Zeshi Li (Jack)

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...

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...

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...

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...

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

There is an interesting read here (posted shortly after the very first preprint): doi.org/10.1242/prel...

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 ⬇️

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...

Hi Dr. Erasmus, here is an updated version: www.biorxiv.org/content/10.1...

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,...

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...

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.

We hope this serves as a heads-up for the community, and propose a simple checkpoint experiment for whichever protocol you are employing👇

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.

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...

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...

Toward single-molecule protein sequencing using nanopores Nature Biotechnology - Maglia and colleagues discuss advances in nanopore technology en route to single-molecule protein sequencing

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

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.

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.

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

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?

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.

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.

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.

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...

Excited to share an update on heparan sulfate (HS)-associated cell-surface RNA (hepRNA):
www.biorxiv.org/content/10.1...

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…

Transcriptome-wide Identification of GlycoRNAs by Clier-seq Pipeline https://www.biorxiv.org/content/10.1101/2025.02.28.639800v1

Proteins are a source of glycans found in preparations of glycoRNA https://www.biorxiv.org/content/10.1101/2025.03.17.643711v1

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