Genetics and Genomics Commons^™

Role Of Giant Transposons (Starships) In Facilitating Fungal Genome Evolution, Savanna A. Ruebsam, Ciara Pike

2023 Midwest Ecology & Evolution Conference

The hetereothallic ascomycete Magnaporthe contains strains capable of infecting > 50 grass species. Despite the predominance of an asexual lifestyle the genomes of ten examined strains exhibit high levels of chromosomal structural diversity. Starships, a novel class of DNA transposons, have been identified in Magnaporthe and are likely involved in fungal genome evolution. Starships capture and relocate fungal genes throughout their host genomes and could function as recombinogenic substrates. These mobile genetic elements are inserted within the fungal chromosomal 5SrRNA genes resulting in gene disruption into two fragments, from positions 1-69 and 56-116. The software programs blastn, FACET, the Integrated …

Evidence For Starship Transposons As Facilitators Of Fungal Genome Evolution, Morgan Morrow, Toni Blake Park

2023 Midwest Ecology & Evolution Conference

Cereal grains (e.g. rice, wheat) comprise up to 50% of worldwide daily caloric intake. One fungal disease affecting these crops that exhibits high pathogenicity and virulence is blast disease. The pathogen is Pyricularia oryzae, a primarily asexual ascomycete fungus. Despite being primarily asexual P. oryzae has a wide host range and been documented to have high phenotypic and pathogenic variability, contradicting Muller’s rachet. It is postulated that other genetic mechanisms are being utilized to generate genome instability and, thus, genetic diversity, such as transposons. Recent findings suggest that a novel class of massive transposons (10kb - >300Kb), termed Starships, inserted …

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.

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 …

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 …

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 …

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?

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

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

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.

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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White Coat Color Of A Black Angus Calf Attributed To An Occurrence Of The Delr217 Variant Of Mitf, Jessica Lynn Petersen, Renae L. Sieck, David J. Steffen

Department of Animal Science: Faculty Publications

A white calf, with minimal pigmented markings, was born to two registered Black Angus parents. Given the possibility of an unknown recessive or de novo dominant mutation, whole-genome sequencing was conducted on the trio of individuals. A 3-bp in-frame deletion in MITF was identified; this mutation was unique to the calf but identical to the delR217 variant reported in both humans and murine models of Waardenburg syndrome type 2A and Tietz syndrome. Given the coat color phenotype and identity of the mutation, our data support that this calf represents the first instance of this recurring MITF mutation in cattle.

Gaming To Learn Genetics, Sarah Wolfe

Undergraduate Honors Thesis Projects

Digital game-based learning is an alternative to traditional lecture learning. It involves active engagement with concepts in a digital game setting and can apply to a variety of subjects, including STEM fields. We examined this type of learning in the context of an undergraduate introductory genetics course: specifically, use of a genetics video game for teaching. There were two groups: an experimental group that played the genetics game Geniventure, and a control group that read and studied Powerpoint lecture slides. Both groups took a pretest and posttest, as well as completed an I/D (interest/deprivation) scale and workload scale. There …

The Status Of Invasive Dusky Slug (Arion) Species In The Upper Great Lakes: A Molecular Approach, Olivia W. Hall

All NMU Master's Theses

I update the distribution of two cryptic slug species, Arion fuscus and Arion subfuscus, in the Upper Great Lakes of the United States using molecular identification methods. Arion fuscus has not previously been reported in the literature in this region, and Arion subfuscus has previously been reported as abundant. However, all previous distribution studies were determined using visual identification tools, which can result in misidentification between cryptic species. To molecularly re-examine these distribution maps, I used a mitochondrial ribosomal subunit 16S PCR amplification and subsequent SSpI and MfeI restriction enzyme digest to identify slug specimens. I collected slugs in …

A Kinome-Wide Crispr Screen Identifies Ck1Α As A Target To Overcome Enzalutamide Resistance Of Prostate Cancer, Jinghui Liu, Yue Zhao, Daheng He, Katelyn M. Jones, Shan Tang, Derek B. Allison, Yanquan Zhang, Jing Chen, Qiongsi Zhang, Xinyi Wang, Chaohao Li, Chi Wang, Lang Li, Xiaoqi Liu

Markey Cancer Center Faculty Publications

Enzalutamide (ENZA), a second-generation androgen receptor antagonist, has significantly increased progression-free and overall survival of patients with metastatic prostate cancer (PCa). However, resistance remains a prominent obstacle in treatment. Utilizing a kinome-wide CRISPR-Cas9 knockout screen, we identified casein kinase 1a (CK1a) as a therapeutic target to overcome ENZA resistance. Depletion or pharmacologic inhibition of CK1a enhanced ENZA efficacy in ENZA-resistant cells and patient-derived xenografts. Mechanistically, CK1a phosphorylates the serine residue S1270 and modulates the protein abundance of ataxia telangiectasia mutated (ATM), a primary initiator of DNA double-strand break (DSB)-response signaling, which is compromised in ENZA-resistant cells and patients. Inhibition of …

Identification Of A Nacc1-Regulated Gene Signature Implicated In The Features Of Triple-Negative Breast Cancer, Chrispus Ngule, Hami Hemati, Xingcong Ren, Oluwafunminiyi Obaleye, Amos O. Akinyemi, Felix Oyelami, Xiaofang Xiong, Jianxun Song, Xia Liu, Jin-Ming Yang

Markey Cancer Center Faculty Publications

Triple-negative breast cancer (TNBC), characterized by a deficiency in estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor2 (HER2), is among the most lethal subtypes of breast cancer (BC). Nevertheless, the molecular determinants that contribute to its malignant phenotypes such as tumor heterogeneity and therapy resistance, remain elusive. In this study, we sought to identify the stemness-associated genes involved in TNBC progression. Using bioinformatics approaches, we found 55 up- and 9 downregulated genes in TNBC. Out of the 55 upregulated genes, a 5 gene-signature (CDK1, EZH2, CCNB1, CCNA2, and AURKA) involved in cell regeneration was positively correlated …

Leukocyte Tyrosine Kinase (Ltk) Is The Mendelian Determinant Of The Axolotl Melanoid Color Variant, Mirindi Kabangu, Raissa Cecil, Lloyd Strohl Ii, Nataliya Y. Timoshevskaya, Jeramiah James Smith, Stephen Randal Voss

Markey Cancer Center Faculty Publications

The great diversity of color patterns observed among amphibians is largely explained by the differentiation of relatively few pigment cell types during development. Mexican axolotls present a variety of color phenotypes that span the continuum from leucistic to highly melanistic. The melanoid axolotl is a Mendelian variant characterized by large numbers of melanophores, proportionally fewer xanthophores, and no iridophores. Early studies of melanoid were influential in developing the single-origin hypothesis of pigment cell development, wherein it has been proposed that all three pigment cell types derive from a common progenitor cell, with pigment metabolites playing potential roles in directing the …

In Situ Microwave Fixation Provides An Instantaneous Snapshot Of The Brain Metabolome, Jelena A. Juras, Madison B. Webb, Lyndsay E. A. Young, Kia H. Markussen, Tara R. Hawkinson, Michael D. Buoncristiani, Kayli E. Bolton, Peyton T. Coburn, Meredith I. Williams, Lisa P. Y. Sun, William C. Sanders, Ronald C. Bruntz, Lindsey R. Conroy, Chi Wang, Matthew S. Gentry, Bret N. Smith, Ramon C. Sun

Markey Cancer Center Faculty Publications

Brain glucose metabolism is highly heterogeneous among brain regions and continues postmortem. In particular, we demonstrate exhaustion of glycogen and glucose and an increase in lactate production during conventional rapid brain resection and preservation by liquid nitrogen. In contrast, we show that these post- mortem changes are not observed with simultaneous animal sacrifice and in situ fixation with focused, high- power microwave. We further employ microwave fixation to define brain glucose metabolism in the mouse model of streptozotocin-induced type 1 diabetes. Using both total pool and isotope tracing analyses, we identified global glucose hypometabolism in multiple brain regions, evidenced by …

Targeting Lncrna Ddit4-As1 Sensitizes Triple Negative Breast Cancer To Chemotherapy Via Suppressing Of Autophagy, Ting Jiang, Jiaojiao Zhu, Shilong Jiang, Zonglin Chen, Ping Xu, Rong Gong, Changxin Zhong, Yueying Cheng, Xinyuan Sun, Wenjun Yi, Jinming Yang, Wenhu Zhou, Yan Cheng

Markey Cancer Center Faculty Publications

In this study, it is found that the lncRNA, DNA damage inducible transcript 4 antisense RNA1 (DDIT4-AS1), is highly expressed in triple-negative breast cancer (TNBC) cell lines and tissues due to H3K27 acetylation in the promoter region, and promotes the proliferation, migration, and invasion of TNBC cells via activating autophagy. Mechanistically, it is shown that DDIT4-AS1 induces autophagy by stabilizing DDIT4 mRNA via recruiting the RNA binding protein AUF1 and promoting the interaction between DDIT4 mRNA and AUF1, thereby inhibiting mTOR signaling pathway. Furthermore, silencing of DDIT4-AS1 enhances the sensitivity of TNBC cells to chemotherapeutic agents such as paclitaxel both …

Face Validation Of A Spanish Non-Invasive Prenatal Screening Knowledge Scale, Kenya Michelle De Leon

Theses and Dissertations

Non-invasive prenatal screening (NIPS) provides risk assessment for chromosome aneuploidy in pregnancy. Previous studies in the United Kingdom and United States have attempted to measure patient knowledge, decisional conflict, and informed choice in cohorts of English-speaking pregnant patients who elected NIPS (Griffin et al., 2023; Lewis et al., 2016). However, knowledge scales utilized in these studies have not been validated. The current study was conducted in order to assess face validity of a Spanish NIPS knowledge scale that was originally written in English. This scale was developed as part of a larger project to ultimately provide more validated research measures …