Systems Biology Commons^™

Nitrogen Dynamics And Transport Along Flowpaths In A Rural Wetland-Stream Complex, Colton Kyro

Graduate Student Theses, Dissertations, & Professional Papers

Human activities have doubled the rate of nitrogen inputs onto the landscape resulting in elevated nitrogen concentrations in our streams. Anthropogenically applied nitrogen is largely transported to stream networks via groundwater movement. Groundwater discharge occurs in distinct points along a stream but whose influences can often persist far beyond that area due to insufficient biogeochemical removal of imported nitrogen potentially causing alterations in community structure and precipitating large algae blooms. To understand the factors governing nitrogen abundance in a historical polluted stream, I used a mass-balance approach to quantify groundwater-surface water interaction and the magnitude of groundwater nitrogen input and …

Comparison Of Standard And Environmental Dna Methods For Estimating Chinook Salmon Smolt Abundance In The Klamath River, California, Doyle Joseph Coyne

Cal Poly Humboldt theses and projects

Evaluating abundance of juvenile salmonids is critical to conservation and management. Current abundance estimation involves use of rotary screw traps and mark-recapture studies. Use of environmental DNA (eDNA) in water samples offers a noninvasive and less expensive approach that may potentially improve or eventually replace traditional monitoring. Here I evaluate the utility of eDNA to predict weekly abundance estimates of outmigrating Chinook salmon (Oncorhynchus tshawytscha) smolts in the Klamath River, California. A total of 15 water samples were collected per week over the 17-week smolt outmigration in both 2019 and 2020. Chinook salmon eDNA concentration in each water …

Evaluating Common Raven Take For Greater Sage-Grouse In Oregon’S Baker County Priority Conservation Area And Great Basin Region, Frank F. Rivera-Milán, Peter S. Coates, Jacqueline B. Cupples, Michael Green, Patrick K. Devers

Human–Wildlife Interactions

The common raven (Corvus corax; raven) is a nest predator of species of conservation concern, such as the greater sage-grouse (Centrocercus urophasianus). Reducing raven abundance by take requires authorization under the Migratory Bird Treaty Act. To support U.S. Fish and Wildlife Service’s take decisions (e.g., those that authorize killing a specified proportion or number of individuals annually in a defined area), including the most recent one for Oregon’s Baker County Priority Area for Conservation (PAC), we modeled raven population dynamics under hypothetical scenarios with take rates ranging from below to above the maximum sustained yield (MSY; …

Development Of Tools For Atom-Level Interpretation Of Stable Isotope-Resolved Metabolomics Datasets, Huan Jin

Theses and Dissertations--Toxicology and Cancer Biology

Metabolomics is the global study of small molecules in living systems under a given state, merging as a new ‘omics’ study in systems biology. It has shown great promise in elucidating biological mechanism in various areas. Many diseases, especially cancers, are closely linked to reprogrammed metabolism. As the end point of biological processes, metabolic profiles are more representative of the biological phenotype compared to genomic or proteomic profiles. Therefore, characterizing metabolic phenotype of various diseases will help clarify the metabolic mechanisms and promote the development of novel and effective treatment strategies.

Advances in analytical technologies such as nuclear magnetic resonance …

Effects Of 4-Methylcyclohexanemethanol On Stress Response Pathway Regulators, In Saccharomyces Cerevisiae, Suk Lan Ser

Graduate Theses, Dissertations, and Problem Reports (ETD)

Hydrotropes are small molecules capable of inducing liquid-liquid phase separation by altering the solubility and conformation states of organic compounds that are increasingly becoming important in organizing chemical reactions and regulating complexes. They prevent protein aggregation causing these proteins to form condensates. Mediator, a highly conserved multi-subunit complex, plays an important role in transcription. Med15, a subunit found within the tail domain of the Mediator complex, works with stress-induced transcription factors and is regulated by many kinases, including CDKs and the AMP kinase, Snf1. Living cells respond by changing molecular and cellular pathways when they are exposed to stressful conditions. …

Resilience: Insights From The U.S. Longterm Ecological Research Network, Jane Cowles, Laura Templeton, John J. Battles, Peter J. Edmunds, Robert C. Carpenter, Stephen R. Carpenter, Michael Paul Nelson, Natalie L. Cleavitt, Timothy J. Fahey, Peter M. Groffman, Joe H. Sullivan, Maile C. Neel, Gretchen J. A. Hansen, Sarah Hobbie, Sally J. Holbrook, Clare E. Kazanski, Eric W. Seabloom, Russell J. Schmitt, Emily H. Stanley, Alan J. Tepley, Natalie S. Van Doorn, Jake M. Vander Zanden

Advanced Science Research Center

Ecosystems are changing in complex and unpredictable ways, and analysis of these changes is facilitated by coordinated, long-term research. Meeting diverse societal needs requires an understanding of what populations and communities will be dominant in 20, 50, and 100 yr. This paper is a product of a synthesis effort of the U.S. National Science Foundation funded Long-Term Ecological Research (LTER) network addressing the LTER core research area of populations and communities. This analysis revealed that each LTER site had at least one compelling story about what their site would look like in 50 or 100 yr. As the stories were …

A New Mathematical Theory For The Dynamics Of Large Tumor Populations, A Potential Mechanism For Cancer Dormancy & Recurrence And Experimental Observation Of Melanoma Progression In Zebrafish, Adeyinka A. Lesi

Dissertations and Theses

Cancer, a family of over a hundred disease varieties, results in 600,000 deaths in the U.S. alone. Yet, improvements in imaging technology to detect disease earlier, pharmaceutical developments to shrink or eliminate tumors, and modeling of biological interactions to guide treatment have prevented millions of deaths. Cancer patients with initially similar disease can experience vastly different outcomes, including sustained recovery, refractory disease or, remarkably, recurrence years after apparently successful treatment. The current understanding of such recurrences is that they depend on the random occurrence of critical mutations. Clearly, these biological changes appear to be sufficient for recurrence, but are they …

The Mayfly Newsletter, Donna Giberson

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

The Prairie Naturalist, Vol. 52, Issue 2, December 2020

The Prairie Naturalist

Comparing Native Bee Communities on Reconstructed and Remnant Prairie in Missouri • Joseph LaRose, Elisabeth B. Webb, and Deborah Finke

Patterns and Potential Causes of Changing Winter Bird Distributions in South Dakota • David L. Swanson, Reza Goljani Amipkhiz, and Mark D. Dixon

Greater prairie-chickens and sharp-tailed grouse have similarly high nest survival in the Nebraska Sandhills • Larkin A. Powell, Walter H. Schacht, Julia P. Ewalt, and Katie R. McCollum

Captive Ring-necked Pheasant Response to Very High Experimental Doses of Lead • Travis J. Runia and Alex J. Solem

Trends in a Greater Prairie Chicken Population Established by Translocation …

A Context-Forward In Vivo Functional Genomics Platform For Target Discovery And Establishing Vulnerability Context In Pancreatic Cancer, Johnathon Rose, Johnathon Lynn Rose

Dissertations and Theses (Open Access)

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a very poor patient prognosis (5-year survival of ≤ 7%). While transcriptional profiling has aided in the classification of this disease into at least two broader subtypes, this alone has so far been insufficient to inform on more nuanced patterns of oncogenic dependency. We hypothesized that a more comprehensive and granular characterization of PDAC disease diversity is required to establish relevant context for targeted therapy. To this end, we sought to establish an integrated platform to: i) more comprehensively characterize differential oncogenic signaling across our tumor models, and ii) establish …

Investigation Of Proliferation Suppressors In Genetic Fitness Screens, Walter Frank Lenoir Iv

Dissertations and Theses (Open Access)

Innovation of CRISPR gene-editing technology has provided scientists genome manipulation tools that allowed rapid advancement of scientific capabilities and thus improved our ability to systematically study mammalian genetic functional profiles. Genome-wide CRISPR knockout screens conducted in collections of human cell lines can knock out genes at multiple loci, and have provided new insights into functional roles for independent genes. This method has launched massive efforts in looking across genetic backgrounds for context specific genetic vulnerabilities within cancer. Much of the research effort thus far has been spent on optimizing phenotype distinctions between essential, genes required for cell fitness, and non-essential, …

Molecular Mechanisms Of Boron Toxicity Tolerance In Plants, Guannan Wang

LSU Doctoral Dissertations

Boron toxicity is a worldwide agricultural problem that limits crop productivity and quality. However, our understanding on the genetic responses and adaption mechanisms to boron toxicity in plants is very limited. To address this gap in our knowledge, I compared boron stress-sensitive model, Arabidopsis thaliana and its stress-adapted relative Schrenkiella parvula to study how plants respond and adapt to excess boron at physiological, genomic, transcriptomic, and metabolic levels.

The overall project goal involved integration of multi-omics datasets to develop genome to phenome interpretations. To achieve this, I developed a python package, GOMCL, to facilitate the extraction of biologically meaningful information …

Estimating The Number Of Discrete Models Of Biological Networks, Brandilyn Stigler

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Mathematical Modelling And In Silico Experimentation To Estimate The Quantity Of Covid-19 Infected Individuals In Tijuana, México, Karla A. Encinas, Luis N. Coria, Paul A. Valle

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Wnt Signaling Determines Body Axis Polarity In Regenerating Hydra Tissue Fragments, R. Wang, R. E. Steele, Eva-Maria S. Collins

Biology Faculty Works

How an animal establishes its body axis is a fundamental question in developmental biology. The freshwater cnidarian Hydra is an attractive model for studying axis formation because it is radially symmetric, with a single oral-aboral axis. It was recently proposed that the orientation of the new body axis in a regenerating Hydra polyp is determined by the oral-aboral orientation of the actin-myosin contractile processes (myonemes) in the animal’s outer epithelial layer. However, it remained unclear how the oral-aboral polarity of the body axis would be defined. As Wnt signaling is known to control axis polarity in Hydra and bilaterians, we …

Homicide And Drug Trafficking In Impoverished Communities In Brazil, Elenice De Souza Oliveira, Braulio Figueiredo Alves Da Silva, Flavio Luiz Sapori, Gabriela Gomes Cardoso

Department of Justice Studies Faculty Scholarship and Creative Works

Many studies demonstrate that homicides are heavily concentrated in impoverished neighborhoods, but not all socially disadvantaged neighborhoods are hotbeds of violence. Conducted in Belo Horizonte, Brazil, this study hypothesizes that the association between high rates of homicide and impoverished areas is influenced by the emergence of a specific type of street drug-dealing common to favelas (slums). The study applies econometric techniques to police data on homicides and drug arrests from 2008 to 2011, as well as 2010 Census data, to test its hypothesis. The findings provide insight into the development of crime prevention policies in areas of high social vulnerability.

Machine Learning Applications For Drug Repurposing, Hansaim Lim

Dissertations, Theses, and Capstone Projects

The cost of bringing a drug to market is astounding and the failure rate is intimidating. Drug discovery has been of limited success under the conventional reductionist model of one-drug-one-gene-one-disease paradigm, where a single disease-associated gene is identified and a molecular binder to the specific target is subsequently designed. Under the simplistic paradigm of drug discovery, a drug molecule is assumed to interact only with the intended on-target. However, small molecular drugs often interact with multiple targets, and those off-target interactions are not considered under the conventional paradigm. As a result, drug-induced side effects and adverse reactions are often neglected …

Preliminary Evidence Of The Role Of Medial Prefrontal Cortex In Self-Enhancement: A Transcranial Magnetic Stimulation Study, Birgitta Taylor-Lillquist, Vivek Kanpa, Maya Crawford, Mehdi El Filali, Julia Oakes, Alex Jonasz, Amanda Disney, Julian Keenan

Department of Biology Faculty Scholarship and Creative Works

Humans employ a number of strategies to improve their position in their given social hierarchy. Overclaiming involves presenting oneself as having more knowledge than one actually possesses, and it is typically invoked to increase one’s social standing. If increased expectations to possess knowledge is a perceived social pressure, such expectations should increase bouts of overclaiming. As the medial prefrontal cortex (MPFC) is sensitive to social pressure and disruption of the MPFC leads to decreases in overclaiming, we predicted that transcranial magnetic stimulation (TMS) applied to the MPFC would reduce overclaiming and the effects would be enhanced in the presence of …

Prioritizing The Largest, Oldest Corals For Disease Intervention In A Coral Disease-Ravaged Area: Southeast Florida Coral Reef Ecosystem Conservation Area, Alysha Brunelle

All HCAS Student Capstones, Theses, and Dissertations

Coral diseases appear to be more devastating than ever before. When a virulent disease ravages a coral ecosystem, it can significantly change the population’s demographics and cause local extinctions. Disease intervention response during such an event is impossible at a landscape scale, therefore priorities must be considered. Saving the largest, oldest colonies of reef-building species is a good choice due to their high fecundity and ecological function. Their size, as a proxy for age, is an indicator of their resistance to previous perturbations which may indicate higher fitness. Their size also provides habitat to many organisms and wave resistance in …

Adapting Biotoxin Monitoring For The Future: An Opportunity For A Harmful Algae Bloom (Hab) Network In Casco Bay, Maine, Zachary B. Gordon

All Theses And Dissertations

Harmful Algae Blooms (HABs) related to marine biotoxins have considerable impacts on coastal communities and have been increasing in size and frequency globally. Maine is recognized as a leader in biotoxin management as it relates to bivalve shellfish, but it has been unclear how current management practices effect the growth of shellfish aquaculture and how they will adapt to future conditions. This research uses a collaborative approach to analyze the current state of biotoxin management in Maine. First, the current management practices in Maine were compared and contrasted with five other states dealing with similar issues. Then, the perspectives of …