Instruments

Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.

a thermometer embedded in a small, sturdy, thick plastic container with a rope attached.  Heave the bucket overboard and it catches water and the thermometer inside reads the temperature.

Rotronics device used to measure air temperature

SOLARIS (Submersible Oceanic Luminescent Analyzer of Reactive Intermediate Species) is a superoxide detector that can be used at deeper depths (up to 4000 meters) and could be incorporated into a deep-sea sampling platform such as WHOI's submersible, Alvin. See: https://doi.org/10.3390/s22051709

The squidpop assay is described in detail in Duffy et al., 2015 (doi: 10.1371/journal.pone.0142994).

In summary, the squidpop consists of a standard prey item: a small piece of dried squid mantle tissue, tethered to a fiberglass plant stake with light monofilament fishing line. The squidpop is assembled by first punching a 1.3-centimeter (cm) diameter disc from the squid mantle using a cork borer. A length of monofilament line is threaded through the squid disc and tied to it securely, then the other end of the line is attached to the end of the plant stake with electrical tape, leaving 1-2 cm of line with the squid piece on the end. The short length of the line helps prevent tangling the tethers when squidpops are bundled together.

Squidpops are deployed by pushing the stakes securely into the substratum. The stakes are typically arranged in one or two rows, but the spatial arrangement is of secondary importance to ensuring that the squidpops can be reliably relocated and retrieved at the end of the deployment. Squidpops are assessed for the presence or absence of the squid bait after some period of time.

Sedgewick Rafter Counting Chambers are transparent slides widely water analysis, culture inspection, and for other applications where particles per unit volume in fluid must be determined. The slide has a base that is ruled in one-thousand 1-millimeter squares. When a liquid is held in the cell by a coverglass, the grid subdivides 1 milliliter of liquid into 1 microliter volume.

An instrument designed for the analysis of dissolved inorganic carbon in samples from various aquatic environments. It comprises of a laser-based CO2 detector (LI-7815), a digital syringe pump, a mass flow controller, CO2 stripping reactor, an electronic cooling system and a computer communication assembly (RS-485, USB). The AS-C6L supersedes the earlier AS-C3 model, which used non-dispersive infra-red CO2 detection (LI-7000, discontinued). The AS-C6L improves on the AS-C3 by incorporating a multi-sampler of one set of standards plus 8 samples, and uses improved Apollo SciTech software. The AS-C6L is suitable for use in either shipboard or land-based laboratories. It maintains a precision of +/-0.1 % for seawater (or +/-2 umol/kg), enables sample volumes ranging from 0.5 - 3.5 ml per analysis, and an analytical rate of approximately 3 minutes.

A benthic lander is an autonom­ous re­search plat­form used in mar­ine re­search to take meas­ure­ments dir­ectly on the sea­floor. Benthic landers are car­rier sys­tems to which dif­fer­ent meas­ur­ing and sampling devices can be at­tached. They trans­port these devices to the sea­floor and back up again. Autonom­ous means that the lander is not con­nec­ted to the ship via a cable. It can thus work in­de­pend­ently on the sea­floor for a long period of time.

Automated trace element sampler (MITESS or ATE unit).

Bell, J., J. Betts, and E. Boyle (2002) MITESS: A Moored In-situ Trace Element Serial Sampler for Deep-Sea Moorings, Deep-Sea Research I: 49:2103-2118 (pdf)

More description: http://boyle.mit.edu/~ed/MITESS/MITESShomepage.html

A manufactured device which is used to remove contaminants from water impeding the flow of particles or solutes. 

A platform used to carry equipment and samples from the surface to the seafloor and back up again. 

The UH remotely operated vehicle (ROV) Lu'ukai is a small work-class ROV that can be operated from the R/V Kilo Moana to conduct investigations in waters up to 6,000 meters deep. After beginning operations in early 2018, the Lu'ukai has supported a study of deep-sea biodiversity and ecological processes in the western Clarion-Clipperton Zone, an area where numerous manganese nodule mining exploration claims are located; has maintained and upgraded sensors at the ALOHA Cabled Observatory, the world's deepest operating ocean observatory; and has recovered a failed telecommunications cable used to support acoustic research in local waters.

An apparatus for counting and sizing particles suspended in electrolytes. It is used for cells, bacteria, prokaryotic cells and virus particles. A typical Coulter counter has one or more microchannels that separate two chambers containing electrolyte solutions.

from https://en.wikipedia.org/wiki/Coulter_counter

A seine net is a very long net, with or without a bag in the centre, which is set either from the shore or from a boat for surrounding a certain area and is operated with two (long) ropes fixed to its ends (for hauling and herding the fish).

Seine nets are operated both in inland and in marine waters. The surrounded and catching area depends on the length of the seine and of the hauling lines.

(definition from: fao.org)

Photon counting is a technique in which individual photons are counted using some single-photon detector (SPD). 

An automated analyzer designed for a wide range of sequencing and fragment analysis applications with the ability to perform comparative sequencing, linkage analysis, STR analysis, SNP detection, discovery and validation, mutation detection, and many other applications.

ROV Ventana is operated by the Monterey Bay Aquarium Research Institute (MBARI). ROV Ventana comes with two manipulators as standard equipment: a Schilling T4, seven-function spatially correspondent arm, and a seven-function Schilling/Oceaneering Atlas Hybrid (rate and spacially correspondent.) Both manipulators can use a variety of end effectors. The ROV has forward-looking camera systems mounted on pan-and-tilt units. The vehicle also has a hydraulic swing arm that deploys from the port side.

Ventana is equipped with a Sea-Bird 19plus V2 CTD package which includes a dissolved oxygen sensor and a transmissometer. Three spatial lasers are mounted on the main camera for quantitative calculations.

For a full description, see https://www.mbari.org/at-sea/vehicles/remotely-operated-vehicles/rov-ventana/.

The Raman microscope is a laser-based microscopic device used to perform Raman spectroscopy. The Raman microscope begins with a standard optical microscope, and adds an excitation laser, laser rejection filters, a spectrometer or monochromator, and an optical sensitive detector such as a charge-coupled device (CCD), or photomultiplier tube, (PMT). One example is the XploRA confocal Raman microscope (information from the manufacturer).

An apparatus composed of two vertically oriented, coaxial cylinders separated by a gap that contains seawater. During operation, the outer cylinder rotates at a prescribed speed causing relative motion between the cylinders and thereby shearing the seawater between them.

A metal detector is an electronic instrument that detects the presence of metal nearby. Metal detectors are useful for finding metal inclusions hidden within objects, or metal objects buried underground. They often consist of a handheld unit with a sensor probe which can be swept over the ground or other objects.

Human Occupied Vehicle (HOV) Alvin is part of the National Deep Submergence Facility (NDSF). Alvin enables in-situ data collection and observation by two scientists to depths reaching 6,500 meters, during dives lasting up to ten hours.

Commissioned in 1964 as one of the world’s first deep-ocean submersibles, Alvin has remained state-of-the-art as a result of numerous overhauls and upgrades made over its lifetime. The most recent upgrades, begun in 2011 and completed in 2021, saw the installation of a new, larger personnel sphere with a more ergonomic interior; improved visibility and overlapping fields of view; longer bottoms times; new lighting and high-definition imaging systems; improved sensors, data acquisition and download speed.  It also doubled the science basket payload, and improved the command-and-control system allowing greater speed, range and maneuverability.

With seven reversible thrusters, it can hover in the water, maneuver over rugged topography, or rest on the sea floor.  It can collect data throughout the water column, produce a variety of maps and perform photographic surveys.  Alvin also has two robotic arms that can manipulate instruments, obtain samples, and its basket can be reconfigured daily based on the needs of the upcoming dive.

Alvin's depth rating of 6,500m gives researchers in-person access to 99% of the ocean floor.  Alvin is a proven and reliable platform capable of diving for up to 30 days in a row before requiring a single scheduled maintenance day.  Recent collaborations with autonomous vehicles such as Sentry have proven extremely beneficial, allowing PIs to visit promising sites to collect samples and data in person within hours of their being discovered, and UNOLs driven technological advances have improved the ability for scientific outreach and collaboration via telepresence

Alvin is named for Allyn Vine, a WHOI engineer and geophysicist who helped pioneer deep submergence research and technology.

(from https://www.whoi.edu/what-we-do/explore/underwater-vehicles/hov-alvin/, accessed 2022-09-09)

A device that isolates a portion of seabed plus overlying water from its surroundings. Either returns the entire system to the surface or incorporates sampling devices and/or in-situ sensors.

Tilt current meters are based upon the property that a tethered object will experience drag inside a current flow. If a restoring force perpendicular to the drag is introduced, the tethered object will tilt until the system of forces is balanced. Therefore, measuring the tilt allows calculation of drag force, from which current speed can be obtained. Measuring the direction of tilt gives current heading.

Tilt current meters operate under the drag-tilt principle and are designed to either float or sink depending on the type. A floating tilt current meter typically consists of a sub-surface buoyant housing that is anchored to the sea floor with a flexible line or tether. A sinking tilt current is similar, but the housing is designed such that the meter hangs from the attachment point. In either case, the housing tilts as a function of its shape, buoyancy (negative or positive) and the water velocity. Once the characteristics of a housing is known, the velocity can be determined by measuring the angle of the housing and direction of tilt.

The Qiagen TissueLyser II is a tissue processor designed to disrupt biological samples through high-speed shaking in plastic tubes with stainless steel, tungsten carbide, or glass beads. It is used for high-throughput disruption of human, animal, and plant tissues, bacteria, and yeast to access biological information for genomics, transcriptomics, and proteomics applications. It automates the purification of DNA, RNA, and protein from 1 to 96 samples. Disruption and homogenization are achieved through the beating and grinding effect of beads on the sample material as they are shaken together in the grinding vessels. Using the appropriate adapter set, up to 48 or 192 samples can be processed at the same time. Alternatively, a grinding jar set can be used to process large samples. A range of beads, bead dispensers, and collection microtubes and caps are also available. It can be programmed to provide variable speeds from 3 to 30 Hz (180-1800 oscillations per minute) and run times from 10 seconds to 99 minutes.

ROV SuBastian is operated from the research vessel Falkor and the R/V Falkor(too). The ROV is outfitted with a suite of sensors and scientific equipment to support scientific data and sample collection, as well as interactive research, experimentation, and technology development. More information available at https://schmidtocean.org/technology/robotic-platforms/4500-m-remotely-operated-vehicle-rov/

This equipment removes dissolved gases from the water samples, traps the extracted compounds on a cold trap and then heats the trap and injects the trapped gases into the gas chromatograph. It is automated and controlled by a laptop computer.

Digestion instrument for UV photolysis of water samples

An epibenthic sled is a semi-quantitative bottom-sampling device designed to trawl just above the bottom at the sediment water interface (the epibenthic zone). The sled consists of a rectangular steel frame with a mesh net (often more than one) attached to it. Towed along the ocean floor, its weight scrapes into the benthos, collecting any organisms on the surface or in the first few centimeters of sediment. It also collects the organisms in the water column just above the benthos.

Descriptions from WHOI and Census of Marine Life.

Hydrolab DataSonde Multiparameter Probes have sensors for temperature, conductivity, salinity, specific conductance, TDS, pH, ORP, dissolved oxygen, turbidity, chlorophyll a, blue-green algae, Rhodamine WT, ammonium, nitrate, chloride, ambient light (PAR), and total dissolved gas.

Instrument that measures forces such as dynamic and quasistatic tensile and compression forces.  Units commonly as Newtons (N).

A chamber specifically designed for the growth of algae in flasks. The chamber typically provides controlled temperature, humidity, and light conditions.

A Soxhlet extractor is a piece of laboratory apparatus designed for the extraction of a lipid from a solid material. The solid is placed in a filter paper thimble which is then placed into the main chamber of the Soxhlet extractor. The solvent (heated to reflux) travels into the main chamber and the partially soluble components are slowly transferred to the solvent.

Instruments that measure the proportion of the sky covered by cloud (cloud amount) and/or the height of the cloud above the ground (cloud base). Also called ceilometers.

Natural or artificial materials deployed in a marine or artificial environment for a given period to act as standardised, passive settlement sampling devices (e.g. settlement plates). They are used to determine the extent of colonization and/or the diversity of settled organisms.

An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).

Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.

The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications.

Examples include Tekran Models 2600 and 2700 

An optode or optrode is an optical sensor device that optically measures a specific substance usually with the aid of a chemical transducer.

An underwater device that collects animals and other samples under gentle suction and deposits them into a collection chamber.  Also known as an oceanographic 'slurp' sampler.  The primary components are an electrical or hydraulic pump, outlet hose connected to collection chamber, and inlet hose. 

A dissolved oxygen sensor which provides analogue (0-5V) and digital output (RS-232) to third party data loggers, gliders and floats. Measurement based on the ability of selected substances to act as dynamic fluorescence quenchers. The fluorescent indicator is a special platinum porphyrin complex embedded in a gas permeable foil that is exposed to the surrounding water. In this standard model, a black optical isolation coating protects the complex from sunlight and fluorescent particles in the water. This sensing foil is attached to a window providing optical access for the measuring system from inside a watertight housing. The foil is excited by modulated blue light, and the phase of a returned red light is measured. For improved stability the 4831 optode also performs areference phase reading by use of a red LED that does not produce fluorescence in the foil. This model is fitted with a standard sensing foil. By linearizing and temperature compensating, with an incorporated temperature sensor, the absolute O2 concentration can be determined. Accuracy +/- 1.5% or 2uM; precision +/- 0.2 uM.

The Aanderaa Recording Current Meter (RCM) is a self-contained instrument that can be moored in the sea and record ocean current, water temperature, conductivity of the water and depth of the instrument. This instrument designation is used when specific make and model are not known. (more from Aanderaa).

The Autonomous Behaving Lagrangian Explorer (ABLE), designed by Tom Wolcott, is a biomimetic robotic drifter that senses in situ environmental stimuli (e.g., variations in PAR, pressure, salinity, or temperature) and can be programmed to respond to these cues with vertical migration behavior like that of the planktonic organism of interest.

An instrument that determines the numbers, types or viability of cells present in a sample.

ADV is the acronym for acoustic doppler velocimeter. The ADV is a remote-sensing, three-dimensional velocity sensor. Its operation is based on the Doppler shift effect. The sensor can be deployed either as a moored instrument or attached to a still structure near the seabed.

Reference:
G. Voulgaris and J. H. Trowbridge, 1998. Evaluation of the Acoustic Doppler Velocimeter (ADV) for Turbulence Measurements. J. Atmos. Oceanic Technol., 15, 272–289. doi: http://dx.doi.org/10.1175/1520-0426(1998)015<0272:EOTADV>2.0.CO;2

A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.

A single channel, networked, gas chromatograph that separates and analyses compounds into separate components and can be used for chemical, petrochemical and petroleum analyses. The sample is introduced into the injector and then vaporised in the instrument. A chemically inert gas (e.g. helium and nitrogen) carries the vaporised solute into the column that is maintained in a temperature controlled oven. As the solute elutes from the column, it enters the heated detector. An electronic signal is generated upon interaction of the solute with the detector. The Agilent 6850 has a similar performance to the Agilent 6890N GC, but is half as wide. The local interface provides run control and status information and the instrument comes network-ready with a built-in LAN communications interface. There is a choice of detectors available, the Flame Ionization Detector (FID), Thermal Conductivity Detector (TCD) or Mass Selective Detector (MSD). There is an option of split/splitless or packed inlets, a variety of automated sample introduction systems and products available for headspace analysis. This model is no longer in production.

 Device for spraying liquid by means of compressed air.

Measures air temperature

WET Labs’ Aquatic Laser Fluorescence Analyzer (ALFA) provides spectrally and
temporally resolved measurements of key bio-environmental variables in oceanic,
coastal, and fresh waters. Operation modes allow underway shipboard measurements
and discrete sample analysis for accurate assessments of pigment biomass,
phytoplankton community structure and physiology.
 
Features
• Spectral deconvolution of overlapped fluorescence bands with Raman normalization
• Improved assessment of chlorophyll concentrations for estimating phytoplankton biomass
• Discrimination of 5 phycobiliprotein pigments for structural phytoplankton characterization
• Fluorescence assessment of chromophoric dissolved organic matter (CDOM)
• Measures variable fluorescence, Fv/Fm, with correction for background CDOM fluorescence
• Instrument software allows real-time data analysis and display with GPS coordinates and time

more information from Wet Labs