SPA Bioinformatics Trip 2019

DAY 1 ~ Bienviendos El Jobo

TRAVEL

Today started with a tired but enthusiastic sendoff from the MSP airport at 3:30 AM! Pia (not Helen) was four minutes late. After a quick flight to Atlanta everyone managed to find snacks and get comfortable for the quick 3 hour jaunt to Liberia.

After landing we boarded the bus and headed for El Jobo! Obviously we stopped for some chicken, rice and beans before the two hour journey to the coast!

R&R (rest and relaxation)

After arriving in El Jobo and meeting our host families we enjoyed some free time. Some played soccer with the younger children, and the most fun ones went to the beach. Also we bought snacks.

After our adequate rejuvenation, we were ready for more learning. We met a nice french woman named Mathilde who gave us a great presentation on the local efforts of turtle conservation. She explained that tomorrow we will be catching and tagging turtles which seems like it will be a blast. Mathilde works for an organization called Equipo Tora Carey which is focused on turtle education.

The food is delicious (this is actually a picture of lunch)

R&B (rice and beans and big bugs)

Yum yum dinnertime. We had a highly anticipated meal of beans, rice, fish, and lettuce. Very good. Dinnertime was very exciting because there were many large bugs, and some students were pretty excited. Dinner and a show for the rest of us.

Adios:)

From your friends Pia Helen and Katie

Day 2: Sea Turtles!

Today started bright and early with breakfast at 6 AM. From breakfast we headed to the beach where we got onto boats and headed out for our first snorkeling adventure. We saw tons of awesome fish, some rays, and even a large nurse shark! In addition, we helped the research crew tag and process two sea turtles. We had lunch on the boat and headed back to shore for an afternoon of rest. Before dinner we spent an hour helping count parrots moving from the feeding grounds to nesting grounds. After dinner we swept two beaches looking for sea turtle nests. We learned a lot about sea turtles and how human actions impact their environment. It was another amazing day in Costa Rica!

Checking out the local sea life from the boat

A scorpion from our hike to the beach to look for sea turtle nests

The Amazing sunset over El Jobo during our parrot count

Capturing a turtle so it can be tagged and processed.

Learning about parrots and how to collect data

The views from the top of the hill



Day 3 - Sea Rays, Beach, and a BBQ

Today was the third and final day in El Jobo for us, and boy oh boy was it a doozy. It started off fresh with a nice, invigorating 8:00 AM breakfast at the houses of our host families. We then took the bus down a hilly, gnarled gravel road to the beautiful *Insert beach name here*. There, we met with Matilde, her son, and several other local youth who were working with Equipo Tora Carey. They proceeded to teach us the strategy to catch the stingrays that were plentiful on the sandy ocean floor near the beach. Armed with a snorkel kit and a net, we were to dive down to the bottom, entrap the stingray with the net, and bring it to the shore for processing. Turns out stingrays are wicked quick and most of the attempts to catch them were unsuccessful, with a few notable exceptions, mostly from the local kids and staff of the organization. Once caught, the stingrays were placed in plastic bins filled with water to await the data collection. This data collection included identification of the ray’s species, measurements of the body and reproductive organs, and observations of any discolorations in the eyes. While one half of the group was occupied with stingrays, the other half worked on a beach cleanup project, where the amounts of different materials found were recorded for another study. Then, as we hit the midday mark, we returned for lunch.

After another delicious fulfilling lunch, we waited out the midday heat with unscheduled relaxations. Playing cards, taking a nap, and picking mangoes from trees kept everyone entertained for multiple hours. Once the weather cooled down, we took bus to the larger town of La Cruz and had some frozen beverages. We had many flavors to choose from ranging from blackberry to “sour sop.” The restaurant had an amazing view and many kids took photos of each other and the landscape. We then went back to the beach and relaxed on the sand, watching the sunset go down. It was a beautiful view. To top off the night, we went back to our little pueblo and the locals cooked us a barbeque with chicken, fish, and sausage.

Buenos Noches!

Sam and Sharee

Lounging at the beach

Catching and studying sting rays

The amazing view from the restaurant

A giant iguana in the wild!

Learning how to process rays

We are having an amazing trip

Playing cards during our downtime.

Getting ready to capture rays! The bright things we are holding are our safety devices for snorkeling

The beach at sunset!

Ms. Seibel Hunt keeps apologizing for the views. I think we can all see why

Great views and great friends!

Playing at the beach with some of the local kids from El Jobo

Our garbage collection data. Lots of plastic!

There are lots of hermit crabs at the beach.

Learning how to capture rays. It is much easier in theory than in practice :)

Writing thank you notes to our amazing host families! We have loved our time in El Jobo!

Day 4 - On to Monteverde

Today we took the bus to Liberia to the supermarket where we stocked up on interesting Costa Rican snacks. Then we continued on up a windy mountain road to the CIEE where we will be doing our bioinformatics research. We immediately jumped in another bus and went to the Monteverde Cloud Forest Preserve where we went on an amazing guided hike and learned all about the biodiversity in this part of Costa Rica. We've settled into our cabinas and can't wait to start our bioinformatics research tomorrow.!!

Buenos Noches!

Maya and Katya

Goodbye to Kembly's where we had many amazing meals in El Jobo

Enjoying the biodiversity in the cloud forest

A sighting of the rare Quetzal!!

The canopy in the cloud forest

Learning about choke vines

Humming birds! There are many different species of hummingbird in Monteverde

These little orange flowers are actually orchids!

We hiked to an amazing waterfall

Listening to our guide explain the interactions between different plant species

Having fun in Costa Rica!

Learning about our new home at the CIEE classroom

Stay away from the pinchers on this bug!!

Day 5 - Zipping through Monteverde and our Research Projects

Today we started off with another delicious breakfast at the lodge and then headed to our first bioinformatics class. We brainstormed ideas for our projects and worked on our proposals with partners. In the afternoon we did an amazing zip line through the cloud forest. We were really lucky and had fantastic, clear weather so we could see Arenal volcano and Lake Arenal in addition to flying above the canopy of the forest! After dinner (and ice cream!) we presented our project proposals wrapping up another fun and productive day in Costa Rica!

Excited about the zipline!

The view from one of the zipline platforms

Learning about bioinformatics from Gabriel - one of our great instructors

A project presentation

Day 6: Birding, Science, and a Night Hike

This morning we all got up early for a 6:30 AM birding hike with staff naturalists from CIEE. While most groups only saw smaller birds (including some really cool hummingbirds), we all learned a lot about the local plant and animal life at the Institute. After breakfast we worked on our projects with our partners including looking up background literature, compiling genome information, and making figures for our final posters. At lunch we took a break and the group that hiked back to the cabinas got to see a group of monkeys play in the trees right off our back decks! The afternoon was another research session and after dinner we ventured out on a nighttime hike.

We started our day with a birding hike

The little flowers you see are actually mistletoe that has grown around this tree.

Our naturalist showed us lots of cool stuff - there are MANY types of wild avocados that grow in Costa Rica.

After lunch, a group of monkeys visited the trees outside the cabinas.

Another monkey picture because - MONKEY!!




Day 7: Coffee, Sugar, and Science

Almost all of the dairy products we eat in the cafeteria at CIEE come from the dairy cows on campus. In the mornings small groups have been getting the chance to help milk the cows. It is really cool to see how sustainable life is at CIEE. Waste from the bathrooms is fed into a biodigester that uses bacteria to break the waste into methane that is piped to the kitchen for cooking fuel, liquid that after 3 months of treatment enters a tilapia pond, and solids that are used to fertilize the crops that in return feed the cows. Food waste from the dining hall is fed to the pigs at the farm.

In addition to spending time on the farm at CIEE, today groups traveled into San Luis to visit small farms that produce coffee and sugar. One group got to see how coffee is processed and roasted and the other got a detailed demonstration on how sugar cane is turned into sugar blocks.

The trip to the farms gave us a great opportunity to explore the local area on foot and we all stopped at the small shop near campus for some snacks on the way home.

We also had time for plenty of science this morning and in the evening. We are all making great progress on our projects and are looking forward to presenting them when we get home.

Half our group toured a local, organic coffee and sugar farm.

We learned about the coffee growing and harvesting process

The farm (and town) were home to many dogs

We also saw a field of sugar cane

There were great views from the hill at the farm.

This machine that processes sugar cane has been in this family for 70 years

The machine is usually powered by oxen, but today we used student-power

At the end we got to taste the results of our labor.

The dairy we eat at CIEE comes from the on site cows

The pigs eat the scraps from our plates.

We got to try our hand at helping to milk the cows

Waste is fed into a biodigester to create water and fertilizer for the fields.





Day 8: Science and Horses

Today's recap is provided in rhyming verse courtesy of Ryan, Evan, and Sydney


For our projects we cited all of our sources

And later we galloped on horses

The horse lifts its tail and out comes its farts

This experience is shaping our minds and our hearts

We've eaten lots of Costa Rican treats

And ridden on many bus seats

We love seeing fuzzy farm critters

And even tarantulas who skitter

We've enjoyed exploring the Cloud Forest

And there's still lots of fun left before us

"Write a poem", said Sydney, "it will be fun!"

She'll show up as soon as we're done

We're not very good at writing rhymes

But we're having a really great time!

















Day 9: All science, all day

Today's post brought to you by Abdel and Lyle

Today we didn't do anything outside of the campus. This gave us a lot of time to finalize our posters and practice our presentations before we had to give our final presentation tomorrow. During the morning classroom session, everyone finished their poster designs and practiced presenting. Then, in the afternoon, everyone got the opportunity to present in front one of the teachers and receive tips on how to improve their projects. We also had a break in the middle of poster design where we all got to play soccer. There was also some yummy yummy cuisine, including cheese tortillas with breakfast and yucca with lunch. Finally, we worked on our projects some more after dinner, including more presentation practice and peer feedback.



Day 10: Morning Research Presentations and Afternoon at the Bat Jungle and Santa Elena

Our final full day was spent presenting our research projects to the group, our instructors Gabriel and Jose, and a few of the naturalists that are on campus at CIEE. See photos below of the researchers and their project titles! After lunch we headed into nearby Santa Elena to enjoy a presentation and visit to the Bat Jungle. From there we had a few hours to check out Santa Elena, the largest town in the Monteverde region. We had the opportunity to get souvenirs, a latte or ice cream, and see this beautiful little town on our last day together.

Jackson Small and Milo Waltenbaugh

The Functions of Microbial Communities within the Fungus Garden of Attine Ants and Pine Beetles

Sydney Therien and Sam Steinhacker

Exploring the Synthetic Estrogen-Degrading Capabilities of the Genus Bacillus and the Pathways on Which They Operate

TJ Isberg and Eddie Gamble

What You Put in is What You Get Out: How Diet Affects the Composition of the Gut Microbiome and Overall Human Health

Evan Barnes and Abdelrahman Mokbel

Analysis of Rhizosphere Microbiomes in Corn, Switchgrass and Miscanthus Plants

Abby Hedberg and Pia Schultz

Cleaning Contaminated Water: A Study of the Oceanic Microbial Community and its Biotic Potential

Lyle Menard and Jackson Biggs

The Effect of Diet on the Efficiency of Cellulose Degradation in the Rumen

Ryan Strobel and Sharee Roman

Common Mastitis-Associated Virulence Factors in E. coli, Staphylococcus aureus, and Streptococcus agalactiae

Pilar Saavedra-Weis and Isabel Medrano

Comparing the Microbiomes of Human Inhabited vs. Non-Human Inhabited Soil

Katie Beran and Helen Bartlett

Groundwater Bioremediation- Comparing Microbial Discrepancies and Methane Functions in Contaminated, Clean, and Bioremediated Groundwater

Katya Sjaastad and Maya Choi

How does a historic hunter-gatherer diet compare to a modern diet regarding the impact on the gut microbiome?