Bioluminescence, pictures, Science

Nagoya Aquarium – Bioluminescent Species

I was only able to find two bioluminescent species at the Nagoya Aquarium. Unfortunately I wasn’t able to observe their bioluminescence, but take a look!

One was the Pinecone fish, also known as the knight fish.  This Japanese species has two small black spots underneath its chin that bioluminesce at night.  The reason for their bioluminescence is still not understood.

Another was the sea pen.  The bioluminescence of this species is dazzling, I saw it once in person after-hours at the Uozu Aquarium in Toyama. When disturbed, the cnidarians withdraw into their coral, and then a green sparkling sweeping light covers the sea pen.  It reminded me of the Eiffel Tower at midnight.

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Bioluminescence, pictures, Science

Sea Creatures of Uozu Aquarium – 1 – Pandalid Shrimp

I recently visited the Uozu Aquarium in Toyama while searching for the Japanese Fireworms in Toyama Bay. The aquarium staff were extremely helpful and hospitable, and our laboratory group had the chance to spend three leisurely hours exploring the aquarium.  I was able to take a lot of videos, so I plan on posting one per day here with short descriptions.

Day 1 – A Pandalid Shrimp

I’m not sure what this species is, but it is a pandalid shrimp – a species that is probably edible! These shrimps are found in cold waters, and aside from being delicious, are economically important.  Most pandalid shrimp start their lives as males, then become females later in life – a life strategy not uncommon in the ocean. Most species live between 3-5 years and can lay thousands of eggs in one season. Fried or fertilized?

Many Heterocarpus shrimp (a genus of pandalids) use bioluminescence to defend themselves by ejecting a blue glowing cloud into the surrounding water when disturbed.  This blue cloud gives the shrimps a chance to escape, like a squid’s ink cloud.

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pictures, Science

Traveling for research.

I am fortunate in that my laboratory takes trips fairly regularly to collect bioluminescent specimens for research. Recently I traveled to Toyama to gather a rare luminous worm that only appears swimming on the ocean surface for three or four days per year.

We were also able to take home luminous mushrooms, two fish specimens with bioluminescent spots, and bioluminescent earthworms that we found outside of an aquarium building.

Fecaloma of what we believe to be a bioluminescent worm.

Fecaloma of what we believe to be a bioluminescent worm. Basically it’s a giant pile of above-ground worm poop.

After sampling for specimens, we sampled the local cuisine, namely their famous sashimi and other fruits de mer, including a local delicacy: the firefly squid.

Firefly squid nicely packaged and dried for consumption.

Firefly squid nicely packaged and dried for consumption.

Currently I am in Okinawa for five days for an insect genome conference and to collect luminous fireflies, millipedes, centipedes, fishes, and snails.

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Blog, pictures, Science

Okinawa Day 1 – Fireflies and Glowing Mushrooms.

Today I left for the Ryukyu islands to attend an insect genome conference and collect specimens. Most people are familiar with Okinawa, which is actually the main island of what was once the Ryukyu Kingdom, independent of Japan.  Excluding hundreds of years of history, The Ryukyu Islands and Okinawa are known today for their (sadly) dying language, interesting music, lion-dog statues everywhere, and unique food. Let’s not forget the tragedy of the Battle of Okinawa during World War II.

I first landed on the main island of Okinawa, but soon flew to the site of the conference, Kume Island. We were greeted by a bus schedule with an Okinawa-dialect ”めんそ〜れ〜,” (men-so-rayyy) which seems to be a mix between “Welcome” and “Hello.”

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The island itself seemed fairly small, so we were looking forward to traveling around the forests in the mountains  for specimens.

Map of Kume Island.

Map of Kume Island.

After unloading our things at the hotel, we headed to the beach to search for bioluminescent worms that live in the sand.  We didn’t have any luck, but the view was certainly nice. This is A-ra beach on Kume island, there’s a nice mountain to the left.

The sand on the beach was made from crushed coral.  You can even see the coral reefs from the shore.

Large bits of coral on the beach.

Large bits of coral on the beach.

There were big chunks of coral lying about. Hopefully these weren’t victims of coral bleaching.

Sad coral.

Sad coral.

Due to some rain, we weren’t able to sample until late at night, but we had quite a catch! We were searching for firefly larvae, and were very successful. One interesting specimen we found, but left alone, was this larva hanging upside down from a twig grasped onto a snail.  Many firefly larvae eat snails, and some are very picky – they only eat one species of snail! Firefly larvae usually live very close to water, both for breeding purposes (some spend their larval stage in water), and for finding food. Maybe all fireflies are French – you know, the whole “escargot” thing.

Here’s a shot of the fluorescent banding on the same specimen.  This photo was illuminated with UV light. Many bioluminescent creatures have chemical compounds in their bodies that glow brightly (usually green!) when they are exposed to UV light. This is the same phenomenon, fluorescence, that occurs when you shine a black light onto highlighters, white t-shirts, and your dad’s groovy pink floyd posters from the 70s.

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We found another species. This guy was a fatty! His light was so bright that it shone through someone’s breastpocket, illuminating most of their shirt. What species could it be?! We’ll find out soon enough after we do some DNA barcoding experiments!

でっかい - HUGE

でっかい – HUGE

I took a short video of some of the firefly larvae scooting around in case you’ve never found one in the wild. You can’t see it now since the lights are on, but their rears glow fairly brightly at regular intervals. It’s not a flash sort of glow, it’s more like a wave of light, fading in and out. _.,-~=^””””^=~-,._<–This is a graph of their luminescence.

Even more exciting for me were the glowing fungi and mushrooms we found. There are many bioluminescent species of fungi, many of which produce mushrooms that emit a continuous, fairly strong glow. It was my first time seeing it, so I was quite surprised at how bright it actually was. People aren’t really sure why mushrooms evolved the ability to glow, but some people think that it attracts insects to distribute their spores, and others think that it’s just a good way to get rid of dangerous chemicals that build up in the mushrooms while they’re glowing.

mushrooms

It’s pretty tough to take pictures of things that glow, I had to expose these photos for about 3 minutes to get them to be this visible. This is a great excuse to buy new camera equipment.

So you might be wondering why we’re bothering to study these glowing organisms. Simply put, by learning more about how these organisms glow, we can use their genes and proteins to make new discoveries in science and medicine. So far bioluminescent proteins have been used to monitor tumor growth, to detect food-borne illnesses on an industrial scale, and used in countless experiments  as a sensitive detector for chemicals and genes.

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Blog, Japanese, Science

Camaraderie in Japanese Laboratories.

Given the working schedule for natural science labs, there isn’t too much time for socialization outside of the lab. In short, being a member of a laboratory is akin to being a member of a Japanese “group,” or an intensive club that typically meets every day to play a sport, or partake in some other activity. “Groups” are defined by the close bond that members build over time, and by the strong senior-junior mentorships and social hierarchy that forms. This feeling is very apparent in the lab, whose members spent long hours in both exciting cooperative learning and in commiseration.

Me, ecstatic to receive a fossil from a labmate.

Me, ecstatic to receive a fossil from a labmate.

I was treated kindly by the other lab members from Day 1. Everyone has helped me at some point with finding an apartment, setting up internet, taking me to purchase a phone, et cetera. People have gone out of their way to help me when I really didn’t need so much help either – they simply wanted to make sure that things go smoothly.

One of my labmates studies bioluminescent fish. This is not a picture of my labmate, it is the Izu Scorpionfish. Scorpaena izensis. Unfortunately it is not bioluminescent.

One of my labmates studies bioluminescent fish. This is not a picture of my labmate, it is the Izu Scorpionfish. Scorpaena izensis. Unfortunately it is not bioluminescent.

Even more surprising, most members of the lab have gone out of their way to help without my request. For example, someone rode their bike for 1 hour to purchase a pair of waterproof boots after the professor stated I would need some for an upcoming trip. I can only hope to repay their kindness somehow someday.

Maybe I can repay them with the delicious bioluminescent squid, Watasenia scintillans. Also called the "firefly squid," they are eaten as a delicacy in Toyama Bay of Japan.

Maybe I can repay them with the delicious bioluminescent squid, Watasenia scintillans. Also called the “firefly squid,” they are eaten as a delicacy in Toyama Bay of Japan.

There are ample casual conversations that happen during the day during mealtimes and in between experiments that have been good opportunities to get to know the lab members on a more personal level. I was even invited to a party of other research students through one lab member. As far as socialization outside of the research circle and other scientists… well, there really isn’t that much. I attended a castle tour with other foreigners and English-speaking Japanese individuals, but mostly found myself interested in the one scientist I found who works on robotics, and the American JET teacher. Soon I hope to branch out and participate in more cultural activities.

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pictures, Science

Academic Life in Japan.

As my project is in the natural sciences, I am a member of a laboratory. More specifically, I am a member of a Japanese laboratory. The scientific culture here consistently seems to be defined by long working hours and a fervor for research that one rarely finds in American laboratories. With that being said, most of my time here has certainly been spent in the laboratory, working and socializing with other science students during mealtimes and tea breaks.

I study things that glow in the lab. Can you see the specimen at the bottom of the tube?

I study things that glow, or bioluminescent organisms. Can you see the specimen at the bottom of the tube?

Typical days in the laboratory begin with me arriving at 9AM to unlock the space, where I have a few minutes to work on readings or translations before we meet as a laboratory beginning around 9:30. The entire staff of scientists (graduate students and the professor) meets every day for some purpose. Many days we simply present recent results and discuss how we plan to move ahead. Once a week we each translate a paragraph of the textbook on bioluminescence into Japanese, and practice reading the sections in both Japanese and English. This practice has benefitted both my understanding of my project material as well as my language skills. Moreover, I am able to assist the other scientists with both English skills, and to verify that their translations are scientifically accurate. I’m not very familiar with Japanese language scientific writing yet, so I acquire much study material this way.

Recent Studies suggest that ghosts are not real.

Recent Studies suggest that ghosts are not real.

Recently I have been editing and co-authoring a book chapter with my advisor (in English), but I foresee beginning experiments soon. During the first week, I found myself working until 8-9PM without hesitation, so I have recently been leaving at 6PM in order to free up time for essential shopping, cultural activities, and exploration of Nagoya.

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