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Articles 1 - 5 of 5
Full-Text Articles in Organisms
Investigating The Origin And Functions Of A Novel Small Rna In Escherichia Coli, Fenil Rashmin Kacharia
Investigating The Origin And Functions Of A Novel Small Rna In Escherichia Coli, Fenil Rashmin Kacharia
Dissertations and Theses
Non-coding small RNAs (sRNAs) regulate various cellular processes in bacteria. They bind to a chaperone protein Hfq for stability and regulate gene expression by base-pairing with target mRNAs. Although the importance of sRNAs in bacteria has been well established, the mode of origination of novel sRNA genes is still elusive, mainly because the rapid rate of evolution of sRNAs obscures their original sources. To overcome this impediment, we identified a recently formed sRNA (EcsR2) in E. coli, and show that it evolved from a degraded bacteriophage gene. Our analyses also revealed that young sRNAs such as EcsR2 are expressed …
Mechanisms Of Adaptation In The Newly Invasive Species Brachypodium Sylvaticum (Hudson) Beauv., Gina Lola Marchini
Mechanisms Of Adaptation In The Newly Invasive Species Brachypodium Sylvaticum (Hudson) Beauv., Gina Lola Marchini
Dissertations and Theses
It is common knowledge that invasive species cause worldwide ecological and economic damage, and are nearly impossible to eradicate. However, upon introduction to a novel environment, alien species should be the underdogs: They are present in small numbers, possess low genetic diversity, and have not adapted to the climate and competitors present in the new habitat. So, how are alien species able to invade an environment occupied by native species that have already adapted to the local environment? To discover some answers to this apparent paradox I conducted four ecological genetic studies that utilized the invasive species Brachypodium sylvaticum (Hudson) …
The Boiling Springs Lake Metavirome: Charting The Viral Sequence-Space Of An Extreme Environment Microbial Ecosystem, Geoffrey Scott Diemer
The Boiling Springs Lake Metavirome: Charting The Viral Sequence-Space Of An Extreme Environment Microbial Ecosystem, Geoffrey Scott Diemer
Dissertations and Theses
Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of establishing a more comprehensive view of virus diversity and evolution, as vast amounts of new sequence data becomes available for comparative analysis.
Metagenomic DNA from virus-sized particles (smaller than 0.2 microns in diameter) was isolated from approximately 20 liters of sediment obtained from Boiling Springs Lake (BSL) and sequenced. BSL is a large, acidic hot-spring (with a pH of 2.2, and temperatures ranging from 50°C to 96°C) located in Lassen Volcanic National …
Metagenomes From High-Temperature Chemotrophic Systems Reveal Geochemical Controls On Microbial Community Structure And Function, William P. Inskeep, Douglas B. Rusch, Zackary J. Jay, Markus J. Herrgard, Mark A. Kozubal, Toby H. Richardson, Richard E. Macur, Natsuko Hamamura, Ryan Dem. Jennings, Bruce W. Fouke, Anna-Louise Reysenbach, Frank Roberto, Mark Young, Ariel Schwartz, Eric S. Boyd, Jonathan H. Badger, Eric J. Mathur, Alice C. Ortmann, Mary Bateson, Gill Geesey
Metagenomes From High-Temperature Chemotrophic Systems Reveal Geochemical Controls On Microbial Community Structure And Function, William P. Inskeep, Douglas B. Rusch, Zackary J. Jay, Markus J. Herrgard, Mark A. Kozubal, Toby H. Richardson, Richard E. Macur, Natsuko Hamamura, Ryan Dem. Jennings, Bruce W. Fouke, Anna-Louise Reysenbach, Frank Roberto, Mark Young, Ariel Schwartz, Eric S. Boyd, Jonathan H. Badger, Eric J. Mathur, Alice C. Ortmann, Mary Bateson, Gill Geesey
Biology Faculty Publications and Presentations
The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site) was obtained for five hightemperature (>65°C) chemotrophic microbial communities sampled from …
Rearrangement Of The Rna Polymerase Subunit H And The Lower Jaw In Archaeal Elongation Complexes, Sebastian Grünberg, Christoph Reich, Mirijam E. Zeller, Michael S. Bartlett, Michael Thomm
Rearrangement Of The Rna Polymerase Subunit H And The Lower Jaw In Archaeal Elongation Complexes, Sebastian Grünberg, Christoph Reich, Mirijam E. Zeller, Michael S. Bartlett, Michael Thomm
Biology Faculty Publications and Presentations
The lower jaws of archaeal RNA polymerase and eukaryotic RNA polymerase II include orthologous subunits H and Rpb5, respectively. The tertiary structure of H is very similar to the structure of the C-terminal domain of Rpb5, and both subunits are proximal to downstream DNA in pre-initiation complexes. Analyses of reconstituted euryarchaeal polymerase lacking subunit H revealed that H is important for open complex formation and initial transcription. Eukaryotic Rpb5 rescues activity of the ΔH enzyme indicating a strong conservation of function for this subunit from archaea to eukaryotes. Photochemical cross-linking in elongation complexes revealed a striking structural rearrangement of RNA …