Cell and Developmental Biology Commons^™

Aerobic Exercise And Scaffolds With Hierarchical Porosity Synergistically Promote Functional Recovery Post Volumetric Muscle Loss, Christina Zhu, Karina Skylar, Yori Endo, Mohamadmahdi Samandari,, Mehran Karvar, Azadeh Mostafavi, Jacob Quint, Chiara Rioldi, Wojciech Swieszkowski, Joshua Mauney, Shailesh Agarwal, Ali Tamayol, Indranil Sinha

School of Veterinary and Biomedical Sciences: Faculty Publications

Volumetric muscle loss (VML) is a composite loss of skeletal muscle tissue (greater than 20%) that heals with minimal muscle regeneration, substantial fibrosis, and subsequent functional deficits. Standard treatment, involving free functional muscle transfer and physical therapy, cannot restore full muscle function following VML. Tissue engineered scaffolds, 3D structural templates that mimic native extracellular matrix, are promising to enhance functional muscle formation and recovery. Bioprinted 3D scaffolds are engineered using bioinks, created from scaffolding material, cells, and growth factors, to replicate skeletal muscle architecture with precise control over their spatial deposition. METHODS: The present study evaluates a 3D-printed foam-like scaffold …

Host-Genetic-Based Outcome Of Co-Infection By Pcv2b And Prrsv In Pigs, Christian W. Eaton, Hiep Vu, Arabella L. Hodges, Seth P. Harris, Stephen D. Kachman, Daniel C. Ciobanu

School of Veterinary and Biomedical Sciences: Faculty Publications

Replication of porcine circovirus type 2 (PCV2), an important worldwide swine pathogen, has been demonstrated to be influenced by host genotype. Specifically, a missense DNA polymorphism (SYNGR2 p.Arg63Cys) within the SYNGR2 gene was demonstrated to contribute to variation in PCV2b viral load and subsequent immune response following infection. PCV2 is known to induce immunosuppression leading to an increase in susceptibility to subsequent infections with other viral pathogens such as porcine reproductive and respiratory syndrome virus (PRRSV). In order to assess the role of SYNGR2 p.Arg63Cys in co-infections, pigs homozygous for the favorable SYNGR2 p.63Cys (N = 30) …

Infection Of Feral Phenotype Swine With Japanese Encephalitis Virus, So Lee Park, Yan-Jang S. Huang, Amy C. Lyons, Victoria B. Ayers, Susan M. Hettenbach, D. Scott Mcvey, Leela E. Noronha, Kenneth R. Burton, Stephen Higgs, Dana L. Vanlandingham

School of Veterinary and Biomedical Sciences: Faculty Publications

Background: Japanese encephalitis virus (JEV) is a mosquito-borne zoonotic flavivirus and the leading cause of pediatric encephalitis in the Asian Pacific region. The transmission cycle primarily involves Culex spp. mosquitoes and Ardeid birds, with domestic pigs (Sus scrofa domestica) being the source of infectious viruses for the spillover of JEV from the natural endemic transmission cycle into the human population. Although many studies have concluded that domestic pigs play an important role in the transmission cycle of JEV, and infection of humans, the role of feral pigs in the transmission of JEV remains unclear. Since domestic and …

Auditory Processing Deficits In Msh2-Ko Mice Are Linked To Aberrant Inhibitory Neuron Function In The Thalamic Reticular Nucleus, Sadia N. Rahman

Dissertations and Theses

DNA repair mechanisms are crucial for both cellular development and function. One highly conserved DNA repair factor is Mut-S Homolog 2 (Msh2), which corrects base-base mismatches and insertion/deletion loops. In humans, defects in this repair pathway are linked to diseases that have severe neurological pathologies. These include Lynch syndrome, Huntington’s disease and demyelination of the corpus callosum. The fundamental role of Msh2 in brain function is unknown. Using an Msh2^-/- mouse model we began an exploration of its impact on the processing of sensory information, a crucial function to an animal’s survival. The goal of this …

Analysis Of Biologically Effective Dose For Retroactive Yttrium-90 Trans-Arterial Radioembolization Treatment Optimization, Mj Lindsey

CMC Senior Theses

Trans-arterial radioembolization (TARE) is a protracted modality of radiation therapy where radionuclides labeled with Yttrium-90 (⁹⁰Y) are inserted inside a patient's hepatic artery to treat hepatocellular carcinoma (HCC). While TARE has been shown to be a clinically effective and safe treatment, there is little understanding of the radiobiological relationship between absorbed dose and tissue response, and thus there is no dosimetric standard for treatment planning. The Biologically Effective Dose (BED) formalism, derived from the Linear-Quadratic model of radiobiology, is used to weigh the absorbed dose by the time pattern of delivery. BED is a virtual dose that can …

Visualization And Characterization Of The Immunological Synapse Between Chlorotoxin Chimeric Antigen (Cltx-Car) Redirected T Cells And Targeted Glioblastoma Tumors, Arianna Livi

CMC Senior Theses

Chimeric Antigen Receptor T (CAR-T) cells have demonstrated anti-tumor activity against aggressive and invasive cancers such as glioblastoma (GBM); however, clinical response rates remain low in clinical trial studies. Tumor heterogeneity and tumor microenvironment conditions pose significant challenges for treatment of GBM, thus continuous optimization of CAR-T cell therapies and identification of novel, widely expressed, and highly specific GBM antigens are vital to better patient outcomes. A newly developed CAR-T cell construct incorporating chlorotoxin (CLTX) as the targeting domain exhibited broad GBM-targeting capabilities and elicited potent cytotoxic effects during preclinical studies and is currently being tested in a phase I …

Endogenous Antioxidant Response And Lipid Peroxidation Levels In Muscle Tissue Of The Cownose Ray (Rhinoptera Bonasus), Bailey Berry

College of Graduate Studies: Theses & Dissertations

Oxidative stress is the result of an imbalance between reactive oxygen species (ROS) and antioxidant response within cells. ROS generation is a natural consequence of ETC activity within the mitochondria and is associated with aerobic metabolism. Oxidative stress data on elasmobranch muscle is limited, with previous studies primarily focusing on mammalian and teleost muscle. Elasmobranch skeletal muscle is generally composed of large proportions of white muscle fibers (anaerobic), low proportions of red muscle fibers (aerobic), and low proportions of pink muscle fibers (anaerobic). The cownose ray, a benthopelagic batoid species, presents an interesting model of study because it contains relatively …

Host Cell Responses Modulate Oncolytic Viral Treatment Of Neuroblastoma Cells, Kritika Kedarinath

Electronic Theses and Dissertations, 2020-2023

Neuroblastoma is an aggressive pediatric cancer that is poorly responsive to traditional cancer therapies. Oncolytic viral (OV) vectors such as Zika virus (ZIKV) and Parainfluenza virus type 5 (P/V virus) are promising neuroblastoma therapeutics, but the role of innate immune responses in the effectiveness of OV killing is not well understood. Previous studies showed the neuroblastoma cell line SK-N-AS (expressing low CD24) had low permissivity for ZIKV infection, and this restriction was relieved by ectopic CD24 expression (CD24-high cells). Compared to permissive CD24-high cells, the non-permissive CD24-low cells had elevated basal levels of IRF-1, NF?B and phosphorylated STAT1; these cells …

Conserved Novel Interactions Between Post-Replicative Repair And Mismatch Repair Proteins Have Differential Effects On Dna Repair Pathways, Anna K. Miller

Theses and Dissertations--Toxicology and Cancer Biology

DNA mismatch repair (MMR) is the DNA repair mechanism that repairs base-base mispairs and small insertions and deletions remaining after replication. MMR is also required for apoptosis after certain types of exogenous DNA damage that result in damage-associated mispairs. The basic MMR mechanism is well understood; however, proteins associated with MMR continue to be identified. The roles of these interacting proteins in MMR are largely unknown. We have identified the yeast protein Rad5 as a novel interactor of the critical MMR proteins Msh2 and Mlh1. Rad5 is a DNA helicase and E3 ubiquitin ligase involved in post-replicative repair. However, to …

Elucidating The Functional Importance Of Peroxiredoxin Iv In Prostate Cancer And Its Secretion Mechanism, Na Ding

Theses and Dissertations--Toxicology and Cancer Biology

Prostate cancer is the most common and second leading cause of cancer death in men. Prevailing theories state that inflammation may drive prostate carcinogenesis via oxidative stress and the generation of reactive oxygen species (ROS) that induce somatic mutagenesis. Since high proliferating cells or cancer cells exhibit aberrant metabolism to satisfy the needs of energy for rapid cell proliferation, they also generate high levels of ROS which stimulates the expression of cellular antioxidants to overcome the dysregulation of redox homeostasis through the regulation of redox-sensitive transcription factors. Among different antioxidants, peroxiredoxin (Prx) family proteins are the highly conserved and mostly …

Beyond Mitosis, Plk1-Mediated Phosphorylation Re-Wires Cancer Metabolism And Promotes Cancer Progression, Qiongsi Zhang

Theses and Dissertations--Toxicology and Cancer Biology

Polo-like kinase 1 (PLK1) is a well- characterized regulator of cell division and is known to be highly expressed in certain types of tumors. It has been demonstrated the multifaceted roles of PLK1 in regulation of transcription, translation, epigenetics, DNA damage and cellular metabolism et al. Despite these findings, the precise mechanisms by which PLK1 regulates these processes beyond mitosis remain unclear. PLK1-mediated phosphorylation and misregulation of its substrates has been linked to tumorigenesis, cancer progression, drug resistance and worse prognosis. In this study, we investigated the non-canonical functions of PLK1 in cancer metabolism and drug resistance. We found that …

Sex-Dependent Effects Of Induced Acute Inflammation On Glucose Homeostasis And Rna Editing Enzymes, Christian A. Rivas

Graduate Theses/Dissertations

The first line of defense against bodily insults, like pathogen invasion, is the innate immune system. Innate immunity sets in motion countless cascades that result in inflammation. Inflammation simultaneously affects multiple biological processes like metabolism and gene expression. Males and females react differently to inflammation. To understand both molecular and physiological sex differences in inflammation, we examined how inflammation affects gene expression and glucose metabolism. Adenosine deaminase acting on RNA (ADAR1) is upregulated by inflammation and catalyzes RNA editing, a process where nucleotides encoded by the genome are modified. ADAR1 also controls the innate immune reaction by decreasing activity of …

Cul3 Negatively Regulates Nlrp12-Mediated Inhibition Of The Canonical Nf-Κb Signaling Pathway, Inyeong Lee

Graduate Theses/Dissertations

Nod-like receptor family pyrin domain-containing protein 12 (NLRP12) is mainly known for its inhibitory function on NF-κB signaling in innate immune cells, and more recently, for its ability to regulate chemokine signaling and ubiquitination of the immune receptor RIG-I. Through a yeast 2-hybrid screen, the Lupfer lab previously discovered that NLRP12 interacts with other ubiquitin-associated proteins including Cullin 3 (CUL3) and RING finger protein 2 (RNF2). This research was conducted to mainly investigate the interaction between NLRP12 and CUL3 in human cells and examine the role in regulating NF-κB signaling. Previously, co-immunoprecipitation, followed by western blot analysis, and confocal microscopy …

Identification Of Proteins Involved In Cell Membrane Permeabilization By Nanosecond Electric Pulses (Nsep), Giedre Silkuniene, Uma Mangalanathan, Alessandra Rossi, Peter A. Mollica, Andrei G. Pakhomov, Olga N. Pakhomova

Bioelectrics Publications

The study was aimed at identifying endogenous proteins which assist or impede the permeabilized state in the cell membrane disrupted by nsEP (20 or 40 pulses, 300 ns width, 7 kV/cm). We employed a LentiArray CRISPR library to generate knockouts (KOs) of 316 genes encoding for membrane proteins in U937 human monocytes stably expressing Cas9 nuclease. The extent of membrane permeabilization by nsEP was measured by the uptake of Yo-Pro-1 (YP) dye and compared to sham-exposed KOs and control cells transduced with a non-targeting (scrambled) gRNA. Only two KOs, for SCNN1A and CLCA1 genes, showed a statistically significant reduction in …

Pre-Clinical Trials With Precision-Medicine Based Therapeutics In Basal-Like Patient-Derived Xenografts, David C. Boyd

Theses and Dissertations

Breast cancer treatments have improved over time, but the diseases seeing the most benefit from these improvements have the estrogen receptor, progesterone receptor, or are positive for HER2. Basal-like breast cancer tends to not have these biomarkers, which necessitates their treatment to be traditional, untargeted therapeutics which are less effective and tend to have harsh adverse effect profiles – this is an important unmet need. These studies utilize a variety of techniques, including tissue culture, viability assays, high-throughput screening, in vivo drug treatments and imaging, pathway analyses, molecular techniques such as Western blot, antibody arrays, RNA sequencing, sc RNA sequencing, …

The Hepatic Immunological Pattern Shaped By Dominant-Subdominant Cellular Interactions Creates A Collective Function Beyond The Function Of Each Cellular Constituent To Orchestrate Progression Of Hepatocellular Carcinoma, Nicholas J. Koelsch

Theses and Dissertations

Abundance of data on the role of inflammatory immune responses in the progression or inhibition of hepatocellular carcinoma (HCC) has failed to offer a curative immunotherapy for HCC. This is largely because of taking reductionist approaches and missing the collective function of the hepatic immune system by focusing on specific immune cell types. To this end, we propose that focusing on the dominant-subdominant patterns of the immune cells would allow understanding of the mechanism by which a collective immune function emerges. To identify the collective immune function through a systems immunology perspective, we performed high-throughput analysis of snRNAseq data collected …

Epithelial Membrane Protein 3 (Emp3b) Is A Novel Regulator Of Sympathetic Nervous System Development In Zebrafish., Jessica M. White

Theses and Dissertations

Notable progress has been made in understanding the development of the neural crest (NC). Neural crest cells (NCCs) can be divided into 4-5 subpopulations. A major lineage among trunk NC derivatives are sympathoadrenal (SA) cells, which give rise to the sympathetic nervous system (SNS). Trunk NCCs follow a ventromedial migration pathway where signals derived from the dorsal aorta instruct migrating NCCs to a SA cell fate. Defects in NC development can result in syndromes known as neurocristopathies. Neuroblastoma is one of the most common forms of pediatric cancer affecting nearly 800 infants each year in the United States (Takita et …

Protacs – A Novel And Rapidly Developing Field Of Targeted Protein Degradation, Hannah R. Gatley

Theses and Dissertations

There is a continued need for new technology and strategies for tackling cancer and other diseases, and within the current century a novel therapeutic strategy has emerged in the realm of targeted protein degradation called Proteolysis-Targeting Chimeras (PROTACs). This technology specifically targets and degrades disease-causing proteins via the ubiquitin-proteasome system, and has seen an explosion of research and intrigue in both academia and industry over the past two decades. The diversity of PROTAC classes based on the E3 ligase recruiting ligand and the target protein allows for a universal molecular structure that can be customized for a specific target and …

Tgif1 Physiological Levels Limit Β-Cell Distress And Neonatal Diabetes, Creighton J. Friend

Theses and Dissertations

TGIF1 belongs to the superfamily of homeodomain proteins, which regulate a wide variety of biological functions, including cell stemness and specification of cell fate during early development. Perhaps surprisingly, we found that enforced expression in pancreatic progenitor cells during embryogenesis resulted in severe diabetes, hinting at the possibility that TGIF1 might regulate pancreas development. Subsequent genetic experiments targeting β-cells showed that TGIF1 affected β-cell function and homeostasis. Transcriptomic analysis revealed that TGIF1 expression inhibits the expression of essential components of UPR signaling, underscoring a potential mechanism in which TGIF1 disrupts protein folding and secretion. Congruently, TGIF1 expression led to a …

Kpt-330 Synergizes With Everolimus To Reduce Mtorc1-Overactive Basal-Like Triple-Negative Breast Cancer Brain Metastasis Burden, Aaron D. Valentine

Theses and Dissertations

Triple-negative breast cancer (TNBC), a highly metastatic breast cancer subtype, accounts for approximately 20% of all breast cancer diagnoses. Basal-like TNBC is notably difficult to treat due to the lack of actionable drug targets such as estrogen and progesterone receptors, as well as HER2. Due to the deficiency in TNBC-targeting drugs that are able to cross the blood-brain barrier (BBB) for breast-to-brain metastasis, there is a need to develop novel BBB-permeable treatments. After preliminary testing, KPT-330 (XPO1 inhibitor) and everolimus (FKBP1A/mTOR inhibitor) were selected as drug candidates for this study. Patient-derived xenograft (PDX) models for in vitro and in vivo …

Development Of A Chemical Biology Approach To Uncover The Influence Of Sequence Variations On Ces1 Activity In Live Cells, Samuel James Knebel

Masters Theses

Drug metabolism is the biochemical process of modifying drugs to detoxify and remove them through enzymatic transformations. These biotransformation’s occur primarily in the liver and are critical to understanding how pharmaceutical compounds are chemically altered inside the human body. Human carboxylesterases (CESs) catalyze the hydrolysis of esters, amides, thioesters, and carbamates. CES-mediated hydrolysis plays an important role in the metabolism of many drugs including the first FDA approved antiviral treatment for COVID-19, remdesivir (Veklury), the seizure control medication rufinamide (Banzel), and the flu antiviral drug oseltamivir (Tamiflu). CES activity is known to be influenced by a variety of factors including …

Application Of Crispr/Cas9 Whole Genome Screens To Advance Macrophage Biology, Kevin Wanniarachchi

Electronic Theses and Dissertations

Advances in CRISPR/Cas9 gene editing technologies present opportunities to better understand the contribution of individual genes to complex eukaryotic cellular processes. I have applied CRISPR whole genome screen technologies to inform further mechanistic understanding of macrophage fitness and neutral lipid metabolism. This work is important because macrophages play critical roles in immune function and are implicated as causative agents in disease states. Chapter One of this dissertation provides insights into how CRISPR genome screening technologies have improved biological discovery and key findings from their application and discusses how this technology can be implemented to advance the discovery of novel macrophage …

Investigating Changes In Er-To-Golgi Protein Transport Following A Short Calcium Pulse: Roles Of Alg-2 And Peflin, Alaa Mohammed Yosri Shaheen

Graduate Student Theses, Dissertations, & Professional Papers

The ER-Golgi interface is a very dynamic environment that involves the movement of protein-loaded vesicles forward and backward. The movement of COPII-coated vesicles from the ER to the Golgi is the initial step in the movement of secreted, organellar, and cell surface proteins toward their final destinations. Many factors can regulate this step, including cytosolic calcium increases. In this study, we examined the effect of a transient calcium pulse on recruitment to ER exit sites of cargo proteins for ER export, the calcium-sensitive regulatory proteins apoptosis-linked gene 2 (ALG-2) and peflin, and the COPII outer coat subunits Sec31A and Sec13. …

A Cladoxylopsid With Complex Vascular Architecture From The Early Devonian Battery Point Formation (Québec, Canada), Jessica Chu

Cal Poly Humboldt theses and projects

Cladoxylopsids are seed-free plants that formed the world’s earliest forests and gave rise to horsetails (sphenopsids), but their evolutionary origins are poorly understood. Here, I describe a new Early Devonian cladoxylopsid from the Emsian (400-395 Ma) Battery Point Formation (Québec, Canada). The structural features of this plant indicate taxonomic affinity to cladoxylalean cladoxylopsids and its phylogenetic position supports placement in genus Cladoxylon (the proposed name, Cladoxylon kespekianum sp. nov., to be formalized by peer-reviewed publication). Specimens of this plant are permineralized in calcium carbonate and were studied using the acetate peel technique with light and electron microscopy. Cladoxylon kespekianum is …

The Effect Of Larval Competition On Adult Life History Traits And The Immune Response Of Adult Cat Fleas (Ctenocephalides Felis), Piper N. Zellner, Lisa D. Brown

Honors College Theses

In holometabolous insects, conditions during the larval stage can affect the adult stage. For instance, in mosquitoes, reduced larval food and high density can make adults more susceptible to infection. Fleas (Siphonaptera), like mosquitoes, go through complete metamorphosis and have adult stages that exclusively feed on the blood of vertebrates, including humans. However, flea larvae have chewing mandibles and rely on nutrients from dried fecal matter containing vertebrate blood proteins. Their limited mobility and unique nutritional needs confine their development to specific areas, likely leading to frequent larval competition in natural conditions. Yet, the influence of larval density on the …

The Effects Of Cucurbitacin B And Silmitasertib On Metastasis And Itga6 Using The Zebrafish Tumor-Xenograft, Alexandra Griffis

College of Graduate Studies: Theses & Dissertations

Ninety percent of cancer deaths are resultant from the metastasis of cancer cells. When cancer cells translocate through blood vessels or the lymphatic system, they may form tumors outside of their primary site. The processes of metastasis can begin quickly; after onset, metastasis is unforgiving, as it does not participate with the body’s physiological systems in an orderly way. In the past, our lab produced results indicating that a cell adhesion molecule, Integrin Alpha-6, may contribute to cancer cells' ability to metastasize. Integrins mediate interactions between the cell and the Extracellular Matrix (ECM), regulating cell attachment and cell migration. With …

How To Build A Cortex: Coordinated Assembly Of Cortical Septins And Actomyosin In The Leader Bleb, Asia Marie Paguntalan

Master's Theses

In confined spaces, migrating cells can undergo mesenchymal-to-amoeboid transitions by altering their cortical dynamics and adhesion with the environment. Septins frequently associate with cortical actin and non-muscle myosin (NMII), but the functional nature of these interactions remains unclear. Upon non-adhesive confinement and NMII enrichment, fibroblasts can switch to a fast, leader bleb-based mode of motility, characterized by the absence of adhesions and stress fibers and formation of a single, elongated leader bleb. During this transition, cortical actin remodeling and polarized NMII contractility drive leader bleb stabilization by generating long-range cortical flows, in coordination with changes in septin localization and assembly …

A Single-Cell Atlas Of Bovine Skeletal Muscle Reveals Mechanisms Regulating Intramuscular Adipogenesis And Fibrogenesis, Leshan Wang, Peidong Gao, Chaoyag Li, Qianglin Liu, Zeyang Yao, Yuxia Li, Xujia Zhang, Jiangwen Sun, Constantine Simintiras, Matthew Welborn, Kenneth Mcmillin, Stephanie Oprescu, Shihuan Kuang, Xing Fu

Computer Science Faculty Publications

Background: Intramuscular fat (IMF) and intramuscular connective tissue (IMC) are often seen in human myopathies and are central to beef quality. The mechanisms regulating their accumulation remain poorly understood. Here, we explored the possibility of using beef cattle as a novel model for mechanistic studies of intramuscular adipogenesis and fibrogenesis.

Methods: Skeletal muscle single-cell RNAseq was performed on three cattle breeds, including Wagyu (high IMF), Brahman (abundant IMC but scarce IMF), and Wagyu/Brahman cross. Sophisticated bioinformatics analyses, including clustering analysis, gene set enrichment analyses, gene regulatory network construction, RNA velocity, pseudotime analysis, and cell-cell communication analysis, were performed to elucidate …

Measuring How Kinetochore-Microtubule Detachment Contributes To Chromosome Movement And The Correction Of Attachment Errors, Melissa K. Parks

Dartmouth College Ph.D Dissertations

The goal of mitosis is to achieve faithful chromosome segregation; ensuring that the daughter cells inherit equal numbers of chromosomes. This is vital to cell health and viability and if mis-regulated can result in birth defects and disease such as cancer. There are many intricately regulated processes that occur throughout mitosis to achieve proper chromosome segregation, and one such example is the dynamic attachments formed between cytoskeletal structures, known as microtubules, and chromosomes, the carriers of genetic material. These attachments occur at structures called kinetochores, and the microtubules attached here are referred to as kinetochore-microtubules (k-MTs). These k-MTs are inherently …

Investigation Of The Segment Polarity Network In The Tardigrade Hypsibius Exemplaris, Taylor R. Harrison

UNF Graduate Theses and Dissertations

Segmentation has facilitated the evolution of the many forms of the panarthropods. Downstream regulation of segmentation is controlled by the highly conserved segment polarity network which includes the genes engrailed (en), hedgehog (hh), wingless (wg), cubitus interruptus (ci), patched (ptc), and smoothend (smo). While a high level of conservation has been seen in both the arthropods and onychophorans, only en has been described in any representatives of Tardigrada. Previous work had already established the loss of wg, which encodes for a Wnt ligand, in the tardigrade H. exemplaris …