Biology Commons^™

Studies On Development In Euphilomedes Ostracods: Embryology, Nervous System Development, And The Genetics Of Sexually Dimorphic Eye Development, Kristina Koyama

University of the Pacific Theses and Dissertations

Model organism studies have been fundamental in understanding evolutionary and developmental biology. However, non-model organisms present opportunities to study unique characteristics and as comparisons to model organisms, leading us toward broader and more relevant perspectives on diversity. The Euphilomedes genus of ostracods is an example of a non-model group with potential for evolutionary and developmental studies.

Ostracoda is an ancient, basally branching lineage of Crustaceans with a complete and prodigious fossil record. Despite the group’s promise for evolutionary studies, much remains unknown about the basic biology of this clade. There are a limited number of embryogenesis studies in Ostracoda; here, …

Identification Of Multiple Functional Receptors For Tyramine On An Insect Secretory Epithelium, Haiying Zhang, Edward M. Blumenthal

Biological Sciences Faculty Research and Publications

The biogenic amine tyramine (TA) regulates many aspects of invertebrate physiology and development. Although three TA receptor subtypes have been identified (TAR1-3), specific receptors have not been linked to physiological responses in native tissue. In the Malpighian (renal) tubule of Drosophila melanogaster, TA activates a transepithelial chloride conductance, resulting in diuresis and depolarization of the transepithelial potential. In the current work, mutation or RNAi-mediated knockdown in the stellate cells of the tubule of TAR2 (tyrR, CG7431) resulted in a dramatic reduction, but not elimination, of the TA-mediated depolarization. Mutation or knockdown of TAR3 (tyrRII, …

Winner's Curse Correction And Variable Thresholding Improve Performance Of Polygenic Risk Modeling Based On Genome-Wide Association Study Summary-Level Data, Jianxin Shi, Ju-Hyun Park, Jubao Duan, Sonja T. Berndt, Winton Moy, Kai Yu, Lei Song, William Wheeler, Xing Hua, Debra Silverman, Montserrat Garcia-Closas, Chao Agnes Hsiung, Jonine D. Figueroa, Victoria K. Cortessis, Nuria Malats, Margaret R. Karagas

Dartmouth Scholarship

Recent heritability analyses have indicated that genome-wide association studies (GWAS) have the potential to improve genetic risk prediction for complex diseases based on polygenic risk score (PRS), a simple modelling technique that can be implemented using summary-level data from the discovery samples. We herein propose modifications to improve the performance of PRS. We introduce threshold-dependent winner’s-curse adjustments for marginal association coefficients that are used to weight the single-nucleotide polymorphisms (SNPs) in PRS. Further, as a way to incorporate external functional/annotation knowledge that could identify subsets of SNPs highly enriched for associations, we propose variable thresholds for SNPs selection. We applied …

Genetic Basis Of Melanin Pigmentation And Sexual Dichromatism In Domestic Pigeons, Shreyas Krishnan

Biology Dissertations - Archive

Deciphering the genetic basis of pigmentation in domestic pigeons (Columba livia) affords a unique opportunity to connect microevolution to macroevolution. Domestic pigeons have far greater phenotypic diversity than other domesticates that often recapitulate traits that occur in nature. By using classical genetic approaches and by leveraging the innumerable meiotic events since the advent of pigeon domestication, and population structure, I have mapped traits to genes and begun to deconstruct more complex traits. In this process of investigation one expects to discover mechanisms that may be generalizable to some extent to other birds; however, their generality may be limited in their …

Genetic And Transcriptional Analysis Of Human Host Response To Healthy Gut Microbiota, Michael B. Burns, Allison L. Richards, Adnan Alazizi, Luis B. Barreiro, Roger Pique-Regi, Ran Blekhman, Francesca Luca

Biology: Faculty Publications and Other Works

Many studies have demonstrated the importance of the gut microbiota in healthy and disease states. However, establishing the causality of host-microbiota interactions in humans is still challenging. Here, we describe a novel experimental system to define the transcriptional response induced by the microbiota for human cells and to shed light on the molecular mechanisms underlying host-gut microbiota interactions. In primary human colonic epithelial cells, we identified over 6,000 genes whose expression changed at various time points following coculturing with the gut microbiota of a healthy individual. Among the differentially expressed genes we found a 1.8-fold enrichment of genes associated with …

Quantitative Perturbation-Based Analysis Of Gene Expression Predicts Enhancer Activity In Early Drosophila Embryo, Rupinder Sayal, Jacqueline M. Dresch, Irina Pushel, Benjamin R. Taylor, David N. Arnosti

Biology

Enhancers constitute one of the major components of regulatory machinery of metazoans. Although several genome-wide studies have focused on finding and locating enhancers in the genomes, the fundamental principles governing their internal architecture and cis-regulatory grammar remain elusive. Here, we describe an extensive, quantitative perturbation analysis targeting the dorsal-ventral patterning gene regulatory network (GRN) controlled by Drosophila NF-kB homolog Dorsal. To understand transcription factor interactions on enhancers, we employed an ensemble of mathematical models, testing effects of cooperativity, repression, and factor potency. Models trained on the dataset correctly predict activity of evolutionarily divergent regulatory regions, providing insights into spatial relationships …

Social And Scientific Implications Of Genetic Testing In The Digital Age, Yaruska A. Ordinola

Senior Honors Projects

From Mendel’s law of inheritance in the 19th century through Watson and Crick’s revolutionary observations of the double helix in the 20th century, genetics has been a fascinating and continuing topic of discussion in the field of science (Collins & McKusick, 2001). Major studies like the Human Genome Project (HGP), initiated in 1990 and completed in 2003, provided a starting point from which scientists could more thoroughly investigate the human condition on a genetic level. Arising from this study, personal genomics is considered a blooming field in genetics- in which rapidly developing technological advances are able to provide easier and …

The Role Of Rapgap1 In Sxl Activation In Drosophila Melanogaster, Katherine M. Barnes

Lewis Honors College Capstone Collection

The master switch of the sexual differentiation and dosage compensation pathway in Drosophila is the sex lethal gene, Sxl. The early promoter, SxlPe, is activated in females, resulting in female-specific splicing of later transcripts (notably the late Sxl transcript SxlPm), while inactive in males. Chromatin immunoprecipitation (ChIP) assays have previously shown association of two conventionally heterochromatin-localized proteins, HOAP and HP1, at SxlPe, and in situ hybridization as well as RT-PCR assays have confirmed a repressive role for HOAP and both repressive and activating roles for HP1. The mechanism for the activity shift of HP1 is currently unknown. Deletions in the …

The Role Of Arp2/3 In Ring Canal Development In Drosophila Melanogaster, Marina Tipold

Undergraduate Honors Thesis Collection

Infertility and impaired fecundity affect 8.2 million women in the United States. Intercellular bridges are essential to the proper formation of germ cells in many organisms; therefore, learning more about how they are formed and regulated during the formation of sperm and eggs could provide insight into how defects in their structure can impact fertility. Intercellular bridges are actin-rich structures that connect developing germ cells to each other and allow the transfer of materials. I used the development of the fruit fly egg as a model system to study formation and regulation of intercellular bridges. Specifically, I investigated the role …

Lack Of Host Specialization On Winter Annual Grasses In The Fungal Seed Bank Pathogen Pyrenophora Semeniperda, Julie Beckstead, Susan E. Meyer, Tony S. Ishizuka, Kelsey M. Mcevoy, Craig E. Coleman

Biology Faculty Scholarship

Generalist plant pathogens may have wide host ranges, but many exhibit varying degrees of host specialization, with multiple pathogen races that have narrower host ranges. These races are often genetically distinct, with each race causing highest disease incidence on its host of origin. We examined host specialization in the seed pathogen Pyrenophora semeniperda by reciprocally inoculating pathogen strains from Bromus tectorum and from four other winter annual grass weeds (Bromus diandrus, Bromus rubens, Bromus arvensis and Taeniatherum caput-medusae) onto dormant seeds of B. tectorum and each alternate host. We found that host species varied in …

Loblolly Pine Genetics Structure Its Mycorrhizal Community, Bridget Joan Piculell

Electronic Theses and Dissertations

Plant populations are constantly exposed to a multitude of biotic and abiotic environmental selection pressures. The ability of a population to persist in or adapt to its environment is heavily influenced by the genetic underpinnings of the traits involved. Thus, in order to understand patterns in current plant populations, and to predict future populations dynamics, an understanding of the genetic basis of adaptive traits is necessary. For example, genetic correlations between traits (driven by pleiotropy or linkage disequilibrium) could influence how species evolve under multiple, conflicting selection pressures, potentially either constraining or enhancing the adaptation of species to each other. …

Genetic Factors That Contribute To The Pathogenesis Of Amyotrophic Lateral Sclerosis, Janet Elizabeth Cady

Arts & Sciences Graduate Student Theses and Dissertations

Amyotrophic lateral sclerosis (ALS) is fatal neurodegenerative disease for which there is no cure. The only treatment available extends survival by only a matter of months. There are over 20 genes that are known to cause ALS. Over half of the ALS cases with a family history of disease (FALS) can be explained by mutations in known ALS genes with hexanucleotide repeat expansions in C9ORF72 accounting for 40% of families. However roughly 90% of cases have no family history of disease (sporadic ALS or SALS) and a much smaller proportion (10%) of these cases can be explained by mutations in …

Polyq-Dependent Rna–Protein Assemblies Control Symmetry Breaking, Changhwan Lee, Patricia Occhipinti, Amy S. Gladfelter

Dartmouth Scholarship

Dendritic growth in fungi and neurons requires that multiple axes of polarity are established and maintained within the same cytoplasm. We have discovered that transcripts encoding key polarity factors including a formin, Bni1, and a polarisome scaffold, Spa2, are nonrandomly clustered in the cytosol to initiate and maintain sites of polarized growth in the fungus Ashbya gossypii. This asymmetric distribution requires the mRNAs to interact with a polyQ-containing protein, Whi3, and a Pumilio protein with a low-complexity sequence, Puf2. Cells lacking Whi3 or Puf2 had severe defects in establishing new sites of polarity and failed to localize Bni1 protein. Interaction …

The Effects Of Hpa Axis Genetic Variation And Early Life Stress On Cortisol Levels In Preschool Age Children And On Amygdala And Hippocampus Volumes, Reactivity, And Connectivity At School Age, David Pagliaccio

Arts & Sciences Graduate Student Theses and Dissertations

Internalizing psychopathology has been linked to increased cortisol reactivity and alterations in limbic brain structure and function, yet the mechanisms underlying these alterations are unclear. One key hypothesis is that stress plays a major causal role in these mechanisms. Animal studies find that chronic stress or glucocorticoid administration lead to alterations in hippocampal and amygdala structure and function. Relatedly, life stress is a major risk factors for depression while candidate gene studies have related variation in hypothalamic-pituitary-adrenal (HPA) axis genes to increased prevalence and severity of depression. The present work tested the hypothesis that genetic profile scores combining variance across …

An Inquiry-Infused Introductory Biology Laboratory That Integrates Mendel's Pea Phenotypes With Molecular Mechanisms, Philip Kudish, E. Schlag, Nicholas J. Kaplinsky

Biology Faculty Works

We developed a multi-week laboratory in which college-level introductory biology students investigate Mendel's stem length phenotype in peas. Students collect, analyze and interpret convergent evidence from molecular and physiological techniques. In weeks 1 and 2, students treat control and experimental plants with Gibberellic Acid (GA) to determine whether uncharacterized short mutant lines are GA responsive. These data allow students to place the mutation in the GA signal transduction pathway. During weeks 2 and 3, plants are genotyped for Mendel's "le" mutation using a derived cleaved polymorphic sequences (dCAPS) PCR assay. This laboratory allows students to make a direct connection between …

Origins Of An Unmarked Georgia Cemetery Using Ancient Dna Analysis, Andrew T. Ozga, Raul Y. Tito, Brian M. Kemp, Hugh Matternes, Alexandra J. Obregon-Tito, Leslie Neal, Cecil M. Lewis Jr.

Biology Faculty Articles

Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and, in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we used ancient DNA extraction methods in well-preserved skeletal fragments from 20 individuals buried in Avondale Burial Place to investigate the origins of the …

An Approach For Determining And Measuring Network Hierarchy Applied To Comparing The Phosphorylome And The Regulome, Chao Cheng, Erik Andrews, Koon-Kiu Yan, Matthew Ung, Daifeng Wang, Mark Gerstein

Dartmouth Scholarship

Many biological networks naturally form a hierarchy with a preponderance of downward information flow. In this study, we define a score to quantify the degree of hierarchy in a network and develop a simulated-annealing algorithm to maximize the hierarchical score globally over a network. We apply our algorithm to determine the hierarchical structure of the phosphorylome in detail and investigate the correlation between its hierarchy and kinase properties. We also compare it to the regulatory network, finding that the phosphorylome is more hierarchical than the regulome.

A Bioinformatics Approach To Revealing The Genetic Basis For Host Range Specificity, Hayley A. Norian

James Madison Undergraduate Research Journal (JMURJ)

Bacteriophages, or phages, are viruses that infect bacteria. Mycobacteriophages are bacteriophages that specifically infect the genus Mycobacterium. This genus of bacteria includes human pathogens such as Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium ulcerans, which cause tuberculosis, leprosy and Buruli ulcer, respectively. The full genome sequences of 654 mycobacteriophages are currently available. Collectively, these 654 phages encode 69,581 genes. Only 20.25% of these genes have at least one known homologue in NCBI, the National Center for Biotechnology Information, leaving roughly 80% of all known mycobacteriophage genes without even a predicted function. Bacteriophages are highly host-specific and typically only infect a small …

Assessment Of A Metaviromic Dataset Generated From Nearshore Lake Michigan, Siobhan C. Watkins, Neil Kuehnle, C Anthony Ruggeri, Kema Malki, Katherine Bruder, Jinan Elayyan, Kristina Damisch, Naushin Vahora, Paul O'Malley, Brianne Ruggles-Sage, Zachary Romer, Catherine Putonti

Bioinformatics Faculty Publications

Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse …

Genetic Structure And Demographic Analysis Of Key Deer (Odocoileus Virginianus Clavium), Vicki Villanova

Electronic Theses and Dissertations

Recent improvements in genetic analyses have paved the way in using molecular data to answer questions regarding evolutionary history, genetic structure, and demography. Key deer are a federally endangered subspecies assumed to be genetically unique (based on one allozyme study), homogeneous, and have a female-biased population of approximately 900 deer. I used 985bp of the mitochondrial cytochrome b gene and 12 microsatellite loci to test two hypotheses: 1) if the Moser Channel is a barrier to gene flow, I should expect that Key deer are differentiated and have reduced diversity compared to mainland deer and (2) if isolation on islands …

High-Throughput Screening Of Age-Related Changes In Caenorhabditis Elegans, Neil Copes

USF Tampa Graduate Theses and Dissertations

This project was developed to identify novel methods for high-throughput culturing and screening of C. elegans to investigate age-related metabolic changes and to survey the proteomic and metabolomic factors associated with age-related changes. To accomplish these goals we developed a novel way to grow C. elegans in liquid culture in 96-well microplates for several weeks without suffering significant fluid loss due to evaporation and without needing to shake or unseal the plates for aeration. We also developed methods for assaying the total volume of live C. elegans in microplate cultures using a fluorescence microplate reader and for performing RNAi experiments …

Natural Selection On Thermal Performance In A Novel Thermal Environment, Michael L. Logan, Robert M. Cox, Ryan Calsbeek

Dartmouth Scholarship

Tropical ectotherms are thought to be especially vulnerable to climate change because they are adapted to relatively stable temperature regimes, such that even small increases in environmental temperature may lead to large decreases in physiological performance. One way in which tropical organisms may mitigate the detrimental effects of warming is through evolutionary change in thermal physiology. The speed and magnitude of this response depend, in part, on the strength of climate-driven selection. However, many ectotherms use behavioral adjustments to maintain preferred body temperatures in the face of environmental variation. These behaviors may shelter individuals from natural selection, preventing evolutionary adaptation …

Phenotypic Robustness And The Assortativity Signature Of Human Transcription Factor Networks, Dov A. Pechenick, Joshua L. Payne, Jason H. Moore

Dartmouth Scholarship

Many developmental, physiological, and behavioral processes depend on the precise expression of genes in space and time. Such spatiotemporal gene expression phenotypes arise from the binding of sequence-specific transcription factors (TFs) to DNA, and from the regulation of nearby genes that such binding causes. These nearby genes may themselves encode TFs, giving rise to a transcription factor network (TFN), wherein nodes represent TFs and directed edges denote regulatory interactions between TFs. Computational studies have linked several topological properties of TFNs - such as their degree distribution - with the robustness of a TFN's gene expression phenotype to genetic and environmental …

Metagenomic Identification Of A Novel Salt Tolerance Gene From The Human Gut Microbiome Which Encodes A Membrane Protein With Homology To A Brp/Blh-Family Beta-Carotene 15,15'-Monooxygenase, Eamonn P. Culligan, Roy D. Sleator, Julian R. Marchesi, Colin Hill

Department of Biological Sciences Publications

The human gut microbiome consists of at least 3 million non-redundant genes, 150 times that of the core human genome. Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. Cloning and heterologous expression of brpA in Escherichia coli confers a significant salt tolerance phenotype. Furthermore, when cultured in the presence of exogenous β-carotene, cell pellets adopt a red/orange pigmentation indicating the incorporation of carotenoids in the cell membrane.

Structural And Functional Studies Of Urea Amidolyase, Yi Lin

Dissertations (1934 -)

Urea amidolyase (UAL) is a key virulence factor that regulates the yeast to hyphae switch in the opportunistic pathogen, Candida albicans. UAL is a multi-domain enzyme with two enzyme activities: urea carboxylase (UC) and allophanate hydrolase (AH). UC is a biotin-dependent carboxylase that adds a carboxyl group to urea to make allophanate by the coordinated action of three domains. Allophanate is subsequently hydrolyzed into NH3 and CO2 in the AH domain. Studies on the structure and function of UAL may lead to treatments for systemic candidiasis and can serve to clarify the molecular basis for multi-functional swinging arm enzymes. In …

Divergent Transcriptional Responses To Low Temperature Among Populations Of Alpine And Lowland Species Of New Zealand Stick Insects (Micrarchus)., Luke T Dunning, Alice B Dennis, Brent J Sinclair, Richard D Newcomb, Thomas R Buckley

Biology Publications

In widespread and genetically structured populations, temperature variation may lead to among-population differentiation of thermal biology. The New Zealand stick insect genus Micrarchus contains four species that inhabit different thermal environments, two of which are geographically widespread. RNA-Seq and quantitative PCR were used to investigate the transcriptional responses to cold shock among lowland and alpine species to identify cold-responsive transcripts that differ between the species and to determine whether there is intraspecific geographical variation in gene expression. We also used mitochondrial DNA, nuclear 28S ribosomal DNA and transcriptome-wide SNPs to determine phylogeographic structure and the potential for differences in genetic …

Earthworm Remyelination Gene Expression Analysis, Shelby Shevik

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

Synthesizing Research And Education: Ecology And Genetics Of Independent Fern Gametophytes And Teaching Science Inquiry And Content Through Simulations, Aaron M. Duffy

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The mission statements of Utah State University and the Department of Biology, as well as the requirements of funding agencies like the National Science Foundation encourage an integration of teaching and research. I have attempted to achieve that in my dissertation work by using tools I originally created to support and inform my biological research projects to teach science content and inquiry to middle school and undergraduate students.

Chapter 2 of this dissertation reports the results of surveys for Hymenophyllum wrightii, a fern with independent gametophyte populations in the Pacific Northwest, which improved our understanding of the range, distribution, …

Identification And Expression Analysis Of Sugar Transporters In Microbotryum Violaceum., Jared Morris Andrews

College of Arts & Sciences Senior Theses

No abstract provided.

Population Genetics And Microbial Communities Of The Gopher Tortoise (Gopherus Polyphemus), Daniel Lyle Gaillard

Dissertations

The gopher tortoise, Gopherus polyphemus, is an endangered species living in the southeastern United States. The recent and drastic decline in tortoise numbers has resulted in a multi-faceted approach to conserve this species. I used a population genetic approach to determine the population structure, genetic diversity and barriers to gene flow at a broad, regional and local scale. Tortoises are divided into five distinct genetic populations at the broad scale, the central populations have the highest levels of genetic diversity and the Tombigbee, Mobile, Apalachicola, Suwannee and St. John’s Rivers appear to be barriers to gene flow. At the regional …