FLIP the Ship!

OFFICE OF NAVAL RESEARCH/CC BY 2.0

"Why is that picture hanging sideways? Oh, wait a minute..."

On June 1st, I was invited to tour the RP FLIP, a famous ship part of the Scripps Institution of Oceanography fleet. The FLIP ship is an oceanographic research vessel with a long, weighted "tail" that is designed to keep the ship steady when rotated vertically by 90 degrees. By not succumbing to wave movements in the open ocean, the FLIP allows researchers to accurately measure wave height, along with other things like ocean conditions and acoustics.

The "tail" section of the FLIP is more than 90 meters long and stabilizes the research platform when rotated 90 degrees into the water.

The FLIP is a one-of-a-kind vertical research platform, but the inside is even more of anomaly. The bathroom has 2 sinks, 2 toilets, and two shower heads--each pair with one that appears to be normally placed and the other at a 90 degree angle next to it. This is so the bathroom can function normally once the vessel completes its 90 degree "flip" in the open ocean. The beds and shelves are able to rotate with the boat so that nothing falls during the flip, and other items, such as chairs are tied to the ceiling so they can be accessed once flipping is complete.

The condiment shelf is able to rotate with the FLIP's 90 degree upright rotation

Chairs are secured to the ceiling with a desk that is secured to the post-flip floor.

During the 20-minute vertical rotation, researchers and crew must hold on to a bar with one foot in position for when the flip completes. The flip is slow, and at the last second jerks upright, so it is a relatively safe process. 

Researchers and crew must hold on to this support with leg in-place during the 20-minute flipping process.

Once the flip is complete, the vessel stays in place until it is ready to flip back and be tugged somewhere else. During this time, however, the sun bakes the barnacles stuck to the hull and the smell of decaying sea critters floods the living quarters, making a difficult environment to work in.

Although extreme, the FLIP is an iconic vessel, and it was such a privilege to explore it. Thank you for a FLIPping great tour!!

A successful hike to the end of the FLIP ship's 90-meter "tail" with the body of the vessel in the background. Thank you for a FLIPping great tour!

Orange Bloom

Bioluminescent algae light-up the waves at La Jolla Shores.
Image courtesy of John H. Moore at The San Diego Union-Tribune. 

"Bioluminescence tonight!" read the email sent over the Scripps list-serve. A group of scientists carefully monitoring the water off of the pier at the Scripps Institution of Oceanography in La Jolla had picked up signals of a bioluminescent bloom to occur later that week.

Bioluminescence is a sort of light given-off by certain organisms. In the ocean, and particularly that week at La Jolla Shores, red algae that glows when disturbed can cause grandiose displays of blue light when their population numbers are high. This is sometimes called a "Red Tide" and can be extremely toxic depending on the species of algae present. 

Beyond the blue, I saw this bloom as an opportunity to try to culture some cool bacterial species from the algae-infested waters. So, when my professor invited me on a bioluminescent night swim with the rest of the lab, I tucked a few Falcon tubes into my dive glove to take some water samples with while swimming through the brilliant blue bloom. 

Upon return to the lab, I spread the samples onto different types of agar plates. Agar has the texture of stiff jelly and is what scientists put in Petri dishes to grow bacteria on in the lab. It contains most of the nutrients certain bacterial species need depending on their preferences. 

After waiting a few days, I noticed a neat little orange spot on one of my plates. It was a sort of iridescent, peachy color, so I isolated it onto a new plate. After the isolate grew up and I saw that it was free of contaminants, I was able to extract the 16S rRNA from the bacterial cells and sequence it.

After making more copies of the 16S rRNA with a technique called PCR, making sure I had bacterial 16S rRNA (instead of fungal) by running a bit of the sample through an agarose gel, and sending the RNA to a sequencing lab (science, science, science), I was able to identify the species name of my mystery bacteria. 

This is an agarose gel that I ran for one of my previous sequencing experiments. The column with many bands on the right is a "ladder". Each band in the ladder represents a different length of base pairs, with the shortest strand at the bottom. The thick bands on the left of the ladder indicate the presence of 16S rRNA from bacteria!

Flammeovirga arenaria--the orange bacterial species I isolated--doesn't seem to have been studied much in the past. From Wikipedia, I know that it was originally isolated from Mexican sands, which leads me to believe it was independent from the bioluminescent bloom. Nevertheless, I still think the mystery work of solving an unknown bacteria's species name is one of the most satisfying tasks in the world!

I always wonder what more there is to find and learn about these small but tenacious organisms. With so little studied on this particular species of bacteria, I wonder what brought it all the way to La Jolla, and what other mysteries its genome could reveal about its function. 

There's always more to discover!

Marine Bacteria Encapsulation--Success!

After months of work and lots failures and successes, my encapsulation technique for marine bacteria finally worked! As mentioned in a previous post, I have been volunteering at the Bradley S. Moore Lab at the Scripps Institution of Oceanography since April 2018. After summer break, I began an independent project that I am still working on and will continue to explore throughout my senior year of college. In short, the lab's overall goal is to discover natural products from bacteria in the sea. Some of these bacteria reside in sponges, but their ability to grow in three-dimensional animals like the sponge makes it difficult to grow them on the flat surfaces or in liquid solutions we traditionally use to grow bacteria in lab.

Because we need to be able to grow bacteria to find and use the chemicals they produce for medicinal purposes, I have been working on a new technique for growing space-dependent bacteria in the laboratory. This technique includes encapsulating bacteria in micro-orbs made of a sugar and chitosan. Encapsulation can be compared to putting bacteria into a jelly-like substance and enclosing the "jelly" in a casing. In the past, I was successful in growing terrestrial bacteria with this technique, but ran into problems when I switched to growing marine bacteria.

Capsules under a microscope.

The issue with the capsules with marine bacteria and in seawater depended on a few things. First, I noticed the marine bacteria were dying once encapsulated. After a bit of thinking and trial-and-error, my mentor and I found that this was because the pH (or acidity) of the sugar I was using was too low. The pH of the ocean is about 8. The acidic nature of the sugar was killing the marine bacteria before they could even be encapsulated in chitosan. 

Second, marine bacteria are used to surviving in salty seawater, and the sugar did not contain salt. The osmotic imbalance of the cells and the sugar may have been popping the cells. We were able to adjust the balance of salt in the sugar mixture to match the balance of different salts commonly found in the ocean to make sure the bacteria were happy, healthy, and staying alive during encapsulation.

Known marine bacterial species, Shewanella japonica, is grown using encapsulation and popped on a plate for visual confirmation of the technique's validity.

Once we were able to make the proper pH and salt adjustments, marine bacteria were able to be encapsulated, grown, and cultured like the original terrestrial species! 

Now, I am experimenting with using the capsules to separate a mixture of many types of bacteria. Stay tuned for more updates to come!

                                                    -Em