Biochemistry Commons^™

Rhizophora Mangle (Red Mangrove) Seedling Success In Different Habitats In Mosquito Lagoon, Florida, Usa, Mekail N. Negash

Graduate Thesis and Dissertation 2023-2024

Mangroves provide many ecosystem services in coastal environments around the world. These include water quality improvement, creating habitats for terrestrial and aquatic species, and stabilizing shorelines. In central Florida, the red mangrove Rhizophora mangle is a common species in coastal wetlands, and recently the number of individuals successfully recruiting to intertidal oyster reefs has greatly increased, possibly because biogeochemical hot spots are present on oyster reefs due to nutrient-rich biodeposits from the live oysters. To understand how well R. mangle responds in terms of survival and growth to the suite of variables associated within these two unique habitats, I tracked …

Synthesis Of Dihydro-Β-Carbolines By Tandem C-H Activation And Aza-Michael Reaction In The Presence Of Rh(Ii)/Squaramide Catalysis: Investigation Of The Mechanism Via Computational Methods, Syed Wasiuddin

Senior Honors Theses and Projects

N-heterocycles are the major component of various bioactive natural products, pharmaceuticals, and their precursors. In particularly, β-carbolines are examples of substituted indole and its derivatives that serve as the basic structures of diverse, therapeutically important molecules with broad pharmacological properties. Rajasekar and Anbarasan have suggested a novel one-pot synthesis for dihydro-β-carbolines involving more than one catalytic system: a rhodium acetate dimer for C-H insertion on the indole and a basic organo-catalyst for the subsequent aza-Michael addition. The product can be obtained enantioselectively by using a chiral squaramide as the organo-catalyst. Since the mechanism of this reaction, including the rate determining …

Malate Dehydrogenase In Parasitic Protozoans: Roles In Metabolism And Potential Therapeutic Applications, Amy L. Springer, Swati Agrawal, Eric P. Chang

Biological Sciences Research

The role of malate dehydrogenase (MDH) in the metabolism of various medically significant protozoan parasites is reviewed. MDH is an NADH-dependent oxidoreductase that catalyzes interconversion between oxaloacetate and malate, provides metabolic intermediates for both catabolic and anabolic pathways, and can contribute to NAD+/NADH balance in multiple cellular compartments. MDH is present in nearly all organisms; isoforms of MDH from apicomplexans (Plasmodium falciparum, Toxoplasma gondii, Cryptosporidium spp.), trypanosomatids (Trypanosoma brucei, T. cruzi) and anaerobic protozoans (Trichomonas vaginalis, Giardia duodenalis) are presented here. Many parasitic species have complex life cycles and depend on the environment …

Revolutionizing Our Understanding Of Specific Platelet-Pathogen Interactions, Hammodah Rawhi Hammodah Alfar

Theses and Dissertations--Molecular and Cellular Biochemistry

Aside from their classical role in maintaining hemostasis, platelets are considered first-line vascular guardians that influence both the innate and adaptive immune systems. This is mediated by either direct interactions with immune cells or through the release of pre-stored cytokines and chemokines upon interacting with pathogens such as viruses. While this establishes platelets as potential players in the response to pathogens, it remains unclear what platelets can do with pathogens and how important that is to immune responses, especially against viruses. Most systemic viremias, such as HIV-1, present with mild thrombocytopenia, which is mediated through several mechanisms such as a …

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 …

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 …

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 …

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 …

C. Compactum Acts As A Comprehensive Climate Archive And Ecological Foundation In The Labrador Sea, Sadie Heckman

CMC Senior Theses

Clathromorphum compactum, a species of crustose coralline algae (CCA), is incredibly valuable for the future of high latitude ocean health, both as a comprehensive archive of changing ocean conditions, and ecologically as a foundational species for promoting biodiversity. Previous work establishes C. compactum as an effective climate proxy, and its life history provides several advantages for this use. C. compactum grow in nongeniculate, generally radial formations on hard substrates, over a wide distribution in mid-to-high latitude oceans and at subtidal depth ranges. Indeterminate growth leads to extreme longevity in C. compactum (Halfar et al., 2008), and growth rates are relatively …

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 ), …

Using Virus Like Particle Conjugates Of Synthetic Targeting Compounds To Deliver Chemotherapeutic Drugs To Cancer Stem Cells, Austen W. Kerzee

Chemistry Theses

Cancer stem cells are a type of cell that have the properties of both cancer cells and stem cells. They can differentiate into other types of cancer cells, are resistant to conventional chemotherapeutics, and seem to contribute greatly to the metastasis and recurrence of cancer. Due to these properties, eliminating cancer stem cells would be greatly beneficial in the treatment of cancer. While there have been approved therapeutic methods for the removal of a few of the cancer stem cells types, treatment for most types of cancer stem cells are still in the experimental phase and have yet to be …

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 …