Biochemistry, Biophysics, and Structural Biology | Open Access Articles

Sd2 Ptov1 Interactomics, Joshua Andersen

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PTOV1 interactome data

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Sd1 14-3-3 Interactome For Ptov1 Manuscript, Joshua Andersen

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14-3-3 interactome

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Sd1 14-3-3 Interactome For Ptov1 Manuscript, Joshua Andersen

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Excel data sheet of MS data from 14-3-3 interactomics

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On The Relationship Of Diabetes And Sleep Apnea: Evolution And Epigenetics, Nancy Wilson

Undergraduate Honors Theses

This thesis gives an overview of the relationship between diabetes, sleep apnea, obesity, and heart disease. It then addresses evidence that the traditional understanding of this relationship is incomplete or misleading. In the process, there is a brief discussion of the evolutionary rationale for the development and retention of sleep apnea in light of blood sugar dysregulation, as an adaptive mechanism in response to environmental stressors, followed by a brief overview of the general concepts of epigenetics. Finally, this paper presents the results of a literature search on the epigenetic marks and changes in gene expression found in sleep apnea …

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Tp-5801 In Vitro Kinase Screen Data, Joshua Andersen

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In vitro kinase screen data for TP-5801 to accompany Chan and Egbert et al., Nature Communications, 2021 (in press)

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A Fret Flow Cytometry-Based Screening Assay For Multiplex Analysis Of Metabolites In T. Brucei, Ronald A. Zegarra

Undergraduate Honors Theses

Kinetoplastid parasites are a significant public health issue in some tropical and subtropical regions of the world. Kinetoplastid parasites all require glycolysis for survival, with host glucose key for ATP production. One such parasite, Trypanosoma brucei, exclusively metabolizes glucose in its bloodstream form. Trypanosomal glycolysis is unique because it displays unconventional structural features. Hence, glucose metabolism has been studied extensively in T. brucei and is a therapeutic target in kinetoplastid parasites.The lack of in vivo analytical techniques for measuring vital glycolytic metabolites in situ has restricted the ability of researchers to test, with high sensitivity and specificity, the essential roles …

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Exploration Of Fluorinated Α,Β-Dehydroamino Acids And Their Structure, Austin Lesueur

Undergraduate Honors Theses

This thesis explores the synthesis of fluorinated α,β-dehydroamino acids, specifically a fluorinated dehydrovaline derivative. Previous work has been done on the equivalent dehydrovaline derivative without fluorine present and this work builds toward the fluorinated version with the goal of comparing the two structurally. The synthesis presented here pulls from previous synthetic strategies employed for dehydrovaline while also exploring the synthetic impact of the electronegative fluorine atoms.

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Telsam-Target Protein Fusions Can Form Diffraction-Quality Crystals Without Direct Inter-Polymer Contacts, Moriah Longhurst

Undergraduate Honors Theses

X-ray diffraction is a robust method for determining the detailed 3D structures of specific proteins. However, this requires the formation of well-ordered protein crystals, a process that is time-consuming, expensive, and only has about a 10-30% success rate. New methods are needed to enable the efficient crystallization of challenging proteins. One such technique is explored here, which utilizes a protein polymer (the sterile alpha motif domain of the human protein translocation Ets leukemia, or TELSAM) as a crystallization chaperone to form a more ordered crystal lattice of target proteins and drive crystallization. This method was successfully used to crystallize, collect …

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In Vitro Screening Of Tp5801 Against Kinases For Nature Communications Publication, Joshua Andersen

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Data from screen of TP-5801 against in vitro kinases

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Improvement In 14-3-3 Binding Site Prediction, Katherine K. Mccormack

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The 14-3-3 family of phospho-binding proteins regulate a variety of major cellular processes through interaction with a network of dynamic proteins. Deregulation of the 14-3-3 interaction network contributes to a variety of degenerative disorders and cancers. Our lab focuses on identifying novel 14-3-3 interactions and understanding how 14-3-3 binding regulates protein function. A major gap in this process is that identifying the phospho-site where 14-3-3 docks on a given protein is time- and resource-consuming. Prediction algorithms have been developed to predict canonical 14-3-3 binding sites, however, there are many non-canonical sites that existing software is unable to predict. To fill …

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Kinase Screen Data For Nature Communications Publication, Joshua Andersen

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A TNK1 peptide encompassing S502 was screened against 245 Ser/Thr kinases. This file contains kinase activity values (against S502) from an n=1 experiment. These data support a manuscript to be published in Nature Communications (Chan and Egbert et al.)

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The Dynamic Spectroscopic Ellipsometry(Se) Data For Aluminum Thin Films Oxidations, David D. Allred, Tahereh G. Avval

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The dynamic spectroscopic ellipsometry(SE) data captured on oxidation of ultra thin evaporated aluminum film over starting a few minutes after evaporation and continued for four hours. The Aluminum layer was ca. 15 nm thick. This data needs to be interpreted with J.A. Woollam CompleteEase software. The Aluminum was modeled with Lorentz model and the Alumina was modeled using Cody-Lorentz.

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Engineering And Application Of A Biosensor With Focused Ligand Specificity, Dennis Della Corte, Hugo L. Van Beek, Falk Syberg, Marcus Schallmey, Felix Tobola, Kai U. Cormann, Christine Schlicker, Philipp T. Baumann, Karin Krumbach, Sascha Sokolowsky, Connor J. Morris, Alexander Grünberger

Faculty Publications

Cell factories converting bio-based precursors to chemicals present an attractive avenue to a sustainable economy, yet screening of genetically diverse strain libraries to identify the best-performing whole-cell biocatalysts is a low-throughput endeavor. For this reason, transcriptional biosensors attract attention as they allow the screening of vast libraries when used in combination with fluorescence-activated cell sorting (FACS). However, broad ligand specificity of transcriptional regulators (TRs) often prohibits the development of such ultra-high-throughput screens. Here, we solve the structure of the TR LysG of Corynebacterium glutamicum, which detects all three basic amino acids. Based on this information, we follow a semi-rational engineering …

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Building An Ins-1 Cdna Library For A Genome-Wide Crispr-Cas9 Screen, Idongesit Ekpo

Undergraduate Honors Theses

By the year 2040, an estimated 642 million people are expected to have diabetes globally. Diabetes results from an elevation of metabolic stressors, such as glucotoxicity, lipotoxicity, oxidative stress and apoptosis. In type 2 diabetes, these stressful conditions contribute to the malfunction and loss of functional insulin-producing β-cells. Current treatment methods for diabetes include insulin therapy, islet transplant and anti-diabetes medication. These treatments are not curative and ignore other factors that contribute to the pathogenesis of diabetes beyond insulin resistance and islet β-cell failure. Previous research on β-cells has focused on ways to replace functional β-cell mass, trigger β-cell proliferation, …

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Sunflower Seedlings Fail To Remove Uranium Pollution In The Navajo Nation: Participatory Science As A Path To Build Community And Address Environmental Injustice, Zak R. Webber

Undergraduate Honors Theses

Mid-20th century mining on Naabeehó Bináhásdzo (Navajo Nation) polluted groundwater with high concentrations of uranium and arsenic. The Navajo Nation and other rural residents of this region use groundwater for drinking, livestock, and irrigation. However, many individuals and communities must purchase and transport treated water from locations that are often hours away. Sunflowers have been shown to preferentially take up heavy metals, including uranium and arsenic, potentially representing a tool to improve water quality through on-site, low-cost phytoremediation. We carried out a collaborative research project with a high school class on the Navajo Nation in 2018 and 2019. The students …

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Evaluation And Improvement Of A Novel Method For Rapid Promoter Characterization In A Zebrafish Model, Hunter Giles

Undergraduate Honors Theses

This thesis examines a novel technique for characterizing promoters using a zebrafish model. The proximal upstream cis-regulatory elements, also known as promoters or promoter regions, are essential for the precise regulation and timing of gene expression. Often the characterization of these regions relies on imprecise methods involving large deletions or bioinformatic predictions rather than experimental data. However, high-throughput sequencing technology could potentially allow large libraries containing hundreds of thousands of variants of a single promoter to be simultaneously analyzed. We have been working to develop a novel method for promoter characterization that takes advantage of this technology. We tested this …

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Functional Implications Of Nlrp1 Variants For Autoimmune Disease, Laura J. Westhoff

Undergraduate Honors Theses

NLRP1 is a protein-coding human gene that plays a crucial role in the NLRP1 inflammasome. Variants to the NLRP1 gene have been associated with autoimmune and autoinflammatory diseases. We examined the effects of polymorphisms at two SNPs on cytokine levels and NLRP1 gene expression in 50 human volunteers without diagnosed autoimmune disease. NLRP1 was genotyped at SNPs rs2670660 and rs12150220 and individuals who were homozygous at one or more SNP were selected for further analysis. Serum IL-18 and IL-1β levels were quantified using ELISA. NLRP1 gene expression was measured using real-time PCR. A strong linkage was found between genotypes of …

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Improving And Modeling Bacteria Recovery In Hollow Disk System, Clifton Anderson

Theses and Dissertations

Identifying antibiotic resistance in blood infections requires separating bacteria from whole blood. A hollow spinning disk rapidly removes suspended red blood cells by leveraging hydrodynamic differences between bacteria and whole blood components in a centrifugal field. Once the red cells are removed, the supernatant plasma which contains bacteria is collected for downstream antibiotic testing. This work improves upon previous work by modifying the disk design to maximize fractional plasma recovery and minimize fractional red cell recovery. V-shaped channels induce plasma flow and increase fractional plasma recovery. Additionally, diluting a blood sample spiked with bacteria prior to spinning it increased the …

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Characterizing Novel Pathways For Regulation And Function Of Ataxin-2, Elise Spencer Melhado

Theses and Dissertations

Ataxin-2 is an RNA-binding protein that is involved in many crucial cellular processes such as R-loop regulation, mRNA stability, TOR signaling regulation, and stress granule formation. Ataxin-2 is highly conserved, found in organisms ranging from Saccharomyces cerevisiae to Caenorhabditis elegans and Homo sapiens. Recently, ataxin-2 has been linked to the neurodegenerative disease Amyotrophic Lateral Sclerosis (ALS). ALS is a fatal disease that causes loss of motor neurons. In addition to ataxin-2 interacting with known ALS risk factor proteins, research into the relationship between ataxin-2 and ALS shows that polyglutamine expansions in ataxin-2 are gain-of-function mutations that lead to overactivity of …

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3d Printed Microfluidic Devices For Bioanalysis, Michael J. Beauchamp

Theses and Dissertations

This work presents the development of 3D printed microfluidic devices and their application to microchip analysis. Initial work was focused on the development of the printer resin as well as the development of the general rules for resolution that can be achieved with stereolithographic 3D printing. The next stage of this work involved the characterization of the printer with a variety of interior and exterior resolution features. I found that the minimum positive and negative feature sizes were about 20 μm in either case. Additionally, micropillar arrays were printed with pillar diameters as small as 16 μm. To demonstrate one …

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Dna Capture Via Magnetic Beads In A Microfluidic Platformfor Rapid Detection Of Antibiotic Resistance Genes, David Hyrum Harris

Theses and Dissertations

Antibiotic resistant infections are a growing health care concern, with many cases reported annually. Infections can cause irreversible bodily damage or death if they are not diagnosed in a timely matter. To rapidly diagnose antibiotic resistance in infections, it is important to be able to capture and isolate the DNA coding for the resistance genes. This is challenging because bacteria are present in blood in minute concentrations. To enrich the DNA to detectable levels, I modified magnetic microbeads with ssDNA sequences complementary to the target DNA to capture the DNA via hybridization. I compared DNA capture efficiency in three different …

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Snfing Glucose To Pass Mitochondrial Dysfunction: The Role Of Two Sensory Protein Kinases In Metabolic Diseases, Kai Li Ong

Theses and Dissertations

Mitochondria is no longer viewed as merely a powerhouse of the cell. It is now apparentthat mitochondria play a central role in signaling, maintaining cellular homeostasis and cell fate.Mitochondrial dysfunction has been linked to many human diseases caused by cellular metabolicderegulation, such as obesity, diabetes, neurodegenerative disease, cardiovascular disease andcancer. Eukaryotic organisms have evolved an efficient way in sensing, communicating andresponding to cellular stress and regulating mitochondrial activity correspondingly through acomplex network of intercommunicating protein kinases and their downstream effectors. Thisdissertation focuses on the interplay of two of the master metabolic regulators in the cell: AMPKand PASK, and characterization of …

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Characterizing The Function Of Pas Kinase In Cellular Metabolism And Neurodegenerative Disease, Jenny Adele Pape

Theses and Dissertations

The second identified substrate of PAS kinase discussed is Pbp1. The human homolog of Pbp1 is ataxin-2, mutations in which are a known risk factor for amyotrophic lateral sclerosis (ALS). As diet and sex have been shown to be important factors regarding PAS kinase function, they also are strong contributing factors to ALS and are extensively reviewed herein. Pbp1 is known to be sequestered by PAS kinase under glucose depravation, and it can sequester additional proteins along with it to regulate different cellular pathways. To shed light on the pathways affected by Pbp1, we performed a yeast two-hybrid assay and …

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You Are What You Eat At Any Age: Carbon And Nitrogen Analysis Of Mummies From An Ancient Egyptian Necropolis, Stephen Funk, R. Paul Evans

Library/Life Sciences Undergraduate Poster Competition 2019

The BYU Egypt Project at Fag el-Gamus necropolis and adjacent Seila Pyramid has studied over 700 mummies excavated over the past 30 years. The necropolis includes an open area with densely located vertical burial shafts and a hill with horizontal burial shafts. The chronological and dietary history of the mummies was assessed using stable isotopy and 14C analysis of accessible biological samples.

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Design And Synthesis Of Ceragenins–Cationic Steroid Antimicrobial Compounds, Structural Improvement And Synthesis Of Cyclopentenone Prostaglandins And Modification And Synthesis Of Derivatives Of Ribityllumazines: Potential Antigens For Activation Of Mait Cells, Yubo Li

Theses and Dissertations

Antimicrobial peptides (AMPs) are ubiquitous and display broad-spectrum antimicrobial activity that can control bacterial colonization of surfaces. Ceragenins are small-molecule mimics of AMPs and have several advantages over AMPs, including cost of manufacture and stability. A ceragenin, CSA-120, modified with an acrylamide group was directly incorporated into fluoropolymer coatings as a means of inhibiting bacterial biofilm formation. The ceragenin-containing coatings displayed improved performance. By conjugating a copper chelating group to the ceragenin, chelation of 64Cu by the conjugate was effective and provided a stable complex that allowed in vivo imaging. This conjugate may provide a means of identifying infection sites …

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Regulation Of Immune Cell Activation And Functionby The Nbmpp2 Protein Andthe Cd5 Co-Receptor, Claudia Mercedes Freitas

Theses and Dissertations

According to the centers for disease control and prevention (CDC) and the world healthorganization (WHO), heart disease and immune related diseases such as diabetes and cancer areamong the leading causes of death around the world. Thus, the regulation of the function ofimmune cell plays a key role in health and disease. Calcium (Ca2+) ions play a critical role inimmune cell activation, function and in a robust immune response. Defects in Ca2+ signalinginfluences the development of cardiac disease, Alzheimer disease, immune cell metabolism,muscle dysfunction, and cancer. Each immune cell is unique in its activation and function,making it relevant to understand how …

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Antibacterial And Antifungal Activity Of Ceragenins, Mimics Of Endogenous Antimicrobial Peptides, Marjan Mohammadihashemi

Theses and Dissertations

The continuous emergence of drug-resistance pathogens is a global concern. As a result, substantial effort is being expended to develop new therapeutics and mechanisms for controlling microbial growth to avoid entering a "post-antibiotic" era in which commonly used antibiotics are no longer effective in treating infections. In this work, we investigate the efficacy and application of ceragenins as non-peptide mimics of antimicrobial peptides (AMPs). First, this work examines the susceptibility of drug-resistant Gram-negative bacteria. The susceptibility of colistin-resistant clinical isolates of Klebsiella pneumoniae to ceragenins and AMPs suggests that there is little to no cross-resistance between colistin and ceragenins/AMPs. Furthermore, …

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Further Understanding Of Bacteriophages That Infect The Bacterial Family Enterobacteriaceae, Paul Flake

Undergraduate Honors Theses

Despite the eclectic nature of bacteriophage genomes, nucleotide comparison is an effective method for grouping phages into cluster and subcluster classifications. This process is facilitated by making preliminary cluster assignations based on the identity of the major capsid protein. As more phages continue to be sequenced and integrated into cluster/subcluster groupings, adjustments may need to be made to the genomic similarity percentages that have previously defined cluster/subcluster classifications. Implementing proteomic comparison in addition to nucleotide homology may provide added clarity to this process. Protein conservation and diversity among lytic phages that infect the bacterial family Enterobacteriaceae is discussed and the …

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Total Synthesis Of Anticancer Agent Deoxypodophyllotoxin And Antiviral F4-4 Demonstrating The Utility Of The Intramolecular Styryl Diels-Alder (Isda) Reaction, Diana Isabel Saavedra Nova

Theses and Dissertations

The intramolecular styryl Diels – Alder (ISDA) reaction is a rare and unique [4+2] cycloaddition with potential in the syntheses of polycycles. Its utility is based on the formation of two rings and one stereocenter in a single step, making it an efficient method for the construction of lignan-type natural product targets. Detailed mechanistic studies with complex esters and the application to natural product synthesis has been limited due to drawbacks including the loss of aromaticity, producing slow reactivity, a potentially problematic thermal [1,3]-hydrogen shift, and electronic mismatch related to the substituents on the aryl functional groups. In this research, …

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Pas Kinase And Tor, Controllers Of Cell Growth And Proliferation, Brooke Jasmyn Cozzens

Theses and Dissertations

Nutrient sensing kinases lie at the heart of cellular health and homeostasis, allowing cells to quickly adapt to changing environments. Target of Rapamycin (TOR) and PAS kinase (PASK, or PASKIN) are two such nutrient kinases, conserved from yeast to man. In yeast, these kinases each have paralogs. The two TOR paralogs in yeast mimic the mammalian TORC1 and TORC2 complexes, except both Tor1 and Tor2 may contribute to TORC1 or TORC2 function. The two PAS kinase paralogs are paired with the TOR paralogs, meaning that both Psk1 and Psk2 regulate TORC1, while Psk2 suppresses a temperature-sensitive allele of Tor2. Herein …

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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Sd2 Ptov1 Interactomics, Joshua Andersen

ScholarsArchive Data

Sd1 14-3-3 Interactome For Ptov1 Manuscript, Joshua Andersen

ScholarsArchive Data

Sd1 14-3-3 Interactome For Ptov1 Manuscript, Joshua Andersen

ScholarsArchive Data

On The Relationship Of Diabetes And Sleep Apnea: Evolution And Epigenetics, Nancy Wilson

Undergraduate Honors Theses

Tp-5801 In Vitro Kinase Screen Data, Joshua Andersen

ScholarsArchive Data

A Fret Flow Cytometry-Based Screening Assay For Multiplex Analysis Of Metabolites In T. Brucei, Ronald A. Zegarra

Undergraduate Honors Theses

Exploration Of Fluorinated Α,Β-Dehydroamino Acids And Their Structure, Austin Lesueur

Undergraduate Honors Theses

Telsam-Target Protein Fusions Can Form Diffraction-Quality Crystals Without Direct Inter-Polymer Contacts, Moriah Longhurst

Undergraduate Honors Theses

In Vitro Screening Of Tp5801 Against Kinases For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

Improvement In 14-3-3 Binding Site Prediction, Katherine K. Mccormack

ScholarsArchive Data

Kinase Screen Data For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

The Dynamic Spectroscopic Ellipsometry(Se) Data For Aluminum Thin Films Oxidations, David D. Allred, Tahereh G. Avval

ScholarsArchive Data

Engineering And Application Of A Biosensor With Focused Ligand Specificity, Dennis Della Corte, Hugo L. Van Beek, Falk Syberg, Marcus Schallmey, Felix Tobola, Kai U. Cormann, Christine Schlicker, Philipp T. Baumann, Karin Krumbach, Sascha Sokolowsky, Connor J. Morris, Alexander Grünberger

Faculty Publications

Building An Ins-1 Cdna Library For A Genome-Wide Crispr-Cas9 Screen, Idongesit Ekpo

Undergraduate Honors Theses

Sunflower Seedlings Fail To Remove Uranium Pollution In The Navajo Nation: Participatory Science As A Path To Build Community And Address Environmental Injustice, Zak R. Webber

Undergraduate Honors Theses

Evaluation And Improvement Of A Novel Method For Rapid Promoter Characterization In A Zebrafish Model, Hunter Giles

Undergraduate Honors Theses

Functional Implications Of Nlrp1 Variants For Autoimmune Disease, Laura J. Westhoff

Undergraduate Honors Theses

Improving And Modeling Bacteria Recovery In Hollow Disk System, Clifton Anderson

Theses and Dissertations

Characterizing Novel Pathways For Regulation And Function Of Ataxin-2, Elise Spencer Melhado

Theses and Dissertations

3d Printed Microfluidic Devices For Bioanalysis, Michael J. Beauchamp

Theses and Dissertations

Dna Capture Via Magnetic Beads In A Microfluidic Platformfor Rapid Detection Of Antibiotic Resistance Genes, David Hyrum Harris

Theses and Dissertations

Snfing Glucose To Pass Mitochondrial Dysfunction: The Role Of Two Sensory Protein Kinases In Metabolic Diseases, Kai Li Ong

Theses and Dissertations

Characterizing The Function Of Pas Kinase In Cellular Metabolism And Neurodegenerative Disease, Jenny Adele Pape

Theses and Dissertations

You Are What You Eat At Any Age: Carbon And Nitrogen Analysis Of Mummies From An Ancient Egyptian Necropolis, Stephen Funk, R. Paul Evans

Library/Life Sciences Undergraduate Poster Competition 2019

Design And Synthesis Of Ceragenins–Cationic Steroid Antimicrobial Compounds, Structural Improvement And Synthesis Of Cyclopentenone Prostaglandins And Modification And Synthesis Of Derivatives Of Ribityllumazines: Potential Antigens For Activation Of Mait Cells, Yubo Li

Theses and Dissertations

Regulation Of Immune Cell Activation And Functionby The Nbmpp2 Protein Andthe Cd5 Co-Receptor, Claudia Mercedes Freitas

Theses and Dissertations

Antibacterial And Antifungal Activity Of Ceragenins, Mimics Of Endogenous Antimicrobial Peptides, Marjan Mohammadihashemi

Theses and Dissertations

Further Understanding Of Bacteriophages That Infect The Bacterial Family Enterobacteriaceae, Paul Flake

Undergraduate Honors Theses

Total Synthesis Of Anticancer Agent Deoxypodophyllotoxin And Antiviral F4-4 Demonstrating The Utility Of The Intramolecular Styryl Diels-Alder (Isda) Reaction, Diana Isabel Saavedra Nova

Theses and Dissertations

Pas Kinase And Tor, Controllers Of Cell Growth And Proliferation, Brooke Jasmyn Cozzens

Theses and Dissertations