Digital Commons Network^™

Annotation Of The Microtubule Star (Mts) Gene In Drosophila Ananassae Using Drosophila Melanogaster As A Reference Organism For Comparative Genomics, Danesh Khazaei, Catherine Reinke

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

Our lab is using comparative genomics protocols to explore the evolution of the insulin-like signaling pathway in Drosophila species spanning 40M years of evolution. This project aims to annotate an ortholog of the Drosophila melanogaster gene microtubule star (mts) in the incompletely characterized Drosophila ananassae genome. Genome annotation is the process of creating gene models, or labelling areas of interest in a species’ genome for further investigation, using genome comparisons and large data sets characterizing gene expression, which is the production of RNA from select regions of genomic DNA. We are using comparative genomics and bioinformatics protocols to …

Modulation Of Voltage-Gating And Hysteresis Of Lysenin Channels By Cu2+ Ions, Andrew Bogard, Pangaea W. Finn, Aviana R. Smith, Ilinca M. Flacau, Rose Whiting, Daniel Fologea

Physics Faculty Publications and Presentations

The intricate voltage regulation presented by lysenin channels reconstituted in artificial lipid membranes leads to a strong hysteresis in conductance, bistability, and memory. Prior investigations on lysenin channels indicate that the hysteresis is modulated by multivalent cations which are also capable of eliciting single-step conformational changes and transitions to stable closed or sub-conducting states. However, the influence on voltage regulation of Cu²⁺ ions, capable of completely closing the lysenin channels in a two-step process, was not sufficiently addressed. In this respect, we employed electrophysiology approaches to investigate the response of lysenin channels to variable voltage stimuli in the presence …

Suitability And Nutritional Analysis Of Spotted Lanternfly Habitats, Kathryn Hickey

Biology Student Scholarship

The spotted lanternfly is an invasive bug that has recently started taking over the Northeastern US, and has even made it to Rhode Island. Although this species is intriguing with its bright red back and spots, it is hurting native plant species and the agriculture industry by feeding on crops, like grapes and cherries. It uses a tongue-like mouthpart to pierce through the plant and feed directly on the sap inside. This punctures plant stems and causes them to drip sap, wither, and even mold. The lanternfly’s most preferred host plant is the invasive tree-of-heaven, which grows and spreads quickly …

Effect Of Decreased Snowfall During An Atypical Winter On A Rare Butterfly’S Host Plant, Breelyn Gilbert

Biology Student Scholarship

In the Northeastern US, one result of climate change is decreased snowfall and earlier snowmelt. Such changes can alter the relationship between climate and the timing of cyclical biological phenomena— the phenology of organisms. This is especially concerning for species that interact with one another such as butterflies and their host plants. For this study, I focused on the host plant of the rare frosted elfin butterfly. The frosted elfin is a species of concern in RI, MA, and CT, among 8 other states, and they are a host plant specialist only laying eggs on yellow wild indigo (Baptisia …

The Effect Of Integrated Pest Management On Honey Bee Behavior And Colony Level Health, Kaitlyn Bresnahan

Biology Student Scholarship

Honey bees are the world’s most commercially valuable pollinators, and they face many threats. The greatest challenge facing honey bees is Varroa mites, which are parasitic mites that feed on bees’ fat bodies, killing bees and spreading diseases. While chemical treatments are available to stop the spread of mites, these treatments are insecticides, which are not ideal to put in a hive of insects. A popular organic method of mite management is using drone comb. Drone brood is preferentially chosen by mites for ovipositing and development because of its larger size and longer development time, so removing drone brood can …

Diversity Of Bees In Trees And Their Foraging Preferences On An Urban College Campus, Aidan Castricone

Biology Student Scholarship

Pollinators collect nutrients from blooming flowers; pollen provides proteins and fats, nectar provides carbohydrates. The few plants that bloom during early Spring are trees such as crabapple (Malus sp). Current research however, mainly focuses on pollinators that forage on the ground and overlooks pollinators foraging in the canopy of trees. Past research showed increased generalization of pollen foraging in bees as seasons move from spring to summer. Here I identified which bee species forage in the canopy on Providence College campus and will analyze the pollen collected using microscopy. This data can inform more specific research on diet breadth, …

Hypo-Osmotic Stress And Pore-Forming Toxins Adjust The Lipid Order In Sheep Red Blood Cell Membranes, Rose Whiting, Sevio Stanton, Maryna Kucheriava, Aviana R. Smith, Matt Pitts, Daniel Robertson, Jacob Kammer, Zhiyu Li, Daniel Fologea

Physics Faculty Publications and Presentations

Lipid ordering in cell membranes has been increasingly recognized as an important factor in establishing and regulating a large variety of biological functions. Multiple investigations into lipid organization focused on assessing ordering from temperature-induced phase transitions, which are often well outside the physiological range. However, particular stresses elicited by environmental factors, such as hypo-osmotic stress or protein insertion into membranes, with respect to changes in lipid status and ordering at constant temperature are insufficiently described. To fill these gaps in our knowledge, we exploited the well-established ability of environmentally sensitive membrane probes to detect intramembrane changes at the molecular level. …

Targeting Energy Intake And Circadian Biology To Engage Mechanisms Of Aging In Older Adults With Obesity: Calorie Restriction And Time-Restricted Eating, Satchidananda Panda, Geraldine Maier, Dennis T Villareal

Faculty, Staff and Students Publications

With the rise in obesity across age groups, it has been a hindrance to engaging in physical activity and mobility in older adults. Daily calorie restriction (CR) up to 25% has been the cornerstone of obesity management even though the safety in older adults remains incompletely understood. Although some adults can follow CR with clinically significant weight loss and improved health metrics, CR faces 2 obstacles-many fail to adopt CR and even among those who can adopt it short term, long-term compliance can be difficult. Furthermore, there is a continuing debate about the net benefits of CR-induced weight loss in …

Clinical Significance And Biology Of Circulating Tumor Dna In High-Risk Early-Stage Her2-Negative Breast Cancer Receiving Neoadjuvant Chemotherapy, Mark Jesus M Magbanua, Lamorna Brown Swigart, Ziad Ahmed, Rosalyn W Sayaman, Derrick Renner, Ekaterina Kalashnikova, Gillian L Hirst, Christina Yau, Denise M Wolf, Wen Li, Amy L Delson, Smita Asare, Minetta C Liu, Kathy Albain, A Jo Chien, Andres Forero-Torres, Claudine Isaacs, Rita Nanda, Debu Tripathy, Angel Rodriguez, Himanshu Sethi, Alexey Aleshin, Matthew Rabinowitz, Jane Perlmutter, W Fraser Symmans, Douglas Yee, Nola M Hylton, Laura J Esserman, Angela M Demichele, Hope S Rugo, Laura J Van 'T Veer

Faculty, Staff and Student Publications

Circulating tumor DNA (ctDNA) analysis may improve early-stage breast cancer treatment via non-invasive tumor burden assessment. To investigate subtype-specific differences in the clinical significance and biology of ctDNA shedding, we perform serial personalized ctDNA analysis in hormone receptor (HR)-positive/HER2-negative breast cancer and triple-negative breast cancer (TNBC) patients receiving neoadjuvant chemotherapy (NAC) in the I-SPY2 trial. ctDNA positivity rates before, during, and after NAC are higher in TNBC than in HR-positive/HER2-negative breast cancer patients. Early clearance of ctDNA 3 weeks after treatment initiation predicts a favorable response to NAC in TNBC only. Whereas ctDNA positivity associates with reduced distant recurrence-free survival …

It Is Better To Light A Candle Than To Curse The Darkness: Single-Cell Transcriptomics Sheds New Light On Pancreas Biology And Disease, Amelia T Cephas, William L Hwang, Anirban Maitra, Oren Parnas, Kathleen E Delgiorno

Faculty, Staff and Student Publications

Recent advances in single-cell RNA sequencing and bioinformatics have drastically increased our ability to interrogate the cellular composition of traditionally difficult to study organs, such as the pancreas. With the advent of these technologies and approaches, the field has grown, in just a few years, from profiling pancreas disease states to identifying molecular mechanisms of therapy resistance in pancreatic ductal adenocarcinoma, a particularly deadly cancer. Single-cell transcriptomics and related spatial approaches have identified previously undescribed epithelial and stromal cell types and states, how these populations change with disease progression, and potential mechanisms of action which will serve as the basis …

Deep Learning For Skin Photoaging, Gokul Srinivasan

Computer Science Senior Theses

Skin photoaging is the premature aging of skin that results from ultraviolet light exposure. It is a major risk factor for the development of skin cancer, among other malignant skin pathologies. Accordingly, understanding its etiology is important for both preventative and reparative clinical action. In this study, skin samples obtained from patients with ranging solar elastosis grades – a proxy for skin photoaging – were sequenced using next-generation sequencing techniques to further understand the genomic, epigenomic, and histological signs and signals of skin photoaging. The results of this study suggest that tissues with severe photoaging exhibit increases in the frequency …

Exploring The Intersection Of Biology And Design For Product Innovations, Ajay P. Malshe, Salil Bapat, Kamlakar Rajurkar, Ang Ang, Jean-Marc Linares

Department of Mechanical and Materials Engineering: Faculty Publications

Design, development, productization, and applications of advanced product concepts are pressing for higher multifunctionality, resilience, and maximization of available resources equitably to meet the growing and continuing demands of global customers. These demands have further accelerated during the recent COVID- 19 pandemic and are continuing to be a challenge. Engineering designs are one of the most effective ways to endow products with functions, resilience, and sustainability. Biology, through millions of years of evolution, has met these acute requirements under severe resource and environmental constraints. As the manufacturing of products is reaching the fundamental limits of raw materials, labor, and resource …

Does Artificial Lighting Cause Sea Turtle Hatchling Disorientations?, Kate Hickey

Biology Student Scholarship

Sea turtle hatchlings run into obstacles from the minute they emerge from their shell. They have a 1 in 1,000 survival rate and new obstacles are on the horizon. Coastal development is increasing and is not planning on slowing down. It supports and funds tourism, but has some negative implications on the wildlife that uses this area, like sea turtles. A particular problem with development is the artificial lighting it emits which is effecting sea turtles nesting. When the hatchlings emerge from the nest, they use the horizon and moon to guide them in the direction of the sea. The …

The Effect Of Nuclear Power On Carbon Intensity, Lukas Mullaney

Biology Student Scholarship

The world is currently facing one of the biggest threats to the environment in its history: the warming of the Earth’s surface due to climate change. One major contributor is the release of greenhouse gases, such as carbon dioxide, into the atmosphere by humans. To reduce these emissions, countries are making a concerted effort to invest in more sustainable energy sources. Nuclear power is one green energy source that can potentially support the transition to lower carbon emissions. Nuclear power plants release no carbon emissions during the generation of electricity. The only emissions are a result of maintenance, such as …

Effect Of Natural Disasters On Coastal Human Populations Of The Southeastern U.S., Caitlin Mchugh

Biology Student Scholarship

Due to climate change, extreme weather events and natural disasters are becoming more prevalent, and the severity of these events is increasing (Sheldon & Zhan, 2022). Over the last 40 years, the number of billion-dollar natural disasters has gone up. The U.S, averaged 3 billion-dollar disasters per year in the 1980s compared to the average 13 per year in the 2010s (USAFacts, 2023). With natural disasters comes loss of life, infrastructure, and resources that can leave a physical and economic toll on communities for many years if not generations. While some global studies have found that natural disasters increase households’ …

The Effect Of Water Temperature On Tiger Shark Location, Philip Gelso

Biology Student Scholarship

The tiger shark is a keystone species in its ecosystem. As an apex predator, the tiger shark keeps the entire ecosystem in balance such as maintaining seagrass and coral reef habitats. The rise of ocean surface temperatures have become an issue over the past decades due to the increase in energy from the sun trapped by greenhouse grasses. This change in ocean surface temperature can have detrimental impacts on the ocean environment and the life cycles of many species including the tiger shark. Therefore, this project evaluates the change in location of tiger sharks in relation to water temperature.BIO …

Element Levels In Soil Depend On Elevation, Sean Harris

Biology Student Scholarship

Elements, such as arsenic, copper, phosphorus, and calcium, in soil can help biological processes if content levels are not too low or excessive. Arsenic in soil is toxic at high levels and so too much is harmful to vegetation. Copper is important for plants because it helps with chlorophyll and seed production. Phosphorus helps with plant growth, especially for new seedlings. Calcium in soil is not completely needed at high levels, but it does strengthen plants’ health. However, with factors such as different environments, average precipitation levels, and elevation levels in different counties in the Northeast, element content level differ. …

Land And Energy, Devan Viani

Biology Student Scholarship

Land use has and will continue to be a complicated topic. We need land to succeed as a country and a species, but it is equally as important to keep the land as pristine as possible to not affect natural ecosystems. As population continues to increase, urbanization and economic growth has inevitably had an impact on climate change.¹ Parallel to an increase in land development is an increase in power generation. As cities grow, technology evolves, and energy use goes up. With this increase in technology, new sources of power generation are emerging. While fossil fuels have always been the …

Precipitation Effects On Butterfly Species Richness, Maggie Ritchie

Biology Student Scholarship

Butterflies are important pollinators that have been impacted due to climate change(1). Studies have looked at how the increasing temperatures and precipitation due to climate change may be playing a role in decreasing populations among some species in Mediterranean climates(2). However, the effects of precipitation have not been considered when looking at changing butterfly populations around the United States. Therefore, increasing precipitation amounts due to climate change may contribute to the decreasing populations of butterflies in Massachusetts.BIO 340 final project

The Impact Of Age And Catch Location On The Mortality Rates Of Striped Bass, Owen Finnegan

Biology Student Scholarship

Striped bass are one of the most popular and sought-after gamefish in the United States for recreation and commercial fishermen. This popularity comes from their size, with many fish reaching 40+ pounds, a prominent dish in seafood restaurants, and their expansive habitat as they inhabit waters from Florida to Canada (1). During the late 1970s/80s, the population began sharply declining due to overfishing, and governments enacted regulations to stabilize the population (1). However, as of 2020, overfishing is still occurring, and regulations are continuously evolving (1). Each state has their own rules and regulations for possessing striped bass for commercial …

Does More Pollen Mean More Sneezing?, Diraliz Cruz

Biology Student Scholarship

Every year millions of people suffer from seasonal allergies, according to the CDC about 25% of adults have to deal with these allergies. Pollen comes from all different things like trees, grasses, and weeds and as climate change increases annually the amount of pollen released into the air also increases. Research has shown that climate change has specifically impacted the amount of birch and oak pollen released annually. Although there is data to show that there has been an increase in pollen release there is little to no information on if the prevalence of allergies has increased or decreased along …

The Influence Of Sampling Frequency On Bee Species Richness, Courtney Caccamo

Biology Student Scholarship

As one of Earth’s most valuable pollinators, bees provide important pollination services to wild plant species and crops alike (Winfree 2010). But, in recent years, bee populations appear to be declining due to a variety of anthropogenic drivers (Potts et al. 2010). Quantifying the extent of bee population decline is difficult because there is currently a lack of a standardized protocol for how best to survey bee populations (Tepedino & Portman 2021). One of the commonly used survey methods is pan trapping, which involves leaving out yellow, white, and blue bowls filled with soapy water to passively sample the species …

Throwing Away The Late Work Penalty, Anthony Orttel

Dissertations, Theses, and Projects

Abstract

This 2023 study examines the academic effects of a penalty-free late work policy. The study focuses on whether taking away penalties for late work significantly decreases the number of missing assignments at the end of an academic quarter. During the third quarter of the 2022/2023 academic school year, students will not receive point deductions for turning in late work. This research took place in South Florida and included approximately 50 10^th grade biology students. Data and results from the study will follow.

Creativity In Biology, Denisse Emeterio

Writing Waves

No abstract provided.

Forecasting Natural Regeneration Of Sagebrush After Wildfires Using Population Models And Spatial Matching, Andrii Zaiats, Megan E. Cattau, David S. Pilliod, Rongsong Liu, Juan Miguel Requena-Mullor, Trevor Caughlin

Human-Environment Systems Research Center Faculty Publications and Presentations

Context Addressing ecosystem degradation in the Anthropocene will require ecological restoration across large spatial extents. Identifying areas where natural regeneration will occur without direct resource investment will improve scalability of restoration actions.

Objectives An ecoregion in need of large scale restoration is the Great Basin of the Western US, where increasingly large and frequent wildfires threaten ecosystem integrity and its foundational shrub species. We develop a framework to forecast where postwildfire regeneration of sagebrush cover (Artemisia spp.) is likely to occur within the burnt areas across the region (>900,000 km²).

Methods First, we parameterized population models …

The Developing Effects Of Potassium Ferricyanide On Tetrahymena, Katelyn Coronell

Whittier Scholars Program

Potassium Cyanide is a highly toxic chemical asphyxiant that interferes with the body's ability to use oxygen, typically by directly affecting the body by ingestion, inhalation, skin contact, or eye contact(CDC, 2011). Due to its high toxicity, the main effect that leads to the downfall of the organism begins with the cessation of aerobic metabolism; it does this by cyanide binding to the ferric ions and inhibiting cytochrome oxidase within the mitochondria (Zhang, 2015). There are no physical dangers the substance causes. Although, there are many chemical dangers. If used at temperatures higher than 70℉ The substance may produce toxic …

Use Of Vocabulary Strategies To Aid English Language Learners In A General Education Biology Classroom, Virginia Perry

All Dissertations

The demographics of the typical American classroom continue to present as a more diverse student population with the increase of English Language Learners (ELL) entering public schools. General education teachers on a secondary level are challenged with incorporating academic language instruction into content instruction for ELLs. Many of these teachers seek appropriate instructional strategies to teach ELLs academic language skills related to literacy to comprehend the specific content taught at the secondary level. A deeper understanding of language and skill acquisition within a secondary classroom can help guide future efforts in implementing effective literacy strategies to address ELLs’ academic language …

Extranodal Tumors And Chromosomal Abnormalities Associated With Non-Hodgkin Lymphoma In T(14;18)-Positive Patients, Alexis Finch

Honors Program: Senior Projects (Public)

Nebraska is mostly an agricultural state with a non-Hodgkin lymphoma (NHL) incidence rate of 20.1 per 100,000 individuals, which is greater than the US incidence rate of 19 per 100,000 individuals. It is possible that the higher incidence rate in Nebraska is due to an increase in pesticide usage. Pesticide exposure is linked to t(14;18), a genetic translocation involving the BCL2 gene that regulates apoptosis. The dysregulation of apoptosis could contribute to the proliferation of NHL. This exploratory study utilized the Nebraska Lymphoma Study Group, which consists of patients with non-Hodgkin lymphoma, Hodgkin disease, or some other neoplastic hematologic disorder …

Investigating The Nectar Preferences Of Bumblebees While Foraging: Are Total Responses A Good Metric?, Alexander Entwistle, Becky Hansis-O'Neill, Aimee Dunlap Dr

Undergraduate Research Symposium

The declining population of bumblebees worldwide poses an unmistakable threat to ecological systems and biodiversity. Therefore, a deep understanding of the factors at play when bees are foraging is crucial to conservation efforts. This research aims to explore the energy that foraging bumblebees are willing to expend at a known food source after the food has stopped, and if these responses reveal sugar concentration preferences. In this experiment a novel approach was used, adapted from psychology research on addiction, to measure bee’s preferences for different concentration of sugar-water (nectar). First, how many rewards the bees earned if they were given …

Automated Classification Of Pectinodon Bakkeri Teeth Images Using Machine Learning, Jacob A. Bahn

MS in Computer Science Project Reports

Microfossil dinosaur teeth are studied by paleontologists in order to better under- stand dinosaurs. Currently, tooth classification is a long, manual, error-ridden process. Deep learning offers a solution that allows for an automated way of classifying images of these microfossil teeth. In this thesis, we aimed to use deep learning in order to develop an automated approach for classifying images of Pectinodon bakkeri teeth. The proposed model was trained using a custom topology and it classified the images based on clusters created via K-Means. The model had an accuracy of 71%, a precision of 71%, a recall of 70.5%, and …