Biochemistry, Biophysics, and Structural Biology Commons^™

Synthesis Of Glycolipids And Evaluation Of Their Nkt Cell Stimulatory Properties, Yang Liu

Theses and Dissertations

Natural killer T (NKT) cells are a subset of T cells that modify a variety of immune responses. NKT cells recognize glycolipid antigen presented by a molecule called CD1d, a nonclassical antigen-presenting molecule. The best known subset of CD1d-dependent NKT cells expresses an invariant T cell receptor Vα (TCR-α) chain. These are referred to as type I or invariant NKT (iNKT) cells. When stimulated by a glycolipid, NKT cells rapidly release large amounts of cytokines. Cytokines released by NKT cells can induce either Th1 or Th2 responses. Th1 cytokines are effective in regulating bacterial, parasitic, and viral infections. But Th1 …

A Kinesin Motor In A Force-Producing Conformation, Elisabeth Heuston, C. Eric Bronner, F Jon Kull, Sharyn A. Endow

Dartmouth Scholarship

Kinesin motors hydrolyze ATP to produce force and move along microtubules, converting chemical energy into work by a mechanism that is only poorly understood. Key transitions and intermediate states in the process are still structurally uncharacterized, and remain outstanding questions in the field. Perturbing the motor by introducing point mutations could stabilize transitional or unstable states, providing critical information about these rarer states.

Rna Processing Of Nitrogenase Transcripts In The Cyanobacterium Anabaena Variabilis, Justin Ungerer, Brenda Pratte, Teresa Thiel

Biology Department Faculty Works

Little is known about the regulation of nitrogenase genes in cyanobacteria. Transcription of the nifH1 and vnfH genes, encoding dinitrogenase reductases for the heterocyst-specific Mo-nitrogenase and the alternative V-nitrogenase, respectively, was studied by using a lacZ reporter. Despite evidence for a transcription start site just upstream of nifH1 and vnfH, promoter fragments that included these start sites did not drive the transcription of lacZ and, for nifH1, did not drive the expression of nifHDK1. Further analysis using larger regions upstream of nifH1 indicated that a promoter within nifU1 and a promoter upstream of nifB1 both contributed to expression of nifHDK1, …

Short-Chain Carboxylic Acids From Gray Catbird (Dumetella Carolinensis) Uropygial Secretions Vary With Testosterone Levels And Photoperiod, Rebecca J. Whelan, Tera C. Levin, Mary C. Garvin

Faculty & Staff Scholarship

The uropygial gland of birds produces secretions that are important in maintaining the health and structural integrity of feathers. Non-volatile components of uropygial secretions are believed to serve a number of functions including waterproofing and conditioning the feathers. Volatile components have been characterized in fewer species, but are particularly interesting because of their potential importance in olfactory interactions within and across species. We used solid-phase microextraction headspace sampling with gas chromatography-mass spectrometry to detect and identify volatiles in uropygial secretions of gray catbirds (Dumetella carolinensis), a North American migratory bird. We consistently detected the following carboxylic acids: acetic, …

Release Of Hmgb1 In Response To Pro-Apoptotic Glioma Killing Strategies: Efficacy And Neurotoxicity, Marianela Candolfi, Kader Yagiz, David Foulad, Gabrielle Alzadeh, Matthew Tesarfreund, Akm Ghulam Muhammad, Mariana Puntel, Kurt Kroeger, Chunyan Liu, Sharon Lee, James Curtin, Gwendalyn D. King, Jonathan Lerner, Katsuaki Sato, Yohei Mineharu, Weidong Xiong, Pedro R. Lowenstein, Maria Castro

Articles

Purpose In preparation for a Phase I clinical trial utilizing a combined cytotoxic/immunotherapeutic strategy using adenoviruses expressing Flt3L (Ad-Flt3L) and thymidine kinase (Ad-TK) to treat glioblastoma (GBM), we tested the hypothesis that Ad-TK+GCV would be the optimal tumor killing agent in relation to efficacy and safety when compared to other pro-apoptotic approaches. Experimental Design and Results The efficacy and neurotoxicity of Ad-TK+GCV was compared with Ads encoding the pro-apoptotic cytokines (TNF-α, TRAIL, FasL), alone or in combination with Ad-Flt3L. In rats bearing small GBMs (day 4), only Ad-TK+GCV or Ad-FasL improved survival. In rats bearing large GBMs (day 9), the …

Getting Up To Speed: Acceleration Strategies In The Florida Scrub Lizard, Sceloporus Woodi, Eric J. Mcelroy, Lance D. Mcbrayer

Biology: Faculty Publications

Small animals typically rely on quick bursts and intermittent pauses when moving in the wild. Hence, the study of acceleration capacity is important for understanding the ecology and evolution of locomotor performance. In this study, we investigate intraspecific variation in the acceleration capacity of a small lizard (Sceloporus woodi). To quantify animal acceleration performance, the momentum‐impulse theorem is applied to data collected from high‐speed video recordings of individuals accelerating from a standstill and over a subsequent distance of 0.4 m. Unlike earlier studies, the momentum‐impulse approach allows one to directly and precisely quantify the per step contribution to …

Experimental Investigation Of A Non-Thermal Atmospheric Pressure Plasma Jet, Asma Begum

Electrical & Computer Engineering Theses & Dissertations

The main objective of this dissertation is to understand the formation of the plasma jet from the plasma pencil, and the propagation of the plasma jet in the ambient atmosphere where the effect of the external electric field is almost zero. Before investigating the formation and propagation phenomenon of the plasma jet, common physical properties of plasma jets are determined by using the imaging technique and optical emission spectroscopy. The first goal of this dissertation is to establish the laminar helium gas flow channel through a plasma pencil.

The formation position, formation time, and the criterion of the plasma jet …

Entry And Fusion Of Emerging Paramyxoviruses, Rebecca Ellis Dutch

Molecular and Cellular Biochemistry Faculty Publications

Paramyxoviruses are a family of non-segmented RNA viruses that includes major human pathogens such as measles virus and respiratory syncytial virus (RSV) and significant animal viruses like rinderpest. In recent years, several new paramyxoviruses have been identified, further increasing the breadth and importance of this viral family. While many elements of the fusion and entry mechanisms of these recently identified pathogens are conserved, there are interesting differences, including variations in receptor binding, cell tropism, fusion (F) protein proteolytic activation, and triggering of membrane fusion. Thus, study of their entry mechanisms has highlighted the diversity of these critical events in the …

Targeting Complex Cyclic Peptides For Synthesis: The Celogentin And Theonellamide Families, Joshua Wayne Robinson

Theses and Dissertations

Celogentin C and theonellamide F are a class of natural products that have potential antimitotic behavior. They both contain interesting bicyclic structures with unusual linkages within a central moiety. Celogentin C's highly functionalized tryptophan moiety has two unusual linkages, a β-substituted Leu connection to the C6 of the indole structure that makes up the left-hand ring, and a τ-N connection of the imidazole to the C2 of the indole constructing the right-hand ring. This right-hand ring connection was solved via a novel oxidative coupling procedure developed in our group and the left-hand ring was initially constructed via a radical conjugated …

Novel Mechanism In Astrocyte Gene Regulation And Function, Sandeep Singh

Theses and Dissertations

This dissertation sheds light on several novel mechanistic findings in astrocyte specific gene regulation and function by the NFI-X transcription factor which can be further extrapolated to astrocyte differentiation and glial tumor invasion. First, we cloned and analyzed human NFI-X3, a novel splice variant of the nfix gene, which contains a unique transcriptional activation (TA) domain completely conserved in primates. In contrast to previously cloned NFI-X1, overexpression of NFI-X3 potently activates NFI reporters, including GFAP reporter, in astrocytes and glioma cells. The expression of NFI-X3 is dramatically upregulated during the differentiation of neural progenitors to astrocytes and precedes the expression …

Alternative Trans-Splicing Of Caenorhabditis Elegans Sma-9/Schnurri Generates A Short Transcript That Provides Tissue-Specific Function In Bmp Signaling, Jianghua Yin, Ling Yu, Cathy Savage-Dunn

Publications and Research

Background Transcription cofactors related to Drosophila Schnurri facilitate the transcriptional programs regulated by BMP signaling in C. elegans, Drosophila, Xenopus, and mouse. In different systems, Schnurri homologs have been shown to act as either agonists or antagonists of Smad function, and as either positive or negative regulators of transcription. How Schnurri proteins achieve this diversity of activities is not clear. The C. elegans sma-9/schnurri locus undergoes alternative splicing, including an unusual trans-splicing event that could generate two non-overlapping shorter transcripts.

Results We demonstrate here that the shorter transcripts are expressed in vivo. Furthermore, we find that one of the short …

Estuarine Nitrifiers: New Players, Patterns And Processes, Anne E. Bernhard, Annette Bollmann

Biology Faculty Publications

Ever since the first descriptions of ammonia-oxidizing Bacteria by Winogradsky in the late 1800s, the metabolic capability of aerobic ammonia oxidation has been restricted to a phylogenetically narrow group of bacteria. However, the recent discovery of ammonia-oxidizing Archaea has forced microbiologists and ecologists to re-evaluate long-held paradigms and the role of niche partitioning between bacterial and archaeal ammonia oxidizers. Much of the current research has been conducted in open ocean or terrestrial systems, where community patterns of archaeal and bacterial ammonia oxidizers are highly congruent. Studies of archaeal and bacterial ammonia oxidizers in estuarine systems, however, present a very different …

Redox Status Affects The Catalytic Activity Of Glutamyl-Trna Synthetase, Assaf Katz, Ranat Banerjee, Merly De Armas, Michael Ibba, Omar Orellana

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Glutamyl-tRNA synthetases (GluRS) provide Glu-tRNA for different processes including protein synthesis, glutamine transamidation and tetrapyrrole biosynthesis. Many organisms contain multiple GluRSs, but whether these duplications solely broaden tRNA specificity or also play additional roles in tetrapyrrole biosynthesis is not known. Previous studies have shown that GluRS1, one of two GluRSs from the extremophile Acidithiobacillus ferrooxidans, is inactivated when intracellular heme is elevated suggesting a specific role for GluRS1 in the regulation of tetrapyrrole biosynthesis. We now show that, in vitro, GluRS1 activity is reversibly inactivated upon oxidation by hemin and hydrogen peroxide. The targets for oxidation-based inhibition were …

Dna Adducts Of Decarbamoyl Mitomycin C Efficiently Kill Cells Without Wild-Type P53 Resulting From Proteasome-Mediated Degradation Of Checkpoint Protein 1, Ernest K. Boamah, Angelika Brekman, Maria Tomasz, Natura Myeka, Maria E. Figueiredo-Pereira, Senyene Hunter, Joel Meyer, Rahul C. Bhosle, Jill Bargonetti

Publications and Research

The mitomycin derivative 10-decarbamoyl mitomycin C (DMC) more rapidly activates a p53-independent cell death pathway than mitomycin C (MC). We recently documented that an increased proportion of mitosene1-β-adduct formation occurs in human cells treated with DMC in comparison to those treated with MC. Here, we compare the cellular and molecular response of human cancer cells treated with MC and DMC. We find the increase in mitosene 1-β-adduct formation correlates with a condensed nuclear morphology and increased cytotoxicity in human cancer cells with or without p53. DMC caused more DNA damage than MC in the nuclear and mitochondrial genomes. Checkpoint 1 …

Celogentin C And Thioviridamide: Synthetic And Structural Studies, Dmitry Nikolayevich Litvinov

Theses and Dissertations

Project I Celogentin C, isolated by Kobayashi from the seeds of Celosia argentea in 2001 exhibits strong inhibitory behavior towards polymerization of tubulin – globular protein, which plays crucial role during the cell division cycle. We have attempted synthesis of the left-hand ring of celogentin C via the intramolecular alkylation and the Knoevenagel condensation strategies. Utilizing synthetic methodologies in the field of nitroacetyl chemistry, developed by Kornblum and Rajappa we have successfully prepared the intermolecular Knoevenagel condensation product – the late-stage precursor to the left-hand ring of celogentin C. Synthesis of this key intermediate subsequently led to the preparation of …

Notch1 Functions As A Tumor Suppressor In A Model Of K-Ras–Induced Pancreatic Ductal Adenocarcinoma, Linda Hanlon, Jacqueline L Avila, Renée M Demarest, Scott Troutman, Megan Allen, Francesca Ratti, Anil K Rustgi, Ben Z Stanger, Fred Radtke, Volkan Adsay, Fenella Long, Anthony J Capobianco, Joseph L Kissil

Rowan-Virtua School of Osteopathic Medicine Departmental Research

K-ras is the most commonly mutated oncogene in pancreatic cancer and its activation in murine models is sufficient to recapitulate the spectrum of lesions seen in human pancreatic ductal adenocarcinoma (PDAC). Recent studies suggest that Notch receptor signaling becomes reactivated in a subset of PDACs, leading to the hypothesis that Notch1 functions as an oncogene in this setting. To determine whether Notch1 is required for K-ras-induced tumorigenesis, we used a mouse model in which an oncogenic allele of K-ras is activated and Notch1 is deleted simultaneously in the pancreas. Unexpectedly, the loss of Notch1 in this model resulted in increased …

Ricin B Chain-Insulin Fusion Protein Immunomodulation Of Type 1 Diabetes, James Edward Carter Iii

Loma Linda University Electronic Theses, Dissertations & Projects

Type 1 diabetes mellitus (T1D) is a debilitating chronic inflammatory disease of the insulin-producing pancreatic islet β-cells that results from a combination of genetic and environmental factors. Attempts to suppress Th1-mediated autoimmune diseases such as T1D by mucosal delivery of autoantigens for immunotolerization have yielded only partial success. Attainment of satisfactory levels of sustained immunological tolerance remains to be accomplished. To restore self-tolerance requires delivery of sufficient amounts of autoantigen to stimulate regulatory T helper cells that function to survey the gut and induce tolerance to consumed antigens such as food. Oral delivery of autoantigens has previously been shown to …

Poisonous Rangeland Plants In San Luis Obispo County, Sara Litten, Amanda Ou

Animal Science

Poisonous Rangeland Plants in San Luis Obispo County is a comprehensive educational guide to rangeland plants that are toxic to domestic livestock. This guide begins with an exploration of how the biological systems are affected by the poisonous plant toxins. The biochemistry behind these toxins is included in the discussion. Next, reference material for fourteen plants that inhabit San Luis Obispo County is provided. This information includes specific toxins found in poisonous plants, affected animals, symptoms of poisoning, stages of growth, lethal dose, and distribution of the plant in California. This section of the guide is filled with helpful photos …

Growth Hormone Alters Components Related To Differentiation, Metabolism And Milk Synthesis And Secretion In Mac-T Cells, Tasha Lynn Johnson

Master's Theses

The mammary alveolar cell-T (MAC-T) cell line is able to uniformly differentiate and secrete casein proteins in response to dexamethasone, insulin and prolactin and is extensively used to study bovine mammary epithelial cell function. Growth hormone (GH) has been shown to increase milk protein synthesis both in vivo and in mammary cell models, and induce cytoskeletal rearrangement in 3T3 fibroblast cell line and a Chinese hamster ovary (CHO) cell line. Few studies have focused on identifying the mechanisms involved in differentiated MAC-T cells’ response to GH. We tested the hypothesis that MAC-T cells would respond directly to GH and that …

Mimosa: A System For Minimotif Annotation, Jay Vyas, Ronald J. Nowling, Thomas Meusburger, David P. Sargeant, Krishna Kadaveru, Michael R. Gryk, Vamsi Kundeti, Sanguthevar Rajasekaran, Martin Schiller

Life Sciences Faculty Research

BACKGROUND:

Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature.

RESULTS:

We have built the MimoSA application for minimotif annotation. The application supports management of …

Intrinsic Contact Geometry Of Protein Dynamics, Yosi Shibberu, Allen Holder, David Cooper

Mathematical Sciences Technical Reports (MSTR)

We introduce a new measure for comparing protein structures that is especially applicable to analysis of molecular dynamics simulation results. The new measure generalizes the widely used root-mean-squared-deviation (RMSD) measure from three dimensional to n-dimensional Euclidean space, where n equals the number of atoms in the protein molecule. The new measure shows that despite significant fluctuations in the three dimensional geometry of the estrogen receptor protein, the protein's intrinsic contact geometry is remarkably stable over nanosecond time scales. The new measure also identifies significant structural changes missed by RMSD for a residue that plays a key biological role in …

Determination Of The Myogenic Potential Of Human Embryonic Stem Cell-Derived Mesenchymal Stem Cells, Rory Coleman

Honors Scholar Theses

Human embryonic stem cells (hESCs) have the potential to

differentiate to all adult somatic cells. This property makes hESCs a very promising area of research for the treatment of disorders in which specific cell populations need to be restored. Despite this potential, research that focuses on producing mesodermally derived cell populations from hESCs is decidedly limited, notwithstanding the prevalence of disorders involving mesodermal tissues for which treatment options are limited. Skeletal muscle myoblasts are derivatives of mesodermal cells and are characterized by the expression of the MyoD gene. These cells are difficult to obtain from hESCs in a reproducible and …

Characterization Of The Putative Xyloglucan Glycosyltransferase Gt14 In Arabidopsis Thaliana, Najam R. Syed

Honors Scholar Theses

Plant cell walls largely consist of matrix polysaccharides that are linked to cellulose microfibrils. Xyloglucan, the primary hemicellulose of the cell wall matrix, consists of a repeating glucose tetramer structure with xylose residues attached to the first three units ('XXXG'). In Arabidopsis thaliana, the core XXXG structure is further modified by enzymatic addition of galactose and fucose residues to the xylose side chains to produce XLXG, XXLG, XLLG and XLFG structures. GT14 is a putative glycosyltransferase in the GT47 gene family. Initial predictions of GT14's hydrophobic regions, based on its translated amino acid sequence, are almost identical to its Arabidopsis …

Alkylphenol Contamination In Homarus Americanus, Jennifer Renee Urban

Honors Scholar Theses

Alkylphenols are pollutants that are present in marine sediments and fishes. In earlier work it has been discovered that alkylphenols are present in the Homarus americanus, or the American lobster. Research suggests that alkylphenols could behave as endocrine disruptors as they have been found to affect juvenile hormone activity. It has been hypothesized that lobsters may be able to rid themselves of alkylphenol contamination through secreting these compounds into the environment or sequestering them in their tissues. In this study, I address the question of how lobsters may rid themselves of alkylphenols by analyzing hemolymph, muscle, gill, and shell samples …

Dopaminergic Innervation Of The Subventricular Zone In The Murine Brain, Linda Beth Drozdowicz

Honors Scholar Theses

The subventricular zone (SVZ) is one of two areas in the brain that, in a healthy mouse, continually generate neurons throughout adulthood. While it was previously thought that only the A9 neurons of the substantia nigra sent dopaminergic afferents to the SVZ, recent studies suggest that the A10 neurons of the ventral tegmental area may innervate this area. This project has aimed to discover which, if either, model is correct.

Examination of the Aphakia (AK) mouse was used to determine the role of distinct midbrain regions in SVZ regulation. Additionally, intraperitoneal injections of the chemical MPTP were used to deduce …

A Computational Biology Approach To The Analysis Of Complex Physiology: Coagulation, Fibrinolysis, And Wound Healing, Nathan Menke

Theses and Dissertations

The birth of complexity research derives from the logical progression of advancement in the scientific field afforded by reductionist theory. We present in silico models of two complex physiological processes, wound healing and coagulation/fibrinolysis based on two common tools in the study of complex physiology: ordinary differential equations (ODE) and Agent Based Modeling (ABM). The strengths of these two approaches are well-suited in the analysis of clinical paradigms such as wound healing and coagulation. The complex interactions that characterize acute wound healing have stymied the development of effective therapeutic modalities. The use of computational models holds the promise to improve …

A Novel Role Of Sirt1 In Sildenafil Induced Cardioprotection In Mice, Mona Shalwala

Theses and Dissertations

Phosphodiesterase-5 inhibitor, sildenafil (SIL) protects against myocardial ischemia/reperfusion (I-R) injury. We hypothesized that SIL-induced protection may be mediated through activation of SIRT1, an enzyme which deacetylates proteins involved in cellular stress response. Adult male ICR mice were treated with SIL (0.7mg/kg ip), Resveratrol (RSV) (5mg/kg ip) (positive control), or saline (0.2 ml ip). The hearts were harvested 24 h later and homogenized for SIRT1 activity analysis. Both SIL and RSV increased cardiac SIRT1 activity (P<0.001) as compared to Saline. Adult mouse ventricular cardiomyocytes pre-treated with either SIL or RSV (1µM) in vitro also upregulated SIRT1 activity (P<0.05). SIL also reduced infarct size following 30 min. ischemia and 24 h reperfusion in vivo. Sirtinol (5mg/kg in 10% DMSO, ip), a SIRT1 inhibitor abolished the infarct-limiting effect of SIL and RSV (P<0.001). In conclusion, activation of SIRT1 by SIL plays an essential role in cardioprotection against I-R injury.

Overexpression And Partial Purification Of Recombinant Human Serine Hydroxymethyltransferase: A Potential Anticancer Target, Suprit Singh Deol

Chemistry and Biochemistry

Serine Hydroxymethyltransferase (SHMT) is a member of the thymidylate synthase cycle that provides pyrimidine nucleotides to actively dividing cells, including cancer cells. The other two enzymes involved in this cycle have been targets for clinical anticancer drugs, suggesting that inhibitors of SHMT may also be used as clinical anticancer drugs. In order to test potential inhibitors against SHMT, human SHMT has been overexpressed in E. coli and partially purified by selective ammonium sulfate fractionation followed by anion-exchange fast protein liquid chromatography. A coupled assay using L-allo-threonine and alcohol dehydrogenase was used to identify active fractions, which were analyzed …

Terminal Deoxynucleotidyl Transferase: The Story Of A Misguided Dna Polymerase, Edward A. Motea, Anthony J. Berdis

Chemistry Faculty Publications

Nearly every DNA polymerase characterized to date exclusively catalyzes the incorporation of mononucleotides into a growing primer using a DNA or RNA template as a guide to direct each incorporation event. There is, however, one unique DNA polymerase designated terminal deoxynucleotidyl transferase that performs DNA synthesis using only single-stranded DNA as the nucleic acid substrate. In this chapter, we review the biological role of this enigmatic DNA polymerase and the biochemical mechanism for its ability to perform DNA synthesis in the absence of a templating strand. We compare and contrast the molecular events for template-independent DNA synthesis catalyzed by terminal …

Non-Natural Nucleotides As Probes For The Mechanism And Fidelity Of Dna Polymerases, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

DNA is a remarkable macromolecule that functions primarily as the carrier of the genetic information of organisms ranging from viruses to bacteria to eukaryotes. The ability of DNA polymerases to efficiently and accurately replicate genetic material represents one of the most fundamental yet complex biological processes found in nature. The central dogma of DNA polymerization is that the efficiency and fidelity of this biological process is dependent upon proper hydrogen-bonding interactions between an incoming nucleotide and its templating partner. However, the foundation of this dogma has been recently challenged by the demonstration that DNA polymerases can effectively and, in some …