Digital Commons Network^™

The Evolution Of Transposable Elements As Cis-Regulatory Elements In Mammals, Alan Y. Du

Arts & Sciences Graduate Student Theses and Dissertations

Transposable elements (TEs) are mobile genetic elements that make up a large proportion of mammalian genomes. Although TEs are highly prevalent genomic sequences, they have been understudied as they were once labeled as “junk DNA.” Despite their initial status as simple genomic parasites, recent studies have implicated TEs as cis-regulatory elements, supplying promoters, enhancers, and boundary elements. Functional testing of regulatory activity, however, remains a significant bottleneck. Nonetheless, due to their repetitive nature, TEs provide a unique model to examine the evolution of cis-regulatory elements, which has traditionally been difficult to study due to lack of homology at the sequence …

Membrane Translocation Process Revealed By In Situ Structures Of Type Ii Secretion System Secretins, Zhili Yu, Yaoming Wu, Muyuan Chen, Tong Huo, Wei Zheng, Steven J Ludtke, Xiaodong Shi, Zhao Wang

Faculty, Staff and Students Publications

The GspD secretin is the outer membrane channel of the bacterial type II secretion system (T2SS) which secrets diverse toxins that cause severe diseases such as diarrhea and cholera. GspD needs to translocate from the inner to the outer membrane to exert its function, and this process is an essential step for T2SS to assemble. Here, we investigate two types of secretins discovered so far in Escherichia coli, GspDα, and GspDβ. By electron cryotomography subtomogram averaging, we determine in situ structures of key intermediate states of GspDα and GspDβ in the translocation process, with resolution ranging from 9 Å …

The Timid Invasion: Behavioural Adjustments And Range Expansion In A Non-Native Rodent, Jana A. Eccard, Valeria Mazza, Celia Holland, Peter Stuart

Publications

Animal behaviour can moderate biological invasion processes, and the native fauna's ability to adapt. The importance and nature of behavioural traits favouring colonization success remain debated. We investigated behavioural responses associated with risk-taking and exploration, both in non-native bank voles (Myodes glareolus, N = 225) accidentally introduced to Ireland a century ago, and in native wood mice (Apodemus sylvaticus, N = 189), that decline in numbers with vole expansion. We repeatedly sampled behavioural responses in three colonization zones: established bank vole populations for greater than 80 years (2 sites), expansion edge vole populations present for 1–4 …

Investigating Cassava Susceptibility To Xanthomonas Induced Bacterial Blight Using Disease Phenotyping And Genome Engineering Strategies, Kiona Rajene Elliott

Arts & Sciences Graduate Student Theses and Dissertations

In nature, plants regularly contend with bacterial, viral, and fungal pathogens, which employ strategies that promote pathogen fitness and subsequently elicit disease in the host. Xanthomonads are a group of bacterial phytopathogens that induce disease in an extensive range of host plants. Mechanisms underlying pathogen disease promotion have been understudied in food staple crops such as cassava. Cassava is a starchy root crop susceptible to cassava bacterial blight (CBB) a disease caused by the pathogen Xanthomonas phaseoli pv. manihotis (Xpm). Xpm and other bacterial pathogens use effector molecules to manipulate host genes that promote disease susceptibility. Xpm has specialized effector …

Tiam1 Coordinates Synaptic Structural And Functional Plasticity Underpinning The Pathophysiology Of Neuropathic Pain, Lingyong Li, Qin Ru, Yungang Lu, Xing Fang, Guanxing Chen, Ali Bin Saifullah, Changqun Yao, Kimberley F Tolias

Faculty, Staff and Students Publications

Neuropathic pain is a common, debilitating chronic pain condition caused by damage or a disease affecting the somatosensory nervous system. Understanding the pathophysiological mechanisms underlying neuropathic pain is critical for developing new therapeutic strategies to treat chronic pain effectively. Tiam1 is a Rac1 guanine nucleotide exchange factor (GEF) that promotes dendritic and synaptic growth during hippocampal development by inducing actin cytoskeletal remodeling. Here, using multiple neuropathic pain animal models, we show that Tiam1 coordinates synaptic structural and functional plasticity in the spinal dorsal horn via actin cytoskeleton reorganization and synaptic NMDAR stabilization and that these actions are essential for the …

Morphological Trait Evolution In Solanum (Solanaceae): Evolutionary Lability Of Key Taxonomic Characters, Rebecca Hilgenhof, Edeline Gagnon, Sandra Knapp, Xavier Aubriot, Eric Tepe, Lynn Bohs, Leandro Giacomin, Yuri Gouvea, Andres Orejuela, Christopher T. Martine, Clara Ines Orozco, Iris E. Peralta, Tina Sarkinen

Faculty Journal Articles

Solanum is one of the world's largest and economically most important plant genera, including 1245 currently accepted species and several major and minor crops (e.g., tomato, potato, brinjal eggplant, scarlet eggplant, Gboma eggplant, lulo, and pepino). Here we provide an overview of the evolution of 25 key morphological traits for the major and minor clades of this giant genus based on stochastic mapping using a well-sampled recently published phylogeny of Solanum. The most evolutionarily labile traits (showing >100 transitions across the genus) relate to plant structure (growth form and sympodial unit structure), herbivore defence (glandular trichomes), pollination (corolla shape …

Context Dependence, Cheating, And Long-Term Conflict In Social Interactions, Trey Scott

Arts & Sciences Graduate Student Theses and Dissertations

Social interactions are widespread in nature and can have important ecological and evolutionary consequences. Interactions are often categorized by who is benefited or harmed by the symbiosis. For example, if both sides benefit, the interaction is cooperative. If one side benefits at the expense of the other, it is an antagonism. The kind of interaction can have important evolutionary implications, but interactions rarely fit neatly into these interaction categories. Instead, interactions often involve elements of cooperation and conflict. My dissertation explores the consequences of interactions and how they can involve both cooperation and conflict using a range of experimental, genomic, …

Presence And Identity Of Babesia Microti In Ireland, A. Zintl, A. Mcmanus, M. Galan, M. Diquattro, L. Giuffredi, N. Charbonnel, J. Gray, C. Holland, Peter Stuart

Publications

Babesia microti is a tick-transmitted protozoan parasite of wildlife that can also cause serious disease in humans. It is now well established that B. microti represents an assemblage of different strains or species, only some of which are important zoonotic pathogens. Therefore, in order to assess the potential public health risk associated with B. microti in any given location, it is important to determine the strains that are present. This is the first study on the presence and identity of B. microti in Ireland. Overall, 314 wood mice (Apodemus sylvaticus), 243 bank voles (Myodes glareolus) and 634 questing Ixodes ricinus …

Skeletal Anatomy Of The Pectoral Fin In Mudskipper Species From Terrestrial And Aquatic Habitats, Haodong Zhou, Cassandra M. Donatelli, Odette Laneuville, Emily M. Standen

Engineering Faculty Articles and Research

Mudskippers are a group of amphibious fishes in the family Oxudercidae, whose species inhabit a range of habitats from mostly aquatic to mostly terrestrial. Most of our understanding about habitat preference comes from natural history observations, particularly where they are collected (i.e., low intertidal vs. high intertidal regions). Mudskippers have undergone several morphological changes to accommodate a terrestrial life, including major changes to the pectoral and pelvic girdles. These changes result in a novel crutching gait, which mudskippers use to move over land. Though the appendicular morphology and crutching gait of mudskippers have been described in some species, few …

Beyond A Vision For The Future: Tangible Steps To Engage Diverse Participants In Inclusive Field Experiences, Robin M. Verble, Corinne L. Richards-Zawacki, Vanessa K.H. Young

Biological Sciences Faculty Research & Creative Works

Synopsis Recent strides toward improving diversity, equity, and inclusion (DEI) in field biology present a unique opportunity for transdisciplinary exploration of the impacts and state of a topic that has remained hereto largely underexplored and under-discussed in the academic setting. Within current literature, themes of racial and gender inequity, power imbalances, unsafe environments, and underdeveloped infrastructure and resources are widespread. Thus, we organized a symposium that addressed these compelling issues in field biology DEI through a multitude of experiential and academic lenses. This article will orient the reader to the special issue and offer summative goals and outcomes of the …

The Art Of A Slugslayer: An Exploration Of The Process Of Extracting Radulae From Lehmannia Valentiana For The Purpose Of Viewing In The Scanning Electron Microscope, Elizabeth Gannon

Mahurin Honors College Capstone Experience/Thesis Projects

A radula is an anatomical structure found exclusively in mollusks that acts as both tongue and teeth in feeding. Its structure has been studied for more than a century, yet published methods for identifying, dissecting, and cleaning radulae for microscopy are almost unintelligible to anyone not already familiar with molluscan anatomy. The purpose of this project was to identify the best method of garden slug radula isolation and present it in a manner that anyone could understand and successfully use.

After identifying the location of the radula in the slug, the easiest means of removal proved to be simply regurgitating …

Effects Of Heterozygous Deletion Of Autism-Related Gene Cullin-3 In Mice, Qiang-Qiang Xia, Angela K. Walker, Chenghu Song, Jing Wang, James A. Mobley, Jeffrey Singer, Anju Singh, Craig M. Powell

Biology Faculty Publications and Presentations

Autism Spectrum Disorder (ASD) is a developmental disorder in which children display repetitive behavior, restricted range of interests, and atypical social interaction and communication. CUL3, coding for a Cullin family scaffold protein mediating assembly of ubiquitin ligase complexes through BTB domain substrate-recruiting adaptors, has been identified as a high-risk gene for autism. Although complete knockout of Cul3 results in embryonic lethality, Cul3 heterozygous mice have reduced CUL3 protein, demonstrate comparable body weight, and display minimal behavioral differences including decreased spatial object recognition memory. In measures of reciprocal social interaction, Cul3 heterozygous mice behaved similarly to their wild-type littermates. In …

An Evolutionary Comparative Study Of Congenital Stationary Night Blindness-Associated Trpm1 Genetic Variants Of Uncertain Significance In Horses And Humans Utilizing Caenorhabditis Elegans, Gabrielle Davis

Theses

Congenital stationary night blindness (CSNB) is a heterogeneous collection of genetic diseases affecting the eyes and vision in horses and humans. Current research has implicated several genetic mutations impacting different genes involved in phototransduction and signal transmission, including TRPM1. In horses, genetic mutations in TRPM1 also result in a leopard spotting pattern or leopard complex. The goal of this study is to examine the potential impact of CSNB associated TRPM1 missense variants of uncertain significance (VUS). Previous research in Caenorhabditis elegans have revealed an orthologous TRPM1 gene known as gon-2 that allows for comparative studies. The evolutionary relationship of …

School Of Biological Sciences News, 2023, School Of Biological Sciences

School of Biological Sciences News

Alumni newsletter of Illinois State University's School of Biological Sciences.

Decision Rules For Egg-Color-Based Rejection By Two Cavity-Nesting Hosts Of The Brown-Headed Cowbird, Alexander J. Di Giovanni, Juliana Villa, Mark T. Stanback, Charles F. Thompson, Scott K. Sakaluk, Mark E. Hauber, Daniel Hanley

Faculty Publications – Biological Sciences

Hosts of obligate avian brood parasites often evolve defense mechanisms to avoid rearing unrelated young. One common defense is egg rejection, for which hosts often rely on eggshell color. Most research has assumed that hosts respond to perceived color differences between their own eggs and parasite eggs regardless of the particular color; however, recent experiments have found that many hosts respond more strongly to brown foreign eggs than to equally dissimilar blue eggs. Yet, none of these prior studies tested a brown-egg-laying species and, with only one exception, all were conducted in open nests where light levels are considered sufficient …

Molecular Mediators Of Axonal Transport And Local Translation Of Cdc42, Rhoa Molecular Mediators Of Axonal Transport And Local Translation Of And Calreticulin Mrnas And Their Implications For Axon Growth And Regeneration, Matthew Davis Zdradzinski

Theses and Dissertations

Neurons are highly polarized cells with expansive cytoplasmic processes, axons and dendrites, which create unique subcellular domains. Localization and translation of mRNAs in these subcellular regions is now recognized as a critical mechanism through which polarized cells establish and maintain the specialized domains that are needed for their functions. RNA profiling studies have uncovered hundreds to thousands of mRNAs in axons and these axonal mRNA profiles differ across neuronal populations, physiological conditions, and developmental growth states. Functionally organizing these mRNA populations into cohorts of coregulated mRNAs via RNA binding proteins allows us to better understand how the transcriptome is regulated …

A Trait-Based Approach To Explain Plant Coexistence In Tropical Forests, Felipe Nery Arantes Mello

Dissertations (1934 -)

Ecology seeks to explain the mechanisms that allow multiple species to coexist in the same habitat without one species outcompeting or driving others to extinction. Niche differentiation is a mechanism that has been proposed to allow species to coexist through specialization on different resources or habitats, which reduces competition and the probability of competitive exclusion. Species can reduce competition by using different combinations of resources and thus partitioning available resources in time and space. Differences in resource use is hypothesized to be influenced by species’ morphological and physiological adaptations, known as functional traits. Links between functional traits and abiotic factors …

Evolutionary Codependency: Insights Into The Mitonuclear Interaction Landscape From Experimental And Wild Caenorhabditis Nematodes, Suzanne Estes, Zachary P. Dietz, Vaishali Katju, Ulfar Bergthorsson

Biology Faculty Publications and Presentations

Aided by new technologies, the upsurgence of research into mitochondrial genome biology during the past 15 years suggests that we have misunderstood, and perhaps dramatically underestimated, the ongoing biological and evolutionary significance of our long-time symbiotic partner. While we have begun to scratch the surface of several topics, many questions regarding the nature of mutation and selection in the mitochondrial genome, and the nature of its relationship to the nuclear genome, remain unanswered. Although best known for their contributions to studies of developmental and aging biology, Caenorhabditis nematodes are increasingly recognized as excellent model systems to advance understanding in these …

Embryonic Development Of Natural Annual Killifish Populations Of The Genus Austrolebias: Evolutionary Parallelism And The Role Of Environment, Hellen Schlueb, Daniel Blanco, Daniel García, Jason Podrabsky

Biology Faculty Publications and Presentations

1. Repeated, independent emergence of the same trait within different phylogenetic lineages is termed parallel evolution. It typically occurs as a result of similar selective pressures. Annual killifish have adapted to survive in the extreme habitat of temporary pools on three continents and present an especially amenable system for studying fundamental principles of evolutionary parallelism. When the pools dry, annual killifish embryos survive through the dry phase in the bottom substrate in a stage of dormancy—a diapause. The diapause is a complex set of three different developmental stages, none of which is obligate, thus leading to a multitude of potential developmental …

Sympatric Soil Microbe Interactions Between Streptomyces And Fusarium Isolates, Lehren A. Olk-Szost

All NMU Master's Theses

Interkingdom interactions between soil bacteria and fungi may play a critical role in occurrence of disease suppressive soils, yet our understanding of these interactions remains limited. Streptomyces are well-known producers of antimicrobial compounds important to medicine and agriculture. Production of these secondary metabolites is often mediated by quorum sensing. Most Streptomyces research occurs in single species experiments, yet new metabolites have been discovered in interspecies co-culture experiments. Interspecies, intergenic, and interkingdom co-culture research will likely reveal many valuable compounds, and strengthen our understanding of complex ecological interactions in soil microbiomes. Interactions between sympatric Streptomyces and Fusarium isolates from disease suppressive …

Soil Moisture Dynamics In Cover Cropping Systems: From Local To Global Scales, Manish Gautam

Theses and Dissertations

Cover cropping systems, which have gained recognition for their ability to enhance soil health and promote sustainability are also associated with potential risks related with declining soil moisture and pose a dilemma for farmers considering the adoption of cover crops in water deficit semi-arid settings worldwide. To address this pressing issue, we conducted a participatory cover cropping trial in the Lower Rio Grande Valley (LRGV) region, encompassing four different farms and supplemented this experiment with a meta-analysis to answer our soil moisture and climate parameters and quantify the impact of cover crops on soil moisture levels. The findings revealed that …

Establishing Effective Conservation Management Strategies For A Poorly Known Endangered Species: A Case Study Using Australia’S Night Parrot (Pezoporus Occidentalis), Nicholas P. Leseberg, Alex Kutt, Megan C. Evans, Tida Nou, Scott Spillias, Zoe Stone, Jessica C. Walsh, Stephen A. Murphy, Mike Bamford, Allan H. Burbidge, Kate Crossing, Robert A. Davis, Stephen T. Garnett, Rodney P. Kavanagh, Robert Murphy, John Read, Julian Reid, Stephen Van Leeuwen, Alexander W. T. Watson, James E. M. Watson, Martine Maron

Research outputs 2022 to 2026

An evidence-based approach to the conservation management of a species requires knowledge of that species’ status, distribution, ecology, and threats. Coupled with budgets for specific conservation strategies, this knowledge allows prioritisation of funding toward activities that maximise benefit for the species. However, many threatened species are poorly known, and determining which conservation strategies will achieve this is difficult. Such cases require approaches that allow decision-making under uncertainty. Here we used structured expert elicitation to estimate the likely benefit of potential management strategies for the Critically Endangered and, until recently, poorly known Night Parrot (Pezoporus occidentalis). Experts considered cat management the …

Comparative Analysis Of Soil Properties, Microbial Community Composition, And Yield Responses To Cover Crops In Different Ecoregions Of South Texas, Daphne Zapsas

Theses and Dissertations

Comprehensive understanding of soil properties, their interdependencies, and the effects of management practices is crucial for designing sustainable agricultural strategies. By adopting site-specific and need-based practices that enhance soil health, farmers can optimize crop growth, increase yield, and contribute to long-term environmental sustainability. Cover crops have been recognized for enhancing soil fertility, promoting microbial activity, and increasing organic matter content. However, while their effectiveness is well documented in temperate regions with readily available water, their impact in water limited systems in subtropical regions remains mixed. The aim of this study is to assess soil conditions in four different farms across …

Cadmium And Salinity Stressor Antagonism On Vallisneria Neotropicalis, Christopher P. Mikolaitis

Graduate Theses and Dissertations (2019 - present)

Submerged macrophytes form the foundation of freshwater ecosystems. These organisms are sessile and are very susceptible to shifts in their environment. Heavy metals are of particular concern as they can be sequestered indefinitely in sediments and are readily taken up by rooted vegetation. In the presence of saltwater intrusions, these metals can interact with salt ions potentially changing their availability to submerged vegetation. In this study a freshwater macrophyte, Vallisneria neotropicalis, was used as a test species for interactive effects between Cd, a non-essential heavy metal, and salt stress. The metrics used to establish the individual as well as …

Long-Chain Fatty Acid Sensing And Catabolism In Commensal Escherichia Coli Impact Murine Gut Colonization, Tessa Carolina Cox

Theses and Dissertations

The gastrointestinal tract is home to trillions of microbes that collectively influence host physiology, immunity, nutrient metabolism, and infectious disease. The overgrowth of naturally-occurring Escherichia coli in the gut is a common signifier of microbiome dysfunction and occurs in many chronic diseases including obesity. Recent studies have shown that higher fat intake is associated with increased gut E. coli growth. However, it remains unknown whether gut E. coli utilize lipids such as long chain fatty acids (LCFAs) as carbon sources to colonize the mammalian gut. Therefore, the central objective of my dissertation was to utilize bacterial genetics and various mouse …

Modulation Of Eif2Α Signaling And The Integrated Stress Response By Targeted Therapeutic Attenuation Of Pkr Activity Contributes To Protection Of Dyt-Prkra Cells From Apoptosis, Kenneth L. Frederick

Theses and Dissertations

Luteolin is a natural flavonoid present in vegetables, fruits, and medicinal herbs that possesses anti-oxidative, anti-cancer, and anti-inflammatory properties. In this study, we investigated the effect of luteolin on the integrated stress response (ISR), which is an evolutionarily conserved intracellular signaling network essential for adapting to environmental stresses to maintain healthy cells. Dysregulated ISR is involved in the etiology of many human diseases including the movement disorder DYT-PRKRA which is caused by mutations in the PRKRA gene. PRKRA encodes for PACT, the protein activator of interferon-induced, double-stranded RNA (dsRNA)-activated protein kinase PKR.PACT-mediated PKR activation regulates the …

Diversity, Function, And Phenotypic Plasticity Of Cryptophyte Phycobiliproteins, Kristiaän Merritt

Theses and Dissertations

Cryptophytes are a group of unicellular eukaryotic algae that can be found in a wide range of underwater habitats. Part of their ecological success can be attributed to their diverse array of cryptophyte phycobiliproteins (Cr-PBPs), a pigment class that captures wavelengths of light that are poorly absorbed by chlorophylls. Cryptophytes gained photosynthesis via secondary endosymbiosis in which their ancestor engulfed a red algal endosymbiont. Following endosymbiosis, they deconstructed the red algal photosynthetic machinery to form the Cr-PBP. Since then, the Cr-PBPs have diversified into at least 9 spectrally distinct forms. I investigated the diversity of Cr-PBP light absorption across 76 …

Biological Flora Of Coastal Freshwater And Brackish Marshes: Cladium Jamaicense Crantz, Richard Stalter, Robert I. Lonard

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Cladium jamaicense Crantz, also known as sawgrass, has a broad distributional range from the Atlantic coast of Virginia to Florida, to southern Texas, the Caribbean, and along the Atlantic coast of Mexico to Central America, and to Brazil. Cladium jamaicense typically occurs in oligotrophic sloughs and fresh and brackish marshes where optimal salinity values range from 0 to 3.5 ppt. This species is a long-lived perennial with a highly developed rhizome system with rhizomes up to 20 cm long and 2.5 to 10 mm in diameter. Asexual reproduction is common. Its fibrous root system comprises short dauciform roots characterized by …

The Impact Of Progerin On Genome Maintenance In Mammalian Cells, Liza Alexandra Joudeh

Theses and Dissertations

Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic condition characterized by accelerated aging. The cause of HGPS is a point mutation in the LMNA gene, which encodes lamins A and the splice variant lamin C. Lamins are components of the nuclear lamina, a complex that plays structural and catalytic roles in the nucleus that are essential to chromatin organization, DNA replication, and DNA repair. The mutation associated with HGPS activates a cryptic splice donor site which alters the lamin A protein in a way that does not allow prelamin A to be fully processed, and ultimately results in the accumulation …

The Effects Of Variations In Light And Nutrient Availability On Phytoplankton And Zooplankton, Jake Anthony Swanson

Theses and Dissertations

Aquatic ecosystems experience a wide range of variation in resource availability; two of the resources that are most essential to phytoplankton and zooplankton are light and nutrients. Light can vary in both its color and intensity; these variations can directly impact phytoplankton by altering the amount and color of light available for photosynthesis. Nutrient variability, particularly increases in nutrient levels, also alter phytoplankton communities by favoring the growth of certain taxa such as cyanobacteria.

To understand whether phytoplankton respond differently to changes in light availability I investigated whether the diversification of cryptophytes, phytoplankton with diverse light-capturing pigments, showed evidence of …