Calin Plesa
@calin.bsky.social
Assistant Prof. @uoknightcampus.bsky.social. Cofounder @synplexity.bsky.social. Gene synthesis, synbio, protein engineering, nanopores, multiplex assays. Opinions my own. www.plesalab.org
The BioE dept in the Knight Campus is a great place to work and is unique in many ways! We are expanding over the next few years with our second building opening in 2026. Come join us, applications begin review on October 15. ...4/n
September 9, 2025 at 5:38 PM
The BioE dept in the Knight Campus is a great place to work and is unique in many ways! We are expanding over the next few years with our second building opening in 2026. Come join us, applications begin review on October 15. ...4/n
Our BioE dept at @uoknightcampus.bsky.social has an open rank search for two complementary tenure-track faculty positions in Neuroengineering focused on: 1) Experimental & Translational Neuroengineering and 2) Computational & Data-Science Neuroengineering.
careers.uoregon.edu/en-us/job/53... ...1/n
careers.uoregon.edu/en-us/job/53... ...1/n
September 9, 2025 at 5:32 PM
Our BioE dept at @uoknightcampus.bsky.social has an open rank search for two complementary tenure-track faculty positions in Neuroengineering focused on: 1) Experimental & Translational Neuroengineering and 2) Computational & Data-Science Neuroengineering.
careers.uoregon.edu/en-us/job/53... ...1/n
careers.uoregon.edu/en-us/job/53... ...1/n
Amazing PhD defense by Dr. Natanya Villegas! She pioneered CRISPR-Cas9 and RNA work in our lab and drove multiple tech-dev projects. She is looking for opportunities in the PNW so reach out -> @trienetoscience.bsky.social
May 29, 2025 at 5:36 PM
Amazing PhD defense by Dr. Natanya Villegas! She pioneered CRISPR-Cas9 and RNA work in our lab and drove multiple tech-dev projects. She is looking for opportunities in the PNW so reach out -> @trienetoscience.bsky.social
Huge congrats to Dr. Andrew Holston on a successful PhD defense!! Andrew has been working on the large-scale characterization and engineering of chimeric receptor histidine kinases. He’s looking for roles in biotech/academia, let’s connect if you’re hiring! -> @hkalltheway.bsky.social
May 27, 2025 at 11:32 PM
Huge congrats to Dr. Andrew Holston on a successful PhD defense!! Andrew has been working on the large-scale characterization and engineering of chimeric receptor histidine kinases. He’s looking for roles in biotech/academia, let’s connect if you’re hiring! -> @hkalltheway.bsky.social
Zooming in: Each homolog typically has ~30 mutants. This granular view lets us see not just overall trends but also some of the individual mutations driving resistance or loss of function. 9/n
January 28, 2025 at 1:42 AM
Zooming in: Each homolog typically has ~30 mutants. This granular view lets us see not just overall trends but also some of the individual mutations driving resistance or loss of function. 9/n
Next, we turned to Trimethoprim resistance. We examined how each homolog behaved across 6 concentrations, with only a few still surviving at the highest concentration tested. 8/n
January 28, 2025 at 1:41 AM
Next, we turned to Trimethoprim resistance. We examined how each homolog behaved across 6 concentrations, with only a few still surviving at the highest concentration tested. 8/n
Patterns in gain-of-function mutants pointed to specific regions critical for restoring function. In DHFR many factors contribute to fitness: catalytic activity, expression level, folding, metabolic flux, coupling to thymidylate synthase, PPIs, … 7/n
January 28, 2025 at 1:39 AM
Patterns in gain-of-function mutants pointed to specific regions critical for restoring function. In DHFR many factors contribute to fitness: catalytic activity, expression level, folding, metabolic flux, coupling to thymidylate synthase, PPIs, … 7/n
The silver lining: gain-of-function mutants. Many poorly complementing homologs gained function with minor changes. Including mutants up to 3 a.a. away increases the fraction of complementing homologs to 91%. 6/n
January 28, 2025 at 1:38 AM
The silver lining: gain-of-function mutants. Many poorly complementing homologs gained function with minor changes. Including mutants up to 3 a.a. away increases the fraction of complementing homologs to 91%. 6/n
Only 50% of the DHFR homologs were able to complement the KO strain well. What does this mean for ML models trained on unlabeled metagenomic data? Could non-functional sequences be "poisoning" the training set? Further work is needed to quantify this effect. 5/n
January 28, 2025 at 1:37 AM
Only 50% of the DHFR homologs were able to complement the KO strain well. What does this mean for ML models trained on unlabeled metagenomic data? Could non-functional sequences be "poisoning" the training set? Further work is needed to quantify this effect. 5/n
We adapted the DHFR KO strain and expression plasmid from the @kreynoldslab.bsky.social and Kortemme labs to assay the functionality of our libraries. Homologs were assayed for their ability to complement the KO or survive exposure to 6 levels of Trimethoprim inhibitor. 4/n
January 28, 2025 at 1:35 AM
We adapted the DHFR KO strain and expression plasmid from the @kreynoldslab.bsky.social and Kortemme labs to assay the functionality of our libraries. Homologs were assayed for their ability to complement the KO or survive exposure to 6 levels of Trimethoprim inhibitor. 4/n
We previously synthesized two 1,536 DHFR libraries in 2 codon versions, representing 19 phyla, 32 classes, 74 orders, 159 families, 330 genera, and 778 species, with most belonging to bacterial phyla such as Actinomycetota, Bacillota, Bacteroidota, Mycoplasmatota, and classes of Pseudomonadota. 3/n
January 28, 2025 at 1:32 AM
We previously synthesized two 1,536 DHFR libraries in 2 codon versions, representing 19 phyla, 32 classes, 74 orders, 159 families, 330 genera, and 778 species, with most belonging to bacterial phyla such as Actinomycetota, Bacillota, Bacteroidota, Mycoplasmatota, and classes of Pseudomonadota. 3/n
This study was many years in the making with talented @carmenvr.bsky.social leading experimental efforts during her undergrad. She will be applying to grad schools soon. Postdoc @kroman.bsky.social led the huge data analysis effort and is now looking for faculty positions. 2/n
January 28, 2025 at 1:30 AM
This study was many years in the making with talented @carmenvr.bsky.social leading experimental efforts during her undergrad. She will be applying to grad schools soon. Postdoc @kroman.bsky.social led the huge data analysis effort and is now looking for faculty positions. 2/n
Need long-read sequencing? We just completed the first ever run on @uoregon.bsky.social GC3F core’s new
@pacbio.bsky.social Revio instrument! Perfect for amplicons too long for Illumina, and with Kinnex, you can get >10x more data. Great pricing, no queue, try it: gc3f.uoregon.edu/pacbio-seque...
@pacbio.bsky.social Revio instrument! Perfect for amplicons too long for Illumina, and with Kinnex, you can get >10x more data. Great pricing, no queue, try it: gc3f.uoregon.edu/pacbio-seque...
November 25, 2024 at 2:53 PM
Need long-read sequencing? We just completed the first ever run on @uoregon.bsky.social GC3F core’s new
@pacbio.bsky.social Revio instrument! Perfect for amplicons too long for Illumina, and with Kinnex, you can get >10x more data. Great pricing, no queue, try it: gc3f.uoregon.edu/pacbio-seque...
@pacbio.bsky.social Revio instrument! Perfect for amplicons too long for Illumina, and with Kinnex, you can get >10x more data. Great pricing, no queue, try it: gc3f.uoregon.edu/pacbio-seque...
3M is discontinuing manufacturing of both Novec HFE-7500 and Fluorinert FC-40 in the next few months. These are the major diluents currently used in most emulsion fluorous oils (combined with fluorinated surfactants). Has anyone been looking for or testing alternatives?
November 12, 2024 at 5:42 PM
3M is discontinuing manufacturing of both Novec HFE-7500 and Fluorinert FC-40 in the next few months. These are the major diluents currently used in most emulsion fluorous oils (combined with fluorinated surfactants). Has anyone been looking for or testing alternatives?
A word of caution: uniformity is key with the use of degeneracy – it's like balancing ingredients in a recipe for the perfect bake, otherwise the differences in the resulting amount of assembled DNA can lead to issues later on. 11/n
December 12, 2023 at 10:42 PM
A word of caution: uniformity is key with the use of degeneracy – it's like balancing ingredients in a recipe for the perfect bake, otherwise the differences in the resulting amount of assembled DNA can lead to issues later on. 11/n
The coverage doesn't decrease as fast as the increase from the additional degeneracy, so the absolute numbers assembled go up. We estimate that an 1,536 bead set with degeneracy of 8 could successfully assembly over 8,000 variants in a single reaction. 10/n
December 12, 2023 at 10:41 PM
The coverage doesn't decrease as fast as the increase from the additional degeneracy, so the absolute numbers assembled go up. We estimate that an 1,536 bead set with degeneracy of 8 could successfully assembly over 8,000 variants in a single reaction. 10/n
We also tested lengths up to 1 kbp, hitting ~8% perfects. 9/n
December 12, 2023 at 10:40 PM
We also tested lengths up to 1 kbp, hitting ~8% perfects. 9/n
We used this to test 4 libraries each having 1-8 variants per barcoded droplet. We see a minimal effect on the percentage perfects. 8/n
December 12, 2023 at 10:39 PM
We used this to test 4 libraries each having 1-8 variants per barcoded droplet. We see a minimal effect on the percentage perfects. 8/n
Adding a 'degenerate' oligo to the mix is like throwing a wildcard into a card game - it spices up the assembly, keeping things interesting and efficient with low marginal cost. 7/n
December 12, 2023 at 10:38 PM
Adding a 'degenerate' oligo to the mix is like throwing a wildcard into a card game - it spices up the assembly, keeping things interesting and efficient with low marginal cost. 7/n
Why rebuild the wheel with every variant (wasting oligos and barcodes)? With this in mind we sought to make multiple gene variants in each droplet. With Degenerate DropSynth, it's like using a blueprint for the core and tweaking the design details. 6/n
December 12, 2023 at 10:38 PM
Why rebuild the wheel with every variant (wasting oligos and barcodes)? With this in mind we sought to make multiple gene variants in each droplet. With Degenerate DropSynth, it's like using a blueprint for the core and tweaking the design details. 6/n
We identified the selection of the fusion point between sensor and kinase as a major failure point. Although DropSynth could make 1536 genes, this would be quickly saturated by all the sensor and fusion variants we wanted to make. 5/n
December 12, 2023 at 10:37 PM
We identified the selection of the fusion point between sensor and kinase as a major failure point. Although DropSynth could make 1536 genes, this would be quickly saturated by all the sensor and fusion variants we wanted to make. 5/n
Our approach relies on making chimeras with a variable sensor module fused to a conserved downstream kinase to enable multiplexing of functional assays. (protein engineering) 4/n
December 12, 2023 at 10:35 PM
Our approach relies on making chimeras with a variable sensor module fused to a conserved downstream kinase to enable multiplexing of functional assays. (protein engineering) 4/n
A major push in the lab is to develop methods to functionally characterize entire protein families. We've been working for a few years on deorphanizing sensor histidine kinases, a family with several million known sensors, so scaling the functional assay is a major concern. 3/n
December 12, 2023 at 10:34 PM
A major push in the lab is to develop methods to functionally characterize entire protein families. We've been working for a few years on deorphanizing sensor histidine kinases, a family with several million known sensors, so scaling the functional assay is a major concern. 3/n
Some background first. DropSynth is a low-cost simple method to carry out multiplexed assembly of oligos into 1,536 designed genes. We isolate gene fragments onto barcoded beads and load them into emulsions for PCA assembly. 2/n
December 12, 2023 at 10:33 PM
Some background first. DropSynth is a low-cost simple method to carry out multiplexed assembly of oligos into 1,536 designed genes. We isolate gene fragments onto barcoded beads and load them into emulsions for PCA assembly. 2/n
We (UOregon Knight Campus) are hiring 1-2 tenure track faculty positions at any level. Focus is on data-enabled approaches to improve human health with applications in regenerative medicine, immunoengineering, synthetic biology, biosensors, human performance, or aging. Deadline is October 16. 1/2
September 5, 2023 at 9:14 PM
We (UOregon Knight Campus) are hiring 1-2 tenure track faculty positions at any level. Focus is on data-enabled approaches to improve human health with applications in regenerative medicine, immunoengineering, synthetic biology, biosensors, human performance, or aging. Deadline is October 16. 1/2