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Zeshi Li (Jack)

@lizeshi.bsky.social
247 followers 477 following 31 posts

Assistant Professor, Chemical Biology and Drug Discovery, Utrecht U. PhD G.-J.Boons Lab; Post-doc C.Joo Lab TUDelft. www.uu.nl/medewerkers/ZLi2

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Zeshi Li (Jack) @lizeshi.bsky.social · 15/08/2026
Dear Bluesky community, does anyone have any insight into what’s going on at the @idtdna.bsky.social plant in Belgium? Many of our oligo orders have been significantly delayed, with several repeatedly failing synthesis/QC cycles. Some colleagues have experienced similar issues.
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Zeshi Li (Jack) @lizeshi.bsky.social · 17/06/2026
The project was led by Lin Rietveld (my first PhD trainee), had been a teamwork with Wei Wu and Filip Zawisza, and received tremendous support from @incarnatolab.bsky.social
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Zeshi Li (Jack) @lizeshi.bsky.social · 17/06/2026
Excited to share the very first #preprint since I started my lab at @utrechtuniversity.bsky.social We explored the area of small molecule- #RNA interaction, and present SOLiD-MaP: a #photoproximity labeling platform for mapping small molecule binding site on RNA. www.biorxiv.org/content/10.6...
biorxiv.org
SOLiD-MaP: A Photoproximity Labeling Platform for Small Molecule Binding Site Mapping on RNA
RNA-targeting small molecules are emerging as promising therapeutic modalities, but their development requires methods that define binding sites and evaluate RNA target selectivity. Existing approache...
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Zeshi Li (Jack) @lizeshi.bsky.social · 13/04/2026
We have a 3-year post-doc position open. Apply now and join BioBeyond_NL to power up mass spec studies with new chemical biology tools! www.uu.nl/en/organisat...
uu.nl
Postdoc Position in Chemical Biology
Join us to design cutting-edge chemical biology tools and reveal molecular mechanisms in complex biological systems.
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Reposted by Zeshi Li (Jack)
Iain Wilson @iainwilsonwien.bsky.social · 16/02/2026
RIP: Professor Dr. Johannes Frederik Gerardus (Hans) Vliegenthart (April 7, 1936 – February 12, 2026) A leading figure in structural Glycobiology. www.uu.nl/en/news/in-m...
uu.nl
In memoriam: Hans Vliegenthart
In memoriam: prof. dr. Hans Vliegenthart (April 7, 1936 – February 12, 2026)
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Reposted by Zeshi Li (Jack)
Ryan Flynn @raflynn5.bsky.social · 28/01/2026
Science update from my postdoc Peiyuan Chai - his work “glycoRNA complexed with heparan sulfate regulates VEGF-A signaling” is now published @nature.com uncovering a new layer or glycoRNA-regulation of growth factor mediated control physiological processes rdcu.be/e1bBX
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Zeshi Li (Jack) @lizeshi.bsky.social · 19/12/2025
Thanks Alexander!
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Zeshi Li (Jack) @lizeshi.bsky.social · 18/12/2025
This project was co-led by former post-doc of Chirlmin Joo @chirlmin.bsky.social lab, Bhayashree Joshi. Jointly supervised by Vered Raz (LUMC).
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Zeshi Li (Jack) @lizeshi.bsky.social · 18/12/2025
Nice Preview from Ling-Ling Chen lab at Shanghai Academy of Natural Sciences. www.sciencedirect.com/science/arti...
sciencedirect.com
A molecular trio anchors RNAs on the cell surface
RNAs are now recognized as functional components of the cell surface, expanding the molecular repertoire of the plasma membrane. In this issue of Mole…
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Zeshi Li (Jack) @lizeshi.bsky.social · 18/12/2025
Link to the paper: www.sciencedirect.com/science/arti...
sciencedirect.com
Cell-surface RNA forms ternary complex with RNA-binding proteins and heparan sulfate to recruit immune receptors
Recent discoveries have shown the presence of ribonucleic acid (RNA) on the cell surface, defying the view that RNA only functions intracellularly. Ho…
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Zeshi Li (Jack) @lizeshi.bsky.social · 18/12/2025
How are RNAs presented on the cell surface without any transmembrane domains? In our paper published at Molecular Cell @cp-molcell.bsky.social, we provide mechanistic insights into this pressing question. They form ternary complexes with RNA-binding proteins and heparan sulfate proteoglycans.
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Reposted by Zeshi Li (Jack)
Nathanael B. Kegel @nathanaelbkegel.bsky.social · 18/11/2025
Now finally peer-reviewed and published in @springernature.com Experimental & Molecular Medicine (EMM)🥳: www.nature.com/articles/s12... Our story was published back-to-back with the intriguing paper by Kim et al.: www.nature.com/articles/s12...
nature.com
Proteins are a source of glycans found in preparations of glycoRNA - Experimental & Molecular Medicine
Glycosylation, a process where sugars attach to molecules, is known to modify proteins and lipids. Recently, researchers discovered that RNA can also be glycosylated. This study explores the presence ...
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Zeshi Li (Jack) @lizeshi.bsky.social · 17/11/2025
Had the pleasure to learn about this cool platform over a Friday afternoon seminar during Matt’s visit at UU.
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Reposted by Zeshi Li (Jack)
U Utrecht-CBDD @uu-cbdd.bsky.social · 15/11/2025
New @angewandtechemie.bsky.social paper jointly supervised by Zeshi Li @lizeshi.bsky.social and Geert-Jan Boons describes the chemoenzymatic synthesis of O-acetylated GD3 as intact glycolipids, and the use there of to study virus binding in cellular context. onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
Chemoenzymatically Synthesized O‐Acetylated GD3 Gangliosides to Examine Viral Receptor Specificities in a Cellular Context
7-O-, 9-O-, and 7,9-di-O-acetylated GD3 gangliosides can be prepared by chemical assembly of a tetrasaccharide as α-glycosyl fluoride that is coupled to sphingosine using a glycosynthase, followed by...
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Zeshi Li (Jack) @lizeshi.bsky.social · 15/11/2025
Our studies call for development of labeling and analytical methods that are really SPECIFIC for glycoRNA. Team effort with Sungchul Kim lab, @chirlmin.bsky.social Joo lab, and @pmiesen.bsky.social Miesen lab
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Zeshi Li (Jack) @lizeshi.bsky.social · 15/11/2025
These glycoproteins behave like glycoRNA biochemically and electrophoretically, so it may confound assays on glycoRNA. E.g. when doing #glycomics analysis, how much glycans are from the contaminant glycoproteins vs. from glycoRNA? This will critically affect your conclusions
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Zeshi Li (Jack) @lizeshi.bsky.social · 15/11/2025
We show that the total #RNA isolated from cell cultures can contain substantial non-RNA glycoconjugates, which was found out to be #glycoproteins (characterized in Kegel et al paper), and those glycoconjugates persist even after protease treatment and rounds of purification.
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Zeshi Li (Jack) @lizeshi.bsky.social · 15/11/2025
#glycotime We hope our b2b publications serve as a heads-up for the #glycoRNA community, and drive the field forward constructively. Links👇 Kim et al. rdcu.be/eP4GQ @nathanaelbkegel.bsky.social Kegel et al. nature.com/articles/s12276-025-01575-1 (Stefan Bauer lab)
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Zeshi Li (Jack) @lizeshi.bsky.social · 15/11/2025
It’ll be interesting to explore whether there are interacting proteins specifically recognizing sialate OAc moieties, or how specific gangliosides cluster with different membrane proteins on cell surface or organelles.
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Zeshi Li (Jack) @lizeshi.bsky.social · 15/11/2025
Regarding where they may play a role, in addition to cell surface, previous literatures suggest gangliosides can function intracellularly in mitochondria and very likely Golgi. Langereis et al 2016 paper showed OAcSias largely colocalizes with Golgi markers.
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Zeshi Li (Jack) @lizeshi.bsky.social · 15/11/2025
Thanks for the question, Chris! How the OAc gangliosides function at molecular level is still largely unknown. We generally believe the sialate OAc group blocks lectin or enzyme recognition. But there has not been any endogenous protein that specifically binds OAcSia or these gangliosides.
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Reposted by Zeshi Li (Jack)
Friedrich Förster @fridof.bsky.social · 04/11/2025
Very happy that NWO supports this major upgrade of our national EM infrastructure. It is great that this initiative got broad support all over NL, and it will EMPower fantastic science - looking forward to that! www.uu.nl/en/news/33-m...
uu.nl
33 million euro investment for national electron microscope facility EMPower
A major new national facility for electron microscopy, called EMPower, has been awarded to a consortium of Dutch universities and medical centers. EMPower aims to pave the way for major discoveries im...
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Reposted by Zeshi Li (Jack)
Daniel Hurdiss @danielhurdiss.bsky.social · 03/11/2025
Thrilled, and admittedly relieved, to see this major investment in Dutch #cryoEM become reality! 🇳🇱🔬 Honoured to be a co-applicant on this national initiative and very excited for the opportunity to advance our work in cellular structural virology! 🦠 www.uu.nl/en/news/33-m...
uu.nl
33 million euro investment for national electron microscope facility EMPower
A major new national facility for electron microscopy, called EMPower, has been awarded to a consortium of Dutch universities and medical centers. EMPower aims to pave the way for major discoveries im...
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Zeshi Li (Jack) @lizeshi.bsky.social · 03/11/2025
Deeply honored to be a co-applicant of #BioBeyond_NL. The team will develop enabling #MassSpec based technologies to advance (glyco)proteomics, glycomics and spatial omics. Stay tuned for PhD/post-doc openings in the near future! www.nwo.nl/en/news/nati...
nwo.nl
National Roadmap: NWO invests 197 million euro in eleven Large-Scale Research Infrastructures | NWO
Eleven consortia from various scientific disciplines are set to launch projects of great value to science. But also to the economic and social prosperity of the Netherlands. For example, a consortium led by TU Delft will start work on a detailed virtual model of the Dutch energy system. In another project, a consortium of UMC Utrecht is developing an MRI scanner that can scan people in motion.
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Reposted by Zeshi Li (Jack)
U Utrecht-CBDD @uu-cbdd.bsky.social · 03/11/2025
Congratulations to CBDD researchers, Geert-Jan Boons and Zeshi Li @lizeshi.bsky.social, and members of #BioBeyond_NL, a consortium co-led by Maastricht, Utrecht, Radboud University and LUMC researchers to advance (glyco)proteomics, glycomics and spatial omics. Read more👇 www.nwo.nl/en/news/nati...
nwo.nl
National Roadmap: NWO invests 197 million euro in eleven Large-Scale Research Infrastructures | NWO
Eleven consortia from various scientific disciplines are set to launch projects of great value to science. But also to the economic and social prosperity of the Netherlands. For example, a consortium led by TU Delft will start work on a detailed virtual model of the Dutch energy system. In another project, a consortium of UMC Utrecht is developing an MRI scanner that can scan people in motion.
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Reposted by Zeshi Li (Jack)
Ryan Flynn @raflynn5.bsky.social · 11/04/2025
Advancing #glycoRNA imaging with FRET-based detection and expanding the scope of their presentation to extracellular vesicles - interestingly high levels of sialoglycoRNAs on blood EVs can be predictive of having cancer @naturecomms.bsky.social www.nature.com/articles/s41...
nature.com
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Reposted by Zeshi Li (Jack)
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 11/04/2025
SCAM ALERT. This is a fake conference that ripped off my and other people’s names to trick people into registering. There is no such conference that I or the others shown were invited or agreed to. We are working to try to get this fraud taken down from the web. chemsymposia.com
chemsymposia.com
Join Chemsymposia 2026: Research & Innovation | ChemSymposia 2026
Join us at Chemsymposia 2026 to discover groundbreaking research in physics applications. Connect with experts, engage in insightful discussions, and explore our venue, registration details, and speak...
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Zeshi Li (Jack) @lizeshi.bsky.social · 01/04/2025
There is an interesting read here (posted shortly after the very first preprint): doi.org/10.1242/prel...
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Reposted by Zeshi Li (Jack)
Jordan Meier @doc-jlmeier.bsky.social · 30/03/2025
Question for glycoRNA proponents: What specific evidence would convince you that these signals are protein contaminants rather than modified RNA? Since so much evidence depends on extraction & analysis of pure RNase-sensitive glycoRNA, this seems like a problem. Worth reading the whole exchange ⬇️
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Zeshi Li (Jack) @lizeshi.bsky.social · 28/03/2025
Hi Dr. Erasmus, here is an updated version: www.biorxiv.org/content/10.1...
biorxiv.org
RNA-Associated Glycoconjugates Highlight Potential Ambiguities in glycoRNA Analysis
A recent ground-breaking study suggested that small RNA from mammalian cells can undergo N-glycan modifications (termed glycoRNA) 1. The discovery relied upon a metabolic glycan labeling strategy in c...
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Zeshi Li (Jack) @lizeshi.bsky.social · 28/03/2025
An independent study from @nathanaelbkegel.bsky.social et al. has led to alike conclusions. The common RNA prep may not give you the RNA as pure as you think. The results also call for the development of glycoRNA-specific labeling methods… A dual labeling? www.biorxiv.org/content/10.1...
biorxiv.org
Proteins are a source of glycans found in preparations of glycoRNA
Recent discoveries show that RNA can be modified with sialylated glycans (termed glycoRNA), thus broadening our understanding of cellular glycosylation beyond traditional proteins and lipids. However,...
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Zeshi Li (Jack) @lizeshi.bsky.social · 28/03/2025
Suppose you are ready to load the glycan-labeled glycoRNA samples into gels. Get half of it, mix with RNases/nucleases, incubate, add sample loading buffer, denature, DIRECTLY load the mixture into gel. Do the rest the same as reported. GlycoRNA gets degraded, the N-glycoconjugate remains intact.
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Zeshi Li (Jack) @lizeshi.bsky.social · 28/03/2025
We hope this serves as a heads-up for the community, and propose a simple checkpoint experiment for whichever protocol you are employing👇
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Zeshi Li (Jack) @lizeshi.bsky.social · 28/03/2025
The non-RNA N-glycoconjugate, is an independent, separate, but potentially co-existing molecular entity in glycoRNA preparations. It even exhibits an apparent RNase sensitivity related to purification methods, but not digestion.
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Zeshi Li (Jack) @lizeshi.bsky.social · 28/03/2025
Here is an updated version of a preprint posted in 2024: It describes a non-RNA glycoconjugate persisted throughout RNA sample processing, with similar electrophoretic properties and enzymatic reactivity as glycoRNA. It confounds gel-/blot-based glycoRNA assays. www.biorxiv.org/content/10.1...
biorxiv.org
RNA-Associated Glycoconjugates Highlight Potential Ambiguities in glycoRNA Analysis
A recent ground-breaking study suggested that small RNA from mammalian cells can undergo N-glycan modifications (termed glycoRNA) 1. The discovery relied upon a metabolic glycan labeling strategy in c...
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Reposted by Zeshi Li (Jack)
Iris @irismarchal.bsky.social · 18/03/2025
Nanopore technology might be able to sequence proteins soon! Read about the road ahead in this exciting Perspective rdcu.be/edWPi in @naturebiotech.bsky.social
rdcu.be
Toward single-molecule protein sequencing using nanopores
Nature Biotechnology - Maglia and colleagues discuss advances in nanopore technology en route to single-molecule protein sequencing
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Reposted by Zeshi Li (Jack)
Protea Glycosciences @proteaglyco.bsky.social · 24/03/2025
We're just completing an R&D sprint to identify an LC additive that increases our glycan identifications 3x and enhances glycan charge states by up to 45%🚀. It's too early to publicly disclose its identity, but here's a results preview. Interested? Message or email us, we'd love to collaborate.
Manuscript figure describing our method for evaluating mobile phase additives for enhanced negative mode LC-MS of glycans. The results show different O-glycan compositions having up to 40% higher charge states.
Interested in how our platform can help you discover more from your samples? Email us at info@proteaglyco.com to collaborate.
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Reposted by Zeshi Li (Jack)
Suyang Zhang @suyangzhang.bsky.social · 24/03/2025
Excited to share our new preprint on co-transcriptional splicing! U1 snRNP is recruited to RNA polymerase II through multiple interaction sites, with elongation factor SPT6 binding directly to the U1 snRNP protein. www.biorxiv.org/content/10.1... #cryoEM #transcription #splicing
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Zeshi Li (Jack) @lizeshi.bsky.social · 24/03/2025
6. KIR2DL5 does directly bind to RNA. Food for thought: what are other classical membrane glycoproteins that can directly bind to RNA as non-canonical RBPs?
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Zeshi Li (Jack) @lizeshi.bsky.social · 24/03/2025
4. SCOOPS validated HS is essential for hepRNA presentation on cell surface in an orthogonal fashion to the originally described TLR7 probe. 5. SCOOPS enabled unveiling hepRNA identities: high-confidence candidates include mRNA, lncRNA (Huang 2020) and snoRNA.
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Zeshi Li (Jack) @lizeshi.bsky.social · 24/03/2025
3. Exploiting the new chemistry, we establish spatial-selective crosslinking followed by orthogonal organic phase separation (Queiroz 2019), or SCOOPS🍨 to isolate these cell-surface RNA-protein crosslink products for biochemical analysis.
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Zeshi Li (Jack) @lizeshi.bsky.social · 24/03/2025
New to this version: 1. A hepRNA-RBP-HS ternary complex model is proposed and validated. 2. A key enabling technique is based on an unexpected finding that photosensitized singlet oxygen can crosslink RNA to RBP.
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Zeshi Li (Jack) @lizeshi.bsky.social · 24/03/2025
Excited to share an update on heparan sulfate (HS)-associated cell-surface RNA (hepRNA): www.biorxiv.org/content/10.1...
biorxiv.org
Cell-Surface RNA Forms Ternary Complex with RNA-Binding Proteins and Heparan Sulfate to Recruit Immune Receptors
Recent discoveries have shown the presence of RNA molecules on the cell surface, defying the traditional view that RNA only functions intracellularly. However, it is not well understood how cell-surfa...
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Zeshi Li (Jack) @lizeshi.bsky.social · 22/03/2025
Candidate list kept updating. But if we piece things together, also taking the recent preprint into account, what get pulled down may include: 1. Non-specifically bead-associated RNA; 2. RNA associated with denatured glycoproteins; 3. Real glycoRNA. Complicated. How big is each part in the pool…
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Reposted by Zeshi Li (Jack)
bioRxivpreprint @biorxivpreprint.bsky.social · 01/03/2025
Transcriptome-wide Identification of GlycoRNAs by Clier-seq Pipeline www.biorxiv.org/content/10.1101/202…
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Reposted by Zeshi Li (Jack)
bioRxivpreprint @biorxivpreprint.bsky.social · 18/03/2025
Proteins are a source of glycans found in preparations of glycoRNA www.biorxiv.org/content/10.1101/202…
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Reposted by Zeshi Li (Jack)
U Utrecht-CBDD @uu-cbdd.bsky.social · 18/12/2024
Hello, Bluesky community! Let our first post be a good news: CBDD researchers Geert-Jan Boons and Rob de Vries (@rpdevrieslab.bsky.social), together with researchers in ErasmusMC Rotterdam, were awarded an #ENW-XL from the Dutch Research Council. Stay tuned for #phd/#post-doc openings! #glycotime
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