Environmental Sample Processor (ESP)

Printing probe arrays

The “ink” of the probe array is made up of a single-stranded DNA probe, complementary to a unique rRNA sequence in the organisms of interest. These probes are chemically linked to biotin and mixed with the protein streptavidin, which binds the whole to the surface of the filter support. Electrostatic charges force the probes to stand upright, ready to attach to any complimentary sequence of nucleic acid. The support is a 25-millimeter circle of filter material that fits in the puck, where the analysis takes place.

To print probe arrays, an XYZ translation gantry positions four piezoelectric-actuated nozzles over the spotting area and delivers 6nL of probe solution per spot.  Each of those probes targets a specific species or group of species. The probes can be printed on the substrate in any shape or pattern, as long as you keep track of the “map”.  Below are two typical maps generated with various printers we have used over the years. Note a target might have 5-8 dedicated spots to provide a pseudo-replicated response of the sample to this array print.

Left, early printing (2000–2013); right, current printing (2014–present).

Left, early printing (2000–2013); right, current printing (2014–present).


With better printing technology, we now can lay down 300+ spots on a 25mm disk.

With better printing technology, we now can lay down more than 300 spots on a 25-millimeter disk.

Using a Scienion sciFlexarrayer S3, we lay down 6nL of probe “ink” on a nitrocellulose membrane. It takes about two hours to print 63 arrays for detecting harmful algae targets.

Technology

Solving challenges
Taking the laboratory into the ocean
Environmental Sample Processor (ESP)
In Situ Ultraviolet Spectrophotometer
Midwater Respirometer System
Mobile flow cytometer
Enabling targeted sampling
Automated Video Event Detection
Environmental Sample Processor (ESP)
Gulper autonomous underwater vehicle
Advancing a persistent presence
Aerostat hotspot
Benthic event detectors
Benthic rover
Fault Prognostication
Long-range autonomous underwater vehicle Tethys
MARS hydrophone for passive acoustic monitoring
Monterey Ocean-Bottom Broadband Seismometer
Shark Café camera
Vehicle Persistence
Wave Glider-based communications hotspot
Emerging and current tools
Communications
Aerostat hotspot
Wave Glider-based communications hotspot
Data management
Oceanographic Decision Support System
Spatial Temporal Oceanographic Query System (STOQS) Data
Video Annotation and Reference System
Instruments
Apex profiling floats
Benthic event detectors
Deep particle image velocimetry
Environmental Sample Processor (ESP)
Persistent presence—2G ESP
How does the 2G ESP work?
Arrays on the 2G ESP
Printing probe arrays
Expeditions and deployments
In Situ Ultraviolet Spectrophotometer
Investigations of imaging for midwater autonomous platforms
Lagrangian sediment traps
Midwater Respirometer System
Mobile flow cytometer
SeeStar Imaging System
Shark Café camera
Smart underwater connector
Power
Wave-Power Buoy
Vehicle technology
Benthic Rover
Gulper autonomous underwater vehicle
Imaging autonomous underwater vehicle
Seafloor mapping AUV
Long-range autonomous underwater vehicle Tethys
Mini remotely operated vehicle
ROV Doc Ricketts
ROV Ventana
Video
Automated Video Event Detection
Deep learning
Video Annotation and Reference System
Technology publications
Technology transfer