Goodbyes are Always the Hardest Part

I have been away from IRRI for almost two weeks now. Spending time at home as made me realize just how much I Los Banos had grown on me. I remember how scared I felt during my first week there, and how comfortable I felt right before I left IRRI. I failed to realize just how much I would miss the mountains and the people of the Philippines. I don’t think I can put into words how much I have grown as a researcher and as a person.

Going in, I expected to learn new lab techniques. I imagined I would get to use new equipment and perfect the techniques I already knew of. I knew I would gain experience working in the lab – which I did – but I also learned a lot more than the technical aspect of research. I learned that research takes a lot of patience and perseverance because you rarely ever get the results you had hoped for on the first try. I learned that it is always a team effort. I learned it is okay to ask people questions, no matter how stupid you might think the questions are. I learned it’s acceptable to make mistakes, as long as you don’t keep repeating the same ones. And above all, I learned that you can learn something from everyone.

I miss the fact that everyone I came across – from the guards to the cafeteria workers to my supervisor and everyone who worked in the lab – was more than willing to talk to me. One of the prime examples is the way the guards’ faces lit up when I said “maganda umaga” (good morning) upon entering the building gave me so much joy. They then taught me “maganda japon” (good afternoon), “mangada gabi” (good evening), and “maganda tanghali” (good noon). It made them happy that I was trying, and that made me want to keep learning new greetings.

I miss everything about the Philippines. I miss local shops. I miss the mountains. I miss going on weekend excursions. More than anything else, I miss the people. I miss their kind and helpful nature. I miss how excited they were to see me and help me when I had questions about how the shuttle schedule worked. But just like all good things, my summer in the Philippines has to come to an end. Paalam Philippines, I hope I get to see you again.

Work Continues

As I am approaching the end of my internship, I have come to the realization that I have learned a lot more in terms of research that I had expected. As I learned new techniques and improved on the ones I had already known, I realized how it all came together. Researching is a lot of like climbing a mountain: you have to do it one step at a time while motivating yourself by keeping your end goal in mind. It takes a lot of patience to get to the top, but once you get there, the view is well worth the work.

In the second half of my internship, I continued to perform PCR, Assays, and Extractions, but I also started performing new lab techniques. Here is a short list:

Here is a short list:

•  Sampling leaves and extracting DNA
  • Cleaning the extracted DNA
  • Measuring the concentration of the cleaned DNA
• A-tailing and Ligation
  • Inoculation
  • Extraction of DNA
  • Performing Colony PCR

I have learned a lot more than I ever thought I would in two very short months thanks to my amazing supervisor, Yvonne Ludwig. The best way to learn is through hands-on experience, and she truly embodies that. She doesn’t just show me what to do,  she lets me do it even though her experiment would go a lot faster if she did it herself.

Adventures Make Life Better

It has been a while since my last blog update because I was too busy living in the moment. The IWU group at IRRI has been trying to travel every weekend, so I will break it down by what we did.

Bukal Falls – 9 July 2016

We took two Jeepneys to get to The Bukal Falls in Majayjay. Once there, we paid the entrance fee and hired a guide to take us to the actual Fall. The hike took around an hour and it anything but easy. Even though the sun was not shining bright, it was still a lot harder than the Taal Volcano hike had been. It was steep and slippery. We had to go up and then down to reach the falls.

Once we reached the Falls, the hike was well worth it. It was cool and the cold water felt phenomenal. We spent some time in the water, ate our sandwiches and snacks, took tons of pictures, and headed back. This was my favorite spot of this summer. It was the perfect combination of a beach (because of the water) and a mountain (because of the hike). I loved absolutely everything about this day, and I would go back in a heartbeat.

GK Farms – 16 July

The IWU group at IRRI, Human Nature, and FNRI for to visit Gawad Kalinga Farms. We got a tour of their compound and what they do. We learned about how they are truly making a difference in the community and giving people great opportunities. Talking with Tito Tony made us realize just how incredible and important the work they do is. They are providing housing and jobs for the poor and producing healthy, organic products at the same time. It is the kind of place where you know that the money you spend is going to a great cause and actually helping people. It was a great experience to learn about the work that GK Farms does.

Mount Makiling – 17 July

The day after our visit to the GK Farms, the IWU crew decided to climb Mount Makiling. We are able to clearly see the mountain from the IRRI campus, so climbing it was a must. It is supposed to be a beginners hike even though it takes 5 hours to get to the top. The hike is long, but it is not terribly difficult. Hiking Mount Makiling helped me realize that I really enjoy hiking. Even if the view at the top is not all that great, I still enjoy the hiking part. The views along the way make the hike worth it. I can officially say I have climbed a mountain, and I hope to climb many more in the future.

Zambales – Weekend of 23 July

The IWU students from IRRI and Human Nature decided to go on another beach weekend. But this time, we did not stay at a beach resort. We stayed at a hostel, The Circle, and slept on hammocks. We rented a van that took us to the hostel and drove us around the town for the weekend. We spent Saturday morning at the beach and went to a waterfall in the evening. Both were incredible. On Sunday, we visited another island, and it was beautiful. We then grabbed a quick lunch and headed back to Manila in order to drop off the students that work for Human Nature. We got dinner to go and took a bus back to Los Banos.

Pandin Lake and Liliw – 30 July

This weekend, a local researcher, Paolo, took the IWU students along with a couple other grad students to Pandin Lake in San Pablo. We rented a raft that took us across the lake. We then climbed a small hill to get to the top and take pictures. After taking pictures, coming back down, and eating some snacks, we got to swim in the lake. After that, we headed to Liliw in order to check out the famous shoe shops. We also ate dinner in town before heading back to IRRI and concluding the day.

As it is pretty evident, I have been exploring every weekend and loving every second of it.

So Much to do, so Little Time

In terms of work, I am in the full swing of things. In my last post about work, I failed to truly express how much work I truly do. Through hands-on experience, I have learned a lot of lab techniques. Usually in class, we read about lab techniques in terms of procedure and purpose, but we fail to learn about it practically. Sure we perform some techniques in lab courses, but we do not get to truly learn from our mistakes. In labs, we make a mistake, acknowledge where we went wrong, and move on.

In an actual research lab, where your research has actual implications, you do not get to simply acknowledge your errors and move on. You have to make changes and repeat until you obtained the needed results. The next step builds on the first one, so you have to be extremely persistent and make it past the first step. Having said all of this, I am learning a lot of lab techniques, and here is a weekly breakdown of what I started doing.

• Week 1:
  • I started designing vectors using a program called Unipro
  • I learned how to run a PCR in order to establish an enzyme assay
    • I had to repeat the process a lot because it was extremely important to only get one band. I could not move on to the next step until I figured out how to only get one band.
• Week 2:
  • I sterilized rice seeds.
    • The seeds need to grow for 8-10 days before we can isolate the protoplast.
  • I started running PCR on Batch 1245 which contains 218 samples.
    • I finally got the single band I needed and my negative control was actually negative, so I was finally allowed to run the PCR on the samples without supervision.
• Week 3:
  • I started establishing T7E1  assay in order to analyze the CRISPR-Cas9 modified products.
    • Since the negative control of my PCR was actually negative, I was confident in using my PCR product to establish the assay.
    • In order to establish an assay, the DNA is hybridized and then digested. Now the hope is to get two bands when the gels are run.
  • I also started the plasmid DNA extraction process as well as the protoplast transformation.
• Week 4
  • I tried to do Direct PCR
    • It is very similar to regular PCR, but we did not see any bands because the plants were just a little too old.
  • I assisted Yvonne (my amazing supervisor) with protoplast extraction.
    • The seeds we sterilized during week 2 had finally grown a bit, so we chopped them into very small pieces, put them in the enzyme solution, and incubated them.
  • Since I had finished establishing the assay in all the samples of batch 1245, I started running PCR for the samples in batch 1246.

Here are some pictures of the seeds as well as several pictures of the stages of protoplast extraction. Additionally, there are some pictures of me in front of the lab equipment I use.

Beach Weekend

Last weekend, our group of six IWU students decided to head to a beach resort. We started our travel at 4:00 AM on Saturday. After taking two jeepneys, one bus, and one tricycle, we finally reached Badladz Beach Resort at around 9:00 AM. We spent the whole day in the water. In the evening, we drank fresh coconut water and also ate the coconut meat. On Sunday, we started back for IRRI around 1:3o PM and reached IRRI at 7:00 PM.  All in all, it was a much needed, relaxing weekend.

We met some French people at the beach. Coincidentally, they worked at the GK Farm and were friends with the IWU students who are also at GK. Additionally, on the trip back, we met a family from Illinois. Talk about a small world.

Sidenote: shout out to Abby, Piotr, and Jamie for doing all the research about resorts, booking the rooms, and making this beach weekend possible

 

Surrounded by Beauty

When there is an island in a lake inside a volcano that is in the middle of the ocean, and you have the opportunity to hike the said volcano, you go up that volcano. And that is exactly what our group of eight IWU students did. We embarked on our adventure are 7:00 AM and what an adventure it was.

We took a boat to the volcano, got out entrance tickets, and started hiking up. Climbing up was a lot harder than I had anticipated because I had failed to take into account the scorching heat as well as the steepness of the mountain. However, one and a half hours and five breaks later, we made it to the top! The view was spectacular and the pictures below do not do the view justice, so you will just have to take my word for it. The view was worth the hike, and I would definitely do it again if I had the chance.  The cooler breeze at the top also helped.

After taking a lot of pictures, we went down the mountain. Going down only took about 15 minutes. We took the boat back to the mainland and drove 45 minutes to get pizza. After eating the pizza, we came back to IRRI to shower and rest for a bit. The group went to a karaoke bar around 6:00 PM. We ended our long day around 8:30 PM.

At the end of the day, my Fitbit tells me I walked 25,337 steps and 10.74 miles.

Routine

After two weeks at IRRI, I have fallen into a routine. I work from 8:00 AM to 5:00 PM, come back and talk to my mom through Skype, eat, shower, and go to bed. It is a simple, yet satisfying routine.

Work has been pretty good so far. I am running PCR for now. PCR is short for Polymerase Chain Reaction, which essentially amplifies a specific sequence of DNA depending on the primers being used. Since there are so many samples to run PCR for, I have spent the last 4 days just doing PCR. It is not a difficult process, but it is very tedious. Even a small amount of contamination means that we have to run PCR again. The process is extremely detail oriented.

Hopefully this week, I will finish running PCR and move on to the next stage.

Below are just a couple pictures of me preparing gels to run and pipetting in order to run the PCR.

Uber Chaos

This weekend was an experience like no other. Abby, Jamie, Piotr, Vishnu and I decided to visit Eric and Liz in Manila for the weekend. We were not entirely sure how to get there, but we were determined. Going there was not too bad. We just took a bus from the South Supermarket and then took a taxi to their condo.

Once we got there, we took an Uber to Old Manila. The trip took about an hour and we were able to witness the chaos that is traffic in Manila. Rush hour traffic in Chicago seems pleasant in comparison to the way people drive in Manila. However, looking back, there was some method to their madness because we did make it there and back in one piece.

By the time we reached Old Manila, it was already 11:00 AM, so we decided to get lunch and make our way to Fort Santiago. It had a lot of rich, sad history behind it, but it was beautiful. A lot of the buildings were degrading, but that just added to its beauty. We walked around bought some souvenirs. We then decided that it was time to try the infamous Halo-Halo that we have been told multiple times to try. It was essentially shaved ice with milk and a lot of fruits. It was refreshing for a hot, humid day.

After walking around a bit more, we took an Uber to U.P Town Center. It was as large as the Woodfield Mall, if not larger! It had a lot of stores and restaurants. Half of the mall was indoor, but the other half was outside. For dinner, we had nachos and they were delicious. Next, I got a mix-in of mango icee and vanilla custard. It was the perfect way to end the night!

The next morning, it was time to head back to Los Banos.We grabbed lunch at the mall and then took an Uber to the bus station. Catching the bus was way more complicated than we had expected, but after a lot of walking, we made it to the right place. We were able to make it back safe and sound, which is all that matters! Even with all the struggling, it was a great a weekend and I regret none of it.

Here’s a little glimpse of what my day was like.

 

 

 

 

Getting my Hands Dirty…Literally…

Living in the suburbs of Chicago, I rarely ever wonder where my food really came from. It is easy to forget that there are actual people out there working incredibly hard in order to grow the food that we simply buy from a grocery store. I still do not know the exact path the food takes to get from the farm to the grocery store, but I do know a little about how hard it is to grow rice.

In theory, it is very simple. You plant some rice, let it grow, collect it, and then finally sell it. In reality, the process is much more complex. The amount the labor it takes to prepare the land before planting the seeds is incredible. I got to use some of the machines that are used to pulverize the land. When I saw that they were motor-run, I assumed it would be easy. I was wrong. It took an incredible amount of upper-body strength to move as well as control those machines. We also got the opportunity to see Gretchen the Water Buffalo at work. I thought I would be controlling her, but she ended up controlling me. By the end of the activity, I was extremely tired and in desperate need of a shower. And I only worked for about ten minutes.

Then came the tedious job of actually planting the rice. It is done through a grid system. The rice seeds are supposed to be planted every 20 cm so there was a grid where all we had to do was insert two to three rice grains at the intersections. It seemed easy enough, but we soon realized that when we step in the plot, we also step on the lines. It was hard to plant rice in a straight line. Just like everything else that day, it ended up being harder than it looked.

Needless to say, this was an eye-opening experience that has helped me appreciate where rice (and even food in general) comes from. It is a lot harder than it seems, but the experience was definitely worth it. Fireants and all.

Here are some pictures of me hard at work as well as a picture of the beautiful Gretchen.

I am Here!

I am finally at the IRRI campus! It is surreal to know that I am in a foreign country where I don’t know anyone. I never thought that the day would come where I would get to go a new country and research. The view around the campus is breathtaking! You can see beautiful mountains in the distance. There are rice fields with palm trees behind them. It is extremely hot and humid, but the views make up for it.

Since the flight was so long and I am incapable of sleeping in planes, I have slept for a total of five hours in the past day and a half. Weirdly enough, I feel energized and ready to take on my first day in the Philippines. So far, I have had breakfast and walked around the campus. This campus has everything one needs to be happy! There is a basketball court, mini soccer field, tennis courts, indoor gym with machines and weights, and a cafeteria. There is even a souvenir shop! With so much going around me, I am very confident that there will never be a dull moment.