Caleb

A day late but STILL IMPORTANT

We named the designation of specific transcripts for processing specification of cap chaperones (SOCCS) and believe it is a new mechanism for regulation of gene expression.

Nuclear RNA cap-chaperones eIF4E and NCBP2 govern distinct fates for 1000s of mRNAs uncovering an unexpected regulatory point in gene expression mRNA processing constitutes a series of steps in the nucleus to generate mature mRNAs that can be translated into protein. This relies on the methyl-7-guanosine (m7G) "cap" on the 5'end of mRNAs which...

The first paper from my postdoc is now out on BioRxiv! I was very lucky to join the Borden lab in time to work on bioinformatics for this project. We find that NCBP2 and eIF4E cause altered splicing when overexpressed, affecting largely distinct sets of transcripts. www.biorxiv.org/content/10.1...

It's so fun explaining the normal academic career path to non academics, because none of them understand why you do it. People look at me like I have two heads when I explain that as a postdoc I'm still considered a trainee most of the time.

The more I use rMATS the more I hate it. It's so annoying trying to get any information more granular than gene level or event level summaries.

I'm so glad the revisions on my grad school paper isn't extensive because I don't know how many weeks of 10 hours work days just to come home and work on revisions I can take.

I'm training someone that mainly does computational stuff in the wet lab and it's funny seeing his reaction when I get honest about procedures. Yes, letting a blot incubate in primary overnight can help the signal, but mainly I just don't want to stay late.

I was talking to my family about the devastation of academic science and it was so frustrating them not getting how bad it is. It feels like being a cow lead to slaughter, each day hearing the sound of the gun getting louder, and then being told they think it's just a thunderstorm.

While moving to my postdoc I lost a flash drive I had been using since high school. I paid the same price to replace it as it originally cost, and got 128GB instead of 8GB. The craziest part is that I wasn't that close to filling up the 8GB because everything moved to cloud storage.

The back of a proteintech antibody product sheet with empty boxes where validation images should be

Thank you protein tech, this validation data is very helpful.

Not telling the university until the media reports it is a great way to make this even more chaotic.

The vibes around campus are about to get really weird. I've already had non-biology grad students I've talked to ask me how everyone is coping with the broader NIH cuts, so this certainly isn't going to help the sense of dread that I think a lot of people are feeling.

in case you're wondering, "what's the harm in claiming an extinct species has been brought back from the dead" when it most certainly has not, our interior secretary is already using it to justify taking animals off the endangered species list

I don't know why I always leave writing methods until last. It's the hardest to do and way too energy draining.

Anyone could have predicted this. Columbia could fire or expel everyone who isn’t a white cis male and they’d still never get a penny of those grants back.

The only way you could think that assistants don't do anything at universities is to have never interacted with academia outside of going to class. They're the ones that make the entire thing run at an administrative level.

Meanwhile… in Chicago ❄️ 🌧️ #StandUpForScience 🧪

It still feels weird to get emails addressed to Dr. Embree and have them not be predatory journal spam.

RNA xkcd.com/3056

I've tested out a couple different electronic lab notebooks, but I honestly think the best one is just Obsidian for note taking and organization + git for version control. Its so much easier to link to bioinformatics stuff, and I can customize everything.

People outside of academics are clueless about the whole process, and I assume don't realize how big of a setback this will be. They really don't understand the time or the number of people that goes into the whole endeavor.

In the coming years it's going to be important to demystify academia.

There's nothing like being ready to leave to make you acutely aware of how long your code takes to run.

I'm very excited to start my postdoc tomorrow. Having a couple weeks off has been nice, but I'm ready to start thinking about science again. Let's hope my coding skills haven't atrophied.

I'm at a bar watching the OSU game, and they found out that I was new to Chicago and made me try a shot of malort. It was not as bad as I had heard, honestly just tasting like a worse version of absinthe.

At least I've done that initiation rite, so I guess I can call myself a Chicagoan.

Every so often I feel like I should.make a personal website, and then look at HTML and decide to postpone for another few months.

Hopefully reviews go well and I can soon write a longer thread talking about specific results when it's been fully published.

Our work also highlights the difficulty in using bulk RNA-seq to identify direct effects on the NMD pathway when there is also more general changes to gene expression happening, like widespread splicing changes.

Broadly, we find that no matter how you disrupt the spliceosome, there will be an increase in abundance of NMD targeted transcripts. In many situations this is likely due to pleiotropic effects on NMD, but we did ID a few spliceosome components that may have more direct effects.

Direct and indirect effects of spliceosome disruption compromise gene regulation by Nonsense-Mediated mRNA Decay Pre-mRNA splicing, carried out in the nucleus by a large ribonucleoprotein machine known as the spliceosome, is functionally and physically coupled to the mRNA surveillance pathway in the cytoplasm ca...

My graduate work from the Singh lab is now out on bioRxiv. In it we look at the impacts on nonsense mediated mRNA decay when the spliceosome is disrupted in different ways.

www.biorxiv.org/content/10.1...

I'm very excited to be starting a postdoc soon, but not at all excited for the logistics of moving to a new city.