2005, Schiel 2008, Simmons et al. 2010). Some factors, such as low …

Effects Of Management Practices On Grassland Plant And Bird Community Composition In Kane County Forest Preserves, Colleen R. Zumpf

All Student Theses

Loss of grassland ecosystems over the past century has increased importance of efforts to improve and restore habitat for native plant species and the biotic communities they support. As a result of these efforts, biotic and abiotic conditions and interactions with the environment are altered. Species evolution based on these particular environmental conditions has caused many species to be mapped onto various environmental gradients which can be defined as niche separation. This study attempted to determine what environmental gradients had the strongest impact upon grassland bird and plant species niche separation, particularly those gradients defined by management activities such as …

Phylogenetic Relationships Of Samydaceae And Taxonomic Revision Of The Species Of Casearia In South-Central Asia, Tharangamala Samarakoon

Dissertations

The flowering plant family Samydaceae was recently reinstated to include 14 genera and about 256 species of tropical trees and shrubs. Preliminary analyses of relationships in the family, however, indicated that the largest genus in the family, Casearia, is not monophyletic and that several smaller groups are probably misplaced. In order to affirm or refute those hypotheses, additional DNA sequence data with broader taxon sampling from the Old World were gathered for phylogenetic analysis. In particular, rapidly evolving plastid (matK, ndhF, psbA-trnH, trnL, and trnL-F) and nuclear (EMB2765 and GBSSI) DNA …

Integrating Phylogenomics, Biogeography And Systematics To Explore The Taxonomy And The Rise Of The Ratsnakes, Xin Chen

Dissertations, Theses, and Capstone Projects

Understanding the evolutionary processes that create the spectacular diversity of organisms, both in species numbers and form, is a primary goal for biologists. Global ratsnakes are a species-rich assemblage with high morphological and ecological diversity and a distribution that encompasses both the Old World (OW) and the New World (NW). To explore the mechanism leading to the divergence of the ratsnakes, I tested the hypotheses regarding the area of origin and global dispersal, and examined the patterns of diversification and trait evolution. Given adaptive radiation via ecological opportunity, a diversity-dependent diversification pattern and an early burst trait evolutionary pattern are …

In-Silico Models For Capturing The Static And Dynamic Characteristics Of Robustness Within Complex Networks, Bhanu K. Kamapantula

Theses and Dissertations

Understanding the role of structural patterns within complex networks is essential to establish the governing principles of such networks. Social networks, biological networks, technological networks etc. can be considered as complex networks where information processing and transport plays a central role. Complexity in these net works can be due to abstraction, scale, functionality and structure. Depending on the abstraction each of these can be categorized further. Gene regulatory networks are one such category of biological networks. Gene regulatory networks (GRNs) are assumed to be robust under internal and external perturbations. Network motifs such as feed-forward loop motif and bifan motif …

The Sensitivity Of Soil Respiration To Soil Temperature, Moisture, And Carbon Supply At The Global Scale, Andrew Hursh

Graduate Student Theses, Dissertations, & Professional Papers

Soil respiration is one of the most important terms in the global carbon budget, yet we know very little about how important environmental factors control this process at the global scale. Soils contain more carbon than terrestrial biomass and the atmosphere combined and contribute ten times more carbon dioxide to the atmosphere each year than the burning of fossil fuels. This study provides new insight on the factors driving soil respiration at the global scale by assimilating satellite observations of soil moisture, temperature, and net primary productivity with the Global Soil Respiration Database (SRDB).While temperature, moisture, carbon supply and other …

Population Differentiation And Habitat Selection Of A Montane Red Fox Population In The Greater Yellowstone Ecosystem, Patrick Cross

Graduate Student Theses, Dissertations, & Professional Papers

Montane red fox (Vulpes vulpes) populations across the western United States are genetically and morphologically distinct from foxes at lower elevations. These montane populations also share a preference for subalpine forest habitats. One hypothesis is that they stem from boreal forest-associated ancestors that expanded during the Pleistocene when boreal forests extended farther south than they do today. Forest habitat selection may therefore aid the persistence of native populations surrounded by non-native conspecifics. Alternatively, this behavior may be an avoidance mechanism in response to competition with larger coyotes (Canis latrans), or a product of the fox's natural adaptability. The red fox …

Graph-Based Regularization In Machine Learning: Discovering Driver Modules In Biological Networks, Xi Gao

Theses and Dissertations

Curiosity of human nature drives us to explore the origins of what makes each of us different. From ancient legends and mythology, Mendel's law, Punnett square to modern genetic research, we carry on this old but eternal question. Thanks to technological revolution, today's scientists try to answer this question using easily measurable gene expression and other profiling data. However, the exploration can easily get lost in the data of growing volume, dimension, noise and complexity. This dissertation is aimed at developing new machine learning methods that take data from different classes as input, augment them with knowledge of feature relationships, …