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Proteome Characterizations Of Microbial Systems Using Ms-Based Experimental And Informatics Approaches To Examine Key Metabolic Pathways, Proteins Of Unknown Function, And Phenotypic Adaptation, Suresh Poudel
Doctoral Dissertations
Microbes express complex phenotypes and coordinate activities to build microbial communities. Recent work has focused on understanding the ability of microbial systems to efficiently utilize cellulosic biomass to produce bioenergy-related products. In order to maximize the yield of these bioenergy-related products from a microbial system, it is necessary to understand the molecular mechanisms.The ability of mass spectrometry to precisely identify thousands of proteins from a bacterial source has established mass spectrometry-based proteomics as an indispensable tool for various biological disciplines. This dissertation developed and optimized various proteomics experimental and informatic protocols, and integrated the resulting data with metabolomics, transcriptomics, and …
Biomass Production Of Herbaceous Energy Crops In The United States: Field Trial Results And Yield Potential Maps From The Multiyear Regional Feedstock Partnership, Do Kyoung Lee, Ezra Aberle, Erik K. Anderson, William Anderson, Brian S. Baldwin, David Baltensperger, Michael Barrett, Jürg Blumenthal, Stacy Bonos, Joe Bouton, David I. Bransby, Charlie Brummer, Pane S. Burks, Chengci Chen, Christopher Daly, Josh Egenolf, Rodney L. Farris, John H. Fike, Roch Gaussoin, John R. Gill, Kenneth Gravois, Michael D. Halbleib, Anna Hale, Wayne Hanna, Keith Harmoney, Emily A. Heaton, Ron W. Heiniger, Lindsey Hoffman, Chang O. Hong, Gopal Kakani, David Williams, Linda Williams
Biomass Production Of Herbaceous Energy Crops In The United States: Field Trial Results And Yield Potential Maps From The Multiyear Regional Feedstock Partnership, Do Kyoung Lee, Ezra Aberle, Erik K. Anderson, William Anderson, Brian S. Baldwin, David Baltensperger, Michael Barrett, Jürg Blumenthal, Stacy Bonos, Joe Bouton, David I. Bransby, Charlie Brummer, Pane S. Burks, Chengci Chen, Christopher Daly, Josh Egenolf, Rodney L. Farris, John H. Fike, Roch Gaussoin, John R. Gill, Kenneth Gravois, Michael D. Halbleib, Anna Hale, Wayne Hanna, Keith Harmoney, Emily A. Heaton, Ron W. Heiniger, Lindsey Hoffman, Chang O. Hong, Gopal Kakani, David Williams, Linda Williams
Plant and Soil Sciences Faculty Publications
Current knowledge of yield potential and best agronomic management practices for perennial bioenergy grasses is primarily derived from small‐scale and short‐term studies, yet these studies inform policy at the national scale. In an effort to learn more about how bioenergy grasses perform across multiple locations and years, the U.S. Department of Energy (US DOE)/Sun Grant Initiative Regional Feedstock Partnership was initiated in 2008. The objectives of the Feedstock Partnership were to (1) provide a wide range of information for feedstock selection (species choice) and management practice options for a variety of regions and (2) develop national maps of potential feedstock …
Genetic Diversity, Genetic Variation And Identification Of Quantitative Trait Loci (Qtl) Associated With Biomass Yield And Establishment-Related Traits In Lowland Switchgrass (Panicum Virgatum L.), Cheryl Ontolan Dalid
Genetic Diversity, Genetic Variation And Identification Of Quantitative Trait Loci (Qtl) Associated With Biomass Yield And Establishment-Related Traits In Lowland Switchgrass (Panicum Virgatum L.), Cheryl Ontolan Dalid
Doctoral Dissertations
Switchgrass is a warm-season C4 grass used for biofuel production. The primary goal of this study is biomass yield improvement for use as a bioenergy feedstock. The research plan was partitioned into three main objectives: (i) evaluate the genetic diversity among lowland switchgrass populations using microsatellite markers; (ii) assess genetic variation in an Alamo half-sib (AHS) population developed through phenotypic selection; (iii) and identify quantitative trait loci (QTL) associated with biomass yield and establishment related seed traits using a Nested Association Mapping (NAM) population. The genetic diversity study on lowland switchgrass showed significant phenotypic variations (P<0.05) among and within germplasm accessions. The Analysis of Molecular Variance (AMOVA) revealed that among genotypes within populations and among populations explained 84 and 16% of molecular genetic variations. The Principal Coordinate Analysis (PCoA) and cluster analysis separated switchgrass populations according to the ancestral background. The study on genetic variation showed significant variation (P<0.05) among AHS for biomass yield, tillering ability, and spring vigor, suggesting the importance of additive genetic variation in these traits. Results also showed great potential for biomass yield improvement through selection based on family performance. Using 10% selection intensity, parental control of two, and a narrow-sense heritability estimate of 0.11, gain per cycle selection from half-sib family selection is estimated to be 23%. The study on identification of QTLs associated with biomass yield and establishment related traits showed significant variation among NAM families and genotypes within families for biomass yield, seed weight, and germination (P<0.05). A total of 785 significant markers for biomass yield were detected (P<0.05) of which 176 were for seed weight and 131 for germination. Composite interval mapping revealed 21 QTLs for biomass yield across locations in 2 years the highest LOD score of 7.6 detected in chromosome Ia that explained a 12.5% of the phenotypic variation. Two QTLs located in chromosome VIIIb for seed weight explained 5.2% and 4.6% phenotypic variation. One QTL for germination located in chromosome IXa explained 5.2% of the phenotypic variation. The results of these studies will be useful for future breeding efforts in switchgrass and other perennial grasses.
Effects Of Hardwood Control And Switchgrass Intercropping On Breeding Bird Communities And Resource Use In Managed Loblolly Pine Stands In Mississippi, Marian Fuller-Morris
Effects Of Hardwood Control And Switchgrass Intercropping On Breeding Bird Communities And Resource Use In Managed Loblolly Pine Stands In Mississippi, Marian Fuller-Morris
Theses and Dissertations
Managed loblolly pine (Pinus taeda) stands are common in the southeastern United States and provide young forest conditions for early successional breeding birds. Common pine management practices (e.g. hardwood control) and novel practices (e.g. switchgrass [Panicum virgatum] intercropping), may influence breeding bird use. I evaluated breeding bird abundance, diversity, and resource use within loblolly stands treated to control hardwood species, intercropped with switchgrass, and with no additional management. Hardwood control and switchgrass intercropping both decreased hardwoods and shrubs, and increased forbs. Switchgrass intercropping increased some early successional bird abundances. However, diversity was not different among treatments. Switchgrass intercropping increased 13C:12C …
Functional Analysis Of Cellulose Synthase Cesa4 And Cesa6 Genes In Switchgrass (Panicum Virgatum) By Overexpression And Rnai-Mediated Gene Silencing, Mitra Mazarei, Holly L. Baxter, Mi Li, Ajaya K. Biswal, Keonhee Kim, Xianzhi Meng, Yunqiao Pu, Wegi A. Wuddineh, Ji-Yi Zhang, Geoffrey B. Turner, Robert W. Sykes, Mark F. Davis, Michael K. Udvardi, Zeng-Yu Wang, Debra Mohnen, Arthur J. Ragauskas, Nicole Labbé, C. Neal Stewart Jr.
Functional Analysis Of Cellulose Synthase Cesa4 And Cesa6 Genes In Switchgrass (Panicum Virgatum) By Overexpression And Rnai-Mediated Gene Silencing, Mitra Mazarei, Holly L. Baxter, Mi Li, Ajaya K. Biswal, Keonhee Kim, Xianzhi Meng, Yunqiao Pu, Wegi A. Wuddineh, Ji-Yi Zhang, Geoffrey B. Turner, Robert W. Sykes, Mark F. Davis, Michael K. Udvardi, Zeng-Yu Wang, Debra Mohnen, Arthur J. Ragauskas, Nicole Labbé, C. Neal Stewart Jr.
Plant Sciences Publications and Other Works
Switchgrass (Panicum virgatum L.) is a leading lignocellulosic bioenergy feedstock. Cellulose is a major component of the plant cell walls and the primary substrate for saccharification. Accessibility of cellulose to enzymatic breakdown into fermentable sugars is limited by the presence of lignin in the plant cell wall. In this study, putatively novel switchgrass secondary cell wall cellulose synthase PvCesA4 and primary cell wall PvCesA6 genes were identified and their functional role in cellulose synthesis and cell wall composition was examined by overexpression and knockdown of the individual genes in switchgrass. The endogenous expression of PvCesA4 and PvCesA6 genes varied …
Identification, Characterization, And Genetic Comparison Of Fusarium Species Isolated From Switchgrass (Panicum Virgatum L.), Tamara Annette Collins
Identification, Characterization, And Genetic Comparison Of Fusarium Species Isolated From Switchgrass (Panicum Virgatum L.), Tamara Annette Collins
Masters Theses
Fusarium spp. are ubiquitous, soilborne and seedborne pathogens that affect over 100 economically important plant hosts annually, resulting in billions of dollars in economic losses. They cause a variety of plant disease symptoms including, crown, root, and stem rots, wilts, and foliar necrosis. Furthermore, they produce harmful mycotoxins that are detrimental to the health of animals and humans. Members of this genus have been isolated from diseased tissues of switchgrass. The objective is to correctly identify and classify Fusarium isolates to species using both classic phenotypic characterization and current genetic technologies of DNA extraction and polymerase chain reaction and create …
Differential Effects Of Warming And Nitrogen Fertilization On Soil Respiration And Microbial Dynamics In Switchgrass Croplands, Jianwei Li, Siyang Jian, Jason P. De Koff, Chad S. Lane, Gangsheng Wang, Melanie A. Mayes, Dafeng Hui
Differential Effects Of Warming And Nitrogen Fertilization On Soil Respiration And Microbial Dynamics In Switchgrass Croplands, Jianwei Li, Siyang Jian, Jason P. De Koff, Chad S. Lane, Gangsheng Wang, Melanie A. Mayes, Dafeng Hui
Agricultural and Environmental Sciences Faculty Research
The mechanistic understanding of warming and nitrogen (N) fertilization, alone or in combination, on microbially mediated decomposition is limited. In this study, soil samples were collected from previously harvested switchgrass (Panicum virgatum L.) plots that had been treated with high N fertilizer (HN: 67 kg N ha−1) and those that had received no N fertilizer (NN) over a 3-year period. The samples were incubated for 180 days at 15 °C and 20 °C, during which heterotrophic respiration, δ13C of CO2, microbial biomass (MB), specific soil respiration rate (Rs: respiration per unit of microbial biomass), and exoenzyme activities were …
Evaluation Of Greenbug And Yellow Sugarcane Aphid Feeding Behavior On Resistant And Susceptible Switchgrass Cultivars, Kyle G. Koch, Teresa Donze-Reiner, Lisa M. Baird, Joe Louis, Keenan L. Amundsen, Gautam Sarath, Jeff Bradshaw, Tiffany Heng-Moss
Evaluation Of Greenbug And Yellow Sugarcane Aphid Feeding Behavior On Resistant And Susceptible Switchgrass Cultivars, Kyle G. Koch, Teresa Donze-Reiner, Lisa M. Baird, Joe Louis, Keenan L. Amundsen, Gautam Sarath, Jeff Bradshaw, Tiffany Heng-Moss
Department of Entomology: Faculty Publications
Switchgrass (Panicum virgatum L.) is an emerging biofuel crop that serves as host for aphids. To discern the effects of plant age and possible resistance mechanisms, the feeding behavior of greenbugs (Schizaphis graminum Rondani.) and the yellow sugarcane aphid (Sipha flava Forbes.) was monitored on three diverse switchgrasses by the electrical penetration graph (EPG) technique. Callose deposition and genes associated with callose metabolism were also analyzed to discern their association with plant resistance. There was a strong host effect on greenbugs feeding on lowland cultivar Kanlow at the V3 stage of development, as compared to the greenbug-susceptible …
Impact Of Drought On Chemical Composition And Sugar Yields From Dilute-Acid Pretreatment And Enzymatic Hydrolysis Of Miscanthus, A Tall Fescue Mixture, And Switchgrass, Amber Hoover, Rachel Emerson, Allison Ray, Daniel Stevens, Sabrina Morgan, Marnie Cortez, Robert Kallenbach, Matthew Sousek, Rodney Farris, Dayna Daubaras
Impact Of Drought On Chemical Composition And Sugar Yields From Dilute-Acid Pretreatment And Enzymatic Hydrolysis Of Miscanthus, A Tall Fescue Mixture, And Switchgrass, Amber Hoover, Rachel Emerson, Allison Ray, Daniel Stevens, Sabrina Morgan, Marnie Cortez, Robert Kallenbach, Matthew Sousek, Rodney Farris, Dayna Daubaras
Department of Agronomy and Horticulture: Faculty Publications
Environmental factors like drought impact the quality of biomass entering a bioconversion process. Drought often reduces the sugar content in lignocellulosic biomass, which could have economic impacts, particularly when compounded with losses in dry biomass yield; however, the effects on conversion efficiency are not completely understood. This study investigated how drought may impact biomass composition and sugar yields from dilute-acid pretreatment and enzymatic hydrolysis of Miscanthus, a tall fescue mixture, and switchgrass from Nebraska, Missouri, and Oklahoma, respectively, grown as part of Regional Feedstock Partnership field trials. Samples were grown and harvested in 2010 during non-drought conditions and in …