Life Sciences Commons^™

Flexible Gating Of Contextual Influences In Natural Vision, Odelia Schwartz

Mathematics Colloquium Series

An appealing hypothesis suggests that neurons represent inputs in a coordinate system that is matched to the statistical structure of images in the natural environment. I discuss theoretical work on unsupervised learning of statistical regularities in natural images. In the model, Bayesian inference amounts to a generalized form of divisive normalization, a canonical computation that has been implicated in many neural areas. In our framework, divisive normalization is flexible: it is recruited only when the image is inferred to contain dependencies, and muted otherwise. I particularly focus on recent work in which we have applied this approach to understanding spatial …

Fine-Grained Bacterial Compositional Analsysis Of The Port Everglades Inlet (Broward County, Fl) Microbiome Using High Throughput Dna Sequencing, Lauren M. O'Connell

HCNSO Student Theses and Dissertations

Port Everglades Inlet is one of the busiest ports in the country and is a point source of pollution to surrounding beaches and offshore corals from heavy boat traffic and urban runoff. Understanding fluctuations of bacterioplankton communities in major port inlets is important due to their impacts on surrounding marine environments. To understand annual microbial fluctuations, the 16s rRNA V4 hypervariable region was sequenced using Illumina high-throughput DNA sequencing technology. Surface samples were taken weekly for one year to generate baseline fluctuations in the microbial community. Total reads of 1.4 million were generated with a final count of 16,384 Operational …

Biodiversity And Ecological Dynamics Of Sciophilous Benthic Communities On Artificial Plates: Emphasis On Reef Sponges, Caidra Elizabeth Hassanzada

HCNSO Student Theses and Dissertations

Low light intensity habitats harbor unique sciophilous benthic communities and are a source of novel and unique sponge fauna. However, the community structure of these habitats is poorly studied to date. Thus, this study attempts to understand the composition and structure of sciophilous sponge populations in southeast Florida. Fifty limestone plates were placed on a shallow reef in Fort Lauderdale for two years (2010-2012). To identify the sponge community and their patterns over time, all plates were photographed at the end of each year. Then, samples were taken from each of the live sponge specimens observed on the plates and …

The First Whole Genome And Transcriptome Of The Cinereous Vulture Reveals Adaptation In The Gastric And Immune Defense Systems And Possible Convergent Evolution Between The Old And New World Vultures, Oksung Chung, Seondeok Jin, Yun Sung Cho, Jeongheui Lim, Hyunho Kim, Sungwoong Jho, Hak-Min Kim, Jehoon Jun, Hyejin Lee, Alvin Chon, Junsu Ko, Jeremy Edwards, Jessica A. Weber, Kyudong Han, Stephen J. O'Brien, Andrea Manica, Jong Bhak, Woon Kee Paek

Biology Faculty Articles

Background: The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.

Results: We sequenced the genome of a cinereous vulture, and mapped it to the bald …

Learning From Lionfish: Modeling Marine Invaded Systems, Matthew Johnston

Mathematics Colloquium Series

Simulating marine invaded systems requires broad consideration of physical oceanographic processes, such as ocean circulation patterns and temperature, and biological traits of the invader, such as their reproductive strategy and tolerances to their environment. Through this understanding of baseline biological and oceanographic function, models can be developed in order to forecast the incursion patterns of marine invasive species - helpful both to predict their spread as well as forewarn of impacts. To facilitate this understanding, computer simulation is useful in order to quickly and efficiently assimilate large biological and oceanographic datasets into digestible products. Data derived from such simulations are …

Gene Loss, Adaptive Evolution And The Co-Evolution Of Plumage Coloration Genes With Opsins In Birds, Rui Borges, Imran Khan, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O'Brien, Agostinho Antunes

Biology Faculty Articles

Background: The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems.

Results: We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal …

The Lli Chronicle Volume 6 Number 3, Nova Southeastern University

Lifelong Learning Institute Newsletters

No abstract provided.

A Scientific Basis For Regulating Deep-Sea Fishing By Depth, Jo Clarke, Rosanna Milligan, David M. Bailey, Francis Neat

Marine & Environmental Sciences Faculty Articles

The deep sea is the world’s largest ecosystem, with high levels of biodiversity and many species that exhibit life-history characteristics thatmake them vulnerable to high levels of exploitation. Many fisheries in the deep sea have a track record of being unsustainable. In the northeast Atlantic, there has been a decline in the abundance of commercial fish species since deep-sea fishing commenced in the 1970s. Current management is by effort restrictions and total allowable catch (TAC), but there remain problems with compliance and high levels of bycatch of vulnerable species such as sharks. The European Union is currently considering new legislation …

Southeast Florida Coral Reef Fishery-Independent Baseline Assessment, Kirk Kilfoyle, Brian K. Walker, Dana P. Fisco, Steven G. Smith, Richard E. Spieler

Marine & Environmental Sciences Faculty Reports

Reef fishes are important biologic, ecologic, and economic resources of the marine ecosystem which must be managed for sustainability. Until recently, there was no long-term monitoring program in place to assess the condition of reef fish resources of the northern Florida Reef Tract (FRT) (northern Miami-Dade, Broward, Palm Beach, and Martin counties). An assessment/monitoring plan for the northern portion of the Florida reef tract was designed through a joint cooperative effort by scientists at the University of Miami, Rosenstiel School of Marine and Atmospheric Science (RSMAS), National Oceanic and Atmospheric Administration (NOAA)-Southeast Fisheries Science Center (SEFSC) and Nova Southeastern University …

A Phylogenetic Revision Of Superfamily Himerometroidea (Echinodermata: Crinoidea), Kristian Taylor

HCNSO Student Theses and Dissertations

Superfamily Himerometroidea AH Clark, 1908 (Echinodermata: Crinoidea) (formerly Mariametroidea) is the second most speciose superfamily in order Comatulida. Although it includes some of the most common species on tropical western Pacific reefs, its phylogeny is poorly understood. Genus- to species-level taxa are currently distinguished by plastic morphological characters. We revised the superfamily from species- to family-levels using a combined morphological and molecular approach. A phylogeny using two nuclear and three mitochondrial markers recovered Colobometridae and Himerometridae as paraphyletic and Mariametridae and Zygometridae as polyphyletic. Within genus Himerometra (Himerometridae), sequence data and detailed morphological examinations of multiple specimens of H. magnipinna, …

Leucothoe Eltoni Sp. N., A New Species Of Commensal Leucothoid Amphipod From Coral Reefs In Raja Ampat, Indonesia (Crustacea, Amphipoda), James Darwin Thomas

Marine & Environmental Sciences Faculty Articles

A new species of leucothoid amphipod, Leucothoe eltoni sp. n., is described from coral reefs in Raja Ampat, Indonesia where it inhabits the branchial chambers of solitary tunicates. With an inflated first gnathopod superficially resembling the genus Paraleucothoe, this new species has a two-articulate maxilla 1 palp characteristic of the genus Leucothoe. While described from coral reef environments in tropical Indonesia and the Philippines, it is an established invasive species in the Hawaiian Islands. The most likely mode of introduction was a US Navy dry dock transported to Pearl Harbor in 1992 from Subic Bay, Philippines.

Genome-Wide Association And Trans-Ethnic Meta-Analysis For Advanced Diabetic Kidney Disease: Family Investigation Of Nephropathy And Diabetes (Find), Sudha K. Iyengar, John R. Sedor, Barry I. Freedman, W. H. Linda Kao, Matthias Kretzler, Benjamin J. Keller, Hanna E. Abboud, Sharon G. Adler, Lyle G. Best, Donald W. Bowden, Allison Burlock, Yii-Der Ida Chen, Shelley A. Cole, Mary E. Comeau, Jeffrey M. Curtis, Jasmin Divers, Christiane Drechsler, Ravi Duggirala, Robert C. Elston, Xiuqing Guo, Huateng Huang, Michael M. Hoffmann, Barbara V. Howard, Eli Ipp, Paul L. Kimmel, Michael J. Klag, William C. Knowler, Orly F. Kohn, Tennille S. Leak, David J. Leehey, Man Li, Alka Malhotra, Winfried Marz, Viji Nair, Robert G. Nelson, Susanne B. Nicholas, Stephen J. O'Brien, Madeleine V. Pahl, Rulan S. Parekh, Marcus G. Pezzolesi, Rebekah S. Rasooly, Charles N. Rotimi, Jerome I. Rotter, Jeffrey R. Schelling, Michael F. Seldin, Vallabh O. Shah, Adam M. Smiles, Michael W. Smith, Kent D. Taylor, Farook Thameem, Denyse P. Thornley-Brown, Barbara J. Truitt, Christoph Wanner, E. Jennifer Weil, Cheryl Winkler, Philip G. Zager, Robert P. Igo Jr., Robert L. Hanson, Carl D. Langefeld, Family Investigation Of Nephropathy And Diabetes (Find) Research Group

Biology Faculty Articles

Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, …

Time-Series Evaluation Of Suspect Rickettsiales-Like Bacteria Presence In Acropora Cervicornis Off Of Broward County From Years 2001–2012, Steven Di Lauro

HCNSO Student Theses and Dissertations

Rickettsiales-like organisms (RLOs) are thought to be related to bacteria in the order Rickettsiales. They have been reported to occur in the staghorn coral (Acropora cervicornis), and this study investigated trends of infection over time, and in relation to the health of infected corals. This study focuses on tissue samples taken mostly from visibly healthy A. cervicornis thickets in Broward County, Florida, and processed for histological examination. Samples were originally collected and analyzed to document reproduction during years 2001 through 2012, and tissue loss diseases (white-band disease [WBD] types I and II, and rapid tissue loss). …

A Comparative Evaluation Of Mitigation Wetlands In Broward County, Florida, Using Chironomid (Ditera) Pupal Exuviae: A Potential Technique For Assessing Mitigation Success, Ryan St. George

HCNSO Student Theses and Dissertations

Wetland resources in South Florida are regulated at three redundant jurisdictional levels: local or municipal regulations set forth by many independent jurisdictions, State regulations derived directly from Florida Statutes, and Federal regulations promulgated primarily under the Clean Water Act. All three levels of government can have jurisdiction over projects that affect regulated wetland resources, yet inconsistent policies and standards remain and continue to confound regulators despite decades of intensive coordination efforts and a rapidly growing scientific research base. The size of a wetland mitigation area is of primary consideration when evaluating its perceived ecological value, although wetland mitigation areas constructed …

Climate Change Resilience And Socioeconomic Impacts Of Mpas And Mpa Networks In The Caribbean - Case Study: Evaluation Of The Effectiveness Of The Management Of Mpas And Coastal Zones In The Dominican Republic, Andrea Isabella Vogel

HCNSO Student Capstones

Many Caribbean nations have established MPAs to preserve marine biodiversity and maintain their economically important marine resources. In some Caribbean nations, in particular the Dominican Republic, most MPAs have failed in these respects and have remained “paper parks” due to being modeled along traditional conservation lines without careful consideration of socioeconomic factors, good management practices or increasingly important climate change factors. Successful Caribbean MPAs and MPA networks effectively function as refuges, attractions, sources of socioeconomic development and ecosystem-based climate change resilience mechanisms. The latter is of utmost importance to Small Island Developing States (SIDS) and other larger island developing states …

Benthic Invertebrate Communities And Habitat Characterization Of The Pourtalès Terrace, Florida With Analysis Of The Deepwater Coral Habitat Areas Of Particular Concern And The East Hump Marine Protected Area, Jana K. Ash

HCNSO Student Theses and Dissertations

The Pourtalès Terrace is a gently curved, narrow triangular platform that parallels the Florida Keys for 213 km running from southern Key Largo to between Key West and the Marquesas Keys. The main Terrace surface begins in 200 m and dips gently to approximately 450 m, where the Pourtalès Escarpment slopes steeply to the deep floor of the southern Straits of Florida. The Terrace platform exhibits a wide variety of Neogene-age geological features, including high-relief ledges, mounds, sinkholes and deep-water biogenic build-ups called bioherms. Previous research revealed dense and diverse benthic assemblages dominated by stylasterid hydrocorals, octocorals and sponges.

Many …

A New Species Of The Ceratioid Anglerfish Genus Lasiognathus Regan (Lophiiformes: Oneirodidae) From The Northern Gulf Of Mexico, Theodore W. Pietsch, Tracey Sutton

Marine & Environmental Sciences Faculty Articles

A new species of the deep-sea ceratioid anglerfish genus Lasiognathus Regan (family Oneirodidae) is described on the basis of three female specimens collected in the northern Gulf of Mexico. Not especially similar to any of the five previously described members of the genus, the new species is unique in having a cylindrical, internally pigmented, anterior escal appendage and a pair of elongate distal escal appendages. The new species is diagnosed and described, and a revised key to the species of the genus is provided.

A Quantitative Assessment Of The January 2010 Cold Spell Effect On Mangrove Utilizing Coral Reef Fishes From Biscayne National Park, Florida, Jeffrey M. Ellis

HCNSO Student Theses and Dissertations

This study examined the effects of the January 2010 cold spell on mangrove utilizing coral reef fishes off the southeast coast of Florida, USA, in the vicinity of Biscayne National Park (BNP). An ongoing, fishery-independent mangrove visual survey documenting fish assemblages in BNP provided data from the years 1998 to 2014 for examination. Of particular interest were the presence, abundance, and size structure for five mangrove utilizing coral reef fishes: sergeant major (Abudefduf saxatilis), yellowfin mojarra (Gerres cinereus), schoolmaster snapper (Lutjanus apodus), gray snapper (Lutjanus griseus), and great barracuda (Sphyraena barracuda …

Assessment Of Nursery-Raised Acropora Cervicornis Transplants In The Upper Florida Keys, Matthew Ware

HCNSO Student Theses and Dissertations

Over the last 40 years, the Caribbean has lost half of its live coral cover, mostly in the form of Acropora cervicornis and A. palmata, due to disease, bleaching from rising water temperatures, and other stressors. To help restore these corals to reefs in Florida, the Coral Restoration Foundation (CRF) created nearshore nurseries and transplanted over 30,000 acroporid colonies across the Florida Keys. The objective of this thesis was to evaluate the growth, survivorship, and condition of nursery-raised A. cervicornis colonies that were part of two transplant projects: 1) photographic analyses of 17 past CRF transplant projects over the …

Connectivity Of Reef Fishes Between Mangroves And Coral Reefs In Broward County, Florida, Jennifer Savaro

HCNSO Student Theses and Dissertations

Many marine fishes use the mangrove ecosystem for foraging, protection, spawning, and as a nursery habitat. To develop a better understanding of energy flow between the coastal mangrove and coral reef ecosystems, the ontogentic migration and trophic connectivity of reef fishes were examined through the use of carbon (C), nitrogen (N), and oxygen (O) stable isotope ratios. Juvenile and adult gray snapper Lutjanus griseus, lane snapper L. synagris, bluestriped grunt Haemulon sciurus, French grunt H. flavolineatum, sailor’s choice H. parra, yellowfin mojarra Gerres cinereus, and great barracuda Sphyraena barracuda were collected from both mangrove …

Staghorn Coral, Acropora Cervicornis, Restoration In South Florida: Growth And Survivorship Of Outplanted Nursery Corals, Meaghan Johnson

HCNSO Student Theses and Dissertations

This thesis provides a detailed analysis of the growth and survivorship of outplanted Acropora cervicornis corals from underwater nurseries within three regions of the Florida Reef Tract. Substantial loss of stony coral cover on Florida’s coral reefs, including the branching staghorn coral, Acropora cervicornis, has occurred for decades due to disturbances such as disease, temperature induced bleaching, hurricanes, sedimentation, and pollution. This rapid population decline contributed to A. cervicornis being listed as a threatened species under the U.S. Endangered Species Act in May 2006. To aid in the recovery of the species, coral fragments were grown in underwater nurseries …

Cross-Shelf And Latitudinal Benthic Community Investigation In The Nearshore Habitats Of The Northern Florida Reef Tract, Katelyn Klug

HCNSO Student Theses and Dissertations

The Florida Reef Tract (FRT) extends from the tropical Caribbean northward along the Florida coast into a warm temperate environment where tropical reef communities diminish with increasing latitude. This study was designed to map the nearshore benthic habitats including coral reefs and evaluate how the benthic communities differ between habitats and along the coast.

Benthic communities across the northern FRT from Key Biscayne to Hillsboro Inlet (25.5°-26.3° N) were digitized from aerial photography taken in 2013 at a 1:1,000 scale. Three main hard-bottom habitat types were identified that ran parallel to shore and consecutively further away from shore: Colonized Pavement, …

A Revision Of The Genera Of Charitometridae With Abruptly Expanded Genital Pinnules, Alois Romanowski

HCNSO Student Theses and Dissertations

Feather star (Echinodermata: Crinoidea: Comatulida) family Charitometridae has not been revised since 1950. Molecular analysis, new specimens of existing species, and the discovery of a new species has revealed the need for a generic-level revision of those genera that exhibit abruptly expanded genital pinnules. A morphological study was conducted using 57 specimens representing 10 species of the Charitometridae. The genus Poecilometra is redescribed, and two species formerly placed in Strotometra have been moved to the genus based primarily on possession of pedunculate genital pinnules and a wide flange on the first pinnular of the proximal pinnules. A new species was …

Thermal Preferences And Critical Temperature Regimes Of The Western North Atlantic Invasive Lionfish Complex (Pterois Spp.), Benjamin Barker

HCNSO Student Theses and Dissertations

Temperature preference, behavioral tolerance, and physiological tolerances were determined for locally captured, invasive juvenile lionfish at four different acclimation temperatures (13°C, 20°C, 25 °C and 32°C). Temperature preferences and avoidance temperatures were evaluated using an automated shuttlebox system that presents subject-driven temperature stimuli to subjects, who control the temperature with their movement throughout the tank for 12 hours. Subjects are tracked by a computer system, with data output approximately every second. Acute preference was calculated from the archived data as the mean temperature that the fish occupied during the first two hours of dynamic experimentation. Acute preference measurements were used …

Modeling Of Epizootics On Four Genera Of Arabian Gulf Corals, John Alexander Kluge

HCNSO Student Theses and Dissertations

Coral colonies, from a reef near Abu Dhabi, United Arab Emirates (UAE), were counted and assessed for condition using photo-transects. An epidemic model, used to track how a communicable disease moves through a population, was constructed to help predict the future condition of this coral reef. In situ data from a disease outbreak that occurred in September 2011 provided a baseline for the model. Coral Populations of Porites, Platygyra, Acropora and Dipsastrea were modelled using condition categories that included Healthy, Black Band Disease Infected, Cyanobacteria Infected, Recovered, Recruits or Dead. Results from the modelling indicate that populations of Platygyra and …

Toll-Like Receptor 9-Mediated Inflammation Triggers Alveolar Bone Loss In Experimental Murine Periodontitis, Paul D. Kim, Xia Xia-Juan, Katie E. Crump, Toshiharu Abe, George Hajishengallis, Sinem E. Sahingur

Biology Faculty Articles

Chronic periodontitis is a local inflammatory disease induced by a dysbiotic microbiota and leading to destruction of the tooth-supporting structures. Microbial nucleic acids are abundantly present in the periodontium, derived through release after phagocytic uptake of microbes and/or from biofilm-associated extracellular DNA. Binding of microbial DNA to its cognate receptors, such as Toll-like receptor 9 (TLR9), can trigger inflammation. In this study, we utilized TLR9 knockout (TLR9^−/−) mice and wild-type (WT) controls in a murine model of Porphyromonas gingivalis-induced periodontitis and report the first in vivo evidence that TLR9 signaling mediates the induction of periodontal bone loss.P. gingivalis-infected …

Repeated, Long-Distance Migrations By A Philopatric Predator Targeting Highly Contrasting Ecosystems, James S. E. Lea, Bradley M. Wetherbee, Nuno Queiroz, Neil Burnie, Choy Aming, Lara L. Sousa, Gonzalo R. Mucientes, Nicolas E. Humphries, Guy Harvey, David W. Sims, Mahmood S. Shivji

Marine & Environmental Sciences Faculty Articles

Long-distance movements of animals are an important driver of population spatial dynamics and determine the extent of overlap with area-focused human activities, such as fishing. Despite global concerns of declining shark populations, a major limitation in assessments of population trends or spatial management options is the lack of information on their long-term migratory behaviour. For a large marine predator, the tiger shark Galeocerdo cuvier, we show from individuals satellitetracked for multiple years (up to 1101 days) that adult males undertake annually repeated, roundtrip migrations of over 7,500km in the northwest Atlantic. Notably, these migrations occurred between the highly disparate …

An International Assessment Of Mangrove Management: Incorporation In Integrated Coastal Zone Management, Haille N. Carter, Steffen W. Schmidt, Amy Hirons

Marine & Environmental Sciences Faculty Articles

Due to increasing recognition of the benefits provided by mangrove ecosystems, protection policies have emerged under both wetland and forestry programs. However, little consistency remains among these programs and inadequate coordination exists among sectors of government. With approximately 123 countries containing mangroves, the need for global management of these ecosystems is crucial to sustain the industries (i.e., fisheries, timber, and tourism) and coastal communities that mangroves support and protect. To determine the most effective form of mangrove management, this review examines management guidelines, particularly those associated with Integrated Coastal Zone Management (ICZM). Five case studies were reviewed to further explore …

Dna Analysis Of Surfactant Associated Bacteria In The Sea Surface Microlayer In Application To Satellite Remote Sensing Techniques: Case Studies In The Straits Of Florida And The Gulf Of Mexico, Bryan Hamilton

HCNSO Student Theses and Dissertations

Several genera of bacteria residing in the sea surface microlayer and in the near-surface layer of the ocean have been found to be involved in the production and decay of surfactants. Under low wind speed conditions, surfactants can suppress short gravity capillary waves at the sea surface and form natural sea slicks. These features can be observed with both airborne and satellite-based synthetic aperture radar (SAR). Using a new microlayer sampling method, a series of experiments have been conducted in the Straits of Florida and the Gulf of Mexico in 2013 to establish a connection between the presence of surfactant-associated …

Acute And Chronic Effects Of Large-Vessel Anchoring On Coral Reef Communities Inside A Designated Commercial Anchorage, Lauren Waters

HCNSO Student Theses and Dissertations

Coral reefs provide economic and environmental services to millions of people as areas for recreation, sources of food, jobs, and shoreline protection; and are now under threat from multiple stresses (NOAA 2002). Anthropogenic impact from acute physical events such as commercial vessel grounding and anchor drags have been well documented throughout the world and southeast Florida. However little data exist on the chronic effects of large commercial vessels anchoring on reef resources. The Port Miami commercial anchorage was designated circa 1927 and was delineated over approximately 700 acres of reef resources. Anchorage use, benthic resources, and substrate composition were surveyed …