Science and Technology Faculty Journal Articles

Polycyclic Aromatic Hydrocarbon Degrading Microorganisms in Great Lakes Sediments

Dan L. McNally et al. — Thu, 21 Jul 2011 15:30:26 PDT

Biodegradation of Three-and Four-ring Polycyclic aromatic Hydrocarbons Under Aerobic and Denitrifying Conditions

Dan L. McNally et al. — Thu, 21 Jul 2011 15:11:05 PDT

PAHs are thought to be particularly persistent in environments where anaerobic conditions exist. This study presents evidence for the biodegradation of three- and four-ringed PAHs (anthracene, phenanthrene, and pyrene) under strict anaerobic, denitrifying conditions. Three pseudomonad strains, isolated from contrasting environments, were used in this study. All three strains were known PAH degraders and denitrifiers.

Biodegration of Mixtures of Polycyclic Aromatic Hydrocarbons Under Aerobic and Nitrate-reducing Conditions

Dan L. McNally et al. — Thu, 21 Jul 2011 15:01:51 PDT

Contaminated sites often contain complex mixtures of aromatic compounds. This complex mixture and the system's redox condition may influence biodegradation patterns. In this study, the biodegradation of PAHs in varying mixture combinations by a pure culture of Pseudomonas putida strain KBM-1 under aerobic conditions showed that the presence of naphthalene (2-ringed PAH) stimulated phenanthrene (3-ringed PAH) degradation five-fold and pyrene (4-ringed PAH) degradation two-fold. However, the presence of phenanthrene inhibited pyrene degradation

Preparation of 1-[N-benzyloxycarbonyl-(1S)-1-amino-2-oxoethyl]-4-methyl-2,6,7-trioxabicylo[2.2.2]octane

Nicholas G. W. Rose et al. — Thu, 07 Jul 2011 16:00:56 PDT

The Effect of NAG–thiazoline on Morphology and Surface Hydrophobicity of Escherichia Coli

Christopher W. Reid et al. — Thu, 07 Jul 2011 15:18:24 PDT

The β-hexosaminidase inhibitor and structural analog of the putative oxazolium reaction intermediate of lytic transglycosylases, N-acetylglucosamine thiazoline (NAG–thiazoline), was synthesized in 46% overall yield and tested as an inhibitor of Escherichia coli growth. NAG–thiazoline, at concentrations up to 1 mg/ml, was not found to affect the viability of E. coli DH5α.

Inhibition of Membrane-bound Lytic Transglycosylase B by NAG-thiazoline

Christopher W. Reid et al. — Thu, 07 Jul 2011 15:11:05 PDT

The lytic transglycosylases cleave the bacterial cell wall heteropolymer peptidoglycan with the same specificity as the muramidases (lysozymes), between the N-acetylmuramic acid and N-acetylglucosamine residues, with the concomitant formation of a 1,6-anhydromuramoyl residue. The putative catalytic residue in the family 3 lytic transglycosylase from Pseudomonas aeruginosa, Glu162 as identified by sequence alignment to the homologous enzyme from Escherichia coli, was replaced with both Ala and Asp by site-directed mutagenesis.

Role of Ser216 in the Mechanism of Action of Membrane-bound Lytic Transglycosylase B: Further Evidence for Substrate-assisted Catalysis

Christopher W. Reid et al. — Thu, 07 Jul 2011 15:04:45 PDT

Lytic transglycosylases cleave the β-(1 → 4)-glycosidic bond in the bacterial cell wall heteropolymer peptidoglycan between the N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues with the concomitant formation of a 1,6-anhydromuramoyl residue. Based on sequence alignments, Ser216 in Pseudomonas aeruginosa membrane-bound lytic transglycosylase B (MltB) was targeted for replacement with alanine to delineate its role in the enzyme’s mechanism of action.

Lytic Transglycosylases: Bacterial Space-making Autolysins

Edie Scheurwater et al. — Thu, 07 Jul 2011 14:54:31 PDT

Lytic transglycosylases are an important class of bacterial enzymes that act on peptidoglycan with the same substrate specificity as lysozyme. Unlike the latter enzymes, however, the lytic transglycosylases are not hydrolases but instead cleave the glycosidic linkage between N-actetylmuramoyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anydromuramoyl product.

Never Take Candy From a Stranger: The Role of the Bacterial Glycome in Host–pathogen Interactions

Christopher W. Reid et al. — Thu, 07 Jul 2011 14:46:51 PDT

Motility and Flagellar Glycosylation in Clostridium Difficile

Susan W. Twine et al. — Thu, 07 Jul 2011 14:36:18 PDT

In this study, intact flagellin proteins were purified fromstrains of Clostridium difficile and analyzed using quadrupoletime of flight and linear ion trap mass spectrometers.

Substrate Binding Affinity of Pseudomonas Aeruginosa Membrane-Bound Lytic Transglycosylase B by Hydrogen−Deuterium Exchange MALDI MS

Christopher W. Reid et al. — Wed, 06 Jul 2011 17:59:13 PDT

Lytic transglycosylases cleave the β-(1→4)-glycosidic bond in the bacterial cell wall heteropolymer, peptidoglycan, between the N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues with the concomitant formation of a 1,6-anhydromuramoyl residue. With 72% amino acid sequence identity between the enzymes, the theoretical structure of the membrane-bound lytic transglycosylase B (MltB) from Psuedomonas aeruginosa was modeled on the known crystal structure of Escherichia coli Slt35, the soluble derivative of its MltB.

Role of Arginine Residues in the Active Site of the Membrane-Bound Lytic Transglycosylase B from Pseudomonas Aeruginosa

Christopher W. Reid et al. — Wed, 06 Jul 2011 17:53:31 PDT

Polyisoprenol Specificity in the Campylobacter Jejuni N-linked Glycosylation Pathway

Mark M. Chen et al. — Wed, 06 Jul 2011 16:38:27 PDT

Campylobacter jejuni contains a general N-linked glycosylation pathway in which a heptasaccharide is sequentially assembled onto a polyisoprenyl-diphosphate carrier and subsequently transferred to the asparagine side chain of an acceptor protein. The enzymes in the pathway function at a membrane interface and have in common amphiphilic membrane-bound polyisoprenyl-linked substrates. Herein we examine the potential role of the polyisoprene component of the substrates by investigating the relative substrate efficiencies of polyisoprene-modified analogs in individual steps in the pathway. Chemically defined substrates for PglC, PglJ and PglB are prepared via semisynthetic approaches. The substrates included polyisoprenols of varying length, double bond geometry, and degree of saturation to probe the role of the hydrophobic polyisoprene in substrate specificity. Kinetic analysis reveals that all three enzymes exhibit distinct preferences for the polyisoprenol carrier whereby cis-double bond geometry and α-unsaturation of the native substrate are important features, while the precise polyisoprene length may be less critical. These finding suggest that the polyisoprenol carrier plays a specific role in the function of these enzymes beyond a purely physical role as a membrane anchor. These studies underscore the potential of the C. jejuni N-linked glycosylation pathway as a system for investigating the biochemical and biophysical roles of polyisoprenol carriers common to prokaryotic and eukaryotic glycosylation.

Affinity-capture Tandem Mass Spectrometric Characterization of Polyprenyl-linked Oligosaccharides: A Novel Tool to Study Protein N-glycosylation Pathways

Christopher W. Reid et al. — Sun, 23 Jan 2011 13:46:56 PST

Analysis of Bacterial Lipid-linked Oligosaccharides Intermediates Using Porous Graphitic Carbon Liquid Chromatography-electrospray Ionization Mass Spectrometry

Christopher W. Reid et al. — Sun, 23 Jan 2011 13:21:47 PST

Thermally and Optically Stimulated Exoelectron Emission from an Electron‐beam Irradiated Glass–ceramic Material

D. L. Carroll et al. — Fri, 07 Jan 2011 07:45:48 PST

The exposure of insulating materials to an electron beam results in the trapping of excess charge on the surface. We have studied the thermally and optically stimulated emission of this excess charge in an electron‐bombarded, fluorophlogopite mica glass–ceramic material (Macor). The total electron emission from the surface is measured either as a function of the sample temperature during heating or the photon wavelength. The emission as a function of temperature has four characteristic peaks whose relative intensity depends on the beam dose, energy, initial sample temperature, and history (accumulation of beam‐induced defects). One peak occurs immediately upon heating and is related to the total surface charge. Two peaks occur at fixed temperatures of 280 and 325 °C and are associated with the discrete energy trap states. The highest temperature peak is only observed after prolonged beam exposure and is due to the annihilation of defects. Illumination in the ultraviolet is required to produce photoemission for an uncharged sample. However, after electron bombardment, electron emission is observed over a broad range of visible wavelengths. In addition, two photoemission thresholds at about 2.7 and 3.1 eV suggest electron trap states which can be associated with the thermally emitted peaks. The thermally and optically stimulated emission is a valuable tool to measure the electron state distribution in charged insulating materials.

Receptive Field Formation in Natural Scene Environments: Comparison of Single Cell Learning Rules

Brian S. Blais et al. — Thu, 06 Jan 2011 10:15:57 PST

We study several statistically and biologically motivated learning rules using the same visual environment: one made up of natural scenes and the same single-cell neuronal architecture. This allows us to concentrate on the feature extraction and neuronal coding properties of these rules. Included in these rules are kurtosis and skewness maximization, the quadratic form of the Bienenstock-Cooper-Munro (BCM) learning rule, and single-cell independent component analysis. Using a structure removal method, we demonstrate that receptive fields developed using these rules depend on a small portion of the distribution. We find that the quadratic form of the BCM rule behaves in a manner similar to a kurtosis maximization rule when the distribution contains kurtotic directions, although the BCM modification equations are computationally simpler.

The Role of Presynaptic Activity in Monocular Deprivation: Comparison of Homosynaptic Mechanisms

Brian S. Blais et al. — Thu, 06 Jan 2011 10:10:50 PST

Although there have been extensive investigations in computational neuroscience, the opportunity (that has made such a marked difference in physical sciences) to test detailed and subtle quantitative consequences of a theory against experimental results is rare. In this paper we outline a testable consequence of two contrasting theories of synaptic plasticity applied to the disconnection in visual cortex of the closed eye in monocular deprivation (MD). This disconnection is sometimes thought to be the consequence of a process that stems from a competition of inputs for a limited resource such as neurotrophin. Such a process leads to what we call spatial competition, or heterosynaptic synaptic modification. A contrasting view, exemplified by the Bienenstock, Cooper, and Munro (BCM) theory, is that patterns of input activity compete in the temporal domain. This temporal competition is homosynaptic and does not require a conserved resource. The two erved resource. The two mechanisms, homosynaptic and heterosynaptic, are the distinguishing characteristics of two general classes of learning rules which we explore, using a realistic environment composed of natural scenes. These alternative views lead to opposite dependence on the level of presynaptic activity of the rate of disconnection of the closed eye in monocular deprivation. This strong and testable consequence sets the stage for a critical distinguishing experiment; the experiment has been done and supports the second view. These results have important implications for the processes of learning and memory storage in neocortex.

Formation of Direction Selectivity in Natural Scene Environments

Brian S. Blais et al. — Thu, 06 Jan 2011 09:35:28 PST

Most simple and complex cells in the cat striate cortex are both orientation and direction selective. In this article we use single-cell learning rules to develop both orientation and direction selectivity in a natural scene environment. We show that a simple principal component analysis rule is inadequate for developing direction selectivity, but that the BCM rule as well as similar higher-order rules can. We also demonstrate that the convergence of lagged and nonlagged cells depends on the velocity of motion in the environment, and that strobe rearing disrupts this convergence, resulting in a loss of direction selectivity.

Statistics of Lateral Geniculate Nucleus (LGN) Activity Determine the Segregation of ON/OFF Subfields for Simple Cells in Visual Cortex

Ann B. Lee et al. — Thu, 06 Jan 2011 09:20:33 PST

The receptive fields for simple cells in visual cortex show a strong preference for edges of a particular orientation and display adjacent excitatory and inhibitory subfields. These subfields are projections from ON-center and OFF-center lateral geniculate nucleus cells, respectively. Here we present a single-cell model using ON and OFF channels, a natural scene environment, and synaptic modification according to the Bienenstock, Cooper, and Munro (BCM) theory. Our results indicate that lateral geniculate nucleus cells must act predominantly in the linear region around the level of spontaneous activity, to lead to the observed segregation of ON/OFF subfields.