Life Sciences Commons^™

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 …

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 …

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 …

Understanding The Expression And Role Of Pros-1 In The Male Gonad Of C. Elegans, Jack Bozik

Undergraduate Theses

The gene pros-1 is a transcription factor that is highly expressed within neuronal sheath cells, glial cells, and excretory canal cells. pros-1 plays a role in cell determination of those cell types in the nematode C. elegans, which promotes organismal development. But the degree to which pros-1 presence is important is still not fully understood, because there are many genes involved in development that when mutated or damaged can result in unexpected phenotypes or even total loss of function to a certain developmental mechanism. What makes pros-1 valuable to research is that it is a functional homologue to a …

Microplastics’ Effects On Painted Lady Butterfly Survivorship, Migratory Behavior, And Fecundity, Kaelin Ferland

Biology Student Scholarship

Kaelin Ferland ’23
Major: Environmental Biology
Faculty Mentor: Dr. Rachael Bonoan, Biology

Human activity is affecting our planet at a microscopic level. In 2021, scientists first discovered microplastics in honeybees. Subsequent research has found that honeybee gut bacteria concentrations decrease because of microplastic ingestion, decreasing honeybee survivorship. The same might be true for other insect pollinators including butterflies. When butterflies visit flowers to feed, they simultaneously collect pollen on their wings. Due to the similar particulate structure of pollen and microplastics, it’s possible that butterflies collect microplastics in addition to food. We used painted lady butterflies to investigate if microplastics …

The Predation Resistance Of Squashed E. Coli, Kathryn Mulvey, Caroline Zielinski

Biology Student Scholarship

Kathryn Mulvey ’23, Major: Biology

Caroline Zielinski ’23, Major: Biology

Faculty Mentor, Dr. Laura Williams, Biology

Predatory bacteria hunt and kill other bacteria, including pathogens that cause disease in humans, which makes them a promising alternative for treating antibiotic-resistant bacterial infections. Currently, it is unknown whether and how pathogens evolve resistance to predation. To investigate this, we are studying interactions between E. coli, which is a model organism for pathogenic bacteria, and predatory Bdellovibrio. When we co-cultured E. coli with a particular strain of predatory Bdellovibrio, we observed the emergence of predation-resistant E. coli that had reduced susceptibility to killing …

See You Later Alligator: Forelimb And Wrist Of Alligators Walking The Treadmill, Erin Trammell, Inthavha Singharaj, Sasha Rudich

Biology Student Scholarship

Erin Trammell ’23, Major: Biology

Inthavha Singharaj ’23, Major: Biology

Sasha Rudich ’23, Major: Biology, Minors: Women and Gender Studies

Faculty Mentor: Dr. Daivd Baier, Biology

We used XROMM, which combines biplanar X-ray video and digital bone models, to measure how the alligator skeleton moves during high walks on a treadmill. The crocodilian high walk and wrist structure are unique compared to other reptiles who walk with a sprawled limb posture. Here, we describe how bones of the forearm, wrist, and hand coordinate during alligator strides. We find that elbow is more than just a simple hinge, the forearm bones …

The Evolution Of Pollution Resistance In The Atlantic Killifish, Matthew Rock

Biology Student Scholarship

Matthew Rock ’23
Major: Environmental Biology
Faculty Mentor: Dr. Jeffrey Markert, Biology

We examined genetic variation in Atlantic Killifish populations to better understand their ability to persist in Superfund sites like New Bedford Harbor, which is polluted with a mix of organic toxicants and heavy metals. As predicted, loci associated with the Aryl Hydrocarbon Receptor (AHR) Detoxification Pathway show large differences in allele frequencies between polluted and non-polluted sites.

Genetic Disruption Of Metabolic Balance In Mouse Cerebellar Neurons Causes Deficits In The Postnatal Development Of Their Dendritic Tree And Mouse Motor Skills, Hayden Lens, Mary Boghos

Biology Student Scholarship

Hayden Lens ’23, Major: Biology

Mary Boghos ’23, Major: Biology

Faculty Mentor: Dr. Ileana Soto Reyes, Biology

The Npc1nmf164 mutant mouse is an animal model for the human disease Niemann-Pick type C (NPC). NPC is a lysosomal storage disease that is acquired by autosomal recessive inheritance. It is mostly caused by mutations in NPC1, a protein that transports cholesterol out of the lysosomes, therefore abnormal accumulation of cholesterol in lysosomes is a hallmark of NPC. Cerebellar Purkinje cells (PCs) are severely affected by NPC, in fact, PCs degenerate first and to a larger extent at childhood stages. Therefore, we have …

Circadian Rhythm Effects Of Social Jetlag And Exercise On Stress Levels And Weight Change Of Fischer Rats, Brian Schwalm

Biology Student Scholarship

Brian Schwalm ’23
Major: Biology
Minor: Economics
Faculty Mentor: Dr. Pamela Snodgrass, Biology

Diversity Of Bees In Trees On Urban College Campus, Aidan Castricone, Courtney Caccamo

Biology Student Scholarship

Aidan Castricone ’24, Major: Environmental Biology

Courtney Caccamo ’23 Majors: Environmental Biology and Psychology

Faculty Mentor: Dr. Rachael Bonoan, Biology

It is well known that insect pollinator populations are declining and a lack of nutrients (i.e flowering plants) may be contributing to this decline. Insect pollinators forage for pollen and nectar, which provides proteins, fats, and carbohydrates, from flowering plants. Current research on pollinator foraging behavior focuses on pollinators that forage on the ground thus overlooking those that forage in trees. Trees such as Kousa dogwood (Cornus kousa) and crabapple (Malus sp.) bloom in early Spring, even before …

Circadian Rhythms Effect On Brain Metabolism In Mutant Flies, Olivia Kozub

Biology Student Scholarship

Olivia Kozub ’23
Major: Biology
Faculty Mentor: Dr. Pamela Snodgrass, Biology

All organisms have an internal clock that drives physiological processes known as circadian rhythms. Being able to predict the environment and prepare for it, rather than simply react, is so critical to survival that this ability has been conserved from single cell organisms all the way to humans. These rhythms can be measured at the gene level, the protein level, the cellular level, the tissue level, all the way to oscillations in behavior. Measuring the metabolic activity of normal fly brains at different times of day will chart the …

Analyzing Behavior In Flies Modeling Frontotemporal Dementia, Colin Mcnulty, Julia Bonavolonta, Connor Barber

Biology Student Scholarship

Colin McNulty ’24, Major: Biology

Julia Bonavolonta ’24, Majors: Biology and Spanish

Connor Barber ’24, Major: Biology

Faculty Mentor: Dr. Marla Tipping, Biology

In this project, the goal is to be able to study the behavioral differences in Drosophila melanogaster who model the neurological disease frontotemporal dementia (FTD). Flies modeling FTD are placed into multiple different tubes and loaded into an activity monitor; the same is done with control flies who do not model FTD. Over time, this machine tracks sleep cycles, movement, eating habits, and other behaviors. These results are filed into a computer where they then are then …

Be Happy, But Not Too Happy: Taiwanese And American Childrearing Differences In Regulation Of Ideal Affect., Samantha Dietel

Biology Student Scholarship

Samantha Dietel ’23
Majors: Psychology and Elementary/Special Education
Faculty Mentor: Dr. Smaranda Lawrie, Psychology

Comparison Of Globalfiler Pcr Amplification Inhibition Due To Humic Acid And Canine Dna, Mckinzie Bundy

Honors Projects

To obtain a DNA profile from a crime scene sample, the DNA must undergo amplification through the Polymerase Chain Reaction (PCR). The PCR process can be inhibited by factors that increase DNase I activity or by factors that interfere with Taq polymerase binding to the DNA. This study compares inhibition to the PCR process caused by dog DNA with inhibition caused by humic acid. The GlobalFiler PCR Amplification Kit was tested using mixtures of dog DNA and human control DNA and mixtures of humic acid and human control DNA. The profiles obtained from these mixtures were then analyzed for instances …

Lesson Plans In Astronomy, Ecology And Biology, Admin Stem For Success

STEM for Success Showcase

This document contains various lesson plan ideas for concepts within the fields of biology, ecology, astronomy, and geology.

Plant Maze, Admin Stem For Success

STEM for Success Showcase

Students plant bean sprouts to observe their growth.

Transcriptional Silencing Of Cdk18 And Its Role In Lung Carcinogenesis Of Brg1-Mutant Lung Cancers, Loryn M. Phillips

Biology ETDs

BRG1 is mutated in 10% of lung cancers, making this mutation clinically relevant. The downstream effects of BRG1 included significantly affecting the cell cycle control and chromosomal replication pathway. CDK18, a cyclin-dependent kinase, was determined to be the gene with significantly decreased expression (p < 0.0001) in the cell cycle control and chromosomal replication pathway. CDK18 is active during the S-phase of the cell cycle and required for genomic stability. Studies were conducted to determine the epigenetic mechanisms that contributed to the repression of CDK18. Histone methylation contributes to the repression of CDK18, and histone deacetylation globally regulates expression of CDK18, while cytosine methylation was found to not contribute to CDK18 expression. Studies were performed to elucidate CDK18 functional role lung carcinogenesis and the genome-wide impact of CDK18 repression. Repression of CDK18 affects cell migration, proliferation, cell-cell signaling, and anchorage-independent growth that contribute to cancer initiation and progression.

The Science Of Baking Bread, Admin Stem For Success

STEM for Success Showcase

Activity plan to teach biology and chemistry using a lesson on the baking of bread.