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Developing Genetic Resources Within The Chenopodium Genus To Advance Quinoa Breeding And The De Novo Domestication Of C. Berlandieri, Clayton David Ludwig

Doctoral Dissertations

Quinoa (Chenopodium quinoa), an orphan crop native to South America, is tolerant of drought and saline soils and produces a highly nutritious grain. Given these qualities, the demand for this pseudocereal has been steadily increasing, and quinoa breeding programs can now be found throughout the world. I believe the introduction of quinoa-like cultivars developed specifically for Northern New England (NNE) with the region’s climate and disease pressures taken into consideration will benefit local farmers and consumers. Quinoa breeding efforts must consider its allopolyploid (2n = 4x = 36: AABB) genome composition as well as its reticulate ancestry, having descended via …

Revolutionary Advances In The Treatment Of Genetic Disease, Emma Kaitlyn Carrigan

Honors Theses and Capstones

No abstract provided.

Current Dog Breeding Practices Impacts On Health And Preservation Of Purebred Dogs, Bridget E. Baker

Honors Theses and Capstones

No abstract provided.

Genetic Dissection Of Non-Host Resistance To The Wheat Stem Rust Pathogen, Using An Interspecific Barberry Hybrid, Radhika Bartaula

Doctoral Dissertations

Stem rust, caused by the macrocyclic fungal pathogen P. graminis (Pg), is one of the most devastating diseases of wheat and other small grains globally; and the emergence of new stem rust races virulent on deployed resistance genes brings urgency to the discovery of more durable sources of genetic resistance. Given its intrinsic durability and effectiveness across a broad range of pathogens, non-host resistance (NHR) presents a compelling strategy for achieving long-term rust control in wheat. However, NHR to Pg (Pg-NHR) remains largely unexplored as a protection strategy in wheat, in part due to the challenge of developing a genetically …

Nitrogen Fixation Mutants Of The Actinobacterium Frankia Casuarinae Cci3, Ken-Ichi Kucho, Daiki Tamari, Shintaro Matsuyama, Takeshi Nabekura, Louis S. Tisa

Molecular, Cellular & Biomedical Sciences

Frankia is a representative genus of nitrogen-fixing (N2-fixing) actinobacteria; however, the molecular mechanisms underlying various phenomena such as the differentiation of a N2 fixation-specific structure (vesicle) and the regulation of N2 fixation (nif) genes, have yet to be elucidated in detail. In the present study, we screened hyphal fragments of Frankia casuarinae that were mutagenized by 1-methyl-3-nitro-1-nitrosoguanidine or gamma rays, and isolated 49 candidate N2 fixation mutants. Twelve of these mutants were selected for further study, and their abilities to grow in NH3-deficient (N-) liquid media and their rates of acetylene reduction activities were evaluated. Eleven mutant strains were confirmed …

Protein Phosphatase 2a Influences Cortical Microtubule Organization In Response To Salt Stress, Gabriella Angelini

Master's Theses and Capstones

As sessile organisms, plants must use molecular mechanisms to cope with stressors, such as NaCl stress. Protein Phosphatase 2A (PP2A) is a highly-conserved enzyme that regulates many processes including auxin transport, gravitropic responses, ABA responses, ionic stress responses, and microtubule organization. PP2A is a heterotrimer comprised of one scaffolding A subunit, one regulatory B subunit, and one catalytic C subunit. Roots of both the A subunit mutant a1rcn1 and the C subunit mutant c4 skewed when grown on vertically-oriented agar plates containing NaCl. Quantitation of cell file orientation in roots indicated that the root skewing phenotype was due to cell …

Genomic Evaluation Of Male Reproductive Adaptations And Responses To Dehydration In Peromyscus Eremicus (Cactus Mouse), Lauren Kordonowy

Doctoral Dissertations

Research elucidating the genetic architecture of physiological mechanisms enabling survival and reproduction in extreme environments is becoming prominent in evolutionary biology. The desert, in particular, poses numerous challenges for its endemic species, and mammals (and often, rodents) have been the focus for survival adaptations pertaining to water-limitation. However, desert rodent adaptation research has focused predominantly on survival, while potential physiological reproductive adaptations to dehydration have received less attention, aside from research evaluating water as reproductive cue. The fact that we do not know the physiological mechanisms enabling reproduction during dehydration is surprising, as desert rodents must possess adaptations to successfully …

Molecular Mechanisms Of Salt And Osmotic Stress Tolerance In Frankia Strains Isolated From Casuarina Trees, Rediet Oshone

Doctoral Dissertations

Globally, 20% of total cultivated and 33% of irrigated agricultural lands are affected by high salinity. By 2050, more than 50% of the arable land will be salinized. The hyper-ionic and hyper-osmotic stresses associated with salt-affected soils threaten the ability of cells to maintain optimal turgor pressure and intracellular ionic concentration for growth and functioning. The nitrogen-fixing soil actinobacterium Frankia shows marked variability in its tolerance to salinity. When in a symbiotic association with actinorhizal plants, Frankia enhances the tolerance of the plants to a range of abiotic stresses, including salinity. The Casuarina-Frankia association has been used to reclaim salt …

Protein Phosphatase 2a Function In Response To Salt Stress In Arabidopsis Thaliana: Defining Pathways And Genetic Interaction Networks, Megan M. Thompson

Doctoral Dissertations

Protein phosphatase 2A (PP2A) is a key regulator of many biological pathways. The PP2A heterotrimer is composed of a scaffolding/regulatory A subunit, regulatory B subunit, and catalytic C subunit. In Arabidopsis thaliana, the A, B and C subunits are encoded by 3, 17, and 5 genes, respectively. Despite the ubiquitous expression and high sequence conservation of the A and C subunits, plants with mutations in specific subunits display phenotypes. A subset of the A and C subunit mutants exhibited root skewing or curling phenotypes when grown on vertically-oriented plates supplemented NaCl. I characterized the root response of a1rcn1 and c4 …

Phylogenetic And Phylogeographic Analyses Reveal A Species Complex In The Estuarine Nudibranch Tenellia Adspersa, Amanda Sobel

Master's Theses and Capstones

Until recently, the nudibranch genus Tenellia (Nudibranchia: Fionidae) was thought to include a single or group of species restricted to temperate estuarine waters. Given the addition of numerous other species from recent studies, the genus now encompasses species from polar, temperate, and tropical oceans from oceanic to estuarine salinities. One such fionid, Tenellia adspersa, is found in temperate estuarine waters globally and its presence is ecologically important as its congeners are capable of decimating colonies of their hydroid prey within a single generation (approx. 20-60 days). The literature is historically vague and conflicted on the morphology, taxonomy, and geographic distribution …

Relating Shell Morphometrics And Heterozygosity To Byssogenesis, Byssal Thread Attachment Strength And Motility In The Blue Mussel, Ellie Daniels

Master's Theses and Capstones

Heterozygote deficiencies have been noted in both wild and farmed populations of Mytilus edulis Linnaeus 1758, yet the underlying causes for this deficit remain unclear. This is especially surprising considering that advantageous fitness traits (i.e., increased fecundity, reduced basal metabolism, higher growth rate in farmed mussels) as well as decreased mortality under environmental stressors (i.e., air exposure, increased water temperature) are positively correlated with heterozygosity in these mussels. The dislodgement hypothesis states that more heterozygous mussels are migrating to the periphery of a rope culture or mussel bed to gain an energetic advantage where they become more susceptible to drop-off. …

The Rate, Spectrum And Effects Of Spontaneous Mutation In Bacteria With Multiple Chromosomes, Marcus M. Dillon

Doctoral Dissertations

Despite their essentiality for evolutionary change and role in many diseases, spontaneous mutations remain understudied because of both biological and technical barriers. Prokaryotic mutation biases are especially understudied and no studies have been conducted on bacteria with multiple chromosomes, leaving major gaps in our understanding of the role of genome content and structure on mutation. The application of mutation accumulation lines to whole-genome sequencing offers the opportunity to study spontaneous mutations in a wide range of prokaryotic organisms. Here, we present a genome-wide view of molecular mutation rates and spectra in Burkholderia cenocepacia, Vibrio fischeri, and Vibrio cholerae, three bacterial …

Bacterial And Phage Interactions Influencing Vibrio Parahaemolyticus Ecology, Ashley L. Marcinkiewicz

Master's Theses and Capstones

Vibrio parahaemolyticus, a human pathogenic bacterium, is a naturally occurring member of the microbiome of the Eastern oyster. As the nature of this symbiosis in unknown, the oyster presents the opportunity to investigate how microbial communities interact with a host as part of the ecology of an emergent pathogen of importance. To define how members of the oyster bacterial microbiome correlate with V. parahaemolyticus, I performed marker-based metagenetic sequencing analyses to identify and quantify the bacterial community in individual oysters after culturally-quantifying V. parahaemolyticus abundance. I concluded that despite shared environmental exposures, individual oysters from the same collection site varied …

Marker Assisted Selection Of Sex Determination In Kiwiberry (Actinidia Arguta And Actinidia Kolomikta), Haley Gustafson

Master's Theses and Capstones

The selection of phenotypic traits in plant breeding has recently become augmented by the implementation of molecular markers. Marker-assisted breeding strategies are used to develop new cultivars of many important crop plants but have yet to be assimilated into breeding programs for many minor crops with untapped economic potential. In the following chapters, I discuss methods of marker development in crop plants, sex determination as a trait of economic interest in plant breeding, and the identification of two male-dominant, PCR-based markers in the commercially viable Kiwiberry species Actinidia arguta and A. kolomikta.

Dominance And Experience: Aggression And The Evolutionary Origins Of Social Behavior, Jacob Withee

Master's Theses and Capstones

Sociality as a life history strategy has many overt benefits, but its origin from solitary living is not fully understood. The cooperation necessary for formation of even basic social groups can present natural selection paradoxes that many models are unable to reconcile. Conversely, aggression is a key component to the formation of dominance hierarchies, a very basic form of social group. These hierarchies can give way to reproductive hierarchies, which are in turn the basis for some of the most complex forms of social organization. The focus of this thesis is to use aggression in an incipiently social bee species …

Iron Uptake In Symbiosis: The Role Of Siderophore In The Association Between Vibrio Fischeri And Euprymna Scolopes, Evan Dasilva

Master's Theses and Capstones

Iron acquisition is well studied in pathogens, and successful virulence is often attributed to iron acquisition by siderophore and heme uptake; however, the role of iron uptake in mutual symbiotic interactions is not as well understood. The mutual symbiosis between Vibrio fischeri and the Hawaiian bobtail squid, Euprymna scolopes, is a well-characterized system in which iron uptake has been implicated as a symbiotic factor. Four studies have implicated iron uptake in the symbiosis: 1) A TnLux reporter assay revealed that siderophore is more highly expressed by V. fischeri in the light organs of juvenile squid compared to V. fischeri in …

Understanding The Evolution Of Pathogenicity Within Geosmithia, Taruna Aggarwal

Master's Theses and Capstones

Geosmithia morbida is a filamentous ascomycete that causes thousand cankers disease in the eastern black walnut tree. This pathogen is commonly found in the western US; however, recently the disease was also detected in several eastern states where the black walnut lumber industry is concentrated. G. morbida is one of two known phytopathogens within the genus Geosmithia, and it is vectored into the host tree via the walnut twig beetle. We present the first de novo draft genome of G. morbida (Chapter 2). It is 26.5 Mbp in length and contains less than 1% repetitive elements. The genome possesses an …

Invasive Plant (Alliaria Petiolata; Garlic Mustard) Homogenizes Fungal Communtiy Composition And Increases Fungal Richness, Mark Anthony

Master's Theses and Capstones

Non-native invasive plants can disrupt native plant communities and soil function (e.g., C and N cycling), but few studies have examined how soil microbial community structure differs in association with invasion. This work focused on Alliaria petiolata (garlic mustard), a non-mycorrhizal Brassicaceae that can displace native plants and reduce aboveground diversity. Garlic mustard produces toxic phytochemicals that can suppress mycorrhizal fungi, but we currently do not know if garlic mustard invasion affects the general fungal community, including specific mycorrhizal fungi, saprotrophic fungi, and plant pathogens and parasites. The objective of this work was to compare uninvaded and invaded soils from …

Establishment Of The Multicolored Asian Lady Beetle, Harmonia Axyridis, As A Model System For The Evolution Of Phenotypic Variation, Lindsay Havens

Master's Theses and Capstones

The mechanisms behind the evolution and maintenance of striking visual phenotypes are as varied as the species that display these phenotypes. Multiple study systems have been well characterized and provide critical information about the evolution of these traits. However, new study systems in which the phenotype of interest can be easily manipulated and quantified are essential to answer many questions about the functionality of core evolutionary processes. One such model is elytral spot number of the multicolored Asian lady beetle, Harmonia axyridis (Chapter 1). I describe Harmonia axyridis as a potential novel model species for examining extreme phenotypic evolution. To …

Genetic And Evolutionary Analysis Of Plant Replication Protein A 1 (Rpa1), Behailu Birhanu Aklilu

Doctoral Dissertations

Challenging human health issues include treatments for genetic diseases and providing improved agricultural crop output to feed the growing world population. The project described here, which focuses on how cells respond to chromosomal (genomic) damage, has significant implications in each example. In humans, accumulation of DNA damage induced mutations can result in genetic diseases such as cancer, and in plants can similarly result in genome instability, reducing productivity. Organisms from human to plants have conserved mechanisms to counteract DNA damage. However, detailed genetic and biochemical information on plant DNA repair systems is still limited. The goal of this dissertation was …

Hybrid Zone Dynamics Between Saltmarsh (Ammodramus Caudacutus) And Nelson's (Ammodramus Nelsoni) Sparrows, Jennifer Walsh

Doctoral Dissertations

Hybrid zones in nature have long been equated to “windows on the evolutionary process” providing unique environments to understand patterns of gene flow and introgression and the role of these mechanisms in maintaining biodiversity. Ongoing hybridization and introgression can lead to a number of conservation and evolutionary outcomes; as such, identifying the role of introgression in natural populations can provide new insights into species interactions while contributing to our understanding of evolutionary theory.

The research presented below characterizes hybrid zone dynamics between two tidal marsh endemics – the Saltmarsh (Ammodramus caudacutus) and Nelson’s (Ammodramus nelsoni) sparrow. Both species co-inhabit salt …

Genomic Resource Development And Candidate Gene Evaluation In Fragaria Vesca (L.), Melanie Eileen Shields

Doctoral Dissertations

The wild strawberry Fragaria vesca (L. Rosaceae) is an important diploid model plant system for the study of processes associated with crop production, plant physiology, and cultivar development of the octoploid cultivated strawberry (F. ×ananassa), an economically important crop plant. A fosmid clone library developed from F. vesca ssp. americana ‘Pawtuckaway’, and a mapping population of 96 F2 progeny (YPF2) resulting from a cross of F. vesca ssp. semperflorens “Yellow Wonder’ with F. vesca ssp. americana ‘Pawtuckaway’, were employed to further develop genetic and genomic resources and advance the search for the molecular identity of the classically defined fruit color …

A Landscape Genetics Approach For Comparing Connectivity Across The Range Of The New England Cottontail, Katrina Papanastassiou

Master's Theses and Capstones

Habitat connectivity is vital for dispersal and metapopulation persistence. Land use change and landscape modification alter the distribution and availability of habitat, thereby altering connectivity and impeding organisms’ dispersal abilities. Reduction of connectivity is a concern for the New England cottontail (Sylvilagus transitionalis), a species of high conservation priority that has experienced a dramatic decline of its required shrubland habitat. To better understand New England cottontail connectivity, I used a landscape genetics approach to assess the impact of landscape features on cottontail dispersal in two geographically isolated study areas, one in southern Maine-seacoast New Hampshire and the other in eastern …

Development Of Genomic Resources And Identification Of Marker-Trait Associations In Strawberry, Lise L. Mahoney

Doctoral Dissertations

Crosses were performed and progeny populations were developed in diploid and octoploid strawberry (Fragaria) species for the purposes of genetic analysis and breeding. A high throughput genotyping platform - the Affymetrix IStraw90® Axiom® strawberry SNP array - was evaluated and employed for these purposes. Phenotyping was conducted with respect to several traits of interest, including flower color, flower and fruit pigment compositions, and verticillium wilt resistance, for the ultimate purpose of identifying marker-trait associations useful in breeding. In the ancestral diploid species Fragaria iinumae, an F2 mapping population was developed from a cross between two accessions previously collected in Hokkaido, …

The Investigation Of Microbe-Nematode Interactions, Chelsea K. Crepeau

Honors Theses and Capstones

No abstract provided.

Identification And Stoichiometric Analysis Of The Monosomal Translational Complex, Xin Wang

Doctoral Dissertations

The identification of the components involved in translational complexes has relied primarily on in vitro studies. Determining which proteins associate together in these complexes, under what conditions they do so, and how the composition of the complexes change under different conditions have became the key issues of in vivo studies. After a one-step affinity purification, using a novel technique of analytical ultracentrifugation with a fluorescence detection system (AU-FDS) I have identified a 77S monosomal translational complex in the yeast Saccharomyces cerevisiae. Major components of the 77S complex include the 80S ribosome, mRNA, and components of the closed-loop structure, eIF4E, eIF4G1/eIF4G2 …

Characterization Of The Expression Profile Of Polyamine Biosynthetic Genes (Spermidine Synthase) And Polyamine Metabolic Regulation In Arabidopsis, Lin Shao

Doctoral Dissertations

Polyamines are ubiquitously distributed cationic compounds, which play important roles in numerous cellular functions in plants. This study was aimed at elaborating the regulation of polyamine biosynthetic gene expression and polyamine metabolism. The organ/tissue specific expression patterns of two genes encoding the polyamine biosynthetic enzyme spermidine synthase ( AtSPDS1 and AtSPDS2) were studied in Arabidopsis at different developmental stages using promoter::reporter approach. The two homologues showed similar ubiquitous expression with subtle differences being observed in certain tissues (e.g. root, siliques, and embryos). Neither transgenic manipulation by over-expression of AtSPDSI alone nor its concomitant expression with genes encoding other biosynthetic enzymes …

Engineering Lipases And Solvents For Trans/-Esterification Of Used Vegetable Oils, Michael Dore Gagnon

Doctoral Dissertations

Diminishing petroleum reserves and increasing environmental awareness has led to an urgent need to develop alternative fuels, such as biodiesel. However, the conventional method to produce biodiesel uses environmentally harmful chemical catalysts. A relatively new development in the production of biodiesel is through enzymatic trans/- esterification with a lipase catalyst. Despite several advantages, there are a few technical and economical obstacles that limit this process: (1) immiscibility of the hydrophilic methanol and hydrophobic triglyceride which results in the formation of an interface leading to mass transfer resistance, (2) insufficient availability of large quantities of inexpensive lipase suitable for catalysis, and …

Patterns Of Cytosine Methylation In The Genome Of Caenorhabditis Elegans, Kazufusa Okamoto

Doctoral Dissertations

Recent large-scale comparative analysis of cytosine DNA methylation across diverse eukaryotes suggest that early features of DNA methylation present in the last common ancestor of all eukaryotes some 1.6 to 1.8 billion years ago included the methylation of gene bodies and transposable elements (Zemach, McDaniel et al. 2010; Parfrey, Lahr et al. 2011). These potentially ancient patterns may reflect a primitive role of methylation in transcriptional fidelity and as a mechanism to protect the germ line from transposon, or repeat, mediated mutation. Because spurious transcription and mutation are hypothesized to be among the critical limiting factors to genome size, an …

Patterns Of Intron Loss And Gain In Caenorhabditis, Gabrielle Giese

Master's Theses and Capstones

Introns, segments of genes that get spliced from the transcript before translation, are prevalent parts of many genomes and yet remain largely mysterious. Although their presence in the genome has been known for over thirty years, we still cannot answer the most fundamental questions about introns, such as where did they originate and, how are they gained and lost? In our most stringent dataset, we compared 137,453 intron positions in 6,257 pan-orthologs among four species of Caenorhabditis using a bioinformatics approach. While 82% of intron positions were conserved, we found a remarkable amount of intron variation. We also found evidence …