Biochemistry, Biophysics, and Structural Biology Commons^™

Placental Co-Transcriptional Activator Vestigial-Like 1 (Vgll1) Drives Tumorigenesis Via Increasing Transcription Of Proliferation And Invasion Genes, Heather Sonnemann

Dissertations and Theses (Open Access)

Vestigial-like 1 (VGLL1) is a co-transcriptional activator that binds to TEA domain containing transcription factors (TEADs). Its expression is upregulated in a variety of aggressive cancer types, including pancreatic and basal-like breast cancer, and increased transcription of VGLL1 is strongly correlated with poor prognosis and decreased overall patient survival. In normal tissues, VGLL1 is most highly expressed within placental trophoblast cells, which share the common attributes of rapid cellular proliferation and invasion with tumor cells. The impact of VGLL1 in cancer has not been fully elucidated and no VGLL1-targeted therapy currently exists. The aim of this study was to evaluate …

The Role Of The Circadian Clock In Disease And Tissue Function, Marvin Wirianto

Dissertations and Theses (Open Access)

The mammalian circadian clock responds to the 24-hour daily cycle and regulates tissue-specific gene expression and downstream physiology. The central pacemaker located in the hypothalamic suprachiasmatic nuclei (SCN) synchronizes the peripheral clocks in different tissues. This dissertation aims to uncover specific circadian regulatory mechanisms in the brain and skeletal muscle.

Alzheimer’s Disease (AD) is the most common type of dementia. It has previously been shown that there is a strong correlation of disease progression with circadian rhythm decline. We showed that circadian modulation by a small molecule Nobiletin (NOB) was able to mitigate AD pathogenesis. Furthermore, NOB significantly alleviated the …

Pragmatism And Feasibility: A Qualitative Study Of Experiences Implementing And Upgrading Care In Geriatric Emergency Departments, Anita Chary, Annika Bhananker, Vivian Ramont, Lauren Southerland, Aanand Naik, Kyler Godwin, Maura Kennedy

Faculty, Staff and Students Publications

OBJECTIVES: Implementation and sustainability of new care processes in emergency departments (EDs) is difficult. We describe experiences of implementing geriatric care processes in EDs that upgraded their accreditation level for the Geriatric Emergency Department Accreditation (GEDA) program. These EDs can provide a model for adopting and sustaining guidelines for evidence-based geriatric care.

METHODS: We performed qualitative interviews with geriatric ED nurse and physician leaders overseeing their ED's geriatric accreditation processes. The interview guide was based on the Consolidated Framework for Implementation Research (CFIR), a framework consisting of a comprehensive set of factors that impact implementation of evidence-based interventions. We used …

Exploring Acetate Metabolism: Genetically Characterizing Acetate Production And Acetate Utilization In The Fungal Pathogen Cryptococcus Neoformans, Rodrigo Catalan-Hurtado

All Dissertations

The basidiomycete Cryptococcus neoformans is an invasive opportunistic fungal pathogen and the most frequent cause of fungal meningitis resulting in approximately 112,000 deaths per year worldwide. Recently, the World Health Organization systematically prioritized fungal pathogens in which C. neoformans was among four fungal pathogens deemed critically important. Current methods of treatment are inadequate for most of the infected population; therefore, it is imperative to find novel therapeutic targets. Previous studies have shown that acetate is a major metabolite found in biopsies of C. neoformans infected mouse brain and lung tissues. Two potential pathways for acetate production have been identified. …

Assessment Of Tce And Chiral Pcb Dechlorination Rate, Congener Diversity, And Enantioselectivity In Town Creek, Sc, Usa Sediment Microcosms, Catherine P. Sumner

All Dissertations

Polychlorinated biphenyls (PCBs) and trichloroethene (TCE) are ubiquitous contaminants and are recognized as persistent organic pollutants due to their extreme chemical stability. PCBs were manufactured by chlorinating biphenyls that created 209 congeners with various structures, of which 19 are chiral and can exist as a pair of stable atropisomers. PCBs have been known to cause developmental and neurological toxicity in humans and wildlife; they can act as endocrine disrupters, carcinogens, and teratogens. Sangamo Weston Inc. was an industrial plant located near Town Creek in Pickens Country, South Carolina, that manufactured capacitors and used Aroclors 1016 and 1254 as dialectic fluids …

Candida Albicans Farnesol Synthesis And Secretion, Daniel J. Gutzmann

School of Biological Sciences: Dissertations, Theses, and Student Research

Candida albicans is a polymorphic fungus and opportunistic commensal found primarily in the gastrointestinal and skin of healthy individuals. Several barriers prevent C. albicans from causing disease including a healthy immune system and microbiome. When these barriers become comprised, C. albicans can transition to a pathogen and disseminate through the intestinal mucosa leading to life-threatening bloodstream and invasive infections with mortality rates of up to 64%. Morphogenic plasticity is key to this transition and impacts virulence, adaptation to different host environments, and evasion of host immune responses. One regulator of morphogenesis is farnesol. Farnesol is a secondary metabolite of …

Metal Assisted O2-Dependent Carbon-Carbon Bond Cleavage Of Β-Diketones And Flavonols, Stephen N. Anderson

All Graduate Theses and Dissertations, Fall 2023 to Present

Almost everything we interact with on a daily basis has been synthesized by chemists ranging from plastics, food preservatives, and medications. The diversity of synthetic molecules are achieved by the formation of new bonds between existing molecules and/or through the cleaving of bonds found in a molecule. There are uncountable amount of conditions reported to facilitate chemical reactions which all depend on the nature of molecules being used and the environment it is used in.

In recent years, more attention has been paid to identify chemical reactions that can use more environmentally favorable conditions and reduce the use of limited …

Synergistic Effects Of Novel Penicillin-Binding Protein 1a Amino Acid Substitutions Contribute To High-Level Amoxicillin Resistance Of Helicobacter Pylori, Alain Cimuanga-Mukanya, Evariste Tshibangu-Kabamba, Patrick De Jesus Ngoma Kisoko, Fabien Mbaya Tshibangu, Antoine Tshimpi Wola, Pascal Tshiamala Kashala, Dieudonné Mumba Ngoyi, Steve Ahuka-Mundeke, Gunturu Revathi, Ghislain Disashi-Tumba

Pathology, East Africa

The growing resistance to amoxicillin (AMX)—one of the main antibiotics used in Helicobacter pylori eradication therapy—is an increasing health concern. Several mutations of penicillin-binding protein 1A (PBP1A) are suspected of causing AMX resistance; however, only a limited set of these mutations have been experimentally explored. This study aimed to investigate four PBP1A mutations (i.e., T558S, N562H, T593A, and G595S) carried by strain KIN76, a high-level AMX-resistant clinical H. pylori isolate with an AMX minimal inhibition concentration (MIC) of 2 µg/mL. We transformed a recipient strain 26695 with the DNA containing one to four mutation allele combinations of the pbp1 gene …

Developing A Comprehensive Genome-Scale Metabolic Model For The Arabidopsis Thaliana Root System, Lohani Esterhuizen

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Arabidopsis thaliana (Arabidopsis) is the most well-established model plant to date. Being the first plant to have its genome mapped, studies on Arabidopsis have provided insurmountable insights into the physiological and biochemical nature of plants. Methods that allow us to computationally study the metabolism of organisms include the use of genome-scale metabolic models (GEMs). Despite its popularity, no GEM currently maps the metabolic activity in the root system of Arabidopsis, which is the first organ to face and respond to stress conditions in the soil. This work aims to develop and implement a comprehensive GEM of the Arabidopsis root system …

L-Arabinose Induced Overexpression For Crystallographic Analysis Of The Spoiie Protein From Clostridioides Difficile, Danielle M. Maynard

Graduate Theses and Dissertations

The SpoIIE protein plays a crucial role in the sporulation process of Clostridioides difficile, a pathogen responsible for severe gastrointestinal diseases. Understanding the structural and functional aspects of SpoIIE is pivotal for deciphering its role in sporulation and exploring its potential as a therapeutic target. This study investigates the impact of varying concentrations of L-arabinose on the overexpression of SpoIIE in C. difficile, aiming to optimize protein yield and purity for subsequent crystallization and structural determination via X-ray crystallography. Using a recombinant expression system in Escherichia coli, different concentrations of L-arabinose were employed to induce SpoIIE overexpression. Protein purification was …

Diatom Abundance In The Polar Oceans Is Predicted By Genome Size, Wade R. Roberts, Adam M. Siepielski, Andrew J. Alverson

Biological Sciences Faculty Publications and Presentations

A principal goal in ecology is to identify the determinants of species abundances in nature. Body size has emerged as a fundamental and repeatable predictor of abundance, with smaller organisms occurring in greater numbers than larger ones. A biogeographic component, known as Bergmann’s rule, describes the preponderance, across taxonomic groups, of larger-bodied organisms in colder areas. Although undeniably important, the extent to which body size is the key trait underlying these patterns is unclear. We explored these questions in diatoms, unicellular algae of global importance for their roles in carbon fixation and energy flow through marine food webs. Using a …

Diapause Specific Proteins Of A Brine Shrimp Form Liquid Droplets Dependent On Salt And Ph Levels, Kolby Sanders, Alex Haydon, Charles Elder, David Grimm, Michael Menze

Undergraduate Research Events

Liquid-Liquid Phase Separation (LLPS) is a process when a polypeptide condenses into a dense and dilute phase in aqueous solutions. Within cells, this process is believed to relate to stress regulation and various cellular processes. Several stress-related proteins found only during the embryonic developmental stage of diapause in the brine shrimp, A. franciscana, have been observed to undergo LLPS in vitro. Our results show that the small heat shock protein (sHSP) p26 has a greater propensity to LLPS under varying salt concentrations compared to LEA6, a late embryogenesis abundant protein (LEA). At a protein concentration of 1.31 mg/ml in …

Computational Modelling And Design Of Antibodies: Benefits From Analysis Of Their Unique Structural Motifs, Katherine M. Mccoy

Dartmouth College Ph.D Dissertations

The complexes that antibodies make with their binding partners, or antigens, are especially valuable to be able to predict and modify due to their unique role in the immune system. Yet, they present significant challenges to computational methods of both modelling and design. Antibodies are unlike most other proteins in that they are composed of a scaffold region, which is a highly conserved structure that is largely the same between antibodies of the same class, and Complementary Determining Regions (CDRs), which are comprised of hypervariable loops that largely determine their binding motifs. Additionally, antibodies and their antigens do not co-evolve …

Elevating Plk1 Overcomes Beti Resistance In Prostate Cancer Via Triggering Brd4 Phosphorylation-Dependent Degradation In Mitosis, Yanquan Zhang, Ka-Wing Fong, Fengyi Mao, Ruixin Wang, Derek B. Allison, Dana Napier, Daheng He, Jinpeng Liu, Yeqing Zhang, Jing Chen, Yifan Kong, Chaohao Li, Guangbing Li, Jinghui Liu, Zhiguo Li, Haining Zhu, Chi Wang, Xiaoqi Liu

Markey Cancer Center Faculty Publications

Bromodomain-containing protein 4 (BRD4) has emerged as a promising therapeutic target in prostate cancer (PCa). Understanding the mechanisms of BRD4 stability could enhance the clinical response to BRD4-tar- geted therapy. In this study, we report that BRD4 protein levels are significantly decreased during mitosis in a PLK1-dependent manner. Mechanistically, we show that BRD4 is primarily phosphorylated at T1186 by the CDK1/cyclin B complex, recruiting PLK1 to phosphorylate BRD4 at S24/S1100, which are recognized by the APC/CCdh1 complex for proteasome pathway degradation. We find that PLK1 overexpression lowers SPOP mutation-stabilized BRD4, consequently rendering PCa cells re-sensitized to BRD4 inhibitors. Intrigu-ingly, we …

Defining A Dynamic Architecture Of Protein Tyrosine Phosphatases, Colin L. Welsh

MUSC Theses and Dissertations

Protein tyrosine phosphatases (PTPs), a critical class of signaling enzymes, are principally responsible for balancing the actions of kinases through the dephosphorylation of tyrosine residues on substrate proteins. As such, this family is involved in myriad pathways and individual members are able to perform both oncogenic and tumor-suppressing roles. However, while clinical success has been achieved in targeting kinases, PTPs have remained therapeutically challenging. Orthosteric inhibition is limited in PTPs due to their highly conserved fold, leading to off-target effects, and their highly charged active site, requiring highly polar molecules with poor bioavailability. These challenges posit the allosteric inhibition of …

Exploring Chilling Stress And Recovery Dynamics In C4 Perennial Grass Of Miscanthus Sinensis, Karolina Sobańska, Monika Mokrzycka, Martyna Przewoźnik, Tomasz Pniewski, Katarzyna Glowacka

Department of Biochemistry: Faculty Publications

The increasing cultivation of perennial C4 grass known as Miscanthus spp. for biomass production holds promise as a sustainable source of renewable energy. Unlike the sterile triploid hybrid of M. × giganteus, which cannot reproduce through seeds, M. sinensis possesses attributes that could potentially address these limitations by effectively establishing itself through seed propagation. This study aimed to investigate how 18 genotypes of M. sinensis respond to chilling stress and subsequent recovery. Various traits were measured, including growth and biomass yield, the rate of leaf elongation, and a variety of chlorophyll fluorescence parameters, as well as chlorophyll …

Mutant Androgen Receptor Induces Neurite Loss And Senescence Independently Of Are Binding In A Neuronal Model Of Sbma, Jordyn Karliner, Y Liu, Diane Merry

Department of Biochemistry and Molecular Biology Faculty Papers

Spinal and bulbar muscular atrophy (SBMA) is a slowly progressing neuromuscular disease caused by a polyglutamine (polyQ)-encoding CAG trinucleotide repeat expansion in the androgen receptor (AR) gene, leading to AR aggregation, lower motor neuron death, and muscle atrophy. AR is a ligand-activated transcription factor that regulates neuronal architecture and promotes axon regeneration; however, whether AR transcriptional functions contribute to disease pathogenesis is not fully understood. Using a differentiated PC12 cell model of SBMA, we identified dysfunction of polyQ-expanded AR in its regulation of neurite growth and maintenance. Specifically, we found that in the presence of androgens, polyQ-expanded AR inhibited neurite …

Functional And Structural Analysis Of The Neimann-Pick Disease Type C Pathway To Include Caveolin-1, Anthony Michael Seat

Chemistry and Chemical Biology ETDs

Human disease is often thought of as an all or nothing prospect, either one has the disease or one does not. This does not bear out in clinical or personal experiences, instead demonstrating that disease occurs within a spectrum ranging from presumed unaffected to demonstrably and detrimentally affected.Neimann-Pick disease is one example of this spectrum look into diseased states, with multiple named versions of a phenotypically similar disease. We focus on Neimann-Picktype C (NPC), which is the result of a disruption in the efflux of cholesterol and sphingolipids from the endocytic pathway. NPC demonstrates this concept of a spectrum of …

Role Of Sds-22/Pp1 Phosphatase In Polarizing The Germplasm Of Caenorhabditis Elegans Embryo, Aparna Nurni Ravi

Dartmouth College Ph.D Dissertations

During asymmetric cell division, cell polarity and cell cycle are tightly coupled to ensure robust segregation of cell fate determinants and generation of cellular diversity. In the one-cell C. elegans embryo, multiple cell cycle kinases regulate cell polarization and posterior segregation of germline fate determinants (germplasm). For example, PLK-1 kinase inhibits the retention of its germplasm substrate POS-1 in the anterior, driving POS-1 segregation to the posterior (Han et al., 2018). Additionally, MBK-2 kinase disassembles P granules in the anterior through phosphorylation of the P granule scaffold MEG-3, helping to drive P granule segregation to the posterior (Wang et al., …

Genetic Diversity Of 1,845 Rhesus Macaques Improves Genetic Variation Interpretation And Identifies Disease Models, Jun Wang, Meng Wang, Ala Moshiri, R Alan Harris, Muthuswamy Raveendran, Tracy Nguyen, Soohyun Kim, Laura Young, Keqing Wang, Roger Wiseman, David H O'Connor, Zach Johnson, Melween Martinez, Michael J Montague, Ken Sayers, Martha Lyke, Eric Vallender, Tim Stout, Yumei Li, Sara M Thomasy, Jeffrey Rogers, Rui Chen

Faculty, Staff and Students Publications

Understanding and treating human diseases require valid animal models. Leveraging the genetic diversity in rhesus macaque populations across eight primate centers in the United States, we conduct targeted-sequencing on 1845 individuals for 374 genes linked to inherited human retinal and neurodevelopmental diseases. We identify over 47,000 single nucleotide variants, a substantial proportion of which are shared with human populations. By combining rhesus and human allele frequencies with established variant prediction methods, we develop a machine learning-based score that outperforms established methods in predicting missense variant pathogenicity. Remarkably, we find a marked number of loss-of-function variants and putative deleterious variants, which …