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Conjecturing In Dynamic Geometry: A Model For Conjecture-Generation Through Maintaining Dragging, Anna Baccaglini-Frank

Doctoral Dissertations

The purpose of this research is to study aspects of the impact of Dynamic Geometry Systems (DGS) in the process of producing conjectures in Euclidean geometry. Previous research has identified and classified a set of dragging schemes spontaneously used by students. Building on these findings, the study focuses on cognitive processes that arise in correspondence to particular dragging modalities in Cabri. Specifically, we have conceived a model describing what seems to occur during a process of conjecture-generation that involves the use of a particular dragging modality, described in the literature as dummy locus dragging. In order to accomplish this goal, …

The Effects Of Didemnum Vexillum Overgrowth On Mytilus Edulis Biology And Ecology, Linda Ann Auker

Doctoral Dissertations

Didemnum vexillum is an invasive colonial ascidian in the Gulf of Maine that readily colonizes hard substrates. These substrates include hard-shelled organisms, such as the common blue mussel Mytilus edulis. Preliminary observations and short-term studies showed potential effects of epibiosis on M. edulis growth, specifically lip thickness and tissue index. This dissertation study further examined the effects of D. vexillum on growth and reproduction of, and predation on, M. edulis. Shell thickness index, tissue index, shell mass to tissue mass ratio, lip thickness and mussel length were measured throughout a 12-month period in control and overgrown mussels. Additionally, histological preparations …

Trematode Parasites Of The Mudsnail Ilyanassa Obsoleta: An Analysis Of Parasite Communities At Different Scales, Irit Altman

Doctoral Dissertations

This research examines the ecological factors that shape trematode parasite communities of mudsnail Ilyanassa obsoleta at three different spatial scales. Nine species of trematode which obligately infect I. obsoleta during larval stages but use numerous estuarine species as second intermediate and definitive hosts are considered. The work provides the most geographically extensive examination to date of this trematode parasite community.

At the broadest scale, I. obsoleta trematodes were examined across their distributional range (Chapter 2) which includes both native and introduced populations. The results demonstrate that introduced trematode communities are characterized by lower abundance and diversity compared to native communities …

Movement And Behavior Of Ocean Sunfish, Mola Mola, In The Northwest Atlantic, Inga F. Potter

Doctoral Dissertations

The ocean sunfish, Mola mola, has a worldwide distribution and is a common resident of the NW Atlantic Ocean. Notable for its unusual anatomy and large size, the biology of the species is largely unknown. I examined the movement and behavior of M. mola using pop-up satellite archival tags (PSAT's). In addition, analysis of aerial survey data was conducted to determine the distribution of ocean sunfish (Family Molidae) in NW Atlantic shelf waters. Data was analyzed from twenty-five PSAT's deployed on M. mola in the northwest Atlantic between 2005 and 2008. Tags were attached from 7-242 days. Results indicate that …

Factors Regulating The Production Of Stx-2 In Escherichia Coli O157:H7, Kate P. Stefani

Doctoral Dissertations

The severity of Escherichia coli O157:H7 disease is due in part to a major virulence factor produced by the microbe, the shiga-like toxin 2 (Stx-2). Antibiotic treatment to reduce pathogen numbers is controversial, as it is thought that antibiotics may increase the levels of Stx-2 released from the pathogen. Currently, recommended treatment for E. coli O157:H7 is palliative The purpose of this study was to examine three critical factors potentially important to disease outcomes, and to determine their effect on expression of the stx2 gene and on release of Stx-2 from the pathogen. Those factors selected for study were: (i) …

Somatic Condition, Growth And Distribution Of Atlantic Bluefin Tuna (Thunnus Thynnus) In The Gulf Of Maine, Walter J. Golet

Doctoral Dissertations

Atlantic bluefin tuna (Thunnus thynnus), a highly migratory apex predator, utilize temperate feeding grounds to place their tissues into positive lipid balance following reproduction and subsequent migration to northern latitudes. Commercial fishermen target Atlantic bluefin tuna between June and October, but landings have declined 70% from 2004-2009 suggesting adult bluefin tuna may no longer be utilizing the Gulf of Maine as a foraging ground. A series of linear and additive models fitted to multiple fishery dependent datasets identified significant declines in the somatic condition of Atlantic bluefin tuna in the Gulf of Maine. Significant changes in the somatic condition of …

Building Better Scientists Through Cross-Disciplinary Collaboration In Synthetic Biology: A Report From The Genome Consortium For Active Teaching Workshop 2010, Michael J. Wolyniak, Consuelo J. Alvarez, Vidya Chandrasekaran, Theresa M. Grana, Andrea Holgado, Christopher J. Jones, Robert W. Morris, Anil L. Pereira, Joyce Stamm, Talitha M. Washington, Yixin Yang

Biological Sciences Research

A common problem faced by primarily undergraduate institutions is the lack of funding and material support needed to adequately expose students to modern biology, including synthetic biology. To help alleviate this problem, the Genome Consortium for Active Teaching (GCAT) was founded in 2000 by Malcolm Campbell at Davidson College to bring genomics into the undergraduate curriculum. GCAT’s first tangible activity was to serve as a central clearinghouse both for the purchase and reading of DNA microarrays and for information on how to execute genomics experiments at undergraduate institutions. In response to the evolution of molecular biology in the last decade, …

Population Genetics, Species Boundaries, And Conservation Of The Jollyville Plateau Salamander, Eurycea Tonkawae, Paul T. Chippindale

KIP Data Sets and Technical Reports

Report submitted to the Texas Parks and Wildlife Department in fulfillment of contract 184467. The report was prepared while the author was affiliated with the University of Texas at Arlington. The author evaluated the genetics variation and population structure of the Jollyville Plateau salamander, Eurycea tonkawae. This information was used to recommend conservation strategies for this species and others found in similar environments. Open Access See Extended description for more information.

Introduction: Protistan Biology, Horizontal Gene Transfer, And Common Descent Uncover Faulty Logic In Intelligent Design, Avelina Espinosa

Arts & Sciences Faculty Publications

THE International Society of Protistologists (ISOP) organized a pre-meeting workshop entitled ‘‘Horizontal Gene Transfer and Phylogenetic Evolution Debunk Intelligent Design,’’ as part of the 1st North American Section meeting held June 11–13, 2009, at Roger Williams University, Bristol, RI, USA. This workshop focused on the acceptance of Darwinian evolution in the United States and the role of intelligent design (ID) in the ongoing controversy between scientific knowledge and popular belief. Intelligent design, a doctrine born in the 1980s, proposes that a ‘‘Designer’’ is responsible for the complexity in biological systems and that Darwinism cannot explain holistically the origin and evolution …

Bacterial Acquisition In Juveniles Of Several Broadcast Spawning Coral Species, Koty H. Sharp, Kim B. Ritchie

Arts & Sciences Faculty Publications

Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, …

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Truncated Mortalin In Animal Cancer, Katrina K. Olson

Master's Theses and Capstones

Hematopoetic neoplasia or clam hemocyte cancer (a leukemia-like disease) has been studied in a number of bivalve molluscs for the last 20 years. Recent molecular studies of the hemocytes of the soft shell clam, Mya arenaria, have demonstrated an interaction between p53 and mortalin, the mitochondrial Hsp70. The former protein is intimately involved in the initiation of cell-cycle arrest, apoptosis, DNA repair, and cell differentiation. In cancerous clams, wild-type p53 is sequestered in hemocyte cytoplasm by mortalin and cannot be translocated to the nucleus. This is critical because although p53 is functions properly, it is unable to enter the nucleus …

Landscape Genetics Of The New England Cottontail: Effects Of Habitat Fragmentation On Population Genetic Structure And Dispersal, Lindsey E. Fenderson

Master's Theses and Capstones

The New England cottontail (Sylvilagus transitionalis) is a species of conservation concern. Population recovery will require knowledge of genetic structure and dispersal patterns. To this end, I used microsatellite loci to assess genetic structure at two spatial scales: across the entire range (broadscale) and within the northernmost population (finescale).

Range-wide, cottontails are separated into five distinct populations. There was little evidence of gene flow among populations and they have experienced extensive genetic drift. Several populations had comparatively reduced genetic diversity.

Intensive fine-scale surveys revealed four genetically differentiated populations. Interstate-95 is a dispersal barrier, though other major roads did not impact …

Variation In Foliar Nitrogen And Albedo In Response To Nitrogen Fertilization And Elevated Carbon Dioxide, Haley F. Wicklein

Master's Theses and Capstones

It has recently been demonstrated that foliar nitrogen is positively correlated with surface albedo over a broad range of plant functional types. However, the mechanism(s) driving the nitrogen-albedo relationship remain elusive. This study investigated leaf spectral properties from three deciduous species subjected to either nitrogen or CO2 fertilization and compared results to measured chemical and structural properties. We measured reflectance and transmittance, foliar nitrogen, leaf mass per unit area, water content, and d13C values for stacks of 1, 2, 4, and 8 leaves. Nitrogen was the best predictor of leaf-level albedo of the traits that we measured. There were no …

Genomic Resource Development For A Diploid Mint: Mentha Longifolia, Zahra Hadadian

Master's Theses and Capstones

This research project aimed to develop genomic resources needed to enable construction of a genetic linkage map of the diploid mint species Mentha longifolia. Such a map would facilitate identification of plant genes involved in resistance to Verticillium fungal infection. For this purpose, a small genomic library was constructed from germplasm accession CMEN 585, 279 genomic inserts were sequenced and annotated and 19 PCR primer pairs were designed and tested on two resistant and two susceptible accessions. The Cleaved Modified Polymorphic Sequence (CAPS) method of molecular marker genotyping was found to detect little variation between crossing parents CMEN 585 (resistant) …

Abiotic Immobilization Of Nitrate In Forest Soil: A Double Level Approach, Richard Graham Maclean

Master's Theses and Capstones

Abiotic immobilization of nitrogen may help explain nitrogen retention in soils under chronic nitrogen addition. Methodological limitations have made differentiating between abiotic and biotic immobilization in live soils difficult. This study attempted to make this differentiation with isotopically labeled nitrate, 15N18O3- . My hypothesis was that during biological reduction and assimilation of 15N, 18O would be lost as labeled water, but some 18O would be retained in abiotic reactions with soil chemicals. Lab incubations of soils from a Pinus resinosa stand were treated with 0.140 mg 15N g-1 dry soil of K15N18O3, for 0.25, 1 and 4 hours. Mean mass …

Regulation Of Photoreceptor Phosphodiesterase By Prenyl Binding Protein And By Other Interacting Proteins In Photoreceptor Cells, Hannah J. Gitschier

Master's Theses and Capstones

Photoreceptor phosphodiesterase (PDE6) is a central component of the visual pathway. While initial PDE6 activation following light stimulation of photoreceptors is well understood, regulation of PDE6 during recovery and light adaptation may require additional components that interact with PDE6. Two approaches were taken to characterize these potential interactions. The first explored the interaction of PDE6 with prenyl binding protein (PrBP/delta) and demonstrated that changes in membrane localization of PDE6 may occur during light adaptation as a result of association with PrBP/delta. The second approach characterized the PDE6 "interactome" by a mass spectrometric identification of 75 proteins that co-purify with PDE6 …

The Genetics Of Sex Determination In Fragaria Virginiana: A Candidate Gene Approach, Benjamin Bryant Orcheski

Master's Theses and Capstones

The evolutionary genetics of plant reproduction is a fascinating aspect of plant biology, involving an astounding diversity of reproductive strategies. While the majority of flowering plants are hermaphroditic (monoecy), many species have opted for an alternate mode, whereby male and female gametes originate on different plants (dioecy).

Wild strawberry, Fragaria virginiana, is a particularly interesting species, as its members can be female, male, or hermaphroditic. Its female flowers display arrested development of male reproductive organs (stamens), evidently conditioned by a single dominant allele of an unknown genetic locus. My aim was to isolate and characterize the gene(s) responsible for male …

A Geometric Approach For Deciphering Protein Structure From Cryo-Em Volumes, Sasakthi Abeysinghe

All Theses and Dissertations (ETDs)

Electron Cryo-Microscopy or cryo-EM is an area that has received much attention in the recent past. Compared to the traditional methods of X-Ray Crystallography and NMR Spectroscopy, cryo-EM can be used to image much larger complexes, in many different conformations, and under a wide range of biochemical conditions. This is because it does not require the complex to be crystallisable. However, cryo-EM reconstructions are limited to intermediate resolutions, with the state-of-the-art being 3.6A, where secondary structure elements can be visually identified but not individual amino acid residues. This lack of atomic level resolution creates new computational challenges for protein structure …

An Evaluation Of Habitat Models For The Common Loon (Gavia Immer), Alexis M. Rudko

Master's Theses and Capstones

The Loon Preservation Committee (LPC) has been collecting field data for the common loon (Gavia immer) in New Hampshire for thirty-six years. A habitat model for lakes throughout New Hampshire was created by Dr. Mark Brennan for the time period 1980--2002. This project re-evaluates Brennan's habitat model using new data from 2003--2008. Two additional models, one with all lakes and another with the three largest lakes excluded, were created and compared to Brennan's model to see if the overall accuracy improved. These models show which lakes have high and low potential for loon habitat. The results of the re-evaluation of …

Role Of Protein Kinase Ck2 And Phosphatase Pp2a In Notch-Mediated Lateral Inhibition, Anasua Bose

Graduate Theses, Dissertations, and Problem Reports (ETD)

The Notch signaling pathway is highly conserved in vertebrates and invertebrates and regulates binary cell fate specifications in diverse developmental contexts. In a process termed lateral inhibition, Notch signaling restricts a particular cell fate to a single cell from a group of multi-potential cells. This mechanism ensures precision in cell fate assignations, which are vital for histogenesis and organogenesis. Studies during Drosophila neurogenesis, specifically development of the compound eye and the mechanosensory bristles, have provided the most detailed insights into the underlying mechanisms. During this process, Notch signaling results in the selection of single R8 photoreceptors or bristle sensory organ …

A Multi-Scale Evaluation Of Eastern Hognose Snake (Heterodon Platirhinos) Habitat Selection At The Northern Extent Of Its Range, Celine Goulet

Master's Theses and Capstones

A complex interaction of biotic and abiotic variables structure landscapes into a hierarchal assemblage of habitats. Species respond to this environmental hierarchy by selecting habitat based upon a set of ecological variables occurring across a range of organizational levels. However, as the criteria for selection may be scale-dependent, it is vital to quantify the influence these variables have on species distribution at each spatial scale. Two years of telemetry data from 17 individuals were used to examine the multi-scale selection process in the northern population of Heterodon platirhinos on the New Boston Air Force Station in New Boston, New Hampshire. …

Aspects Of The Reproduction Of An Invasive Crab, Hemigrapsus Sanguineus, In Northern And Southern New England, Emily F. Gamelin

Master's Theses and Capstones

Populations of the invasive shore crab, Hemigrapsus sanguineus , were studied in northern and southern New England to determine if crabs differ in reproductive behavior or characteristics between these regions. Additionally, effects of temperature on reproductive activity were quantified through laboratory experimentation.

Number of broods per season increased with temperature, but the seasonal total was limited to three broods in laboratory experiments. Broods experienced limited success at the lowest temperature, 10°C. The reproductive season was longer at lower latitudes, and females at this site had smaller average ovigerous size. Patterns of ovigery varied between the regions, suggesting the production of …

Investigating Pheromone Variability In A Terrestrial Woodland Salamander, Adam James Chowinard

Master's Theses and Capstones

The communication system of Plethodontid salamanders relies heavily upon chemical signaling. Pheromone molecules convey a tremendous amount of information to conspecifics, and facilitate a wide variety of the essential social functions of these animals. Much of the information contained within the pheromone mixture is variable from one individual to the next, such as the ability to recognize specific individuals, the size of the sender, and the relative "quality' of the signal. In order for variable information to be conveyed through chemical signals, the corresponding variability must be contained within the pheromone mixture itself. This variability may exist as a gradient …

Elucidating The Microbial Community Within A Trichloroethene Contaminated Competent Bedrock Aquifer Located At Pease International Tradeport, Portsmouth, Nh, Michelle M. Majko

Master's Theses and Capstones

A trichloroethene (TCE)-contaminated competent bedrock aquifer exists at Pease International Tradeport in Portsmouth, NH. Characterization by the Bedrock Bioremediation Center (BBC) at the University of New Hampshire showed active in situ anaerobic degradation of TCE. Formation water from discrete, hydraulically connected fractures was extracted to characterize and enumerate the prevalent TCE biodegradation processes using Fluorescent in situ hybridization (FISH). Eubacteria (90%), Archaea (5%), and sulfate reducing bacteria within Desulfobacteriaceae (1--26%) were present at all depths (13--30 meters). Two probes targeting the anaerobic TCE-dechlorinating genus, Dehalococcoides (4--10%) were developed. FISH in combination with Flow Cytometry was employed to automate the analysis; …

Modeling Permafrost Stability In Peatlands With Climate Change And Disturbance, Claire Treat

Master's Theses and Capstones

Boreal and arctic regions are predicted to warm faster and more severely than temperate latitudes. They contain large stocks of below- ground soil carbon in peatlands and frozen soil, and the flux of the soil C to the atmosphere may be a strong feedback to climate change.

Increases in air temperature due to climate change will increase surface soil temperatures, soil temperatures at depth, active layer depths, and growing season length, but not degrade permafrost by 2100 at this site. Both wildfire and climate change increase active layer depths by 25 cm, but effects of wildfire diminish following vegetation recovery.

Nifh Diversity Associated With Montastraea Cavernosa Identified Using An Optimized Primer Protocol, Nathan D. Olson

Master's Theses and Capstones

The diversity of nitrogen fixing bacteria in any system must be identified to in order to fully understand their ecological role. PCR is commonly used to investigate bacterial diversity. To capture the full diversity PCR primers must bind to and amplify all targeted DNA sequences. For this study I analyzed published universal nifH primers' ability to capture the full diversity of nitrogen fixing bacteria. Based on this work I developed a new protocol for capturing the full diversity of nifH sequences. Using this optimized protocol I investigated community differences in nitrogen fixing bacteria between orange and brown color morphs of …

Phenotypic Characterization Of Palmitoyltransferase Mutants Of Arabidopsis Thaliana, Ulkucan Kaplan

Master's Theses and Capstones

This study seeks to understand the effects of loss of palmitoylation catalyzed by PAT14 on the phenotype of Arabidopsis thaliana. In this project, I focused on two T-DNA insertion mutants of the PAT14 gene in Arabidopsis thaliana: pat14-1 and pat14-2. PAT14 is one of 23 PAT genes encoding palmitoyltransferase (PAT) proteins in Arabidopsis thaliana. PAT proteins are responsible for palmitoylation, one of several cellular mechanisms to modify proteins by lipidation. The purpose of this research was to describe the effect of T-DNA insertion mutations in the PAT14 gene on the phenotype of Arabidopsis thaliana plants. Characterization of palmitoyltransferase mutants of …

Microbial Interactions With Oysters From The Great Bay Estuary: Characterization Of Endemic Vibrio Choleraeand Oyster Metagenetics, Brian Michael Schuster

Master's Theses and Capstones

Within the last two decades the number of gastroenteritis seafood-borne outbreaks due to Vibrio species has increased. These infections are usually caused by the consumption of raw or undercooked shellfish. I took two approaches to describe the ecology of Vibrios in the Great Bay Estuary, Durham, New Hampshire. First, I performed a phenotypic and multi-locus sequence analysis of 31 V. cholerae strains isolated from oysters, water and sediment in 2008 and 2009. I concluded that the V. cholerae population is endemic, diverse and highly recombinatory, but none of the isolates contain the virulence markers indicative of clinical strains. Next, I …

The Influence Of Stocking Density And Acoustic Conditioning On The Behavior And Growth Of Atlantic Cod, Gadus Morhua, Daniel Ward

Master's Theses and Capstones

The goal of experiment one (Chapter One) was to determine if stocking density had an influence of the swimming behavior and spatial distribution of adult cod that were being raised in an aquaculture cage at the University of New Hampshire's Coastal Marine Laboratory. Acoustic telemetry and underwater video were used to quantify the behavior and distribution of cod that were stocked at four densities (5, 10, 25 and 45 kg/m³). At the lowest density (5 kg/m³) cod remained deep in the cage and spent 64.3 +/- 0.8% of their time below 1.80m (of a 2.70m cage). This contrasts to the …