Final thoughts for future SSFer’s

All good things must come to an end, and with the changing weather comes an ebb and flow of students in the Woods Hole community. Unfortunately, I am in the former since I will be leaving Saturday morning. For the next round of summer student fellows, consider some practical tips for living at Woods Hole in the summer:

  • Program dates: most students arrive from mid May to mid June and leave sometimes in August. In terms of the pros and cons of arriving/leaving earlier vs later, I’ve found that arriving in the middle of the pack was fantastic because of it maximizes the amount of time spent with other SSFers. However, if I had to choose between arriving later or earlier, I’d choose later because of the availability of advice for living logistics/getting settled in your project from SSFers who have already been there for a few weeks. Having said that, it does get lonely towards the end of the summer when most cohorts start leaving/taking their end of August vacations
  • Living tips: try to share supplies with roomates. The end of the summer not only brings me sadness in the friends that I will miss, but also at the dramatic amount of food and household supplies that are wasted by merely 30 people. A little bit of planning can save quite a bit of money down the road
  • no worries about the lack of things to do in a small town. It never fails to amaze me how busy I’ve found myself with work and recreational activities, so much so that I haven’t even opened the GRE books that I lugged from Canada with high hopes of studying. I would suggest planning to take the GRE’s at another time rather than the summer, since the summer on the Cape is much more enjoyable outside or meeting the wonderful scientific community rather than reading GRE books
  • many bikes are bought and left neglected since there are so many short-term visiting students in the summer. Ask around before purchasing one at your own expense
  • do not be afraid to speak with other scientists about their research or offer to volunteer in other scientist’s labs to gain more experience. WHOI is a refreshingly welcoming place, and the scientists take time to speak to interested students about their research
  • take time to make friends in this area. In addition to beautiful sailing trips they can take you on, the people are very kind and offer a potentially lasting network should you decide to return
  • Travelling tip: consider avoiding purchasing a return ticket from Peter Pan (just the one-way from Boston is enough). i. you do not get much of a discount with a return purchase (I think one way is $32, while return is $56). ii. their customer service is terrible – you cannot return tickets, and could only exchange them for a fee. Tickets are also non-transferrable. iii. there are many people driving out of Woods Hole at the end of the summer and it is incredibly easy to arrange a ride, since the housing arrangement is somewhat flexible as well. Should I have known this, I would have saved a decent chunk of money that could have been spent towards other more justifiable purchases (such as spending time at the Kidd!)
Last sunset at OP!

My last sunset at Oyster Pond!

This was one of the most enriching experiences of my life. I’ve met a very diverse and intelligent bunch of scientists, fell in love with the community here, and found that this is a wonderful place to pursue graduate studies.

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!

Provincetown sunrise

The perfect sunrise finally happened for us in Provincetown, one of the easternmost points on the Cape that’s about an hour and a half away from Woods Hole. No words can describe this beauty: 20130804_05271120130804_052642 20130804_052911 20130804_0543012013-08-04 16.45.36It was low tide so my friend and I basked by the sailboats while waiting for the sunrise. All photos by Jack Hildick-Smith, a Cornell student who works at the Marine Biological Laboratory this summer and takes amazing panoramic shots.

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.

Casey and Mary Ann’s research

Mary Ann is a SSF from Ohio Wesleyan University, working with graduate student Casey this summer with advisor Dr. Aran Mooney in the Biology department. Their lab has a fantastic ocean acidification (OA) setup and are investigating how OA affects the development of squid paralarvae. Casey’s project entails subjecting the developing larvae to acidified conditions, then measuring several developmental and morphological traits to quantify the effects of OA on their development. Mary Ann is then looking at how their subsequent swimming behaviour may be influenced by these changes. Since I am interested in investigating transcriptomic responses to OA for a PhD and most likely will be using a similar OA setup, I was interested in how the Mooney lab’s setup looked like and Casey was kind enough to give me a tour of the lab.

Casey looking proudly onto his work baby, which he built from scratch

Casey looking proudly onto his work baby, which he built from scratch

Wild squid during spawning season (now) are caught and kept in tanks until they deposit the eggs mats, pictured here. The developing egg mats are kept in specific CO2 conditions using the setup

Wild squid during spawning season (now) are caught and kept in tanks until they deposit eggs mats, pictured here. The developing egg mats are kept in specific CO2 conditions using the setup

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Various CO2 concentrations are colour coded and delivered individually to the small holding tanks

CO2 tank and filters

CO2 tank and filters

Regulators, which control the concentration of CO2 through the mix of normal air with that from the CO2 tank

Regulators, which control the concentration of CO2 through the mix of normal air with that from the CO2 tank

The Mooney lab also does research in sensory ecology using cuttlefish, which are very interesting creatures that can change colours use their chromatophores

The Mooney lab also does research in sensory ecology using cuttlefish, which are very interesting creatures that can change colours using their chromatophores

Squid paralarvae under the dissecting microscope. You can see the small chromatophores as coloured dots, and the two stratoliths (calcified bones used for balance) as the white dots in the head region

Adorable squid paralarvae under the dissecting microscope. You can see the small chromatophores as coloured dots, and the two statoliths (calcified bones used for balance) as the white dots in the head region

Since the statolith is made from calcification (and may be hence impacted by OA), their size is one of the morphological traits Casey will be looking at. After Mary Ann’s swimming behaviour observations, Casey will be dissecting the larvae and taking measurements of the statolith to try to address weather a smaller, poorly developed statolith under OA may be correlated with abnormal swimming/balance in the larvae. Keep in mind that these larvae are about 2-3mm across, so dissecting them would definitely be an interesting endeavour. I will certainly try to drop by again one afternoon to witness it!

Katie Skinner’s research

Katie Skinner is a SSF from Princeton University working with Mike Purcell in the Applied Physics and Ocean Engineering department. Her project is to design a lightweight REMUS, which stands for remote environmental monitoring units. It is an autonomous underwater vehicle with a range of uses including ocean exploration, environmental monitoring, and scientific sampling. She is working with the REMUS 6000, which is a deep ocean vehicle that goes up to 6000 meters. It is autonomous and untethered, so missions are preprogrammed for the vehicle, which then follows these directions on its own.

the REMUS 6000

the REMUS 6000

Her main goal this summer is to extend the endurance of the REMUS 6000 to up to 36 hours, a 50% increase in endurance. This will allow the vehicle to carry out longer and more efficient missions to search over larger areas or collect more images or samples. The longer it can stay in the water, the fewer times it has to be recovered and relaunched to complete a given mission.

Solving this problem starts with reducing the weight of the vehicle. Once it weighs less, the syntactic foam that provides buoyancy can be cut back to decrease the diameter and size. Cutting back the foam we will reduce drag, leading to increased efficiency while maintaining stability, security, and control of the vehicle. To reduce the weight of different components of REMUS, she is working from a solidworks model to go through different parts of the whole assembly. Potential changes include looking for materials with a higher strength-to-weight ratio or higher buoyancy.  In addition, integrating more recent designs to some instruments (the original 6000 was designed about a decade ago) results in smaller instruments. Changing various sensor attachments and supports also cuts down on weight. With a smaller vehicle, some of these parts can be reduced. Overall, her project entails developing new technological methods for sampling and surveying, a frontier for oceanography.

July 4th festivities

Lots of red, white, and blue, as well as jokingly shouting “‘Murica!” abound yesterday as independence day was celebrated at Woods Hole. The day started off with a parade at noon, featuring many people dressed up in sea-related paraphernalia. Yay, science!

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Horseshoe crab!

Horseshoe crab!

I have no idea what this is supposed to be

I have no idea what this is supposed to be

Awesome street ink fight

Awesome street ink fight

It was amazing how crowded Woods Hole got (and now I finally understand the contrast between the “summer people” and “winter people”) on this day of festivities, and by the time fireworks rolled around, there was a ton of traffic and barely any spot on the beach. We didn’t feel like braving the traffic up to Falmouth, where the fireworks were, and decided on a spot just off Oyster Pond. Unfortunately, the weather has to be your friend here, and similar to the sunrise earlier, the sky was completely clear, except for just the area where the fireworks come out. We were reduced to fawning over misty splotches of colour behind the clouds. It was pretty, but I’d recommend spending the day in Falmouth instead and trying to watch it from there.

It's like the sky was mocking us. Maybe there are just permanent clouds over that area.

Deja vu. It’s like the sky was mocking us. Maybe there are just permanent clouds over that area.

OceanQuest cruise

One of my good friends from University of Toronto visited me this weekend. Since we didn’t want to infringe on WHOI residences’ no overnight guest policy, she found nice couchsurfing hosts from MBL to stay with. They were extremely engaging and kind; we met for pizza and chatted about things to do around Woods Hole such as scallopping later in the summer, bioluminescent dinoflagellate blooms, and the OceanQuest cruise, which one of them works for. The pier for the cruise is right across from the Marine Biological Laboratory campus near WHOI.

Being suckers for educational, touristy shenanigans, we immediately decided to try it out. For $25, you get an 1.5 hour cruise around WHOI and the Elizabeth Islands, which extend southwest from WHOI, and learn about the cool creatures around Woods Hole’s waters, as well as the geological history of the area. Although this cruise was tailored towards tourists and children, I was impressed with the scientific accuracy of the descriptions, and some of the animals were fantastic to play with!

They use lobster traps to catch these animals, keep them on board for a few days for educational purposes, then release them

They use lobster traps to catch these animals, keep them on board for a few days for educational purposes, then release them

Horseshoe crab - the coolest creatures!

Horseshoe crab – the coolest creatures! You can place them on your head for a head massage (I tried, but it wasn’t the most comfortable unfortunately)

Another crab that likes to live in rocks - you can see it would be very well camouflaged

Another crab that likes to live in rocks – you can see it would be very well camouflaged

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!