Facilities & Resources
Facilities
The Department of Biology and Marine Science is housed in the Reid Medical Sciences Building, the Nelms Buildings, and the Marine Science Research Institute. There is also the Life Sciences Museum that includes an impressive collection of specimens.
Our facilities have a working wet lab with an aeration system, aquaria to maintain marine and freshwater organisms, an aquaculture compound dedicated to freshwater fish aquaculture, and a variety of spectrophotometers, centrifuges, incubators and microscopes for the use of students and faculty in laboratory and research settings.
Our newly renovated Anatomy & Physiology laboratories allow students to engage in hands-on exploration using anatomical models, simulation software, including Vernier physiological tools, and specimens. New additions include newly designed air control systems and storage solutions. Utilizing these spaces, students have the opportunity to explore the body from the cellular level to the whole organism, all the while gaining an appreciation for how the systems work together.
We have the capacity to teach students how to culture mammalian cells, amplify DNA using the polymerase chain reaction, use fluorescence microscopy to count cells and view subcellular structures, and measure antibodies and antigens via ELISA assays.
Shimadzu AXIMA Performance MALDI TOF/TOF mass spectrometer
Funded by the State of Florida through the St. Johns River Initiative
The MALDI mass spectrometer allows the analysis of a wide range of molecules (toxins, carbohydrates, polymers, metabolites, oligonucleotides, protein, peptides, bacteria, etc.) that are pure as well as in complex mixtures, including environmental samples with minimal sample preparation.
How MALDI-TOF MS works: Analytes are crystallized in a matrix and then loaded into the instrument. After the instrument obtains a high vacuum, the researcher shoots the sample with laser pulses, releasing the analytes into the gas phase as ions. An electric field is applied, and the molecular ions are accelerated, which travel through a vacuum tube and strike a detector at the end. The time it takes an ion to travel the vacuum tube and strike the detector is dependent on its mass and charge. The resulting data are used in a variety of ways, depending on the application. The TOF/TOF feature allows MS/MS analysis of the analytes, which is a tandem mass spectrometry technique where molecules in the instrument are fragmented with helium atoms, providing structural information.
AXIMA-iDPlus: Our MALDI-TOF/TOF mass spectrometer is configured for and combined with the SARAMIS software and database to identify a wide range of bacteria, yeasts, molds, and spores. This technique relies on producing mass “fingerprints” of the microorganism and comparing it to the extensive database.
Features of the instrument:
- Mass range 1-80kDa in reflectron mode; 1-500kDa in linear mode
- Mass range 1-500kDa in linear mode; 1-80kDa in reflectron mode
- Mass resolution 20000 FWHM in reflectron mode; 5000 FWHM in linear mode
- Mass accuracy <5ppm in reflectron mode
- Sensitivity 250 amol in reflectron mode
- High energy MS/MS using helium collision gas to fragment molecules
- structural information for the molecule
- amino acid sequences can be obtained from peptides
- MASCOT database search integration for identifying proteins using peptide mass fingerprints
- SARAMIS software and database for microorganism identification
Students and faculty use the instrument to identify and characterize proteins, toxins, and bacteria by analyzing intact proteins, peptides from digested proteins, algal toxins from local waters, and bacteria from local waters and oysters.
Watch two videos of how some of our students have used the mass spectrometer which were filmed at the Science on the St. Johns community event at the JU Marine Science Research Institute:
Bio-Rad CFX96 Touch Real-Time PCR Instrument
Funded by the State of Florida through the JU EPIC program
The Bio-Rad CFX96 instrument is used to conduct the polymerase chain reaction (PCR), which is a molecular biology technique that copies and amplifies specific targets of DNA. The real-time feature means that the concentrations of specific genes can be determined as well as the ability to monitor the reaction as it happens (in real-time).
How real-time PCR works:
The polymerase chain reaction uses a DNA replicating enzyme (Taq polymerase) to synthesize copies of target DNA. This technique is the basis for DNA analysis of crime scenes and suspects, where short tandem repeats are amplified from biological material (blood, saliva, semen, etc.) and the resulting data are compared. Real-time PCR additionally incorporates molecules that cause an increase in fluorescence when increasing amounts of DNA are copied.
Features of the instrument:
- Ten orders of magnitude dynamic range
- Melting curve analysis
- Thermal gradient
- Three targets with different fluorophores can be analyzed simultaneously
- Takes 96 well plates, individual tubes, or strips
Students and faculty use the instrument to analyze Alu repeats in humans, to identify bacteria such as Vibrio cholerae (causes cholera) and Staphylococcus aureus (causes staph infections), and perform conventional (dark) PCR with subsequent analysis via agarose gel electrophoresis. Student projects can cover a range of target DNA.
FlowCam 8400
Donated by an anonymous donor
The FlowCam 8400 is a dynamic particle imaging and analysis system, which combines flow cytometer and microscopic camera features with computerized identification, enumeration, and biometric measurement capabilities.
Features of the instrument:
- Counts, captures, and saves images of particles
- Quickly (6 minutes) processes a 1 mL sample <100 µm particulates
- Measures and collects size, shape, fluorescence, and concentration statistics (typically up to 10,000 images/minute)
- Identifies and characterizes organisms based on fluorescence
- Calculates biovolumes, concentrations, and community size distributions
- Sorts, filters, and classifies organisms with semi-automated imaging software
Students and faculty can use the FlowCam to image particles, ranging from 3um to 1mm in size, from both aquatic and sedimentary field samples. The images and accompanying data can be used for purposes such as: harmful algal bloom monitoring, larval population ecology studies, microplastic enumeration, reconstructing historic weather and current patterns (through analysis of sediment core particulates), and identifying cryptic species when used in conjunction with fluorescing probes. The FlowCam can also be used in controlled laboratory experiments to monitor growth rates and determine survival thresholds under various parameters.
Biotage SP1 Flash Chromatograph
Donated by Dr. Larry Sutton
The Biotage SP1 is a Flash Liquid Chromatography system that can purify organic compounds in an accelerated manner.
Features of this instrument:
- Window-based LCD touch screen interface
- Solvent and waste monitoring
- Variable wavelength detector (200 to 320nm)
Student and faculty can use the Biotage SP1 Flash Chromatography instrument for separation and purification of organic compounds, siderophores, antibiotics, and others chemical compounds.
Bio-Rad iMark Microplate Absorbance Reader
Funded by the State of Florida through the JU EPIC program
Features of the instrument:
- 400 nm – 750 nm wavelength range; dual wavelength readings
- Takes 96 well plates or strips
- Kinetic analysis
- Built-in shaker
Students and faculty can use this instrument for ELISA analysis, bacterial growth curves, protein assays, enzyme assays for kinetics, and more.
SpectraMax Plus 385 Microplate Reader
Donated by Dr. Larry Sutton
The SpectraMax plus can run as both a standard spectrophotometer and a microplate reader.
Features of this instrument:
- Reads one sample or up to 384 reads in a single microplate.
- Temperature control and shaking capabilities
- Kinetic measurements
- Nucleic Acid and protein quantitation
Students and faculty can use the SpectraMax Plus 384 microplate reader for ELISA, Nucleic Acid quantitation, enzyme assays, protein quantitation, bacterial growth, antibiotic assays, and more.
GE AKTA Start Protein Purification System
Donated by Dr. Larry Sutton
The AKTA protein purification system is a Fast Protein Liquid Chromatography system (FPLC).
Features of this instrument:
- Touchscreen display and real time monitoring
- Quick start methods and templates for common purification techniques
- Runs in either manual or automated modes
- Fraction collection
- UNICORN control software
Students and faculty can use the FPLC to analyze and purify proteins.
Genscript eStain L1
Donated by Dr. Larry Sutton
The Genscript eStain L1 is a PAGE gel staining system.
Features of this instrument
- Has a sensitivity of ≤ 12.5 ng of protein
- Stains and destains in 10 minutes
Faculty and student can use the eStain.to stain/destain two protein PAGE gels
Biosafety Cabinet
Funded by the State of Florida through the JU EPIC program
The microbiology biosafety cabinet is used by students and faculty to work in a sterile environment. Uses include handling bacteria, including pathogens, and preparing samples for PCR analysis.
Leica DM IRB Inverted Fluorescent Microscope
Funded by the National Science Foundation
Students and faculty have used this microscope to detect specific proteins in cells using immuno-labeling, follow macrophage activity, determine and quantify live and dead bacteria, and visualize photosynthetic cells and subcellular components.
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Oceanographic Equipment
RBRduo3 CTDO2 (Conductivity, Temperature, Depths, Dissolved Oxygen) sensor
A CTD is one of the most common instruments in Physical Oceanography that measures
how temperature and salinity change in relation to depth.
Features of the instrument:
- 240M readings Standard sampling up to 1Hz
- Up to 32Hz sampling
- USB-C download
- Real time communications
- Twist activation
- Wi-Fi ready
Student and faculty can use the CTD from the side of a ship or the dock, or moored, to estimate water densities and ocean currents that are caused by density variations, chemical and biological processes, find areas of upwelling and sediment movement, calculate sound velocity and discover areas of low oxygen that might impact fish population.
Pathfinder DVL Acoustic Doppler Current Profiler (ADCP)
ADCP’s are used to measure the movement of water through the use of an acoustic ping.
The sound is emitted by the instrument, traveling through the water where it is scattered
and reflected back by suspended particles. The change in sound waves caused by this,
allows us to calculate the speed with which the water is moving.
Features of the instrument:
- Small size and weight allows the pathfinder to be installed on board the smallest vehicles or on small floating platforms.
- Phased Array: Unique phased array transducer design delivers enhanced position accuracy at a reduced size, eliminates the need for speed of sound correction, and reduces susceptibility to biofouling.
- Flexible Design: Self-contained or remote-head options available to meet your unique
vehicle needs.
Profiling capability. - Ethernet Compatible: Plug-n-play with today’s interfaces.
- Extended Range: New optional XRT (Extended Range Tracking) delivers up to a 60% increase in bottom tracking range
Students and faculty can use the ADCP to measure the flow of the St. Johns river and Ocean, and how this flow changes at different times of the day, in different regions, and during different conditions.
Aquarium Facilities
The Marine Science Research Institute houses the wetlab complete with aquarium and aquaculture tanks for freshwater and seawater projects.
Photos: Francisco Ortiz
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Vessels
The Marine Science Research Institute and Department of Biology and Marine Science have a number of vessels available for student use. They include:
New! Jon Boat donated by North Florida Marine Association
18 ft. Flat Bottom Jon Boat
17 ft. Mako Run-About
RV Dolphin, 25 ft. Boston Whaler
Seabattical, 31 ft. Fountain
RV Larkin, 48 ft. Floating Classroom Pontoon Boat
For daily rates, please contact Director of the MSRI, Dr. Franks: bfranks@ju.edu.
Resources
OCEARCH at JU Scholarly Research
OCEARCH is a nonprofit with a focus on generating critical scientific data related to tracking (or telemetry) and biological studies of keystone marine species, including great white and tiger sharks, while simultaneously continuing its efforts in the areas of conservation and education, all on a measurable yet global scale. OCEARCH shares real-time scientific data through its Global Shark Tracker and leverages that data to engage students with interactive lesson plans and inspire the next generation of explorers, scientists, and stewards of the ocean.
Ocean Observatory Initiative
The National Science Foundation’s Ocean Observatories Initiative (OOI) has constructed a network of sustained ocean measurements to study climate variability, ocean circulation, ecosystem dynamics, air-sea exchange, seafloor processes, and plate-scale geodynamics. The program also invested in making the data available to the public through a series of web-based software tools that link data driven activities to the live data being collected by the OOI.
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