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63 results for “tubulin”
Figure 4 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information
Figure 4. Bayesian trees based on different data sets showing phylogenetic relationships amongst Spirotrichea. '-' reflects disagreement between the maximum likelihood/ maximum parsimony method and the reference Bayesian tree at a given node. The fully supported (1.00/100%/100%) branches are marked with solid circles. Species sequenced in the present study are shown in bold type. The scale bar corresponds to 10/2 substitutions per 100 nucleotide positions. A, phylogenetic analyses inferred from alpha-tubulin gene sequences data set. B, phylogenetic analyses inferred from alpha-tubulin amino acids data set.
STORM Vectashield datasets (Tubulin)
<p>Data generated at EPFL (LEB) under the supervision of Suliana Manley.</p> <p>Microscope: IX71 (Olympus) with 100x 1.3NA objective (Olympus, UplanFL) mounted on a piezo objective scanner (P-725 PIFOC, Physik Instrumente) +1.6x magnification lens (except Fig1 dataset, 160nm px)</p> <p>Laser: 641 nm (Coherent, CUBE 640–100C) and 561 nm (Coherent Sapphire) (Fig7, Cy3) Intensity on the sample ≈ 1–2 kW/cm<sup>2</sup></p> <p>Filters: multiband dichroic (89100bs, Chroma) + bandpass emission filter (ET700/75, ET600/75 (Cy3) Chroma),</p> <p>Camera: IxonEM+ (Andor) with an effective 100 nm pixel size and using the conventional CCD amplifier (except when specified, check the _readme.txt files in each dataset) See spec sheet ("Spec-Sheet_iXon.JPG")</p> <p>"FigX" datasets were used to generated the figures of the article "Simple Buffer for 3D STORM Microscopy" (<a href="https://doi.org/10.1364/BOE.4.000885">https://doi.org/10.1364/BOE.4.000885</a>):</p> <p>Fig1: STORM Imaging of Alexa647 in pure Vectashield (px 160nm)</p> <p>Fig4: STORM Imaging of Alexa647 in 25% and 50% Vectashield in Glycerol-TRIS</p> <p>Fig5: STORM Imaging of Alexa647 in 25% Vectashield - 75% TRIS-Glycerol + 1% NPG / 20 mM DABCO /10 mM Lipoic Acid</p> <p>Fig6: 3D-STORM Imaging of Alexa647 in 20% Vectashield - 80% TRIS-Glycerol (astigmatism)</p> <p>Fig:7: STORM Imaging of Alexa647 in 25% Vectashield - 75% TDE and 50% Vectashield- 50% PBS</p> <p>Fig8: STORM Imaging of CEP152-Cy3 in 40% Vectashield + 1% NPG + 20 mM DABCO</p> <p>Fig9: STORM Imaging of CF647 and Cy5 in Vectashield</p> <p>HD datasets: 2D (& one 3D) high density datasets, one of which ("2DHD6") was used for the 2013 IEEE ISBI SMLM challenge, while another ('2DHD_3") was used in "FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data" (<a href="https://doi.org/10.1038/srep04577">https://doi.org/10.1038/srep04577</a>)</p> <p>"Vecta_20pc_1" was used to generate Fig S13 in "FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data" (<a href="https://doi.org/10.1038/srep04577">https://doi.org/10.1038/srep04577</a>) - similar conditions and samples as with High Density but with Low Density.</p> <p>"_STD' files correspond to the standard deviation of the raw datasets.</p> <p>"_STORM" files correspond to STORM reconstructions obtained with <em>Detection of Molecules (DoM) plugin for ImageJ (<a href="https://github.com/UU-cellbiology/DoM_Utrecht">https://github.com/UU-cellbiology/DoM_Utrecht</a>).</em>"</p> <p>Sample preparation:</p> <p>Cell Culture: COS-7 were cultured in DMEM 10% FBS and plated on Ethanol-cleaned 25 mm size 1 cover-glass (Menzell) or 25mm Hestzig cover-glass (with embedded gold colloids fiducials)</p> <p>Fixation: Cells were pre-extracted for 10s in 0.5% Triton X-100 (Triton) in BRB80 (80 mM PIPES, 1 mM MgCl<sub>2</sub>, 1 mM EGTA, adjusted to pH 6.8 with KOH) supplemented with 4 mM EGTA, washed in PBS, fixed for 10 min in − 20°C-Methanol and washed again in PBS.</p> <p>Immunostaining (all done at room temperature): Blocking 30 min in 5% BSA, then incubation 1.5h with 1:1000 primary antibody in PBS - 1% BSA - 0.2% Triton (PBST), 3 washes with PBS-0.2% Triton, then incubation 45min in PBST with 1:1000 secondary antibody and 3 washes with PBS-0.2% Triton.</p> <p>Primary antibody (except when specified in readme.txt file): mouse anti alpha-tubulin (Sigma-Aldrich, T5168)</p> <p>Secondary antibody (except when specified in readme.txt file): goat anti-mouse Alexa-647 F(ab)2 secondary antibody fragments (Life Technologies, A-21237).</p> <p> </p>
Single and half-cell RNA-sequencing in Stentor coeruleus control and beta-tubulin knockdown cells
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Data from: The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications
<p></p><p>Microtubules are cytoskeletal structures involved in stability, transport and organization in the cell. The building blocks, the α- and β-tubulin heterodimers, form protofilaments that associate laterally into the hollow microtubule. Microtubule also exists as highly stable doublet microtubules in the cilia where stability is needed for ciliary beating and function. The doublet microtubule maintains its stability through interactions at its inner and outer junctions where its A- and B-tubules meet. Here, using cryo-electron microscopy, bioinformatics and mass spectrometry of the doublets of Chlamydomonas reinhardtii and Tetrahymena thermophila, we identified two new inner junction proteins, FAP276 and FAP106, and an inner junction-associated protein, FAP126, thus presenting the complete answer to the inner junction identity and localization. Our structural study of the doublets shows that the inner junction serves as an interaction hub that involves tubulin post-translational modifications. These interactions contribute to the stability of the doublet and hence, normal ciliary motility.</p><p></p>
Tau accelerates tubulin exchange in the microtubule lattice
<p>This dataset contains the data and source code for Figures 1-4 and and the source code for Supplementary Figures S5-S10 from the following publication: </p> <div> <p>Tau accelerates tubulin exchange in the microtubule lattice</p> </div> <div>by</div> <div> </div> <div>Subham Biswas, Rahul Grover, Cordula Reuther, Chetan S. Poojari, M. Reza Shaebani, Mona Grünewald, Amir Zablotsky, Jochen S. Hub, Stefan Diez, Karin John, Laura Schaedel</div> <div> </div> <div>doi: https://doi.org/10.1101/2024.10.05.616777</div>
Data for: The conserved centrosomin motif, γTuNA, forms a dimer that directly activates microtubule nucleation by the γ-tubulin ring complex (γTuRC)
<p>To establish the microtubule cytoskeleton, the cell must tightly regulate when and where microtubules are nucleated. This regulation involves controlling the initial nucleation template, the γ-tubulin ring complex (γTuRC). Although γTuRC is present throughout the cytoplasm, its activity is restricted to specific sites including the centrosome and Golgi. The well-conserved γ-tubulin nucleation activator (γTuNA) domain has been reported to increase the number of microtubules (MTs) generated by γTuRCs. However, previously we and others observed that γTuNA had a minimal effect on the activity of antibody-purified Xenopus γTuRCs in vitro (Thawani et al., eLife, 2020; Liu et al., 2020). Here we instead report, based on improved versions of γTuRC, γTuNA, and our TIRF assay, the first real-time observation that γTuNA directly increases γTuRC activity in vitro, which is thus a bona fide γTuRC activator. We further validate this effect in Xenopus egg extract. Via mutation analysis, we find that γTuNA is an obligate dimer. Moreover, efficient dimerization as well as γTuNA's L70, F75, and L77 residues are required for binding to and activation of γTuRC. Finally, we find that γTuNA's activating effect opposes inhibitory regulation by stathmin. In sum, our improved assays prove that direct γTuNA binding strongly activates γTuRCs, explaining previously observed effects of γTuNA expression in cells and illuminating how γTuRC-mediated microtubule nucleation is regulated.</p>
RNA-seq and label-free quantitative proteomics data from: KDM4A serves as an α-tubulin demethylase regulating microtubule polymerization and cell mitosis
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Data for: Mechanistic insights into TTLL11 polyglutamylase-mediated primary tubulin chain elongation
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Data from: The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications
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Data for: The conserved centrosomin motif, γTuNA, forms a dimer that directly activates microtubule nucleation by the γ-tubulin ring complex (γTuRC)
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Tubulin regulates stability and localization of STMN2 by binding preferentially to its soluble form
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Tubulin regulates the stability and localization of STMN2 by binding to its soluble form
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S6 molecular dynamics simulation trajectories of tubulin in electric field: 1e8V/m, 2e8 V/m, 3e8 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p><a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_centered_08.xtc">traj_centered_08.xtc </a>1e8 V/m<br> <a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_centered_3_08.xtc">traj_centered_3_08.xtc </a> 3e8 V/m<br> <a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_ricentrata_2_08.xtc">traj_ricentrata_2_08.xtc </a> 2e8 V/m</p> <p> </p>
S6 molecular dynamics simulation trajectories of tubulin in electric field: no field, 2e7 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p><a href="https://zenodo.org/api/files/81479d2b-9168-43d1-8573-9c979435b8f0/traj_centered_no_field.xtc">traj_centered_no_field.xtc </a> no field</p> <p><a href="https://zenodo.org/api/files/81479d2b-9168-43d1-8573-9c979435b8f0/traj_centered_2_07.xtc">traj_centered_2_07.xtc </a> 2e7 V/m</p> <p> </p>
S6 molecular dynamics simulation trajectories of tubulin in electric field: 1e7V/m, 5e7 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p>t<a href="https://zenodo.org/api/files/cba74eb5-a746-4cdf-80e4-1c06a1ec0462/traj_centered_07.xtc?versionId=62da1fac-7265-4aeb-a239-481088fb396a">raj_centered_07.xtc </a> 1e7 V/m</p> <p><a href="https://zenodo.org/api/files/cba74eb5-a746-4cdf-80e4-1c06a1ec0462/traj_centered_5_07.xtc?versionId=c0b8015d-b977-4eda-b678-9d4b719a90e2">traj_centered_5_07.xtc </a> 5e7 V/m</p> <p> </p> <p><br> <br> <br> </p>
FIGURE 3 in Four new taxa of Ilyonectria and Thelonectria (Nectriaceae) revealed by morphology and combined ITS and -tubulin sequence data
FIGURE 3. One of thirty-six equally most parsimonious trees inferred from combined ITS and β-tubulin partial sequences. Abbreviations: Neo. = Neonectria, I. = Ilyonectria, T. = Thelonectria, N. = Nectria. Tree length = 1169, CI = 0.6296, HI = 0.3704, CI excluding uninformative characters = 0.5856, HI excluding uninformative characters = 0.4144, RI = 0.8426, Rescaled consistency index = 0.5305. Bootstrap values ≥50% from 1000 replicates are noted above internodes. Asterisks indicate sequences of ITS and β- tubulin gene were from different strains as shown in TABLE 1.
FIGURE 2 in Four new taxa of Ilyonectria and Thelonectria (Nectriaceae) revealed by morphology and combined ITS and -tubulin sequence data
FIGURE 2. Thelonectria yunnanica (holotype). A. Median section of an ascoma; B. Structure of lateral perithecial wall; C. Colony on PDA; D−F. Macroconidia; G, H. Conidiophores and microconidia; I. Asci with ascospores.
FIGURE 1 in Four new taxa of Ilyonectria and Thelonectria (Nectriaceae) revealed by morphology and combined ITS and -tubulin sequence data
FIGURE 1. Thelonectria beijingensis (holotype). A. Median section of an ascoma; B. Colony on PDA; C. Conidiophores and macroconidia; D Asci with ascospores; E. Microconidia; F, G. Macroconidia.
Data from: Utility of internally transcribed spacer region of rDNA (ITS) and β-tubulin gene sequences to infer genetic diversity and migration patterns of Colletotrichum truncatum infecting Capsicum spp.
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Data for the publication "Mechanical communication within the microtubule through network-based analysis of tubulin dynamics"
<p>Repository containing all the necessary data to replicate the study "Mechanical communication within the microtubule through network-based analysis of tubulin dynamics", published in Biomechanics and Modeling in Mechanobiology (https://doi.org/10.1007/s10237-023-01792-5).</p>
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