Biochemistry, Biophysics, and Structural Biology Commons^™

Investigations In The Cellular And Molecular Biology Of Human Airway Mucociliary Tissue, Vincent Manna

Graduate School of Biomedical Sciences Theses and Dissertations

Our laboratory has integrated the use of a human-derived, in vitro model of airway mucociliary tissue. We isolate human nasal epithelial cells (HNECs) from the nasal mucociliary tissue of donors with a small brush and expand the airway progenitor cells in culture. The HNECs are then seeded onto semi-permeable transwell inserts. The inserts are in contact with the media in the lower chamber but don’t contain media in the upper chamber therefore the cells are exposed to the air while drawing nutrients from the media below, this is called the Air-Liquid Interface (ALI). HNECs cultured at the ALI initiate a …

Effects Of Trans-Acting Factors On The Translational Machinery In Yeast, Brandon M. Trainor

Graduate School of Biomedical Sciences Theses and Dissertations

Synthesis of proteins, or translation, is a complex biological process requiring the coordinated effort of numerous protein and RNA factors. Central to translation is the ribosome, a complex macromolecular complex consisting of both ribosomal RNA (rRNA) and ribosomal protein (r-protein). Ribosomes are essential and are one of the oldest and most abundant biomolecules across all forms of life. In addition to the ribosome, translation requires messenger RNA (mRNA), transfer-RNA conjugated to an amino acid (aa-tRNA), translation factors, and energy in the form of ATP and GTP. Translation universally occurs in four major stages, initiation, elongation, termination, and recycling, with initiation …

College Of Natural Sciences Newsletter, August 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 8.

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3 Student Summer Research
Page 4 Media Coverage of CNS
Page 5 Wintrode Student Success Center
Page 6-7 Welcome to our new Faculty & Staff!
Page 8 One Day for State: Thursday, Sept. 2nd
Page 7 Open PRAIRIE Data; Fall Faculty Retreat 2021

Modification Of Cell Wall Polysaccharide Guides Cell Division In Streptococcus Mutans., Svetlana Zamakhaeva, Catherine T Chaton, Jeffrey S. Rush, Sowmya Ajay Castro, Cameron W Kenner, Alexander E Yarawsky, Andrew B Herr, Nina M Van Sorge, Helge C Dorfmueller, Gregory I Frolenkov, Konstantin V Korotkov, Natalia Korotkova

Molecular and Cellular Biochemistry Faculty Publications

In ovoid-shaped, Gram-positive bacteria, MapZ guides FtsZ-ring positioning at cell equators. The cell wall of the ovococcus Streptococcus mutans contains peptidoglycan decorated with serotype c carbohydrates (SCCs). In the present study, we identify the major cell separation autolysin AtlA as an SCC-binding protein. AtlA binding to SCC is attenuated by the glycerol phosphate (GroP) modification. Using fluorescently labeled AtlA constructs, we mapped SCC distribution on the streptococcal surface, revealing enrichment of GroP-deficient immature SCCs at the cell poles and equators. The immature SCCs co-localize with MapZ at the equatorial rings throughout the cell cycle. In GroP-deficient mutants, AtlA is mislocalized, …

Polycyclic Aromatic Hydrocarbons And The Microbiomes Of Two Benthic Species, Samantha Ells

Master's Theses

The presence of oil has been shown to affect the microbiomes of the water column, sediments, and organisms, both by altering the diversity and the composition of those microbial communities. If the microbiome is altered it may no longer provide benefits to its host organism, impacting its ability to survive. Thus, it is important to understand the effects of large-scale contamination events including the Deepwater Horizon oil spill. This study set out to examine the effects of oil exposure on the microbiome of two benthic species, southern flounder (Paralichthys lethostigma) and eastern oysters (Crassostrea virginica) to further understand the effects …

Cyclic Sulfones From Double Conjugate Addition Of Rongalite, Hao Zong

Theses, Dissertations and Culminating Projects

We report a cyclic sulfone synthesis method from the addition of sodium hydroxymethanesulfinate to doubly electrophilic dienone substrates. The novel synthesis of the cyclic sulfone thus avoided the using the toxic and odorous sulfides, and also oxidizing reagents. We prepared both the symmetrical and unsymmetrical substrates, and then used the substrate for the synthesis of cyclic sulfone.

Molecular Simulation Of Rna Conformational Dynamics : An Example Of Micro-Rna Targeting Messenger Rna : Mir-34a-Msirt1, Parisa Ebrahimi

Legacy Theses & Dissertations (2009 - 2024)

MicroRNA (miRNA), as a distinct class of biological regulators and a ”guide” member of non-coding RNA-protein complexes (RNPs), regulates more than 60% of protein-coding genes expression through base-pairing with targeted messenger RNA (mRNA) in the RNA-Induced Silencing Complex (RISC). Most of miRNAs identified in human, are conserved in other animals, which have preferentially conserved interaction sites particularly in 3’ untranslated regions (3’UTRs) of many human messenger mRNAs.The capability of a single miRNA to target more than hundreds of mRNAs, suggests that miRNAs influence essentially all developmental process and diseases, which also makes them interesting candidates as therapeutics agents. The primary …

Molecular Simulation Of Rna Conformational Dynamics : An Example Of Micro-Rna Targeting Messenger Rna : Mir-34a-Msirt1, Parisa Ebrahimi

Legacy Theses & Dissertations (2009 - 2024)

MicroRNA (miRNA), as a distinct class of biological regulators and a ”guide” member of non-coding RNA-protein complexes (RNPs), regulates more than 60% of protein-coding genes expression through base-pairing with targeted messenger RNA (mRNA) in the RNA-Induced Silencing Complex (RISC). Most of miRNAs identified in human, are conserved in other animals, which have preferentially conserved interaction sites particularly in 3’ untranslated regions (3’UTRs) of many human messenger mRNAs.The capability of a single miRNA to target more than hundreds of mRNAs, suggests that miRNAs influence essentially all developmental process and diseases, which also makes them interesting candidates as therapeutics agents. The primary …

Molecular And Cellular Characterizations Of Glucosylceramide Transferase (Synthase) In Giardia Lamblia, Vanessa Enriquez

Open Access Theses & Dissertations

Giardiasis, caused by an intestinal protozoan, Giardia lamblia, is a major public health problem worldwide. Giardia infection is spread through the fecal-oral route via contaminated water and food. It is estimated that over 280 million people are infected with Giardia across the globe. Giardia is a non-invasive parasite and consists of a two-stage life cycle: trophozoites and cysts. Ingested cysts undergo excystation in the proximal small intestine, releasing two trophozoites (excyzoites). Upon reaching the distal small intestine and colonizing there, trophozoites transform into cysts by encystation. It has been reported earlier that the process of encystation induced the synThesis of …

Stimuli Responsive Dye-Containing Peg-Pla Block Copolymer Micelles And Computationally Assisted Design Of A Stapled Peptide Bundle, Tyler L. Odom

Graduate Theses/Dissertations

In this thesis, I report the preparation and characterization of dye-containing PEG-b-PLA block copolymer micelles and the computational design of a novel coiled-coil peptide bundle. The PEG-b-PLA micelles encapsulate hydrophobic molecules into their core and have strong potential as nanocontainers or delivery vesicles. In theory, these internalized molecules can be released upon exposure to mechanical forces that disrupt the micellar structures. This force-responsive nature is one of the inherent properties of micellar systems. However, there is a stark lack of research that utilize this property in applications. Along those lines, I have studied the behavior of …

The 4d Living Genome, Julianna Arlene Sherman Goelzer

Boise State University Theses and Dissertations

Over the last few decades great advances have been made in our understanding of gene expression and the human genome. In 2003 the human genome was sequenced for the first time, allowing us to discover its true importance in human health. While sequencing the human genome was a great advance, it ultimately created more questions than it answered. It is known that the genomic sequence is extremely important in genome regulation, however recent studies have shown that the 4D (spatiotemporal) organization and dynamics of the living genome plays an equally critical role in regulation of gene expression. A key factor …

Engineering Of Recombinant Fortilin For Structure Activity Studies, Maranda S. Cantrell

Boise State University Theses and Dissertations

Cardiovascular disease (CVD) is the leading cause of death worldwide affecting approximately 40% of all adults over the age of 20 and is responsible for an economic burden upwards of $3 billion annually. Treatments for CVD are limited to either hypertension medication to treat symptoms, and/or statin-based drugs to reduce low-density lipoprotein (LDL) cholesterol formation. However, recent studies suggest that approximately 50% of patients diagnosed with CVD have normal to low LDL cholesterol levels. Therefore, a critical need exists to develop new treatments for CVD that are independent of cholesterol lowering statins. Fortilin, also known as translationally controlled tumor protein …

Collagen Xi Impact On Structure And Function Of The Vertebrate Inner Ear In A Zebrafish Model, Makenna Hardy

Boise State University Theses and Dissertations

The ear is essential to maintaining balance and hearing; both of which can be linked to one another and significantly impact a person’s quality of life. Although aging and damage are more common reasons for hearing loss, congenital ear defects still have a considerable impact on our population. The function of the ear can be affected by structural deformities to the ear and its components which results in hearing loss. Mutations and single nucleotide polymorphisms in the gene encoding Collagen XI alpha one chain (COL11A1) protein can play a role in hearing and balance dysfunction in humans as seen in …

Npsd4: A New Player In Sumo-Dependent Dna Repair, Erin Atkinson

Dissertations and Theses (Open Access)

The human genome is under constant threat from sources of damage and stress. Improper resolution of DNA damage lesions can lead to mutations, oncogene activation, and genomic instability. Difficult-to-replicate-loci present barriers to DNA replication that, when not properly resolved, lead to replication fork stalling and collapse and genomic instability.

DNA damage and replication stress trigger signaling cascades potentiated by multiple types of post-translational modifications, including SUMOylation. Through proteomic analysis of proteins involved in SUMOylation following DNA damage, our lab identified an uncharacterized protein that we named New Player in SUMO-dependent DNA damage repair 4 (NPSD4). Through an additional proteomic screen, …

Investigations Of Elastin Recoil On Molecular And Macroscopic Levels., Nour Mohammad Jamhawi

Electronic Theses and Dissertations

Elastin is one of the most hydrophobic proteins, and it is extremely flexible when hydrated. The driving force for recoil is the decrease in entropy of the protein and/or the hydrating solvent. This dissertation is a study of both mechanisms. Following an introduction (Chapter 1), Chapters 2 and 3 investigate the recoil mechanism on the molecular level in the hydrating solvent and in the protein, respectively. Chapter 4 examines macroscopic properties of recoil by thermomechanics. Conclusions are discussed in Chapter 5. Using double quantum NMR, the deuterated water ordering at the elastin surface was studied quantitatively as a function of …

Development Of High Value Oil Traits Using The Model Oilseed Crop Camelina Sativa, Evan Updike

Department of Biochemistry: Dissertations, Theses, and Student Research

Plant oils are an important source of food, fuel, and feed in our society today. The oil found in the seeds of plants is composed almost entirely of triacylglycerol (TAG) molecules, which consist of three fatty acids esterified to a glycerol backbone. As crude oil supplies decline, vegetable oils are gaining traction as a renewable substitute to petroleum-based materials in fuels, lubricants, and specialty oleochemicals. However, as it currently stands vegetable oils do not possess the properties necessary to fill the void of a petroleum free world.

To address this problem, plant biotechnologists have done extensive work on genetic engineering …

Characterization Of Sphingolipid Biosynthesis And Modification In Plants, Dongdong Zhang

Department of Biochemistry: Dissertations, Theses, and Student Research

Sphingolipids are ubiquitous membrane lipids in eukaryotic cells. Ceramides, the backbone of sphingolipids, are synthesized by ceramide synthases (CerSs), which form amide bonds between long-chain bases (LCBs) and the acyl groups of acyl-CoAs. Class I CerS works predominantly towards C16-CoA, whereas Class II CerS works towards C24-CoA. Plant sphingolipids generally have 16-carbon and 24-carbon as the major acyl groups. However, the sphingolipids of Oryza sativa and Zea mays have 20-carbon and 24-carbon as the predominant acyl groups. This dissertation aims to understand the substrate preference of CerSs in monocots such as rice. Phylogenetic analysis shows the Class I CerSs from …

Pacific Black Duck Ecology And Habitat Assessment In Aunu'u, American Samoa, And Their Relationship To Other Mallard-Like Ducks Of Oceania, Greater Indonesia, And The Philippines, Marissa Kaminski

Open Access Theses & Dissertations

Determining a species’ ecological needs, assessing the quality of their habitat, and determining genetic differentiation and connectivity among populations is essential to their conservation. My dissertation focuses on obtaining such a holistic view for a population of Pacific Black Ducks recently established on the Island of Aunu’u, American Samoa. Specifically, I present the first evaluation of the ecology and habitat of a recently established population of Pacific Black Ducks on the Island of Aunu’u, American Samoa, in Chapter 1, while I assess the genetic connectivity and relationship of this population to other Mallard-like ducks found in Greater Indonesia, Oceania, and …

The Role Of Calcium Ions In Signaling And Regulation Of Efflux Pump Genes In Staphylococcus Aureus, Amy Rebecca Nava

Open Access Theses & Dissertations

Calcium ions (Ca2+) play an important role in eukaryote cell signaling and regulation of physiological functions. Although evidence of a similar role for Ca2+ in prokaryotes has been difficult to demonstrate, there is mounting evidence that Ca2+ acts as a cell regulator in bacteria. The purpose of this study was to investigate Ca2+ signaling and the effect of Ca2+ on gene expression of various multidrug resistant (MDR) efflux pumps and their regulator MgrA in Staphylococcus aureus and clinically isolated MRSA. We hypothesized that the presence of Ca2+ increased gene expression of multidrug resistance pumps, LmrS, NorA, and the regulator, MgrA. …

In The Search For Novel Treatments For Chagas' Disease Using Cutting-Edge Imaging Technology, Karsten Dieter Amezcua Winter

Open Access Theses & Dissertations

Chagas disease (ChD) is caused by Trypanosoma cruzi (T. cruzi), an intracellular protozoan parasite. ChD has a global mortality of 15,000 annual deaths, and approximately, 8-10 million people are infected. There is growing concern in the United States as autochthonous cases of ChD have been reported in the southern region. The two available treatments are only partially effective and highly toxic. N-aroyl derivatives and α, β-unsaturated ketones have been previously tested against Leishmania, a closely related parasite, demonstrating selective toxicity towards the microorganism. The objective of this study is to evaluate a drug library consisting of 21 α, β-unsaturated ketones …

Anatomy And Physiology Preparatory Course Textbook (2nd Edition), Carlos Liachovitzky

Open Educational Resources

The goal of this preparatory textbook is to give students a chance to become familiar with some terms and some basic concepts they will find later on in the Anatomy and Physiology course, especially during the first few weeks of the course.

Organization and functioning of the human organism are generally presented starting from the simplest building blocks, and then moving into levels of increasing complexity. This textbook follows the same presentation. It begins introducing the concept of homeostasis, then covers the chemical level, and later on a basic introduction to cellular level, organ level, and organ system level. This …

Investigation Of Techniques And Their Application For The Cryopreservation Of Algal Species, Jazmine Leija

Theses and Dissertations

An alternative source for petroleum-based crude oils are algae derived biofuels. Fossil fuels are harmful for the environment, expensive and becoming scarce. There has been an increase in research on environmentally sustainable energy, using lipids derived from microalgae, which can be converted into biofuel. The use of microalgae as a source for biofuels has a lot of benefits including decreasing greenhouse gas emissions, rapid fuel production, absorption of carbon dioxide, and production of a renewable source of energy.

Algae cryopreservation aids in the maintenance of the best algae strains selected for producing lipids for biofuels. Cryopreservation will help minimize genetic …

Cd148 Deficiency In Fibroblasts Promotes The Development Of Pulmonary Fibrosis, Konstantin Tsoyi, Xiaoliang Liang, Giulia De Rossi, Stefan W Ryter, Kevin Xiong, Sarah G Chu, Xiaoli Liu, Bonna Ith, Lindsay J Celada, Freddy Romero, Matthew J Robertson, Anthony J Esposito, Sergio Poli, Souheil El-Chemaly, Mark A Perrella, Yuanyuan Shi, James Whiteford, Ivan O Rosas

Faculty, Staff and Students Publications

Rationale: CD148/PTRJ (receptor-like protein tyrosine phosphatase η) exerts antifibrotic effects in experimental pulmonary fibrosis via interactions with its ligand syndecan-2; however, the role of CD148 in human pulmonary fibrosis remains incompletely characterized.

Objectives: We investigated the role of CD148 in the profibrotic phenotype of fibroblasts in idiopathic pulmonary fibrosis (IPF).

Methods: Conditional CD148 fibroblast-specific knockout mice were generated and exposed to bleomycin and then assessed for pulmonary fibrosis. Lung fibroblasts (mouse lung and human IPF lung), and precision-cut lung slices from human patients with IPF were isolated and subjected to experimental treatments. A CD148-activating 18-aa mimetic peptide (SDC2-pep) derived from …

Neurovascular Regulation In Diabetic Retinopathy And Emerging Therapies, Liyang Ji, Hong Tian, Keith A Webster, Wei Li

Faculty, Staff and Students Publications

Diabetic retinopathy (DR) is the leading cause of vision loss in working adults in developed countries. The disease traditionally classified as a microvascular complication of diabetes is now widely recognized as a neurovascular disorder resulting from disruption of the retinal neurovascular unit (NVU). The NVU comprising retinal neurons, glia and vascular cells coordinately regulates blood flow, vascular density and permeability to maintain homeostasis. Disturbance of the NVU during DR can lead to vision-threatening clinical manifestations. A limited number of signaling pathways have been identified for intercellular communication within the NVU, including vascular endothelial growth factor (VEGF), the master switch for …

Characterization Of The Structural Forces Governing The Reversibility Of The Thermal Unfolding Of The Human Acidic Fibroblast Growth Factor, Shilpi Agrawal, Vivek Govind Kumar, Ravi Kumar Gundampati, Mahmoud Moradi, Thallapuranam Krishnaswamy Suresh Kumar

Chemistry & Biochemistry Faculty Publications and Presentations

Human acidic fibroblast growth factor (hFGF1) is an all beta-sheet protein that is involved in the regulation of key cellular processes including cell proliferation and wound healing. hFGF1 is known to aggregate when subjected to thermal unfolding. In this study, we investigate the equilibrium unfolding of hFGF1 using a wide array of biophysical and biochemical techniques. Systematic analyses of the thermal and chemical denaturation data on hFGF1 variants (Q54P, K126N, R136E, K126N/R136E, Q54P/K126N, Q54P/R136E, and Q54P/K126N/R136E) indicate that nullification of charges in the heparin-binding pocket can significantly increase the stability of wtFGF1. Triple variant (Q54P/K126N/R136E) was found to be the …

Sugar-Sweetened Beverage Consumption May Modify Associations Between Genetic Variants In The Chrebp (Carbohydrate Responsive Element Binding Protein) Locus And Hdl-C (High-Density Lipoprotein Cholesterol) And Triglyceride Concentrations, Danielle E Haslam, Gina M Peloso, Melanie Guirette, Fumiaki Imamura, Traci M Bartz, Achilleas N Pitsillides, Carol A Wang, Ruifang Li-Gao, Jason M Westra, Niina Pitkänen, Kristin L Young, Mariaelisa Graff, Alexis C Wood, Kim V E Braun, Jian'an Luan, Mika Kähönen, Jessica C Kiefte-De Jong, Mohsen Ghanbari, Nathan Tintle, Rozenn N Lemaitre, Dennis O Mook-Kanamori, Kari North, Mika Helminen, Yasmin Mossavar-Rahmani, Linda Snetselaar, Lisa W Martin, Jorma S Viikari, Wendy H Oddy, Craig E Pennell, Frits R Rosendall, M Arfan Ikram, Andre G Uitterlinden, Bruce M Psaty, Dariush Mozaffarian, Jerome I Rotter, Kent D Taylor, Terho Lehtimäki, Olli T Raitakari, Kara A Livingston, Trudy Voortman, Nita G Forouhi, Nick J Wareham, Renée De Mutsert, Steven S Rich, Joann E Manson, Samia Mora, Paul M Ridker, Jordi Merino, James B Meigs, Hassan S Dashti, Daniel I Chasman, Alice H Lichtenstein, Caren E Smith, Josée Dupuis, Mark A Herman, Nicola M Mckeown

Faculty, Staff and Students Publications

BACKGROUND: ChREBP (carbohydrate responsive element binding protein) is a transcription factor that responds to sugar consumption. Sugar-sweetened beverage (SSB) consumption and genetic variants in the

METHODS: Data from 11 cohorts from the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium (N=63 599) and the UK Biobank (N=59 220) were used to quantify associations of SSB consumption, genetic variants, and their interaction on HDL-C and triglyceride concentrations using linear regression models. A total of 1606 single nucleotide polymorphisms within or near

RESULTS: In a meta-analysis, rs71556729 was significantly associated with higher HDL-C concentrations only among the highest SSB consumers …

Modulation Of Glucose Homeostasis By Nucleotide P2y2 Receptor And Biological Sex, Hailee Anne Marino

Graduate Theses/Dissertations

Recent insights into the pathological role of Nucleotide P2Y₂ receptor suggest P2Y₂R involvement in high fat diet-induced obesity and potentiates insulin resistance. However, these recent insights do not demonstrate how P2Y₂R modulates glucose homeostasis under physiological conditions. Further, it remains unknown how sex biological factors influence P2Y₂R receptor signaling in the regulation of glucose homeostasis. The research objective for the present study is to elucidate the novel roles of P2Y₂ in fasting blood glucose and glucose tolerance (basal insulin sensitivity) under resting conditions in males and females. We expected that under physiological …

Nucleotide P2y₂ Receptor-Dependent Leukocyte-Endothelial Interaction, Spencer E. Thomas

Graduate Theses/Dissertations

Extracellular nucleotides (ATP, UTP) released from cells act on nucleotide receptors to promote vascular inflammation. Increased leukocyte-endothelial interaction is a hallmark of vascular inflammation. The nucleotide P2Y₂ receptor (P2Y₂R), activated by extracellular ATP≈UTP, plays a role in cardiovascular homeostasis and immune regulation. Moreover, accumulating evidence from studies in vitro and in vivo models have implicated the P2Y₂R in the inflammatory response significantly contributing to the progression and pathogenesis of asthma, atherosclerosis, sepsis, and ischemia. I hypothesized that P2Y₂R activation by UTP, an agonist of the receptor, increased leukocyte rolling and adhesion in the microvasculature from baseline. To test the hypothesis, …

Neuronal Migration In Developmental Hyperserotonmia: Assessment Of Vesicular Glutamate In The Raphe Nuclei, Trey M. Shupp

Graduate Theses/Dissertations

The neurotransmitter serotonin is involved in the early development of the central nervous system and the organization of neurons throughout the cerebral cortex and cerebellum. It is proposed that serotonin indirectly interacts with cells in the marginal zone of the cerebral cortex known as Cajal-Retizus (CR) cells. These cells secrete the extracellular matrix protein reelin, which is known for its role in neuronal organization and migration during early neural development. It has been observed that low levels of serotonin are associated with similarly low levels of reelin during development and have been reported to result in disorganization of neurons in …

Unveiling Global Roles Of G-Quadruplexes And G4-22 In Human Genetics, Ruth Barros De Paula

Dissertations and Theses (Open Access)

G-quadruplexes are non-B DNA structures formed by four or more runs of repeated guanines that confer unique features to living organism’s genomes. These sequences are enriched in regulatory regions, such as promoters and 5’ UTRs, and have distinct regulatory roles in both health and disease states. Even though previous studies showed the impact of G4 in gene expression, none of them summarized the location-specific effect of G4. Also, there is no broad understanding about the most common G4 repeat in the human genome, named here as G4-22, and how it links to the evolution of mammals and their biology. In …