Harnessing synthetic biology to enhance ocean health

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Glossary

Amnesic shellfish poisoning (ASP)

an illness in humans caused by domoic acid exposure through ingestion of contaminated seafood that causes excitotoxic brain damage and organ failure in mammals, including humans.

Biodegradable plastics

plastics that can be broken down by the action of living organisms, usually microbes, producing biomass, water, and carbon dioxide as products.

Biotransformation

the biological conversion of an organic chemical or contaminant into a metabolite that can be utilized by natural metabolic processes.

Chaperones

a functional category of proteins or protein complexes that assist in a cell’s protein folding functions.

Coral bleaching

a process in which the coral–algal symbiosis collapses, resulting in expulsion of the algae from the coral host. The corals become energy starved and are at risk of death. The bleaching effect is due to the loss of the algae, which provides the color to many coral species.

CRISPR-Cas nucleic acid sensors

biosensors that use CRISPR enzymes to recognize nucleic acid sequences and produce an output signal. The enzymes currently in use include Cas12a for dsDNA detection and Cas13a for RNA detection.

Directed evolution

an optimization method in which variations of a biomolecule of interest are generated and subjected to a selection scheme. Desired ‘improved’ variants are selected and then used to seed subsequent cycles of variant generation and selection. In this way, a path can be traced along the fitness landscape to obtain optimized versions of the parent molecule.

Domoic acid (DA)

a small-molecule neurotoxin produced by some species of algae, most notably Pseudo-nitzschia australis and Chondria armata. It enters the food chain through contaminated shellfish and small fish that feed off the algae and bioaccumulates in higher trophic levels.

Ecoengineering

the bioengineering of ecosystems, with the goal of maintaining or restoring the health of a niche or general biome.

Eutrophication

an influx of nutrients and/or minerals into a body of water which affects the natural ecosystem. Usually caused by sewage discharge, industrial waste dumping, or fertilizer runoff from farms.

Guide RNA (gRNA)

a synthetically derived RNA that binds to a CRISPR enzyme to program its sequence specificity.

Harmful algal bloom (HAB)

an explosive overgrowth of unicellular algae populations in a localized area, caused by favorable nutrient conditions, warm waters, and certain weather conditions. The resulting bloom and decomposition of dying algae cause hypoxic zones, which can kill fish and other organisms in the area.

Heat shock proteins (HSP)

a highly conserved family of chaperone proteins that have evolved to play key roles in maintaining proper protein folding.

Holobiont

an ecological unit composed of the entire aggregate network of an organism, including the host and any mutualistic partners, colonizing protists, microbes, fungi, or viruses.

Microbiota

the contingent of microorganisms that colonize a host organism and may consist of bacteria, archaebacteria, fungi, and viruses.

Microplastics

fragments of plastic waste less than 5 mm in size. Microplastics can readily contaminate food chains and permeate throughout the ecosystem.

PET

polyethylene terephthalate, colloquially known as polyester. PET is one of the most widely used plastics in the world and is highly recyclable.

PETase

an esterase class of enzymes that efficiently catalyze the hydrolysis of polyethylene terephthalate (PET) plastics to monomeric mono-2-hydroxyethyl terephthalate (MHET).

Plastics

synthetic polymers typically made from petroleum-based compounds.

Polymers

natural or synthetic substances consisting of very large molecules, composed of many repeating subunits.

SHERLOCK

specific high-sensitivity enzymatic reporter un-locking, a CRISPR-Cas diagnostic platform that uses a gRNA-programmable CRISPR nuclease and a nucleic-acid probe reporter to detect RNA or DNA sequences with high sensitivity and specificity.

Thermotolerance

the ability of an organism to survive changes in temperature.

Upwelling

an oceanic phenomena whereby nutrient-rich deeper and colder water rises to the ocean surface to replace warmer surface waters.

Zooxanthellae algae

unicellular photosynthetic dinoflagellates known to serve as endosymbionts to a wide range of marine invertebrate organisms.

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