Biochemistry Commons^™

Lipocalin-2 Ameliorates The Signs And Outcomes Of Diabetes Mellitus In An Animal Model, Saeeda Mohammed Al Jaberi

Theses

Lipocalin-2 (LCN2) is a new adipocytokine consisting of 198 amino acids. It is also referred to as neutrophil gelatinase-associated lipocalin, siderocalin, uterocalin, α1-microglobulin related protein, or 24p3. LCN2 belongs to a large group of transport proteins that are capable of carrying small and lipid-soluble molecules in blood circulation. It has two membrane receptors, megalin/glycoprotein GP330, which binds human LCN2 and SLC22A17 or 24p3R, which forms complexes with mouse Lcn2 protein. LCN2 is encoded by a gene located at chromosome locus 9q34.11. LCN2 was initially isolated from neutrophil granules released at the site of infection and inflammation in humans and from …

High Performance Mixed-Matrix Electrospun Membranes For Ammonium Removal From Wastewaters, Shu-Ting Chen, Sumith Ranil Wickramasinghe, Xianghong Qian

Chemical Engineering Faculty Publications and Presentations

Mixed-matrix electrospun membranes were developed to investigate ammonium removal from low ammonium concentration wastewaters for the first time. Particles derived from the inexpensive zeolite 13X were successfully incorporated into polyethersulfone (PES) matrices. The fabricated mixed-matrix electrospun membranes demonstrate high ammonium removal capacity reaching over 55 mg/g_zeolite, more than 2.5 times higher than the previously fabricated mixed-matrix membranes via non-solvent induced phase inversion. Moreover, the membranes fabricated exhibit high permeability and ease of regeneration. Over 90% of total ammonium nitrogen (TAN) can be removed from low TAN wastewaters such as aquaculture wastewaters. In addition to zeolite 13X, other zeolite …

An In Vitro Model Of Tumor Heterogeneity Resolves Genetic, Epigenetic, And Stochastic Sources Of Cell State Variability, Corey A. Hayford, Darren R. Tyson, C. Jack Robbins Iii, Peter L. Frick, Vito Quaranta, Leonard Harris

Biomedical Engineering Faculty Publications and Presentations

Tumor heterogeneity is a primary cause of treatment failure and acquired resistance in cancer patients. Even in cancers driven by a single mutated oncogene, variability in response to targeted therapies is well known. The existence of additional genomic alterations among tumor cells can only partially explain this variability. As such, nongenetic factors are increasingly seen as critical contributors to tumor relapse and acquired resistance in cancer. Here, we show that both genetic and nongenetic factors contribute to targeted drug response variability in an experimental model of tumor heterogeneity. We observe significant variability to epidermal growth factor receptor (EGFR) inhibition among …

Reconstituting The Cyanobacterial Circadian Clock In Vitro, Pyong Hwa Kim

Dissertations

Cyanobacteria are photosynthetic organisms that are known to be responsible for oxygenating Earth’s early atmosphere. Having evolved to ensure optimal survival in the periodic light/dark cycle on this planet, their genetic codes are packed with various tools, including a sophisticated biological timekeeping system. Among the cyanobacteria is Synechococcus elongatus PCC 7942, the simplest clock-harboring organism with a powerful genetic tool that enabled the identification of its intricate timekeeping mechanism. The three central oscillator proteins—KaiA, KaiB, and KaiC—drive the 24 h cyclic gene expression rhythm of cyanobacteria, and the "ticking" of the oscillator can be reconstituted inside a test tube just …

Investigating The Mechanism Of The Escherichia Coli Atp-Binding Cassette (Abc) Transporter Metni, Matthew Foronda

Master's Theses

Chemical homeostasis is a baseline requirement for any cell to survive. ATP-binding cassette (ABC) transporters play a vital role in homeostasis by importing nutrients and exporting toxins against their concentration gradients by utilizing the energy of ATP hydrolysis. Malfunctioning ABC transporters cause a variety of health problems, including cystic fibrosis, Stargardt’s disease (vision loss), and the development of drug-resistant tumors. An important step in solving these medical issues is to first understand the structure and mechanism of ABC transporters. Various studies have made great strides in depicting the structure and details of different ABC transporters and their mechanisms, however, many …

Assessment Of The Quality And Quantity Of Organic Matter In The Rufiji Mangrove Surface Sediments Using Biochemical Composition, Daniel A Shilla

Tanzania Journal of Science

This study was carried out to investigate spatial changes in the quality and quantity of sedimentary organic matter in the Rufiji mangrove system, Tanzania. Sediment samples were collected from three sampling sites. Total organic matter in mangrove sediments ranged from 7.28 ± 2.02% to 10.58 ± 1.34%. Protein concentrations varied from 1,145.33 ± 20.33 μg/g to 2,747.50 ± 25.14 μg/g in the mangrove sediments. Total carbohydrates, lipids and biopolymeric carbon in mangrove sediments ranged between 1,110.50 ± 16.31 μg/g and 1,914.17 ± 27.79 μg/g, 1,436.50 ± 24.13 μg/g and 6,373.50 ± 25.79 μg/g, and 4,496 μg C/g and 10,231.50 μg …

Genetic Engineering Of Lesquerella With Increased Ricinoleic Acid Content In Seed Oil, Grace Q. Chen, Kumiko Johnson, Tara J. Nazarenus, Grisel Ponciano, Eva Morales, Edgar B. Cahoon

Department of Biochemistry: Faculty Publications

Seeds of castor (Ricinus communis) are enriched in oil with high levels of the industrially valuable fatty acid ricinoleic acid (18:1OH), but production of this plant is limited because of the cooccurrence of the ricin toxin in its seeds. Lesquerella (Physaria fendleri) is being developed as an alternative industrial oilseed because its seeds accumulate lesquerolic acid (20:1OH), an elongated form of 18:1OH in seed oil which lacks toxins. Synthesis of 20:1OH is through elongation of 18:1OH by a lesquerella elongase, PfKCS18. Oleic acid (18:1) is the substrate for 18:1OH synthesis, but it is also used by fatty acid desaturase 2 …

Diversity And Substrate-Specificity Of Green Algae And Other Micro-Eukaryotes Colonizing Amphibian Clutches In Germany, Revealed By Dna Metabarcoding, Sten Anslan, Maria Sachs, Lois Rancilhac, Henner Brinkmann, Jörn Petersen, Sven Künzel, Anja Schwarz, Hartmut Arndt, Ryan R. Kerney, Miguel Vences

Biology Faculty Publications

Amphibian clutches are colonized by diverse but poorly studied communities of micro-organisms. One of the most noted ones is the unicellular green alga, Oophila amblystomatis, but the occurrence and role of other micro-organisms in the capsular chamber surrounding amphibian clutches have remained largely unstudied. Here, we undertook a multi-marker DNA metabarcoding study to characterize the community of algae and other micro-eukaryotes associated with agile frog (Rana dalmatina) clutches. Samplings were performed at three small ponds in Germany, from four substrates: water, sediment, tree leaves from the bottom of the pond, and R. dalmatina clutches. Sampling substrate strongly …

Assessment Of Endogenous Biomass Decay As A Source Of Precursors For Microbially-Mediated Toluene And P-Cresol Production, Samuel J. Reynolds

LSU Master's Theses

The research reported in this thesis was conducted to investigate whether protein hydrolysis associated with endogenous decay of biomass produced following the addition of a readily fermentable substrate is a potential source of precursors that can ultimately be transformed to toluene and p-cresol in environments undergoing enhanced bioremediation.

A packed column intended to represent a laboratory-scale section of an aquifer was seeded with groundwater and then supplied with molasses-amended groundwater for a two-day interval. The injected molasses concentration and surface loading rate were selected to be representative of conditions in the vicinity of injection wells at a Superfund Site …

Heat Shock Proteins: Classification, Functions And Expressions In Plants During Environmental Stresses., Sara Khan, Raheela Jabeen, Farah Deeba, Ummara Waheed, Plosha Khanum, Nadia Iqbal

Journal of Bioresource Management

HSPs proteins are found mostly in every cell from prokaryotes to eukaryotes. HSPs have been comprehensively studied in animals and humans. Recently their role in plants was thoroughly studied. HSPs were described as a result of heat shock conditions, but now get activate by various stresses like Ultraviolet light, cold, wound healing, drought, salinity and pathogenic infections (Lindquist et al., 1988). The term “heat shock protein” is now incorrect because HSPs are not expressed only under high temperature, also expressed under other stresses. HSPs are essential in maintaining balanced cell internal conditions under optimum and damaged growth conditions about in …

Effect Of Diabetes Mellitus And Anti-Diabetic Drugs On Bone Health-A Review, Farah Deeba, Sidra Younis, Nida Qureshi, Tahmina Mustafa, Nadia Iqbal, Saira Hussain

Journal of Bioresource Management

Osteoporosis and diabetes mellitus (DM) are widespread diseases and have a significant health burden. Type-1 diabetes mellitus (T1DM) and Type-2 diabetes mellitus (T2DM) are associated with an increased bone fracture. In T1DM, the increased risk of bone fracture is associated with low bone mass. In patients with T2DM, the risk of fracture of the bone is increased due to low quality of bone, despite increased bone mineral density (BMD). In type 2 diabetic patients, bone fragility depends on the quality of bone instead of a reduction in bone mass. Thiazolidinediones (TZD) cause differentiation of adipocytes and inhibit differentiation of osteoblast …

Binding Affinity Of Flavins To The Dehydrogenase Domain Of Spnox, Quinesha Williams

Master of Science in Chemical Sciences Theses

NADPH oxidases (NOX’s) are enzymes that catalyze the production of superoxide through single electron transfer. This superoxide production leads to the production of other reactive oxygen species (ROS). ROS affect many metabolic processes throughout the body that can cause several different diseases, making this an ideal target for drug discovery. The general structure of NOX contains a transmembrane (TM) domain and a dehydrogenase (DH) domain connected by a linker. The DH domain contains binding sites for FAD and NADPH/NADH that both participate in the electron transfer necessary for producing superoxide. Structural information of NOX’s is still relatively new to the …

Salicylic Acid Response To Simulated Herbivory In Geographically Distinct T. Heterophylla And H. Discolor Populations, Amy E. Castle

Honors Projects

It is commonly known that plants may produce salicylic acid as a chemical defense response to wounding, although the phenomenon has usually been observed with regard to insect herbivory. Stem and leaf tissue of two species, Tsuga heterophylla and Holodiscus discolor, which are often eaten by deer, were extracted in methanol and analyzed by HPLC to quantify salicylic acid concentration in experimentally wounded or control samples. No salicylic acid response was detectable in T. heterophylla, suggesting it is a less useful candidate species for future study. Some but not all H. discolorsamples had a measurable salicylic acid …

Expression And Purification Of Proteins For A Structural Determination: Orf8, Paivy1, Paivy2, Sarah Fashinasi, Avery Moss

Symposium of Student Scholars

Protein purification is a crucial procedure in order to analyze the behavior, structure, and function of a select protein. The Orf8 protein is an increasingly mutable accessory protein found within the SARS-CoV2 virus, however the complex and unpredictable nature of this protein has been met by its inability to be purified thus far. By purifying the model proteins, PaIVY1 and PaIVY2, we believe that we can denote a sound purification method to apply to the Orf8 protein. In our procedure, we transformed BL21(DE3)pLysS cells and inoculated them in LB media. The cells were then placed into a centrifuge to isolate …

Investigating The Sars-Cov-2 Orf 8 Accessory Protein: Expression, Purification, And Structural Determination, Laney Hedgeman, Caroline Salha

Symposium of Student Scholars

Abstract

In order to provide insight into potential therapeutic breakthroughs for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more research must be done to understand the structure and function of its proteins. The open reading frame 8 (ORF 8) accessory protein is particularly unstable on its own outside of the viral envelope but can be stabilized when bound to the small ubiquitin-related modifier (SUMO) protein. The stable ORF 8-SUMO protein complex can be expressed and purified using familiar techniques and later characterized with nuclear magnetic resonance (NMR) spectroscopy, thus allowing us to gain knowledge about the role it plays …

Bioanalytical Determination Of Glucose Concentration In Sports Drinks Using Uv/Vis Spectroscopy, Laney Hedgeman, Brianna Bond

Symposium of Student Scholars

Abstract

The purpose of our project is to indirectly monitor the enzymatic activity of glucose oxidase as it reacts with the glucose present in sports drinks through the quantitative analysis of the generated ferricyanide. As glucose oxidase catalyzes the oxidation of beta-D-glucose in the presence of oxygen, D-glucono-1,5-lactone is produced along with hydrogen peroxide. The hydrogen peroxide is used in a subsequent reaction with ferrocyanide catalyzed by horse radish peroxidase to produce water and the chromophore ferricyanide. This compound absorbs in the ultraviolet/visible spectrum at 420 nm, which can be quickly measured using Ultraviolet/Visible Spectroscopy. Since the molar ratio of …

Host–Guest Interactions In A Metal–Organic Framework Isoreticular Series For Molecular Photocatalytic Co2 Reduction, Philip M. Stanley, Johanna Haimerl, Christopher Thomas, Alexander Urstoeger, Michael Schuster Prof. Dr., Natalia B. Shustova Prof. Dr., Angela Casini Prof. Dr., Bernhard Rieger Prof. Dr., Julien Warnan Dr., Roland A. Fischer Prof. Dr.

Faculty Publications

A strategy to improve homogeneous molecular catalyst stability, efficiency, and selectivity is the immobilization on supporting surfaces or within host matrices. Herein, we examine the co-immobilization of a CO2 reduction catalyst [ReBr(CO)3(4,4′-dcbpy)] and a photosensitizer [Ru(bpy)2(5,5′-dcbpy)]Cl2 using the isoreticular series of metal–organic frameworks (MOFs) UiO-66, -67, and -68. Specific host pore size choice enables distinct catalyst and photosensitizer spatial location—either at the outer MOF particle surface or inside the MOF cavities—affecting catalyst stability, electronic communication between reaction center and photosensitizer, and consequently the apparent catalytic rates. These results allow for a rational understanding of an optimized supramolecular layout of catalyst, …

Multi-Strategy Engineering Greatly Enhances Provitamin A Carotenoid Accumulation And Stability In Arabidopsis Seeds, Tianhu Sun, Qinlong Zhu, Ziqing Wei, Lauren A. Owens, Tara Fish, Hyojin Kim, Theodore W. Thannhauser, Edgar B. Cahoon, Li Li

Department of Biochemistry: Faculty Publications

Staple grains with low levels of provitamin A carotenoids contribute to the global prevalence of vitamin A deficiency and therefore are the main targets for provitamin A biofortification. However, carotenoid stability during both seed maturation and postharvest storage is a serious concern for the full benefits of carotenoid biofortified grains. In this study, we utilized Arabidopsis as a model to establish carotenoid biofortification strategies in seeds. We discovered that manipulation of carotenoid biosynthetic activity by seed-specific expression of Phytoene synthase (PSY) increases both provitamin A and total carotenoid levels but the increased carotenoids are prone to degradation during …

Determining The Role Of Methylglyoxal (Mgo) And The Trpa1 Channel In Inducing Astrocyte Senescence And Neurodegeneration, Natalie Hill

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Aging is the largest risk factor for the development of Alzheimer’s disease (AD) and related dementias. A recently proposed driver of age-related pathologies is cellular senescence, a phenotype that consists of cell-cycle arrest and an inflammatory response known as the senescence-associated secretory phenotype (SASP). Although there is a link between the accumulation of senescent cells and neurodegeneration, much remains unknown about how senescent cells arise in the brain. Astrocytes are the most abundant cell type in the brain that serve important roles like supporting neurons and proliferating in response to stress. Methylglyoxal (MGO) is a glycolytic byproduct that can react …

In Vivo Tissue-Specific Chromatin Profiling In Drosophila Melanogaster Using Gfp-Tagged Nuclei, Juan Jauregui-Lozano, Kimaya Bakhle, Vikki M. Weake

Department of Biochemistry Faculty Publications

The chromatin landscape defines cellular identity in multicellular organisms with unique patterns of DNA accessibility and histone marks decorating the genome of each cell type. Thus, profiling the chromatin state of different cell types in an intact organism under disease or physiological conditions can provide insight into how chromatin regulates cell homeostasis in vivo. To overcome the many challenges associated with characterizing chromatin state in specific cell types, we developed an improved approach to isolate Drosophila melanogaster nuclei tagged with a GFPKASH protein. The perinuclear space-localized KASH domain anchors GFP to the outer nuclear membrane, and expression of UAS-GFPKASH can …

Design, Synthesis, And Evaluation Of Carbapenem And Cephalosporin Antibiotics To Counter Resistant 21st Century Pathogens, Maha Alqurafi

Chemistry Theses and Dissertations

Antibiotics represent one of mankind’s most important discoveries, enabling longer, more productive lives. Carbapenem antibiotics are one of the most potent classes of β-lactams and often represent the last resort used to treat patients who are seriously stricken by bacterial infections. Carbapenems possess a broad spectrum of antibacterial activity including efficacy against the majority of Gram-positive and Gram–negative bacteria. Unfortunately, the emergence of antibiotic resistant strains is posing a serious threat to existing antibiotics. New discoveries in the antibiotic field are desperately needed to counter the threat of rapidly evolving bacterial resistance. Despite the investment of billions of dollars, and …

Regulation Of Dna Replication Licensing And Re-Replication By Cdt1, Hui Zhang

Chemistry and Biochemistry Faculty Research

In eukaryotic cells, DNA replication licensing is precisely regulated to ensure that the initiation of genomic DNA replication in S phase occurs once and only once for each mitotic cell division. A key regulatory mechanism by which DNA re-replication is suppressed is the S phase-dependent proteolysis of Cdt1, an essential replication protein for licensing DNA replication origins by loading the Mcm2-7 replication helicase for DNA duplication in S phase. Cdt1 degradation is mediated by CRL4 ubiquitin E3 ligase, which further requires Cdt1 binding to proliferating cell nuclear antigen (PCNA) through a PIP box domain in Cdt1 during DNA synthesis. Recent …

Steady-State Transmembrane Water Exchange In Proliferating Cultures Of Saccharomyces Cerevisiae, Joseph O'Malley Armstrong

Dissertations and Theses

Cellular water exchange is often considered in terms of a change in volume, where a net flux of water moves across the cell membrane due to a change in osmotic pressure. Osmotic pressure can cause a cell to shrink or swell, however, rapid water exchange persists across the membrane even when the volume of the cell is constant. Steady-state transmembrane water exchange describes the exchange of water across the cell membranes which results in no net change in cell volume. This exchange is astonishingly rapid; the entire pool of intracellular water of a Saccharomyces cerevisiae cell may exchange 2-5 times …

Beyond Structural Motifs: The Frontier Of Actinide-Containing Metal–Organic Frameworks, Corey R. Martin, Gabrielle A. Leith, Natalia B. Shustova Prof. Dr.

Faculty Publications

In this perspective, we feature recent advances in the field of actinide-containing metal–organic frameworks (An-MOFs) with a main focus on their electronic, catalytic, photophysical, and sorption properties. This discussion deviates from a strictly crystallographic analysis of An-MOFs, reported in several reviews, or synthesis of novel structural motifs, and instead delves into the remarkable potential of An-MOFs for evolving the nuclear waste administration sector. Currently, the An-MOF field is dominated by thorium- and uranium-containing structures, with only a few reports on transuranic frameworks. However, some of the reported properties in the field of An-MOFs foreshadow potential implementation of these materials and …

Beyond Structural Motifs: The Frontier Of Actinide-Containing Metal–Organic Frameworks, Corey R. Martin, Gabrielle A. Leith, Natalia B. Shustova

Faculty Publications

In this perspective, we feature recent advances in the field of actinide-containing metal-organic frameworks (An-MOFs) with a main focus on their electronic, catalytic, photophysical, and sorption properties. This discussion deviates from a strictly crystallographic analysis of An-MOFs, reported in several reviews, or synthesis of novel structural motifs, and instead delves into the remarkable potential of An-MOFs for evolving the nuclear waste administration sector. Currently, the An-MOF field is dominated by thorium- and uranium-containing structures, with only a few reports on transuranic frameworks. However, some of the reported properties in the field of An-MOFs foreshadow potential implementation of these materials and …

Reeling In New Antibiotics: Synthesis And Antimicrobial Susceptibility Testing Of Zinc-Binding Clavanins From Styela Clava (Sea Squirt), Eduardo Badillo-Colberg

Honors Scholar Theses

Clavanins have been a quite rarely studied antimicrobial peptide (AMP) family. Though the data in the few studies published on the matter and in theoretical experimental data presented by the Wang lab in their peptide library creation [14], in that the members of this family could potentially be quite effective novel antimicrobial candidates. Among those that have been targets of studies, Clavanin A has been at the forefront of this endeavor of finding effective novel antimicrobial peptides[14]. In these aforementioned studies, Clavanin A has been shown to be quite effective against many different bacterial strains, which begs the question as …

Probing Interactions Between Canonical Nox Domains, Akua Acheampong

Master of Science in Integrative Biology Theses

NAPDH oxidase enzymes (NOXes) reduce molecular oxygen to superoxide and other ROS. NOXes contain a catalytic core comprising a heme-containing transmembrane (TM) domain and a cytoplasmic dehydrogenase (DH) domain that binds the substrate NADPH and the cofactor. Previously, NOXes were only characterized in eukaryotes, but have recently been identified in prokaryotes, namely bacteria. Due to their constitutive activity and solubility in detergent, bacterial NOXes, such as Streptococcus Pneumoniae NOX, have emerged as a model for studying NOXes. Past research studies in NOXes have identified conserved, putative interacting regions at the interface of the TM and DH domains: the TM B-loop, …

Designing A Reactive Warhead To Bind And Inhibit Pseudomonas Aeruginosa’S Periplasmic Protein, Inhibitor Of Vertebrate Lysozyme, Leah Greinke

Master of Science in Chemical Sciences Theses

Pseudomonas aeruginosa is a Gram-negative bacterium commonly found throughout the environment. It is a significant cause of disease and mortality in immunodeficient patients such as those suffering from cystic fibrosis (CF). Due to the emerging antibiotic resistance of P. aeruginosa, it is becoming increasingly more challenging to treat an infection by traditional means. Further complicating treatment, P. aeruginosa secretes a protein known as Inhibitor of Vertebrate Lysozyme (PaIVY) that binds to and inhibits C-type lysozyme, thus preventing the degradation of the bacterium. A reactive chemical warhead was synthesized from a rhenium(I) tricarbonyl derivative inorder to bind to and irreversibly …

Changes In Fecal Glucocorticoid Levels And Possible Microbiome Profile Changes During Positive Enrichment In A Captive Population Of Tigers (Panthera Tigris), Sylvia R. Ramsey

Undergraduate Theses

Cortisol is a hormone that is released in response to stress. Cortisol can be damaging in high amounts and it is ideal to maintain at a low level. Captive animals can experience high baseline levels of cortisol during their captivity, verses their non-captive counterparts, (Terio, Marker, & Munson, 2004). Enrichment, a stimulus that encourages an animal to perform natural behavior, is offered to captive animals to allow the animal to exhibit natural behaviors and hopefully lower stress levels. This experiment analyzes if exposure to a positive enrichment significantly impacts an animal’s fecal cortisol levels. Fecal cortisol levels are indicative of …

Secreted Mucin 5ac-Mediated Epithelial And Stromal Modulations Augment Pancreatic Cancer Aggressiveness, Koelina Ganguly

Theses & Dissertations

The mucosal layer that shields the epithelium of the body cavities is made up of high molecular weight, heavily glycosylated proteins called mucins that are broadly categorized into transmembrane and secreted members. Aberrant expression of secreted mucin MUC5AC has been implicated in lung, stomach, and colon cancer pathologies. MUC5AC is expressed de novo in the pancreas upon oncogenic insult, and its abundance in pancreatic tumor and circulation correlates to disease progression. However, few studies have explored beyond the diagnostic and prognostic significance of MUC5AC in pancreatic cancer (PC).

In this dissertation, we sought to investigate the mechanistic contribution of MUC5AC …