Marine Biology Commons^™

Effects Of Hypoxia And 4-Tert-Octylphenol On Gene Expression Profiles Of The Sheepshead Minnow (Cyprinodon Variegatus), Arthur Alan Karels

Dissertations

Hypoxia occurs in estuaries of northern Gulf of Mexico and world-wide, with increasing frequency/severity via eutrophication and anthropogenic influences. Hypoxia inducible factors (HIFs) form transcriptional complex and bind DNA at hypoxia responsive elements (HREs) in promoter regions of genes needed for systemic and cellular adaptation of fish to low dissolved oxygen (hypoxia, DO <2.0 mg/ml). Hypoxia-induced activation of HIF-αs can lead to a cascade of downstream activation, such as erythropoietin (EPO). Return to normal DO levels (normoxia), prolyl hydroxylases (PHDs) are activated to degrade HIF-αs back to baseline. Fish are affected by environmental estrogen mimics, like 4-tert-octylphenol (4tOP), binding estrogen receptor alpha (ERα) at estrogen responsive elements (EREs) and activating genes vitellogenin (VTG). Previous research showed overlap or crosstalk between these two mechanistic pathways. Hypoxia triggers unknown factors regulating ERE-mediated ERα signaling pathway, and stressor combinations could increase/decrease hypoxic or endocrine pathway. Research examined molecular/physiological effects of hypoxia (acute and chronic, moderate and severe) and 4tOP (~60μg/L)on adult male and/or female sheepshead minnow (Cyprinodon variegatus). Three genes identified, cloned, and sequenced (HIF-1α, HIF-2α, and PHD3), plus previously identified genes EPO and VTG, were examined in liver/testes exposed to hypoxia and/or 4tOP for cellular/physiological changes. Endpoints examined included mRNA expression from real-time PCR of HIF-1α, HIF-2α, PHD3, EPO, and VTG using cDNA from total RNA extracts, and microarray analyses of genes expressed during the transition from hypoxia back to normoxia. Phylogenetic analyses confirmed isolation of two HIF-α isofoms (HIF-1α and HIF-2α) and the PHD3 isoform. Significant up-regulation of PHD3 occurred within 10 hrs of chronic hypoxia, and persisted when severe (1.5 mg/L) and declined when moderate (~2.5mg/L). Significant up-regulation of HIF-1α and EPO occurred within 30 minutes to 2 hours of onset of acute severe and very severe (~1.08mg/L) hypoxia. Hypoxia acted similar to an estrogen mimic, with huge up-regulation of VTG gene expression in males, and increased VTG levels (additive effect) when hypoxia was combined with 4tOP. Microarray analyses showed 125 genes with significant transcriptional change, with up- or down-regulation from transitions of: (1) hypoxia (72 hrs) to normoxia (74 hrs) and (2) hypoxia+4tOP (72 hrs) to normoxia+4tOP (74 hrs).

Comparison Of Creel Survey Data To Traditional Sampling Techniques In Pit-Lake Fisheries Of Muhlenberg County, Kentucky, Derek L. Rupert

Masters Theses & Specialist Projects

Populations of largemouth bass, Micropterus salmoides, and bluegill, Lepomis macrochirus, were evaluated from five pit-lakes in Muhlenberg County, Kentucky, to determine if accurate proportional stock density (PSD) data can be obtained from a mandatory creel survey. It was hypothesized that the proportion of stock-to-quality (300-400mm) and quality (+400mm) largemouth bass from four years (2007-2010) of creel survey data would be statistically similar to those generated through on-site sampling in 2011. Fish were collected via a combination of gill netting, seining, hook-and-line fishing, and boat-mounted electro-fishing. In two of the pit-lakes, the sampling-generated length frequency data was not significantly …

Predictive Model Of Ocean Sediment Binding, Erica Delaney

Honors Senior Capstones and Theses

This project explored the relationship between sediment size, sediment composition and the concentration of mercury. The samples were taken from Narragansett Bay in Rhode Island. Knowledge and understanding of the binding ability of heavy metals, specifically mercury, will help to improve remediation efforts in the future. Analysis of elemental composition was conducted using the Elementar Analyzer and much troubleshooting of the instrument was necessary. End result of the project was the ability to work successfully with an advisor, as well as the ability to troubleshoot, operate and maintain the instrument.

Red Sea Coral Reef Trajectories Over 2 Decades Suggest Increasing Community Homogenization And Decline In Coral Size, Bernhard Riegl, Andrew W. Bruckner, Gwilym Rowlands, Samuel J. Purkis, Philip Renaud

Marine & Environmental Sciences Faculty Articles

Three independent line intercept transect surveys on northern Red Sea reef slopes conducted in 1988/9 and 1997/8 in Egypt and from 2006–9 in Saudi Arabia were used to compare community patterns and coral size. Coral communities showed scale-dependent variability, highest at fine spatial and taxonomic scale (species-specific within and among reef patterns). At coarser scale (generic pattern across regions), patterns were more uniform (regionally consistent generic dominance on differently exposed reef slopes and at different depths). Neither fine- nor coarse-scale patterns aligned along the sampled 1700 km latitudinal gradient. Thus, a latitudinal gradient that had been described earlier from comparable …

Use Of Injectable Eugenol For Euthanasia And Anesthesia Of American Lobsters (Homarus Americanus) And Similar Species, Carlton Huntsberger

Biology Theses

Crustaceans are economically and ecologically significant, but current treatment and diagnostic protocols for crustacean health are limited. According to standards given by the American Veterinary Medical Association there are no current methods of euthanizing lobsters, nor are there effective methods of quick release anesthesia. The objective of this research demonstrated that eugenol by direct injection is a safe, efficient and reliable method for euthanizing or anesthetizing crustaceans. Anesthetic levels were determined by behavior responses, death was determined by a lack of response to stimuli. The results presented here suggest eugenol can be used as a euthanizing agent for American lobsters …

Investigating The Roles Of Lhx1a, Lhx1b, And Lhx5 In Zebrafish Spinal Cord Interneuron Specification And Function, Samantha Balakirsky

Renée Crown University Honors Thesis Projects - All

Located in the vertebral column, the human spine is responsible for regulating body movements and receiving sensory input about pain and touch. Currently, few treatments for neurological diseases and spinal cord injuries exist, partly because we know little about how a fully functioning spinal cord is constructed. As such, studying spinal cord development, specifically neuronal specification and patterning, should be useful for developing better treatments for people with spinal cord injuries and diseases. Zebrafish are a prime model organism for studying neuronal specification because their transparent embryos develop outside the mother, allowing us to easily examine gene expression, cell movements …

Potential Impact Of Herbivorous Fish On Ulva Bloom Biomass, Tanja Schollmeier

Senior Honors Projects

Potential Impact of Herbivorous Fish on Ulva Bloom Biomass

Tanja Schollmeier

Sponsor: Carol Thornber, Biological Sciences

The addition of anthropogenically produced nitrogen and phosphorous to coastal habitats is a major problem that frequently results in the rapid growth, or bloom, of macroalgae. Within Narragansett Bay, RI, blooms are commonly formed by two species: Ulva compressa and U. rigida. These blooms co-occur with a number of invertebrates that have been previously studied for their impacts on bloom biomass. However, few studies have examined the abundance or potential grazing impacts of herbivorous fish. To address this information gap, we conducted surveys …

Big Blue And You: An Interdisciplinary Look At Science And The Ocean, A Students Teaching Students Course, Megan M. Nepshinsky, Alexa Kretsch, Benjamin Negrete

Senior Honors Projects

This class is the second project under the new Honors Program initiative, Students Teaching Students (STS). STS was brought to URI and implemented by Bridget Griffith as part of her Senior Honors Project in 2011. Students apply in their Junior year to design, research, and teach an honors course on a topic about which they are passionate. The STS program allows motivated honors students to have a unique opportunity to lead a class as student professors. This allows students a freedom of creativity on the topic, assignments, and teaching style. Drawing on our own experiences, we were able to create …

Application Of A Hybrid 3d-Var Data Assimilation System In The Monterey Bay To Study Regional Dynamics Of The California Current System, Chudong Pan

Dissertations

A data assimilation system combining 3-dimensional variational scheme and Navy Coastal Ocean Model was applied to the Monterey Bay area to assimilate temperature and salinity glider data collected in August 2003. The hybrid background error covariance model in the present 3-dimensional variational system incorporates both the static and the flow-dependent background error covariance. To explore the impact of high temporal resolution on the overall skill of the assimilation system, the intended data assimilation interval was set to 1 hour in the present study. A Floating Temporal Window approach is designed to keep the computational efficiency of the scheme and to …

Evaluation Of Electrophoretic Protein Extraction And Database-Driven Protein Identification From Marine Sediments, Eli K. Moore, Brook L. Nunn, Jessica F. Faux, David R. Goodlett, H. Rodger Harvey

OES Faculty Publications

Intact proteins comprise a major component of organic carbon and nitrogen produced globally and are likely an important fraction of organic matter in sediments and soils. Extracting the protein component from sediments and soils for mass spectral characterization and identification represents a substantial challenge given the range of products and functionalities present in the complex matrix. Multiple forms of gel electrophoresis were evaluated as a means of enhancing recovery of sedimentary protein before proteomic characterization and compared with a direct enzymatic digestion of proteins in sediments. Resulting tryptic peptides were analyzed using shotgun proteomics and tandem mass spectra were evaluated …

Thermal Impacts Of A Coal Power Plant On The Plankton In An Open Coastal Water Environment, Keun-Hyung Choi, Young-Ok Kim, Joon-Baek Lee, Soon-Young Wang, Man-Woo Lee, Pyung-Gang Lee, Dong-Sik Ahn, Jae-Sang Hong, Ho-Young Soh

Journal of Marine Science and Technology–Taiwan

Over a five-year period, this study examined the overall impact of coal power plant cooling processes on entrained copepods and the local plankton community on the west coast of Korea. Mortality differences between the intake and discharge water of the single most dominant copepod, Acartia hongi, were positively correlated with temperature differences between the two locations. Laboratory tests showed copepod sensitivity to temperature increase, and with very low chlorine concentration applied, thermal stress was the major source of copepod mortality. Chlorophyll a concentration, ciliate abundance, and total copepod abundance at the intake showed no discernable differences from the values at …

Double-Power Double-Heterostructure Light-Emitting Diodes In Microalgae, Spirulina Platensis And Nannochloropsis Oculata, Cultures, Yean-Chang Chen, Meng-Chou Lee

Journal of Marine Science and Technology–Taiwan

The growth conditions of two microalgae, Spirulina platensis and Nannochloropsis oculata, were tested under various light sources including white cold DDH GaAlAs LED, traditional fluorescent lamps and natural light cultures, with no difference found in the growth of biomass, indicating that white cold DDH GaAlAs LED could replace traditional fluorescent lamps, thus providing for large saving on electricity costs and preservation of cultural space. To date, the use of white cold DDH GaAlAs LEDs as light source for microalgal cultures seems to be largely unstudied.

Eelgrass Habitat Creation In Nantucket Harbor, Massachusetts, David M. Burdick, Gregg Moore, Chris Peter

Natural Resources & the Environment

In response to eelgrass habitat losses associated with development and marine activities in and around Nantucket Harbor, a plan to restore a meadow by transplanting eelgrass to previously vegetated areas was developed in conjunction with the Nantucket Land Council. Over 6,000 eelgrass shoots were sustainably harvested from an extensive bed within the Harbor that was located just west of First Point and near the inlet to Nantucket Sound. Four weeks following collection, impacts from our collection were shown by a 24% decline in shoot density, but live eelgrass cover did not decline significantly. After 12 weeks, no effects of collecting …

A Streamlined Dna Tool For Global Identification Of Heavily Exploited Coastal Shark Species (Genus Rhizoprionodon), D. Pinhal, Mahmood S. Shivji, Pedro G. Nachtigall, Demian D. Chapman, Cesar Martins

Marine & Environmental Sciences Faculty Articles

Obtaining accurate species-specific landings data is an essential step toward achieving sustainable shark fisheries. Globally distributed sharpnose sharks (genus Rhizoprionodon) exhibit life-history characteristics (rapid growth, early maturity, annual reproduction) that suggests that they could be fished in a sustainable manner assuming an investment in monitoring, assessment and careful management. However, obtaining species-specific landings data for sharpnose sharks is problematic because they are morphologically very similar to one another. Moreover, sharpnose sharks may also be confused with other small sharks (either small species or juveniles of large species) once they are processed (i.e., the head and fins are removed). Here …

Crommet Creek Conservation Area Management Plan, Joanne Glode, Dea Brickner-Wood, Ed Robinson, Wendy Weisiger, Peter Wellenberger, Rachel Stevens

PREP Reports & Publications

The Crommet Creek Conservation Area comprises the largest block of natural lands in the immediate Great Bay watershed, and in New Hampshire’s North Atlantic Coast Ecoregion. It includes the entire watershed of two tidal creeks that flow directly into the Great Bay Estuary. The area has been identified by the Great Bay Resource Protection Partnership as a protection priority due to the size of the natural area; the diversity of habitats and wildlife it supports; and it’s integral role in protecting the regional water quality and resources within the Great Bay Estuary. The Conservation Area includes headwater wetlands, and the …

Genetic Connectivity In Scleractinian Corals Across The Northern Gulf Of Mexico: Oil/Gas Platforms, And Relationship To The Flower Garden Banks, Daniel A. Brazeau, Paul W. Sammarco, James Sinclair

Pharmaceutical Sciences Faculty Publications

The 3,000 oil/gas structures currently deployed in the northern Gulf of Mexico (GOM) provide hard substratum for marine organisms in a region where such has been rare since the Holocene. The major exception to this are the Flower Garden Banks (FGB). Corals are known to have colonized oil/gas platforms around the FGB, facilitating biogeographic expansion. We ask the question, what are the patterns of genetic affinity in these coral populations. We sampled coral tissue from populations of two species occurring on oil and gas platforms: Madracis decactis (hermatype) and Tubastraea coccinea (invasive ahermatype). We sampled 28 platforms along four transects …

Diversity Of Tanaidacea (Crustacea: Peracarida) In The World's Oceans - How Far Have We Come?, Gary Anderson, Magdalena Blazewicz-Paszkowycz, Roger Bamber

Faculty Publications

Tanaidaceans are small peracarid crustaceans which occur in all marine habitats, over the full range of depths, and rarely into fresh waters. Yet they have no obligate dispersive phase in their life-cycle. Populations are thus inevitably isolated, and allopatric speciation and high regional diversity are inevitable; cosmopolitan distributions are considered to be unlikely or non-existent. Options for passive dispersion are discussed. Tanaidaceans appear to have first evolved in shallow waters, the region of greatest diversification of the Apseudomorpha and some tanaidomorph families, while in deeper waters the apseudomorphs have subsequently evolved two or three distinct phyletic lines. The Neotanaidomorpha has …

Predicting The Influence Of Seed And Commercial Oyster Fisheries On Metapopulation Genetic Connectivity Using Model Simulations, Daphne Munroe, Eileen E. Hofmann, Eric N. Powell, John M. Klinck

CCPO Publications

No abstract provided.

How Do Marine Protected Area Strategies Influence Metapopulation Genetic Connectivity? A Modeling Study With Oysters, Daphne Munroe, Eric N. Powell, John M. Klinck, Eileen E. Hofmann

CCPO Publications

No abstract provided.

Assessing The Variability In Distribution Of Four Shark Species Within The Mississippi Sound, Daniel Crear

All Theses And Dissertations

Global declines in shark populations have been observed, including several species indigenous to the northwest Atlantic Ocean and the Gulf of Mexico (GOM). Attributing to these declines is a lack of abundance and distribution data of early life stages, particularly within essential habitats such as nursery grounds. Previous research has defined the Mississippi Sound as a multispecies shark nursery, therefore determining how abundance and distribution patterns change will aid in verifying where these species are throughout the year within this shark nursery. Thus, the objectives of the current study were to describe the variability in distributions of four shark species …

Two- And Three-Dimensional Photogrammetric Mass Estimation Techniques For Two Phocid Species: Halichoerus Grypus And Phoca Vitulina Concolor, Jennifer Harris

All Theses And Dissertations

Collecting mass measurements of seals is a common technique used to determine health. To determine the mass of Western North Atlantic Grey seal (Halichoerus grypus) and Atlantic Harbor seal (Phoca vitulina concolor) pups, a researcher must physically measure each animal. This produces stress for both pups and their mothers. Photogrammetric analysis (PGA) (evaluating photographs to obtain characteristics of a subject) has been used to determine physical measurements in a number of marine mammals. The purpose of this study was to develop a nonintrusive method for determining the mass of grey and harbor seal pups. Through this …

Coupled Physical And Biological Modeling Of Atlantic Surfclam Larval Transport And Sub-Population Connectivity In The Middle Atlantic Bight And Georges Bank, Xinzhong (Peter) Zhang, Dale B. Haidvogel, John M. Klinck, Roger Mann, Eric N. Powell

CCPO Publications

No abstract provided.

Effects Of The Parasitic Dinoflagellate Hematodinium Sp. On Blue Crab (Callinectes Sapidus) Activity Predation And Habitat Selection, John M. Tiggelaar Ii

Biological Sciences Theses & Dissertations

The blue crab Callinectes sapidus occurs along the Atlantic and Gulf coasts of the United States, and in high salinity regions, they are subject to lethal infection by the parasitic dinoflagellate Hematodinium. In Virginia's seaside estuaries, the prevalence of Hematodinium infection of C. sapidus can sometimes exceed 50%, threatening the commercial fishery for this species. Indeed, other commercially important crustacean fisheries have approached collapse due to Hematodinium infections. Most studies of this host-parasite interaction have focused on epidemiology, host-pathogen dynamics, and pathogen transmission, and little is known about the impact of the parasite on host behavior and population dynamics. …

Invasionsoft: A Web-Enabled Tool For Invasive Species Colonization Predictions, Matthew W. Johnston, Samuel J. Purkis

Marine & Environmental Sciences Faculty Articles

Predicting and averting the spread of invasive species is a core focus of resource managers in all ecosystems. Patterns of invasion are difficult to forecast, compounded by a lack of user-friendly species distribution model (SDM) tools to help managers focus control efforts. This paper presents a web-based cellular automata hybrid modeling tool developed to study the invasion pattern of lionfish (Pterois volitans/miles) in the western Atlantic and is a natural extension our previous lionfish study. Our goal is to make publically available this hybrid SDM tool and demonstrate both a test case (P. volitans/miles) and a …

Coral Recruitment To Two Vessel Grounding Sites Off Southeast Florida, Usa, Alison L. Moulding, Vladimir N. Kosmynin, David S. Gilliam

Marine & Environmental Sciences Faculty Articles

Over the last two decades, more than 10 major vessel groundings have occurred on coral reefs offshore southeast Florida. Lack of any published information on coral settlement, post-settlement survival, and juvenile coral growth in the southeast Florida region inhibits efforts to determine if coral populations will be able to effectively re-establish themselves. The goal of this study was to examine these processes to obtain background data needed to determine the potential for natural recovery. Over a three year period annual coral recruitment, juvenile growth, and mortality rates were measured in 20 permanent quadrats at each of two ship grounding and …

Insights Into Migration And Development Of Coral Black Band Disease Based On Fine Structure Analysis, Aaron Miller, Patricia Blackwelder, Husain Al-Sayegh, Laurie L. Richardson

Biology Faculty Articles

In many diverse ecosystems, ranging from natural surfaces in aquatic ecosystems to the mammalian gut and medical implants, bacterial populations and communities exist as biofilms. While the process of biofilm development has been well-studied for those produced by unicellular bacteria such Pseudomonas aeruginosa, little is known about biofilm development associated with filamentous microorganisms. Black band disease (BBD) of corals is characterized as a polymicrobial biofilm (mat) community, visually-dominated by filamentous cyanobacteria. The mat migrates across a living coral host, completely lysing coral tissue and leaving behind exposed coral skeleton. It is the only known cyanobacterial biofilm that migrates across …

A Retrospective Analysis Of Sustainable Oyster Harvest From The Louisiana State Primary Seed Grounds, 1999-2010: A Shell-Neutral Modeling Approach, Thomas M. Soniat, Mahdi Abdelguerfi, Eric N. Powell, John M. Klinck, Eileen E. Hofmann, Shengru Tu, Nathan Cooper, Janak Dahal, John Finigan, Benjamin S. Eberline, Jerome F. La Peyre, Megan K. La Peyre, Keith B. Ibos, Brian Lezina, Patrick Banks

CCPO Publications

No abstract provided.

Siting Study For A Hydrokinetic Energy Project Located Offshore Southeastern Florida: Protocols For Survey Methodology For Offshore Marine Hydrokinetic Energy Projects, Charles Vinick, Charles Messing, Brian K. Walker, John K. Reed, Stephanie Rogers

Marine & Environmental Sciences Faculty Reports

Dehlsen Associates, LLC was awarded a grant by the United States Department of Energy (DOE) Golden Field Office for a project titled “Siting Study Framework and Survey Methodology for Marine and Hydrokinetic Energy Project in Offshore Southeast Florida,” corresponding to DOE Grant Award Number DE-EE0002655 resulting from DOE funding Opportunity Announcement Number DE-FOA- 0000069 for Topic Area 2, and it is referred to herein as “the project.”

The purpose of the project was to enhance the certainty of the survey requirements and regulatory review processes for the purpose of reducing the time, efforts, and costs associated with initial siting efforts …

Weak Prezygotic Isolating Mechanisms In Threatened Caribbean Acropora Corals, Nicole D. Fogarty, Steven V. Vollmer, Don R. Levitan

Marine & Environmental Sciences Faculty Articles

The Caribbean corals, Acropora palmata and A. cervicornis, recently have undergone drastic declines primarily as a result of disease. Previous molecular studies have demonstrated that these species form a hybrid (A. prolifera) that varies in abundance throughout the range of the parental distribution. There is variable unidirectional introgression across loci and sites of A. palmata genes flowing into A. cervicornis. Here we examine the efficacy of prezygotic reproductive isolating mechanisms within these corals including spawning times and choice and no-choice fertilization crosses. We show that these species have subtly different mean but overlapping spawning times, suggesting …

Spatial Analyses Of Benthic Habitats To Define Coral Reef Ecosystem Regions And Potential Biogeographic Boundaries Along A Latitudinal Gradient, Brian K. Walker

Marine & Environmental Sciences Faculty Articles

Marine organism diversity typically attenuates latitudinally from tropical to colder climate regimes. Since the distribution of many marine species relates to certain habitats and depth regimes, mapping data provide valuable information in the absence of detailed ecological data that can be used to identify and spatially quantify smaller scale (10 s km) coral reef ecosystem regions and potential physical biogeographic barriers. This study focused on the southeast Florida coast due to a recognized, but understudied, tropical to subtropical biogeographic gradient. GIS spatial analyses were conducted on recent, accurate, shallow-water (0–30 m) benthic habitat maps to identify and quantify specific regions …