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Filtering by: Creator Sullivan, Nichole D. Remove constraint Creator: Sullivan, Nichole D. Non-Academic Affiliation Oregon State University. Center for Genome Research and Biocomputing Remove constraint Non-Academic Affiliation: Oregon State University. Center for Genome Research and Biocomputing

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Creating High Throughput Low Cost Analysis of Different Labor-Intensive Repetitive Research Processes

Creator:

Sullivan, Christopher M.

Abstract:

Many research projects suffer from limited data causing poor statistical analysis or limited results. The movement to high throughput methods has been building for many years and cross many different disciplines. Lots of these methods start out using pathways that generate large amounts of data but have limited methods to...

Resource Type:

Masters Thesis

Full Text:

THE THESIS OF Christopher M. Sullivan for the degree of Master of Science in Molecular and Cellular
Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Creator:

Kasschau, Kristin D., Fahlgren, Noah, Chapman, Elisabeth J., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., and Carrington, James C.

Abstract:

Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants...

Resource Type:

Article

Full Text:

siRNAs Kristin D. Kasschau 1,2 , Noah Fahlgren 1,2,3 , Elisabeth J. Chapman 1,2,3 , Christopher M
High-Throughput Sequencing of Arabidopsis microRNAs : Evidence for Frequent Birth and Death of MIRNA Genes

Creator:

Fahlgren, Noah, Howell, Miya D., Kasschau, Kristin D., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., Law, Theresa F., Grant, Sarah R., Dangl, Jeffrey L., and Carrington, James C.

Abstract:

In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep...

Resource Type:

Article

Full Text:

microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes Noah Fahlgren1,2, Miya D. Howell1, Kristin D
The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

Creator:

Fischer, Sylvia E. J., Montgomery, Taiowa A., Zhang, Chi, Fahlgren, Noah, Breen, Peter C., Hwang, Alexia, Sullivan, Christopher M., Carrington, James C., and Ruvkun, Gary

Abstract:

Endogenous small interfering RNAs (siRNAs) are a class of naturally occuring regulatory RNAs found in fungi, plants, and animals. Some endogenous siRNAs are required to silence transposons or function in chromosome segregation; however, the specific roles of most endogenous siRNAs are unclear. The helicase gene eri-6/7 was identified in the...

Resource Type:

Article

Full Text:

. Bars are color coded according to the most abundant size class of small RNAs within each interval. (D
Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

Creator:

Wiemann, Philipp, Sieber, Christian M. K., von Bargen, Katharina W., Studt, Lena, Niehaus, Eva- Maria, Espino, Jose J., Huß, Kathleen, Michielse, Caroline B., Albermann, Sabine, Wagner, Dominik, Bergner, Sonja V., Connolly, Lanelle R., Fischer, Andreas, Reuter, Gunter, Kleigrewe, Karin, Bald, Till, Wingfield, Brenda D., Ophir, Ron, Freeman, Stanley, Hippler, Michael, Smith, Kristina M., Brown, Daren W., Proctor, Robert H., Munsterkotter, Martin, Freitag, Michael, Humpf, Hans-Ulrich, Guldener, Ulrich, and Tudzynski, Bettina

Abstract:

The fungus Fusarium fujikuroi causes "bakanae" disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we...

Resource Type:

Article

Full Text:

Kleigrewe3, Till Bald4, Brenda D. Wingfield7, Ron Ophir8, Stanley Freeman9, Michael Hippler4, Kristina M
Transcriptomic Analyses of Crop Plants using Next-Generation Sequencing Technology

Creator:

Geniza, Matthew J.

Abstract:

Advancements in molecular biology and computer science have enabled researchers the ability to investigate the transcriptome – the quantification of an organism’s RNA transcripts in response to its environment on a system wide scale. The collective chapters of this thesis utilize high-throughput RNA sequencing, which produces hundreds of millions of...

Resource Type:

Dissertation

Full Text:

Award. To my study group; Edward Davis, Kai Tao, Estefania Elorriaga, and Chris Sullivan – without
Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum

Creator:

Kimbrel, Jeffrey A., Thomas, William J., Jiang, Yuan, Creason, Allison L., Thireault, Caitlin A., Sachs, Joel L., and Chang, Jeff H.

Abstract:

Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing...

Resource Type:

Article

Full Text:

clusters of orthologous genes and generate a whole-genome phylogeny of the 17 strains plus two d
Investigating Transcriptional Control of Specialized Gene Expression in Plants

Creator:

Fraser, Valerie N.

Abstract:

Specialized or secondary metabolism is a collection of pathways and small molecules that, while beneficial to an organism, are not strictly necessary for survival. Plants use secondary metabolites to, among other things, attract pollinators, defend against biotic and abiotic stressors, and form symbioses. Natural products from plants have seen an...

Resource Type:

Dissertation

Full Text:

(Zhang et al., 2012b; Zhang et al., 2012a; Pajoro et al., 2014; Sullivan et al., 2014; Maher et al
Comparative Aquatic Toxicology of Pesticides and Plastics Using the Model Estuarine Fish, Inland Silverside

Creator:

Hutton, Sara J.

Abstract:

Based on current trends both pesticide and plastic production are expected to continue to rise in the coming decade. A growing global population coupled with the effects of climate change are the main drivers of increased pesticide use. Throughout this dissertation pesticides refer to herbicides, fungicides, and insecticides. Plastic production...

Resource Type:

Dissertation

Full Text:

D – Supplemental Information to Chapter 5 .......................................... 162 Appendix
Host-Selective Toxins of Pyrenophora tritici-repentis Induce Common Responses Associated with Host Susceptibility

Creator:

Pandelova, Iovanna, Figueroa, Melania, Wilhelm, Larry J., Manning, Viola A., Mankaney, Aakash N., Mockler, Todd C., and Ciuffetti, Lynda M.

Abstract:

Pyrenophora tritici-repentis (Ptr), a necrotrophic fungus and the causal agent of tan spot of wheat, produces one or a combination of host-selective toxins (HSTs) necessary for disease development. The two most studied toxins produced by Ptr, Ptr ToxA (ToxA) and Ptr ToxB (ToxB), are proteins that cause necrotic or chlorotic...

Resource Type:

Article

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Academic Affiliation

Botany and Plant Pathology6
Environmental and Molecular Toxicology2
Statistics2
Biochemistry and Biophysics1
College of Pharmacy1

Advisor

Brander, Susanne M.1
Jaiswal, Pankaj1
Megraw, Molly1
Pankaj Jaiswal1
Tanguay, Robert L.1
more Advisors »

Commencement Year

Commencement Year range begin – Commencement Year range end

Current results range from 2018 to 2023

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Unknown 7

Committee Member

Fowler, John2
Anderson, Jeffrey C.1
Coopley, Richard1
Fowler, John E.1
Freitag, Michael1
more Committee Members »

Creator

Sullivan, Christopher M.4
Carrington, James C.3
Cumbie, Jason S.3
Fahlgren, Noah3
Givan, Scott A.2
more Creators »

Contributor

Tyler, Brett M.1

Date

Date range begin – Date range end

Current results range from 2007 to 2023

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Decade

2020-20294
2010-20199
2000-20092

Degree Field

Molecular and Cellular Biology5
Toxicology3

Degree Level

Doctoral7
Master's1

Degree Name

Doctor of Philosophy (Ph.D.)7
Master of Science (M.S.)1

Language

English [eng]15

License

All rights reserved8
Attribution 3.0 United States5
CC0 1.0 Universal2

Non-Academic Affiliation

Oregon State University. Center for Genome Research and Biocomputing[remove]15
Hatfield Marine Science Center1

Peer Reviewed

No7
Yes7

Resource Type

Article7
Dissertation7
Masters Thesis1

Rights Statement

In Copyright12
No Copyright - United States2
In Copyright - Non-Commercial Use Permitted1

Subject

Alternative toxicity testing1
Gene expression1
Lipids1
Machine learning1
Membrane proteins1
more Subjects »

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