Heterogeneity Of Nitrogen Fixation In The Mesopelagic Zone Of The South China Sea,
2024
Xiamen University
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 …
Cd46 Isoforms And Viral Receptor For Adenovirus Type 64d,
2024
University of Richmond
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,
2024
University of Richmond
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 …
Development Of A Diaryl Oxazole-Based Cleavable Linker For Peptides,
2024
University of Richmond
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 …
Structural Phylogenetics Of A Family Dna Polymerases,
2024
University of Richmond
Structural Phylogenetics Of A Family Dna Polymerases, Yagmur Bingul
Honors Theses
The transition from the RNA to the DNA world stands as an important event, demanding the emergence of enzymatic activities for DNA precursor synthesis, retro-transcription of RNA templates, and replication of single and double-stranded DNA molecules. The distribution of protein families associated with these activities across the three domains of life—Archaea, Eukarya, and Bacteria—adds layers of complexity to the narrative. While Archaea and Eukarya often share similar protein structures, structural biology shows homologous, but distinct, structures in Bacteria. On the other hand, viral polymerases emerge as a crucial part of genome replication and transcription. Their versatility, including RNA-dependent RNA polymerase, …
Heterocycles As Peptide-Based Cleavable Linkers,
2024
University of Richmond
Heterocycles As Peptide-Based Cleavable Linkers, John Blobe
Honors Theses
As cancer cases continue to rise, the need for advancing the treatment options for cancer is ever increasing. Current cancer therapeutics, while effective at treating localized cancers and a fraction of advanced cancers, generally lack the specificity needed to target more advanced cancers. Recent advancements in cancer treatments have leveraged antibodies to target certain cancers. A class of drugs that utilize antibodies to deliver anti-cancer therapy preferentially to cancer cells, termed antibody-drug conjugates (ADCs), have been quite effective in treating certain advanced forms of certain cancers. These ADCs could be more effective if they could allow for the facile release …
Functionalized Gold Nanoparticles And Halogen Bond Interactions With Neonicotinoid Pesticides,
2024
University of Richmond
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 …
Hybridization And Duplex Stability Of Peptide Nucleic Acid Containing An Azobenzene Switch,
2024
Georgia Southern University
Hybridization And Duplex Stability Of Peptide Nucleic Acid Containing An Azobenzene Switch, Carmen J. Velasquez
College of Graduate Studies: Theses & Dissertations
Light-driven molecular switches that can be turned on and off on demand have found many biological applications. For DNA, RNA, and synthetic derivatives, the switch can be used to interfere with a hybridization event with a complementary strand. To explore this potential, we have synthesized three light-sensitive PNA which have an azobenzene group (PNA-5azo5 and PNA-4azo4), and two azobenzene groups (PNA-2azo5azo2) as part of the PNA backbone. UV experiments were used to verify the conversion to the cis-isomer from the initial trans state for all of the single-stranded Azo-PNA ( PNA-5azo5, PNA-4azo4, and PNA-2azo5azo2) by irradiating at 365 nm …
Discovery Of Dna Aptamers As Probes For Detecting Ranavirus Mcp,
2024
Montclair State University
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 …
Csn-5: A Tumor's Friend Or Foe In The C. Elegans Germline?,
2024
University of Montana, Missoula
Csn-5: A Tumor's Friend Or Foe In The C. Elegans Germline?, Kellie C. Kuch
Graduate Student Theses, Dissertations, & Professional Papers
The COP9 signalosome is a highly conserved eukaryotic complex regulating protein degradation via deneddylation of Cullin-RING E3 ligases. CSN5, the COP9’s fifth component, contains the catalytically active domain for CSN deneddylation. The complex is inactive without CSN5; however, CSN5 engages in COP9-independent binding with several other proteins, typically promoting either destruction or stabilization of its partners. Many of its confirmed interaction partners are also implicated in tumorigenesis (prominent examples being p27 and p53) and a complex cancer interactome has been established for CSN5. Additionally, CSN5 overexpression has been documented in a staggering array of cancers of diverse origins. This discovery …
Chemical Synthesis Of Sensitive Dna,
2024
Michigan Technological University
Chemical Synthesis Of Sensitive Dna, Komal Chillar
Dissertations, Master's Theses and Master's Reports
Over the past decades, researchers have tried various chemical methods to synthesize modified oligodeoxynucleotides (ODNs, i.e. short segments of DNAs). Traditional ODN synthesis methods require strong basic, and nucleophilic conditions for the deprotection and cleavage of the ODN from the solid support. However, the sensitive ODNs containing labile functionalities are vulnerable to such harsh conditions. Sensitive ODNs have a wide range of applications in research and pharmaceuticals. To synthesize sensitive ODNs, researchers devised different strategies but no practical methods have been developed. To overcome these challenges, we developed alkyl Dim alkyl Dmoc technology. This innovative technology uses weakly basic and …
Synthesis Of Long Oligodeoxynucleotides,
2024
Michigan Technological University
Synthesis Of Long Oligodeoxynucleotides, Yipeng Yin
Dissertations, Master's Theses and Master's Reports
Synthetic long oligodeoxynucleotides (ODNs) have found wide applications in diverse fields such as chemical biology, synthetic biology, and genes and genomes synthesis. Those applications leading to a significant demand for their production. However, traditional methods for purifying synthetic ODNs present notable drawbacks, particularly their inability to purify long ODNs, rendering long ODN synthesis challenging. To address these issues, chemical synthesis techniques for long ODNs coupled with non-chromatographic purification methods have been developed. This technology makes the purification of long synthetic ODNs feasible and offers a viable pathway for producing genes and genomes with extensive repeats or stable secondary structures, which …
Immune Signaling And Pathogenesis Of Enterocytozoon Hepatopenaei Infection In Pacific White Shrimp Litopenaeus Vannamei,
2024
Faculty of Science
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 …
Synthesis And Biophysical Analysis Of Modified Cell-Penetrating Peptides,
2024
Wilfrid Laurier University
Synthesis And Biophysical Analysis Of Modified Cell-Penetrating Peptides, Joel Mitchell
Theses and Dissertations (Comprehensive)
Cell-penetrating peptides (CPPs) are a family of peptides that have the ability to penetrate biological membranes. They were discovered in the late 1980s and have been the topic of many studies. Much of the interest in CPPs has been due to their ability to translocate biological membranes, and the possibility that they could offer a novel drug delivery method by conjugation to biologically active molecules. Linear CPPs can be modified to form cyclic structures. This change in structure has been observed to enhance the stability and penetrative ability of the CPPs which have been studied. The current thesis focuses on …
Cloning And Characterization Of Endolevanase From Bacillus Amyloliquefaciens Pd9,
2024
Faculty of Science
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, …
Characterization Of Mannanase From Bacillus Subtilis Hm7 And Prebiotic Production,
2024
Faculty of Science
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,
2024
Faculty of Science
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, …
Development Of Nanomaterial-Based Electrochemical Detection Devices For Point-Of-Care Testing,
2024
Faculty of Allied Health Sciences
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 ), …
The Role Of Ferroptosis In Cholangiocarcinoma,
2024
Faculty of Allied Health Sciences
The Role Of Ferroptosis In Cholangiocarcinoma, Apiwit Sae-Fung
Chulalongkorn University Theses and Dissertations (Chula ETD)
Cholangiocarcinoma (CCA) is a highly heterogeneous and aggressive malignancy of the bile ducts, characterized by a poor prognosis and high mortality rate. Despite advancements in treatment, effective targeted therapies and reliable prognostic biomarkers remain limited. Ferroptosis, a regulated form of cell death, has emerged as a potential therapeutic target in various cancers. However, its role in CCA remains poorly understood. In this study, we conducted a comprehensive analysis of ferroptosis-related genes (FRGs) to predict the prognosis of CCA and identify potential therapeutic targets. Using the least absolute shrinkage and selection operator (LASSO) Cox regression analysis on a training dataset, followed …
Utilizing Plasmid Dna Hydrogels For Cell-Free Protein Production,
2024
University of New Hampshire, Durham
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 …
