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A Summary Of Three Antibiotic Resistant Bacteria Studies Of Plaster Creek, Yeaeun Lee, David P. Warners

Faculty and Professional Research

No abstract provided.

Nine Year Assessment Of Soil Treatment On Aguacatillo (Nectandontisii And Ocotea Austinii, Lauraceae) Seedling Success In The Restoration Of A Costa Rican Cloud Forestra Cufo, Sheila Devries, David Warners

Faculty and Professional Research

We tracked seedling growth of two species of aguacatillo (Nectandra cufodontisii (O. C. Schmidt) C. K. Allen and Ocotea austinii C. K. Allen) that were planted into an early successional cloud forest hillside in San Gerardo de Dota, Costa Rica over nine years. Seedlings were collected from underneath nearby mother trees and transplanted into one of three soil treatments: indigenous soil; a 50:50 mixture of horse manure and indigenous soil; and a 50:50 mixture of kitchen compost and indigenous soil. After seedlings were transplanted they were measured and each specific location was evaluated for light exposure. Two months later seedlings …

Single-Molecule Analysis Of Alzheimer's Β-Peptide Oligomer Disassembly At Physiological Concentration, Chen Chen

Theses and Dissertations--Chemistry

The diffusible soluble oligomeric amyloid β-peptide (Aβ) has been identified as a toxic agent in Alzheimer’s disease that can cause synaptic dysfunction and memory loss, indicating its role as potential therapeutic targets for AD treatment. Recently an oligomer-specific sandwich biotin-avidin interaction based assay identified the Aβ oligomer dissociation potency of a series of dihydroxybenzoic acid (DHBA) isomers. Because the sandwich assay is an ensemble method providing limited size information, fluorescence correlation spectroscopy (FCS) was employed to provide single molecule resolution of the disassembly mechanism.

Using FCS coupled with atomic force microscopy, we investigated the size distribution of fluorescein labeled synthetic …

Stability Studies Of Membrane Proteins, Cui Ye

Theses and Dissertations--Chemistry

The World Health Organization has identified antimicrobial resistance as one of the top three threats to human health. Gram-negative bacteria such as Escherichia coli are intrinsically more resistant to antimicrobials. There are very few drugs either on the market or in the pharmaceutical pipeline targeting Gram-negative pathogens. Two mechanisms, the protection of the outer membrane and the active efflux by the multidrug transporters, play important roles in conferring multidrug resistance to Gram-negative bacteria. My work focuses on two main directions, each aligning with one of the known multidrug resistance mechanisms.

The first direction of my research is in the area …

Increase Of Basal Oxidative Stress Levels And Impairment Of Heme Oxygenase-1/Biliverdin Reductase Post-Translational Modification By The Defect Of Parkinson-Related Gene Of Pink1, Zhaoshu Zhang

Theses and Dissertations--Chemistry

Parkinson disease (PD) is the most common movement disorder and the second most common neurodegenerative disease. PINK1, PTEN-induced kinase 1, functions as a serine/threonine kinase as well as a protector of mitochondrial function. Mutations in PINK1 gene result in either mitochondria dysfunction or disruption of kinase signaling pathways involved in the pathogenesis of PD.

In this thesis, oxidative stress levels were examined in the brain of PINK1 knockout mice, and also how heme oxygenase-1 and biliverdin reductase are affected in brain of PINK1 knockout mice. In addition, posttranslational modifications are a way to control the behavior of proteins, so posttranslational …

Bases For Breadth - Insights Into How The Mechanism And Dynamics Of Nitroreductase Can Explain This Enzyme's Broad Substrate Repertoire, Warintra Pitsawong

Theses and Dissertations--Chemistry

Nitroreductase from Enterobacter cloacae (NR) is a member of a large family of homologues represented in all branches of the tree of life. However the physiological roles of many of these enzymes remain unknown. NR has distinguished itself on the basis the diverse sizes and chemical types of substrates it is able to reduce (Koder et al 1998). This might be an evolved characteristic suiting NR for a role in metabolism of diverse occasional toxins. While there are numerous studies of determinants of substrate specificity, we know less about mechanisms by which enzymes can be inclusive. Therefore, we present …

The Differences Between Iron And Iron-Substituted Manganese Superoxide Dismutase With Respect To Hydrogen Peroxide Treatment, Jianing Wang

Theses and Dissertations--Chemistry

Iron-substituted manganese superoxide dismutase (Fe(Mn)SOD) was produced using an in vivo preparation method. It’s an inactive enzyme in catalyzing superoxide radical dismutation owing to the mis-incorporation of Fe in the active site evolved to use Mn. To investigate the possible toxicity of human Fe(Mn)SOD proposed by Yamakura, we studied the properties of Fe(Mn)SOD upon H₂O₂ treatment and compared to that of FeSOD. It’s found that the responses to H₂O₂ treatment were different, including the changes of optical spectra, variations of active site coordination and secondary structures. Fe³⁺ reduction was not observed in Fe(Mn)SOD …

Bioc 435: Advanced Topics In Biochemistry—A Peer Review Of Teaching Project Benchmark Portfolio, Edward N. Harris

UNL Faculty Course Portfolios

BIOC 435 or Advanced Topics in Biochemistry is an ACE 10 (Achievement centered education)course for students in their senior year. This is a capstone course for Biochemistry majors and is the last of several biochemistry courses that they will take in their undergraduate enrollment. The course is also open to non-majors in a related science such as Biology and Biological Sciences, although these students typically do not do as well as the majors. Students who take this course should be well-prepared in the basic concepts of biochemistry with regards to nucleic acids and proteins as well as some familiarity with …

High Fat Diet Increased Serum Glutamate Dehydrogenase More Than Chronic Acetaminophen Dosing In Female Mice, Elizabeth Ruth Behmer

All Graduate Theses, Dissertations, and Other Capstone Projects

This laboratory study examined the effects of acetaminophen overdose in normal fed and high-fat fed female mice. Forty female mice were placed on normal and high-fat diets at 4 weeks old. When the mice were significantly different in weight (between 6 and 9 months old), half the mice were dosed with acetaminophen. These mice were daily given an overdose of acetaminophen for 14 days. The dose used was 300 mg/kg mouse (LD50 = 338 mg/kg). The control group was given 10 µl water/g mouse. Levels of serum glutamate dehydrogenase (GDH) were measured to indicate liver damage. GDH is released from …

Modulation Of Cholera Toxin Structure And Function By Host Proteins, Helen Burress

Electronic Theses and Dissertations

Cholera toxin (CT) moves from the cell surface to the endoplasmic reticulum (ER) where the catalytic CTA1 subunit separates from the holotoxin and unfolds due to its intrinsic thermal instability. Unfolded CTA1 then moves through an ER translocon pore to reach its cytosolic target. Due to the instability of CTA1, it must be actively refolded in the cytosol to achieve the proper conformation for modification of its G protein target. The cytosolic heat shock protein Hsp90 is involved with the ER-to-cytosol translocation of CTA1, yet the mechanistic role of Hsp90 in CTA1 translocation remains unknown. Potential post-translocation roles for Hsp90 …

Dimethylarginine Dimethylaminohydrolase Ii Overexpression Attenuates Lps-Mediated Lung Leak In Acute Lung Injury, Saurabh Aggarwal, Christine M. Gross, Sanjiv Kumar, Christiana Dimitropoulou, Shruti Sharma, Boris A. Gorshkov, Supriya Sridhar, Qing Lu, Natalia V. Bogatcheva, Agnieszka J. Jezierska-Drutel, Rudolf Lucas, John D. Catravas, Stephen M. Black

Bioelectrics Publications

Acute lung injury (ALI) is a severe hypoxemic respiratory insufficiency associated with lung leak, diffuse alveolar damage, inflammation, and loss of lung function. Decreased dimethylaminohydrolase (DDAH) activity and increases in asymmetric dimethylarginine (ADMA), together with exaggerated oxidative/nitrative stress, contributes to the development of ALI in mice exposed to LPS. Whether restoring DDAH function and suppressing ADMA levels can effectively ameliorate vascular hyperpermeability and lung injury in ALI is unknown, and was the focus of this study. In human lung microvascular endothelial cells, DDAH II overexpression prevented the LPS-dependent increase in ADMA, superoxide, peroxynitrite, and protein nitration. DDAH II also attenuated …

The Burden Of Avian Influenza Viruses In Community Ponds In California, Zin Htway

Walden Dissertations and Doctoral Studies

Emerging influenza viruses continue to challenge public health. The problem is public health science professionals have been battling emerging human influenza diseases with tactile and reactionary methods because there is a lack of knowledge and data at the human-animal interface. This research was a baseline study of the proportion of influenza A virus (IAV) in urban and rural communities in California. The population was artificial recirculating water ponds in the geographic locations of rural and urban Californian communities. Surface water samples [N = 182] were collected from artificial recirculating ponds in California. Positivity for IAV was verified by real time …

Investigation Of The Cellular And Molecular Mechanisms Of Radiation-Induced Bystander Effects, Hayley Furlong

Doctoral

The overall aim of this study was to investigate the cellular and molecular mechanisms involved in radiation-induced bystander effects in HaCaT cells, predominantly at low-doses of irradiation. They do not follow the original dose-response theory and exhibit a unique cascade of signalling events, which are under intense investigation for radiation risk purposes. An in vitro system was first used to observe the bystander effect, comparing two cell viability assays while measuring apoptotic cell death in these known reporter HaCaT cells and established the most sensitive assay for bystander responses Downstream bystander signalling events were then investigated through gene expression studies …

Methanol And Ethanol Modulate Responses To Danger- And Microbe- Associated Molecular Patterns In Tomato, Tobacco And Arabidopsis, Claire Teresa Hann

Theses and Dissertations

Methanol is a byproduct of cell wall modification. It is released through the action of pectin methylesterases (PMEs), which demethylate cell wall pectins. Plant PMEs play not only a role in developmental processes but also in responses to herbivory and infection by fungal or microbial pathogens, resulting in increased methanol release. To break down the cell wall barrier, pathogens employ their own PMEs. Interestingly, the infection process also regulates the expression of certain plant PMEs. Methanol is toxic to a number of herbivores and reduces their fitness. At high concentrations, it upregulates signaling and defense genes. However, molecular mechanisms that …

Catalytic Mechanism And Maturation Of The Metalloenzyme Nitrile Hydratase, Natalie I. Gumataotao

Dissertations

Nitrile hydratases are metalloenzymes that catalyze the hydration of nitriles to their corresponding amides in a specific manner at ambient pressures and temperatures at neutral pH. Traditional industrial methods require high temperature and pressure, extreme pH, and heavy metals. NHases are used as biocatalysts in the large scale industrial production of amide precursors to textiles, animal feedstock, and polymers. Notably, NHase is used in the production of ~100,000 tons of acrylamide annually by the Mitsubishi Corporation.

Despite being used extensively in industry, questions remain about NHase. The catalytic mechanism is not defined. Understanding the way in which the nitrile is …

Investigating The Role Of The Pgf2 Alpha/Calcineurin-Signaling Pathway In The Regulation Of Adipogenesis, Damodaran Annamalai

Dissertations

Prostaglandin F2α (PGF2α) is a potent physiological inhibitor of adipocyte differentiation. In previous studies, we demonstrated that PGF2α inhibits adipogenesis via activation of the calcium-regulated protein phosphatase, calcineurin. In this current study, we have now extended these findings to identify the IL-11 cytokine and the Nurr1 orphan nuclear hormone receptor as functionally important downstream transcriptional targets of the PGF2α/calcineurin-pathway involved in the inhibition of adipocyte differentiation. In the case of IL-11, we show that this cytokine acts in an autocrine fashion to inhibit adipogenesis via the essential actions of the gp130 cytokine co-receptor signaling subunit. Further, by using a well-characterized …

Mutations In Phospholamban Alter The Structure And Function Of The Calcium Atpase Regulatory Complex, Neha Abrol

Dissertations

Phospholamban (PLB) is an integral membrane protein that plays an important role in regulation of cardiac calcium handling and contractility. PLB exists as a homopentamer in the membrane, which upon deoligomerization into active monomers reversibly inhibits sarco/endoplasmic reticulum calcium ATPase (SERCA). Mutations in PLB that change the PLB monomer-pentamer equilibrium result in dysregulation of SERCA. To determine the structural and regulatory role of the C-terminal residues of PLB in the membranes of living cells, we fused fluorescent protein tags to PLB and SERCA. We then studied the effect of C-terminal alanine substitutions and truncation mutations on PLB oligomerization and SERCA …

The Dape-Encoded N-Succinyl-L,L-Diaminopimelic Acid Desuccinylase (Dape) From Haemophilus Influenzae As A Prospective Target For The Development Of Novel Antibiotics, Anna Starus

Dissertations

The rapid emergence of bacteria that are resistant to todayfs antibiotics makes them more and more ineffective. Consequently, the need for a novel class of antibacterial agents is rapidly increasing. The importance of this project is emphasized by the emergence of several pathogenic bacterial strains that are resistant to all currently available antibiotics on the market today. One way to approach this problem is to develop drugs that target essential bacterial biosynthetic pathways. Based on bacterial genetic information, the meso]diaminopimelate (mDAP)/lysine biosynthetic pathway offers several potential anti]bacterial targets that have not been yet explored. One of these, the dapE-encoded N-succinyl-L,L-diaminopimelic …

Lineage-Specific Transcriptional Profiles Of Symbiodinium Spp. Unaltered By Heat Stress In A Coral Host, Daniel J. Barshis, Jason T. Ladner, Thomas A. Oliver, Stephen R. Palumbi

Biological Sciences Faculty Publications

Dinoflagellates of the genus Symbiodinium form an endosymbiosis with reef building corals, in which photosynthetically derived nutrients comprise the majority of the coral energy budget. An extraordinary amount of functional and genetic diversity is contained within the coral-associated Symbiodinium, with some phylotypes (i.e., genotypic groupings), conferring enhanced stress tolerance to host corals. Recent advances in DNA sequencing technologies have enabled transcriptome-wide profiling of the stress response of the cnidarian coral host; however, a comprehensive understanding of the molecular response to stress of coral-associated Symbiodinium, as well as differences among physiologically susceptible and tolerant types, remains largely unexplored. Here, …

Atm, Brca1, And Aurora A: Mechanisms Of G2/M Checkpoint Control In Human Embryonic Stem Cells, Jason Beckta

Theses and Dissertations

When cultured in vitro, human embryonic stem cells (hESCs) acquire genetic abnormalities that have slowed their therapeutic use. As hESCs have a “leaky” G1/S boundary, the pressure of ensuring genetic integrity falls on the G2/M checkpoint, which can be activated by failed chromosomal decatenation (among other stimuli). It is hypothesized that hESCs have a deficient decatenation checkpoint, but little data supports this. Evidence suggests that the ataxia telangiectasia mutated (ATM) kinase controls the G2/M decatenation and DNA damage checkpoints, though previous reports are conflicting on this point. My work demonstrates that inhibition of decatenation activates ATM and arrests hESCs in …

The Cytotoxic Effect Of The Bcl-2 Family Of Proteins In Breast Cancer Cells, Yamileth Chin

Theses and Dissertations

Breast cancer is the second leading cause of death amongst women ages 20 to 59. Despite advancements in cancer therapies, more research is necessary to improve the diagnoses and treatment of several types of breast cancer. Paclitaxel (Taxol) is a commonly utilized anti-cancer drug for various types of solid tumors. However, the molecular mechanism utilized by paclitaxel to induce cell death is still elusive. Previous studies in our laboratory have shown that the pro-apoptotic BCL-2 family protein, BAK (BCL-2 homologous antagonist/killer) plays an important role in paclitaxel-induced cell death. In untreated breast cancer cells, BAK is associated with the anti-apoptotic …

Folate Conjugated Dendrimers For Targeted Anticancer Therapy, Shannon Andrews

Theses and Dissertations

Anticancer therapeutics are often limited to suboptimal doses due to their lack of selectivity for tumor cells and resultant damage to healthy tissue. These limitations motivated researchers to develop tumor-specific delivery systems for improved therapeutic efficacy and reduced unintended cytotoxicity. Polyamidoamine dendrimers offer an ideal platform for designing targeted therapeutics with tunable characteristics that optimize pharmacokinetic behavior and targeting specificity. Ligand conjugation to dendrimer provides the biochemical interaction necessary to activate tumor-specific receptors for receptor-mediated endocytosis and effective internalization of polyplexes. Tumor-specific receptors overexpressed in carcinomas, like folate receptor-alpha (FOLRα), are targeted by ligand-conjugated dendrimer to allow enhanced internalization of …

Regulation Of Ykl-40 In Sterile Inflammation And Its Role In Glioblastoma In Vivo, Reetika Bhardwaj

Theses and Dissertations

YKL-40 is a secreted glycoprotein, which is a shared biomarker of chronic inflammation and oncogenic transformation. Indeed, YKL-40 expression is up-regulated in many diseases including multiple sclerosis, Alzheimer disease, viral encephalitis, HIV-associated dementia, brain infarction, and traumatic brain injury. YKL-40 is also expressed by several solid tumors, such as osteosarcoma, ovarian carcinoma and glioblastoma multiforme (GBM). It promotes the migration and invasion of astrocytes as well as GBM cells. Serum YKL-40 levels have been shown to directly correlate with tumor grade and potentially tumor burden in GBM. In contrast to the numerous reports documenting elevated expression of YKL-40, relatively little …

Developing A Caenorhabditis Elegans Model For Marfan Syndrome, Pauline Fotopoulos

Theses and Dissertations

Marfan Syndrome (MFS) is one of the most common monogenic diseases and affects approximately 1 in 5,000 individuals worldwide. The syndrome is characterized by elongated extremities, tall stature, slender frame, and cardiac, and vision abnormalities due to severe connective tissue defects. It is caused by mutations in the fbn1 gene, which encodes an extracellular matrix glycoprotein, and is required for proper cardiac and skeletal development and for sequestration of TGFβ (transforming growth factor beta) and BMP (bone morphogenetic protein) within the extracellular matrix (ECM). The primary objective of this study was to establish a C.elegans MFS model and use this …

Template-Based C8-Scorpion: A Protein 8 State Secondary Structure Prediction Method Using Structural Information And Context-Based Features, Ashraf Yaseen, Yaohang Li

Computer Science Faculty Publications

Background: Secondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining high resolution 3D models.

Methods: In this work, we investigate a template-based approach to enhance 8-state secondary structure prediction accuracy. We construct structural templates from known protein structures with certain sequence similarity. The structural templates are then incorporated as features with sequence and evolutionary information to train two-stage neural networks. In case of structural templates absence, heuristic structural information is incorporated instead. …

Vibrational Spectroscopic Analysis Of Body Fluids: Avoiding Molecular Contamination Using Centrifugal Filtration, Franck Bonnier, Matthew Baker, Hugh Byrne

Articles

The use of centrifugal filtration for protein purification and concentration represents an important improvement for the application of vibrational spectroscopy to analysis of bodily fluids based on protein fractions with specific molecular weight. Vibrational spectroscopic techniques are highly specific and can potentially detect small variations in the protein content indicating the presence of different diseases, therefore usable as markers for early diagnostic. However, due to the high sensitivity of the techniques, it is essential to verify that no molecular contamination occurs during the preparation of the samples. Concentration of the blood serum using commercially available centrifugal filters has been shown …

Integrating Phage Therapy Into Western Medicine, Jacob B. Jaminet

UROP Posters

The World Health Organization has described the rise of antibiotic use as a “global heath security emergency” (who.int). With the growing concern about antibiotic resistant bacteria, there has been an increased interest in bacteriophages. Bacteriophages are high-specific viruses that only infect bacteria. The use of bacteriophages medicinally to treat bacteria is called phage therapy. Research in phage therapy gained momentum until the introduction of antibiotics. While the USA and other Western countries accepted antibiotics, the Soviet Union and their satellite nations still continued to research phages. Since the funding for research was supplied by the Soviet military, the results of …

Basic Features Of A Cell Electroporation Model: Illustrative Behavior For Two Very Different Pulses, Reuben S. Son, Kyle C. Smith, Thiruvallur R. Gowrishankar, P. Thomas Vernier, James C. Weaver

Bioelectrics Publications

Science increasingly involves complex modeling. Here we describe a model for cell electroporation in which membrane properties are dynamically modified by poration. Spatial scales range from cell membrane thickness (5 nm) to a typical mammalian cell radius (10 μm), and can be used with idealized and experimental pulse waveforms. The model consists of traditional passive components and additional active components representing nonequilibrium processes. Model responses include measurable quantities: transmembrane voltage, membrane electrical conductance, and solute transport rates and amounts for the representative "long" and "short" pulses. The long pulse-1.5 kV/cm, 100 μs-evolves two pore subpopulations with a valley at ~5 …

Disassembly Of Actin Structures By Nanosecond Pulsed Electric Field Is A Downstream Effect Of Cell Swelling, Andrei G. Pakhomov, Shu Xiao, Olga N. Pakhomova, Iurii Semenov, Marjorie A. Kuipers, Bennett L. Ibey

Bioelectrics Publications

Disruption of the actin cytoskeleton structures was reported as one of the characteristic effects of nanosecond-duration pulsed electric field (nsPEF) in both mammalian and plant cells. We utilized CHO cells that expressed the monomeric fluorescent protein (mApple) tagged to actin to test if nsPEF modifies the cell actin directly or as a consequence of cell membrane permeabilization. A train of four 600-ns pulses at 19.2 kV/cm (2 Hz) caused immediate cell membrane poration manifested by YO-PRO-1 dye uptake, gradual cell rounding and swelling. Concurrently, bright actin features were replaced by dimmer and uniform fluorescence of diffuse actin. To block the …

Sumoylation Affects Ns1'S Ability To Neutralize The Interferon Response, Jeanette Cecilia Gonzalez

Open Access Theses & Dissertations

It is of huge concern the possibility that at some point in the future we may face a new pandemic involving a highly pathogenic virus due to our current preventive and treatment options to fight this viral disease. The main reason for such limitations is the ability of the virus to go over constant antigenic shifts and drifts on its viral surface proteins HA and NA. The constant mutations that affect this virus cause the need of developing new vaccines for each influenza season. Periodically, the World Health Organization (WHO) reports that around 10% of the world population gets infected …