Life Sciences Commons^™

Validation Of A Short Tandem Repeat Multiplex Typing System For Genetic Individualization Of Domestic Cat Samples, Nikia Coomber, Victor A. David, Stephen J. O'Brien, Marilyn Menotti-Raymond

Biology Faculty Articles

Aim To conduct developmental validation studies on a polymerase chain reaction (PCR) based short tandem repeat (STR) multiplex typing system, developed for the purpose of genetic individualization and parentage testing in domestic cat samples.

Methods To evaluate reproducibility of the typing system, the multiplex was amplified using DNA extracted from hair, blood, and buccal samples obtained from the same individual (n = 13). Additional studies were performed to evaluate the system’s species’ specificity, using 26 North American mammalian species and two prokaryotes Sacchromyces and Escherichia coli, sensitivity, and ability to identify DNA mixtures. Patterns of Mendelian inheritance and mutation …

First Observations On The Re-Established Southeast Florida Recreational Swordfish Tournament Fishery, Juan C. Levesquee, David W. Kerstetter

Marine & Environmental Sciences Faculty Articles

Recreational tournaments for swordfish (Xiphias gladius) existed in the Florida Straits between 1977 and 1983 before disappearing due to low catch rates and an overexploitation of the stock. The first recent swordfish tournament occurred in 2001 off southeast Florida with 13 participating vessels. In 2002, three swordfish tournaments were observed and anglers were interviewed to determine catch and gear characteristics of the re-established recreational fishery. A total of 156 vessels participated in these three tournaments, catching 112 swordfish and hooking an additional 48 animals. The combination of the recovery of the North Atlantic swordfish stock and the continuation …

Primate Tnf Promoters Reveal Markers Of Phylogeny And Evolution Of Innate Immunity, Andres Baena, Alan R. Mootnick, James V. Falvo, Alla V. Tsytsykova, Filipa Ligeiro, Ousmane M. Diop, Claudia Brieva, Pascal Gagneux, Stephen J. O'Brien, Oliver A. Ryder, Anne E. Goldfeld

Biology Faculty Articles

Background. Tumor necrosis factor (TNF) is a critical cytokine in the immune response whose transcriptional activation is controlled by a proximal promoter region that is highly conserved in mammals and, in particular, primates. Specific single nucleotide polymorphisms (SNPs) upstream of the proximal human TNF promoter have been identified, which are markers of human ancestry.

Methodology/Principal findings. Using a comparative genomics approach we show that certain fixed genetic differences in the TNF promoter serve as markers of primate speciation. We also demonstrate that distinct alleles of most human TNF promoter SNPs are identical to fixed nucleotides in primate TNF promoters. Furthermore, …

Regulatory Polymorphisms In The Cyclophilin A Gene, Ppia, Accelerate Progression To Aids, Ping An, Li Hua Wang, Holli Hutcheson-Dilks, George Nelson, Sharyne Donfield, James J. Goedert, Charles Rinaldo, Susan Buchbinder, Gregory D. Kirk, Stephen J. O'Brien, Cheryl Winkler

Biology Faculty Articles

Human cyclophilin A, or CypA, encoded by the gene peptidyl prolyl isomerase A (PPIA), is incorporated into the HIV type 1 (HIV-1) virion and promotes HIV-1 infectivity by facilitating virus uncoating. We examined the effect of single nucleotide polymorphisms (SNPs) and haplotypes within the PPIA gene on HIV-1 infection and disease progression in five HIV-1 longitudinal history cohorts. Kaplan-Meier survival statistics and Cox proportional hazards model were used to assess time to AIDS outcomes. Among eight SNPs tested, two promoter SNPs (SNP3 and SNP4) in perfect linkage disequilibrium were associated with more rapid CD4⁺ T-cell loss (relative hazard = …

Prevalence And Diversity Of Avian Hematozoan Parasites In Asia: A Regional Study, Farah Ishtiaq, Eben Gering, Jon H. Rappole, Asad R. Rahmani, Yadvendradev V. Jhala, Carla J. Dove, Christopher M. Milensky, Storrs L. Olson, Mike A. Peirce, Robert C. Fleischer

Biology Faculty Articles

Tissue samples from 699 birds from three regions of Asia (Myanmar, India, and South Korea) were screened for evidence of infection by avian parasites in the genera Plasmodium and Haemoproteus. Samples were collected from November 1994 to October 2004. We identified 241 infected birds (34.0%). Base-on-sequence data for the cytochrome b gene from 221 positive samples, 34 distinct lineages of Plasmodium, and 41 of Haemoproteus were detected. Parasite diversity was highest in Myanmar followed by India and South Korea. Parasite prevalence differed among regions but not among host families. There were four lineages of Plasmodium and one of …

Evaluation Of Methods To Enhance Reef Restoration, David S. Gilliam, Alison L. Moulding, Vladimir N. Kosmynin, Vanessa I. P. Brinkhuis, Richard E. Dodge

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

The coral reefs of southeast Florida are offshore a highly urbanized area with a population exceeding 5 million people and three major shipping ports with over 6000 ships calling on an annual basis. Reef injury events are common and have been caused by ship groundings and marine construction activities such as channel dredging and cable placement. Restoration activities generally only include the reattachment of dislodged stony corals, removal of rubble, and boulder stabilization. The Florida Department of Environmental Protection has recognized these limited activities and is collaborating with Nova Southeastern University’s Oceanographic Center to study ways to accelerate coral reef …

Analysis Of Factors Influencing Southeast Florida Coral Reef Community Composition, M. A. Phillips, David S. Gilliam, L. K. B. Jordan, Richard E. Dodge, Louis E. Fisher

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

The southeast Florida reef system lies offshore a heavily populated and urbanized coast. These high latitude reefs are not only affected by their geography but also by anthropogenic factors that accompany an urban area such as dredging activities, ship groundings, waste water outfalls, runoff and beach erosion. Sedimentation has been shown to influence stony coral community composition including dominance, abundance, cover, diversity, and colony size. Using annual monitoring data collected since 2000, the southeastern Florida reef community is being analyzed to examine if and how sedimentation and other factors such as depth, distance from shore and distance from port channels …

Regulation Of Cell Diameter, For3p Localization, And Cell Symmetry By Fission Yeast Rho-Gap Rga4p, Maitreyi Das, David J. Wiley, Saskia Medina, Helen A. Vincent, Michelle D. Larrea, Andrea Oriolo, Fulvia Verde

Chemistry and Physics Faculty Articles

Control of cellular dimensions and cell symmetry are critical for development and differentiation. Here we provide evidence that the putative Rho-GAP Rga4p of Schizosaccharomyces pombe controls cellular dimensions. rga4Δ cells are wider in diameter and shorter in length, whereas Rga4p overexpression leads to reduced diameter of the growing cell tip. Consistent with a negative role in cell growth control, Rga4p protein localizes to the cell sides in a “corset” pattern, and to the nongrowing cell tips. Additionally, rga4Δ cells show an altered growth pattern similar to that observed in mutants of the formin homology protein For3p. Consistent with …

Rapid Response And Restoration For Coral Reef Injuries In Southeast Florida: Guidelines And Recommendations, Chantal Collier, Richard E. Dodge, David S. Gilliam, Kelly Gracie, Lisa Gregg, Walter Jaap, Mike Mastry, Nikki Poulos

Marine & Environmental Sciences Faculty Reports

From the time an injury to coral reef resources is reported, a well-coordinated and implemented plan is critical to the success of response and restoration efforts. There are three major plan components, each of which is equally important: (1) the Initial Response period immediately following notification of the incident; (2) the Response period, during which the Responsible Party (RP) is identified, the Trustees and RP carry out their respective responsibilities, a Primary Restoration plan is developed, authorizations and contractors to conduct restoration activities are sought and obtained, and primary restoration activities are conducted; and (3) the Post-Response period, which is …

Southeast Florida Coral Reef Evaluation And Monitoring Project 2006 Year 4 Final Report, Jennifer Wheaton, Carl Beaver, Sandra Brooks, Michael Callahan, Shannon Wade, Jeff Beal, Chantal Collier, Laura Herren, Jamie Monty, David S. Gilliam, Vanessa I. P. Brinkhuis, Daniel P. Fahy, Shaun M. Gill, Lindsey Habakuk Klink, M. A. Philips, Nicole R. Stephens, Brian K. Walker, Joanna C. Walczak, Richard E. Dodge, Tim Mcintosh, Steven Blair, Kenneth Banks, Louis E. Fisher, David Stout, Joe Ligas, Janet Phipps

Marine & Environmental Sciences Faculty Reports

No abstract provided.

New Species And Host Associations Of Commensal Leucothoid Amphipods From Coral Reefs In Florida And Belize (Crustacea:Amphipoda), James Darwin Thomas, Kristine N. Klebba

Marine & Environmental Sciences Faculty Articles

Six new amphipod species in the genus Leucothoe from the tropical western Atlantic Ocean are described and illustrated. Extensive field collecting and specialized underwater collecting techniques have documented 43 new invertebrate host records for these new taxa. Four of these new species inhabit interior canals of sponges; Leucothoe barana n.sp., Leucothoe garifunae n.sp., Leucothoe saron n.sp., and Leucothoe ubouhu n.sp. A remarkable new species, Leucothoe flammosa n.sp., nestles in the gills of seven species of bivalve mollusks. A single species, Leucothoe wuriti n.sp., appears restricted to the branchial chamber of two species of solitary ascidians. Detailed illustrations and scanning electron …

Clouded Leopard Phylogeny Revisited: Support For Species Recognition And Population Division Between Borneo And Sumatra, Andreas Wilting, Valerie A. Buckley-Beason, Heike Feldhaar, Jurgen Gadau, Stephen J. O'Brien, K. Eduard Linsenmair

Biology Faculty Articles

Background

The clouded leopard (Neofelis nebulosa) is one of the least known cat species and depletion of their forested habitats puts it under heavy pressure. Recently reclassification of Bornean clouded leopards (N. nebulosa diardi) to species level (N.diardi) was suggested based on molecular and morphological evidence. Since the genetic results were based solely on three Bornean samples we re-evaluated this partition using additional samples of Bornean clouded leopards (N = 7) and we were also able to include specimens from Sumatra (N = 3), which were lacking in previous analysis.

Results

We found strong …

Meso- And Bathypelagic Fish Interactions With Seamounts And Mid-Ocean Ridges, Tracey Sutton, Filipe M. Porteiro, John K. Horne, Cairistiona I. H. Anderson

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

The World Ocean's midwaters contain the vast majority of Earth's vertebrates in the form of mesoand bathypelagic ('deep-pelagic,' in the combined sense) fishes. Understanding the ecology and variability of deep-pelagic ecosystems has increased substantially in the past few decades due to advances in sampling/observation technology. Researchers have discovered that the deep sea hosts a complex assemblage of organisms adapted to a “harsh” environment by terrestrial standards (i.e., dark, cold, high pressure). We have learned that despite the lack of physical barriers, the deep-sea realm is not a homogeneous ecosystem, but is spatially and temporally variable on multiple scales. While there …

Spring 2007, Nsu Oceanographic Center

Currents

No abstract provided.

Stalked Crinoid Locomotion, And Its Ecological And Evolutionary Implications, Tomasz K. Baumiller, Charles G. Messing

Marine & Environmental Sciences Faculty Articles

In the past two decades, much direct evidence has been gathered on active crawling by stalked crinoids, a group generally thought to be sessile. Detailed descriptions of crawling mechanics of isocrinids in aquaria revealed only exceedingly slow movements (~0.1 mm sec^-1). Crawling at such speeds severely restricted the range of roles that this behavior could play in stalked crinoid biology and, consequently, in its potential impact on their ecology and evolutionary history. Here, we provide evidence collected in situ by submersible near Grand Bahama Island at a depth of 420 m for a different mode of crawling in …

Development Of Gis Maps For Southeast Florida Coral Reefs, Bernhard Riegl, Brian K. Walker, Greg Foster, Kristy Foster

Marine & Environmental Sciences Faculty Reports

The present report outlines the results of an integrated mapping project undertaken to provide habitat maps of the shallow Palm Beach County seafloor between the 6m and 35m contours. This study is a continuation of a similar mapping study undertaken in Broward County, and results were produced such that a seamless and fully compatible mapping product is now available for both counties. The study area stretched from 26.4429o (E. Linton Blvd) in the south to 26.9590o (Jupiter Inlet) in the north. Compatibility with other, in particular NOAA, mapping products was also assured. Data types used in this mapping effort included …

The Molecular Basis Of High-Altitude Adaptation In Deer Mice, Jay F. Storz, Stephen J. Sabatino, Federico G. Hoffmann, Eben Gering, Hideaki Moriyama, Nuno Ferrand, Bruno Monteiro, Michael W. Nachman

Biology Faculty Articles

Elucidating genetic mechanisms of adaptation is a goal of central importance in evolutionary biology, yet few empirical studies have succeeded in documenting causal links between molecular variation and organismal fitness in natural populations. Here we report a population genetic analysis of a two-locus α-globin polymorphism that underlies physiological adaptation to high-altitude hypoxia in natural populations of deer mice, Peromyscus maniculatus. This system provides a rare opportunity to examine the molecular underpinnings of fitness-related variation in protein function that can be related to a well-defined selection pressure. We surveyed DNA sequence variation in the duplicated α-globin genes of P. maniculatus …

Preliminary Observations On The Reproductive Cycle And Uterine Fecundity Of The Yellow Stingray, Urobatis Jamaicensis (Elasmobranchii: Mylioba Tiformes: Urolophidae) In Southeast Florida, U.S.A., Daniel P. Fahy, Richard E. Spieler, William C. Hamlett

Marine & Environmental Sciences Faculty Articles

The yellow stingray, Urobatis jamaicensis is the most common elasmobranch observed among the coral reefs and associated habitats of Southeast Florida, U.S.A. In coastal waters off Broward County, Florida, gravid females were observed throughout the year. Urobatis jamaicensis is an aplacental viviparous species with evidence of a short gestation period (five to six months). Vitellogenesis occurs concurrently with gestation, with the females having both term fetuses and mature ova simultaneously. It is likely that the females have a bi-annual reproductive cycle where each female is capable of producing two broods annually. The ovulation period in the spring/summer reproductive cycle ranged …

Genetic Protection Against Hepatitis B Virus Conferred By Ccr5Δ32: Evidence That Ccr5 Contributes To Viral Persistence, Chloe L. Thio, Jacquie Astemborski, Arman A. Bashirova, Timothy L. Mosbruger, Spencer Greer, Mallory D. Witt, James J. Goedert, Margaret Hilgartner, Audrey Majesk, Stephen J. O'Brien, David L. Thomas, Mary Carrington

Biology Faculty Articles

Recovery from acute hepatitis B virus (HBV) infection requires a broad, vigorous T-cell response, which is enhanced in mice when chemokine receptor 5 (CCR5) is missing. To test the hypothesis that production of a nonfunctional CCR5 (CCR5Δ32 [a functionally null allele containing a 32-bp deletion]) increases the likelihood of recovery from hepatitis B in humans, we studied 526 persons from three cohorts in which one person with HBV persistence was matched to two persons who recovered from an HBV infection. Recovery or persistence was determined prior to availability of lamivudine. We determined genotypes forCCR5Δ32 …

Creating And Presenting A Poster At The Undergraduate Student Symposium, Beatrix Aukszi, Christopher A. Blanar, Weylin Sternglanz

Chemistry and Physics Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

Joint United States-Brazil Billfish Research In The Western South Atlantic, David W. Kerstetter, Fabio H.V. Hazin, J. C. Pacheco, John E. Graves

Marine & Environmental Sciences Faculty Reports

A joint research project between Brazilian and U.S. scientists was initiated in 2004 to investigate the interaction of istiophorid billfishes with pelagic longline fisheries in the western equatorial South Atlantic Ocean. This project incorporates two general themes (1) an investigation into several aspects of pelagic longline operations by comparing catch results between circle and “J” style hooks, time-of-capture with hook time recorders, and by direct monitoring of pelagic longline gear behavior, and (2) an additional evaluation of billfish trophic ecology using a combination of satellite tag technology and traditional analyses (e.g., gut contents and ageing). Data obtained from this research …

Post-Release Survival Of Sailfish (Istiophorus Platypterus) Captured On Commercial Pelagic Longline Gear In The Southern Gulf Of Mexico, David W. Kerstetter, John E. Graves

Marine & Environmental Sciences Faculty Reports

To estimate post-release survival of sailfish caught incidentally to regular commercial pelagic longline fishing operations in the southern Gulf of Mexico targeting mixed swordfish and tunas, ten pop-up satellite archival tags were deployed for ten days on incidentally captured animals. All ten tags transmitted following the full deployment period, transmitting 25-82% of the archived data. Repeated, short-duration movements at depth and horizontal displacement data from were consistent with survival of those nine of the ten animals for the ten-day deployment period. The results of this study indicate that sailfish can survive the trauma resulting from interaction with pelagic longline gear …

Preliminary Results Of Circle And J-Style Hook Comparisons In The Brazilian Pelagic Longline Fishery, David W. Kerstetter, J. C. Pacheco, Fabio H.V. Hazin, P. E. Travassos, John E. Graves

Marine & Environmental Sciences Faculty Reports

Preliminary studies in western North Atlantic pelagic longline fisheries indicate that a change in terminal gear from J-style hooks to circle hooks may reduce bycatch mortality. However, such studies have not examined the impact of this change in the equatorial fishery. Catch composition, catch rates, hooking location, and condition at haulback were monitored during 26 sets in the commercial longline fishery operating in the western equatorial South Atlantic where circle (size 18/0, non-offset) and J-style (size 9/0 and 10/0, 10° offset) hooks were deployed in an alternating fashion. Catch rates for yellowfin tuna, swordfish, and a composite “all fishes” category …

The Crinoid Fauna (Echinodermata: Crinoidea) Of Palau, Charles G. Messing

Marine & Environmental Sciences Faculty Articles

Taxonomic revisions and a recent survey using scuba place the number of shallow-water (< 50 m) crinoid species known from Palau at 22. Five are new records: Clarkcomanthus littoralis, Comanthus suavia, Alloeocomatella pectinifera, Oxycomanthus comanthipinna, and O. exilis. A submersible survey (to 310 m) recovered five additional new records, four of which are the first representatives of their families from Palauan waters:Eudiocrinus venustulus (Eudiocrinidae), Glyptometra sp. (Charitometridae), Cosmiometra belsuchel Messing, n. sp. (Thalassometridae), and Porphyrocrinus verrucosus(Phrynocrinidae), the first stalked crinoid recorded from Palau. Two of the three specimens of the latter have regenerating crowns, suggesting that this species may be subject to substantial predation or an …

Surface Associated Amoebae On The Ctenophore, Mnemiopsis Sp., Connie S. Versteeg

HCNSO Student Theses and Dissertations

Previous work by Moss et al. (2001) reported surface associated protists on the ctenophore Mnemiopsis sp. They frequently observed the ciliate Trichodina ctenophorii and a Flabellula-like amoeba attached to the comb plate surface. They noted that the ciliate and the amoeba were found on the subsagittal, subtentacular, and the auricular comb plates. The amoeba had a maximum width of about 15 μm and cells were crescent shaped. Ultrastructural evidence suggested that these protists were parasites although the exact nature of the association remained to be determined. This was the background for the present study.

The present investigation documented the …

Comparison Of Fish Assemblages Between Mitigation Boulder Reef And Neighboring Natural Hardbottom In Broward County, Florida, Usa, Jessica A. Freeman

HCNSO Student Theses and Dissertations

A beach renourishment project was initiated in May 2005 and completed in February 2006 to restore 11.1 km of shoreline in Broward County, Florida, USA. For mitigation of predicted nearshore hardbottom burial, a boulder reef totaling 3.6 ha was deployed in 2003. To examine the replacement value of the mitigation relative to fishes, this study compared fish assemblages on boulder reef to those on adjacent natural hardbottom. Twenty-five natural hardbottom sites and twenty-five boulder reef sites were surveyed six times between March 2005 and August 2007. Two non-destructive visual census methods, a transect count (30 m long x 2 m …

Winter 2007, Nsu Oceanographic Center

Currents

No abstract provided.

Polymorphisms Of Cul5 Are Associated With Cd4+ T Cell Loss In Hiv-1 Infected Individuals, Ping An, Priya Duggal, Li Hua Wang, Stephen J. O'Brien, Sharyne Donfield, James J. Goedert, John Phair, Susan Buchbinder, Gregory D. Kirk, Cheryl Winkler

Biology Faculty Articles

Human apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (Apobec3) antiretroviral factors cause hypermutation of proviral DNA leading to degradation or replication-incompetent HIV-1. However, HIV-1 viral infectivity factor (Vif) suppresses Apobec3 activity through the Cullin 5-Elongin B-Elongin C E3 ubiquitin ligase complex. We examined the effect of genetic polymorphisms in the CUL5 gene (encoding Cullin 5 protein) on AIDS disease progression in five HIV-1 longitudinal cohorts. A total of 12 single nucleotide polymorphisms (SNPs) spanning 93 kb in the CUL5 locus were genotyped and their haplotypes inferred. A phylogenetic network analysis revealed that CUL5 haplotypes were grouped into two clusters …

Two Yeast Plasmids That Confer Nourseothricin-Dihydrogen Sulfate And Hygromycin B Resistance In Neurospora Crassa And Cryphonectria Parasitica, Robert P. Smith, Myron L. Smith

Biology Faculty Articles

Two plasmids that were previously used with yeast, pRS41N and pRS41H, were found to confer clonNAT and hygromycin B resistance, respectively, in the filamentous fungi Neurospora crassa and Cryphonectria parasitica. These plasmids are suitable for routine cloning and for use in forcing heterokaryons and are available through the FGSC.

Validity, Identification, And Distribution Of The Roundscale Spearfish, Tetrapturus Georgii (Teleostei: Istiophoridae): Morphological And Molecular Evidence, Mahmood S. Shivji, Jennifer E. Magnussen, Lawrence R. Beerkircher, George Hinteregger, Dennis W. Lee, Joseph E. Serafy, Eric D. Prince

Marine & Environmental Sciences Faculty Articles

The roundscale spearfish, Tetrapturus georgii Lowe, 1840, is known only from four specimens from the Mediterranean and eastern North Atlantic. Additional specimens have not been identified since 1961, making the validity and distribution of this species unclear. Analysis of 16 billfish specimens from the western North Atlantic on the basis of scale morphology, anus position, and mitochondrial DNA confirms the validity of this species and extends its distribution. Mid-lateral scales are soft, notably rounded anteriorly, and bear 2–3 points distinct from those of the sympatric longbill spearfish (Tetrapturus pfluegeri Robins and de Sylva, 1963) and white marlin (Tetrapturus …