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Posts by Nilimesh Das

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Linker histone H1 functions as a liquid-like glue to organize chromatin in living human cells Single-molecule imaging and MD simulations reveal how histone H1 acts as a liquid-like “glue” to compact chromatin in cells.

Linker histone H1 functions as a liquid-like glue, dynamically holding nucleosomes together, and keeping chromatin fluid and accessible
to organize chromatin in living human cells | Science Advances

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

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Glad we could contribute to this beautiful work from Claire Dudley et al! I remain forever in awe of Dr. Daniel Foust’s amazing data visualization skills.

1 week ago 7 2 0 0
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Fluorescence Lifetime-Based FRET Biosensors for Monitoring N Terminal Domain-Dependent Interactions of TDP-43 in Living Cells: A Novel Approach for ALS and FTD Drug Discovery Pathological aggregates of TDP-43 are implicated in Alzheimer’s disease, frontotemporal dementia, and amyotrophic lateral sclerosis. While therapeutic efforts have traditionally focused on mitigating ...

Fluorescence Lifetime-Based FRET Biosensors for Monitoring N Terminal Domain-Dependent Interactions of TDP-43 in Living Cells: A Novel Approach for ALS and FTD Drug Discovery | ACS Chemical Neuroscience pubs.acs.org/doi/10.1021/...

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Last day to register for the SMC meeting 2026!

3 weeks ago 6 7 0 1
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Lipid-conjugated DNA enables on-demand delivery of lipids and proteins to synthetic cells
doi.org/10.64898/202...

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RNA-specific local translation is patterned by condensates for multinucleate cell growth - Nature Cell Biology Geisterfer, Jalihal et al. show spatially distinct effects of Whi3 condensates on target translation in Ashbya syncytia. In vitro, translation is enriched at condensate–solute interfaces but repressed...

Condensates are powerful ways to break symmetry and cells do remarkable things with them. Here we show that in a multinucleate fungus, a condensate regulates translation of a cyclin and a formin in distinct locations.
www.nature.com/articles/s41...

1 month ago 110 43 1 0
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Algal pyrenoids—condensates that mediate ~1/3 of Earth’s CO2 fixation—change size and number as cells divide. Our data suggest a simple control mechanism: a kinase that continuously ejects material from the condensate! ☀️🌍🔬💧 #Biophysics #Photosynthesis
www.biorxiv.org/content/10.1...

6 months ago 35 14 0 2
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Biomolecular condensates as cellular memory modules: Thermodynamic principles and plant stress adaptation Organisms frequently encounter abiotic stresses such as drought, salinity, and extreme temperatures, requiring sophisticated adaptive mechanisms. Stress memory enables them to respond more efficiently...

Biomolecular condensates as cellular memory modules: Thermodynamic principles and plant stress adaptation: Biophysical Journal www.cell.com/biophysj/ful...

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Structural Heterogeneity and Hydrodynamics of an Intrinsically Disordered Protein Condensate Biology demonstrates precise control over the free-energy landscape through the selective partitioning of biomacromolecules into membraneless organelles, enabling essential functions such as biochemic...

Structural Heterogeneity and Hydrodynamics of an Intrinsically Disordered Protein Condensate | Journal of the American Chemical Society pubs.acs.org/doi/10.1021/...

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Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch - Nature Communications Riboswitches are RNA elements that regulate gene expression through dynamic changes in secondary structure. Here, the authors reveal how the glycine tandem riboswitch integrates sequential signals via...

How does a riboswitch regulate genes?
glycine tandem riboswitch follows a stepwise 5’ to 3’ folding pathway guided by polymerase pausing and stepwise ligand binding, leading to cooperativity through non-equilibrium mechanisms, not classical concerted model.
www.nature.com/articles/s41...

2 months ago 0 0 0 0
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MYC binding to nascent RNA suppresses innate immune signaling by R-loop-derived RNA-DNA hybrids RNA-binding-mediated multimerization of MYC concentrates RNA-degrading factors around double-stranded RNAs and R-loops. This prevents aberrant RNAs from accumulating and leaking into the cytosol. Thro...

RNA-binding protein MYC binds to nascent, intronic RNA.
It then forms multimers, and suppresses the accumulation of R-loop to prevent innate immune signalling: Cell www.cell.com/cell/fulltex...

2 months ago 1 0 0 0
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Structural dynamics of mixed-subunit CaMKIIα/β heterododecamers filmed by high-speed AFM Nature Communications - High-speed AFM reveals CaMKIIα/β subunits are mixed within 12-unit rings, with βs frequently neighboring. Activated heterooligomers form stable kinase...

HS-AFM revaealed the architecture of CaMKIIα/β, a protein essential for memory!

Dynamic HS-AFM imaging shows how α and β subunits mix and stabilize the active state.

rdcu.be/e3VCP

2 months ago 1 0 0 0
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Intrinsically disordered regions facilitate target search to drive promoter selectivity by a yeast transcription factor Nature Communications - The study reveals how intrinsically disordered regions enable a yeast transcription factor to locate and selectively bind its target promoters by promoting DNA association...

Non-specific interaction plays a big role on how selectivity emerges in cells!!
Intrinsically disordered regions power the search facilitating initial non-specific association with DNA to find promoter.
rdcu.be/e0mIF

2 months ago 1 0 0 0
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Stag2 dependent chromatin remodeling enforces the erythroid-specific Gata1 cistrome The transcription factor GATA1 has pleiotropic hematopoietic functions, particularly in erythroid and megakaryocytic ontogeny. While mechanistic investigations have uncovered many facets of GATA1 biol...

🚨 Excited to share our new preprint: Stag2 dependent chromatin remodeling enforces the erythroid-specific Gata1 cistrome. This work was led by Columbia VP&S MD student Varun Sudunagunta (‼️ Program Directors: Varun is applying to IM residencies this year!) www.biorxiv.org/content/10.1...

6 months ago 5 3 2 0
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Confocal scanning laser microscopy, fluorescence lifetime imaging & Raman analyses allowed @nhm-london.bsky.social, @slcuplants.bsky.social & @cambridge-ee.bsky.social researchers to resolve plant & fungal structures fossil
Read in @newphyt.bsky.social
doi.org/10.1111/nph....

@dromius.bsky.social

5 months ago 37 12 1 2
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Unraveling Protein Clumps: Using Fluorescence to Study Aggregation at the Nano Scale This study uses advanced fluorescence techniques to track how proteins like bromelain clump together at extremely low concentrations. The authors compare different methods, highlighting how fluorescen...

Protein aggregation in cells can start at nanomolar levels as tiny clusters that are hard to see with standard methods. This study uses fluorescence correlation spectroscopy to spot and study these invisible early aggregates.

www.growkudos.com/publications...

3 months ago 1 0 0 0
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Formation of multicompartment structures through aging of protein-RNA condensates Cells can dynamically organize reactions through the formation of biomolecular condensates. These viscoelastic networks exhibit complex material properties and mesoscale architectures, including the a...

In aged condensates, weaker protein–RNA interactions release RNA from the dense phase. Aging plus slow macromolecular diffusion then tarts nucleatiin, producing double-emulsion.

Formation of multi compartment structures through aging of protein-RNA condensates: www.cell.com/biophysj/ful...

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Cryo-EM snapshots of Wadjet show how ATP fuels a 360° dimer rotation to trap DNA and set the stage for loop extrusion

5 months ago 2 0 0 0
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Ancient amino acid sets enable stable protein folds Early proteins likely arose from a chemically limited set of amino acids available through prebiotic chemistry, raising a central question in molecular evolution: could such primitive compositions yie...

You don't need all 20 amino acids to build proteins! Here, authors showed
a reduced 10-amino-acid alphabet form exceptionally stable and resistant to mutations proteins!!
A key insight into the #OriginOfLife and a new foundation for minimalist #ProteinDesign.

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

5 months ago 2 0 0 0
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How Water Shapes Protein Behavior in Crowded Spaces This study explores how proteins behave under crowded conditions, mimicking the complex environment inside cells. Using bromelain (a protein found in pineapple) and Ficoll-70 (a sugar-based crowding a...

link.growkudos.com/1b8sjkvls00

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Diagram to represent the interrelated factors involved in the photo-regulatory mechanisms of Arabidopsis CRY complexes. Dual mechanisms of action, including the “Lock-and-Key” and the “Liquid-Liquid Phase Separation (LLPS)” mechanisms, explain, at least partially, the structural diversity of CRY-interacting proteins and the functional diversity of the CRY photoreceptors.

Diagram to represent the interrelated factors involved in the photo-regulatory mechanisms of Arabidopsis CRY complexes. Dual mechanisms of action, including the “Lock-and-Key” and the “Liquid-Liquid Phase Separation (LLPS)” mechanisms, explain, at least partially, the structural diversity of CRY-interacting proteins and the functional diversity of the CRY photoreceptors.

💪 Small but mighty! This JIPB mini-review explores the remarkable dual-action mechanism of #Arabidopsis cryptochromes. PlantScience onlinelibrary.wiley.com/doi/10.1111/...

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