A Conference in Jeju - Part Deux

Not long after we arrived in Jeju, our professors decided that the conference seminars were not that important and we would instead go sightseeing around the island. I did get an inkling that it was a foregone conclusion before we even left Seoul, but to ponder such matters is not very useful. Jeju is one of the highlights of Korea and well worth the short flight from Seoul.


First up on the agenda was horse riding. I once rode a horse at Wirrina Cove in Australia, which was a rather mediocre affair. Our horse riding in Jeju started off in the same way, but then the horse-guy came up and slapped our horse's rumps with a stick. The instant reaction was for the horse to increase speed, not quite to a gallup, but to a 'heightened state of urgency'.

It was a little bit scary and a little bit difficult to walk afterwards.


Because horses are herbivores, their eyes are spaced widely on their head. This helps them spot approaching predators more easily, but at the expense of being able to see straight ahead. If you think about lions and tigers on the other hand, they have their eyes positioned straight forwards, which helps them chase a target.



I've always thought of horses as rather gracious animals. These ones were funny though. An ajumma came out with a box of carrots and all of the horses instantly came wandering up like little kids looking for candy.
I learned from a documentary once that horses communicate extensively with body language. Which, incidentally, is something they have in common with sharks.


Then we arrived by coach bus at this idyllic looking beach. It's on the south coast of the island somewhere, but I can't remember the name. There are quite a few nice beaches around the island.


Here's Professor Moon's lab from Daejeon. Behind them is a wind farm. I like the idea of wind energy, but apparently one of their drawbacks is that they chop up bats who fly through them at night.

Echolocation can only give you so much information.


Tide pools usually contain an interesting array of life. Being sheltered from the drag of the waves helps small communities of life establish themselves. This tide pool only had a couple of snails in it, probably because investigative children had plucked everything else out already. If you tried to raise anemones or other pool life in a salty aquarium, you'd have problems though. That's because tide pools are constantly cleaned and refreshed with new food every time the tide comes in.


And speaking of nourishment, this is what we had for lunch that day. It's abalone porridge or jeonbok juk. Wikipedia just told me that the colour is green because it's cooked with the abalone's digestive organs.

Well, it tasted better than it looks.


Next on the conference agenda was a ride in a jet boat. I believe the purpose was to get first hand knowledge of wave function dynamics on an extensively hydrated surface. Which, I might add, is abstractly related to our studies in molecular biology.


It was a lot faster than expected, reaching speeds of probably 70 km/hr. The driver did a few roundabout spins in the water to make sure we were all sufficiently drenched. That made my studies on wave dynamics particularly difficult.



The jet boat ride is on the south side of the island and lasts for about twenty minutes. Also available is a ride in a small submersible which can take you under the water.


The final destination was Sangumburi, which is a volcanic crater that exploded upon eruption many eons ago. The remaining geological feature is like a miniature Wilpena Pound, and only takes about 30 minutes to make it to the top. The cliffs on the far side drop directly into the ocean.


Our professor was once a student at Berkeley, where he was also the number 2 tennis player. He's smiling in this photo because he appreciates geological artefacts that have weathered the storms of a millenia.


And here's me with Seung-Mo and Sang-Min from Daejeon. Sang-Min in particular has the worst command of the English language, but we get along like a house on fire. In Korean, he often says "Lee ootgyoyo", which means "Lee is funny."


Here's the view from the top. The mound in the far distance is a parasitic cone that originated from Mount Halla. There are around 360 of them scattered across the island.


Us four guys had to share the same room in the boarding house that we stayed at, which was roughly 3 X 3 metres square. On the first day Sang-Min happily announced to us "I snore every night."


And here are the biotech ladies of the future. Biotechnology has its pros and cons, but in the far distant future humans will probably colonise Mars. And that would be greatly accelerated with biotechnology if we want to sustain a population there. In the photo above are possibly the early pioneers of the field.

How's that for a thought?


And this is me and Mi-Ok at the top of the crater. Mi-Ok is the kind of person who will talk to you cheerfully even if you spend the whole day frowning at her.


Remember Se-Kyung taking a photo of herself in the last blog post? Well I managed to see her preparing herself for another one, so I snuck in at the last minute. Her reaction upon review was well worth the effort.


And on the end of the last night, we all had some drinks at a local bar. In the photo above is our professor defeating Seung-Mo in an arm wrestle. Although our professor is quite strong, theoretically in Korean culture no one would really try and beat him anyway.

So that's all for this post. Jeju is quite different to the rest of Korea and something to think about if you've been on the mainland for too long. And if you can go there on a business trip or a conference, all the more power to you.

See you soon!

2009 KSPP Fall Meeting, 1st Japan-Korea Joint Symposium

The highlight of grad student life, apart from graduation, is when you get to go to a conference. The idea of a conference is to present your work and see what others have been up to. Although the tangible benefits of conferences are difficult to measure, to even question whether they are worthwhile or not is taboo. The reasons are threefold, (1) It's an excuse to travel (2) It's paid for by your academic institution and (3) There's drinking involved.


The first conference I ever went to was to Ballarat in Australia, which was pretty good. Recently I went to my second conference here in Korea, for the 2009 Korean Society of Plant Pathologists fall meeting, and the 1st symposium between Japan and Korea. We went to Kimpo airport in the morning and teamed up with our lab colleagues from Daejeon and Sejong University.


One of the things Se-Kyung likes to do, constantly, is take photos of herself on her camera phone. It's quite common in Korea, for girls especially. I do find the behaviour somewhat curious, but it seems to keep them happy.


And this is Se-Kyung's reaction when she realises I've been documenting her unusual behaviour.


This is me, wandering around the poster displays with my complimentary symposium paraphenalia. The conference was held on Jeju Island, which is Korea's version of Australia's Tasmania.
Or America's Hawaii.
Scientists will create posters for displaying their unpublished work at meetings. Usually they're crammed with details and a lot of effort is put into their creation. And then when they're on display, people just wander past them, and you might be lucky to have one or two people who are remotely interested.


I made an effort to network, but it's pretty difficult when most people are working on things that you don't know much about. The sciences in general become very specific to the point where only people in a very narrow field will be able to understand your particular project in any detail. I met a virologist from Tokyo University and we struck up a conversation. But it's hard to keep the ball rolling when you get a sentence like "Yeah, I've been studying post-transcriptional gene silencing in TBSV for 7 years now."

The correct response to that sentence, which I appropriately gave, was "Really?"


Here's our professor eating with Professor Moon from Daejeon. The predominating topics of conversation between two such quirky intellectuals range from future project funding to the work of colleagues who I've never heard of.

Not that I would think of eavesdropping on two academics in the midst of feeding.


And this is my plate. The problem with buffets is that because they have everything to choose from, you never know what to choose.


We regularly woke up at 6am, which professors seem to be fond of. It had been a while since I saw the sun come up.


Here are the combined lab groups of SNU, Daejeon and Sejong University at the base of Mount Halla. We all get along pretty well, although our work is only loosely related.


We climbed Mt Halla, the tallest mountain in South Korea, which ended up taking us around 7 hours for the round trip. In the photo above is Jae-Eun on the left and Professor Jwa on the right. They're from Sejong University and I go to their lab every once in a while to use their microscopy equipment. Their lab group is one of my favourites because they're friendly and helpful.


This is Eun-Hye. She exercises in the gym regularly during the week, so when we go hiking she's usually walking up in front somewhere.
Back when I was in the Scouts, we used to designate a 'Tail-End Charlie', whose job it was to walk slowest and make sure no one gets left behind. So as long as you could see the Tail-End Charlie, you knew that everyone was still close by.


Mount Halla is a massive shield volcano that erupted thousands of years ago. The hike up to the top is worthwhile, but it will take you a day to complete and probably 2 days to recover from the ordeal. The mountain is a cultural icon and a popular tourist destination so the local council have been constructing walkways that make the climb a little easier.


I carried up four litres of water, due in no small part to my hiking experiences in Australia. But the weather was freezing cold and I ended up bringing 3 litres back down with me.

Better safe than sorry, as my old man used to say.


What do you do when you get to the top of a mountain? Look around for 2 minutes and then take a group photo.

The foremost reason being so that you can have fun in the lab later, tagging everyone on Facebook.


Here's Eun-Hye, Se-Kyung and me. In the lab they often talk to me in Korean, a little too fast. I'm lazy with languages, so often I can't keep up with what they're saying. When I don't concentrate properly, they sound to me like clucking chickens.


We all brought up a dosirak (Korean lunchbox). It had a whole fish in it, and some dried squid and other unidentifiable things. When you've been walking for so long, you lose the motivation to question otherwise questionable food.

Which reminds me of an old Indian proverb "To the man who hasn't eaten in three days, the only god is bread."


My friend Hong is getting into photography these days, which reminded me of the times when I used to be a bit of an amateur photographer as well. To get some nice photos, you just have to be in the right place at the right time. Tree branches against the sky always work pretty well. I like the way they appear as some kind of distorted organic fractal pattern.

Fractals occur when you have simple repeating patterns, which can actually be expressed as a maths formula. The reason we see them in nature is because crystal lattices, snowflakes and even DNA are bound at a very fundamental level by simple mathematical rules. At the heart of all applied sciences is the most purest form of logic, which is mathematics.


Sang-Min from Daejeon was also keen to be involved in photography. He wanted to pose on this rock, so I told him to point at the sky to add a dramatic atmosphere.

Didn't really turn out the way I expected though.


And this is a bear next to a slippery dip. Nothing unusual here.

Moving along.


That night we went fishing. Fishing is one of my official hobbies, although I've only been about three times in my life. One day, when I have time, I think I'll buy a nice little boat and go fishing on Sundays. In the photo above is Yun-Seong, from Sejong University. He's a nice guy and we once ate barbecued intestines together.

Anyway, Part II of our conference in Jeju coming soon!

GFP Biolistics Bombardment, Onion Epidermal Peel

Although laboratory work comprises about 80% of my waking life, only a small proportion seems to be making it onto this blog. The main reason for that is because lab work is not very interesting to most people, so I try to keep the focus more on life in Korea.
But I found out through my over-performing Sitemeter that some readers are starting to find this blog through science related searches. Often times I'll try looking for a protocol on Google, and the only results that come through are too technical to be useful.


To that end, I've decided to occasionally put some of our lab work up here, in the hopes that some of it will be useful to a perplexed undergrad student somewhere.
The protocol that we're going through today is GFP biolistics bombardment (only the machine part). A protocol is the science name for the 'recipe' of an experiment, and GFP is a fluorescent protein (think of deep-sea jellyfish or glowsticks). Biolistics involves coating gold or tungsten bullets with modified DNA and literally shooting it into the heart of a living cell. It was pretty revolutionary a few years ago, but has since been eclipsed by Agrobacterium-mediated transformation. In the photo above, Chen-Jing is peeling onions, in preparation for the experiment.


But first, let's have a look at this list they've posted up at the biolistics lab at Sejong University. I'd say it pretty much sums up the working conditions of Korean graduate students.

Except that we normally work longer than that.


This is what bacteria looks like when you grow it in a test tube. Bacteria are obviously too small to see, but the liquid they're in will turn cloudy when there's enough of them. In a typical inoculation, a few hundred cells will multiply into billions in just 16 hours. So imagine a classroom of kids multiplying into the population of the world overnight.


This is the biolistics machine. It's basically a crude particle accelerator that uses helium gas to propel the charge downwards. Make sure you've opened the main tank valve and connected the vacuum pump securely. The device is remarkably simple to use, but don't operate it by yourself the first time.


The first thing you need to do is unscrew the large metal nozzle in the chamber. Use tweezers to transfer a sterilised rupture disk into it and make sure it sits flat. The purpose of the rupture disk is to hold back the air pressure to a specific point, like 1000 psi, after which it will burst and fire the charge. You can change the specific pressure by changing the value of the disk.

But why do you need to change the pressure? It's because some plants have thicker skins than others, and you have to make sure you get the pellets inside the cell.


Then you take out the tray that normally sits directly under the rupture disk. Take it apart and put a gauze mat in it. This protects your sample from getting obliterated by the macrocarriers.


Next, put your macrocarrier holder facing downwards onto the circular top of the tray. The macrocarrier holder is the brown plastic circle that has your dried DNA on it. Prior to this, you need to have coated the metal pellets with your DNA and dried it with ethanol. The black spot in the middle is the tungsten residue.


Then you screw the metal clasp on top. It should all fit together very simply, like a Meccano set.


Put the tray into the chamber and get your sample ready. The best thing to use for GFP is onion cells, because they're big and clear so you can see them easily under the microscope. Unfortunately though, they don't have chloroplasts (green things responsible for photosynthesis), which means you can't really extrapolate the results to situations in leaves. They also have rather large vacuoles (empty spaces) right in the middle of each cell, so you need to be careful when you interpret your photos. But anyway, they're a good starting point.

You need to peel the slivers of onion skin that come from the middle of the onion when you cut it. An onion is just layers of bulbs, like Russian dolls, all layered on top of each other. Take the bulb in the middle that is around half the circumference of the entire onion and you'll find it has a thin skin sheath around it (like all of them). Cut a little square out of that and put it on 0.5% Murashige and Skoog media.


Okay, so now you put the sample underneath the firing apparatus. Remember to take the lid off the plate.


Close the door tightly. Hold the middle vacuum switch down until you can see the pressure gauge reach 27. When this happens, quickly switch it over to 'Vent', and the value should stay constant. Then hold down the 'Fire' button until the secondary pressure gauge (the one on top of the vacuum chamber) reaches around 1000 psi. You keep holding it until you here a popping sound, which is the sound of the rupture disk breaching.


Release the button, remove the plate from the chamber and wrap it in aluminium foil. Store overnight for around 12 hours, in the dark at 28 degrees C. The next day, prepare microscope slides and dye stains of your samples.


And this is what you'll see in the microscope the next day if you've done everything right. Dazzling, bright and beautiful. Make sure you have the right filter set on, and you shouldn't have to search very far. Real GFP fluorescence jumps out at you in a very conspicuous way. If you find yourself squinting at a faint blur and wondering if it's a real signal or not, you might need to adjust your incubation time or plasmid concentration.


My first picture was nice and bright, but it was too intense to be useful. After a bit of fine tuning I ended up getting this photo above, which shows some nicer details of the onion cells. The green blobs are localisation positions of my fusion protein, and the blue colour is DAPI staining, which highlights the nucleus.
So basically, what you're seeing is the DNA of a glowing jellyfish protein, fused to a bacterial protein, that was then shot into an onion cell which managed to translate it. It's the convergence of three kingdoms of nature, brought together through biotechnology. Cool, hey?

If you're having trouble with your protocol, send me an email and some of your photos and I'll try and help you out.

That's all for me this time. Happy bombarding everybody!

Another Year and What We're Eating

The new year came and went without much ado. I heard a guy on TV recently say "On New Year's Eve, no one really knows what to do apart from stay up late." And for our case at least, I'd have to agree. Heather and I felt like doing something special, but it was really cold and we had to wake up early. So we were fast asleep by 11:30pm, which was the first time I'd slept through the countdown in probably 20 years.

Is this the dawn of our middle-age?


Lotteria is Korea and Japan's version of McDonald's. I don't eat much fast food in general, but the odd McDonald's breakfast sometimes works its way into a late night out. Fast food in Australia is relatively cheap, but in Korea it's more expensive than kimbap cheonguk. So I'll usually go for the healthier option.
It would be nice to say that Lotteria is better than McDonald's, but that would be false. Lotteria doesn't put a lot of effort into making its food palatable, and comes up with all sorts of intriguing burger non-ideas. I tried their old 'Australian Burger' once, which had harder bread (supposedly resembling damper) and their 'Tropical Burger', which had a sad looking slice of tinned pineapple on an otherwise even-less-exciting meat patty. Now, to celebrate their 30 years of unremarkableness, they've released a Meat and Shrimp burger. That's what happens when you try to reconcile the overwhelming output from a hamburger company's creativity department. I believe it is colloquially known as the Shreat burger.

Or was it Mrimp?


Heather seems to be enjoying her time off. Most days I have to eat near the lab, but on weekends we usually get a couple of good meals together. I cooked that beef thingy in the middle, which was a 2 hour stew.

Wasn't too bad.


International food companies have long known that people's tastes are regional. That's why Vegemite doesn't sell in Korea (although now that I think about it, it probably would), and why Yoplait have successfully released this pumpkin yoghurt here.
Now, the funny thing isn't that they sell pumpkin yoghurt, it's that Heather bought it without batting an eyelid and still can't fathom why anyone would find it peculiar.


Every once in a while our professor likes to take us out to eat somewhere flash. As you can see from the photo, Se-Kyung becomes particularly excitable when such moments occur.


We had a buffet at the Ritz-Carlton that night. When I was younger I always saw a buffet as a challenge to eat more in value than the price you pay. Now a much wiser and indigestion-wary variant of myself approaches buffets with due caution.


That's me on the left and our professor on the right. He happens to be very good at science and knows a lot about bacterial genetics.

But I'm probably better at Starcraft.


The guy sitting in the middle is Dr Jin-Woo Kim, who recently came back from the US. He's a graduate from our lab and has been doing a post-doc at Indiana University.


And here are the girls of the plant bacteriology lab, Se-Kyung, Chen Jing and Eun-Hye. Grad students in general are pretty strange people, but I would have to say that the girls in our lab resemble normal humans more than the boys do.


Seoul National University has its pros and cons. It seems to be half-heartedly making progress away from endemic traditionalism and looking toward a more creative future. In global rankings like the Times Higher Education Supplement, it tends to lose points due to a shortage of international students and faculty. As the only Western student in the department, my suggestion for improvement would be to discourage the enormous socially-preserved gap between the status of the professors and those of the students. Professors deserve respect, but to the point where the students are discouraged from speaking their mind is a little contrary to the spirit of education.


But as long as they give us free food, we'll stay happy for a while at least. Recently, our department decided to acknowledge its foreign constituents with a dinner for all of the international students. I don't know what prompted it, but it was a nice gesture and duly appreciated.


And here's a breakfast that I cooked for wifey and me. Breakfast was one of the first things I learned how to cook, because my parents used to like breakfast-in-bed. The second thing I learned was how to make instant noodles. When we were young, my sister and I were addicted to Maggi 2-minute noodles. They were the highlight of our weekends.

Well it's back to lab work for me now. Blogging seems like a good way to take my mind off things. See you soon!