@AvasthiReading's saved articles

Prachee Avasthi Recommended Reading

Length control of cytoskeletal filaments and superstructures is a really interesting area of study given maintenance of length is typical critical for polymer function. This new interesting model attempts to describe to actin filaments across various superstructures found in different cell/tissue types. Ultimately, a balance of assembly and disassembly can’t explain the observed length variance of filaments alone but considering crosslinked actin bundles (with filaments exponentially distributed within and defined by the length of the longest filament) can explain the observed variance relative to mean bundle length. There’s an interesting side prediction of the decay of bundle width as a function of distance from the assembly site which is consistent with observed width changes in yeast actin cables.

Prachee Avasthi Recommended Reading

Cilia proteins often have extra ciliary roles but this is a particularly interesting result because the protein in question is CEP290, a protein whose function seems so localization dependent. It’s thought to comprise the Y-links that can be seen by electron microscopy to link the ciliary microtubule core to the ciliary membrane in a region known to gate what goes in and what stays out of the cilium (called the transition zone). Authors find here that there are extra ciliary roles in microtubule dynamics and cell adhesion for CEP290 in IMCD3 cells when they are cycling and don’t have cilia. It would be interesting to note any CEP290 functions in a cell that was truly cilium-incompetent like Jurkat T cells.

Prachee Avasthi Recommended Reading

Really well written article showing for the first time that non-muscle myosin 2, largely thought to be contractile rather than processive, has the ability to move toward the leading edge of cells on parallel actin bundles (against retrograde actin flow).

Prachee Avasthi Recommended Reading

This paper is a neat example of correlating cell level traits (ribbon-like Golgi) with protein evolution (interaction of Golgi architecture proteins predicted using alpha fold) to make hypotheses about the origin of cellular structures and associated functions

Prachee Avasthi Recommended Reading

Totally fascinating and surprising (to me) study suggesting more frequent mating in Chlamy results in worse rather than better adaptation to a challenging environment (high salt)

Prachee Avasthi Recommended Reading

With diffusion being inversely correlated with viscosity, this super interesting modeling study got me thinking about intracellular transport based on viscosity gradients (viscophoresis) or non-homogeneous viscosity within a cell. They call this “diffusive lensing” and speculate it drives a lot of biological processes at the meso scale.

Prachee Avasthi Recommended Reading

Pkd2 mutations result in autosomal dominant polycystic kidney disease (PKD), characterized as a ciliopathy due to the ciliary localization and impact of protein dysfunction, though the relationship with cilium structure and function for PKD remains murky given cilium disruption on a pkd2 mutant background can ameliorate cystic phenotypes. Studying functions of this protein OUTSIDE cilia via a model that lacks cilia entirely (yeast) is sure to be informative in teasing apart these complex interdependencies

Prachee Avasthi Recommended Reading

There are few things I enjoy more than a comparative analysis of actin probes. Another of my all time favorites is this: https://www.tandfonline.com/doi/full/10.1080/19490992.2014.1047714

Prachee Avasthi Recommended Reading

This is an unbelievably interesting study on mictotubule and MTOC behavior during phagocytosis of apoptotic cells by microglia during zebrafish development. Check out the relative contributions of actin and mictotubules in branch mediated engulfment in figures 2E and F and the role of centrosome movement into these branches in figures 4 and 5 for successful phagocytosis, which can explain the one at a time behavior typically seen in these cells. This is tested further by artificially increasing centrosome number by centrin 4 over-expression and concurrent phagocytic events. They even look at vesicular trafficking and mechanisms of centrosome reorientation. Honestly this feels like several papers worth of work.

Prachee Avasthi Recommended Reading

Understanding ARPC5 and its isoforms, a component of the branched actin nucleating Arp2/3 complex is a fascinating topic. They find here (in addition to effects on ARPC1 and ENA/VASP) that knocking out both isoforms eliminates lamellipodia (the branched actin sheets at the leading edge of migrating cells). Some fun facts: Chlamydomonas cells don’t seem to have an ARPC5 (though we are working to confirm this), nor lamallipodia AND ARPC5 is the target of a microRNA miR-133a that is up-regulated in many human cancers. There are lots of interesting migration/metastasis related implications for ARPC5 regulation.

Prachee Avasthi Recommended Reading

If you’ve ever worked in a model or non-model system, finding putative orthologs can be difficult given low sequence homology. Structure is much more well conserved across taxa and given recent advancements in structural prediction made possible by AlphaFold2 and methods built upon it (here ColabFold), structural homology based functional annotation of proteins across phyla is easier than ever!

Prachee Avasthi Recommended Reading

A useful tool that can be used for testing functions of localized mRNAs and consequences of disrupting their targeting. Condensate scaffolds and chemically inducible condensates are engineered to test effects of motor proteins on mRNA/RNP localization. The scaffolds move based on typical motor direction (minus end microtubule motors were much faster for transport of non-functionalized condensate scaffolds, possibly due to availability of scaffolds and molecular crowding in different parts of the cell). Chemically inducible condensate formation on motors was achieved and mRNA recruitment to condensates successfully disrupted endogenous localization.

Prachee Avasthi Recommended Reading

I somehow missed this the first time but this [revision] is unbelievably cool. APC can bind the 3’UTR of RNAs as an adaptor for kinesin-1 and -2 (the ciliary kinesin!) for trafficking on mictotubules. This is shown via in vitro reconstitution experiments and it appears that these complexes track plus ends in an EB1 dependent manner but can stay associated in shrinking MTs in an EB1-independent manner.

Prachee Avasthi Recommended Reading

This is awesome. Multifunctional cell permeable ligands (fluorophore+biotin) that can be used with haloTag fusion proteins for both visualization and affinity capture!

Prachee Avasthi Recommended Reading

Omg this is so cool! A peptide phage display approach to screen for functionally relevant phospho-sites. They do some structural, evolutionary and other analyses to prioritize phosphorites within intrinsically disordered regions containing short linear motifs that often mediate phospho-dependent interactions. They then screen through expression/binding to uncover novel interactions mediated by phosphorylation that they are able to validate in many instances. Neat approach and a wealth of data to be mined. Check out the supplemental tables.