Author Archives: gsteners

The Two With Lots of Photos P1

In the next two blog posts, I will post some of the many pictures taken in the Philippines and describe what is going on. This album mostly focuses on the Rice Planting day and the subsequent tour of Los Banos the other Wesleyan interns and I went on.

Above you can see Aidan prepare to use a tool designed to plant rice seeds across the field in an efficient manner.

In the three images above, the Indian and Wesleyan Interns practice seed broadcasting, the act of throwing rice seeds in a large arc onto the field.

In the above two photos, the head instructor describes different methods for ensuring the rice seeds are safe from predators.

At the end of the day, all the interns posed for a group photo.

After the rice planting day, the Wesleyan students and I went on a tour of Los Banos. Here we are in front of Lake Laguna at the “I Love LB” sign.

Here are some more pictures of the surrounding beauty of the Philippines.

And a Fish!!

Working at IRRI

During my internship at IRRI, I participated in 3 projects: analyzing rice panicles structures with P-TRAP, writing a recommendation for two rice loci for future use, and performing a total starch percent assay.

Analysis of Rice Panicle Structure

Much of the work I have done here I described in detail in two of my previous blog posts. I still am not allowed to share specifics of my results, but I did analyze 210 plants and create corrplots, biplots, and histograms of the entire data set. I then wrote up a summary of these results.

Gene Loci Recommendation

The second project I worked on was writing a short recommendation on two rice loci for future research. This project began by compiling rice loci of interest into a single spreadsheet then finding orthologous genes and the putative functions of them. Based on the putative function’s relation to flowering and rice panicle branching, Lala and I selected 7/31 gene for further research. This further research included the use of databased like StringDB and SNP-Seek, and analysis from readings in the literature. StringDB is a visual tool used to show closely related proteins or genes to the loci of interest. For example as shown below, the red orb, the loci of interest whose name has been censored, has a line connecting it to CML30 indicating a close relationship. If CML30 is found to relate to flowering in other plants, then the loci of interest may also play a role in flowering in rice.

Source: Me

The other program I used was SNP-Seek. Before I began this project, IRRI test grow a population of plants with a known genetic code. These plants were divided into two camps: ones that were less branching and ones that were more branching. I loaded these plants into the program as the Y axis and along the X axis is the genetic code at the loci of interest from a representative rice plant. Only areas in the gene where SNPs (Single Nucleotide Polymorphism) occur are shown. I then look at clumpings of high branching rice plants (green) or low branching rice plants (red) and see if these clumps share many SNPs that the green plants lack. As seen below there is a clump of low branching plants at the top that all share 5 SNPs. Since a SNP may cause the functioning of the gene to be changed, if many low branching plants share the same SNP and many high branching plants don’t, that gene loci probably serves a function in rice branching and the SNP may be inhibiting the proper functioning of that gene.

Source: Me

In the end, I chose two loci for future research. Because of IRRI policy, I cannot share their names, but their putative functions related to CAMK kinases and cytochrome P450 both known to play a role in flowering in other plants.

Total Starch Percent Assay

The final project I assisted with was the Total Starch Assay in the biochemistry lab. For all of my time up until now, I have been working in a cubicle on my laptop, dry lab, but now I will be in the physical laboratory, the wet lab. However, because of scheduling difficulties and running out of time in my internship, I only spent 3 days in the wet lab, so I was only able to learn part of 1 assay, the total starch assay. The goal of the total starch assay is to measure the starch content in rice. This assay is part of a larger project to try to make rice healthier by lowering its glycemic index while still maintain its edibility. We measure the starch content by breaking the starch molecule into glucose molecules, which we can then dye and run in a machine which will detect the relative amount of glucose through light absorption. Much of the experiment is dedicated to creating the proper conditions for the enzymes to deconstruct the starch and to ensure the dye adheres to the glucose.

Work Culture

Finally, I’d like to revisit the difference in Filipino and American work culture. I have found that Filipinos are more lax than Americans in some ways, but more strict in others. As I have mentioned before, it is common for Filipinos to take communal snack breaks in the morning and afternoon. These breaks are not given a strict time limit and their length depends more on the conversation and if there is a timed experiment occurring rather than a strict time limit. In addition, when the work was done we’d be able to leave early. In contrast, the jobs I have had in America have expected you to closely monitor the length of your breaks and leaving early was not allowed. However, these differences may have more to do with the jobs I have had in the states being paid hourly, while those who work at IRRI maybe salaried.

Filipino Food

For these last few blog posts, instead of doing a full recap of each week, I am going to focus on one specific part of my experience in the Philippines. This blog post will be about food.

Ordering Food

This aspect of the culinary experience is very similar to America. Many of the interns used an app called Foodpanda to order delivery which was very similar to American apps such as Doordash or Grubhub. In addition, both places have many restaurants that cater to food from outside their respective cultures. For example, the Wesleyan students ate at restaurants specializing in Italian, Korean, Vietnamese, and even American style cuisine. At these restaurants, the ordering experience is similar to America. You arrive at a restaurant and are seated or seat yourself, a waiter arrives to take your order, then after you eat you receive a bill. One notable fact is that in the Philippines you do not need to tip. However, one restaurant I went to had a different dining style. At the Samgyupsalamat, a Korean barbeque place, instead of a chef cooking your food, you cook it yourself. You pay for unlimited meat for 2 hours, then the waiter will bring in more chicken or pork for you to cook yourself at a small grill in the middle of your table. I believe rice, noodles, and other sides are available for an extra price. Below is a picture showing the setup.

Credit: https://www.ivankhristravels.com/2018/05/samgyupsalamat-unlimited-korean-barbecue-review.html

Restaurants

The other Wesleyan Students and I tried a few of the many restaurants in the Los Banos area. Personally, I was known for my unluckiness in selecting dishes from some of these menus, but still many of these places had good food. One of our favorite restaurants was Seoul Kitchen, another Korean restaurant. There I had the Spicy Pork Bulgogi. Essentially, it is a seasoned strips of pork served with rice, a small salad, and a spicy sauce. When eaten together, these foods make a sum greater than their parts. In addition, I had a side of kimchi for the first time, which I also liked. Finally, we shared an order of Bingsu for desert. The Bingsu we had was a scoop of ice cream atop shaved ice, with Oreos crumbled on top. If you are ever in Los Banos I definitely recommend this restaurant. Below is an “action shot” of the Bingsu we ordered.

Credit: Me

One thing to be careful of when ordering food is that the pictures shown of the food will not always match up with the food ordered, as I learned the hard way.

Fast Food

On the less glamorous side of the dining spectrum lies the fast food of the Philippines. This space is dominated by two brands, Jollibee and McDonalds. Much like Burger King and McDonalds in America, these two chains are always found near each other with similar offerings. One notable difference between Filipino and American fast food is that Filipino fast food serves spaghetti, normally with pieces of hot dog in the sauce. In addition, the sauce for spaghetti is much sweeter than what is normally found in America. Other menus differences include the existence of burger steak, which is a hamburger patty served with mushroom gravy, and almost every meal comes with a side of rice.

Fruit

No discussion about Filipino food would be possible without mentioning fruit. In the Philippines, many fruits considered exotic in America are common. At many roadside stands, fruits such as durian, avocados, and mango are commonplace and cheap. Coconuts are found everywhere in the Philippines. They are even used in one of their signature desserts, buko pie, which is made from the skin of a young coconut.

Conclusion

There is much more that can be discussed about Filipino food, but I have other things to blog about. Hopefully, I have given you a taste of what food in Los Banos and the Philippines is like.

Blog Post 6/26

This week I began to work full time. Sadly, my adviser was out sick for the entire week, so I continued to check the images that have been processed by P-TRAP. Overall, this week was an enjoyable working experience. I was able to listen to a podcast while I worked, and the building has good AC. In addition, everyone here is very nice and friendly. Interestingly, Filipinos take numerous snack and coffee breaks throughout the day. Coffee and snacks is served at around 930 or 10, lunch is normally at noon, then at around 4/5 they break for an afternoon snack. They even have a table in the center of where most of them work dedicated to snacks and drinks. I tried a fried banana which was very good. Towards the end of the week, I finished processing the images and was able to move to the next phase of analysis which involved using R to create three different graphical models of the data.

Histogram Source:https://www.investopedia.com/terms/h/histogram.asp
Correlation Plot Source: https://stackoverflow.com/questions/40509217/how-to-have-r-corrplot-title-position-correct
Biplot Source: https://blog.bioturing.com/2018/06/18/how-to-read-pca-biplots-and-scree-plots/

These three different models each have unique uses in analyzing the data gleamed from the rice data. Again sadly, I cannot share my own pretty models. The histogram is useful for seeing how close the data is to a normal distribution (a bell curve) and any outliers. The correlation plot measures the correlation between variable. A strong positive correlation indicates that as one variable increases, the other also increases. A strong negative correlation indicates that as one variable increases, the other decreases. A weak correlation indicates that values move independently of each other. Finally, the biplot shows how closely related analyzed individuals are. It does this through a principal component analysis which simplifies all the variables analyzed into as few variables as possible, called principal components. The straight lines represent the original variables while the dots represent the analyzed individuals.

That weekend, I and the other Wesleyan students along with the Indian students were invited to an adviser’s home for dinner. There we introduced the Indian students to the card game Cards Against Humanity, and they introduced us to some of their popular music. The food I had there was very good, but definitely different from what I normally have in the states.

Week 1 Blog for 6/19

This week I have more to report.
Despite some delays with my ID card, I was able to start working this week on Tuesday. I began learning the R programming language and I began to work with P-TRAP, a computer software program which helps a user classify rice panicle structure and count the number of rice granules.

credit: AL-Tam, F., Adam, H., Anjos, A.d. et al. P-TRAP: a Panicle Trait Phenotyping tool. BMC Plant Biol 13, 122 (2013). https://doi.org/10.1186/1471-2229-13-122

Above is an example of the analyzing structure part of my job. I am not allowed to share the results I have worked with so far, but above is an example from the paper originally describing the function of this software. The software is not that good at developing the above structure on its own, so my job is to fix it.

On Friday, IRRI had a day in the field for all the student workers. The Illinois Wesleyan Students, along with some students from India, were able to be rice farmers for the day. We got to use both traditional and mechanized ways of planting rice, even using an ox to plow a rice field. We also practiced different methods of planting rice, including planting by hand and machine. Also, I learned that around 70% of Filipino rice is still planted by hand, but mechanization is being slowly adopted. I am still waiting on getting some photos back from IRRI, but once they are here, I will upload them to my blog.

After the rice picking, Froilan, the main person at IRRI who has helped us get settled, offered to take us on a tour of Los Banos. He showed us parts of the campus, The Philippines’s largest lake, and brought us to a dairy shop where I tried carabao milk, a cow native to the Philippines and the same kind used to plow Filipino rice fields. It tasted like slightly bitter whole milk. Finally, our group had Buko pie, a coconut based pie that tasted very good.

Finally, on Saturday, some of the other Wesleyan students and I decided to go on a hike partially up a nearby mountain to see a mud spring. We left early in the morning and walked by a bazaar, a group of outdoor shops that sell food. They had lots of different options of food, and music was being played on a speaker. We then worked our way through town towards the entrance of the trail. Once we were there, we had to check in, then begin our climb. During our climb, we saw many cyclists, and people enjoying the trail. It was a steep hike, especially for someone used to the Midwest. The trail was paved, really a narrow road. There were even motorbikes and a few cars driving on the trail. As we approached our destination, we were surprised to find a few snack/touristy shops that was relatively busy. Shortly afterwards, we finally reached our destination: the mud spring.

From the mud spring there a slight smell of sulfur, and you could see some plants have died from being too close to the boiling mud. There was a barbed fence that surrounded the pit with signs warning of severe injury if you touched the mud. We then returned to campus and picked up McDonald’s on the way back.

Blog Post Number 1 6/13/22

Travelling and Quarantining

This first blog post will most likely be shorter than my future posts. We flew from O’hare to Doha, 8 hour layover, then a flight to Manilla. Much of the time on the plane was spent either sleeping or watching shows. The Doha airport was big and had interesting architecture. Also it was interesting many ads featured soccer players similar to how adds in the United States will feature football or basketball players. Then once we landed we were dropped off at IRRI to sleep. The next day we began an orientation to learn some Filipino phrases and etiquette and ended the day by going to a buffet with good food including chicken adobe.

Then the IRRI people split off from the rest of the group and began a week long quarantine. Not much happened during this time. We did go shopping twice at the southern mall/grocery store. In many ways it was similar to an American grocery store but with some minor differences. Snacks were divided into imported and local, milk was not refrigerated, and guards would check your receipt before you left. In addition, before you entered the shopping area there were a couple of small food/snack places. There I tried a shawarma place and a seasoned French fry place, both of which were tasty. Besides shopping, during my quarantine I was given some readings relating to what I will be doing during my internship. Once my internship starts, I will get into more detail about what I’m doing. Today (Monday), was supposed to be my first day, but due to delays and miscommunications I was unable to start working, but I did move out of my quarantine dorm into my dorm for the next two months. Tomorrow I finally get to start my internship which I am excited for.