We’re Cuckoo for Copepods

The alarm goes off on my phone. I simultaneously acknowledge and try to ignore it. Try. It’s 4 am and too early to be alive, and yet here I am, trying to calculate how many times I can press snooze and still be on time.

Today is sample day.

I eventually dredge myself out of bed and get ready. Now that my brain is booting up, I start to feel excited again. After all, this is the first time I’ve ever done fieldwork for my major, so it doesn’t matter that it’s just a sample collection. My phone buzzes: they’re here. After a final check to be sure I have everything, I hurry outside and get into our sketchy looking lab van.

Location: Point Dume
Date:  July 3, 2019
Party: Sam the man, they call me Logan, and Asher pod catcher.
Objective: collect all the samples, disturb some ecosystems, protect UCSB

After a short drive, we finally reach Point Dume state beach, where we unload our weapons of choice: tupperware and turkey basters. We prowl the edges of the rocky beach, flashing our lights into the various tide pools hidden within the craggy boulders. Our target: Tigriopus californicus, sometimes known as the tiger copepod. Although they’re small, tigs have a remarkable tolerance to conditions that would kill many other creatures, such as low pH, high temperatures, and low levels of oxygen. Furthermore, many scientific papers show that these tolerances vary based on the climate and location of where the tigs live. Our research project aims to find what role, if any, genetics plays in these differences. But before we can get to that, we first need to awaken our inner pokemon fan and catch some tigs.

100% skill and precision.

 

Back at UCSB, we began the process of labeling our samples and testing the range of tolerances of our tigs. For this experiment, we specifically focus on thermal tolerances to explore how different populations will be able to handle increasing ocean temperatures. To do this, we calculate the lethal temperature 50% (LT50) by putting our tigs through an almost-literal trial by fire. The most accurate way to determine a population’s LT50 is by slowly increasing the temperature of the tig’s environment up to a high temperature, then maintaining that temperature for a while. Luckily, a thermal cycler can do just that, and tigs are small enough that we can comfortably fit 5 of them into a PCR well. We do this through the incredible and highly competitive process known as tig loading.

The set-up is a dream. The prep work is a nightmare.

 

Thermal Tolerance Testing

Ingredients:
12    8-well PCR tube strips
480    T. californicus (if doing a complete 96 well plate)
1    Micropipette, set at 24 microliters
1    Thermal cycler
∞    Amounts of patience

Start by preheating programming your cycler with a temperature gradient of 36-38°C.

Contemplate your life choices as you meticulously fish out 480 tigs using the micropipette as an inefficient vacuum.

Catching multiple tigs at once gives you bonus points.

Panic when you realize you lost your place loading the wells.

Place loaded wells into your cycler for 3 hours total: two to slowly bring the temperature up, then one hour at that temperature.

Remove and serve hot.

We then fully accept our fate as hunchbacks and use a dissecting microscope to look for survivors in each well. By counting the number of fatalities, we can calculate the proportion of survival at each individual temperature. This gives us survivor proportion as a dependant variable with respect to temperature, which can be easily plotted onto a graph using RStudio. The best part about using RStudio is that the different thermal tolerance graphs we plot can be combined with each other into a single graph, giving us an easy-to-read visual comparison between populations.

Pretending that you know how to use R is an important step.

And that’s a wrap! Between the early morning collecting and giving myself nearsighted blindness, I think I’m ready to call it a day. This was definitely one of the more eventful days I’ve had in the lab, but I really enjoyed it. It’s really starting to feel like I’m contributing to the lab and project. Tomorrow will be another busy day setting up cultures for out tigs, and a few days later will be another sampling trip. I can hardly wait!

A Day in the Cleanroom

When you walk by Engineering Science Building, you can always see people in the cleanroom wearing bunnysuits doing magical things. But it has been somewhat mysterious as of what people actually do in there. In this blog, I’ll show you what I have done so far in the cleanroom as an intern.

Storage Bay

After you get gowned and enter the cleanroom, you would first collect your tools and glassware from this bay. Each group has their own assigned area for storing boxes.


Solvent Bench

It is necessary to clean your wafer before you start to process it and the cleaning is done at the solvent bench. At each bench, there is a laminar flow fume hood to prevent exposure to the fumes and vapors from solvents. There are also nitrogen guns for drying purposes. One typical solvent people use to clean the wafer is Acetone.

(Photo credit: UCSB Nanofab)


Spin Coat Bench

At this bench, people can spin photoresist coating on their wafer. The procedures are to put wafer on the spinner chuck, evacuate the spinner to fix the wafer on the chuck, drip photoresist, set the spinning speed and time (there are built-in recipes to choose from), start spinning, vent the spinner once it stops, and take the wafer off. There are hotplates set at different temperatures (105°C, 110°C, 115°C, etc.) to bake the photoresist coating.

(Photo credit: UCSB Nanofab)


Atomic Layer Deposition (ALD)

This equipment is a plasma-enhanced system for precise layer growth. One of the chambers is used for metal growth, and the other is used for dielectric growth. You only need to load your wafer into the load lock chamber and you can operate the equipment via the computer. There are also well-written process recipes for ALD, and you only need to change the number of cycles to run the recipe depending on the film thickness you want.

 

(Photo Credit: UCSB Nanofab)

Working in the cleanroom is both exciting and challenging. A lot of things could go wrong through the fabrication process, but you can always learn new skills and new perspectives of thinking.

From an Innocent Girl, to Undergraduate Actuarial Researcher

A year ago, I finished my high school degree in the United States, and was able to go back to China, the place I lived for 15 years. I visited my grandparents who raised me up and took care of my for my entire life in China, but I was shock by how much was changed to their health condition. People I care about the most is getting older and older, and suffering from different chronic deseases. I was sorrowful, and wanted to do something. That was the first time I truely realized my value of existing is to bring something valuable to the world, and to people.

I was lucky, because I got a chance that summer to explore this thing called research. I was selected to attend a 2 week research summer program: SIMS. That was my very first peak to the world of research. I was asked to rank a list of research projects as my favor to work with, when I saw one about investing cancer tumor cells, I put that on my top one without any doubt.

Two weeks passed really fast with an extremely packed schedule. I tasted my first fruit from the research experience: we truely got a data that can be a tiny contribution to approach cancer cure. I realized that research is such a fastinating thing that can really be a way for me to help people and the world. So I started to dig in more to learn about different research fields. I want to find the right one for me.

As an actuarial science major student, I didn’t realize there could be so many research topics to help with the world for this type of subjects as well until I met Mr. Duncan in actuarial association at UCSB. Besides being a professor at school, he is a successful actuary working in industry for over 30 years. But he is always passionate about researching and encouraging young researchers. I was totally amazed by how much papers and books he has published, and how respectful he is in actuarial field. At that moment, I realized I can do research and help people as well with math and statistics, these tools I am more comfortable with.

This summer, I am honored to work with Mr. Duncan on a research project about developing a predictive model on hospital readmission rate. While health care is often unaffordable for us normal people, especially those without health care insurance. With our model, we want to predict the hospital readmission rate for different types of patients, so that hospitals can provide enough care and attention ahead, so that hopefully to reduce the hospital readmission rate, and also, reduce the costs to go to hospital for patients. To make health care affordable is a big goal, but every little effort is worth trying and can approach to the goal closer and closer. I am sure that is true for all fields of research.

I have a great goal, that is to change the way people live, and help make our life and the world better. Innovation and research is the best way to real that goal. It might be a brand new area for those who never get in touch with research, but as you work hard, and find more opportunities, your research skills get better and better, and eventually, everyone can do their parts to help with the world.

When your research results glow

E. coli glowing: Agar plate of E. coli, some with the red fluorescent protein gene

Staring at our plate, my lab partner and I couldn’t help but smile, tears and sweat dripping down our faces.

We had actually done it.

Our teacher had told us this would be a long, hard journey, and that some of us would not be successful. After this week-long quest, we obtained the red fluorescent treasure at the end. We were successful.

Everyone surrounded our plate and us, staring at it in awe as well.

My lab partner looked at me and said, “Our E. coli are literally glowing red! We did it!”

I first realized my passion for microbiology and research when performing a week-long experiment in my A.P. Biology course as a junior in high school. We conducted a bacterial transformation using recombinant DNA technology to insert our gene of interest– a red fluorescent protein gene– in a bacterium, Escherichia coli. As seen in the picture above, this gene allowed the bacteria to, well, glow red! It was a long process that, if not you did not follow the procedure exactly as stated and if you were not paying attention to detail, you would not get the end result.

This short but sweet experiment is a small scale example of what research is like. The process to get to an end result might be long and daunting, but once you get the result, it is like eating that cake after a week of being on a “diet.” I am painting the process as being unenjoyable, but on the contrary, it is full of exciting moments as well and each step encourages you to keep going. Even on setbacks, you learn from them and find new ways to tackle what you were working on.

As I mentioned earlier, my passion for research really started when doing this experiment. I had done other experiments, such as what factors affect the rate of photosynthesis in leaves and understanding the physiology of roly-poly bugs, but none really caught my attention as the bacterial transformation experiment. There are many branches of research that people can go into. You can be in a lab with a microscope, 60 feet underwater in the middle of the Pacific, or in the valley with hiking boots and a large bottle of water. I prefer to be with a microscope and pipette, looking at organisms that are much smaller than I am and understanding their importance and complexity.

Phytoplankton: Different species of phytoplankton collected at the Sea Center

Since there is such a diverse range of research topics, you may not know what you want to go into or what you enjoy most. It is important to try different research areas first. I knew I enjoyed microbiology, but that is still a broad category. I first combined my interest in the ocean with the smallest creatures that live in it: phytoplankton. I was in a laboratory that researched how climate-induced changes affect the physiological and community composition of phytoplankton.

Even though I enjoyed studying phytoplankton, I was drawn more towards the biomedical side of research. I downsized in the organisms I was studying to viruses, which are even smaller and less complex than phytoplankton but have huge impacts on individual people and communities at large.

In general, research allows you to explore your interests while also teaching you patience, new skills, and how to follow a procedure, because trust me, you’ll need to pay attention to all the details in order for your end result to glow as our E. coli did.

chloe

How my Research Perceptions Changed

When I first envisioned research, I thought of a white coat scientist in a laboratory setting. I would never have guessed the EUREKA program would expose me to so many different fields of research. Research projects range from analyzing biochemical processes to coding computer programs and working with participants to examining complex mathematical functions. Although the term “research” can be associated to the cliche white coat lab setting and specific areas of study, the beauty of research is that it can be applied interdisciplinarily with the same goal of advancing knowledge and bettering society. Aside from that, I perceived research as a lone activity. With the experience I’ve gained so far in my lab, I’ve realized that I am constantly communicating with lab members about data analysis and various machinery. Research is a cohesive, team-effort and even includes communicating with people outside the lab such as official personnel and other faculty advisors. In fact, communication and connections are one of the most crucial factors leading to success in a research project.

On the other hand, I completely expected to be surrounded by intelligent and inspiring people such as my project’s faculty advisor, post doctoral, graduate students, and research assistants. Each colleague is an opportunity to learn something completely new and deepen my understanding of the project at hand. Additionally, I knew that research rewards hard work and continuous effort. Whether you are running a participant, analyzing data, or keeping up with the literature, you are responsible to have the initiative to do those things. By doing such tasks efficiently, you gain more information and skills directly tied into the betterment of your future. On top of that, expressing your interests and initiative to the lab members allows them to find ways to make your experience as beneficial as possible.

All the experiences I have gained from research were beyond what I imagined for myself and it’s a journey that every researcher takes. Research takes you down a road you never expect, and from there you decide what you can do with those skills. Ultimately, everyone’s research experience will be different and your perception of research will change over time in hopes to gain a better grasp of being a more valuable researcher.