Biochemistry Commons^™

A Facile Strategy For The Fabrication Of Cell-Laden Porous Alginate Hydrogels Based On Two-Phase Aqueous Emulsions, Wen Xue, Donghee Lee, Yunfan Kong, Mitchell Kuss, Ying Huang, Taesung Kim, Soonkyu Chung, Andrew T. Dudley, Seung-Hyun Ro, Bin Duan

Department of Biochemistry: Faculty Publications

Porous alginate (Alg) hydrogels possess many advantages as cell carriers. However, current pore generation methods require either complex or harsh fabrication processes, toxic components, or extra purification steps, limiting the feasibility and affecting the cellular survival and function. In this study, a simple and cell-friendly approach to generate highly porous cell-laden Alg hydrogels based on two-phase aqueous emulsions is reported. The pre-gel solutions, which contain two immiscible aqueous phases of Alg and caseinate (Cas), are cross-linked by calcium ions. The porous structure of the hydrogel construct is formed by subsequently removing the Cas phase from the ion-cross-linked Alg hydrogel. Those …

Conformal Electrodeposition Of Antimicrobial Hydrogels Formed By Self-Assembled Peptide Amphiphiles, Gervasio Zaldivar, Jiachen Feng, Leonardo Lizarraga, Yafan Yu, Luana De Campos, Kelly Mari Pires De Oliveira, Kurt Piepenbrink, Martin Conda-Sheridan, Mario Tagliazucchi

Department of Biochemistry: Faculty Publications

The colonization of biomedical surfaces by bacterial biofilms is concerning because these microorganisms display higher antimicrobial resistance in biofilms than in liquid cultures. Developing antimicrobial coatings that can be easily applied to medically-relevant complex-shaped objects, such as implants and surgical instruments, is an important and challenging research direction. This work reports the preparation of antibacterial surfaces via the electrodeposition of a conformal hydrogel of self-assembling cationic peptide-amphiphiles (PAs). Hydrogels of three PAs are electrodeposited: C₁₆K₂, C₁₆K₃, and C₁₈K₂, where C_n is an alkyl chain of n methylene …

Treponema Denticola Synthesizes C-Di-Amp And Encodes The Cdaa-Type Diadenylate Cyclase Cdaa, Claire R. O'Brien

Theses and Dissertations

Periodontitis is a form of oral disease characterized by dysbiosis of the oral microbiome, leading to inflammation, bone resorption, and in severe cases, entire tooth loss, affecting 42% of adults in the US. One of the bacteria most associated with periodontal disease progression is Treponema denticola (Td), an oral spirochete which inhabits the mouth in small quantities during health but which can dominate the biofilms that form during periodontal disease. The ability of Td to survive in a disease environment and contribute to the progression of disease requires the use of robust signaling networks. Analysis of Td cultures …

Engineering Ph-Dependent Antibody Interactions Through Introduction Of Linked Protonation Equibria Within The Antigen Binding Interface Or Linked Oligomeric Interfaces, Tosha Laughlin

Graduate Research Theses & Dissertations

Antibodies are widely applied as affinity reagents across a variety of fields, due to their high affinity and specificity. While high affinity across a range of conditions is useful for many applications, the ability to modulate affinity with environmental conditions (e.g., pH) opens new opportunities for antibody applications. This dissertation focuses on exploring the impact of an antibody’s interface size on engineered pH dependence, as well as exploring engineered pH-dependence through perturbing oligomerization equilibria that are linked to target binding. An anti-maltose binding protein (MBP) Fab 7O antibody fragment was used as a large protein-protein interface model to explore a …

Development Of A Chemical Biology Approach To Uncover The Influence Of Sequence Variations On Ces1 Activity In Live Cells, Samuel James Knebel

Masters Theses

Drug metabolism is the biochemical process of modifying drugs to detoxify and remove them through enzymatic transformations. These biotransformation’s occur primarily in the liver and are critical to understanding how pharmaceutical compounds are chemically altered inside the human body. Human carboxylesterases (CESs) catalyze the hydrolysis of esters, amides, thioesters, and carbamates. CES-mediated hydrolysis plays an important role in the metabolism of many drugs including the first FDA approved antiviral treatment for COVID-19, remdesivir (Veklury), the seizure control medication rufinamide (Banzel), and the flu antiviral drug oseltamivir (Tamiflu). CES activity is known to be influenced by a variety of factors including …

Evaluating The Contribution Of Adjacent Charges On The Observed Ph-Dependent Binding Profile For A Vhh/Antigen Interaction With A Linked Histidine Protonation Equilibria, Kiruthika Arulmoly

Graduate Research Theses & Dissertations

pH dependent protein-protein interactions are of great importance for various biological processes. In addition, the generation of engineered pH-dependent therapeutic antibodies opens opportunities for the extension of therapeutic half-life, thereby reducing drug dosage or frequency of administration, as well as providing pH-dependent targeting, such as the tumor microenvironment. Engineering pH-dependent antibody-antigen interaction is mostly achieved through the incorporation of ionizable residues within the antigen binding interface. These ionizable residues must undergo a change in environment upon forming a protein-protein complex, which causes a change in the ionizable group’s pKa value. This coupled protonation equilibria is responsible for the observed pH-dependent …

Bioanalytical Studies Of Disease Protein Profiles: Maldi-Tof Ms, Prajkta Satish Chivte

Graduate Research Theses & Dissertations

Coronavirus disease-2019 (COVID-19), which is caused by a novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has ravaged the world for the past 3 years. Even today, there still exists a need for rapid, accurate, economical and non-invasive diagnostic testing platforms that yield high specificity and sensitivity towards the constantly mutating SARS-CoV-2. Research has consistently indicated saliva to be a more amenable specimen type for early detection of SARS-CoV-2, compared to the oral and nasopharyngeal swabs. Considering the limitations and high demand of the existing COVID-19 testing platforms, this dissertation work studies used MALDI-ToF MS (matrix-assisted laser desorption/ionization-time of …

Analyzing The Impact Of Zip Subfamily Ii Mutations On The Zinc And Iron Transport Of Zupt From Escherichia Coli, Bradley Vandecar

Wayne State University Theses

The disfunction or misregulation of the ZIP family of metal ion transporters has been linked to a plethora of diseases and cancers in humans. Zn2+ is the primary substrate for ZIPs and is transported through the M1 metal binding site, though this activity is stimulated through the binding of Fe2+ in the M2 metal binding site. The members of ZIP Subfamily II are predicted to have an inactive M2 site due to the lack of Fe2+ transport and from a previously generated homology model. This work utilizes homology modelling, whole cell metal ion uptake assays, and growth studies in minimal …

In Silico Drug Discovery For Sars-Cov-2 Papain-Like Protease, Olivia Haskin

Wayne State University Theses

SARS-CoV-2 Papain-like protease is an essential viral protein for viral replication. In our lab, we hypothesize that successful inhibition of this protease will stop viral replication and allow for clearance of the infection by the host. The work described here aimed to design and execute an in silico drug discovery workflow for successfully selecting PLpro inhibitors from the Mcule purchasable compound database. This work reports such a workflow and nine potential compounds for in vitro testing. This work also describes structural activity relationship analysis of a proprietary set of PLpro inhibitors synthesized by medicinal chemistry collaborators and makes recommendations for …

Approaches To Avoid Proteolysis During Protein Expression And Purification, Gary T. Henehan, Barry J. Ryan, Gemma K. Kinsella

Books/Book Chapters/ Proceedings

All cells contain proteases, which hydrolyze the peptide bonds between amino acids of a protein backbone. Typically, proteases are prevented from nonspecific proteolysis by regulation and by their physical separation into different subcellular compartments; however, this segregation is not retained during cell lysis, which is the initial step in any protein isolation procedure. Prevention of proteolysis during protein purification often takes the form of a two-pronged approach: first, inhibition of proteolysis in situ, followed by the early separation of the protease from the protein of interest via chromatographic purification. Protease inhibitors are routinely used to limit the effect of the …

Isotopic Evidence For Sources Of Dissolved Carbon And The Role Of Organic Matter Respiration In The Fraser River Basin, Canada, Britta M. Voss, Timothy I. Eglinton, Bernhard Peucker-Ehrenbrink, Valier Galy, Susan Q. Lang, Cameron Mcintyre, Robert G.M. Spencer, Ekaterina Bulygina, Zhaohui Aleck Wang, Katherine A. Guay

OES Faculty Publications

Sources of dissolved and particulate carbon to the Fraser River system vary significantly in space and time. Tributaries in the northern interior of the basin consistently deliver higher concentrations of dissolved organic carbon (DOC) to the main stem than other tributaries. Based on samples collected near the Fraser River mouth throughout 2013, the radiocarbon age of DOC exported from the Fraser River does not change significantly across seasons despite a spike in DOC concentration during the freshet, suggesting modulation of heterogeneous upstream chemical and isotopic signals during transit through the river basin. Dissolved inorganic carbon (DIC) concentrations are highest in …

Structural And Spectroscopic Study Of New Copper(Ii) And Zinc(Ii) Complexes Of Coumarin Oxyacetate Ligands And Determination Of Their Antimicrobial Activity, Muhammad Mujahid, Natasha Trendafilova, Georgina Rosair, Kevin Kavanagh, Maureen Walsh, Bernadette Creaven, Ivelina Georgieva

Articles

Tackling antimicrobial resistance is of increasing concern in a post-pandemic world where overuse of antibiotics has increased the threat of another pandemic caused by antimicrobial-resistant pathogens. Derivatives of coumarins, a naturally occurring bioactive compound, and its metal complexes have proven therapeutic potential as antimicrobial agents and in this study a series of copper(II) and zinc(II) complexes of coumarin oxyacetate ligands were synthesised and characterised by spectroscopic techniques (IR, 1H, 13C NMR, UV-Vis) and by X-ray crystallography for two of the zinc complexes. The experimental spectroscopic data were then interpreted on the basis of molecular structure modelling and subsequent spectra simulation …

Identification Of A Dna Polymerase Alpha Gene Sequence In Thermomyces Lanuginosus Fungus, Nathan Williams

Honors Program Theses

With cell growth being the main focus of our research, we chose to study DNA polymerase alpha. DNA polymerase alpha is likely to be involved in cell growth as it is the enzyme that starts DNA replication. Control of this enzyme might lead to decreased cell growth in cancer or increased cell growth in damaged spinal cord tissue. We chose the thermophilic fungus Thermomyces lanuginosus for the study of the enzyme due to the ability to compare the enzyme’s activity during fungal growth at different temperatures. Thermomyces exhibits rapid growth at high temperatures and slow growth at low temperatures. Studying …

Specialized Metabolism In Retina, Retinal Pigmented Epithelium, And Testis, Siyan Zhu

Graduate Theses, Dissertations, and Problem Reports (ETD)

The retina and its neighboring retinal pigmented epithelium (RPE) are high energy-demanding and metabolically active tissues with specialized and complementary metabolism. They are metabolically interdependent and impact each other’s viability. Interestingly, many of the metabolic features in the retina and RPE are shared with the testis. For example, testis is also energy costly due to continuous sperm differentiation and it has similar metabolic inter-dependence between different testis cells. Both the retina and testis are vulnerable to mitochondrial metabolic impairments.

We conducted three research projects to understand 1) the nutrient utilization and communication in retina and RPE; 2) The profiling of …

Extension Of The Ergot Alkaloid Gene Cluster, Samantha Joy Fabian

Graduate Theses, Dissertations, and Problem Reports (ETD)

Specialized metabolites produced by fungi impact human health. A large portion of the pharmaceuticals currently on the market are derived from metabolites biosynthesized by microbes. Ergot alkaloids are a class of fungal metabolites that are important in the interactions of environmental fungi with insects and mammals and also are used in the production of pharmaceuticals. In animals, ergot alkaloids can act as partial agonists or antagonists at receptors for 5-hydroxytryptamine (serotonin), dopamine, and noradrenaline as ergot alkaloids have chemical structures similar to those neurotransmitters. Therefore, they affect insects and mammals that consume them and can be used to produce drugs …

Concentrated Wastewater Treatment Using A Ferric Iron-Dosed Anaerobic Upflow Sludge Blanket Reactor For Recovery Of Phosphorus And Ammonium, Carley E. Shingleton

Graduate Theses, Dissertations, and Problem Reports (ETD)

This study evaluated the performance of a novel, ferric iron-dosed anaerobic bioreactor to recover two separate nutrient products from concentrated wastewaters -- phosphorus as vivianite (Fe₃(PO₄)₂×8H₂O) and an ammonium-containing effluent with low organics. A bench-scale upflow anaerobic sludge blanket (UASB) reactor fed with a synthetic wastewater (458.0 mg/L total organic carbon, 282.7 mg/L ammonium, and 84.4 mg/L phosphate) was dosed with a ferric chloride solution at an org. C/Fe³⁺ molar ratio ~17.5 to facilitate organic carbon oxidation coupled to iron reduction. The reactor design allowed natural settling of vivianite to its …

Elucidating Mechanisms Of Proteasome Modulation By Small Molecules To Treat Neurodegenerative Diseases And Cancer, Janelle Joo Yee Chuah

Graduate Theses, Dissertations, and Problem Reports (ETD)

Maintaining protein homeostasis, or proteostasis, is crucial for cellular function, and protein degradation through the proteasome plays a pivotal role in this process. Dysregulation of the proteasome can lead to proteostasis collapse and has been linked to the development of neurodegenerative diseases and cancers. Neurodegenerative diseases often exhibit proteasome impairment, whereas proteasome upregulation is frequently observed in cancer. Although the use of proteasome inhibitors as a pharmaceutical approach has shown success in certain cancers, it has yet to demonstrate efficacy in neurodegenerative diseases due to the absence of drug-like small molecules capable of effectively reversing proteasome impairment and/or activating the …

Heat Shock Protein 90 (Hsp90) System In Health And Disease., Daniella Munezero

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cells rely on heat shock proteins (HSP) to facilitate and regulate the folding of the substrate proteins into their native state, and degradation if misfolding cannot be prevented. HSP90, a member of the HSP family, is a potential target for treatment of cancer and neurodegenerative diseases. Unfortunately, several clinical trials for cancer treatment have been discontinued due to cell toxicity accompanying HSP90 inhibition. HSP90 has four distinct but structurally similar paralogs. HSP90 inhibitors target all the paralogs despite increasing proof of functional differences among the paralogs. Understanding the in vivo function of HSP90 and the role played by each paralog …

Mitochondrial Division: Synergizing In Mitochondrial Divisome, Ao Liu

Dartmouth College Ph.D Dissertations

Mitochondria are the energy factories of the cell. The dynamic nature of cells demands routine changes in mitochondrial morphology by fusion and division. The dynamin GTPase Drp1 is a central mitochondrial division protein, driving constriction of the outer mitochondrial membrane via oligomerization. At least four regulatory factors control Drp1 activity on the outer mitochondrial membrane (OMM): 1) receptor proteins (Mff, MiD49, MiD51, and Fis1); 2) actin filaments; 3) the mitochondrial phospholipid cardiolipin (CL); and 4) Drp1 post-translational modifications, of which two phosphorylation sites (S579 and S600) are the most well studied. However, the molecular mechanism of how these factors work …

Development Of Multivalent Dna-Peptide Nucleosome Mimetics And Multi-Domain Protein Inhibitors That Directly Or Indirectly Target The E3 Ligase Uhrf1, Li Gu

University of the Pacific Theses and Dissertations

UHRF1 is an E3 ubiquitin ligase and a key epigenetic regulator establishing a crosstalk between DNA methylation and histone modification. Despite the important biochemical role of UHRF1 in cells, its overexpression has been found in almost all primary cancer types including breast cancer, lung cancer and so on. Numerous evidence indicates a strong link between tumorigenesis and UHRF1 overexpression, supporting its potential as a universal biomarker for cancer. However, UHRF1 is “yet-to-be drugged” and no highly potent chemical probes have been developed to target UHRF1 to date. In this study, we proposed two drug design approaches for UHRF1. The first …