Biochemistry Commons^™

Electrochemical Reduction Of Carbon Dioxide Using Ruthenium And Amines, Sydney Moise

Honors Theses

With an increased concern for climate change in the recent years, a significant area of research has been devoted to the reduction of greenhouse gases. Carbon dioxide (CO2) resides in the atmosphere between 300 – 1000 years, making the reduction of the molecule a substantial field of study.1 Amines have been used as CO2 scrubbing agents in literature historically, due to their ability to form bonds to carbon.2 Although studies involving metal catalysts and amines have been reported numerous times, research involving chemical reduction of CO2 using purely amines is scarce. In this paper, amines, in addition to hydride donors …

Potential Use Of The Gel Extract Of Butterfly Pea Flower As Topical Therapy To Prevent Photodamage By Downregulating Tnf-Α And Caspase-3 Expression Levels In Uvb-Exposed Rats, Elvana Cahyani, Agung Putra, Prasetyowati Subchan

Makara Journal of Health Research

Background: Prolonged exposure to UVB radiation causes DNA damage in skin cells by raising the levels of reactive oxygen species, resulting in the production of inflammatory factors and skin issues. Plant extracts are frequently used to counteract photodamage due to their antioxidant properties. One example is the floral extract of the butterfly pea plant, which contains flavonoid antioxidants. However, the effect of the extract on inflammatory factors is unknown. This study investigated how tumor necrosis factor-alpha (TNF-α) and caspase-3 expression changed when a butterfly pea flower extract gel was applied topically to UVB-exposed animals.

Methods: Experimental and control …

Investigating The Helicase Activity Of Methylated Vs Unmethylated Ded1, Hannah Lukow

Honors Theses

Ded1 is an RNA helicase protein of the DEAD-box subfamily in eukaryotic organisms (Sharma & Jankowsky, 2014) which can act as an activator or initiation factor, during translation (Hilliker et al., 2011). Ded1 has several functions in yeast including assembly of translational initiation factors, scanning the mRNA for the start codon, and unwinding any double stranded segments of mRNA with its helicase ability. Ded1 was discovered to be methylated at four arginine sites in vivo (Low et al., 2013), with a fifth methylation site being discovered recently (Low et al., 2020), however the purpose of such post-translational modifications is still …

The Role Of Sars-Cov-2 Orf8 Protein Arks Motif On Novobiocin Binding, Si Chun Chiu, My T. Nguyen

Celebrating Scholarship and Creativity Day (2018-)

The discovery of the SARS-CoV-2 virus during the COVID-19 pandemic required scientists to develop medical solutions to reduce infectivity, severity of symptoms, and death. Although vaccines and drugs provided urgent assistance, the need to continue developing better drugs is necessary long term, and understanding the structure of the virus and finding potential inhibitors would prove vital to discovering solutions to this worldwide health problem. This experimental project focuses on targeting the unique accessory protein, Open Reading Frame 8 (ORF8) in SARS-CoV-2 through studying its interactions with a repurposable drug, novobiocin. Importantly, ORF8 specializes in helping evade immune system checks by …

Genome Announcement For E Cluster Phage Tarkin, Katherine Cleary

Chemistry & Biochemistry Student Scholarship

Katherine Cleary ’23
Major: Biochemistry
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

The Role Of Cerium(Iii) In Bacterial Growth And The Microbial Transformation Of Aromatic Hydrocarbons, Shruti Sathish

Honors Theses

Biofilms are communities of surface-attached bacterial cells encased in an exopolymeric matrix. In this state, they are more resistant to antimicrobial treatment and can have adverse effects in medical, agricultural, and industrial settings. Whereas, as biocatalysts, biofilms from nonpathogenic bacteria enhance their performance and stability in catalysis. Unfortunately, there are several challenges when using bacteria in organic transformations due to their complex cellular chemistry. Trivalent lanthanide metals were discovered to serve regulatory roles in some bacterial catalytic processes, including those of Pseudomonas putida KT2440 (P. putida), a non-infectious Gram-negative bacterium. The main goal of our research is to use cerium(III) …

Toward The Design, Synthesis, And Characterization Of Abiotic Coiled-Coil Peptides Via Solid-Phase Copper-Catalyzed Azide-Alkyne Cycloaddition (Sp-Cuaac) Click Reaction For The Preparation Of Controlled Self-Assembly Molecular Building Block, Liaquat Ali

Chemistry Theses

The production of cutting-edge materials, the development of novel medications, drug delivery systems, technological advancements, and biosynthesizing all depend on molecular building blocks. Proteins are required for the creation of intricate, well-organized structures, and coiled-coil protein domains are vital subunits for the oligomerization of protein complexes, gene expression, and the structural components of biological materials. The numerous interactions between a wide variety of amino acids make it difficult to assemble protein complexes with a particular shape. In the current study, we successfully designed and synthesized four different 32-residue peptides, each of which had two modified amino azide residues. These peptides …

Apoptosis Induction In Jurkat T-Lymphocytes By Proton Pump Inhibitors (Ppis), Shreya Murali, Randall Reif

Departmental Honors & Graduate Capstone Projects

Apoptosis, commonly known as programmed cell death, constantly occurs in humans. As a cancer cell increases in acidity, apoptosis is induced. In healthy cells, proton pump proteins allow for H⁺ ions to permeate cellular membranes, regulating pH. However, proton pump inhibitors (PPIs), such as omeprazole, prevent proton movement. In previous studies, omeprazole induced cell death in Jurkat T lymphocytes; however, there was no confirmation of whether the cells died through apoptosis, or through necrosis, where the cell bursts. By using Annexin-V staining, the effects of omeprazole, dexlansoprazole, and esomeprazole on apoptosis induction can be measured. Cell death was observed …

From Deep Mutational Mapping Of Allosteric Protein Landscapes To Deep Learning Of Allostery And Hidden Allosteric Sites: Zooming In On “Allosteric Intersection” Of Biochemical And Big Data Approaches, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approaches have been developed and actively deployed to facilitate computational and experimental studies of protein dynamics and allosteric mechanisms. In this review, we discuss in detail new developments along two major directions of allosteric research through the lens of data-intensive biochemical approaches and AI-based computational methods. Despite considerable progress in applications of AI methods for protein structure and dynamics studies, the intersection between allosteric …

Assessment Of Histone Acetyltransferase Homologs In Cryptococcus Neoformans, Phoebe Bridy, Felice Kho, Yuqi Wang

Liberty University Research Week

Undergraduate

Basic

Study Of Protein Extraction Techniques For M. Foliorum Phages, Lola Sibaud, Anna Elgersma

Student Academic Conference

Characterizing phages is becoming increasingly important in biochemistry and biotechnology due to their potential to treat bacterial infections without need for antibiotics. Last year, students attempted to isolate proteins from Microbacterium foliorum infecting phages Babydotz and Rosadiaz. Proteins were successfully extracted; however, after further analysis it was shown that the obtained proteins belonged to the host bacteria and not the phages. The purpose of this study was to find a method to separate phage from host bacterial debris to successfully isolate phage proteins and analyze them later. Isolating phage proteins could help us characterize more phages and know more about …

Novel Plant Peroxidase Investigation For Use In Various Biochemical And Practical Applications, Sally Hess

Liberty University Research Week

Undergraduate

Basic

Activation Of Nrf2 Pathway By Natural Products, Genesis Schat, Madelyn Sedlachek

Liberty University Research Week

Undergraduate

Basic

Characterization Of Select Lysine Mutations Of The Cystine/Glutamate Transporter, System XC-, Anna Koppin, Claire Buck, Amanda Gibson

22nd Annual Celebration of Undergraduate Research and Creative Activity (2023)

System xc- is a membrane transport system that plays a critical role in mitigating oxidative stress. As such, its regulation is critical for proper brain functioning. Recent work in our lab has shown that System xc- activity increases immediately during an oxidative insult by undergoing a change in localization to the plasma membrane, but we have yet to identify the specific mechanism for the redistribution of the transporter. Previous studies have demonstrated that post-translational modifications of proteins can lead to differential protein distribution within cells. Therefore, in this study, we sought to determine if post-translational modification (PTM) of the transporter …

Does Phosphorylation On Serine 26 Of System Xc- Lead To Changes In Cell Surface Expression?, Katherine Lane

22nd Annual Celebration of Undergraduate Research and Creative Activity (2023)

System x_c^- is involved in transporting cystine into cells and glutamate out of cells, and ultimately in production of the antioxidant glutathione. Antioxidants are important in protecting cells from oxidative stress which can occur when waste products like H₂O₂ build up in the cell. Previous studies have shown that a critical regulator mTORC regulates system xc- by phosphorylating serine 26 (S26) on the N-terminus of the cystine/glutamate antiporter xCT, leading to a reduction in transport activity. The specific objective of this study is to determine the mechanism by which phosphorylation of S26 affects activity. To …

Creation Of An N-Terminal Xct Mutant Lacking Lysines For Use In Protein Turnover Studies, Alexandria Switzer

22nd Annual Celebration of Undergraduate Research and Creative Activity (2023)

xCT plays a role in protecting cells from oxidative stress as well as intracellular glutathione synthesis. If this process is impeded, reactive oxygen species accumulate in the cell, leading to cellular damage, and if left unchecked, it can lead to neuronal loss. Ubiquitin is a small protein that some evidence suggests can negatively affect the stress response pathway modulated by xCT, as well as induce cell death. It is hypothesized that ubiquitin binds to xCT on the N-terminal lysine residues, and there are six conserved lysines in the N-terminal domain at positions K4R, K12R, K30R, K37R, K41R, and K43R. Previous …

Early Life Δ9-Tetrahydrocannabinol Exposure Of F0 Zebrafish Causes Hyperactivity In F1 Offspring, Jenna Cripe

Honors Theses

As cannabis increases in its accessibility, potency, and acceptance across the United States, investigation into the multigenerational effects of Δ9-tetrahydrocannabinol (THC) exposure during key stages of development is critical. The aim of this study was to evaluate whether there would be behavioral impacts in the F1 offspring following a dose-response of THC exposure (0.08, 0.4, or 1 µM) during development in the F0 generation. Zebrafish (Danio rerio) were utilized in this study. Behaviors (locomotive activity and anxiety-like behavior) in the F1 generation were evaluated at 120 hours post-fertilization (hpf) with the larval photometer response (LPR) assay, and at 3, 11, …

A Fisher Indole Synthesis Approach To Phidianidine Analogues, Anna Tingler, Trinity Ghering, Samuel Ross

Undergraduate Research Competition

Naturally occurring products are molecules that are found in the natural world without the aid of humans. Aspirin and opium are famous examples of this classification of molecule. Another example of natural products that are less known are the phidianidines. Phidianidines A & B were isolated from a shell-less mollusk, Phidiana militaris. These molecules are comprised of a 1,2,4-oxadiazole ring, an indole and an aminoalkylguanadio group. These compounds have exhibited striking pharmacological behavior such as that of neutralizing reactive oxygen species and acting as an agonist for the μ-opioid receptor. In recent years, the synthesis of phidianidine analogues has replaced …

A New Approach To The Core Of Flinderole C, Ana Pettijohn, Claire Romain

Undergraduate Research Competition

The flinderoles A-C are a class of anti-malaria bisindole alkaloids from plants of the Flindersia genus. Flinderole C was specifically from the Papua New Guinean plant called F. amboinensis and is the most potent antimalarial of the group. Malaria is a parasitic infectious disease usually found in the hot, tropic regions of the world, such as parts of Africa. It is estimated that nearly half the world's population lives in an area where it is endemic. Furthermore, malaria was estimated to have caused over 600,000 deaths in 2020. While measures to limit the spread of the disease lessen its impact, …

Discovery And Characterization Of A Prophage Encoded Anti-Crispr Against The Type Iv-A Crispr System, Andrew Williams

Student Research Symposium

CRISPR Systems are adaptive immune systems in bacteria used to defend against mobile genetic elements such as bacteriophages, or bacterial viruses, and plasmids. They use a protein complexed with a guide RNA to target the protein to a foreign invader and neutralize it by cleaving its genetic information. In order to survive and keep infecting bacteria, bacteriophages likewise have developed machinery used to inhibit CRISPR immunity in the form of anti-CRISPR (Acr) proteins. The type IV-A system is a recently discovered and characterized system by the Jackson lab. It has been shown to defend against plasmids, but further data on …

Cycloaddition Of Aryldiazoacetates With Terminal Alkynes And Nitriles Via A Bioinspired Cobalt Complex, Liming Tan

Student Research Symposium

In this study, we present a novel method for the efficient cycloaddition of aryl diazoacetates with both terminal alkynes and nitriles, employing a bioinspired cobalt complex as a catalyst. Our findings indicate that terminal alkynes react with aryl diazoacetates to yield a cyclopropenation product through a 2+1 cycloaddition reaction. Meanwhile, nitriles react with aryl diazoacetates to produce an oxazole product via a 2+3 cycloaddition reaction. These results have significant implications for the development of new synthetic routes towards cyclopropenation and oxazole compounds.

Developing A Safe And Effective Papillomavirus Screen To Be Used On College Students, Nicole Frantz

Undergraduate Research Competition

Human papillomavirus (HPV) is the most common sexually transmitted infection that accounts for approximately 5% of all cancers worldwide and affects more than 80 million people in the US alone, according to the CDC and National Cancer Institute. Human papillomaviruses are small, nonenveloped, icosahedral DNA viruses that infect squamous epithelial cells. The viral particles consist of a single double stranded DNA molecule bound to histones and contained within a protein capsid composed of structural proteins late (L)1 and L2. To date, over 100 different genotypes of HPV have been identified, and approximately 15 types are considered oncogenic in cervical, vulvar, …

Environmental Bacteriophage Presence In The Drainage Ponds At Coastal Carolina University, Alexei Chesnutwood

Undergraduate Research Competition

The purpose of this research is to detect naturally occurring, lytic bacteriophages and identify the environmental factors that influence their presence on Coastal Carolina University’s campus. Bacteriophages are non-living viruses that only infect bacteria, and these viruses are found in abundance in every environment. Likewise, coliphages are viruses that exclusively infect coliform bacteria. Eleven treated and untreated freshwater sample sites were chosen for weekly sampling on CCU’s campus. During water sample collection, ambient environmental conditions were measured. In addition, precipitation was tracked over the collection period as runoff relates to the proliferation of bacteriophages. If plaque assays indicated the presence …

Analysis Of Attitudinal Student Learning Benefits From A Course-Based Undergraduate Research Experience (Cure) Adapted For Online Format, Ambika Kapil, Luis C. Gonzalez Isoba, Niraj Pathak, Arthur Sikora, Santanu De

FDLA Journal

Course-based Undergraduate Research Experiences (CUREs) are an increasingly utilized model for exposing students to research. The lack of robust assessments is a major hurdle to wider adoption of CUREs. The Coronavirus Infectious Disease 2019 (COVID-19) pandemic necessitated a drastic shift of in-person courses to the online format. Using the Participant Perception Indicator (PPI) survey, we measured students’ self-reported changes in learning from such a biochemistry course at a large university in south Florida based on the Biochemistry Authentic Scientific Inquiry Lab (BASIL) model. By doing this, we were able to better understand the student-benefits of CUREs and how these benefits …

The Application Of Microbial Source Tracking To Aid In Site Prioritization For Remediation In Lower Michigan, John J. Hart

Masters Theses

Non-point source fecal pollution is a threat to both the environment and public health. Climate change, aging infrastructure, and intensified agricultural practices are predicted to accentuate this issue. In Michigan, due to the high instance of aging infrastructure and intensified agriculture, non-point source fecal pollution has caused many waterbodies to exceed the state standards posing a risk to recreational activities and source water. Due to this threat, there is an increased effort to identify and remediate these sources. My study focused on improving the identification of non-point source fecal pollution through a combination of culture-based and molecular fecal indicator bacteria …

Characterizing Marr Homologs That Mediate Bacterial Fitness And Survival, George Chukwuemeka Nwokocha

LSU Doctoral Dissertations

Plant disease outbreaks are on the rise, threatening food security in many parts of the globe. To address these enormous challenges, new intervention strategies like bio-controls are being used as an important sustainable alternative to mitigate the negative effects of pathogens and increase the quality and productivity of agricultural crops. MarR family transcriptional regulators have been studied for their involvement in regulating bacterial virulence genes that help colonize plant hosts and therefore could serve as targets for biocontrol. The transcriptional regulator PecS, a member of the MarR family, is encoded by select bacterial pathogens and we show here that PecS …

Serving Justice Case By Case, Michael Becker

WRIT: Journal of First-Year Writing

Forensic Science is an integral part of serving justice in today's society, and majority of the world has little understanding of what forensics is. Read this article on forensic science and how it relates to writing in today's world.

Ins And Outs Of Rocker Switch Mechanism In Major Facilitator Superfamily Of Transporters, Stephanie Sauve, Joseph Williamson, Adithya Polasa, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

The major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles, known as the rocker-switch mechanism. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters of the MFS superfamily. We reviewed a variety of experimental and computational structural data on a select number of antiporters, symporters, and uniporters from the MFS family to compare the similarities and differences …

A Kinome-Wide Crispr Screen Identifies Ck1Α As A Target To Overcome Enzalutamide Resistance Of Prostate Cancer, Jinghui Liu, Yue Zhao, Daheng He, Katelyn M. Jones, Shan Tang, Derek B. Allison, Yanquan Zhang, Jing Chen, Qiongsi Zhang, Xinyi Wang, Chaohao Li, Chi Wang, Lang Li, Xiaoqi Liu

Markey Cancer Center Faculty Publications

Enzalutamide (ENZA), a second-generation androgen receptor antagonist, has significantly increased progression-free and overall survival of patients with metastatic prostate cancer (PCa). However, resistance remains a prominent obstacle in treatment. Utilizing a kinome-wide CRISPR-Cas9 knockout screen, we identified casein kinase 1a (CK1a) as a therapeutic target to overcome ENZA resistance. Depletion or pharmacologic inhibition of CK1a enhanced ENZA efficacy in ENZA-resistant cells and patient-derived xenografts. Mechanistically, CK1a phosphorylates the serine residue S1270 and modulates the protein abundance of ataxia telangiectasia mutated (ATM), a primary initiator of DNA double-strand break (DSB)-response signaling, which is compromised in ENZA-resistant cells and patients. Inhibition of …

Identification Of A Nacc1-Regulated Gene Signature Implicated In The Features Of Triple-Negative Breast Cancer, Chrispus Ngule, Hami Hemati, Xingcong Ren, Oluwafunminiyi Obaleye, Amos O. Akinyemi, Felix Oyelami, Xiaofang Xiong, Jianxun Song, Xia Liu, Jin-Ming Yang

Markey Cancer Center Faculty Publications

Triple-negative breast cancer (TNBC), characterized by a deficiency in estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor2 (HER2), is among the most lethal subtypes of breast cancer (BC). Nevertheless, the molecular determinants that contribute to its malignant phenotypes such as tumor heterogeneity and therapy resistance, remain elusive. In this study, we sought to identify the stemness-associated genes involved in TNBC progression. Using bioinformatics approaches, we found 55 up- and 9 downregulated genes in TNBC. Out of the 55 upregulated genes, a 5 gene-signature (CDK1, EZH2, CCNB1, CCNA2, and AURKA) involved in cell regeneration was positively correlated …