Pristina single cell atlas

We have a new pre-print out, which is the result of a wonderful collaboration with Jordi Solana’s lab.

It is the first adult single cell atlas of an annelid, one of our favorite annelids, Pristina leidyi Smith, 1896 bioRxiv

Here is Jordi’s tweetorial about the preprint, and here are some details from me.

This was basically one of those collaborations where we were better than sum of our parts, and we loved working on this together! Jordi writes about it here, and I am forever grateful I got to work with him and his team on this project.

Conference/Talks Coming Up

Duygu will give a talk at UW-Madison Wisconsin next week (May 5th)

She will then be at the Gordon Conference on Tissue Repair and Regeneration as an invited speaker in late May/early June.

Duygu and Ranny will teach at the Embryology Course at the MBL in Woods Hole this summer. Then Duygu, Ryan, and Ranny will be at the SDB Meeting in Chicago.

A short note on Duygu's Twitter decision

A while ago, after Twitter was acquired by a somebody with severely low emotional intelligence, and that somebody started attacking trans people, scientists, disabled folks etc, I decided to leave Twitter. Even though initially I wasn’t sure about leaving, it became an obvious choice, especially folks switching to Mastodon. This has been a very interesting experience that had some unexpected outcomes for me. In this blog post, I want to briefly talk about those outcomes, and then explain what I plan to do next about my social media presence.

1) In making the switch to Mastodon, I started spending a lot less time on social media.

Because there was not as much activity on Mastodon. This helped me realize that I was spending way more time on social media than I liked. It was difficult at first, but because I had left Twitter out of a principle that was so important to me, I could not flake and just get back on it. This helped a lot in limiting my social media use.

2) I used to tell myself I learn a lot via Twitter.

And that is not incorrect, but the type of learning that happens wasn’t as meaningful as I wanted it to be, especially for the time spent. For example, I learn more meaningful things by reading a journal article in 1 hour, compared to the 1 hour spent on Twitter. One could argue you learn many more smaller things, but really, do they ever stick as real knowledge? Maybe a small portion. Since leaving Twitter I have been reading so much more, and feel happier.

3) But it is not all black and white, there are good things about social media.

I don’t mean this to be a blog post about how bad social media is. It isn’t. I love #WormWednesday, I love reading other academics thoughts in a less formal space, I love the power of social media in raising awareness. So, I realized I do not want to be completely off social media, but I really want to limit the time spent (like really, 10 minutes/day for Twitter, 10 minutes for Mastodon, 10 minutes for Instagram).

4) Oh so, does this mean I am back on Twitter, after all that I have said, despite how much I despise the owner?

The revolution I hoped (a mass move out of Twitter to a de-centralized platform) unfortunately did not happen. In the meantime, multiple earthquakes devastated Türkiye. So much of the earthquake aid and communication was happening via Twitter inevitably. I realized it is not possible to isolate myself, and the reality is, the social media revolution hasn’t happened. Initially, I decided to be back on Twitter only for earthquake relief efforts. But the experience also made me accept the fact that I need the platform for spreading the word about my lab’s work.

5) So what’s next?

Basically, I will be on Twitter only for announcing my lab’s works, job posts, other professional announcements etc. Stuff that can be done via 10 minutes/day. If something like a disaster requires more time spent, then I will spend more time. I have already been feeling the good effects of the limited time on social media on my mental health. So, in some ways, I am grateful for the toddler man who forced me to explore this new way of existence on social media. <3

Here is where you can find me (but find me IRL and let’s have coffee or something):
Mastodon (the ideal, decentralized social media platform, despite room for improvement for its user interface)
Twitter (out of obligation because y’all haven’t left)
Instagram (for science-art, also I know Facebook is evil too)

Welcome Grace

Grace is visiting from Stephan Schneider’s Lab in Taiwan to learn how to inject Platynereis embryos.

Welcome Kaitlyn Hong

Welcome to Kaitlyn, our new undergraduate researcher at the lab! Kaitlyn will be working with Ranny on establishing sex-specific markers in Platynereis dumerilii.

David Remsen

I heard the news of losing Dave on Wednesday night. Since then, most of my awake hours have been filled with thinking of him, Dana, and his family. Dave was my colleague and friend. He was the director of Marine Resources Center (MRC) at the MBL. Being here in St. Louis, so far from everybody else who know and love Dave, it has been difficult to grieve his unexpected death. So, I decided to write about him.

Dave was one of the best humans you could meet. My office at the MBL was in the same building as Dave’s, and I saw him quite often. It was always a delight to run into him and have a quick chat. He was so knowledgable, kind, caring, supportive. An example human being in every sense I could tell. He set the tone with his personality at the MRC. His staff is just like him: they always go out of their way to help, even though they are often stretched thin with so many people and animals they are helping and taking care of throughout the day.

I would often see Dave with a bunch of visitors, him telling them about MRC, MBL’s mission, the beloved animals, the building’s history. Always with excitement. You could bask in his positivity, knowledge, and kindness.

Most people probably never noticed, but I have had Dave’s face on my powerpoint slides that I use for public science education since 2017. Him and Louie Kerr. During these public outreach talks, I tell the story of how, as a little girl, I dreamed of becoming an explorer like Jacques Cousteau.

I follow up saying that, even though I thought I was going to be in deep oceans in a submersible, or out in the jungles, instead I became a lab biologist. But I still feel like that explorer, I feel like with all the resources available to me, and especially thanks to the experts helping me make my scientific dreams get realized, I get to explore the tiny “planets” that are embryos and organisms.

This is the next slide I show, where I have Dave and Louie photoshopped on that image above:

Here is a close-up:

Because how can you achieve anything without the amazing people like Dave (and Louie)? Him and his team were essential in establishing my animal cultures at the MBL, all the while they made it a joy to be an inhabitant of the MRC. (Except, damn that building’s climate control, but that is nobody’s fault.)

I don’t know how to imagine that building without Dave, I don’t know how to process this.

I trusted Dave’s opinion so much that, anytime I needed to hire a new Research Assistant, first I would go to him and ask if he had any great volunteers or summer workers he may recommend. That is how I had the luck and pleasure to work with some great people at my lab. He just knew how good people looked like, because he was one of the greatest of people.

Dave, my friend, you left a big void that will never be filled. I know I will miss seeing you anytime I visit MBL.

Help us train our robot

Ryan Null has been working to create an AI model that can count segment numbers instantly in Platynereis. We would like to crowdsource the training data and if you like, you can help us. Go here and annotate some images!

Goodbye Jamie!

Jamie was a research assistant while we were still in Woods Hole, helped move the lab to St. Louis and spent the summer with us there. She is back at the MBL. We will miss her very much (worms will miss her even more so!).

Welcome Brandon McCrow-Bennett

Brandon joined us as our first undergraduate research assistant as a part of the Enter program. We are so excited to have you Brandon!

Goodbye Emma!

Emma is moving onto a new adventure to work on cephalopods at the Albertin Lab at the MBL. Emma, you will be sorely missed, your work and tools you have developed will be used at the lab years to come! We are excited for you!

Welcome Faith Stemmler

Faith Stemmler joined the lab as our new lab manager. Faith is a native St. Louisan, she studied plankton in the past when she lived in Alaska, and brings a ton of aquaculture knowledge to the lab. Welcome Faith!

Embryology 2022 at MBL

Özpolat Lab ran the Annelid module at the Embryology Course 2022. We had a great time with the students, and ended up experiencing one of the best worm hunts ever!





Photo by Jana Sipkova

We are in St. Louis!

Our lab has arrived in St. Louis, with Emma back in Woods Hole keeping our animals alive until they get sent. We are so excited to be here and can’t wait to welcome new students, and team members to the lab.