Life Sciences Commons^™

Reconstructing The Genomic Architecture Of Mammalian Ancestors Using Multispecies Comparative Maps, William J. Murphy, Guillaume Bourque, Glenn Tesler, Pavel Pevzner, Stephen J. O'Brien

Biology Faculty Articles

Rapidly developing comparative gene maps in selected mammal species are providing an opportunity to reconstruct the genomic architecture of mammalian ancestors and study rearrangements that transformed this ancestral genome into existing mammalian genomes. Here, the recently developed Multiple Genome Rearrangement (MGR) algorithm is applied to human, mouse, cat and cattle comparative maps (with 311-470 shared markers) to impute the ancestral mammalian genome. Reconstructed ancestors consist of 70-100 conserved segments shared across the genomes that have been exchanged by rearrangement events along the ordinal lineages leading to modern species genomes. Genomic distances between species, dominated by inversions (reversals) and translocations, are …

Coastal Observatory Investigates Energetic Current Oscillations On Southeast Florida Shelf, Alexander Soloviev, Rebekah J. Walker, Robert H. Weisberg, Mark E. Luther

Marine & Environmental Sciences Faculty Articles

Coastal circulation along the southeast Florida shelf is strongly related to the dynamics of the Florida Current. The current follows the steep bottom terrain along the shelf break separating the deep ocean from the coastal zone (Figure 1 a, b). Energetic and complex flow regimes arise along the current's western edge, causing transient features such as sub-meso-scale eddies [Lee and Mayer, 1977; Shay et al., 2000] and energetic internal oscillations [Mooers, 1975; Soloviev et al., 2003], which affect mixing between the shelf and deeper ocean waters. Understanding of these regimes is important for modeling and prediction of the …

Fall 2003, Nsu Oceanographic Center

Currents

No abstract provided.

Use Of Pop-Up Satellite Archival Tags To Demonstrate Survival Of Blue Marlin (Makaira Nigricans) Released From Pelagic Longline Gear, David W. Kerstetter, Brian E. Luckhurst, Eric Prince, John E. Graves

Marine & Environmental Sciences Faculty Articles

No abstract provided.

Who Is Eating Most Of The Zooplankton In The Oceanic Gulf Of Mexico? The Impact Of Mesopelagic Fishes, Tracey Sutton, Scott E. Burghart

Marine & Environmental Sciences Faculty Proceedings, Presentations, Speeches, Lectures

Deep-sea pelagic fishes are the most abundant vertebrates on Earth, yet their role in the overall economy of these is poorly known. Low latitude oligotrophic regimes, typified by the eastern Gulf of Mexico, constitute most of the world ocean and consequently support the largest global ecosystems. Thus, we have little information on the trophic role of most of Earth's vertebrates. To address this, the diets of an entire midwater fish assemblage (164 species, constituting > 99% of assemblage numbers) were analyzed to assess feeding guilds and predation impact. Zooplanktivory was the dominant feeding mode (80% of prey biomass taken), followed by …

Summer 2003, Nsu Oceanographic Center

Currents

No abstract provided.

A Rapid Assessment Of Coral Reefs Near Hopetown, Abaco Islands, Bahamas (Stony Corals And Algae), Joshua Feingold, Susan L. Thornton, Kenneth W. Banks, Nancy J. Gasman, David S. Gilliam, Pamela Fletcher, Christian L. Avila

Marine & Environmental Sciences Faculty Articles

Coral reefs at 13 sites ranging in depth from 1-16 m near Hopetown, Abaco Islands, Bahamas were surveyed utilizing the Atlantic and Gulf Rapid Reef Assessment (AGRRA) benthos protocol. A total of 35 species of scleractinian corals and 2 species of calcareous hydrocorals were observed. The overall coral cover averaged just over 14%. Among corals that were at least 10 cm in diameter, small colonies (< 40 cm diameter) predominated in all sites except for the Fowl Cay pinnacles where 68% were larger than 60 cm in diameter. Large colonies (> 40 cm diameter) were also found in the Lynyard Cay spur-and-groove formations and the Sandy Cay fore reef. Zero-4% of the colonies were affected by disease. Total (recent + old) partial-colony mortality ranged from …

Phytoplankton Response To Intrusions Of Slope Water On The West Florida Shelf: Models And Observations, John J. Walsh, Robert H. Weisberg, Dwight A. Dieterle, Ruoying He, Brian P. Darrow, Jason K. Jolliff, Kristen M. Lester, Gabriel A. Vargo, Gary J. Kirkpatrick, Kent A. Fanning, Tracey Sutton, Ann E. Jochens, Douglas C. Biggs, Bisman Nababan, Chuanmin Hu, Frank E. Muller-Karger

Marine & Environmental Sciences Faculty Articles

Previous hypotheses had suggested that upwelled intrusions of nutrient-rich Gulf of Mexico slope water onto the West Florida Shelf (WFS) led to formation of red tides of Karenia brevis. However, coupled biophysical models of (1) wind- and buoyancy-driven circulation, (2) three phytoplankton groups (diatoms, K. brevis, and microflagellates), (3) these slope water supplies of nitrate and silicate, and (4) selective grazing stress by copepods and protozoans found that diatoms won in one 1998 case of no light limitation by colored dissolved organic matter (CDOM). The diatoms lost to K. brevis during another CDOM case of the models. In …

Comparative Genome Organization Of Human, Murine, And Feline Mhc Class Ii Region, Naoya Yuhki, Thomas W. Beck, Robert M. Stephens, Yoko Nishigaki, Kymberly Newmann, Stephen J. O'Brien

Biology Faculty Articles

To study comparative molecular dynamics in the genesis of the major histocompatibility complex (MHC), we determined a complete nucleotide sequence spanning 758,291 bp of the domestic cat (Felis catus) extended and classical class II region. The feline class II MHC includes 44 genes (31 predicted to be expressed) which display DNA sequence homology and ordered gene synteny with human HLA and mouse H2, in extended class II and centromere proximal regions (DM to DO) of the classical class II region. However, remarkable genomic alterations including gene gain and loss plus size differentials of 250 kb are …

Energetic Baroclinic Super-Tidal Oscillations On The Southeast Florida Shelf, Alexander Soloviev, Mark E. Luther, Robert H. Weisberg

Marine & Environmental Sciences Faculty Articles

Historical and recent data reveal a very energetic regime on the shelf off southeast Florida. In addition to spin off eddies, large-amplitude tidal velocity fluctuations with amplitudes exceeding 0.5 ms⁻¹ are observed. Recent exploratory measurements conducted as a part of the South Florida Ocean Measurement Center (SFOMC) show that the time scale of these oscillations is about 10 hrs. This period does not coincide either with the inertial period (27 Hrs) or with the semidiurnal M₂ (12.42 hrs) or S₂ (12 hrs) tidal constituents. In addition, these internal oscillations appear to be modulated seasonally. A possible explanation …

Past Stony Coral Growth (Extension) Rates On Reefs Of Broward County, Florida: Possible Relationships With Everglades Drainage, Richard E. Dodge, Kevin P. Helmle

Marine & Environmental Sciences Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

Restoration Of Coral Reef Habitats Within The National Park System, Jim Tilmant, Linda Canzanelli, Rick Clark, Richard Curry, Bruce Graham, Monika Mayr, Alison L. Moulding, Robert Mulcahy, Shay Viehman, Tamara Whittington

Marine & Environmental Sciences Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

Spring 2003, Nsu Oceanographic Center

Currents

No abstract provided.

Biology And Ecologyof Epigean Crayfish That Inhabit Everglades Environments Procambarus Alleni (Faxon) And Procambarus Fallax (Hagen), Peggy G. Vanarman

HCNSO Student Theses and Dissertations

Two species of epigean crayfish, Procambarus alleni (the Everglades crayfish) and Procambarus fallax (slough crayfish), may be keystone species that inhabit wetlands in south Florida and the Everglades. Recent field studies showed that although these two species occur in sympatric and syntopic distribution, Everglades crayfish prefer shallow water and short hydroperiod conditions, whereas slough crayfish prefer areas that are more permanently flooded (Hendrix 2000). Slough crayfish have invaded some areas within the range occupied by Everglades crayfish, and may be the more successful competitor. Because of their critical role throughout the trophic structure of Everglades wetlands, shifts in relative abundance …

Habitat Utilization By Bottlenose Dolphins (Tursiops Truncatus) In Biscayne Bay, Florida, Christine A. Hudak

HCNSO Student Theses and Dissertations

Bottlenose dolphins (Tursiops truncatus) exhibit variable distribution patterns, depending upon their geographic location. Habitat utilization patterns in Biscayne Bay, Florida, were examined using the Biscayne Bay Bottlenose Dolphin Photo-ID database obtained from the National Oceanic and Atmospheric Administration (NOAA) Southeast Fisheries Science Center (SEFSC) Miami Laboratory. Habitat coverages in Biscayne Bay were obtained from the Atlas of Marine Resources Version 1.3B CD and the Biscayne Bay National Park CD. Dolphin sightings were overlaid on the habitat coverages using GIS Arcview software.

The effects of habitat, season, behavior, zone (sectioned area of Biscayne Bay), and depth on patterns …

A Monte Carlo Demographic Analysis Of The Silky Shark (Carcharhinus Falciformis): Implications Of Gear Selectivity, Lawrence R. Beerkircher, Mahmood S. Shivji, Enric Cortes

Marine & Environmental Sciences Faculty Articles

No abstract provided.

Histidine-Decarboxylase Knockout Mice Show Deficient Nonreinforced Episodic Object Memory, Improved Negatively Reinforced Water-Maze Performance, And Increased Neo- And Ventro-Striatal Dopamine Turnover, Ekrem Dere, Maria A. De Souza-Silva, Bianca Topic, Richard E. Spieler, Helmut L. Haas, Joseph P. Huston

Marine & Environmental Sciences Faculty Articles

The brain's histaminergic system has been implicated in hippocampal synaptic plasticity, learning, and memory, as well as brain reward and reinforcement. Our past pharmacological and lesion studies indicated that the brain's histamine system exerts inhibitory effects on the brain's reinforcement respective reward system reciprocal to mesolimbic dopamine systems, thereby modulating learning and memory performance. Given the close functional relationship between brain reinforcement and memory processes, the total disruption of brain histamine synthesis via genetic disruption of its synthesizing enzyme, histidine decarboxylase (HDC), in the mouse might have differential effects on learning dependent on the task-inherent reinforcement contingencies. Here, we investigated …

Assessment Of The Coral Reefs Of The Turks And Caicos Islands (Part 2: Fish Communities), Kaho Hoshino, Marilyn Brandt, Carrie Manfrino, Bernhard Riegl, Sascha C. C. Steiner

Marine & Environmental Sciences Faculty Articles

Ecologically and commercially significant coral reef fishes were surveyed at 28 sites in the Turks and Caicos Islands during August 1999. Our results constitute the first quantitative census of these fishes and can serve as baseline information for subsequent studies. Their density and size generally were highest off West Caicos and lowest in Mouchoir Bank. Herbivore density overall showed no correlation with macroalgal index (a proxy for biomass) or live stony coral cover, but surgeonfish density was positively correlated with macroalgal index. Species richness of these select fishes was positively correlated with the species richness of stony corals that were …

Assessment Of The Coral Reefs Of The Turks And Caicos Islands (Part 1: Stony Corals And Algae), Bernhard Riegl, Carrie Manfrino, Casey Hermoyian, Marilyn Brandt, Kaho Hoshino

Marine & Environmental Sciences Faculty Articles

Major constituents of the benthic reef community (stony corals, algae) were assessed in 28 reefs on the Caicos, Turks and Mouchoir Banks. Living stony coral cover ranged from 8-28%, averaging 18% overall. Montastraea annularis and M. faveolata of “intermediate” sizes (cm) dominated all examined reefs. Acropora palmata and A. cervicornis were scarce. The most frequently recruiting scleractinians were Porites astreoides and Agaricia agaricites; Montastraea recruits were uncommon. Old partial-colony mortality (overall mean = 23%) was greater than recent partial-colony mortality (mean = 3%). Crustose coralline algae and turf algae were generally more abundant than macroalgae. Mouchoir Bank, with the …

The State Of Coral Reef Ecosystems Of The United States And Pacific Freely Associated States: 2002, Donna D. Turgeon, Rebecca G. Asch, Billy Causey, Richard E. Dodge, Walter Jaap, Kenneth Banks, Joanne Delaney, Brian Keller, Richard E. Spieler, Cruz A. Matos, Jorge R. Garcia, Ernesto Diaz, Don Catanzaro, Caroline Rogers, Zandy Hillis-Starr, Richard Nemeth, Herman Taylor, Marcia Taylor, George P. Schmahl, Margaret W. Miller, David A. Gulko, James E. Maragos, Alan Friedlander, Cynthia L. Hunter, Russell E. Brainard, Peter Craig, Robert H. Richmond, Gerry W. Davis, John Starmer, Michael Trianni, Peter Houk, Charles E. Birkeland, Ahser Edward, Yimnang Golbuu, Jay Gutierrez, Noah Idechong, James E. Maragos, Gustav Paulay, Andrew Tafileichig, Nancy Vander Velde

Marine & Environmental Sciences Faculty Reports

Called for by the U.S. Coral Reef Task Force’s (USCRTF) National Action Plan to Conserve Coral Reefs, this is the first biennial report on the condition of coral reefs. It is the scientific baseline for subsequent reports on the health of U.S. coral reef ecosystems that are to be used by NOAA and others to evaluate the efficacy of coral reef conservation and management practices. The National Oceanic and Atmospheric Administration’s National Ocean Service led the development of this report. It was authored by 38 experts and supported by 79 contributors from government agencies and non-governmental organizations across the nation …

Habitat Standardization Of Cpue Indices: Research Needs, C. Phillip Goodyear, David Die, David W. Kerstetter, Donald Olson, Eric Prince, Gerald P. Scott

Marine & Environmental Sciences Faculty Reports

Habitat standardization for billfish CPUE offers a potentially useful alternative to the statistical procedures used in the past. However, most of the assumptions of the current habitatstandardization methodology remain untested and some are not consistent with current knowledge about the behavior of billfish. This paper outlines research required to ensure the methods for habitat standardization produce robust estimates of CPUE.

Habitat Preferences Of Istiophorid Billfishes In The Western North Atlantic: Applicability Of Archival Tag Data To Habitat-Based Stock Assessment Methodologies, John E. Graves, David W. Kerstetter, Brian E. Luckhurst, Eric D. Prince

Marine & Environmental Sciences Faculty Reports

The Japanese pelagic longline fishery, which has a broad temporal and spatial coverage in the Atlantic Ocean, provides an important time series used in assessments of istiophorid billfishes. Past assessments of Atlantic blue marlin and white marlin by the ICCAT SCRS indicate a pronounced decrease in stock abundance of both species over the past fifty years. The current biomass of the white marlin is estimated to be 15% of that necessary for maximum sustainable yield (BMSY), while blue marlin are estimated to be at 0.4 BMSY. Over the past fifty years Japanese pelagic longline fishing operations have moved from shallow …

Sea Turtle Conservation Program, Broward County, Fl 2003 Report, Curtis M. Burney, Stefanie Ouellette

Marine & Environmental Sciences Faculty Reports

No abstract provided.

Status Of Coral Reefs Of Little Cayman, Grand Cayman And Cayman Brac, British West Indies, In 1999 And 2000 (Part 1: Stony Corals And Algae), Carrie Manfrino, Bernhard Riegl, Jerome L. Hall, Robert Graifman

Marine & Environmental Sciences Faculty Articles

A benthic assessment of the isolated Cayman Islands was completed at 42 sites. Major changes in the reef community structure were documented by comparison with earlier studies. Acropora palmata and A. cervicornis, once abundant as shallow framework builders, were uncommon. Diseased stony corals were seen in >90% of the study sites, with the highest averages in Little Cayman, especially at Bloody Bay which is one of the most highly regulated marine parks in the Cayman Islands. The Montastraea annularis species complex accounted for two-thirds of the diseased corals which, along with other massive species, were affected largely by white-plague …

Marine Biological Monitoring In Broward County, Florida: Year 3 Annual Report, David S. Gilliam, Richard Dodge, Richard E. Spieler, Lance K. B. Jordan, Jamie A. Vernacchio

Marine & Environmental Sciences Faculty Reports

A study has been undertaken to monitor Broward County, Florida (southeast Florida) coral communities, reef fish assemblages and sedimentation rates in relation to possible effects from a proposed extensive beach renourishment (restoration) project. Coral communities and reef fish assemblages will be monitored at a total of 23 stations distributed offshore Broward County. This monitoring effort will characterize and quantify populations of scleractinian (stony) corals, octocorallian (gorgonian) corals, sponges, and reef fishes. In addition, sediment traps located at each station will be sampled and analyzed.

This document reports the data collected during the third year of this project. Coral communities and …

Growth And Survivorship Of Meandrina Meandrites And Montastrea Cavernosa Transplants To An Artificial Reef Environment, And The Effectiveness Of Plugging Core Holes In Transplant Donor Colonies, Elizabeth Glynn Fahy

HCNSO Student Theses and Dissertations

The growth and survivorship of two species of scleractinian coral transplants, Meandrina meandrites and Montastrea cavernosa, were investigated. Identically sized replicate transplants were obtained from the second reef, off Dania Beach, using a hydraulic drill fitted with a 4” core barrel. The transplants were fixed to Reef Ball™ substrates using an adhesive marine epoxy. Drill holes in the donor corals (core holes) were filled with concrete plugs to prevent the detrimental effects of bioeroders. Control corals, of comparable size to both the donor colonies and the transplant corals, were selected for comparison. The transplant corals, donor corals, and controls …

Winter 2003, Nsu Oceanographic Center

Currents

No abstract provided.

Feline Immunodeficiency Virus Integration In B-Cell Lymphoma Identifies A Candidate Tumor Suppressor Gene On Human Chromosome 15q151, Julia Beatty, Anne Terry, Julie Macdonald, Elizabeth Gault, Stanley Cevario, Stephen J. O'Brien, Ewan Cameron, James C. Neil

Biology Faculty Articles

Infection with immunosuppressive lentiviruses is associated with increased cancer risk,but most studies have implicated indirect mechanisms as the tumor cells generally lack integrated viral sequences.An exception wasfound in a B-cell lymphoma (Q254) where the tumor cells contained a single integrated feline immunodeficiency virus genome. Additional analysis now indicates that feline immunodeficiency virus integration in lymphoma Q254 resulted in promoter insertion and truncation of a conserved gene on feline chromosome B3, whereas the unaffected allele of the gene appeared to be transcriptionally down-regulated. The orthologous human gene (FLJ12973), is expressed ubiquitously and encodes a WD-repeat protein with structural similarity …

Sequencing The Genome Of The Domestic Cat Felis Catus, Stephen J. O'Brien, Eric S. Lander, M. E. Haskins, Urs Giger, Niels C. Pederson, David E. Wildt, William J. Murphy, Naoya Yuhki, Marilyn Menotti-Raymond

Biology Faculty Articles

No abstract provided.

Fall 2002, Nsu Oceanographic Center

Currents

No abstract provided.