Life Sciences Commons^™

Effects Of Cyclic Hypoxia On Gene Expression And Reproduction In A Grass Shrimp, Palaemonetes Pugio, Nancy J. Brown-Peterson, C. Steve Manning, Vishal Patel, Nancy D. Denslow, Marius Brouwer

Faculty Publications

Cyclic changes in dissolved oxygen occur naturally in shallow estuarine systems, yet little is known about the adaptations and responses of estuarine organisms to cyclic hypoxia. Here we examine the responses of Palaemonetes pugio, a species of grass shrimp, to cyclic hypoxia (1.5-8 mg/l dissolved oxygen; 4.20-22.42 kPa) at both the molecular and organismal levels. We measured alterations in gene expression in hepatopancreas tissue of female grass shrimp using custom cDNA macroarrays. After short-term (3-d) exposure to cyclic hypoxia, mitochondrial manganese superoxide dismutase (MnSOD) was upregulated and 70-kd heat shock proteins (HSP70) were downregulated. After 7-d exposure, nuclear genes encoding …

Coral Reefs Of Miskitus Cays, Nicaragua, Ana C. Fonseca

Gulf and Caribbean Research

The Miskitus Cays, on the Caribbean coast of Nicaragua, consist of eighty mangrove and two sand and gravel cays, surrounded by seagrass beds, octocoral gardens, patch reefs, reef crests, extended algae platforms, short reef walls, and two marginal reefs around the sand cays. Seventy sites were inspected and eighteen sites were selected for rapid assessments in order to determine the status of the coral reefs. Linear transects and the intercept point methods were used to determine the relative benthic cover, and the density, size and health of coral colonies was estimated following the AGRRA protocol. Water was highly turbid due …

Seagrass Distribution In The Pensacola Bay System, Northwest Florida, Michael A. Lewis, Richard Devereux, Pete Bourgeois

Gulf and Caribbean Research

Aerial surveys of seagrass coverage in the Pensacola Bay system (PBS) have been conducted during 1960, 1980, 1992 and 2003. This report summarizes the results for the 2003 survey and compares the results to those previously reported for other surveys. The estimated coverage of seagrass for the PBS during 2003 was 1,654 ha. Continuous and patchy coverages ranged from 0 to 684 ha and 11 to 543 ha, respectively, for five PBS subsystems. In 2003, the majority of seagrass coverage occurred in Santa Rosa Sound (76%). Declines in total coverage occurred for East Bay (93%) and Escambia Bay (75%) whereas …

Variability In Estimating Abundance Of Postlarval Brown Shrimp, Farfantepenaeus Aztecus (Ives), Migrating Into Galveston Bay, Texas, Geoffrey A. Matthews

Gulf and Caribbean Research

Three sets of monitoring data were used to examine the variability associated with abundance estimation of postlarval brown shrimp, Farfantepenaeus aztecus (Ives) in Bolivar Roads, Texas—the main connection between the Gulf of Mexico and Galveston Bay. Abundance of postlarvae (PL) caught with Renfro beam trawl varied greatly in different years on the same dates. A “spring peak” of brown shrimp PL migrating into Galveston Bay was found for 2 April with a quadratic regression fit to 6-day moving averages of daily mean abundance from 22 yrs of monitoring data: Ln(PL+1) = 0.8736 + 0.09037Day - 0.0004934Day² (adj-R² = …

Occurrence Of Larval And Juvenile Fish In Mangrove Habitats In The Sian Ka'an Biosphere Reserve, Quintana Roo, Mexico, Matthew Campbell, Kim Withers, James Tolan

Gulf and Caribbean Research

Mangrove forests are ubiquitous in low lying coastal areas of tropical and subtropical zones of the world, including the lagoons of the Sian Ka’an Biosphere Reserve, Quintana Roo, Mexico. Mangroves are habitat for juvenile fish of both oceanic and estuarine origin (Vásquez-Yoemans 1992, Vásquez-Yoemans et al. 1992, Laegdsgaard and Johnson 1995). Development of the Caribbean coast of Mexico north and south of the Sian Ka’an Reserve is in large part focused on tourism-related endeavors such as destination resorts, scuba diving and fishing. While some of the development is innocuous, land acquisition for development of resorts has fragmented mangrove habitats in …

Carpoapseudes Heardi N. Sp. (Tanaidacea: Apseudomorpha) From Caribbean Waters Near Tobago, Tom Hansknecht, Katia Christol Dos Santos

Gulf and Caribbean Research

Carpoapseudes heardi n. sp. is described from samples collected from depths of 421 and 537 m off Tobago and is the first Caribbean record for the genus. The new species bears a resemblance to Carpoapseudes serratospinosus Lang, 1968 and other related species in the shortened dactylus unguis combination of pereopod 1, but has parallel eyespines like Carpoapseudes bacescui Guţu, 1975 and Carpoapseudes simplicirostris (Norman and Stebbing, 1886). Other diagnostic characters include pereopods 2 and 3 with basal spurs, labrum with paired lobes, labial palp with two terminal setae, maxillipedal bases with outer crenulations, and pleopods with 1-articled rami. It was …

Habitat Condition And Associated Macrofauna Reflect Differences Between Protected And Exposed Seagrass Landscapes, Chet F. Rakocinski, Cynthia A. Moncreiff, Mark S. Peterson, Katherine E. Vanderkooy, Todd A. Randall

Gulf and Caribbean Research

Seagrass landscape configurations associated with different physical settings can affect habitat-structure and plant-animal relationships. We compared shoal grass (Halodule wrightii) habitat and macrofaunal variables between two fragmented seagrass landscapes at barrier-island locations subject to different disturbance regimes. Five seagrass habitat variables including above ground biomass (AGB), shoot number, per shoot biomass, epiphyte biomass and below ground biomass (BGB), differed significantly between the island landscapes. Per shoot biomass and epiphyte biomass also varied significantly over the seagrass growing season; and epiphyte biomass showed a strong landscape-time interaction. Abundances of microgastropods normalized to AGB differed significantly between landscapes. An inverse …

Seasonal Patterns Of Juvenile Fish Abundance In Seagrass Meadows In Teague Bay Bank Barrier Reef Lagoon, St. Croix, U.S. Virgin Islands, Ivan Mateo, William J. Tobias

Gulf and Caribbean Research

Considerable knowledge has been gained regarding fish use of nearshore habitats such as seagrass meadows or mangrove lagoons in the Caribbean (e.g., evaluation of nursery value, trophic linkages). However, few studies have been conducted on fish recruitment to seagrass habitat around the Caribbean. Juvenile reef fish in seagrass meadows at Teague Bay, St. Croix, U.S. Virgin Islands were surveyed from October 1998 through September 1999 using a visual census technique. Grunts (Haemulidae) were the most abundant juveniles observed (60% of all fish), followed by wrasses (Labridae, 20%) and parrotfishes (Scaridae, 13%). French grunt, Haemulon flavolineatum, were the most numerous …

An Unusual Reaction And Other Observations Of Sperm Whales Near Fixed-Wing Aircraft, Mari A. Smultea, Joseph R. Mobley Jr., Dagmar Fertl, Gregory L. Fulling

Gulf and Caribbean Research

Reported behavioral reactions by sperm whales to aircraft are sparse, highly variable, and largely anecdotal as summarized below. Observers since the whaling era began have noted that sperm whales tend to be skittish (Whitehead 2003). When documented, sperm whale reactions to both planes and helicopters range from no reaction (Clarke 1956, Gambell 1968, Green et al. 1992) to reactions such as increased surface intervals and dramatic behavioral changes (Clarke 1956, Fritts et al. 1983, Mullin et al. 1991, Würsig et al. 1998, Richter et al. 2003, 2006). Given the lack of supporting data for either case, it is important that …

Documentation Of A Gulf Sturgeon Spawning Site On The Yellow River, Alabama, Usa, Brian R. Kreiser, J. Berg, M. Randall, F. Parauka, S. Floyd, B. Young, K. Sulak

Gulf and Caribbean Research

The Gulf Sturgeon Recovery Plan (USFWS, GSMFC and NMFS 1995) stressed the need to provide maximum protection to Gulf sturgeon spawning habitat. The approach employed by various Gulf sturgeon researchers, including ourselves, to document spawning has been to identify potential spawning habitat on the basis of physical characteristics and/or tracking data, collect eggs, and then raise the eggs in the laboratory until the point where the larval fish can be identified (e.g., Marchant and Shutters 1996, Sulak and Clugston 1998, 1999). However, collecting eggs in any appreciable number is usually difficult, and these eggs may not always be viable upon …

Preliminary Survey Of Fish Community Composition In Seagrass Habitat In Two Back-Reef Lagoons Of The Southern Mexican Caribbean, Lauren A. Yeager, J. Ernesto Arias-Gonzalez

Gulf and Caribbean Research

Little is known about seagrass fish communities in the southern Mexican Caribbean. Diurnal and nocturnal fish community structure in seagrass habitat were compared between back-reef lagoons using a visual census technique in a natural protected area within a national park (Xcalak) and an unprotected area (Mahahual). Seagrass fish communities differed significantly between the two locations in the daytime and Xcalak supported greater total fish densities. Species richness did not differ statistically between locations. Observed nighttime fish communities were characterized by low species richness and low fish abundance when compared to diurnal communities. Heavy tourist use and coastal development may have …

Shell Utilization Pattern By The Hermit Crab Isocheles Sawayai Forest And Saint Laurent, 1968 (Anomura, Diogenidae) From Margarita Island, Caribbean Sea, Venezuela, Lee A. Galindo, Juan A. Bolanos, Fernando L. Mantelatto

Gulf and Caribbean Research

Isocheles sawayai is a hermit crab that is occasionally mentioned in the literature, and recently its distribution was extended to Venezuelan waters. Because no information on the biology and shell use patterns of this species inhabiting Caribbean waters is available, we provide the first information on shell occupation patterns of I. sawayai from Venezuela. Specimens were collected monthly from January to December 2000 along the sandy shore of Margarita Island, Venezuela. The 942 specimens collected showed different shell use patterns between the sexes and according to the reproductive condition of the females. The gastropods Leucozonia nassa (37.37%), Engoniophos unicinctus (25.37%), …

First Record Of Ceratapsis Monstrosa, A Larval Oceanic Penaeoid Crustacean, From The Gulf Of Mexico, James S. Franks, Adrienne Russell Flowers

Gulf and Caribbean Research

The genus Cerataspis (Gray, 1838) (Crustacea, Decapoda), assigned to the Penaeoidea by Burkenroad (1936) and Heegaard (1966), has circumglobal distribution between 40ºN and 40ºS (Morgan et al. 1985) and is represented in the Atlantic Ocean by two rarely collected species, C. monstrosa and C. petiti. Descriptions of both species are based on the larval forms since their adult form remain undescribed (Morgan et al. 1985). Although the larval development of Cerataspis is described by five mysis stages (I-V) (Heegaard 1966), the large larva is very un-mysid like and appears more like that of a megalops with the abdomen bend …

Behavior Of An Escolar Lepidocybium Flavobrunneum In The Windward Passage As Determined By Popup Satellite Archival Tagging, D.W. Kerstetter, P.H. Rice, E.D. Prince

Gulf and Caribbean Research

In June 2003, fisheries research was conducted in the Windward Passage using a chartered commercial pelagic longline vessel (Rice and Snodgrass 2003). This paper describes the habitat use by an escolar in this location tagged with a pop-up satellite archival tag (PSAT) that remained attached to the fish for 14 d. Data recovered from the PSAT were used to directly document diel vertical migration and ambient temperature range for the first time in a mesopelagic teleost.

Arabian Sea Response To Monsoon Variations, Raghu Murtugudde, Richard Seager, Prasad Thoppil

Faculty Publications

This study aims to quantify the impact of strong monsoons on the mixed layer heat budget in the Arabian Sea by contrasting forced ocean general circulation model simulations with composite strong and weak monsoon winds. Strong (weak) monsoons are defined as years with zonal component of the Somali Jet being greater (smaller) by more than a standard deviation of the long-term mean of the National Centers for Environmental Prediction reanalysis winds. Coastal upwelling is shown to be demonstrably stronger for strong monsoons leading to significant surface cooling, shallower thermoclines, and deeper mixed layers. A coupled ecosystem model shows that surface …

A Regional Modeling Study Of The Entraining Mediterranean Outflow, Xiaobiao Xu, E. P. Chassignet, J. F. Price, T. M. Özgökmen, H. Peters

Faculty Publications

[1] We have evaluated a regional-scale simulation of the Mediterranean outflow by comparison with field data obtained in the 1988 Gulf of Cadiz Expedition. Our ocean model is based upon the Hybrid Coordinate Ocean Model (HYCOM) and includes the Richardson number-dependent entrainment parameterization of Xu et al. (2006). Given realistic topography and sufficient resolution, the model reproduces naturally the major, observed features of the Mediterranean outflow in the Gulf of Cadiz: the downstream evolution of temperature, salinity, and velocity profiles, the mean path and the spreading of the outflow plume, and most importantly, the localized, strong entrainment that has been …

A Statistical Appraisal Of Disproportional Versus Proportional Microbial Source Tracking Libraries, Brian J. Robinson, Kerry J. Ritter, Rudolph D. Ellender

Faculty Publications

Library-based microbial source tracking (MST) can assist in reducing or eliminating fecal pollution in waters by predicting sources of fecal-associated bacteria. Library-based MST relies on an assembly of genetic or phenotypic "fingerprints" from pollution-indicative bacteria cultivated from known sources to compare with and identify fingerprints of unknown origin. The success of the library-based approach depends on how well each source candidate is represented in the library and which statistical algorithm or matching criterion is used to match unknowns. Because known source libraries are often built based on convenience or cost, some library sources may contain more representation than others. Depending …

Laboratory Method To Estimate Rain-Induced Splitting In Cultivated Blueberries, Donna A. Marshall-Shaw, James M. Spiers, Stephen J. Stringer, Kenneth J. Curry

Faculty Publications

Preharvest rainfall that occurs when fruit are fully ripe or approaching full ripeness can result in detrimental fruit splitting in rabbiteye and southern highbush blueberries. This study was initiated to develop a laboratory method to model rain-related incidence of splitting in cultivated blueberries with the goal of predicting the incidence of splitting in blueberry cultivars and selections. Multiyear field surveys of rabbiteye and southern highbush cultivars show that the incidence of rain-related splitting is strongly cultivar-dependent. Laboratory values for forced splitting and naturally occurring rain-related field splitting data show a strong correlation indicating that the incidence of fruit splitting can …

Evalution Of The Efficacy Of The Photosystem Ii Inhibitor Dcmu In Periphyton And Its Effects On Nontarget Microorganisms And Extracellular Enzymatic Reactions, Steven N. Francoeur, Audrey C. Johnson, Kevin A. Kuehn, Robert K. Neely

Faculty Publications

We examined the efficacy of the photosystem II inhibitor 3-(3,4-diclorophenyl)-1,1-dimethyl urea (DCMU) for inhibition of algal photosynthesis in periphyton associated with submerged decomposing litter of Typha angustifolia. We also investigated the possible nontarget effects of DCMU exposure on heterotrophic microorganisms (i.e., bacteria and fungi) and extracellular enzyme activity associated with decaying litter. Standing-dead Typha leaf litter was submerged for 34 and 73 d, returned to the laboratory, and used for controlled laboratory experiments that examined the effect of DCMU on algal ([¹⁴C]bicarbonate, pulse-amplitude modulated fluorometry), bacterial ([³H]leucine), and fungal ([¹⁴C]acetate) production. Simultaneous assays …

Reproductive Function For A C-Terminus Extended, Male-Transmitted Cytochrome C Oxidase Subunit Ii Protein Expressed In Both Spermatozoa And Eggs, Rumela Chakrabarti, Jennifer M. Walker, E.G. Chapman, S.P. Shepardson, R.J. Trdan, J.P. Curole, G.T. Watters, D.T. Stewart, S. Vijayaraghavan, W.R. Hoeh

Faculty Publications

Our previous study documented expression of a male-transmitted cytochrome c oxidase subunit II protein (MCOX2), with a C-terminus extension (MCOX2e), in unionoidean bivalve testes and sperm mitochondria. Here, we present evidence demonstrating that MCOX2 is seasonally expressed in testis, with a peak shortly before fertilization that is independent of sperm density. MCOX2 is localized to the inner and outer sperm mitochondrial membranes and the MCOX2 antibody’s epitope is conserved across >65 million years of evolution. We also demonstrate the presence of male-transmitted mtDNA and season-specific MCOX2 spatial variation in ovaries. We hypothesize …

Cloning, Analysis And Functional Annotation Of Expressed Sequence Tags From The Earthworm Eisenia Fetida, Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S. Inouye, Kuan Yang, Edward J. Perkins, Youping Deng

Faculty Publications

Background

Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR.

Results

A total of 3144 good quality ESTs (GenBank dbEST accession number EH669363–EH672369 and EL515444–EL515580) were obtained from the raw clone …

Comparison Of Probabilistic Boolean Network And Dynamic Bayesian Network Approaches For Inferring Gene Regulatory Networks, Peng Li, Chaoyang Zhang, Edward J. Perkins, Ping Gong, Youping Deng

Faculty Publications

Background: The regulation of gene expression is achieved through gene regulatory networks (GRNs) in which collections of genes interact with one another and other substances in a cell. In order to understand the underlying function of organisms, it is necessary to study the behavior of genes in a gene regulatory network context. Several computational approaches are available for modeling gene regulatory networks with different datasets. In order to optimize modeling of GRN, these approaches must be compared and evaluated in terms of accuracy and efficiency.

Results: In this paper, two important computational approaches for modeling gene regulatory networks, …

Sammd: Staphylococcus Aureus Microarray Meta-Database, Vijayaraj Nagarajan, Mohamed O. Elasri

Faculty Publications

Background

Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation …

Algal Regulation Of Extracellular Enzyme Activity In Stream Microbial Communities Associated With Inert Substrata And Detritus, Steven T. Rier, Kevin A. Kuehn, Steven N. Francoeur

Faculty Publications

We tested the hypothesis that algae influence the activities of extracellular enzymes involved in mineralization processes within microbial assemblages in streams. We tested the prediction that the factors that influence algal biomass and photosynthesis (i.e., diel fluctuations in photosynthetically active radiation [PAR], long-term variations in light regime, and community development stage) would have a corresponding effect on extracellular enzyme activities. We also tested the prediction that algae would influence enzyme activities on inorganic substrata and in detrital communities where they ultimately would influence plant litter decomposition rates. We allowed microbial communities to develop on inert substrata (glass-fiber filters) or on …

A Multi-Scale Examination Of Stopover Habitat Use By Birds, Jeffrey J. Buler, Frank R. Moore, Stefan Woltmann

Faculty Publications

Most of our understanding of habitat use by migrating land birds comes from studies conducted at single, small spatial scales, which may overemphasize the importance of intrinsic habitat factors, such as food availability, in shaping migrant distributions. We believe that a multi-scale approach is essential to assess the influence of factors that control en route habitat use. We determined the relative importance of eight variables, each operating at a habitat-patch, landscape, or regional spatial scale, in explaining the differential use of hardwood forests by Nearctic-Neotropical land birds during migration. We estimated bird densities through transect surveys at sites near the …

Variability In The Bulk Composition And Abundance Of Dissolved Organic Matter In The Lower Mississippi And Pearl Rivers, Shuiwang Duan, Thomas S. Bianchi, Alan M. Shiller, Karl Dria, Patrick G. Hatcher, Kevin R. Carman

Faculty Publications

[1] In this study, we examined the temporal and spatial variability of dissolved organic matter (DOM) abundance and composition in the lower Mississippi and Pearl rivers and effects of human and natural influences. In particular, we looked at bulk C/N ratio, stable isotopes (delta N-15 and delta C-13) and C-13 nuclear magnetic resonance (NMR) spectrometry of high molecular weight (HMW; 0.2 mu m to 1 kDa) DOM. Monthly water samples were collected at one station in each river from August 2001 to 2003. Surveys of spatial variability of total dissolved organic carbon (DOC) and nitrogen ( DON) were also conducted …

Fecundity And Survival Of The Calanoid Copepod Acartia Tonsa Fed Isochrysis Galeana (Tahitian Strain) And Chaetoceros Mulleri, Angelos Apeitos

Master's Theses

Historically, red snapper (Lutjanus campechanus) larviculture at the Gulf Coast Research Lab (GCRL) used 25 ppt artificial salt water and mixed, wild zooplankton composed primarily of Acartia tonsa, a calanoid copepod. Acartia tonsa was collected from the estuarine waters of Davis Bayou and bloomed in outdoor tanks from which it was harvested and fed to red snapper larvae. We are developing a more controlled copepod mass culture system to support finfish larviculture. To that end, I examined the effect of single species versus mixed species of algae as food for the copepods. Wild A. tonsa were isolated and reared in …

Revision Of The Nonequilibrium Thermal Dissociation And Stringent Washing Approaches For Identification Of Mixed Nucleic Acid Targets By Microarrays, Alex E. Pozhitkov, Robert D. Stedtfeld, Syed A. Hashsham, Peter A. Noble

Faculty Publications

Microarray experiments typically involve washing steps that remove hybridized nonspecific targets with the purpose of improving the signal- to- noise ratio. The quality of washing ultimately affects downstream analysis of the microarray and interpretation. The paucity of fundamental studies directed towards understanding the dissociation of mixed targets from microarrays makes the development of meaningful washing/ dissociation protocols difficult. To fill the void, we examined activation energies and preexponential coefficients of 47 perfect match ( PM) and double- mismatch ( MM) duplex pairs to discover that there was no statistical difference between the kinetics of the PM and MM duplexes. Based …

Upper-Ocean Response To Hurricane Ivan In A 1/25 Degrees Nested Gulf Of Mexico Hycom, T. G. Prasad, Patrick J. Hogan

Faculty Publications

[ 1] A 20-layer, 1/25 degrees nested Gulf of Mexico (GoM) Hybrid Coordinate Ocean Model (HYCOM) has been employed to examine the evolving three-dimensional ocean response to Hurricane Ivan during 14 - 16 September 2004. Results from several combinations of numerical experiments with and without assimilation of satellite-altimetry sea-surface height (SSH) are being analyzed and compared for the September 2004 hurricane period. A comparison of simulated zonal and meridional velocities using data assimilation shows improved agreement with profiler observations. The amplitude of the cold wake ( similar to 6 degrees C) produced by these simulations compared reasonably well with the …

Investigation Of The Summer Kara Sea Circulation Employing A Variational Data Assimilation Technique, G. Panteleev, A. Proshutinsky, M. Kulakov, Dmitri A. Nechaev, W. Maslowski

Faculty Publications

[ 1] The summer circulations and hydrographic fields of the Kara Sea are reconstructed for mean, positive and negative Arctic Oscillation regimes employing a variational data assimilation technique which provides the best fit of reconstructed fields to climatological data and satisfies dynamical and kinematic constraints of a quasi-stationary primitive equation ocean circulation model. The reconstructed circulations agree well with the measurements and are characterized by inflow of 0.63, 0.8, 0.51 Sv through Kara Gate and 1.18, 1.1, 1.12 Sv between Novaya Zemlya and Franz Josef Land, for mean climatologic conditions, positive and negative AO indexes, respectively. The major regions of …