Biochemistry, Biophysics, and Structural Biology Commons^™

Ectopic Expression Of A Cyanobacterial Flavodoxin In Creeping Bentgrass Impacts Plant Development And Confers Broad Abiotic Stress Tolerance, Zhigang Li, Shuangrong Yuan, Haiyan Jia, Fangyuan Gao, Qian Hu, Dongfa Sun, Hong Luo

Publications

Flavodoxin (Fld) plays a pivotal role in photosynthetic microorganisms as an alternative electron carrier flavoprotein under adverse environmental conditions. Cyanobacterial Fld has been demonstrated to be able to substitute ferredoxin (Fd) of higher plants in most electron transfer processes under stressful conditions. We have explored the potential of Fld for use in improving plant stress response in creeping bentgrass (Agrostis stolonifera L.). Overexpression of Fld altered plant growth and development. Most significantly, transgenic (TG) plants exhibited drastically enhanced performance under oxidative, drought and heat stress as well as nitrogen (N) starvation, which was associated with higher water retention and …

Group I Intron Internal Guide Sequence Binding Strength As A Component Of Ribozyme Network Formation, Elizabeth Satterwhite, Jessica Anne Mellor Yeates, Niles Lehman

Chemistry Faculty Publications and Presentations

Origins-of-life research requires searching for a plausible transition from simple chemicals to larger macromolecules that can both hold information and catalyze their own production. We have previously shown that some group I intron ribozymes possess the ability to help synthesize other ribozyme genotypes by recombination reactions in small networks in an autocatalytic fashion. By simplifying these recombination reactions, using fluorescent anisotropy, we quantified the thermodynamic binding strength between two nucleotides of two group I intron RNA fragments for all 16 possible genotype combinations. We provide evidence that the binding strength (K_D) between the 3-nucleotide internal guide sequence …

Study Of The Structure-Related Functions Of Eukaryotic Primase-Pol Alpha Complex During Replication, Yinbo Zhang

Theses & Dissertations

During eukaryotic replication primase•polymerase α (prim•polα) complex synthesizes de novo chimeric primers composed of about 10 nt RNA and 20 nt DNA, which are subsequently extended by main replicative DNA polymerases (pol), polε and polδ, on leading and lagging strands, respectively. It is estimated that prim•polα initiates more than 10 millions of lagging strand Okazaki fragments in human genome in each replication cycle. A concerted action of the two active sites, RNA pol and DNA pol, is required to ensure the efficient priming. A remarkable feature of the prim•polα complex is the “programmed” synthesis of the chimeric primer, where the …

Role Of Ddr1 In Pancreatic Cancer, Huocong Huang

Theses & Dissertations

Pancreatic ductal adenocarcinomas are highly malignant cancers, characterized by extensive invasion into surrounding tissues, metastasis to distant organs at a very early stage, and a limited response to therapy. One of the main features of pancreatic ductal adenocarcinomas is desmoplasia, which leads to extensive deposition of collagen I. We have demonstrated that collagen I can induce epithelial-mesenchymal transition (EMT) in pancreatic cancer cells. A hallmark of EMT is an increase in the expression of a mesenchymal cadherin, N-cadherin. Our previous studies have shown that up-regulation of N-cadherin can promote tumor cell invasion and that collagen I-induced EMT is through two …

Interleukin-6 Increases Matrix Metalloproteinase-14 (Mmp-14) Levels Via Down-Regulation Of P53 To Drive Cancer Progression, Jillian Cathcart, Anna Banach, Alice Liu, Jun Chen, Michael S. Goligorsky, Jian Cao

NYMC Faculty Publications

Matrix metalloproteinases (MMPs) play critical roles in cancer invasion and metastasis by digesting basement membrane and extracellular matrix (ECM). Much attention has focused on the enzymatic activities of MMPs; however, the regulatory mechanism of MMP expression remains elusive. By employing bioinformatics analysis, we identified a potential p53 response element within the MMP-14 promoter. Experimentally, we found that p53 can repress MMP-14 promoter activity, whereas deletion of this p53 response element abrogated this effect. Furthermore, we found that p53 expression decreases MMP-14 mRNA and protein levels and attenuates MMP-14-mediated cellular functions. Additional promoter analysis and chromatin immunoprecipitation studies identified a mechanism …

Interactions Of Nucleic Acid Bases With Temozolomide. Stacked, Perpendicular, And Coplanar Heterodimers, Okuma Emile Kasende, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Temozolomide (TMZ) was paired with each of the five nucleic acid bases, and the potential energy surface searched for all minima, in the context of dispersion-corrected density functional theory and MP2 methods. Three types of arrangements were observed, with competitive stabilities. Coplanar H-bonding structures, reminiscent of Watson–Crick base pairs were typically the lowest in energy, albeit by a small amount. Also very stable were perpendicular arrangements that included one or more H-bonds. The two monomers were stacked approximately parallel to one another in the third category, some of which contained weak and distorted H-bonds. Dispersion was found to be a …

App Regulates Microglial Phenotype In A Mouse Model Of Alzheimer's Disease, Gunjan Manocha, Angela Floden, Keiko Rausch, Joshua Kulas, Brett Mcgregor, Lalida Rojanathammanee, Kelley Puig, Kendra Puig, Sanjib Karki, Michael Nichols, Diane Darland, James Porter, Colin Combs

Chemistry & Biochemistry Faculty Works

Prior work suggests that amyloid precursor protein (APP) can function as a proinflammatory receptor on immune cells, such as monocytes and microglia. Therefore, we hypothesized that APP serves this function in microglia during Alzheimer's disease. Although fibrillar amyloid β (Aβ)-stimulated cytokine secretion from both wild-type and APP knock-out (mAPP−/−) microglial cultures, oligomeric Aβ was unable to stimulate increased secretion from mAPP−/− cells. This was consistent with an ability of oligomeric Aβ to bind APP. Similarly, intracerebroventricular infusions of oligomeric Aβ produced less microgliosis in mAPP−/− mice compared with wild-type mice. The mAPP−/− mice crossed to an APP/PS1 transgenic mouse line …

Autophagic Turnover Of Inactive 26s Proteasomes In Yeast Is Directed By The Ubiquitin Receptor Cue5 And The Hsp42 Chaperone, Richard S. Marshall, Fionn Mcloughlin, Richard D. Vierstra

Biology Faculty Research

Highlights

• The yeast 26S proteasome is degraded by Atg8-mediated autophagy
• Nitrogen starvation and inactivation stimulate proteaphagy via distinct pathways
• Proteasome inhibition is accompanied by extensive ubiquitylation of the complex
• Proteaphagy engages the Cue5 autophagy receptor and the Hsp42 chaperone

Summary

The autophagic clearance of 26S proteasomes (proteaphagy) is an important homeostatic mechanism within the ubiquitin system that modulates proteolytic capacity and eliminates damaged particles. Here, we define two proteaphagy routes in yeast that respond to either nitrogen starvation or particle inactivation. Whereas the core autophagic machineries required for Atg8 lipidation and vesiculation are essential for both routes, the upstream Atg1 …

Monitoring The Charge Distribution During Proton And Sodium Ion Conduction Along Chains Of Water Molecules And Protein Residues, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are used to determine the level of delocalization of the charge of a cation as it translates along a chain of water molecules or glycine residues. Charge dispersal is monitored via the molecular electrostatic potential and the dipole moment of the entire system. The positive charge is largely localized on the water molecule on which the proton is situated, but becomes more intense and extended as the proton moves along the chain. The positive charge is more delocalized in protonated polyglycine, where it extends over at least an entire residue. Displacement of the proton along the chain intensifies …

Mapping Mayapple Growth In Restored Forest, Jonathan Walt, Stephanie Praamsma, Tanner Vincent, David P. Warners

Student Papers and Reports

No abstract provided.

In Vitro Motility Of Actin Filaments Powered By Plant Myosins Xi, Cesar A. Quintana-Cataño, Christopher J. Staiger, Weiwei Zhang

The Summer Undergraduate Research Fellowship (SURF) Symposium

The actomyosin network is thought to support fundamental processes of plant development and cell expansion such as polarized elongation of root hairs and the diffuse growth of epidermal and mesophyll cells. Inhibition of myosins via pharmacological treatments represents one of the key approaches for understanding of their roles in different cellular processes. However, the use of the standard plant myosin inhibitor, 2,3-butanedionemonoxime (BDM), is questioned as it requires a high concentration and may not be as specific as desired. By testing drugs that inhibit animal and yeast myosins V, the Staiger laboratory previously found pentabromopseudilin (PBP) as a potential inhibitor …

Nanobubbles Provide Theranostic Relief To Cancer Hypoxia, Christopher M. Long, Pushpak N. Bhandari, Joseph Irudayaraj

The Summer Undergraduate Research Fellowship (SURF) Symposium

Hypoxia is a common motif among tumors, contributing to metastasis, angiogenesis, cellular epigenetic abnormality, and resistance to cancer therapy. Hypoxia also plays a pivotal role in oncological studies, where it can be used as a principal target for new anti-cancer therapeutic methods. Oxygen nanobubbles were designed in an effort to target the hypoxic tumor regions, thus interrupting the hypoxia-inducible factor-1α (HIF-1α) regulatory pathway and inhibiting tumor progression. At less than 100nm, oxygen nanobubbles act as a vehicle for site-specific oxygen delivery, while also serving as an ultrasound contrast agent for advanced imaging purposes. Through in vitro and in vivo studies, …

The Effect Of An Enhanced Isopentenyl Monophosphate Pool On Terpenoid Biosynthesis In Vivo, Evan T. Adams, Laura K. Henry, Dr. Natalia Dudareva

The Summer Undergraduate Research Fellowship (SURF) Symposium

Found in all living organisms, terpenoids make up the largest group of natural products and are essential compounds for many major processes, including photosynthesis, respiration, hormone production, and electron transport. Additionally, they have commercial and medical value in products including fragrances, cosmetics, and medicines. Terpenoids originate from the five-carbon building blocks isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are synthesized by the mevalonic acid (MVA) and methylerithritol phosphate (MEP) pathways. An alternative MVA pathway was discovered in Archaea with the final two enzymes being phosphomevalonate decarboxylase (MPD) and isopentenyl phosphate kinase (IPK). Even though this alternative pathway is not …

Mutational And Biochemical Analysis Of Isoprenylcysteine Carboxyl Methyltransferase, Sahej Bains, Amy L. Funk, Christine A. Hrycyna

The Summer Undergraduate Research Fellowship (SURF) Symposium

Ninety percent of pancreatic cancers are attributed to mutations in the Ras protein, making it paramount to concentrate on Ras activity. This study focuses on Ras activity by targeting a post-translational modifying enzyme of Ras called Isoprenylcysteine carboxyl methyltransferase (Icmt). Elucidation of the binding site of Icmt will allow the development of therapeutics that effectively inhibit Icmt causing the mislocalization of Ras, and in turn, aid in the treatment of Ras driven cancers. Currently, the hydrophobic substrate binding site of Icmt is unknown. In order to characterize the substrate binding site of Icmt, site-directed mutagenesis was used to design mutations …

Biochemical And Structural Characterization Of Cdc14 Phosphatases From Pathogenic Fungi, John Whitney, Kyle Wettschurack, Mark Hall, Jeremy Lohman, Aaron Benjamin, Lee M. Stunkard

The Summer Undergraduate Research Fellowship (SURF) Symposium

Cyclin-dependent kinases (Cdk) drive cell cycle progression and reversal of Cdk phosphorylation is essential for mitotic exit. Cdc14 is a widely conserved family of protein phosphatases that reverse Cdk phosphorylation. Recently, Cdc14 was also found to be essential for pathogenicity of some fungal plant pathogens. Fungal pathogens, like Ustilago maydis, decrease agricultural crop yield costing global agriculture by some accounts $60 billion per year. Since Cdc14 is absent in plants, a fungi specific Cdc14 inhibitor could be made to reduce the pathogenicity of U. maydis and other fungal plant pathogens to increase crop yields. To guide inhibitor development, a …

Role Of Sumoylation In Mitochondrial Division In Tetrahymena Thermophila, Ramya Modi, James Forney

The Summer Undergraduate Research Fellowship (SURF) Symposium

SUMOylation is a post translation modification that involves the addition of a small protein called SUMO, Small Ubiquitin-like MOdifier to a target protein. It is an important mechanism for the regulation of gene expression, the maintenance of genomic stability and in modifying nuclear proteins. More recently evidence has emerged for its importance in regulating mitochondrial fission and fusion in mammalian cells. This study evaluates the parameters for optimal staining of Tetrahymena thermophila mitochondria using two different dyes and then examines different cell lines with defects in the SUMOylation pathway. The first staining method uses Mitotracker Green, a vital stain that …

Expression And Site-Directed Mutagenesis Of Type Iii Polyketide Synthases, Logan R. Richards, Odessa Goudy, Lee M. Stunkard, Aaron B. Benjamin, Bethany P. Manning, Jeremy Lohman

The Summer Undergraduate Research Fellowship (SURF) Symposium

Natural products are a well-established source of drugs, and evolution has yielded polyketides such as leinamycin and iso-migrastatin that have demonstrated anti-tumor activity. Polyketides are large metabolites with a high degree of chemical variability and are commonly produced by soil bacteria. Polyketide synthases (PKS) exist as three different archetypes, and the reaction mechanisms of ketosynthases from all archetypes is not understood. Type III PKSs exist as an independently functioning ketosynthase (KS), which primarily use coenzyme A (CoA), with some exceptions, for the biosynthesis of polyketides. We elected to focus our studies on ketosynthases, because they are responsible for forming the …

Runoff Volume Reduction From Subbasins In Plaster Creek Watershed, Kent County, Mi, Julie Wildschut, Dena De Kryger

Student Papers and Reports

No abstract provided.

The Green Team And The Restoration Of Plaster Creek, Leira Lew, Micah Warners, Gail Heffner, David P. Warners

Student Papers and Reports

No abstract provided.

Sweetening Of Glutamine Metabolism In Cancer Cells By Rho Gtpases Through Convergence Of Multiple Oncogenic Signaling Pathways, Thambi Dorai, John T. Pinto, Arthur J. L. Cooper

NYMC Faculty Publications

Comment on: Lukey MJ, Greene KS, Erickson JW, et al. The oncogenic transcription factor c-Jun regulates glutaminase expression and sensitizes cells to glutaminase-targeted therapy. Nat Commun 2016;7:11321.

Protein Crystallization Tray Protocol Development, Brooke Connell

STAR Program Research Presentations

In the field of protein crystallography the transfer of the protein crystals from the crystallization plate/tray, where the crystals are initially grown, to the site of analysis is a difficult and lengthy process. A new crystallization tray has been designed and 3D printed to eliminate this intermediate step which is called crystal fishing. The crystallization tray allows crystals to be grown directly on grids that are attached to the pins that are used for analysis of the crystal. The efficacy of protein crystallization using the aforementioned tray was tested in order for a protocol to be developed for potential users …

Comparative Analysis Of In Situ Fibronectin Using Tof-Sims, Spi-Ms, And Dropdesi-Ms In A Microfluidic Reactor, Shannon Fasing, Xiao-Ying Yu, Juan Yao, Jiachao Yu

STAR Program Research Presentations

Fibronectin is an important biomolecule due to its role in cell differentiation, growth, kinesis, and adhesion. Such biological responses are mediated through membrane recognition and signaling; where fibronectin is found. Studying the outer molecular surface of fibronectin allows deeper insight into the microbiological reactions that occur during these processes. In situ mass spectrometry analysis in aqueous solution accurately represents fibronectin’s chemical components, made possible by a vacuum compatible microfluidic reactor, SALVI (System for Analysis at the Liquid Vacuum Interface). SALVI was paired with the analytical tools: time-of-flight secondary ion mass spectrometer (ToF-SIMS), single photon ionization mass spectrometer (SPI-MS) and drop …

Investigation Of An Energetic Coupling Between Ligand Binding And Protein Folding, Nathan W. Gardner

Open Access Dissertations

The cellular environment presents a protein with many small molecules with which it may interact. Many novel interactions between proteins and non-substrate metabolites are being uncovered through proteome-wide screens. The homodimeric Escherichia coli cofactor-dependant phosphoglycerate mutase (dPGM) was identified as an ATP binding protein in a proteome-wide screen, but dPGM does not use ATP for catalysis. This dissertation elucidates the effect of ATP and other non-substrate metabolites on dPGM. Initial investigations revealed a partially unfolded, monomeric intermediate of dPGM that forms during equilibrium unfolding. ATP binding was found to occur at the active site of dPGM and to be energetically …

Intestinal Cytoplasmic Lipid Droplets, Associated Proteins, And The Regulation Of Dietary Fat Absorption, Theresa M. D'Aquila

Open Access Dissertations

Dietary fat provides essential nutrients, contributes to energy balance, and regulates blood lipid concentrations. These functions are important to health, but can also become dysregulated and contribute to diseases such as obesity, diabetes, and cardiovascular disease. The small intestine absorbs dietary fat through an efficient multi step process of digestion, uptake, metabolism, and secretion or storage. When dietary fat is taken up by the absorptive cells of the small intestine, enterocytes, it can be secreted into circulation where it contributes to blood lipid levels or temporarily stored in cytoplasmic lipid droplets (CLDs). The objective of this dissertation is to investigate …

Curb-Cut Rain Garden Research, Patrick Jonker, David P. Warners

Student Papers and Reports

No abstract provided.

Parameterization Of Single-Scattering Albedo (Ssa) And Absorption Ångström Exponent (Aae) With Ec/Oc For Aerosol Emissions From Biomass Burning, Rudra P. Pokhrel, Nick L. Wagner, Justin M. Langridge, Daniel A. Lack, Thilina Jayarathne, Elizabeth A. Stone, Chelsea E. Stockwell, Robert J. Yokelson, Shane M. Murphy

Chemistry and Biochemistry Faculty Publications

Single-scattering albedo (SSA) and absorption Ångström exponent (AAE) are two critical parameters in determining the impact of absorbing aerosol on the Earth's radiative balance. Aerosol emitted by biomass burning represent a significant fraction of absorbing aerosol globally, but it remains difficult to accurately predict SSA and AAE for biomass burning aerosol. Black carbon (BC), brown carbon (BrC), and non-absorbing coatings all make substantial contributions to the absorption coefficient of biomass burning aerosol. SSA and AAE cannot be directly predicted based on fuel type because they depend strongly on burn conditions. It has been suggested that SSA can be effectively parameterized …

The Effect Of R382w Mutation On Citrus Paradisi Flavonol Specific 3-O-Glucosyltransferase, Kathleen King

Undergraduate Honors Theses

Flavonoids are a class of plant metabolites with C6-C3-C6 structure responsible for many biological functions, including coloration and defense. Citrus paradisi, grapefruit, contains a wide variety of flavonoids which are grouped by the extent of modification, examples of which are flavonols, flavones, and flavanones. A major modification is the addition of glucose by glucosyltransferases (GTs) to stabilize the structure and provide ease of transport. Glucosyltransferases can be highly substrate and regiospecific. With Cp3OGT, glucose is added at the 3-hydroxy position. This 3GT only accepts flavonols as its substrate; however, a Vitis vinifera (grape) 3-GT can accept both flavonols and …

Snp-Based High Density Genetic Map And Mapping Of Btwd1 Dwarfing Gene In Barley, Xifeng Ren, Jibin Wang, Lipan Liu, Genlou Sun, Chengdao Li, Hong Luo, Dongfa Sun

Publications

A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of …

Vascular Endothelial Growth Factor-A Gene Electrotransfer Promotes Angiogenesis In A Porcine Model Of Cardiac Ischemia, Anna A. Bulysheva, Barbara Hargrave, Nina Burcus, Cathryn G. Lundberg, Len Murray, Richard Heller

Bioelectrics Publications

This study aimed to assess safety and therapeutic potential of gene electrotransfer (GET) as a method for delivery of plasmid encoding vascular endothelial growth factor A (VEGF-A) to ischemic myocardium in a porcine model. Myocardial ischemia was induced by surgically occluding the left anterior descending coronary artery in swine. GET following plasmid encoding VEGF-A injection was performed at four sites in the ischemic region. Control groups either received injections of the plasmid without electrotransfer or injections of the saline vehicle. Animals were monitored for 7 weeks and the hearts were evaluated for angiogenesis, myocardial infarct size and left ventricular contractility. …

Enhancing Silymarin Fractionation Via Molecular Modeling Using The Conductor-Like Screening Model For Real Solvents, Emma C. Brace

Open Access Theses

The market for bio-based products from plant sources is on the rise. There is a global challenge to implement environmentally clean practices for the production of fuels and pharmaceuticals from sustainable resources. A significant hurdle for discovery of comparable plant-derived products is the extensive volume of trial-and-error experimentation required. To alleviate the experimental burden, a quantum mechanics based molecular modeling approach known as the COnductor-like Screening Model for Real Solvents (COSMO-RS) was used to predict the best biphasic solvent system to purify silymarins from an aqueous mixture. Silymarins are a class of flavonolignans present in milk thistle ( Silybum marianum …