How to look under the hood of protein sequence functional annotations? We have a DUF that is sometimes labeled with 2 different types of "___ase". One traces back to google's ProtNLM (natural language model) (I think), the other ... ? No clear structural homologs with experimental functions.

'Cribraria Cluster – A cluster of 1.5mm tall, immature Cribraria rufa slime moulds in ancient woodland, south Buckinghamshire, England.'
Photograph: Barry Webb

www.theguardian.com/artanddesign...

Large Serine Integrase fans: Multiple structures of 2 different integrases, with and without their RDFs. Amazing machines, different details, same concepts!
Our work on SPbeta: www.biorxiv.org/content/10.1...
Or friends' work on PhiC31:
www.biorxiv.org/content/10.1...

#SyntheticBiology #phage

Vibrant color portrait of Jane S. Richardson, the visionary biophysicist and artist who revolutionized structural biology with her invention of ribbon diagrams. She gazes warmly at the camera with a bright, knowing smile that radiates quiet brilliance and decades of curiosity. Her silver-blonde hair woven with gentle waves. Large, elegant dangling earrings catch the light, and she wears a richly patterned brown blouse embroidered with intricate turquoise paisley motifs and delicate beadwork that echoes the molecular elegance she has spent her life depicting. Behind her floats a luminous, dreamlike backdrop of glowing molecular structures--interlocking hexagonal and ribbon-like forms in electric blues, teals, and greens--blending science and art in a single, living canvas.

Hand-drawn and hand-colored (by Jane Richardson) scientific artwork known as a Richardson ribbon diagram (or “ribbon model”), one of the iconic visual inventions of Jane Richardson that transformed the way we see and understand protein structures. A graceful, three-dimensional tangle of protein backbone ribbons twists and spirals through space, rendered in soft pencil lines and luminous watercolor hues. Smooth golden-brown coils represent α-helices that curl like elegant ribbons, while broad teal-green arrows trace the flat, pleated strands of β-sheets slicing through the molecule with directional purpose. Thin, looping golden threads connect the secondary structures, creating a delicate, almost dance-like choreography of biology’s hidden architecture. The entire form is framed by a simple olive-green mat and dark border, giving the drawing the quiet dignity of both fine art and precise scientific illustration—a timeless bridge between molecular reality and human imagination.

Jane Richardson was born #OTD in 1941

+ Developed the Richardson (ribbon) diagram to represent proteins' 3D structure (becoming a standard representation for protein structures)
+ MacArthur Fellow, 1985
+ Elected, Nat'l Academy of Sciences, 1991
+ President, Biophysical Society, 2012

#WomenInSTEM

Great resource!

This line graph illustrates the percentage change in agency staff levels from the previous year for nine major U.S. federal scientific and health organizations between the fiscal years 2016 and 2025. The agencies tracked include the CDC, Department of Energy, EPA, FDA, NASA, NIH, NIST, NOAA, and NSF. For the majority of the timeline between 2016 and 2023, the agencies show relatively stable fluctuations, generally staying within a range of +5% to -5% change per year. However, there is a dramatic and uniform plummet starting in the 2024–25 period. Every agency depicted shows a sharp downward trajectory, with staffing losses ranging from approximately -15% to over -25%. The Environmental Protection Agency (EPA) shows the most significant decline, dropping to roughly -26%, while the National Institute of Standards and Technology (NIST) shows the least severe but still substantial drop at approximately -15%.

This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again.

www.nature.com/immersive/d4...

Bummer! Hope all is cleaned up soon.

Sun trying to shine through freezing fog rising from a partially- frozen Lake Michigan. Trying to come up with a political analogy about making rainbows out of less-than-pleasant circumstances, but failing, so please just enjoy the pic.

What's larger, a protein or its templating mRNA ?

> The mRNA is much larger.

⬛ 𝐀 𝐬𝐞𝐧𝐬𝐞 𝐨𝐟 𝐬𝐜𝐚𝐥𝐞 -- 𝐪𝐮𝐚𝐧𝐭𝐢𝐭𝐚𝐭𝐢𝐯𝐞 𝐢𝐧𝐭𝐮𝐢𝐭𝐢𝐨𝐧 & 𝐜𝐨𝐧𝐬𝐭𝐫𝐚𝐢𝐧𝐭𝐬 -- 𝐢𝐬 𝐚 𝐩𝐨𝐰𝐞𝐫𝐟𝐮𝐥 𝐞𝐧𝐚𝐛𝐥𝐞𝐫 𝐨𝐟 𝐫𝐞𝐬𝐞𝐚𝐫𝐜𝐡.

The figure shows myoglobin protein drawn to scale next to its mRNA template. The coding sequence of an mRNA ...

The historic largest library of NASA, linked to the development of the Hubble and James Webb telescopes, is being closed by the Trump administration, resulting in job losses and strong criticism regar... The Donald Trump administration shut down the library at NASA's Goddard Space Flight Center, threatening its unique scientific collection.

🧵For those who don't know, this has been in the works for a while.

There have been plans in the works to close down and consolidate some of the libraries with NASA.

But the closure of the Goddard library was never part of the plan.

Planning was being done to make Goddard the hub/main library.

Something hopeful to ponder

Tidied up an old desk drawer, found this. It was transcribed from a Brandeis science library bathroom wall in the 1980s:

I don't remember requests like this before! No deadline either. Have others been getting them?

Yikes, hang in there!

A physics demo seen from Chicago this AM: steam rising from our side of Lake Michigan into sunny but frigid air, and condensing into snow clouds on the Michigan side.

Thank you for publicizing what is going on! Even us grateful NSF grantees find it hard to know.

Wonderful history, but that picture with the positive supercoiling node has always bugged me.

The top 10 people of 2025 @nature.com who shaped science.
Recognizes Dr. Susan Monarez, the CDC Director who was "fired for holding the line on scientific integrity"
www.nature.com/immersive/d4...

love it!

Anybody else bugged by the loose definitions in headlines like this? For example, "Breakfast cereal" could be plain oatmeal or shredded wheat, or it could be candy-in-a-bowl. They're not the same thing!

while home sick yesterday I watched a history channel thing that claimed the discovery really came from Fleming's hobby of "agar art" with different-colored bacteria. Was there any truth to that?

OMG this is amazing.

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge.

Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...

Different repair pathways support intact or truncated insertions by R2 retrotransposon protein Non-LTR retrotransposon proteins copy their RNA template into a genome via coordinated nicking and reverse transcriptase activities of target-primed reverse transcription. Mechanisms by which the firs...

Awesome paper from Kathy Collins' lab

Different repair pathways support intact or truncated insertions by R2 retrotransposon protein | Science www.science.org/doi/10.1126/...

way to go @cnn.com to put this little tidbit of info behind a paywall.

After faculty raise concerns, UNC-Chapel Hill Chancellor says university will not sign Trump's higher ed compact Lee Roberts called the "preferential treatment" proposal a clear infringement on academic freedom.

👏 👏 👏

www.wunc.org/education/20...

Chicago Fellows The Chicago Fellows Program is an internationally competitive postdoctoral fellowship program to support the career advancement of truly exceptional and creative scientists in the biological and biome...

Postdoctoral fellowship opportunity at the U of Chicago:
biologicalsciences.uchicago.edu/research/chi...

working from home on an autumn (?) morning