Kasturika Shankar

Gigantic birth study paints most detailed picture of pregnancy’s toll on body Data from 300,000 births reveal how essential biological measurements are altered by carrying and delivering a baby.

Biologists have built one of the most detailed pictures ever of the changes that occur in women’s bodies before and after pregnancy, by pooling and studying around 44 million physiological measurements from more than 300,000 births

https://go.nature.com/4236GSV

🎈 The final_final_paper of my PhD is now online.
This protocol can also be used to study other full-length peripheral membrane proteins with limited solubility. I hope this paper will be useful to other biochemists.
Cheers!
bio-protocol.org/en/bpdetail?...

Transfer RNA acetylation regulates in vivo mammalian stress signaling An ancient tRNA modification is used by mammalian cells to coordinate protein translation and adaptive signaling.

www.science.org/doi/10.1126/...

Structural basis for Ebola virus nucleocapsid assembly and function regulated by VP24 pubmed.ncbi.nlm.nih.gov/40064872/ #cryoEM

Science Advances’ special issue on women’s health highlights a growing wave of research focusing on women’s unique biological and psychological experiences. Articles cover a range of studies from the interplay between menopause and Alzheimer’s risk to the menstrual cycle’s influence on the brain-heart connection. It also describes the opportunities pregnancy provides to research aspects of both physical and mental health. By prioritizing women’s unique physiological and psychological experiences, research can expand the frontiers of knowledge in ways that benefit everyone.

A special issue on #WomensHealth in #ScienceAdvances highlights a growing wave of research focusing on women’s unique biological and psychological experiences.

Learn more: scim.ag/3R59fPe (THREAD 🧵)

The graphene-based affinity cryo-EM grid for the endogenous protein structure determination pubmed.ncbi.nlm.nih.gov/40060550/ #cryoEM

eft: A 2D CryoSXT projection of an HSV-1 evelopment event. Right: A 3D rendering of the budding assembly stage captured by CLXT.

A new combination of microscopy methods has revealed exquisite detail of the virus assembly process used by herpes simplex virus during replication.
buff.ly/43aqR3G

Do you LOVE organelles??
Well I am THRILLED to announce that Nellie has been published in @naturemethods.bsky.social!

Nellie a fully automated pipeline for organelle segmentation, tracking, and hierarchical feature extraction in 2D, 3D, timelapse, multichannel live-cell microscopy

🧵1/N

A conserved class of viral RNA structures regulates translation reinitiation through dynamic ribosome interactions Certain viruses with bicistronic mRNAs use reinitiation to translate the downstream open reading frame. Sherlock et al. use bioinformatics to find new examples of RNA structures that mediate reinitiat...

www.cell.com/cell-reports...

Tumor extracellular vesicle–derived PD-L1 promotes T cell senescence through lipid metabolism reprogramming PD-L1 from tumor extracellular vesicles induces T cell senescence through lipid metabolism.

Tumor extracellular vesicle–derived PD-L1 promotes T cell senescence through lipid metabolism reprogramming

www.science.org/doi/10.1126/...

Wow! It's an amazing finding!!

Enteroviruses and their "hyper-functional" proteins!⭐️

Deep-tissue transcriptomics and subcellular imaging at high spatial resolution Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. Here, we introduce cycle Hybridization Chain Reaction (HCR), a method that integrates ...

www.science.org/doi/10.1126/...

Internal cap-initiated translation for efficient protein production from circular mRNA - Nature Biotechnology Placement of an m7G cap internally on circular RNAs promotes their translation in vivo.

www.nature.com/articles/s41...

Guess aspartic acid (D), glutamic acid (E), and isoleucine (I) are too woke to be part of a protein.

ProtGPS classifies protein compartment with high performance.

Generative modeling creates novel proteins that concentrate in a desired condensate.

Pathogenic mutations are predicted to alter protein compartmentalization

A protein language model trained to predict subcellular localization for human proteins can generate de novo sequences with the desired localization and identify pathological mutations.

@itamarchinn.bsky.social @pgmikhael.bsky.social

www.science.org/doi/10.1126/...

thanks Lars!

The most recycled first slide of my academic career. Have been using it for the last 7 years to give updates on my work.
#academia

First ribosome purification using poly-lysine beads (RAPPL, developed by @djuranoviclab.bsky.social & collaborators: www.biorxiv.org/content/10.1...). Full process—from lysis to grid prep—in just 3 hours. Look how pretty it is (even if a bit too diluted)! This is a game-changer🚀.

Visualizing sub-organellar lipid distribution using correlative light and electron microscopy Lipids and proteins compartmentalize biological membranes into nanoscale domains which are crucial for signaling, intracellular trafficking and many other cellular processes. Studying nanodomain funct...

Ooh nice preprint! Studying membrane nanodomains needs nanoscale lipid localization - current methods fall short. 'Lipid-CLEM', correlative light & EM with click chemistry to map lipids. In endosomes, it shows sphingomyelin’s differential partitioning beautifully.
www.biorxiv.org/content/10.1...

Western blot is bloting ;))

Goooo #Bills #NFL 🏈🏈🏈

A scalable system using mini-organs to test personalized RNA therapy Platform to accelerate the testing of antisense oligonucleotides.

A rapid and efficient method developed to create stem-cell-based 3D mini-organs derived from the cells of patients offers a way to evaluate personalized treatments using RNA therapies for rare genetic diseases

https://go.nature.com/3POiHpJ

Sequencing technologies to measure translation in single cells - Nature Reviews Molecular Cell Biology Recent sequencing-based methods, including novel ribosome profiling, ribosome affinity purification and spatial translation methods, have enabled the measurement of translation at single-cell resoluti...

Several new technologies have enabled translation profiling in single cells. In our article in @natrevmcb.bsky.social, Alexander and I discuss these single-cell methods for measuring ribosome profiles, ribosome-associated transcripts, and spatial translation 🧵 www.nature.com/articles/s41...

so cool! (or hot I should say)

Cryo-electron tomography pipeline for plasma membranes - Nature Communications Cryo-electron tomography requires thin samples. Few cell-thinning techniques have been standardized. Here, the authors provide and validate a method to prepare, label, and image proteins at mamma...

www.nature.com/articles/s41...

This is a scientific figure from the paper mentioned in the post. It shows fluorescence and electron microscopy images and associated schematics for using the ferritag to image clathrin coated pit proteins.

I'd like to draw your attention to this truly excellent paper from the Taraska lab on cryoET of plasma membrane associated proteins. Everyone who is thinking about probes in the cryoET space should also see what they could do with ferritag (fig 6) www.nature.com/articles/s41...

Mapping the complete influenza A virus infection cycle through single vRNP imaging Cell-to-cell heterogeneity is a common feature of viral infection that can generate enormous complexity, complicating understanding of infection progression and interpretation of differences between v...

Our new paper is out: "Mapping the complete influenza A virus infection cycle through single vRNP imaging". Combining newly-developed single-molecule imaging approaches with in situ viral transcriptomics, we identify numerous non-canonical infection pathways.

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

The very informative 2023-2024 #RNA review series in @embojournal.bsky.social has been completed. Throwback to our contribution, reviewing how #coronaviruses modulate host cell translation 🔬🦠
www.embopress.org/page/journal...
www.embopress.org/doi/full/10....