Time Flies When You're Working with... Flies? @genetics2019 - Tumblr Blog

Day x. March 29, 2019.

It’s crazy to think that the work I have been doing in my CSL placement has come to an end. Time flies!

As my BIO 2133 course is also coming to an end, I’ve made many connections between the ideas presented in class and with some of the things I have witnessed or done in the lab.

From my very first post, Day 0, I talked about what makes a good model organism in genetics research. On Day 1, my first real day working in the lab, I mentioned the ways in which chromosomes are represented on labels, using semicolons and slashes. I was able to recognize different phenotypes of Drosophila melanogaster. I even got my first taste of lab maintenance. In my case, it was taking care of flies. On Day 2, I learned even more about fruit fly phenotypes and genotypes.

Skipping ahead, on Day 4, I set some goals for myself. I reached the majority of them!

✓ I hope to continue to improve my skills handling the flies and using a microscope.

✓ I want to become more efficient while performing virgin collections.

✓ Over the next few days that I am in the lab, my goal is to learn how to perform assays.

✓ I hope to learn how to dissect select parts of the fruit fly.

▶︎ I want to learn how to make different kinds of fruit fly food.

▶︎ My ultimate goal is to successfully complete a fruit fly dissection and isolate the fruit fly’s brain.

I never got a chance to learn how to make fruit fly food. I was too busy improving my skills while handling flies, using the microscope, and collecting and recognizing virgin fruit flies. I successfully completed two assays and I learned a little bit about dissecting fruit flies, too! As for my ultimate goal, I certainly needed more practice dissecting the brain of a fruit fly. It was really difficult!

On Day 6 and Day 10, I completed assays mentioned above. This was my first taste of real research while working in the lab. I wouldn’t be surprised if my future career involved research similar to the work I did in the Kim Lab. Without a doubt, I’ll be using the skills I practiced with the microscope in the future.

Overall, I really enjoyed this experience. This CSL placement has taught me a lot, even if I know more about flies now than I thought I would ever want to know!

#flyingaway

Day 11. March 26, 2019.

It’s been quite some time since I’ve been at the lab!

Unfortunately, today was also my last day. Working in the Kim Lab has been such a great, hands-on experience. I’ll be writing about my experience as a whole and how it relates to the BIO2133 course I’m taking with Professor Montpetit in my next post.

#timeflies

Day 10. February 26, 2019.

Today, I performed an assay to confirm findings from an assay that one of the students working in the lab had already conducted. We needed to confirm the findings from the original assay because the result wasn’t conclusive.

In day 6, I explained how I set up an assay. I basically did the same thing today, but this assay was not for practice. I used a total of four mating chambers, as shown in the first picture. One experimental group contained male flies that were kept in a group setting (these will be referred to as naive for the rest of the post) and the other experimental group contained male flies that were isolated from each other (referred to as single).

Obviously, we can’t raise flies individually. It would take up a huge amount of space in the lab for each fly to have its own vial. Instead, we create a paradigm, a model, for this. In the second and third pictures, you can see my groups of flies in the 25℃ incubator. In the incubator, my flies are in the box on the top. On the left, I have vials of groups of flies. There are 20 flies in each vial. These flies are part of the naive experimental group. On the right, you can see that I have many more vials. These vials contain only one fly each. These flies are part of the single experimental group. I put cotton balls into their vials to keep them from viewing each other.

I kept the flies in this paradigm for 5 days. It is meant to make these flies act like they were raised in these conditions.

In the fourth picture, you can see what the mating chambers look like right before I remove the clear plastic divider between the male and female flies. I added “X” on cells that did not have a pair of flies- the cells were either empty, only had one fly, or had two flies, but one was dead or severely injured.

When my assay was complete, one of the students working in the lab added my data (shown on the last picture!) to his. With the addition of this new data, he was able to make a conclusion about this experiment.

The bottom text on the last picture represents the genotype of the flies that we were experimenting with. The explanation of the genotype goes far beyond what I want to cover in my blog. Put simply, this assay was used to determine if the genotype affected the LMD, longer mating duration, induced by rival male flies. When flies are raised with rival male flies, they mate for longer durations. When flies are isolated from other males, they mate for a shorter duration. My data was able to show that the genotype did not affect the LMD induced by rival flies.

I thought that this was great experience. I finally got a taste of real research.

#timeflies

Day 9. February 18, 2019.

I didn’t do anything super exciting in the lab today. My main responsibility was to collect virgin female flies. Here’s a picture of a fly in a vial with soy food!

I wanted to take the time to reflect on my experiences so far in the lab. I’ve learned and experienced a lot more than I was expecting to (discussed on Day 0). At first, I was a little nervous stepping into the lab. I wasn’t sure what to expect. I thought the lab was going to be more strict. I assumed everyone working in the lab would be too busy to have time to converse. Overall, I thought it would be a lot more intense. I was pleasantly surprised when I got to know the people working in the lab. They weren’t intense and they took the time to help me. They also took the time to help me learn everything I wanted to.

Working in the lab thus far has shown me that I am capable of working in a research lab. As a biopharmaceutical science student who doesn’t plan on going to med school, working in a lab is a very real possibility for my future career. Although I want to pursue a career geared more towards pharmaceuticals, the time spent working in the Kim lab is great, hands-on experience nonetheless.

I have gotten a lot of practice using microscopes, as well as being responsible while working around other expensive equipment. I’ve learned to have patience when trying new things (i.e. learning to dissect a fly brain!). I’ve also been able to see that putting effort into learning new things pays off.

I’ve gained some new, valuable skills working in the Kim lab. Many are fly-related; I can sex and sort flies easily. I can distinguish fly genotypes quite easily. I’ve improved immensely with my methods of fly handling. If my future profession is fruit fly related, I’m all set!

#flyingaway

Day 8. February 12, 2019.

Today was a slow day in the lab. I spent my time collecting virgin female flies in the morning. After that, I worked on updating the lab’s stock list which is kept in a huge google sheets file. Each box, like the one pictured, works like a “table” in the fly stock list online. This picture shows the front view of the box. The vial with the yellow label on the left is identified as location 1-1. The vial with the red label second from the left is identified as location 1-2. The first number stands for the box. In this case, this is box 1. The second number stands for the spot number in the box. This means that the vial with the green label on the right is identified as 1-10. Each vial contains flies with a particular genotype.

I was very impressed by the organization within the google sheets file. If a person working in the lab wanted to use a specific genotype, they could easily search the genotype code (such as cyO, the code for curly wings) and find the exact location of those flies.

This particular box was/has been used for research in the lab concerning ALS, amyotrophic lateral sclerosis. It’s also known as Lou Gehrig’s disease. I didn’t ask any questions about the research, but hopefully I can find out more about the research that had been or is being conducted.

#flyflies

Day 7. February 10, 2019.

On Day 4, I talked about my goals while working in the Kim lab. My ultimate goal is to be able to successfully dissect a fly brain!

I was told that it is extremely difficult to successfully do this, but I wanted a challenge. I discovered that it takes a lot of practice and patience! I used this youtube video to prepare myself for my first dissection: https://www.youtube.com/watch?v=aGcnJeqEVEk

The first picture shows what a male fly looks like under the microscopes used in the lab for dissection. Because the flies are so small to begin with, it’s important to have the microscope focused correctly. For dissection, the flies are in liquid and and not fixed on a flat, glass slide. I had to choose which parts of the fly I wanted to be in focus. The flies are dissected using very, very sharp forceps. I had to use caution when handling the forceps because even though they are made of metal, the tips are very fragile.

With the whole fly under the microscope, the first step for dissection of the brain is to remove the head capsule, the head, of the fly from its body. This was definitely the easiest part. You can see what the head capsule looks like in the second picture. I was able to do this with no problem.

After isolating the head capsule, the next step is to remove the fly’s “nose”. After that, a small cut is made between the two antennae to remove the two eyes on either side of the head. When the two eyes are removed, the brain is then cleaned up; all other tissue is removed.

You might have noticed that I didn’t include pictures of all of the steps! I wasn’t able to successfully remove the fly’s “nose” to continue with the dissection. I practiced on about ten flies and could see an improvement between my first fly and the last. I’m eager to practice more.

#learningtofly

Day 6. February 5, 2019.

Today I performed a “test assay” to practice setting up an assay in preparation for one that would actually be used for research in the lab. As a reminder, the lab studies mating behaviors of fruit flies in comparison to the genotype the flies posses. Here are the steps I followed to set up the test assay:

▶︎ Prior to today, I collected male flies of the desired genotype. Only males of the desired genotype are needed because the lab is only concerned with the male flies for primary findings. For this test assay, I used CS flies that weren't needed in the lab.

▶︎ Today, I prepared two mating chambers, which are pictured above. Each mating chamber contains 36 cells which are separated into two sections by a removable, clear plastic strip (not pictured). Each chamber has a damp paper towel to better allow the flies to cling to a surface for mating.

▶︎ I placed a virgin female fly into each cell of the two chambers, then placed the clear plastic strip over the top to create a divider in each cell.

▶︎ Normally each assay will have a control group. Because my assay was just a test, I didn’t include a control group. I just wanted to practice performing an assay. Without a control group, I just placed a normal male CS fly into each cell of the two chambers.

▶︎ I placed the two chambers in the 25℃ incubator for 15 minutes (normally, this would be done for 1.5 hours or longer) to help the effects of the CO₂ wear off. The effects of the CO₂ could affect data from the assay.

▶︎ I began the assay. The flies are monitored for an hour. I started my timer immediately after I removed the plastic strip separating the male and female flies.

▶︎ Using the table pictured above, I record the time when each fly pair starts mating. I included a labeled picture (picture 2) above to show what flies look like when they mate. It’s exactly as you’d imagine it (lol).

▶︎ When the flies stop mating, I recorded the time on the table in a square under the square of the start time. In picture 1, I labeled two squares with “start” and “end” in blue ink to help visualize this.

▶︎ At the end of the hour of monitoring the flies, I compiled the data on an excel spreadsheet to analyze the data.

I’ll be able to post the results of an actual assay when I perform it, complete with a control and experimental group!

#flyingfruit

Day 5. January 31, 2019.

This is where I’ll explain the fruit fly life cycle.

Day 4. January 29, 2019.

This is what I see in the eyepiece of the microscope in the fly lab when I first start my virgin collection. It’s a pile of flies. It’s a little overwhelming, right?

I forgot to mention how I have been getting pictures from the microscope! The microscopes in the lab do not have the ability to take pictures to upload to a computer. I’ve actually been using my cellphone to take pictures though the microscopes’ eyepieces. They aren’t the best, but they get the job done.

I have really been enjoying my time volunteering at the lab. Now that I have a better idea of what is expected of me and what I am able to learn, I have set new goals for myself.

▶︎I hope to continue to improve my skills handling the flies and using a microscope.

▶︎I want to become more efficient while performing virgin collections.

▶︎Over the next few days that I am in the lab, my goal is to learn how to perform assays. I’ll post more about this later.

▶︎I want to learn how to make different kinds of fruit fly food.

▶︎I hope to learn how to dissect select parts of the fruit fly.

▶︎My ultimate goal is to successfully complete a fruit fly dissection and isolate the fruit fly’s brain.

My ultimate goal might be a little bit of a reach, but I am confident that I will be able to reach my other goals with no problem.

#fruitflieslikeabanana

Day 3. January 24, 2019.

On my blog post titled Day 2, I talked about the need to separate virgin female flies from the rest of the population. Here is a picture of two virgin female flies!

Fly b is a fully developed virgin female fly. You can see that her body is a paler white color compared to the flies she is next to. Although it is not visible in this picture, she also has a small dark mark on the underside of her abdomen.

Fly a is a female fly that has just emerged from its pupa. You can think of the pupa as a butterfly’s cocoon... But the insect that emerges is a lot less beautiful and pleasant. This fly’s wings have not fully opened yet, nor would we be able to see the dark mark on its abdomen. We can rightfully say that this female fly is a virgin because it is not yet fully developed.

#timeflieslikeanarrow

Day 2. January 17, 2019.

Did you know that fruit flies have a tendency to move upwards? Even though the food is at the bottom of the vial, these flies just want to climb (or fly!) up.

Upon arriving at the lab, I sat down with a phD student working in the lab to discuss some of the mutations I would be seeing most often in the lab. We discussed Sp and CyO mutations on the second chromosome. I explained these on a previous blog post titled Day 1. We also talked about TM2 and TM6B mutations on the third chromosome. TM2 is a mutation that affects the haltere, a ’weight’ near the base of the wing that helps with flight. TM6B is a mutation that affects the bristles on the thorax, close to the head.

My main responsibility today was to separate female virgin flies from the rest of the population of flies in multiple bottles. After practicing on my own, I found it quite easy to sex the flies. It’s slightly harder to confirm that the fly is a virgin. Virgin flies are often slightly larger than the common fly and have a lighter (usually white!) body. Virgin flies also have a spot of darker pigment, usually in the shape of a circle, on their abdomens. You can distinguish female and male flies by their genitalia. I’ll post a picture of a female virgin fly in one of my next blog posts.

The purpose of separating the virgin female flies from the rest of the population stems from the need to perform genetic crosses. Female flies can store sperm from male flies even after laying eggs. After another male fly mates with the female, the female is even able to choose which sperm to use. If we crossed flies that were not virgins, we wouldn't be able to know which genes were being passed on to the next generation.

#onthefly

Day 1. January 15, 2019.

Today was my first real day in the lab. My main responsibility was flipping, transferring living flies from old, dirty vials to clean, new vials with new food. The first picture shows one flipping method, with a dirty vial and a clean vial. The second picture shows what a clean vial with living flies looks like. Basic fruit fly husbandry calls for the replacement of dirty vials about once every other week.

Check out the third (middle) picture. Because the lab is studying the mutations in fruit flies, each vial is labeled with the group number and the chromosome mutations. When I was flipping this vial, I noticed that the flies could not fly. Upon further inspection, I realized that the flies had white eyes and deformed wings. Check out the last two pictures to see these flies!

Fruit flies without mutations are called “wild-type”. They have red eyes; brown bodies; rounded, full wings; and long, straight bristles on their abdomens in very specific places.

Chromosome 1 controls some eye genotypes, so W- indicated that these flies have white eyes. The semicolon acts as an indicator that the next information on the label will correspond to the next chromosome. Chromosome 2 controls some wing genotypes and some bristle genotypes, so sp/CyO indicated that these flies have and curly wings (CyO) and an irregular bristle pattern (sp) that’s actually really hard to visualize. You can clearly see the flies with white eyes and curly wings in the pictures. Maybe I’ll draw out a chart of possible fly mutations in a later post!

Among other factors, wing and eye phenotypes affect mating. I’ll talk about this more later.

#flyingaround

Day 0. January 11, 2019.

Welcome to my first blog post!

Today I attended a short informational meeting at the Kim Lab. Five other students and I met with Dr. Jae Woo Kim and toured the lab.

The Kim Lab studies the genetics of fruit flies, Drosophila melanogaster. Fruit flies are useful models in the lab because they are cheap, reproduce easily and quickly, and are genetically “simple” compared to humans. These flies have four chromosomes. Research done by others in the past have mapped out their chromosomes. We know which gene is located on which chromosome, and where the locust is for each gene. Simply put, this lab is observing the mating behaviors of these flies and comparing the behaviors to one or many mutations that a collection of flies have. The lab wants to know more about neuropeptides, cells, and how the mutations on a chromosome affects the interactions between these three things.

My main goal while working in this lab is to gain experience working in a real lab; a real work environment. I want to learn how to conduct myself in a lab setting. I want to see what genetic research looks like- as I’m hoping that my career path will lead me to work within the realm of genetics. In comparison to the undergraduate biology course labs, I think that I will feel like I’m actually contributing to something worthwhile. Real research is being conducted. The researchers have real goals. I want to experience firsthand what real research is like.

Dr. Kim briefly spoke about what our roles will be while working in the lab. As I understand it now, I will be responsible for caring for the flies; providing them with good husbandry. I may also be responsible for making fly food.

I have always viewed flies as pests, but these scientists view them as their subjects. I’m really looking forward to volunteering.

#learningtofly

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