Artificial oyster reefs seek to restore reef ecosystem services, such as water filtration, shoreline protection, and habitat for nekton. This study established three objectives to address the dispersed nature of artificial reef information in the Gulf of Mexico (GoM) and lack of post-construction monitoring assessments. First, to document the extent of activities in the GoM, we developed a database of all inshore artificial oyster reefs created for restoration purposes. Of the 422 reefs in the resultant database, a third or less provided records of entities involved (27%), restoration goals (24%), area (20%), monitoring efforts (15%), relief (9%), and costs (8%). Material (89%) and age (66%) records showed reefs were primarily built with rock (48.6%, limestone or concrete) or shell (12.8%) materials; a quarter of projects (26%) occured after Hurricane Katrina (2005). Second, in a field study we examined the success of artificial subtidal reefs using the presence of (a) living oysters and (b) hard substrate as indicators of success. This field study sampled historic (N=7) and artificial shell (N=5) and rock (N=8) reefs in 8 bays along the northern GoM. Rock artificial reefs were more successful on average than shell, providing significantly higher mean adult oyster density and hard substrate volume. In addition to material effects, design (i.e., relief) and placement specific environmental variations (i.e., hydrodynamics) may have affected success. Lastly, to assess artificial reef use by nekton communities, we sampled nekton assemblages with 3 gear types (gillnet, castnet, and shrimp trawl), during 4 trips in summer 2011. Overall, abundance, richness and diversity were similar between historic reefs and both artificial reef materials (shell, rock). It is probable that biophysical variations may have affected nekton use, more than reef structure. Of the reefs sampled, only 65% of the artificial reefs were fully successful in providing reefs with hard substrate and living oysters, while all reefs provided similar nekton support. This project highlights the need to better track restoration projects in order to inform future activities. Identifying aspects of design and/or location that influence reef success is critical for improving restoration activities.

Insulin resistance in type 2 diabetes is associated with impaired glucose and protein metabolism in skeletal muscle. The impaired insulin signaling in skeletal muscle affects muscle mass by tilting the balance between skeletal muscle protein synthesis and degradation toward degradation, a process that is primarily regulated by the ubiquitin-proteasome system. Studies have shown that an extensively characterized ethanol extract of Artemisia dracunculus L (Russian Tarragon), termed PMI 5011, enhances insulin signaling in human primary skeletal muscle cells and in a rodent model of insulin resistance. The aim of this project is to determine if the effect of PMI 5011 on insulin signaling extends to regulation of ubiquitin-proteasome activity in skeletal muscle. To evaluate the effect of PMI 5011 on the ubiquitin-proteasome system, we used two in vitro models of insulin resistance in C2C12 myotubes and the KKAy mouse model of insulin resistance in vivo. Our studies show that PMI 5011 enhances the inhibitory effect of insulin on proteasome activity and ubiquitylation in skeletal muscle in vitro and in vivo. In addition, PMI 5011 inhibits non-proteasomal protein degradation in vivo, indicating that PMI 5011 is a potent inhibitor of skeletal muscle protein degradation. PMI 5011 also regulates the expression of Atrogin-1 and MuRF-1, muscle-specific ubiquitin ligases that are required for ubiquitin-dependent protein degradation in skeletal muscle. Both Atrogin-1 and MuRF-1 gene and protein expression is elevated with impaired insulin signaling and our studies show that PMI 5011 reduces the expression of these ligases while enhancing Akt phosphorylation. In summary, these studies demonstrate that PMI 5011 regulates the ubiquitin-proteasome in insulin resistant states in vitro and in vivo. PMI 5011 may therefore be a therapeutic target for enhancing insulin sensitivity leading to conservation of muscle mass in type 2 diabetes.

Crayfish harvested from the Atchafalaya River Basin (ARB) represent the majority of Louisiana wild crayfish landings. However, excluding water level influences, it is difficult to elucidate inter-annual harvest differences and intra-annual population variability among habitats. This research investigated ecological influences on population characteristics of red swamp crayfish Procambarus clarkii in the southeastern ARB as well as physiological biomarkers of hypoxic stress in P. clarkii. Biotic and abiotic effects on P. clarkii populations were examined throughout the 2008 and 2009 commercial crayfish seasons. P. clarkii catch per unit effort (CPUE) at sampling locations increased nearly 600% between sample years despite similar hydrologic and physicochemical conditions. The passage of Hurricane Gustav between sample years caused near anoxic conditions for several weeks throughout the lower ARB. Increased allochthonous inputs and reduced fish predation associated with Gustav likely contributed to the increased P. clarkii CPUE observed during 2009. During 2008, P. clarkii CPUE was highest at sample locations characterized by high dissolved oxygen (DO) concentrations and lowest at locations with relatively low DO levels. In addition, chronically hypoxic sampling locations yielded lower mean CPUE and carapace length during 2008. An increase in P. clarkii mean CPUE and a concomitant decrease in mean carapace length during the 2009 crayfish season indicated density-dependent growth. While abiotic factors undoubtedly influenced crayfish population characteristics, relative density appeared to have the largest effect on P. clarkii carapace length and may have depressed any physicochemical influences. Lactate, glucose, and protein concentrations in P. clarkii hemolymph were examined in individuals from chronically hypoxic ARB habitats and laboratory simulated hypoxia experiments. P. clarkii from normoxic and hypoxic natural habitats did not display significantly different hemolymph lactate or glucose concentrations, however, mean hemolymph protein concentration was significantly lower in crayfish from hypoxic areas. P. clarkii exposed to severe hypoxia in laboratory experiments had significantly higher hemolymph lactate and glucose concentrations, whereas large differences in protein concentrations were not observed. A hand-held lactate meter and refractometer proved to be reliable methods for determination of P. clarkii hemolymph lactate and protein concentrations, respectively.

Wetland birds are likely to be influenced by habitat at multiple spatial scales, yet few studies have investigated bird responses at both broad and fine scales. Northern Gulf Coast marshes are dynamic ecosystems, and they provide an ideal place to examine habitat across spatial and temporal scales. My research focused on the secretive marsh bird guild (i.e. bitterns, rails, gallinules, grebes) with an emphasis on the king rail (Rallus elegans), a species of high conservation concern. My objectives were to investigate the wetland bird-environment relationship across scales, and to model annual changes in bird distribution. Study sites were in the fresh and intermediate (oligohaline) marshes of the Chenier Plain coastal region of southwest Louisiana and southeast Texas. I captured king rails for a two year radio telemetry study, and conducted point count surveys of marsh birds from March to mid-June of 2009-2011 using call-back methods to elicit responses. I visited each point six times per year, and >100 points were surveyed each year (n=304). Localized, field-based measures (e.g. water depth), management, and broad marsh types were related to bird abundance, and species distribution models were developed for four species based on Landsat satellite imagery. Home ranges of king rails varied from 0.8-32.8 ha (n=22), rails selected for open water, and smaller home ranges were associated with greater open water within the home range (20-30%). Point counts showed fine-scale habitat models, usually incorporating water depth, were improved with the addition of broad-scale marsh type and management, classified as permanently impounded, drawdown, or unmanaged. For 12 of 13 species, a multi-scale model was better than any single spatial scale. Species distribution models showed satellite-based measures of habitat corresponded well to marsh birds as they explained 37-79% of the variation in abundance. Temporary water was the most important variable, and species' models were distinct for fresh and intermediate marshes. The spatial distribution of birds varied greatly among years, especially with migratory birds in the highly variable fresh marsh. Overall, marsh birds responded to the environment at a variety of spatial scales, and satellite-based distribution models showed broad-scale patterns and dynamic distributions among years.

One major drawback of biomass fuel is its bulky nature and the resulting high cost of transporting the fuel to the facility where the energy is being produced. Hence, supply chain of biomass residues plays a crucial role in determining the financial viability of bioenergy production. Transporting biomass for energy purposes more than 50 miles (80 km) is not considered economically feasible in most conditions. In the wood energy scenario, the maximum distance is more often restricted to distances of less than 200 km between production and consumption (via road). A study was done to determine logging residues and agricultural residues production for the 64 parishes in Louisiana and to compare the three different modes of transportation (freight) for wood biomass, namely rail, road and water. The average annual production for logging residues in the state from 2000 to 2010 was estimated around 3,073,978 bone dry tons (BDT) and for agricultural crop residue it was approximately 6,773,985 BDT annually (2005- 2011). The greatest production of logging residues was in the western and northern parishes of Louisiana, away from the population centers. The road network was the most extensive means of transportation. For long distances (greater than about 150 km), the Mississippi/Red River complexes could provide a very cheap source of transportation, followed by rail, but they had their own set of logistical problems. The river or rail networks were limited for the major logging residues producers (such as Winn, Vernon, Bienville, Union, etc.) and utilizing parishes. For agricultural residues, north-eastern and central parishes like Morehouse, Madison, Franklin, East Carroll and Pointe Coupee were the major producers. Soybean, rice, corn and sugarcane constituted the majority of the agricultural residue production. All the major agricultural parishes were in close proximity to ports in the state, which opened them to the waterway system.

Mottled ducks (Anas fulvigula) are the most abundant breeding waterfowl in the coastal marshes of Louisiana and Texas. Mottled ducks are non-migratory and heavily dependent on coastal marsh habitats; they must satisfy all of their annual resource needs from within the Gulf Coast region. Coastal marsh habitats are being rapidly lost or degraded in Louisiana and Texas. The hydrology of many coastal marsh habitats has been altered by anthropogenic activity and natural factors. Parameters related to Mottled Duck habitat use and movements in this altered environment are poorly understood, and managers need information on vital rates of Mottled Ducks in coastal Louisiana and Texas. Information on use of habitats, breeding pair densities, and movements of female Mottled Ducks could benefit managers charged with conservation of Mottled Ducks and coastal marsh habitats and be used to guide resource allocation for restoration and conservation in this region. Additionally, information on breeding propensity would satisfy a need to establish vital rates used for population modeling. I employed radio-telemetry techniques to evaluate use of habitats and movements by female Mottled Ducks in the Gulf Coast region. I used a transect survey as an index to pair densities in different habitats, and evaluated examination of postovulatory follicles as a method to assess breeding propensity in Mottled Ducks. Mottled Ducks used fresh and intermediate marsh heavily and pair densities were greatest in fresh marsh habitats. Mottled ducks had low movement distances and moved inland away from storm surge caused by hurricanes. Macroscopic examination of postovulatory follicles was not appropriate for evaluation of breeding propensity in Mottled Ducks. Conservation of natural coastal marsh habitats in Louisiana and Texas will benefit Mottled Ducks in the Western Gulf Coast region.

Although watershed land use effects on in-stream fish habitat and fish-macrohabitat associations have been widely studied in the past, low-gradient, coastal Louisiana streams have been poorly described in the literature. In this thesis, I report the results of a two-year study exploring relationships among regional land use, in-stream physical habitat, and headwater stream fish assemblages. In chapter two, I examined in-stream habitat variables such as depth, flow, and substrate combined with three-pass electrofishing depletion estimates at thirteen 100-m stream sites. I used a combination of principle component analysis and structural equation modeling to determine if trends were present in the habitat, fish composition, and species trait data. I found that a species-based structural equation model was a better predictor of relationships among fish, land use, and in-stream habitat variables, when compared to species grouped by functional traits. In addition, it appears that the amount of agricultural land may not have as detrimental effects on fishes in these coastal streams as has been reported in other aquatic systems and substrate type may be the most important manageable habitat parameter. In chapter three, I measured various in-stream habitat variables (i.e. dominant substrate, depth, flow) for two dominant macrohabitats (pools vs glides). I collected fish from each macrohabitat via point-electrofishing and compared these data using canonical correlation analysis (CCorA) to determine if trends were present in macrohabitat, fish composition, and species trait data. I found that species- and functional trait-based CCorAs were able to determine correlations with various macrohabitats and variables within macrohabitats. Results indicate that species traits may be better measures of assemblage structure when macrohabitat-scale management, conservation, or restoration is the goal. Although I expected land use to heavily influence in-stream habitat and fish assemblage composition, my research indicated that in-stream habitat was be more influential than land use in determining species composition of Louisiana headwater stream fish assemblages. I also expected species- and trait-based models to successfully predict fish-macrohabitat associations. The findings of this study confirmed my predictions that multiple techniques for assessing fish-macrohabitat associations exist, although the most appropriate method may depend on specific management, restoration, or conservation goals.

Riverine fisheries management programs often do not focus on non-sport and non-commercial fishes, such as catostomids, yet many suckers have become threatened or endangered throughout river systems in the United States because of habitat alterations. In the Pearl River, sedimentation, dam construction, and other hydrologic modifications have negatively impacted habitats used by southeastern blue suckers Cycleptus meridionalis, a species of concern in both Louisiana and Mississippi. The principal objective of this project was to investigate habitat use of likely historically abundant southeastern blue suckers in the lower Pearl River. During electrofishing surveys in 2010 and 2011, we observed no southeastern blue suckers in the west branch of the Pearl River, and significantly lower catch rates in the main branch of the Pearl River (Mean Catch Per Unit Effort (CPUE) = 0.053/minute) relative to three other common benthic Pearl River fishes, including smallmouth buffalo Ictiobus bubalus (P< 0.0018), channel catfish Ictalurus punctatus (P< 0.0001) and flathead catfish Pylodictus olivaris (P< 0.0017). However, CPUE for southeastern blue suckers was similar to quillback Carpiodes cyprinus (P=0.999) and highfin carpsucker Carpiodes velifer (p=0.999). A mark and recapture population analysis was unable to generate a reasonable population estimate for southeastern blue suckers in this section of the Pearl River. The low CPUE values for other non-buffalo catostomids indicates that the availability of suitable habitat may be limiting populations of benthic suckers in the southern portions of the river. Habitat use of radio-tagged southeastern blue suckers indicated a strong affinity for deeper, outside river bends with accumulations of large woody debris and gravel, with high habitat specificity indicated by extended periods of little movement from these areas. Limited movements suggest a low potential for colonization of new areas or recolonization of abandoned habitats within the river. Raising the threat status for southeastern blue suckers, both globally and in Louisiana, may be warranted given their high habitat specificity, low recolonization potential, and susceptibility to the continuing degradation of their preferred habitats from sedimentation.

Hydrologic alterations frequently lead to vegetation changes in floodplain ecosystems. In Louisiana, there has been an expansion of water-elm (Planera aquatica) and to a lesser extent baldcypress (Taxodium distichum) at Catahoula Lake, a Ramsar Wetland of International Importance. Water-elm and baldcypress both are flood tolerant species; baldcypress growth is known to be influenced by hydrologic conditions more than climate. The expansion of these woody trees has reduced herbaceous vegetation valuable for waterfowl. In this study, I tested two hypotheses that establishment of water-elm trees into the lake increased after the construction of water control structures in the nearby Black River and a diversion canal and water-control structure on the lake in 1971; and that growth rates of water-elm and baldcypress are more correlated with hydrologic regimes than with local climate. Water-elm trees have been found in the lake for at least 140 years, but most (171 of 219) sampled trees were established in the period following the construction of water-control. In addition, 48 of 67 plots consisted of trees established entirely in the post-control period. Hydrologic conditions in the lake changed with the modifications, including reduced variability in June and August lake levels and reduced fall flooding. These changes coincided with apparently increased establishment of water-elm trees during the post-control period. Finally, there are several sources of uncertainty that prevent clear interpretation of the effects of water control on water-elm establishment including prevailing climatic conditions, control measures by Louisiana Department of Wildlife and Fisheries and cattle grazing. My second hypothesis that growth of water-elm and baldcypress would be more correlated with hydrologic regimes than with climate was partially supported. Growth of water-elm was more related to climatic variables than with lake levels, whereas baldcypress radial growth was more correlated with lake levels than with climatic variables. The response of water-elm radial growth to lake hydrology was limited to a negative relationship with late spring lake levels in the pre-control period; baldcypress had a consistent positive response with lake levels during several seasons in both the pre-and post-control periods.

The goal of this dissertation was to integrate multiple disciplines for application of high-throughput sperm cryopreservation to aquatic species. The blue catfish Ictalurus furcatus was selected for research due to its role in production of hybrid catfish with eggs from channel catfish Ictalurus punctatus. A high-throughput cryopreservation pathway was developed by systematically evaluating each process factor and using automated processing systems. Large quantities of cryopreserved sperm produced from this protocol were evaluated in commercial-scale hatcheries in cooperation with aquaculture producers. To develop production for commercial requirements, quality characteristics of materials and products were identified and recorded during processing and analyzed using industrial engineering methods to regulate quality. More than 1 million channel catfish eggs from 300 females were fertilized with thawed sperm, which was larger than any previous large-scale fertilization trial performed in fish. This demonstrated that the fertilization capability of cryopreserved sperm was equivalent to fresh sperm in production of hybrid fry. Quality regulation was presented within a quality assurance plan designed specifically for this process using quality standards (specifications) and quality variation data (quality control). This quality assurance plan is potentially the first of its kind for cryopreserved sperm of any species. After being scaled up by automation and standardized by the quality assurance plan, the cryopreservation process produced reliable products for hatcheries. Proper use of these products (i.e., as a dose of 3704 eggs/straw) can provide a basis for industry standards for artificial spawning. A quantitative evaluation was developed based on the defined dose and the production efficiency. To increase the efficiency for large-scale production, simulation model computing was used to create a virtual process. The simulation model was validated based on the existing process, and provides a valuable tool for future improvements. This dissertation took the initiative to apply high-throughput cryopreservation in aquaculture and expand the process from planning to operation at the production line, to terminal use of products by customers. This enables cryopreserved sperm to become a practical form of genetic resources applicable for aquatic genetic improvement and conservation.