USF Making Waves REU
NSF Research Experience for Undergraduates (REU), Making Waves REU program will be hosted by the College of Marine Science, School of Geosciences, Morsani College of Medicine, and the Department of Journalism and Digital Communication at the University of South Florida (USF). Making Waves REU has five projects for 2024.
Project 1: Dr. Brad Rosenheim
Project 2: Dr. Larry Dishaw
Project 3: Dr. Pamela Hallock Muller
Project 4: Dr. Frank Muller-Karger
Project 5: Dr. Mark Luther
Project 1: Faculty mentor: Dr. Brad Rosenheim
Carbon cycling in one of the most dynamic sedimentary routing systems on Earth –the Amazon River and associated coastal sediments
Dr. Brad Rosenheim will involve REU participants in a research project aiming to revise the world’s carbon budget by applying new analytical techniques to one of the most dynamic sedimentary routing systems on Earth –the Amazon River and associated coastal sediments. The project aims to constrain the role that the coastal ocean plays in storing or incinerating the organic carbon stored in sediments eroded from the Amazon basin, transported to the ocean, and then moved up the Guianas coast for thousands of kilometers. Conventional wisdom held that most of this carbon was returned to the atmosphere due to the dynamic nature of the marine deposits, however Dr. Rosenheim’s group unearthed contradictory evidence. The team set out on an ocean-going expedition in the summer of 2023 to core sediments and to sample water and particulate matter from the water column. The REU participants for this project will play a crucial role in testing hypotheses related to this work. Students with backgrounds in chemistry can analyze porewaters, the waters within the sediment pore spaces that equilibrate with the sediments, to determine what minerals and elements are mobilized by microbial activity. Students with background or interests in Earth sciences can explore relationships between sediment parameters such as grain size, surface area, and elemental makeup and distribution of radiocarbon in sedimentary organic matter. In either case, REU participants will be introduced to the dynamic and transdisciplinary world of coastal marine sediment geochemistry and will learn transferrable laboratory and analytical skills important for today’s STEM workforce. Experimental design, hypothesis testing, and geochemical tools will be the focus of this work.
Project 2: Faculty mentor: Dr. Larry Dishaw
Marine invertebrate chordate model system to study gut microbial immune interactions
Dr. Larry Dishaw, from USF Health Morsani College of Medicine, will involve REU participants to explore in vitro and in vivo functional attributes of lysogens and their cured counterparts (recently established in our lab). REU participants will conduct biofilm assays and co-culture experiments, focusing on strain variants. REU participants will also learn the Ciona model and leverage the germ-free approaches (Leigh et al. 2016) to determine if lysogens colonize the gut in unique ways. The necessary methods have been developed and a variety of strains are now available, so this project is feasible in the time constraints of the program by allowing the REU participants to characterize various strain combinations in ways that maximize opportunities to complete a project. REU participants will learn to ‘map’ the prophage genomes in the context of other bacterial genes and predict interactions within metabolic pathways using various online resources (e.g., Kyoto Encyclopedia of Genes and Genomes, MetaCyc, or BioCyc Database). REU participants will learn to design qPCR primers so that after the pandemic he/she will be able to collaborate with future students who will continue the project and perform in vitro assays to test these predicted metabolic interactions. Additionally, the REU participants may work on a project designed to understand the pharynx as a sensory organ delivering signals to the developing gut; for example, we are trying to understand mechanosensory inputs via PIEZO calcium channels or g-protein coupled sensory receptors, GPCRs, and how they may respond as part of the sensory system delivering signals to the developing gut. REU participant s will learn about the various methods necessary to map proteomics data to genome and transcriptome data in the hopes to understand the complex dialogue between host and the associated microbial community.
Project 3: Faculty Mentor: Dr. Pamela Hallock Muller
Seasonal differences in sediment texture and composition and characterization of benthic macrofauna associated with upside-down jellyfish blooms at selected sites in Jobos Bay, Puerto Rico
Dr. Pamela Hallock Muller will involve the REU participant in a study at Jobos Bay National Estuarine Research Reserve (JBNERR) on the southeast coast of Puerto Rico. Recent studies have indicated that timing of major storm passage can be more important than “wet/dry” seasonality. The REU student will analyze sediment grain-sizes, percent calcium carbonate, percent organic carbon, and sediment constituents from samples collected previously, conduct data entry and verification, and carry out basic data analyses. Additionally, tropical estuaries, such as JBNERR, have witnessed the invasion of the upside-down jellyfish Cassiopea spp., triggering blooms due to their rapid population growth and limited predation pressure. This project also aims to uncover the macrofaunal communities linked with Cassiopea blooms in JBNERR and the REU student will perform video annotations using the free source program BIIGLE where they will quantify and identify macrofauna associated to areas of upside-down jellyfish blooms. The participant will gain experience performing environmental DNA analysis (eDNA) to confirm species identified by pictures and translation of the tool with the field observations. REU student will gain transferable skills, such as familiarity of scientific literature, mapping procedures, quality assurance and quality control, data collection, data entry, data verification, creation and use of data spreadsheets, identify, and verify data outliers, and report writing and revision.
Project 4: Faculty Mentor: Dr. Frank Muller-Karger
Ground and satellite observations related to biodiversity to inform ecosystem-based management
Dr. Frank Muller-Karger will involve REU participants in the Marine Biodiversity Observation Network (MBON), which seeks to integrate ground and satellite observations related to biodiversity to inform ecosystem-based management. This includes supporting Federal and State Ecosystem Assessment (IEA) efforts, the National Marine Fisheries Southeast Fisheries, National Marine Sanctuary (FKNMS) Program, National Estuarine Research Reserve (NERR), and international groups such as the Global Ocean Observing System. The objectives are to 1) Further integrate and synthesize information from ongoing monitoring programs through the Integrated Ocean Observing System (IOOS); and 2) Refine details for practical marine Essential Biodiversity Variables (EBVs) and Essential Ocean Variables (EOVs). The MBON has an international dimension in the UN Decade of Ocean Science for Sustainable Development (the Ocean Decade) as it served as the lead for several partners to propose the Marine Life 2030 Program, which has been endorsed by the Ocean Decade. The REU participants will participate in MBON and Marine Life 2030 meetings. They will help coordinate volunteer groups specifically to help identify existing biodiversity measurements, help investigators understand standards for data storage and sharing through an international relational database called the Ocean Biodiversity Information System (OBIS). The REU participants will participate in joint analyses of the data that may be used for Condition Reports for the Florida Keys National Marine Sanctuary. The REU participants will learn about marine biodiversity, tools available to assess ecosystem status including satellite data, advance protection of marine resources, and promote conservation.
Project 5: Faculty Mentor: Dr. Mark Luther
Forecasting anomalous coastal ocean conditions relevant to maritime navigation at major US ports using artificial intelligence
Dr. Mark Luther will involve REU participants in development of new tools that will improve the safety and efficiency of navigation in the coastal waters of major US seaports by converging the sciences of physical oceanography, artificial intelligence (AI), and data analytics. Luther has an extensive history with the NOAA National Ocean Service (NOS) Center for Operational Oceanographic Products and Services (CO-OPS), having operated NOAA’s Physical Oceanographic Real-Time System (PORTS®) for Tampa Bay for over 25 years in close collaboration with the Tampa Bay port community (one of the largest in the US). Students will be actively engaged in operation and maintenance activities for Tampa Bay PORTS® during their research projects. REU participants will gain experience in real-time ocean observing systems, numerical forecast models, AI techniques, and port operations and infrastructure. State-of-the-art AI techniques, such as recursive neural networks, graph neural networks, and deep reinforcement learning will be utilized to integrate available observations and model hindcasts/nowcasts/forecasts with vessel tracking data.AI decision support tools developed will produce improved forecasts of optimal vessel arrival times to meet published Vessel Handling Guidelines for tide, current, and wind conditions. The AI tools also can guide optimal vessel loading and sailing windows for bulk cargo, such as that for the phosphate industry in Tampa Bay, and can automatically detect anomalous or suspicious vessel movements for port safety and security applications. This project in part consists of data analysis and code development.