Digital Commons Network^™

Addressing Barriers In Comprehensiveness, Accessibility, Reusability, Interoperability And Reproducibility Of Computational Models In Systems Biology, Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M. Keating, David Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomáš Helikar, Sylvain Soliman, Laurence Calzone

Department of Biochemistry: Faculty Publications

Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to improve the reusability of these models and their ability to reproduce virtual experiments becomes critical. Correct and effective model annotation in community-supported and standardised formats is necessary for this improvement. Here,we present recent efforts toward a common framework for annotated, accessible, reproducible and interoperable computational models in biology, and discuss key challenges of the field.

Scientists from different systems biology fields have long been developing community-driven guidelines and best practices for annotation, …

Development, Structure, And Mechanism Of Synthetic Antibodies That Target Claudin And Clostridium Perfringens Enterotoxin Complexes, Benjamin J. Orlando, Pawel K. Dominik, Sourav Roy, Chinemerem P. Ogbu, Satchal K. Erramilli, Anthony A. Kossiakoff, Alex J. Vecchio

Department of Biochemistry: Faculty Publications

Strains of Clostridium perfringens produce a two-domain enterotoxin (CpE) that afflicts humans and domesticated animals, causing prevalent gastrointestinal illnesses. CpE’s C-terminal domain (cCpE) binds cell surface receptors, followed by a restructuring of its N-terminal domain to form a membranepenetrating β-barrel pore, which is toxic to epithelial cells of the gut. The claudin family of membrane proteins are known receptors for CpE and also control the architecture and function of cell-cell contacts (tight junctions) that create barriers to intercellular molecular transport. CpE binding and assembly disables claudin barrier function and induces cytotoxicity via β-pore formation, disrupting gut homeostasis; however, a structural …

The Follicular Lymphoma Epigenome Regulates Its Microenvironment, Rada Amin, Mounia S. Braza

Department of Biochemistry: Faculty Publications

Follicular lymphoma (FL) is a B-cell non-Hodgkin lymphoma of germinal center (GC) origin with a distinctive tumor microenvironment (TME) and a unique spectrum of mutations. Despite the important therapeutic advances, FL is still incurable. During B-cell development, the GC reaction is a complex multistep process in which epigenetic regulators dynamically induce or suppress transcriptional programs. In FL, epigenetic gene mutations perturb the regulation of these programs, changing GC B-cell function and skewing differentiation towards tumor cells and altering the microenvironment interactions. FL pathogenesis and malignant transformation are promoted by epigenetic reprogramming of GC B cells that alters the immunological synapse …

Feedlot Diets Containing Different Starch Levels And Additives Change The Cecal Proteome Involved In Cattle’S Energy Metabolism And Inflammatory Response, Leone Campos Rocha, Andrey Sávio De Almeida Assunção, Renata Aparecida Martins, Victor Valério De Carvalho, Alexandre Perdigão2, Marília Afonso Rabelo Buzalaf, Jiri Adamec, Camila Pereira Braga, Danilo Domingues Millen, José Cavalcante Souza Vieira, Pedro De Magalhães Padilha

Department of Biochemistry: Faculty Publications

Diets for feedlot cattle must be a higher energy density, entailing high fermentable carbohydrate content. Feed additives are needed to reduce possible metabolic disorders. This study aimed to analyze the post-rumen effects of different levels of starch (25%, 35%, and 45%) and additives (monensin or a blend of essential oils and exogenous α-amylase) in diets for Nellore feedlot cattle. The cecum tissue proteome was analyzed via two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and then differentially expressed protein spots were identified with liquid chromatography–tandem mass spectrometry (LC–MS/MS). The use of blends of essential oils associated with α-amylase as a feed additive promoted …

Endothelial Cell-Specific Deletion Of A Microrna Accelerates Atherosclerosis, Dafeng Yang, Stefan Haemmig, Jingshu Chen, Michael Mccoy, Henry S. Cheng, Haoyang Zhou, Daniel Pérez-Cremades, Xiao Cheng, Xinghui Sun, Jorge Haneo-Mejia, Shamsudheen K. Vellarikkal, Rajat M. Gupta, Victor Barrera, Mark W. Feinberg

Department of Biochemistry: Faculty Publications

Background and aims: Chronic vascular endothelial inflammation predisposes to atherosclerosis; however, the cell-autonomous roles for endothelial-expressing microRNAs (miRNAs) are poorly understood in this process. MiR-181b is expressed in several cellular constituents relevant to lesion formation. The aim of this study is to examine the role of genetic deficiency of the miR-181b locus in endothelial cells during atherogenesis.

Methods and Results: Using a proprotein convertase subtilisin/kexin type 9 (PCSK9)-induced atherosclerosis mouse model, we demonstrated that endothelial cell (EC)-specific deletion of miR-181a2b2 significantly promoted atherosclerotic lesion formation, cell adhesion molecule expression, and the influx of lesional macrophages in the vessel wall. Yet, …

The Impact Of Plant Secondary Metabolites On Auxin And Cytokinin Signaling, Timothy E. Shull

Theses and Dissertations--Plant and Soil Sciences

Secondary metabolites are a broad class of specialized compounds that mediate plant-environment interactions and mitigate stress. It is increasingly clear that many phenylalanine-derived secondary metabolites are nearly indispensable for plant survival and that plants adjust their growth according to their secondary metabolic outputs. Consequently, many phenylalanine-derived secondary metabolites have influence over hormone activity. For instance, multiple phenylpropanoid intermediates and catecholamines alter the sensitivity of plants to the central hormone auxin, which in concert with cytokinin directs most aspects of plant growth and development. This dissertation reviews previous research on the influence of phenylpropanoid intermediates and catecholamines on plants, with a …

ฤทธิ์การเหนี่ยวนำร่วมระหว่างสารพฤกษเคมีกลุ่มฟลาโวนอยด์และแนพโทควิโนนกับสารสะแมคไมเมติกต่อการตายของเซลล์มะเร็งที่กระตุ้นภูมิคุ้มกันในเซลล์มะเร็งท่อน้ำดี, ภัทธร ใจกล้า

Chulalongkorn University Theses and Dissertations (Chula ETD)

มะเร็งท่อน้ำดีเป็นมะเร็งที่เกิดขึ้นบริเวณท่อทางเดินน้ำดี โดยมีความหลากหลายของเซลล์มะเร็งบริเวณเนื้อเยื่อมะเร็งและมีความรุนแรง มะเร็งท่อน้ำดีจัดเป็นสาเหตุหลักในการเสียชีวิตของผู้ป่วยในประเทศไทย เนื่องจากผู้ป่วยได้รับการวินิจฉัยเมื่อมะเร็งเจริญพัฒนาไปยังระยะท้ายและยังขาดวิธีการรักษาที่มีประสิทธิภาพ การรักษามะเร็งท่อน้ำดีด้วยวิธีมาตรฐานในปัจจุบันในผู้ป่วยที่ไม่สามารถผ่าตัดได้ หรือในผู้ป่วยหลังการผ่าตัด คือ การรักษาด้วยยาเคมีบำบัด ชนิดเจมไซทาบีนหรือยาเจมไซทาบีนร่วมกับยาซิสพลาติน แต่อย่างไรก็ตามผู้ป่วยส่วนใหญ่พบปัญหาการดื้อต่อยาเคมีบำบัดนำไปสู่การพยากรณ์โรคที่ไม่ดี ดังนั้นการพัฒนาการรักษาที่มีประสิทธิภาพมากยิ่งขึ้นถือว่ามีความจำเป็นเร่งด่วน โดยได้มีการศึกษาการตายของเซลล์มะเร็งแบบใหม่ที่ทำให้เซลล์มะเร็งตาย และกระตุ้นการทำงานของระบบภูมิคุ้มกันแบบจำเพาะ เรียกว่า การตายของเซลล์ที่กระตุ้นภูมิคุ้มกัน โดยการตายของเซลล์แบบเนคโครปโทซิส จัดว่าเป็นการตายของเซลล์ที่กระตุ้นภูมิคุ้มกัน โดยได้มีการศึกษาอย่างแพร่หลายในมะเร็งหลายชนิด โดยพบว่าการกระตุ้นให้เซลล์มะเร็งตายแบบเนคโครปโทซิสสามารถกระตุ้นระบบภูมิคุ้มแบบจำเพาะและยับยั้งการเจริญพัฒนาของก้อนมะเร็งในหนูทดลอง การศึกษาภายในห้องปฏิบัติการก่อนหน้าของคณะผู้วิจัยพบว่าการเหนี่ยวนำร่วมกันระหว่างยาเคมีบำบัดเจมไซทาบีนและสารสะแมคไมเมติกสามารถเหนี่ยวนำให้เซลล์มะเร็งท่อน้ำดีตายแบบเนคโครปโทซิสในสภาวะที่มีการยับยั้งการทำงานของเอนไซม์แคสเปส ทั้งนี้จากข้อจำกัดที่ยาเคมีบำบัดมีความเป็นพิษที่สูง การศึกษานี้จึงมีจุดมุ่งหมายเพื่อค้นหาสารที่สามารถนำมาทำการเหนี่ยวนำร่วมกับสารสะแมคไมเมติก โดยมีสมมติฐานของงานวิจัย คือ สารพฤกษเคมีที่มีฤทธิ์ทำให้เกิดการทำลายของดีเอ็นเอและหยุดวัฏจักรของเซลล์จะสามารถเสริมฤทธิ์กับสารสะแมคไมเมติก โดยกระตุ้นการตายของเซลล์แบบในคโครปโทซิสในเซลล์มะเร็งท่อน้ำดี โดยงานวิจัยนี้ได้ทำการศึกษาฤทธิ์ยับยั้งการแบ่งตัวและการตายเซลล์มะเร็งท่อน้ำดีของสารพฤกษเคมี ได้แก่ ชิโคนิน พลัมบาจิน เควอซิติน โดยพบว่าสารเควอซิตินมีค่าความเข้มข้นของสารที่ยับยั้งการรอดชีวิตของเซลล์ได้ 50% (IC50) ที่ต่ำที่สุดเมื่อเปรียบเทียบกับสารพฤกษเคมีชนิดอื่นๆ ในการวิเคราะห์ด้วยวิธีการทางชีวสารสนเทศน์พบว่าสารเควอซิตินมีเป้าหมายไปยังยีนที่มีบทบาทในการควบคุมวัฏจักรเซลล์ระยะ G2/M และยีนเป้าหมายของสารเควอซิตินมีการแสดงออกที่เพิ่มมากขึ้นอย่างมีนัยสำคัญในเนื้อเยื่อมะเร็งท่อน้ำดีเมื่อเปรียบเทียบกับเซลล์ปกติ การทดลองในเซลล์มะเร็งท่อน้ำดี (in vitro) พบว่าสารเควอซิตินสามารถหยุดวัฏจักรเซลล์ที่ระยะ G2/M นอกจากนี้สารเควอซิตินช่วงความเข้มข้นค่าต่ำที่มีความเป็นพิษน้อยในรูปแบบสารเดี่ยว เมื่อนำไปเหนี่ยวนำร่วมกับสารสะแมคไมเมติกชนิด LCL-161 แล้วพบว่าสามารถเสริมฤทธิ์กันกระตุ้นการตายของเซลล์มะเร็งท่อน้ำดี โดยเมื่อทำการวิเคราะห์ชนิดการตายของเซลล์เพิ่มเติมพบว่ามีการแสดงออกที่เพิ่มขึ้นของโปรตีนเอ็มแอลเคแอลที่ถูกเติมหมู่ฟอสเฟต (phosphorylated MLKL; pMLKL) ซึ่งเป็นตัวบ่งชี้ที่จำเพาะต่อการตายแบบเนคโครปโทซิส นอกจากนั้นยังพบว่าการตายของเซลล์ถูกยับยั้งเมื่อมีการเติมตัวยับยั้งที่จำเพาะกับโปรตีนที่สำคัญต่อการเกิดเนคโครปโทซิส แสดงให้เห็นว่าการเหนี่ยวนำเซลล์ด้วยสารเควอซิตินร่วมกับสารสะแมคไมเมติกสามารถกระตุ้นให้เซลล์มะเร็งท่อน้ำดีตายผ่านเนคโครปโทซิส การศึกษาเพิ่มเติมเพื่อศึกษาการตายของเซลล์ที่กระตุ้นภูมิคุ้มกัน โดยการวิเคราะห์การเคลื่อนย้ายของโปรตีนเอชเอ็มจีบีวัน (HMGB-1) จากภายในนิวเคลียสมายังบริเวณไซโตพลาสซึมด้วยวิธีการย้อมแบบอิมมูโนฟลูออเรสเซนส์ พบว่าการเหนี่ยวนำเซลล์มะเร็งท่อน้ำดีด้วยสารเควอซิตินร่วมกับสารสะแมคไมเมติกสามารถกระตุ้นการตายของเซลล์ที่กระตุ้นภูมิคุ้ม กล่าวโดยสรุป การเหนี่ยวนำร่วมกันระหว่างสารเควอซิตินและสารสะแมคไมเมติกในสภาวะที่มีการยับยั้งเอนไซม์แคสเปสสามารถเสริมฤทธิ์กันโดยกระตุ้นการตายของเซลล์มะเร็งท่อน้ำดีแบบเนคโครปโทซิสและการตายของเซลล์ที่กระตุ้นภูมิคุ้มกัน ดังนั้นงานวิจัยนี้อาจนำไปสู่การพัฒนากลยุทธ์การรักษามะเร็งท่อน้ำดีแบบใหม่ที่เพิ่มประสิทธิภาพในการรรักษาในอนาคต อย่างไรก็ตาม งานวิจัยนี้ยังต้องมีการศึกษาเพิ่มเติม เช่น การศึกษากลไกการเสริมฤทธิ์และการกระตุ้นการตายของเซลล์ การศึกษาฤทธิ์ในเซลล์มะเร็งท่อน้ำดีชนิดอื่นๆ และการเมินความเป็นพิษในเซลล์ปกติ เป็นต้น

Histological Comparison Of Shark Dermis Across Various Ecomorphologies, Olivia Schuitema

UNF Graduate Theses and Dissertations

The integument plays essential roles in the structural support, protection, and hydrodynamic capability among fishes. Most shark skin research has been done on the external epidermal layer containing the dermal denticles, while the larger dermis layer has been mostly ignored. The dermis layer in sharks is composed of two layers, the upper stratum laxum and the lower stratum compactum, holding supportive collagen and elastin fibers. There may be morphological and compositional differences in the dermis layers across various species of sharks, although the extent of such is unknown. These potential differences may be represented by various dermal thicknesses and different …

Nutrient Scarcity And Cellular Cooperation In A Clonal Hydroid, Weam S. El Rahmany

Graduate Research Theses & Dissertations

Biological complexity forms when lower-level units (e.g., genes, cells, organisms) cooperatively band together. This complexity may be exemplified by multicellularity, the cooperation between the cells of the same species, or symbiosis, cooperation between the cells of different species. This cooperation is under continual threat, as defection, the opposite of cooperation, is favored by default by lower-level units (i.e., cells). Animal cancers may be the most well-known phenomena that exemplify the concept of cellular defection. Cancer cells have been shown to feature morphological and metabolic traits, developed through differential gene expression or mutations, that favor their growth at the cost of …

Copper(Ii) And Silver(I)‑1,10‑Phenanthroline‑5,6‑Dione Complexes Interact With Double‑Stranded Dna: Further Evidence Of Their Apparent Multi‑Modal Activity Towards Pseudomonas Aeruginosa, Anna Clara Milesi Galdino, Lívia Viganor, Matheus Mendonça Pereira, Michael Devereux, Malachy Mccann, Marta Helena Branquinha, Zara Molphy, Sinéad O'Carroll, Conor Bain, Georgia Menounou, Andrew Kellett, André Luis Souza Dos Santos

Articles

Tackling microbial resistance requires continuous efforts for the development of new molecules with novel mechanisms of action and potent antimicrobial activity. Our group has previously identified metal-based compounds, [Ag(1,10-phenanthroline-5,6-dione)2]ClO4 (Ag-phendione) and [Cu(1,10-phenanthroline-5,6-dione)3](ClO4)2.4H2O (Cu-phendione), with efficient antimicrobial action against multidrug-resistant species. Herein, we investigated the ability of Ag-phendione and Cu-phendione to bind with double-stranded DNA using a combination of in silico and in vitro approaches. Molecular docking revealed that both phendione derivatives can interact with the DNA by hydrogen bonding, hydrophobic and electrostatic interactions. Cu-phendione exhibited the highest binding affinity to either major (− 7.9 kcal/mol) or minor (− 7.2 kcal/mol) …

Xrcc4 And Mre11 Roles And Transcriptional Response To Repair Of Talen-Induced Double-Strand Dna Breaks, Ronald Benjamin, Atoshi Banerjee, Xiaogang Wu, Corey Geurink, Lindsay Buczek, Danielle Eames, Sara G. Trimidal, Janice M. Pluth, Martin R. Schiller

Health Physics and Diagnostic Sciences Faculty Research

Double-strand breaks (DSB) are one of the most lethal forms of DNA damage that, if left unrepaired, can lead to genomic instability, cellular transformation, and cell death. In this work, we examined how repair of transcription activator-like effector nuclease (TALEN)-induced DNA damage was altered when knocking out, or inhibiting a function of, two DNA repair proteins, XRCC4 and MRE11, respectively. We developed a fluorescent reporter assay that uses TALENs to introduce DSB and detected repair by the presence of GFP fluorescence. We observed repair of TALEN-induced breaks in the XRCC4 knockout cells treated with mirin (a pharmacological inhibitor of MRE11 …

Investigation Of A Carbon Monoxide Dehydrogenase From An Uncultured Archaeon, Luke Moore

Dissertations, Master's Theses and Master's Reports

The Nickel based Carbon Monoxide Dehydrogenase (CODH) is an anaerobic metalloenzyme responsible for the reversible conversion of CO and water into CO2 and 2 protons and 2 electrons. This enzyme has importance in the environment as one of Earth’s first carbon fixation pathways, and for human uses as a potential source of biofuels and other commodity chemicals. CODH enzymes are present in a wide array of taxa, many of which are uncultured. In this study we express and purify the catalytic subunit (CooS) of the anaerobic CODH from an uncultured Hydrothermarchaeota JdFR-17 co-expressed with the nickel insertion accessory protein (CooC) …

Botanical Inventory And Management Consideration For Potential Park At 32 Nd Street Property: City Of Grand Rapids Parks And Recreation, David Warners, William Hofmann, Hayden Janssen, Martin Vanderschoot, Garrett Crow

Faculty and Professional Research

During the spring and summer of 2022, a botanical inventory and floristic quality assessment was carried out by Calvin University students and faculty for the 32 nd Street Property proposed as a 17-acre potential City Park, located at 2163 32 nd Street SE in Grand Rapids, Michigan. The purpose of this inventory was to inform the staff of the Grand Rapids Parks and Recreation Department of the botanical significance of this newly sectioned property and also to provide information for the City to share with neighbors of the plants that could be found in this parcel. The research conducted as …

Synthesis Of 6,6- And 7,7-Difluoro-1-Acetamidopyrrolizidines And Their Oxidation Catalyzed By The Nonheme Fe Oxygenase Lolo, Nabin Panth

Theses and Dissertations--Chemistry

One of the remarkable steps in loline alkaloid biosynthesis is the installation of an ether bridge between two unactivated C atoms in 1-exo-acetamidopyrrolizidine (AcAP). LolO, a 2-oxoglutarate-dependent nonheme Fe oxygenase, catalyzes both the hydroxylation of AcAP and the resulting alcohol's cycloetherification to give N-acetylnornoline (NANL). The mechanism of hydroxylation is well understood, but the mechanism of the oxacyclization is not. I synthesized difluorinated analogs of AcAP in an attempt to further understand the mechanism of the unusual cycloetherification step.

I prepared 6,6-F₂-AcAP in eight steps from N,O-protected 4-oxoproline. The key step was a Dieckmann …

The Role Of Charge On Dna Packaging And Integrity Within Reconstituted Peptide-Dna Assemblies, Ehigbai Oikeh

Theses and Dissertations--Chemistry

In nature, DNA exists primarily in a highly compacted form. The compaction of DNA in vivo is mediated by cationic proteins; histone in somatic nuclei and arginine-rich peptides called protamines in sperm chromatin. The packaging in the sperm nucleus is significantly higher than somatic nuclei resulting in a final volume roughly 1/20^th that of a somatic nucleus. This tight packaging results in a near crystalline packaging of the DNA helices. While the dense packaging of DNA in sperm nuclei is considered essential for both efficient genetic delivery as well as DNA protection against damage by mutagens and oxidative species, …

Development Of Fluorescence Based Approaches To Understand Astrocyte Biology In The Context Of Nicotine And Nicotinic Receptor Activity, Surya P. Aryal

Theses and Dissertations--Chemistry

Smoking and tobacco use (STU) is a major global health problem and worldwide more than six million people die due to tobacco related diseases each year. Although majority of smokers try to quit smoking several times in their life, traditional therapeutic approaches, which focus only on neuronal cells, have a very low success rate. Understanding the effect of nicotine on glial cells, synaptic communication and blood vasculature in the brain can provide further insights on the neurobiology of substance abuse and can potentially help to design better therapeutic approaches. Glial cells are non-excitable cells in the brain which do not …

Structural Basis Of Bacterial Flagellin For Naip5 Binding And Nlrc4 Inflammasome Activation And The Mechanism Of Flagellin Induced Release Of Cytokines In Vivo, Jian Cui

Theses and Dissertations--Chemistry

The bacterial flagellum is a whip-like structure that protrudes from the cell membrane and is one of the most complex and dynamic biological molecular machines that propels bacteria to swim toward beneficial environments and the sites of infection. It is composed of a basal body, a hook, and a long filament. The flagellar filament contains thousands of copies of the protein flagellin (FliC) monomer arranged helically and ending with a filament cap composed of oligomer protein FliD. The overall structure of the filament core is preserved across bacterial species, while the outer domains exhibit high variability, and in some cases …

Mechanism Of Antibiotic Permeability Through The Gram-Negative Bacterial Envelope, Olaniyi Alegun

Theses and Dissertations--Chemistry

The outer membrane of Gram-negative bacteria (GN) makes them distinct among superbugs that are associated with the development of antibiotic resistance. The outer membrane, and inner membrane, separated by the periplasm, form a double-membrane barrier to the entry of antibiotics into the cell. Several studies have been conducted to examine the role of outer membrane modifications such as porins, lipopolysaccharides, and efflux pumps on antibiotic resistance. However, there is a paucity of knowledge on how antibiotics behave in the periplasm, to gain access into their target region. My thesis focuses on understanding the mechanism of antibiotic permeability through the cellular …

Antibiotic Permeation In Gram-Negative Bacteria And Contribution Of Inflammasome Activation And Pyroptosis In Pathogenesis Of Salmonella Systemic Infection, Ankit Pandeya

Theses and Dissertations--Chemistry

Antibiotic resistance is one of the major global issues in the field of public health and medicine. Good antibiotic candidates need to be selectively toxic, inhibit cellular target, and effectively penetrate and accumulate in bacterial cells. The last factor is a formidable barrier in the development of antimicrobials effective in Gram-negative bacteria, due to the presence of two layers of cell envelope. The first half of my thesis focuses on understanding the permeation of small molecules through this formidable cell envelope, distribution inside the cell of Gram-negative bacteria, and design of novel methods to make small molecules effectively cross the …

Course Portfolio For Bioc934: Genome Dynamics And Gene Expression, Nicole R. Buan

UNL Faculty Course Portfolios

A graduate degree in Biochemistry or any molecular life science field requires a strong foundation in molecular biology. BIOC934 Genome Dynamics and Gene Expression is a course designed to challenge graduate students whose research interests lie in the areas of biochemistry, molecular biology, synthetic biology, bioinformatics, and systems biology of prokaryote and eukaryote systems. Graduate students in these disciplines require a rigorous and thorough examination of core concepts in addition to practice applying theory to new observations while traversing unfamiliar disciplinary terrain. This portfolio describes the design of BIOC934, its implementation, and observed outcomes to identify strengths of the course …

Alternative Splicing Regulates The Innate Immune Response To Viral Infection, Luke A. White

Graduate Student Theses, Dissertations, & Professional Papers

Rift Valley fever virus (RVFV) is a mosquito-borne RNA virus that infects humans and livestock in sub-Saharan Africa and the Arabian peninsula, causing disease ranging from a mild flu-like illness to liver damage, blindness, hemorrhagic fever, death, and, especially in livestock animals, high rates of abortive pregnancies. There is no approved vaccine for RVFV, and as a disease with a high rate of spread that causes severe illness, it is listed as a Category A pathogen by the USA CDC. A better understanding of RVFV’s molecular virology will be instrumental to combating RVFV as climate change causes its mosquito host …

Microbial Community Analysis: Biofilm Inhibition & Algae Associated Community Structure, Michelle V. Fong

University of the Pacific Theses and Dissertations

Natural products chemistry is the pursuit of bioactive small molecules from living organisms. These can be classified as primary metabolites if they are essential to survival, and secondary metabolites if they are accessory, playing a role in communication, defense, recruitment, etc.. Natural products have made a significant contribution to society – of 1,881 FDA-approved drugs from 1981 to 2019, 4% were pure natural products, 19% were natural products derived, and 3% were synthetic drugs with a natural products pharmacophore targeting a wide range of diseases and infections (Newman & Cragg, 2020). Pharmacophores are structural components of drugs that are responsible …

The Role Of Rad51 In Trichomonas Vaginalis, Dominique Hall

University of the Pacific Theses and Dissertations

Drug resistance to the current treatments on the market is on the rise, therefore there is strong interest in understanding what could be causing the resistance, how resistance could be spreading through the population, and finding some possible new drug targets. One protein of interest is Radiation Sensitive Protein 51 (Rad51). It is a protein that is involved in homologous recombination as well as other processes such as DNA damage repair. While Trichomonas vaginalis traditionally has been known to replicate via binary fission, a modified form of closed mitosis, there is some evidence that meiosis, or at least some form …

Analysis Of The Antimicrobial Activity Of The Novel Chemotherapeutic Drug, Tpp1, Against Pseudomonas Aeruginosa And The Hydrogel Delivery Of Water-Soluble Antimicrobial Compounds, Alex Gasper

Senior Independent Study Theses

Cancer is one of the leading causes of death in the world, and it is commonly linked with bacterial infections that often complicate treatments. Recently, chemotherapeutics have been developed that are able to act as anti-cancer agents using delocalized lipophilic cations (DLCs) that are able to specifically target mitochondrial membranes of cancer cells. TPP1 is a newly developed chemotherapeutic drug that has activity against bladder cancer and melanoma cell lines in vitro. In order to determine if TPP1 has antimicrobial activity, TPP1 was tested against a common bacteria, Pseudomonas aeruginosa, to determine if antimicrobial activity was present. This testing was …

Design And Synthesis Of Purine Based Neuroprotectors And Novel Synthetic Methods For The Trifluoromethylation Of Aldehyde Hydrazones, Puspa Aryal

Doctoral Dissertations

"Purine-derived compounds are widely investigated as cyclin-dependent kinase inhibitors that have broad applications in the design of pharmaceuticals for treating diseases, such as diabetes, atherosclerosis, and cancers. Towards the goal of effective AGE-inhibitors, and neuroprotector compounds we have synthesized a series of novel purine-based triazoles and investigated their neuroprotective effects, using SHSY-3Y human neuroblastoma cell line. Through these studies, we have identified purine-based neuroprotector compounds that favorably modulate oxidative stress induced by the Fenton reaction-generated reactive oxygen species (ROS).

The C(sp²−H)-trifluoromethylation of hydrazones would give access to the αtrifluoromethylated hydrazones that can serve as intermediates in the synthesis …

Abl2 Promotes Alcohol-Associated Liver Disease Via Ppar Gamma Regulation, Gregory Malnassy

Dissertations

Alcohol-associated liver disease (AALD) is an umbrella term for a spectrum of diseases resulting from chronic alcohol (e.g. ethanol) abuse ranging in severity from reversible conditions such as alcohol-induced steatosis to advanced and largely irreversible liver pathologies including alcoholic steatohepatitis (ASH), alcoholic hepatitis (AH), fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). AALD is one of the primary causes of chronic liver disease worldwide and accounts for 44% of liver disease deaths in the United States. Drinking rates, both in the United States and globally, have increased year over year for the past three decades, a trend which has resulted in significantly …

Toward A Topology-Based Therapeutic Design Of Membrane Proteins: Validation Of Napi2b Topology In Live Ovarian Cancer Cells, Leisan Bulatova, Daria Savenkova, Alsina Nurgalieva, Daria Reshetnikova, Arina Timonina, Vera Skripova, Mikhail Bogdanov, Ramziya Kiyamova

Faculty, Staff and Student Publications

NaPi2b is a sodium-dependent phosphate transporter that belongs to the SLC34 family of transporters which is mainly responsible for phosphate homeostasis in humans. Although NaPi2b is widely expressed in normal tissues, its overexpression has been demonstrated in ovarian, lung, and other cancers. A valuable set of antibodies, including L2 (20/3) and MX35, and its humanized versions react strongly with an antigen on the surface of ovarian and other carcinoma cells. Although the topology of NaPi2b was predicted

Optimization And Standardization Of Dms Chemical Mapping Experiments For Probing Rna 3d Structure, Sarah Brady

Honors Program: Senior Projects (Public)

RNA plays a significant and crucial role in biological processes. The properties of RNA are ultimately responsible for each molecule’s unique function. The configuration and structural integrity of RNA is important for its functionality. Chemical mapping detailed in this thesis can be used to analyze the 3D structure of an RNA sequence. RNA is modified via methylation of adenine and cytosine bases using dimethyl sulfate, then reverse transcribed to DNA, then sequenced. The sites where the bases were methylated become mutations in the DNA sequence, allowing for identification of these locations when analyzing sequencing data. Conditions for modification can be …

Roles Of Regulated Cell Death In Cholangiocarcinoma And Pancreatic Ductal Adenocarcinoma, Thanpisit Lomphithak

Chulalongkorn University Theses and Dissertations (Chula ETD)

Cholangiocarcinoma (CCA) and pancreatic ductal adenocarcinoma (PDAC) are complex and heterogeneous cancers. Conventional therapy approaches often fail to elicit significant responses in patients, resulting in low survival rates compared to other cancer types. This could be due to their immunosuppressive and desmoplastic tumor microenvironment, which renders cancer cells resistant to conventional therapies, highlighting the urgent need for more effective therapeutic approaches. Regulated cell death pathways have been extensively studied in recent years as a promising target for developing new strategies in cancer treatment. Specifically, necroptosis and ferroptosis, two forms of regulated necrosis, hold promise as novel targets for treating cancer, …

Role Of Jak/Stat Signaling Pathway During Viral Infection In Black Tiger Shrimp Penaeus Monodon, Pasunee Laohawutthichai

Chulalongkorn University Theses and Dissertations (Chula ETD)

Janus Kinase/signal transducers and activators of transcription (JAK/STAT) signaling pathway plays an important role for antiviral immunity. To stimulate the pathway, the cytokines, interferons, or other stimulators activate the receptor, which is then dimerized and activate JAKs, causing phosphorylation of the tyrosine residues of the receptor. Consequently, STATs are phosphorylated, dimerized and localized into the nucleus to regulate their target gene transcription. This study aims to better understand the role of JAK/STAT signaling pathway in Penaeus monodon during viral infection. From tissue distribution, PmDOME, PmJAK and PmSTAT transcripts were expressed in all tested tissues and up-regulated about 2-fold upon WSSV …