@loltrogge
 Berkeley, CA
Joined October 2008
  • Tweets22
  • Following56
  • Followers52
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Luke Oltrogge retweeted
Maria Lukarska@MariaLukarskaJul 24
I’m happy to share our pre-print exploring the activity and specificity trade-offs in adenine base editors. Thanks to my amazing co-authors @loltrogge, Hunter Nisonoff and all the other contributors @CynthiaTerrace @jlistgarten @dfsavage @SavageCatsOnly biorxiv.org/content/10.64898… 🧵

Activity and specificity trade-offs in adenine base editors

Adenine base editors (ABEs) are CRISPR effectors that introduce A-T to G-C transitions in the genome using a nucleotide deaminase fused to a Cas protein. ABEs have been evolved to have very high...

biorxiv.org
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Luke Oltrogge retweeted
Savage Lab@SavageCatsOnly11 Jul 2023
In the first preprint of the weekend, @loltrogge et al. find that the size of α-carboxysomes is strongly specified by CsoS2 and, in particular, the relative abundance of M- and C-type peptide repeats. ⬇️biorxiv.org/content/10.1101/…

α-carboxysome size is controlled by the disordered scaffold protein CsoS2

Carboxysomes are protein microcompartments that function in the bacterial CO2 concentrating mechanism (CCM) to facilitate CO2 assimilation. To do so, carboxysomes assemble from thousands of constit...

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Luke Oltrogge retweeted
Avi Flamholz@flamholz1 Dec 2022
New work online today! Eli and I used synbio tools to trace the evolution of bacterial CO2 fixation with @DNAmanipulation @Jjdesmarais2 @loltrogge Woody Fischer, Steve Singer & @SavageCatsOnly pnas.org/doi/10.1073/pnas.22…

Trajectories for the evolution of bacterial CO2-concentrating mechanisms | PNAS

Cyanobacteria rely on CO2-concentrating mechanisms (CCMs) to grow in today’s atmosphere (0.04% CO2). These complex physiological adaptations requir...

pnas.org
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Luke Oltrogge retweeted
Avi Flamholz@flamholz28 Jun 2022
Now that preprint v2.0 is out with correctly rendered equations, it's tweetsplainer time. "Trajectories for the evolution of bacterial CO2-concentrating mechanisms" A thread: biorxiv.org/content/10.1101/…

Trajectories for the evolution of bacterial CO2-concentrating mechanisms

Cyanobacteria rely on CO2 concentrating mechanisms (CCMs) that depend on ≈15 genes to produce two protein complexes: an inorganic carbon (Ci) transporter and a 100+ nm carboxysome compartment that...

biorxiv.org
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Luke Oltrogge retweeted
Neil Kaye@neilrkaye9 Dec 2020
Earth is warming but not the same everywhere. This #dataviz shows the warming from 1960 to 2020 at different latitudes. It shows that in 2016 the Arctic was already 3°C warmer than the 1961-1990 average, The last decade is more than 2°C warmer! #globalwarming #climatechange
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Probably dumb question from a non-biologist: Once you know the protein structure, how do you use that to predict macro-visible effects?
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Luke Oltrogge retweeted
Martin Jonikas@JonikasLab23 Nov 2020
One-third of the global carbon cycle is mediated by a phase-separated #pyrenoid. Just out: how the CO2-fixing enzyme Rubisco assembles to form the pyrenoid matrix. nature.com/articles/s41477-0… Free full text: rdcu.be/cbcI6 Teal: Rubisco; Red: EPYC1 linker protein. #LLPS
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Here's a small perspective on recent developments regarding Rubisco droplets and other metabolic condensates. This was keeping me busy during solitary quarantine in Taiwan in early May. authors.elsevier.com/a/1bmrP…
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Luke Oltrogge retweeted
Daniel Swain
@Weather_West10 Sep 2020
A meteorological feature I don't think I've seen before--a "smoke cyclone?" Looks like a mid-level low pressure swirl over North Coast--entirely encircled by dense smoke! Plus, bit of shallow convection atop smoke layer to south? Hmmm... cc @nplareau @NWSBayArea @NickyNaus #CAwx
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As the winds weaken aloft, gravity will take over as the primary vertical transport of the smoke. Suspended smoke will descend closer to the surface and could lead to darker skies and worsening air quality today. This is beyond the scope of our models so we rely on your reports!
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Luke Oltrogge retweeted
Avi Flamholz@flamholz28 May 2020
So happy that our new manuscript "Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli" is up on @bioRxiv biorxiv.org/content/10.1101/…

Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli

Many photosynthetic organisms employ a CO2 concentrating mechanism (CCM) to increase the rate of CO2 fixation. CCMs catalyze ≈50% of global photosynthesis, yet it remains unclear which genes and...

biorxiv.org
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So happy to see our pre-print online!! We discovered an characterized a new prokaryotic organelle - a novel family of encapsulins! With the help of @bjlafrance and the @NogalesLab we determined the structure of the compartment to 2.2 Angstrom resolution!! biorxiv.org/content/10.1101/…

Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur...

Prokaryotic nanocompartments, also known as encapsulins, are a recently discovered proteinaceous organelle in prokaryotes that compartmentalize cargo enzymes. While initial studies have begun to...

biorxiv.org
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Luke Oltrogge retweeted
Savage Lab@SavageCatsOnly4 Mar 2020
Luke and Benz's new paper on the intrinsically disordered repeat protein, Csos2, that brings the carboxysome together; a summary thread! nature.com/articles/s41594-0…
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Luke Oltrogge retweeted
Savage Lab@SavageCatsOnly2 Mar 2020
Big congrats to Luke and Benz on the culmination of untold hours scrutinizing csos2! Now we finally understand how this strange disordered repeat protein brings rubisco to the carboxysome. #savagecats #upwardsandonwards nature.com/articles/s41594-0…
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