Digital Commons Network^™

Exploring Gene Functions And Phage-Host Protein Interactions In Mycobacteriophage Island3, Annika Stecker, Steven Van Meeteren, Gracelyn Wager, Abigail Clarke, Jordyn Kramer, Lauren Pavich, Emily Schmidt, Krista Starr, Kaarina Van Berkum, Ashley Van Egdom

Celebration of Research

Island3 is an I1 mycobacteriophage that infects Mycobacterium smegmatis mc²155. It has a total of 76 protein coding genes, but only 17 of these genes have functions assigned by bioinformatics. To discover the functions of the additional genes, we cloned 72 of Island3’s genes and are assaying each gene product for two functions when expressed in the host M. smegmatis: the ability to reduce growth of the host (cytotoxicity) and the ability to protect the host from infection by Island3 or another phage (defense). So far, we have assayed more than 60 of Island3’s genes and found 14 genes that …

Genomic Annotation Of Bacteriophages Clayda5, Gshelby23, Santhid, And Wrigley, Abigail Bastian, Marcus Blankespoor, Gideon Fynaardt, Sadie Gilmeister, Emily Hurley, Madison Jones, Erika Mckenney, Alexa Olguin, Micah Rens, Garrett Snyder, Anneka Sterk, Sophie Swart, Chelsea Thurm, Alaena Trevino, Ashley Van Egdom, Morgan Veach, Lauren Pavich, Byron Noordewier, Sara S. Tolsma

Celebration of Research

We annotated the genomes of four recently discovered Actinobacteriophages. Clayda5 and GShelby23 were isolated on Microbacterium foliorum NRRL B-24224. Clayda5 is a lytic, cluster EB phage, one of only 47 discovered to date. It has 10 base pair 3’ sticky overhanging ends and a GC content is 67.2%. It has 70 protein-coding genes and two tRNA genes in its 39,894 bp genome. Clayda5 was purified from soil collected in Hull, IA. GShelby23 was isolated from soil collected in Storm Lake, IA. It is a cluster EM phage, one of only six discovered to date. Its genome is circularly permuted and …

Investigating The Putative Reca-Like Recombinase Gene, Kaytlyn Keeler, Blake Anderson, Abigail Clarke, Kip Cullinan, Lindsey Groen, Travis Grover, Benjamin Kingery, Jordyn Kramer, Noah Kryfka, Kaitlyn Mccracken, Emilien Meray, Mitchell Oostra, Dominick Pickard, Mitchell Rentschler, Annika Stecker, Ashley Van Egdom, Morgan Veach, Elizabeth Heeg

Celebration of Research

Our Biochemistry: Molecular Genetics class has partnered with the Immunology class to investigate the expression of JacoRen57’s gene 50.

The bacteriophage JacoRen57 – found in Sioux Center, Iowa (accession: MK279840). JacoRen57’s genome has sequenced by Pittsburg SEA-PHAGES Institute and fully annotated by Northwestern College students in 2018. A region between gene 49 and 50 caught our attention as there is a large gap between these genes. Almail et al., investigated if this is a transcription regulatory region for genes 49 and/or 50 (2021). This work demonstrated the region has a regulatory function in the direction of gene 50. Based on …

Analysis Of A Putative Promoter In Mycobacteriophage Jacoren57, Kip Cullinan, Kaitlyn Mccracken, Emilien Meray, Lane Mulder, Daniel A. Nordquist, Lauren Pavich, Mitchell Rentschler, Annika Stecker, Sara S. Tolsma

Celebration of Research

JacoRen57 is a cluster AB mycobacteriophage that infects Mycobacterium smegmatis mc²155. We recently reported on the characterization of a putative promoter in JacoRen57 using an mCherry reporter construct. This promoter is present in a gap upstream of a gene that is present in all AB phages. In all cases, these are forward genes immediately following a long series of reverse genes. The genes are most frequently identified as a RecA-like DNA recombinases but also as RepA by bioinformatics. To further analyze this putative promoter and gene product, NWC Molecular Genetics students cloned the RecA-like DNA recombinase into an E. coli …

Microplastic Concentrations In Orange City Wastewater, Garrett Raymon, Garrett Snyder, April Van Tol, Lindsey Craig, Marshall Kleinhesselink, Lane Mulder, Daniel Strand, Gideon Fynaardt, Kaytlin Wojciechowski, Todd Tracy

Celebration of Research

Microplastics are increasingly polluting both terrestrial and aquatic ecosystems. Researchers have found that wastewater treatment plants are an entry point for microplastics into surface waters, and we wondered how effective our local wastewater treatment plant is in removing microplastics from wastewater, given that it was not engineered for the removal of microplastics. We sampled effluent water from the new wastewater treatment plant (WWTP) in Orange City, Iowa, to determine the amount of microplastics released from the plant into Orange City Slough. We found concentrations of 498 pieces of microplastic/cubic meter (0.498/L) in the effluent water, which is similar to published …

Invertebrate Pitfall Surveys At Glacial Hills Preserve And Buena Vista County Park, April Van Tol, Lindsey Craig, Marshall Kleinhesselink, Garrett Raymon, Garrett Snyder, Katie Meyer, Gideon Fynaardt, Kaytlin Wojciechowski, Lane Mulder, Daniel Strand, Laurie Furlong, Todd Tracy

Celebration of Research

Invertebrates are integral members of the ecosystems they inhabit. However, they are often overlooked and understudied. We performed two pitfall surveys in Buena Vista County in September 2021 to study the diversity and abundance of invertebrate species in the presence and absence of two invasive species: Eastern Redcedar (Juniperus virginiana) and Garlic Mustard (Alliaria petiola). We collected pitfall samples and brought them back to the lab for identification. We found no significant differences in invertebrate abundance between cedar and non-cedar samples, nor between mustard and non-mustard samples. We propose further research focusing on seasonal changes, as these invasives may have …

The Effect Of Cold Stratification On The Germination Of Grassland Seeds, Katie Meyer, Gideon Fynaardt, Kaytlin Wojciechowski, April Van Tol, Marshall Kleinhesselink, Lindsey Craig, Garrett Snyder, Garrett Raymon, Lane Mulder, Daniel Strand, Todd Tracy

Celebration of Research

One factor that must be considered when reconstructing a prairie is how the prairie seeds being planted need to be prepared for germination. The probability of successful germination of these seeds is dependent on many factors, including exposure to cold temperatures for a prolonged period of time. To explore this idea, we collected seeds from 13 species of forbs and grasses, both native and non-native, and stored them at various temperatures for several weeks. We predicted that the germination of the seeds of native grassland species would be enhanced by cold stratification, while non-natives (especially forbs common to flower gardens) …

Environment And Co-Occurring Native Mussel Species, But Not Host Genetics, Impact The Microbiome Of A Freshwater Invasive Species (Corbicula Fluminea), Marlène Chiarello, Jamie R. Bucholz, Mark Mccauley, Stephanie N. Vaughn, Garrett W. Hopper, Irene Sánchez González, Carla L. Atkinson, Jeffrey D. Lozier, Colin R. Jackson

Faculty and Student Publications

The Asian clam Corbicula fluminea (Family: Cyneridae) has aggressively invaded freshwater habitats worldwide, resulting in dramatic ecological changes and declines of native bivalves such as freshwater mussels (Family: Unionidae), one of the most imperiled faunal groups. Despite increases in our knowledge of invasive C. fluminea biology, little is known of how intrinsic and extrinsic factors, including co-occurring native species, influence its microbiome. We investigated the gut bacterial microbiome across genetically differentiated populations of C. fluminea in the Tennessee and Mobile River Basins in the Southeastern United States and compared them to those of six co-occurring species of native freshwater mussels. …

Alewife (Alosa Pseudoharengus) Contributions To Lake Phosphorus Budgets: Implications For Management, Meg "Rue" Farley Thurrell Ms

Student Scholarship

As human-made dams are removed and fish passage at dams is improved in

support of restoration efforts, anadromous alewives (Alosa pseudoharengus) gain

access to historic spawning grounds. As they migrate to spawn, adult alewives import

marine derived nutrients to lakes and impoundments. Young of year alewives (juveniles)

export nutrients as they emigrate to the sea. These nutrients support primary

production and are incorporated into freshwater food webs. However, many lakes in

New England are mesotrophic or eutrophic. Additional nutrients, specifically

phosphorus (P), may exacerbate water quality issues. To examine these issues, I

compared outputs ofan alewife nutrient and population model …

Impact Of Hydrologic Alteration On Brazos River Pelagophilic Minnows, Christopher M. Taylor, Kevin B. Mayes

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

The lower Brazos River has been profoundly altered since the construction of multiple impoundments. The resulting river regulation poses problems for organisms adapted to a natural flow regime and is thought to play a major role in the imperilment of seven native minnows that synchronize spawning during high flow pulses. Four of the species are presumably extirpated from the region, but their declines and losses differed across time. To address potential reasons for species’ declines, we assessed pre- and post-impoundment changes in flow regime from five gaging stations across the lower Brazos River to identify river flow characteristics that depart …

Host-Pathogen Coevolution Between Tasmanian Devils (Sarcophilus Harrisii) And Devil Facial Tumor Disease, Dylan Garret Gallinson

USF Tampa Graduate Theses and Dissertations

Coevolution is a driving force of rapid evolution, yet the complexity of coevolutionary interactions has made it difficult to characterize the genomic basis of traits mediating such relationships. Coevolutionary dynamics are especially important in host-pathogen systems where the host and pathogen must constantly adapt to one another. The Tasmanian devil and its species-specific transmissible cancer, devil facial tumor disease (DFTD), provide the rare opportunity to study host-pathogen coevolution in a complex natural system. Extensive spatiotemporal devil sampling, high linkage disequilibrium in devils, and a large selective pressure imposed by DFTD facilitate a system tractable for study. Here, we characterized devil …

Spata7 Is Required For Maintenance Of The Retinal Connecting Cilium, Jiaxiong Lu, Kaitlyn Xiong, Xinye Qian, Jongsu Choi, Yoon-Kyung Shim, Jacob Burnett, Graeme Mardon, Rui Chen

Faculty, Staff and Students Publications

SPATA7, an early onset LCA3 retinal disease gene, encodes a putative scaffold protein that is essential for the proper assembly of the connecting cilium (CC) complex in photoreceptors. Previous studies have shown that SPATA7 interacts with other photoreceptor-specific ciliary proteins, such as RPGR and RPGRIP1, and maintains the integrity of CC integrity. However, although it is known that Spata7 is required for early formation of the CC, it is unclear if Spata7 is also required for the maintenance of the CC. To investigate Spata7 function in the retina at the adult stage, loss of function was induced in the …

Leaf Phenology Of Callery Pear: Frost Damage, Margaret E. Maloney, Abby Hay, Eric B. Borth, Ryan W. Mcewan

Five Rivers MetroParks Collaboration Data Archive

This dataset is one of three affiliated with the paper "Leaf phenology and freeze tolerance of the invasive tree Pyrus calleryana Roseaceae) and potential native competitors."

The other two datasets are:

• Leaf Phenology of Callery Pear: Spring
• Leaf Phenology of Callery Pear: Fall

Leaf Phenology Of Callery Pear: Spring, Margaret E. Maloney, Abby Hay, Eric B. Borth, Ryan W. Mcewan

Five Rivers MetroParks Collaboration Data Archive

This dataset is one of three affiliated with the paper "Leaf phenology and freeze tolerance of the invasive tree Pyrus calleryana Roseaceae) and potential native competitors."

The other two datasets are:

• Leaf Phenology of Callery Pear: Fall
• Leaf Phenology of Callery Pear: Frost Damage

Exploring The Functionality Of Putative Bop3 Post-Translational Modifications, Liliya Tkachuk

Honors Scholars Collaborative Projects

All eukaryotic cells require that transcribed mRNAs undergo export form the nucleus to the cytoplasm where they can be translated into proteins. This process requires a host of proteins which are conserved between the unicellular budding yeast, S. cerevisiae, and humans. During this process, Mex67 and other associated proteins facilitate the mRNA to travel across the nuclear pore complex (NPC), doorways embedded in the nuclear envelope. Upon the exit of mRNA, Mex67 is released and recycled back into the nucleus to facilitate the export of more mRNA. This occurs through the action of Dbp5, whose activity is regulated through …

Engaging Students Equitably In Biological Systems Modeling, Sowmya Anjur

Faculty Publications & Research

It has been my goal as an educator to engage students in meaningful and innovative assessments that are hands-on, engage their creativity and improve their interdisciplinary understanding. At the same time, the engagement need to be equitable as well, to recognize each student for their individuality and creativity. To this end, I created my Pathophysiology course with the objective of teaching students how to model biological systems. The course is a one semester course that is based on homeostasis maintenance in the body and how homeostatic disruptions result in symptoms of pathologies. Students are required to understand how homeostasis is …

Developing An Electroporation Method For Transforming Streptomyces Nymphaeiformis, Heather Knott, Stephen Baron

Honors Projects

Streptomyces species are notoriously difficult to transform. Streptomyces nymphaeiformis is no different, so a method of electroporation was used to attempt to transform the cells. Multiple growth stages were used in order to alter the degree of development of the cell wall. The procedure did not kill the cells, but the cells were not transformed. Due to the lack of transformation with S. nymphaeiformis, transformation was attempted on two other Streptomyces strains, S. lividans and S. coelicolor. Neither was successfully transformed to thiostrepton (tsr) resistance, nor did they grow on a plate lacking thiostrepton. One possibility for the …

Ecological Stressors Impact Soil Biodiversity, Kaleb Frierson, John Carlile

Transformations: Presentation Slides

Soil biodiversity serves ecologically important roles like nutrient cycling and is used as an indicator of community disturbance. North American forests host a multitude of ecological stressors, including invasive plants, earth worms, and deer abundance. While relationships between deer and invasive species, as well as relationships between macroinvertebrates and worms have been heavily investigated, the effects of invasive plant species like Pale Swallowwort on soil biodiversity are unknown. To test our hypothesis that Pale Swallowwort affects soil biodiversity, we collected leaf litter from three state parks throughout Central New York at sites with and without the invasive plant. Samples were …

Cingulin Binds To The Zu5 Domain Of Scaffolding Protein Zo-1 To Promote Its Extended Conformation, Stabilization, And Tight Junction Accumulation, E. Vasileva, D. Spadaro, F. Rouaud, Jonathan M. King, A. Flinois, J. Shah, S. Sluysmans, I. Méan, L. Jond, J. R. Turner, S. Citi

Biology Faculty Research

Zonula occludens-1 (ZO-1), the major scaffolding protein of tight junctions (TJs), recruits the cytoskeleton-associated proteins cingulin (CGN) and paracingulin (CGNL1) to TJs by binding to their N-terminal ZO-1 interaction motif. The conformation of ZO-1 can be either folded or extended, depending on cytoskeletal tension and intramolecular and intermolecular interactions, and only ZO-1 in the extended conformation recruits the transcription factor DbpA to TJs. However, the sequences of ZO-1 that interact with CGN and CGNL1 and the role of TJ proteins in ZO-1 TJ assembly are not known. Here, we used glutathione-S-transferase pulldowns and immunofluorescence microscopy to show that CGN and …

Behavioral Choices Of Apple Snails, Pomacea Maculata, Under Varied Chemical Landscapes, Andrea Adams

Theses

Habitat choice is a critical behavior for organisms to successfully survive and reproduce. These choices are dictated by available environmental information about potential predation risks or food patches that form the organism’s sensory landscape. This study specifically focused on the behavioral choices of two invasive apple snail (Pomacea maculata) populations exposed to varying predation threats. We collected snails from Florida and Alabama which were used in laboratory experiments with varied sensory landscapes. Trials consisted of controls with no cues (FL: n = 7, AL: n= 7), an attractive treatment with introduced food cues (FL: n = 4, AL: …

Variation In Student Perceptions Of Higher Education Course Quality And Difficulty As A Result Of Widespread Implementation Of Online Education During The Covid-19 Pandemic, Joseph Cavanaugh, Stephen J. Jacquemin, Christine Junker

Biological Sciences Faculty Publications

The onset of the COVID-19 global pandemic affected higher education in a myriad of ways. One of the most notable effects however was the rapid and sudden transition of nearly all courses at most institutions to an online environment. And while there are a growing number of courses offered online already, this transition to nearly 100% remote education presented numerous challenges for instructors and students of face-to-face and hybrid style courses. Since student perceptions are closely tied to recruitment and retention, it is important to know if there are differences in student perceptions present in the way different courses are …

The Effect Of Gallate Esters On T Cell Immunity, Brianna Cervantes

Longwood Senior Theses

Parabens are used to prevent bacterial growth and are commonly found in cosmetics and personal care products. The structure of parabens is similar to estrogen and can cause increased estrogen activity which unfortunately has been linked to breast cancer. Parabens are endocrine disrupting compounds, which means they disrupt many hormone-regulated systems and could contribute to immune dysfunctions, reproductive disorders, birth defects, or developmental and behavioral disorders. One example of an effect on the immune system is that estrogen regulates CD4 T cell differentiation during pregnancy to induce anti-inflammatory Th2 and Treg phenotypes and reduce the differentiation of inflammatory Th1 and …

The Effects Of Impaired Water On Zebrafish Muscle Development And Startle Responses, Cecily Hayek

Longwood Senior Theses

For over 100 years, the presence of coliform bacteria in water has been used as environmental risk indicators for the occurrence of human pathogens (Salmonella, enteric viruses, etc.). Although these measurements typically are used to protect humans from potential exposure to toxins, little has been researched about the effect on organisms that live in these waters. Our current study utilizes a long-term water monitoring program within the Appomattox River watershed of south-central Virginia, as it examines the effect of raw water containing varying bacteria levels on the first 72 hours of aquatic vertebrate development, using a zebrafish model. Water samples …

Costimulatory Domains Alter The Efficacy And Safety Of Chimeric Antigen Receptor-Expression Gamma Delta T Cells, Stephanie Willis

Longwood Senior Theses

Engineering T cells with a chimeric antigen receptor (CAR) recognizing proteins specifically expressed on tumor cells is a new cancer therapy. While CAR T cells can successfully treat hematopoietic malignancies, CAR T cells have not shown success in treating solid tumors. In addition, one side effect observed after CAR T cell infusion is Cytokine Release Syndrome (CRS) which causes damaging inflammation. There are many factors that may enhance CAR T cell efficacy and safety for solid tumor treatment, including costimulatory domains to increase T cell functions and switching T cell type from alpha beta to gamma delta T cells. We …

Establishing A Drosophila Colon Cancer Model To Study Interactions And Therapeutic Targets Of Oncogenic Pathways, Kathleen T. Mccaslin

Honors Theses

The objective of this project is to develop an in vivo colorectal cancer (CRC) model in Drosophila melanogaster to test the role of Ras and Wnt pathways in gastrointestinal cancer as potential therapeutic targets. To do so, we have (a) developed a CRC model in flies, (b) tested the levels of Ras and Wnt pathway activity in this model, and (c) will use drugs to find inhibitors of these pathways. Using fly mutants and transgenic flies we have created small patches of cancerous cells in the fly intestine in which have activated oncogenic Ras (mutation RasV12) and dominant negative p53 …

Phylogenetic Placement Of Owl Monkey, Genus Aotus, Using Alu Retrotransposons, Morgan Brown

Honors Capstones

No abstract provided.

Characterization Of Non-Coding Alpha, Beta, And Gamma Heat Shock Tran, Lauren Meyer

Honors Capstones

No abstract provided.

Expression Of Heat Shock Proteins And Glucocorticoid Receptors In Response To Metabolic And Reproductive Stressors In The African Cichlid Fish, Astatotilapia Burtoni, Jeong Hyerin

Honors Capstones

No abstract provided.

Attenuation Of Maternal Obesity Before And During Pregnancy Restores Pro- Angiogenic Factors And Reduces Pro-Inflammatory Cytokines In The Bph/5 Mouse Model Of Preeclampsia, Brianna Rogers

Honors Capstones

No abstract provided.

Measuring Volatile Emissions From Moss Gametophytes: A Review Of Methodologies And New Applications, Danlyn L. Brennan, Leslie M. Kollar, Scott Kiel, Timea Deakova, Aurélie Laguerre, Stuart F. Mcdaniel, Sarah Eppley, Elliott T. Gall, Todd Rosenstiel

Center for Life in Extreme Environments Publications

Mosses inhabit nearly all terrestrial ecosystems and engage in important interactions with nitrogen-fixing microbes, sperm-dispersing arthropods, and other plants. It is hypothesized that these interactions could be mediated by biogenic volatile organic compounds (BVOCs). Moss BVOCs may play fundamental roles in influencing local ecologies, such as biosphere–atmosphere–hydrosphere communications, physiological and evolutionary dynamics, plant–microbe interactions, and gametophyte stress physiology. Further progress in quantifying the composition, magnitude, and variability of moss BVOC emissions, and their response to environmental drivers and metabolic requirements, is limited by methodological and analytical challenges. We review several sampling techniques with various analytical approaches and describe best practices …