Life Sciences Commons^™

Sequences, Annotation And Single Nucleotide Polymorphism Of The Major Histocompatibility Complex In The Domestic Cat, Naoya Yuhki, James C. Mullikin, Thomas W. Beck, Robert M. Stephens, Stephen J. O'Brien

Biology Faculty Articles

Two sequences of major histocompatibility complex (MHC) regions in the domestic cat, 2.976 and 0.362 Mbps, which were separated by an ancient chromosome break (55–80 MYA) and followed by a chromosomal inversion were annotated in detail. Gene annotation of this MHC was completed and identified 183 possible coding regions, 147 human homologues, possible functional genes and 36 pseudo/unidentified genes) by GENSCAN and BLASTN, BLASTP RepeatMasker programs. The first region spans 2.976 Mbp sequence, which encodes six classical class II antigens (three DRA and three DRB antigens) lacking the functional DP, DQ regions, nine antigen processing molecules (DOA/DOB, DMA/DMB, TAPASIN, and …

Selfishness As Second-Order Altruism, Omar Tonsi Eldakar, David Sloan Wilson

Biology Faculty Articles

Selfishness is seldom considered a group-beneficial strategy. In the typical evolutionary formulation, altruism benefits the group, selfishness undermines altruism, and the purpose of the model is to identify mechanisms, such as kinship or reciprocity, that enable altruism to evolve. Recent models have explored punishment as an important mechanism favoring the evolution of altruism, but punishment can be costly to the punisher, making it a form of second-order altruism. This model identifies a strategy called “selfish punisher” that involves behaving selfishly in first-order interactions and altruistically in second-order interactions by punishing other selfish individuals. Selfish punishers cause selfishness to be a …

The State Of Coral Reef Ecosystems Of Southeast Florida, Chantal Collier, Rob Ruzicka, Kenneth Banks, Luiz Barbieri, Jeff Beal, David Bingham, James A. Bohnsack, Sandra Brooke, Nancy Craig, Richard E. Dodge (Editor), Louis E. Fisher, Nick Gadbois, David S. Gilliam, Lisa Gregg, Todd Kellison, Vladimir N. Kosmynin, Brian Lapointe, Erin Mcdevitt, Janet Phipps, Nikki Poulos, John Proni, Patrick Quinn, Bernhard Riegl, Richard E. Spieler, Joanna Walczak, Brian K. Walker, Denise Warrick

Marine & Environmental Sciences Faculty Reports

No abstract provided.

Spring 2008, Nsu Oceanographic Center

Currents

No abstract provided.

Identifying Selected Regions From Heterozygosity And Divergence Using A Light-Coverage Genomic Dataset From Two Human Populations, T. K. Oleksyk, Kai Zhao, Francisco M. De La Vega, Dennis A. Gilbert, Stephen J. O'Brien, Michael W. Smith

Biology Faculty Articles

When a selective sweep occurs in the chromosomal region around a target gene in two populations that have recently separated, it produces three dramatic genomic consequences: 1) decreased multi-locus heterozygosity in the region; 2) elevated or diminished genetic divergence (F_ST) of multiple polymorphic variants adjacent to the selected locus between the divergent populations, due to the alternative fixation of alleles; and 3) a consequent regional increase in the variance of F_ST (S²F_ST) for the same clustered variants, due to the increased alternative fixation of alleles in the loci surrounding the selection target. In …

Functions, Structure, And Read-Through Alternative Splicing Of Feline Apobec3 Genes, Carsten Munk, Thomas W. Beck, Jorg Zielonka, Agnes Hotz-Wagenblatt, Sarah Chareza, Marion Battenberg, Jens Thielebein, Klaus Cichutek, Ignacio G. Bravo, Stephen J. O'Brien, Martin Lochelt, Naoya Yuhki

Biology Faculty Articles

Background:

Over the past years a variety of host restriction genes have been identified in human and mammals that modulate retrovirus infectivity, replication, assembly, and/or cross-species transmission. Among these host-encoded restriction factors, the APOBEC3 (A3; apolipoprotein B mRNA-editing catalytic polypeptide 3) proteins are potent inhibitors of retroviruses and retrotransposons. While primates encode seven of these genes (A3A to A3H), rodents carry only a single A3 gene.

Results:

Here we identified and characterized several A3 genes in the genome of domestic cat (Felis catus) by analyzing the genomic A3 locus. The cat genome presents one A3H gene and three …

Mercury Transport And Bioaccumulation In The Alvarado Lagoon System, Veracruz State, Mexico, Edward O. Keith, Jane L. Guentzel

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

The Alvarado Lagoon System (ALS) consists of shallow rivers and lagoons connected to the Gulf of Mexico (GOMEX) by a narrow channel. We collected samples of water and seafood in the wet (September 2005) and dry (March 2003 and 2005) seasons, and human hair and sediment in 2005. Total Hg in sediments ranged from 27.5 to 90.5 μg Hg/g dry weight, while fish and shellfish Hg levels ranged from 0.01 to 0.35 μg Hg/g wet weight. Total Hg in human hair ranged from 0.10 to 3.36 μg Hg/g (n = 47) and 58 % of the hair samples were above …

Who's Eating Whom? Identification And Quantification Of Deep-Pelagic Prey Fishes In The North Atlantic Ocean, A. Heger, Tracey Sutton

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

Understanding the structure and functioning of marine ecosystems requires accurate knowledge of trophic interactions. Trophic ecology studies generally underestimate prey diversity due to the difficulties imposed by digestion. Further, this degradation leads to uncertainty in the quantification of prey biomass (i.e., energy flow between various ecosystem components). Trophic interactions in the deep sea are poorly known relative to coastal ecosystems due to an incomplete inventory of meso-and bathypelagic species composition. The CoML field project MAR-ECO has increased our knowledge of the faunal structure of the mid-North Atlantic. Deep-pelagic fish specimens from the 2004 MARECO expedition provided a basis for an …

Bathypelagic Fish Diversity In The Sargasso Sea, Northwestern Atlantic Ocean, Tracey Sutton, Peter Wiebe, Ann Bucklin, Laurence P. Madin

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

Of the various marine habitats, one of the (if not the) most daunting to quantify is the under-sampled bathypelagic zone (> 1000 m depth), which at 60% of the ocean’s volume is the largest habitat on Earth. One project addressing this challenge is the Census of

Marine Zooplankton (CMarZ), whose goal is the assessment of biodiversity of animal plankton throughout the world’s oceans. The 2006 CMarZ cruise in the Western North Atlantic provided an unprecedented opportunity to sample bathypelagic micronekton using a large midwater trawl (10-m2 MOCNESS) outfitted with fine (0.335-mm) mesh netting. This netting allowed non-destructive sampling of the …

The Importance Of Stealth: Recent Findings With The Eye-In-The-Sea Deep-Sea Observatory, Edith A. Widder, E. H. Raymond, Tracey Sutton

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

The Eye-in-the-Sea (EITS) observatory was designed to be acoustically quiet and to use far-red illumination to observe deep-sea animals unobtrusively. The EITS has clearly demonstrated the critical importance of stealth in research ocean observatories. Its use has revealed both animals and behaviors never seen before. Additionally recordings of animal activity under different lighting conditions and in the presence or absence of different sound-producing vehicles (ROVs and submersibles) have revealed to what extent tools for exploration bias observations. Recent recordings made during a 2007 NOAA Ocean Exploration mission to deep waters around the Bahamas provide excellent additional examples of the importance …

The Adaptive Evolution Of The Mammalian Mitochondrial Genome, Rute R. Da Fonseca, Warren E. Johnson, Stephen J. O'Brien, Maria J. Ramos, Agostinho Antunes

Biology Faculty Articles

Background

The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures.

Results

Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation to …

Construction, Alignment And Analysis Of Twelve Framework Physical Maps That Represent The Ten Genome Types Of The Genus Oryza, Hyeran Kim, Bonnie Hurwitz, Yeisoo Yu, Kristi Collura, Navdeep Gill, Phillip Sanmiguel, James C. Mullikin, Christopher Maher, William Nelson, Marina Wissotski, Michele Braidotti, David Kudrna, José Luis Goicoechea, Lincoln Stein, Doreen Ware, Scott A. Jackson, Carol Soderlund, Rod A. Wing

Biology Faculty Articles

We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.

A Seascape Approach To Predicting Reef Fish Distribution, Brian K. Walker

Oceanography Faculty Theses and Dissertations

Linking small-scale measurements of species distributions to broad-scale seascapes is necessary to understanding and predicting organismal distributions and their dynamics. This applies to reef fish populations as well. Reef fish studies are often limited to small spatial scales because of logistical and economic constraints; however, viewing the data at larger spatial scales might elucidate unforeseen relationships and patterns and facilitate regional management and conservation efforts. To address this growing need, an empirical model was created to predict reef fish abundance and species richness for the entire seascape using the relationship between the fish, benthic habitats, and GIS-derived topographic complexity metrics …

Genomic Organization, Sequence Divergence, And Recombination Of Feline Immunodeficiency Virus From Lions In The Wild, Jill Pecon-Slattery, Carrie L. Mccracken, Jennifer L. Troyer, Sue Vandewoude, Melody E. Roelke, Kerry Sondgeroth, Christiaan Winterbach, Stephen J. O'Brien

Biology Faculty Articles

Background

Feline immunodeficiency virus (FIV) naturally infects multiple species of cat and is related to human immunodeficiency virus in humans. FIV infection causes AIDS-like disease and mortality in the domestic cat (Felis catus) and serves as a natural model for HIV infection in humans. In African lions (Panthera leo) and other exotic felid species, disease etiology introduced by FIV infection are less clear, but recent studies indicate that FIV causes moderate to severe CD4 depletion.

Results

In this study, comparative genomic methods are used to evaluate the full proviral genome of two geographically distinct FIV subtypes …

Genetic Characterization Of Feline Leukemia Virus From Florida Panthers, Meredith Brown, Mark W. Cunningham, Alfred L. Roca, Jennifer L. Troyer, Warren E. Johnson, Stephen J. O'Brien

Biology Faculty Articles

From 2002 through 2005, an outbreak of feline leukemia virus (FeLV) occurred in Florida panthers (Puma concolor coryi). Clinical signs included lymphadenopathy, anemia, septicemia, and weight loss; 5 panthers died. Not associated with FeLV outcome were the genetic heritage of the panthers (pure Florida vs. Texas/Florida crosses) and co-infection with feline immunodeficiency virus. Genetic analysis of panther FeLV, designated FeLV-Pco, determined that the outbreak likely came from 1 cross-species transmission from a domestic cat. The FeLV-Pco virus was closely related to the domestic cat exogenous FeLV-A subgroup in lacking recombinant segments derived from endogenous FeLV. FeLV-Pco sequences were …

Real-Time Coral Stress Observations Before, During, And After Beach Nourishment Dredging Offshore Se Florida, L. Fisher, Kenneth Banks, David S. Gilliam, Richard E. Dodge, D. Stout, Bernardo Vargas-Ángel, Brian K. Walker

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

Beach nourishment in Southeast Florida involves dredging sand source borrow areas located between offshore reefs. From May 2005 to February 2006 Broward County, FL. nourished 10.9 km of beach with 1.5 ×106 m3 of sand. As part of a program to monitor potential reef community impacts, a visual stress index was developed from laboratory experiments and histological analyses for three stony coral species (Montastrea cavernosa, Solenastrea bournoni, and Siderastrea siderea). Scoring involved healthy = 0; moderately stressed = 1 (polyp swelling, increased mucus); markedly stressed = 2 (coloration changes, increased mucus secretion, tissue thinning); and severely stressed = 3 (severe …

Patterns In Southeast Florida Coral Reef Community Composition, M. P. Sathe, David S. Gilliam, Richard E. Dodge, L. E. Fisher

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

The Southeast (SE) Florida coral reef system is the northern extension of the Florida reef tract. This high latitude system lies offshore a heavily populated and urbanized coast and therefore is affected by numerous environmental and anthropogenic stressors. Using annual monitoring data collected in 2004, the southeast lorida reef community was analyzed to investigate patterns in community composition in various habitat types. Data was collected by SCUBA divers who conducted a 30m2 belt transect survey at 24 sample sites offshore Broward County (SE), Florida. Sites ranged in depth range from six to 18 meters. The 24 sites occurred on five …

Long-Term Monitoring Of A High-Latitude Coral Reef System Off Southeast Florida, Usa: A Partnership Between Academia And Resource Management, David S. Gilliam, Kenneth Banks, Michael Callahan, Chantal Collier, Richard E. Dodge, Louis E. Fisher, Jennifer Wheaton

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

Significant coral reef community development exists along the eastern shelf of the United States from the Dry Tortugas through the Florida Keys (Monroe County) and Southeast (SE) Florida (Miami-Dade, Broward, Palm Beach, and Martin Counties). State and county resource managers have partnered with academia to monitor the health of the SE Florida reef system. Since 2000, more than 20 sites have been monitored annually offshore Broward County. Quantitative data includes stony coral species cover, colony size, density, and condition (bleaching, disease, etc.) and gorgonian and sponge density. The SE Florida Coral Reef Evaluation and Monitoring Project (SECREMP) was established in …

Winter 2008, Nsu Oceanographic Center

Currents

No abstract provided.

Additional Records Of Deep-Sea Fishes From Off Greater New England, Karsten E. Hartel, Christopher P. Kenaley, John K. Galbraith, Tracey Sutton

Marine & Environmental Sciences Faculty Articles

Recent review of deep-sea fishes captured deeper than 200m off greater New England, from the Scotian Shelf at 44°N to the southern New England Shelf at about 38°N, documented 591 species. Subsequent trawling activity and reviews of deep-sea taxa occurring in the area have revealed that an additional 40 species in habit the deep sea off New England. Thirty-two of these new records were captured in the course of 44 bottom trawls and 94 mid-water trawls over or in the proximity of Bear Seamount (39°55'N, 67°30'W). Five of the 40 species have been described as new to science, at least …

Diverse Bacterial Pks Sequences Derived From Okadaic Acid-Producing Dinoflagellates, Roberto Perez, Li Liu, Jose V. Lopez, Tianying An, Kathleen S. Rein

Marine & Environmental Sciences Faculty Articles

Okadaic acid (OA) and the related dinophysistoxins are isolated from dinoflagellates of the genus Prorocentrum and Dinophysis. Bacteria of the Roseobacter group have been associated with okadaic acid producing dinoflagellates and have been previously implicated in OA production. Analysis of 16S rRNA libraries reveals that Roseobacter are the most abundant bacteria associated with OA producing dinoflagellates of the genus Prorocentrum and are not found in association with non-toxic dinoflagellates. While some polyketide synthase (PKS) genes form a highly supported Prorocentrum clade, most appear to be bacterial, but unrelated to Roseobacter or Alpha-Proteobacterial PKSs or those derived from other Alveolates …

The State Of Coral Reef Ecosystems Of Southeast Florida, Chantal Collier, Rob Ruzicka, Ken Banks, Luiz Barbieri, Jeff Beal, David Bingham, James Bohnsack, Sandra Brooke, Nancy Craig, Richard E. Dodge, Lou Fisher, Nick Gadbois, David S. Gilliam, Lisa Gregg, Todd Kellison, Vladimir Kosmynin, Brian Lapointe, Erin Mcdevitt, Janet Phipps, Nikki Poulos, John Proni, Patrick Quinn, Bernhard Riegl, Richard E. Spieler, Joanna Walczak, Brian K. Walker, Denise Warrick

Marine & Environmental Sciences Faculty Reports

The northern extension of the Florida reef tract and a complex of limestone ridges run parallel to the subtropical Atlantic coastline of southeast Florida. Spanning 170 km from the northern border of Biscayne National Park (BNP) in Miami-Dade County to the St. Lucie Inlet in Martin County, the reefs and hardbottom areas in this region support a rich and diverse biological community (Figure 5.1). Nearshore reef habitats in southeast Florida include hardbottom areas, patch reefs and worm reefs (Phragmatopoma spp.) exhibiting abundant octocoral, macroalgae, stony coral and sponge assemblages. Offshore, coral reef associated biotic assemblages occur on linear Holocene Acropora …

The Colonial Zoanthid Palythoa Caribaeorum: Population Dynamics On Southeast Florida Reefs, Joanna C. Walczak

HCNSO Student Theses and Dissertations

The colonial zoanthid Palythoa caribaeorum (Cnidaria, Zoanthidea) (Duchassaing and Michelotti 1861) is a major benthic component of most Caribbean reefs and is an extremely aggressive spatial competitor (Suchanek and Green 1981). This study looks at annual visits to 16 permanent monitoring sites over 3 reef designations (Inshore Ridge Complex, Middle Reef, and Outer Reef) in Broward County, Florida from 2002-2006. The data obtained in this study fills an informational void regarding the role of zoanthids in the southeast Florida reef benthic community. The study was conducted in two parts. Part One used digital imagery analysis to quantify the spatial cover …

Behavior Of An Escolar Lepidocybium Flavobrunneum In The Windward Passage As Determined By Popup Satellite Archival Tagging, David Kerstetter, P. H. Rice, Derke Snodgrass, Eric Prince

Marine & Environmental Sciences Faculty Articles

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.

Histopathological Assessment And Comparison Sedimentation And Phosphate Stress On The Staghorn Coral, Acropora Cervicornis, Erin Christine Hodel

HCNSO Student Theses and Dissertations

Traditional coral reef monitoring efforts lack assessment of coral health at tissue and cellular levels. This thesis investigated tissue, cellular, and gross morphological responses of the Caribbean staghorn coral, Acropora cervicornis, to elevated sedimentation and phosphate using state-of-the-art histological techniques. Branch fragments of A. cervicornis were collected offshore Broward County, FL, acclimated for 12 weeks, subjected to a 4-week experimental period, and given a 1-week recovery period in laboratory aquaria. Treatments consisted of high doses (200 mg cm^-2 day^-1) of sedimentation (S), phosphate (4 μM) (P), and a combination of these two (S + P), in …

Fish And Coral Reef Communities Of The Parque Nacional Sistema Arrecifal Veracruzano (Veracruz Coral Reef System National Park) Veracruz, Mexico: Preliminary Results, Marcos Alberto Rangel Avalos, Lance K. B. Jordan, Brian K. Walker, David S. Gilliam, Elvira Carvajal Hinojosa, Richard E. Spieler

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

Effective resource management requires robust baseline datasets and efficient monitoring programs to identify and quantify temporal change. The Parque Nacional Sistema Arrecifal Veracruzano (Veracruz Coral Reef System National Park) encompasses a total of 52000ha including 23 coral reefs in two island groups separated by the mouth of the Jamapa River; one near the port of Veracruz, Mexico and one approximately 20km south near Punta Antón Lizardo. Both groups receive substantial fisheries pressure and other anthropogenic impacts. Using non-destructive, visual methods we surveyed fish and benthic assemblages at 18 sites, which included 10 individual coral reefs within the Park. For fishes, …

Initial Sequence And Comparative Analysis Of The Cat Genome, J. U. Pontius, James C. Mullikin, Douglas R. Smith, Agencourt Bioscience Corporation, Kerstin Lindblad-Toh, Sante Gnerre, Michele Clamp, Jean Chang, R. Stephens, Beena A. Neelam, Natalia Volfovsky, Alejandro A. Schaffer, R. Agarwala, Kristina Narfstrom, William J. Murphy, Urs Giger, Alfred L. Roca, Agostinho Antunes, Marilyn Menotti-Raymond, Naoya Yuhki, Jill Pecon-Slattery, Warren E. Johnson, Guillaume Bourque, Glenn Tesler, Nisc Comparative Sequencing Program, Stephen J. O'Brien

Biology Faculty Articles

The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and …

Documenting Lineages From My ‘Littlest Ancestor’ To My Deep Ancestral Roots, Emily F. Schmitt Lavin

Biology Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

Summer/Fall 2007, Nsu Oceanographic Center

Currents

No abstract provided.

The Statistics Of Natural Shapes In Modern Coral Reef Landscapes, Samuel J. Purkis, Kevin E. Kohler, Bernhard Riegl, Steven O. Rohmann

Marine & Environmental Sciences Faculty Articles

Spatial heterogeneity is a fundamental characteristic of modern and ancient depositional settings, and the scaling of many carbonate environments has been shown to follow power function distributions. The difficulty in obtaining information on the horizontal persistence of sedimentary lithotopes at the basin scale has, however, hampered evaluation of this fact over larger geographic areas. In recent years, large‐scale maps of reef facies derived from remotely sensed data have become widely available, allowing for an analysis of reef‐scale map products from 26 sites spread through four reef provinces, covering >7000 km² of shallow‐water habitat in the U.S. territorial Pacific. For …