Life Sciences Commons^™

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 …

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 …

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 …

Interaction Of Fish Aryl Hydrocarbon Receptor Paralogs (Ahr1 And Ahr2) With The Retinoblastoma Protein, Rebeka R. Merson, Sibel I. Karchner, Mark E. Hahn

Faculty Publications

The aryl hydrocarbon receptor (AHR) mediates the toxic effects of 2,3,7,8-tetrachlorodibenzo-pdioxin (TCDD) and related compounds. In some mammalian cell lines, TCDD induces G1 cell cycle arrest, which depends on an interaction between the AHR and the retinoblastoma tumor suppressor (RB). Mammals possess one AHR, whereas fishes possess two or more AHR paralogs that differ in the domains important for AHR-RB interactions in mammals. To test the hypothesis that fish AHR paralogs differ in their ability to interact with RB, we cloned RB cDNA from Atlantic killifish, Fundulus heteroclitus, and studied the interactions of killifish RB protein with killifish AHR1 and …

Species Vs. Height As Predictors Of Increased Growth Rate In New England Canopy Trees, Kiely Schultz

Honors Projects

As part of a larger study on the effect of an experimentally-created gap within a forest on adult canopy trees, focuses on the possible effect of tree height versus type of species on radial growth response to gap creation. Sample includes fifty trees within four transects next to a gap in the Yale-Myers Experimental Forest in Connecticut, with results showing that type of species affects radial growth response.

Localization Of Ufd2a Transcripts In Adult And Fry Zebrafish, Serena J. Kankash

Honors Projects

Examines the spacio-temporal expression of the three alternative splice forms of UFD2A in zebrafish to further understanding of UFD2A's role in muscle development

Expression Of Three Novel Alternative Splice Forms Of Ufd2a During Zebrafish Development, Nicole Gadbois

Honors Projects

Ufd2a is a ubiquitylation enzyme that is involved in protein degradation, cell division, and apoptosis signaling. Data has shown that cardiac and skeletal muscle cells of adult rodents and humans express alternatively spliced isoforms of Ufd2a. Ufd2a I (exons 1-6, 8-27) has been found to be expressed in murine myoblasts, but, upon differentiation, myotubes began to express Ufd2a II (includes exon 7), followed by Ufd2a III (includes exon 7a). Since zebrafish are an ideal in vivo model organism, this study examines the spatial-temporal expression patterning of Ufd2a and its isoforms in zebrafish embyros during development.

Dna Sequence Analysis Of A Bioluminescent Marine Bacterium, Benjamin Ryder

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

Studies the sequencing of the DNA fragment containing the gene phaC (PHA synthase) and undertakes the search for open reading frames and putative gene matches in a bioluminescent marine bacterium.

A Tale Of Two Investigations In Molecular Biology: The Use Of Pcr Technology To Identify Bacteria Containing Genes For Pha Synthesis And The Antibiotic Sensitivity Profile Of Vibrio Species B-18, Diana B. Lizarazo

Honors Projects

The Vibrio species, B-18, produces PHA, a bacterial storage material with application as a biodegradable plastic. Phase one of this project aimed at determining if PCR technology could be used to find other bacteria that produce a similar type of PHA. Results showed that the primer sets utilized were not able to identify bacteria with PHA genes. Phase two hoped to discover if it would be possible to introduce Escherichia coli plasmids into B-18 using electroporation. Results demonstrated that electroporation was not useful for introducing plasmids into B-18.

A Unified View Of Base Excision Repair, Karen H. Almeida, Robert W. Sobol

Faculty Publications

Base excision repair (BER) proteins act upon a significantly broad spectrum of DNA lesions that result from endogenous and exogenous sources. Multiple sub-pathways of BER (short-path or longpatch) and newly designated DNA repair pathways (e.g., SSBR and NIR) that utilize BER proteins complicate any comprehensive understanding of BER and its role in genome maintenance, chemotherapeutic response, neurodegeneration, cancer or aging. Herein, we propose a unified model of BER, comprised of three functional processes: Lesion Recognition/Strand Scission, Gap Tailoring and DNA Synthesis/Ligation, each represented by one or more multiprotein complexes and coordinated via the XRCC1/DNA Ligase III and PARP1 scaffold proteins. …