Biochemistry, Biophysics, and Structural Biology Commons^™

Spt5 Affects The Rate Of Mrna Degradation And Physically Interacts With Ccr4 But Does Not Control Mrna Deadenylation, Yajun Cui, Yueh-Chin Chiang, Palaniswamy Viswanathan, Darren J. Lee, Clyde L. Denis

New Hampshire Agricultural Experiment Station Publications

The CCR4-NOT complex has been shown to have multiple roles in mRNA metabolism, including that of transcriptional elongation, mRNA transport, and nuclear exosome function, but the primary function of CCR4 and CAF1 is in the deadenylation and degradation of cytoplasmic mRNA. As previous genetic analysis supported an interaction between SPT5, known to be involved in transcriptional elongation, and that of CCR4, the physical association of SPT5 with CCR4 was examined. A two-hybrid screen utilizing the deadenylase domain of CCR4 as a bait identified SPT5 as a potential interacting protein. SPT5 at its physiological concentration was shown to immunoprecipitate CCR4 and …

Design And Synthesis Of Cationic Steroid Antimicrobial Compounds, Synthesis Of Glycolipids Recognized By Natural Killer T Cells And Development Of Tlr-1, Tlr-6 Heterodimer Binders And Studies Of Their Immunology Activities, Yanshu Feng

Theses and Dissertations

Cationic steroid antimicrobial agents (CSAs) are a family of bile acid derivatives. These compounds are amphiphilic and mimic endogenous antimicrobial peptides. The antimicrobial activities of CSA-13 have been investigated and due to portent bactericidal activities and low toxicity, a large amount of CSA-13 is demanded for clinic trails and other antimicrobial applications. During our studies, we optimized the synthetic route of CSA-13, so that it can be prepared at the kilogram, even in tons scale. We investigated three routes and one of them is suitable for industry, because only recrystallization is needed in the synthesis. Natural killer T cells (NKT …

Synthesis Of Resveratrol Esters And Aliphatic Acids., Stanley Mofor Jing

Electronic Theses and Dissertations

Resveratrol (RV) is a naturally occurring phytoalexin of the stilbenoid family produced by some plant species, and present in grape skin, peanuts, and red wine. It has been found to exhibit anti-cancer, anti-inflammatory, anti-viral, anti-aging, cardio protective, and anti-oxidant properties. Bioavailability is a huge setback that limits the potentials of RV. As a result, efforts have been made to design and synthesize RV esters and aliphatic acids in an attempt to increase its bioavailability, solubility in water, and possibly improving its biological activities. Resveratrol esters, 3,5,4'-triacetyloxystilbene (2) and Methyl 1,1',1''- (3,4',5-stilbenyl)-1,6-hexanedioate (3) have been synthesized. Compound 3 is a new …

Reactions With Platinum (Ll) Complexes And Selenium-Containing Amino Acids, Stephanie Robey

Mahurin Honors College Capstone Experience/Thesis Projects

We have reacted [Pt(Me₄en)(D₂O)₂]²⁺ [Me₄En=N,N,N’N’-tetramethylethylenediamine] with Selenomethionine (SeMet), Methionine (Met), and Methylselenocysteine (MeSeCys). When MeSeCys was reacted with [Pt(Me₄en)(D₂O)₂]²⁺, we observed both stereoisomers of Se,N chelates, as well as [Pt(Me₄en)(MeSeCys)Cl]⁺ from ­¹­H NMR Spectroscopy; the latter formed due to the presence of Cl^- in the solution. Both isomers of the chelate seemed to form proportionally to one another, not favoring a specific stereoisomer. Eventually the [Pt(Me₄en)(MeSeCys)Cl]⁺ products became Se,N chelates. We incubated SeMet with …

Influence Of Weak Interactions On Supramolecular Binding: Characterization Of Cucurbituril Complexes With Alkylmonoammonium Ions Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Ruijan Shi

Theses and Dissertations

This thesis focuses on using mass spectrometry-based techniques for characterizing the structure and behavior of cucurbituril complexes in the gas phase. Both solvent and counter ion effects can be completely eliminated in the gas phase and the intrinsic interactions in the system are directly shown in the experimental results. Chapter 1 introduces the structures, properties and host-guest chemistry of cucurbituril, and FTICR mass spectrometry including instrumentation, performance and working principles. Two mass spectrometry-based methods for supramolecular characterization, sustained off-resonance irradiation collision induced dissociation (SORI CID) and ion molecule equilibrium measurements, are also discussed in this chapter. Chapter 2 characterizes the …

Discrimination And Aggregative Patterns Among And Between Populations Of Entamoeba Spp., Katelyn M. Higgins

Honors Senior Capstones and Theses

Kin recognition facilitates the evolution of cooperation in animals, but its relevance in microorganisms and their behavior toward relatives remains unclear. The Entamoeba lineage constitutes an ideal model to determine the behavioral and signaling cues needed for aggregative preference. Chemical cues have been reported for E. histolytica but not E. dispar, suggesting cell-communication between con-specifics and behavioral differences with relevance for disease. Entamoeba varieties have been reported as ‘morphologically undistinguishable’. Two strains of E. invadens have been isolated from different hosts (VK-1: NS - Varanus komodoensis and IP1- serpentes) but were classified within the same ‘species’. Trophozoites …

Son Maintains Accurate Splicing For A Subset Of Human Pre-Mrnas, Alok Sharma, Michael P. Markey, Keshia Torres-Munoz, Sapna Varia, Madhavi P. Kadakia, Athanasios Bubulya, Paula A. Bubulya

Biochemistry and Molecular Biology Faculty Publications

Serine-arginine-rich (SR) proteins play a key role in alternative pre-mRNA splicing in eukaryotes. We recently showed that a large SR protein called Son has unique repeat motifs that are essential for maintaining the subnuclear organization of pre-mRNA processing factors in nuclear speckles. Motif analysis of Son highlights putative RNA interaction domains that suggest a direct role for Son in pre-mRNA splicing. Here, we used in situ approaches to show that Son localizes to a reporter minigene transcription site, and that RNAi-mediated Son depletion causes exon skipping on reporter transcripts at this transcription site. A genome-wide exon microarray analysis was performed …

Mechanism Of G Protein Beta-Gamma Assembly Mediated By Phosducin-Like Protein 1, Chun Wan Jeffrey Lai

Theses and Dissertations

G-protein coupled receptor signaling (GPCR) is essential for regulating a large variety of hormonal, sensory and neuronal processes in eukaryotic cells. Because the regulation of these physiological responses is critical, GPCR signaling pathways are carefully controlled at different levels within the cascade. Phosducin-like protein 1 (PhLP1) can bind the G protein βγ dimer and participate in GPCR signaling. Recent evidence has supported the concept that PhLP1 can serve as a co-chaperone of the eukaryotic cytosolic chaperonin complex CCT/TRiC to mediate G βγ assembly. Although a general mechanism of PhLP1-mediated G βγ assembly has been postulated, many of the details about …

Co-Crystallization And Polymorphism Of Naturally Occurring Peptide Derivatives, Kevin Crowley

Honors Theses

Carnosine is a dipeptide compound that is found in many dietary supplements and food products. Carnosine has many functions in the body, such as alleviating oxidative stress on tissues by acting as an antioxidant compound. Carnosine, therefore, has important anti-aging properties. Carnosine is also capable of forming protective sequestration structures around heavy metal ions; this process of chelating metals ions in solutions is very beneficial for maintaining the well-being of cells in the body. Thus, carnosine could be useful in pharmaceutical products for creating anti-aging drugs that would reduce tissue stress and promote a healthy cellular environment. I attempted to …

Map Kinases Couple Hindbrain-Derived Catecholamine Signals To Hypothalamic Adrenocortical Control Mechanisms During Glycemia-Related Challenges, Arshad Khan, Kimberly Kaminski, Graciela Sanchez-Watts, Todd Ponzio, J. Kuzmiski, Jaideep Bains, Alan Watts

Selected Works Temporary Series

No abstract provided.

Map Kinases Couple Hindbrain-Derived Catecholamine Signals To Hypothalamic Adrenocortical Control Mechanisms During Glycemia-Related Challenges, Khan, Kimberly Kaminski, Graciela Sanchez-Watts, Todd Ponzio, J. Kuzmiski, Jaideep Bains, Alan Watts

Departmental Papers (Biology)

No abstract provided.

Juvenile Hormone Regulates Vitellogenin Gene Expression Through Insulin-Like Peptide Signaling Pathway In The Red Flour Beetle, Tribolium Castaneum, Zhentao Sheng, Jingjing Xu, Hua Bai, Fang Zhu, Subba R. Palli

Entomology Faculty Publications

Our recent studies identified juvenile hormone (JH) and nutrition as the two key signals that regulate vitellogenin (Vg) gene expression in the red flour beetle, Tribolium castaneum. Juvenile hormone regulation of Vg synthesis has been known for a long time in several insects, but the mechanism of JH action is not known. Experiments were conducted to determine the mechanism of action of these two signals in regulation of Vg gene expression. Injection of bovine insulin or FOXO double-stranded RNA into the previtellogenic, starved, or JH-deficient female adults increased Vg mRNA and protein levels, thereby implicating the pivotal role for …

Regulation Of High Light Responses In Synechocystis Sp. Pcc6803, Waqar Majeed

Theses and Dissertations

Cyanobacteria have evolved various acclimation mechanisms to enable them to thrive under harsh environmental conditions. There are a total of more than 80 sensory kinases and response regulators on the genome of the cyanobacterium Synechocystis sp. PCC 6803, which coordinate the molecular responses to changes in environmental conditions. However, it is not clearly understood how these regulators control the stress-responsive genes. This dissertation focuses on analysis of the functions of two regulators, RpaA and DspA, by targeted mutagenesis. Upon deletion of RpaA, a significant reduction in chlorophyll fluorescence from photosystem I at 77K was observed in whole cells and the …

Characterizing The Phosphorylation State Of Tie2 Using Sh2 Domain Fusion Proteins, Kenneth Yuth

Theses and Dissertations

The cardiovascular system develops through two distinct processes in embryogenesis: vasculogenesis, whereby the primary plexus in the heart is formed along with embryonic and extraembryonic vasculature, and angiogenesis, which begins after vasculogenesis and results in the refinement and maturation of the branched vessel system. In pathological angiogenesis, tumors expand by releasing pro-angiogenic factors in response to hypoxic conditions. The Tie receptors, Tie1 and Tie2, are receptor tyrosine kinases that are integral to angiogenic pathways. A family of Angiopoietins, Ang1-4, have been shown to act as ligands for Tie2, of which Ang1 and Ang2 are best characterized. Activation of the receptor …

Gene Expression And Physiological Analyses To Study Metabolic Shifts In Medicago Truncatula Subjected To Biotic Stresses, Michelle Ryan Martin

Graduate Theses and Dissertations

Plants are frequently under attack from pests and deploy various defense mechanisms to fight off predators. Many plant defenses are induced following herbivory or pathogen infection. An investment in defense could potentially lead to a diversion of metabolic resources away from primary metabolism, including reduction in plant commitment to photosynthesis. In this thesis, changes in expression levels of representative genes for primary and secondary metabolism were studied using real-time polymerase chain reaction (PCR) in Medicago truncatula Gaertner subjected to beet armyworm (Spodoptera exigua H¨¹bner) damage or Phoma medicaginis Malbr. & Roum. infection. Photosynthetic yield was also measured using chlorophyll fluorescence …

Characterization Of De Novo Fatty Acid Biosynthesis In Soybean Somatic Embryo Plastids, Karen Clark

All Theses

A method for the isolation of intact physiologically active plastids from rapidly developing soybean (Glycine max L.) somatic embryos has been developed for the in vitro study of lipid metabolism. Using de novo fatty acid biosynthesis from 14C-acetate as a marker for physiological functionality, the greatest rates of fatty acid biosynthesis were recovered in 3000 x g fractions that were isolated in the presence of 0.5 M sorbitol, with essentially no activity occurring in the 3000 x g supernatant. Plastids purified on 10% Percoll were approximately 70 and 97 % free from mitochondrial and ER contamination, respectively, as judged …

Impact Of Collateral Enlargement On Smooth Muscle Phenotype, Alexander Jerome Bynum

Master's Theses

Peripheral Artery Disease is a very serious disease characterized by an arterial occlusion due to atherosclerotic plaques. In response to an arterial occlusion, arteriogenesis occurs, causing smooth muscle cells to transition from a contractile to synthetic state. Also following an arterial occlusion, functional impairment was seen in the collateral circuit. An immunofluorescence protocol was developed in order to assess the impact of collateral enlargement (arteriogenesis) on smooth muscle phenotype at various time points. Smooth muscle α-actin was used to mark all smooth muscle cells, Ki-67 was used to label proliferating smooth muscle cells, and a fluorescent nuclear stain was used …

Cellular Poly(C) Binding Proteins 1 And 2 Interact With Porcine Reproductive And Respiratory Syndrome Virus Nonstructural Protein 1Β And Support Viral Replication, Lalit Beura, Phat X. Dinh, Fernando A. Osorio, Asit K. Pattnaik

School of Veterinary and Biomedical Sciences: Faculty Publications

Porcine reproductive and respiratory syndrome virus (PRRSV) infection of swine results in substantial economic losses to the swine industry worldwide. Identification of cellular factors involved in PRRSV life cycle not only will enable a better understanding of virus biology but also has the potential for the development of antiviral therapeutics. The PRRSV nonstructural protein 1 (nsp1) has been shown to be involved in at least two important functions in the infected hosts: (i) mediation of viral subgenomic (sg) mRNA transcription and (ii) suppression of the host’s innate immune response mechanisms. To further our understanding of the role of the viral …

Impact Of Crop And Residue Management On The Physical And Chemical Stabilization Of Soil Organic Matter At Farm Level, Ana B. Wingeyer

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

This dissertation explores changes over time in soil organic matter (SOM) stabilization of two irrigated production fields: a continuous maize sequence that was converted from no-till to conservation deep tillage (Site 1), and a no-till maize-soybean rotation (Site 2). An integrated approach using humic acid extractions and density-based physical fractionation of SOM within aggregate size classes was developed to evaluate the changes in SOM stabilization (physical protection, organo-mineral associations and humification). At Site 1, loss of SOM in the surface layer was compensated for by increased SOM in deeper soil layers with no net change in C stocks. Whole field …

A Polymerase Chain Reaction Method For The Detection Of Selenomonas Noxia, Arthuro Mehretu

UNLV Theses, Dissertations, Professional Papers, and Capstones

In recent studies, periodontal health has been linked to being overweight and/or obese. Among common oral bacteria, Selenomonas noxia has been implicated in converting periodontal health to disease. Selenomonas spp. have also been found in gastric ulcers, and were misdiagnosed as Helicobacter -like organisms, but no further studies were conducted. The increasing clinical and epidemiological importance of S. noxia necessitates the development of a rapid detection method. In this study, a TaqMan 16S rRNA based real-time Polymerase Chain Reaction (PCR) method was developed, optimized and evaluated for the rapid and specific detection of S. noxia . The 16S PCR assay …

Visualizing The Spatial Localization Of Active Matrix Metalloproteinases (Mmps) Using Maldi Imaging Ms, Sasirekha Muruganantham

Graduate Theses and Dissertations

Biomaterial implantation induces the foreign body response (FBR). Development of longer-term implants relies on the thorough understanding of the FBR. The progression of the FBR is regulated by a number of biomolecules including cytokines, chemokines, and matrix metalloproteinases (MMPs). The nature of the FBR requires the spatial and temporal regulation of these mediators. MMPs are an extremely large and diverse group of enzymes that play key roles in regulating the FBR. Precise spatiotemporal regulation of MMPs defines their proteolytic activities. The aim of this project is to develop a new bioanalytical method to visualize the localization of active MMPs at …

In Vitro Selection Of Aptamers Against Avian Influenza Virus H5n1, Jingjing Zhao

Graduate Theses and Dissertations

Over $10 billion losses in the poultry industry were caused by avian influenza (AI) so far. Rapid and specific detection of avian influenza virus is urgently needed with the concerns over the outbreaks of highly pathogenic H5N1 influenza virus and cases of animal and human infection. Aptamers are oligonucleic acid or peptide molecules that bind a specific target molecule with good affinity. They show better thermal stability than antibodies. The goal of this research was to select DNA-aptamers as the specific recognition element of AI H5N1virus to be used in detection assays specific for field application. In this study, Systematic …

The Role Of Receptor Tyrosine Kinase Axl In Pancreatic Ductal Adenocarcinoma And Its Regulation By Hematopoietic Progenitor Kinase 1, Xianzhou Song

Dissertations and Theses (Open Access)

Pancreatic ductal adenocarcinoma (PDA) is one of the most aggressive malignancies with less than 5% of five year survival rate. New molecular markers and new therapeutic targets are urgently needed for patients with PDA. Oncogenic receptor tyrosine kinase Axl has been reported to be overexpressed in many types of human malignancies, including diffuse glioma, melanoma, osteosarcoma, and carcinomas of lung, colon, prostate, breast, ovary, esophagus, stomach, and kidney. However, the expression and functions of Axl in PDA are unclear. We hypothesized that Axl contributes to the development and progression of PDA. We examined Axl expression in 54 human PDA samples …

Homologous Recombination In Nannochloropsis: A Powerful Tool In An Industrially Relevant Alga, Donald P. Weeks

Department of Biochemistry: Faculty Publications

The availability of facile methods for targeted gene knockout and gene replacement based on homologous recombination in bacteria and yeast systems has driven rapid progress in understanding many of the complex metabolic and regulatory networks in prokaryotic and eukaryotic cells. The lack of such tools in other organisms is a major impediment to progress both in fundamental research and in research that is directed toward practical economic and societal outcomes. For example, the current goal to replace fossil fuels with renewable energy sources produced by plants and algae is hampered in both the short term and the long term by …

Conformational Changes In The Extracellular Domain Of Glutamate Receptors, Anu Rambhadran

Dissertations and Theses (Open Access)

The family of membrane protein called glutamate receptors play an important role in the central nervous system in mediating signaling between neurons. Glutamate receptors are involved in the elaborate game that nerve cells play with each other in order to control movement, memory, and learning.

Neurons achieve this communication by rapidly converting electrical signals into chemical signals and then converting them back into electrical signals. To propagate an electrical impulse, neurons in the brain launch bursts of neurotransmitter molecules like glutamate at the junction between neurons, called the synapse. Glutamate receptors are found lodged in the membranes of the post-synaptic …

Definition Of The Landscape Of Chromatin Structure At The Frataxin Gene In Friedreich’S Ataxia, Eunah Kim

Dissertations and Theses (Open Access)

Friedreich’s ataxia (FRDA) is caused by the transcriptional silencing of the frataxin (FXN) gene. FRDA patients have expansion of GAA repeats in intron 1 of the FXN gene in both alleles. A number of studies demonstrated that specific histone deacetylase inhibitors (HDACi) affect either histone modifications at the FXN gene or FXN expression in FRDA cells, indicating that the hyperexpanded GAA repeat may facilitate heterochromatin formation. However, the correlation between chromatin structure and transcription at the FXN gene is currently limited due to a lack of more detailed analysis. Therefore, I analyzed the effects of the hyperexpanded GAA …

Global And Specific Controls Of Protein Synthesis In Hibernators, Peipei Pan

UNLV Theses, Dissertations, Professional Papers, and Capstones

Mammalian hibernation is a highly dynamic physiological process that is composed of a series of torpor bouts, wherein hibernators oscillate between periods of torpor and interbout arousal. Although normally vital to homeostasis, many energetically consumptive processes such as translation or protein synthesis are virtually ceased during hibernation. Earlier studies indicated that protein synthesis had fallen to almost negligible levels. Cap-dependent initiation of translation is well regulated by eukaryotic translation initiation factor 4E (eIF4E) and its binding partner eIF4E-binding protein 1 (4E-BP1) when hibernators cycle in and out the torpor state. Herein, I investigated well-characterized regulatory mechanisms of global and specific …

Proteome Based Development Of Novel Affinity Tail For Immobilized Metal Affinity Chromatography And Hydrophobic Interaction Chromatography, Neha Tiwari

Graduate Theses and Dissertations

At industrial scale, reducing the step in purification and recovery is desired; this not only decreases the cost but also increases the yield. Hydrophobic Interaction Chromatography (HIC) and Immobilized Metal Affinity Chromatography (IMAC) both are not harsh on biological structure or activity of proteins; also both the techniques are economical and therefore a suitable choice at industrial level. This dissertation comprises of three parts. Purpose for the Part I was to identify and characterize Escherichia coli proteins which display affinity towards both IMAC and Hydrophobic Interaction Chromatography (HIC). Co (II) IMAC was chosen as the primary capture step, followed by …

Host-Virus Interactions Of Infectious Laryngotracheitis Virus Infection In Cultured Cells, Jeong Yoon Lee

Graduate Theses and Dissertations

Infectious laryngotracheitis virus (ILTV; Gallid herpesvirus 1) causes upper respiratory diseases in mainly chickens and exhibits 90-100% of high morbidity and up to 70% of mortality, resulting in huge economic losses in the poultry industry worldwide.

To study host-ILTV interactions, the changes in genome-wide gene expressions in response to wild-type and vaccine ILTV infections in primary chicken embryo lung cells were investigated using microarray analysis. Results provide crucial insights into host cell pathogenic and immunogenic responses against wild-type and vaccine ILTV infections. Using microarray method and Ingenuity Pathway Analysis (IPA) bioinformatics tool, 273 and 306 differentially expressed genes were identified …

Design And Fabrication Of Nanofluidic Systems For Biomolecule Characterizations, Orain Ansel Hibbert

Graduate Theses and Dissertations

Nanofluidic channel systems were designed and fabricated by combining MEMS microfabrication with AFM nanolithography. In the fabrication process flow, photolithography was first utilized to pattern microfluidic channels and reservoirs on a 4" Pyrex substrate. Subsequently, atomic force microscopy (AFM) based nanolithography was used to mechanically fabricate nanochannels to connect the microreservoirs which formed the inlet and outlet of the nanofluidic system. A Tap190 Diamond-Like Carbon (DLC) AFM tip with a force constant of 48 N/m and a radius of less than 15 nm was used as the nanolithography tool. The resultant nanochannel ranges from 20 to 80 µm in length …