Life Sciences Commons^™

Study Of Secondary Metabolite Gene Expression In Marine Microbial Co-Cultures Using Quantitative Real-Time Pcr, Crystal A. Conway

HCNSO Student Theses and Dissertations

Interactions among microbial organisms often cannot be observed directly, but they can be inferred genetically using new molecular techniques. The analysis of secondary metabolite gene expression produced by co-cultured marine microbial species allows us to see how these organisms interact with one another when kept in the same environment. Co-cultures of three different strains of marine bacteria, P. aeruginosa PAO1, Roseobacter denitrificans OCH114, and Salinispora arenicola CNS-205 were grown in a laboratory setting, and using the Real-Time qPCR method gene expression levels of two different secondary metabolite producing genes from each organism was accessed across three time points. P. aeruginosa …

Genome Sequence Of The Palaeopolyploid Soybean, Jeremy Schmutz, Steven B. Cannon, Jessica Schlueter, Jianxin Ma, Therese Mitros, William Nelson, David L. Hyten, Qijian Song, Jay J. Thelen, Jianlin Cheng, Dong Xu, Uffe Hellsten, Gregory D. May, Yeisoo Yu, Tetsuya Sakurai, Taishi Umezawa, Madan K. Bhattacharyya, Devinder Sandhu, Babu Valliyodan, Erika Lindquist, Myron Peto, David Grant, Shengqiang Shu, David Goodstein, Kerrie Barry, Montona Futrell-Griggs, Brian Abernathy, Jianchang Du, Zhixi Tian, Liucun Zhu, Navdeep Gill, Trupti Joshi, Marc Libault, Anand Sethuraman, Xue-Cheng Zhang, Kazuo Shinozaki, Henry T. Nguyen, Rod A. Wing, Perry Cregan, James Specht, Jane Grimwood, Dan Rokhsar, Gary Stacey, Randy C. Shoemaker, Scott A. Jackson

Biology Faculty Articles

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but …

Diurnal Movements And Site Fidelity Of The Florida Manatee, Trichechus Manatus Latirostris, In Fort Lauderdale, Fl., Kym Walsh

HCNSO Student Theses and Dissertations

The diurnal movements of Florida manatees (Trichechus manatus latirostris) in warmwater refugia are poorly understood and these may prove critical in accurately estimating populations of these animals. Previous studies indicate that manatee populations in such refuges in Tampa Bay, FL, peak mid-day and decline towards evening when the animals leave to forage. This trend suggests that variation in the timing of aerial manatee population surveys may hamper accurate estimation of the true population size. Aerial survey counts are known to underestimate population size, yet the extent of the underestimation may be greater than expected. In this study data …

The Royal Dames, Robert Bogorff

NSU Archives Papers

A brief overview of the philanthropic efforts of the Royal Dames in the development of the Leo Goodwin Institute for Cancer Research and the organization's contribution to the advancement of cancer research at Nova University in the 1970s.

Fall 2010, Nsu Oceanographic Center

Currents

No abstract provided.

2010 Tropical Coral Reefs (Appendix 10), Joana Figueiredo

Marine & Environmental Sciences Faculty Reports

SUMMARY

• Coral reef ecosystems are global biodiversity hotspots that depend on the massive calcium carbonate structures mainly deposited by scleractinian (i.e., “hard”) corals. Scleractinian coral distribution is primarily limited by sea-surface temperature, light, depth, ocean pH, sea water salinity, nutrients and sediment loads. These ecosystems are currently threatened by localized stresses such as overfishing and destructive fishing practices, pollution, terrestrial nutrient and sediment run-off, but are increasing impacted by direct and indirect impacts of rising CO2 concentrations and climate change.
• Coral reefs provide a broad range of ecosystems services with high socio-economic value: tourism, fisheries (food and employment), nutrient cycling, …

Sailfish (Istiophorus Platypterus) Habitat Utilization In The Southern Gulf Of Mexico And Florida Straits With Implications On Vulnerability To Shallow-Set Pelagic Longline Gear, David W. Kerstetter, Shannon Michael Bayse, John E. Graves

Marine & Environmental Sciences Faculty Reports

A total of 19 pop-up satellite archival tags (PSATs) were deployed on sailfish in the southern Gulf of Mexico between 2005 and 2007 aboard a commercial pelagic longline vessel (n = 18) and a recreational rod-and-reel vessel (n = 1). All PSATs were programmed to collect pressure (depth), temperature, and light-level data for 10 days at approximately 90-second intervals. These point-level data were not summarized prior to transmission, allowing the reconstruction of vertical movement patterns. Three tags suggested mortality events and were excluded from subsequent analyses. We present the preliminary data analyses from the remaining 16 PSATs. Sailfish are primarily …

Standardized Catch Rates Of Sandbar Sharks And Dusky Sharks In The Vims Longline Survey: 1975-2009, Jason G. Romine, Kristene T. Parsons, R. Dean Grubbs, John A. Musick, Tracey Sutton

Marine & Environmental Sciences Faculty Reports

The Virginia Institute of Marine Science has conducted a fishery-independent longline survey during summer months since 1974. Data for sandbar sharks and dusky sharks captured in the survey between 1975 and 2009 are presented. Most of the sandbar sharks encountered by the survey were immature, with females composing almost all of the mature sandbar catch. Almost all dusky sharks captured were immature. Most of the catch since the early 1990’s has been composed of 0-4 year age classes. Nominal and standardized catch rates are presented. CPUE for both species decreased from the early 1980’s to minima in 1992. CPUE then …

Marine Resources Of The Falklands' Shallow Marine Environment, Karen L. Neely, Paul Brickle, Vladimir Laptikhovsky

Marine & Environmental Sciences Faculty Reports

No abstract provided.

Seasonal And Salinity Effects On The Distribution Of Higher Filamentous Marine Fungi At Rookery Bay, Fl., Julia Ossler

HCNSO Student Theses and Dissertations

More than 500 species of higher marine fungi in over 300 genera have been described. Many marine fungi are highly specialized for marine environments relative to their terrestrial counterparts, having appendaged ascospores and conidia to aid in buoyancy, entrapment, and adherence to substrates. They have been reported to inhabit a wide variety of substrates including decaying wood, leaves, calcareous and chitinous substrates, seaweeds, and seagrasses. Most early studies on marine fungi were carried out in temperate regions. Investigations have now shifted to tropical locations in order to better evaluate the abundance and diversity of marine fungi on a global basis. …

The Leo Goodwin Institute For Cancer Research Of Nova University: 1969-1980, Robert Bogorff

NSU Archives Papers

Brief history of the establishment of the Leo Goodwin Institute for Cancer Research (LGICR) at Nova University on June 1, 1969 until its dissolution in March 1979.

Winter 2010, Nsu Oceanographic Center

Currents

No abstract provided.

Light Whole Genome Sequence For Snp Discovery Across Domestic Cat Breeds, James C. Mullikin, Nancy F. Hansen, Lei Shen, Heather Ebling, William F. Donahue, Wei Tao, David J. Saranga, Adrianne Brand, Marc J. Rubenfield, Alice C. Young, Pedro Cruz, Carlos Driscoll, Victor David, Samer W. K. Al-Murrani, Mary F. Locniskar, Mitchell S. Abrahamsen, Stephen J. O'Brien, Douglas R. Smith, Jeffrey A. Brockman

Biology Faculty Articles

Background

The domestic cat has offered enormous genomic potential in the veterinary description of over 250 hereditary disease models as well as the occurrence of several deadly feline viruses (feline leukemia virus -- FeLV, feline coronavirus -- FECV, feline immunodeficiency virus - FIV) that are homologues to human scourges (cancer, SARS, and AIDS respectively). However, to realize this bio-medical potential, a high density single nucleotide polymorphism (SNP) map is required in order to accomplish disease and phenotype association discovery.

Description

To remedy this, we generated 3,178,297 paired fosmid-end Sanger sequence reads from seven cats, and combined these data with the …

Commentary Of Off-Label Prescribing: A Call For Heightened Professional And Government Oversight, Mark A. Jaffe

Biology Faculty Articles

No abstract provided.

Molecular Evolution And The Role Of Oxidative Stress In The Expansion And Functional Diversification Of Cytosolic Glutathione Transferases, Rute R. Da Fonseca, Warren E. Johnson, Stephen J. O'Brien, Vitor Vasconcelos, Agostinho Antunes

Biology Faculty Articles

Background: Cytosolic glutathione transferases (cGST) are a large group of ubiquitous enzymes involved in detoxification and are well known for their undesired side effects during chemotherapy. In this work we have performed thorough phylogenetic analyses to understand the various aspects of the evolution and functional diversification of cGSTs. Furthermore, we assessed plausible correlations between gene duplication and substrate specificity of gene paralogs in humans and selected species, notably in mammalian enzymes and their natural substrates.

Results: We present a molecular phylogeny of cytosolic GSTs that shows that several classes of cGSTs are more ubiquitous and thus have an …

Accounting For Multiple Comparisons In A Genome-Wide Association Study (Gwas), Randall C. Johnson, George W. Nelson, Jennifer L. Troyer, J. A. Lautenberger, Bailey Kessing, Cheryl Winkler, Stephen J. O'Brien

Biology Faculty Articles

Background

As we enter an era when testing millions of SNPs in a single gene association study will become the standard, consideration of multiple comparisons is an essential part of determining statistical significance. Bonferroni adjustments can be made but are conservative due to the preponderance of linkage disequilibrium (LD) between genetic markers, and permutation testing is not always a viable option. Three major classes of corrections have been proposed to correct the dependent nature of genetic data in Bonferroni adjustments: permutation testing and related alternatives, principal components analysis (PCA), and analysis of blocks of LD across the genome. We consider …

Analyzing Spatial Patterns In Reefscape Ecology Via Remote Sensing, Benthic Habitat Mapping, And Morphometrics, Shanna K. Dunn

HCNSO Student Theses and Dissertations

A growing number of scientists are investigating applications of landscape ecology principles to marine studies, yet few coral reef scientists have examined spatial patterns across entire reefscapes with a holistic ecosystem-based view. This study was an effort to better understand reefscape ecology by quantitatively assessing spatial structures and habitat arrangements using remote sensing and geographic information systems (GIS).

Quantifying recurring patterns in reef systems has implications for improving the efficiency of mapping efforts and lowering costs associated with collecting field data and acquiring satellite imagery. If a representative example of a reef is mapped with high accuracy, the data derived …

Climate Change, Coral Reef Ecosystems, And Management Options For Marine Protected Areas, Brian D. Keller, Daniel F. Gleason, Elizabeth Mcleod, Christa M. Woodley, Satie Airame, Billy D. Causey, Alan M. Friedlander, Rikki Grober-Dunsmore, Johanna E. Johnson, Steven Miller, Robert S. Steneck

Marine & Environmental Sciences Faculty Articles

Marine protected areas (MPAs) provide place-based management of marine ecosystems through various degrees and types of protective actions. Habitats such as coral reefs are especially susceptible to degradation resulting from climate change, as evidenced by mass bleaching events over the past two decades. Marine ecosystems are being altered by direct effects of climate change including ocean warming, ocean acidification, rising sea level, changing circulation patterns, increasing severity of storms, and changing freshwater influxes. As impacts of climate change strengthen they may exacerbate effects of existing stressors and require new or modified management approaches; MPA networks are generally accepted as an …

Spatial Distribution Of Petroleum Hydrocarbons In Sediment Cores From Blind Pass, St. Pete Beach, Florida, Charles M. Featherstone, John Proni, Thomas P. Carsey, Cheryl J. Brown, Madeleine M. Adler, Patricia Blackwelder, Husain Alsayegh, Teresa A. Hood, Christina Piela, Donald S. Mccorquodale Jr.

Marine & Environmental Sciences Faculty Reports

One hundred and one sediment cores were collected to characterize the spatial distribution of petroleum hydrocarbons within and just outside Blind Pass, St. Pete Beach, Florida. Twenty-five percent of the cores exhibited levels of petroleum hydrocarbons above detection limits of the gas chromatograph/flame ionization detector (GC/FID) (0.01 mg/Kg), but at generally low concentrations. Petroleum hydrocarbon speciation studies of these samples (gas chromatography/mass spectroscopy [GC/MS]) indicate above-detection level (1 μg/Kg) petroleum hydrocarbons are similar to the non-volatile petroleum hydrocarbons found in a Bouchard 155 reference sample collected after the 1993 oil spill in the area, but are in a much degraded …

Extraction And Analysis Of Coral Reef Core Samples From Broward County, Florida., Anastasios Stathakopoulos

HCNSO Student Theses and Dissertations

The reefs off Broward County exist as three shore-parallel, sequentially deeper terraces named the "inner", "middle", and "outer" reefs and also a shallower, nearshore ridge complex. These structures span the continental coast of southeast Florida from Palm Beach County to southern Miami-Dade County and were characterized as relict, early Holocene shelf-edge and mid-shelf reefs along with limestone ridges. Presently, the reefs are colonized by a fauna characteristic of West Atlantic/Caribbean reef systems. Scleractinian coral cover is low except for a few dense patches of Acropora cervicornis, while Acropora palmata is absent except for a few individual living colonies.

Coral …

Common Genetic Variation And The Control Of Hiv-1 In Humans, Jacques Fellay, Dongliang Ge, Kevin V. Shianna, Sara Colombo, Bruno Ledergerber, Elizabeth T. Cirulli, Thomas J. Urban, Kunlin Zhang, Curtis Gumbs, Jason P. Smith, Antonella Castagna, Alessandro Cozzi-Lepri, Andrea De Luca, Philippa Easterbrook, Huldrych F. Gunthard, Simon Mallal, Cristina Mussini, Judith Dalmau, Javier Martinez-Picado, Jose M. Miro, Niels Obel, Steven M. Wolinsky, Jeremy J. Martinson, Roger Detels, Joseph Margolick, Lisa Jacobson, Patrick Descombes, Stylianos E. Antonarakis, Jacques S. Beckmann, Stephen J. O'Brien, Norman L. Letvin, Andrew J. Mcmichael, Barton F. Haynes, Mary Carrington, Sheng Feng, Amalio Telenti, David B. Goldstein, Niaid Center For Hiv/Aids Vaccine Immunology (Chavi)

Biology Faculty Articles

To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of …

Diet Composition Of Swordfish, Xiphias Gladius, Within The Straits Of Florida, Amy Marie Heemsoth

HCNSO Student Theses and Dissertations

A diet study of swordfish, Xiphias gladius, was conducted in the Straits of Florida from April 2007 to December 2008. The stomachs of 131 swordfish were analyzed. Thirteen species of teleosts, three species of cephalopods, and one species of crustacean were observed in the diet. Cephalopods dominated the swordfish diet by weight (73.38%), number (69.90%), and occurrence (80.91%) and ranked highest in importance in the diet when calculating the index of relative importance (IRI). Teleosts followed by weight (25.16%), number (26.34%), occurrence (68.18%), and IRI (3,510.97). The prey species with the greatest dietary importance was Illex sp followed by …

Genome 10k: A Proposal To Obtain Whole-Genome Sequence For 10000 Vertebrate Species, David Haussler, Stephen J. O'Brien, Oliver A. Ryder, F. Keith Barker, Michele Clamp, Andrew J. Crawford, Robert Hanner, Olivier Hanotte, Warren E. Johnson, Jimmy A. Mcguire, Webb Miller, Robert W. Murphy, William J. Murphy, Frederick H. Sheldon, Barry Sinervo, Byrappa Venkatesh, Edward O. Wiley, Fred W. Allendorf, George Amato, C. Scott Baker, Aaron Bauer, Albano Beja-Pereira, Eldredge Bermingham, Giacomo Bernardi, Cibele R. Bonvicino, Sydney Brenner, Terry Burke, Joel Cracraft, Mark Diekhans

Biology Faculty Articles

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16203 representative vertebrate species spanning evolutionary diversity across living …

Every Genome Sequence Needs A Good Map, Harris A. Lewin, Denis M. Larkin, J. U. Pontius, Stephen J. O'Brien

Biology Faculty Articles

No abstract provided.

Molecular And Chromosomal Evidence For Allopolyploidy In Soybean, Navdeep Gill, Seth Findley, Jason G. Walling, Christian Hans, Jianxin Ma, Jeff Doyle, Gary Stacey, Scott A. Jackson

Biology Faculty Articles

Recent studies have documented that the soybean (Glycine max) genome has undergone two rounds of large-scale genome and/or segmental duplication. To shed light on the timing and nature of these duplication events, we characterized and analyzed two subfamilies of high-copy centromeric satellite repeats, CentGm-1 and CentGm-2, using a combination of computational and molecular cytogenetic approaches. These two subfamilies of satellite repeats mark distinct subsets of soybean centromeres and, in at least one case, a pair of homologs, suggesting their origins from an allopolyploid event. The satellite monomers of each subfamily are arranged in large tandem arrays, and intermingled …

Trophic Structure Of The Northwest Hawaiian Islands And Resident Monk Seals (Monachus Schaundslandi) During The Twentieth Century, Nina M. Thompson, Amy Hirons, Charles W. Potter, Charles Littnan

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

The Hawaiian monk seal (Monachus schauinslandi) is an endangered species only found within the Hawaiian Archipelago. The majority of the breeding population for this seal is located around six islands in the Northwest Hawaiian Island chain (NWHI). Overall, both juvenile and adult seals have a wide range in δ¹³C and δ¹⁵N from 1912-2006 (δ¹³C: -12.5‰; δ¹⁵N: 12.6‰). Seals in the northern NWHI were enriched in δ¹³C by nearly 2‰ and depleted in δ¹⁵N by nearly 6‰ during the 96 years. Meanwhile, seals within the middle and …

Leucothoidae, Kristine N. White, James Darwin Thomas

Marine & Environmental Sciences Faculty Articles

Four genera and 17 species of leucothoids, the majority of these belonging to the genus Leucothoe, are herein reported from the Great Barrier Reef. Fifteen species are new to science and only Anamixis bazimut has been previously reported from the Great Barrier Reef.

Net And Acoustic Examination Of Bathypelagic Nekton On The Mid-Atlantic Ridge, C. I. H. Anderson, J. Horne, Tracey Sutton

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

Spatial distributions of organisms play a key role in facilitating trophic interactions, which influence pelagic ecosystem structure and function. This study combines discrete net trawl sampling with continuous acoustic measurements to investigate the distribution of bathypelagic (1000- 3000 m depth) nekton biomass along the Mid-Atlantic Ridge from Iceland to the Azores. Two, previously unknown, acoustic scattering layers (ASLs) were observed using 18 kHz echosounder data. The first extended approximately 200 m from 2000 m depth and was ubiquitous wherever bottom depth allowed. The second, found within the 1500-2000 m depth stratum, only occurred south of the Sub-Polar Front. Backscatter from …

Preliminary Results On Feeding Ecology Of Stomiiforme Fishes Of The Northern Mid-Atlantic, Vanda Carmo, Odd Aksel Bergstad, Tone Falkenhaug, Gui Menezes, Tracey Sutton

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

Few previous studies have focused specifically on the role of the mid-ocean ridges in the ecology of pelagic fishes. This study targets on a dominant nekton component of the mid- Atlantic mesopelagic ichthyofauna - the Stomiiformes - and their food resources including zooplankton and other nekton. Its main goal is to characterize the diets of several species of these midwater fish towards understanding the trophic pathways of the deep-pelagic nekton of the northern MAR. The study material was provided by the G. O. Sars 2004 Expedition under the International project MAR-ECO. On the lab fish were dissected and diet items …

Relationship Of Reef Fish Assemblages And Topographic Complexity On Southeastern Florida Coral Reef Habitats, Brian K. Walker, Lance K. B. Jordan, Richard E. Spieler

Marine & Environmental Sciences Faculty Articles

Reef fish assemblage relationships with in situ and lidar topographic measurements across the seascape were analyzed to evaluate the possibility of using lidar metrics as a proxy for prediction models. In situ topographic complexity (i.e., linear rugosity) was measured from 346 point-count fish surveys spanning the reef seascape. Lidar topographic measurements (i.e., surface rugosity, elevation, and volume) were obtained from a high-resolution lidar bathymetric dataset of each survey's footprint. The survey sites were characterized by an independently derived benthic habitat map. Reef fish abundance and species richness appeared to increase with increasing topographic complexity. Although significant, the relationship was weak. …