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Caribbean Reef-Building Coral-Symbiodiniaceae Network: Identifying Symbioses Critical For System Stability In A Changing Climate, Shaman Patel 2022 Nova Southeastern University

Caribbean Reef-Building Coral-Symbiodiniaceae Network: Identifying Symbioses Critical For System Stability In A Changing Climate, Shaman Patel

All HCAS Student Capstones, Theses, and Dissertations

Increasing global ocean temperatures and frequency of marine heatwaves pose dire consequences for coral reefs. High temperatures often lead to disruptions in coral symbiosis resulting in coral bleaching, increasing the mortality of corals. However, corals can potentially avoid bleaching peril by associating with thermally tolerant symbionts. Here we provide a tool for understanding symbiosis network stability of Caribbean reef-building corals. We created a network of Caribbean hermatypic corals and their associated Symbiodiniaceae phylotypes. A bleaching model was applied to this network to test for resilience and robustness (R50) to thermal stress. It was also layered with trait data for coral …


Role Of Parp1 And Nad+ Bioavailability In Base Excision And Single-Strand Break Repair, Kate M. Saville 2022 University of South Alabama

Role Of Parp1 And Nad+ Bioavailability In Base Excision And Single-Strand Break Repair, Kate M. Saville

Theses and Dissertations

High-grade gliomas (HGGs) are malignant, highly metabolically active brain tumors. HGGs are associated with poor patient outcome, attributed to resistance to current therapies, with a survival rate between 12 to 15 months. Gliomas are highly complex tumors, making targeted therapy difficult, highlighting the need for novel approaches and new treatment options. In addition, a large percentage of HGGs are comprised of glioma stem cells (GSCs) that further contribute to therapeutic resistance. Notable characteristics of GSCs are a heightened DNA damage response (DDR) and elevated replication stress that could provide opportunities for therapeutic targeting. A notable feature of many glioma tumors …


Systematic Evaluation Of Database Builds In Metaproteomics For The Advancement Of Microbiome Research, Katherine E. Ostrouchov 2022 University of Tennessee, Knoxville

Systematic Evaluation Of Database Builds In Metaproteomics For The Advancement Of Microbiome Research, Katherine E. Ostrouchov

Masters Theses

The microscopic life that inhabits a human shares a unique bond with its host. Microbes perform many functions that are vital to the survival of the human species and have long been shown to regulate the absorption of nutrients and to promote immune function. A lack of exposure to certain microbes early in life, excessive antibiotic usage, and improper diet can perturb human microbiomes and lead to disease. Since the emergence of omic sequencing technologies, it has now become possible to measure and monitor the genes and proteins made by these microorganisms to better understand how they contribute to host …


Taxonomic Revision And Morphometric Analysis Of Selected Anthurium (Araceae) Species From Bolivia And Peru, Daniel M. Tarazona Ocana 2022 University of Missouri-St. Louis

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 2022 University of Florida

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 2022 Tufts University

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 2022 Iowa State University

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 2022 School of Food and Drug, Luoyang Normal University, China

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 2022 The Graduate Center, City University of New York

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 2022 Wright State University - Lake Campus

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 2022 Mississippi State University

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 …


Efficient Network Domination For Life Science Applications, Stephen K. Grady 2022 University of Tennessee, Knoxville

Efficient Network Domination For Life Science Applications, Stephen K. Grady

Doctoral Dissertations

With the ever-increasing size of data available to researchers, traditional methods of analysis often cannot scale to match problems being studied. Often only a subset of variables may be utilized or studied further, motivating the need of techniques that can prioritize variable selection. This dissertation describes the development and application of graph theoretic techniques, particularly the notion of domination, for this purpose. In the first part of this dissertation, algorithms for vertex prioritization in the field of network controllability are studied. Here, the number of solutions to which a vertex belongs is used to classify said vertex and determine its …


Tau-Dependent Neurodegeneration And Alleviation By Etas®50, Clifford TyRee Castleberry 2022 Texas Southern University

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 2022 Washington University in St. Louis

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

McKelvey School of Engineering 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 2022 Southwestern Oklahoma State University

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 2022 Wright State University - Main Campus

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 2022 The Graduate Center, City University of New York

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 2022 George Mason University

Inferring Dynamics Of Biological Systems, Tracey G. Oellerich

Biology and Medicine Through Mathematics Conference

No abstract provided.


Multi-Omic Systems Biological Analysis Of Host-Microbe Interactions, Piet Jones 2022 University of Tennessee, Knoxville

Multi-Omic Systems Biological Analysis Of Host-Microbe Interactions, Piet Jones

Doctoral Dissertations

Systems biology offers the opportunity to understand the complex mechanisms of various biological phenomena. The wealth of data that is produced, at an increasing rate, provides the potential to meet this opportunity. Here we take an applied approach to integrate multiple omic level data sources in order to generate biologically relevant hypotheses. We apply a novel analysis pipeline to model both, in concert, the microbial and transcriptomic signature from COVID-19 positive patients. We show patients may suffer from an increased microbial burden, with an increased pathogen potential. Gene expression evidence further shows patients may exhibit a compromised barrier immunity, owing …


Exploiting Chemogenetic And Genetic Interactions In Human Cells As An Avenue For New Therapeutic Opportunities, Medina Colic 2022 The Texas Medical Center Library

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

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences 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, …


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