Tampere at Night

Source Tracking is Hot!

It must have been good enough, because it convinced them to scrape 2500 euros off of wherever they could scrape it from. “But we need some sexy language,” my adviser informs me. “For scientists, this is good, but non-scientists need to know why microbial source tracking is sexy.” Huh? Sexy?

I had a meeting with my advisers on Thursday where I presented the basics of microbial source tracking (MST) and my proposed study design. It was a good idea to have this meeting because I’ve been doing A LOT of learning, A LOT of literature reviewing, and A LOT of meeting with people who know more than me on such topics as MST and molecular tools. Molecular tools are beginning to govern the environmental engineering field. But the techniques are vast and the methods are complicated. For example, you can be an expert in environmental engineering and know very little about MST.

If you don’t want to read the long winded version, I’ll skip to the punch-line. MST is hot because:

• It’s fast! It can prevent people from getting sick, or even dieing of waterborne diseases, by letting them know their water is contaminated much quicker than ever before.
• It’s informative! In addition to finding out that the water is contaminated, we may be able to find out who is responsible and how big of a risk it is.
• The technology is getting easier and quicker and will be automatable for long term monitoring in places like drinking water treatment plants or swimming beaches.
• The same protocols may be applicable from Lilongwe to Santiago, that’s one of the things I’m testing (though not those two particular locations).

If you would like to learn some new cocktail party words and some science, keep on reading.

I may have read more papers during my first month in Tampere than I read for my entire thesis. There’s nothing to show it-- no data, no concrete scientific conclusions, no eloquently crafted proposals-- unless I present what I’ve learned to someone else. Thus the adviser meeting.

Tuula is right. Microbial Source Tracking is sexy. If our drinking or swimming water is contaminated, we’ve never been able to tell who is responsible, what type of animal the contamination came from, or where we need to focus our management efforts. With microbial source tracking, this is all possible. One of the biggest challenges of living with so many people on earth is keeping human and animal waste separate from drinking water. It’s an enormous industry for lucky people who have municipalities with drinking and wastewater infrastructure. However, it’s an enormous risk for many rural areas, particularly in less developed nations, that do not have this infrastructure.

Historically, we have monitored water contamination by growing indicator organisms (E. coli, fecal coliform, Enterococci, etc.) from drinking water samples. This tells us if the water is contaminated. It does not tell us what to do about it or where the contamination came from. The options have been either to guess where the contamination came from, or to post signs warning people not to swim if contaminant levels are high. Monitoring indicator organisms is relatively easy, but takes two days (of potentially exposing swimmers to waterborne pathogens) to get the results.

The basic concept of MST is to match microbes from a polluted site to their animal or human hosts. To understand MST, you have to know that microbes are everywhere, on your hands, in your mouth, in the air, on surfaces, and most importantly all over your digestive tract. Most of them don’t cause us problems, and many of them help us. MST capitalizes on microbes to trace contamination to its source. Matching genotypic or phenotypic microbial profiles suggests a link between the origin (septic tank) and contamination site (reservoir or swimming beach). It’s important in watershed management and risk assessment. Microbial source tracking has the potential to be fast. It can also be automated for utilities, once we work out the kinks. We’ll know within a few hours if our water is contaminated and if we should contain the septic tank across the street or the upstream factory farm.

In my study on Finnish well water, I’ll be looking for either cow or human fecal contamination (or both). I’ll use Bacteroides, a type of bacteria found in human and animal digestive systems. Bacteroides is a good MST indicator because:

1. it cannot grow in the presence of oxygen (it cannot grow in the environment, only in digestive systems)
2. it is abundant in human and animal digestive tracts
3. it only grows in rumen, digestive tracts, and body cavities (not on rocks, on bugs, in the soil, etc.—if it’s in the environment, it came from something with a digestive tract)
4. its DNA varies consistently, depending on the host (animal) in which it resides

I’m using PCR to test for the presence of a DNA sequence in Bacteroides. PCR is a way of amplifying DNA sequences to concentrations that are high enough to visualize using agarose gel electrophoresis. From reading papers on other MST projects, I’ve found some regions of Bacteroides DNA that are found only in humans, and some other regions that are found only in cows. These are the regions that I will amplify.

If the cow specific regions amplify, dairy farms are a likely source. If the human regions amplify, local septic tanks are a likely source. If nothing amplifies, either the well is not contaminated or there’s some other source besides cows or humans (I’ll pick wells that do not have any other likely sources, but nothing is ever 100% certain in science).

Proud to be Tamperelainen

Guess what! I'm already tamperelainen! I was never Quiteňa, Borboneňa, or even Mexicana, after living there for months. I wasn't even always a Seattleite after living in Seattle for three years. Occasionally people in Seattle would get on my case for being a Californian and contaminating the Seattle area with my... Californianess. However, my Finnish professor told me that you become tamperelainen, immediately after you move to Tampere. For someone who's only ever truly been Californian, it's very liberating.

Chains!

We were talking about traveling to different places in Finland. Kirsi, who’s teaching me everything I need to know about molecular techniques, and her husband are planning to head to her folks' house this weekend. Her parents live in a little village, 600 km north of Tampere.

“If we’re lucky, we’ll get there by midnight on Friday,” she said.

“Yeah, but it depends on the weather too,” Katariina chimed in. She was pointing out that it might take even longer. Apparently Kirsi’s village has already had one snow storm this year, even though it’s only the beginning of October.

So, I was thinking about Kirsi, and her trip through snowy terrain and… yikes! Driving in the snow? “So will you bring chains?” I asked. You know, then if it doesn’t snow, she wouldn’t have to put them on; if it does snow, she could just pull right over to the side of the road and put them on… piece a cake.

Katariina almost died laughing. “Chains! Can you imagine!” And then she laughed a whole lot more. “We’re covered in snow for at least five months per year.”

I realized I had said something wrong. But the Southern California part of my brain couldn’t figure out what it was.

“We don’t use chains in Finland, Laura. We use snow tires here.”

Oooooh yeah, I’ve heard of snow tires before. I’ve never used them, but my friends Patrick and Jenny talked about putting them on their car one winter.

Shoot, I’ve never even used chains before. Boy, it’s gonna be an interesting winter for me.

“Chains, ha!”

Sieni Mushrooms?

It started with a conversation at lunch today. Several of us from my department eat lunch together. We talk about cultural differences, stuff that happens in Finland, UFOs, and sometimes they come up with things for me do. Anna asked if I liked orienteering... as if I were familiar with orienteering, had tried it a bunch, and then decided if I liked it or not. I do vaguely remember orienteering at Girl-scout camp when I was ten. I think it mostly involved practicing inside a lodge. Maybe the next day, after we got some experience, we were allowed to try it outdoors. It was all very slow: following directions, writing down coordinates. It was very boring.

"I've never tried it," I told her. It was almost the truth. There were six of us at the table. As it turned out, all five (other than me) had been on fairly extensive orienteering expeditions... in the actual forest. Most people didn't like it, or claimed to be bad at it.

"My sense of direction is so bad that I get lost even with a map and a compass." or "I used to like it, until I missed a whole lake and had to find my way home without it." Apparently, the Finns learn to orienteer as part of their upbringing. It seemed kind of like Americans learning to play soccer or softball. Some of us are good at it, some of us aren't, but we all know the basics.

Anna likes it. And she invited me to join her orienteering team. I didn't realize it was a competitive sport... with teams. "Do you like to run?" she asked. Run? While orienteering?

There were three of us on the 4km team (Anna, Ari, and me), and one person was her own one-man 3km team. We drove for about 30 minutes to the starting point. You see, orienteering courses have to be in a different location every week because those darn orienteerers learn their way around the forest quickly.

Ari lent me a compass. That was key. The other key was having Ari and Anna on my team. I actually have a poor sense of direction. When we first pulled into the parking lot (the starting point), I couldn't help but notice the outfits on the other competitors... oh the outfits! People really get into this. There was a variety of attire, but the hardest core people were wearing... superhero-like costumes: bright blue tights, a red shirt with a fluorescent green vest over it, and plastic leg warmers (apparently to keep their legs dry when crossing lakes!). They were dressed... like Night Captain, but brighter. We were often in the middle of the forest (away from all trails), looking at our compasses and maps, and then, out of nowhere, a brightly colored bundle of energy would come plowing through, leaping over tree stumps, flying through the air. We had to be careful to keep out of their way. The forest outside of Tampere is like the Olympic National Forest in some ways. There was about six inches of moss covering the ground and growing on trees. Running through it required agility. I only fell down once, but I had a few other close calls. Our team was of moderate competitiveness level, compared to the other teams. We ran, and we took it seriously, but once in a while someone would stop and say something like "oh hey, look at this mushroom. What kind of a mushroom is it? How to you say mushroom in English?" And then we'd start running again.

I was surprized how fun it was. You don't really notice that you're running because you're too busy looking for rocks, mounds, valleys, and other hints on the map. It was a good way to see the forest... as long we you didn't mind the periodic superheros leaping by. I heard that we had it easy this week. Sometime you have to climb trees and cross rivers!

We finished the 4km course in one hour, nine minutes, and 55 seconds. It was an all-time record for me! I'm totally doing it every week!

Tampere!

This is International Student Housing, where I live. It's a fairly modular building (inside and out), and it's concrete blockish nature takes some adjusting at first. The pink stripes across the front crack me up! Finland is not afraid of the color pink!

Tampere! It's Finland's third largest city, and its 200,000 inhabitants feel that they live in the city (not a suburban town, but an honest city). People continually tell me about the cultural differences between Finnish cities and rural areas. Once I asked some co-workers how to say "excuse me," in Finnish. One of them asked if I wanted to say it in the country or in the city.

"In the country you can just bump into somebody and then keep on walking. You don't need to say excuse me." Then he chuckled, and everyone else argued with him.

"Why do you always say things like that? I always say excuse me if I bump into someone."

So it might be debatable, but most people tend to agree that city folk are more outgoing. Though it seems small to me, Tampere has a central downtown area with tall buildings, theatres, clubs, two universities, lots of shops, a soccer team, and a famous ice hockey hall. It even has a Fringe Festival in November, regularly scheduled Finnish music shows, and it's (ironically) a bit of an afro-cuban salsa dancing hub. Compared to my hometown (of 300,000 people that barely makes the U.S. map), there's a lot to do in Tampere.

I'm working on a well water contamination project at the Tampere University of Technology (TUT). My adviser and one other student have been characterizing the groundwater flow, and measuring chemical and microbial indicators of contamination from surrounding farms and septic tanks for the past year. I've officially joined the project, and I'm planning to use microbial source tracking methods to show the a link between the source of the contaminants and the wells. My adviser, the faculty in my institute, and the other students and researchers have been incredibly supportive both academically and in getting me moved in. People have lent me curtains, blankets, dishes, a bike, and much good advice on getting started as a student at TUT and one of the 200,000 residents of Tampere.

So, even though I accidentally erased my hard drive installing Windows XP last night, I feel pretty settled into my apartment with (post Windows XP installation) functioning Internet access, curtains, bed sheets, dishes... avocado green vinyl flooring-- everything I need.



This is the bike that one of my co-workers has let me borrow for the year. I can't wait to cruise around the endless bike trails between Tampere and Hervanta. There's only one gear working right now, but one gear is all I really need.



These are the bikes of the people that live in my building. I noticed the nice shelter to protect them from the weather, but what's even more noticeable is that many of these bikes have no locks!