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Integration Of Raman Spectroscopy And Python-Based Data Analysis For Advancing Neurobiological Research, Natalie E. Dunn

Doctoral Dissertations

The field of Raman spectroscopy continues to expand into biological applications due to its usefulness as a non-invasive technique that can be utilized qualitatively and quantitatively. However, the inherent weakness of Raman scattering leads to the need for each collected spectra to undergo a preprocessing step to remove noise, background drift, and cosmic rays. Biological research in particular needs large datasets due to the increased variability in samples. As datasets grow, the need to perform preprocessing on each individual spectra becomes daunting. Often, these steps are done by hand with the help of specialized software programs. Preprocessing can be accelerated …

Evaluation Of The Epigenetic Regulation Of Two X-Linked, Autism Candidate Genes: X-Linked Lymphocyte Regulated 3b And Transketolase-Like 1, Glenn W. Milton

Doctoral Dissertations

According to the CDC the prevalence of Autism Spectrum Disorder (ASD) in males compared to females is approximately 5:1. Skuse et al. hypothesized that imprinted genes on the X chromosome could account for this sex bias. Genomic imprinting is defined as differential gene expression dependent upon the parental origin of the allele. While genomic imprinting on autosomes has been well classified, no imprinting mechanism on the sex chromosomes has been discovered. This work presents an investigation into the regulation of expression governing the imprinted locus of X-Linked Lymphocyte Regulated 3b/4b/4c (Xlr3/4), and closely linked ASD candidate gene, Transketolase-Like …

Development Of Protein Display Systems And Genetic Tools For Spore-Forming Bacteria, Erin Drufva

Doctoral Dissertations

One major area of synthetic biology is to engineer microbial cells and subcellular systems for diverse applications including biosynthesis, biocatalysis, therapeutics, drug delivery, and bioremediation. For most applications, robust cellular systems are preferred for longer activity half-life and resistance to harsh environments. Two projects related to robust cellular systems involving Gram-positive bacteria are presented in this work. One is to develop thermostable genetic reporters for Geobacilli species and the other is to display an enzyme on the Bacillus subtilis spore surface to enhance its robustness and present an alternative to purified enzymes for industrial applications.

Bacillus subtilis and Geobacillus thermoglucosidans …

Use Of Multimedia Games For Biology Vocabulary Instruction, Ian Murray

Doctoral Dissertations

Vocabulary knowledge is considered fundamental to learning. However, students typically find learning scientific vocabulary quite difficult, and that is especially true for biology vocabulary. Games are well established as effective tools for vocabulary instruction. Multimedia instruction is likewise recognized as aiding vocabulary learning. To date, however, there seems have been little examination of the use of multimedia games in biology vocabulary instruction. This study, therefore, compared the effectiveness of digital multimedia games and traditional instruction in teaching biology vocabulary.

A two-group, quasi-experimental study was carried out over the course of 61 days. Participants were a convenience sample of 10 high …

Development Of Novel Bio- And Heterogeneous Catalysts For The Production Of Bio- And Green Diesel, Ye Deng

Doctoral Dissertations

Diminishing petroleum reserves and increasing environmental awareness has led to an urgent need to develop alternative fuels, such as biodiesel. Enzymatic trans/-esterification of waste cooking oils with a lipase catalyst is a promising environmentally-friendly process to produce biodiesel, compared to the current industrial chemical process. Despite several advantages, there are a few technical and economical obstacles that limit this process, such as insufficient availability of large quantities of inexpensive lipase suitable for catalysis, and bad performance at low temperatures due to biodiesel’s low cetane number. These limitations are addressed in this dissertation using genetic engineering of plants to produce the …

Genomic Evaluation Of Male Reproductive Adaptations And Responses To Dehydration In Peromyscus Eremicus (Cactus Mouse), Lauren Kordonowy

Doctoral Dissertations

Research elucidating the genetic architecture of physiological mechanisms enabling survival and reproduction in extreme environments is becoming prominent in evolutionary biology. The desert, in particular, poses numerous challenges for its endemic species, and mammals (and often, rodents) have been the focus for survival adaptations pertaining to water-limitation. However, desert rodent adaptation research has focused predominantly on survival, while potential physiological reproductive adaptations to dehydration have received less attention, aside from research evaluating water as reproductive cue. The fact that we do not know the physiological mechanisms enabling reproduction during dehydration is surprising, as desert rodents must possess adaptations to successfully …

Channeled Whelk (Busycotypus Canaliculatus) Ecology In Relation To The Fishery In Vineyard And Nantucket Sounds, Massachusetts, Shelley Ann Edmundson

Doctoral Dissertations

Channeled whelks (Busycotypus canaliculatus) are predatory marine gastropods that support lucrative commercial fisheries along the east coast of the United States, with areas around Massachusetts supplying the largest landings. In the absence of a more thorough and comprehensive understanding of channeled whelk biology, it is unclear how to sustainably manage their fisheries. Within this dissertation, various aspects of whelk ecology were investigated to determine how to protect this species, while effectively managing the local fishery.

Early life history experiments revealed channeled whelk egg strings may incubate for 8 to 9 months in MA water temperatures. Incubation period decreased with increasing …

Estimation Problems In Complex Field Studies With Deep Interactions: Time-To-Event And Local Regression Models For Environmental Effects On Vital Rates, Krzysztof M. Sakrejda

Doctoral Dissertations

Field studies that measure vital rates in context over extended time periods are a cornerstone of our understanding of population processes. These studies inform us about the relationship between biological process and environmental noise in an irreplaceable way. These data sets bring ``big data'' and ``big model'' challenges, which limit the application of standard software (e.g., \textbf{BUGS}). The environmental sensitivity of vital rates is also expected to exhibit interactions and non-linearity, which typically result in difficult model selection questions in large data sets. Finally, long-term ecological data sets often contain complex temporal structure. In commonly applied discrete-time models complex temporal …

The Foliose Bangiales (Rhodophyta) In The Northern Part Of The North Atlantic And The Relationship With The North Pacific Foliose Bangiales - Diversity, Distribution, Phylogeny And Phylogeography, Agnes Mols-Mortensen

Doctoral Dissertations

Foliose Bangiales species have a long history of study in the North Atlantic, but regions, especially in the northern parts, need more attention. Based on both new collections and herbarium material from Iceland, the Faroe Islands, West Greenland, UK, Norway, Sweden, Denmark and the Northwest Atlantic coast (from Newfoundland to Florida) the aim was to document diversity and distribution of foliose Bangiales species in the North Atlantic and to make floristic comparisons between the geographical areas. Species Identification was based on DNA sequences using the mitochondrial cox1, chloroplast rbcL and 3' rbcL + 5' rbcL-S markers. The North Atlantic species …

Intermittent Swim Stress Effects On Anxiety Behavior, Timothy A. Warner

Doctoral Dissertations

Millions of Americans are suffering from depression each year, leading to a significant number of individuals who seek treatment for their ailment. However, fewer than 50 percent of depressed individuals fully recover using current methods. The comorbidity between depression and anxiety could be a contributing factor in the lower rates of recovery. The demonstrated correlation between anxiety and depression has led to the term "anxious depression," which is associated with difficulty in coping, a poorer rate of recovery, and more severe symptoms of depression. The purpose of this dissertation was to expand on an existing animal model of depression (intermittent …

Mechanisms Of Nutrient Limitation And Nutrient Acquisition In Managed And Unmanaged Forest Ecosystems, Matthew A. Vadeboncoeur

Doctoral Dissertations

Understanding the interactions between global change, human and natural disturbances, and other factors on biogeochemical processes in forests is necessary to ensure the sustainability of forest management. Here I report the results of several investigations into nutrient acquisition processes in the forests of New Hampshire. I begin with a meta-analysis of fertilization studies showing that phosphorus (P) and calcium (Ca) as well as nitrogen (N) may limit primary production in deciduous forests of the region. Because these limiting nutrients are all removed from the ecosystem when trees are harvested, I compared nutrient budgets under a range of harvesting scenarios with …

Identification And Stoichiometric Analysis Of The Monosomal Translational Complex, Xin Wang

Doctoral Dissertations

The identification of the components involved in translational complexes has relied primarily on in vitro studies. Determining which proteins associate together in these complexes, under what conditions they do so, and how the composition of the complexes change under different conditions have became the key issues of in vivo studies. After a one-step affinity purification, using a novel technique of analytical ultracentrifugation with a fluorescence detection system (AU-FDS) I have identified a 77S monosomal translational complex in the yeast Saccharomyces cerevisiae. Major components of the 77S complex include the 80S ribosome, mRNA, and components of the closed-loop structure, eIF4E, eIF4G1/eIF4G2 …

Interactions Of Shiga-Like Toxin-2 (Stx-2) From Escherichia Coli O157:H7 And The Bcl-2 Family Of Proteins During Host Cell Programmed Cell Death, Lia K. Jeffrey

Doctoral Dissertations

Stx-2 is a major contributor to the pathogenesis of Escherichia coli 0157:H7. Prior reports suggest that Stx-2 increases necrosis and apoptosis of a variety of host cells including those of endothelial origin as well as immune cells such as neutrophils (156). However, the role Stx-2 plays in delayed apoptosis of neutrophils is not fully understood given that previous studies have shown conflicting results (118, 51). The process of apoptosis is mediated by the Bcl-2 protein family (2, 46, 226). The purpose of this research was to define the molecular mechanisms of Stx-2 and Bcl-2 protein family interactions. These studies examined …

Characterization Of The Expression Profile Of Polyamine Biosynthetic Genes (Spermidine Synthase) And Polyamine Metabolic Regulation In Arabidopsis, Lin Shao

Doctoral Dissertations

Polyamines are ubiquitously distributed cationic compounds, which play important roles in numerous cellular functions in plants. This study was aimed at elaborating the regulation of polyamine biosynthetic gene expression and polyamine metabolism. The organ/tissue specific expression patterns of two genes encoding the polyamine biosynthetic enzyme spermidine synthase ( AtSPDS1 and AtSPDS2) were studied in Arabidopsis at different developmental stages using promoter::reporter approach. The two homologues showed similar ubiquitous expression with subtle differences being observed in certain tissues (e.g. root, siliques, and embryos). Neither transgenic manipulation by over-expression of AtSPDSI alone nor its concomitant expression with genes encoding other biosynthetic enzymes …

Engineering Lipases And Solvents For Trans/-Esterification Of Used Vegetable Oils, Michael Dore Gagnon

Doctoral Dissertations

Diminishing petroleum reserves and increasing environmental awareness has led to an urgent need to develop alternative fuels, such as biodiesel. However, the conventional method to produce biodiesel uses environmentally harmful chemical catalysts. A relatively new development in the production of biodiesel is through enzymatic trans/- esterification with a lipase catalyst. Despite several advantages, there are a few technical and economical obstacles that limit this process: (1) immiscibility of the hydrophilic methanol and hydrophobic triglyceride which results in the formation of an interface leading to mass transfer resistance, (2) insufficient availability of large quantities of inexpensive lipase suitable for catalysis, and …

Characterization Of The Prokaryotic Community Associated With The Giant Barrel Sponge, Xestospongia Muta Across The Caribbean, Cara L. Fiore

Doctoral Dissertations

Sponges have long been known to be ecologically important members of the benthic fauna on coral reefs. Recently, it has been shown that sponges, and their symbiotic microbes, are also important contributors to the nitrogen biogeochemistry of coral reefs. Here, I investigate the ecology and physiology of the microbial community associated the ecologically dominant sponge, Xestospongia muta. A natural experiment was conducted with X. muta form three different locations (Florida Keys, USA; Lee Stocking Island, Bahamas, and Little Cayman, Cayman Islands) to compare nitrogen cycling and prokaryotic community composition. The dissolved inorganic nitrogen (DIN) fluxes of sponges were studied using …

The Effects Of Biotic And Abiotic Factors On Byssogenesis, Growth And Movement Patterns Of The Blue Mussel, Mytilus Edulis, Yvette Louise Garner

Doctoral Dissertations

Blue mussels create extensive aggregations on intertidal and low subtidal shores in the Gulf of Maine, in which they modify habitat, trap sediments and create microclimates for many organisms. Mussels are an important aquaculture species worldwide, and play a major part of the economy of New England. Blue mussels produce collagenous byssal threads to anchor themselves to the substrate on wave swept shores. Byssogenesis, growth and movement abilities of mussels are influenced by a host of biotic and abiotic factors. In this dissertation I quantified byssogenesis and growth of the blue mussel, Mytilus edulis, affected by wave exposure, temperature, and …

Regulation Of The Catalytic And Allosteric Properties Of Photoreceptor Phosphodiesterase (Pde6) By The Glutamic Acid-Rich Protein-2 (Garp2), Wei Yao

Doctoral Dissertations

The photoreceptor phosphodiesterase (PDE6) must be precisely regulated to control the sensitivity, amplitude, and kinetics of the photoresponse during excitation, termination and adaptation to light stimulation in rod and cone photoreceptors. The central hypothesis of this thesis is that one PDE6 binding partner, the glutamic acid-rich protein (GARP2), may regulate PDE6 to reduce its "dark noise", enhance its sensitivity and conserve metabolic energy during rod photoresponse saturation.

The first aim of this research is to better understand the unique biochemical and biophysical characteristics of GARP2 in order to reveal its functional attributes for regulating PDE6 during phototransduction in rod photoreceptors. …

Movements, Dive Behavior And Trophic Ecology Of Leatherback Turtles (Dermochelys Coriacea) In The Northwest Atlantic, Kara Dodge

Doctoral Dissertations

The endangered leatherback turtle is a highly migratory predator that feeds exclusively on gelatinous zooplankton. Leatherbacks spend most of their lives submerged or offshore, and their at-sea biology (particularly that of males and sub-adults) is poorly understood throughout much of their range. I used satellite telemetry to monitor movements and dive behavior of nine adult and eleven sub-adult leatherbacks captured off Massachusetts, USA, and tracked throughout the NW Atlantic. Leatherback movements and environmental associations varied by oceanographic region, with slow, sinuous, area-restricted search behavior and shorter, shallower dives occurring in cool, productive, shallow shelf habitat at temperate latitudes. Leatherbacks were …

Patterns Of Cytosine Methylation In The Genome Of Caenorhabditis Elegans, Kazufusa Okamoto

Doctoral Dissertations

Recent large-scale comparative analysis of cytosine DNA methylation across diverse eukaryotes suggest that early features of DNA methylation present in the last common ancestor of all eukaryotes some 1.6 to 1.8 billion years ago included the methylation of gene bodies and transposable elements (Zemach, McDaniel et al. 2010; Parfrey, Lahr et al. 2011). These potentially ancient patterns may reflect a primitive role of methylation in transcriptional fidelity and as a mechanism to protect the germ line from transposon, or repeat, mediated mutation. Because spurious transcription and mutation are hypothesized to be among the critical limiting factors to genome size, an …

Tracking Environmental Trends In The Great Bay Estuarine System: An Examination Of Water Quality And Nuisance Macroalgal Blooms, Jeremy C. Nettleton

Doctoral Dissertations

Monitoring macroalgae populations is an effective means of detecting long term water quality changes in estuarine systems. To investigate the environmental status of New Hampshire's Great Bay National Estuarine Research Reserve, this study assessed the abundance/distribution of macrophytes, particularly Gracilaria and Ulva species, relative to eutrophication patterns; compared historical (1970s-1990s) and current algal biomass/cover at several sites; and compared Ulva and Gracilaria tissue N/P content to ambient and historical levels. Nitrogen and phosphorus testing revealed that the estuarine system has become eutrophic, and Ulva and Gracilaria biomass/cover have increased significantly. The percent cover of Ulva species, at seasonal maxima, was …

The Impact Of Seasonal Movements By Ovigerous American Lobsters (Homarus Americanus) On Egg Development And Larval Release, Jason Seth Goldstein

Doctoral Dissertations

The American lobster (Homarus americanus) supports one of the most economically successful fisheries in the Gulf of Maine. The continued success of this fishery is attributed in part to vigilant broodstock conservation through the preservation of ovigerous (egg-bearing) females. Previous studies of ovigerous lobster movements indicate that some, if not most, display seasonal inshore-to-offshore movement patterns. While it has been assumed that these movements serve to expose eggs to thermal regimes that are optimal for development, this theory has never been rigorously tested. In Chapter 1, I present results from ultrasonic tracking studies designed to determine if lobsters in coastal …

Calcium Homeostasis In Escherichia Coli, Muhammad Arif

Doctoral Dissertations

While the role of calcium ions as secondary chemical messengers has been well described in eukaryotic cells, little is known about calcium homeostasis in bacteria at the physiological and molecular level. No calcium influx gene has been identified so far. This dissertation focuses on calcium regulation of gene expression by (i) determining the effects of elevated and depleted calcium levels on global gene expression in wild-type cells (MG1655), (ii) employing transposon mutants (calcium-sensitive) and mutants that are defective in calcium transport, and (iii) performing quantitative analysis of a specific subset of 15 genes to elucidate their possible involvement in calcium …

Effects Of Nitrogen-Fixing Symbiotic Cyanobacteria On The Microbial Ecology Of The Coral, Montastraea Cavernosa, Jessica K. Jarett

Doctoral Dissertations

Corals form the physical structure of coral reefs, one of the most ecologically and economically important ecosystems in the world. The abundant and broadly distributed Caribbean coral Montastraea cavernosa forms a symbiosis with intracellular nitrogen-fixing cyanobacteria in some, but not all colonies, which make up approximately 30% of the population and display a characteristic orange fluorescence. Diverse and functionally important microbial communities of dinoflagellates, bacteria, Archaea, viruses, fungi, and other organisms are also associated with corals and together with the host compose what is termed the coral holobiont. Whether the cyanobacteria are mutualists, commensals, or parasites, and their effects on …

Ecological Effects Of Ditching And Ditch-Plugging In New England Salt Marshes, Robert E. Vincent

Doctoral Dissertations

Anthropogenic activities in New England salt marshes have altered hydrologic flows in various ways, but unintended consequences from some of these habitat modifications have received little attention. Specifically, ditches have existed on salt marshes for decades, but the effects of these hydrologic alterations are only poorly understood. Ditch-plugging is a more recent methodology used for salt marsh habitat enhancement and mosquito control, but the long-term effects from this management practice are also unclear. I used natural tidal creeks and pools as controls to examine the effects resulting from ditching and plugging, respectively, on hydrology, soil characteristics, marsh surface elevation, plant …

The Role Of Red-Backed Salamanders In Ecosystems, Daniel J. Hocking

Doctoral Dissertations

Ecosystems provide a vast array of services that benefit human societies, which can be divided into provisioning, regulating, cultural, and supporting services. Amphibians provide provisioning services in the form of food and use in medical advances. As one of the major vertebrate groups, amphibians also play an important part in cultures throughout the world. Finally, amphibians can be extremely abundant and play important roles in ecosystem supporting services, including altering both physical structure and ecosystem functions. In aquatic systems, tadpoles can alter sedimentation, water clarity, and filamentous algae growth. Additionally, amphibians affect ecosystem functions, including nutrient cycling, decomposition, and primary …

An Investigation Of Non-Spatial Cognitive Abilities In An Asocial Corvid, The Clark's Nutcracker (Nucifraga Columbiana), Jan K. Tornick

Doctoral Dissertations

A great deal of research suggests that the cognitive abilities of birds in the family Corvidae (crows and jays) are comparable in many aspects to that of apes. Scientists have posited competing hypotheses to explain how complex cognitive abilities arise in a species or group of animals. One such hypothesis, the social-intelligence hypothesis, states that the demands of living in a large, dynamic group drive an animal's need for complex cognitive skills. The ecological-intelligence hypothesis, predicts that generalist foragers develop more highly flexible behaviors and a wider cognitive repertoire than specialist foragers. To date, cognitive research on corvids has focused …

Development Of Bio-Optical Algorithms To Estimate Chlorophyll In The Great Salt Lake And New England Lakes Using In Situ Hyperspectral Measurements, Shane Richard Bradt

Doctoral Dissertations

Chlorophyll is widely used to evaluate lake water quality, effectively integrating the chemical, physical and biological state of a lake. Assessment of chlorophyll conditions in lakes can be greatly enhanced by the use of remote sensing, allowing information to be gathered at spatial and temporal scales not possible with traditional limnological sampling methods. In order for remote sensing methods to provide accurate estimates of chlorophyll concentration, algorithms need to be developed with high-quality spectral data paired with water quality measurements and optimized for regional lake differences.

In this study, in situ hyperspectral optical measurements were used to develop algorithms to …

The Historical Fisheries In The Mediterranean Sea: A Reconstruction Of Trawl Gear, Effort And Trends In Demersal Fish Stocks, Giacomo Chato Osio

Doctoral Dissertations

An extensive search of historical data sources and publications has been carried out in different countries of the Mediterranean. This lead to the construction of the largest compilation of historical fisheries information existing in the Mediterranean region. The goal first here was to quantify historical trawling effort. This shows that Mediterranean demersal communities underwent a much longer and more systematic exploitation than previously thought, very likely the longest known exploitation by means of trawls in Europe and North America. Analysis of the data available for the Catalonian, Italian and French areas showed a clearly emerging pattern: fishing capacity increased in …

The Use Of Multibeam And Split-Beam Echo Sounders For Assessing Biomass And Distribution Of Spring-Spawning Atlantic Cod In The Gulf Of Maine, Christopher William Damon Gurshin

Doctoral Dissertations

This research focused on advancing the application of split-beam and multibeam echo sounding to remotely locate and describe spatial distribution, and to provide a relative measure of abundance of the spring-spawning Atlantic cod (Gadus morhua) in the western Gulf of Maine. Specifically, the main objectives of this research were 1) to test the feasibility of a multibeam echo sounder to detect changes in volume backscatter proportional to incrementally decreasing quantities of cod held in a submerged cage, and to compare results to a split-beam echo sounder; 2) to describe the spatio-temporal distribution and estimate biomass of spring-spawning cod in the …