Life Sciences Commons^™

Incremental Genetic K-Means Algorithm And Its Application In Gene Expression Data Analysis, Yi Lu, Shiyong Lu, Farhad Fotouhi, Youping Deng, Susan J. Brown

Faculty Publications

Background

In recent years, clustering algorithms have been effectively applied in molecular biology for gene expression data analysis. With the help of clustering algorithms such as K-means, hierarchical clustering, SOM, etc, genes are partitioned into groups based on the similarity between their expression profiles. In this way, functionally related genes are identified. As the amount of laboratory data in molecular biology grows exponentially each year due to advanced technologies such as Microarray, new efficient and effective methods for clustering must be developed to process this growing amount of biological data.

Results

In this paper, we propose a new clustering algorithm, …

Spring Phytoplankton Photosynthesis, Growth, And Primary Production And Relationships To A Recurrent Coastal Sediment Plume And River Inputs In Southeastern Lake Michigan, Steven E. Lohrenz, Gary L. Fahnenstiel, David F. Millie, Oscar M.E. Schofield, Tom Johengon

Faculty Publications

[1] A recurrent coastal sediment plume (RCP) is an episodic event in the southern basin of Lake Michigan that typically coincides with the spring diatom bloom. Strong winter storm activity during El Nino conditions in 1998 resulted in a large and intense RCP event. Consistently higher values of the light-saturated rate of photosynthesis, P-max(B), were observed in spring 1998 compared to 1999 and 2000. Higher values of P-max(B) in 1998 appeared to be related to increased availability of phosphorus, as evidenced by significant correlations of P-max(B) with soluble reactive phosphorus (SRP). Light-saturated growth rates were also significantly correlated with SRP …

On The Approximation Of The Coriolis Terms In C-Grid Models, Dmitri A. Nechaev, Max Yaremchuk

Faculty Publications

A new representation of the Coriolis terms on the Arakawa C grid is proposed. The approximation dumps the grid-scale noise that arises because of spatial averaging of the Coriolis terms when the grid spacing is larger than the deformation radius. The proposed approximation can also be applied in C-grid schemes with semi-implicit treatment of the Coriolis terms. The new scheme is analyzed in the context of the linear inertial-gravity waves and its advantageous behavior is demonstrated with respect to the conventional technique.

Rationale For A New Generation Of Indicators For Coastal Waters, Gerald Niemi, Denice Wardrop, Robert Brooks, Susan Anderson, Valerie Brady, Hans Paerl, Chet Rakocinski, Marius Brouwer, Barbara Levinson, Michael Mcdonald

Faculty Publications

More than half the world'S human population lives within 100 km of the coast, and that number is expected to increase by 25% over the next two decades. Consequently, coastal ecosystems are at serious risk. Larger coastal populations and increasing development have led to increased loading of toxic substances, nutrients and pathogens with subsequent algal blooms, hypoxia, beach closures, and damage to coastal fisheries. Recent climate change has led to the rise in sea level with loss of coastal wetlands and saltwater intrusion into coastal aquifers. Coastal resources have traditionally been monitored on a stressor-by-stressor basis such as for nutrient …

Impacts Of A Recurrent Resuspension Event And Variable Phytoplankton Community Composition On Remote Sensing Reflectance, Trisha Bergmann, Gary Fahnenstiel, Steven Lohrenz, David Millie, Oscar Schofield

Faculty Publications

In order to characterize the impact of turbidity plumes on optical and biological dynamics, a suite of environmental parameters were measured in southern Lake Michigan during the springtime recurrent sediment plume. In-water measurements of inherent optical properties (IOPs) were entered into the Hydrolight 4.2 radiative transfer model and the output was compared with measured apparent optical properties (AOPs) across a wide range of optical conditions. Hydrolight output and measured underwater light fields were then used to clarify the effects of the sediment plume on primary production, phytoplankton community composition, and nearshore remote sensing ocean color algorithms. Our results show that …

Decadal Variability Of Circulation In The Arctic Ocean Retrieved From Climatological Data By A Variational Method, Dmitri A. Nechaev, Max Yaremchuk, Motoyoshi Ikeda

Faculty Publications

[1] An inverse 3D finite-element ocean circulation model has been designed and used to study variability of the Arctic Ocean circulation in the last 4 decades. We obtained stationary model solutions with the temperature and salinity fields close to the ones given by the Environmental Working Group (EWG) [1998] atlas. Transports at the open boundaries, wind forcing and hydrographic fields are treated as unknowns, which are varied to minimize a quadratic cost function subject to model constraints. The inverse problem is solved for 10 gridded hydrographic data sets that were obtained as winter and summer averages of EWG data over …

A New Method For Estimation Of The Sensible Heat Flux Under Unstable Conditions Using Satellite Vector Winds, Jiayi Pan, Xiao-Hai Yan, Young-Heon Jo, Quanan Zheng, W. Timothy Liu

Faculty Publications

It has been difficult to estimate the sensible heat flux at the air - sea interface using satellite data because of the difficulty in remotely observing the sea level air temperature. In this study, a new method is developed for estimating the sensible heat flux using satellite observations under unstable conditions. The basic idea of the method is that the air - sea temperature difference is related to the atmospheric convergence. Employed data include the wind convergence, sea level humidity, and sea surface temperature. These parameters can be derived from the satellite wind vectors, Special Sensor Microwave Imager (SSM/I) precipitable …

Translocation As A Strategy To Rehabilitate The Queen Conch (Strombus Gigas) Population In The Florida Keys, Gabriel A. Delgado, Claudine T. Bartels, Robert A. Glazer, Nancy J. Brown-Peterson, Kevin J. Mccarthy

Faculty Publications

Queen conch (Strombus gigas) stocks in the Florida Keys once supported commercial and recreational fisheries, but overharvesting has decimated this once abundant snail. Despite a ban on harvesting this species since 1985, the local conch population has not recovered. In addition, previous work has reported that conch located in nearshore Keys waters are incapable of spawning because of poor gonadal condition, although reproduction does occur offshore. Queen conch in other areas undergo ontogenetic migrations from shallow, nearshore sites to offshore habitats, but conch in the Florida Keys are prevented from doing so by Hawk Channel. The present study was initiated …

Seasonal Use Of Bridges By Rafinesque's Big-Eared Bat, Corynorhinus Rafinesquii, In Southern Mississippi, Austin W. Trousdale, David C. Beckett

Faculty Publications

We conducted surveys of concrete bridges in southern Mississippi from 2000–2002 to determine the phenological pattern of use by Rafinesque's big-eared bat, Corynorhinus rafinesquii. The earliest dates on which we located maternity colonies were 9 March 2000, 20 April 2001, and 15 May 2002. Maternity colonies increased in size and abundance as spring progressed. Pups were born in mid- to late May (first observed 12 May 2000, 15 May 2001, 27 May 2002) and nursed through midsummer (lactating females last captured 14 July 2000, 25 July 2001, 16 July 2002). Colony size and percentage of bridges occupied by bats declined …

Hydrogen Peroxide In Deep Waters Of The North Pacific Ocean, Jinchun Yuan, Alan M. Shiller

Faculty Publications

Hydrogen peroxide is a reactive oxygen intermediate that can play a role in a variety of redox cycles. In the ocean, it is generally considered to be dominantly photo-produced with negligible concentrations in deep waters. We have utilized a highly sensitive analytical method to investigate hydrogen peroxide in deep waters of the North Pacific Ocean. We present evidence that hydrogen peroxide exists in low nanomolar concentrations in these deep waters with an apparent minimum in the depth range of the oxygen minimum. A consideration of possible mechanisms and rates suggests both a short (similar to12 day) residence time as well …

Diel Vertical Distribution Of Atlantic Croaker, Micropogonias Undulatus, Larvae In The Northcentral Gulf Of Mexico With Comparisons To Red Drum, Sciaenops Ocellatus, Bruce H. Comyns, Joanne Lyczkowski-Shultz

Faculty Publications

Atlantic croaker Micropogonias undulates (Linnaeus, 1766) larvae < 6 mm showed a distinct pattern of vertical stratification in inner-shelf waters (< 25 m depth) of the northcentral Gulf of Mexico. Discrete-depth plankton collections were taken at night, early morning after daylight, and at mid-day or early afternoon at 1, 5, and 11–16 m. No consistent pattern among cruises was evident in the vertical stratification of Atlantic croaker larvae found in mid-day and afternoon collections, but at night the highest abundances were observed at the deepest depths sampled. Atlantic croaker larvae were least abundant in surface waters (1 m) at night. Of the 66,913 Atlantic croaker larvae collected, only 346 specimens (< 1%) were found in 1 m collections at night, and 266 of these larvae were from a single collection of large specimens (mean = 6.7 mm). By morning the vertical distribution of larvae suggested that Atlantic croaker had moved up in the water column, and highest abundances were usually found at 5 m. There was no indication that patterns of larval distribution reflected hydrographic stratification within the water column, prey availability, size of larvae, or moonlight intensity.

Effects Of Salinity On Growth And Molting Of Sympatric Callinectes Spp. From Camaronera Lagoon, Veracruz, Mexico, Sergio Cházaro-Olvera, Mark S. Peterson

Faculty Publications

Megalopae of Callinectes rathbunae Contrareras, 1930 and C. sapidus Rathbun, 1896 were exposed to salinities of 5, 15, and 25 at 25.0degreesC (through crab stage 16) to determine if there were species-specific differences in survival, growth, and intermolt duration. Survival of C. rathbunae decreased significantly at higher salinities, but there was no salinity effect for C. sapidus. Callinectes rathbunae had significantly higher survival than C. sapidus in salinities of 5 and 15, but survival was not different in a salinity of 25. There was no difference in survival of C. rathbunae by gender; survival of both genders was generally lowest …

Long-Lived Worms And Aging, Yuan Luo

Faculty Publications

Several investigators have generated long-lived nematode worms (Caenorhabditis elegans) in the past decade by mutation of genes in the organism in order to study the genetics of aging and longevity. Dozens of longevity assurance genes (LAG) that dramatically increase the longevity of this organism have been identified. All long-lived mutants of C. elegans are also resistant to environmental stress, such as high temperature, reactive oxygen species (ROS), and ultraviolet irradiation. Double mutations of some LAGS further extended life span up to 400%, providing more insight into cellular mechanisms that put limits on the life span of organisms. With …

Survey Of Salamanders In Mississippi Limestone Caves, John G. Himes, David C. Beckett, Austin W. Trousdale

Faculty Publications

During 2000-2002 we surveyed for salamanders in the larger limestone caves of Mississippi, all within the Vicksburg Group rock unit. We found four species: Plethodon mississippi was the most abundant, followed by Eurycea guttolineata, Eurycea cirrigera, and Desmognathus conanti. We did not find Pseudotriton montanus in any of the caves, and question the validity of an investigator's statement made nearly 45 years ago that, "it is one of the most numerous salamanders in Mississippi. limestone caves." The salamander fauna we found is similar to that of the only other comprehensive survey of salamanders in Mississippi caves, conducted almost thirty years …

Artificial Reef Matrix Structures (Arms): An Inexpensive And Effective Method For Collecting Coral Reef-Associated Invertebrates, Todd L. Zimmerman, Joel W. Martin

Gulf and Caribbean Research

Collecting reef-associated invertebrates usually involves disturbance of the reef area, often damaging the habitat and sometimes damaging live corals. We introduce a nondestructive, inexpensive, and effective method for collecting coral reef-associated invertebrates using approximations of small coral heads constructed of concrete, PVC pipes, nylon cleaning pads, and other materials easily obtainable in most tropical (coral-rich) countries. An example showing the effectiveness of the method is presented based on fieldwork in the eastern Caribbean.

Seasonal Occurrence Of Reef-Related Medusae (Cnidaria) In The Western Caribbean Sea, Gloria Ramos, Lourdes Segura-Puertas

Gulf and Caribbean Research

Seasonal fluctuations in composition and abundance of medusae collected in a reef lagoon of the Mexican Caribbean were analyzed. Plankton samples and hydrological data were taken monthly from January to September 1994 at 2 stations: coastal and near-reef. The highest densities of medusae were recorded in March (17,687 ind/100 m³) and August (2,433 ind/100 m³) at the coastal station. Medusae were less abundant at the nearreef station, but diversity indices were higher in comparison to the coastal station. Twenty-five species (24 hydroidomedusae and 1 scyphomedusa) were identified, with Linuche unguiculata (Swartz, 1788) and Eirene lactea (Mayer, …

Formation Of A Stress-Induced Check Mark On The Otoliths Of Juvenile Fishes: Implications For Mesocosm Studies, Thomas R. Reinert, Donald M. Baltz

Gulf and Caribbean Research

Daily otolith increment widths of spot Leiostomus xanthurus and spotted seatrout Cynoscion nebulosus were examined experimentally in field mesocosms for 5 to 7 days in various habitat types. Daily otolith increments were used as a surrogate for daily somatic growth so that growth prior to capture and handling could be examined. For both species, possible effects of habitat types were confounded by an overall decrease in daily increment widths during the experimental period when compared to increment widths prior to capture. Several spotted seatrout inadvertently captured during mesocosm deployment provided a means for assessing if there was a significant mesocosm …

The First Larval Stage Of Microprosthema Semilaeve (Von Martens, 1872) (Crustacea: Decapoda: Stenopodidea) Obtained In The Laboratory, Joel W. Martin, Joseph W. Goy

Gulf and Caribbean Research

The first larval stage of Microprosthema semilaeve (von Martens, 1872) is described from ovigerous females collected off Sombrero Key, Florida Keys, USA, and Guana Island, British Virgin Islands, Caribbean. The larvae are characterized by a broad, triangular telson bearing posterolateral spines and an “anomuran seta,” a first maxilliped that differs markedly from the very similar (to each other) second and third maxillipeds, and the presence of the first pereiopod as a swimming appendage upon hatching, as is apparently true of all stenopodidean first stage larvae. Characters of the larvae are compared to those described from the Indian Ocean by Raje …

Embryogenesis In The Dwarf Seahorse, Hippocampus Zosterae (Syngnathidae), James T. Wetzel, John P. Wourms

Gulf and Caribbean Research

Embryogenesis of the dwarf seahorse, Hippocampus zosterae, was studied by scanning electron microscopy of a series of developmental stages. Stages ranged from initial cleavage of the egg through term embryos. Embryos hatch from their egg envelopes about midway through development, yet remain nestled in stromal chambers of vascularized epithelium within the male brood pouch until their yolk reserves are consumed. The difference in body shape between the pipefish and seahorse first becomes discernible during mid-development, just before hatching. At this stage, embryos begin to develop their characteristic prehensile tail in contrast to the straight body and typical caudal fin …

Stomatopoda (Crustacea: Hoplocarida) From The Shallow, Inshore Waters Of The Northern Gulf Of Mexico (Apalachicola River, Florida To Port Aransas, Texas), John M. Foster, Brent P. Thoma, Richard W. Heard

Gulf and Caribbean Research

Six species representing the order Stomatopoda are reported from the shallow, inshore waters (passes, bays, and estuaries) of the northern Gulf of Mexico limited to a depth of 10 m or less, and by the Apalachicola River (Florida) in the east and Port Aransas (Texas) in the west. With the exception of the “live bottom” gonodactylid, Neogonodactylus bredini (Manning), these predatory crustaceans usually inhabit burrows in mud, sand-mud, and sand substrata in coastal and shelf waters. The species treated in this paper are Neogonodactylus bredini (Manning), Lysiosquilla scabricauda (Lamarck), Bigelowina biminiensis (Bigelow), Coronis scolopendra Latreille, Squilla empusa Say, and Gibbesia …

Northern Range Extensions For Caprella Scaura Templeton, 1836 (Crustacea: Amphipoda: Caprellidae) On The Florida Gulf Coast And In South Carolina, John M. Foster, Richard W. Heard, David M. Knott

Gulf and Caribbean Research

Previous northwestern Atlantic records for the caprellid amphipod Caprella scaura Templeton, 1836 were confined to St. Croix (US Virgin Islands), St. Barthélemy, and Puerto Rico, islands bordering the northern Caribbean Sea. Based on recent collections, C. scaura is now reported from the Gulf of Mexico (St. Andrew Bay, Florida) and the US east coast (Charleston Harbor, South Carolina). These constitute the first records for this apparently non-indigenous species in waters of the continental eastern United States, establishing considerable northern range extensions for C. scaura in the northwest Atlantic.

Introduction To Special Section On Research Activities At The Iztacala Campus Of The Universidad Nacional Autónoma De México, México, Mark S. Peterson, Nancy J. Brown-Peterson

Gulf and Caribbean Research

In October 2002, we had the opportunity to initiate a long-term collaboration with colleagues from the Iztacala campus of the Universidad Autónoma de México (UNAM), whose research interests focus on coastal and nearshore fishes and decapod crustaceans of Veracruz state, Mexico. This is an undergraduate campus with a strong Biology department whose faculty also maintain research programs despite limited sources of funding and a heavy teaching load. During the course of our initial visit, we realized that there is a wealth of unpublished undergraduate student research on understudied fish species.

Feeding Habits And Sexual Dimorphism Of The Violet Goby, Gobioides Broussoneti Lacepede (Pisces: Gobiidae), In The Estuarine System Of Tecolutla, Veracruz, Mexico, Sergio Mata-Cortes, Jose Antonio Martinez-Perez, Mark S. Peterson

Gulf and Caribbean Research

Gobioides broussoneti were sampled in Silveña estuary, a branch of the Tecolutla estuary, Veracruz, Mexico, during 2 trips made between February 1998 and June 1999 to evaluate diet and sexual dimorphism. A total of 65 G. broussoneti ranging from 49–401 mm SL (0.7–124.2 g WW) were collected. There was a 1:1.2 sex ratio in favor of females. Seven food types were noted, with filamentous algae (25.4%) and detritus (21.3%) representing the principal food types. A 24 h feeding study revealed that this species feeds continuously throughout the day. The ovaries of all female G. broussoneti contained previtellogenic oocytes, characteristic of …

Helminths From Dormitator Maculatus (Pisces: Eleotridae) In Alvarado Lagoon, Veracruz, Mexico, And Supplemental Data For Clinostomum Complanatum Rudolphi, 1814 From Egretta Caerulea (Aves: Ardeidae), Jesus Montoya-Mendoza, Rafael Chavez-Lopez, Jonathan Franco-Lopez

Gulf and Caribbean Research

Fishes are important hosts of helminths with aquatic life stages, yet little information is available on host-parasite relationships in tropical low salinity ecosystems. In this paper we report helminth parasites of the fat sleeper, Dormitator maculatus, in the Alvarado lagoon system, Veracruz. Mexico. Four parasite species were recorded from D. maculatus, including trematode metacercariae of Clinostomum complanatum, as well as nematode larvae of Spyroxis sp. and Camallanus sp. and adults of Neochinorhynchus golvani. In addition, we obtained adult C. complanatum from the esophagus of the little blue heron, Egretta caerulea. Dormitator maculatus is a new …

Predators And The Distribution And Abundance Of Blennies On Offshore Petroleum Platforms, Tommy J. Rauch

Gulf and Caribbean Research

Predation may be important in structuring fish assemblages but studies of the intensity of predation on marine fish assemblages are uncommon. Predator avoidance behavior was used to identify the predators of an assemblage of blennies found on offshore petroleum platforms in the northern Gulf of Mexico. The distribution of predators was then compared with the distribution of 3 species of blennies to see if predation intensity was related to the vertical zonation of blennies. Predator approaches and blenniid activity were compared in low and high surface current events. Results did not support a hypothesis of predation controlling the distribution and …

Studies On The Crustacea Of The Turks And Caicos Islands, British West Indies. V. Records Of Mysids From Pine Cay, Fort George Cay, Water Cay, And Adjacent Waters, W. Wayne Price, Richard W. Heard

Gulf and Caribbean Research

Only 2 species of mysids, Heteromysis spottei and Stygiomysis clarkei, have been previously reported from the Turks and Caicos Islands. Between 1988 and 1990, 21 species of mysids were collected from reef (to 38 m) and shallow non-reef habitats surrounding Pine Cay, Fort George Cay, and Water Cay, Turks and Caicos Islands. One species collected, Anchialina typica, is distributed throughout tropical and subtropical seas. Twelve species (Bowmaniella johnsoni, Dioptromysis paucispinosa, Heteromysis bermudensis, H. guitarti, H. mayana, Mysidium columbiae, M. gracile, M. integrum, Mysidopsis bispinulata, M. brattstromei, Parvimysis …

Spatial Patterns Of Estuarine Habitat Type Use And Temporal Patterns In Abundance Of Juvenile Permit, Trachinotus Falcatus, In Charlotte Harbor, Florida, Aaron J. Adams, David A. Blewett

Gulf and Caribbean Research

The life history of many marine fishes is a 2-phase cycle: juveniles and adults make up a demersal phase, whereas larvae are planktonic. Determining ontogenetic patterns of habitat type use of the demersal phase has important management and habitat conservation implications for species that use coastal habitat types as juveniles. Juvenile permit, Trachinotus falcatus, are presumed to be limited to beaches exposed to open ocean, but few studies have addressed juvenile permit use of estuarine habitat types. Ten years of fisheries-independent monitoring data from a subtropical estuary were analyzed to determine habitat type use patterns and seasonality of juvenile …

First Record Of Bonefish, Albula Vulpes, From Mississippi Coastal Waters, K.J. Cuevas, James S. Franks, M.V. Buchanan

Gulf and Caribbean Research

Bonefish (Albula spp.), Family Albulidae, occur worldwide in coastal waters of tropical and warm temperate seas (Crabtree et al. 1997), and 2 species, A. vulpes and A. nemoptera, are recognized from the western Atlantic Ocean (Rivas and Warlen 1967). The normal range of A. vulpes in the western Atlantic extends from Bermuda to Brazil, including the Bahamas, Cuba, Mexico, Central America and the Antilles (Hildebrand 1963), but in US waters, A. vulpes typically occurs off south Florida (Crabtree et al. 1997). In contrast, A. nemoptera has been reported from Panama, Colombia, Venezuela, Jamaica and Hispaniola (Uyeno et al. …

Notes On Aquarium Brood Release And Feeding Of The Opossum Pipefish, Microphis Brachyurus Lineatus, Sarah Frias-Torres

Gulf and Caribbean Research

The opossum pipefish, Microphis brachyurus lineatus, is a migratory syngnathid with a salmon-like life history (Frias-Torres 2002). Adults breed in freshwater and oligohaline habitats associated with emergent vegetation, mostly Panicum sp. and Polygonum sp.; breeding occurs during the wet season (May to November) (Gilmore and Hastings 1983). In southern Mexico, opossum pipefish associate with Ruppia maritima, and reproduction is year-round (Miranda-Marure et al. 2004). Pelagic juveniles are found in the Atlantic Ocean and are associated with Sargassum sp. (Böhlke and Chaplin 1968). Juveniles eventually recruit into oligohaline habitats. The species range is from Sao Paulo, Brazil, to New …

Overview Of Study Areas And Unam-Iztacala Student Research, Jonathan Franco-Lopez, Jose Antonio Martinez-Perez

Gulf and Caribbean Research

The State of Veracruz is located on the east coast of Mexico and consists of many shallow marine systems such as estuaries and coastal lagoons. These estuarine systems are ecological sites of great importance due to the interactions that occur between the intertidal zones and adjacent areas. This importance is reflected in the variety of natural components present in these sites as well as the large number of species that depend on this aquatic zone, such as birds, mammals, molluscs, crustaceans and fishes. Many of the crustaceans and fishes are consumed by the local inhabitants and distributed in commercial areas …