student research

The major histocompatibility complex (MHC) is a family of genes that has become an important marker in measuring the diversity of immune response in a wide range of species. The MHC complex can be thought of as a transport device; it carries the pathogenic peptide to the surface of the cell and presents it to the T-cell receptor initiating the body's immune response against potential pathogens. Since MHC's first discovery in mid 1930's by Peter Gorer, this multigene family has been identified in every mammalian species studied to date. The diversity of MHC influences an individual's susceptibility to disease and autoimmunity (Ackerman & Brigil, 2011)

Mesophotic reefs have historically been understudied, leading to a dearth of information on the corals that compose these reefs. Recent advancements in technology have enabled researchers to have greater access to reefs at mesophotic depths, generating a greater interest in the microbial communities in both mesophotic and shallow reefs, in order to determine the relative bacterial community differences. Samples of coral mucus from Montastraea cavernosa were collected from Flower Garden Banks National Marine Sanctuary (FGBNMS) in the summer of2010 and 2011. Bacterial community DNA was extracted from the coral mucus and amplified using LH-PCR. Length Heterogeneity PCR is a technique used to amplify the hypervariable Vl and V2 region of the 16s rRNA gene in order to detennine relative base pair length and abundance of microbial connnunities. During the PCR product verification, contamination became apparent in the gel. Through contamination troubleshooting, the source was determined; however, not soon enough to continue with analyzing the samples. This project will be continued in the future in order to add to the mesophotic bacterial community database. The DNA extraction protocol frequently utilized in the laboratory will be modified to increase DNA yields, PCR conditions will be optimized, and the samples will be fully analyzed.

The ocean engineering summer internship project focused on designing, modeling, constrncting and virtually testing a fully functional undetwater housing for a novel instrnment called a fluorolidar.

With the current decline in world fisheries it is necessary to develop more sustainable methods of marine resource production. An Integrated Multi-Trophic Aquaculture (IMTA) system is one such method. In an IMT A system the waste nutrients of fed species are used to culture other species, thus increasing the efficiency of feed use. A land-based IMTA (LB-IMTA) system was utilized in the cunent study in which one of the waste nutrient utilizing species was oysters. Oysters in this system were determined to be not getting an adequate amount of waste nutrient feed necessary for normal growth. Therefore, oysters would need supplemental microalgae to grow normally, however the addition ofmicroalgae to the LB-IMTA might have detrimental effects, e.g., spreading throughout the system and changing the balance of nutrient flow or blooming throughout the system. Therefore, a study was designed to determine the fate of microalgae added to an LB-IMTA under a worst case scenario. With no oysters in the LB-IMTA system (total volume 61,740 L), 30 L ofmicroalgae (average density= 6.3x106 cells/mL) were added into the oyster tanks. Microalgae cells were tracked over time by sampling at distinct sites throughout the LB-IMTA system. Microalgae concentrations (i.e., #/mL) in the samples were determined with the aid of a Flocam®. Three microalgae species were individually tested: Dunaliella tertiolecta, Chaetoceros gracilis, and Isochrysis galbana Caribbean strain. Overall, the data indicated that all three micro algae species spread to almost all parts of the system after only 15 minutes, but nearly all of the microalgae was gone after 3 hrs; avg. = 8 cells/mL, which was 0.26% of the average theoretical homogenous concentration (3061 cells/mL). The primary removal of microalgae was most likely by the bead filters, which remove fine particles. The filtration components of the HBOI LB-IMTA were able to remove the excess microalgae and should limit any potentially detrimental effects caused by an overabundance of microalgae.

Various bivalve species were sampled at three sites in the Indian River Lagoon in Fort Pierce, Florida to determine whether the change in the seasonal prevalence of Bonamia spp. in the Indian River Lagoon as determined by PCR could be confirmed histologically using standard hematoxylin and eosin (H&E) staining and fluorescent in situ hybridization (FISH). Parasite location was noted in tissue samples and determinations were made as to whether the infection was external (gills, mantle) or internal (connective tissue). Bonamia spp. was found to be more prevalent in the fall at all three study sites. Fluorescent in situ hybridization confirmed the majority ofPCR-positive samples. A large
percentage of Bonamia spp. infections at North Causeway Park and Wabasso Causeway Bridge were external infections. In addition, a large percentage of Bonamia spp. infections at Wildcat Cove and Wabasso Causeway Bridge were in the gills and mantle. This indicates that most of the bivalves sampled are filtering the parasite from their surrounding environment but are not being negatively affected and those that are infected are not heavily infected. Bonamia spp. has not been reported to negatively impact bivalve populations in Florida, however the impacts of this parasite on various oyster and mussel species in Florida has not been thoroughly examined. This project may determine what steps need to be taken to prevent the losses in oyster and associated bivalve populations in the Indian River Lagoon.

Bivalves are important aquatic species that are an integral part of food web dynamics and nutrient cycling. As filter feeding organisms, bivalves impact on aquatic habitats, includes their ability clean up the surrounding water which allows under water plants to receive sunlight, increase oxygen and provide additional habitat to that provided by created oyster reefs. Oyster diseases such as Bonamiosis caused by the parasite Bonamia spp. may decimate bivalve populations, causing a potential threat to the
habitat of other aquatic organisms. The objective of this study was to identify the seasonal prevalence of Bonamia spp. in bivalve populations and correlate that to its environmental preference (i.e. salinity, temperature.). The results of this study show that Bonamia spp. is not only present in multiple sites and multiple bivalve species in the Indian River Lagoon, FL but is more prevalent in the fall compared to the other seasons as is seen with other oyster parasites, such as Perkinsus spp. This points for the need for additional studies to determine if Bonamia spp are having an impact on the bivalve populations in Florida and whether this parasites is causing an impact to the surrounding environment.

The interaction between seagrass and macroalgae affects the growth and distribution of both photosynthetic communities. The Central Indian River Lagoon displays a wide variety of seagrass and macroalgae, both of which are in constant flux due to seasonal variations. The purpose of this study was to ascertain a relationship between seagrass and macroalgal communities along a latitudinal gradient in the Central Indian River Lagoon. It is predicted that there will be a positive relationship between seagrass and macroalgae; an increase in percent cover for seagrass will yield a conctment increase for
macroalgae. Our data do not support this claim, but rather the opposite; there is an inverse relationship between seagrass and macroalgae. We attribute this relationship partially to competition of attached algae and sea grass, but mostly to the hydrodynamic properties of the Indian River Lagoon which greatly affects the movement of drift algae in and around seagrass beds.

This paper discusses the development of a automated system which will be used to monitor manatee abundance and behavior 24 hours a day. The main motivation for doing this project is that recent observations suggest manatees utilize the HBOI channel as a thermal refuge. It has also been observed that manatees are drinking from a drainage pipe pumping fresh water into the channel. The main objective of the project is to gain better insight into the manatee behavior in relation to environmental factors. This purpose was achieved by developing software that can control the camera with several functions: taking still images, video recording, zooming in/out, full screen option, patrol channel function and function to see if water is flowing from the pipe. The next step was to develop an algorithm to detect movement, different colors and contours in the channel. I show study at this problem in water enviromnent in this research paper. The software was developed in Microsoft Visual C# 2010 Express in programming language C#. I also developed a system to save the pictures and recordings made by the camera according to the date and time at which they were taken. The steps I have taken during my time working on the project will allow the scientists studying the manatees to more easily keep track of their data.

As a result of increased oil exploration and an increased risk of oil spills in the marine environment, the ability to detect and characterize spilled oil with spectral fingerprinting has major significance. First, a spectrometer and fluorometer were used to characterize and compare spectral properties of parent polycyclic aromatic hydrocarbon (PAHs) and their alkylated homologs in relation to oil and the weathering processes. Next, prepared parent PAH compounds were tested for sensor responses to seven commercially available off-the-shelf instruments with varying optical parameters that measure the fluorescence of hydrocarbon molecules. Lastly, the seven fluorometer responses were tested in response to oil in water solutions. From absorbance and Excitation Emission spectra, the spectral properties of parent and alkylated PAHs are very similar. For each parent PAH, the Cl-Alkylated homolog had a lower concentration and less defined absorbance spectrum than the parent PAH. The Chelsea UviLux and Cyclops-7 Refined Oil sensors had an extremely linear and sensitive response to Fluorene. The C3-Crude Oil fluorometer surprisingly did not have strong response to the 1.4 g/L North Sea Crude water accommodated fraction. The Chelsea UviLux T-Piot sensor output detects lower concentrations of oil in water and provides higher resolution data than the DAQ Plotter for both water accommodated and chemically dispersed solutions.

Seagrasses are fully submersed, marine angiosperms that provide crucial ecological functions. Yet, seagrass communities in the Indian River Lagoon (IRL), Florida, and elsewhere have been in decline as a result of point and non-point source pollution The major factor in seagrass decline in the IRL can be associated with the degradation of water quality, which has been influenced by human urbanization. Monitoring projects, restoration, and inquiries into the resilience of these declining seagrass communities have been initiated due to the detrimental effects of human-caused and environmental sources. Therefore, a small-scale monitoring project was conducted throughout the central IRL, using traditional transect method'i in order to observe trends based on spatial gradients, water depth, seagrass bed length, sparseness, and abundance, and any factor that might be affecting the growth and distribution of these seagrasses. A second component of the study incorporates obsen,ations on seagrass reproduction and recovery potential from environmental stressors via seed development and germination. In terms of percent coverage, shoot counts, canopy height, and overall transect length, the Southern sites had higher averages for almost every species of seagrass and for totals of all species compared to the Northern sites. Throughout the ten sites that were monitored, a seed bank was identified as being present. However, the abundance of seeds found was smaller than that found according to many other studies dealing with seed banks. Further inquiries into both aspects of the study would allow for a better understanding of the distribution, abundance, and relationships between seagrass beds, seed bank characteristics, and the surrounding environment.