@dabiophysicist

Postdoctoral scholar in @veeslerlab @UW. Former @UCSFBiophysics @SFSU & @ucsc & @exploratorium explainer. Tiny pictures.

 Seattle, WA
bsky.app/profile/dabiophysicist.bsky.social
Joined March 2017
  • Tweets936
  • Following726
  • Followers486
34Media
💔😢
259
As we celebrate the PDB, let's also remember the prolific but underrecognized structural biologists who contributed so much to our field, and to us personally as trainees. Scientists like @UCSF @UCSFBiophysics legend Janet Finer-Moore, with 125 depositions from 1987 to 2024! 🎉🥳
rcsb pdb 💉🧬💻🔬💊🌱🧠🦠@buildmodels20 Oct 2024
Happy Birthday PDB, announced #OTD in 1971 In Nature New Biology. Today we celebrate the 53rd anniversary of the Protein Data Bank and the PDB depositor community, and congratulate the 2024 Nobel Prize in Chemistry Awardees rcsb.org/news/feature/670ffe…

The Nobel Prize in Chemistry 2024

Congratulations to David Baker, who was recognized for computational protein design, and to Demis Hassabis and John M. Jumper, who were recognized for protein structure prediction. These achievements...

rcsb.org
3
16
1,763
Hey cryo-EM tweeps - I wonder if anyone has seen anything weird with significant 3xFLAG peptide in your samples? (Like 100 uh/mL after eluting)
1
1
572
The uh is of course the unit of confusion used to quantify bad grids (ug)
294
🌟Exciting news!🌟 I’m thrilled to share our latest preprint, which marks a special milestone. This manuscript, authored by my brilliant PhD student @ciara_pugh is her first scientific paper with my group and presents the first high-resolution cryo-EM structure from my group!
4
6
3
70
6,312
Daniel Asarnow retweeted
The Veesler Lab@veeslerlab9 Jul 2024
How many times did coronaviruses evolve the ability to use ACE2 as receptor for infection? Find out by reading this @biorxivpreprint in collab with Huan Yan (Wuhan Univ) Led by Ma CB, Liu C @YoungjunPark11 Tang J & Chen J @HHMINEWS @UWBiochemistry 1/9 biorxiv.org/content/10.1101/…

Multiple independent acquisitions of ACE2 usage in MERS-related coronaviruses

The angiotensin-converting enzyme 2 (ACE2) receptor is shared by various coronaviruses with distinct receptor-binding domain (RBD) architectures, yet our understanding of these convergent acquisition...

biorxiv.org
3
41
1
119
15,218
Two Mondays, two Salems, two eclipses - no witchcraft
1
9
713
Daniel Asarnow retweeted
The Veesler Lab@veeslerlab1 Apr 2024
Sharing our work on developing counter-measures against porcine-deltacoronavirus (PDCoV) which is also infecting humans! Led by @RexhepajMegi @YoungjunPark11 & Lisa Perruzza w Fabio Benigni @HHMINEWS @UWBiochemistry biorxiv.org/content/10.1101/… 1/15

Broadly neutralizing antibodies against emerging delta-coronaviruses

Porcine deltacoronavirus (PDCoV) spillovers were recently detected in children with acute undifferentiated febrile illness, underscoring recurrent zoonoses of divergent coronaviruses. To date, no...

biorxiv.org
1
22
51
12,670
Nice idea - I've done something quite similar in 3D, using particle orientation. In general I find it doesn't improve the resolution or replace 3D classification, but large proportions of particles (~3/4 in some cases) can be excluded with no loss.
Yasuhiro Arimura@ArmrYshr22 Jan 2024
Duplicated Selection To Exclude Rubbish particles (DuSTER) is a method for facilitating the structural analysis of small biomolecules. DuSTER uses the reproducibility of the particle centering during 2D classification to exclude the low S/N. biorxiv.org/content/10.1101/…
1
17
3,409
Here's my poster about it (thought the code was already buried in my github somewhere, but not so, I'll have to post it later) github.com/asarnow/posters/b…
2
1
7
1,235
If these phenotypes worry you... nucleofection maybe?
Min WU@WUMIN_LAB9 Mar 2024
😍 " moment of the entry of Lipofectamines into the cell via endosome-rupture" So many wonderful cell biology ideas behind how John Heuser captured these rare, transient, asynchronous moments. Read them here: early #EM_Monday @HaniehFalahati biorxiv.org/content/10.1101/…
6
593
"Deliberately and for private reasons" 😂
This Post is from an account that no longer exists. Learn more
3
623
CTFFIND5 provides improved insight into quality, tilt and thickness of TEM samples biorxiv.org/cgi/content/shor… #biorxiv_biophys
10
2
30
4,866
Paul Doherty taught me the Nakamura lock 20 years ago @exploratorium & I'm sure I'm not the only one who remembers him for it (any many other things) 💔
Massimo
@Rainmaker197326 Feb 2024
How to make an effective paper plane [📹 Fuzail Ansari / mr.fuzail_art] xitter.cf/i/status/1762192…
1
1
366
exploratorium.edu/education/…

Paul Doherty: Teacher Institute Staff (in Memoriam) | Exploratorium

Paul Doherty graduated from the Massachusetts Institute of Technology with a PhD in physics. He was a tenured professor of physics for twelve years at Oakland University, Michigan, where he taught...

exploratorium.edu
1
139
We used to talk about this idea in @yifan_ucsf lab, but my lab mate chose to start with hydrophobins and never got past initial playing-around. So cool to see folks actually tried it and it works!
Ci Ji Lim@cijilim9 Feb 2024
1/6: #CryoEM Exhausted with fighting the air-water interface (AWI) problem during sample grid plunge freezing? We may have an easy solution for you! Read our latest preprint on how we use LEA proteins as AWI sample protectants for challenging samples: biorxiv.org/content/10.1101/…

Small LEA proteins as an effective air-water interface protectant for fragile samples during...

Sample loss due to air-water interface (AWI) interactions is a significant challenge during cryo-electron microscopy (cryo-EM) sample grid plunge freezing. We report that small Late Embryogenesis...

biorxiv.org
1
1
14
1,961
Replying to @t0nyyates
This is like saying debunking the Laffer curve is pointless, because it merely reflects a preexisting political conclusion
1
2
162
It's important to say that incorrect, politically motivated reasoning is motivated AND that it's wrong - because otherwise it's going to be used again and again in service of the same politics
1
140
This is cool but feels like the real lesson is that @RolandDunbrack rocks
Structure@Structure_CP5 Jan 2024
One bead per residue can describe all-atom protein structures dlvr.it/T10wLK

One bead per residue can describe all-atom protein structures

Heo and Feig describe a machine-learning-based protocol for accurate recovery of atomistic detail from coarse-grained models of proteins. The method can be applied to add atomistic details to...

cell.com
1
1
3
1,511
Unless I'm reading it wrong, the state of the art neural network is performing slightly better than a program the Dunbrack lab first published over 25 years ago
3
295
When foundational discovery turns into "common knowledge" so quickly, the ink is hardly dry before folks argue whether to even cite a source, we risk forgetting what made a new idea challenging - why we believed in the old paradigm and what kind of thinking can change the game
1
2
336
more replies
Tonight I'm remembering a lecture (Biochem 100C, Spring '08) where we discussed the rise and fall of what he called the "Orthodox model" over this then-recent press release newsarchive.berkeley.edu/new…
1
162
TL;DR Bob Ludwig was a great teacher, emblematic of how greatly @UCSCscience values pedagogy, and also colocalization of lactate dehydrogenase and the malate antiporter is still a big deal, if it's 15, or 30, or (probably) a hundred million years later
1
145
Load more