Molecular Biology Commons^™

Electrosensory Ampullary Organs Are Derived From Lateral Line Placodes In Bony Fishes, Melissa S. Modrell, William E. Benis, R. Glenn Northcutt, Marcus C. Davis, Clare V.H. Baker

Faculty and Research Publications

Electroreception is an ancient subdivision of the lateral line sensory system, found in all major vertebrate groups (though lost in frogs, amniotes and most ray-finned fishes). Electroreception is mediated by 'hair cells' in ampullary organs, distributed in fields flanking lines of mechanosensory hair cell-containing neuromasts that detect local water movement. Neuromasts, and afferent neurons for both neuromasts and ampullary organs, develop from lateral line placodes. Although ampullary organs in the axolotl (a representative of the lobe-finned clade of bony fishes) are lateral line placode-derived, non-placodal origins have been proposed for electroreceptors in other taxa. Here we show morphological and molecular …

Interspecies Comparison Of Αii-Spectrin Abundance Between Chinook Salmon And Steelhead, Brielle D. Kemis, Ann L. Miracle, Katie A. Wagner, Christa M. Woodley

STAR Program Research Presentations

Salmonids, such as Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss), are a staple economic, recreational, tribal, and environmental resource, yet many populations are unsustainable. This study was part of a broad scale effort to monitor the impact of downstream migration obstacles on juvenile salmonid health and survival, which is an essential step towards increasing Smolt-to-Adult Return ratios (SARs). The objective of this study was to determine if juvenile Chinook salmon and steelhead exhibit differing quantities of alphaII-Spectrin Breakdown Products (SBDPs) over two consecutive spring migration periods, indicative of neurogenesis rate and/or biological response to head …

Gata-Family Transcription Factors In Magnaporthe Oryzae, Cristian F. Quispe

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The filamentous fungus, Magnaporthe oryzae, responsible for blast rice disease, destroys around 10-30% of the rice crop annually. Infection begins when the specialized infection structure, the appressorium, generates enormous internal turgor pressure through the accumulation of glycerol. This turgor acts on a penetration peg emerging at the base of the cell, causing it to breach the leaf surface allowing its infection.

The enzyme trehalose-6- phosphate synthase (Tps1) is a central regulator of the transition from appressorium development to infectious hyphal growth. In the first chapter we show that initiation of rice blast disease requires a regulatory mechanism involving an …

Characterization Of Arginine-82 Mutants With Non-Native Chromophores, Vivek Alaigh

Honors Scholar Theses

Bacteriorhodopsin, found in most halobacteria, is an integral protein that contains seven transmembrane alpha helices and an organic chromophore, all-trans retinal. Light energy is captured by the protein and results in a series of spectrally discrete intermediates that conclude with a proton being pumped across the membrane from the cytoplasmic side to the extracellular milieu. The most blue-shifted photo-intermediate, the M state, has been of interest for protein-based holographic memory storage devices. Bacteriorhodopsin mutants were prepared with either a 4-hydroxy retinal or 3,4-dihydro retinal analog: R82A, R82C, R82H, R82K, R82N and R82Q. The objective of this research was to investigate …

Modeling Human Immune Response To The Lyme Disease-Causing Bacteria, Yevhen Rutovytskyy

Honors Scholar Theses

The purpose of this project is to develop and analyze a mathematical model for the pathogen-host interaction that occurs during early Lyme disease.

Based on the known biophysics of motility of Borrelia burgdorferi and a simple model for the immune response, a PDE model was created which tracks the time evolution of the concentrations of bacteria and activated immune cells in the dermis. We assume that a tick bite inoculates a highly localized population of bacteria into the dermis. These bacteria can multiply and migrate. The diffusive nature of the migration is assumed and modeled using the heat equation. Bacteria …

Expression Of The Porcine Reproductive And Respiratory Syndrome Virus Non-Structural Protein 3 (Nsp 3) In Escherichia Coli, Lidia Beka

Honors Scholar Theses

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is single-stranded, positive-sense RNA virus in the family Arteriviridae, order Nidovirales. PRRSV is the most economically significant viral infection of swine herds in the United States. The single-stranded RNA genome is 15 kb in length and encodes 9 open reading frames (ORF1a, ORF1b, ORF2a, ORF2b and ORFs 3 through 7). ORFs 1a and 1b encode for 13 non-structural proteins (nsp) that are suggested to be involved in transcription and viral genome replication. The exact role of non-structural proteins in PRRSV cycle is still unknown. Moreover, there is a limited availability of reagents such …

Design And Bio-Production Of A Nanoparticle Avian Influenza Vaccine, Kashif N. Ather

Honors Scholar Theses

Influenza is one of the most common diseases in the world and the cause for numerous deaths every year. The primary method of combating the disease is the influenza vaccine, which is produced by inoculating chicken eggs with inactivated virus. An emerging solution is to use Self-Assembling Polypeptide Nanoparticles (SAPN) to elicit an immune response in the body, rather than using inactivated viruses. This project focuses on the synthesis, purification, and refolding of two peptide constructs, BN5C and S43, which are specific protein sequences that under the right conditions will refold into the 3-dimensional structures necessary for producing an immune …

Quorum Sensing In Archaea, Charles Mackin

Honors Scholar Theses

Bacteria coordinate cell density dependent behaviors by communicating through chemical intermediaries in a process called quorum sensing. In a bacterial culture, individual cells will constitutively produce signal molecules, termed autoinducers, and export them into the environment. When the concentration of autoinducers reaches a threshold, the cells sense that they are in a specific situation, which requires the upregulation of certain genes. This upregulation causes the bacteria to produce proteins that allow them to take part in a coordinated population-wide behavior.

In bacteria that are naturally competent, or capable of importing DNA from the environment, the expression of competence genes is …

Characterizing The Role Of The Bacterial Metallothionein, Smta, In Mammalian Infection, Stephanie R. Davis

Honors Scholar Theses

Mammalian metallothioneins (MT) are induced by various immunomodulatory molecules and are involved in a spectrum of immune processes such as essential metal homeostasis, detoxification of certain heavy metals, inflammation, and immune cell trafficking [1-3]. A bacterial metallothionein, SmtA, shares some sequence homology with mammalian MT as well as its metal-binding capabilities [4]. In addition to its ability to sequester heavy metals, eukaryotic MT has also been shown to scavenge free radicals such as reactive oxygen and nitrogen species (ROS, RNS), interfering with their toxic effects on cells and potentially influencing their regulatory roles in cell proliferation and differentiation [5, 6]. …

Biomarker Signature Classification Of Various Stress Forms, Chana L. Rich

Honors Scholar Theses

Various types of stressful conditions can have unique and important effects on immunity and can lead to dramatic consequences to health. For my University Scholar project, the characteristic biomarker signatures produced from a set of diverse stressors (e.g. psychological, biological and chemical) are being investigated. A biomarker signature is a distinctive biological indicator of a specific condition. High-throughput tools for the measurement of different cellular products have the potential to further our understanding of human disease and facilitated the identification of new biomarkers in all areas of medicine. The hypothesis that each form of stress, psychological, chemical and physical, will …

Arctic Mustard Flower Color Polymorphism Controlled By Petal-Specific Downregulation At The Threshold Of The Anthocyanin Biosynthetic Pathway, Cynthia A. Dick, Jason Buenrostro, Timothy Butler, Matthew L. Carlson, Daniel J. Kliebenstein, Justen B. Whittall

Biology

Intra- and interspecific variation in flower color is a hallmark of angiosperm diversity. The evolutionary forces underlying the variety of flower colors can be nearly as diverse as the colors themselves. In addition to pollinator preferences, non-pollinator agents of selection can have a major influence on the evolution of flower color polymorphisms, especially when the pigments in question are also expressed in vegetative tissues. In such cases, identifying the target(s) of selection starts with determining the biochemical and molecular basis for the flower color variation and examining any pleiotropic effects manifested in vegetative tissues. Herein, we describe a widespread purple-white …

Dynamic Glucoregulation And Mammalian-Like Responses To Metabolic And Developmental Disruption In Zebrafish, Agata Jurczyk, Nicole M. Roy, Rabia Bajwa, Philipp Gut, Kathryn Lipson, Chaoxing Yang, Laurence Covassin, Waldemar J. Racki, Aldo A. Rossini, Nancy Phillips, Didier Y. R. Stainier, Dale L. Greiner, Michael A. Brehm, Rita Bortell, Philip Diiorio

Biology Faculty Publications

Zebrafish embryos are emerging as models of glucose metabolism. However, patterns of endogenous glucose levels, and the role of the islet in glucoregulation, are unknown. We measured absolute glucose levels in zebrafish and mouse embryos, and demonstrate similar, dynamic glucose fluctuations in both species. Further, we show that chemical and genetic perturbations elicit mammalian-like glycemic responses in zebrafish embryos. We show that glucose is undetectable in early zebrafish and mouse embryos, but increases in parallel with pancreatic islet formation in both species. In zebrafish, increasing glucose is associated with activation of gluconeogenic phosphoenolpyruvate carboxykinase1 (pck1) transcription. Non-hepatic Pck1 protein is …

Connecting Motors And Membranes: A Quantitative Investigation Of Dynein Pathway Components And In Vitro Characterization Of The Num1 Coiled Coil Domain, Bryan J. St. Germain

Masters Theses 1911 - February 2014

In the budding yeast, Saccharomyces Cerevisiae, dynein, a minus-end directed motor, is involved in nuclear migration and proper orientation of the mitotic spindle during mitosis. Our lab has developed a model that involves the loading of cytoplasmic dynein onto the plus-end of astral microtubules through interactions with Pac1/LIS1 and Bik1/CLIP-170. Dynein is then delivered to the cell cortex and anchored through a cortical receptor protein, Num1. Num1 is a 313KDa protein that localizes to the cell cortex and is an essential component of dynein mediated nuclear migration.

Using quantitative fluorescence techniques I was able to create a molecular inventory of …

Sex Difference In Calbindin Cell Number In The Mouse Preoptic Area: Effects Of Neonatal Estradiol And Bax Gene Deletion, Richard F. Gilmore Iii

Masters Theses 1911 - February 2014

The sexually dimorphic nucleus of the preoptic area (SDN-POA) was first discovered in rats and is one of the most famous and best studied sex differences in the field of neuroscience. Though well documented in rats (larger in males than females), this sex difference was only recently able to be observed in mice due to the discovery of the protein calbindin-D28k as a marker. Recent studies have shown a larger, more distinct calbindin-immunoreactive (ir) cell cluster in male mice compared to females. However, the exact location of the cluster and whether the sex difference is one of total cell number …

In Vivo Investigations Of Polymer Conjugates As Therapeutics, Elizabeth M. Henchey

Masters Theses 1911 - February 2014

Polymer conjugates offer a way to introduce materials into the body that would normally be rejected or cause toxicity. Two polymers are investigated in vivo for uses in chemotherapeutic delivery, protein therapeutics, and DNA transfection. A novel polymer, polyMPC, has the ability to increase doxorubicin loading and its solubility, and is conjugated in a way to release its payload in a low pH environment. Through its conjugation, blood clearance time of doxorubicin is increased, and thus tumor exposure to the drug is increased with a single administration. It can be administered at ten times the concentration of free doxorubicin, and …

Performance Screening Of Chemostat Adapted Recombinant Zymomonas Mobilis Strains, Deirdre M. Beard, Nancy Dowe

STAR Program Research Presentations

Corn stover biomass can be pretreaed and hydrolyzed into soluble sugars to be fermented by microorganisms to ethanol. NREL has developed a recombinant bacteria Zymomonas mobilis 8b that metabolizes both five and six carbon sugars. During pretreatment, toxic inhibitors such as furfural and acetate are produced. NREL has made an attempt to adapt two sub-strains of Z. mobilis 8b to acetate and furfural by using a chemostat method. During the chemostat process, cultures were frozen back in glycerol and saved. In this study, those frozen cultures were revived and analyzed for performance in environments with varying concentrations of furfural and …

An Apoptosis Targeted Stimulus With Nanosecond Pulsed Electric Fields (Nspefs) In E4 Squamous Cell Carcinoma, Wei Ren, Stephen J. Beebe

Bioelectrics Publications

Stimuli directed towards activation of apoptosis mechanisms are an attractive approach to eliminate evasion of apoptosis, a ubiquitous cancer hallmark. In these in vitro studies, kinetics and electric field thresholds for several apoptosis characteristics are defined in E4 squamous carcinoma cells (SCC) exposed to ten 300 ns pulses with increasing electric fields. Cell death was [95% at the highest electric field and coincident with phosphatidylserine externalization, caspase and calpain activation in the presence and absence of cytochrome c release, decreases in Bid and mitochondria membrane potential (Δψm) without apparent changes reactive oxygen species levels or in Bcl2 and Bclxl levels. …

Quantifying Agonist Activity At G Protein-Coupled Receptors, Frederick J. Ehlert, Hinako Suga, Michael T. Griffin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

When an agonist activates a population of G protein-coupled receptors (GPCRs), it elicits a signaling pathway that culminates in the response of the cell or tissue. This process can be analyzed at the level of a single receptor, a population of receptors, or a downstream response. Here we describe how to analyze the downstream response to obtain an estimate of the agonist affinity constant for the active state of single receptors.

Receptors behave as quantal switches that alternate between active and inactive states (Figure 1). The active state interacts with specific G proteins or other signaling partners. In the absence …

Expression Of Genes Involved In A Radiation-Induced Bystander Effect, Hayley Furlong

Conference Papers

The radiation induced bystander effect is relevant to carcinogenesis, it may have significant implications for risk estimation for radiation exposure. Currently the mechanisms and cellular events are the subject of intense investigation, because little is known. It is thought that the radiation induced bystander response is due to a bystander factor secreted in the medium post irradiation. However the biological nature of this factor is currently unknown, but it is thought to be a protein of some sort that may be involved in the apoptosis cascade. Materials and Methods: HaCaT epithelial cells were used in this study and exposed to …

Disorder Predictors Also Predict Backbone Dynamics For A Family Of Disordered Proteins, Gary W. Daughdrill, Wade M. Borcherds, Hongwei Wu

Molecular Biosciences Faculty Publications

Several algorithms have been developed that use amino acid sequences to predict whether or not a protein or a region of a protein is disordered. These algorithms make accurate predictions for disordered regions that are 30 amino acids or longer, but it is unclear whether the predictions can be directly related to the backbone dynamics of individual amino acid residues. The nuclear Overhauser effect between the amide nitrogen and hydrogen (NHNOE) provides an unambiguous measure of backbone dynamics at single residue resolution and is an excellent tool for characterizing the dynamic behavior of disordered proteins. In this report, we show …