Friday, December 26, 2008

Last post of 2008

This Christmas week I've done my best to keep from missing folks back home but have not been too successful. On Monday, Jenny, Spike, and I did the Cadbury's/Speight's tour double. The Dunedin Cadbury's factory occupies a city block just east of the Octagon and on weekdays delivers chocolatey aromas to homes and businesses nearby. The 45 minute tour was much less informative than I was expecting, but we did learn that chocolate was first eaten by the Aztecs in Mexico and that there are three varieties of chocolate: milk, dark, and white (which contains cocoa butter but no cocoa solids so isn't real chocolate). After the tour guide told us a little about the history and production of chocolate, she took us into a purple silo and up a circular staircase where a ton of liquid chocolate was dumped 10 meters or so and then pumped up to the top of the tower for the next tour group. I was very angry the tour guide did not tell us what was going to happen because I would have at least stuck out my nalgene into the chocolate waterfall. We didn't see any of the real factory whatsoever. At the gift shop I bought several chocolate bars including one called Energy Scroggin with nuts and fruits in it that is not sold outside New Zealand.

We next walked to the Speight's Brewery and while we waited for the tour to begin, filled our water bottles with spring water from a tap coming out the side of the building. This water used to make the beer is free to the public, and hundreds of people fill jugs of it to take home each day. On the tour we learned that beer is somewhat older than chocolate, being first brewed by the ancient Egyptians around 6000 B.C. We learned that beer's ingredients are water, hops, barley, sugar, and yeast and got to see the giant copper vats where the mashed barley is boiled. In contrast to chocolate-making, brewing beer apparently produces some disagreeable odors, and the Dunedin girls high school uphill from Speight's has repeatedly written to the brewery asking them to do something about the smells, but Speight's has always replied that they were there first so deal with it. After being forced to sit through a horribly cheesy infomercial for Speight's, we were offered unlimited samples of half a dozen types of beer. I prefered the traditional "Gold Medal Ale" and the dark Porter. Everyone laughed when Spike turned beet red after drinking a single cup of booze.

On Christmas Eve Jenny rented a bicycle and we rode out on the peninsula. We attempted to visit Larnach Castle, the only castle in New Zealand, but were turned away by the high admission fee. That night we had a traditional Asian hot pot meal, a dramatic contrast from the usual shrimp and rolls we have back home on Christmas Eve. We found a large electric wok in the kitchen cupboard, boiled some water, and inserted various ingredients that Jenny had purchased from the Asian market, including taro (dense vegetable like cassava or yam), tofu, spinach, rice cakes, udon noodles, eggs, and corn. When one desired, one reached in with chopsticks and picked out some item and dipped it in a thick sauce Jenny had prepared from sesame paste, hoisin sauce, soy sauce, and chili. Soon enough we were joined by two curious surfer bums who have been staying in Carrington for over a week now. Orginally from England, they were living out of a van, traveling throughout New Zealand and Australia in search of the perfect wave but instead have happened across a girl they both fancy in the form of Kate. We also offer free showers, beds, and kitchen equipment, so it is unclear exactly how long they will stay.

Christmas Day I hiked up Mt. Cargill and took a side trip to the organ pipes, which are rather disappointing as rock formations but still feature a fantastic view of the surrounding countryside. I saw many other trampers, so hiking on Christmas must be quite popular with Kiwis. I managed a number of excellent bike rides this week as well, including one along the Pacific coast to the mouth of the Taieri River and another loop on the Taieri plain. I've done very little in the lab; part of me feels like this is okay since the whole department is dark and deserted, but my scholarly conscience has forced me nonetheless to print out and read several reviews on Alzheimer's.

Tomorrow I'm taking the bus to Queenstown where I'm meeting Peter Nunns, Williams '08. We'll be tramping the Rees and Dart track, which ordinarily takes five days, including a day trip to the Cascade Glacier. We may attempt to squeeze two days into one in order to be back in town for New Years festivities.

Saturday, December 20, 2008

Of fire, mountains, and nirvana

After last weekend's protein purification marathon, this week has been less labwork but no less busy. First a few photos from last Saturday's trek up the Mt. Cargill track.



Holiday parties of various kinds have occupied a large amount of my time the past several days. On Wednesday we had drinks and snacks at Carrington where I met a number of new summer students. Logan and Henry in particular were very welcoming and insisted that I come camping with them on a deserted beach a few hundred kilometers to the south. I said I would be "keen." I got the impression these Otago students really like to have fun, with alcohol taking center stage perhaps moreso than it does at Williams. The next evening we all went to dinner at one of the four Thai restaurants in town with the exact same menu but different names: Thai Hanoi, Thai Kar Tom, Thai Land (ha), and Thai Over (this evening's choice). Santa Claus arrived and dished out some $5 presents to folks who had brought something to exchange, and then we headed to someone's apartment and watched a fire poi shoe by Logan, who runs a pyrotechnics business called "Highly Flammable." He explained to me how fire breathing and fire eating work. In fire breathing, one spews refined jet fuel out of their mouth, like someone spitting out wine in the movies, while holding a match to it. In fire eating, one positions one's throat completely vertical such that the heat from the flame rises out of the mouth. Wet mucus lining the throat and mouth protects against burning in the short term. And to extinguish the flame, one closes one's mouth and the flame goes out immediately due to lack of oxygen. A couple photos from the show:
I'm hoping to buy a pair of poi myself (the glow kind to begin). After the fire show, we danced until 3 am at two clubs playing non-disco music, which was quite fun.

Friday was the Biochemistry Department Christmas social. The highlight was playing a game called "Heads or Tails" to win Cadbury's chocolate. The department chair and an assistant flipped two coins, and everyone in the group of sixty or seventy placed their hands either both on their head, both on their "tail," or one on each. If you guessed the flips, then you remained in the game, and the last one standing won. Of course the best strategy is to always put one hand on your head and one hand on your tail, since that gives you a 50% chance of being correct (heads tails or tails heads) while the other options give you only a 25% chance each. So every flip I used this strategy, but after several games I didn't win a thing, leaving me quite annoyed.

Today is Saturday and I just returned from another tramp on the Pineapple Track, my second journey there this week. This time around I was hiking with two Chinese, Jenny and Spike, who I had a great time with. As Jenny is Buddhist, I learned her views on reincarnation and karma and how the ultimate goal is to reach nirvana, which is a state of mind rather than a place. Since she believes that every living thing has a spirit living within it, she is vegetarian and does her best to minimize harm to all creatures; she walks around grass, for example, to avoid crushing insects (grass is too small a plant to harbor spirits, but other larger plants do contain them). Buddhism is a very flexible philosophy (and not a religion, per se); the important thing is to find one's own way. So there are Buddhists who don't believe in reincarnation or are not vegetarian. I told her that I would be very interested to read some books on Buddhism and she recommended one by an Australian author who writes on adapting the philosophy to everyday life.

At the top of Flagstaff Mountain we stood on top of a geodesic marker and snapped photos with my new waterproof and shockproof camera (to be seen next post). On the way down we played the always entertaining "Pancakes or Waffles" in which one begins by choosing between the two breakfast items and eventually is forced with decisions such as "Being the first person on Mars" or "Curing cancer." When Jenny was asked "Have a healthy and happy family" or "Save 1,000 people from dying of malaria" she chose the latter option without hesitation. I found this fascinating because a few days before, while on that same track with a couple non-Buddhists, a firm consensus was reached that there was nothing more important than being in a happy family with a loving spouse and children. Jenny explained that the people she helped would all be part of her family. For Spike, being not religious, money was most important, except when offered with the prospect of a supermodel wife.

After coming off the mountain, we returned to town in a light rain, which must come at some point during a walk near Dunedin, and Spike showed us to his favorite Chinese restaurant where we feasted on mushroom and bean soup, tofu and vegetables, and whole fish with onion. There I learned more about Chinese culture and language and how Asians in general tend to be very reserved with emotion, such that hugging and saying things like "I love you," even in private, are generally not done. My education in chopstick usage was also continued, although my hands were somewhat frozen after the wet and chilly walk so I seemed to have made negative progress in that department. Jenny insisted that it is bad karma to leave grains of rice in one's bowl, so they had a good time of it as I made a fool of myself for a quarter of an hour.

Sunday, December 14, 2008

Eat, sleep, breathe, run chromatography columns

I would rate the past 72 hours as the most intense (and at times stressful) yet rewarding in my lab experience thus far. It all began last week when I was preparing some DnaK mutant protein to ship to Sigurd, who is currently traveling all over the U.S.--from his hometown in Oregon to Princeton to Stanford, where he will be performing Small Angle X-ray Scattering (SAXS) experiments. On Tuesday I finished dialyzing the protein, which Sigurd and I had purified together several weeks ago, and per his instructions packed it in a styrofoam box with water ice and poured liquid nitrogen on top. I then sealed the box with tape and brought it to the administers upstairs, where a man from TNT picked up the thankfully no longer smoking box and sent it on its way to Palo Alto. Sigurd sent me a letter to attach to the package explaining that the recombinant protein was non-pathogenic and purified from the harmless lab bacterium E. coli.

Three days later, on Friday, I received a call in lab from the secretary saying they needed to see me immediately regarding the protein shipment to Stanford. I was sure that the package had exploded due to evaporation of the liquid nitrogen I poured on top and headed to the secretary expecting the worst. It turned out that the package had not exploded but was being held at U.S. customs because the description of the protein was not adequate. I called and emailed Sigurd, who soon sent me a longer letter to send to TNT customer service in the States. The letter explained the fragility of the protein, that it was sent only on water ice, and that it had to be kept cold. I forwarded the letter to TNT and apparently Sigurd has still not heard about the status of the package. We can only hope that it is being chilled while the paperwork is completed.

In the meantime, Sigurd requested that I purify a variant of the original protein to give to his wife Erika in a thermos. Erika is flying out to join Sigurd this Wednesday, and we arranged for her to pick up the protein Tuesday afternoon. She said in an email that she couldn't wait to tell airport security that she was carrying a thermos containing biological materials from a man she barely knew.

And so my mission, if I chose to accept, was to purify a DnaK mutant beginning only with a plasmid encoding the protein, and have it ready by Tuesday afternoon. This meant transforming E. coli with the plasmid, growing up "heaps" of bacteria, lysing the cells, and then running three chromatography columns plus several rounds of dialysis with various buffers. I had done all of these things once before under the watchful eye of Sigurd (he also did some parts without me there while I took care of administrative issues the first couple weeks) and in twice the amount of time that I currently had.

As I began the challenge, I already had a draft of the email to Sigurd in my mind explaining the horrible mistake I had made and how I lost all the protein in some massive waste beaker or something. I was really not expecting to be successful--there were too many complex steps that I had observed only once or not at all. There was bound to be a major error at some point. And when the transformation and cell lysis went smoothly, I thought to myself 'Things are going too well, I'm going to screw up the chromatography.'

On Saturday morning, I got up at 7 AM and arrived in lab at 8 to spin down cells for lysis. I had them chilling on ice by 9 and and ran back to Carrington to meet up with the other summer students to go hiking. I had promised that I would take everyone up the Mt. Cargill trail and we would go to Capers for a pancake brunch afterward. When I told them that we actually wouldn't be back until 2 or 3, they protested that brunch is strictly between breakfast and lunch. Haven't they heard of Greylock brunch night? If you're eating pancakes, no matter the time, you're having brunch. The others were non-hikers but good sports who did well on the 5 hour round-trip journey (pictures soon). We returned to town to find Capers closed, causing temporary despair until we decided on hamburgers at Velvet Burger. When we finished at 4 pm, I walked back to lab to lyse cells and begin the first column, a DEAE anion exchange column. The main problem I ran into was setting up the plumbing connecting the pump to the column. Fishing through multiple boxes of metric and U.S. adapters and tubing, I got pretty creative in setting up a system that seemed to work with no leaks. At 11 pm I went into town for a quick dinner and shower, then back to lab until 5:30 am, equilibrating the column, loading the sample, collecting the appropriate fractions, running gels to see which fractions had the DnaK, cleaning the column, and then setting up the dialysis for "overnight" (i.e. while I slept).

I woke up at 2 pm on Sunday and headed back to lab to run column #2, the ATP affinity column. DnaK has high affinity for ATP, so this is the primary column in the purification. The main challenge this time was that the column kept going over the pressure limit and had to be run at a miniscule flow rate, I imagine because the column was old and needed to be re-set, thus dramatically augmenting the time required. By early evening I set up a program to load the sample and elute in fractions with the appropriate buffer and took off for the University gym for some much-needed exercise. A couple hours later I returned, completely prepared for A) the column to have exploded, B) the fraction collector to have malfunctioned, leaving my sample in a pool on the benchtop, C) the program to have pumped in the incorrect buffer, D) something worse. Miraculously, everything seemed to be working well and a gel confirmed which fractions contained DnaK. I was in bed early at 3 AM.

I arrived today back in lab by noon and was happy to see that the program I had run while asleep to equilibrate column #3, gel filtration, had worked swimmingly. I injected the sample onto the gel filtration column and watched the computer as a beautiful UV absorbance peak emerged right where it was expected. I just finished running gels on fractions jam packed with DnaK.

All that is left is two more dialysis runs and some flash freezing and she'll be ready for Erika. The weekend taught me A) working in the lab alone to Young Gs by P. Diddy at 4 am is quite enjoyable, B) coffee actually tastes pretty good, C) don't doubt myself so much.

Sunday, December 7, 2008

Tramping in the Silver Peaks

Here are some random photos from Dunedin on a rainy day:

Yesterday I went on my first Otago Tramping Club tramp in the Silver Peaks, the mountain range immediately west of Dunedin. There were 12 people on the hike, including a woman from the Biochemistry Department I persuaded to come. All the folks were very friendly and fun to talk with except one spectacularly arrogant woman originally from the U.S. who cackled annoyingly after every sentence she said. It was a fairly epic day hike, about 9 hrs and 27 km long, featuring beautiful grassy hills, creek crossings, blustery peaks, a steep Devil's Staircase climb, and some "bushbashing" through the hardy vegetation.



Also this weekend I went for another bike ride along the coastline and cooked up a pretty tasty noodle dish for an Iron Chef potluck dinner we had at the college. Much to my disappointment, the vegetarians and Buddhist in the group insisted that "everybody's a winner," thus there was no voting for the best dish or crowning of the Iron Chef.

Friday, December 5, 2008

Back in the saddle again

Friday morning was awesome. Woke up, threw on my bike shorts, ran down to the main street and went to the first ATM I saw. "Cannot process transaction at this time." A minor hiccup. The next ATM churned out 40 crisp 20s and I was on my way. Gave the money to the guy at the shop (I was still 20 short, but will pay that today), he helped me get the bike set up to my specifications and body size on the indoor trainer, and I was off. It was the first seriously sunny day in a while, and the bay was gorgeous. I did an out-and-back on the peninsula low road. The wind was in the perfect direction so I was suffering on the way out and jamming back home. Here she is, that beaut:

In other news, I went to the Otago Tramping Club meeting on Thursday night. The club is very well organized and they have their own clubhouse with walls covered in topo maps and pictures. They run day hikes and weekend hikes every weekend, and I'm going on the hike tomorrow to Pulpit Rock.

Last night we saw High School Musical 3, which I thought was the best one yet. Smash hits included "The Boys are Back," "I Can't Choose," and "I Want it All." Seems like a long time ago when we returned to Westmont College to see Grant, Bill, and Corey passed out on the floor, stuffed to the gills with ice cream and donuts and raving about HSM 1.

Wednesday, December 3, 2008

Searching for Christmas cheer in summer

Due to lack of bicycle, this past week I've continued to explore Dunedin and surroundings on foot. Most notably I hiked the Pineapple track, which winds up a steep hill north of town through dense, seemingly tropical forest and emerges on a ridge covered in yellow wildflowers. Although the Pineapple track was restricted to walking, it ended at a junction with several mountain bike trails. Earlier this week I headed to the ocean beach in the pouring rain in search of the Tunnel Beach walk, which is advertised online as a superb seaside hike. I didn't find the crucial tunnel to access the trail, but walked along the beach anyway. It was just me, the rain, a chilly wind, and the waves, until I discovered Dunedin's Lovers Lane, which was full of a dozen parked cars aimed at the beach.

I plan to go to the Otago Tramping Club weekly meeting tonight. A free supper is included for first time attendees. Their friendly website advertizes weekend day hikes and overnight trips. I'm also hoping they can recommend a good track for a Chirstmastime tramp I'm planning with Peter Nunns, Williams class of '08 who is currently in Wellington.

On Tuesday night I saw my first movie in New Zealand, Quantum of Solace. The movie theater seats are like La-Z-Boys, but otherwise the experience was equivalent to an American cinema, including the never-ending previews. After the movie we went to a bar with an open mike, where a middle-aged gentleman was wailing away and freestyling about how he went to the supermarket to buy some good karma.

Last night the wardens of Carrington College invited us for pre-dinner drinks in the college lounge. I'm learning that residential colleges here are more akin to fraternities than dormitories in the U.S. Students must apply to live in a college and a spot is not guaranteed to first-years. Although the colleges are affiliated with the university, they each have their own reputation and traditions. Some are for pre-med students, some for religious Christians, others for international students. The wardens showered us with gifts of kitchen equipment, including baking pans, a cheese grater, and a full set of knives.

I have picked out a new bicycle, significantly higher end than the one that was stolen, but will not be able to take it from the shop until tomorrow. Since my debit card fails to work here (it worked in Tanzania), I can only get money through the ATM, which has a daily limit of NZ$800. I put down some money today, the rest tomorrow.

In the lab I proposed an idea for a project to Sigurd related to Alzheimer's Disease, and he appeared interested. It will take a while to assemble all the components for the experiments, so for now I'll be working on the basics of the FRET method.