Manikandan
@manikandanp.bsky.social
#RNA #biophysics #structuralbiology
Postdoc @EMBL.org #smFRET
Previously - PhD @IISc on #bacterial defense
#Nature lover #Science student
Postdoc @EMBL.org #smFRET
Previously - PhD @IISc on #bacterial defense
#Nature lover #Science student
Reposted by Manikandan
Reposted by Manikandan
Bacterial ncRNAs influence various cellular functions & often have complex 3ry structures. ModT is a conserved #ncRNA found in 2,500 bacterial spp, shown here to regulate growth transition & sporulation in #Cdifficile via changes in c-di-GMP @helmholtz-hiri.bsky.social #PLOSBiology plos.io/4iIpgYm
December 17, 2024 at 1:31 PM
Bacterial ncRNAs influence various cellular functions & often have complex 3ry structures. ModT is a conserved #ncRNA found in 2,500 bacterial spp, shown here to regulate growth transition & sporulation in #Cdifficile via changes in c-di-GMP @helmholtz-hiri.bsky.social #PLOSBiology plos.io/4iIpgYm
Super cool #RNA stuff!
Our miRNA story is now in @science.org ! We found a microRNA, not a protein, that finally solved a long-standing evolutionary mystery of wing coloration in butterflies and moths. (1/n)
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
A microRNA is the effector gene of a classic evolutionary hotspot locus
In Lepidoptera (butterflies and moths), the genomic region around the gene cortex is a “hotspot” locus, repeatedly implicated in generating intraspecific melanic wing color polymorphisms across 100 mi...
www.science.org
December 12, 2024 at 9:34 AM
Super cool #RNA stuff!
Reposted by Manikandan
Our latest work is out in Nature today! Using smFRET, we directly visualized recruitment of the eIF4F complex to the 5' cap of eukaryotic mRNAs and formation of an activated mRNA. Our findings reveal new and surprising roles for each eIF4F component. 1/3 www.nature.com/articles/s41...
December 11, 2024 at 9:35 PM
Our latest work is out in Nature today! Using smFRET, we directly visualized recruitment of the eIF4F complex to the 5' cap of eukaryotic mRNAs and formation of an activated mRNA. Our findings reveal new and surprising roles for each eIF4F component. 1/3 www.nature.com/articles/s41...
Reposted by Manikandan
Huping Wang and Manu Hegde, in @cellbiol-mrclmb.bsky.social have found a factor that accelerates protein deliveries to the endoplasmic reticulum
Click here to read more about it: www2.mrc-lmb.cam.ac.uk/discovery-of...
#LMBResearch
Click here to read more about it: www2.mrc-lmb.cam.ac.uk/discovery-of...
#LMBResearch
November 29, 2024 at 9:43 AM
Huping Wang and Manu Hegde, in @cellbiol-mrclmb.bsky.social have found a factor that accelerates protein deliveries to the endoplasmic reticulum
Click here to read more about it: www2.mrc-lmb.cam.ac.uk/discovery-of...
#LMBResearch
Click here to read more about it: www2.mrc-lmb.cam.ac.uk/discovery-of...
#LMBResearch
Reposted by Manikandan
First paper of our lab today @natureportfolio.bsky.social by Nussi!
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
December 4, 2024 at 8:53 PM
First paper of our lab today @natureportfolio.bsky.social by Nussi!
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
Reposted by Manikandan
Meet Romain Linares, cryo-electron microscopy (cryo-EM) expert at EMBL Grenoble.
In this interview, he talks about his role in managing the cryo-EM platform to explore molecules at the atomic level and his passion for stargazing.
🧪 🧬🧶 #MolBiol
www.embl.org/news/people-...
In this interview, he talks about his role in managing the cryo-EM platform to explore molecules at the atomic level and his passion for stargazing.
🧪 🧬🧶 #MolBiol
www.embl.org/news/people-...
December 4, 2024 at 8:16 AM
Meet Romain Linares, cryo-electron microscopy (cryo-EM) expert at EMBL Grenoble.
In this interview, he talks about his role in managing the cryo-EM platform to explore molecules at the atomic level and his passion for stargazing.
🧪 🧬🧶 #MolBiol
www.embl.org/news/people-...
In this interview, he talks about his role in managing the cryo-EM platform to explore molecules at the atomic level and his passion for stargazing.
🧪 🧬🧶 #MolBiol
www.embl.org/news/people-...
Reposted by Manikandan
EMBL Group Leader @olivierduss.bsky.social and his research team discovered how two molecular machines in bacteria work together and watched their interactions as a real-time movie.
Discover how they put snapshots in motion 👉 www.embl.org/news/science...
#MolBiol 🧪 @natureportfolio.bsky.social
Discover how they put snapshots in motion 👉 www.embl.org/news/science...
#MolBiol 🧪 @natureportfolio.bsky.social
December 4, 2024 at 4:05 PM
EMBL Group Leader @olivierduss.bsky.social and his research team discovered how two molecular machines in bacteria work together and watched their interactions as a real-time movie.
Discover how they put snapshots in motion 👉 www.embl.org/news/science...
#MolBiol 🧪 @natureportfolio.bsky.social
Discover how they put snapshots in motion 👉 www.embl.org/news/science...
#MolBiol 🧪 @natureportfolio.bsky.social
Reposted by Manikandan
Congratulations, Olivier Duss, Simone Köhler, and Eva Kowalinski! 👏
The three EMBL Group Leaders have received ERC Consolidator Grants #ERCCoG for their innovative research projects aimed at understanding fundamental cellular mechanisms.
#MolBiol 🧪👇
Read more here: www.embl.org/news/awards-...
The three EMBL Group Leaders have received ERC Consolidator Grants #ERCCoG for their innovative research projects aimed at understanding fundamental cellular mechanisms.
#MolBiol 🧪👇
Read more here: www.embl.org/news/awards-...
December 3, 2024 at 11:05 AM
Congratulations, Olivier Duss, Simone Köhler, and Eva Kowalinski! 👏
The three EMBL Group Leaders have received ERC Consolidator Grants #ERCCoG for their innovative research projects aimed at understanding fundamental cellular mechanisms.
#MolBiol 🧪👇
Read more here: www.embl.org/news/awards-...
The three EMBL Group Leaders have received ERC Consolidator Grants #ERCCoG for their innovative research projects aimed at understanding fundamental cellular mechanisms.
#MolBiol 🧪👇
Read more here: www.embl.org/news/awards-...
Reposted by Manikandan
Cool new work from Jenn Prescher and coworkers @ucirvine.bsky.social, “RNA lantern” technology for bioluminescence imaging of RNA transcripts
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A modular platform for bioluminescent RNA tracking - Nature Communications
Studying RNA dynamics in vivo often relies on fluorogenic approaches, but these can be hampered by factors such as limited sensitivity and sample autofluorescence. Here, the authors describe an ultras...
www.nature.com
December 3, 2024 at 12:31 AM
Cool new work from Jenn Prescher and coworkers @ucirvine.bsky.social, “RNA lantern” technology for bioluminescence imaging of RNA transcripts
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Very cool work on single mRNA visualisation inside cells!
We designed MS2 and PP7 binding coat proteins that are degraded in cells except when bound by their hairpin RNAs.
You can check out our pre-print here: tinyurl.com/27p7hyt9,
and listen to a Google AI-generated podcast on it here: notebooklm.google.com/notebook/d71...
You can check out our pre-print here: tinyurl.com/27p7hyt9,
and listen to a Google AI-generated podcast on it here: notebooklm.google.com/notebook/d71...
December 1, 2024 at 9:53 AM
Very cool work on single mRNA visualisation inside cells!
Reposted by Manikandan
‘Dark proteome’ survey reveals thousands of new human genes | Science www.science.org/content/arti...
‘Dark proteome’ survey reveals thousands of new human genes
Database confirms that overlooked segments of the genome code for a multitude of tiny proteins
www.science.org
November 30, 2024 at 12:32 PM
‘Dark proteome’ survey reveals thousands of new human genes | Science www.science.org/content/arti...
Reposted by Manikandan
We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered???
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Stereochemistry in the disorder–order continuum of protein interactions - Nature
Studies on protein–protein interactions using proteins containing d- or l-amino acids show that stereoselectivity of binding varies with the degree of disorder within the complex.
www.nature.com
November 27, 2024 at 8:31 PM
We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered???
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Manikandan
Very excited that our paper describing a critical role for the PNUTS-PP1 phosphatase complex in transcription pause release is up online! This was a massive team effort with @edimitrova.bsky.social and the rest of the @robklose.bsky.social lab www.cell.com/molecular-ce... A short thread: (1/8)
The PNUTS phosphatase complex controls transcription pause release
Kelley et al. discover that the PNUTS phosphatase complex plays an essential role
in gene transcription by controlling RNA polymerase II pause release. PNUTS achieves
this through its TND, which recog...
www.cell.com
November 26, 2024 at 4:18 PM
Very excited that our paper describing a critical role for the PNUTS-PP1 phosphatase complex in transcription pause release is up online! This was a massive team effort with @edimitrova.bsky.social and the rest of the @robklose.bsky.social lab www.cell.com/molecular-ce... A short thread: (1/8)
Reposted by Manikandan
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 27, 2024 at 4:13 AM
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Manikandan
sunburn is from ribosomes stalled by UV damage to RNA? super cool www.sciencedirect.com/science/arti...
The ribotoxic stress response drives acute inflammation, cell death, and epidermal thickening in UV-irradiated skin in vivo
Solar UVB light causes damage to the outermost layer of skin. This insult induces rapid local responses, such as dermal inflammation, keratinocyte cel…
www.sciencedirect.com
November 27, 2024 at 1:22 AM
sunburn is from ribosomes stalled by UV damage to RNA? super cool www.sciencedirect.com/science/arti...
Reposted by Manikandan
Super method linking GROseq/DMSMaPseq shedding light on co-transcriptional #RNA folding. Really enjoyed seeing this presented recently. #RNAStructure www.biorxiv.org/content/10.1...
Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis
An RNA′s catalytic, regulatory, or coding potential depends on RNA structure formation. Because base pairing occurs during transcription, early structural states can govern RNA processing events and d...
www.biorxiv.org
November 27, 2024 at 7:15 AM
Super method linking GROseq/DMSMaPseq shedding light on co-transcriptional #RNA folding. Really enjoyed seeing this presented recently. #RNAStructure www.biorxiv.org/content/10.1...
Reposted by Manikandan
Do you want to go further with your proteomics? Looking for something new in cancer?
Check out microproteins!
Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social
www.science.org/content/arti...
🔎 microprotein
🧬 💻
Check out microproteins!
Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social
www.science.org/content/arti...
🔎 microprotein
🧬 💻
‘Dark proteome’ survey reveals thousands of new human genes
Database confirms that overlooked segments of the genome code for a multitude of tiny proteins
www.science.org
November 26, 2024 at 6:05 PM
Do you want to go further with your proteomics? Looking for something new in cancer?
Check out microproteins!
Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social
www.science.org/content/arti...
🔎 microprotein
🧬 💻
Check out microproteins!
Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social
www.science.org/content/arti...
🔎 microprotein
🧬 💻
Reposted by Manikandan
How long does an mRNA stay in the nucleus? How long does it stay in the cytoplasm? In an amazing collaboration with @landthalerm.bsky.social, we used metabolic labeling, cell fractionation and mathematical modeling to quantify mRNA flow through the cell. Finally out in MSB: doi.org/10.1038/s443...
November 21, 2024 at 2:56 PM
How long does an mRNA stay in the nucleus? How long does it stay in the cytoplasm? In an amazing collaboration with @landthalerm.bsky.social, we used metabolic labeling, cell fractionation and mathematical modeling to quantify mRNA flow through the cell. Finally out in MSB: doi.org/10.1038/s443...
Reposted by Manikandan
The final version of our article describing a modernized procedure for cotranscriptional RNA structure probing is online! www.nature.com/articles/s41...
Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing ...
RNA begins to fold as the nascent transcript emerges from a transcribing RNA polymerase. Here, the authors develop a concise method for mapping RNA folding pathways that couples in vitro transcription...
www.nature.com
November 29, 2023 at 2:46 PM
The final version of our article describing a modernized procedure for cotranscriptional RNA structure probing is online! www.nature.com/articles/s41...
Reposted by Manikandan
Reposted by Manikandan
A language model-based deep learning approach for #RNA 3D structure prediction www.nature.com/articles/s41...
Accurate RNA 3D structure prediction using a language model-based deep learning approach - Nature Methods
RhoFold+ is an end-to-end language model-based deep learning method to predict RNA three-dimensional structures of single-chain RNAs from sequences.
www.nature.com
November 21, 2024 at 3:15 PM
A language model-based deep learning approach for #RNA 3D structure prediction www.nature.com/articles/s41...
Reposted by Manikandan
First attempt in a (loosely defined) Single-Molecule Biophysics starter pack. Please share and (self-) nominate. go.bsky.app/CteFZM5
November 13, 2024 at 8:23 AM
First attempt in a (loosely defined) Single-Molecule Biophysics starter pack. Please share and (self-) nominate. go.bsky.app/CteFZM5