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High throughput screening of eukaryotic release factor 1 variants to enhance noncanonical amino acid incorporation

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Reposted by Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts

Jim Van Deventer @vandeventerjim.bsky.social · 27d

Today, I’m grateful that I can finally share Briana Lino’s @blino237.bsky.social work on engineering eukaryotic release factor 1 (eRF1) for enhanced noncanonical amino acid incorporation. I highlight some key findings in this thread (1/n).

www.biorxiv.org/content/10.1...

Noncanonical amino acids (ncAAs) enable diversification of protein functions, but the efficiency of genetic code expansion (GCE) in eukaryotes is hindered by competition between suppressor tRNAs and r...

Tufts Will Be Tuition-Free for U.S. Families Earning Less Than $150,000

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Reposted by Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts

Jim Van Deventer @vandeventerjim.bsky.social · 29d

Today, I'm grateful to Tufts University--the university is trying to do good in the world, at a time when it's very easy for institutions of higher learning to stray wildly from their core missions.

(Disclosure: Tufts is my employer)

now.tufts.edu/2025/09/09/t...

Tufts University announces that U.S. students from families earning less than $150,000 will not have to pay undergraduate tuition.

now.tufts.edu

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Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Aug 22

I'm very excited to lead the @darpa.mil #SWITCH effort on #sustainable #biomanufacturing at #TuftsUniversity with Matt McNulty, Amin Nikkhah, and Todd Chappell! See more here:
now.tufts.edu/2025/08/19/w...

Working Toward Reducing Chemical Industry Dependence on Petroleum

Tufts researchers receive up to $4.5 million from DARPA to create robust, flexible biosynthetic manufacturing

now.tufts.edu

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Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Aug 1

New pre-print from the lab! We show for the first time that tagatose can be synthesized from glucose! After assessing several pathways, we identified a phosphatase specific to gal-1-P. We also perform modeling to understand the molecular determinants of specificity.
www.biorxiv.org/content/10.1...

A Novel Phosphatase Reverses the Leloir Pathway to Promote Tagatose Synthesis from Glucose

D-Tagatose is a natural, low-calorie, rare monosaccharide that has gained substantial interest as an alternative sweetener. It offers numerous benefits, including a low glycemic index, prebiotic prope...

Here are the nearly 2,500 medical research grants canceled or delayed by Trump

Reposted by Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts

ChemKritzer @chemkritzer.bsky.social · Jun 4

Great piece @nytimes.com with a database of thousands of NIH grants ended or delayed.

No matter the intention, the effects are clear: a huge slowdown in biomedical research into diseases & new therapeutics.

Share with your Rep & Senators, and spread awareness!

www.nytimes.com/interactive/...

Some cuts have been starkly visible, but the country’s medical grant-making machinery has also radically transformed outside the public eye.

www.nytimes.com

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Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Apr 22

The Nair lab is looking for a #post-doc experienced in yeast pathway and genome engineering. Please DM or email me if you are interested!! Please spread the word! #synbio #metabolicengineering

Tufts says federal authorities detained graduate student

Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Apr 12

Congratulations 🍾

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Reposted by Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts

Joe Katz @joekatz45.bsky.social · Mar 26

ICE kidnapped another student.

This time a grad student at Tufts, Rumeysa Ozturk. Turkish national, in the United States on a student visa. Her lawyer does not know where she is being held.

Rumeysa wrote op-eds criticizing the university's response to student demands on Gaza.

The university received reports that an international graduate student was taken into custody from an off-campus apartment Tuesday night, President Sunil Kumar wrote in a letter to the school communit...

www.wbur.org

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Reposted by Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts

Jim Van Deventer @vandeventerjim.bsky.social · Mar 18

The Van Deventer Lab’s first manuscript describing chemically expanded antibody discovery is now published! The genetically encoded “Clickable CDR-H3 Library” can become many, chemically diverse antibody libraries, enabling new drug discovery opportunities (1/n).

pubs.acs.org/doi/full/10....

Design, Construction, and Validation of a Yeast-Displayed Chemically Expanded Antibody Library

In vitro display technologies, exemplified by phage and yeast display, have emerged as powerful platforms for antibody discovery and engineering. However, the identification of antibodies that disrupt...

pubs.acs.org

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Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Feb 24

I'm excited to be named a senior member of the NAI! Thank you to all my group members and colleagues at Tufts for supporting my group's research!
now.tufts.edu/2025/02/20/f...

Five Tufts Faculty Named Senior Members of National Academy of Inventors

Tufts faculty newly named to the National Academy of Inventors have led to innovations in healing wounds, assessing health, treating rare disorders, and more

now.tufts.edu

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Reposted by Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts

Graham Leverick (he/him) @grahamleverick.bsky.social · Feb 4

Want hands-on battery research experience? Join the Battery Research Summer School!

4 days of real labs, real data, real problem-solving. Learn to cycle, test & troubleshoot Li-ion batteries.

📅 June 3-6 | 📍 Tufts University
📌 More info: www.eventbrite.com/e/1234043610...

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Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Jan 8

This pre-print is now published and available in final form here:

www.sciencedirect.com/science/arti...

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Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 25

Finally, we show that engineered spores can be used to degrade plastic PET films #plasticdegradation

Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 25

We compare coat proteins for surface availability and protection from inactivating agents (e.g., heat, protease), and their effect on sporulation efficiency. We also assess how different coat proteins can be co-utilized to increase display levels.

Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 25

Allelic tagging allows us to examine the activation timing and strength of promoters associated with spore coat structural proteins.

Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 25

In addition, this work investigates scarless allelic tagging of spore coat proteins using genome editing by co-transformation, analyzing factors affecting genome editing by congression.

Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 25

🚨🆕New manuscript🆕🚨from the lab!! Started by @biotechalchemist.bsky.social and completed by Todd Chappell. This work assesses the utility of >30 #spore coat proteins for #surfacedisplay - almost 3x currently described! We found that SscA is a great carrier not used before‼️
biorxiv.org/cgi/content/...

biorxiv.org

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Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 25

Allelic tagging allows us to examine the activation timing and strength of promoters associated with spore coat structural proteins.

Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 25

In addition, this work investigates scarless allelic tagging of spore coat proteins using genome editing by co-transformation, analyzing factors affecting genome editing by congression.

Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 21

Here!

Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 4

This effort was led by post-doc Damayanti Chakravarty (Nair) + @DolginJames (Kaplan) w/ support from Pomai Yamaguchi (Lee) + many others from the Nair & Kaplan groups.

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Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 4

Work showed that both, protein + metabolites, in VN lysate are needed to support fast growth. The cells were less stressed on VN lysate when compared to other serum alternatives and could be differentiated after several passages.

Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 4

We found that different cell lines are compatible with different microbial lysates. We were able to adapt bovine satellite cells for long-term growth on Vibrio natriegens lysate. After adaptation, their growth rate on VN lysate was similar to that on serum.

Nair (Synthetic Biology & Systems Bioengineering) Lab @Tufts @nair-lab.bsky.social · Nov 4

🆕New pre-print🆕! Our first foray into 🥩cultivated meat🍖 with David Kaplan, Kyong Lee, and supported by Tufts University for Cellular Agriculture, Consortium! We report that microbial lysates can be used as serum alternatives for in vitro animal cell proliferation.
www.biorxiv.org/content/10.1...