Alex Naka
@gottapatchemall.bsky.social
ML & protein engineering at http://science.xyz | into papers, pens, plots, puppies, proteins
algorithmic.ink
https://x.com/gottapatchemall
algorithmic.ink
https://x.com/gottapatchemall
We also did a low-tech experiment we call the curtain test. It's basically peekaboo: cover the rig with a curtain for a while, then open it again. WAChRs respond pretty well.
Simple - but a sanity check for being able to do something like optogenetic vision restoration.
Simple - but a sanity check for being able to do something like optogenetic vision restoration.
September 18, 2025 at 2:06 PM
We also did a low-tech experiment we call the curtain test. It's basically peekaboo: cover the rig with a curtain for a while, then open it again. WAChRs respond pretty well.
Simple - but a sanity check for being able to do something like optogenetic vision restoration.
Simple - but a sanity check for being able to do something like optogenetic vision restoration.
In particular, WAChRs can drive decent photocurrents with very low intensity light.
September 18, 2025 at 2:06 PM
In particular, WAChRs can drive decent photocurrents with very low intensity light.
We picked three finalists that offer a trade-off between speed and sensitivity: WAChR-f/m/s
We benchmarked these against some existing optogenetic tools on our manual patch clamp rig ("Patchrig Swayze").
We think they offer superior performance for a lot of applications.
We benchmarked these against some existing optogenetic tools on our manual patch clamp rig ("Patchrig Swayze").
We think they offer superior performance for a lot of applications.
September 18, 2025 at 2:06 PM
We picked three finalists that offer a trade-off between speed and sensitivity: WAChR-f/m/s
We benchmarked these against some existing optogenetic tools on our manual patch clamp rig ("Patchrig Swayze").
We think they offer superior performance for a lot of applications.
We benchmarked these against some existing optogenetic tools on our manual patch clamp rig ("Patchrig Swayze").
We think they offer superior performance for a lot of applications.
We kept Mr. Patchino very busy while we iteratively searched for improvements - several hundred new WAChR variants for this project (and 1750+ so far in our broader campaign).
September 18, 2025 at 2:06 PM
We kept Mr. Patchino very busy while we iteratively searched for improvements - several hundred new WAChR variants for this project (and 1750+ so far in our broader campaign).
We ran an ML-guided directed evolution campaign to optimize WAChR. To do this, we developed a system that uses automated patch clamp to quickly screen opsin functional properties.
(We named him Al Patchino)
(We named him Al Patchino)
September 18, 2025 at 2:06 PM
We ran an ML-guided directed evolution campaign to optimize WAChR. To do this, we developed a system that uses automated patch clamp to quickly screen opsin functional properties.
(We named him Al Patchino)
(We named him Al Patchino)
We used the K+ selective opsin WiChR as a starting point pmc.ncbi.nlm.nih.gov/articles/PM...
WiChR is a strong, sensitive optogenetic silencer. We applied a mutation that breaks K+ selectivity, which converts it into an excitatory channel. We call this mutant WAChR (pronounced "watcher").
WiChR is a strong, sensitive optogenetic silencer. We applied a mutation that breaks K+ selectivity, which converts it into an excitatory channel. We call this mutant WAChR (pronounced "watcher").
September 18, 2025 at 2:06 PM
We used the K+ selective opsin WiChR as a starting point pmc.ncbi.nlm.nih.gov/articles/PM...
WiChR is a strong, sensitive optogenetic silencer. We applied a mutation that breaks K+ selectivity, which converts it into an excitatory channel. We call this mutant WAChR (pronounced "watcher").
WiChR is a strong, sensitive optogenetic silencer. We applied a mutation that breaks K+ selectivity, which converts it into an excitatory channel. We call this mutant WAChR (pronounced "watcher").
My group at Science has been running a big campaign to engineer new channelrhodopsins.
Excited to share the first results from it today: a suite of highly sensitive new opsins.
We call them "WAChRs".
Everyday indoor office lighting is enough to activate them pretty strongly.
Excited to share the first results from it today: a suite of highly sensitive new opsins.
We call them "WAChRs".
Everyday indoor office lighting is enough to activate them pretty strongly.
September 18, 2025 at 2:06 PM
My group at Science has been running a big campaign to engineer new channelrhodopsins.
Excited to share the first results from it today: a suite of highly sensitive new opsins.
We call them "WAChRs".
Everyday indoor office lighting is enough to activate them pretty strongly.
Excited to share the first results from it today: a suite of highly sensitive new opsins.
We call them "WAChRs".
Everyday indoor office lighting is enough to activate them pretty strongly.
Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies
www.cell.com/cell/fulltex...
broad spectrum antivenom
www.cell.com/cell/fulltex...
broad spectrum antivenom
May 2, 2025 at 3:34 PM
Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies
www.cell.com/cell/fulltex...
broad spectrum antivenom
www.cell.com/cell/fulltex...
broad spectrum antivenom
ATLAS: a rationally designed anterograde transsynaptic tracer
www.nature.com/articles/s41...
very cool
www.nature.com/articles/s41...
very cool
May 1, 2025 at 5:42 PM
ATLAS: a rationally designed anterograde transsynaptic tracer
www.nature.com/articles/s41...
very cool
www.nature.com/articles/s41...
very cool
complete and total vindication
March 14, 2025 at 6:55 PM
complete and total vindication
this is cool
Rational multienzyme architecture design with iMARS
Rational multienzyme architecture design with iMARS
January 23, 2025 at 5:18 PM
this is cool
Rational multienzyme architecture design with iMARS
Rational multienzyme architecture design with iMARS
A muddy fall hike with Lily and puppy QWERTY
From Nov 2022
From Nov 2022
November 26, 2024 at 7:25 AM
A muddy fall hike with Lily and puppy QWERTY
From Nov 2022
From Nov 2022
unless i'm misunderstanding there are n=2 people in their series B bin
November 18, 2024 at 6:06 PM
unless i'm misunderstanding there are n=2 people in their series B bin
Another old plot, from november 2020
November 17, 2024 at 10:07 PM
Another old plot, from november 2020
Getting back into plotting
November 14, 2024 at 7:27 AM
Getting back into plotting
November 21, 2023 at 6:00 PM
Lily likes the view from the new apartment
November 18, 2023 at 8:58 PM
Lily likes the view from the new apartment
