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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 …

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 …

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 …

Trace Metal Applications In Atmospheric And Watershed Dynamics: Case Studies Of Mercury Deposition In New England And Bedrock Groundwater-Surface Water Mixing, Melissa A. Lombard

Doctoral Dissertations

The studies presented in this dissertation focus on the environmental chemistry of two trace metals, mercury (Hg) and strontium (Sr). Both are naturally occurring and exist in the environment at trace levels.

Chapters II-IV of this dissertation focus on understanding the atmospheric chemistry of Hg and the wet and dry deposition of this toxic element. Chapter II presents results from Hg wet deposition measurements and ambient reactive gaseous Hg (RGM) measurements collected at Thompson Farm located in Durham, NH over a 3 year time period. The duration of this study allowed for seasonal and inter-annual comparisons. Seasonally, Hg wet deposition …

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 …

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 …

Educative Encounters: An Analysis Of Dewey, Buber And Noddings To Understand The Role Of Encountering Self, Others And The World In Teaching And Learning In Higher Education, Carrie Maureen Nolan

Doctoral Dissertations

This dissertation provides a novel conception of educative encounter as a means of providing a pedagogical framework for directing experience in the classroom for the purpose of cultivating growth, and specifically cultivating care (N. Noddings, 2003a). By honing in on encounter as the relational aspect of experience, emphasizing the importance of the relational quality of the learning experience, and articulating a different approach to teaching in higher education, this conception helps educators attend to strengthening learning outcomes oriented towards the growth of students. This serves towards the illumination of learning through and for educative encounter by addressing both the meaning …

Comparative Systems Analysis Of Thermochemical And Biochemical Recycling Of Organic Waste Towards Industrial Feedstocks, Philip Nuss

Doctoral Dissertations

Shifting the resource base for chemical and energy production from fossil feedstocks to renewable raw materials is seen by many as one of the key strategies towards sustainable development. The utilization of biomass for the production of fuels and materials has been proposed as an alternative to the petroleum-based industry. Current research and policy initiatives focus mainly on the utilization of lignocellulose biomass, originating from agriculture and forestry, as second generation feedstocks for the production of biofuels and electricity. These activities act on the assumption that significant amounts of biomass for non-food purposes are available.

However, given a certain productivity …

Can We Get There From Here? Ecosystem Based Governance In The Bay Of Fundy/Gulf Of Maine Region, John R. Coon

Doctoral Dissertations

Decades, even centuries, of resource extraction and exploitation by humans have taken a toll on the Bay of Fundy/Gulf of Maine ecosystems. The very real threats posed by population growth and coastal development, climate change, habitat loss, overharvesting, chemical pollution, nutrient overloading, and invasive species invasions show no sign of abating. Traditional methods of managing the human activities that impact the Bay of Fundy/Gulf of Maine are proving unable to keep pace with the growing threats. The Gulf of Maine Council and others have joined in the chorus calling for a broader, more holistic ecosystem approach to the governance of …

Anxious Lives: Tracing The Life Course Of A Medical Diagnosis Through Illness Narratives, Jennifer J. Esala

Doctoral Dissertations

This dissertation is a study of medical diagnosis, specifically anxiety disorder diagnosis, from the perspective and through the narratives of people who have been diagnosed. In this study, I address two core research questions. First, how does social materiality (e.g., bodies and objects) contribute to, shape, and lend empirical understanding to the experience of an anxiety disorder and the experience of illness in general? Second, how does medical diagnosis translate from the medical institution into the lives of people who have been diagnosed, and how do those diagnoses transform in and through the social lives of people? To address these …

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 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 …

Flatfish Stock Enhancement: Examining Conditioning Strategies To Promote Success, Michelle Lynn Walsh

Doctoral Dissertations

Conditioning is the process of providing individuals reared for stock enhancement with some degree of "wild" experience prior to release. Flatfish trained for "wild" conditions may more easily and successfully transition to natural environments. This dissertation identifies strategies that optimize feeding-related performance of flatfish in the hatchery and subsequently post release in the wild.

The influence of live feed conditioning on feeding performance of juvenile winter flounder, Pseudopleuronectes americanus, was investigated. In the hatchery, fish reared on live feeds exhibited significantly higher survival (P < 0.0001) and growth (P < 0.01) than those reared on formulated feed. Once released into cages in the wild, amphipodreared fish had higher mean Stomach Contents Index and RNA/DNA of all feed types, including wild fish. Wild and worm-reared fish exhibited the most similar survival, baseline RNA/DNA values, overall stomach fullness, and diet composition profiles over time.

Pre-release, experimental cage conditioning was conducted for stocking Japanese flounder, Paralichthys olivaceus, in Wakasa Bay, Japan. …

On The Reproductive Biology Of The Western Atlantic Bluefin Tuna, Thunnus Thynnus, Jessica M. Knapp

Doctoral Dissertations

The Atlantic bluefin tuna, Thunnus thynnus, is a highly migratory species capable of traversing great distances throughout the North Atlantic Ocean, but spawning is known to occur only in the Mediterranean Sea and the Gulf of Mexico/Straits of Florida. The regulatory body charged with managing Atlantic bluefin tuna, the International Commission for the Conservation of Atlantic Tunas (ICCAT), currently recognizes two spawning stocks, eastern and western, separated by a management line at 45° W. The eastern stock spawns from May through July in the Mediterranean Sea with an age at first maturity of 3--4 years. Due in part to a …

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 …

Fairness In A Data Center, Mikkel Hagen

Doctoral Dissertations

Existing data centers utilize several networking technologies in order to handle the performance requirements of different workloads. Maintaining diverse networking technologies increases complexity and is not cost effective. This results in the current trend to converge all traffic into a single networking fabric. Ethernet is both cost-effective and ubiquitous, and as such it has been chosen as the technology of choice for the converged fabric. However, traditional Ethernet does not satisfy the needs of all traffic workloads, for the most part, due to its lossy nature and, therefore, has to be enhanced to allow for full convergence. The resulting technology, …

Interaction Between The Coastal Ocean And The Estuarine Systems, Shivanesh Arvinda Rao

Doctoral Dissertations

Fluctuating winds change the interaction between an estuary and its adjacent coastal ocean. This change in the interaction determines how the wind-induced changes in the estuary influence the near-shore coastal ocean and vice-versa.

The first chapter examines the water properties in the near-shore coastal region close to estuaries after coastal upwelling. In regions where the time-integrated upwelling and down-welling wind stresses are comparable, there exists a region in the direction of a coastal Kevin wave propagation from an estuary, where the arrival of the plume in the near-shore region prevents the upwelled front from returning to the coast. The weakened …

The Ecological Role Of Feeding Disturbances Of The Atlantic Horseshoe Crab, Limulus Polyphemus, Wan-Jean Lee

Doctoral Dissertations

This study examined the influence of localized disturbances on the heterogeneity of ecological communities at multiple temporal and spatial scales. Foraging disturbances by the epibenthic predator, Atlantic Horseshoe Crab Limulus polyphemus, on the intertidal mudflats of Great Bay estuary, New Hampshire, USA were used as the study system.

This study overcame methodological hurdles in the study of small localized disturbance over extensive areas of soft-sediments. Using a novel, low-cost technique to monitor Limulus foraging disturbances, Great Bay's tidal flats were found to be critical feeding habitats from late spring till fall. Foraging Limulus disturbed the benthos of Great Bay at …

Eating Quality And Variability In Carotenoid Content And Profiles In Winter Squash And Sweet Potato, Jennifer Bonina Noseworthy

Doctoral Dissertations

A comprehensive study at the New Hampshire Agricultural Experiment Station (NHAES) of 16 winter squash cultigens (Cucurbita spp.), including inbred lines and open pollinated and F1 hybrid cultivars from the University of New Hampshire breeding program, was undertaken to determine dry weight (%DW), soluble solids contents (%SSC) and carotenoid contents of mesocarp tissue, major attributes for determining acceptable eating quality and nutritional content. Data were recorded at harvest, either 40 or 60 days after pollination (DAP), and after 30 and 60 days of storage at 14 °C. Carotenoid contents were determined spectrophotometrically and using high performance liquid chromatography (HPLC).

The …

Producing Science That Gets Used By Coastal Communities: What Funders Should Do To Link More Science With Decisions, Kalle Matso

Doctoral Dissertations

Many reports have noted that a significant portion of coastal science that is funded to help society address resource management issues does not actually link to decisions. Here, I report on 13 case studies involving new tools and science to help diverse decision makers better protect coastal resources. My qualitative analysis indicates that the programs' efforts to better link science with decisions have had varied results: some encouraging and some less so. In contrast, all 13 project case studies clearly confirm that the funding programs could have done more to link science with decisions. These case studies, combined with this …

Nonideality In High Concentration Solutions, Ronald Toth

Doctoral Dissertations

Our current understanding of molecular interactions, the kinetics, equilibria, and thermodynamics of biochemical reactions, is based mostly on research conducted in dilute solutions. Recent interest in the implications of true physiological concentrations has led to the development of new tools and techniques. In vivo biological systems differ so significantly from dilute solutions that a model is required to conceptualize them. The excluded volume theory is one such model. In this framework macromolecules are regarded as hard spherical volumes, holding only the property of size, and not those of shape or charge. Alternatively, the proximity energy framework considers molecules as having …

Ratiometric Copper(Ii) Indicators Based On Poly(N-Isoproprylacrylamide) And Fluorescence Resonance Energy Transfer, Shaojun Yao

Doctoral Dissertations

An approach to ratiometric fluorescence detection of Cu(II) ions was devised by copolymerizing N-isopropylacrylamide with small percentages of bipyridine and amine monomers. The copolymer was divided into two portions. The amine group on one portion was functionalized with AlexaFluor555 (donor fluorophore) and the other with AlexaFluor647 (acceptor fluorophore). The indicator consists of a mixture of these two portions. Aggregation above the lower critical solution temperature (LCST) of this copolymer brings about a large increase in fluorescence resonance energy transfer (FRET). Addition of Cu(II) to the aggregated copolymer introduces charge onto the backbone, causing the copolymer to deaggregate with a resulting …

Exposure To Silver Nanoparticles Inhibits Selenoprotein Synthesis And The Activity Of Thioredoxin Reductase, Milan Srivastava, Sanjay Singh, William T. Self

Faculty Bibliography 2010s

BACKGROUND: Silver nanoparticles (AgNPs) and silver (Ag)-based materials are increasingly being incorporated into consumer products, and although humans have been exposed to colloidal Ag in many forms for decades, this rise in the use of Ag materials has spurred interest into their toxicology. Recent reports have shown that exposure to AgNPs or Ag ions leads to oxidative stress, endoplasmic reticulum stress, and reduced cell proliferation. Previous studies have shown that Ag accumulates in tissues as silver sulfides (Ag2S) and silver selenide (Ag2Se). OBJECTIVES: In this study we investigated whether exposure of cells in culture to AgNPs or Ag ions at …

Virk Is A Periplasmic Protein Required For Efficient Secretion Of Plasmid-Encoded Toxin From Enteroaggregative Escherichia Coli, Gabriela Tapia-Pastrana, Lucia Chavez-Dueñas, Humberto Lanz-Mendoza, Ken Teter, Fernando Navarro-Garcí

Faculty Bibliography 2010s

Despite the autotransporter (AT) moniker, AT secretion appears to involve the function of periplasmic chaperones. We identified four periplasmic proteins that specifically bound to plasmid-encoded toxin (Pet), an AT produced by enteroaggregative Escherichia coli (EAEC). These proteins include the 17-kDa Skp chaperone and the 37-kDa VirK protein. We found that the virK gene is present in different Enterobacteriaceae. VirK bound to misfolded conformations of the Pet passenger domain, but it did not bind to the folded passenger domain or to the beta domain of Pet. Assays with an EAEC Delta virK mutant and its complemented version showed that, in the …

Detection Of Toxin Translocation Into The Host Cytosol By Surface Plasmon Resonance, Michael Taylor, Tuhina Banerjee, Neyda Vanbennekom, Ken Teter

Faculty Bibliography 2010s

AB toxins consist of an enzymatic A subunit and a cell-binding B subunit(1). These toxins are secreted into the extracellular milieu, but they act upon targets within the eukaryotic cytosol. Some AB toxins travel by vesicle carriers from the cell surface to the endoplasmic reticulum (ER) before entering the cytosol(2-4). In the ER, the catalytic A chain dissociates from the rest of the toxin and moves through a protein-conducting channel to reach its cytosolic target(5). The translocated, cytosolic A chain is difficult to detect because toxin trafficking to the ER is an extremely inefficient process: most internalized toxin is routed …

Detecting Transcription Of Ribosomal Protein Pseudogenes In Diverse Human Tissues From Rna-Seq Data, Peter Tonner, Vinodh Srinivasasainagendra, Shaojie Zhang, Degui Zhi

Faculty Bibliography 2010s

Background: Ribosomal proteins (RPs) have about 2000 pseudogenes in the human genome. While anecdotal reports for RP pseudogene transcription exists, it is unclear to what extent these pseudogenes are transcribed. The RP pseudogene transcription is difficult to identify in microarrays due to potential cross-hybridization between transcripts from the parent genes and pseudogenes. Recently, transcriptome sequencing (RNA-seq) provides an opportunity to ascertain the transcription of pseudogenes. A challenge for pseudogene expression discovery in RNA-seq data lies in the difficulty to uniquely identify reads mapped to pseudogene regions, which are typically also similar to the parent genes. Results: Here we developed a …

Ant Distribution In Relation To Ground Water In North Florida Pine Flatwoods, Walter R. Tschinkel, Tyler Murdock, Joshua R. King, Christina Kwapich

Faculty Bibliography 2010s

Longleaf pine savannas are one of the most threatened ecosystems in the world, yet are under-studied. Ants are a functionally important and diverse group of insects in these ecosystems. It is largely unknown how local patterns of species diversity and composition are determined through the interaction of this dominant animal group with abiotic features of longleaf pine ecosystems. Here we describe how an important abiotic variable, depth to water table, relates to ant species distributions at local scales. Pitfall trapping studies across habitat gradients in the Florida coastal plains longleaf pine flatwoods showed that the ant community changed with mild …

Use Of Airborne Lidar To Delineate Canopy Degradation And Encroachment Along The Guatemala-Belize Border, John F. Weishampel, Jessica N. Hightower, Arlen F. Chase, Diane Z. Chase

Faculty Bibliography 2010s

Tropical rainforest clearing and degradation significantly reduces carbon sequestration and increases the rate of biodiversity loss. There has been a concerted international effort to develop remote sensing techniques to monitor broad-scale patterns of forest canopy disturbance. In addition to loss of natural resources, recent deforestation in Mesoamerica threatens historic cultural resources that for centuries lay hidden below the protective canopy. Here, we compare satellite-derived measures of canopy disturbance that occurred over a three decade period since 1980 to those derived from a 2009 airborne LiDAR campaign over the Caracol Archaeological Reserve in western Belize. Scaling up fine-resolution canopy height measures …

Casein Kinase 2 Reverses Tail-Independent Inactivation Of Kinesin-1, Jing Xu, Babu J. N. Reddy, Preetha Anand, Zhanyong Shu, Silvia Cermelli, Michelle K. Mattson, Suvranta K. Tripathy, Matthew T. Hoss, Nikita S. James, Stephen J. King, Lan Huang, Lee Bardwell, Steven P. Gross

Faculty Bibliography 2010s

Kinesin-1 is a plus-end microtubule-based motor, and defects in kinesin-based transport are linked to diseases including neurodegeneration. Kinesin can auto-inhibit via a head-tail interaction, but is believed to be active otherwise. Here we report a tail-independent inactivation of kinesin, reversible by the disease-relevant signalling protein, casein kinase 2 (CK2). The majority of initially active kinesin (native or tail-less) loses its ability to interact with microtubules in vitro, and CK2 reverses this inactivation (approximately fourfold) without altering kinesin's single motor properties. This activation pathway does not require motor phosphorylation, and is independent of head-tail auto-inhibition. In cultured mammalian cells, reducing CK2 …