This week in the lab I continued to run PCRs working through the markers. I got the hang of the larger-scale PCRs and gels so I started running two PCRs a day in order to make more progress through the markers. I also learned how to properly record all of the gel images so that I could actually keep track of what is what. Because I’m going to be running so many PCRs if I don’t record everything correctly and promptly then it is easy to get lost with all of the images of gels. To keep track I just put each gel image on a PowerPoint slide with a template that indicates what DNA is in each lane. I also write down the PCR number for the gel and the marker numbers next to each of the six rows of wells in the gel. After doing that I look at each row and record whether or not I got duplication from the PCR, with the first two wells having DNA that acts as a control and should always duplicate.
This weekend we also went on a trip down to a resort on the beach. The spot we went to was recommended by one of our supervisors and he knew people who ran a resort there so we were able to get a pretty good deal. He also provided us with instructions on how to get there using public transportation which was a lot cheaper than hiring a driver. We took Friday off and started our trip in the morning. All we had to do was take one jeepney and one tricycle to get to the bus terminal. Once we got there we just asked around to find the right bus. We didn’t even have to buy tickets we just took seats and paid on the bus. While we were waiting for the right bus we ran into a group of Filipinos who were also going to the same area as us. We got to talking with them and learned they were a basketball team who were taking a weekend vacation. They invited us to go join them in their activities the next day and we decided to accept. After getting off the bus we took a tricycle to our resort. By the time we had arrived after all of the traveling, it was already time for dinner so we ordered some food from the resort. They had Italian food and I got some pasta which was quite good. I also got a mango crepe which was delicious. The next day we got up early to see the sunset before joining the people we met. In the morning we went out on boats with them and visited a couple beaches. We also went snorkeling for an hour or two. After we were done we went back with them to where they were staying and they started preparing lunch. While they were doing that they also had us try some unripe mangos, kamias, and fresh coconut all of which they picked from trees in the yard. For lunch, they cooked a bunch of rice and grilled squid, pork, chicken, and fish and spread everything out on a banana leaf. Then we all sat around the table and dug in. The food was really good and it was great to get to experience a typical way of eating. The next day some of us hiked to a waterfall in the morning. The trail was on the tougher side, including an almost vertical part that required some climbing, so we didn’t make it all the way to the big waterfall but we did get to see some of the smaller ones along the way. After that, we headed back to our resort before starting the journey back to IRRI. The trip back was just as easy as the trip down and we pretty much had to do everything in reverse, just going to a different bus station.
This week marked the start of the real lab work for me. On Monday I went to the greenhouse with my supervisor and collected leaves from rice plants to use for DNA extraction. We collected the leaves from fairly young rice plants that had been planted in seed beds. The extraction didn’t require much material so we only had to collect a couple of inches of leaf from each plant. One part of one leaf was sufficient and was torn up before being placed in the tubes I prepared last week. The leaf collection was simple but we had to do it for about 100 plants while outside so it did get hot by the time we had finished. After we had collected all the leaves we went back to the lab and started the actual DNA extraction process. The first whole extraction process was actually very simple thanks to the fact that my supervisor had developed a method that provided good results but didn’t require the use of certain chemicals, such as chloroform, which other extractions do. This was beneficial because chloroform is difficult to handle. Once the extraction was complete we took we had to dilute the DNA to create a working stock. I am only working with some of the DNA we extracted, specifically the DNA of wild rice species accounting for some of the different rice genome types. Once I had the working stock ready I moved on to PCR. My supervisor created the markers that I used for the PCR based on the BB genome which is available online. The PCR was similar to what I did in genetics lab except adapted to a bigger scale. As a result, some stuff did take some getting used to. However, by the end of the week, I had gotten the hang of everything. That weekend I joined the students from India on their trip to a water park close to Los Banos. In order to get there, we used public transportation. This was my first experience going on a long trip using public transportation in the Philippines and honestly, it was quite easy. All it took was two jeepneys and two tricycles and we made it to the water park. Traveling as a group definitely made it easier, as did knowing exactly what we needed to do beforehand. We got to the park in the afternoon when some rides had already closed but it was still a bunch of fun and it was cool to spend time with students who go to college in a different country. The park also had a blow-up course similar to wipeout and I managed to make it all the way through only falling a couple of times. On the way back we stopped by a mall to grab something to eat before returning to IRRI.
This week was a lot more notable than last week. Our seven days of self-monitoring ended over the weekend so on Monday we all moved out of our quarantine rooms in Swaminathan Hall and over into our actual rooms in Harrar Hall. The rooms themselves are pretty similar so it wasn’t too much of a change but the internet in our new rooms is significantly better which has been a very helpful change. We also were able to actually start our internships this week although the transition into actually working wasn’t too smooth. Due to the restrictions that they have in place, we needed to be on a list to be allowed to go past the security guards. However, despite completing our seven days of self-monitoring we still weren’t on the list. As a result, we were unable to go meet with our supervisors on Monday. However, Froilan was on top of the problem, and by Tuesday afternoon we were allowed past the security stop and got to go to our labs for the first time. I’m working in the same lab as another IWU student so we both went to the same place and the people there gave us a tour of their lab. The first lab we toured was the grain quality and nutrition lab which is responsible for analyzing the quality of the grains in a wide array of ways within three main categories: physical characteristics, biochemical composition, and cooking or eating quality. After that I went to the lab I would be working in which focuses on rice breeding and genetics. There I got to meet everybody who works in the lab and talk a little about what I would be doing for the next seven weeks. For the next couple of days, I just did some prep work in the lab including preparing some seeds for planting and preparing some tubes for DNA extraction. However, on Friday, we had a rice planting activity in the morning, which will be its own post, and a tour of Los Banos in the afternoon. During this tour we got to see a lot more of Los Banos than we had before, including some specific spots that were really cool. One spot was called magnetic hill where it seemed like if you put the car in park you would roll back up the hill thanks to an optical illusion. We also got to go up the mountain here and buy some fruit from the market up there. The fruit there is all organic and is collected from the mountain. I got a couple of avacados and dragonfruits. The avacodos were not very flavorful but were good on bread but the dragonfruit was absolutely amazing. We also visited a couple other spots including an I love Los Banos sign. Finally, on the way back we got to try some buko pie, which is a local specialty of Los Banos. The buko pie was definelty my favorite food I’ve tried so far and I’ve already decided I want to try making it myself when I get back home.
The first week of this internship has been relatively uneventful. The flight here was pleasant enough and even our eight-hour layover wasn’t too bad. Once we arrived we went straight to the IRRI dorm. When we arrived it was already pretty late so I went straight to sleep. Since I hadn’t slept much on the flight here I actually ended up being so tired that I didn’t feel jet-lagged. The next day we had a cultural orientation where we learned a little about the Philippines and learned some phrases in Tagalog. After the orientation, they took all of us out for dinner and we got to try some Filipino dishes including sinigang na baboy, pork and chicken adobo, and halo-halo, all of which were very good. After that, all of the IRRI interns then had to complete seven days of self-monitoring so we weren’t really allowed to do much. All I did during that time was get food from the cafeteria, watch shows on Netflix, and fill out some documents to prepare to start the internship at IRRI. However, the seven days of self-monitoring end next week so we should be able to start soon which I am looking forward to.
This blog will be dedicated to documenting my experiences at the International Rice Research Institute and will be updated weekly. Thanks to the IWU Freeman Asia program and IRRI for making this a possibility.