Category Archives: Research/the Daily Grind

R/V Tioga

The Summer Student Fellowship program includes a day trip on the research vessel Tioga to show us various sampling techniques used in oceanography. The day trip starts out at 8:30am and sailed out westward to Buzzard’s Bay. Many students had a chance to have a hands-on experience on using one the sampling equipments.

Using a probe to measure water temperature, salinity, and dissolved oxygen.

Using a probe to measure water temperature, salinity, and dissolved oxygen

Looking cheeky as the probe descends

Looking happy as the probe descends

Using a claw-like apparatus to sample sediments

Using a claw-like apparatus to sample sediments

The sediments collected were clay-based and described as "very good for your skin"

The sediments collected were clay-based and described as “very good for your skin”

fellow SSF Vincent obviously took that above comment to heart as he examines the critters under the microscope

Fellow SSF Vincent obviously took that above comment to heart as he examines the critters under the microscope

Tubeworm that was extracted from the mud

Tubeworm that was extracted from the mud

It usually hides its soft, fragile body within this hard casing

It usually protecs its soft, fragile body within this hard casing, but we took it out for examination

Other cool critters

Other cool critters

Using a net to catch ctenophores, a jellyfish-like bioluminescent cnidarian

Using a net to catch ctenophores, a bioluminescent, jellyfish-like creature that glow up when you accidentally bump into them during night swims

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Ctenophores are very cute but definitely prettier at night when they bioluminesce when you accidentally bump into one. Since they are so abundant, the crew encouraged us to taste them and they tasted exactly like one would expect - a bag of salty seawater. Guess these guys are pretty good at keeping equilibrium with the seawater to minimize the energetic costs of osmosis

Cute ctenophores. Since they are so abundant, the crew encouraged us to taste them and they tasted exactly like one would expect – a bag of salty seawater. Perhaps these guys are pretty good at keeping equilibrium with the seawater to minimize the energetic costs of osmosis?

Our final activity was learning how to navigate by measuring angles of three landmarks. This gave us three lines on this map that located us to the area where they crossed. The GPS (star) confirmed that we were right on!

Our final activity was learning how to navigate by measuring angles of three landmarks. This gave us three lines on this map that located us to the area where they crossed. The GPS (star) confirmed that we were right on!

Out and about and having a grand old time

Out and about and having a grand old time

Overall, it was a beautiful day spent with a wonderful crew!

MBL open house

The MBL (Marine Biological Laboratory) celebrates its 125th anniversary today. The MBL is another marine sciences institution situated in Woods Hole and everyone in the village was invited to join the festivities.

2013-07-17 17.00.45 2013-07-17 17.00.53 2013-07-17 17.01.03 2013-07-17 17.04.18 In addition to the festivities, Dr. Osamu Shimomura, Nobel Prize Laureate and discoverer of green fluorescent protein, gave a talk on his scientific career. He was incredibly humble and said that he wanted to study bioluminescent jellyfish simply because it was “cool”, and I couldn’t agree more. They’re awesome (and ctenophores are so fun to poke around because they bioluminesce more when disturbed – an hypothesized antipredatory response).

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Experimental crunch time

Since our experiments are highly dependent on when spawns of larvae are ready, once they were finally developed, we visited Martha’s Vineyard shellfish group to pick them up. I’ve never been to Martha’s Vineyard (MV for short) and was extremely excited at the prospect of getting on the ferry, especially since I hear MV was simply a more touristy version of Woods Hole and wouldn’t have went out of my way to visit there otherwise.

Martha's Vineyard ferry (Steamship Authority)

Martha’s Vineyard ferry (Steamship Authority)

Yup, looks like Woods Hole

Yup, looks like Woods Hole

Algae grown at the hatchery, which we took some with us to feed the oyster larvae

Algae grown at the hatchery; we took some with us for feeding the oyster larvae

After getting the larvae, which were collected on 200um filters so we have a lower size limit, we check for their competency to settle by looking for eyespots (which develop in late-stage larvae).

Can you see the eyespots?

Can you see the eyespots?

Since these larvae are already competent to settle, our experiments are extremely time-sensitive. We have to transfer them into bleached culture buckets, set up the airstone system, feed them, and start the experiment as soon as possible. We typically have 2-3 days after larval acquisition to perform the experiments, and multiple people in the lab take shifts to realize the continuous stint of data collection in these 2-3 days.

One million larvae transported on filter paper

One million larvae transported on filter paper

Jeanette and I adding larvae into the tank prior to experimental data collection. The camera is to the left of the tank and the laser is calibrated to the right. Photo by Tom Kleindinst

Jeanette and I adding larvae into the tank prior to experimental data collection. The camera is to the left of the tank and the laser is calibrated to the right. Photo by Tom Kleindinst

Safety first! This caution light always have to be on outside of our environmental chamber when the laser is turned on for data collection

Safety first! This caution light always have to be on outside of our environmental chamber when the laser is turned on for data collection

These laser goggles look pretty badass, no?

Don’t these laser goggles look pretty badass?

I have to admit that it was a tiring three days, but Lauren, our advisor, was super supportive, took quite a few shifts herself, and was kind enough to bring us food and munchkins (did you know that this was the “Timbits” of the US? so cute!). Additionally, after some level of sleep deprivation, random things become hilarious, so we had a pretty great time derping around the lab while waiting for the data to finish downloading after each collection (each dataset contains several gigabytes of images). Overall, the experiments went very well and we’ve successfully collected enough data to work on through the next few months.

Developing a project

When I first spoke to Lauren regarding project ideas, I was given two choices of current projects to work on: larval settlement behaviour in turbulence (focused on Matlab analyses) or on deep-sea hydrothermal vent larvae identification (focused on microscopy). Being a sucker for statistics and data analyses, I naturally picked the former. Additionally, the lab’s work using particle image velocimetry (PIV) is a relatively new method of quantifying larval behaviour, and I wanted to gain some exposure to a new field since I’ve already done some larval identification work for a previous field course.

PIV. The vectors between the two annuli in bold are used to calculate local flow (Wheeler et al., 2013)

PIV. The vectors between the two annuli, in bold, are used to calculate local flow (Wheeler et al., 2013)

Larvae of benthic organisms, such as those of our study organism the eastern oyster (C. virginica), may adopt sensitivity to specific settlement cues for habitat optimization (there may be strong selection against those who don’t, who may then likely settle in unfortunate places such as the open ocean). Benthic regions such as oyster reefs are characterized by turbulent conditions, and it has been speculated that oyster larvae may use turbulence as a settlement cue. There has been mixed results in whether turbulence does induce settlement, and controversy over the possible confounding effects of artificial particles used in PIV (since an effective control, without particles, does not exist in these experiments since one cannot calculate relative larval velocity to the same degree of accuracy without them).

My project attempts to address 1. whether particles indeed affect the larvae (done by comparing the relative observed larval abundance and absolute verticle velocities in water seeded with algae and with particles); 2. whether turbulence affects the frequency of larval helical swimming behaviour (done by programming a script that can identify helical tracts); 3. how turbulence can affect phototaxis (done by the addition of light in turbulence experiments, which are typically done in the dark).

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Experimental tank setup that we will be using for turbulence experiments. The two grids stir the tank at various frequencies to emulate different turbulence levels (Wheeler et al., 2013)

The experimental work, which will commence once the hatcheries have larvae available in mid-July, is done in a separate wet lab, the Shore lab. Although we will be using another tank set-up for the experiment (above), Jeanette Wheeler (a third-year graduate student) is piloting a new flume tank set-up, and we had a chance to poke around some of the setup there last week:

Dangerous Class IV laser

Class IV laser used to light the field of view

Larval injector (from which the larvae can enter the water column) with the camera setup. Since this tank is much bigger than the typical experimental tank, it is more budget-friendly to inject the larvae upstream of the camera field, rather than distribute them randomly throughout the tank

Larval injector (from which the larvae can enter the water column) with the camera setup. Since this tank is much bigger than the older experimental tank, it is more budget-friendly to inject the larvae upstream of the camera field of view, rather than distribute them randomly throughout the tank

Visualizing turbulence characteristics as the water flows around the injector (to emulate what the larvae would feel) using fluorescein

Visualizing turbulence characteristics as the water flows around the injector (to emulate what the larvae would face) using fluorescein

Flourescein is pretty cool

Flourescein is pretty cool

As fun as Matlab is (<- I’m actually being completely serious), I’m definitely looking forward to the experimental work in mid-July. I wonder if I can raise baby oysters in a tank/watch them under a dissecting microscope when we’re done using them? One can certainly hope!

Meeting James Cameron

An email was sent to the SSFers earlier this week, something about greeting the Deepsea Challenger and James Cameron at the WHOI dock yesterday. My head must have been so far up in my Matlab script, because it took a Google search to realize that the director of Terminator, Titanic, and Avatar, along with the first single-manned submersible vehicle to explore the deepest parts of Mariana Trench, was going to be here!

It was clearly marked with a banner, in case you confused it with something else...

It was clearly marked with a banner, in case you confused it with something else…

James Cameron stayed inside that tiny white ball for the entire duration of the 9 to 12-hour dives

James Cameron stayed inside that tiny white ball for the entire duration of the 9 to 12-hour dives

Inside the white ball

Inside the white ball

The team

The team

WHOI represent!

I don’t think it’s physically possible to have more WHOI paraphernalia in this photo

The event started off with speeches from Susan Avery, the Director of WHOI, James Cameron, a tour of the Deepsea Challenger, and finished off with a question period. After that, I knew what the big deal was about: he is one of three people to have actually seen the deepest bottom of the ocean floor, an area apparently the size of North America, and he is donating the vehicle that he did it in to WHOI. The press bulwarked our attempts to interact with him, but I was lucky enough to shake his hand (!), get a question in, and thanks to the help of Susan, get a photo of this momentous occasion:

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SSFers with Susan Avery and James Cameron

It is refreshing to see such a famous director, who is capable of reaching so many people, share his passion for oceanography and become involved with the scientific community WHOI. His speech focused around the importance of promoting curiosity and educating the next generation about the importance of scientific discovery. As he says, perhaps when we empower the voters with knowledge, funding and support for the sciences will follow.  As an aspiring oceanographer, I definitely hope that it will, and his speech has further encouraged me to continue my involvement in departmental and outreach activities. For now though, let me just revel at how awesome he is, and how lucky we were to be able to be here.

Update: a fellow SSFer Camille just informed me that she’s on the news release video, and another, Claire, was in the article. Yay!

Dogs in the lab

Look who came up to greet me yesterday morning!

It's the dog from "Up"!

It’s the dog from “Up”!

Try concentration on work with this guy at your feet

Try concentrating on work with this guy at your feet

Pretty much sums up Roscoe’s style

What a delightful way to start a otherwise bleak Friday morning (full with a tropical storm warning). Lauren brings Roscoe in on rainy days when she takes the car, so it’s either the sun or the dog. Win-win.

Matlab

Matlab is apparently a very popular software amongst oceanographers at WHOI (especially since they have paid for its license) and many of us SSFers are starting to learn to navigate around it. The platform appears to be much more user-friendly than R and I’m happy about this opportunity to learn such an awesome program. I found this extremely helpful tutorial today that gives a great overview of how the workspace is set up.