Biochemistry, Biophysics, and Structural Biology Commons^™

Regional-Scale Simulations Of Fungal Spore Aerosols Using An Emission Parameterization Adapted To Local Measurements Of Fluorescent Biological Aerosol Particles, Matthias Hummel, Corinna Hoose, M. Gallagher, D. A. Healy, J. Alex Huffman, D. O'Connor, U. Pöschl, C. Pöhlker, N. H. Robinson, M. Schnaiter, J. R. Sodeau, M. Stengel, E. Toprak, H. Vogel

Chemistry and Biochemistry: Faculty Scholarship

Fungal spores as a prominent type of primary biological aerosol particles (PBAP) have been incorporated into the COSMO-ART (Consortium for Small-scale Modelling- Aerosols and Reactive Trace gases) regional atmospheric model. Two literature-based emission rates for fungal spores derived from fungal spore colony counts and chemical tracer measurements were used as a parameterization baseline for this study. A third, new emission parameterization for fluorescent biological aerosol particles (FBAP) was adapted to field measurements from four locations across Europe. FBAP concentrations can be regarded as a lower estimate of total PBAP concentrations. Size distributions of FBAP often show a distinct mode at …

Fluorescence Imaging Of Analyte Profiles In An Inductively Coupled Plasma With Laser Ablation As A Sample Introduction Source, Lance Moses

Theses and Dissertations

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has risen to among the top tier techniques for the direct analysis of solid samples. However, significant problems remain that must be solved to achieve the full analytical potential of LA-ICP-MS. Inefficient conversion of aerosol to ions within the ICP or transmission through the MS interface may decrease precision, sensitivity, and/or accuracy. Although fundamental mechanisms that govern ion production and transmission have been studied extensively in solution-nebulization (SN) ICP-MS instruments, significant gaps in our understanding remain. Furthermore, it is unclear to what extent differences between the aerosols generated during SN and LA …

Physiological Function Of Fus: An Rna Binding Protein In Motor Neuron Disease, Liuqing Yang

Theses and Dissertations--Molecular and Cellular Biochemistry

FUS is an RNA binding protein implicated in the motor neuron disease— amyotrophic lateral sclerosis (ALS, also called Lou Gehrig’s disease). ALS is a fatal neurodegenerative disease characterized by progressive motor neuron death. Mutations in the FUS gene cause about 4% of familial ALS (FUS ALS). Mutated FUS protein mislocalizes from the motor neuron nucleus to the cytoplasm and forms inclusions in the cytoplasm. It is unclear how FUS mislocalization induces motor neuron dysfunction and degeneration. This dissertation research was designed to investigate the physiological functions of FUS in the nucleus, with a purpose to shed light on the pathogenesis …

Physical Interactions Between Neuropilin And Vegfrs, Integrins In Regulating Endothelial Cell Functions, Xiaobo Li

Theses and Dissertations--Molecular and Cellular Biochemistry

The neuropilin (Nrp) family consists of multifunctional cell surface receptors with critical roles in a number of different cell and tissue types. A core aspect of Nrp function is ligand-dependent cellular adhesion and migration, where it controls the multistep process of cellular motility through integration of ligand binding, receptor coupling and signaling via the coordinated action of its extracellular and intracellular domains. While Nrp regulates cellular adhesion and motility in the cardiovascular and nervous systems under physiological conditions, the emerging pathological role of Nrp in tumor cell migration and metastasis has been identified and provides motivation for continued efforts toward …

Beryllium Nitrate Supports Fibroblast Migration As An Essential Component Of Skin And Limb Regeneration In Axolotls, Adam Boyd Cook

Theses and Dissertations--Biology

Tissue regeneration in salamanders is a robust process that is not easily interrupted or altered. Therefore, inhibiting regeneration provides a means to interrogate the underlying cellular and molecular mechanisms regulating this complex event. Here we show that application of a relatively low concentration of beryllium nitrate solution (100mM) causes a delay in skin regeneration and severely alters normal limb regeneration. We provide evidence showing a beryllium-induced reduction in dermal fibroblast migration in vivo and in vitro. We link this phenomenon to delayed regeneration of the skin and abnormal blastema formation resulting in limb patterning defects during regeneration. Though our …

Analysis Of Chromatin Accessiblity Of The Human C-Myc Replication Origin, Tu Thien Danh

Browse all Theses and Dissertations

The best characterized eukaryote replication model is of the budding yeast Saccharomyces cerevisiae. Replication origins of S.cerevisiae are 100 to 200 bp in size and contain an essential 11-bp autonomous replicating sequence (ARS) consensus sequence (ACS). The origin recognition complex (ORC) binds to the ACS in order to recruit additional replication factors (Cdt1, Cdc6, MCM, Cdc45) and together they form the pre-replication complex (pre-RC).

Unlike budding yeast, the mammalian cells contain dispersed replication origins in which multiple elements distributed over large distances act as replication start sites. Mammalian DNA replication origins, such as the c-myc origin, contain a DNA unwinding …

Confocal Fluorescence Microscopy: An Ultra-Sensitive Tool Used To Evaluate Intracellular Antiretroviral Nano-Drug Delivery In Hela Cells, Subhra Mandal, You Zhou, Annemarie Shibata, Christopher J. Destache

School of Veterinary and Biomedical Sciences: Faculty Publications

In the last decade, confocal fluorescence microscopy has emerged as an ultra-sensitive tool for real-time study of nanoparticles (NPs) fate at the cellular-level. According to WHO 2007 report, Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome (HIV/AIDS) is still one of the world’s major health threats by claiming approximately 7,000 new infections daily worldwide. Although combination antiretroviral drugs (cARV) therapy has improved the life-expectancy of HIV-infected patients, routine use of high doses of cARVhas serious health consequences and requires complete adherence to the regimen for success. Thus, our research goal is to fabricate long-acting novel cARV loaded poly(lactide-co-glycolic acid) (PLGA) nanoparticles (cARV-NPs) as …

Spiral Ganglion Degeneration And Hearing Loss As A Consequence Of Satellite Cell Death In Saposin B-Deficient Mice, Omar Akil, Ying Sun, Sarath Vijayakumar, Wujuan Zhang, Tiffany Ku, Chi-Kyou Lee, Sherri Jones, Gregory A. Grabowski, Lawrence R. Lustig

School of Veterinary and Biomedical Sciences: Faculty Publications

Saposin B (Sap B) is an essential activator protein for arylsulfatase A in the hydrolysis of sulfatide, a lipid component of myelin. To study Sap B’s role in hearing and balance, a Sap B-deficient (B^-/-) mouse was evaluated. At both light and electron microscopy (EM) levels, inclusion body accumulation was seen in satellite cells surrounding spiral ganglion (SG) neurons from postnatal month 1 onward, progressing into large vacuoles preceding satellite cell degeneration, and followed by SG degeneration. EM also revealed reduced or absent myelin sheaths in SG neurons from postnatal month 8 onwards. Hearing loss was initially seen …

First Evidence For Substrate Channeling Between Proline Catabolic Enzymes A Validation Of Domain Fusion Analysis For Predicting Protein-Protein Interactions, Nikhilesh Sanyal, Benjamin W. Arentson, John J. Tanner, Donald F. Becker

Department of Biochemistry: Faculty Publications

Background: PRODH and P5CDH from Thermus thermophilus are monofunctional enzymes in proline catabolism.

Results: Steady-state kinetics and intermediate trapping data show the PRODH and P5CDH reactions are coupled by a channeling step.

Conclusion: Substrate channeling in monofunctional enzymes is achieved via weak interactions.

Significance: Evidence for substrate channeling between monofunctional proline catabolic enzymes is shown and confirms the Rosetta Stone hypothesis.

Triacylglycerol Synthesis During Nitrogen Stress Involves The Prokaryotic Lipid Synthesis Pathway And Acyl Chain Remodeling In The Microalgae Coccomyxa Subellipsoidea, James W. Allen, Concetta C. Dirusso, Paul N. Black

Department of Biochemistry: Faculty Publications

Triglyceride (TAG) synthesis during nitrogen starvation and recovery was addressed using Coccomyxa subellipsoidea by analyzing acylchain composition and redistribution using a bioreactor-controlled time course. Galactolipids, phospholipids and TAGs were profiled using liquid chromatography tandem mass spectroscopy (LC–MS/MS). TAG levels increased linearly through 10 days of N starvation to a final concentration of 12.6% dry weight (DW), while chloroplast membrane lipids decreased from 5% to 1.5% DW. The relative quantities of TAG molecular species, differing in acyl chain length and glycerol backbone position, remained unchanged from 3 to 10 days of N starvation. Six TAG species comprised approximately half the TAG …

Correction For Sandai Et Al., The Evolutionary Rewiring Of Ubiquitination Targets Has Reprogrammed The Regulation Of Carbon Assimilation In The Pathogenic Yeast Candida Albicans, Doblin Sandai, Zhikang Yin, Laura Selway, David Stead, Janet Walker, Michelle D. Leach, Iryna Bohovych, Iuliana V. Ene, Stavroula Kastora, Susan Budge, Carol A. Munro, Frank C. Odds, Neil A.R. Gow, Alistair J.P. Brown

Department of Biochemistry: Faculty Publications

No abstract provided.

Role Of Micrornas In Alcohol-Induced Multi-Organ Injury, Sathish Kumar Natarajan, Joseph M. Pachunka, Justin L. Mott

Department of Biochemistry: Faculty Publications

Alcohol consumption and its abuse is a major health problem resulting in significant healthcare cost in the United States. Chronic alcoholism results in damage to most of the vital organs in the human body. Among the alcohol-induced injuries, alcoholic liver disease is one of the most prevalent in the United States. Remarkably, ethanol alters expression of a wide variety of microRNAs that can regulate alcohol-induced complications or dysfunctions. In this review, we will discuss the role of microRNAs in alcoholic pancreatitis, alcohol-induced liver damage, intestinal epithelial barrier dysfunction, and brain damage including altered hippocampus structure and function, and neuronal loss, …

Some Of The Most Interesting Casp11 Targets Through The Eyes Of Their Authors, Andriy Kryshtafovych, John Moult, Arnaud Basle, Alex Burgin, Timonthy K. Craig, Robert A. Edwards, Deborah Fass, Marcus D. Hartmann, Mateusz Korycinski, Richard J. Lewis, Donald Lorimer, Andrei N. Lupas, Janet Newman, Thomas S. Peat, Kurt H. Piepenbrink, Janani Prahlad, Mark J. Van Raaij, Forest Rohwer, Anca M. Segall, Victor Seguritan, Eric J. Sundberg, Abhimanyu K. Singh, Mark A. Wilson, Torsten Schwede

Department of Biochemistry: Faculty Publications

The Critical Assessment of protein Structure Prediction (CASP) experiment would not have been possible without the prediction targets provided by the experimental structural biology community. In this article, selected crystallographers providing targets for the CASP11 experiment discuss the functional and biological significance of the target proteins, highlight their most interesting structural features, and assess whether these features were correctly reproduced in the predictions submitted to CASP11.

Secretoglobin And Transferrin Expression In Bronchoalveolar Lavage Fluid Of Horses With Chronic Respiratory Disease, M. Miskovic Feutz, Laurent Couetil, C.P. Riley, X. Zhang, J. Adamec, R.E. Raskin

Department of Biochemistry: Faculty Publications

Background: Lower expression of secretoglobin and transferrin has been found in the bronchoalveolar lavage fluid (BALF) of a small number of horses with experimentally induced signs of recurrent airway obstruction (RAO) compared to healthy controls.

Hypothesis/Objectives: Secretoglobin and transferrin BALF expression will be similarly decreased in horses with naturally occurring clinical signs of RAO and in horses with experimentally induced clinical signs of RAO as compared to healthy controls and intermediate in horses with inflammatory airway disease (IAD).

Animals: Recurrent airway obstruction-affected and control horses were subjected to an experimental hay exposure trial to induce signs of RAO. Client-owned horses …

Altered Connexin 43 Expression Underlies Age-Dependent Decrease Of Regulatory T Cell Suppressor Function In Nonobese Diabetic Mice, Michel Kuczma, Cong-Yi Wang, Leszek Ignatowicz, Robert Gourdi, Piotr Kraj

Biological Sciences Faculty Publications

Type 1 diabetes is one of the most extensively studied autoimmune diseases, but the cellular and molecular mechanisms leading to T cell–mediated destruction of insulin-producing β cells are still not well understood. In this study, we show that regulatory T cells (T_regs) in NOD mice undergo age-dependent loss of suppressor functions exacerbated by the decreased ability of activated effector T cells to upregulate Foxp3 and generate T_regs in the peripheral organs. This age-dependent loss is associated with reduced intercellular communication mediated by gap junctions, which is caused by impaired upregulation and decreased expression of connexin 43. Regulatory …

Characterization Of The Sufc Atpase During Fe-S Cluster Assembly By The Suf Pathway In Escherichia Coli, Khaleh Mykel Thomas

Theses and Dissertations

The gram-negative bacterium E. coli encodes the Suf pathway to assemble iron-sulfur (Fe-S) clusters under iron starvation and oxidative stress conditions. The ATPase activity of SufC is critical for in vivo Fe-S cluster assembly by the Suf pathway. SufC shares homology with the nucleotide binding domain (NBD) of ATP-binding cassette (ABC) transporters and belongs to the AAA+ (ATPases Associated with diverse cellular Activities) ATPase superfamily, a family of proteins that utilizes energy from ATP hydrolysis to perform a variety of cellular functions. SufC forms a stable SufBC2D complex with partner proteins SufB and SufD. The SufBC2D complex serves as a …

Characterization Of A Novel Protease In Staphylococcus Aureus, Adam L. Johnson

Theses and Dissertations

A newly discovered cysteine protease, Prp, has been shown to perform an essential, site-specific cleavage of ribosomal protein L27 in Staphylococcus aureus. In Firmicutes and related bacteria, ribosomal protein L27 is encoded with a conserved N-terminal extension that must be removed to expose residues critical for ribosome function. Uncleavable and pre-cleaved variants were unable to complement an L27 deletion in S. aureus, indicating that this N-terminal processing event is essential and likely plays an important regulatory role. The gene encoding the responsible protease (prp) has been shown to be essential, and is found in all organisms …

Dysregulation Of Micrornas In Blood As Biomarkers For Diagnosing Prostate Cancer, Rhonda W. Daniel

Theses and Dissertations

Prostate cancer is the most common noncutaneous cancer among men, yet current diagnostic methods are insufficient and more reliable diagnostic markers need to be developed. The answer that can bridge this gap and enable more efficient diagnoses may lie in microRNAs. These small, single stranded RNA molecules impact protein expression at the translational level and regulate important cellular pathways. Dysregulation of these small RNA molecules can have tumorigenic effects on cells and lead to many types of cancers.

Currently the Prostate-Stimulating Antigen (PSA) is used as a diagnostic marker for prostate cancer. However, many factors can elevate PSA levels such …

Pemetrexed, A Modulator Of Amp-Activated Kinase Signaling And An Inhibitor Of Wild Type And Mutant P53, Stuti Agarwal

Theses and Dissertations

New drug discoveries and new approaches towards diagnosis and treatment have improved cancer therapeutics remarkably. One of the most influential and effective discoveries in the field of cancer therapeutics was antimetabolites, such as the antifolates. The interest in antifolates increased as some of the antifolates showed responses in cancers, such as mesothelioma, leukemia, and breast cancers. When pemetrexed (PTX) was discovered, our laboratory had established that the primary mechanism of action of pemetrexed is to inhibit thymidylate 22 synthase (TS) (E. Taylor et al., 1992). Preclinical studies have shown that PTX has a broad range of antitumor activity in human …

Mysteries Of The Trypanosomatid Maxicircles: Characterization Of The Maxicircle Genomes And The Evolution Of Rna Editing In The Order Kinetoplastida, Preethi Ranganathan Iyengar

Theses and Dissertations

The trypanosomatid protists belonging to Order Kinetoplastida are some of the most successful parasites ever known to mankind. Their extreme physiological diversity and adaptability to different environmental conditions and host systems make them some of the most widespread parasites, causing deadly diseases in humans and other vertebrates.

This project focuses on their unique mitochondrion, called the kinetoplast, and more specifically involves the characterization of a part of their mitochondrial DNA (also called kinetoplast DNA or kDNA), the maxicircles, which are functional homologs of eukaryotic mitochondrial DNA in the kinetoplastid protists. We have sequenced and characterized the maxicircle genomes of 20 …

Regulation Of Tie2 Extracellular Complex Formation In Angiogenesis, Annamarie Dalton

Theses and Dissertations

Pathological angiogenesis is an essential component of tumor growth, development, and metastasis for which few effective therapeutic options exist. Though many cancer therapies target the function of cell surface receptors, mechanisms regulating membrane receptor crosstalk remain unclear. Two important families of receptors in angiogenesis, the Ties and Integrins, respond to the extracellular environment via outside-in and, in the case of Integrins, also inside- out signaling. Recent reports showed that the endothelial specific tyrosine kinase receptor, Tie2, forms complexes with two of the endothelial Integrin heterodimers, α₅β₁ and α_Vβ₃, providing a convenient mechanism for …

Effects Of Refuges On The Evolution Of Resistance To Transgenic Corn By The Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Jennifer Deitloff, Mike W. Dunbar, David A. Ingber, Bruce E. Hibbard, Aaron J. Gassmann

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

BACKGROUND: Diabrotica virgifera virgifera LeConte is a major pest of corn and causes over a billion dollars of economic loss annually through yield reductions and management costs. Corn producing toxins derived from Bacillus thuringiensis (Bt) has been developed to help manageD. v. virgifera.However, previous studies have demonstrated the ability of this species to evolve resistance to Bt toxins in both laboratory and field settings.

RESULTS: We used an experimental evolution approach to test the refuge strategies for delaying resistance of D. v. virgifera to corn producing Bt toxin Cry34/35Ab1. In the absence of refuges, D. v. virgifera developed resistance to …

Efficacy Of Ultraviolet Radiation To Control Lactic Acid Bacteria In Wine Must, Brian D. Williams

All Master's Theses

The use of shortwave ultraviolet (UV_c) radiation to control lactic acid bacteria (LAB) in wine production was studied. A simulated wine sterilizer was built using a commercially sourced ultraviolet (UV) sterilizer commonly used in aquariums and ponds. After growing cultures in test tubes, samples of five different species of LAB were introduced into white grape juice adjusted for brix and pH to match that of wine must commonly found in the Yakima Valley American Viticultural Area. The mixture was then agitated and allowed time to evenly distribute the bacteria throughout the juice. The juice was sent through the …

Non-Destructive Dna Extraction Methods That Yield Dna Barcodes In Spiders, Reva Ann Bork

Honors Program Theses

DNA barcodes are short sequences of nucleotides that differ from species to species (Hebert et al., 2003; Hebert & Gregory, 2005). DNA barcoding is very important in helping to reconstruct phylogenetic trees and to confirm the identity of threatened or endangered species in the wild. Additionally, it has become increasingly popular in the food industry to test the accuracy of the food being sold in fast food chains (Wong and Hanner, 2008). For scientific purposes, nondestructive DNA extraction techniques need to be explored because they allow for preservation of the voucher specimen, which is particularly important for rare or extinct …

Rheb Dynamics On Lysosomal Membranes Determines Mtorc1 Activity After Loss Of P53 Or Activation Of Ampk, Catherine M. Bell

Theses and Dissertations

The tumor suppressor TP53 is the most frequently altered gene in human cancers. The growth-promoting complex, mTORC1 plays a part of the oncogenic profile caused by dysfunctional p53. mTORC1 sits downstream of AMPK and other crucial tumor suppressors/oncogenes, PTEN, LKB1, and Akt. The antifolate pemetrexed was found by this laboratory to activate AMPK via the inhibition of the enzyme AICART in de novo purine synthesis. This work presents a mechanism of mTORC1 activation with p53 loss, as well as of mTORC1 inhibition by pemetrexed-induced AMPK. We have found that mTORC1 activity was substantially upregulated by the loss …

Nitric Oxide Synthase Activity And Its Modulation In The Treatment Of Colorectal Cancer, Asim Alam

Theses and Dissertations

The American Cancer Society estimates more than 141,000 new cases of and about 50,000 deaths from colorectal cancer every year. Treatment options include surgery, radiation therapy and targeted therapies such as anti-angiogenics. However, no therapies address the key driving factor of colorectal cancer: inflammation. It is well known that chronic inflammatory conditions such as Crohn’s Disease, ulcerative colitis, diabetes, obesity and cigarette smoking all elevate the risk of developing colorectal cancer. One of the hallmarks of chronic inflammation is the elevated levels of reactive oxygen/nitrogen species (ROS/RNS). A primary source of these ROS/RNS is uncoupled Nitric Oxide Synthase (NOS). Under …

Synthesis And Characterization Of Core-Shell Zinc Silica Nanoparticles And Zinc Silica Nanogels For Agricultural Applications., Megan Berroth

Electronic Theses and Dissertations

Plant pathogens are a serious problem facing the agricultural industry today. Current methodologies use copper based biocides as the main form of defense. Unfortunately this can lead to damaging environmental effects and increased rates of antimicrobial resistance. In this study, antimicrobial activity of multiple alternative zinc-based nanoformulations were tested against three important plant pathogens: Xanthomonas alfalfae, Pseudomonas syringae, and Clavobacter michiganensis. Xanthomonas sub species cause Citrus canker, a devastating disease that affects millions of citrus trees worldwide while the latter two affect tomato crops. Materials synthesis was completed and the resulting nanoformulations were characterized by Atomic Absorption Spectroscopy, Scanning Electron …

Fmf Assay For Assessing Vaccine Generated Antibodies In A Biomimetic Manner, Vipra Dhir

Electronic Theses and Dissertations

Traditional functional assays such as hemagglutination inhibition (HAI) and micro-neutralization (MN) assays have been routinely used for assessing the vaccine response, since influenza vaccine has been administered in people (1940). Such assays are not always predictive regarding the protection conferred by the influenza vaccine and are not able to monitor neutralization related to stem region of influenza hemagglutinin responsible for virus membrane fusion in the endosomes. In order to study Influenza vaccine response in a more biomimetic manner and overcome the deficiencies of the traditional functional assays, we developed a fluorescent membrane fusion assay (fMF). The assay uses viruses labeled …

Functional Identification Of Nucleus Tractus Solitarius (Nts) Barosensitive Neurons: Effect Of Chronic Intermittent Hypoxia (Cih), Jenya Kolpakova

Electronic Theses and Dissertations

Chronic Intermittent Hypoxia (CIH) is a model used to study obstructive sleep apnea (OSA). Previously, we showed that baroreflex control of heart rate (HR) (baroreflex sensitivity) is reduced in CIH rats. While afferent function and HR in response to vagal efferent stimulation are enhanced, the effect of CIH on the central components, in particular NTS, is still not completely understood. F344 rats (3-4 mo) were exposed either to CIH or room air (RA) for 35-50 days. Following CIH exposure, rats were anaesthetized with Ket/Ace. Using single-unit extracellular recording technique, we recorded NTS barosensitive neurons in response to arterial pressure (AP) …

Nanoparticle Behavior In Biological Gels And Biofluids: The Impact Of Interactions With Charged Biogels And The Formation Of Protein Coronas On Nanoparticles, Xiaolu Zhang

Theses and Dissertations--Chemistry

With the rapid growth of nanotechnology, situations where nanomaterials will interact with biological systems will unquestionably grow. Therefore, it is increasingly understood that interactions between nanomaterials and biological environments will play an essential role in nanomedicine. Biological polymer networks, including mucus and the extracellular matrix, serve as a filter for the exchange of molecules and nanoparticles. Such polymer networks are complex and heterogeneous hydrogel environments that regulate transport processes through finely tuned particle-network interactions. In chapters 3 and 4, we investigate the role of electrostatics on the basic mechanisms governing the diffusion of charged molecules inside model polymer networks by …