Week 3 in the Harvey Lab- Phytos go M.I.A. during a P.I.A.

Back in Georgia, Week 3 was off to a great start. The phytoplankton culture looked strong, there were fresh crudes to test in my phytoplankton inhibition assay (PIA) like the one above, and we had a solid game of pickup soccer among the lab members.

But by Wednesday, the abundance of phytoplankton in my PIA was dropping across the board. This is not the type of cell death I am looking for, because even the phytos who hadn’t been treated with possibly algicidal crude extracts were disappearing.

Then I remembered what a helpful lab technician had told me about my phyto culture.

—-“They typically don’t like this kind of bottle, and the cap was on a little too tight,” she said as she showed me her beakers of phytoplankton strains, which were covered in loose-fitting aluminum foil.—-

Even though they appeared to be doing OK, I was suffocating my phytoplankton!! Just like land plants, my phytos can’t grow without CO2, and these stressed out cells were not reproducing as they normally do, which is about doubling daily.

The only way to rescue them was to…well, I couldn’t really rescue them because the experiment was flawed…so I poured the remaining ones into a container of 10% bleach labeled “Unhappy Phytos” and restarted the experiment with a new strain borrowed from the technician.

The experiment is now back on track, and the only consequence is having to come into the lab a few times on the weekend. Luckily my barracks is only 200 yards from the lab.

Week 2 in the Harvey Lab- Dilutions off Bermuda

It’s 2:45 am. I’m 80 kilometers off the coast of Bermuda. I’ve been awake for close to 20 hours. I’ve eaten at least 10 cookies and muffins from the galley. And I’ve watched 180 minutes of Season 6 of Game of Thrones, a show I’ve never seen before so I have no idea what’s going on, to pass the nighttime before 3 am.

“It’s up!” I hear from down the main passageway. Now’s my time to shine.

I trudge out on the deck, zip up a lifevest, twist on a hard hat, and grab some rope. My first job is to retrieve the ship’s yellow-framed CTD, a pretty darn cool instrument that measures conductivity, temperature and depth of the ocean water.

“Hold the rope farther from the cleat,” the marine technician on the other rope warns me. “They look innocent, but I knew a guy who lost a hand doin’ what you’re doin’.” Enough said; I took three healthy steps back from the cleat.

We lowered the CTD down snug onto it’s landing pad and I started filtering water from its ring of grey Niskin bottles. Dr. Harvey’s experiments need someone to take saltwater samples every six hours, so they can be diluted and measured for grazing of phytoplankton. Since I’m more of a night person than a morning person at sea, I have the 3 am shift, and Dr. Harvey has the 9 am.

It was a whirlwind research cruise. Not a lot of sleep, but a lot of good samples and a lot of fun! The rest I’ll leave to the pictures:

There was safety (first as always)…

There were sunsets…

There were colleages/friends/jokesters…

There was a sloth…

And at the end of it all, the were two delicious chickens (not pictured) inside a pig (pictured)…

Thank you to the crew of the R/V Atlantic Explorer!

Week 1 in the Harvey Lab- On and Over the Atlantic

My first week stationed at the Skidaway Institute of Oceaniography (SkIO), affiliated with the University of Georgia, was an exciting one!

Nothing beats waking up and running some fresh new experiments on phytoplankton. Within just three days of testing, I determined which fractions of my crude bacterial extracts were algicidal, because the phytoplankton populations plummeted when treated with these compounds.

This new intel was sent straight back to Haverford, where more fractionation will help us crack the phytoplankton-killing code.

In the meantime, my SkIO advisor, Dr. Liz Harvey, and I prepared for a four-day cruise in the North Atlantic off the coast of Bermuda! Dr. Harvey has been wanting to study the night-day differences, or “diel” variation, in rates of phytoplankton grazing, that is, other microorganisms eating phytoplankton. And I have the privilege of helping her on the voyage, which will take us to the Bermuda Atlantic Time Series (BATS)!


I volunteered to model proper immersion-suit entry. Immersion-suits are often called “Gumby Suits.” Can you see why?

We arrived at the Bermuda Institute of Ocean Sciences on Thursday, met with our colleagues from Oregon, Virginia, California, and Bermuda, and gathered materials like deionized water and 10-liter carboys for taking samples.

When the ship, the R/V Atlantic Explorer, is fully loaded and the tide is right, we will set sail on Saturday!

Week 4 in the Whalen Lab- Boom goes the [calcium] dynamite



Experimenting with ionomycin is about as close as one can get to playing with explosives in microbiology. And the Forth of July may be next week, but Mia and I saw a few fireworks this week when we triggered calcium release in our phytoplankton cells using this chemical trigger, or “agonist”. The algicidal compound of our research focus also caused some calcium release, but it didn’t deliver the same kind of boom we saw in our positive control. Here is how it all happened:

1. We stained our cells with a dye that becomes fluorescent in the presence of calcium ions.

2. We anchored our cells to a microscope cover slip so they wouldn’t move.

2. We flushed dilutions of ionomycin and our algicidal compound over the cells.

3. We used a microscope camera and its software to measure their change in fluorescence intensity.

4. We took our data into an Excel spreadsheet and saw that when we added these compounds, the cellular calcium went BOOM!

It wasn’t always easy to do these four steps smoothly; actually, we had plenty of not-so-shining moments and went through our share of duds. On some days, the cells seemed to be playing hide and seek with us, and when we did find them in a good cluster, they were often fluorescing too dimly to measure. We also ended up having a love-hate relationship with the microscope-camera-software conglomerate. Yes we needed it for data, but on more than one occasion (15 is more that one, right?), the cells and “junk” and everything would disappear from view completely. It was the dreaded “Diver Error”, and the only way we found to consistently fix this problem was to shut down the whole conglomerate, precisely in reverse order mind you, and then restart it again in reverse-reverse order.

As a result, I sometimes wake up in the night because I think there’s a “Driver Error” in my room but I turn on the light and it’s just…! No, that doesn’t happen but it was really annoying. And in all honesty, I’m not sure I would have held it together through this full week of microscopy without a lab partner toughing it out with me.

But I’ll have to leave Mia and the rest of the Whalen Lab behind as I ride the rails down the East Coast to Savannah, Georgia, where I’ll begin “Part 2” of my campaign at the Skidaway Institute of Oceanography.

Image result for Skidaway institute of oceanographyThis new post is pretty out there^, but I’ve been there once before and know where not to go to avoid the gators.

Goodbye Haverford until the Fall; new correspondence will come from the Harvey Lab!