Optodes are really cool

Summer’s been exceptionally hot and steamy in Ithaca, which means it’s been a fantastic time to be in the lab with good air conditioning. Our aquarium room is currently at 70oF (tracking Cape Cod water temperatures) – which is a great escape! For the last week, Jay and Ian have been hard at work in the lab progressing on two separate (but perhaps inter-related) projects. You’d never guess that it was summer on Cornell’s campus (normally super quiet) – the place is incredibly busy!!

Jay’s been hard at work extracting RNA and applying our RT-LAMP protocol to detect aiFVs in sea cucumber tissues collected by Kyle Hebert in Ketchikan last month. This is a new approach for our lab, and we’re using it as a ‘first cut’ screening tool to detect tissue samples positive for the virus(es). To date he’s detected 18 samples which have at least some reactivity to the assay – equating to around 6% of all samples tested, which is not unexpected. Following positive detection by RT-LAMP, we’ve tried a qRT-PCR approach for quantitative analysis of their viral load in tissues, but this has proven problematic (twice). While normally qRT-PCR is fairly straightforward, for whatever reason aiFVs aren’t at all – we’ve seen interesting things with the standards and while positive controls come up, samples come up well after standards… so we’re not sure what to make of it. Hence, we’ve turned back to conventional PCR to try and amplify aiFV nonstructural gene 5, for which we’ve had some limited success. We should know in the next couple of weeks what the diversity of aiFVs in these samples looks like.

Meanwhile, Jordan spent last week in the West Falmouth Harbor working with Bob Howarth’s group collecting samples for his microbiome work. On that note, the seagrass cores he collected in early June are still thriving in the lab! This bodes well since it will allow him the opportunity to perform experiments in our aquarium system well after the end of the ‘field season’, and test hypotheses relating to copiotroph proliferation and sulfide oxidation.

Seagrasses in the aquarium room looking pretty good!

Ian’s also been working on optimizing the ‘optode’ which is a thin film of polystyrene that changes color when oxygen is absent (or more correctly the plastic fluorescence is quenched by oxygen). It’s turning up with some very cool results (see below). The hope is to deploy this against sea cucumbers, seagrasses (and maybe sea stars too!) to measure how oxygen concentrations change atop surfaces when enriched with organic matter. Already we’ve seen some cool results – oxygen definitely depletes within hours around seagrass leaves even when they’re under grow lights… and on OM enrichment this magnifies the boundary layers.

Progression of hypoxia above sediments under organic matter enrichment. The three panels on the right illustrate oxygen concentration where blue and green = anoxic (no oxygen) conditions. See how this increases over time?

So onto the second half of summer!

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