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Laura White

@laurakwhite.bsky.social

2.6K followers 3.4K following 460 posts

Colorado RNA biologist & tRNA enthusiast exploring the wild frontiers of nanopore direct RNA sequencing at the intrepid venn diagram of northern blots & machine learning.

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Laura White @laurakwhite.bsky.social · Aug 22

Our paper is out in its final form! Back in April 2023, my coauthor Aleks Radakovic, then a PhD student, approached me after a talk in Chicago to ask what I thought an aminoacylated tRNA would look like if we pulled it through a @nanopore.
doi.org/10.1038/s414...

Nanopore sequencing of intact aminoacylated tRNAs - Nature Communications

Accurate protein synthesis depends on aminoacylated tRNAs, but their identities have been hard to measure. Here, authors present aa-tRNA-seq, a nanopore-based method that reveals the amino acid, seque...

doi.org

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Reposted by Laura White

Rosa Lafer-Sousa @rosalafersousa.bsky.social · 1d

Over the weekend ICE abducted an NIH contractor when he showed up to a courthouse for his green card hearing. He is documented. His wife is a citizen.

He is also member of the skeleton crew of animal care staff that works through a shutdown, to ensure the health and wellbeing of research animals.

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Laura White @laurakwhite.bsky.social · 1d

no but no one's sneezed on it yet

Laura White @laurakwhite.bsky.social · 1d

v0.2's organizational defaults also make it difficult (though not impossible) for a user to accidentally push large input OR output datafiles to GitHub and have to work backwards to unfuck the situation.

As always, development is informed by personal experience. 🤦

Laura White @laurakwhite.bsky.social · 1d

Previously: bsky.app/profile/laur...

Laura White @laurakwhite.bsky.social · Jul 8

Built a thing to solve my annoyance setting up Python + Quarto projects in Positron (& teaching others to do the same)

For anyone moving from .Rmd to .qmd who wants a cleaner on-ramp: meet Quoncierge.

🔗 github.com/lkwhite/Quoncierge

#positron #quarto #rstats #datascience #reproducibility #jupyter

GitHub - lkwhite/Quoncierge: Automate initializing reproducible Quarto + Jupyter + GitHub projects

Automate initializing reproducible Quarto + Jupyter + GitHub projects - lkwhite/Quoncierge

github.com

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Laura White @laurakwhite.bsky.social · 1d

Quoncierge updates: v0.2 adds an alternative, even more opinionated setup with organization and auto-routing of notebook outputs, intended for users who do lots of interactive exploratory data analysis. Sometimes the notebooks ARE the work, so let's make them reproducible. github.com/lkwhite/Quon...

GitHub - lkwhite/Quoncierge: Automate initializing reproducible Quarto + Jupyter + GitHub projects

Automate initializing reproducible Quarto + Jupyter + GitHub projects - lkwhite/Quoncierge

github.com

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Laura White @laurakwhite.bsky.social · 1d

But more importantly for #RNAsky #RNAbiology, I don't want your finger nucleases touching the ice touching my tubes holding my RNA. pubmed.ncbi.nlm.nih.gov/13715349/

Evidence for the liberation of a nuclease from human fingers - PubMed

Evidence for the liberation of a nuclease from human fingers

pubmed.ncbi.nlm.nih.gov

Laura White @laurakwhite.bsky.social · 1d

Michael, is this the right time to tell you I sometimes use my ice bucket as liquid waste disposal?

Mostly for ethanol/isopropanol washes, but still.

Reposted by Laura White

闵娅(Min Ya; Minya) PhD @minyaaa.bsky.social · 3d

And look at this graphic abstract….. 😱🤯

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Reposted by Laura White

Nature Cell Biology @natcellbio.nature.com · 4d

☕Pan, David, Chevrier & co show that the microbial #metabolites queuine and preQ1 modify the same host tRNA. PreQ1-tRNA reduces cell proliferation, slows #tumor growth, decreases the translation of ribosomal proteins and is cleaved by IRE1 on the ER #ribosome.
👉https://rdcu.be/eJqFc
bit.ly/46BPXtJ

Two microbiome metabolites compete for tRNA modification to impact mammalian cell proliferation and translation quality control - Nature Cell Biology

Zhang, Lahry, Cipurko et al. show that the microbial metabolites queuine and preQ1 modify the same host tRNA. PreQ1-tRNA reduces cell proliferation, slows tumour growth, decreases the translation of ribosomal proteins and is cleaved by IRE1 on the ER ribosome.

bit.ly

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Reposted by Laura White

Monica Maalouf, MD @maaloufmd.bsky.social · 5d

My husband was detained by ICE today

Juan Muñoz, an American citizen, father of 2, and local government official, was peacefully protesting w. other elected officials. He was assaulted and taken away

I have had zero contact or updates since

#SOS
@duckworth.senate.gov @durbin.senate.gov

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Reposted by Laura White

Susan Shao @sshaolab.bsky.social · 5d

Beautiful reconstitution of amino acid stress-dependent ISR activation by my @harvardcellbio.bsky.social colleagues presenting a unifying mechanism for GCN2 activation, which requires ribosome collisions and is enhanced by cognate uncharged tRNA in the A site! www.science.org/doi/10.1126/...

GCN1 couples GCN2 to ribosomal state to initiate amino acid response pathway signaling

During nutrient deprivation, activation of the protein kinase GCN2 regulates cell survival and metabolic homeostasis. In addition to amino acid stress, GCN2 is activated by a variety of cellular stres...

www.science.org

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Laura White @laurakwhite.bsky.social · 6d

This looks useful.

Francisco Rodriguez-Sanchez @frodsan.bsky.social · 6d

Finally using {pins} #rstats package to share heavy files that can't be shared among collaborators through GitHub, and it works like a breeze! Supports data versioning, cache, etc. Thanks @posit.co

Here using Google Drive to share files, but can use many different servers, see pins.rstudio.com

library("pins")

# specify folder in Google Drive to store objects
board <- board_gdrive("https://drive.google.com/drive/folders/FOLDER_ID")

# upload file
board |> pin_write(big_dataset, "big_dataset.csv", type = "csv")

# retrieve file (e.g. in another computer)
board |> pin_read("big_dataset.csv")

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Laura White @laurakwhite.bsky.social · 7d

The grad student organizers of Colorado's long-running RNA Club have been putting together this event to demystify the PhD application process for the past few years. Pass along to folks applying to grad school this cycle 🍁

It's a flyer for Colorado RNA Club's Undergrad Day event on Oct 21st at 1:30PM.

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Reposted by Laura White

Ryan Marino, MD @ryanmarino.bsky.social · 8d

This is why we fund scientists to study things like oyster slobber even if you don’t think it sounds important

Leah McElrath @leahmcelrath.bsky.social · 9d

⚠️ Chinese researchers have invented bone glue that mimics how oysters stick to surfaces underwater.

The adhesive can reportedly repair orthopedic fractures in 2-3 minutes, even in blood-rich environments, and is bioabsorbable.

interestingengineering.com/science/chin...

China's oyster-inspired 'bone glue' bonds fractures in minutes

A new oyster-inspired Bone-02 adhesive can revolutionize bone repair without metal fasteners.

interestingengineering.com

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Laura White @laurakwhite.bsky.social · 8d

Fun fact: the Japanese Spider Crab’s Latin name (M. kaempferi) refers to this 17th century Dutchman who “discovered” it in… a restaurant. 🙄

A wood and glass case in McGill’s Redpath museums containing a Japanese spider crab. The crab is roughly a meter across.

A sign inside the glass case at the Redpath museum reads: WHAT’S IN A NAME? Dr. Englebert Kaempfer, after whom the species is now named, first described the Japanese Spider Crab. A doctor and naturalist in the Dutch East Indian Company, Kaempfer visited Japan in 1690 and discovered the crab in a restaurant in Suruga, Japan.

The text is accompanied by an image of our intrepid explorer.

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Reposted by Laura White

Craig Kaplan @triggerloop.bsky.social · 8d

I think the R01 is basically a non-starter at NIGMS now. Data from NIH Reporter for new and competing awards, comparing number of R01s issued relative to R35s (MIRA). This has major ramifications for basic science and basic science investigators that are not yet in the MIRA pool

Graph showing total R35+R01 awards issued by NIGMS from 2020 to 2025. R01 in black showing a steep decline. R35 showing an increase. Total awards in 2025 slightly up from 2024 but these years are lower than 2020-2023

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Laura White @laurakwhite.bsky.social · 9d

Thank you! Super cool story so far.

Laura White @laurakwhite.bsky.social · 9d

Thanks, I think I caught most of that looking at the preprint. I suppose I always have my molecular biologist hat on when I ask why. 🤠

Do you think it’s intrinsic to the translational machinery, such that the effect would be recapitulated in an in vitro assay run at different temperatures?

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Laura White @laurakwhite.bsky.social · 9d

Very cool work! Mechanistically, do you have any idea *how* the opal codon is temperature sensitive in this context?

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Laura White @laurakwhite.bsky.social · 9d

US National Parks close if there’s a government shutdown due to Congress failing to pass a budget. The elk won’t notice. 🦌

Laura White @laurakwhite.bsky.social · 10d

Every single one of these leaves is a bug.

It’s a display case containing 20 or so bugs that look like leaves, at the Montreal Insectarium. Most of the bigs are brown, but some are light teal. The glass is labeled “Just like a bug” in English and French.

Zoom in on a whole bunch of brown not-leaves arranged naturalistically on a branch.

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Reposted by Laura White

Jason Williams @jasonwilliamsny.bsky.social · 13d

Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.

The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP

jasonjwilliamsny.github.io/grfp2025/

An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program

jasonjwilliamsny.github.io

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Reposted by Laura White

Terry McGlynn @hormiga.bsky.social · 20d

I have the (dubious) pleasure of serving as the chair of my campus's Academic Senate.

This means I have a (sometimes) office on the top floor of the admin building, along with the President, Provost, and VPs.

I will share something scandalous with you. This office has a thermostat. AND IT WORKS.

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Reposted by Laura White

Beth Popp Berman @epopppp.bsky.social · 21d

You know things are rough when the AAUP's advice on how to use social media is just "set all your accounts to private."

Kevin Reuning @reuning.bsky.social · 21d

The @aaup.org just shared guidance for academic workers on how to protect themselves online www.aaup.org/news/advisor...

Advisory to Academic Workers

In a moment when it is becoming increasingly difficult to predict the consequences of our online speech and choices, the AAUP and Faculty First Responders are issuing guidance to AAUP members and othe...

www.aaup.org

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Laura White @laurakwhite.bsky.social · 21d

Are you sure that’s not a blurry nighttime photo of a lit-up building and its reflection in the lake in front of it

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