Biochemistry Commons^™

Broad-Spectrum Lignin-Based Adhesives Using Thiol–Silyl Ether Crosslinkers, Yishayah Bension, Siteng Zhang, Tristan Menninger, Ting Ge, Chuanbing Tang

Faculty Publications

Lignin is a renewable feedstock that is abundant and inexpensive but still presents challenges for its valorization. In this work, we converted functionalized lignin into broad-spectrum adhesives using thiol–silyl ether crosslinkers. The curing behavior of adhesives was investigated via rheology of their resin forms. These materials exhibit good adhesion on diverse substrates, including wood, glass, steel, aluminium, carbon fiber, and different plastics, with the most adhesion strength in the range of 1–3 MPa. These adhesives were also explored for applications, ranging from wet conditions to different mechanically responsive materials. The mechanism of adhesion was further examined to understand the bonding …

The Impact Of Mutations In The Arabidopsis Apetela (Ap3) Gene, Hazel R. Frans, Tara Phelps-Durr

SACAD: Scholarly Activities

The purpose of this research is to understand the molecular functioning of the Arabidopsis thaliana Apetela (Ap3) gene. We created mutations in two sites of the gene, AP3-3 and AP3-5. These are predicted to change AP3 protein structure, which may result in a mutated flower. Analyzing the effects of new mutations allows an understanding of protein formation both in plants and humans.

Parp2 Promotes Break Induced Replication-Mediated Telomere Fragility In Response To Replication Stress, Daniela Muoio, Natalie Laspata, Rachel L Dannenberg, Caroline Curry, Simone Darkoa-Larbi, Mark Hedglin, Shikhar Uttam, Elise Fouquerel

Department of Biochemistry and Molecular Biology Faculty Papers

PARP2 is a DNA-dependent ADP-ribosyl transferase (ARTs) enzyme with Poly(ADP-ribosyl)ation activity that is triggered by DNA breaks. It plays a role in the Base Excision Repair pathway, where it has overlapping functions with PARP1. However, additional roles for PARP2 have emerged in the response of cells to replication stress. In this study, we demonstrate that PARP2 promotes replication stress-induced telomere fragility and prevents telomere loss following chronic induction of oxidative DNA lesions and BLM helicase depletion. Telomere fragility results from the activity of the break-induced replication pathway (BIR). During this process, PARP2 promotes DNA end resection, strand invasion and BIR-dependent …

Hedgehog Signaling And Congenital Disorders; The Case Of Anencephaly And Polydactyly, Joshua Towery

First-Year Research Immersion (FRI) Scholarship

The Hedgehog pathway is a fundamental signaling pathway in the human body; involved in carcinogenesis, stem cell maintenance, as well as limb patterning in embryonic development. Originally discovered in drosophila, their initial discovery, and subsequent analysis revealed many novel pieces of information about the mechanisms inside the human body, as many core components of the signaling pathway are carried over from fruit flies to humans. Because of the key roles hedgehog signaling plays in human development, dysfunction and mutations in the pathway can be detrimental. This review will focus on two congenital birth defects thought to be caused by hedgehog …

Neurotensin Modulates Ovarian Vascular Permeability Via Adherens Junctions, Andrew Pearson, Ketan Shrestha, Thomas E. Curry, Diane M. Duffy

UK CARES Faculty Publications

Neurotensin (NTS) is a 13-amino acid peptide which is highly expressed in the mammalian ovary in response to the luteinizing hormone surge. Antibody neutralization of NTS in the ovulatory follicle of the cynomolgus macaque impairs ovulation and induces follicular vascular dysregulation, with excessive pooling of red blood cells in the follicle antrum. We hypothesize that NTS is an essential intrafollicular regulator of vascular permeability. In the present study, follicle injection of the NTS receptor antagonist SR142948 also resulted in vascular dysregulation. To measure vascular permeability changes in vitro, primary macaque ovarian microvascular endothelial cells (mOMECs) were enriched from follicle aspirates …

A Review On Irisin, The Beta 3-Adrenergic Receptor, And Zinc Alpha 2-Glycoprotein’S Impact On Metabolic Health, Dawson Troutman

Honors College Theses

This thesis aims to provide insight into how Irisin, the beta 3-adrenergic receptor, and zinc alpha 2-glycoprotein can impact human metabolism. Analyzing studies on the impact these species have on thermogenesis and lipolysis help provide a clearer picture on their use in potential management of metabolic issues.

Cifa And Cifb Expression In Response To Piwi And Aub Knockdown In Jw18 D. Melanogaster Cells, Julieta Alarcon

Posters - 2024

Wolbachia is an intracellular bacterium that is known for inducing cytoplasmic incompatibility (CI) in its Drosophila melanogaster hosts. CI is characterized by embryonic death when males that express cifA and cifB genes mate with unaffected females (Shropshire, Rosenberg, and Bordenstein 2020). PIWI proteins play important roles such as germline determination, spermiogenesis, and transposon silencing (Thomson and Lin 2009). Previous studies have shown that Piwi expression decreases in a developmental window called the “Piwiless pocket” or Pilp. When Aub is depleted in the Pilp, then Piwi expression increases (Théron et al. 2018). We will determine if Piwi and Aub FANA ASO …

Exploring Cation Exchange: Unveiling Its Significance In Biochar And Bioenergetics Applications, Gyanendra Kharel

Chemistry & Biochemistry Theses & Dissertations

Cation exchange, a cornerstone of soil chemistry and nutrient cycling, is a fundamental chemical process that occurs in soils, sediments, membranes, and other solid materials. It involves the interchange of positively charged ions, or cations, between a solid matrix and a surrounding solution. This process is crucial in various natural and engineered systems, leading to a range of applications across different fields.

This dissertation presents an extensive investigation into the applications of cation exchange in the fields of biochar and bioenergetics, encompassing three distinct aims. The first aim concentrates on the surface oxygenation of biochar through ozonization, aiming to achieve …

Decreasing The Antibiotic Survival Of Multi-Drug Resistant Gram-Positive Organisms, Areej Malik

Biomedical Sciences Theses & Dissertations

Biofilm production plays a crucial role in bacterial antibiotic tolerance and novel approaches are needed to combat it. The stringent response (SR), activated by nucleotide alarmones (pp)pGpp, is crucial for bacterial transcriptional reprogramming. In Clostridioides difficile, the SR is implicated in antibiotic survival, contributing to infection recurrence. Despite its known roles in sporulation and biofilm production in other bacterial species, the broader influence of the SR on C. difficile physiology remains undiscovered. This study deletes the C. difficile SR gene relQ, revealing the pivotal role of RelQ in regulating SR-dependent phenotypes in this organism. The absence of RelQ …

A Comparison Of In Vitro Studies Between Cobalt(Iii) And Copper(Ii) Complexes With Thiosemicarbazone Ligands To Treat Triple Negative Breast Cancer, Duaa R. Alajroush, Chloe B. Smith, Brittney F. Anderson, Ifeoluwa T. Oyeyemi, Stephen J. Beebe, Alvin A. Holder

Undergraduate Research Symposium

Triple negative breast cancer (TNBC) is one of the most aggressive forms of breast cancer, and disproportionately affects African American women. TNBC cells lack the common hormone receptors that many pre-existing cancer treatments target. Fortunately, metal-based complexes with thiosemicarbazone ligands have gained significant attention for their potential as anti-cancer agents. Cobalt(III) complex ([Co(phen)2(MeATSC)](NO3)3•1.5H2O•C2H5OH]) and Copper(II) complex ([Cu(acetylethTSC)Cl]Cl•0.25C2H5OH) specifically have properties of high toxicity, which can contribute to decreased cancer cell activity. The effects of these complexes are currently being investigated on cancerous and non-cancerous breast cell lines. The cytotoxic effect of the cobalt(lll) complex and the copper(ll) complex was analyzed …

Myeloid-Derived Suppressor Cell Mitochondrial Fitness Governs Chemotherapeutic Efficacy In Hematologic Malignancies, Saeed Daneshmandi, Jee Eun Choi, Qi Yan, Cameron R. Macdonald, Manu Pandey, Mounika Goruganthu, Nathan Roberts, Prashant K. Singh, Richard M. Higashi, Andrew N. Lane, Teresa W-M Fan, Jianmin Wang, Philip L. Mccarthy, Elizabeth A. Repasky, Hemn Mohammadpour

Markey Cancer Center Faculty Publications

Myeloid derived suppressor cells (MDSCs) are key regulators of immune responses and correlate with poor outcomes in hematologic malignancies. Here, we identify that MDSC mitochondrial fitness controls the efficacy of doxorubicin chemotherapy in a preclinical lymphoma model. Mechanistically, we show that triggering STAT3 signaling via β2-adrenergic receptor (β2-AR) activation leads to improved MDSC function through metabolic reprogram- ing, marked by sustained mitochondrial respiration and higher ATP generation which reduces AMPK signaling, altering energy metabolism. Furthermore, induced STAT3 signaling in MDSCs enhances glutamine consumption via the TCA cycle. Metabolized glutamine generates itaconate which downregulates mitochondrial reactive oxygen species via regulation of …

Blocking The Dimerization Of Polyglutamine-Expanded Androgen Receptor Protects Cells From Dht-Induced Toxicity By Increasing Ar Turnover, Allison Lisberg, Yuhong Liu, Diane E. Merry

Department of Biochemistry and Molecular Biology Faculty Papers

Spinal and bulbar muscular atrophy (SBMA) is a neuromuscular degenerative disease caused by a polyglutamine expansion in the androgen receptor (AR). This mutation causes AR to misfold and aggregate, contributing to toxicity in and degeneration of motor neurons and skeletal muscle. There is currently no effective treatment or cure for this disease. The role of an interdomain interaction between the amino- and carboxyl-termini of AR, termed the N/C interaction, has been previously identified as a component of androgen receptor-induced toxicity in cell and mouse models of SBMA. However, the mechanism by which this interaction contributes to disease pathology is unclear. …

In Silico Analysis Of C-Type Lectins As Co-Infection Receptors Of Dengue And Chikungunya Viruses In Aedes Aegypti, Munawir Sazali, R. C. Hidayat Soesilohadi, Nastiti Wijayanti, Tri Wibawa, Arif Nur Muhammad Ansori

Makara Journal of Science

Aedes aegypti is a primer vector of dengue virus (DENV) and chikungunya virus (CHIKV). The susceptibility of mosquitoes to DENV and CHIKV depends on their recognition receptor of pathogens. C-type lectins (CTLs) are an important mediator of virus infection in A. aegypti. This study aims to identify potential receptors and determine the binding affinity between ligand–receptor interaction, CTLs and virus envelopes (DENV-1, 2, 3, and 4 and CHIKV) interaction based on in silico analysis. Sample sequences were obtained from GenBank (NCBI), and 10 CTLs were acquired from VectorBase. Homology modeling based on a minimum standard of 20% was processed …

Altered Lipid Metabolism In Apc-Driven Colorectal Cancer: The Potential For Therapeutic Intervention, Courtney O. Kelson, Yekaterina Y. Zaytseva

Markey Cancer Center Faculty Publications

Altered lipid metabolism is a well-recognized feature of solid cancers, including colorectal cancer. In colorectal cancer, upregulation of lipid metabolism contributes to initiation, progression, and metastasis; thus, aberrant lipid metabolism contributes to a poor patient outcome. The inactivating mutation of APC, a vital tumor suppressor in the Wnt signaling pathway, is a key event that occurs early in the majority of colorectal cancer cases. The potential crosstalk between lipid metabolism and APC-driven colorectal cancer is poorly understood. This review collectively highlights and summarizes the limited understanding between mutations in APC and the upregulation of Wnt/beta- catenin signaling and lipid metabolism. …

Coomassie Brilliant Blue Dye As A Method For Analyzing Fracture Markings In Bone, Abigail Hoffmeister, David Harutunyan, Matthew Aizawa, Everett Baker, Brandon Mendoza, Chase Freeman, Siran Iskanian

Seaver College Research And Scholarly Achievement Symposium

Coomassie Brilliant Blue Dye is a dye commonly used to stain proteins. Because of its ability to adhere to proteins, this research has focused on perfecting a method of dyeing a fractured flat bone in order to most accurately observe and analyze fracture markings within the trabecular layer. Stereoscopic microscopy was the chosen technique of analysis for this research because of its proven effectiveness in glass and ceramic fractography to observe varying depths. In order to most effectively apply stereoscopic microscopy to this research, the following variables were manipulated to maximize color contrast in the trabecular layer in order to …

Effects Of Diminazene Aceturate On Drosophila Melanogaster: A Lipidomic Analysis, Gabriela Suarez

USF Tampa Graduate Theses and Dissertations

Pesticides are agents designed to eradicate living organisms to preserve agricultural needs.¹ Today the most commonly used pesticides are termed “modern pesticides”, they are characterized by lower lipophilicity and limited stability, making them less time persistent in the environment. Among these modern pesticides are organophosphorus, urea, phenoxy alkanoic, triazine, chloroacetanilide, and glyphosate-based pesticides.² The issue faced with most of these pesticides is that they affect more than just the targeted pest and pose a danger to not only humans, but also entire ecosystems.^1,3,4 While there are many different types of pesticides, insecticides show the most variance and …

Two Dot1 Enzymes Cooperatively Mediate Efficient Ubiquitin-Independent Histone H3 Lysine 76 Tri-Methylation In Kinetoplastids, Victoria Frisbie, Hideharu Hashimoto, Yixuan Xie, Francisca De Luna Vitorino, Josue Baeza, Tam Nguyen, Zhangerjiao Yuan, Janna Kiselar, Benjamin Garcia, Erik Debler

Department of Biochemistry and Molecular Biology Faculty Papers

In higher eukaryotes, a single DOT1 histone H3 lysine 79 (H3K79) methyltransferase processively produces H3K79me2/me3 through histone H2B mono-ubiquitin interaction, while the kinetoplastid Trypanosoma brucei di-methyltransferase DOT1A and tri-methyltransferase DOT1B efficiently methylate the homologous H3K76 without H2B mono-ubiquitination. Based on structural and biochemical analyses of DOT1A, we identify key residues in the methyltransferase motifs VI and X for efficient ubiquitin-independent H3K76 methylation in kinetoplastids. Substitution of a basic to an acidic residue within motif VI (Gx₆K) is essential to stabilize the DOT1A enzyme-substrate complex, while substitution of the motif X sequence VYGE by CAKS renders a rigid active-site …

The Polyglutamine Domain Is The Primary Driver Of Seeding In Huntingtin Aggregation, Adam Skeens, Chathuranga Siriwardhana, Sophia E. Massinople, Michelle M. Wunder, Zachary L. Ellis, Kaitlyn M. Keith, Tyler Girman, Shelli L. Frey, Justin Legleiter

Chemistry Faculty Publications

Huntington’s Disease (HD) is a fatal, neurodegenerative disease caused by aggregation of the huntingtin protein (htt) with an expanded polyglutamine (polyQ) domain into amyloid fibrils. Htt aggregation is modified by flanking sequences surrounding the polyQ domain as well as the binding of htt to lipid membranes. Upon fibrillization, htt fibrils are able to template the aggregation of monomers into fibrils in a phenomenon known as seeding, and this process appears to play a critical role in cell-to-cell spread of HD. Here, exposure of C. elegans expressing a nonpathogenic N-terminal htt fragment (15-repeat glutamine residues) to preformed htt-exon1 fibrils induced …

The Effect Of Ethanol Treatment On The Protein Content Of Difi Exosomes, Kenzie Rushing

[Archive] Belmont University Research Symposium (BURS)

Colorectal cancer (CRC) is the second most common cause of cancer death in the United States in both men and women combined, second only to lung cancer.1 CRC metastasis is the primary cause of mortality largely due to therapy resistant cancer cells.2 Therefore, detection before metastasis is of great importance and could potentially lead to earlier detection and decreased mortality. Extracellular vesicles (EVs), including exosomes, are lipid bound vesicles secreted by cells3 that are involved in cell-cell communication and have been found to promote CRC progression and metastasis.4 The proteome of exosomes is thought to reflect that of the originating …

Identification Of A Novel Target For Declustering Supernumerary Centrosomes In Triple Negative Breast Cancer, Priyanga J

Theses and Dissertations

Triple-negative breast cancer (TNBC) confers considerable interventional challenge owing to its massive heterogeneity, aggression and metastatic prowess. These facets are attributed to chromosomal instability (CIN), a feature consequent to TNBC cell’s ability to harbor more than two centrosomes (supernumerary centrosomes; SNCs).

In principle, if a normal cell possesses SNCs, uneven pull forces are generated consequent to multipolar spindle, which activates cellular surveillance. This ensures error-free mitosis by either repairing the error or, in an irreparable condition, driving cells to death. This averts the possibility of aneuploidy (fundamental to tumorigenesis).

Unfortunately, TNBC cells, despite harboring SNCs, have devised a survival strategy …

Evaluation Of Ergosterol And Its Metabolites As Lxr Agonists And Their Anticancer Potential In Colon Cancer, Yogain Taank, Navneet Agnihotri

Research Symposium

Purpose: Aberrant cholesterol homeostasis is a well-recognized hallmark of cancer and implicated in metastasis and chemotherapeutic resistance, the two major causes of cancer associated mortality. Liver X receptors (LXRs) are the key transcription factors that induce cholesterol efflux via enhancing the expression of ABCA1 and ABCG1.

Methods: Molecular docking and dynamic simulation studies were done to assess the binding affinity and stability of the receptor ligand complexes. Activation of LXRs was evaluated using the luciferase reporter assay. qRT-PCR and western blotting was done to analyse the mRNA and protein expression of cholesterol homeostasis genes. Flow cytometric analysis was carried out …

Differentially Disrupted Spinal Cord And Muscle Energy Metabolism In Spinal And Bulbar Muscular Atrophy, Danielle Debartolo, Frederick Arnold, Y Liu, Elana Molotsky, Hsin-Yao Tang, Diane Merry

Department of Biochemistry and Molecular Biology Faculty Papers

Prior studies showed that polyglutamine-expanded androgen receptor (AR) is aberrantly acetylated and that deacetylation of the mutant AR by overexpression of nicotinamide adenine dinucleotide-dependent (NAD+-dependent) sirtuin 1 is protective in cell models of spinal and bulbar muscular atrophy (SBMA). Based on these observations and reduced NAD+ in muscles of SBMA mouse models, we tested the therapeutic potential of NAD+ restoration in vivo by treating postsymptomatic transgenic SBMA mice with the NAD+ precursor nicotinamide riboside (NR). NR supplementation failed to alter disease progression and had no effect on increasing NAD+ or ATP content in muscle, despite producing a modest increase of …

Structure-Based Targeting Of The Nemo:Ikk Interaction For Canonical Nf-Κb Inhibition, Amy Kennedy

Dartmouth College Ph.D Dissertations

The NF-κB pathway is important for cell survival and proliferation, inflammation, and innate immunity, and its dysregulation is a common theme in many cancers, autoimmune disorders, and other disease states. The protein-protein interaction between the scaffolding protein NEMO and the kinase IKK in the NF-κB pathway represents a compelling target for selective NF-κB inhibition because it occurs only in the canonical branch of the NF-κB pathway. Disruption of the NEMO:IKK interaction has been established for decades in the literature as a safe and effective way to selectively inhibit overactivation of the canonical branch of the NF-κB pathway. The benchmark in …

Dna-Pkcs Rnaseq Data: Dna-Pkcs Wilde-Type Or Kinase-Dead Protein Regulate Basal And Etoposide-Induced Gene Expression Changes, Amanda Ashley

Chemistry & Biochemistry: Datasets

No abstract provided.

Facile One-Pot Synthesis And Anti-Microbial Activity Of Novel 1,4-Dihydropyridine Derivatives In Aqueous Micellar Solution Under Microwave Irradiation, Asmita Goswami, Navneet Kaur, Manvinder Kaur, Kishanpal Singh, Harvinder Singh Sohal, Haesook Han, Pradip K. Bhowmik

Chemistry and Biochemistry Faculty Research

The current study describes a novel and eco-conscious method to synthesize 1,4-dihydropyridine derivatives utilizing an aqueous micellar solution containing aluminum dodecyl sulfate, Al(DS)3, using readily available starting material. The final products were synthesized with excellent yields within remarkably quick reaction durations, promoting remarkable atom economy and minimizing environmental impacts. The present protocol has several advantages over other methodologies in terms of high yield (up to 97%) with excellent purity. Further, the synthesized 1,4-DHPs exhibit favorable to excellent resistance against examined bacterial and fungal species. Intriguingly, polar groups on the phenyl ring (5b, 5c, 5i and 5j) make the 1,4-DHPs equally …

Spontaneous Alignment Of Myotubes Through Myogenic Progenitor Cell Migration, Lauren E. Mehanna, Adrianna R. Osborne, Charlotte A. Peterson, Brad J. Berron

Chemical and Materials Engineering Faculty Publications

In large-volume muscle injuries, widespread damage to muscle fibers and the surrounding connective tissue prevents myogenic progenitor cells (MPCs) from initiating repair. There is a clinical need to rapidly fabricate large muscle tissue constructs for integration at the site of large volume muscle injuries. Most strategies for myotube alignment require microfabricated structures or prolonged orientation times. We utilize the MPC’s natural propensity to close gaps across an injury site to guide alignment on collagen I. When MPCs are exposed to an open boundary free of cells, they migrate unidirectionally into the cell-free region and align perpendicular to the original boundary …

Ellagic Acid Inhibits Α-Synuclein Propagation And Alleviates The Neurotoxicity By Enhancing Autophagic Flux In Animal Model Of Parkinson’S Disease, Nada Akram Abdellatif

Theses

Parkinson’s Disease (PD) is the second most common neurological disorder pathologically characterized by loss of dopaminergic neurons in the Substantia Nigra pars compacta (SNc) as well as the formation of Lewy bodies composed mainly of α-synuclein (α-syn) aggregates. It has been documented that abnormal aggregation of α-syn is one of the major causes of developing PD. Ellagic Acid (EA) is a widely known dietary supplement found in pomegranates as well as a plethora of berries and nuts. EA has been shown to prevent α-syn aggregates’ toxicity in cellular model of PD. In the current study we aim to evaluate whether …

Antioxidant Properties Of Kombucha Beverage Infused With Ganoderma Lucidum And Green Tea From Camellia Sinensis (L.) Kuntze With Several Fermentation Times, Rizki Rabeca Elfirta, Pamungkas Rizki Ferdian, Iwan Saskiawan, Tri Hadi Handayani, Kayla Faza Gustafri Mandalika, Rini Riffiani, Kasirah Kasirah, Ukhradiya Magharaniq Safira Purwanto

Karbala International Journal of Modern Science

Kombucha is a functional beverage produced through the fermentation of infused tea or Camelia sinensis (L.) Kuntze (CS) by a symbiotic culture of bacteria and yeast. Apparently, the substrate of kombucha can be substituted to enhance its functional properties. Ganoderma lucidum (GL) is a potential substrate reported to have health benefits. This study aims to evaluate antioxidant properties by comparing different formulations and fermentation times. The formulations prepared in the present study varied in the compositions of GL and CS substrates, namely F1 (100% GL), F2 (75% GL: 25% CS), F3 (50% GL: 50% CS), F4 (25% GL: 75% CS), …

Raw Nmr Data For Tripeptides, David J. Michaelis, Scott R. Burt, Mariur Rodriguez Moreno, Nye C. Johnson, Christopher B. Stewart, Mary L. Setelin, Adam X. Wayment, Braxton M. Felix

ScholarsArchive Data

This data set contains primary data for 50 tripeptides that were generated as part of an advanced undergraduate laboratory experience in solid phase peptide synthesis. The raw data can be processed sing NMR interpretation software and can be used as problems for exams and quizzes or as supplementary materials for a laboratory experience

Vitamin E Biofortification: Enhancement Of Seed Tocopherol Concentrations By Altered Chlorophyll Metabolism, Ping Qin, Peng Chen, Yuanwei Zhou, Wei Zhang, Yunyun Zhang, Jingjing Xu, Lu Gan, Yingnan Liu, Jill Romer, Peter Dörmann, Edgar B. Cahoon, Chunyu Zhang

Department of Biochemistry: Faculty Publications

Homogentisate Phytyltransferase (HPT) catalyzes condensation of homogentisate (HGA) and phytyl diphosphate (PDP) to produce tocopherols, but can also synthesize tocotrienols using geranylgeranyl diphosphate (GGDP) in plants engineered for deregulated HGA synthesis. In contrast to prior tocotrienol biofortification efforts, engineering enhanced tocopherol concentrations in green oilseeds has proven more challenging due to the integral role of chlorophyll metabolism in supplying the PDP substrate. This study show that RNAi suppression of CHLSYN coupled with HPT overexpression increases tocopherol concentrations by >two-fold in Arabidopsis seeds. We obtained additional increases in seed tocopherol concentrations by engineering increased HGA production via overexpression of …