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A list by Prachee Avasthi Recommended Reading

See what researchers at Prachee Avasthi’s lab are reading to discover some interesting new work.

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  6. Universal length fluctuations of actin structures found in cells

    1. Aldric Rosario
    2. Shane G. McInally
    3. Predrag R. Jelenkovic
    4. Bruce L. Goode
    5. Jane Kondev

    • Curated by eLife

      eLife assessment

      This is a theoretical analysis that gives compelling evidence that length control of bundles of actin filaments undergoing assembly and disassembly emerges even in the absence of a length control mechanism at the individual filament level. Furthermore, the length distribution should exhibit a variance that grows quadratically with the average bundle length. The experimental data are compatible with these fundamental theoretical findings, but further investigations are necessary to make the work conclusive concerning the validity of the inferences for filamentous actin structures in cells.

    Reviewed by eLife

    3 evaluationsAppears in 2 listsLatest version Latest activity

    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.

  7. Ciliary protein CEP290 regulates focal adhesion via microtubule system in non-ciliated cells 1

    1. Kazuhiko Matsuo
    2. Yoshiro Nakajima
    3. Masaki Shigeta
    4. Daisuke Kobayashi
    5. Shinichiro Sakaki
    6. Satoshi Inoue
    7. Naoki Takeshita
    8. Atsuko Ueyama
    9. Kousuke Nishikawa
    10. Rie Saba
    11. Takahiko Yokoyama
    12. Kenta Yashiro

    Reviewed by Arcadia Science

    2 evaluationsAppears in 2 listsLatest version Latest activity

    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.

  8. Nonmuscle myosin 2 filaments are processive in cells

    1. Eric A. Vitriol
    2. Melissa A. Quintanilla
    3. Joseph J. Tidei
    4. Lee D. Troughton
    5. Abigail Cody
    6. Bruno A. Cisterna
    7. Makenzie L. Jane
    8. Patrick W. Oakes
    9. Jordan R. Beach
    Appears in 1 listLatest version

    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).

  9. Evolution of the ribbon-like organization of the Golgi apparatus in animal cells

    1. Giovanna Benvenuto
    2. Serena Leone
    3. Emanuele Astoricchio
    4. Sophia Bormke
    5. Sanja Jasek
    6. Enrico D’Aniello
    7. Maike Kittelmann
    8. Kent McDonald
    9. Volker Hartenstein
    10. Valentina Baena
    11. Héctor Escrivà
    12. Stephanie Bertrand
    13. Bernd Schierwater
    14. Pawel Burkhardt
    15. Iñaki Ruiz-Trillo
    16. Gáspár Jékely
    17. Jack Ullrich-Lüter
    18. Carsten Lüter
    19. Salvatore D’Aniello
    20. Maria Ina Arnone
    21. Francesco Ferraro
    Appears in 1 listLatest version

    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

  11. Diffusive lensing as a mechanism of intracellular transport and compartmentalization

    1. Achuthan Raja Venkatesh
    2. Kathy H Le
    3. David M Weld
    4. Onn Brandman

    • Curated by eLife

      eLife assessment

      The authors discuss an effect, "diffusive lensing", by which particles would accumulate in high-viscosity regions – for instance in the intracellular medium. To obtain these results, the authors rely on agent-based simulations using custom rules performed with the Ito stochastic calculus convention. The "lensing effect" discussed is a direct consequence of the choice of the Ito convention without spurious drift which has been discussed before and its adequacy for the intracellular medium is insufficiently discussed and relatively doubtful. Consequently, the relevance of the presented results for biology remain unclear and based on incomplete evidence.

    Reviewed by eLife

    7 evaluationsAppears in 2 listsLatest version Latest activity

    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.

  12. Functionally conserved Pkd2, mutated in autosomal dominant polycystic kidney disease, localizes to the endoplasmic reticulum and regulates cytoplasmic calcium homeostasis in fission yeast

    1. Takayuki Koyano
    2. Kazunori Kume
    3. Kaori Onishi
    4. Makoto Matsuyama
    5. Masaki Fukushima
    6. Takashi Toda
    Appears in 1 listLatest version

    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

  13. Comparative analysis of actin visualization by genetically encoded probes in cultured neurons

    1. Attila Ignácz
    2. Domonkos Nagy-Herczeg
    3. Angelika Hausser
    4. Katalin Schlett

    Reviewed by ASAPbio crowd review

    1 evaluationAppears in 2 listsLatest version Latest activity

    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

  14. A role for the centrosome in regulating the rate of neuronal efferocytosis by microglia in vivo

    1. Katrin Möller
    2. Max Brambach
    3. Ambra Villani
    4. Elisa Gallo
    5. Darren Gilmour
    6. Francesca Peri

    • Curated by eLife

      eLife assessment

      This paper is an important contribution to the microglia field and will be of interest to a broad readership in the fields of neurobiology, cell biology and immunology. This work describes fundamental mechanisms of efferocytosis by microglia and uses impressive imaging in zebrafish, in combination with molecular manipulations, to provide compelling data of how centrosome movements synchronize with phagocytic cup formation during microglial efferocytosis of neuronal corpses in vivo.

    Reviewed by eLife

    4 evaluationsAppears in 2 listsLatest version Latest activity

    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.

  15. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning

    1. Florian Fäßler
    2. Manjunath G. Javoor
    3. Julia Datler
    4. Hermann Döring
    5. Florian W. Hofer
    6. Georgi Dimchev
    7. Victor-Valentin Hodirnau
    8. Jan Faix
    9. Klemens Rottner
    10. Florian K.M. Schur
    Appears in 1 listLatest version

    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.

  16. Cross-phyla protein annotation by structural prediction and alignment

    1. Fabian Ruperti
    2. Nikolaos Papadopoulos
    3. Jacob M. Musser
    4. Milot Mirdita
    5. Martin Steinegger
    6. Detlev Arendt
    Appears in 1 listLatest version

    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!

  17. Condensate functionalization with microtubule motors directs their nucleation in space and allows manipulating RNA localization

    1. Audrey Cochard
    2. Adham Safieddine
    3. Pauline Combe
    4. Marie‐Noëlle Benassy
    5. Dominique Weil
    6. Zoher Gueroui
    Appears in 1 listLatest version

    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.

  18. APC couples neuronal mRNAs to multiple kinesins, EB1 and shrinking microtubule ends for bidirectional mRNA motility

    1. Sebastian J. Baumann
    2. Julia Grawenhoff
    3. Elsa C. Rodrigues
    4. Silvia Speroni
    5. Maria Gili
    6. Artem Komissarov
    7. Sebastian P. Maurer
    Appears in 1 listLatest version

    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.

  19. Multifunctional fluorophores for live-cell imaging and affinity capture of proteins

    1. Pratik Kumar
    2. Jason D. Vevea
    3. Edwin R. Chapman
    4. Luke D. Lavis

    Reviewed by preLights

    1 evaluationAppears in 3 listsLatest version Latest activity

    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!

  20. Large-scale identification of phospho-modulated motif-based protein-protein interactions

    1. Johanna Kliche
    2. Dimitriya Hristoforova Garvanska
    3. Leandro Simonetti
    4. Dilip Badgujar
    5. Doreen Dobritzsch
    6. Jakob Nilsson
    7. Norman Davey
    8. Ylva Ivarsson
    Appears in 1 listLatest version

    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.

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