Saved Articles

Showing page 2 of 9 pages of list content

1. Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq

   This article's authors

   1. Bassel Ghaddar
   2. Subhajyoti De

   Annotation by AvasthiReading

   Huh clever. Leveraging incomplete dissociation in scRNA-seq experiments to infer tissue architecture/cell-cell interactions.

2. Conserved degronome features governing quality control-associated proteolysis

   This article's authors

   1. Bayan Mashahreh
   2. Shir Armony
   3. Kristoffer Enøe Johansson
   4. Alon Chappleboim
   5. Nir Friedman
   6. Richard G. Gardner
   7. Rasmus Hartmann-Petersen
   8. Kresten Lindorff-Larsen
   9. Tommer Ravid

   Annotation by AvasthiReading

   How interesting! A peptide screen to identify degrons with E3 ubiquitin ligase specificity in yeast followed by extraction of conserved properties identifies transmembrane domain containing peptides as likely degrons.

3. Integrating bulk and single cell RNA-seq refines transcriptomic profiles of specific C. elegans neurons

   This article's authors

   1. Alec Barrett
   2. Erdem Varol
   3. Alexis Weinreb
   4. Seth R. Taylor
   5. Rebecca M. McWhirter
   6. Cyril Cros
   7. Manasa Basaravaju
   8. Abigail Poff
   9. John A. Tipps
   10. Maryam Majeed
   11. Berta Vidal
   12. Chen Wang
   13. Eviatar Yemini
   14. Emily A. Bayer
   15. HaoSheng Sun
   16. Oliver Hobert
   17. David M. Miller
   18. Marc Hammarlund

   Annotation by AvasthiReading

   Recognizing the utility of not using exclusively cutting edge methods for everything, this important study combines bulk RNAseq (high sensitivity due to capturing more low expression and noncoding RNAs) and single cell RNAseq (high specificity) for a more comprehensive transcriptomic picture.

4. Bio-hybrid micro-swimmers propelled by flagella isolated from C. reinhardtii ^†

   This article's authors

   1. Raheel Ahmad
   2. Albert J Bae
   3. Yu-Jung Su
   4. Samira Goli Pozveh
   5. Eberhard Bodenschatz
   6. Alain Pumir
   7. Azam Gholami

   Annotation by AvasthiReading

   This is wild! Chlamydomonas flagella were isolated, demembranated, attached to polystyrene beads and reactivated to reconstitute flagellar movement. This yields some interesting insights through experimentation and simulation: Increased calcium concentration affects flagellar waveform and trajectory of bead movement and surprisingly, larger beads have increased rather than decreased velocity.

5. ARP2/3 complex associates with peroxisomes to participate in pexophagy in plants

   This article's authors

   1. Jan Martinek
   2. Petra Cifrová
   3. Stanislav Vosolsobě
   4. Jana Krtková
   5. Lenka Sikorová
   6. Kateřina Malínská
   7. Zdeňka Mauerová
   8. Ian Leaves
   9. Imogen Sparkes
   10. Kateřina Schwarzerová

   Annotation by AvasthiReading

   Interesting role for ARP2/3 complex in peroxisome autophagy in plants!

6. Rapid Rerouting of Myosin Traffic at the T Cell Immunological Synapse

   This article's authors

   1. Robert Mąka
   2. Natalia Plewa
   3. Urszula Cichoń
   4. Katarzyna Krysztofiak
   5. Jagoda J. Rokicka
   6. Ronald S. Rock

   Annotation by AvasthiReading

   This polarity of actin networks and myosin traffic is interesting in light of the parallels between cilium biogenesis and the immune synapse function.

7. Structural basis of actin filament assembly and aging

   This article's authors

   1. Wout Oosterheert
   2. Björn U Klink
   3. Alexander Belyy
   4. Sabrina Pospich
   5. Stefan Raunser

   Annotation by AvasthiReading

   A 2.2 angstrom resolution structures of muscle actin filaments in ATP, ADP-Pi and ADP states. Many new insights here about the surprising stability of ADP actin, mechanism of ATP hydrolysis, cofilin binding and more.

8. Genome-wide functional analysis reveals key roles for kinesins in the mammalian and mosquito stages of the malaria parasite life cycle

   This article's authors

   1. Mohammad Zeeshan
   2. Ravish Rashpa
   3. David J Ferguson
   4. Steven Abel
   5. Zeinab Chahine
   6. Declan Brady
   7. Sue Vaughan
   8. Carolyn A. Moores
   9. Karine G. Le Roch
   10. Mathieu Brochet
   11. Anthony A. Holder
   12. Rita Tewari

   Annotation by AvasthiReading

   Truly exquisite characterization of kinesins in the malaria parasite. Check out the spectacular expansion microscopy images in figure 7A!

9. The molecular organization of flat and curved caveolae indicates bendable structural units at the plasma membrane

   This article's authors

   1. Claudia Matthaeus
   2. Kem A. Sochacki
   3. Andrea Dickey
   4. Dmytro Puchkov
   5. Volker Haucke
   6. Martin Lehmann
   7. Justin W. Taraska

   Annotation by AvasthiReading

   This is a beautiful characterization of caveolae. In addition to platinum replica EM of these plasma membrane invaginations in various cell types, this work includes molecular identification of proteins associated with caveolae of different curvatures by STED-CLEM (very high-resolution correlative light electron microscopy).

10. Early Endosome Capture Proteomics and its Application to Amyloid Precursor Protein Intramembrane Processing by β and γ-Secretases

    This article's authors

    1. Hankum Park
    2. Qing Yu
    3. Frances V. Hundley
    4. Katherine Overmyer
    5. Lia Serrano
    6. Joao A. Paulo
    7. Julia C. Paoli
    8. Sharan Swarup
    9. Joshua J. Coon
    10. Steven P. Gygi
    11. J. Wade Harper

    Annotation by AvasthiReading

    Whoa! Successful ID of early endosomal cargoes via pull-down of an early endosomal marker followed by proteomics.

11. Systematic analysis of cilia characteristics and Hedgehog signaling in five immortal cell lines

    This article's authors

    1. Arianna Gómez
    2. Julie Craft Van De Weghe
    3. Malaney Finn
    4. Dan Doherty

    Annotation by AvasthiReading

    I love this kind of study that challenges our assumptions of what cells and models we should use. This is an important comparative characterization of cilium-based hedgehog signaling across a variety of cultured cell types.

12. The actin assembly requirements of the formin Fus1 to build the fusion focus

    This article's authors

    1. Ingrid Billault-Chaumartin
    2. Laetitia Michon
    3. Caitlin A Anderson
    4. Sarah E Yde
    5. Cristian Suarez
    6. Justyna Iwaszkiewicz
    7. Vincent Zoete
    8. David R Kovar
    9. Sophie G Martin

    Annotation by AvasthiReading

    This is a great demonstration (using chimeras of formin FH2 and FH1 domains from a diverse range of formins) that tuning the actin nucleation and elongation rates of formins affects actin architecture. This can help explain how various cell types can generate unique actin structures optimized for a particular function as in this case for Fus1’s role in assembling the structure required for fusion of fission yeast cells during mating.

13. Vimentin intermediate filaments organize organellar architecture in response to ER stress

    This article's authors

    1. Tom Cremer
    2. Lenard M. Voortman
    3. Erik Bos
    4. Daphne M. van Elsland
    5. Laurens R. ter Haar
    6. Roman I. Koning
    7. Ilana Berlin
    8. Jacques Neefjes

    Annotation by AvasthiReading

    Interesting function of intermediate filaments though an ER embedded protein: this protein, a ubiquitin ligase, links the perinuclear ER with vimentin-based intermediate filaments for ER and stress-dependent endosome positioning. The work was done in U2OS cells.

14. High-resolution secretory timeline from vesicle formation at the Golgi to fusion at the plasma membrane in S. cerevisiae

    This article's authors

    1. Robert M. Gingras
    2. Abigail M. Sulpizio
    3. Joelle Park
    4. Anthony Bretscher

    Annotation by AvasthiReading

    This is a must-read spatio-temporal characterization of secretory pathway events during yeast exocytosis. This will undoubtedly impact our thinking about secretory traffic during processes like encystment and ciliogenesis across a range of unicellular eukaryotes.

15. Imaging tools generated by CRISPR/Cas9 tagging reveal cytokinetic diversity in mammalian cells

    This article's authors

    1. Mathieu C. Husser
    2. Imge Ozugergin
    3. Tiziana Resta
    4. Vincent J. J. Martin
    5. Alisa J. Piekny

    Annotation by AvasthiReading

    This paper is a good reminder of the heterogeneity in phenotypes that can be observed when visualizing molecular players at physiological levels.

16. Atypical small GTPase RABL3 interacts with RAB11 to regulate early ciliogenesis in human cells

    This article's authors

    1. Tetsuo Kobayashi
    2. Tatsuya Ikeda
    3. Reo Ota
    4. Takafumi Yasukawa
    5. Hiroshi Itoh

    Annotation by AvasthiReading

    A new GTPase player in ciliogenesis in human (RPE1) cells binds directly to rab11 and is needed for ciliary vesicle formation.

17. Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies

    This article's authors

    1. Marie Locard-Paulet
    2. Oana Palasca
    3. Lars Juhl Jensen

    Annotation by AvasthiReading

    Interesting framing…identifying genes that are robustly correlated with cell proliferation not to find novel mechanisms of division but to eliminate confounding contributions of cell proliferation in cellular processes analyzed by large data sets.

18. Alterations to the broad-spectrum formin inhibitor SMIFH2 improve potency

    This article's authors

    1. Marina Orman
    2. Maya Landis
    3. Aisha Oza
    4. Deepika Nambiar
    5. Joana Gjeci
    6. Kristen Song
    7. Vivian Huang
    8. Amanda Klestzick
    9. Carla Hachicho
    10. Su Qing Liu
    11. Judith M. Kamm
    12. Francesca Bartolini
    13. Jean J. Vadakkan
    14. Christian M. Rojas
    15. Christina L. Vizcarra

    Annotation by AvasthiReading

    Thanks to @cdmacquarrie for alerting me to this one! Synthesis of SMIFH2 derivatives identifies more potent versions (5-fold decrease in IC50) that are able to inhibit all human formins. This increased potency may reduce off target inhibition of myosins at higher concentrations. Myosins aren’t directly tested in this study.

19. Transient accumulation and bidirectional movement of KIF13B in primary cilia

    This article's authors

    1. Alice Dupont Juhl
    2. Zeinab Anvarian
    3. Stefanie Kuhns
    4. Julia Berges
    5. Jens S. Andersen
    6. Daniel Wüstner
    7. Lotte B. Pedersen

    Annotation by AvasthiReading

    Worm cilia are perhaps not as unique as we thought. A kinesin-3 accumulates in a subset of cilia in human cultured cells and undergoes bursts of bidirectional motor domain dependent movement.

20. The dynamics of protein localisation to restricted zones within Drosophila mechanosensory cilia

    This article's authors

    1. Wangchu Xiang
    2. Petra zur Lage
    3. Fay G. Newton
    4. Guiyun Qiu
    5. Andrew P. Jarman

    Annotation by AvasthiReading

    Very interesting study tackling the sub-compartmentalization of cilia. In fly chorodonal neurons, cilia have differences in outer and inner dynein arm complexes along the apical-distal axis of the axoneme. This paper highlights different modes of establishing this subcompartmentalization whether by restriction to proximal regions (ODAs) or by uniform localization and maturation to final proximal restriction (IDAs). Access to the axonemal interior, binding affinities via docking complexes, tubulin modification and pruning of IDA localization by retrograde IFT-mediated removal are suggested as possible factors.