Biochemistry, Biophysics, and Structural Biology Commons^™

Campylobacter Ureolyticus: An Emerging Gastrointestinal Pathogen?, Susan Bullman, Daniel Corcoran, James O'Leary, Brigid Lucey, Deirdre Byrne, Roy D. Sleator

Department of Biological Sciences Publications

A total of 7194 faecal samples collected over a 1-year period from patients presenting with diarrhoea were screened for Campylobacter spp. using EntericBios, a multiplex-PCR system. Of 349 Campylobacter-positive samples, 23.8% were shown to be Campylobacter ureolyticus, using a combination of 16S rRNA gene analysis and highly specific primers targeting the HSP60 gene of this organism. This is, to the best of our knowledge, the first report of C. ureolyticus in the faeces of patients presenting with gastroenteritis and may suggest a role for this organism as an emerging enteric pathogen.

Measurements Of Gas‐Phase Inorganic And Organic Acids From Biomass Fires By Negative‐Ion Proton‐Transfer Chemical‐Ionization Mass Spectrometry, P. Veres, James M. Roberts, I. R. Burling, C. Warneke, Joost De Gouw, Robert J. Yokelson

Chemistry and Biochemistry Faculty Publications

[1] Emissions from 34 laboratory biomass fires were investigated at the combustion facility of the U.S. Department of Agriculture Fire Sciences Laboratory in Missoula, Montana. Gas-phase organic and inorganic acids were quantified using negative-ion proton-transfer chemical-ionization mass spectrometry (NI-PT-CIMS), open-path Fourier transform infrared spectroscopy (OP-FTIR), and proton-transfer-reaction mass spectrometry (PTR-MS). NI-PT-CIMS is a novel technique that measures the mass-to-charge ratio (m/z) of ions generated from reactions of acetate (CH₃C(O)O⁻) ions with inorganic and organic acids. The emission ratios for various important reactive acids with respect to CO were determined. Emission ratios for isocyanic acid (HNCO), 1,2 …

Genotype And Breed Trend Influences On Citric Acid And Coagulation Times Of Raw Milk, Melissa Looney

Dairy Science

The objective of the study was to determine if citric acid levels measured in milk was related to genetic variants identified in Holstein and Jersey cows. The data used were milk samples collected from both Holstein and Jersey cows at Cal Poly, San Luis Obispo. Citric acid levels and other constituents were measured using FTIR methods with the FOSS MilkoscanTM FT2 on each sample. Genotypes were obtained for the DGAT 1 locus using polymerase chain reaction and an enzymatic digestion using the MWO I restriction enzyme. Observations were obtained on 13 Holsteins and 12 Jersey cows. Results indicated that citric …

Lateral Blood Flow Velocity Estimation Based On Ultrasound Speckle Size Change With Scan Velocity, Tiantian Xu, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Conventional (Doppler-based) blood flow velocity measurement methods using ultrasound are capable of resolving the axial component (i.e., that aligned with the ultrasound propagation direction) of the blood flow velocity vector. However, these methods are incapable of detecting blood flow in the direction normal to the ultrasound beam. In addition, these methods require repeated pulse-echo interrogation at the same spatial location. A new method has been introduced which estimates the lateral component of blood flow within a single image frame using the observation that the speckle pattern corresponding to blood reflectors (typically red blood cells) stretches (i.e., is smeared) if the …

Development Of A Genetic Modification System In Clostridium Scatologenes Atcc 25775 For Generation Of Mutants, Prasanna Tamarapu Parthasarathy

Masters Theses & Specialist Projects

3-Methyl indole (3-MI) is a malodorant in food and animal waste and Clostridium scatologenes ATCC 25775 is the model organism for the study of 3-MI production. 3-MI is an anaerobic degradation product of L-tryptophan and can cause pulmonary disorders and death in cattle and goats. To elucidate the 3-MI biosynthesis pathway and the underlying genes, it is necessary to develop a system to allow genetic modification in Clostridium scatologenes ATCC 25775. Bacteriophages and transposons are useful tools to achieve this goal. Isolation of Clostridium scatologenes ATCC 25775 bacteriophage was attempted by prophage induction and enrichments using environmental sources. To induce …

[Accepted Article Manuscript Version (Postprint)] Pex5 Mutants That Differentially Disrupt Pts1 And Pts2 Peroxisomal Matrix Protein Import In Arabidopsis, Bibi Khan, Bethany Zolman

Biology Department Faculty Works

PEX5 and PEX7 are receptors required for the import of peroxisome-bound proteins containing one of two peroxisomal targeting signals (PTS1 or PTS2). To better understand the role of PEX5 in plant peroxisomal import, we characterized the Arabidopsis (Arabidopsis thaliana) pex5-10 mutant, which has a T-DNA insertion in exon 5 of the PEX5 gene. Sequencing results revealed that exon 5, along with the T-DNA, is removed in this mutant, resulting in a truncated pex5 protein. The pex5-10 mutant has germination defects and is completely dependent on exogenous Suc for early seedling establishment, based on poor utilization of seed-storage fatty acids. This …

Expression Of Functional Bacterial Undecaprenyl Pyrophosphate Synthase In The Yeast Rer2{Delta} Mutant And Cho Cells., Jeffrey S. Rush, Sergey Matveev, Ziqiang Guan, Christian R H Raetz, C J Waechter

Molecular and Cellular Biochemistry Faculty Publications

During evolution the average chain length of polyisoprenoid glycosyl carrier lipids increased from C55 (prokaryotes) to C75 (yeast) to C95 (mammalian cells). In this study, the ability of the E. coli enzyme, undecaprenyl pyrophosphate synthase (UPPS), to complement the loss of the yeast cis-isoprenyltransferase in the rer2Δ mutant was tested to determine if (55)dolichyl phosphate (Dol-P) could functionally substitute in the protein N-glycosylation pathway for (75)Dol-P, the normal isoprenologue synthesized in S. cerevisiae. First, expression of UPPS in the yeast mutant was found to complement the growth and the hypoglycosylation of carboxypeptidase Y defects suggesting that the (55)polyprenyl-P-P intermediate was …

Intraspecific Variation In Two Cosmopolitan Myxomycetes, Didymium Squamulosum And Didymium Difforme (Physarales: Didymiaceae), Katherine Elizabeth Winsett

Graduate Theses and Dissertations

The myxomycetes (plasmodial slime molds or myxogastrids) are one of three groups considered to be true slime molds (class Eumycetozoa sensu Olive 1975). Two vegetative states--amoebae and plasmodia--along with a spore-producing fruiting body characterize the life cycle of the myxomycetes. These organisms are associated with decaying plant material and are found in all terrestrial habitats worldwide. A number of species are considered cosmopolitan, being found worldwide, where they are associated with a diversity of microhabitats and substrates. A review of the literature, including molecular investigations in all three groups of slime molds, is presented, and this is followed by four …

Applications Of Site-Specific Recombination Systems In Transgene Expression And Marker Gene Removal, Mehmet Aydin Akbudak

Graduate Theses and Dissertations

Site Specific Recombination systems, such as FLP-FRT and Cre-lox, have been successfully used for site-specific gene integration and marker-gene deletion in plant systems. They are very useful tools in the integration of single-copy full-length transgene cassettes into the genome because the transgene integration via conventional methods often generate multi-copy locus. Such complex locus containing direct and inverted repeats of full-length and truncated copies of the transgene cassette generate aberrant RNA resulting in gene silencing. Therefore, for stable gene expression, a single copy transgene locus is preferred. However, even single copy locus sometimes succumbs to gene silencing. Although the mechanism is …

Development Of Novel Biomarkers In Cancer: Detection Of Circulating Mir-141 As A Potential Prognostic Marker For Prostate Cancer, Jason Cadaoas Gonzales

UNLV Theses, Dissertations, Professional Papers, and Capstones

Prostate cancer (CAP) is the most common epithelial malignancy and the second leading cause of cancer deaths in American men. The identification of predictive and prognostic biomarkers in CAP patients is critical for improving clinical outcomes. Although the measurement of prostate-specific antigen (PSA) and radiographic studies are clinically approved to predict response to therapy, these tests can oftentimes prove to be inadequate in certain patients. Thus, it is important to discover new biomarkers to improve chances of survivability. We and others have shown that longitudinal measurements of circulating tumor cells (CTC) and lactate dehydrogenase (LDH) may aid in predicting response …

The In Situ Function Of A Microbial Community Profiled By Ft-Ir: A Snapshot In Time, Ryan Roberts

Department of Biochemistry: Dissertations, Theses, and Student Research

Photographs of an ecosystem are an important tool in macro-community ecology. The photograph is a permanent record of species phenotype. In microbiology, biochemical activity provides the most descriptive information of an organism’s phenotype. A method for fingerprinting all biochemical activities occurring within a microbial community is analogous to a photograph. Infrared spectroscopy in the region between wavelengths 2500 to 20,000 nm (mid-IR) is a well established instrumental method for fingerprinting the total biochemical profile of axenic cultures. Spectra are complex and sensitive as demonstrated by the ability to discriminate between strains of bacteria, fungi, and algae. This thesis develops the …

Transcriptional Regulation Of Shigella Virulence Plasmid-Encoded Genes By Virb And Crp, Christopher Thomas Hensley

UNLV Theses, Dissertations, Professional Papers, and Capstones

Shigella flexneri is a species of Gram-negative intracellular pathogens that causes bacillary dysentery in humans. Shigella relies on the precise transcriptional regulation of virulence genes, encoded by a large virulence plasmid, for invasion and infection of human colonic epithelial cells. The transcription of most identified virulence genes are regulated through a cascade controlled by the primary regulator of virulence genes, VirF, and the global transcriptional regulator, VirB. Currently, few studies have addressed how individual Shigella virulence genes are precisely regulated for optimal expression during specific stages of pathogenesis and within the constraints of the regulatory cascade. This work addresses how …

Tryptophan Anchored Peptides In Lipid Bilayer Membranes: Control Of Peptide Orientation And The Phase Behavior Of Cholesterol-Containing Ternary Lipid Mixtures, Johanna Maria Rankenberg

Graduate Theses and Dissertations

Model WALP peptides and "next generation" WALP-derived hydrophobic model peptides were employed to discover principles that govern protein-lipid interactions in biological membranes.

Ternary cholesterol-containing lipid mixtures were examined in the presence of WALP peptides of different lengths (acetyl-GWW(LA)_nLWWA-ethanolamide, with n between 3 and 8). Deuterium NMR spectra from labeled lipids reveal that WALP peptides may stabilize lipid ordered "raft" domains and therefore promote lipid phase separation, albeit to a minor extent. The results depend upon whether dioleolyl- or diphytanoyl-phosphatidylcholine is present as the fluid lipid component.

Several WALP peptides were modified to remove anchoring Trp residues from one …

Mechanism Of N-Methylation By The Trna M1g37 Methyltransferase Trm5., Thomas Christian, Georges Lahoud, Cuiping Liu, Katherine Hoffmann, John J Perona, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

Trm5 is a eukaryal and archaeal tRNA methyltransferase that catalyzes methyl transfer from S-adenosylmethionine (AdoMet) to the N(1) position of G37 directly 3' to the anticodon. While the biological role of m(1)G37 in enhancing translational fidelity is well established, the catalytic mechanism of Trm5 has remained obscure. To address the mechanism of Trm5 and more broadly the mechanism of N-methylation to nucleobases, we examined the pH-activity profile of an archaeal Trm5 enzyme, and performed structure-guided mutational analysis. The data reveal a marked dependence of enzyme-catalyzed methyl transfer on hydrogen ion equilibria: the single-turnover rate constant for methylation increases by one …

High Flow Air Sampling For Field Detection Using Gas Chromatography-Mass Spectrometry, Jacolin Ann Murray

Theses and Dissertations

The ability to rapidly detect and identify hazardous analytes in the field has become increasingly important. One of the most important analytical detection methods in the field is gas chromatography-mass spectrometry (GC-MS). In this work, a hand-portable GC-MS system is described that contains a miniature toroidal ion trap mass analyzer and a low thermal mass GC. The system is self-contained within the dimensions of 47 x 36 x 18 cm and weighs less than 13 kg. Because the instrument has a small footprint, it was used as the detector for an automated near-real-time permeation testing system. In permeation testing, materials …

Targeted Insertion Of Cysteine By Decoding Uga Codons With Mammalian Selenocysteine Machinery, Xue-Ming Xu, Anton A. Turanov, Bradley A. Carlson, Min-Hyuk Yoo, Robert A. Everley, Renu Nandakumar, Irina Sorokina, Steven P. Gygi, Vadim N. Gladyshev, Dolph L. Hatfield

Department of Biochemistry: Faculty Publications

Cysteine (Cys) is inserted into proteins in response to UGC and UGU codons. Herein, we show that supplementation of mammalian cells with thiophosphate led to targeted insertion of Cys at the UGA codon of thioredoxin reductase 1 (TR1). This Cys was synthesized by selenocysteine (Sec) synthase on tRNA^[Ser]Sec and its insertion was dependent on the Sec insertion sequence element in the 3′ UTR of TR1 mRNA. The substrate for this reaction, thiophosphate, was synthesized by selenophosphate synthetase 2 from ATP and sulfide and reacted with phosphoseryl-tRNA^[Ser]Sec to generate Cys-tRNA^[Ser]Sec. Cys was inserted in vivo at UGA …

Elucidating Functional Roles For Myogenin In Adult Skeletal Muscle Metabolism, Exercise Capacity, And Regeneration, Jesse Flynn

Dissertations and Theses (Open Access)

The four basic helix-loop-helix myogenic transcription factors, myogenin, Myf5, MRF4, and MyoD are critical for embryonic skeletal muscle development. Myogenin is necessary for the terminal differentiation of myoblasts into myofibers during embryogenesis, but little is known about the roles played by myogenin in adult skeletal muscle function and metabolism. Furthermore, while metabolism is a well-studied physiological process, how it is regulated at the transcriptional level remains poorly understood. In this study, my aim was to determine the function of myogenin in adult skeletal muscle metabolism, exercise capacity, and regeneration. To investigate this, I utilized a mouse strain harboring the Myogflox …

Agrobacterium Virb10 Contributions To Type Iv Substrate Secretion, T-Pilus Biogenesis, And Outer Membrane Pore Formation, Isaac Garza

Dissertations and Theses (Open Access)

The VirB/D4 type IV secretion system (T4SS) of Agrobacterium tumefaciens functions to transfer substrates to infected plant cells through assembly of a translocation channel and a surface structure termed a T-pilus. This thesis is focused on identifying contributions of VirB10 to substrate transfer and T-pilus formation through a mutational analysis. VirB10 is a bitopic protein with several domains, including a: (i) cytoplasmic N-terminus, (ii) single transmembrane (TM) α-helix, (iii) proline-rich region (PRR), and (iv) large C-terminal modified β-barrel. I introduced cysteine insertion and substitution mutations throughout the length of VirB10 in order to: (i) test a predicted transmembrane topology, (ii) …

Dynamic Remodeling Of The Stressed Heart: Role Of Protein Degradation Pathways, Deborah Vela

Dissertations and Theses (Open Access)

The heart is a remarkable organ. In order to maintain its function, it remodels in response to a variety of environmental stresses, including pressure overload, volume overload, mechanical or pharmacological unloading and hormonal or metabolic disturbances. All these responses are linked to the inherent capacity of the heart to rebuild itself. Particularly, cardiac pressure overload activates signaling pathways of both protein synthesis and degradation. While much is known about regulators of protein synthesis, little is known about regulators of protein degradation in hypertrophy. The ubiquitin-proteasome system (UPS) selectively degrades unused and abnormal intracellular proteins. I speculated that the UPS may …

Resistance And Dna Repair Mechanisms Under Nitrosative Stress In Mammalian And Microbial Systems, Hyun-Wook Lee

All Dissertations

Living organisms are exposed a nitrosative stress mediated by reactive nitrogen species (RNS) that can cause DNA damage and mutation. DNA base deamination is a typical damage occurred under nitrosative stress, which results in conversion of cytosine (C) to uracil (U), adenine (A) to hypoxanthine (I), and guanine (G) to xanthine (X) or oxanine (O). Base excision repair (BER) is an important pathway to remove deaminated DNA lesions in mammalian and microbial systems. My dissertation work concerns with genes and enzymes involved in resistance to nitrosative stress and DNA glycosylases in the BER pathway. In chapter one, I will briefly …