Biochemistry Commons^™

Elucidation Of The Pax/Six Gene Regulatory Network In Ephydatia Muelleri, Anna Rued

Honors Theses

The evolution of gene regulatory networks accounts for much of the diversity we observe in the animal kingdom. In particular, the Pax/Six/Eya/Dac gene network has been known to play critical roles in development of all bilaterians and cnidarians. However, this network has not been characterized in Porifera. These studies focus on tracing the evolutionary history of the PSED network back to the most basal organism in the metazoan phylogeny through demonstrating the presence of a direct gene regulatory network between PaxB and Six1/2 orthologs in sponges. To this end, putatitve Six1/2 cis- regulatory elements were identified while the PaxBprd transcription …

Alteration In 5ht1a Receptor Activity From A Prenatal Exposure To Dexamethasone In A Stressed And Non-Stressed Adult Male Rat, Darshan S. Shah

Honors Theses

Synthetic glucocorticoids (GC) are used as a clinical therapeutic to stimulate lung development in fetuses that present the risk of preterm delivery. Previous studies have shown that a prenatal exposure to Dexamethasone (DEX) causes a disturbance in normal GC mediation of neuritic outgrowth, cell signaling, and serotonergic systems. Our hypothesis is that a prenatal exposure to DEX during the third trimester of pregnancy alters 5HT1A receptor function. Pregnant dams were injected daily with 150μg/ml/kg of DEX from gestation day 14 through 19. Control dams were treated with and equal volume of saline. Swim stress followed by elevated plus maze testing …

The Optimization Of A One-Pot Heteroconjugate Addition-Oxidation-Diels-Alder Reaction, Christina Vivelo

Honors Theses

Ynoate esters are ideal reagents for one-pot reactions due to their ability to undergo multiple addition reactions in one flask. Ethyl propiolate undergoes a heteroconjugate addition reaction with aromatic thiol nucleophiles, producing an enoate which is then oxidized by m-CPBA and is able to undergo a Diels–Alder reaction with cyclopentadiene. The work presents the optimization of a three-step heteroconjugate addition-oxidation-Diels–Alder reaction to yield cyclic compounds favoring endo stereochemistry, which may be used in further synthesis of biologically active compounds such as (+)-Methyl-5-epi-Shikimate or Deipeptyl-IV-Peptidase inhibitor.

The Role Of Histidines In Neurosteroid Binding Of Nmda Glun2b And D Subunits, Sarah Rhoads

Honors Theses

Implicit in cellular mechanisms essential for learning and memory, NMDA receptors are heterotetrameric members of the family of ionotropic glutamate receptors. Activation of the glutamate-specific receptor subunits results in the opening of ion channels, triggering an excitatory pathway, which can be moderated by certain endogenous and exogenous compounds. Previous research with the endogenous neurosteroids pregnenolone sulfate (PS) and 3α-hydroxy-5-β-20-one sulfate (PregS) have indicated that the binding of these neurosteroids to NMDA receptors containing the four A-D isoforms of the GluN2 subunit affects current flow through them1. Binding of PS to NMDA receptors containing GluN2A or GluN2B subunits causes an increased …

Determination Of The Atomic Resolution Structure Of A Dna Polymerase I Isolated From Rhodothermus Marinus, Natalie S. Omattage

Honors Theses

DNA polymerase I employs a multistep mechanism for sorting correctly paired nucleotides from mismatches. We aim to characterize reaction intermediates during nucleotide selection to better understand how this class of enzymes achieves high DNA replication fidelity. DNA polymerase I from R. marinus contains an unusual and disruptive proline in the mobile O helix near the active site. To characterize this enzyme, the structure of the large (5´-to-3´ exo-deficient) fragment of the R. marinus DNA polymerase I (RF) was solved to 2.95 Å (R = 0.234) using multi-wavelength anomalous dispersion. Alignment …

Design Of In Vivo Assays For Study Of Transport, Biocompatibility And Toxicity Of Nanoparticles, Kerry Jean Lee

Theses and Dissertations in Biomedical Sciences

This dissertation focuses on the design of new in vivo assays for study of transport, biocompatibility and toxicity of nanoparticles (NPs) in zebrafish embryos. We synthesized and purified spherical silver (Ag) NPs with diameters, ranging from 12 to 95 nm, that are stable (non-aggregated) in egg-water media. We developed new imaging approaches to characterize the sizes of single Ag NPs in zebrafish embryos at nanometer resolution by measuring their size-dependent plasmonic spectra and scattering intensity using dark-field optical microscopy and spectroscopy (DFOMS). We used single Ag NPs because they exhibit the high quantum yield (QY) of Rayleigh scattering and resist …

Composition And Evolution Of The Vertebrate And Mammalian Selenoproteomes, Marco Mariotti, Perry G. Ridge, Yan Zhang, Alexei V. Lobanov, Thomas H. Pringle, Roderic Guigo, Dolph L. Hatfield, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Background: Selenium is an essential trace element in mammals due to its presence in proteins in the form of selenocysteine (Sec). Human genome codes for 25 Sec-containing protein genes, and mouse and rat genomes for 24.

Methodology/Principal Findings: We characterized the selenoproteomes of 44 sequenced vertebrates by applying gene prediction and phylogenetic reconstruction methods, supplemented with the analyses of gene structures, alternative splicing isoforms, untranslated regions, SECIS elements, and pseudogenes. In total, we detected 45 selenoprotein subfamilies. 28 of them were found in mammals, and 41 in bony fishes. We define the ancestral vertebrate (28 proteins) and mammalian …

Correction To Fully Enclosed Microfluidic Paper-Based Analytical Devices, Kevin M. Schilling, Anna L. Lepore, Jason A. Kurian, Andres W. Martinez

Chemistry and Biochemistry

There is an error in the units of the concentrations of potassium iodide and trehalose described in the experimental details on page 1581. The correct concentrations are 0.6 M potassium iodide and 0.3 M trehalose.

Connections Between Sphingosine Kinase And Phospholipase D In The Abscisic Acid Signaling Pathway In Arabidopsis, Liang Guo, Girish Mishra, Jennifer E. Markham, Maoyin Li, Amanda Tawfall, Ruth Welti, Xuemin Wang

Department of Biochemistry: Faculty Publications

Background: Sphingosine kinase (SPHK) and phospholipaseD(PLD) produce different lipid mediators involved in abscisic acid (ABA) response.

Results: Ablation of SPHKs and PLDα1 attenuates ABA-induced production of LCBPs and PA. Phyto-S1P closes stomata in sphk1, sphk2, but not in pldα1, whereas PA closes stomata in all mutants.

Conclusion: SPHK acts upstream of PLDα1, whereas PLDα1 promotes SPHK.

Significance: The roles of lipid messengers in the ABA signaling pathway are clarified.

Novel Phosducin-Like Protein Binding Partners: Exploring Chaperone And Tumor Suppressor Protein Interactions, Amy Jetaun Gray

Theses and Dissertations

Many proteins cannot fold into their native state without the assistance of one or more molecular chaperones. Chaperonins are an essential class of chaperones that provide an isolated chamber for proteins to fold. CCT, a group II chaperonin found in eukaryotes assists in the folding of actins, tubulins, and many other cellular proteins. PhLP1 is a member of the phosducin protein family that assists CCT in the folding of Gβ and its subsequent assembly with Gγ. However, previous studies have not addressed the scope of PhLP1 and CCT-mediated Gβγ; assembly. The data presented in Chapter 2 shows that PhLP1 plays …

Follicular Dendritic Cells, Human Immunodeficency Virus Type 1, And Alpha 1 Antitrypsin, Xueyuan Zhou

Theses and Dissertations

HIV/AIDS is raging and causing millions of deaths around the world. The major challenge in treating HIV/AIDS is the establishment of HIV reservoirs where the viruse escapes both drug and immune system attempts at eradication. Throughout the course of HIV/AIDS, productive HIV infection occurs primarily in the lymphoid follicles or germinal centers (GC) surrounding follicular dendritic cells (FDC). In the GCs, FDCs trap and maintain infectious HIV for years and provide these infectious viruses to the host cells. FDCs also attract B and T cells into the GCs and increase the ability of CD4+ T cells to be infected. Additionally, …

Optical And Mass Spectrometric Studies Of A Helium Dielectric-Barrier Atmospheric-Pressure Plasma Jet Used As An Ambient Desorption Ionization Source, Matthew Spencer Heywood

Theses and Dissertations

Recently there has been a surge in the field of mass spectrometry centered around the concept of rapid analysis of target analytes with minimal or no sample preparation. The target analyte undergoes desorption from its surface of origin and is subsequently ionized under ambient conditions. The technique is termed ambient desorption/ionization mass spectrometry (ADI-MS). Since the introduction of ADI-MS in 2004, there has been an explosion of research based around the development of novel ambient desorption/ionization (ADI) sources with the capability of desorbing and ionizing a variety of target analytes from various sampling surfaces. One type of ADI source uses …

Development Of A Humanized Hla-A2.1/Dp4 Transgenic Mouse Model And The Use Of This Model To Map Hla-Dp4-Restricted Epitopes Of Hbv Envelope Protein, Zhitao Ru, Wenjun Xiao, Anthony Pajot, Zhihua Kou, Shihui Sun, Benard Maillere, Guangyu Zhao, David M. Ojcius, Yu-Chun Lone, Yusen Zhou

All Dugoni School of Dentistry Faculty Articles

A new homozygous humanized transgenic mouse strain, HLA-A2.1^+/+HLA-DP4^+/+ hCD4^+/+mCD4^−/−IAβ^−/−β2m^−/− (HLA-A2/DP4), was obtained by crossing the previously characterized HLA-A2^+/+β2m−/− (A2) mouse and our previously created HLA-DP4^+/+ hCD4^+/+mCD4^−/−IAβ^−/− (DP4) mouse. We confirmed that the transgenes (HLA-A2, HLA-DP4, hCD4) inherited from the parental A2 and DP4 mice are functional in the HLA-A2/DP4 mice. After immunizing HLA-A2/DP4 mice with a hepatitis B DNA vaccine, hepatitis B virus-specific antibodies, HLA-A2-restricted and HLA-DP4-restricted responses were observed to be similar to those in naturally infected humans. Therefore, the present …

Antifungal Activity Of Lactobacillus Against Microsporum Canis, Microsporum Gypseum And Epidermophyton Floccosum, Jiahui Guo, Brid Brosnan, Ambrose Furey, Elke K. Arendt, Padraigin Murphy

Department of Biological Sciences Publications

A total of 220 lactic acid bacteria isolates were screened for antifungal activity using Aspergillus fumigatus and Aspergillus niger as the target strains. Four Lactobacillus strains exhibited strong inhibitory activity on agar surfaces. All four were also identified as having strong inhibitory activity against the human pathogenic fungi Microsporum canis, Microsporum gypseum and Epidermophyton floccosum. One of the four lactobacilli, namely Lb. reuteri ee1p exhibited the most inhibition against dermatophytes. Cell-free culture supernatants of Lb. reuteri ee1p and of the non-antifungal Lb. reuteri M13 were freeze-dried and used to access and compare antifungal activity in agar plate assays …

Proteins: Form And Function, Roy D. Sleator

Department of Biological Sciences Publications

An overwhelming array of structural variants has evolved from a comparatively small number of protein structural domains; which has in turn facilitated an expanse of functional derivatives. Herein, I review the primary mechanisms which have contributed to the vastness of our existing, and expanding, protein repertoires. Protein function prediction strategies, both sequence and structure based, are also discussed and their associated strengths and weaknesses assessed.

Dynamics Of The Solvent Exchange Reaction Of Weakly Bound Organic Solvents To Group 6 Transition Metal Carbonyls And The Molybdenum Hexacarbonyl Mediated Pauson-Khand Reaction, Richard J. Gates

Theses and Dissertations

Many organometallic reactions are solvent-dependent, suggesting solvent molecules interact with reaction intermediates. Studies of the solvent exchange reaction of group 6 transition metal carbonyls with moderately binding ligands have provided insight into these interactions, however, studies of the mechanism for this reaction with weakly binding ligands have not been performed. Experiments were conducted on the nanosecond time scale in methylcyclohexane over the temperature range of 4 to 44 °C using Step Scan FTIR (SS FTIR) spectroscopy with weakly binding ligands benzene and mesitylene. Upon photolysis of the metal hexacarbonyls, the kinetically favored product (M(CO)5(solv)), decays following pseudo-first-order kinetics to the …

Cryo-Em Structure Of The Archaeal 50s Ribosomal Subunit In Complex With Initiation Factor 6 And Implications For Ribosome Evolution, Basil J. Greber, Daniel Boehringer, Vlatka Godinic-Mikulcic, Ana Crnkovic, Michael Ibba, Ivana Weygand-Durasevic, Nenad Ban

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The …

Roles Of Trna In Cell Wall Biosynthesis, Kiley Dare, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Recent research into various aspects of bacterial metabolism such as cell wall and antibiotic synthesis, degradation pathways, cellular stress, and amino acid biosynthesis has elucidated roles of aminoacyl‐transfer ribonucleic acid (aa‐tRNA) outside of translation. Although the two enzyme families responsible for cell wall modifications, aminoacyl‐phosphatidylglycerol synthases (aaPGSs) and Fem, were discovered some time ago, they have recently become of intense interest for their roles in the antimicrobial resistance of pathogenic microorganisms. The addition of positively charged amino acids to phosphatidylglycerol (PG) by aaPGSs neutralizes the lipid bilayer making the bacteria less susceptible to positively charged antimicrobial agents. Fem transferases utilize …

The Mechanical Properties Of Epoxy Composites Filled With Rubbery Copolymer Grafted Sio2, Jianing Gao, Junting Li, Brian C. Benicewicz, Su Zhao, Henrik Hillborg, Linda S. Schadler

Faculty Publications

This study demonstrated a method for toughening a highly crosslinked anhydride cured DGEBA epoxy using rubbery block copolymer grafted SiO2 nanoparticles. The particles were synthesized by a sequential reversible addition-fragmentation chain transfer (RAFT) polymerization. The inner rubbery block poly(n-hexyl methacrylate) (PHMA) had a glass transition temperature below room temperature. The outer block poly(glycidyl methacrylate) (PGMA) was matrix compatible. A rubbery interlayer thickness of 100% and 200% of the particle core radius was achieved by grafting a 20 kg/mol and a 40 kg/mol PHMA at a graft density of 0.7 chains/nm² from the SiO₂ surface. The 20 kg/mol rubbery …

Fully Enclosed Microfluidic Paper-Based Analytical Devices, Kevin M. Schilling, Anna L. Lepore, Jason A. Kurian, Andres W. Martinez

Chemistry and Biochemistry

This article introduces fully enclosed microfluidic paper-based analytical devices (microPADs) fabricated by printing toner on the top and bottom of the devices using a laser printer. Enclosing paper-based microfluidic channels protects the channels from contamination, contains and protects reagents stored on the device, contains fluids within the channels so that microPADs can be handled and operated more easily, and reduces evaporation of solutions from the channels. These benefits extend the capabilities of microPADs for applications as low-cost point-of-care diagnostic devices.

[Accepted Article Manuscript Version (Postprint)] Plant Peroxisomes: Biogenesis And Function, Jianping Hu, Alison Baker, Bonnie Bartel, Nicole Linka, Robert Mullen, Sigrun Reumann, Bethany Zolman

Biology Department Faculty Works

Peroxisomes are eukaryotic organelles that are highly dynamic both in morphology and metabolism. Plant peroxisomes are involved in numerous processes, including primary and secondary metabolism, development, and responses to abiotic and biotic stresses. Considerable progress has been made in the identification of factors involved in peroxisomal biogenesis, revealing mechanisms that are both shared with and diverged from non-plant systems. Furthermore, recent advances have begun to reveal an unexpectedly large plant peroxisomal proteome and have increased our understanding of metabolic pathways in peroxisomes. Coordination of the biosynthesis, import, biochemical activity, and degradation of peroxisomal proteins allows for highly dynamic responses of …

"Fine-Tuning" Of Ribosomal Structure And Functions By Pseudouridylation And Rna-Protein Interactions, Jun Jiang

Wayne State University Dissertations

ABSTRACT

"Fine-tuning" of ribosomal structure and functions by pseudouridylation and RNA-protein interactions

by

JUN JIANG

AUGUST 2012

Advisor: Prof. John SantaLucia Jr.

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Ribosomal structure and functions appear to be "fine-tuned" by pseudouridylation and RNA-protein interactions. Pseudouridylation may promote base stacking interactions by mediating the base stacking between residues on both sides. In the RNA duplex region, this enhanced stacking interaction contributes to stabilization of duplex folding. In the loop region, enhanced stacking in one structural motif may destabilize the conformation of adjacent structural residues. This hypothesis is supported by both UV-melting experiments, where …

Conformational Properties Of Cardiolipin-Bound Cytochrome C, Jonas Hanske, Jason R. Toffey, Anna M. Morenz, Amber J. Bonilla, Katherine H. Schiavoni;, Ekaterina V. Pletneva

Dartmouth Scholarship

Interactions of cytochrome c (cyt c) with cardiolipin (CL) are important for both electron transfer and apoptotic functions of this protein. A sluggish peroxidase in its native state, when bound to CL, cyt c catalyzes CL peroxidation, which contributes to the protein apoptotic release. The heterogeneous CL-bound cyt c ensemble is difficult to characterize with traditional structural methods and ensemble-averaged probes. We have employed time-resolved FRET measurements to evaluate structural properties of the CL-bound protein in four dansyl (Dns)-labeled variants of horse heart cyt c. The Dns decay curves and extracted Dns-to-heme distance distributions P(r) …

Domain Architecture Of A Calcium-Permeable Ampa Receptor In A Ligand-Free Conformation, Charles R. Midgett, Avinash Gill, Dean R. Madden

Dartmouth Scholarship

Ligand-gated ion channels couple the free energy of agonist binding to the gating of selective transmembrane ion pores, permitting cells to regulate ion flux in response to external chemical stimuli. However, the stereochemical mechanisms responsible for this coupling remain obscure. In the case of the ionotropic glutamate receptors (iGluRs), the modular nature of receptor subunits has facilitated structural analysis of the N-terminal domain (NTD), and of multiple conformations of the ligand-binding domain (LBD). Recently, the crystallographic structure of an antagonist-bound form of the receptor was determined. However, disulfide trapping of this conformation blocks channel opening, suggesting that channel activation involves …

Changing Water Quality In Great Pond: The Roles Of Lake Sediments, Invasive Macrophytes, And The Watershed, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: Great Pond (2012, 2010, 1998)

Eutrophication as a result of human activity is a threat to lake water quality globally and within the state of Maine. Great Pond, in the Belgrade Lakes region of Maine, has traditionally been an oligotrophic lake that is experiencing early signs of eutrophication and is currently classified as a mesotrophic lake. In the fall of 2012, the Colby Environmental Assessment Team (CEAT) measured the primary sources of nutrient loading to Great Pond including the catchment and the lake sediment, current water quality in Great Pond, and the potential impact of the variable milfoil invasion on the lake’s water quality. An …

Detailed Comparison Of The Pnicogen Bond With Chalcogen, Halogen And Hydrogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The characteristics of the pnicogen bond are explored using a variety of quantum chemical techniques. In particular, this interaction is compared with its halogen and chalcogen bond cousins, as well as with the more common H-bond. In general, these bonds are all of comparable strength. More specifically, they are strengthened by the presence of an electronegative substituent on the electron-acceptor atom, and each gains strength as one moves down the appropriate column of the periodic table, for example, from N to P to As. These noncovalent bonds owe their stability to a mixture in nearly equal parts of electrostatic attraction …

Bacterial Host Interactions In Cystic Fibrosis, Máire Callaghan, Siobhan Mcclean

Articles

Chronic infection is a hallmark of cystic fibrosis (CF) and the main contributor to morbidity. Microbial infection in CF is complex, due to the number of different species that colonise the CF lung. Their colonisation is facilitated by a host response that is impaired or compromised by highly viscous mucous, zones of hypoxia and the lack of the cystic fibrosis transmembrane regulator (CFTR). Successful dominant CF pathogens combine an effective arsenal to establish infection and counter-attack the host response, together with an ability to adapt readily to an unfavourable environment. Hypermutability is common among CF pathogens facilitating adaptation and as …

First Steps In Growth Of A Polypeptide Toward Β-Sheet Structure, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The full conformational energy surface is examined for a molecule in which a dipeptide is attached to the same spacer group as another peptide chain, so as to model the seminal steps of β-sheet formation. This surface is compared with the geometrical preferences of the isolated dipeptide to extract the perturbations induced by interactions with the second peptide strand. These interpeptide interactions remove any tendency of the dipeptide to form a C5 ring structure, one of its two normally stable geometries. A C7 structure, the preferred conformation of the isolated dipeptide, remains as the global minimum in the full molecule. …

Extrapolation To The Complete Basis Set Limit For Binding Energies Of Noncovalent Interactions, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A means of extrapolating from double and triple-valence basis sets to a complete basis set is examined in the context of the pnicogen bonds in the BH2P⋯NH3 complexes, with B = CH3, H, NH2, CF3, OH, Cl, F, and NO2. Binding energies converge smoothly, and the trends for the various substituents B are unaffected by the basis set size, extrapolation, or level of inclusion of electron correlation, including MP2 and CCSD(T). The approach appears to be successful also for H-bonded systems, in particular the water dimer. In the event that full extrapolation within the context of CCSD(T) is not feasible, …

Tgd1, -2, And -3 Proteins Involved In Lipid Trafficking Form Atp-Binding Cassette (Abc) Transporter With Multiple Substrate-Binding Proteins, Rebecca Roston, Jinpeng Gao, Monika W. Murcha, James Whelan, Christoph Benning

Department of Biochemistry: Faculty Publications

Background: ATP-binding cassette transporters exist in all life forms and usually require only one substrate-binding domain.

Results: The TRIGALACTOSYLDIACYLGLYCEROL (TGD) complex contains 8–12 substrate-binding proteins.

Conclusion: Multiple substrate-binding proteins may be needed by the TGD complex to enhance its putative lipid transport activity.

Significance: Knowing the subunit stoichiometry of the TGD complex furthers understanding of lipid transfer between chloroplast membranes.