Browsing by Author "Amy Grunden, Member"

Now showing 1 - 20 of 59

A Synthetic Carbon Fixation Cycle to Increase Carbon Assimilation in Plants.
(2021-12-13) Wilson, Nathan John; Heike Inge Sederoff, Chair; Amy Grunden, Member; Cranos Williams, Member; Terri Long, Member; Henry Schaffer, Graduate School Representative
Activity-based protein profiling and labeling of bacterial monooxygenase enzymes.
(2017-08-09) Bowen, Kristen Bennett; Michael Hyman, Chair; Eric Miller, Member; Amy Grunden, Member; Reza Ghiladi, Member
Alkene and Alkane Oxidation by the 2-Methylpropene-Metabolizing Strain Mycobacterium sp. ELW1.
(2014-04-29) Kottegoda, W. G. Samanthi Subashi; Michael Hyman, Chair; Eric Miller, Member; Hosni Hassan, Member; Amy Grunden, Member; Reza Ghiladi, Graduate School Representative
An Artificial Root System to Study Effect of Plant Root Exudates on the Rhizosphere Microbiome
(2022-07-15) Loucanides, Althea J; Oliver Baars, Chair; Amy Grunden, Member; Alejandra Huerta Vazquez, Member; Marc Cubeta, Member
Application of Integration Tools for Functional Genomic Analysis of Lactobacilli.
(2011-08-22) Douglas, Grace; Todd Klaenhammer, Chair; Amy Grunden, Member; Dahlia Nielsen, Member; Robert Kelly, Minor
Biochemical, Regulatory, and Metabolic Assessment of Hemicellulose Conversion by the Extreme Thermophile Caldicellulosiruptor bescii.
(2022-10-13) Crosby, James Ryan; Robert Kelly, Chair; Amy Grunden, Member; Nathan Crook, Member; Albert Keung, Member
Biodiversity of and Lignocellulosic Modes of Action by the Extremely Thermophilic Caldicellulosiruptor.
(2018-05-04) Lee, Laura Lynn; Robert Kelly, Chair; Balaji Rao, Member; Chase Beisel, Member; Amy Grunden, Member; Robert Kelly, Minor
Characterization of Disinfectant and Phage Resistance Determinants of Listeria monocytogenes.
(2011-09-09) Dutta, Vikrant; Sophia Kathariou, Chair; Amy Grunden, Member; James Brown, Member; Ilenys Perez Diaz, Member; Vivek Fellner, Graduate School Representative
Characterization of Escherichia coli O157:H7 Stationary Phase Acid Resistance and Assessment of Survival in a Mock Vegetable Fermentation System.
(2018-12-18) Jones, Clara Margaret; Frederick Breidt, Chair; Carlos Goller, Member; Amy Grunden, Member
Characterization of the protein component of Methanococcus jannaschii RNase P
(2001-09-07) Bates, Ginger; James W. Brown, Chair; Amy Grunden, Member; Steve Libby, Member
RNase P is the ribonuclease responsible for the 5' maturation of precursor transfer RNA (pre-tRNA). In Bacteria RNase P is composed of a single 14kDa protein accompanied by a single catalytic RNA subunit that is capable of cleave pre-tRNA without the protein cofactor in vitro. The RNA subunit of archaeal RNase P resembles those found in Bacteria, however holoenzymes characterized from the Archaea indicate that the accompanying protein component is much larger than in the bacterial enzyme. Purified RNase P from the Euryarchaeon Methanococcus jannaschii possesses approximately eight protein subunits and has an RNA that is incapable of cleaving pre-tRNA alone in vitro. Four putative M. jannaschii RNase P proteins have been identified by their similarity to RNase P proteins of Methanothermobacter thermoautotrophicus. Here we confirm the presence of two of these proteins, MJ0464 and MJ1139, as well as the presence of several other hypothetical proteins (MJ0332.1, MJ0376, MJ1128, and MJ1625), two 30S ribosomal protein subunits (S6E and S8E), and a nicotinamide-nucleotide adenylyltransferase in M. jannaschii RNase P preparations. Eukaryotic RNase P holoenzymes also contain multiple protein subunits and it is thought that these "extra" proteins are required for function in the increased compartmentalization of the eukaryotic cell. Archaeal cells do not have the distinct compartmentalization seen in eukaryotic cells and it is unclear what purpose the protein subunits described here would have in vivo. One possibility is protein-substrate interactions to facilitate formation of the substrate-enzyme complex. M. jannaschii RNase P RNA lacks certain secondary structures present in E. coli RNase P RNA that have been shown in the bacterial model to interact with pre-tRNA substrate. Archaeal RNase P RNAs that possess these elements, such as that of M. thermoautotrophicus, are capable of cleaving substrate in vitro without protein, although only at very high salt concentration. M. jannaschii RNase P RNA does not have any extra secondary structural elements to compensate for the lack of substrate binding helices and it is possible that the protein component has evolved to assume these responsibilities. In order to test this hypothesis, circularly permuted transfer RNAs containing a photoagent positioned in the T loop were used in ultra-violet cross-linking reactions.
Clostridium autoethanogenum Fermentation Using Sugar and Gaseous Carbon Substrates.
(2018-11-02) Slivka, Rachel Marie; Mari Chinn, Chair; Amy Grunden, Member; Praveen Kolar, Member; Michael Goshe, Minor; Frederick Breidt, Graduate School Representative
Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridia.
(2021-09-01) Reed, Amber Dawn; Casey Theriot, Chair; Jose Bruno-Barcena, Member; Amy Grunden, Member; Robert Kelly, Minor
CRISPR-Cas Systems and Functional Genomics of Lactic Acid Bacteria.
(2023-09-12) Pan, Meichen; Rodolphe Barrangou, Chair; Manuel Kleiner, Member; Amy Grunden, Member; Matthew Koci, Member
CRISPR-Cas Systems and Genetic Organization in Lactic Acid Bacteria.
(2018-03-19) Crawley, Alexandra Briner; Rodolphe Barrangou, Chair; Daniel Burke, Graduate School Representative; Casey Theriot, Member; James Brown, Member; Amy Grunden, Member
Determinants for Hot Acid Microbial Lifestyles: Chemolithoautorophic Physiology of the Extremely Thermoacidophilic Archaeal Lineage Sulfolobales.
(2019-11-20) Counts, James Aaron; Robert Kelly, Chair; Carlos Goller, Member; Balaji Rao, Minor; Amy Grunden, Member
Developing Cell Surface-Display of Enzymes in Thermophilic Geobacillus.
(2020-03-27) Greenstein, Jennifer Lynn; Paul Hamilton, Chair; Amy Grunden, Member; Jose Bruno-Barcena, Member; Steven Peretti, Member
Development of a Genetic Toolbox for Geobacillus kaustophilus using Novel Bacteriophages GBK1 and GBK2.
(2020-01-03) Marks, Timothy James; Paul Hamilton, Chair; Eric Miller, Member; Amy Grunden, Member; Gary Gilleskie, Member
Development of the Extreme Thermophiles Pyrococcus furiosus and Sulfolobus acidocaldarius as Metabolic Engineering Platforms.
(2016-06-21) Loder, Andrew James; Robert Kelly, Chair; Balaji Rao, Minor; Gregory Reeves, Member; Amy Grunden, Member
Discovering, Characterizing, and Applying CRISPR-Cas Systems in Bacteria.
(2017-09-18) Leenay, Ryan Thomas; Chase Beisel, Chair; Robert Kelly, Minor; Rodolphe Barrangou, Member; Amy Grunden, Member
Effects of Three Chemical Compounds on Ralstonia solanacearum Physiological Functions and Disease Development.
(2019-03-26) Tseng, Hsien Tzer; David Ritchie, Chair; Marc Cubeta, Member; Amy Grunden, Member; Richard Zobel, Graduate School Representative; Lindsey Thiessen, Member