Biochemistry, Biophysics, and Structural Biology Commons^™

Modulation Of Biological Responses To 2 Ns Electrical Stimuli By Field Reversal, Esin B. Sözer, P. Thomas Vernier

Bioelectrics Publications

Nanosecond bipolar pulse cancellation, a recently discovered Phenomenon, is modulation of the effects of a unipolar electric pulse exposure by a second pulse of opposite polarity. This attenuation of biological response by reversal of the electric field direction has been reported with pulse durations from 60 ns to 900 ns for a wide range of endpoints, and it is not observed with conventional electroporation pulses of much longer duration (> 100 mu s) where pulses are additive regardless of polarity. The most plausible proposed mechanisms involve the field-driven migration of ions to and from the membrane interface (accelerated membrane discharge). …

Regulation Of Cyp3a5 In Pancreatic Ductal Adenocarcinoma, Jessica D. Hoyer

Theses and Dissertations (ETD)

CYP3A5 is a drug metabolism enzyme that is polymorphically expressed in normal tissues and expressed in high amounts in some cancers, including pancreatic ductal adenocarcinoma (PDAC). There have been several published studies regarding CYP3A5 regulators, but there is still much to be discovered concerning CYP3A5 regulation in cancer. To further understand the regulation of CYP3A5, a high-throughput screen was performed in the AsPC-1 PDAC cell line. This screen employed small interfering RNA (siRNA) targeting transcription factors and chromatin-associated proteins. We identified siRNA that decreased CYP3A5 mRNA and protein levels in AsPC-1 cells and probed into the potential mechanisms. Taken together, …

Genetic Variation Of Human Leukocyte Antigen (Hla) Alleles Among Rheumatiod Arthritis Patients In Fujairah, Amna Abdulla Harib Al-Dhmanie

Biology Theses

Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammation that affects the joints. It occurs when the immune system attacks the body's own tissues and organs. The precise cause of RA is not fully understood but evidence suggests that genes, hormones and environmental factors could be involved. It has been established that human leukocyte antigen (HLA) loci is a strong risk factor of RA. Specifically, the shared epitope (SE) region of HLA-DRB1 and variations at position 11 and 13 of HLA-DRB1 and position 77 of HLA-A have shown strong association with RA. The hypothesis of this study was …

Study Of Paper Microbial Fuel Cells For Use In On-Site Wastewater Testing, William A. Tolmasoff

Master's Theses

This study demonstrated a technique for fabricating simple, low-cost Paper Microbial fuel cells (PMFC’s) in the model of a previous study to, for the first time, produce voltage from wastewater effluent. The PMFC’s were created by stacking and gluing the main components of an MFC together: reservoir layer; anode; cation exchange membrane (CEM); air cathode. A wax printer was used to create the hydrophobic borders of the PMFC’s on filter paper, and graphite paint was applied to the paper to create the anode. The CEM’s considered were filter paper, wax, and Nafion, with Nafion being the most efficient. Finally, the …

The Statistical Optimisation Of Recombinant Β-Glucosidase Production Through A Two-Stage, Multi-Model, Design Of Experiments Approach, Albert Uhoraningoga, Gemma K. Kinsella, Jesus Maria Frias, Gary T. Henehan, Barry J. Ryan

Articles

β-glucosidases are a class of enzyme that are widely distributed in the living world, with examples noted in plants, fungi, animals and bacteria. They offer both hydrolysis and synthesis capacity for a wide range of biotechnological processes. However, the availability of native, or the production of recombinant β-glucosidases, is currently a bottleneck in the widespread industrial application of this enzyme. In this present work, the production of recombinant β-glucosidase from Streptomyces griseus was optimised using a Design of Experiments strategy, comprising a two-stage, multi-model design. Three screening models were comparatively employed: Fractional Factorial, Plackett-Burman and Definitive Screening Design. Four variables …

Electrochemically Reactive Membranes For Efficient Biomass Recovery, Pollutant Degradation And Commercialization, Likun Hua

Dissertations

Micropollution in natural waters such as rivers and groundwater aquifers is a widespread problem that prevents these potentially potable sources from being used as drinking water. In the United States, approximately two-thirds of the over 1,200 most serious hazardous waste sites in the nation are contaminated with trichloroethylene (TCE), a potentially carcinogenic compound. Other emerging and environmentally persistent organic micropollutants include polyromantic hydrocarbons (PAHs), organophosphate flame retardants, endocrine disrupting compounds (EDCs), pesticides, herbicides, pharmaceuticals and personal care products (PPCPs). Membrane filtration is one of the most efficient separation processes widely used for water treatment and pollutant removal. However, traditional membrane …

Genistein Has Antiviral Activity Against Herpes B Virus And Acts Synergistically With Antiviral Treatments To Reduce Effective Dose, Julia C. Lecher, Nga Diep, Peter W. Krug, Julia K. Hilliard

Faculty Articles

Herpes B virus is a deadly zoonotic agent that can be transmitted to humans from the macaque monkey, an animal widely used in biomedical research. Currently, there is no cure for human B virus infection and treatments require a life-long daily regimen of antivirals, namely acyclovir and ganciclovir. Long-term antiviral treatments have been associated with significant debilitating side effects, thus, there is an ongoing search for alternative efficacious antiviral treatment. In this study, the antiviral activity of genistein was quantified against B virus in a primary cell culture model system. Genistein prevented plaque formation of B virus and reduced virus …

Recombinant Production Of Catfish Interleukin-22 As A Natural Immune Stimulant For Improving Aquaculture Fish Health, Lana Elkins

Student Theses and Dissertations

As the world population increases and wild caught fisheries decline, aquaculture offers an important sustainable solution addressing this global challenge. In fact, aquaculture now provides more than half the world’s food fish. With this rapid rise in production, has come the problem of disease management. Current options are limited and there is a great need for innovative solutions to this problem. The cytokine interleukin-22 (IL-22) has emerged as a therapeutic target for fish and is correlated with protection under pathogen challenge. Plant bioproduction has the potential to effectively manufacture recombinant IL-22 and offer advantages of low cost for commodity markets, …

Examining Lateral Line Development Through Cxcl14 Modulation Of Cxcl12-Cxcr4 Mediated Gene Expression In Danio Rerio, Ariana Calderon-Zavala

Lawrence University Honors Projects

The lateral line is a mechanosensory system used by fish to sense the movement of water. It is evolutionarily related to the inner-ear in humans. For both organisms, the binding of the CXCL12 (SDF-1 ligand) to the CXCR4 receptor induces conformational changes needed to activate signal transduction. This signaling results in numerous cellular responses such as cell fate, chemotaxis, and gene transcription. Interestingly, researchers have found that another signaling molecule, CXCL14, can also bind to the CXCR4 receptor with high affinity (Tanegashima et al., 2013). As a result, we hypothesize that CXCL14 modulates CXCL12-mediated chemotaxis, presumably acting as an allosteric …

Nf-Κb In Biomphalaria Glabrata: A Genetic Fluke?, Paige Stocker

Lawrence University Honors Projects

Biomphalaria glabrata is the intermediate host to the disease causing parasitic worm, Schistosoma mansoni. Previous work has identified homologs of NF-κB, a known immune related transcription factor, in B. glabrata and work has also been done to establish putative κB sites. It has also been observed that the p65 homologous subunit has an extended N-terminal region not present in other homologs. The goal of the present study is twofold: investigate DNA binding affinity of two NF-κB subunits, Bg-p65 and Bg-p50, and characterize the nature of the N-terminal extension of Bg-p65. In the current work, it is shown through the …

Acid Sphingomyelinase Regulates The Localization And Trafficking Of Palmitoylated Proteins, Xiahui Xiong, Chia-Fang Lee, Wenjing Li, Jiekai Yu, Linyu Zhu, Yongsoon Kim, Hul Zhang, Hong Sun

Chemistry and Biochemistry Faculty Research

In human, loss of acid sphingomyelinase (ASM/SMPD1) causes Niemann–Pick disease, type A. ASM hydrolyzes sphingomyelins to produce ceramides but protein targets of ASM remain largely unclear. Our mass spectrometry-based proteomic analyses have identified >100 proteins associated with the ASM-dependent, detergent-resistant membrane microdomains (lipid rafts), with >60% of these proteins being palmitoylated, including SNAP23, Src-family kinases Yes and Lyn, and Ras and Rab family small GTPases. Inactivation of ASM abolished the presence of these proteins in the plasma membrane, with many of them trapped in the Golgi. While palmitoylation inhibitors and palmitoylation mutants phenocopied the effects of ASM inactivation, we demonstrated …

Understanding How Map Kinases Influence Endothelial Nitric-Oxide Synthase Activity, Xzaviar Solone

Master of Science in Integrative Biology Theses

Mitogen activated protein kinases (MAPK) p38 and ERK have both been reported to bind endothelial nitric oxide synthase (eNOS) with submicromolar affinity via proposed interactions with a pentabasic non-canonical MAPK binding sequence in the autoinhibitory insertion of eNOS. The neuronal isoform, which lacks the pentabasic motif, did not bind either MAPK significantly. In the present study, the pentabasic motif was validated using predictive modeling programming, and eNOS phosphorylation by MAPKs (P38, ERK and JNK) was examined using in vitro kinase assays and immunoblotting. JNK phosphorylation at Ser¹¹⁴ contrasts with ERK, which phosphorylated Ser⁶⁰⁰, and p38, which phosphorylated …

Expanding The Toolbox With Site-Specific Methods Of Bioconjugation, Tiauna S. Howard

Seton Hall University Dissertations and Theses (ETDs)

Bioconjugation is an important tool for studying complex biological systems, with site-specificity being the major challenge. Reactions based on amino acid derived organocatalysts have been widely used in organic synthesis, particularly for the asymmetric synthesis of small molecules but this concept has not been vastly explored on biomolecules. To combat these limitations, two chemical strategies are developed to effectively attach synthetic molecules site specifically to proteins. First, a protein modification technique based on conjugation at a non-native functional handle, an aldehyde or ketone, is developed. This functional handle is chemically introduced onto the biomolecules before undergoing the organocatalyzed aldol reaction, …

Applications Of Sirna For Cancer Gene Therapy, Christopher Nicholas Cultrara

Seton Hall University Dissertations and Theses (ETDs)

Gene therapy is a potent and versatile nano-medicine strategy in the treatment of cancer. Of the many tools currently used in this application, short-interfering RNA (siRNA) are among the most commonly employed due to their ability to silence oncogenic mRNA with high precision through the RNA interference (RNAi) pathway potentially leading to cancer cell death. Our work revolves around silencing the Glucose-Regulated Proteins (GRPs) whose expressions are upregulated in cancerous tissues and are implicated in the proliferative, pro-survival, and anti-apoptotic pathways that govern tumor biology. Here we present a variety of applications to improve the potency and functionality of GRP-targeting …

Analysis Of Septum Defects In Arabidopsis Organ Boundary Mutants, Katherine T. Anderson

Honors Theses

Arabidopsis thaliana, a model plant species, has been heavily studied to determine the genetic contributions that lead to gynoecium development. The Arabidopsis fruit is created from two carpels that form a gynoecium, which contains the stigma, style, and ovary. The ovary is divided into two sub-compartments by a septum, and the ovules develop within the ovary. The fruit’s purpose is to protect, nurture, and eventually disperse the mature ovules, or seeds, and if the septum does not fuse properly, the plant’s fertility will be impacted. SHOOT MERISTEMLESS (STM) and ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1) are two genes that are known …

Molecular Signatures Of Calpain 10 Isoforms Sequences, Envisage Functional Similarity And Therapeutic Potential, Bushra Chaudhry, Farina Hanif, Kausar Saboohi

Department of Biological & Biomedical Sciences

Calpain 10 plays a role in insulin secretion, action and susceptibility to type 2 diabetes. The mechanism through which it influences the insulin secretion and action is not completely defined. A structural bioinformatics approach is applied to envision its mechanism of action using available tools on NCBI (blastp and blastn), EMBL-EBI, Ensembl, Swiss Model Repository websites, I-TASSER, PROCHECK program and Discovery Studio software. Homology of domain I and II of calpain10 (isoform a) was established with super family cysteine proteinase domains (II a and II b, e=1.30e-77, 1.00e-20). Remaining sequences of domain III and T from (isoform a and c) …

Microrna Profiling And Engineering Of Cho Cell Lines Stably Expressing Difficult-To-Express Lysosomal Protein, Ifeanyi Amadi

KGI Theses and Dissertations

Difficult-to-express (DTE) recombinant proteins like multi-specific proteins, DTE monoclonal antibodies and lysosomal enzymes, have seen difficulties in manufacturability using Chinese hamster ovary (CHO) cells and other mammalian cells as production platforms. CHO cells are preferably used for protein production because of their innate ability to secrete human-like recombinant proteins with post-translational modification, resistance to viral infection and familiarity with drug regulators. However, despite huge progress made in engineering CHO cells for high volumetric productivity, expression of DTE proteins like recombinant lysosomal sulfatase represent one of the poorly understood proteins. Furthermore, there are growing interest in the use of microRNAs (miRNAs) …

Targeted Genome-Scale Gene Activation And Gene Editing In Human Cells To Understand Disease Models, Michael De La Cruz

KGI Theses and Dissertations

Since the discovery of sequence directed DNA editing reagents such as CRISPR-Cas9 RNA-guided and TALEN DNA endonucleases, there has been a snowball of advances in the life sciences due to the ability to efficiently edit and control genomes within living cells. CRISPR-Cas9 based genomic tools, which facilitate the high-throughput precise manipulation of genes, allow for unbiased functional genomic screens. We used a human CRISPR-Cas9 Synergistic Activation Mediator pooled library which utilizes an engineered protein complex for transcriptional activation of 23,430 endogenous genes to investigate the development of novel resistance mechanisms to lung cancer targeted therapy, Erlotinib. We set out to …

Molecular Characterization Of The Putative Nucleotide- Binding And Hydrolyzing Activities Of The Ellis Van Creveld (Evc) Protein, Giang Nguyen

Electronic Theses and Dissertations

Ellis–van Creveld (EvC) syndrome is a rare autosomal recessive disorder that is characterized by short-limb dwarfism, extra fingers or toes, malformed teeth and nails, and congenital heart defects. Mutations in two genes, EVC and EVC2, which are located on chromosome 4, have been shown to be responsible for EvC syndrome. The protein products of these genes, EVC and EVC2 physically interact and together, they are tethered to the base of the primary cilium of cells. This multi-protein assembly positively regulates the Sonic and Indian hedgehog signaling pathways by promoting downstream processes after activation of the smoothened receptor (Smo), by the …

Generation Of Full-Length Wild-Type Gata4 Protein And Characterization Of Its Binding To Unc-45 Domains, Morgan Anderson

Electronic Theses and Dissertations

Striated muscle UNC-45 (SM UNC-45) protein acts as a chaperone for cardiac and skeletal muscle myosins; regulating their folding, assembly into thick filaments, interaction with other sarcomeric proteins, and degradation. GATA4 is an important transcription factor that regulates the expression of several cardiac muscle proteins, including myosin. A previous study demonstrated for the first time that SM UNC-45 (also known as UNC-45B) physically interacted with GATA4. The major revelation from this study is that SM UNC-45 has the potential to exert both short-term (protein level) and long-term (gene level) controls over myosin and therefore muscle structure and function. The aim …

Synthesis, Stabilization, And Modification Of Zinc Oxide Nanoparticles For Biological Applications, Allison Kimberly Freese

Graduate Theses/Dissertations

Nanoparticles have become very useful as delivery systems in biomedicine. The nanoparticles can be layered with different compounds to produce a vessel for transport of biological materials. Specifically, gold nanoparticles layered with a reducing agent, lysozyme, and polyelectrolytes can be synthesized to transport lysozyme into a cell. However, zinc oxide nanoparticles are cheaper, biocompatible nanoparticles that can be used for the same process. Here in, zinc oxide nanoparticle conjugates were synthesized, modified, and analyzed to be used as a biological material delivery system. The zinc oxide nanoparticles were synthesized using zinc chloride and sodium hydroxide. The particles were then layered …

Kinetics Of Hiv-1 Uncoating In C20 Microglial Cells, Melanie Anne Taylor

Graduate Theses/Dissertations

Uncoating is a poorly understood yet required step of HIV-1 replication that is defined as the disassembly of the viral capsid structure. The goal of this project is to characterize uncoating in C20 microglial cells. These cells are a natural target of HIV-1 that are infected to establish latent viral reservoirs and HIV-associated neurological disorders. A stable C20 cell line that expresses TRIM-CypA was established to study the kinetics of uncoating with the CsA washout assay. The expression of TRIM-CypA was confirmed by western blot and the functionality of the protein was confirmed by a viral infectivity assay. Using this …

Further Characterization Of The Skeletal Phenotype In A Hurler Syndrome Mouse Model And The Ethical Treatment Of Children In Medicine, Anna Marie Mcwoods

Graduate Theses/Dissertations

Mucopolysaccharidosis type I (MPS I) is a rare, autosomal recessive disorder caused by the deficiency of the lysosomal enzyme α-L-iduronidase (IDUA). Absence of IDUA results in the accumulation of dermatan and heparin sulfate and ultimately causes multi-system dysfunction. The most severe form of MPS I is Hurlers syndrome, a rapidly progressive disorder that, if left untreated, is fatal. Current treatment options for diagnosed individuals includes hematopoietic stem cell transplantation (HSCT) and enzyme replacement therapy (ERT). These treatments are able to ameliorate the majority of symptoms with the exception of the bone phenotype. This investigation aimed to further characterize the bone …

Stochastic Modeling Of Neuronal Transport In Various Cellular Geometries, Abhishek Choudhary Mr., Peter Kramer

Biology and Medicine Through Mathematics Conference

No abstract provided.

Role Of The Drosophila Beaf Protein In Chromatin Domain Insulator And Promoter Function, Mukesh Maharjan

LSU Doctoral Dissertations

Proper folding of eukaryotic genomes is required to allow correct interactions between different parts of chromosomes. Precise and timely interactions among different parts of a chromosome allow proper functioning inside a nucleus, including gene regulation, DNA replication and DNA repair. Eukaryotic regulatory elements that facilitate folding and interactions include enhancers, promoters and insulator elements. Insulator elements and their binding proteins play an important role in regulating correct chromatin structure and function. The Drosophila melanogaster special chromatin structure (scs’) is one such insulator. The Boundary Element Associated Factor (BEAF) binds to scs’. BEAF is a 32 kDa protein that has two …

Role Of The Glycerophosphocholine Acyltransferase, Gpc1, In Phosphatidylcholine (Pc) Biosynthesis And Remodeling In Saccharomyces Cerevisiae, Sanket Anaokar

Electronic Theses and Dissertations

Biomembranes are permeable barriers that enclose the cell and the intracellular organelles in a cell. The selective nature of these robust barriers acts as the first line of defense towards the harsh factors that can compromise cell survival. Biomembranes primarily consist of membrane lipids that are organized into layers to form a dynamic bilayer structure. The dynamic nature of the membrane requires the synchronized modulation of lipid composition through de novo synthesis, degradation, intracellular movement, and remodeling. Phospholipids are the major membrane lipid class, and phosphatidylcholine (PC) is the most abundant phospholipid in most eukaryotic biomembranes.

PC is primarily produced …

Characterization Of Bacterial Isolates Obtained From Commercial Poultry Feed And Retail Food Using Whole Genome Sequence Analysis And Selected Biochemical Tests, Elena George Olson

Electronic Theses & Dissertations

The goals of this study is two-fold. The first part investigates bacterial isolates from commercial poultry feed and the second part deals with bacterial isolates recovered from retail food. In order to reduce pathogen contamination in poultry products identification of overall microbial populations in poultry production processing steps have always been considered an important monitoring tool for assessing sanitizer effectiveness and the corresponding responses of bacteria load levels on poultry carcasses. Bacterial isolates recovered from corn-based chicken feed were purified on aerobic plate count agar and eleven morphologically different colonies were selected for whole genome sequencing. In this part, the …

The Effect Of Simulated Storm Passage On The Behavior Of Whitespotted Bamboo Sharks, Chiloscyllium Plagiosum And Golden Shiners, Notemigonus Chrysoleucas, Jordan A. Healy

Honors Theses

Environmental changes during a storm can affect animal behavior; for example, tagged sharks leave shallow waters during tropical storms. While changes in shark behavior during storm passage have been documented, there have been no experimental tests to determine which environmental parameters are responsible. In this study, we experimentally manipulated two environmental cues: barometric pressure, and thunder sounds, to determine their effect on whitespotted bamboo sharks, Chiloscyllium plagiosum, and golden shiners, Notemigonus crysoleucas. Elasmobranchs do not have a swim bladder to detect pressure change; therefore, we used golden shiners to compare the reaction of a fish with a swim bladder. The …

On The Ability Of Pnicogen Atoms To Engage In Both Σ And Π-Hole Complexes. Heterodimers Of Zf2C6H5 (Z = P, As, Sb, Bi) And Nh3, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When bound to a pair of F atoms and a phenyl ring, a pyramidal pnicogen (Z) atom can form a pnicogen bond wherein an NH₃ base lies opposite one F atom. In addition to this σ-hole complex, the ZF₂C₆H₅ molecule can distort in such a way that the NH₃ approaches on the opposite side to the lone pair on Z, where there is a so-called π-hole. The interaction energies of these π-hole dimers are roughly 30 kcal/mol, much larger than the equivalent quantities for the σ-hole complexes, which are only 4–13 kcal/mol. On …

Probing The Formation Of Reactive Oxygen Species By A Porous Self- Assembled Benzophenone Bis-Urea Host, Baillie A. Dehaven, Hannah K. Liberatore, Alexander Greer, Susan D. Richardson, Linda S. Shimizu

Publications and Research

Herein, we examine the photochemical formation of reactive oxygen species (ROS) by a porous benzophenone-containing bis-urea host (1) to investigate the mechanism of photooxidations that occur within the confines of its nanochannels. UV irradiation of the self-assembled host in the presence of molecular oxygen generates both singlet oxygen and superoxide when suspended in solution. The efficiency of ROS generation by the host is lower than that of benzophenone (BP), which could be beneficial for reactions carried out catalytically, as ROS species react quickly and often unselectively. Superoxide formation was detected through reaction with 5,5- dimethyl-1-pyrroline N-oxide in the presence of …