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Exploring Natural Competence Of Escherichia Coli Through Biofilm Formation, Thulni Liyanaarachchi

University Honors Theses

Escherichia coli is a species not known for natural competence; however, specific growth conditions can induce the process in this bacterium due to the presence of homologous competence genes. These conditions could be met with biofilm formation through an active growth phase in the two-layer architecture. Therefore, my thesis examined whether natural competence is exhibited in E. coli during biofilm formation as determined by the genetic transfer of ampicillin and chloramphenicol-resistance genes between two separate strains. The experiments were broken into three aims to determine the morphology of the biofilm in inter-strain co-cultures and cell-DNA mixes, the effect of …

Investigating A Link Between Dna Repair And Dna Replication In Escherichia Coli Using A Bacterial Two-Hybrid System, Lo Cooper

University Honors Theses

Cells rely on nucleotide excision repair (NER) to remove bulky DNA lesions, such as those caused by UV light. In Escherichia coli, NER involves the UvrABC complex, and includes two main pathways, global genomic repair and transcription-coupled repair (TCR). While TCR, which preferentially removes lesions that block RNA polymerase on the transcribed strand of active genes, is well studied, less is known about whether a similar coupling between repair proteins and replisomes blocked by damaged DNA exists. Such a process has been suggested by a high throughput interactome study, using the replisome subunit HolC as bait and the damage …

Bile Acid Regulation Of Xenobiotic Nuclear Receptors On The Expressions Of Orosomucoids In The Liver, Ji Ho Suh, Inyoung Cheon, Hyun-Jung Jung, Sung Ho Lee, Mi Jeong Heo, Matthew Deberge, Clavia Ruth Wooton-Kee, Kang Ho Kim

Children’s Nutrition Research Center Staff Publications

The constitutive androstane receptor (CAR) and pregnane X receptor (PXR) are xenobiotic nuclear receptors activated by various xenobiotics, drugs, hormones, and bile acids (BAs). Upon activation, these nuclear receptors play critical roles in regulating systemic energy homeostasis. However, precise mechanisms through which CAR and PXR influence systemic metabolism remain incompletely understood. Here, we investigated the impact of CAR and PXR on the liver-secreted hormone (i.e., hepatokine) expressions in response to BA stress such as cholic acid (CA) feeding. Our analysis revealed that several BA-activated genes, including the well-known CAR/PXR target, aldo-keto reductase family 1, member B7 (Akr1b7 …

Kinetic Analysis Reveals T6a-Protein Specificity For T6a And Hn6a Trna Modifications, Cassandra Mae Harker

University Honors Theses

Transfer RNA (tRNA) is essential for accurate translation of genetic information and plays a role in cellular processes such as lipid aminoacylation and bacterial conjugation. Base modifications help tRNA fold correctly and function properly. An important base modification, N6-threonylcarbamoyladenosine (t6A) occurs at position A37 in the anticodon-stem-loop of tRNA. This modification is crucial for decoding ANN codons. Interestingly, an Archeal organism, Methanocaldococcus jannaschii, can have either t6A and hydroxynorvalylcarbamoyl-6- adenosine (hn6A) modification at the same position on tRNAs. As Tsa proteins catalyze the formation of both t6A and hn6A modifications, this raises the question of whether discrimination between these …

Exploring Vaccine Efficacy And Safety For Ms Patients On Immunosuppressant Treatment In Light Of The Covid-19 Pandemic, Rain Pross

University Honors Theses

Multiple sclerosis (MS) is a chronic neurodegenerative autoimmune disorder affecting approximately 2.8 million people worldwide. Despite decades of research to understand the molecular mechanisms of MS pathology, little is known about why the neurodegeneration caused by this illness occurs. For this reason, current treatments for MS target two broader aspects of the disease: relapse management and prevention via disease-modifying therapies. These treatments often involve immunosuppressive mechanisms, creating vulnerability to infectious diseases that became particularly concerning during the COVID-19 pandemic. This literature review examines the safety and efficacy of vaccination for MS patients on immunosuppressant therapies, highlighting the novel mRNA vaccines …

The Role Of Excitatory Neuromodulation In Managing Variability Of Neural System Output, Omar Itani

Dissertations

Neural systems can generate consistent outputs across a population despite substantial variability in the underlying components of individuals. This dissertation aims to identify mechanisms through which neuromodulation influences the relationship between parametric and output variability in neural systems. Through a combination of theoretical analysis, computational modeling, and data-driven approaches, the research addresses how excitatory neuromodulation can shape population-level activity variability and identifies key patterns that govern the production of consistent neural population output despite underlying parameter variability.

The theoretical foundation is established by considering how excitatory neuromodulation affects population variability in simplified neuronal models. Two fundamental patterns of variability reduction …

Rapid Riparian Ecosystem Decline In Rocky Mountain National Park, David J. Cooper, E William Schweiger, Jeremy R. Shaw, Cherie J. Westbrook, Kristen Kaczynski, Hanem Abouelezz, Scott M. Esser, Koren Nydick, Isabel De Silva, Rodney Chimner

Michigan Tech Publications

Understanding the drivers of ecosystem collapse is critical for resource management, particularly for protected areas mandated to preserve biodiversity. In Rocky Mountain National Park, Colorado, tall willows (Salix spp.) dominated riparian vegetation, and a beaver-willow state was the natural ecosystem type in the Colorado River headwaters. However, willows comprise a portion of elk diets and are a preferred food for recently introduced moose, and the vegetation structure has changed dramatically since the early 2000s. To assess ecosystem changes, we analyzed time-series data on willow height from 1997 to 2021 inside and outside 3 exclosures built to exclude ungulates, area of …

Cohabitation At Threshold: Carpenter House Reimagined For Multispecies Living, Zhixiao Yang

Masters Theses

With the rapid growth of the human population, we are encroaching further into wildlife habitats, particularly those surrounding urban environments. This accelerating urbanization leads to biodiversity loss, the degradation of ecological services essential to human health and well-being, and a diminishing connection between city dwellers and the natural world.

Today, urban planners, architects, economists, and other advocates for the future of humanity and the health of the planet are actively questioning how we might build greener, more resilient cities. While much of the focus has been on large-scale interventions — such as the use of sustainable materials, the creation of …

Neuroinflammation In The Ventral Tegmental Area Of Chronically Stressed Rats, Marie M. Hafez

Honors Projects

Chronic stress has been associated with maladaptive behaviors in both human and animal research models, but the underlying mechanisms are unclear. In this research study, we sought to define whether stress induces neural inflammation in the ventral tegmental area, the brain region primarily responsible for regulating reward consumption, learning, memory, and addictive behaviors through moderating dopamine release in other brain areas. To do this, male Sprague-Dawley rats were subjected to a chronic intermittent stress paradigm that included stressors such as wet bedding, delayed feedings, social isolation, strobe lights, and forced swims. Following the chronic stress intervention, brain sections were collected …

Gamified Gait Rehabilitation Via Real-Time Biofeedback And Adaptive Hip-Exoskeleton Control, Mariya Huzaifa Tohfafarosh

Theses

Gait impairments arise from systemic diseases, age-related degeneration, musculoskeletal dysfunctions, or neurological conditions. While traditional rehabilitation can be effective, they often face challenges such as high costs, inaccessibility, and low patient engagement. To address these challenges, my work introduces a virtual reality-based rehabilitation (VRBR) system, integrating real-time motion and electromyographic (EMG) muscle activation feedback with a gamified virtual environment for enhanced adaptability and engagement. The system includes a custom-designed hip-exoskeleton that provides adaptive spring-like assistance or resistance, supporting both mobility-impaired users and strength training. Assistance levels can be tuned to match the user's progress. Additionally, a custom pressure insole was …

Analytical Approaches For Identification Of Essential Genomes Of Plasmodium Knowlesi And Babesia Divergens, Sida Ye

Graduate Doctoral Dissertations

Apicomplexa constitute a large phylum of single-celled, obligate intracellular protozoan parasites. Notably, Plasmodium spp. and Babesia spp. are apicomplexan parasites that infect red blood cells. Plasmodium species are the causative agent of malaria and are transmitted by Anopheles mosquitoes, affecting large human populations, whereas Babesia spp., transmitted through the bite of Ixodes ticks cause babesiosis.

In this dissertation, we investigate the essential genome of these parasites using high-throughput transposon mutagenesis. Identifying the essential genome is key to finding new drug targets and understanding resistance mechanisms, a crucial pursuit given the rising resistance to frontline antimalarial drugs and the challenges …

Fire Fossils: Biomineral Infrastructures In Untangling Climates, Tanmayee More

Masters Theses

Diatoms drift, sediments sink, wildfires generate their own weather. Lightning strikes can blast sand into glass, and microscopic organisms do the same in the cold recesses of the ocean. What alchemies and metabolisms catalyze space, time, and energy? What are the thermodynamics of infrastructure in Climate Change?

Places, materials, and beings are afterimages. Through alchemical experiments, and multi-scalar imaging, I develop simulations of wildfires, and their profound, reverberating effects. In this thesis, a glass-meets-landscape experimental process enters these obscured conditions and renders new material relations for the built environment.

Ecospiritual Entanglement, Ali Vedad Yüner

Masters Theses

Land breeds culture. It gives us the resources to thrive, and in that process we establish a relationship with its constituents. With a multitude of beings inhabiting the land, a complex web of relationships develop. Biology describes these relationships as food webs; the mass entanglement of organisms in a manner that each organism nourishes the other. These webs are not just mere scientific structures but rather an interpretation of existential connections that every organism in the world, humans included, are indebted to. Food webs are the first stepping stone in the formation of culture, as they account for the engagement …

Tree Story, Jia Hu

Masters Theses

What is Nature?

Nature is a system of intelligence. It means designing for efficiency—often by learning from strategies that have evolved over time. In my research, I use patterns to interpret and decode nature.

To explore nature, I began with the red cedar tree, aiming to simulate and predict its growth patterns—forms shaped by both internal biology and external forces. By analyzing its geometry, I sought to understand how trees embody the dynamic relationship between organism and environment. These patterns reveal the adaptive logic of life.

Patterns are central to understanding nature. While tree geometry may appear chaotic, it follows …

Field Journal: The Excluded Middle, Carrie E. Kouts

Masters Theses

What does it look like to engage with organisms and landscapes at the periphery of anthropocentric value structures? How does one break the internalized myth that the “built” environment is excluded from the natural world? When does a hyper-mobile and hyper-commodified society confront the exponential crisis of animal death? Within this series of journal entries, field notes, collection observations, weird prose, and sensory musings, one will find questions on the nature of being human and the complex narratives of care we encounter in a world shared with more-than-humans. Each handwritten vignette and photograph from daily life weaves a non-linear and …

Development Of A Novel Biomarker Platform For Profiling Key Protein-Protein Interactions To Predict The Efficacy Of Bh3-Mimetic Drugs, Andrew J Kinloch, Faiyaz Rahman, Bahriye Karakas, Muhammad Shahid, Bora Lim, Stephanie J Bouley, James A Walker, Erinna F Lee, Walter D Fairlie, Kevin R Kelly, Michael H Cardone

Faculty, Staff and Student Publications

One of the hallmarks of cancer cells is their failure to respond to the cellular mechanism of apoptosis. The B-cell lymphoma 2 (BCL-2) family of proteins regulate apoptosis. Their ability to do so can be measured using several methods that in turn anticipate the fate of the cancer cell in response to apoptosis-inducing treatment. These assays ultimately identify the readiness of the cancer cell to undergo apoptosis, which is referred to as the mitochondrial priming state. These metrics, however, have been challenging to implement in the clinic.

Genetic Factors Of Campylobacter Jejuni Required For Its Interactions With Free-Living Amoeba, Deepti Pranay Samarth, Asim Z. Abbasi, Young Min Kwon

Poultry Science Faculty Publications and Presentations

Acanthamoeba, a free-living amoeba ubiquitous in environmental water, has been considered as the environmental reservoir of certain bacterial pathogens, including Campylobacter jejuni, an intracellular human pathogen causing self-limiting gastroenteritis. Acanthamoeba-C. jejuni interaction mechanisms may help clarify how the otherwise fastidious bacterium C. jejuni survives in environmental waters. In this study, we constructed single deletion mutants of C. jejuni strain 81-176 for the 10 selected genes (motAB, ciaB, kpsE, virB11, cheY, flaAB, cstII, docB, sodB, and cadF) previously shown to be important for the interaction (invasion and intracellular survival) of C. jejuni with mammalian hosts. We used a modified gentamicin protection …

Anti-Viral Cd8 Central Memory Veto Cells As A New Platform For Car T Cell Therapy, Wei-Hsin Liu, Anat Globerson Levin, Assaf Lask, Galit Horn, Tova Waks, Bar Nathansohn Levi, Irit Milman Krentsis, Einav Shoshan, Xiaohua Su, Maksim Mamonkin, Richard E Champlin, Yair Reisner, Esther Bachar Lustig

Faculty, Staff and Student Publications

Central memory CD8 T cells exhibit marked veto activity enhancing engraftment in several mouse models of T cell-depleted bone marrow (TDBM) allografting. Graft-versus-host disease (GVHD) can be prevented by stimulation of mouse or human memory CD8 T cells against their cognate antigens under cytokine deprivation, in the early phase of culture followed by further expansion with IL21, IL15, and IL7. Thus, human anti-viral CD8 central memory veto T cells generated from CMV and EBV-positive donors are currently evaluated in a clinical trial at MD Anderson Cancer Centre (MDACC). Results in 15 patients indicate a low risk of GVHD. Considering that …

Diversity And Activity Of Ground-Dwelling Spiders (Araneae) In Four Sub-Communities In A Degraded Oak Woodland At The Chicago Botanic Garden, Cook County, Illinois, James F. Steffen, Michael L. Draney

The Great Lakes Entomologist

Ground-dwelling spiders were sampled using pitfall traps over a twelve-month period from four sub-communities within a 40-ha oak woodland complex in northern Cook County, Illinois. Mesic and dry mesic oak woodland, mesic upland forest, buckthorn dominated mesic oak savanna and a mesic woodland control, where no restoration management is planned, were sampled. Fifty-five species within 44 genera and 18 families were trapped. The results suggest negative correlations between non-native spider abundance and spider species richness. Also, phenology of the various species indicates that a year-round inventory is necessary to adequately sample ground-dwelling spider assemblages. Possibilities of using Bathyphantes concolor (Wider) …

Biology And Larval Morphology Of Agrilus Subcinctus (Coleoptera: Buprestidae), With Comparisons To The Emerald Ash Borer, Agrilus Planipennis, Toby R. Petrice, Robert A. Haack, John S. Strazanac, Jonathan P. Lelito

The Great Lakes Entomologist

Emerald ash borer (EAB), Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), is an exotic invasive pest of ash (Fraxinus spp.) trees that was first discovered in North America in 2002. There has been concern that surveyors could confuse immature stages of EAB with A. subcinctus Gory, an ash borer native to North America. We conducted studies in 2006-2009 in southern Michigan to determine biological and morphological characters for distinguishing immature A. subcinctus and EAB life stages. Agrilus subcinctus adults were captured on yellow sticky cards from late May through mid-August, with peak flight occurring in June. Agrilus subcinctus egg laying began in …

Odonata Of Coastal Peatland Habitats Adjacent To Lake Superior In Wisconsin, Robert B. Dubois, Julie M. Pleski, William A. Smith, Eric J. Epstein

The Great Lakes Entomologist

We sampled adults and exuviae of Odonata in eleven coastal fens and poor fens near Lake Superior in Douglas, Bayfield, and Ashland counties in Wisconsin to determine species that were breeding in these areas, and gain knowledge about their relative abundances, flight periods, and nymphal habitats. The flora in these fens was characterized by mats of Sphagnum mosses, a variety of ericaceous shrubs, and a number of sedges, among which Carex lasiocarpa Ehrhart (slender sedge) was most dominant. We averaged seven visits per site from early June through September, 2004, to cover the flight periods of most species of Odonata …

Habitat Distribution Of Carabid Beetles (Coleoptera: Carabidae) In Northern Hardwood Forests Of Michigan, Holly A. Petrillo, John A. Witter

The Great Lakes Entomologist

We compared carabid beetle communities in northern hardwood forests and divided these forests into three categories based on overstory composition and geographic location: Northern red oak-American beech (Quercus rubra L.-Fagus grandifolia Ehrh.) in the Lower Peninsula (OBLP), sugar maple- American beech (Acer saccharum Marsh.) in the Lower Peninsula (MBLP), and sugar maple- American beech in the Upper Peninsula (MBUP). Carabid beetles were collected using pitfall traps in 36 stands in 2003-2004. We found that carabid composition changed throughout the collection periods. Pterostichus pensylvanicus LeConte and Sphaeroderus lecontei Dejean comprised 76% of the trap catches in May while Synuchus impunctatus (Say) …

Spatiotemporal Variation Of Violet-Feeding Large Fritillaries (Euptoieta, Speyeria) (Lepidoptera: Nymphalidae) In Central And Northern Wisconsin, Ann B. Swengel, Scott R. Swengel

The Great Lakes Entomologist

We analyzed the relative abundance of the large fritillaries Euptoieta claudia (Cramer) (immigrant), Speyeria cybele (Fabricius) and S. atlantis (Edwards) (generalists), S. aphrodite (Fabricius) (grassland species), and S. idalia (Drury) (prairie specialist) in transect surveys at grasslands and pine barrens during 1990-2006 for variation and correlation over time (measured both as chronological year and as years since last management treatment) among six subregions in central and northern Wisconsin. Population trends (correlations of abundance with chronological year) were few and not significantly skewed toward either negative or positive trends. Spatial synchrony between pairs of subregions was significantly different among species, and …

The Native And Introduced Bark And Ambrosia Beetles Of Michigan (Coleoptera: Curculionidae, Scolytinae), Anthony I. Cognato, Nicolas Barc, Michael Philip, Robert Mech, Aaron D. Smith, Eric Galbraith, Andrew J. Storer, Lawrence R. Kirkendall

The Great Lakes Entomologist

Our knowledge of the biogeography of Scolytinae of eastern temperate North America is very patchy. We used data from hand collecting, trapped material (from 65 of 83 counties), and museum collections, supplemented by literature records, to compile a list comprising 107 bark beetle species in 45 genera for Michigan, a state with an especially rich diversity of woody plants. We provide detailed collection data documenting 32 species not previously catalogued for Michigan, 23 of which are new state records; the genera Trypophloeus and Trischidias are reported from Michigan for the first time. Fifteen Michigan scolytines are not native to North …

Fleas Of The Norway Rat In The Superior, Wisconsin, Harbor Area (Siphonaptera: Ceratophyllidae, Hystrichopsyllidae), Darol L. Kaufmann, Norman D. Radtke

The Great Lakes Entomologist

The occurrence of the fleas of the Norway rat, Rattus noruegicus (Berkenhout) was monitored in Superior, Wisconsin, for 12 months. A total of 441 fleas was recovered from 300 rat hosts. Nosopsyllus fasciatus (Bosc), the northern rat flea, was the most abundant species found (94.1%) while Ctenophthalmus pseudagyrtes pseudagyrtes Baker (5.4%) and Megabothris asio asio (Baker) (0.5%) were also present. The flea index was highest (4.8) in July and lowest (0.2) in February and March. Forty-four percent of the rats examined were infested.

Simulation Of The Effects Of Stand Factors On Spruce Budworm (Lepidoptera: Tortricidae), W. P. Kemp, J. P. Nyrop, G. A. Simmons

The Great Lakes Entomologist

A model was developed to simulate the life history of instar-I through instar-I1 spruce budworm, Choristoneura fumiferana (Clemens). Particular emphasis was given to the redistribution phases during spring and fall and the factors affecting budworm survival. Analyses included the effects of aggregated stand types, temperature, cloud cover, open areas, and the species distribution, on redistribution mortality. Of those stand factors examined, open area and non-host percentages were the most important in regulating redistribution survival.

Size Reduction Southward In Michigan's Mustard White Butterfly, Pieris Napi (Lepidoptera: Pieridae), W. H. Wagner Jr., Michael K. Hansen

The Great Lakes Entomologist

[Excerpt]

The mustard white, Pieris napi (Linnaeus) is generally considered to be a circumboreal species or species-complex. Much disagreement exists regarding the classification in this group, the members of which are extremely diverse, especially in Eurasia. There is evidently "a continuous range of differentiation, from local populations, through subspecies, to species, which nomenclature cannot fully reflect" (Bowden 1972). In North America the major controversy has been whether the so-called West Virginia white, P. virginiensis Edwards, should be separated as a distinct species. Most writers today agree that it should. Of the mustard white in the Great Lakes area, the local …

An Annotated List Of The Checkered Beetles (Coleoptera: Cleridae) Of Michigan, D.C. L. Gosling

The Great Lakes Entomologist

[Excerpt]

The checkered beetles (Cleridae) have been included in local lists of Michigan Coleoptera by Andrews ( 1916, 192 1, 1929), Hatch (1924), Hubbard and Schwarz (1878). LeConte (1850), and Wolcott (1909). The present list is the first to include records from throughout the state, and is based on the collections of the University of Michigan Museum of Zoology (UMMZ), those of the Department of Entomology, Michigan State University (MSUC), and the private collections of E. F. Giesbert, D. K. Young, and the author. This list records 35 species of Cleridae from the state, and I believe it is essentially …

Seroprevalence And Associated Risk Factors Of Caprine Arthritis Encephalitis (Cae) And Peste Des Petits Ruminants (Ppr) Among Deer In An Institutional Farm In Malaysia, Krishnan Nair Balakrishnan, Faez Firdaus Abdullah Jesse, Bura Thlama Paul, Shalonagiftsal Stephen C Charles, Ummul Rifhan Najiha Noor Zaman, Eric Lim Teik Chung, Nur Amira Azhar, Abdirahman Barre, Muhammed Mikail, Mohd Azmi Mohd Lila

The Thai Journal of Veterinary Medicine

Caprine arthritis encephalitis (CAE) and peste des petits ruminants (PPR) are significant viral diseases impacting small ruminants, leading to substantial economic losses and posing a potential threat to livestock health. Although seroprevalence evidence of these viruses has been documented in ruminants, there is a lack of data regarding their presence among farmed deer in Malaysia. This preliminary study aimed to determine the seroprevalence and associated risk factors for CAEV and PPRV infections among deer in Malaysia. A total of ninety-two blood sera from an institutional deer farm were screened for CAEV and PPRV antibodies using commercially available indirect ELISA test …

A New Genus And New Synonyms For Liburnia Reducta Van Duzee, 1907 (Hemiptera: Auchenorrhyncha: Delphacoidea: Delphacidae), Charles R. Bartlett, Adam M. Wallner

Insecta Mundi

The delphacid species Liburnia reducta Van Duzee is transferred to the new genus Calkinodelphax Bartlett and Wallner (Hemiptera: Auchenorrhyncha: Delphacoidea: Delphacidae) and is designated the type species of this genus under the name Calkinodelphax reductus (Van Duzee), new combination. Calkinodelphax reductus is broadly distributed from Florida, the Antilles, Central America, and northern South America. Calkinodelphax reductus is the subjective senior synonym of Pissonotus striolus Osborn, Delphacodes cornuta Beamer, and Euides fasciatella auct. (nec. Osborn). A new lectotype is designated for Liburnia reducta Van Duzee. The female holotype and male allotype of Liburniella fasciatella Osborn were reviewed and found to …