Tag Archives: tomato research

My Time at Davis

1 Aug

Well, the trip is officially over. I am back from Davis and this time to stay. (I came back for the July 4th weekend and last weekend as one of the YSP fieldtrips).

Looking back I have to say that I had a good time. Originally, I was nervous and very unprepared for the unexpected. I was almost ready to call the director and tell him that I had changed my mind, especially since I felt that I was going to miss out on baking internships/jobs/classes. But you know what? I’m glad I went to Davis. There are no regrets.

The research part of the program was especially interesting. I was able to work with tomato seeds all the way from the beginning. I chose the little seeds from the tomato library in the Plant Science building with my lab partner, Jina. We counted ten seeds per tomato introgression line (IL). And for those who don’t know what an IL is – and don’t feel bad because I didn’t know what it was until I got to Davis – is a domestic tomato genome that contains a small, known genetic region from the wild tomato (S. pennilli).
The project was to germinate the IL seeds to see what the wild tomato region in the domestic tomato genome produced. Previously, the lab had already categorized the traits that belonged to the domestic tomato and the wild tomatoes so they could compare the IL’s physical traits to the known traits. If the IL exhibited a trait that belonged to the wild tomato, then the IL was said to contain a quantitative trait loci (QTL), which contains that gene responsible for the physical trait. It’s kind of confusing, I know, but if you’re truly interested in more of the research just comment and I’ll go into depth further.

Once I had the seeds, I put them into sterilized plates that contained a nutrient-rich agar media so we didn’t have to open the plates and risk contamination. I kept the seeds in there until seven days after germination and scanned the plates daily.

Basically the results of the experiment was that certain IL seeds did contain QTL responsible for a specific trait. In the future, the lab will work on genetically identifying the genes within the QTL to establish a gene-to-gene relationship network within the wild tomato. This network will detail how genes interact with other genes, and and how transciption factors and promoters affect gene expression (phenotypes).

Wild vs. Domestic Tomato

A- Wild tomato(left) and domestic tomato(right) B-domestic tomato; contains three cortex layers and linear xylem cell structure in middle C-wild tomato; contains two cortex layers and clumped xylem cell structure

IL seeds on microscope slides

IL seeds on microscope slides. The seeds were made transparent using chloralhydrate so I could count the number of lateral roots (emerged and initiated).

Analyzing lateral roots

Analyzing the IL roots for lateral roots (emerged and initiated).

Planting the IL Seeds

Transfering two IL seeds from the sterilized plates to plastic containers

IL seeds planted

IL seeds planted. Containers are placed in a special plant chamber that provides 16 hours of light and 8 hours of darkness.

The whole IL family

The whole IL family in the plant chamber.

So these are the photos that I am allowed to put up. It kind of gives you a glimpse of what I’ve been doing these past few weeks. It was very nice to work in a lab especially with this project because it was brand new. The lab researchers were literally just starting the project when I got there so these are the first big batch of ILs (36 ILs out of 72 ILs). I set up the experiment, gathered the data, analyzed the data, and then presented the data and conclusions at my program’s symposium on July 30th.

As far as the presentation goes, I was really stressing out for it. Maybe I wasn’t “stressing” per say, but I was panicking on the inside. I made sure my powerpoint was decent enough and then wrote out my transitions from slide to slide because otherwise everything just seemed awfully incoherent. Because of the number of times I practiced, I actually ended up memorizing my slides and what was on it. I didn’t memorize word for word and I didn’t write everything that I was going to say on the slides so the presentation actually turnedĀ  out alright.

My presentation was after lunch so I told myself that I shouldn’t eat too much before it because I knew that when I started getting nervous, I’d get the butterflies in mystomach, and when my stomach is full, I’d get a stomach ache. But, I ate anyway. A lot. Like a lot more than I usually do because it was the last time I’d be in the Dining Commons for lunch. I ended having to wait for my mom and family friendĀ  (Eric) at the dorms because they didn’t know how to get to the lecture hall. This kind of made me more nervous. And then once we got to the hall, we had to wait outside for the presentation inside to finish. Once inside, I sat down near the back but I moved forward because I was up after the guy that was speaking. But then, my researcher (Mily) comes and takes me out of the hall to tell me that my data was somewhat inconclusive for the lateral root counts and that I’d have to mention that in my presentation. I basically nodded my head and said that was fine and went back in. Three minutes later, it was my turn.

I got up out of my seat with an already flushed face from the heat, running around, and nervousness. I thought about my best friend and how she always smiles during class presentations and I figured I’d be okay. Once in front of everyone, I just opened my powerpoint and then looked at everyone. There must have been at least 50 people (39 of which were the YSP scholars like myself). I kinda smiled and told myself, “This is it. Showtime”.

Once I saw my slide and started my introduction, the words just flowed. I glanced at my slides when I needed to and when I was changing topics. I was dreadfully nervous up there though because the seats are ascending so the people in the back are not only far away but really tall. I tried to do hand motions but that kind of failed so I just kept still most of the time, and it turned out okay.

After each presentation, there are about five minutes for questions so when I ended, I waited for questions. Surprisingly, I understood the questions so I could answer them. I felt really accomplished after the presentation because I’m not much of a public speaker. I have a soft-spoken voice – so I’m told – and big crowds can just be a little intimidating. But it worked out, so I’m glad. Best of all, my mom was extremely proud of me. My whole research team and friends even greeted afterwards. Pictures were taken to capture the happy (relieved) faces of all of us who were done presenting.

With friends after my presentation

Hanging with my friends after my presentation. Check out all our spiffy outfits!

I also wrote a paper on my research, but I might submit it to a scientific journal so I can’t reveal anything on it really. All I can say is that it had to look like a published scientific journal and mine came real close. I had the all the parts (abstract, introduction, materials and methods, discussion, etc) and the right format (two columns with headers and footers). It looks really nice, “looks” being the keyword. :)

But enough of the research, the friends I made in the program are hopefully friends for life. I know that I’d love to keep in touch with them if they’d be willing to too. After all, friendship is a two-way street. Now, I’ll be posting up some photos of our fieldtrips, adventures around town or in our dorm, and anything food related.

Plant Life Science Building Potluck

Theme: Food Inspired by Scientists and Their Discoveries

Theme: Food Inspired by Scientists and Their Discoveries

Photosynthesis Salad

Photosynthesis Salad

Indian Rice

Corn Bread

Corn Bread

Allie and Da Hae preparing the pasta

Researchers Allie and Da Hae preparing the pasta

"Mold" Jello
“Mold” Jello. It’s supposed to be how we spread yeast over plastic plates/slides.

Berry Tartletts

Berry Tartlets

My plate of food

My plate of food :)

Making Brownies in My Dorm (Rm. 312)

The set-up and ingredients

The set-up and ingredients

Mixing, mixing, mixing

Mixing, mixing, mixing

Brownies in the oven

Brownies in the oven

Brownies all done

Absolutely perfect for dorm brownies :)

Tahoe Fieldtrip

Tahoe Research Center

Tahoe Research Center

In the Tahoe Researh Center

In the Tahoe Researh Center

Ice Cream Shop at Tahoe

Ice Cream Shop at Tahoe; friends Jina and Ben are shown walking :)

Making wishes at a wishing well

Making wishes at a wishing well

Wish Description

Wish Description

Tahoe Beach

Choosing a spot at the Tahoe Beach

Tahoe Beach 2

Group Photo

YSP Group Photo ... missing a couple of people

Group Photo - full

All of us :)

Professor’s BBQ

The infamous peahen

The infamous peahen that woke up us all up at 5 am.

Jina (lab partner) and Coline (best roomie ever)

Jina (lab partner) and Coline (best roomie ever)

My plate

My plate: portebello burger, chicken alfredo, salad, fruit salad, etc

Professor's tomatoes

Professor's tomatoes in her backyard

Trip to San Francisco & Alcatraz

Ferry ride

Ferry ride

The Alzatraz Tour

The Alzatraz Tour - had to wear funky headphones

Boudin for lunch

Boudin for lunch - the breadbowls were so good! And the tomato soup was actually a good match for the sourdough too.

At Fort Point under the Golden Gate  Bridge

At Fort Point under the Golden Gate Bridge - it was so windy and cold. Don't we just all look wind whipped-lashed?

Move-Out Day

Saying the last goodbyes

Saying the last goodbyes with friends (Ben, Jina and Daniel)

With all these photos, I’m sure you’ve gotten a pretty good view of my time in Davis. There were definitely some crazy moments of pure randomness – my roommate Coline can vouch for that – as well as times of pure scholarly chaos with turning in journals to counselors, writing research papers, and making it to rooms before room curfew. :) But these moments are probably what made my time at Davis the best. And these moments couldn’t have existed without the people there. For sure I’ll never forget anyone from that program let alone the people I spent a lot of time with. Like I mentioned before, the friends I made are friends for life.

Here’s a video my friend Ben made.

YSP 2010 from Ben Yang on Vimeo.