Genetics and Genomics Commons^™

Temperate Eurasian Origins Of Hawaiian Chenopodium (Amaranthaceae) Plus Description Of A New Species Endemic To Moloka‘I, Jason T. Cantley, Angela J. Mcdonnell, J Branson, S R. Long, W Garnett, Christopher T. Martine

Faculty Journal Articles

Chenopodium taxa of Hawai‘i are tetraploids distinguished from other members of the circumglobally distributed genus by minute morphological characters. Because of these reasons, the geographic origin of Hawaiian Chenopodium has remained unclear. Across the Hawaiian Archipelago, Chenopodium taxa are morphologically variable and grow in highly disparate xeric habitats, especially in terms of precipitation, temperature, wind, salt spray, and solar irradiation. Habitats include dry subalpine shrublands, sandy beach strand of atolls in the Northwest Hawaiian Islands, dry forests, and precipitously tall sea cliffs of northwestern Moloka‘i. From the Moloka‘i sea cliffs, which are battered by high energy winds, salt spray, and …

Investigation Into The Roles Of Her9 And Capn5 During Retinal Development And Regeneration, Cagney Coomer

Theses and Dissertations--Biology

The formation of a healthy and functioning eye requires coordinated interactions between numerous signaling pathways and gene regulatory networks within the developing neural retina. Tight regulation of gene expression is required for cell specification and differentiation in this multilayered, light sensitive tissue. The photoreceptors are the light detecting cells of the retina, capable of functioning in both intense sunlight and dim light at night. When pigment cells of the photoreceptor outer segment are activated by light, a complex chain of events called phototransduction leads to the electrical signal cascade that is transmitted through the retina and ultimately to the brain …

Combination Of Investigational Cell-Based Therapy And Deep Brain Stimulation To Alter The Progression Of Parkinson’S Disease, Nader El Seblani

Theses and Dissertations--Pharmacy

Parkinson’s disease (PD) is the second most common neurodegenerative disorder and the motor symptoms are caused by progressive loss of midbrain dopamine neurons. There is no current treatment that can slow or reverse PD. Our current “DBS-Plus” clinical trial (NCT02369003) features the implantation in vivo of autologous Schwann cells (SCs) derived from a patient’s sural nerve into the substantia nigra pars compacta (SNpc) in combination with Deep Brain Stimulation (DBS) therapy for treating patients with advanced PD.

The central hypothesis of our research is that transdifferentiated SCs within conditioned nerve tissue will deliver pro-regenerative factors to enhance the survival of …

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

Honors Theses and Capstones

No abstract provided.

Biological Pathways Associated With Wild And Domestic Animals, Cayla Steemer, Laura Carson, Jim Hu, Gloria Regisford

Pursue: Undergraduate Research Journal

Background: Zoonotic diseases are problematic, in that, they impact both wild and domestic animals alike. Thus, there is a need to investigate the genomes of wild and domestic. Gene ontology (GO) is a major bioinformatics initiative, whereby descriptions of gene products across the database are developed and unified to describe all species. This process is performed by biocurators, who gather, annotate, and validate information on the databases, consequently affording easy access to accurate and updated data. In this study, we investigated the biocuration of two biological processes, DNA integration, which is used for DNA coding, and the tricarboxylic acid (TCA) …

Spatial And Temporal Genetic Structure Of Winter-Run Steelhead (Oncorhynchus Mykiss) Returning To The Mad River, California, Steven R. Fong

Cal Poly Humboldt theses and projects

Distinct populations of steelhead in the wild are in decline. The propagation of steelhead in hatcheries has been used to boost population numbers for recreational fisheries and for use in conservation. However, hatchery breeding practices of steelhead can result in changes in genetic structure. I investigated the genetic structure of winter-run steelhead (Oncorhynchus mykiss) returning to the Mad River, California, where a hatchery has been used enhance production for recreational fisheries since 1971. Genetic variability in Mad River steelhead was evaluated using 96 single nucleotide polymorphisms (SNPs) among 4203 individuals, including the Mad River and nearby locations, and …

Plasticity And The Impact Of Increasing Temperature On A Tropical Ectotherm, Adam A. Rosso

College of Graduate Studies: Theses & Dissertations

Organisms may respond to climate change through behavior, genetic adaptation, and/or phenotypic plasticity. Tropical ectotherms are thought to be especially vulnerable to climate change because most have a narrow range of thermal tolerance while living close to their upper thermal tolerance limits. Additionally, many tropical species live in closed-canopy forests, which provide homogenous thermal landscapes that prevent behavioral compensation for stressfully warm temperatures. Finally, tropical ectotherms are thought to have decreased capacity for phenotypic plasticity because they have evolved in thermally stable environments. We tested gene expression patterns and phenotypic plasticity in the Panamanian slender anole by a) measuring changes …

Floral Trait Architecture In Crop Sunflower (Helianthus Annuus) Under Drought Conditions, Lauren Segarra

All Master's Theses

Longer and more intense droughts are predicted to become more common in the coming century due to anthropogenic climate change. Drought can reduce crop yield and decrease food security. In order to mitigate the negative effects of drought on crop production, it is important to elucidate the underlying mechanisms that promote drought stress resistance in crop plants. Floral traits impact yield, especially in oilseed crops such as sunflower (Helianthus annuus), but their susceptibility to drought stress is understudied. The goal of this study was to describe the floral trait architecture of H. annuus crop lines under drought versus …

Roadmap For Naming Uncultivated Archaea And Bacteria, Alison Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T. Konstantinidis, Christopher E. Lane, R. Thane Papke, Anna-Louise Reysenbach, Multiple Additional Authors

Biology Faculty Publications and Presentations

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code …

A Mechanism For Sex Determination In Dioecious Cultivated Spinach, Nicholas West

Wayne State University Dissertations

While unisexual flowers have evolved repeatedly throughout angiosperm families, the actual identity of sex determining genes has been elusive, and their regulation within populations remains largely undefined. Additionally, sex liability is often observed in unisexual plants and has been correlated to external and internal cues, suggesting that the genes responsible for unisexual morphology are not necessarily segregating but rather differentially regulated. Understanding these processes will be of significant theoretical and agronomical importance.

Cultivated spinach is a dioecious species in which an individual will bear alternative sexual organs. Previous work has identified spinach B class floral organ identity genes, SpAP3 and …

The Regulatory Role Of Tnac In The Universal Expression Regulation Of Rf-2 Dependent Regulons, Chi Pham

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

The Functional Importance Of Methyl Cpg Binding Domain Proteins 2 And 3 In Regulating Fetal Hemoglobin Expression In Human Adult Erythroid Cells, Alexander Azzo

Theses and Dissertations

Humans undergo two developmental switches in the predominantly expressed β-like globin chain during embryogenesis and fetal development. The first switch from embryonic (ε) to fetal (γ) occurs around week 5 of embryonic development, while the second switch from fetal to adult (β) globin occurs shortly after birth. By adulthood, fetal hemoglobin represents only 1-2% of total hemoglobin in the blood. As sufficiently elevated levels of fetal hemoglobin are beneficial for improving clinical outcomes in sickle cell disease and β-thalassemia, the mechanisms that enforce silencing of fetal hemoglobin expression postnatally are of great clinical significance. The methyl-CpG binding domain protein MBD2 …

Analysis Of Adult Neural Retina Extracellular Vesicle Release, Rna Transport And Proteomic Cargo, Jason Mighty, Jing Zhou, Alberto Benito-Martin, Sami Sauma, Samer Hanna, Onyekwere Onwumere, Cui Shi, Martin Muntzel, Moira Sauane, Michael Young, Henrik Molina, Dianne Cox, Stephen Redenti

Publications and Research

PURPOSE. Extracellular vesicles (EVs) contain RNA and protein cargo reflective of the genotype and phenotype of the releasing cell of origin. Adult neural retina EV release, RNA transfer, and proteomic cargo are the focus of this study.

METHODS. Adult wild-type mouse retinae were cultured and released EV diameters and concentrations quantified using Nanosight. Immunogold transmission electron microscopy (TEM) was used to image EV ultrastructure and marker protein localization. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze retinal cell transcripts present in EVs. Super-resolution microscopy was used to image fluorescent (green) RNA and (red) lipid membrane labeled EVs, released …

From Genes To Species: Ecological Speciation With Gene Flow In Neodiprion Pinetum And N. Lecontei, Emily E. Bendall

Theses and Dissertations--Biology

My dissertation focuses on how differences accumulate across the genome during ecological speciation with geneflow. To do this I used two species of Neodiprionpine sawflies, which are plant-feeding hymenopterans with high host specificity. I used experimental crosses to measure both intrinsic and extrinsic postzygotic isolation and to understand the contribution of specific traits to reproductive isolation. Despite substantial genetic divergence and haploid males in which all recessive incompatibilities should be expressed, I found surprisingly little evidence of intrinsic postzygotic isolation. Recombination in hybrid males may reconstitute viable genotypes and counteract the effects of haploidy in males. Nevertheless, hybrids have …

Vertical‑Surface Navigation In The Neotropical Whip Spider Paraphrynus Laevifrons (Arachnida: Amblypygi), Patrick Casto, Daniel D. Wiegmann, Vincent J. Coppola, Daniele Nardi, Eileen A. Hebets, Verner P. Bingman

Eileen Hebets Publications

Studies on whip spider navigation have focused on their ability to locate goal locations in the horizontal plane (e.g., when moving along the ground). However, many species of tropical whip spiders reside and move along surfaces in the vertical plane (e.g., trees). Under controlled laboratory conditions, the current study investigated the ability of the tropical whip spider, Paraphrynus laevifrons, to return to a home shelter on a vertical surface in the presence of numerous, similar, and competing refuge sites, as well as the distribution of navigational errors in the vertical, horizontal, and diagonal plane. We also assessed the relative …

Functional Analysis Of Fam83d And Dupd1 – Two Novel Neruogenic Skeletal Muscle Atrophy-Induced Genes, Lisa Michelle Cooper

UNF Graduate Theses and Dissertations

Fam83d and Dupd1 have been identified as novel genes in skeletal muscle that are upregulated in response to neurogenic atrophy in a mouse model. qPCR analysis reveaed both genes are expressed in skeletal muscle with Fam83d expression being highest during myoblast proliferation, while Dupd1 expression is highest during myotube differentiation. Overexpression of either protein results in inhibition of proper muscle cell differentiation as evidenced by repression of both myosin heavy chain and myogenin expression. Characterization of transcriptional activity revealed both genes are modulated by myogenic regulatory factors and additionally, Dupd1 expression is enhanced by dexamethasone treatment. Assessment of subcellular localization …

Neurodegenerative Modeling: Tau Protein, Degradative Pathways, And Gene Expression Profiling Of Human Ipsc-Derived Neural Precursors And Differentiated 3-D Neural Sphere Versus 2-D Monolayer Cultures, Kyle H. Anthoney

Cal Poly Humboldt theses and projects

Human induced pluripotent stem cells offer a model for human brain development and disease by differentiation into brain organoids; however, current neural culture systems lack the microenvironment, neuronal circuits and connectivity, vascular circulation, and immune system that exist in vivo. After differentiation and development of neuronal and non-neuronal cell types within two formats of cell cultures, we can visualize and recapitulate in vivo protein accumulation, gene expression, and degradative processes such as autophagy. Using RNA extraction, purification methods and reverse transcription I compared traditional monolayer cultures and novel 3-D neural sphere cultures via gene expression analysis. This analysis indicated …

Interspecific Gene Flow Potentiates Adaptive Evolution In A Hybrid Zone Formed Between Pinus Strobiformis And Pinus Flexilis, Mitra Menon

Theses and Dissertations

Species range margins are often characterised by high degrees of habitat fragmentation resulting in low genetic diversity and higher gene flow from populations at the core of the species range. Interspecific gene flow from a closely related species with abutting range margins can increase standing genetic diversity and generate novel allelic combinations thereby alleviating limits to adaptive evolution in range margin populations. Hybridization driven interspecific gene flow has played a key role in the demographic history of several conifer due to their life history characteristics such as weak crossability barriers and long generation times. Nevertheless, demonstrating whether introgression is adaptive …

The Exploration Of Nanotoxicological Copper And Interspecific Saccharomyces Hybrids, Matthew Joseph Winans Phd

Graduate Theses, Dissertations, and Problem Reports (ETD)

Nanotechnology takes advantage of cellular biology’s natural nanoscale operations by interacting with biomolecules differently than soluble or bulk materials, often altering normal cellular processes such as metabolism or growth. To gain a better understanding of how copper nanoparticles hybridized on cellulose fibers called carboxymethyl cellulose (CMC) affected growth of Saccharomyces cerevisiae, the mechanisms of toxicity were explored. Multiple methodologies covering genetics, proteomics, metallomics, and metabolomics were used during this investigation. The work that lead to this dissertation discovered that these cellulosic copper nanoparticles had a unique toxicity compared to copper. Further investigation suggested a possible ionic or molecular mimicry …

Gmr36a08, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 49927

• ID - GMR36A08
• Location - 2R: 18120673, 18124576
• Base pairs - 3903

Gmr40e08, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 41238

• ID - GMR40E08
• Location - 2R: 18162090, 18165058
• Base pairs - 2968

Gmr36a10, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 49373

• ID - GMR36A10
• Location - 2R: 18116788, 18120701
• Base pairs - 3913

Gmr39h01, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 50066

• ID - GMR39H01
• Location - 2R: 18153797, 18156108
• Base pairs - 2311

Gmr42e10, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR42E10
• Location - 2R: 18133506, 18137474
• Base pairs - 3968

Gmr41c04, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR41C04
• Location -2R: 18143594, 18147064
• Base pairs - 3470

Gmr42h01, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 48150

• ID - GMR42H01
• Location - 2R: 18158419, 18162751
• Base pairs - 4332

Gmr35a04, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR35A04
• Location - 2R: 18125755, 18128365
• Base pairs - 2610

Gmr41h07, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 46241

• ID - GMR41H07
• Location - 2R: 18150920, 18154671
• Base pairs - 3751

Gmr41f05, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 50133

• ID - GMR41F05
• Location - 2R: 18139042, 18142672
• Base pairs - 3630

Gmr40c05, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 45682

• ID - GMR40C05
• Location - 2R: 18141630, 18144381
• Base pairs - 2751