Life Sciences Commons^™

Complete Mitogenome Sequences Of Smooth Hammerhead Sharks, Sphyrna Zygaena, From The Eastern And Western Atlantic, Derek S. Guy, Cassandra L. Ruck, Jose V. Lopez, Mahmood S. Shivji

Biology Faculty Articles

We report the first mitogenome sequences of the circumglobally distributed, highly mobile, smooth hammerhead shark, Sphyrna zygaena, from the eastern and western Atlantic. Both genomes were 16,729 bp long with 13 protein-coding genes, two rRNAs, 22 tRNAs and a non-coding control region. The two Atlantic shark sequences differ from each other by 13 SNPs, and by 43 and 44 SNPs from the published mitogenome of an S. zygaena specimen from the eastern Pacific Ocean. The cross-Atlantic mitogenome sequences reported here provide a resource to assist with population genetics studies of this widely exploited species of conservation concern.

Hardbottom Mapping And Community Characterization Of The West-Central Florida Gulf Coast, December 2011 - June 2016, Brian K. Walker, Rene Baumstark, Sean Keenan, Cory Ames

Marine & Environmental Sciences Faculty Datasets

The continental shelf off Florida’s west coast is a mosaic of fish habitats including seagrass beds and carbonate reef outcroppings (hard bottom) classified by the National Marine Fisheries Service (NMFS) as Essential Fish Habitat. Habitat maps and community baseline data, however, are nonexistent for a majority of the region. This collaborative effort between Nova Southeastern University, Florida Fish and Wildlife Conservation Commission, NMFS and other scientists will characterize and map continental shelf seagrass and hard bottom habitats in nearshore areas fished by many recreational fishermen. Objectives include: 1) map hard bottom and seagrass beds using various data types including sonar …

Complete Bacterial Symbiont Genome Sequences From Anglerfish Cryptopsaras Couesii And Melanocetus Johnsonii, Lindsay L. Freed, Dana Fadera, Dante Fenolio, Tracey Sutton, Jose V. Lopez

DEEPEND Datasets

These are the complete bacterial symbiont genome sequences from anglerfish Cryptopsaras couesii (individual CC26) and one individual Melanocetus johnsonii. These data were generated and analyzed by the laboratory of Dr Tory Hendry (Cornell University). The full sequences of two symbiotic bacterial genomes have been submitted to public DDBJ/ENA/GenBank repositories under the accessions CP020660- CP020663 (CC26 Cryptopsaras couesii) and NBYY01000001-NBYY01000039 (Melanocetus johnsonii). The total genome size for each of the symbiont species is about 2-2.6 Mb.

Composition And Quantification Of Polycyclic Aromatic Hydrocarbons In Deep-Pelagic Fauna. Cruises Dp02, Dp03, And Dp04 From August 2015 - August 2016, Isabel C. Romero

DEEPEND Datasets

Samples were collected in the northern Gulf of Mexico on cruises DP02, DP03 and DP04 from August 2015 - August 2016. Polycyclic Aromatic Hydrocarbons (PAH) data were integrated with those from population dynamics and stable isotope analysis to provide evidence for effects of oil exposure to deep pelagic communities. The target fish species include Argyropelecus spp., Ceratoscopelus warmingii, Chauliodus sloani, Diaphus spp., Lampanyctus alatus, Lepidophanes guentheri, and Sigmops elongatus. Analysis of PAHs was conducted on different fish tissues (muscle, guts, gills, and eggs) following modified EPA method 8270D and QA/QC strict protocols. Detection and quantification of PAH homologues was performed …

Beginning Experiment: Nanoparticle Uptake In Arpe-19 Cells, Nitya Nunna

Trick to the Treat of Internships and Research

No abstract provided.

Cleveland Clinic Summer Scholars Program, Chethani Chitraacharige

Trick to the Treat of Internships and Research

No abstract provided.

Practicum In Biology, Sarah Amaris

Trick to the Treat of Internships and Research

No abstract provided.

Cano Health Clinical Studies Internship Program, Stephanie Hernandez

Trick to the Treat of Internships and Research

No abstract provided.

The Austria Summer Biology Internship, Max Cedeno-Hahn, Laura Enzinna

Trick to the Treat of Internships and Research

No abstract provided.

Rumbaugh Goodwin Institute Of Cancer Research, Christopher Garcia

Trick to the Treat of Internships and Research

No abstract provided.

The International Human Cadaver Prosection Program, Wilford Miranda, Christopher Garcia

Trick to the Treat of Internships and Research

No abstract provided.

Science Alive, Allan Barraza, Ahjay Bhatia, Gwen Bui, Sophia Nguyen

Trick to the Treat of Internships and Research

No abstract provided.

Major Complications And Management Options Of Obesity, Shreja Patel, Mir Saleem

Biology Faculty Articles

Obesity is a disorder that consists of many factors, which has become a global epidemic since it is associated with various crucial diseases, such as diabetes, cardiovascular diseases, hypertension, stroke, sleep apnea, as well as other conditions. In order to manage obesity, a variety of strategies are taken into account in order to direct attention on those with current weight problems as well as those that are at a high risk of developing obesity. Therefore, obesity prevention should be focused during the early ages as there is a high risk of developing it in the later years. This article focuses …

Inventory Of Gulf Of Mexico Oceanic Fauna Data Including Species, Weight, And Measurements From R/V Point Sur (Cruises Dp03 And Dp04) May-August, 2016, April Cook, Tracey Sutton

DEEPEND Datasets

This data set includes the biological and environmental data for all of the species collected during the DP03 (May 2016) and DP04 cruises (August 2016). The main gear type used was a 10-m2 Multiple Opening Closing Net and Environmental Sensing System (MOCNESS). The MOCNESS was fitted with 6 nets which were opened according to the following depth scheme: net 0 from the surface to 1500m, net 1 from 1500-1200m, net 2 from 200-1000m, net 3 from 1000-600m, net 4 from 600-200m, and net 5 from 200m to the surface. Two trawls were conducted at each station sampled to capture diel …

How Do Former Undergraduate Mentors Evaluate Their Mentoring Experience 3-Years Post-Mentoring: A Phenomenological Study, Kari L. Nelson, Christine E. Cutucache

The Qualitative Report

This phenomenological study involves a unique, longitudinal assessment of the lived experiences of former undergraduate mentors (n=7) in light of their current experiences (i.e., career or advanced schooling). The objective of a phenomenological study is to engage in in-depth probing of a representative number of participants. Specifically, we followed up with graduates of the Nebraska STEM 4U (NE STEM 4U) intervention 3 years post-program, with the overall goal of describing the mentors’ experiences using the lens of their current experiences. This type of longitudinal perspective of mentoring is greatly lacking in the current literature. At the time of the interviews, …

Multiple Opening Closing Net Environmental Sensing System (Mocness) Instrument Data For Cruise Dp05 R/V Point Sur In-Situ Deep Seawater And Associated Fauna, May 1-11, 2017, Viosca Knoll Gom, Gray Lawson, Travis Richards

DEEPEND Datasets

The Multiple Opening Closing Net and Environmental Sensing System(s) (MOCNESS) deployed during the DEEPEND field program collects data (e.g., pressure, temperature, conductivity, volume filtered, horizontal and vertical velocity, latitude, and longitude) from several sensors while the instrument is in use. These data help characterize the environment and assess the orientation and speed of the MOCNESS. The flow and net angle can be used to calculate the volume of water filtered for each net. The biological data and ship data collected during this cruise are available in GRIIDC datasets R4.x257.226:0005 and R4.x257.226:0014 respectively.

Meditation Experience Associated With Structural Neuroplasticity, Mir Saleem, Pallavi Samudrala

Biology Faculty Articles

The intention of the review is to evaluate several studies regarding meditation and its association with structural neuroplasticity. The analysis of the studies would be evaluated based on its methods and results, with respect to the implications of various physiological findings as well as the different ways in which neuroplasticity is measured. Sources were gathered from numerous journals and literature posted online. Databases at the Alvin Sherman Library were utilized to further the research process. To synthesize ideas, a holistic approach was taken to the research process, and studies regarding meditation's effects on the chemical, molecular, and genetic aspects of …

Methodological Approach To The Ex Vivo Expansion And Detection Of T. Cruzi-Specific T Cells From Chronic Chagas Disease Patients, Gonzalo R. Acevedo, Silvia A. Longhi, Alcinette Bunying, Nazila Sabri, Augusto Atienza, Maria P. Zago, Radleigh Santos, Valeria A. Judkowski, Clemencia Pinilla, Karina A. Gomez

Mathematics Faculty Articles

The discovery of T cell epitopes is essential not only for gaining knowledge about host response to infectious disease but also for the development of immune-intervention strategies. In Chagas disease, given the size and complexity of the Trypanosoma cruzi proteome and its interaction with the host’s immune system, the fine specificity of T cells has not been extensively studied yet, and this is particularly true for the CD4+ T cell compartment. The aim of the present work was to optimize a protocol for the generation of parasite-specific memory T cell lines, representative of their in vivo precursor populations and capable …

The Sunflower Genome Provides Insights Into Oil Metabolism, Flowering And Asterid Evolution, Hélène Badouin, Jérôme Gouzy, Christopher Grassa, Florent Murat, S. Evan Staton, Ludovic Cottret, Christine Lelandais-Brière, Gregory Owens, Sébastien Carrère, Baptiste Mayjonade, Ludovic Legrand, Navdeep Gill, Nolan Kane, John Bowers, Sariel Hubner, Arnaud Bellec, Aurélie Bérard, Hélène Bergès, Nicolas Blanchet, Marie-Claude Boniface, Dominique Brunel, Olivier Catrice, Nadia Chaidir, Clotilde Claudel, Cécile Donnadieu, Thomas Faraut, Ghislain Fievet, Nicolas Helmstetter, Matthew King, Steven Knapp, Zhao Lai, Marie-Christine Le Paslier, Yannick Lippi, Lolita Lorenzon, Jennifer Mandel, Gwenola Marage, Gwenaëlle Marchand, Elodie Marquand, Emmanuelle Bret-Mestries, Evan Morien, Savithri Nambeesan, Thuy Nguyen, Prune Pegot-Espagnet, Nicolas Pouilly, Frances Raftis, Erika Sallet, Thomas Schiex, Justine Thomas, Céline Vandecasteele, Didier Varès, Felicity Vear, Sonia Vautrin, Martin Crespi, Brigitte Mangin, John Burke, Jérôme Salse, Stéphane Muños, Patrick Vincourt, Loren Rieseberg, Nicolas Langlade

Biology Faculty Articles

The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought1. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives2,3, including numerous extremophile species4. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences5 and required single-molecule real-time sequencing technologies for …

Dna Sequences Of The Mitochondrial Cytochrome C Oxidase I (Coi) Genes From Deep Sea Fishes. Cruises Dp01 And Dp02 From May 2015 - August 2015, Andrea Bernard, Max Weber, Kimberly A. Finnegan, Mahmood S. Shivji, Ron Eytan

DEEPEND Datasets

The deep sea ecosystem is believed to contain the highest biomass of fish in the oceans. However, the taxonomic diversity in this ecosystem is incompletely described and likely to be vastly underestimated. DNA sequence data (barcodes) have become a key tool to discover hidden biodiversity. We generated mitochondrial DNA barcode datasets based on the Cytochrome c oxidase I (COI) gene from deep sea fishes. These data were analyzed using phylogenetic and statistical methods to reveal cryptic species and make taxonomic linkages between adult fishes and their early life stages. These datasets were generated from fishes collected in the Northern Gulf …

Growth Of Orbicella Faveolata In La Parguera, Puerto Rico, Darren B. Marshall

HCNSO Student Theses and Dissertations

Reef-building corals are subject to high amounts of stress, including pollution and rising sea surface temperatures due to climate change. These factors can affect the ability of corals to produce their calcium carbonate skeletons. Evaluation of the effects of climate change may be facilitated by evaluation of records of coral skeletal growth over a long period of time. The aim of this study was to evaluate skeletal growth of the coral Orbicella faveolata in La Parguera, Puerto Rico over a 32-year period. For this, 14 Orbicella faveolata core samples were collected from corals at two reefs (1.2 km apart) in …

Exploring The Potential For Artificial Reefs In Coral Reef Restoration: Responses And Interactions Of Associated Biota To Varying Experimental Treatments In The Mexican Caribbean, Audie Kirk Kilfoyle

HCNSO Student Theses and Dissertations

Coral reefs are being negatively impacted by various causes worldwide, and direct intervention is often warranted following disturbance to restore or replace lost ecosystem structure and function. An experimental coral reef restoration study involving standardized artificial reef modules (Reefballs^TM) was conducted in Mexico’s Yucatan Peninsula in the towns of Puerto Morelos and Akumal. The purpose was to explore the use of artificial structure for restoration and mitigation applications in a highly diverse and dynamic Caribbean coral reef environment by applying and evaluating the performance of select experimental treatments hypothesized to accelerate development of the associated biota. The first …

Presence/Absence And Density Data For Epipelagic Tows From 48 Stations In The Northern Gulf Of Mexico From R/V Blazing Seven Cruises Lf2015a And Lf2015b June 2015 And July 2015, Jay R. Rooker, R.J. David Wells

DEEPEND Datasets

Larval catch data after the oil spill is being used to improve our understanding of the causes of temporal variability as it relates to the Deep Water Horizon oil spill (DWHOS). Bongo and neuston net tows were conducted at 48 stations in both June and July, 2015 in the northern Gulf of Mexico. Cruise data collected at each site included latitude/longitude, date, time and environmental data (temperature, salinity, dissolved oxygen). The occurrence and density of selected epipelagic (e.g., billfishes, tunas, dolphinfishes, flyingfishes) and deep pelagic (e.g., lanternfishes, bristlemouths, marine hatchetfishes) fish larvae were quantified and are being used to extend …

Cooperation And Competition Shape Ecological Resistance During Periodic Spatial Disturbance Of Engineered Bacteria, Cortney E. Wilson, Allison J. Lopatkin, Travis J. A. Craddock, William W. Driscoll, Omar T. Eldakar, Jose V. Lopez, Robert P. Smith

Biology Faculty Articles

Cooperation is fundamental to the survival of many bacterial species. Previous studies have shown that spatial structure can both promote and suppress cooperation. Most environments where bacteria are found are periodically disturbed, which can affect the spatial structure of the population. Despite the important role that spatial disturbances play in maintaining ecological relationships, it remains unclear as to how periodic spatial disturbances affect bacteria dependent on cooperation for survival. Here, we use bacteria engineered with a strong Allee effect to investigate how the frequency of periodic spatial disturbances affects cooperation. We show that at intermediate frequencies of spatial disturbance, the …

The Human Microbiome: An Emerging Tool In Forensics, Jarrad T. Hampton-Marcell, Jose V. Lopez, Jack A. Gilbert

Biology Faculty Articles

No abstract provided.

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp01 And Dp02 From May 2015 - August 2015, Cole Easson, Jose V. Lopez

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during two planned DEEPEND cruise expeditions to the GOM. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable region was generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Bioinformatics analyses in QIIME and R was used to quality filter and assess microbial community diversity and taxonomic composition. These baseline characterizations track alpha and beta diversity at different depths ranging from 0 – …

Cruise Data For Neuston Net And Paired Bongo Net Tows From 48 Stations In The Northern Gulf Of Mexico From R/V Blazing Seven Cruises Lf2015a And Lf2015b June 2015 And July 2015, Jay R. Rooker, R.J. David Wells

DEEPEND Datasets

Shelf and slope waters in the Deep Water Horizon oil spill (DWHOS) area are known to serve as critical spawning, nursery, and foraging habitat of several important oceanic species including billfishes (e.g. blue marlin, white marlin, sailfish), tunas (bluefin tuna, yellowfin tuna), and other pelagic taxa (swordfish, dolphinfishes). The aim of this component was to further investigate potential ecological effects of the DWHOS on pelagic fishes during the early life period. Larval fishes were sampled from 48 stations in the northern Gulf of Mexico and cruise data was collected at each site including latitude/longitude, date, time and environmental data (sea …

Comparative Transcriptomics Of Elasmobranchs And Teleosts Highlight Important Processes In Adaptive Immunity And Regional Endothermy, Nicholas J. Marra, Vincent P. Richards, Angela Early, Steve M. Bogdanowicz, Paulina D. Pavinski Bitar, Michael J. Stanhope, Mahmood S. Shivji

Biology Faculty Articles

Background: Comparative genomic and/or transcriptomic analyses involving elasmobranchs remain limited, with genome level comparisons of the elasmobranch immune system to that of higher vertebrates, non-existent. This paper reports a comparative RNA-seq analysis of heart tissue from seven species, including four elasmobranchs and three teleosts, focusing on immunity, but concomitantly seeking to identify genetic similarities shared by the two lamnid sharks and the single billfish in our study, which could be linked to convergent evolution of regional endothermy.

Results: Across seven species, we identified an average of 10,877 Swiss-Prot annotated genes from an average of 32,474 open reading frames within each …

First Record Of The Megamouth Shark, Megachasma Pelagios, (Family Megachasmidae) In The Tropical Western North Atlantic Ocean, Grisel Rodriguez-Ferrer, Bradley M. Wetherbee, Michelle Schärer, Craig Lilyestrom, Jan P. Zegarra, Mahmood Shivji

Biology Faculty Articles

Background: A new record of Megachasma pelagios is here reported for the tropical western North Atlantic Ocean from Puerto Rico. Results: On December 10, 2016, a tourist reported an unusual stranded shark on Mojacasabe Beach, Cabo Rojo, on the southwestern coast of Puerto Rico. Visual examination of the carcass and mitochondrial DNA analysis from a dorsal fin sample revealed it to be a 457 cm female megamouth shark. Conclusion: This record represents the first record of M. pelagios for the tropical western North Atlantic Ocean within the Caribbean Sea of southwest Puerto Rico and only the second record of M. …