Shihoko Kojima found her high school science classes interesting, but what she really wanted to chase was research. Put simply, she thought it sounded really cool. 

“I wanted to do something different,” she said, “I didn’t want to wear business attire or work in a small office everyday. Research sounded like a way to achieve that.” 

Shihoko Kojima

Shihoko went on to earn undergraduate and postgraduate degrees in Japan. As she approached her pHD she wanted to change her field of study and eventually came across circadian rhythms at a conference she attended. 

“I was flipping through the abstracts that were going to be presented and came across a few that mentioned clock genes. That’s how I became interested in circadian rhythms. It was so clear to me what those genes could be doing in your body. The idea of figuring out how those genes control behaviour, that was fascinating to me.”

Today she’s an Assistant Professor and circadian rhythm Researcher at Virginia Tech. Shihoko explained for us, in lay terms, how clock genes impact us, how she investigates them at the cellular level and how her team is moving forward despite COVID-19…

  • Before we get ahead of ourselves, how would you explain a circadian rhythm? 
  • They’re rhythms that run every 24 hours and control the body’s functions, like sleep. It’s not just humans that have them either. All animals and plants have them – humans aren’t special in that way.
  • What is a ‘clock gene’ exactly?
  • They are genes that rotate one another, if you will. If you want to think of it visually, one set of clock genes forms one gear and another set of clock genes form a second gear and so on. They interact with one another and turn each other on and off. Clock genes control a lot of things like metabolism, the immune system, the reproductive system and neuronal activities. There are clock genes in almost every cell. Immune cells, for example, defend the body from viruses. The clock genes within immune cells can moderate, at the cellular level, the best time to do different activities in order fight off pathogens.
  • What does your lab at Virginia Tech focus on?
  • Right now we’re trying to understand the function of a new gene we found a few years ago. 
Shihoko and some of her lab members.
  • You found a new gene?
  • Yes, but what we’ve found doesn’t quite fit the typical gene description. It’s called a non-coding gene. We weren’t looking for it, but we accidentally found it and we call it Per2AS. Right now we’re trying to understand how it functions but because it isn’t a typical gene we can’t use the normal strategies to understand it. We have to think outside the box. We’re using experimental tools and mathematical analysis to learn more about it.
  • What have you learned about Per2AS so far?
  • Our first attempt was to predict its functions using mathematical tools. We predicted Per2AS would have some impact on circadian rhythms and we designed an experiment to test the prediction. We’re working on a paper about it right now.
  • What does your lab look like?
  • Well I’m a molecular biologist really so I spend about 50% of my time at the bench and 50% of my time in the office doing informational and mathematical work (when I am not teaching). I have four full time scientists, including graduate students, and two undergraduate students working on my team. We use LabArchives to track all of our data, and I use it every minute, actually.
Shihoko’s lab uses LabArchives to record all their work.
  • What shape does your data take?
  • We do A LOT of gene expression analysis and generate a ton of QPCR data, so we end up with Excel files, image files and PDFs. We keep all of that in LabArchives. The inventory function has been really helpful for us too, since we work with so many cells and DNA sequences, and need to be planning for future experiments all the time. It makes it easy for us to look and see what we have and what we need to buy.
  • Has your lab been able to continue work during COVID-19?
  • We’re using this time to write papers and grants. To do this we need to go back to our data. We’re so grateful that our data is in all one place. We didn’t even have to bring our lab notebooks home and there’s no need to flip through them as we write our papers. Virginia Tech told researchers to only do “essential” work during the COVID-19 outbreak. Luckily my team had already stored all our data online in LabArchives. We were ready to work from home. We did this before the pandemic but it’s even more relevant now, everything has to be done remotely.
Shihoko and her team (pictured here) are using this time to work on papers and grants.
  • How do you think this pandemic will change research?
  • I guess it won’t change what we do in the lab necessarily. But people do have to realise that data accessibility is crucial especially during difficult times. Nowadays a lot of experimental data is digital, and we need to be able to store and share that data to do effective research. I hope this situation helps people realise the power of digital storage and shareable data. Working this way also helps lab members learn to take better notes and makes it easy for everyone to check what you did. Working this way has changed how we document research for the better.