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Variational Principles In Statistical Mechanics And Their Application In Biology And Evolution, Luca Agozzino

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The Maximum Entropy Principle (Max Ent) was introduced by E.T. Jaynes in 1957 as a method to infer the most likely probability distribution given some known partial information about data. This principle was given a theoretical grounding by Shore and Johnson in 1980, who framed it in terms of self-consistency conditions on the laws of probability themselves. They showed how the concept of entropy and its maximization is not limited to equilibrium thermal systems. More recently, it has been extended to non-thermal systems at equilibrium as well as dynamical systems. After a brief overview of the principle itself, and its …

Temporary Membrane Permeabilization Via The Pore-Forming Toxin Lysenin, Nisha Shrestha, Christopher A. Thomas, Devon Richtsmeier, Andrew Bogard, Rebecca Hermann, Malyk Walker, Gamid Abatchev, Raquel J. Brown, Daniel Fologea

Physics Faculty Publications and Presentations

Pore-forming toxins are alluring tools for delivering biologically-active, impermeable cargoes to intracellular environments by introducing large conductance pathways into cell membranes. However, the lack of regulation often leads to the dissipation of electrical and chemical gradients, which might significantly affect the viability of cells under scrutiny. To mitigate these problems, we explored the use of lysenin channels to reversibly control the barrier function of natural and artificial lipid membrane systems by controlling the lysenin’s transport properties. We employed artificial membranes and electrophysiology measurements in order to identify the influence of labels and media on the lysenin channel’s conductance. Two cell …

Does Population Density Affect The Singing Behavior Of Female Canyon Wrens (Catherpes Mexicanus)?, Lorraine Dargis

Master's Theses

Bird song has historically been considered from the perspective of temperate males despite females in many bird species being prolific singers. In this study, I investigated one species with female song, the canyon wren (Catherpes mexicanus). Canyon wrens do not duet like many other species with female song or other wrens. Instead, males and females sing sex-specific songs. The resource defense function of male canyon wren song is well-described, and males sing often during the breeding season. Females have only been observed to sing sporadically during the breeding season but sing reliably and often when exposed to playback of other …

A Comparison Of Egg Desiccation Tolerance And Development Under Different Temperatures For Three Common Aedes Mosquitoes, Shelby A. Hosch

Honors Theses

With the rise in global temperatures, invasive mosquito species like Aedes albopictus may be able to reach regions that were previously inhospitable to these species. Therefore, if A. albopictus were to potentially reach Puerto Rico, it would come into contact with the species of Aedes aegypti and Aedes mediovittatus in local containers, and it is unclear how the tropical temperatures and precipitation patterns would affect the co-occurrence of these three species. Egg desiccation and temperature dependent growth among the species were measured to test how these species hatched and developed during different humidity and temperature. It was hypothesized that there …

An Investigation Of The Impacts Of Traditional, Virtual, And Hybrid Biological Laboratories On College Students’ Achievement And Motivation To Learn Biology, Shavonda Jackson

Dissertations

Virtual courses function in a different manner than traditional courses, therefore they require teaching methods and assessment techniques geared specifically to maximize this learning experience. Internet-based learning and distance-education are no longer new concepts in the science field. Because of this, many collegiate biology programs have created courses that can be taken virtual or hybrid. A number of experimental studies have had great influence in terms of the effects and impacts of educational technology in relation to virtual laboratories.

However, not many studies emphasize the impact of hybrid laboratories on student achievement or assess students’ motivation to learn in a …

Investigating The Effects Of Temperature On Lesser Celandine, Regina Bellian

The Downtown Review: An Interdisciplinary Journal Written and Peer-Reviewed by Mandel Honors College Students at Cleveland State University

This paper explores invasive species Ficaria verna (Lesser celandine) and the effects of temperature on its growth. Trials were completed with two treatments, 13OC cold temperature and 20OC ambient temperature. Germinated bulbils of Lesser celandine were planted on February 15, 2017 and placed in their respective growing chambers. The plants were watered weekly and monitored for growth until harvest on March 29, 2017. Upon harvest, the plants’ height, largest leaf diameter and biomass were measured after extraction from soil and the removal of the leftover soil debris. Average height was found to be 11.66cm for the cold treatment and 5.14cm …

Clean Meat: Did We Under Or Over Estimate How Far This New Industry Could Grow?, Tyler R. Glick

Honors Theses - Providence Campus

Soon lab-grown meat will be on the market for everyday consumers to purchase, but will it be successful as the companies producing it are predicting? Scholarly discussions on lab-grown meat are in their beginning stages with most attention being directed toward the production process (Kowitt 2017; Mitchell 2017: Schwartz & Conley 2018). The late decade of the 2010’s saw an increasing amount of coverage and interest in lab-grown meat. As the technology continues to advance, I hypothesize thatlab-grown meat will become more readily available to consumers; however, I question whether or not consumers are ready for such a change even …

Yeast Bxi1p/Ybh3p Is A Ph-Sensitive Calcium Channel In Escherichia Coli., Amanda Raffa, John Kalhorn

Biology Student Scholarship

Amanda Raffa ’21
Major: Biology

John Kalhorn ’21
Major: Biology

Faculty Mentor: Fr. Nicanor Austriaco, Biology

39 And Me: The Evolution Of Dogs Through The Study Of Genomics, Lauren Flynn, Kathleen Kuhl, Jordan Pagliuca, Megan Russel

Biology Student Scholarship

Lauren Flynn ’21
Major: Biology and Mathematics

Jordan Pagliuca ’21
Major: Biology

Kathleen Kuhl ’22
Major: Biology

Megan Russell ’20
Major: Biology

Faculty Mentor: Dr. Elisabeth Arévalo, Biology

Our lab is interested in utilizing the dog model to explore the relationship between genes, evolution, and physical traits. The human selection and manipulation of different desirable traits in dogs has led to mutations that create the unique traits and diversity of breeds. Our lab uses different molecular methods to assess genetic mutations and different inheritable traits ranging from physical characteristics to disease in a variety of dog breeds. Statistical analysis and …

Autophagy And Lipid Metabolism In C.Elegans, Cristina De Corral, Samantha Otalvaro

Biology Student Scholarship

Cristina de Corral ’22
Major: Biology

Samantha Otalvaro ’22
Major: Biology

Faculty Mentor: Dr. Melissa Silvestrini, Biology

The synthesis, storage, delivery and breakdown of lipids in the cell is crucial for organismal homeostasis. Dysfunction in lipid metabolism can lead to a variety of pathologies including diabetes, heart disease, and even neurodegenerative disorders such as Parkinson’s. One common link between these metabolic diseases is the cellular recycling process of autophagy. Autophagy plays a complex role in lipid metabolism as it is required for both lipid storage and breakdown. In C. elegans, loss of autophagy during development impairs production of neutral lipids. …

In Vitro Assessment Of Acute Neuro-Inflammation In A Model Of The Blood Brain Barrier, Cassandra Phillips, Dak Ojuka, Ramon G. Ortega-Alvarez, Anne-Deyssa Victor, Kathryn Fama

Biology Student Scholarship

Cassandra Phillips ’20
Major: Biology and Psychology

Dak Ojuka '20
Major: Biology Minor: Business and Innovation

Anne-Deyssa Victor '21
Major: Biology

Ramon G. Ortega-Alvarez ’20
Major: Biology

Kathryn Fama ’21
Major: Biology

Faculty Mentor: Dr. Charles Toth, Biology

The purpose of this experiment was to develop an in vitro model of the blood brain barrier that incorporated brain endothelial microvascular cells (BMEC) and co-cultures composed of neurons, astrocytes, and macrophages. All cell types were derived from human induced pluripotent stem cells. A transendothelial electrical resistance (TEER) assay and immunofluorescence were used to evaluate barrier function. In addition, the model was …

Modeling Parkinson’S Disease In The Budding Yeast, Saccharomyces Cerevisiae, Yuri Takenaka

Biology Student Scholarship

Major: Biology and Mathematics
Faculty Mentor: Fr. Nicanor Austriaco O.P., Biology

Parkinson’s Disease (PD) is the second most common, incurable neurodegenerative disorder worldwide. PD patients have accumulations of abnormal proteins called Lewy Bodies (LBs) within their neurons that trigger cell death. Damaged and dead neurons lead to decline in dopamine levels, triggering the symptoms of Parkinson’s such as muscle stiffness, tremors, and slowed movement. Numerous studies have shown that the human protein, alpha-synuclein and Tau, are two major components of Lewy Bodies. To study the relationship between protein aggregation and cell death, I have created a system to co-overexpress human …

Distribution Of The Cold Water Coral Astrangia In The Waters Of Narrangansett Bay, Jared Getgano, Sarah Ramsaran, Victoria Hartley, Noah Mina

Biology Student Scholarship

No abstract provided.

Drosophila Models Of Neurodegenerative Diseases, Ella Clifford, Jackson Diltz, Emily Teixeira

Biology Student Scholarship

Ella Clifford ’20
Major: Biology and Psychology

Jackson Diltz ’22
Major: Biology

Emily Teixeira ’22
Major: Biology

We are working to determine if there are structural differences in the brains of flies modeling neurodegenerative diseases such as Frontotemporal Dementia and Alzheimer’s Disease in comparison to wild type flies. Our project is a complement to another study our lab is conducting on the metabolic activity of fruit fly models of neurodegenerative diseases. By analyzing cell size, cell pattern, and number of cells, we want to determine if the functional differences found in the metabolic study are mirrored in the structure of …

Mycobacteriophage Morphology As A Diagnostic For Cluster Assignment, Ethan Dionne

Chemistry & Biochemistry Student Scholarship

Major: Biochemistry

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

Phages are viral bodies that infect bacterial hosts, and have shown promising applications as alternatives to antibiotics for the treatment of bacterial infections. This project examines the morphology of siphoviridae mycobacteriophage, which have long, flexible, non-contractile tails as well as the characteristic head, called a capsid. Using electron microscopy photos of sequenced phages, tail length and capsid diameter were measured and compared to further characterize morphological relationships between genetically distinct phages. The data presented has the potential to work as a diagnostic tool to classify unsequenced phages to genetically …

Investigating Metabolic Reprogramming In Neurodegenerative Disease, Sidney Mackinnon, Samantha Nicodemus

Biology Student Scholarship

Sidney MacKinnon ’21
Major: Biology

Samantha Nicodemus ’20
Major: Biology and Psychology, Neuroscience Certificate

Faculty Mentor: Dr. Marla Tipping, Biology

Pmsf And Sfn Reduce Alpha-Synuclein Aggregation In A Yeast Model Of Parkinson’S Disease, Noah Kozub, Taylor Brysgel, Christopher Yerxa

Biology Student Scholarship

Noah Kozub ’22
Major: Biology

Faculty Mentor: Fr. Nicanor Austriaco O.P, Biology

Studying Cardiovascular Disease Using Human Stem Cell-Derived 3d Cardiomyocytes, Nicholas Dash, Veronica Bohl

Biology Student Scholarship

Veronica Bohl ’20
Major: Biology and Psychology, Neuroscience Certificate Program

Nicholas Dash ’20
Major: Biology

Faculty Mentor: Dr. Charles Toth, Biology

This experiment provides insight on how using metabolites derived naturally from the microbiome can influence cardiac inflammation.3D cardiomyocytes were derived from human induced pluripotent stem cells through the utilization of small molecules and growth factors. Quantitative PCR was performed to verify that the organoids expressed genes associated with cardiomyocyte cells. Primers for the genes FOXa2, TNNT2, MYH7, AHR, CACNA1, and KCNH2 were used for the qPCR, as these genes are expressed more prominently in cardiomyocyte cells than the undifferentiated …

There’S A New Species Of Thief Ant Hiding In The Pine Barrens Of Rhode Island, Justin Andries

Biology Student Scholarship

Major: Biology and Sociology
Faculty Mentor: Dr. James Waters, Biology

Ants are often missed underfoot and overlooked, but they are among the most ecologically dominant groups of animals on the planet. There are more than 200 species of ants which have been scientifically recorded in New England but samples from Rhode Island represent less than a percent of the overall survey of our regional taxa. To discover the species that are found in Rhode Island, we are engaged in a multi-year and multi-location effort to systematically trap and accurately identify the ant species found in diverse rural and urban habitats …

Cancer: The Role Of Bax Inhibitor In C. Elegans, Ibrahim Abaherah, Michael Bittner, Kevin Ly

Biology Student Scholarship

Ibrahim Abaherah ’20
Major: Biology

Michael Bittner '21
Major: Biology

Kevin Ly '23
Major: Biology

Faculty Mentor: Dr. Melissa Silvestrini, Biology

Bax inhibitor-1 is an evolutionarily conserved regulator of apoptosis and ER stress in cells. Bax inhibitor-1 is regulated by IRE-1, a transmembrane protein in the ER that is responsible for detection of ER-induced stress and activation of downstream targets involved in the unfolded protein response (UPR) to maintain homeostasis. Our goal is to determine whether the C. elegans Bax inhibitor-1 homolog tmbi-4 is dependent on the IRE1 pathway in C. elegans. Our preliminary data in the lab suggest that …

Comparison Of Branching Allometry Between Ginkgo Biloba And Several Native Michigan Trees, Collin Fox, Noah Holkeboer

Student Scholars Day Posters

Ginkgo biloba is the only extant species of the gymnospermous order Ginkgoales. Like angiosperms, ginkgo is deciduous with broad leaves and vessel tubes. However, unlike angiosperms, ginkgo possesses a long-shoot x short-shoot branching system, the latter producing most of the leaves, and open-dichotomous leaf venation. Given that branching reflects optimization of photosynthetic capture through structural support and hydraulic efficiency, we compared the degree to which these functions were optimized for ginkgo relative to three native species. DBH, neighbor density and size were measured in field and branch dimensions were measured from photographs and analyzed per Murray’s Law for hydraulic optimization …

Lifelines Spring 2020, Southern Adventist University

Lifelines - Biology Department Newsletter

The Spring 2020 issue of Lifelines contains articles on Insights from the Professor, Students in Service, Departments Happenings, and The Amazing Gift of Hearing.

Using Stable Isotopes And Diet Analysis To Assess The Potential For Competition And Coexistence Among Coyotes (Canis Latransl, Red Foxes (Vulpes Vulpes), And Gray Foxes (Urocyon Cinereoargenteus) In Maine, Henry M. Masters

Student Scholarship

When two species compete for food, one species typically outcompetes the other. Subordinate species can alleviate costs of competition by reducing diet overlap, promoting coexistence. Non-native coyotes (Canis latrans) and historically native gray foxes (Urocyon cineroargenteus) have expanded their range in Maine and may compete with native red foxes (Vulpes vulpes). To investigate competition, I analyzed stable isotopes and stomach contents to determine if coyotes, red foxes, and gray foxes differed in use of anthropogenic foods and trophic position. I predicted that coyotes utilize anthropogenic foods the least (lowest δ13C), and red foxes utilize …

Thing 1 And Thing 2 Are In A New Zoo: Changes In Behavior Of Amur Tigers Following Introduction To John Ball Zoo, Caitlin Gerke, Faith Hensley

Student Scholars Day Posters

Animals alter their behavior in response to changes in their environment such as alterations to their enclosure, social group, or husbandry routine. In 2018, two related, young adult Amur tigers (Panthera tigris altaica) were transferred to the John Ball Zoo (JBZ). The male siblings were given access to a spacious, wooded outdoor enclosure (area = 920 m²). We used Zoomonitor in 2018 and 2019 to conduct focal-animal sampling of the two males. We recorded state behaviors in 30 sec intervals of scan sampling, and all occurrences of event behaviors, both during 30 min sampling sessions. Our study objective …

Great Starts: Amy Holzer '20, Amy Holzer

2020

From time to time, we like to showcase a new SNC grad who’s entered the workplace or grad school. Success stories like these are pretty common. Amy Holzer '20 shares her story.

The Effects Of A New Mutation In Lis1 And Its Potential Role In Autism Spectrum Disorder, John A. Slovensky

Senior Theses

LIS1 is a protein, particularly concentrated in the brain, that is important in regulating the movement and transport capabilities of dynein. Dynein is protein that can move along pathways in the cell, carrying various cellular components and also helping brain cells migrate. These two proteins are crucial during the development of the nervous system, and mutations in them can lead to lissencephaly, a disorder in which the brain does not form properly. This disease causes patients to develop cognitive-motor defects and seizures that can lead to early death. While all previously identified mutations in LIS1 are known to cause lissencephaly, …

Membrane Lipid Extraction Methods From Sorghum Bicolor, Max Regester

Honors Program: Senior Projects (Public)

Plants are the basis of the world as we know it. As sessile beings, there are often subject to many environment stressors like drought, extreme temperatures, etc. One way of analyzing how plants respond to these stressors is by monitoring changes in their lipid compositions. Having a better understanding of how plants respond to different stressors can have very important implications when it comes to cultivating crops. When testing lipid composition, it is important to measure levels as they were in the living tissue. The problem is, enzymes known as lipases are active during extraction and can greatly change the …

Adaptations Of Interferon Regulatory Factor 3 During Transition From Terrestrial To Aquatic Life, Monica Angeletti

Honors Program: Senior Projects (Public)

Interferon regulatory factor 3 (IRF3) and IRF7 are closely related IRF members and play a major role in the induction of interferons, which are a key component in vertebrate innate immunity. However, there is limited knowledge regarding the evolution and adaptation of these IRFs to the environment. Two unique motifs in IRF3 and 7 were identified. One motif, GASSL, is highly conserved throughout the evolution of IRF3 and 7 and located in the signal response domain. Another motif, DPHK, is in the DNA-binding domain. The ancestral protein of IRF3 and 7 seemed to possess the DPHK motif. In the ray-finned …

Teaching Natural And Artificial Selection In Production Agriculture, Madhav P. Nepal, Clayton W. Scott

iLEARN Teaching Resources

In this lesson, students will learn how natural selection and artificial selection impact both production agriculture and biological sciences. A natural selection is a mechanism that favors heritable traits that increase species survival and reproduction. Artificial selection is a selective breeding, where humans select for desirable traits in agricultural products.

03. Botany, Southwestern Oklahoma State University

Oklahoma Research Day Abstracts

No abstract provided.