Biochemistry Commons^™

The Multifunctional Catalytic Hemoglobin Fromamphitrite Ornata: Protocols On Isolation, Taxonomic Identification, Protein Extraction, Purification, And Characterization, Anna L. Husted, Lauren A. Presnar, R. Kevin Blackburn, Joseph L. Staton, Stephen A. Borgiani, Edward L. D'Antonio

Natural Sciences Faculty Publications

The multifunctional catalytic hemoglobin from the terebellid polychaete Amphitrite ornata, also named dehaloperoxidase (AoDHP), utilizes the typical oxygen transport function in addition to four observed activities involved in substrate oxidation. The multifunctional ability of AoDHP is presently a rare observation, and there exists a limitation for how novel dehaloperoxidases can be identified from macrobenthic infauna. In order to discover more infaunal DHP-bearing candidates, we have devised a facilitated method for an accurate taxonomic identification that places visual and molecular taxonomic approaches in parallel. Traditional visual taxonomic species identification by the non-specialist, at least for A. ornata or even for other …

Heterogeneity Of Nitrogen Fixation In The Mesopelagic Zone Of The South China Sea, Siqi Wu, Xianhui Sean Wan, Moge Du, Xirong Chen, Corday R. Selden, Mar Benavides, Sophie Bonnet, Carolin R. Löscher, M. Robert Hamersley, Margaret R. Mulholland, Xiuli Yan, Shuh-Ji Kao

OES Faculty Publications

Biological dinitrogen (N₂) fixation, the energetically expensive conversion of N₂ gas to ammonia, plays an essential role in balancing the nitrogen budget in the ocean. Accumulating studies show detectable N₂ fixation rates below the euphotic zone in various marine systems, revealing new insights of marine N₂ fixation. However, the reported rates are highly variable and frequently fall close to detection limits, raising the question of the ubiquity and significance of N₂ fixation in the global dark ocean. Using highly sensitive isotopic labeling incubation including a set of control incubations, we confirm the occurrence of mesopelagic N₂ fixation in the South …

Primary Cilia And Intraflagellar Transport Are Essential Regulators Of Lymphangiogenesis And Modulate Cellular Trafficking Of Ve-Cadherin, Delayna Paulson

Electronic Theses and Dissertations

No abstract provided.

Iron–Sulfur Cluster Assembly Scaffold Protein Iscu Is Required For Activation Of Ferric Uptake Regulator (Fur) In Escherichia Coli, Huangen Ding

Faculty Publications

No abstract provided.

Development Of Innovative Flocculation Technologies For Agricultural Water Treatment, Noor Haleem

Electronic Theses and Dissertations

The development of innovative flocculation technologies is essential for addressing the challenges of agricultural water treatment. These technologies play a crucial role in removing contaminants such as suspended solids and nutrients, thereby ensuring safer water for irrigation and livestock consumption. By enhancing water quality and wastewater management, they contribute significantly to environmental sustainability and public health in agricultural communities. This comprehensive thesis extensively explores various dimensions of flocculation, with a focused effort on methodologies and resources aimed at strengthening sustainability and efficiency. A pivotal aspect of the research involves synthesizing cationic starch (CS), a flocculant derived from an underutilized resource, …

Design, Synthesis, And Evaluation Of Class Iia Histone Deacetylase (Hdac) Inhibitors, Lauren Nicole Kotsull

Wayne State University Dissertations

Histone deacetylase (HDAC) proteins are linked to disease states, including cancer, and have become important targets for therapeutic development. Many inhibitors have been developed to target HDAC proteins, including FDA-approved inhibitors Vorinostat (SAHA), Belinostat, Romidepsin, and Panobinostat. These inhibitors non-specifically influence most of the 11 metal-dependent HDAC isoforms, which might contribute to the side effects that patients experience during treatment. The lack of selectivity also diminishes the use of HDAC inhibitors as biomedical research tools. To address these drawbacks, the development of selective inhibitors has been heavily studied. Yet, reported inhibitors are predominantly selective for class I HDAC isoforms (HDACs …

Utilizing Plasmid Dna Hydrogels For Cell-Free Protein Production, Tinotenda Duche

Honors Theses and Capstones

Proteins play an important role in various biological processes and are crucial components in biomedical research and therapeutics. Cell-free protein synthesis (CFPS) has provided a valuable approach for rapid protein production outside living cells, involving both transcription and translation processes. However, traditional CFPS methods encounter challenges such as high cost, relatively low yields, and scalability. The end goal of our project is to incorporate our template into the hydrogel. In this work, we report advancements towards that by trying to optimize our solution of CFPS. Unfortunately, the standards for pDNA hydrogel synthesis are not met by the pDNA production and …

Assessing Lipid Composition Of Cell Membrane In Escherichia Coli Under Aerobic And Anaerobic Conditions, Isabelle Johnson

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Escherichia coli is a highly studied model organism that is tightly tied to the mammalian gastrointestinal system. This microorganism has the capability to be a beneficial gut microbe or a life-threatening pathogen. In this study, the lipid membrane of Escherichia coli was investigated using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) to observe the change in its composition in aerobic and anaerobic conditions. Evidence of desaturation was discovered in the spectra, though more investigation is needed to understand the metabolic processes and drives that result in this change. Elucidation of these pathways in the future could result in …

Discovery Of Dna Aptamers As Probes For Detecting Ranavirus Mcp, Corbin Hudson

Theses, Dissertations and Culminating Projects

Global amphibian populations have been declining since the late 20th century; one of the most significant contributors to these declines is a genus of viral pathogens known as Ranavirus (Rv). Frog virus 3 is one of these viral agents and is currently found affecting frog populations throughout NJ, MD, PA, DE, and VA. While Frog virus 3 is most known for afflicting frogs, the Ranavirus genus can also infect bony fish species as well as reptiles, allowing for a wide vector of transmission and making its spread a danger both locally and globally. In the absence of a cure, it …

Chemical Biology Approach To Study Rna Modifications, Ya Ying Zheng

Legacy Theses & Dissertations (2009 - 2024)

Nucleic acid modifications have gained compelling interest for their pivotal roles in cellular and biological processes. These modifications introduced a new layer of regulation without altering the original genetic sequence. In this burgeoning field of epitranscriptomics, many of the chemical modifications have emerged as potential biomarkers in therapeutic applications. Inosine is an essential post-transcriptional RNA modification that has functional roles in modulating the fate of all RNAs. The enzyme ADAR catalyzes the deamination of adenosine to inosine. This can also lead to change in the eukaryotic transcriptome due to A-G miscoding since inosine preferentially base pairs with cytosine. Moreover, hyper-editing …

"Hunter-Killer" Peptoid-Peptide Conjugate To Target And Eliminate Cancer Stem Cells, Breanne F. Mcelderry

Chemistry Theses

In the contemporary paradigm concerning the emergence of therapy-resistant recurrent cancer, recent studies posit the existence of a limited population of self-renewing malignant progenitors known as cancer stem cells (CSCs). The presence of CSCs explains why tumors often relapse despite clinical remission with initial therapeutic interventions. Consequently, the development of innovative therapeutic modalities specifically tailored to target and eliminate CSCs represents a highly promising strategy for eradicating cancer without the risk of recurrence. In previous research, we successfully developed a synthetic peptoid-based ligand CL-1-19-1 that selectively binds to CSC over non-CSC. However, CL-1-19-1 did not exhibit any significant inhibitory effect …

Developing Methods For Analysis Of Chiral Small Molecules And D-Amino Acid Containing Peptides, Joshua I. Putman

Chemistry & Biochemistry Dissertations - Archive

This dissertation covers the development of methods to analyze chiral small molecules and d-amino acid containing peptides. The first section covers the development of liquid chromatographic chiral screening approaches for newly synthesized chiral molecules. The next part of the dissertation covers methodologies for the analysis of d-amino acid containing peptides. Lastly the bacterial degradation of three commonly used pesticides by bacteria harvested from Colorado potato beetles (Leptinotarsa decemliniata) is presented.

Twelve new azole compounds and eleven racemic ethanolamine derivatives were synthesized. These twenty-three compounds were evaluated using eight chiral columns, four macrocylic glycopeptides, a cyclodextrin derivative …

Characterization Of Mannanase From Bacillus Subtilis Hm7 And Prebiotic Production, Kornwarin Chumnankul

Chulalongkorn University Theses and Dissertations (Chula ETD)

Mannan oligosaccharides (MOS) have been utilized as food and feed additives due to their various advantages, including modulation and regulation of gut microbiota. Moreover, MOS can enhance tight junction activity by activating the AMPK signaling pathway. MOS can be produced by β-mannanase, a widely used enzyme in various industries. This study aims to clone, express, purify, and biochemically characterize the β-mannanase (MAN26HM7/A), and determine substrate specificity and hydrolytic products from konjac, copra meal, and coffee bean. Man26HM7/A was successfully cloned into pET-21b, resulting in pETMan26HM7/A. pETMan26HM7/A was expressed in E. coli BL21, induced by 0.4 mM IPTG at 37 °C …

Identification Of Inhibitors And Inhibitory Mechanisms For Sars-Cov-2 Papain-Like Protease, Auwal Auwal Rabiu

Chulalongkorn University Theses and Dissertations (Chula ETD)

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in late 2019 in Wuhan, China, and rapidly spread worldwide. The continuous emergence of SARS-CoV-2 variants necessitates the investigation of viral proteins as potential drug targets. While the main protease (Mpro) has been extensively studied, papain-like protease (PLpro) remains relatively underexplored despite its critical roles in viral replication and the inhibition of host innate immune responses. This study aims to identify and characterize potential inhibitors of SARS-CoV-2 PLpro using a combination of in vitro protease activity assays, enzyme kinetics, molecular docking, molecular dynamics simulations, …

Cloning And Characterization Of Endolevanase From Bacillus Amyloliquefaciens Pd9, Theerapat Tangsupatawat

Chulalongkorn University Theses and Dissertations (Chula ETD)

Endolevanase (EC 3.2.1.65) from Bacillus amyloliquefaciens PD9 (ENLENPD9) belongs to the glycoside hydrolase family 32 (GH32) that hydrolyzes β-2,6-fructofuranosyl linkages in levan to produce levan-type fructooligosaccharide(L-FOS) of various lengths. The gene encoding this enzyme (enlenPD9), consisting of 1,545 base pairs, was cloned into the pET-21b expression vector to produce ENLENPD9 both with (polyHis-ENLENPD9; 522 amino acids) and without a six-histidine residue tag (6xpolyHis tag) at the C-terminal (ENLENPD9; 514 amino acids) variants. ENLENPD9 and polyHis-ENLENPD9 were optimally expressed in Escherichia coli BL21(DE3) for 3 hours in TB medium with 0.4 mM IPTG and LB medium with 0.25 mM IPTG, respectively, …

Development Of Nanomaterial-Based Electrochemical Detection Devices For Point-Of-Care Testing, Khageephun Permpoka

Chulalongkorn University Theses and Dissertations (Chula ETD)

Electrochemical detection aligns with the REASSURED criteria established by the World Health Organization. Nanomaterials also play a crucial role in enhancing detection performance. Therefore, this research integrates nanomaterials into the development of pointof-care testing (POCT) devices for detecting prostate cancer biomarkers and monitoring wound infection status. Timely diagnosis can significantly reduce the physical burden of illness, ease pressure on healthcare systems, and lessen the broader socioeconomic impact. The first part of the research involves the development of a paper-based analytical device for detecting the enzyme myeloperoxidase (MPO). Glucose oxidase (GOx) was immobilized on paper to produce hydrogen peroxide (H2O2 ), …

Effect Of Dietary Flavonoids On Growth In Saccharomyces Cerevisiae, Vivian Rivera

Mahurin Honors College Capstone Experience/Thesis Projects

Plant foods contain a diversity of biologically active compounds called phytochemicals, produced by plant species as secondary metabolites. A phytochemical group known as flavonoids has received much scientific attention in recent times with respect to their antioxidative and anti-inflammatory roles. This investigation examined how quercetin and naringenin, the most common dietary flavonoids, affect growth potential of yeast under optimal and stress conditions (temperature, glucose, and oxidative stress). Using Saccharomyces cerevisiae as a model, a dose dependency effect of quercetin and naringenin was observed under optimal conditions when liquid cultures were treated with three different concentrations (75 μM, 150 μM, and …

Abl1/2 And Ddr1 Cooperate To Stabilize Braf/Craf To Drive Erk1/2 Reactivation And Promote Mek Inhibitor Resistance In Nras-Mutant Melanomas, Anastasia Lyon

Theses and Dissertations--Pharmacology and Nutritional Sciences

This study addresses the escalating incidence of NRAS-mutant melanomas, a type of skin cancer lacking FDA-approved targeted therapies. Despite ongoing research targeting the RAF/MEK/ERK pathway, existing drugs fail to enhance progression-free survival due to acquired resistance. This project identifies a novel role for ABL1/2 and DDR1 kinases in driving drug resistance and proliferation of NRAS-mutant melanoma cells. ABL1/2 and DDR1 cooperate to promote RAF homodimerization and protein stability in order to reactivate MEK/ERK signaling to drive MEK1/2 inhibitor (MEKi) resistance and promote survival of resistant cells. By targeting ABL1/2 and DDR1 with nilotinib, a FDA-approved anti-leukemic inhibitor, we …

The Delineation Of Platelet Pathology In Cardiometabolic Disease, Chi Peng

Theses and Dissertations--Pharmacology and Nutritional Sciences

Obesity is a multifactorial disease with many comorbidities leading to multiorgan dysfunction. Current studies point towards dysregulation of platelet signaling as a driver for increased risk of cardiovascular disease and stroke. The exact mechanisms remain elusive due to the complex interplay of factors involved, warranting the need to further understand how platelets are affected. Our preliminary data evaluating changes in platelet and coagulation parameters from bariatric patients showed that obesity did not affect platelet count or clotting time as demonstrated in INR values. However, female patients had increased bleeding events before surgery that were decreased after surgery. Due to limitations …

Development Of Functional Plasmonic Nanoceria For The Ultrasensitive Detection Of Ebola Glycoprotein, Carissa A. Sutton

Graduate Theses/Dissertations

Infectious diseases have been increasing in both severity and prevalence, leading to increasing economic burdens and health concerns. Ebola hemorrhagic fever is an infectious disease that is both highly communicable and highly fatal. Current detection methods for the virus have high specificity and sensitivity but have long and/or complicated procedures that do not allow for early virus detection in highly affected areas. Compared to the lengthy procedure of reverse transcription-polymerase chain reaction (RT-PCR), real-time RT-PCR is more time-efficient; however, specificity and sensitivity are reduced. Since early detection of the virus is the only way to increase survival rates, sensitive detection …

Inflammation And Tumor Progression: The Differential Impact Of Saa In Breast Cancer Models, Daniel Wilhelm Olivier, Carla Eksteen, Manisha Du Plessis, Louis De Jager, Lize Engelbrecht, Nathaniel Wade Mcgregor, Preetha Shridas, Frederick C. De Beer, Willem J. S. De Villiers, Etheresia Pretorius, Anna-Mart Engelbrecht

Saha Cardiovascular Research Center Faculty Publications

Background: Previous research has shown that the Serum Amyloid A (SAA) protein family is intricately involved in inflammatory signaling and various disease pathologies. We have previously demonstrated that SAA is associated with increased colitis disease severity and the promotion of tumorigenesis. However, the specific role of SAA proteins in breast cancer pathology remains unclear. Therefore, we investigated the role of systemic SAA1 and SAA2 (SAA1/2) in a triple-negative breast cancer mouse model.

Methods: Syngeneic breast tumors were established in wild-type mice, and mice lacking the SAA1/2 (SAADKO). Subsequently, tumor volume was monitored, species survival determined, the inflammatory profiles of mice …

Development Of A Diaryl Oxazole-Based Cleavable Linker For Peptides, Evan Wolff

Honors Theses

The development of new cleavable linkers increases the diversity of compatible conditions for peptide discovery platforms. Potential applications for these linkers include high-throughput pharmaceutical candidate screening when utilized in Peptide Encoded Libraries (PELs). This thesis describes the development of a bifunctional diaryl oxazole-based cleavable linker that may be incorporated into compounds through Solid-Phase Peptide Synthesis (SPPS). This oxazole-based linker may be rapidly cleaved by cerium ammonium nitrate in aqueous conditions and is compatible with most natural amino acids and a variety of unnatural amino acids. This linker represents the first single-electron oxidant labile linker described to our knowledge and it …

N(Alpha)-Acetyltransferase 40-Mediated Histone Acetylation Plays An Important Role In Ecdysone Regulation Of Metamorphosis In The Red Flour Beetle, Tribolium Castaneum, Sharath Chandra Gaddelapati, Smitha George, Anilkumar Moola, Karthi Sengodan, Subba Reddy Palli

Entomology Faculty Publications

Histone acetylation, a crucial epigenetic modification, is governed by histone acetyltransferases (HATs), that regulate many biological processes. Functions of HATs in insects are not well understood. We identified 27 HATs and determined their functions using RNA interference (RNAi) in the model insect, Tribolium castaneum. Among HATs studied, N-alpha-acetyltransferase 40 (NAA40) knockdown caused a severe phenotype of arrested larval development. The steroid hormone, ecdysone induced NAA40 expression through its receptor, EcR (ecdysone receptor). Interestingly, ecdysone-induced NAA40 regulates EcR expression. NAA40 acetylates histone H4 protein, associated with the promoters of ecdysone response genes: EcR, E74, E75, and HR3, and causes an increase …

The Mechanoreceptor Piezo Is Required For Spermatogenesis In Bombyx Mori, Zhongjie Zhang, Xiaojing Liu, Bo Hu, Kai Chen, Ye Yu, Chenxin Sun, Dalin Zhu, Hua Bai, Subba Reddy Palli, Anjiang Tan

Entomology Faculty Publications

Background The animal sperm shows high diversity in morphology, components, and motility. In the lepidopteran model insect, the silkworm Bombyx mori, two types of sperm, including nucleate fertile eupyrene sperm and anucleate unfertile apyrene sperm, are generated. Apyrene sperm assists fertilization by facilitating the migration of eupyrene spermatozoa from the bursa copulatrix to the spermatheca. During spermatogenesis, eupyrene sperm bundles extrude the cytoplasm by peristaltic squeezing, while the nuclei of the apyrene sperm bundles are discarded with the same process, forming matured sperm.

Results In this study, we describe that a mechanoreceptor BmPiezo, the sole Piezo ortholog in B. mori, …

Illuminating Function And Enabling Inhibition At The Protein-Membrane Interface Of Glutathione Peroxidase 4., Courtney L. Labrecque

Theses and Dissertations

Membrane proteins act as gateways to cells and are responsible not only for signaling, lipid transport, and cellular homeostasis, but they are also integral in disease pathologies. One class of membrane proteins, peripheral membrane proteins (PMPs), reside in aqueous compartments of the cell until they are recruited to the membrane to perform their function. Glutathione peroxidase 4 (GPx4) is a PMP enzyme responsible for engaging the membrane and reducing lipid hydroperoxides, thereby preventing cellular death via ferroptosis. Due to its central function surrounding ferroptosis, GPx4 is an interesting drug target that has recently gained interest for inflammatory diseases as well …

Functionalized Gold Nanoparticles And Halogen Bond Interactions With Neonicotinoid Pesticides, Molly Mccuen “Mackey” Sherard

Honors Theses

Neonicotinoid (NN) pesticides have emerged globally as one of the most widely used agricultural tools for protecting crops from pest damage and boosting food production. Unfortunately, some NN compounds, such as extensively employed imidacloprid-based pesticides, have also been identified as likely endangering critical pollinating insects like honey bees. To this end, NN pesticides pose a potential threat to world food supplies. As more countries restrict or prohibit the use of NN pesticides, tools are needed to effectively and quickly identify the presence of NN compounds like imidacloprid on site (e.g., in storage areas on farms or pesticide distribution warehouses). This …

Impact Of Hdac Inhibitors On The Efficiency Of Cardiomyocyte Differentiation, Lauren Mary Sargent

Honors Theses and Capstones

Heart disease and injury is the leading cause of death worldwide, with much of its severity caused by the low regenerative capacity of cardiomyocytes (CMs). One of the strategies to counteract the poor regeneration of CMs is the production of CMs via differentiating stem cells. However, the low efficiency of obtaining CMs from stem cells is an issue because there are numerous inconsistencies in the process. Histone deacetylase (HDAC) inhibitors have been researched as ways to increase efficiency of CM differentiation by increasing histone acetylation, and thereby allowing differentiation to occur more efficiently. In this study, the HDAC inhibitor, trichostatin …

Immune Signaling And Pathogenesis Of Enterocytozoon Hepatopenaei Infection In Pacific White Shrimp Litopenaeus Vannamei, Nutthapon Sangklai

Chulalongkorn University Theses and Dissertations (Chula ETD)

Enterocytozoon hepatopenaei (EHP) is an intracellular microsporidian parasite causing hepatopancreatic microsporidiosis (HPM), a disease that impairs the digestion and nutrients absorption of shrimp and leads to growth retardation and size variation. Our studies aim to comprehensively investigate the host’s immune responses to the EHP infection and the pathogenesis of the parasite. It was found that genes in Toll and JAK/STAT pathways, as well as antimicrobial peptides, were highly upregulated upon the EHP infection. Importantly, suppression of the JAK/STAT pathways resulted in a significant reduction of the c-type lysozyme (LvLyz-c) expression and the elevation of EHP copy numbers. These indicate a …

Cd46 Isoforms And Viral Receptor For Adenovirus Type 64d, Corina Stasiak

Honors Theses

Adenovirus Type 64 (Ad.64) belongs to the adenovirus subgroup D, which causes epidemic keratoconjunctivitis (EKC), otherwise known as viral pink eye. There is currently no known effective treatment for EKC. Membrane Cofactor Protein (CD46) is an integral membrane glycoprotein that, in previous studies, has been identified as a protein receptor for the closely related Ad.37. It has been determined that Ad.64 uses CD46 as a receptor on the cell surface in HeLa cells. CD46 is alternatively spliced when expressed to have different isoforms of interest, including the BC and C isoforms. Certain cell types, like A549 lung carcinoma cells, express …

Cd46 Is A Protein Receptor For Human Adenovirus Type 64, Alexander Michael Robertson

Honors Theses

Adenoviruses are important gene delivery vectors and causative agents for a variety of human diseases such as the common cold and gastrointestinal infections. Human adenovirus type 64 (Ad64; formerly 19c) and type 37 are associated with epidemic keratoconjunctivitis. Based upon its high homology and similar disease tropism to Ad37, we hypothesized that Ad64 would have the same protein receptor, CD46 (membrane cofactor protein), as Ad37. We show that a recombinant Ad64 containing an enhanced Green Fluorescent Protein transgene (Ad64.eGFP) enters Chinese hamster ovary cells expressing human CD46 (CHO-CD46) on the surface. Entry into human cervical carcinoma (HeLa) cells is increased …