Life Sciences Commons^™

Dorsal Fin Innervation Of The Bluegill, Lepomis Macrochirus, Amanda Torick

Honors Projects

Recent work has shown that the dorsal fins in fish operate not only as locomotive appendages, but also as sensory structures that aid in proprioception. To investigate how fish use these structures for sensing, the innervation of the dorsal fins in bluegill sunfish (Lepomis macrochirus) was assessed through immunohistochemistry assays. I conducted staining using anti-acetylated tubulin (AAT), a non-specific neuron marker, calcitonin-gene related peptide (CGRP) which stains sensory neurons and cytokeratin 20 (CK20), which binds to mechanoreceptor structures. Stained samples of bluegill dorsal fins were imaged under a laser scanning epifluorescence microscope to visualize mechanoreceptors, as well as sensory and …

Legacy Effects Of Forest Clearcutting On Ecosystem Function And Biogeochemical Cycling In A New England Forest, Andre Solomon Gomes

Honors Projects

Terrestrial soils comprise the largest reservoirs of carbon (C) in the biosphere holding some 2500 Gt C, which is 4x the amount found in plant biomass and 3x the C content of the atmospheric pool. Approximately 1500 Gt of soil C is in an organic form, thus making it available to mineralization by heterotrophic organisms [10]. Changes to the drivers of mineralization such as climate change and aeration due to anthropogenic land use, such as logging, have the potential to strongly affect global carbon and associated nutrient cycles, plant production, and atmospheric composition. With the aim of better understanding the …

Understanding The Effects Of N-Terminal Acetylation On The Oligomeric State Of Tau, Miguel Jose Martinez Guzman

Honors Projects

Protein production, purification, and analysis done in order to find the effects of N-terminal acetylation on microtubule associated protein tau.

The Effects Of Temperature And Phasins On Polyhydroxyalkanoic Acid (Pha) Accumulation In Heterologous Hosts Containing A Pha Synthase From Vibrio Species B-18, Edward R. Lyons

Master's Theses, Dissertations, Graduate Research and Major Papers Overview

Polyhydroxyalkanoic acids (PHA) are bacterial carbon reserves with application as biodegradable biocompatible plastics. PHA synthase, encoded by phaC, creates the PHA polymer. Evidence presented by many researchers has emphasized the role of phasin proteins in PHA accumulation. Phasins have been implicated in PHA granule localization, PHA synthase activation, and possibly chaperone and nucleoid binding functions. The phaC gene from Vibrio species B-18 with and without an upstream gene showing homology to phasin genes (orf2) were placed into runaway replication vectors, which use temperature to control gene expression. The aim of this thesis is to explore earlier observations that lower temperatures …

Expression And Purification Of N-Terminally Acetylated Microtubule Binding Protein Tau, Abigail Fleurima

Honors Projects

The microtubule-associated protein Tau (MAPT) plays a critical role in many neurodegenerative diseases. Tau functions to stabilize microtubule structures that are essential for transport within the neuron, and transport disruption leads to loss of neuronal function. Tau binding is regulated by phosphorylation with the help of kinases that add phosphate groups which block microtubule binding sites, and phosphatases that remove phosphate groups and expose the microtubule-binding regions. Tau can be found in hyper-phosphorylated states, which causes Tau to self-assemble into aggregates and prevent microtubule binding. It's clear that post-translational modifications (PTMs) of Tau play a key role in the dysregulation …

Function Of Spiny Dorsal Fin Erector Muscles In The Bluegill, Lepomis Macrochirus, Zakiyat Djabakatie

Honors Projects

Local motor control directly contributes to stability, which can be compromised by injury or multiple neuromuscular disorders. In addition, lack of sensory perception as experienced by decreased limb sensation can further deteriorate one‚Äôs quality of life. The goal of this study is to use bluegill (Lepomis macrochirus) fins as model systems to study and gain insights on local motor control and sensory perception to improve stability and locomotion in humans, especially in a rehabilitative state. We hypothesize that 1) when exposed to turbulence (T), bluegill will use the spiny dorsal fin to recover stability and muscle intensity and duration will …

Investigating The Role Of Alx4a In Mitfa Repression And Iridophore Fate Biasing, Melanie Cragan

Honors Projects

Investigating the role of the transcription factor alx4a on chromatophore fating in zebrafish.

What’S Water Got To Do With It? Place-Related Symbolic Meanings Alter Residents’ Perceived Effects Of Coastal Infrastructure, Bryce B. Dubois, Katherine Lacasse, Aaron J. Ley

Faculty Publications

The symbolic meanings residents associate with their local bodies of water and coastal infrastructure can shape their perceptions of the infrastructure’s effects. In this case, we conduct a survey (N = 168) to examine residents’ perceptions of visibly disruptive, yet environmentally

protective cooling towers attached to a long-standing coal-fired power plant on Mount Hope Bay. Residents’ symbolic meanings of the bay corresponded predominantly with aesthetic,

ecological, or recreational themes, whereas their symbolic meanings of the towers also focused on aesthetics as well as the towers’ function or uselessness. Although residents generally perceived the towers as having negative effects on …

Detecting Aggregated Superoxide-Dismutase Protein Using Aggregate Specific Antibodies, Helen Magana

Honors Projects

Amyotrophic lateral sclerosis is neurodegenerative disease characterized by late-onset, loss of motor neurons, paralysis, and eventual death. SOD1 is a free radical scavenger that normally resides in the cytoplasm, nucleus, and intermembrane space of the mitochondria. Mutations in SOD1, a ubiquitously expressed free-radical scavenger, are one cause of ALS. Degeneration of motor neurons is thought to be triggered by aggregation of mutant SOD1 followed by propagation to adjacent cells though cell-cell contacts. Here, we present immunohistochemical findings on tissues of a Drosophila melanogaster expressing mutant dsod1 alleles at the endogenous locus. Aggregate-specific antibodies were used to assess the presence of …

The Purification And Characterization Of N-Terminally Acetylated Ssal From Saccharomyces Cerevisiae, Alijah A. Griffith

Honors Projects

Molecular chaperones are highly conserved, ubiquitous enzymes that maintain proteostasis by mediating protein structure in vivo. Post-translational modifications (PTMs) can act as a functional switch between chaperone pathways, allowing for cells to enact a coordinated response to cellular perturbations. Several PTMs are well characterized in the context of chaperone function, though the role of N-terminal acetylation is commonly overlooked, leading to an overwhelming lack of scientific understanding in this area of study. Ssa1, a Hsp70 class chaperone endogenous to Saccharomyces cerevisiae, is likely N-terminally acetylated, though in vitro studies of Ssa1 are limited by current purification methods which are resource-intensive. …

Homology Modeling Of The Squalus Acanthias Ahr1 To Locate Structural Determinants Of Function, Timothy Bock

Master's Theses, Dissertations, Graduate Research and Major Papers Overview

The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that mediates a toxic response to many environmental contaminants. Cartilaginous fishes, due to gene duplication events, express 4 distinct AHR genes. Squalus acanthias AHR1 (SaAHR1) does not bind to typical AHR agonists, including dioxin-like chemicals (DLCs), whereas SaAHR2 binds to DLCs and subsequently upregulates genes containing dioxin responsive elements. Three-dimensional homology models were created based upon both human HIF1α and human HIF2α structural templates. These models yielded different secondary structural characteristics, most notably in the length of the β-strand on the C-terminal end of the ligand binding domain, which is …

Building An In Vivo Model Of Tau Aggregation In Saccharomyces Cerevisae, Jessica Anderson

Honors Projects

Protein aggregates, which can result in cellular toxicity, are found in the brains of people afflicted with neurodegenerative diseases. One of the proteins found to aggregate is Tau, a protein that stabilizes microtubules in neuronal cells. Based on its amino acid sequence, Tau is likely to be N-terminally acetylated by the complex NatA, which is responsible for the acetylation of a majority of proteins with this post-translational modification. Mutations in the NatA complex result in a variety of pleiotropic detrimental phenotypes, showing that acetylation is a crucial modification for many proteins. Without the presence of NatA – and therefore without …

Monitoring Of Dna Polymerase Theta Movements Through Fret Analysis, Ashley Rebelo

Honors Projects

DNA polymerases are enzymes used for DNA replication during cell division and can be specialized for DNA repair. DNA Polymerase Theta (Pol θ) is the predominant polymerase involved in alternative double-stranded break repair and is upregulated in breast cancer. It is errorprone as it does not accurately match the nucleotide on a DNA template with the correct complementary base. This inaccuracy affects the overall fidelity of the enzyme, a biochemical process that looks at the ability of a polymerase to “read” the template DNA and select the right nucleotide before polymerization. Polymerization for most DNA polymerases involves a global conformational …

Hydrodynamic Function Of Dorsal Fins In Spiny Dogfish And Bamboo Sharks During Steady Swimming, Anabela Maia, George V. Lauder, Cheryl D. Wilga

Faculty Publications

A key feature of fish functional design is the presence of multiple fins that allow thrust vectoring and redirection of fluid momentum to contribute to both steady swimming and maneuvering. A number of previous studies have analyzed the function of dorsal fins in teleost fishes in this context, but the hydrodynamic function of dorsal fins in freely swimming sharks has not been analyzed, despite the potential for differential functional roles between the anterior and posterior dorsal fins. Previous anatomical research has suggested a primarily stabilizing role for shark dorsal fins. We evaluated the generality of this hypothesis by using time-resolved …

Haplotyping Small Hive Beetle (Aethina Tumida) Reveals Na1 And Na2 Distribution In Rhode Island Apis Mellifera Hives, Katelyn St. George

Honors Projects

The small hive beetle (Aethina tumida) is a parasite of honeybee hives (Apis mellifera) and native to South Africa. Invasive in North America since 1996, the species has spread to hives throughout the continent, including many in Rhode Island and nearby states. To better understand migration patterns for this invasive species, we haplotyped small hive beetles (SHB) based on mitochondrial Cytochrome Oxidase Part 1 (COI) gene sequences. To analyze spatial and temporal haplotype distribution, we mapped haplotype data along with previously analyzed population numbers using ArcGIS. All identified beetles fell into one of two previously described haplotypes, either NA1 or …

Diversity As Opportunity: Insights From 600 Million Years Of Ahr Evolution, Rebeka R. Merson, Mark E. Hahn, Sibel I. Karchner

Faculty Publications

The aryl hydrocarbon receptor (AHR) was for many years of interest only to pharmacologists and toxicologists. However, this protein has fundamental roles in biology that are being revealed through studies in diverse animal species. The AHR is an ancient protein. AHR homologs exist in most major groups of modern bilaterian animals, including deuterostomes (chordates, hemichordates, echinoderms) and the two major clades of protostome invertebrates [ecdysozoans (e.g. arthropods and nematodes) and lophotrochozoans (e.g. molluscs and annelids)]. AHR homologs also have been identified in cnidarians such as the sea anemone Nematostella and in the genome of Trichoplax, a placozoan. Bilaterians, cnidarians, and …

Creating A Drosophila Sod1 Mutant Through Homologous Recombination, Saman Nayyab Stilwell

Honors Projects

This works describes the creation and partial phenotypic analysis of a point mutation within the endogenous Drosophila sod gene. The sodS111C allele was generated through a process of mutagenesis and homologous recombination in vivo. SodS111C stocks were created to analyze the mutation’s influence on protein aggregation, if any. We were able to test the effects of this mutant by assessing the function of the protein using genetic assays. To examine the effect of sodS111C on the second chromosome in the presence of sodG85R on the third chromosome appropriate genetic crosses were performed and it was determined that there was no …

Cimrf Suppression Of Endogenous Tissue Developments In Ciona Intestinalis Embryos, Emmanuel Kofi Asieidu

Honors Projects

Trans-differentiation of non-muscle tissue to muscle tissue is a well-established property of vertebrate myogenic regulatory factors (MRFs). For instance the vertebrate MRF, MyoD, has been shown to convert nonmuscle cells to muscle cells. During this trans-differentiation, however, endogenous gene activity of the nonmuscle cells is down regulated. To test if this property is also found in invertebrate MRFs our lab has developed a system to analyze the ability of the MRF of Ciona intestinalis, CiMRF, to suppress endogenous gene activity during trans-differentiation. We did this by misexpressing CiMRF in the notochord and endoderm of Ciona embryos, two nonmuscle …

Intraspecific Variation In Leaf Traits Across An Environmental Gradient In The Cape Floristic Provence Of South Africa, Bruce H. Ramos

Honors Projects

Intraspecific variability has been an overlooked and under-investigated driving force behind biodiversity. Both interspecific and intraspecific variability contribute to species community assembly, and the South African Cape Floristic Region (CFR), as an area of remarkable biodiversity, provides the perfect opportunity to the latter. The objective of this research is to study intraspecific variability in leaf traits across three biomes that span rainfall and temperature gradients, and to assess the partitioning of that variability across biomes, across shrubs within biomes, and within shrubs of four focal species - Rushia intricata, Aridaria noctiflorum, Diospyros austro-africana and Chrysocoma ciliata. All …

Trflp Analysis Of The Effect Of A Forest-To-Gap Ectone On Soil Microbial Diversity, Ronald Smith

Master's Theses, Dissertations, Graduate Research and Major Papers Overview

To investigate how soil microbial diversity is influenced by the formation of an experimental edge-creating gap within a southern New England oak-hickory forest, I used a molecular fingerprinting technique known as terminal restriction fragment length polymorphism (TRFLP). Sequence variability in the 16S ribosomal RNA (rRNA) gene in soil bacterial communities is detected by differences in the length and abundance of fragments produced by digesting PCR products amplified from rRNA genes. The different patterns observed are assumed to represent unique phylotypes.

How does the forest-gap ecotone influence soil bacterial diversity? Based on other studies, I hypothesized that the edge would contain …

Streamwise Vortices Destabilize Swimming Bluegill Sunfish, Anabela Maia, Alex P. Sheltzer, Eric D. Tytell

Faculty Publications

In their natural environment, fish must swim stably through unsteady flows and vortices, including vertical vortices, typically shed by posts in a flow, horizontal cross-flow vortices, often produced by a step or a waterfall in a stream, and streamwise vortices, where the axis of rotation is aligned with the direction of the flow. Streamwise vortices are commonly shed by bluff bodies in streams and by ships’ propellers and axial turbines, but we know little about their effects on fish. Here, we describe how bluegill sunfish use more energy and are destabilized more often in flow with strong streamwise vorticity. The …

Effects Of Early Experience And Plasticity On Neuronal Morphology Within The Prefrontal Cortex In A Rodent Model Of Hypoxia-Ischemia, Zarah M. Melendez

Honors Projects

Hypoxia-ischemia (HI) is low oxygenation to the brain paired with low blood supply that can disrupt normal patterns of brain development. HI injury is characterized by many long-term cognitive and behavioral deficits including working memory. Neuronal plasticity due to early sensory or learning experience has been suggested to facilitate recovery of function after neonatal brain injury. Plasticity is the ability for the nervous system, more specifically neurons, and their synapses to modify their function and morphology due to experiences, which in turn correlate with changes in behavior. The objective of the present study was to investigate the effects of neonatal …

Examining Escherichia Coli Plasmid Gene Expression In Vibrio Species B-18, Roberto Ramirez

Honors Projects

The goal of this experiment was to determine if lower temperatures could serve to induce runaway replication for the expression of the lacZ gene in Vibrio species B-18 carrying a different runaway replication vector, pJM9487. One experiment compares β-galactosidase activity in cells incubated at 35, 37, and 39°C while the second experiment examines the enzyme levels for cells incubated at either a low temperature or a high temperature in the presence and absence of the chemical inducer used for the promoter (ptrp) that controls the expression of the lacZ gene on this plasmid.

Comparison Of Guekensia Demissa Populations Along A Nitrogen Loading Gradient In Narragansett Bay, Ri, Janis Hall

Master's Theses, Dissertations, Graduate Research and Major Papers Overview

Anthropogenic eutrophication of coastal estuaries impacts these vital ecosystems by increasing primary production, hypoxic conditions, pathogen concentration, and greenhouse gas emissions, all of which are leading to the degradation of shorelines, disease transmission, and hypoxia-related fish kills. Narragansett Bay is a prominent feature of Rhode Island, making up over 500 km of coastline and acting as a watershed for over 2,000 square meters of land in both Massachusetts and Rhode Island. This estuary is important to both the economy of the state of Rhode Island and its fringing ecosystems are necessary for a healthy shoreline. The beaches of Narragansett Bay …

Investigating The Leaf Cuticle Of The Moss Physcomitrella Patens, Eric John Ricci

Master's Theses, Dissertations, Graduate Research and Major Papers Overview

To minimize water loss, the aerial parts of vascular land plants are covered with a hydrophobic layer called a cuticle. The cuticle typically consists of two major components: cutin and waxes. In contrast to vascular plants, research reports indicate that some primitive nonvascular plants, such as mosses, lack a cuticle. This study attempts to reconcile contradictory literature reports about the presence of a waxy cuticle on the leaves of the moss Physcomitrella patens.

Histochemical staining was utilized to investigate the presence of a cuticle on Physcomitrella leaves. Experiments employing dyes that stain hydrophobic substances were generally consistent with the …

Effects Of Hypoxia-Ischemia And Anti-Inflammatory Prophylactic Treatment On Cortical And Hippocampal Volumes In The Developing Rat Brain, Llian Mabardi

Honors Projects

Very low body weight as a result of premature birth is a common problem all around the world. Many of these infants have medical issues that arise as a direct result of their very low body weight. One of the biggest issues is a lack of oxygen, which is also known as hypoxia. Hypoxia and ischemia (lack of blood flow) are a problem at any age, but they can be especially devastating to infants who have not undergone critical periods of brain development. Hypoxia-ischemia (or HI) can cause problems that start as inflammation and end with large-scale cell death in …

Living In An Age Of Technology: College Students' Perception Of The Role Of Genetic Engineering And Reproductive Technology In Today's Society, Kayla Quadros

Honors Projects

This study examines attitudes about prevalent issues in genetics and reproduction among the college population. Eighteen interviews were conducted with students at Rhode Island College. Respondents were asked questions about their moral standpoints concerning utilizing genetic engineering for disease control and aesthetic purposes, employing assisted reproductive technologies (ARTs), regulation of such procedures, and also about media sources for which they have heard of these topics. Findings suggest that, generally, participants felt that genetic engineering for health issues is permissible, yet reprehensible for the purpose of aesthetically "designing" a baby, though four students (three of which were female) found the enhancement …

Investigating The Role Of P53 In The Germ Cell Apoptotic Pathway, Jamie Lamkin

Master's Theses, Dissertations, Graduate Research and Major Papers Overview

Investigation of the role of p53 in germ cell apoptosis pathways.

Ufd2a Isoforms With Vsp/P97 And Its Ibmpfd Mutants, Amanda St. Germain

Honors Projects

Using the Yeast2Hybrid system, the binding affinities between Ufd2a variants and VCP/p97 mutants were analyzed. Several VCP/p97 mutants are associated with Inclusion body myositis in association of Paget's disease of the bone and fronto temperal dementia (IMBPFD). It was found that Ufd2a bound strongest to the VCP disease causing mutant A232E. It was also determined that the muscle specific isoform of Ufd2a, Ufd2a III, did not interact with VCP/p97.

Trace Metals (Cu, Zn, Cd And Pb) In Juvenile Fish From Estuarine Nurseries Along The Portugese Coast, Rita P. Vasconcelos, Patrick Reis-Santos, Anabela Maia, Miguel Ruano, Maria J. Costa Universidade De Lisboa

Faculty Publications

Organic and inorganic pollution can impact organisms directly and affect condition, growth and survival of juvenile fish which use estuaries as nurseries, and thereby affect marine adult populations quantitatively and qualitatively. Trace element contamination (Cu, Zn, Cd, Pb) in juveniles of commercial fish Solea solea, Solea senegalensis, Platichthys flesus, Diplodus vulgaris and Dicentrarchus labrax collected in putative nurseries of the main Portuguese estuaries (with diverse intensities and sources of anthropogenic pressures) was determined via atomic absorption spectrometry. Contamination was significantly different among species. Similar levels of contamination were found among estuaries, except for D. vulgaris. Cu and Zn concentrations …