Life Sciences Commons^™

Identifying The Role Of Janus Kinase 1 In Mammary Gland Development And Breast Cancer, Barbara Swenson

Theses & Dissertations

The development of the postnatal mammary gland is tightly controlled by peptide hormones and cytokines. The signaling of these extracellular ligands through their corresponding receptors rely on Janus Kinases (JAKs) that activate downstream Signal Transducers and Activators of Transcription (STATs). The JAK/STAT signaling pathway is crucial for processes such as growth, proliferation, and cell survival of the epithelial tissue, but also for the breakdown and remodeling of the mammary gland via IL-6 class inflammatory cytokines (e.g. LIF and OSM). JAK1 and JAK2, which are expressed in the mammary gland, are thought to have redundant functions. However, our previous studies demonstrated …

Transcriptome Profiling Of Cleft Palate Intgf-Beta3 Knockout Mice Alleles: Rna-Seq Analysis Of Tgf-Beta3 Mice, Kelsey White

Theses & Dissertations

Background: Orofacial clefts are the most common craniofacial birth defect with a complex, combinatorial etiology. Tgf-b3 regulates palatal fusion in mice; Tgf-b3 knockout mice have cleft palate (CP) lacking other major deformities. The genes downstream of Tgf-b3 during palatogenesis remain largely unexplored. Our objective was to analyze the global transcriptome changes and their contribution to CP and identify novel Tgf-b3 associated genes involved in formation of CP. We used RNA-sequencing to analyze and compare the whole transcriptome of Tgf-b3 alleles during palatal growth and fusion in mice.

Results: …

Role Of Ezrin In Colorectal Cancer Cell Survival Regulation, Premila Leiphrakpam

Theses & Dissertations

Colorectal cancer (CRC) is the second most common cause of cancer related deaths in the United States, mainly due to metastasis to the distant organ sites. However, the molecular basis of CRC metastasis is poorly understood. Therefore, identification and characterization of novel potential anti-cancer therapeutic targets CRC is of urgent need. Utilizing a 2D-DIGE proteomics approach ezrin was identified as a protein that is differentially expressed between primary colon tumors xenografts, orthotopically implanted in athymic nude mice, and corresponding and liver metastatic deposits. Ezrin, a cytoskeletal protein belonging to the ezrin–radixin–moesin (ERM) family plays important roles in cell motility, invasion …

Perturbing Anti-Apoptotic Proteins To Develop Novel Cancer Therapies, Jacob Contreras

Theses & Dissertations

The apoptotic pathway involves a tightly regulated network of proteins which respond to various stimuli. Previous studies have indicated Mcl-1 and Bcl-xL are intimately involved in determining cell fate, and if both are concurrently neutralized, it activates the apoptotic pathway. The inactivation of Bcl-xL and Mcl-1 as a mechanism to trigger the intrinsic apoptotic response can be used as a platform to develop therapeutic strategies to target cancer cells. The apoptotic pathway is largely dysregulated and often leads to therapy resistance in cancer cells. Although direct inhibitors of Bcl-xL have been developed and have advanced to clinical trials, development of …

Metabolic Reprogramming Of Pancreatic Ductal Adenocarcinoma Cells In Response To Chronic Low Ph Stress, Jaime Abrego

Theses & Dissertations

Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal of all cancers with a 5-year survival rate of only 8.2%. This is because PDAC is diagnosed in its advanced stages and is characterized by radio and chemotherapy resistance. Aggressiveness of PDAC tumors is attributed to its high metabolic phenotype, which is characterized by increased glycolysis rate and lactate secretion, while oxidative metabolism is reduced. These metabolic features are required to fulfill the biosynthetic demands of proliferating PDAC cells. However, this increase in metabolic activity results in acidification of the extracellular space because the dense fibrotic stroma of PDAC tumors limits …

Role Of Transforming Growth Factor (Tgf) – Β Signaling In Craniofacial Development, Malignancies And Regeneration, Jingpeng Liu

Theses & Dissertations

The transforming growth factor (TGF) – β signaling pathway regulates a diversity of fundamental cellular processes such as cell growth and proliferation, cell differentiation, migration, apoptosis and other biological functions, both during embryogenesis and in adult tissue homeostasis. TGF-β is known to play a critical role in palatal development as in TGF-β knockout murine models, TGF-β deficiency causes cleft palate, a common craniofacial deformity in humans due to the abnormality of growth, elevation or fusion of the two palatal shelves. In order to investigate the mechanisms of how TGF-β regulates palatogenesis, we generated TGF-β3 knockout (-/-) murine models, performed systematic …

Diet And Activity Patterns Of Five Bat Species In North-Central Kansas, Holly G. Wilson

Master's Theses or Doctor of Nursing Practice

My study focuses on six bat species that occur in north-central Kansas. Although each species is widely distributed, information about their diet and activity patterns is lacking, especially within Kansas. Increased knowledge about bat species in Kansas can provide a baseline for future studies and conservation efforts for the species included in my study; big brown bat (Eptesicus fuscus), eastern red bat (Lasiurus borealis), hoary bat (Lasiurus cinereus), northern myotis (Myotis septentrionalis), evening bat (Nycticeius humeralis), and tricolored bats (Perimyotis subflavus) were captured and fecal samples were examined for diet diversity. I captured bats in mist nets in the Kansas …

Habitat Selection, Survival, And Movement Ecology Of The American Woodcock (Scolopax Minor) In Louisiana Usa, Elisa Constancia Elizondo

LSU Master's Theses

The American Woodcock (Scolopax minor) is a migratory upland game species occurring across much of eastern North America. Across its breeding range in the northern U.S. and southern Canada, this species has experienced significant, pervasive declines over the last half century. As woodcock populations continue to decline, active habitat management for this species has become increasingly important.

The state of Louisiana has substantial amounts of woodcock habitat and receives wintering birds from across the woodcock range. However, few data exist regarding survival rates, habitat utilization, and movement patterns across the state.

In order to better manage for woodcock …

Defining The Role Of Neuropilin-2 In Macrophages: Implications In Tumor Associated Macrophages In Pancreatic Cancer, Sohini Roy

Theses & Dissertations

Macrophages are extremely heterogeneous and highly plastic hematopoietic cells that reside in all tissues and act as a bridge between the innate and adaptive arms of the immune responses. Besides, they undertake a wide array of housekeeping functions like, clearance of cellular debris that arise due to regular turnover in tissues, iron homeostasis, immune surveillance as well as tissue repair processes post inflammation. They are also causally associated with several clinical conditions, including cancer where the infiltration of macrophages contribute to disease progression, metastasis and therapy resistance, and thereby poor clinical outcome.

Neuropilins (NRPs) are non-tyrosine kinase cell surface glycoproteins …

Focus: A Graph Approach For Data-Mining And Domain-Specific Assembly Of Next Generation Sequencing Data, Julia Sommer

Theses & Dissertations

Next Generation Sequencing (NGS) has emerged as a key technology leading to revolutionary breakthroughs in numerous biomedical research areas. These technologies produce millions to billions of short DNA reads that represent a small fraction of the original target DNA sequence. These short reads contain little information individually but are produced at a high coverage of the original sequence such that many reads overlap. Overlap relationships allow for the reads to be linearly ordered and merged by computational programs called assemblers into long stretches of contiguous sequence called contigs that can be used for research applications. Although the assembly of the …

Understanding The Paradox Of Genetic Diversity In Uropathogenic E. Coli: The Uncommon Evolution Of A Common Pathogen, Henry Louis Schreiber

Arts & Sciences Graduate Student Theses and Dissertations

Urinary tract infections (UTIs) are the second most common bacterial infection of people in the U.S.A and are frequently recurrent, as an initial UTI is quickly followed by a second episode in 30-35% of cases despite appropriate antibiotic treatment and clearance of the bacteria from the urine. The vast majority, >80%, of UTIs are caused by uropathogenic Escherichia coli (UPEC). UPEC that colonize the bladder are thought to originate in the gut, where they live as commensal organisms. UPEC can be shed in feces to colonize the vagina and/or periurethral area, and then can ascend into the bladder to start …

Knowledge Driven Approaches And Machine Learning Improve The Identification Of Clinically Relevant Somatic Mutations In Cancer Genomics, Benjamin John Ainscough

Arts & Sciences Graduate Student Theses and Dissertations

For cancer genomics to fully expand its utility from research discovery to clinical adoption, somatic variant detection pipelines must be optimized and standardized to ensure identification of clinically relevant mutations and to reduce laborious and error-prone post-processing steps. To address the need for improved catalogues of clinically and biologically important somatic mutations, we developed DoCM, a Database of Curated Mutations in Cancer (http://docm.info), as described in Chapter 2. DoCM is an open source, openly licensed resource to enable the cancer research community to aggregate, store and track biologically and clinically important cancer variants. DoCM is currently comprised of 1,364 variants …

Roles Of Peroxisomes And Peroxisome-Derived Products In Controlling Plant Growth And Stress Responses, Elizabeth May Frick

Arts & Sciences Graduate Student Theses and Dissertations

The peroxisome is a vital organelle conserved through the entire eukaryotic lineage. In all examined species, peroxisomes are responsible for such essential processes as fatty acid beta-oxidation and metabolism of reactive oxygen species (ROS). In plants, peroxisomes have taken on additional specialized roles, such as production of some plant hormones and vitamins. In this work, I have uncovered novel factors regulating peroxisome number in model species Arabidopsis thaliana, and novel mechanisms governing how peroxisomes respond to salt stress. I discovered a role for Arabidopsis MAP KINASE17 (MPK17) as a negative regulator of peroxisome division that acts in the salt-stress response …

A Generalized Biophysical Model Of Transcription Factor Binding Specificity And Its Application On High-Throughput Selex Data, Shuxiang Ruan

Arts & Sciences Graduate Student Theses and Dissertations

The interaction between transcription factors (TFs) and DNA plays an important role in gene expression regulation. In the past, experiments on protein–DNA interactions could only identify a handful of sequences that a TF binds with high affinities. In recent years, several high-throughput experimental techniques, such as high-throughput SELEX (HT-SELEX), protein-binding microarrays (PBMs) and ChIP-seq, have been developed to estimate the relative binding affinities of large numbers of DNA sequences both in vitro and in vivo. The large volume of data generated by these techniques proved to be a challenge and prompted the development of novel motif discovery algorithms. These algorithms …

Longitudinal Cerebrospinal Fluid Biomarkers Of Alzheimer Disease: Movement Toward The Diagnosis, Prognosis And Staging Of Disease, Courtney Sutphen

Arts & Sciences Graduate Student Theses and Dissertations

Alzheimer’s disease (AD) is a devastating neurodegenerative disease that slowly claims the memories and experiences that comprise the life experiences of individuals that suffer from the disease. Despite a continually accelerating pace of research and discovery, a viable therapeutic intervention for AD has yet to be realized. There are a multitude of factors that may contribute to this difficulty including the challenge of separating the overall disease of Alzheimer’s from the clinically recognizable memory loss that occurs in what is now known to be the end-stage of the disease. Efforts to treat AD have increasingly turned toward very early disease …

Response Of Appetite And Appetite Regulating Hormones To Acute Hypoxia, Morgan Busboom, Robert Shute, Dustin Slivka

Journal of Human Performance in Extreme Environments

AIM: To determine the acute response of appetite and appetite regulating hormones after exposure to simulated altitude. METHODS: Seven males and five females (height: 178.9 ± 2.3 cm; weight: 77.3 ± 7.2 kg; body fat: 18.4 ± 1.7%) participated in two, three-hour trials in a hypoxic (5000 m) and normoxic (350 m) environment. Blood samples were collected prior to and immediately following three hours of exposure for the measurement of leptin, adiponectin, and acylated ghrelin. Appetite, acute mountain sickness, heart rate, blood oxygenation, tissue oxygenation, respiration rate, and whole body gases were also measured. RESULTS: Leptin was not different between …

Prevention Of Childhood Obesity And Diabetes, Karen Carig

Master's Projects and Capstones

One of the public health concerns that have been on the rise is childhood obesity and diabetes. The National Health and Nutrition Examination Survey indicate that approximately one-third of children in the United States are overweight or obese with 17% meeting criteria for obesity (Pulgaron and Delamater, 2014). This crisis exists nationally and internationally which can effect children in the following ways: physically, socially, psychologically and mentally. Although, genetics also play a role in these diseases, environmental factors, lifestyle preferences and cultural environmental play have a major influence. My internship with the Food Education Project covers a better understanding to …

Evaluation Of Genetic Diversity And Stability Of Colocasia Cultivars Using Issr, Seukmin Hong

Electronic Theses and Dissertations

Using 44 ornamental Colocasia cultivars planted at Stephen F. Austin State University (Nacogdoches, TX), cultivar assessment, genetic diversity, stability, and relationship were examined with banding patterns produced from Inter-simple sequence repeat (ISSR) markers. Comparing banding patterns of vegetatively propagated clones of each cultivar, genetic stability was examined. Unweighted pair group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCO) were performed to examine genetic relationship that can explain a need for the new classification Colocasia gigantea and recent movement of re-classifying Colocasia antiquorum. Average Shannon’s diversity index for all loci was found to quantify genetic diversity. The genetic …

Effects Of Crude Oil On Tumor Suppressor P53 Polymorphisms In Laboratory-Exposed Atlantic Killifish, Fundulus Heteroclitus, Allison Margaret Nadler

Seton Hall University Dissertations and Theses (ETDs)

Polycyclic aromatic hydrocarbons (PAHs), constituents of crude oil, are implicated as a potent source of adverse toxicological effects on living organisms. To model the effects of PAHs in response to environmental oil spill disasters a species of killifish (Fundulus heteroclitus) was captured and exposed to crude oil in a laboratory-controlled setting. Over a period of 7 days, fish were dosed with crude oil by gavage, culled, and organs were harvested for analysis. Excitation-emission matrix spectroscopy (EEMS) of gall bladder tissue homogenates was used to verify exposure. Effects of PAHs on the p53 gene were evaluated as an indicator …

Binding Affinity And Specificity Of Sh2 Domain Interactions In Receptor Tyrosine Kinase Signaling Networks, Tom Ronan

McKelvey School of Engineering Graduate Student Theses & Dissertations

Receptor tyrosine kinase (RTK) signaling mechanisms play a central role in intracellular signaling and control development of multicellular organisms, cell growth, cell migration, and programmed cell death. Dysregulation of these signaling mechanisms results in defects of development and diseases such as cancer. Control of this network relies on the specificity and selectivity of Src Homology 2 (SH2) domain interactions with phosphorylated target peptides. In this work, we review and identify the limitations of current quantitative understanding of SH2 domain interactions, and identify severe limitations in accuracy and availability of SH2 domain interaction data. We propose a framework to address some …

Identification Of Prognostic Cancer Biomarkers Through The Application Of Rna-Seq Technologies And Bioinformatics, Nathan Wong

McKelvey School of Engineering Graduate Student Theses & Dissertations

MicroRNAs (miRNAs) are short single-stranded RNAs that function as the guide sequence of the post-transcriptional regulatory process known as the RNA-induced silencing complex (RISC), which targets mRNA sequences for degradation through complementary binding to the guide miRNA. Changes in miRNA expression have been reported as correlated with numerous biological processes, including embryonic development, cellular differentiation, and disease manifestation. In the latter case, dysregulation has been observed in response to infection by human papillomavirus (HPV), which has also been established as both oncogenic in cervical cancers and oropharyngeal cancers and favorable for overall patient survival after tumor formation. The identification of …

Characterizing Anisotropy In Fibrous Soft Materials By Mr Elastography Of Slow And Fast Shear Waves, John Larson Schmidt

McKelvey School of Engineering Graduate Student Theses & Dissertations

The general objective of this work was to develop experimental methods based on magnetic resonance elastography (MRE) to characterize fibrous soft materials. Mathematical models of tissue biomechanics capable of predicting injury, such as traumatic brain injury (TBI), are of great interest and potential. However, the accuracy of predictions from such models depends on accuracy of the underlying material parameters. This dissertation describes work toward three aims. First, experimental methods were designed to characterize fibrous materials based on a transversely isotropic material model. Second, these methods are applied to characterize the anisotropic properties of white matter brain tissue ex vivo. Third, …

Characterization Of Structural Dynamics Of The Human Head Using Magnetic Resonance Elastography, Andrew Arun Badachhape

McKelvey School of Engineering Graduate Student Theses & Dissertations

In traumatic brain injury (TBI), the skull-brain interface, composed of three meningeal layers: the dura mater, arachnoid mater, and pia mater, along with cerebrospinal fluid (CSF) between the layers, plays a vital role in transmitting motion from the skull to brain tissue. Magnetic resonance elastography (MRE) is a noninvasive imaging modality capable of providing in vivo estimates of tissue motion and material properties. The objective of this work is to augment human and phantom MRE studies to better characterize the mechanical contributions of the skull-brain interface to improve the parameterization and validation of computational models of TBI. Three specific aims …

Accurate Determination And Application Of Local Strain For Studying Tissues With Gradients In Mechanical Properties, John Boyle

McKelvey School of Engineering Graduate Student Theses & Dissertations

Determination of the mechanical behavior of materials requires an understanding of deformation during loading. While this is traditionally accomplished in engineering by examining a force displacement curve for a whole sample, these techniques implicitly ignore local geometric complexities and local material inhomogeneities commonly found in biologic tissues. Techniques such as normalized cross correlation have been classically applied to address this issue and resolve deformation at the local level; however, these techniques have proven unreliable when deformations become large, if the sample undergoes a rotation, and/or if strain fields become incompatible (e.g. at or near failure).

Presented here is a toolbox …

Multiscale Imaging Of The Mouse Cortex Using Two-Photon Microscopy And Wide-Field Illumination, Jonathan Richard Bumstead

McKelvey School of Engineering Graduate Student Theses & Dissertations

The mouse brain can be studied over vast spatial scales ranging from microscopic imaging of single neurons to macroscopic measurements of hemodynamics acquired over the majority of the mouse cortex. However, most neuroimaging modalities are limited by a fundamental trade-off between the spatial resolution and the field-of-view (FOV) over which the brain can be imaged, making it difficult to fully understand the functional and structural architecture of the healthy mouse brain and its disruption in disease. My dissertation has focused on developing multiscale optical systems capable of imaging the mouse brain at both microscopic and mesoscopic spatial scales, specifically addressing …

Mechanics Of The Developing Brain: From Smooth-Walled Tube To The Folded Cortex, Kara Ellspermann Garcia

McKelvey School of Engineering Graduate Student Theses & Dissertations

Over the course of human development, the brain undergoes dramatic physical changes to achieve its final, convoluted shape. However, the forces underlying every cinch, bulge, and fold remain poorly understood. This doctoral research focuses on the mechanical processes responsible for early (embryonic) and late (preterm) brain development.

First, we examine early brain development in the chicken embryo, which is similar to human at these stages. Research has primarily focused on molecular signals to describe morphogenesis, but mechanical analysis can also provide important insights. Using a combination of experiments and finite element modeling, we find that actomyosin contraction is responsible for …

Regulation Of Gene Expression By Rna Binding Proteins And Micrornas, Kyle Cottrell

Arts & Sciences Graduate Student Theses and Dissertations

Regulation of gene expression is essential to life. Post-transcriptional regulation of gene expression is a complex process with many inputs that lead to changes in localization, translation and stability of mRNAs. The translation and stability of many mRNAs is regulated by cis-elements, such as mRNA-structure or codon optimality; and by trans-acting factors such as RBPs and miRNAs. Here I report on the complex interactions between RBPs, miRNAs and characteristics of their target mRNAs in respect to effects on translation and RNA stability.Using a reporter based approach we studied modulation of microRNA-mediated repression by various mRNA characteristics. We observed the influence …

Extrinsic And Intrinsic Control Of Integrative Processes In Neural Systems, Anirban Nandi

McKelvey School of Engineering Graduate Student Theses & Dissertations

At the simplest dynamical level, neurons can be understood as integrators. That is, neurons accumulate excitation from afferent neurons until, eventually, a threshold is reached and they produce a spike. Here, we consider the control of integrative processes in neural circuits in two contexts. First, we consider the problem of extrinsic neurocontrol, or modulating the spiking activity of neural circuits using stimulation, as is desired in a wide range of neural engineering applications. From a control-theoretic standpoint, such a problem presents several interesting nuances, including discontinuity in the dynamics due to the spiking process, and the technological limitations associated with …

Phyllium (Phyllium) Brossardi Sp. Nov. (Phasmida, Phylliidae), A New Species Of Leaf Insect From Northern Borneo, Royce T. Cumming, Stéphane Le Tirant, Sierra N. Teemsma

Insecta Mundi

A new species of leaf insect, Phyllium (Phyllium) brossardi Cumming, Le Tirant, and Teemsma, new species (Phasmida, Phylliidae), is described from a series of three males. A key to males of the currently known species from the siccifolium species group from Borneo is provided.

The Vibe, Sarah P. Douglass

Capstones

The Vibe is a long-form narrative about where tech is taking the female orgasm. The piece concludes that physiological research is a required next step when creating the climax of the future.

http://sarahpdouglass.com