Biology Commons^™

A Long‐Term Obesogenic High‐Fat Diet In Mice Partially Dampens The Anti‐Frailty Benefts Of Late‐Life Intermittent Fasting, Yoko Henderson, Nazmin Bithi, Jie Yang, Christopher Link, Aili Zhang, Benjamin Baron, Eran Maina, Christopher Hine

Senior Honors Projects

The global obesity pandemic coupled with ever-growing life expectancies equates to hundreds of millions of individuals with potentially longer but not healthier lives. Aging is one of the risk factors for numerous maladies such as metabolic dis- order and frailty, which are exacerbated under obesity. Thus, therapeutic approaches that address obesity to ultimately improve afected individuals’ quality of life and extend their lifespan are needed. We previously reported that the every other day (EOD) fasting initiated late-life improved metabolic, musculoskeletal, and cognitive endpoints in standard rodent diet-fed mice. In the present study, using the same dietary intervention methodology, we tested …

Determination Of Taxonomic Placement Of Falsely-Branched Taxa In Soils Of San Nicolas Island And Reassessment Of The Tolypothrichaceae., Natalie Soliman

Senior Honors Projects

This study was conducted to determine the taxonomic placement of falsely-branched taxa in the soil crusts of San Nicolas Island, which is the largest of the Channel Islands lying off the coast of California. After microscopic analysis of the strains collected from the island, a phylogenetic analysis of 16S rRNA genes, and an analysis of the 16S-23S ITS region, we have identified that these strains belong to the soil genus Spirirestis, which is in the Tolypothrichaceae family. The Tolypothrichaceae is a wellcharacterized monophyletic lineage of non-attenuated, false-branching heteropolar types containing the genera Spirirestis, Hassallia, Tolypothrix, Coleodesmium, and Rexia. The strains …

Temporal And Spatial Comparison Of Pseudo-Nitzschia Species Composition And Domoic Acid In Narragansett Bay, Rhode Island And The Northeast U.S. Shelf, Isabella Church, Bethany D. Jenkins

Senior Honors Projects

Diatoms are unicellular algae that make up a significant portion of phytoplankton biomass at the base of marine food webs. Narragansett Bay (NB), RI is home to several species of the diatom genus Pseudo-nitzschia (P-n), some of which are known to cause harmful algal blooms through the production of the potent neurotoxin domoic acid (DA). This toxin can lead to Amnesic Shellfish Poisoning in humans through the consumption of affected shellfish. Although the presence of P-n has been well established in NB for over 50 years, DA levels have only recently become a problem, with shellfish harvest closures …

Ciliate Endosymbiont Imaging Methodology, Aidan Boving, Roxanne Beinart

Senior Honors Projects

Ciliates, a phylum of diverse microbial eukaryotes, are found in a wide range of environments, including anoxia. Anaerobic ciliates host intracellular methanogenic archaea – a unique type of symbiosis. Despite their importance, anaerobic ciliates and their symbiotic relationships remain understudied. Included in this is the ability to image and quantify the intracellular methanogenic symbionts in a precise, timely and replicable procedure. This project aimed to improve the current fluorescence microscopy methodology used for endosymbiont quantification. The proposed method is intended for use with the Opera Phenix, a high throughput spinning disk confocal microscope which can count large amounts of individual …

Sulfated Flavonoids In The Asteraceae, Alyssa Rice

Senior Honors Projects

Gypsum soils are a unique soil type with high levels of calcium and sulfur, which creates a harsh living environment for plants. To survive these conditions, plants have evolved a suite of mechanisms to survive these excess minerals, such as sulfur. In this study we aimed to determine if gypsum status was related to sulfated flavonoid production in plants of the Asteraceae. Flower and leaf tissues were collected from herbarium specimens representing gypsophiles, gypsovags, and gypsofuges. These tissues were analyzed for the presence of sulfated flavonoids using Thin Layer Chromatography (TLC). We observed sulfated flavonoid production in leaf and flower …

Particle Tracking Reveals Pelagic Red Crabs As Indicators Of Climate-Driven Range Expansion In The California Current, Elizabeth Saraf

Senior Honors Projects

Since their first recorded occurrence in 1859, Pelagic Red Crabs (PRC; Pleuroncodes planipes) have experienced increased frequency of episodic mass stranding events in the Eastern Pacific Ocean. PRC’s are transported over 1,000 km northward of their central domain from the coast of central Baja California, Mexico. They have been reported by the thousands on the beaches of central and southern California. Their presence influences the surrounding ecosystem and commercial fisheries because they are nutritional prey items and large predators change their diet to incorporate PRC’s when they are available. Seasonal coastal currents and the California Undercurrent transport warmer waters …

The Journey To Reach Herd Immunity: The United State's Efforts Towards Controlling Sars-Cov-2, Natalina Mastroianni

Senior Honors Projects

COVID-19 is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged in December of 2019 and has been the leading global health concern since. SARS-CoV-2 is a positive sense single-stranded RNA virus coated with viral spike proteins that has led to over 500,000 deaths in the United States and is approaching 3,000,000 deaths worldwide. As COVID-19 persists globally in such high numbers, the virus has been able to undergo mutations, leading to three prominent variants: the United Kingdom variant (B.1.1.7), the South Africa variant (B.1.351), and the Brazil variant (P.1). These variants are more transmissible, …

The Journey To Reach Herd Immunity: The United State's Efforts Towards Controlling Sars-Cov-2, Natalina Mastroianni

Senior Honors Projects

COVID-19 is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged in December of 2019 and has been the leading global health concern since. SARS-CoV-2 is a positive sense single-stranded RNA virus coated with viral spike proteins that has led to over 500,000 deaths in the United States and is approaching 3,000,000 deaths worldwide. As COVID-19 persists globally in such high numbers, the virus has been able to undergo mutations, leading to three prominent variants: the United Kingdom variant (B.1.1.7), the South Africa variant (B.1.351), and the Brazil variant (P.1). These variants are more transmissible, …

Phylogenetic Placement Of Seven Strains Of Synechococcales (Cyanobacteria) Isolated From Desert Soils In Zion National Park., Kevin Houk

Senior Honors Projects

Seven strains of cyanobacteria of the order Synechococcales were isolated from the sandstone derived soil of Zion National Park. These strains were analyzed using 16S rRNA and 16S-23S phylogenetic analysis, percent dissimilarity of the ITS sequence, morphology, and the similarity of the 16S rRNA sequence. One strain was placed within the genus Plectolyngbya, but the Bayesian inference and 16S rRNA similarity analysis support the conclusion that Plectolyngbya should not considered a valid genus, and that it should be integrated into the taxonomically prioritized Leptolybya. Two of the strains were found to be similar to Phormidesmus morphologically, but the …

Heat And Chemical Cues Enhance Germination Rates In Fire-Dependent Chaparral Species, Zachary Litwinowicz

Senior Honors Projects

Climate change has caused an increase in the frequency and intensity of fire cycles in chaparral ecosystems. In environments impacted by wildfires, some plant species depend on complex fire cues to germinate. Determining how to best replicate wildfire cues is essential to using fire-recruiter species in restoration efforts. This study examines the effects of various simulated fire cues on four chaparral species: Arctostaphylos manzanita, A. viscida, Ceanothus cuneatus, and C. jepsonii. Seeds were exposed to heat, charate, liquid smoke, or combinations of treatments. Other germination cues, such as cold exposure for all species and acid exposure for Arctostaphylos species, were …

A Guide To Freshwater Aquariums, Noah Savastano

Senior Honors Projects

The objective of this project was to create a complete guide, useful for someone of any aquarium expertise level, describing how to set up and care for an aquarium. This guide explains the science behind processes involved in setting up and maintaining an aquarium. It also educates the reader on how to properly prioritize the safety of the fish. A full text was first created including all relevant information gathered from scholarly texts and online sources. Original photographs were incorporated as a supplement to the text. Fish and aquatic plants were drawn to further illustrate the concepts that were described …

Surveying Apicomplexan Diversity And Dynamics In Narragansett Bay, Evelyn Spencer

Senior Honors Projects

Parasites play an important role in marine ecosystems and their diversity is generally understudied. Apicomplexans, a group of parasitic protists in the phylum Alveolata, infect a wide variety of animal hosts and are abundant in ecosystems spanning from Polar Regions to Neotropical rainforests. Previous data generated from marine sediments in Antarctica, Naples Bay, and off the coast of Oslo, exhibit high diversity and numbers of apicomplexans. Abundance and diversity of these protists are unknown for Narragansett Bay, despite the fact that they infect many commercially important species. The aim of my study was to obtain abundance data and understand genetic …

Evaluating Implicit Self-Compassion In College Students, Emily Kutok

Senior Honors Projects

Typically, research on self-compassion and mental health has used the measurement tool of self-report (explicit) surveys to examine self-compassion. Implicit Association Tests (IAT) can be applied to a number of di erent constructs, some of which include racial biases, gender stereotypes, and suicidal ideation. ey are used to measure the strength of a person’s automatic association between two concepts (in this case, between self and compassion). By measuring implicit self-compassion, a researcher can expect less self-report bias related to self- presentational concerns and the limits of introspection, and they can capture psychological processes that occur without full conscious awareness but …

Tao-1 And Its Function At The Drosophila Melanogaster Neuromuscular Junction, Kathryn Puhalla

Senior Honors Projects

Tao-1 is a gene that controls the growth of mitotic tissues in Drosophila melanogaster through the Hippo signaling pathway. We have found that Tao-1 also functions independently of this pathway, in regulating the growth of synapses and formation of boutons at Drosophila neuromuscular junctions. We hypothesized that Tao-1 could be exerting its effects at the neuromuscular junction by working through a signaling pathway involving Par-1 and the microtubule associated protein, tau, to affect the microtubule cytoskeleton, which is essential for proper synaptic growth. We overexpressed or knocked down (by RNAi) the expression of each of these genes presynaptically in order …

The Role Of Gene Therapy In Neurodegenerative Disease Treatment, Elaina Bohanon

Senior Honors Projects

No abstract provided.

Comparing The Middle And C-Terminal Domains Of The Soxe Proteins, Abigail Beer

Senior Honors Projects

Osteoarthritis is the most common form of arthritis and affects millions of adults in the United States. Osteoarthritis is a degenerative joint disease that is characterized by irreversible loss of cartilage. Cartilage develops when stem cells differentiate into chondrocytes, the cells found in cartilage, through a process called chondrogenesis. Several proteins are needed for chondrogenesis, including the SOXE family of proteins. The SOXE proteins act as transcriptional activators and consist of three members: SOX8, SOX9, and SOX10. The three proteins share the same basic structure consisting of two transactivation domains. A transactivation domain is a region of a protein that …

The Role Of Cellulose Synthase-Like D Genes In Tip Growth Of Physcomitrella Patens, Erin E. Killeavy, Arielle Chaves, Alison Roberts

Senior Honors Projects

Physcomitrella patens is a non-vascular plant with a relatively small genome and is amongst the few eukaryotic organisms that have a high rate of homologous recombination. This is valuable in biological research because it allows for targeted genetic modification of the organism. In vascular plants like Arabidopsis thaliana, a model organism, Cellulose Synthase-like D (CSLD) genes have been discovered to be important in tip growth. This type of growth is observed in the pollen tubes and root hairs of these plant types. The CSLD genes in Arabidopsis were found to play a crucial role in the growth of …

Social And Scientific Implications Of Genetic Testing In The Digital Age, Yaruska A. Ordinola

Senior Honors Projects

From Mendel’s law of inheritance in the 19th century through Watson and Crick’s revolutionary observations of the double helix in the 20th century, genetics has been a fascinating and continuing topic of discussion in the field of science (Collins & McKusick, 2001). Major studies like the Human Genome Project (HGP), initiated in 1990 and completed in 2003, provided a starting point from which scientists could more thoroughly investigate the human condition on a genetic level. Arising from this study, personal genomics is considered a blooming field in genetics- in which rapidly developing technological advances are able to provide easier and …

A Putative Dual Role For Yorkie In Hippo Pathway Signaling, Caroline Hall

Senior Honors Projects

The Hippo pathway inactivates genes involved in organ size and when aberrant, can lead to cancer. To control organ size, the Hippo pathway inhibits Yorkie (Yki), a transcriptional coactivator that works with Scalloped (Sd), a DNA binding protein. When active, Yki translocates into the nucleus and initiates transcription. Conversely, when inactive, Yki remains in the cytoplasm. However, my work shows that cytoplasmic, inactive Yki interacts with other proteins in the Hippo pathway by recruiting them to the plasma membrane. Accordingly, this study challenges the notion that cytoplasmic Yki is inactive and instead, may play a dual role in the Hippo …

Seed Germination Requirements For Four Fire-Recruiter Chaparral Shrubs, Kati Mcclain

Senior Honors Projects

Wildfires are a natural part of chaparral ecosystems, as they are essential to vegetative regrowth and plant recruitment. For many chaparral species, fire stimulates germination of dormant seeds in the seed bank. This study explored fire-related cues necessary for seed to break dormancy, germinate, and emerge in four chaparral species (Ceanothus cuneatus, C. jepsonii, Arctostaphylos manzanita, A. viscida). Seed were exposed to various treatments mimicking wildfire conditions, including boiling water and charred wood (charate), as well as physical scarification by concentrated acid, and monitored for germination. Our data indicate that Ceanothus seed require heat cues to germinate, but fire-related chemical …

Phenotyping Cesa4ko Mutants In P. Patens, Kristina Bischak

Senior Honors Projects

In order to study the cellulose deposition mechanisms of plants like Physcomitrella patens, understanding the function of CesA genes is crucial. The CesA genes, better known as the Cellulose Synthase gene superfamily, are responsible for the formation of cellulose in developing plants. Cellulose is an important biological molecule necessary for proper plant growth, particularly in non-vascular plants such as P. patens. There are seven known CesA genes in P. patens: CesA 3, 4, 5, 6, 7, 8, and 10. The effects of these cellulose synthase genes on the developing plant can be observed by removing specific CesA …

Experts As Teachers: Can We Abate The Disconnect Between Expert And Student?, Bailey Mallon

Senior Honors Projects

Studies have found that experts often fail as good teachers, mainly because there is a lack of communication within their specific area (Feldon, 2007). Experts may routinely underestimate how difficult a task can be for a newcomer (Hinds, 1999) and even when attempting to make a task easier, they omit information a novice would find valuable (Hinds, Patterson, & Pfeffer, 2001) because they unintentionally assume that non-experts are aware of and possess knowledge that only those already familiar in the field might have, and would thus know what they are talking about. Furthermore, there are factors controllable by the professor, …

Plant-Soil Relations On Gypsum And Non-Gypsum Soils Of The Chihuahuan Desert, Clare Muller

Senior Honors Projects

No abstract provided.

Alkaloid-Based Chemical Defenses In The Brazilian Poison Frog Melanophryniscus Simplex Inhibit Mycobacterial Growth, Megan A. Boyk

Senior Honors Projects

This study investigated the antimycobacterial properties of M. simplex alkaloids from geographically isolated populations against two species of mycobacteria, M. smegmatis, a soil-dwelling species, and M. phlei, a saprophytic species (Berney et al. 2014; Egamberdieva 2011). Both of these species are fast-growing, commonly found in the environment, and typically nonpathogenic in healthy animals (Balazova et al. 2014, Berney et al. 2014, Egamberdieva 2011). Both M. smegmatis and M. phlei are commonly used as model strains for the study of antimycobacterial agents (Zhang et al. 2014, Bruce-Micah et al. 2009). Optical density and colony-forming unit assays were used to evaluate …

What Are The Effects Of Circadian Rhythms On The G-Protein Coupled Receptors Involved With Glucose Metabolism?, Mary Skiffey

Senior Honors Projects

Circadian rhythms (CR) are 24-hour cycles that regulate physiological processes of the human body, such as sleep and blood glucose levels. They allow organisms to coordinate behavioral, physiological, and molecular processes with the 24-hour light/dark cycle. CRs influence metabolism through transcriptional-translation mechanisms of time-keeping, which are activated by environmental stimuli. It is known that circadian rhythms influence glucose metabolism through a variety of ways including G-protein coupled receptors (GPCRs); however, the extent to which these mechanisms operate are unknown. Disrupted CRs lead to inappropriate GPCR pathway signaling, pancreatic beta-cell failure, and misregulation of gene expression, which results in a predisposition …

Age-Dependent Modifications Of Axons, Mitochondrial Dynamics, And Ca2+ Homeostasis Underlie The Vulnerability Of Aging White Matter To Ischemia, Katharine E. Stahon

Senior Honors Projects

Aging white matter (WM) is increasingly susceptible to neurodegenerative diseases and stroke. Among others, changes in ATP production, mitochondrial dynamics, and Ca²⁺ homeostasis contribute to increased susceptibility of aging WM to stroke. We utilized a pure white matter tract, mouse optic nerve (MON), obtained from 2- and 12-month old mice to quantify axon structure and function using electrophysiology, 3D-EM, immunoblots, and ATP assays. Functionally, aging axons did not recover as well after ischemia compared to young axons. Structurally, aging axons became thicker with lower G ratios, indicating increased myelin thickness, as well as increased internodal distances and nodal lengths. …

Is Green Tea The Panacea We’Ve Been Searching For? A Review Of The Scientific Literature On Green Tea And Human Health, Eleanor L. Axson

Senior Honors Projects

There are many claims surrounding the health benefits of consuming green tea, some of which involve its use in the treatment of medical conditions as wide ranging as cancer, diabetes, and neuro-degenerative disorders. The desire for the use of non-toxic and natural drugs to treat various diseases makes any health-benefitting claims about green tea and its components important to investigate for their potential public health benefits. I conducted a critical review of the research literature on green tea and its effects on human health and synthesized the results. There is convincing epidemiological evidence pointing to the health benefits derived from …

Defining The Sites Of Interaction Of The Fancd2, Fance, And Fancl Proteins, Joseph Mcclanaghan

Senior Honors Projects

Fanconi anemia (FA) is a rare genetic disease characterized by congenital defects, bone marrow failure and increased cancer susceptibility. FA is caused by mutations in any one of 16 genes. These genes encode for proteins that function in the FA-BRCA pathway to repair damaged DNA. Because of its important r­­­ole in DNA repair, this pathway is considered a major cellular tumor suppressor pathway, i.e. is critical for the prevention of cancer. Underscoring this fact, several of the FA genes - including BRCA2, BRIP1, PALB2, and RAD51C - are bona fide breast and ovarian cancer susceptibility genes.

My …

Molecular Dynamics Simulations As A Characterization Method Of Biologically Relevant Segments Of Dna, Carman Polsinelli

Senior Honors Projects

Biologically relevant short sequences of DNA have previously been shown to possess high affinity and specificity for binding of small polyamide structures to their minor groove. These structures, or minor groove binders, have the potential to control access to specific regulatory regions of DNA. Before modeling the binding of these polyamides to the DNA, the small segments of DNA must be characterized for better understanding of the impact the minor groove binder will have on the structure of the DNA. The method for such a characterization is a molecular dynamics computer simulation including the solvent effects for a length of …

Geographic Variation In Alkaloid-Based Microbial Defenses Of The Strawberry Poison Frog, Oophaga Pumilio, Annemarie Mina

Senior Honors Projects

Frogs of the family Dendrobatidae use alkaloids as a chemical defense against predators. Alkaloids are not manufactured by frogs, but instead sequestered from a diet of arthropods. Alkaloid defenses in dendrobatids differ with geographic location, mainly because arthropod availability varies with location. It has been postulated that alkaloids also function as a defense against microbes and different frog alkaloids might be more/less effective against microbes. We assessed this hypothesis by testing the effectiveness of alkaloids in the dendrobatid frog Oophaga pumilio from five geographic locations in Costa Rica and Panama against different microbes. Alkaloids were tested against the bacteria Escherichia …