Digital Commons Network^™

Repurposing Drugs To Treat Heart And Brain Illness, Maranda S. Cantrell, Alejandro Soto-Avellaneda, Jackson D. Wall, Aaron D. Ajeti, Brad E. Morrison, Lisa R. Warner, Owen M. Mcdougal

Chemistry and Biochemistry Faculty Publications and Presentations

Drug development is a complicated, slow and expensive process with high failure rates. One strategy to mitigate these factors is to recycle existing drugs with viable safety profiles and have gained Food and Drug Administration approval following extensive clinical trials. Cardiovascular and neurodegenerative diseases are difficult to treat, and there exist few effective therapeutics, necessitating the development of new, more efficacious drugs. Recent scientific studies have led to a mechanistic understanding of heart and brain disease progression, which has led researchers to assess myriad drugs for their potential as pharmacological treatments for these ailments. The focus of this review is …

Addressing A Complex Resource Conflict: Humans, Sea Otters, And Shellfish In Southeast Alaska, Sonia Natalie Ibarra

Fisheries

Complex resource conflicts may benefit from the inclusion of social-ecological systems approaches that recognize the complex linkages between humans and their environment. Competition for shared shellfish resources by sea otters and humans in Southeast Alaska has caused food security concerns, cultural and economic losses, and uncertainty about the future of various fisheries, including rural subsistence-based fisheries. In rural Alaska Native communities, access to subsistence resources are critical to maintaining a way of life, with deeply rooted knowledge systems that are tied to the land, water, and natural resources. This dissertation documents Indigenous and local knowledge of Alaska Native customary and …

The Presence Of Transposable Elements In Actinopterygii, The Ray Finned Fish, Matthew Rock

Biology Student Scholarship

Purpose: My project developed after I was introduced to the idea of horizontal gene transfer in various species. I wanted to further understand one of the largest known mechanisms of horizontal gene transfer, SINE and LINE elements. This project is centered around the analysis of Transposable Elements in various Actinopterygii populations. Transposable Elements are extremely common in The Ray Finned Fish, however analysis of their frequency and position has yet to be done in a majority of the class. I plan to identify their presence in three groups of Ray Finned Fish – Atlantic Killifish, African Cichlids, and Guppies – …

The Effect Of Circadian Phase Shifts On Cellular Respiration In Wild Type And Flies With Mutant Circadian Genes, Shannon Maguire, Michael Yarrows, Kathryn Donohue

Biology Student Scholarship

Shannon Maguire ’22, Major: Biology
Michael Yarrows ’22, Majors: Biology and Health Policy and Management
Kathryn Donohue ’22, Majors: Biology and Spanish

Faculty Mentor: Dr. Pamelas Snodgrass-Belt, Biology

Over the past semester, our team’s research has focused on circadian rhythms in wild type and mutant flies. Circadian rhythms, our body’s internal clock, are the biological processes which regulate the sleep/wake cycle as well as other physiological rhythms in all living organisms. Following a 24-hour light/dark cycle, circadian rhythms influence eating habits, physical activity, and metabolism. An organism’s circadian rhythms can be disrupted by an offset light/dark cycle, food availability, or …

Construction And Analysis Of Three Multi-Partite Synthetic Microbial Communities, Alexander J. Lazzara, Jacob K. Fanning

Honors Theses

Microbial Communities are of interest to molecular biologists hoping to understand the nature of metabolic interactions between co-existing, or possibly mutualistic, organisms. These interactions are ubiquitous in nature, but understanding the molecular mechanisms involved remains challenging and not well understood. Here, we design three tri-partite microbial circuits based on possible interactions among involved microbes, which are discussed and may suggest mutualistic interactions. Carbon and nitrogen molecular pathways and the intracellular metabolism of each microbe is discussed. We present minimal growth media that will ensure that organisms utilize available resources, which may originate from metabolic processes in neighboring microbes, simulating a …

Pectin And Alginate Extraction To Treat Liquid Cafo Manure, Clare Sunderman

Honors Projects

For this project, various extraction methods were used to extract pectin from Pastinaca Sativa and alginate from Macrocystis. These extractions were then dried and used in treating 250mL of manure along with a CaCl₂ or FeCl₃ coagulant. It was found that CaCl₂ was not as effective as FeCl₃ in coagulating manure. But the results obtained suggest that pectin and alginate obtained with a simpler extraction method is just as effective as the highly purified and refined pectin and alginate produced for the food industry, in the treatment of CAFO manure. The liquid portion of the …

Negotiating Disciplinary Literacy Instruction In Secondary Science: A Multi-Case Study, Arsenio Silva

All Dissertations

National science proficiency scores in America have failed to show significant improvement for years (www.nationsreportcard.gov, 2019). Although policy reforms have come and gone in attempt to influence these trends, Disciplinary Literacy (DL) theory currently stands center-stage as one of the most recently espoused approaches to improving students’ scientific illiteracy. However, the field of DL theory is ideologically fragmented and offers little in terms of applicable strategies for practitioners (Fang, 2012a). Consequently, enacting DL instruction requires teachers to draw on highly specialized disciplinary knowledge and experience to inform their application of an incomplete DL theoretical framework (Saraceno, 2019). Yet, research shows …

Infectious Diseases In A Warming World: Using A Modified Sir Model To Investigate The Incidence Rates Of Lyme Disease In The New England Area, Carly Sullivan

Honors Projects in Science and Technology

The effects of climate change are global and unprecedented in scale. Public health is likely to suffer as a result of the warming climate, and one particular risk is the increase in the occurrence of vector-borne diseases (VBDs) in different regions across the world. The purpose of this project is to investigate the impact of rising temperatures on the incidence rates of Lyme disease in the New England area. Following a review of the existing literature relating to the impact of climate factors on VBDs, an SIR model modified for temperature conditions will be utilized to produce several simulated scenarios. …

Stuck In Hot Water: Environmental Conditions Affecting Mysid Populations, Kristian Tomasic, Lauren Flynn, Jordan Pagliuca

Biology Student Scholarship

Kristian Tomasic ’21, Biology major
Lauren Flynn ’21, Biology major
Jordan Pagliuca ’21, Biology and Mathematics major
Faculty Mentor: Dr. Elisabeth Arévalo

Computational Modeling, Energy State Calculations, And Determination Of The Barriers To Rotation Of Atropisomeric Β-Carbolines, Lorenzo Battistoni

Chemistry & Biochemistry Student Scholarship

Major: Biochemistry
Faculty Mentor: Dr. Seann Mulcahy

Axially chiral molecules that have high barriers to rotation about a single bond are called atropisomers. This project aims to expand information on atropisomeric β-carbolines by utilizing computational chemistry to generate energy profiles and determine the barriers to rotation of a library of atropisomeric β-carboline compounds using the program Spartan. Various substituents on the atropisomeric β-carboline scaffold can impact steric strain, electronic effects, and intramolecular hydrogen bonding in the molecule. These factors can impede bond rotation. We will be able to determine which atropisomeric β-carbolines are the best suited to synthesize experimentally using …

An Investigation Of K2 Mycobacteriophage Lysin A Proteins, Ethan Dionne

Chemistry & Biochemistry Student Scholarship

Major: Biochemistry
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Elbow Motion In Walking Alligators, Thao Pham, Luciana Emmanuelli, Megan Rowlings, Nina Pitre

Biology Student Scholarship

Thao Pham ’21, Biology
Megan Rowlings ’21, Biology
Nina Pitre ’22, Biology
Luciana Emmanuelli ’23, Biology
Faculty Mentor: Dr. David Baier, Biology

Crocodylia regularly use a “high-walk” during terrestrial locomotion unlike other non-mammals, thus drawing interest from both biomechanical and evolutionary research communities. Here, we employ the highly accurate XROMM (X-ray Reconstruction of Moving Morphology) method to measure joint motion between the three forelimb bones (humerus, ulna, and radius) of alligators performing high-walks on a treadmill. This method literally “re-animates” bone motion by combining bi-planar X-ray video with digital bone models from CT scans in the animation program Maya (Autodesk).

The Big Picture: Consolidating National Government And Cites Records Of Animal Trade In The Philippines From 1975 To 2019, Ronald Allan L. Cruz, Catherine Genevieve B. Lagunzad

Biology Faculty Publications

The Philippines has exceptionally high biodiversity but is also a hotspot. It is a recognized source; destination; and transit point for the global wildlife trade; which drives biodiversity loss. There is an abundance of data from the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) on the Philippines; but this data has not been assessed for historical trends. Confiscation data reflecting the illegal trade is scarcer; coming from recent (2008 onward) records of the Department of Environment and Natural Resources ___ Biodiversity Management Bureau (DENR-BMB) and the Palawan Council for Sustainable Development (PCSD). CITES data …

Sending Mixed Signals: A Study Of The Melanocortin-1-Receptor, Savannah Simmons, Isabella Kloha, Whitney Wells

Linfield University Student Symposium: A Celebration of Scholarship and Creative Achievement

Skin tone varies considerably among humans across the world. These variations are due in part to different types of skin pigments known as melanin. The two main types of melanin are eumelanin and pheomelanin. Eumelanin, a brown/black pigment, is produced in response to ultraviolet radiation (UVR) and provides protection from harmful UV rays. On the other hand, pheomelanin is a red/yellow pigment and is not photoprotective. According to the World Health Organization, skin cancer is one of the most common forms of cancer. Individuals who produce predominantly pheomelanin typically have fair skin, red or blonde hair, are unable to tan, …

Gene Annotation Of Glys In Drosophila Species, Bronwyn M. Boyd, Hanna Shields, Lottie R. Steward, Catherine Reinke

Linfield University Student Symposium: A Celebration of Scholarship and Creative Achievement

In collaboration with scientists and undergraduate members of the Genomics Education Partnership, we are using genomic data and bioinformatics tools to engage in comparative genomics research. By analyzing sequence and gene expression data from numerous Drosophila species, we are generating gene models for orthologs of genes found in the model organism Drosophila melanogaster. A gene model is a representation of a gene’s exons and introns (coding and noncoding regions). We are building and analyzing gene models in their genomic context. The gene models we produce are illuminating the evolution of the structure and function of the insulin signaling pathway, …

The Effect Of Antibiotic Selective Pressure On Mdr1 And Asct2 Expression In Human Hepatocellular Carcinoma, Isabella G. Guizzetti, Barrie P. Bode, Paige Jay Bothwell

Honors Capstones

Our laboratory has used the CRISPR-Cas9 gene editing system to eliminate the expression of the SLC1A5 gene, which encodes the ASCT2 amino acid transporter, which is implicated in driving the glutamine-dependent growth of several cancers. At last year’s URAD event, the isolation of clones confirmed for knockout (KO) of ASCT2 in two human hepatocellular carcinoma (HCC) cell lines – Huh7 and SK-Hep1 - was described. As these ASCT2 knockout (ASCT2KO) cell lines are currently being deployed in studies assessing the role of this transporter in tumorigenesis, we asked two fundamental questions: 1) Does the removal of antibiotic selective pressure – …

Sciadopitys Verticillata (Japanese Umbrella Pine), #1065-1067, Grace C. Kubat

BIO 140 Arboretum Project

Over the course of the 2021 spring semester, I observed a grove of Japanese Umbrella Pines. These trees are a part of the University's arboretum. In addition to making weekly observations, I researched the cultural significance of the Umbrella Pines. My research will hopefully contribute to future projects regarding the trees and help to enrich the University's arboretum project.

An Alternative Approach To Nucleic Acid Memory, George D. Dickinson, Golam Md Mortuza, William Clay, Luca Piantanida, Christopher M. Green, Chad Watson, Eric J. Hayden, Tim Andersen, Wan Kuang, Elton Graugnard, Reza Zadegan, William L. Hughes

Materials Science and Engineering Faculty Publications and Presentations

DNA is a compelling alternative to non-volatile information storage technologies due to its information density, stability, and energy efficiency. Previous studies have used artificially synthesized DNA to store data and automated next-generation sequencing to read it back. Here, we report digital Nucleic Acid Memory (dNAM) for applications that require a limited amount of data to have high information density, redundancy, and copy number. In dNAM, data is encoded by selecting combinations of single-stranded DNA with (1) or without (0) docking-site domains. When self-assembled with scaffold DNA, staple strands form DNA origami breadboards. Information encoded into the breadboards is read by …

Density Dependent Growth Of Pseudomonas Fluorescens In The Presence And Absence Of C. Elegans Predation In Liquid Media, Jack Landmann

Honors Theses

The purpose of this study was to understand the predator-prey relationship between C. elegans worms and P. fluorescens bacteria in liquid media. We were aiming to create a predation model of the relationship between these two species.

This study was performed through three experiments. Using 96-well plates, we were able to measure the change in optical density (OD) of these wells and calculate the growth rate. This growth rate was then graphed and analyzed. The first experiment contained P. fluorescens and KB liquid media, this study demonstrated that the bacterial population has a carrying capacity. We were also able to …

Evaluation Of Online Lab Platforms Against Best Practices For An Undergraduate Neurobiology Course, Maria Wallace

Celebrating Scholarship and Creativity Day (2018-)

No abstract provided.

Fagus Sylvatica (European Beech), #1009, Megan L. Trafford

BIO 140 Arboretum Project

No abstract provided.

Tilia Cordata (Littleleaf Linden) #1059, Heather Noel Mckee

BIO 140 Arboretum Project

In this paper I studied the Tilia cordata, more commonly known as the Littleleaf Linden, over the course of three months. I included the history and uses of the Linden tree along with its symbolic value in European culture. This tree symbolizes friendship and peace which coincides with the critical concerns of the Sisters of Mercy.

Zoo And Aquarium Animal Welfare, Michael Cerbo

Library Impact Statements

No abstract provided.

Morphological And Biological Variation Of The Self Progeny Of Pennisetum Purpureum, Chenglong Ding, Hongru Gu, Nengxiang Xu

IGC Proceedings (1977-2023)

No abstract provided.

Black Apollo Of Science: The Life Of Ernest Everett Just - Summarizing Timeline, Sumitography And Concept Poster, Lillie R. Jenkins

Perkins Faculty Research and Special Events

This two-part chronology is based on Kenneth R. Manning’s biography, Black Apollo of Science: The Life of Ernest Everett Just (1983). Like other such timelines, this one details Just’s life and pioneering research work. Additionally, and distinctively, this timetable lays out Just’s pioneering fund-seeking and his work mentoring African American female co-researchers (Part 1). A sumitography featuring the United States Postal Service’s postage stamp (1996) recognizes Just’s innovative thinking in biology (Part 2). Following this logic, the author includes a proof-of-concept poster commending E.E. Just’s work as a forward-thinking administrator. This timeline summarizes, chronicles, and aims to re-frame Just’s …

Examining Arctic Melt Pond Dynamics Via High Resolution Satellite Imagery, Austin Abbott, Victoria Hill

College of Sciences Posters

The Arctic Ocean is a rapidly changing environment, and a key observational system for monitoring climate change. The Arctic is going under a rapid transition from thicker, multi-year ice, to thinner first-year ice, that may have many potential consequences. As first year Arctic sea ice begins to retreat in the spring and early summer, melting snow and ice form ponds on the surface- “melt ponds”. These melt ponds increase light transmission to the water column, resulting in warming and increased primary production under the ice. Recent advances in high resolution satellite imagery now allow us to monitor the development and …

Tracking Single Cell Lineages In Saccharomyces Cerevisiae, Guste Urbonaite

Yale Graduate School of Arts and Sciences Dissertations

The ability to measure the number of gene-specific mRNA molecules in individual mammalian cells has transformed the transcriptomics field. Among the key technologies enabling single-cell mRNA sequencing has been Droplet Sequencing (Drop-Seq). While this method works efficiently for mammalian cells, its direct application to yeast cells has been problematic due to cell-type specific differences such as size, doublet formation rate, and cell wall. Here we introduce yeast DropSeq, a single-cell RNA sequencing method for the study of transcriptomics in yeast. I modified and optimized the original Drop-Seq method to address the issues that emerged from smaller cell sizes and the …

Genomic Analysis Of Rare Human Diseases, Weilai Dong

Yale Graduate School of Arts and Sciences Dissertations

Many rare human diseases have a strong genetic basis. Rare germline and somatic mutations exert risks to Mendelian diseases and cancer, respectively. The development of next-generation sequencing and genomic analysis approaches facilitate the characterization of rare causal variants to human diseases. This thesis describes the genomic approaches to identify underlying genetic factors in three rare human diseases focusing on analysis of three distinct genetic mechanisms: congenital heart disease caused by recessive genotypes, congenital hydrocephalus caused by dominant genotypes, and uterus leiomyosarcoma, caused by somatic mutations. Congenital heart disease (CHD) is a structural malformation of the heart and great vessels present …

Comparing Expression Of Green Fluorescent Protein (Gfp) With Different Plasmids, Tinsae Alem, Charles Curbeam, Mackenzie Woody

Spring Showcase for Research and Creative Inquiry

How do different plasmids carrying different promoters affect the Green Fluorescent Protein (GFP) expression? If the appropriate promoter is not used within the bacterias, then the bacterias will not be able to survive and glow.

Techniques Learned By Students To Determine Which Agar Coated Plates Will Show Bacterial Growth And Glow., Lilly Rogers, Hannah Spencer

Spring Showcase for Research and Creative Inquiry

The process in which students conducted a series of experiments to find if agar plates would produce the GFP gene.