Combining Network Modeling And Experimental Approaches To Predict Drug Combination Responses, Deepraj Sarmah

All Dissertations

Cancer is a lethal disease and complex at multiple levels of cell biology. Despite many advances in treatments, many patients do not respond to therapy. This is owing to the complexity of cancer-genetic variability due to mutations, the multi-variate biochemical networks within which drug targets reside and existence and plasticity of multiple cell states. It is generally understood that a combination of drugs is a way to address the multi-faceted drivers of cancer and drug resistance. However, the sheer number of testable combinations and challenges in matching patients to appropriate combination treatments are major issues.

Here, we first present a …

Data-Driven Biomarker Panel Discovery In Ovarian Cancer Using Heterogenous Data Fusion On Exosomal And Non-Exosomal Microrna Expression Data, Paritra Mandal

All Dissertations

Ovarian cancer (OC) is an aggressive gynecological cancer and is currently the 5th leading cause of deaths due to cancer in women. High mortality rates are attributable to the vague pathogenesis and asymptomatic nature of the early stages. The development of a liquid biopsy for routine OC screening could help identify the disease at an earlier stage, making treatments more likely to be effective thereby increasing survival rates. Exosomes, small (~100nm) extracellular vesicles present in body fluids, have been shown to contain cancer-progression, onset, and related factors, making them good candidates for use in liquid biopsies. However, to date, only …

Taxonomic Revision And Morphometric Analysis Of Selected Anthurium (Araceae) Species From Bolivia And Peru, Daniel M. Tarazona Ocana

Theses

The genus Anthurium (Araceae) consists of around 1,200 species distributed in the Neotropics, particularly in Central and South America. The montane forests in the eastern flank of the Andes, ranging from northern Ecuador to central Bolivia; hereafter, the East Andes Gradient region, are particularly rich in terms of species diversity, and include an understudied group of Anthurium species endemic to the region. Within this group of species, some taxa are difficult to distinguish from each other mainly due to the lack of identification keys, incomplete species descriptions and unknown synonyms. In this study, a combination of traditional taxonomic techniques and …

Modularity And Boolean Network Decomposition, Matthew Wheeler

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Nonlinearity Of Regulation In Biological Networks, Santosh Manicka, Kathleen Johnson, Michael Levin, David Murrugarra

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Modularity In Gene Regulatory Networks, Mehak Kapoor, Claus Kadelka

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Systems Pharmacology Dissection Of The Mechanisms And Therapeutic Potential Of Cassiae Semen For Hepatoprotection And Brightening Eyes, Jing-Xiao Zhang, Zi-Yi Chen, Xue-Zhen Huang, Lin-Yue Qi, Wei Zhou

Journal of Food and Drug Analysis

Cassiae semen has been shown to play significant roles in reversing “liver fire” to improve vision. The systems mechanism of Cassiae semen for hepatoprotection and brightening eyes has not been fully explored. The systems pharmacology approach is proposed to dissect the potential pharmacological mechanism of Cassiae semen for hepatoprotection and brightening eyes. The results showed that 26 active components of Cassiae semen that connected with 230 targets were obtained. Gene ontology enrichment, network and pathway analysis explored that Cassiae semen is responsible for hepatoprotection and brightening eyes. The current study will contribute to the research and development of functional foods.

Prenatal Choline Supplementation During Maternal Obesity Alters Offspring Response To Western Diets, Hunter W. Korsmo

Dissertations, Theses, and Capstone Projects

Maternal obesity has led to an increase in adverse offspring developmental outcomes and a greater risk for long-term metabolic diseases. Choline, a semi-essential nutrient, can be incorporated into phosphatidylcholine (PC) as well as sphingomyelin (SM) and donate its labile methyl group for the remethylation of homocysteine after choline is oxidized to betaine. Prenatal choline insufficiency has been related to maternal obesity and metabolic diseases, such as metabolic associated fatty liver disease (MAFLD). Choline may interact with maternal obesity to influence the programming offspring.

Chapter 1 presents an introduction of choline and the various clinical outcomes associated with choline supplementation during …

Drone-Based Water Sampling And Characterization Of Three Freshwater Harmful Algal Blooms In The United States, Regina Hanlon, Stephen J. Jacquemin, Johnna A. Birbeck, Judy A. Westrick, Charbel Harb, Hope Gruszewski, Andrew P. Ault, Durelle Scott, Hosein Foroutan, Shane D. Ross, Javier González-Rocha, Craig Powers, Lowell Pratt, Harry Looney, Greg Baker, David G. Schmale

Biological Sciences Faculty Publications

Freshwater harmful algal blooms (HABs), caused mostly by toxic cyanobacteria, produce a range of cyanotoxins that threaten the health of humans and domestic animals. Climate conditions and anthropogenic influences such as agricultural run-off can alter the onset and intensity of HABs. Little is known about the distribution and spread of freshwater HABs. Current sampling protocols in some lakes involve teams of researchers that collect samples by hand from a boat and/or from the shoreline. Water samples can be collected from the surface, from discrete-depth collections, and/or from depth-integrated intervals. These collections are often restricted to certain months of the year, …

Methods And Tools To Improve Performance Of Plant Genome Analysis, Drew Ferrell

Theses and Dissertations

Multi -omics data analysis and integration facilitates hypothesis building toward an understanding of genes and pathway responses driven by environments. Methods designed to estimate and analyze gene expression, with regard to treatments or conditions, can be leveraged to understand gene-level responses in the cell. However, genes often interact and signal within larger structures such as pathways and networks. Complex studies guided toward describing dynamic genetic pathways and networks require algorithms or methods designed for inference based on gene interactions and related topologies. Classes of algorithms and methods may be integrated into generalized workflows for comparative genomics studies, as multi -omics …

Tau-Dependent Neurodegeneration And Alleviation By Etas®50, Clifford Tyree Castleberry

Theses (2016-Present)

Brain growth factors are a broad group of molecules that enable the brain to adapt to stress. In a study on Alzheimer’s mice (APP), we tested the role of an asparagus supplement, ETAS®50, to mitigate the stress caused by the Alzheimer’s condition in this mouse model. Gene expression data revealed regulation of genes related to neuronal growth and function, such as tau, which were severely stressed in the APP mice to be alleviated.

The Effects Of Host-Like Environmental Signals And Gene Expression On Capsule Growth In Cryptococcus Neoformans, Yu Min Jung

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cryptococcus neoformans is a fungal pathogen that causes cryptococcosis, a disease that kills almost 200,000 people worldwide each year. A unique feature of this deadly yeast is its polysaccharide capsule, which is known to be associated with its virulence. Here, we systematically explore the effects of all possible combinations of 4 capsule-inducing signals on gene expression, cell size, and capsule size. These signals are medium (YPD, DMEM or RPMI), temperature (30°C or 37°C), CO₂ (room air or 5%), cAMP (0 mM or 20 mM), and pH buffer (HEPES/no HEPES). We explore the effects of exogenous cAMP at a range …

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.

Parasitism Of Corn Earworm, Helicoverpa Zea (Boddie) (Lepidoptera: Noctuidae), By Tachinid Flies In Cultivated Hemp, Armando Falcon-Brindis, John O. Stireman Iii, Zenaida J. Viloria, Raul T. Villanueva

Biological Sciences Faculty Publications

In a survey on hemp grown in western Kentucky we found an average of 27.8 CEW larvae per plant. We recorded 45% parasitism of CEW in these fields by two species of tachinid flies, Winthemia rufopicta and Lespesia aletiae. Most parasitized larvae were third to sixth instars at the time of collection. We found up to 22 tachinid eggs per host larva, 89% of which typically bore between 1 and 5 eggs on the thorax. 45.9% of CEW bearing eggs died. The number of tachinid eggs per host was unrelated to host body mass, but both the number of tachinid …

Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer

Dissertations, Theses, and Capstone Projects

The description of a complex system like gene regulation of a cell or a brain of an animal in terms of the dynamics of each individual element is an insurmountable task due to the complexity of interactions and the scores of associated parameters. Recent decades brought about the description of these systems that employs network models. In such models the entire system is represented by a graph encapsulating a set of independently functioning objects and their interactions. This creates a level of abstraction that makes the analysis of such large scale system possible. Common practice is to draw conclusions about …

Inferring Dynamics Of Biological Systems, Tracey G. Oellerich

Biology and Medicine Through Mathematics Conference

No abstract provided.

Combining Pharmacokinetics And Vibrational Spectroscopy: Mcr-Als Hard-And-Soft Modelling Of Drug Uptake In Vitro Using Tailored Kinetic Constraints, David Perez-Guaita, Guillermo Quintas, Zeineb Farhane, Roma Tauler, Hugh Byrne

Articles

Raman microspectroscopy is a label-free technique which is very suited for the investigation of pharmacokinetics of cellular uptake, mechanisms of interaction, and efficacies of drugs in vitro. However, the complexity of the spectra makes the identification of spectral patterns associated with the drug and subsequent cellular responses difficult. Indeed, multivariate methods that relate spectral features to the inoculation time do not normally take into account the kinetics involved, and important theoretical information which could assist in the elucidation of the relevant spectral signatures is excluded. Here, we propose the integration of kinetic equations in the modelling of drug uptake and …

Exploiting Chemogenetic And Genetic Interactions In Human Cells As An Avenue For New Therapeutic Opportunities, Medina Colic

Dissertations and Theses (Open Access)

The advent of CRISPR technology and its adaptation to the mammalian genome made whole-genome knockout screens possible directly in human cells. Gene knockout answers how essential that gene is for cell fitness and proliferation. Genes showing moderate to severe fitness defects are called essential genes and provide insights into disease-specific candidate therapeutic targets. Additionally, CRISPR offers other applications for genome editing. Two applications this dissertation is based on are 1) combination of gene knockout and drug treatment, which enables the identification of chemogenetic interactions, or gene mutations that enhance or suppress the activity of a drug, and 2) combinatorial editing, …

Elucidating The Cellular Physiology Of Glyphosate Resistance In Palmer Amaranth (Amaranthus Palmeri) Using Integrated Omics Approaches, Pawanjit Kaur Sandhu

All Theses

The evolution of resistance to herbicides in weeds poses a major threat to agricultural production systems. To date, herbicide resistance has been reported against 21 modes of action in 266 weed species across 71 countries. More than 50 weed species have developed resistance against glyphosate, the most widely used herbicide worldwide. Although several mechanisms of glyphosate resistance have been discovered, our understanding of alterations in the cellular physiology of glyphosate-resistant weed biotypes, and the induction of the resistance mechanisms remains limited. This knowledge is critical to developing sustainable weed management practices and for a comprehensive understanding of plant stress adaptations. …

Periodic Spatial Disturbances Alter The Expression Of Quorum Sensing Virulence Factors In Pseudomonas Aeruginosa, Laura García-Diéguez

All HCAS Student Capstones, Theses, and Dissertations

Pseudomonas aeruginosa is an opportunistic pathogen associated with severe acute and chronic illnesses. Current antibiotic-based approaches fail to effectively treat P. aeruginosa infections due to the effectiveness and robustness of the quorum sensing signaling system (QS). Pathogenic bacteria, such as P. aeruginosa, employ this population density-dependent communication mechanism to confer antimicrobial resistance, propagate infection, and coordinate the expression of virulence factors, through the production and detection of autoinducing signaling molecules (AI). As such, there is a growing interest in developing novel non-antibiotic-based techniques to attenuate the pathogenicity of P. aeruginosa by disrupting the functionality of its QS system. Previous …

Variation In Student Perceptions Of Higher Education Course Quality And Difficulty As A Result Of Widespread Implementation Of Online Education During The Covid-19 Pandemic, Joseph Cavanaugh, Stephen J. Jacquemin, Christine Junker

Biological Sciences Faculty Publications

The onset of the COVID-19 global pandemic affected higher education in a myriad of ways. One of the most notable effects however was the rapid and sudden transition of nearly all courses at most institutions to an online environment. And while there are a growing number of courses offered online already, this transition to nearly 100% remote education presented numerous challenges for instructors and students of face-to-face and hybrid style courses. Since student perceptions are closely tied to recruitment and retention, it is important to know if there are differences in student perceptions present in the way different courses are …

Effective Dose Fractionation Schemes Of Radiotherapy For Prostate Cancer, Jose Alvarez, Kathleen M. Storey, Pavitra Kannan, Heyrim Cho

Spora: A Journal of Biomathematics

Radiation therapy remains as one of the main cancer treatment modalities. Typical regimens for radiotherapy comprise a constant dose administered on weekdays, and no radiation on weekends. In this paper, we examine adaptive dosages of radiation treatment strategies for heterogeneous tumors using a dynamical system model that consist of radiation-resistant and parental populations with unique interactive properties, namely, PC3 and DU145 prostate cancer cell lines. We show that stronger doses of radiation given in longer time intervals, while keeping the overall dosage the same, are effective in PC3 cell lines, but not in DU145 cell lines. In addition, we tested …

Effects Of Foliar Application Of Zno Nanoparticles On Lentil Production, Stress Level And Nutritional Seed Quality Under Field Conditions, Marek Kolenčík, Dávid Ernst, Matej Komár, Martin Urík, Martin Šebesta, Ľuba Ďurišová, Marek Bujdoš, Ivan Černý, Juraj Chlpík, Martin Juriga, Ramakanth Illa, Yu Qian, Huan Feng, Gabriela Kratošová, Karla Čech Barabaszová, Ladislav Ducsay, Elena Aydın

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

Nanotechnology offers new opportunities for the development of novel materials and strategies that improve technology and industry. This applies especially to agriculture, and our previous field studies have indicated that zinc oxide nanoparticles provide promising nano-fertilizer dispersion in sustainable agriculture. However, little is known about the precise ZnO-NP effects on legumes. Herein, 1 mg·L⁻¹ ZnO-NP spray was dispersed on lentil plants to establish the direct NP effects on lentil production, seed nutritional quality, and stress response under field conditions. Although ZnO-NP exposure positively affected yield, thousand-seed weight and the number of pods per plant, there was no statistically significant …

The Future Of The Big Sagebrush Ecosystem: Plant Community Response To Grazing, Wildfire, And Invasive Annual Grass In A Changing Climate, Margaret Eleanor England

Theses, Dissertations and Capstones

Climate change is increasingly affecting the plant communities across the world. In the Western United States, these changes are affecting plant communities and their risk of invasive species, as well as the frequency and severity of wildfire. Big sagebrush (Artemisia tridentata Nutt.) ecosystems of the Western United States are facing threats of increasingly frequent wildfire and invasion of the annual grass cheatgrass (Bromus tectorum L.), which may be exacerbated by global climate change. Past studies have found cheatgrass to exhibit a positive feedback loop with wildfire, and climate change is expected to facilitate expansion of the cheatgrass …

Second Twenty-Five Year Index: Volumes 26–50, 1994–2018, Jane E. Austin

The Prairie Naturalist

The first 50 years of the Prairie Naturalist reside on the shelves of libraries and personal collections. The articles and notes published over those years provide invaluable knowledge about Great Plains biota, communities, conservation, and landscape ecologies. Awareness of the wealth of information in those 50 print volumes has been limited, relying on references from other published papers or the limited number of articles that have been made available online by authors. This index serves as resource for individuals to digitally tap into the information published since 1994. This index, together with the first 25-year index, serves to complement the …

Review Of The Duck Factory: A History Of Waterfowl In North Dakota, By Mike Jacobs And Erik Fritzell, Douglas Johnson

The Prairie Naturalist

It was by geological accident that North Dakota became the heart of duck production in the continental United States. When the Wisconsin glaciation retreated some 11,000 years ago, it left an uneven layer of glacial till over much of North Dakota and nearby states and provinces, an area termed the Prairie Pothole Region. Large blocks of ice in the glacial till eventually melted and formed depressions that became wetlands, or prairie potholes. These were embedded in a matrix of soil that, with millennia of growth by deep-rooted prairie plants, became rich topsoil. The wetlands, surrounded by luxuriant grassland, were ideal …

Review Of Loon Lessons: Uncommon Encounters With The Great Northern Diver, By James D. Paruk, Kristin Bianchini

The Prairie Naturalist

Gavia immer Brunnich (Common Loon) is a bird that has captivated bird watchers, wildlife enthusiasts, campers, cottagers, and others interested in the natural world for centuries. The loon also features prominently in Native American mythology. For many, the loon symbolizes the wildness of the north, and it is often used as a sentinel of lake health. Indeed, the Common Loon has inspired a wealth of literature, both scientific and popular, describing this species’ ecology, behavior, and fitness in the face of environmental changes. To this literature, Loon Lessons: Uncommon Encounters with the Great Northern Diver adds a complete and accurate …

Review Of Methods For Ecological Research On Terrestrial Small Mammals, By Robert Mccleery, Lynda R. Lafond

The Prairie Naturalist

Small mammals are used in ecological studies throughout the world, yet the subject has lacked a clear reference that included upto- date methods pertaining to passive detection, molecular, and statistical approaches. In Methods for Ecological Research on Terrestrial Small Mammals, McCleery and his coauthors build on previous research references (Braun 2005, Sutherland 2006, Krebs 2014, Silvy 2020) and present methodologies specific to the study of small mammals that are applicable globally. Written as an asset for novice and experienced small mammal researchers alike, Methods for Ecological Research on Terrestrial Small Mammals is organized in a logical format, providing readers …

Review Of Spiders Of North America, By Sarah Rose, Michael L. Draney

The Prairie Naturalist

A field guide to spiders, the dominant terrestrial predator group, has long been a desire for North American naturalists, biologists, and spider fans, but not surprisingly, the first “real” field guide has been a long time coming. The diversity of spiders, with over 50,000 known species globally (World Spider Catalog 2022) and around 4,000 in North America north of Mexico (Rose 2022), is well beyond the diversity of more traditional field guide targets such as birds (about 1,000 species north of Mexico; American Birding Association 2022) or butterflies (about 725 species north of Mexico; North American Butterfly Association 2022). Also, …

Developing A Circuit Model To Study The Mechanisms Of Dna Damage And Repair Feedback Dynamics In Cancer Cells, Thomas M. Deangelo

Honors Theses

Cancer therapies over the last decade have promoted a growing interest in the manipulation of DNA damage and repair pathways due to its beneficial consequences on cancer cell viability. Simultaneously attacking genetic code with DNA-damaging chemotherapies while eliminating mechanisms of DNA repair – the protectors of our genome – has enormous therapeutic potential. Biological circuit engineering interfaces biochemistry and systems biology with electrical engineering analyses to accurately model and simulate biological pathways such as DNA damage and repair. Circuit models can also be used to identify weaknesses within pathways, highlighting the most efficient protein targets for drugs that aim to …