Browsing by Author "Heuberger, Adam L., committee member"

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Open Access
Community structure and pathogenomics of Pinaceae-infecting Fusarium spp.
(Colorado State University. Libraries, 2024) Dobbs, John, author; Stewart, Jane E., advisor; Kim, Mee-Sook, committee member; Sloan, Daniel B., committee member; Heuberger, Adam L., committee member
Due to a warming climate, the need for nursery grown conifer seedlings is continually increasing. However, several Fusarium spp. that cause pre- and post-emergent damping-off and root disease can hinder production of conifer seedlings. These soil or seed-borne Fusarium pathogens of conifers infect seedlings through the developing roots, and their similar effects on conifer hosts suggests that these pathogens may share a common evolutionary history. The shared ecological function of these Fusarium pathogens is likely associated with lineage-specific (LS) chromosomes or virulence gene(s) that are shared among these species. Identifying these potentially shared chromosomes or gene(s) and their functionality is best approached through the use of multiple 'omics technologies. Taken together, genomics, transcriptomics, proteomics, and metabolomics provide a comprehensive overview of the plant-microbial interactions at the time of Fusarium infection. This research accentuates how a combination of these technologies, such as genomics and transcriptomics, can be used to elucidate the biology of Fusarium pathogens and identify the presence of virulence-associated LS chromosomes or virulence gene(s) that facilitate the development of tools to rapidly identify and track these important pathogens. Chapter two, published in Frontiers in Plant Science, presents the observed regional effect on community structure of Fusarioid fungi collected from conifer seedlings among nurseries across the contiguous USA. The need for a global consensus to establish and maintain databases based on Fusarioid species type strains as references due to the continuing taxonomic disputes about the appropriate classification of Fusarium spp. designations was also discussed. For this reason, phylogenetic placement of the isolates was used for species identification; however, it is recognized that more research, such as whole genome sequencing, is needed to further validate the taxonomic identify of the isolates used in this study. Chapter three presents the whole genome comparisons of 17 Fusarium spp. isolates collected from conifer seedlings. Based on phylogenetic analyses of 16 conserved loci and composition of predicted genes, species were shown similar within and among Fusarium species complexes. Putative profiles of pathogenicity/virulence genes, including secreted in xylem (SIX) genes 2, 3, 9, and 14, and secondary metabolites, including the mycotoxins fumonisin and deoxynivelanol, were identified among the species complexes, but validation of expression of these genes is needed to demonstrate their functionality. Chapter four explores the mechanisms of pathogenicity and/or virulence of two understudied Fusarium spp., F. commune and F. annulatum, on conifer and non-conifer hosts and the differential gene expression in a susceptible conifer species. Further, the putative secretome profiles of Fusarium spp. within species complexes were identified, containing secreted carbohydrate-active enzymes, major facilitator supergroup transporters, apoplastic effectors, and gene products involved in secondary metabolite biosynthesis such as prolipyrone B/gibepyrone D, aurofusarin, and deoxinivelanol. Results from this study showed F. annulatum and F. commune caused disease on young conifer and non-conifer seedlings and identified putative genes associated with broad pathogenicity, and possibly indicating age-related resistance within the conifer host to certain upregulated pathogenicity genes. Due to the threat of spreading fungal pathogens from nurseries to field sites through latent infected seedlings and seed, this research highlights the need for robust early detection methods, while also providing insight into the biology of 17 Fusarium spp. that are potentially pathogenic to conifer seedlings. This research will help further develop technologies that aid managers for controlling Fusarium damping-off and root disease and mitigating the spread of novel haplotypes across regions.
Open Access
Genetic and metabolomic analyses of barley and cowpea: implications on quality and nutrition of finished foods
(Colorado State University. Libraries, 2021) Sayre-Chavez, Brooke, author; Muñoz-Amatriaín, María, advisor; Ryan, Elizabeth P., committee member; Heuberger, Adam L., committee member
The finished foods of a cereal (barley) and a legume (cowpea) were subjects of this thesis and analyzed in two separate studies. High quality barley that meets malting standards, is economically worth billions each year to the malting and brewing industry. The prevalence of craft brewing has been on the rise and with that, an increased interest in understanding the basis of beer flavor. Malt has been the subject of most research on beer flavor, and currently there is a lack of understanding on the contributions that the barley variety has to product flavor. The second crop that was subject of this thesis is cowpea. Cowpea is a nutritious food, that grows well in sub-Saharan Africa, where malnutrition is prevalent. It is well adapted to the resource-poor farming practices common in these regions, and highly valued as a food security crop. Despite the known health benefits, potential to alleviate malnutrition, and use in nutritional studies, there are no biomarkers identified for cowpea and its metabolic profile is currently not well characterized. The research goals of this thesis are broken down by crop. Regarding barley, the goals were to 1) test the hypothesis that barley genotype contributes to beer flavor, 2) to identify regions of the genome that control traits associated with flavor, and 3) identify candidate genes that control traits associated with flavor. Regarding cowpea, the goals were to 1) characterize the metabolic profile of three cowpea flours from varieties commonly consumed in sub-Saharan Africa (Ghana, specifically), and 2) test the hypothesis that there are metabolites unique to cowpea (and cowpea varieties). Metabolomic approaches were applied to both crops as finished foods, with additional genetic analysis of barley. We concluded that barley genotype does contribute to beer flavor, and that cowpea has distinct and characterizable metabolomic differences from other legumes. In barley, QTLs (quantitative trait loci) for malt quality, beer sensory, and metabolite traits were mapped, and candidate genes identified. The results of this study set a foundation for future genetic and breeding efforts surrounding barley and beer flavor, allowing for integration of various quality attributes. In cowpea, comparisons were made between cowpea, pigeon pea (another legume common to sub-Saharan Africa), and common bean on two non-targeted mass spectrometry platforms. Comparisons between the legumes illuminated metabolites that were either common to, or unique to each legume type or variety. The annotated metabolites from both analyses were from a diverse set of classifications and metabolic pathways, many with numerous known nutritional benefits. The metabolomic profiling of cowpea (and cowpea varieties) will allow for easier identification of nutritional biomarkers in future feeding studies.
Open Access
Influence of post-mortem aging time and method on flavor and tenderness of beef, and comparison of retail cutting yields, times, and value in thirteen beef subprimals from beef and Holstein cattle
(Colorado State University. Libraries, 2018) Foraker, Blake Austin, author; Woerner, Dale R., advisor; Belk, Keith E., committee member; Engle, Terry E., committee member; Heuberger, Adam L., committee member
The objective of this study was to identify flavor and tenderness differences in beef aged for different lengths of time and using different methods. Strip loin sections from commodity, USDA Choice beef carcasses (n = 38) were randomly assigned to 1 of 8 aging treatments: 1) 3 d wet-aged; 2) 14 d wet-aged; 3) 28 d wet-aged; 4) 35 d wet-aged; 5) 49 d wet-aged; 6) 63 d wet-aged, 7) 21 d dry-aged; and 8) 14 d wet-aged followed by 21 d dry-aged (combination). Trained sensory panelists rated the cooked product for flavor and textural attributes, and samples were evaluated for Warner-Bratzler and slice shear force, fatty acid composition, amino acid composition, and volatile flavor compounds. Wet-aging of beef up to 35 d caused no changes (P > 0.05) in flavor notes. However, beef wet-aged for 49 d or longer was rated lowest (P < 0.01) for the attribute of beef flavor ID and greatest (P ≤ 0.02) for metallic, sour, oxidized, nutty, musty/earthy, and liver-like. No differences (P > 0.05) were identified between wet-aging, dry-aging, or the combination of both for any flavor attributes. Fatty acid profiles did not differ (P > 0.05) by aging length of time or method. Concentrations of amino acids and volatile flavor compounds increased (P < 0.01) during the wet-aging period, but minimal differences in these compounds were noted between wet- and dry-aged beef. Additionally, beef that was wet-aged for 3 d was toughest (P < 0.01). Nonetheless, tenderness improvement only occurred up to 28 d of wet-aging, where no subsequent differences (P > 0.05) were noted. Results suggested that wet-aging to extreme lengths of time may have a dramatic effect on flavor profile of beef, without necessarily improving tenderness. Additionally, eating quality characteristics do not necessarily differ between wet- and dry-aged beef. Holsteins comprise approximately 20% of the U.S. fed beef slaughter, and the carcass characteristics of Holsteins tend to differ (on average) from those of traditional beef breeds. Retail cutting yields, cutting times, and resulting value were evaluated in thirteen subprimal cuts from carcasses of fed Holstein (n = 398) and beef-breed (n = 404) origin. Generally, subprimals from carcasses of beef-breeds were heavier (P < 0.05) than those derived from Holsteins. Greater (P < 0.01) saleable yields of retail cuts were noted for ribeye rolls, short loins, and inside rounds (individual muscle) from carcasses of Holsteins, and bottom round flats from carcasses of beef-breeds. Saleable yields of all other subprimal cuts did not differ (P > 0.05) between cattle types. Only the amount of time taken to cut center-cut top sirloin butts derived from beef-breeds were faster (P < 0.01) than those for cuts from carcasses of Holsteins; in all other instances, times for cutting subprimals derived from Holstein carcasses were either faster (P < 0.05) or not different (P ≥ 0.05). Retail prices among cuts from differing breed types were minimal, but true differences (P < 0.05) in cutting yields for ribeye rolls and short loins from carcasses of Holsteins may generate greater values to a steak cutter or retailer. Such advantages could be attributed to smaller, more manageable, and leaner cuts produced from carcasses of Holsteins. Therefore, further research regarding retail cutting differences between cattle types may provide insight for operations seeking maximum retail yields and profit.
Open Access
The curious case of chemotaxis in soft rot Pectobacteriaceae
(Colorado State University. Libraries, 2021) Nasaruddin, Afnan Shazwan, author; Charkowski, Amy O., advisor; Leach, Jan E., committee member; Trivedi, Pankaj, committee member; Heuberger, Adam L., committee member
Soft rot Pectobacteriaceae, Dickeya and Pectobacterium, are notorious for causing blackleg and soft rot diseases on more than 50% angiosperms such as potato, tomato, carrot, cabbage, and rice. In the United States, soft rot Pectobacteriaceae causes at least $40 million losses of potato each year. Flagellar motility is important for soft rot Pectobacteriaceae virulence. Chemotaxis, which controls flagellar motility towards a conducive environment or away from hostile conditions, is essential for initial stages of infection. Chemotaxis is mediated by chemoreceptors known as methyl-accepting chemotaxis proteins. Genomic analyses of soft rot Pectobacteriaceae and closely related animal pathogens and non-pathogenic bacteria in order Enterobacteriales showed that soft rot Pectobacteriaceae genomes are enriched in methyl-accepting chemotaxis proteins. Furthermore, soft rot Pectobacteriaceae methyl-accepting chemotaxis proteins contain more diverse ligand binding domains compared to other species in Enterobacteriales. This study suggests the importance of chemotaxis for soft rot Pectobacteriaceae pathogenicity and opens up possibilities for future research in targeting chemotaxis for plant disease management. In E. coli, the alternative sigma factor FliA is required for transcription initiation in motility and chemotaxis genes. To determine how chemotaxis is regulated in Dickeya, we conducted an RNA-sequencing experiment using a wild-type strain and a fliA mutant of D. dadantii 3937 grown in minimal media with glycerol or glucose. We found that the FliA sigma factor did not regulate methyl-accepting chemotaxis genes in Dickeya, several virulence genes were upregulated in glucose, and some genes postulated to be regulated by PecS were upregulated in glycerol. It is still a mystery as to which sigma factor regulates the chemotaxis genes in Dickeya, however, my work demonstrates that the regulation of chemotaxis in plant pathogens differs from closely related animal pathogens in the same order.