Genetics and Genomics Commons^™

Which Vole Is Which: Dna-Based Species Identification For Wisconsin’S Three Microtus Species, Madeline Noel Opie

Theses and Dissertations

Accurate species identification is necessary to implement conservation strategies in the wild. When traditional morphology-based species identification is challenging due to phenotypic plasticity, overlapping characteristics, or the species are otherwise cryptic, DNA-based species identification may be more suitable. Of the three species of Microtus in Wisconsin, two are listed as threatened at the state level. Both M. ochrogaster and M. pinetorum have stable population levels at the national level but are along the northern edge of their ranges in Wisconsin. Small and vulnerable populations of M. ochrogaster and M. pinetorum are limited to isolated patches in the southwestern portion of …

Exploring Soil Microbial Dynamics In Southern Appalachian Forests: A Systems Biology Approach To Prescribed Fire Impacts, Saad Abd Ar Rafie

Doctoral Dissertations

Prescribed fires in Southern Appalachian forests are vital in ecosystem management and wildfire risk mitigation. However, understanding the intricate dynamics between these fires, soil microbial communities, and overall ecosystem health remains challenging. This dissertation addresses this knowledge gap by exploring selected aspects of this complex relationship across three interconnected chapters.

The first chapter investigates the immediate effects of prescribed fires on soil microbial communities. It reveals subtle shifts in porewater chemistry and significant increases in microbial species richness. These findings offer valuable insights into the interplay between soil properties and microbial responses during the early stages following a prescribed fire. …

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Du Undergraduate Showcase: Research, Scholarship, And Creative Works, Caitlyn Aldersea, Justin Bravo, Sam Allen, Anna Block, Connor Block, Emma Buechler, Maria De Los Angeles Bustillos, Arianna Carlson, William Christensen, Olivia Kachulis, Noah Craver, Kate Dillon, Muskan Fatima, Angel Fernandes, Emma Finch, Colleen Cassidy, Amy Fishman, Andrea Francis, Stacia Fritz, Simran Gill, Emma Gries, Rylie Hansen, Shannon Powers, Jacqueline Martinez, Zachary Harker, Ashley Hasty, Mykaela Tanino-Springsteen, Kathleen Hopps, Adelaide Kerenick, Colin Kleckner, Ci Koehring, Elijah Kruger, Braden Krumholz, Maddie Leake, Lyneé Alves, Seraphina Loukas, Yatzari Lozano Vazquez, Haley Maki, Emily Martinez, Sierra Mckinney, Mykaela Tanino-Springsteen, Audrey Mitchell, Kipling Newman, Audrey Ng, Megan Lucyshyn, Andrew Nguyen, Stevie Ostman, Casandra Pearson, Alexandra Penney, Julia Gielczynski, Tyler Ball, Anna Rini, Christina Rorres, Simon Ruland, Helayna Schafer, Emma Sellers, Sarah Schuller, Claire Shaver, Kevin Summers, Isabella Shaw, Madison Sinar, Claudia Pena, Apshara Siwakoti, Carter Sorensen, Madi Sousa, Anna Sparling, Alexandra Revier, Brandon Thierry, Dylan Tyree, Maggie Williams, Lauren Wols

DU Undergraduate Research Journal Archive

DU Undergraduate Showcase: Research, Scholarship, and Creative Works

Development Of Three Novel Edna Assays For Detecting Coastal Sharks, Kristina Dawn Flanigan

Electronic Theses and Dissertations

Environmental DNA (eDNA) analysis is an emerging, non-invasive community monitoring tool. This study aimed to determine if eDNA methods can be reliably used in a large brackish, partially mixed estuary by developing and testing three novel eDNA primers, for Sandbar Sharks (Carcharhinus plumbeus), Blacknose Sharks (Carcharhinus acronotus), and Bonnetheads (Sphyrna tiburo). These primers were designed to target 109, 156, and 120 base pair (bp) fragments, respectively, of the highly conserved NAD2 gene in the mitochondrial genome of each species. Primer function was validated through testing against 102 known genomic source samples and 25 filtered water samples from aquaria in which …

Role Of Age And Sex In The Effects Of Repeated Methamphetamine Exposure On Hedonic Tone In Sprague Dawley Rats, Cameron Lewis, Conor Strumberger, Joshua M. Gulley

PRECS student projects

Anhedonia is defined as a reduced or complete loss of pleasure from a previously pleasurable stimulus, and it is comprised of two dimensions:

• Hedonic anhedonia consists of a distinct loss of pleasure in consumption of a normally pleasurable stimulus.
• Motivational anhedonia involves the goal directed behavior to obtain a reward.

Withdrawal induced anhedonia following use of methamphetamine (METH) is thought to contribute to relapse behaviors^1,2 . The anhedonic effects of drug withdrawal largely depend on dose, frequency, and the duration of drug exposure^4,5,6.

The role of sex and age of exposure in this context has yet to …

How Fungicide Alters The Hidden Mycobiome Of A Restored Prairie System, Mya Reyes, Noah Brown, Anthony Yannarell

PRECS student projects

• Fungal Endophytes are microscopic fungi that live inside plant tissues and form a symbiotic relationship that influences the fitness of both parties.

• Fungicides are a widely used method of crop disease control in agriculture, but fungicides can be carried into other environments by water and wind.

• This experiment looks at how long-term fungicide exposure affects diversity of fungal endophytes that are grown in vitro as well as screens them for phosphate solubilization ability.

• Phosphate is a vital macronutrient that is essential for making nucleic acids (DNA, RNA) as well as playing a vital role in energy transfer throughout the plant's …

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Effect Of Varied Macronutrient Ratios On Honey Bee Tolerance To Iapv Infection, Caitlin Lennon-Puthoff, Alex Payne, Adam Dolezal

PRECS student projects

Honey bees are killed by Israeli acute paralysis virus (IAPV). Because this virus has no cure, it is important to lessen its impact on bees through proper nutrition. This project explores the effects of differing protein to lipid (P:L) ratios in pollen on honey bee susceptibility to this virus.

Over three trials, bees in cages were incubated for 3 days to resemble hive conditions. Two doses of IAPV (10^-3 & 10^-2) and a negative control were used, along with five P:L ratios (1.5, 2.5, 11.5, 16.5, & 21.5:1) and a sucrose-only diet. These treatment groups were combined …

Evaluating The Enzymatic Activity Of Transformed X. Cucurbitae, Emily Beger, Iris Lee, Sarah Hind

PRECS student projects

Introduction

• The United States’ pumpkin industry exceeds one billion dollars [1], with Illinois contributing to over 90% of processing pumpkin production.
• Pumpkin growers face a rising concern due to the increasing occurrence of Xanthomonas cucurbitae , the pathogen that causes bacterial spot disease in cucurbits, including pumpkins.
• X. cucurbitae infection leads to the appearance of small, sunken, beige spots on cucurbit fruits and leaves.
• Over time, the bacterium can compromise fruit integrity by breaking down the epidermis and cuticle. • Bacterial spot disease also creates opportunities for other bacteria and fungi to infiltrate the affected fruits, leading to fruit rot …

The Tomato Strikes Back: Plant Response To Environmental Stress, Maya K. Davis, Erinn Dady, Esther N. Ngumbi

PRECS student projects

Introduction

• Tomato is an important vegetable. Its production is threatened due to altered weather patterns which increase environmental stressors such as flooding^{1, 2} and herbivory³ to crops.
• Plants respond in many ways. Stressed plants strike back to environmental stress by altering their chemistry⁴:

1. Volatile Organic Compounds (VOCs) emissions
2. Defensive secondary metabolites²

• Stress induced physiological changes in plants impact growth and development of insects.
• This study is broken into two experiments:

1. The plant response to flooding stress
2. The insect performance on flooded plants

Confirming Presence And Mobilization Of Partner Quality Genes In Sinorhizobium Meliloti, Ethan Perez, Ivan Sosa Marquez, Katy Heath

PRECS student projects

• Mutualism is an interaction in which two organisms benefit from each other.
• The symbiotic relationship between the bacterium Sinorhizobium meliloti and the plant Medicago truncatula is dictated by the bacterial plasmids.
• The Heath lab has a collection of 191 Sinorhizobium meliloti strains with different symbiotic plasmids that vary across populations (Riley et al., 2022).
• Each strain can be a better or worse partner for its plant host in symbiosis with the variation in fitness being called partner quality (Fig. 1)
• These traits can be traced back to the genetic elements that underlie this effect (Batstone et al.,
• These genetic elements …

Revisiting The Reproductive Behaviors Of Blackspotted Stickleback, Cassidy Constant, Megan Tucker, Colby Behrens, Alison M. Bell

PRECS student projects

Why Blackspotted Stickleback?

How Behaviors Evolve Comparing closely related species can give insights into how behavior evolves.

Well studied: Three-spined Stickleback (Gasterosteus aculeatus)

• Model organism for natural variation in behavioral evolution 1.
• Divergence in parental care in two ecotypes1,2.
• White and common ecotypes recently diverged 2.

Lesser studied: Blackspotted Stickleback (Gasterosteus wheatlandi)

• Three-spined’s closest living relative.
• Possible behavioral intermediate of commons & whites.
• Blackspotted egg dispersal is similar to white three-spined 3.

Fusarium Isolates Adapt To Specific Wheat Tissues, Liam Kent, Mara Krone, Santiago Mideros

PRECS student projects

Introduction

Tissue specificity is a pathogen’s preference for infecting one section of tissue (i.e., root, stem, or head) over another. 1 Having a better understanding of a pathogen’s ability to cause disease on specific tissues could contribute to new mechanisms of disease control. This will allow growers to make the best decision on effective pathogen management. In 2022, Fusarium isolates were collected from wheat heads and roots across Illinois. These isolates were used in a pathogen aggressiveness assay on wheat roots, in an in vitro growth rate experiment , and in the development of a spore quantification protocol. The phenotypic …

Identifying Genes Influencing The Efficiency Of Photosynthesis, Jason M. Rivera, Steven Burgess

PRECS student projects

• Photosynthesis adapts to environmental conditions over time.¹

• Varying environmental conditions lead to stress accumulation on the plant.²

• A genetic library has been assembled for forward genetic screening of Arabidopsis thaliana.³

• Arabidopsis Thaliana is a model plant used as a model organism in growth experiments.

• This research project aims to identify and analyze candidate genes that impact the efficiency of photosynthesis.

• These genes can be transplanted into commercial crops to increase efficiency of photosynthesis and crop yields.

Potential Implications Of Elevated Co2 For Enhanced Rock Weathering In Croplands, Hannah Maher, Megan Allen, Lisa Ainsworth

PRECS student projects

• Atmospheric carbon dioxide (CO₂) levels are increasing by 2.37 ppm year, and levels have increased from about 370 ppm in 2000 to about 420 ppm in 2023¹
• Increased CO₂ levels result in climate change, including increased temperatures and drought which impacts soybean crops
• Enhanced Rock Weathering (ERW) is the process of spreading basalt on fields to accelerate the natural reaction between rocks, CO2, and water²
• Enhanced Rock Weathering is a possible way to combat increasing CO₂ levels because of its carbon sequestration properties²

Acth Challenge: Stress Response Across Tadpole Development, Lauren W. Mobo, Lucas Jimenez, Lisa L. Surber-Cunningham, Eva K. Fischer

PRECS student projects

Research Questions

1. Do tadpoles excrete more cortisol or corticosterone?
2. Do tadpoles excrete more corticosterone after ACTH injections?
3. Does the ACTH stress response change across development?

Margalefidinium Polykrikoides Cyst Resuspension In The Lafayette River, A Sub-Tributary Of The Chesapeake Bay, Gabrielle Greaney, Eduardo Perez Vega, Katherine Crider, Dreux Chappell, Kimberly Powell, Richard Hale, Peter Bernhardt, Margaret Mulholland

Undergraduate Research Symposium

Harmful Algal Blooms are a collection of algae in a body of water that can cause serious environmental issues and health problems in both people and aquatic organisms. Dinoflagellates are microscopic, unicellular, and eukaryotic organisms that are well known for forming harmful algal blooms because of eutrophication. Coastal Virginia suffers from HABs in the Chesapeake Bay and its tributaries. A common species of dinoflagellate, known as Margalefidinium polykrikoides exists in the Chesapeake Bay. The purpose of this study is to determine if sediment resuspension produced by wind generated surface gravity waves cause cysts (dinoflagellate resting stages) to be suspended into …

Rhetorics Of Species Revivalism And Biotechnology – A Roundtable Dialogue, Eva Kasprzycka, Charlotte Wrigley, Adam Searle, Richard Twine

Animal Studies Journal

This informal dialogue contextualises and explores contemporary practices of nonhuman animal gene-modification in de-extinction projects. Looking at recent developments in biotechnology’s role in de-extinction sciences and industries, these interdisciplinary scholars scrutinise the neoliberal impetus driving ‘species revivalism’ in the wake of the Capitalocene. Critical examinations of species integrity, cryo-preservation, techno-optimism, rewilding initiatives and projects aimed at restoring extinct animals such as the woolly mammoth and bucardo are used to map some of the necessary restructuring of conservation policies and enterprises that could secure viably sustainable – and just – futures for nonhuman animals at risk of extinction. The authors question …

Variability And Genetic Structure Of The Montezuma Quail Cyrtonyx Montezumae In The Northern Limit Of Its Distribution, Eduardo Sánchez Murrieta, Alberto Macías-Duarte, Reyna A. Castillo-Gámez, Angel B. Montoya, Alejandro Varela-Romero, Nohelia G. Pacheco Hoyos

National Quail Symposium Proceedings

A species’ geographic distribution of genetic variability is influenced by different factors including size of geographic distribution, dispersal capability, mating system, and migration. For instance, a low migration rate among populations may cause a decrease in genetic variation. Such is the case of the Montezuma quail (Cyrtonyx montezumae), a popular game bird with a limited flight capacity that prevents long-distance dispersal. In the northern limit of the species’ distribution in Arizona, New Mexico, and Texas in the United States, the species inhabits oak forests that are separated from one another by deserts. Consequently, Montezuma quail populations are distributed …

Chromosome Number Evolution, Phylogeography, And The Effects Of Climate Change On Species Distributions In Polyploid Plant Systems, Courtney H. Babin

University of New Orleans Theses and Dissertations

Polyploidy, a term used to describe organisms with cells having more than two paired sets of chromosomes, is a significant driver of diversification among land plants. Over a century of research has advanced our understanding of polyploidization in some taxa, but polyploid organisms remain understudied. In this dissertation, I investigate chromosome number evolution, phylogeographic structure, genetic differentiation, and the effects of climate change on ploidy level distribution using polyploid plant systems. In the first chapter, I inferred a molecular phylogeny of Allium, an economically important genus that includes cultivated crops and ornamentals, to investigate evolutionary transitions in chromosome number …

Genomic Analysis And Characterization Of Surface Properties Of Naphthalene Degrading Acinetobacter Isolates, Gunn Emilie Berge

<strong> Theses and Dissertations </strong>

No abstract provided.

The Importance Of Understanding And Developing Identification Techniques In Wildlife Crime, Savannah Nguyen

D.U.Quark

Wildlife crime continues to grow annually and globally, impacting several species and ecosystems. New advancements of technologies and techniques can track criminals and aid the affected victims. Highlighting the complexity of conservation and the development of identification techniques helps tackle this widespread dilemma. New developing techniques in wildlife forensics can differentiate an animal between wild and poached to pave the way for further advancement in understanding wildlife crimes. Hence, though the wildlife forensics field is still new, emphasizing the need for intricate identification techniques can help save threatened species.

Genetic Structure Of Urban White-Tailed Deer In West Michigan, Jacob David Brand

Masters Theses

In urban areas, green spaces are used by humans and wildlife. The proximity between them can lead to both positive and negative interactions, which can make managing urban wildlife difficult. Managers are challenged due to conflicts between wildlife population sizes that can be naturally supported versus those that are socially tolerable. White-tailed deer (Odocoileus virginianus) thrive in urban environments because their habitat requirements are met within green spaces and backyard vegetation. Matrilineal groups of urban white-tailed deer live within the same areas, at times forming high densities that can lead to the spread of diseases or environmental pests, including hemlock …

Root Phenotyping Of Peptide-Treated Glycine Max, Salem Jackson

Biological Sciences Undergraduate Honors Theses

Plant elicitor peptides (Peps) – endogenous chains of amino acids involved in natural plant defense – have been shown to decrease damage from herbivores and pathogens by inducing an immune response, increasing the emission of volatile organic compounds (VOCS), transcripts, and metabolites. Exogenous treatment of soybean seeds with plant elicitor peptide GmPep3 has been shown to induce these broad-spectrum defenses and offers a new method for increasing crop yield. However, the effects of GmPep3 on indicators of soybean health – root characteristics, growth stages, etc. – have not been fully realized.

Using the root-phenotyping platform RhizoVision Explorer, several root traits …

The Effects Of Temperature Changes On Bioluminescent Dinoflagellates (How Climate Change May Affect Our Ocean's Raves), Kayleigh X. Ambrose, Molly Fleming, Carla Caceres

PRECS student projects

Many species of Dinoflagellates are capable of producing bioluminescence. Most species will have an optimal temperature range for bioluminescence production. With sea surface temperatures expected to rise, we have designed an experiment to test the relationship between temperature and bioluminescence in Pyrocystis fusiformis.

Bacterial Metabolism Of Glucosinolates From Brassica: Association With Isothiocyanate Production, Stephanie Thomas, Jiaxuan Li, Michael J. Miller

PRECS student projects

Study Focus: To explore the alternative metabolic pathways of GSLs in bacteria, present on the surface of brassica vegetables.

Hypothesis: The alternative pathways used to metabolize GSLs in bacteria located on the surface of brassica vegetables, may contribute to the high variance of human gut GSL conversion to ITC.

Concentrating On Carbon Concentration In Algae, Chandra Davies, Steven Burgess

PRECS student projects

Carbon Concentrating Mechanisms Improve Photosynthesis Rates in Low-Carbon Environments. CCMs allow the aggregation of carbon near the site of rubisco, that way even small amounts of available carbon are being utilized.

Yes, this is important to you!

Albeit somewhat indirectly, but massively nonetheless! Algae are a driving force behind the global carbon cycle, they sequester CO2 in the oceans. Understanding the mechanisms behind the tiny marine alga O. tauri gives us a better understanding of a vital global process.

Polinators In Peril - Are Illinois Native Bees Getting Smaller?, Anthony Lamb, Tristan Barley, Adam Dolezal

PRECS student projects

Why it matters.

Pollination services provided by native bees are an important natural process, providing ~150 billion dollars globally in agricultural gains.

A bee’s body size is a trait that is an important indicator of the nutritional environment. A loss of habitat results in a loss of rich nutritional environments as flowers and resource become more fragmented and scarcer.

It has been discovered that a bee’s body size is a determinant of their foraging range. The smaller the bee, the less distance they can travel for food, therefor, the more susceptible they are to habitat loss and resource limitation.

Exploring Amaranth’S Color Palette: Linking Phenotype, Plant Adaptation, And Human Health, Sarah Redman, Chance Riggins Ph.D.

PRECS student projects

Amaranthus is a genus containing species that are highly desirable, yet underutilized crops and species that are highly despised pernicious agricultural weeds.

• Cultivated species are primarily grown as nutritious pseudograins, colorful ornamentals, or leafy greens and are recognized for tolerance to heat, drought, and salinity.
• Weedy amaranths possess similar adaptive traits, in addition to evolved resistance to numerous herbicides, and pose severe challenges to global agriculture.
• Plant pigments (i.e., betalains, carotenoids) are central to understanding this impressive diversity of phenotypes and adaptive traits.

Exploration Of Squash Plant Floral Volatiles Influencing Beetle Attraction, Olivia Barrett, Nicholas Seiter, Esther Ngumbi, Joseph Spencer, Sarah Hind

PRECS student projects

Flowers emit volatiles to attract pollinators, but these volatiles can also attract pest insects. Our study builds on earlier findings that showed that cucumber beetle attraction to squash flowers is mediated by volatile release and cucurbitacin accumulation (Theis, 2014, DOI: 10.3732/ajb.1400171). Of the three main domesticated squash species, only a few varieties of Cucurbita maxima had large quantities of floral volatiles and cucurbitacin (Andersen and Metcalf, 1987, doi: 10.1007/BF01020152); however, these studies were limited in the number of varieties that were examined. Here, we increased the number of C. maxima varieties examined, to identify patterns in floral volatile production, with …