Digital Commons Network^™

Development Of Sacb-Based Counterselection For Efficient Allelic Exchange In Fusobacterium Nucleatum, Peng Zhou, Bibek G C, Bo Hu, Chenggang Wu

Faculty, Staff and Student Publications

Fusobacterium nucleatum, prevalent in the oral cavity, is significantly linked to overall human health. Our molecular comprehension of its role in oral biofilm formation and its interactions with the host under various pathological circumstances has seen considerable advancements in recent years, primarily due to the development of various genetic tools for DNA manipulation in this bacterium. Of these, counterselection-based unmarked in-frame mutation methods have proved notably effective. Under suitable growth conditions, cells carrying a counterselectable gene die, enabling efficient selection of rare, defined allelic exchange mutants. The sacB gene from Bacillus subtilis, encoding levansucrase, is a widely used …

Evaluation Of Green Tea Yoghurt Enriched With Lacticaseibacillus Paracasei E1 Microcapsules On Macrophage M1 Profile In High Fat-Fructose Diet Mice, Esha Ardiansyah, Nur Alfi Maghfirotus Sa’Adah, Rahmi Izati, Belinda Nabiila Al Faizah, Dawama Nur Fadlilah, Septhyanti Aprilia Kavitarna, Mochammad Fitri Atho’Illah, Siti Nur Arifah, Yoga Dwi Jatmiko, Muhaimin Rifa’I

Karbala International Journal of Modern Science

Obesity is caused by an energy imbalance that increases chronic low-grade inflammation, including macrophage cell infiltration. Adipose tissue macrophages are polarized into pro-inflammatory macrophage type 1 (M1), secrete large amounts of pro-inflammatory cytokines, and activate transcription factors. Yoghurt with probiotics is popular at all ages for its health benefits and must be protected by microencapsulation. Green tea (Camellia sinensis L.) fortification provides yoghurt nutrients while improving its functional qualities and bioactivity. This study aimed to evaluate the effect of microencapsulation of Lacticaseibacillus paracasei E1 in green tea yoghurt (GTY) on the profile of M1 macrophages in mice fed a …

Exploring Nutritional Needs In Spinal Cord Injury: Dietitian Perspectives, Bowel Health, And Dietary Recommendations, Ayse Gul Zengul

All ETDs from UAB

Spinal cord injury (SCI) is a global condition affecting millions of people and leading to life-altering health complications. It profoundly alters body composition and metabolic rate, which need to be addressed with SCI-specific nutritional strategies. Muscle atrophy, fat accumulation, and decreased energy expenditure often lead to secondary health complications such as chronic diseases and SCI-related health problems, including pressure injuries and bowel dysfunction. Although nutrition plays a critical role in SCI management, our understanding of specific dietary needs for this population remains incomplete. This dissertation aims to comprehensively investigate the nutritional challenges and needs of individuals with SCI, ultimately developing …

Role Of Ring-Box E3 Ligases In Runx2 And Sp7 Protein Turnover During Osteoblast Differentiation, Abeera Sikandar

All ETDs from UAB

The bone matrix synthesis by osteoblast during skeletogenesis is regulated by several transcription factors and signaling pathways. Runx2 and Sp7 are master regulators of osteoblast differentiation and bone formation. Deletion of both genes in mice results in the complete failure of ossification. In humans, Sp7 and Runx2 genes mutations cause osteogenesis imperfecta and cleidocranial dysplasia, respectively. The progression of osteoblast differentiation requires a coordinated and temporal expression of Runx2 and Sp7 genes. Posttranslational modifications regulate the cellular levels and function of Runx2 and Sp7 proteins. Ubiquitination controls protein turnover through targeted degradation. The multi-subunit SCF-complex is the largest class of …

Characterization Of The Roles Of U1-70k In Alternative Splicing And Nuclear Speckle Formation, Trenton Myers Paul

All ETDs from UAB

RNA-binding proteins (RBPs) play critical roles in RNA processing and regulation. Among these RBPs, U1-70K is a key protein involved in RNA processing, nuclear speckle formation, and has implications in neurodegenerative diseases such as Alzheimer's. Despite its significance in transcription, RNA processing, nuclear speckle formation, and nonsense-mediated decay, studies on U1-70K have been limited primarily to its well-structured N-terminal domain due to challenges in solubilizing and expressing the full-length protein. In this dissertation, we address these challenges by optimizing cell strain and co expressing DnaK and DnaJ, enabling the successful expression, solubilization, and purification of full-length U1-70K. Using fluorescence polarization …

Controlled By Disorder: Modifications To An Unstructured C-Terminal Region Alter Srsf1'S Intramolecular Interactions And Tendency To Phase Separate, Talia Fargason

All ETDs from UAB

The protein Serine-Arginine-rich Splicing Factor 1 (SRSF1) is essential in multiple stages of the mRNA lifecycle, including alternative splicing, nonsense-mediated decay, and nuclear export. SRSF1’s dysfunction is linked to cancers, viral evasion, and developmental disorders. Its function depends on interactions between structured and unstructured regions, modulated by phosphorylation. However, the unstructured regions, while critical for regulation, contribute to protein insolubility, hindering full-length studies. Prior to the work presented here, structural studies of SRSF1 were limited to analysis of its isolated domains. This dissertation develops new techniques to characterize SRSF1, focusing on its intermolecular interactions driving phase separation and intramolecular interactions …

Metal-Rich Lacustrine Sediments From Legacy Mining Perpetuate Copper Exposure To Aquatic-Riparian Food Webs, Brittany G. Perrotta, Karen A. Kidd, Kate M. Campbell, Marie-Noële Croteau, Tyler J. Kane, Amy Marcarelli, R Blaine Mccleskey, Gordon Paterson, Craig A. Stricker, David M. Walters

Michigan Tech Publications

Historic copper mining left a legacy of metal-rich tailings resulting in ecological impacts along and within Torch Lake, an area of concern in the Keweenaw Peninsula, Michigan, USA. Given the toxicity of copper to invertebrates, this study assessed the influence of this legacy on present day nearshore aquatic and terrestrial ecosystems. We measured the metal (Co, Cu, Ni, Zn, Cd) and metalloid (As) concentrations in sediment, pore water, surface water, larval and adult insects, and two riparian spider taxa collected from Torch Lake and a nearby reference lake. Overall, elevated metal and metalloid concentrations, particularly Cu, were measured in all …

Intrinsic Adaptive Plasticity In Mouse And Human Sensory Neurons, Lisa A Mcilvried, John Smith Del Rosario, Melanie Y Pullen, Andi Wangzhou, Tayler D Sheahan, Richard A Slivicki, Theodore J Price, Bryan A Copits, Robert W Gereau

Faculty, Staff and Student Publications

In response to changes in activity induced by environmental cues, neurons in the central nervous system undergo homeostatic plasticity to sustain overall network function during abrupt changes in synaptic strengths. Homeostatic plasticity involves changes in synaptic scaling and regulation of intrinsic excitability. Increases in spontaneous firing and excitability of sensory neurons are evident in some forms of chronic pain in animal models and human patients. However, whether mechanisms of homeostatic plasticity are engaged in sensory neurons of the peripheral nervous system (PNS) is unknown. Here, we show that sustained depolarization (induced by 24-h incubation in 30 mM KCl) induces compensatory …

Optimizing Biofilm Assay Reproducibility And Characterizing The 12-Hydroxystearic Acid On Escherichia Coli, Khilola Khusanova

Theses and Dissertations

Biofilm formation in Escherichia coli plays a critical role in microbial chemical communication and surface-associated persistence. This study investigates the antibiofilm activity of 12-hydroxystearic acid (12-HSA), evaluating its R and S enantiomers as well as a racemic mixture. E. coli BL21, biofilms were grown under standardized laboratory conditions and quantified using the Crystal Violet staining assay. Treatment with 12-HSA resulted in a measurable reduction in biofilm biomass, with differences observed between the individual enantiomers and the mixture. These findings suggest that 12-HSA influences early adhesion and biofilm development, supporting its potential as a small-molecule modulator of bacterial surface behavior. This …

The Effects Of Active Substances Of Clinically Important Drugs On The Survival, Development, And Some Adult Traits Of Drosophila Melanogaster Meigen (Diptera: Drosophilidae), Gökçe Üstündağ, Kemal Büyükgüzel, Ender Büyükgüzel

Turkish Journal of Zoology

Drosophila melanogaster Meigen (Diptera: Drosophilidae) was used as a model organism and fed on an artificial diet with different clinically important drugs under laboratory conditions. The effects of fluconazole, acyclovir, and piperazine on the survivorship, development, adult longevity, fecundity, and hatching rate of the insect were investigated. The results showed that the highest concentration of fluconazole (1250 mg/L) significantly decreased both the rate of larvae reaching the 3rd instar and the rate of pupation from 93.00 ± 2.95% to 11.00 ± 2.59% (χ2 = 134.696; df = 1; p = 0.0001). The highest concentration of acyclovir (200 mg/L) significantly reduced …

A Flexible Training Approach To Improving Concurrent Training Outcomes In Remote Trainees, Christopher Bonilla, Justin R. Kilian, Robert L. Herron

International Journal of Exercise Science

International Journal of Exercise Science 18(8): 43-55, 2025. This study aimed to evaluate the effectiveness of a flexible, trainee-driven training program in improving concurrent training outcomes for individuals training remotely. The study employed a repeated-measures, parallel group design with 18 participants randomized into either a control group with fixed workouts or an experimental group with flexible workout selection based on perceived readiness. Participants were recreationally trained at baseline. Over a 16-week period, both groups completed assessments of strength and endurance, including deadlift, push-ups, and a two-mile run. The results indicated no significant difference in overall fitness improvements between the two …

An Exploratory Study Comparing The Metabolic Responses Between The 12-3-30 Treadmill Workout And Self-Paced Treadmill Running, Michael W.H. Wong, Dustin W. Davis, Olivia R. Perez, Bianca Weyers, Devin Green, Alan Garcia, James W. Navalta

International Journal of Exercise Science

International Journal of Exercise Science 18(6): 56-64, 2025. The fitness movement in the United States has evolved substantially since its emergence in the late 20th century, with social media platforms like YouTube and TikTok now playing a pivotal role in disseminating fitness programs and associated claims. One program that has gained considerable popularity is the 12-3-30 treadmill workout (12-3-30), which involves walking at a 12% grade at 3 mph for 30 minutes. Despite widespread claims about its effectiveness in burning fat and calories, there is a lack of peer-reviewed scientific studies evaluating these claims. The present study investigated metabolic responses …

Growing South Dakota (Winter 2025), College Of Agriculture, Food And Environmental Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

[Page] 2 Native Plant Initiative on a mission
[Page] 4 Gees give back
[Page] 7 Christensen named assistant dean
[Page] 8 Fennell honored in plant biology
[Page] 9 New ag communication faculty
[Page] 10 SDSU Extension awards
[Page] 12 Veterinary medicine class welcomed
[Page] 13 Coulter honored
[Page] 14 National beef award winners
[Page] 15 Department celebrates 100 years
[Page] 16 Southeast Research Farm growing
[Page] 18 Saving the flock
[Page] 22 Energize conference inspires
[Page] 24 BeefSD helping producers
[Page] 25 SDSU Extension retirements
[Page] 26 New food safety testing service
[Page] 27 Bringing back bison
[Page] 28 Jackrabbits …

The Importance Of Older Seniors Attempting To Stay Fit, Moses A. Hutchens

CSU Tower Day

Fitness is important to all but is indeed important to seniors. Partaking in fitness positively contributes to seniors in all fascists of life. Seniors attempting to stay fit is essential as it improves their mental health, physical health, and social well-being while stimulating independence and longevity. Mentally, exercise helps relieve depression and anxiety, boosts cognitive function, and improves sleep. Staying active also promotes better balance and mobility, reducing the risks of falls and making daily duties easier. Regular exercise strengthens muscles and bones, improves heart health, weight management, and enhances joint function. These help reduce the risk of conditions like …

Dignity In Detention: Addressing Gynecological Healthcare Needs Of People Detained By U.S. Immigration Authorities, Glykeria Teji, Esq., Shira Wisotsky, Esq.

Annals of Health Law and Life Sciences

People who require gynecological and obstetric care and who are detained by U.S. federal immigration authorities face unique challenges. This article examines how the current legal and administrative landscape fails to hold those responsible for providing healthcare accountable, effectively blocking access to gynecological care, and, assuming no immediate abolition of immigrant detention facilities, how international human law principles can and should guide a reimagining of the system. We also propose interim steps that U.S. authorities can take to protect access to basic and needed gynecological care for the people that they detain. Beginning with an overview of immigration detention as …

Measuring Spatial And Temporal Variation In Species Composition Of Ephemeral Pond Amphibian Assemblages Using Metabarcoding, Elizabeth Strasko

Masters Theses & Specialist Projects

Amphibian populations worldwide face severe threats, heightening the need for reliable monitoring methods. In this thesis, I explored and tested environmental DNA (eDNA) metabarcoding protocols to survey amphibian assemblages in ephemeral ponds of the the Green River Preserve in central Kentucky, USA. First, I evaluated whether the commonly used mitochondrial cytochrome c oxidase subunit I (COI) gene could effectively capture species-level variation in local amphibians for eDNA metabarcoding. Extensive primer design and testing revealed significant challenges in amplifying fragmented eDNA from water samples. In a second study, I applied a metabarcoding approach using the mitochondrial 12S ribosomal RNA (12S) gene …

Which Of The Environmental Aspects Affecting The Gut Microbiome Of The Neonate Has The Largest Lifelong Impact?, Roza Heershzon

The Science Journal of the Lander College of Arts and Sciences

The development of new DNA sequencing techniques has led to new discoveries on the gut microbiome’s critical influence on metabolic processes and immune development. Therefore, understanding the most influential factors in the development of the gut microbiome during early infancy, which impacts the individual’s long-term health, is vital. This paper explores how environmental factors, including delivery method and nutrition, shape the gut microbiome’s devel- opment in early life. In addition, it discusses their long-term health implications. The paper highlights how the mode of delivery significantly affects initial microbial colonization. Vaginal births promote a microbial community that is rich in beneficial …

Investigating The Interactions Between Elm1 And Hsl7 In The Morphogenesis Checkpoint Of Saccharomyces Cerevisiae, Rachel Foster

Masters Theses & Specialist Projects

Cell shape is essential to understanding the normal regulatory processes that occur within the cell and can indicate there are abnormalities present when there is dysfunction in the cell's development, which can have broader implications regarding human disease. The morphogenesis pathway couples cell division to the timely formation of a daughter bud in Saccharomyces cerevisiae and consists of Elm1, Hsl1, Hsl7, and Swe1 proteins which interact with septins at the bud neck to provide stability for the bud and to facilitate cell division. Elm1 is needed for the recruitment of Hsl1 and subsequently Hsl7. Hsl7 will then tether Swe1 to …

Examining The Probiotic Potential Of Pseudoalteromonas Rubra Situated In The Scholarly And Public Spheres, Sam Ruemmler

Honors Senior Capstones and Theses

Climate change is affecting our oceans negatively in many ways, such as rising temperatures and increased disease outbreaks. While there are many diseases that are affecting marine organisms, bacteria of the genus Vibrio are present globally and are known to favor warmer waters, which means increasing temperatures will cause an uptick in infections. One species, V. coralliilyticus, has been identified as a pathogen responsible for coral disease and death as well as mortality in rainbow trout, brine shrimp, and Pacific oyster larvae. A possible solution to the rising prevalence of disease is the use of probiotics. One such probiotic candidate …

The Cdk8 Kinase Module: A Novel Player In The Transcription Of Translation Initiation And Ribosomal Genes, Brittany Friedson, Stephen D Willis, Natalia Shcherbik, Alicia N Campbell, Katrina F Cooper

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Survival following stress is dependent upon reprogramming transcription and translation. Communication between these programs following stress is critical for adaptation but is not clearly understood. The Cdk8 kinase module (CKM) of the Mediator complex modulates the transcriptional response to various stresses. Its involvement in regulating translational machinery has yet to be elucidated, highlighting an existing gap in knowledge. Here, we report that the CKM positively regulates a subset of ribosomal protein (RP) and translation initiation factor (TIF)-encoding genes under physiological conditions in Saccharomyces cerevisiae. In mouse embryonic fibroblasts and HCT116 cells, the CKM regulates unique sets of RP and TIF …

The Possible Role Of Cysteine Synthesis In E. Coli Mastitis, Caz Cullimore, David Erickson

Library/Life Sciences Undergraduate Poster Competition 2025

Clinical mastitis is an infection of the udders of dairy cows

Mastitis is the leading cause of economic losses to the dairy industry

E. coli is the most common cause of clinical mastitis (Gonçalves)

Genetic factors may affect the ability for E. coli to establish an infection

Genome-wide association studies (GWAS) can detect genetic variants correlating with disease. However, most GWASes aren’t validated experimentally

Optimizing Carbon Nanotube Diameter And Copper Coating To Inhibit Pseudomonas Aeruginosa Biofilm Growth, Owen Cramer, Jenny Finlinson, Lucy C. Bowden, Bradford K. Berges Ph.D.

Library/Life Sciences Undergraduate Poster Competition 2025

• ~30% of surgical implant failure is caused by infection¹
• 10-23% of all implant-associated bone and joint infections are caused by gram-negative bacteria²
• Pseudomonas aeruginosa, a gram-negative bacterium, forms biofilms (bacterial communities encased in a matrix) that are extremely difficult to treat
• Carbon-Infiltrated Carbon Nanotubes (CICNT) have a surface structure that prevents the formation of biofilms³
• The mechanism of biofilm disruption on CICNT is still unknown.
• Our current research is focused on creating the optimal CICNT conditions that result in the greatest reduction of adherent P. aeruginosa.

The Effects Of Exosomes In Lead And Lps Induced Inflammation In Microglia, Yitzchak Lax

Theses and Dissertations

Exosomes are membrane bound subcellular vesicles formed through membrane budding of a cell and play important roles in cell-cell communication. Studies have demonstrated inflammatory changes in various cell types depending on the etiology of the exosomes such as exosomes from cancer cells or exosomes derived from mesenchymal stem cells. The purpose of this study was to determine the inflammatory consequences of exosomes in microglial cells following exposure to lead, lipopolysaccharides (LPS) and lead+LPS. The cultured mouse microglial cells were treated at 0.01 μM, 0.1 μM and 1 μM of lead,- three environmentally relevant levels and LPS was used at 10 …

Analysis And Authentication Of An Optical Method For Early Detection Of Harmful Algal Blooms, Cody Schumacher

Theses, Dissertations and Capstones

The proliferation and frequency of harmful algal blooms (HABs) attributed to eutrophication, storm events and a changing climate have been an increasing concern in both lotic and lentic freshwater ecosystems. Methods of detecting HABs have been explored through fluorescent measurement and sample analysis, but are often expensive and time-consuming. A novel smart device application is in development to detect HABs based on images captured and analyzed by machine learning algorithms trained to distinguish potential cyanobacterial blooms. The HABs App model accurately detected cyanobacteria in strong relationship with biovolume concentrations (R² = 0.996) within the Greenup Pool of the Ohio …

The Involvement Of Camp In The Secretion Of Il-10, Jyanna J. Mendola

SURF Posters 2025

Schwann cells have been found to play a key role in inflammation and repair following nerve injury. During nerve injury, the myelin sheath becomes damaged, stimulating Schwann cells to secrete cytokines and initiate an inflammatory response. They begin the process of repair by stimulating macrophages to make pro-inflammatory cytokines, such as Tumor Necrosis Factor-Alpha (TNF-a), and anti-inflammatory cytokines, such as Interleukin 10 (IL-10) which promotes healing and injury. Although it is clear Schwann cells play a role in nerve repair, there is still yet to be known regarding the exact mechanisms by which they do so. In vitro, Lipopolysaccharide (LPS), …

Ms Environmental Biology Capstone: Evaluating Environmental Risks And Conflicts In Golf Course Landscapes, Meredith Boos

Regis University Student Publications (comprehensive collection)

1) This review investigates the relationship between pesticide use on golf courses and in agriculture to determine whether the adverse health effects documented in agricultural settings also apply to golf course environments. While the negative health effects from agricultural pesticide use are well established, golf courses use pesticides with greater frequency and intensity, suggesting a potentially higher exposure risk for both workers and players.

2) This study proposes methods to quantify pesticide bioaccumulation on golf courses and adjacent lands. We hypothesize that areas surrounding golf courses will exhibit a spatial gradient of pesticide accumulation, increasing with proximity to treated sites …

Competitive Bacteria Inhibiting Yersinia Ruckeri Growth – A Strategy To Prevent Enteric Redmouth Disease (Erm) In Freshwater Fish, Kyler Linton, David Erickson

Library/Life Sciences Undergraduate Poster Competition 2025

Pacific freshwater fish are less likely than Atlantic freshwater fish to exhibit Enteric Redmouth Disease (ERM), or Yersiniosis as caused by Yersinia ruckeri. Based on the hypothesis that these fish may harbor commensal bacteria that inhibit Y. ruckeri growth, we isolated many kinds of commensal bacteria from fish intestines that we have collected from Alaska and local streams. Using co-culture experiments, we have conducted competitive assays to determine if the bacteria found in the gut biomes of these fish inhibit the growth of Y. ruckeri. These may be potential probiotic organisms that could provide resistance to ERM disease.

Mechanism Of Copper-Coated Cicnt Inhibition Of Staphylococcus Aureus Biofilm Formation, Emilia Gregory, Lucy Bowden, Bradford Berges

Library/Life Sciences Undergraduate Poster Competition 2025

Staphylococcus aureus is a leading cause of healthcare-associated infections, particularly through biofilm formation on medical devices, leading to severe and recurrent complications¹. The resistance of S. aureus biofilms to traditional antibiotics requires new strategies to mitigate these infections. Our previous findings indicate that the anti-biofilm properties of carbon-infiltrated carbon nanotubes (CICNT) significantly inhibit the growth of S. aureus biofilms². We will further explore if copper, an innately antimicrobial material, will enhance this effect.

To determine the impact that copper would have on bacterial growth, we coated the CICNT with a thin layer of copper and used …

Looking For Manna, Dung, And Craters - Uncovering Hidden Diversity In Circinaria Lichens, Lizzie Perry, Ginny Basset, Steve Leavitt

Library/Life Sciences Undergraduate Poster Competition 2025

• Lichens, symbiotic partnerships between fungi and photosynthetic organisms, are often overlooked in biodiversity studies due to their cryptic nature. The lichen genus, Circinaria —historically, described as “Manna Lichens”, “crater lichens”, “pigeon dung lichens”, and “excrement of the earth”¹ —remains understudied.
• This genus includes approximately 40 formally described species worldwide, however, only 13 have been documented in North America³.
• To better understand species-level diversity of Circinaria in Western North America, we used an integrated data set – DNA, morphology, and ecology – to characterize diversity and delimit potential candidate species.

Effect Of Ph And Iron Chelate On The Growth Of Basil And Soybean In Soilless Media, Christian Baker, Bruce Bugbee

Nutrients

Iron (Fe) deficiencies are common in alkaline root zones and can cause chlorosis and reduce growth. The most common approach to prevent deficiency is using synthetic chelates that keep iron in solution at high pH. Here we report the effects of pH and chelate type on the development of chlorosis and biomass in soybeans and basil. We grew the plants at a pH ranging from 6.0-7.8. Fe was chelated with either a less expensive EDTA chelate or a more expensive EDDHA chelate. There was no significant difference between chelates at pH 6.0 in either soybeans or basil. In soybeans, there …