Author Archives: Michelle Lee

Episode 8- The End of Season Finale

It’s almost hard to believe that 2 months can seem to go by so quickly and yet have been filled with such a variety of ideas, people, and experiences. It’s really helped to put into perspective where I want to go with my future career plans, though I still imagine that they’re liable to change.

Most importantly, I think, is that this summer has really solidified the idea that I want to continue doing research into the foreseeable future. One of my worries was what I’d do if it turned out that being in a lab was more a nightmare than a dream, even though I was pretty certain that a laboratory environment would be the one for me. Luckily, I was correct and I found it to be great, particularly that I’m only really working closely with a small group of people with an overall goal, but each part of the goal is handled fairly independently by each person with some overlapping reliance on others. The flexible schedule with some routine but enough variation to keep things from becoming stale is also an appealing aspect.

It’s also helped me really consider where I want to go with my education in biology. I thought that perhaps I would find my love for genetics once again by being in the lab I’m currently in, but I’ve found that maybe that won’t be the case. Actually, during the summer I’ve looked into other subjects thanks in part to the speakers we heard throughout the summer and I really think I might want to learn more about microbiology, behavior, and the application of biology in industry. While I know that’s bound to change again, this summer has really renewed and invigorated my love for science. I do plan to remain in the lab I’m in to see if maybe I need more time and exposure to the ideas central to the research since it is fairly interesting and two months doesn’t seem like enough time to really come to a sound conclusion (and also my somewhat distant feeling about the research might come from the lack of progress over the past two months. It can be a bit difficult to engage a subject when you’re main exposure to it has been its stubbornness to cooperate).

As far as my ideas about science, I can’t really say how they’ve changed in any particular way. There have been no real “ah-ha!” moments over this past summer, but it’s not as if those moments happen particularly often. Many of the ideas I’ve heard this past summer have been ones I’ve heard before said in a slightly different way or from a different perspective, but with the same central idea. However, that’s not to say that my ideas and perspectives haven’t changed. They have, but in a way that is more nebulous and hard to express concisely. It’s like when you look back over the past year or so of your life and you know you’ve changed and grew since then, but the growth is small across such a variety of aspects that each by itself seems like hardly anything and there are too many to really spend your time considering each one, but together they seem to produce some sense of change. But overall, I can say that I feel closer to what makes science, science, whether it be because of the people who have changed it, understanding its principles, respecting its power to bring forth knowledge about our world, just from being able to be a small, small part of it for a short time, or a number of other things.

Science is amazing, and even though sometimes I, like many of us, need a bit of a break from reading and thinking and talking about it, I hope I don’t ever lose sight of that.

Episode 7- Some Super Summer Seminars

Having all these seminars this summer has really made me appreciate the huge variety of faculty at Duke and how amazing many of the people here are. The fact that I can contact many of them and have a discussion is even more extraordinary. As a result, I find it difficult to select just one presentation that I found the most fascinating, and instead I wanted to focus on my two favorites and how the ideas they presented have overlapped in my mind.

First was Dr. Mohamed Noor’s research on the sister species of Drosophila, D. simulans and D. pseudoobscura, and how they have very similar songs that are slightly modified to avoid interbreeding between the species. This got me rather curious about fruit fly songs and so I took a cursory look around at what had been published. I was really surprised to learn that fruit flies aren’t born knowing what song to sing, but instead they learn it from other flies around them (link). Yes, you know those small things that, no matter how many times you swat them away, will return time and again to annoy you while trying to enjoy your lunch? Apparently, they actually can learn and they’re just terribly rude. But in all seriousness, flies can learn! Something that appears so simple and lacking anything beyond what its genetics programmed for it is actually notably more sophisticated. Perhaps I was just underestimating other animals, but when one is often thinking of organisms at the cellular and genetic level and functioning more as biological machines, sometimes one forgets about the complexities and capabilities of the whole creature.

Secondly, there was Dr. Steve Nowicki’s research on bird song and what it reveals about animal communication and behavior. In particular, I was fascinated by this idea that behavioral responses were caused by stimuli that are sorted into categories as opposed to a linear relationship between the stimulus and the behavior. Like the above, it’s something that I hadn’t ever considered since it always just seemed logical for behavioral responses to be linear. However, reflecting on this new insight, it actually makes sense for it to be categorical since the brain often cut corners where it can and categorization would be an easier system for it to implement compared to having a wide array of responses to a spectrum of intensity of a certain stimulus.

Now, how do those to come together? Well, I’ve been thinking a lot about how categorization may occur in intraspecies interactions besides in birds and humans. Then I thought back to Dr. Noor’s seminar and began wondering if there was categorization occurring in the sister fly species and if changing the duration, frequency, and order of the “notes” in the flys’ songs could change the females likelihood of accepting or rejecting the male, and if the change would look like the categorization that Dr. Nowicki was seeing or if would be more linear. Whether or not that’s an idea worth looking at, I don’t know, but I find it kind of interesting.

Overall, I really enjoyed all the seminars over this summer, though I must admit that I found myself most interested when our speakers were discussing the work they had done or are currently working on. However, the seminars have gotten me to really consider the idea of pursuing a PhD, and there are a few words of wisdom that were shared that I expect to be keeping in mind as I go through my future career.

Episode 6- Abstract and Possible Progress?

Progress on my project has unfortunately been quite slow, due mostly to unavoidable issues that cropped up earlier into the process. In particular, the change from using FL green sea urchins to NC green sea urchins. Given that the project started originally with using the genomic information gathered from FL urchins and the vast genetic variation between population of sea urchins, the guide RNA created for the FL urchins, while successful on those urchins, has proven to be little effective on the NC variety. The reason for the switch from FL to NC urchins is the season in which the animals are reproductively active and thus when their eggs are most healthy for injections.

However, with the lack of genomic sequencing of NC-originating Lytechinus urchins, it has been impossible to create gRNA specifically for the urchins we are currently using. Luckily, one of the members in the lab has recently been sequencing some sections of the NC sea urchin genome, so we may soon be able to design new guides that have a higher effectiveness, assuming that section of the genome has been sequenced and the gRNAs initially created are indeed different enough to warrant new guides.

On a brighter note, I’ve been practicing injections most days of the week and have been able to better hone my skills on the practice as it can often take months to learn how to inject efficiently. Early on, I would often take up to an hour trying to inject a single plate of embryos and awhile to setup my materials for the day. Now, I’ve managed to better refine the protocol and can have everything ready in an hour and do one plate every 20 minutes. Though that’s still a bit long (the optimum time being 15 minutes) and I still need to work on injecting more embryos in that time frame, I feel as though I’ve improved quite a lot and learned a number of things in the process.

Abstract- What Are the Functions of Genes in the GRN of Sea Urchins?

Sea urchins are one of the most useful model organisms for studying early development; however, much is still unknown about the specific functions of genes within the network that regulates urchin development. One gene that has been well-studied is Endo16 and its importance in gut formation. Using CRISPR/Cas9 technology, this project has focused on producing successful knockouts of Endo16 by targeting the gene’s enhancer region. Thus far, there has been moderate success with knocking out Endo16 in Lytechinus embryos, though further experiments are needed to improve the success of the Cas9 knockouts by taking into consideration the significant genetic variation between populations of Lytechinus. Once the percentage of embryos that are injected produce Endo16 knockouts equivalent to the percentages seen in similar studies using other gene silencing techniques, the project will move forward with knocking out other genes whose functions are less well-understood compared to Endo16. This will further our understanding of the gene functions and relationships within the gene regulatory network of sea urchins, and allow comparative studies of gene function in Lytechinus and the closely-related, yet developmentally very different, species, Heliocidaris erythrogramma.

Episode 5- A Day in the Life (in the Lab)

For me in the Wray lab, everyday is pretty close to the same (so long as there are sea urchins in stock). As soon as I get to the lab, I check on the sea urchins I injected the day before if I did injections. Then, I check the dry erase board to see if there’s anyone planning to spawn an urchin before 1 since any time after that is too late. If there isn’t anything written on the board, I go ahead and make the injection mixtures I’m going to be doing that day and set them on ice. Then, I grab the urchin tray and bring it to the urchin room.

Once I’ve spawned some eggs, I have to wash them several times to remove the jelly so the eggs don’t stick together and dirty the water. While waiting for the eggs to settle during the wash, I set up what I need to row the eggs on some plates. After the wash,  put the eggs in a glass dish, swirl them into the center, and place them under a microscope to begin collecting them.

Using a mouth pipette, I suck up some eggs and then blow them out gently onto a plate filled with sea water and PABA (Para-Aminobenzoic Acid) which keeps the eggs soft enough to inject. If done right, the eggs stick to the bottom and don’t roll around much from where they were placed. Then, I add some sperm to each plate and swirl them around to make sure the eggs get fertilized. Now, they’re ready for injection.

To set up for the injection, I take a needle and place it into a nozzle and place a plate on the microscope stage. After a minute or two of adjusting the needle and stage positions, I can see the needle and inject the fertilized eggs. Once injection is finished, all the plates are placed in a plastic case and into an incubator to develop.

Four to five hours later, I can take the embryos out of the incubator and begin transferring them to a 12 well plate. I use the mouth pipette again to select the glowing embryos since those were the ones injected and I move them to different plates depending on the treatment and how brightly they are glowing. Afterwards, all the plates go back into the incubator to develop more overnight. The embryos have to be transferred because spending too much time in the PABA makes them sick and develop poorly.

The following morning, I check the results and see how many of the embryos/larvae have developed and if there appear to be any significant differences in the way the injected versus control animals have developed. After that, I wash and throw out the plates and begin another batch of injections.

Episode 4- Chalk the Talk

As interesting as it was to hear about everyone’s projects and learn a thing or two from each one, I think we’re all pretty glad that’s over with. For now, anyway. Hopefully, the posters will be easier since we’ll have everything written down to be presented as is and we’ve already got our thoughts collected.

Out of all the intriguing projects from last week, I believe that the one that caught my interest most was Michael’s investigation on the epigenetic effects in the offspring of mice after the male parent’s usage of THC. In particular, it was curious though concerning that the F1 mice appeared to exhibit some symptoms of ADD and expression of genes associated with ASPD and schizophrenia, though from what I understood, those results are not conclusive.

However, if those current findings prove to be further supported, then that leads one to wonder if THC usage could have similar effects in the children of those who use it. It’s already well-known that women shouldn’t use a variety of drugs or consume fish with high mercury content while pregnant, but it could also be that men should avoid certain substances before planning on having a child, outside of certain drugs that are known to lower sperm count (unless the transgenerational effects of other drugs have been studied and shown to be detrimental?). That also makes me wonder how long the effects of THC on sperm lasts, though I would imagine it would be about however long it takes to produce new sperm.

But anyway, everybody’s projects were pretty cool, and I’m curious to see how the posters turn out at the end of this program!

Episode 3- The Interview (starring Dr. Wray)

His education and topic of interest:

Dr. Wray got his undergraduate degree in biology at William and Mary before arriving at Duke with the mindset of going the MD-PhD route. Though is changed, he always had the intent of going into research, particularly with a focus on biology. After he obtained his PhD from Duke, he completed his postdoctoral training in Indiana University and the University of Washington and later returned to Duke as a faculty member.

How have his interests changed:

When he was a child, Dr. Wray was interested in becoming a marine biologist, though, admittedly, more from the idealized image he had of marine biologists spending time diving around coral reefs than from an the reality of spending long hours in a lab conducting research. Eventually, however, he became an evolutionary biologist with a focus on how gene regulation evolved, and he spoke about the importance of being able to reinvent yourself as time goes on and you become more attuned to what your interests and strengths are.

What he teaches/has taught here at Duke:

Originally, he taught Bio 201 and did so for 4 years. Currently, he does seminars for seniors and graduate students that are about genomics. He also does guest lectures from time to time throughout the year.

What he enjoys about science:

To Dr. Wray, one of the most enjoyable parts about science is its entrepreneurial nature in that there is much freedom to be found in doing research and to make progress, one sometimes has to take risks in what they decide to investigate. However, one should still be mindful and reasonable in the approach taken; safe, but not too safe. He also enjoys this environment because its freedom fosters creativity and is far from the mechanical process that people sometimes consider scientific research to be.

What he dislikes about science:

There really isn’t much that Dr. Wray genuinely dislikes about science. Though he understands and has felt the frustration of how long it can take for research to be done and even then, it may simply fail to work, these things are just part of the process and everything done in research is valuable anyway, success or failure. Really, any dislike that Dr. Wray has that relates to science is the way that society perpetually ignores the life-changing advancements made by using science, and that the majority of people (in the US, in particular) could name 10 professional sports players with no trouble at all, but would hardly be able to name 2 or 3 living scientists.

Disasters in the lab:

Luckily, there have never been any major problems to happen in the lab, though there was one instance when someone left the water on in the lab and upon returning, there was water flowing down to the lower floors, much to the annoyance of the lab below.

How projects make it into his lab:

Generally, projects arrive in Dr. Wray’s lab from students that have ideas about what they would like to investigate. Though those ideas are usually not very interesting or possible to do in his lab, from time to time there will be an idea that seems worthwhile to pursue. Once the project begins, Dr. Wray becomes invested in the student’s topic of interest so that he can provide them with the support they need, but he also tries to allow the student room to make their own decisions about how they approach their research.

Why there are toy dinosaurs on his bookshelf:

One of the classes that Dr. Wray used to teach was a class on dinosaurs that was meant as a way for students in non-science oriented majors to receive their science credit in a fun, easy class as opposed to taking Bio 201 or 202. As a result, he amassed a collection of toy dinosaurs to use as props in the class. Though he is no longer doing  that class, he has kept the dinosaurs. When ask about which species is his favorite, he said that it was impossible for him to choose as there are so many with their own unique qualities that make them fascinating.

Book recommendations:

If anyone happens to be looking for something to read on the general topic of science and how to think about science , Dr. Wray recommended reading Naturalist, an autobiography by E. O. Wilson. Additionally, he also recommended reading Why We Get Sick: The New Science of Darwinian Medicine by Randolph M. Nesse as a good novel for those interested in science.

Gregory A. Wray, PhD


Episode 2- Project Boogaloo

Before you wonder about the title, no, my project does not involve a study on the popular 1960’s dance (I just thought it was a fun title). The project I’m actually working on in the Wray lab is to use CRISPR/Cas9 to knockout particular genes in sea urchin embryos and observe their development. As of right now, I’m soon going to start trying to knockout endo16, a gene in sea urchins that necessary for the development of their gut (link).

The reason that I am first testing that particular gene is because its function is already known, so I should be able to easily identify if the knockout was successful. Once I’m able to get the results that are expected, I’ll be able to move on to working on genes whose functions are not yet known.

Interestingly enough, though sea urchins are considered to be great model organisms to study early development since their embryos are clear and easy to maintain, there are still many regions of the genome that have not been fully defined, as far as their function and interaction with other genes goes. However, understanding how genes within organisms produce changes at different points in development goes beyond looking at them as individuals, but through understanding them as pieces within a far more complex system, which is referred to as the genomic regulatory network (GRN) (link). This idea is what the sea urchin research in the Wray lab revolves around.

Essentially, by experimenting with individual genes and observing what developmental pathway they effect and when they effect it, those genes can be placed within the overall GRN. The interactions between that gene and other genes that regulate that pathway can be identified, creating a much richer understanding of how genomes operate. This, in conjunction with how these interactions are mediated by cis-reulatory systems, can provide us a greater understanding into how changes in development occur and how these drive evolution of species (link).

Though I haven’t gotten particularly far in my project so far as I’m still practicing the skills required to ensure the embryos are able to develop normally post micro-injection, I hope to get started on CRISPR/Cas9 by the end of this week or the beginning of next week. I’m quite excited to see what I might discover!

Episode 1- Great Expectations

My expectations for this summer research experience are all about discovery, particularly about myself, science, and my relationship with science. Sure, there will be ups and downs, breakups and makeups, but, as with most things, the experience tends to be worthwhile.

As for discovery of myself, there are somethings I hope to learn: how do I function within a laboratory setting? Do I ask enough questions? Do I ask the right ones, and the right person to answer them? What should I do if I need help, and do I realize when I need help? Should I try to be more confident in what I do or say, or should I be more cautious? Are the notes I take useful? The lab setting is something so different from what I’m used to (especially since I’ve never had a job before), that I feel as if I’m going to need to learn a new set of skills or refine those I already have to really thrive in this environment, but before I can do that, I first need to have a better understanding of what I need to work on for myself. I hope I begin to develop an idea of those things throughout this summer.

Then there’s discovery of science, which comes with its other set of expectation. There have been a variety of papers that I’ve been suggested to read, and others I’ve found on my own that I thought would be helpful or interesting. As I progress through the summer, I hope that I’ll become more accustomed to the language used in these papers so I won’t have to stop every couple of sentences to look up what a particular phase or jumble of letters mean, and subsequently become distracted by other interesting research papers. Additionally, it’s nice to be able to understand what others in the lab are talking about so I can participate in discussion. I also hope that perhaps I might come across something in the literature that sparks an idea for research of my own to do in the future.

Lastly, thought most importantly, there’s how science and I interact with one another, since, after all, research is a two-way street. Not only do we impact science through every bit of research we do, either successful or unsuccessful, by showing what works and what doesn’t, but also science impacts how we analyze the world around us and can become heavily integrated into our lives. What I expect from these internship more than anything is insight into whether or not this kind of lab-focused science is the right one for me, or if research is for certain what I wish to dedicate my life to. Perhaps I won’t find that answer in a mere 8 weeks, but at the very least I expect that it might help turn me in the direction that I’m better suited for, whether it be lab work or another broad area of science. So far, I feel pretty at home in the lab, but there’s still a ways to go.

Anyway, here’s me using a microscope to look at some sea urchin embryos that I was practicing injecting with fluorescent dye:

And here’s a bonus photo of a small, scaly friend (broad-headed or five-lined skink?) I found sunning in the garden earlier this week: