Esmé W.

2023-2024

4/18/24

After many urchins with only eggs, the final urchin had sperm. I am following the procedure for gamete extraction and have diluted the sperm and combined them with the eggs, so I’ll check for fertilization hopefully today but if not definitely tomorrow. I’m very excited to have done one more successful gamete extraction before I leave, and I’m hoping without aptasia they may grow further than last time.

4/16/24

Board retreat was a success! It went from roughly 8:45-2:30, and we have a fantastic new board taking over next year. I’m very happy with how everything went, and am both happy and sad to pass on my WISRD responsibilities to a new group of students.

4/8/24

I’ve been dismantling the ceramic printer and working towards gathering important topics of conversation for the board retreat on 4/16/24. After the retreat, I will do another gamete extraction and either monitor it myself or pass it on to the people interested in marine bio next year to get initial experience.

3/21/24

The gametes did not end up developing any more in the tank despite our efforts to create an environment mimicking the one in our larger tank. I will be doing another extraction after spring break in an effort to create new urchins again. Recently, I have been setting up and troubleshooting with the ceramic 3D printer. It has some extrusion issues right now, so I reached out to Joe who offered to help when he is back from his trip. I am working on finishing my poster and dismantling the printer before the break.

2/22/24

The zygotes did very well the first few days, and once they reached the final developmental stage we put them in the tank. Since then, we’ve been able to see some of them but now we’re not sure the next steps. Both the large tank and the mini tank have aptasia infestations unfortunatley, so we are getting fish/nudibranchs to eat them. Hopefully once they are put in the tank to eat them we can continue work with the urchins.

2/8/24

The gamete extraction was successful! The cells have so far been progressing as expected, but we’ve reached the point where there is not much published work on how to continue. We have been splitting the plates every day or couple of days to ensure no overcrowding and feeding them 20 microliters of algae dilution per well. Currently, I have added 5 of the six-well plates to the mini tank we set up. I checked to see if I could find any of them in the tank to check on, but to no avail. I added algae dilution to the tank as well, and asked Megan to add some live rock/live sand to some of the six plate wells.

1/18/24

I have been waiting to do another gamete extraction, and will finally be able to next week. Between the short time from Thanksgiving to Winter break and the four day weekend messing up this week and last week, I haven’t had a long enough window to be able to study potential samples. Next week is finally a full week, so I’m going to create a buffer solution tomorrow and start next week. I also am drafting my Inquirer article and finishing up mid-year lab assessments with the board next week.

11/30/23

I eventually deemed the last batch of samples unfit and discarded them. With Thanksgiving/Winter break, there hasn’t been a long enough stretch of time to cultivate new samples. In these shorter stretches, I have instead pivoted to completing thorough research on the most efficient way to foster gamete growth so the next round of collection can hopefully go smoother. That research can be found here. For now, the urchins have been fitted with new hats with some larger sizes and brighter colors to monitor their reaction. I’m also 3D printing a sheet of connected pieces that functions almost like filament-based fabric, with the hope that the urchins will pick it up and use it as a more all-encompassing shelter that covers more of their surface area rather than just the partial sections they can cover with the hats. They love to pick up the kelp we drop in the tank, so I’m hoping access to something that covers more of their bodies will drive them to pick up the new print.

9/22/23

The old journal didn’t work out, so I’ve started a Google Doc that contains updated entries and photos.

9/18/23

The cells in sample 1 inexplicably seem to have become single orbs again rather than the dividing behavior we’ve seen on the other days. I’m not sure if this indicates progression or regression, but I’m trying to research different urchin egg behaviors to help me understand what’s happening. Sample 2 is still looking normal, as is the combination sample 3 I created on Friday. Both still only contain single eggs and don’t seem to have divided or multiplied. As far as I can tell, nothing is new in the mini tank and the pipette of sample 1 I put into it on the 14th has not yet developed into anything. 

9/15/23

As I’ve been doing every day I took a sample from tubes 1 and 2 to look at under the microscope. I took another photo and time-lapse of sample 1, which is still dividing/evolving, and I’m going to try to research what this phenomenon actually is. I also noticed living organisms in the mini tank that I placed the divided eggs into, so I checked that out too and took a photo of what seems to be a sand mite I found. I also took a small amount of sample 2 (non-divided eggs) and the spontaneous Tuxedo urchin release to create a sample 3 in order to monitor whether or not the same process will take place. This will help me determine what happened with sample 1, as well as confirm whether or not the spontaneous release was sperm. 

9/14/23

The cells still look to be dividing, so I’m monitoring, photographing them, and updating a new journal I created for them daily. Sample 1 is the sample with the eggs that are splitting. Sample 2 is also Tuxedo urchin eggs, but they are unfertilized and not dividing like sample 1. I’ve taken a time-lapse of sample 1 over the course of 10-20 minutes, and the eggs are definitely moving/spinning in circles. I put a small amount of the eggs from the sample into one of the mini tanks and will be observing if they are able to grow in actual tank conditions over the coming weeks. 

9/13/23

Today we discovered what seems to be the splitting of the collected urchin eggs. I have no idea how this would have happened, as the samples and urchins were all quarantined after I did the extractions. The first two images show the eggs that seem to be developing, and the third image is a reference of urchin cell development under a microscope. 

9/11/23

Two of the samples collected seem to be insignificant, leaving us with the other two samples that contain the same eggs(?) that we got a sample of last year. Despite not being new, I hope to stain the eggs and look at them closer than I got a chance to last year. We had an urchin spontaneously release gametes today, and I sampled them from the tank to look at. To the naked eye and under the microscope there doesn’t seem to be anything in the sample, but it’s turned the water in the tube a murky white and I’m hoping letting it settle in the fridge for a day or two will reveal something more.

9/8/23

Today I was able to perform more gamete extractions on the Tuxedo and reef urchins. To do the extractions, I used a buffer solution of 1.865g KCl and 50ml of distilled water. I mixed this solution and then placed one urchin into a petri dish filled a quarter to halfway with water from the tank. I then injected the urchin and let it sit before picking it up to check for release. If successful, I pipetted anything I found into a small tube and labeled it. If unsuccessful, I placed the urchin into a deeper bowl of water from the tank in order to allow more time to release and identify which urchins I had already injected. All extractions yielded something, but I don’t think all of them were necessarily gametes. It does, however, seem that we successfully got two egg extractions again. I looked at all the products under the microscope, and hope to do more research soon to identify my findings. This is the procedure I followed: https://depts.washington.edu/embryology/index.php?id=gametes. The reef urchins seem to be bouncing back from their health scare, and all the new Tuxedos have acclimated to the tank well.

9/7/23

Over the past week, I’ve been doing a lot of microscopy with items of interest found in the tank. There don’t seem to be any new or dangerous additions with the most recent batch of urchins, but we did get a sea star from the ocean water. We set up two smaller tanks for my Honors advanced bio project, and plan on putting one Tuxedo in one tank and one reef urchin in the other tank in order to monitor kelp consumption. I will also be helping Max run experiments for his kinesiology lab.

8/24/23

Today is the first day of WISRD this year. I plan to pick up where I left off with urchin gamete extractions, but I also want to explore some deeper questions with the urchins this year. I think potentially folding in aspects of Ann Marie’s neuroscience and advanced bio classes could also be something I want to explore (dissections, microscopy, art, etc).

2022-2023

8/25/22

Our first day of WISRD was Tuesday. I’m thinking of moving on from the RoCCS group and moving toward the new aquatics projects in WISRD. Max A. (’24) and I want to start the aquatics sector as co-PIs. In theory, there would be a fish tank and an urchin tank used for various data collections. I’ve also reached out to a marine biologist in order to gather ideas for animals to study. The first board meeting is next Thursday, September 1st.

8/30/22

Max has purchased and started setting up the fish tank for the freshwater fish being brought into the aquatics project. Megan has forwarded me a lot of research about urchins and how they live, so if we decide to buy urchins we have some concrete ground to start with. I also am hunting for a science-based internship for the coming semester.

9/1/22

We had our first board meeting today. It went well, and afterwards I checked in with Ann Marie about her interest in the urchin project. It would be great to work with her, so I sent our documents along. The saltwater tank for the urchins is here, and I’ve been drafting documents on the care and keeping of them. The freshwater section is not set up yet. I am also still acting as PI of the RoCCS group as well as co-PI in the aquatics lab.

9/8/22

The analog refractometer seemed to be giving a bad reading, so I tried to re-calibrate it using distilled water. The reading turned out to be accurate enough to use, so I tested it against the digital refractometer. The digital refractometer only gave a reading in parts per million, but upon further examination I figured out how to get a reading of the salinity of the water in a percentage. This is a much more useful measurement, so I’ll be continuing to use the digital refractometer to keep track of the salinity in the tank. All of the supplies to set up the tank before ordering the urchins will be here within the week, so I’ll start setup next class period.

9/14/22

The tank has been partially set up, only missing a few items. The urchins have been ordered as well so they will be placed in the tank soon. I’m also working on finishing up my thermistor whitepaper.

9/22/22

Megan suggested buying a second tank identical to the freshwater group’s, as their tank is better suited for the experiments we want to conduct and is more conducive to the urchin’s needs. The tank we initially set up might be used as a test tank, potentially being used to test alterations to the urchin’s ecosystem before we introduce them. The urchins arrive October 4th, so we are working on getting the tank and the necessary food set up before then.

9/27/22

The saltwater tank is currently awaiting the arrival of our urchins. The saltwater content seems good, but I’m not sure exactly what the percentage should be so I have to check with Megan. The urchins arrive next Tuesday, so I’m working on checking everything necessary off the list before they come.

10/6/22

The urchins arrived Tuesday, 10/4. The tank has been fully set up for them. The urchins were acclimated in their shipping bags to the new water, then their water was drained and they were put into the tank. One urchin died in transit, and two have died since from stress. Two to three of the urchins currently seem stressed, and it seems like the rest are doing well. I performed a feeding today by warming frozen shrimp, cutting them into smaller pieces, and dropping them into the tank using our forceps. If another urchin dies between today and tomorrow, it is also a possibility to perform a dissection. Otherwise, everything is going smoothly so far.

10/7/22

I fed the urchins again today, and it seems like they need daily to every other day feedings. Two more urchins died, and I’m saving one to dissect and learn the anatomy of. I have been spending time in the library during class trying to research the care and keeping of our species of urchins. It’s hard to find good info, but the Wikipedia page is very helpful. The new tank comes Tuesday.

11/1/22

All of the first batch of urchins sadly died. We observed bacteria on their backs, and think that this may have contributed to their trouble surviving. We ordered a second set, and they have arrived. This colony consists of tuxedo urchins and three larger reef urchins. I also built a new tank for them that we got from Amazon and is the same as the freshwater tank. These urchins are doing very well, and have adapted to their new home well. We also had the poster session, which was a much larger success than expected and drew in a lot of people.

11/9/22

I’ve been mostly working on the draft of my article for the WISRD Inquirer. Dr. Moreno completed the first round of edits and I met with her on Saturday 11/5. It was very helpful, and I’ve spent a lot of time restructuring my draft so she can run through it a second time for additional edits. In addition, I’ve also been trying to complete my WISRD poster draft to get it out of the way. I have three of the sections done, and an additional three to write. The urchins are doing very well, and we put a castle in their tank that they’re loving.

11/17/22

The urchins are still doing very well! We added shells and other bits and pieces to the tank for them to pick up and hide under. They love the castle, and today I added a little hobbit hole decoration in order to help fill in some space. Megan also recently changed five gallons of the water, and we have algae and other greenery on the way to add to the tank as well. I’ve been looking into potential research questions, and my three main avenues are gamete study/reproduction, clay prints/3D prints, and potentially looking into their invasive nature with kelp. Megan is helping me with this, and in the week after break one of our MORI collaborators is coming to check out the tank and also potentially help formulate a research question. I finished going through Dr. Moreno’s second round of edits, and my article is turned in for Scott and Noe to edit. I also finished my poster draft, which Megan will be going over at some point.

11/18/22

On the final day before Thanksgiving break, our new algae arrived. I put the algae in the tank using our forceps and Megan acclimated a new batch of anthropods to the tank. After break, we’ll be getting fish to help control the anthropods and add life to the tank.

12/1/22

We are back from Thanksgiving break. Our urchins did very well over the break thanks to Megan’s care, and we have new urchins and anthropods coming in for Anne-Marie’s tank. We have continued looking into research questions for the tank, and we’ve started 3D printing our hats in preparation for the poster session. I have a finished poster, lab report, and Inquirer article draft. Once the poster session and Christmas break are done, I hope to have made more progress in coming up with our research question.

12/13/22

The WISRD server is back up! We had the Fall poster session last week (12/7), and it went very well. I got a lot of interest in my urchins and when the next semester starts I want to work really hard on finding a research question. The lecturer was very interesting and I was able to Tweet about the session right after. I also turned in the final draft of my article, so hopefully that goes over well.

1/4/23

We are back from winter break, and this semester I really want to develop a concrete research question and experiment. Before I jump into the experiment 3D printing different colors to introduce to the tank, I’m doing some research on studies conducted on invasive species as well as characteristics and more information on the invasive purple urchins that I’m basing this study on. Here is an article I thought was interesting on invasive purple urchins:

https://www.npr.org/2021/03/31/975800880/in-hotter-climate-zombie-urchins-are-winning-and-kelp-forests-are-losing

1/10/23

In the coming weeks I would love to get started on 3D printing different colors, shapes, and sizes to test dropping into the tank. Unfortunately, the printers are both currently broken, so for today I’m just continuing research and checking the clay for the ceramic printer.

1/11/23

The printers are back and we’ve printed a crown and a top hat. This is hopefully the beginning of testing preferential treatment with these urchins and the different shapes of the hats. The crown is in the tank, so we will see if they take to it.

1/12/23

We have printed three hats and I’m currently hunting for more textures and shapes to print for the urchins to test out. One has taken to one of the hats and is wearing it, and the other hats float around the tank. We are also looking into gamete collection in order to propel our research this semester.

2021-2022

8/30/21

I hope to join the Coral Reef project, but we are waiting on an update from St. Monica’s. Hopefully once Izze has a meeting we can figure out where to go from here and I can officially sign on.

9/20/21

Izze S. (24′) and I are trying to use the Arduino to design a thermistor circuit to be used as a temperature probe. We ran a test to find out it’s an NTC thermistor, and a test to run code to blink an LED. From here have to hook up the thermistor to the Arduino. We have a meeting with St. Monica’s tomorrow to figure out where to take the project from here.

9/21/21

We met with St Monica’s for the first time after summer today. Izze and I need to finish setting up the temperature probe and thermistor within the next week-ish to deliver to MORI next week/beginning of the week after.

10/4/21

Joe set up the voltage sensor to input graph points to the Pasco while the temperature sensor measures in a different column. We’ve set up a hot plate to boil the water and get the highest point at 100º Celcius, then set up an ice bucket on a stirring plate to put the boiling water beaker in to lower the temperature and measure points along the way. The Pasco graph measures points every minute. Once all our data is collected, we need to do a curve fitting and create an equation from voltage to temperature.

10/12/21

This week Izze and I have created the voltage to temperature equation as well as the voltage to DS (digital signal) equation. We’re working on coding the Arduino to read out in temperature instead of the current numbers in the serial monitor. We have a readout that’s in temperature format, but isn’t accurate to the climate it should be reading from. We’re changing the Arduino code to try to fix this.

11/1/21

Last week we fixed the Arduino’s code and it now gives a comprehensive temperature readout in degrees Celcius. I have to package the circuit and send the code to MORI probably within the next week or two. We’re also working towards finishing the RoCCS poster for the Fall poster session. The ceramic printer will be back up and running for the first time since summer this week, and I cut and packaged some clay to fill it with today. We should be able to run a test Wednesday.

11/8/21

Today we had the Fall poster session. We met the MORI group in person for the first time and each delivered our presentations together. The clay printer had some issues but otherwise everything went smoothly and we’re moving on to packaging the probe for delivery.

11/15/21

After cutting, stripping, and soldering all the wires in order onto the breadboard, I moved on to solder and shrink wrap the thermistor pins. This went smoothly and I plugged the Arduino into the Rasberry Pi. I can now access the temperature readout from the VNC Viewer, at home or from WISRD.

12/2/21

After trying to cut a section from the breadboard with a hacksaw and the Glowforge, I decided our best option was to have Chance cut it on the CNC. He finished cutting the small section today and from there I met with Wills to design a box to hold our probe for delivery to MORI. Wills will be making a spacer so I can determine where to place the board on the Arduino and how short my wires can be, and from there I’ll re-solder all the wires on.

1/13/22

Since we’ve been back, I’ve been working collaboratively with Wills while he works on a design prototype to hold our circuit for delivery to MORI. We’ve had two prints so far and are incorporating feedback to create the final product. Once the print is successful and we’ve changed what needs to be changed, I’m going to re-solder the wires and arrange everything in our box. After the final design is printed, I can finally get the temperature probe to the tank at MORI for use.

1/31/22

Over the past couple weeks a lot of progress has been made. We’ve gone through many models of the box to hold the Arduino as well as re-soldering the wires and testing the code twice. As of now, the soldering is finalized and the code is working. The last things to do before delivery are re-print a model of the top of the box to hold the thicker wires and figure out a way to hold the thermistor in the tank. I reached out to Luca with questions about the tank, so I should be able to figure out a way to implement a wood beam to hold it over the tank. Once Wills’ print is done and I have a support beam, the probe will be ready for delivery/pickup to MORI. Toby also reached out asking about printing a new clay model Luca had designed, so after the probe is delivered I’ll start re-setting up the printer.

2/3/22

Wills finished the final top for the Arduino and I got the dimensions of the tank from Luca, so the last thing to do before dropoff is cut a piece of wood to hang the thermistor over the tank. I was asked to be interviewed for the WISRD podcast, so I spent today filling out the questions Ian sent.

2/8/22

Today I had Jackson cut a hole in the block of wood that’s going to hold the thermistor over the tank. The final steps are to find a clamp for the wire and drop the probe off at MORI with Joe. The interview might take place on Thursday.

2/10/22

I helped Honor and Canada run tests with the EMOTIV today in the library and set up my test profile. I also did the interview with Ian after school for the podcast, which went quite well and he offered to nominate me for the board next year.

3/1/22

We found out the copper in the brass thermowell of the thermistor is toxic to coral in certain volumes, so I have to wait for the new stainless steel probe to come to re-calibrate it and set everything up all over again. This is a big setback, but hopefully the calibration won’t take as long as it did last time. We finally figured out the issues with the Cura on the Recon laptop and Joe did the first print since poster night.

3/21/22

We’re currently trying to re-calibrate the new thermistor. The probes are conducting heat differently so we have a different curve when measuring temperature going up vs going down. Brass conducts heat better than steel, so the temperature is hitting the steel probe slower than the previous brass probe. The temperature probe it’s being measured against is giving readouts much quicker than the thermistor, which makes the data inaccurate. The new experiment needs to consist of bringing the water to a specific constant temperature, waiting, measuring the temperature/voltage, then doing it again for multiple other points. I’ve also done a couple of new prints with the new files, the first came out well and the second failed. Poster presentations are also semi-soon, so we need to start the outline of ours or think about what it would look like to write a whitepaper instead.

3/25/22

The new thermistor has (hopefully) been calibrated correctly and I did one of the most successful clay prints I’ve done. The poster presentation is coming up soon, and because St. Monica’s has different spring break scheduling to rehearse is becoming difficult. We don’t have a poster outline yet because I’ve been working so we have to start soon. Today I’m going to de-solder the breadboard and try to work on getting it onto the new thermistor.

4/19/22

The new thermistor was set up fully (aside from a missing screw), and last Wednesday I dropped it off at MORI with Joe and Megan. It was my first time in their labs so Luca gave me a tour of the tanks and lab. The thermistor successfully read the temperature in Celcius, and I can now VNC in to see their readings. The WISRD board retreat was yesterday as well, and I was officially elected to the board. I will be running for Program Director in the coming weeks. Currently, Izze is working to calibrate the pH sensor and all my effort is going into the poster for Spring poster presentations.

4/28/22

Our Spring poster session was Monday the 26th and I set up the clay printer to run for it. It worked for half of the print then had a motor overload so it didn’t complete the print but otherwise things went smoothly. Yesterday I fixed the overloaded motor with Joe and let a print run while I was out of class. It seems to have gone fine but has some cracks and is not a viable print to drop off at MORI.

5/3/22

I finished taking apart the printer and the final print that I did I don’t think will be viable to be dropped off at MORI. It had a lot of cracks that I patched and cracked again, and I don’t think drying it with wet paper towels worked as well as with a rag. I’m finishing up my vitae in the last four weeks and Izze and I need to brainstorm where we want this project to go next year, as our role has shifted from ceramics to more technical aspects and probe building.

5/17/22

Everything ceramics-wise and probe-wise has wound down, so I’m working on writing a whitepaper about our thermistor setup procedure. It’s been through one round of edits from Joe and Megan and needs some more along with adding photos. I have four more WISRD periods before the end of the year, so I’d like to finish the paper in that time in case other work comes up over the summer. Joe and Luca are building a mechanized machine over the summer to insert and remove the probes from the saltwater. The temperature probe is supposedly having some issues giving a readout, but I haven’t had any luck accessing VNC to see what the issue is.

5/24/22

Today is my final WISRD period of the year. I finished looking over my thermistor whitepaper, and am waiting for final edits from Joe. I think I’ll miss the publication deadline in this journal, but it can always be submitted in the future. Joe’s retirement party was today as well and we gave him the guardian bells and notes.