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Microtubules

Microtubules are cytoskeletal structures found in the cytoplasm of eukaryotic cells.
They are composed of tubulin dimers and play crucial roles in cell division, intracellular transport, and maintaining cell shape.
Microtubules are highly dynamic, undergoing constant assembly and disassembly, which is regulated by various cellular processes.
Studying microtubule structure, function, and regulation is crucial for understanding fundamental cellular mechanisms and developing therapies for microtubule-related diseases, such as cancer and neurodegenerative disorders.
Reserchers can optimize their microtubule studies by utilizing the power of PubCompare.ai, an AI-driven platform that helps locate the best protocols from literature, preprints, and patents, while comparing them to identify the most accurate and reproducible methods.
This tool can take your microtubule research to new heights and facilitate breakthroughs in this important field of cell biology.

Most cited protocols related to «Microtubules»

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Publication 2011
5'-deoxy-5'-phosphonomethyladenosine phosphate Axoneme Chlamydomonas reinhardtii Cone-Beam Computed Tomography DNA Replication Epistropheus Hypersensitivity Maritally Unattached Mental Orientation Microtubule-Associated Proteins Microtubules NADH Dehydrogenase Complex 1 Optimism Plant Embryos Radius Seizures Tomography Yarrowia lipolytica
We performed complementation analysis, genetics, molecular biology, western blotting, immunostaining and generation of transgenic animals using standard techniques4 (link). Multiple new lines of the full-length ‘short’ isoform of Mical, the MicalΔredox mutation (MicalG→W; ref. 4 (link)) and the other transgenic animals were generated and used for all experiments. Adult bristles were examined and quantified by crossing adults at 25 °C: adult offspring from these crosses were first sorted according to genotype and then examined under a dissecting microscope. We genotyped pupae using a Zeiss Discovery M2 Bio fluorescence stereomicroscope, and all preparation, staging and dissection of pupae were done using standard approaches. We imaged, drew and quantified the adult bristles with the aid of the Discovery M2 Bio stereomicroscope, a motorized focus and zoom, a Zeiss AxioCam HR camera and three-dimensional-reconstruction software (Zeiss AxioVision, version 4.6.3, and Extended Focus software). All other bright-field, dark-field, differential interference contrast and fluorescence visualization, and imaging of bristles, embryos and growth cones, was done using a Zeiss Axio Imager upright microscope with motorized focus and zoom and an ApoTome module, and images were captured and quantified using the AxioCam HR camera and AxioVision software. All electron microscopy of pupae and negative staining of purified proteins was done using a FEI Tecnai G2 Spirit BioTWIN transmission electron microscope. We purified recombinant Mical proteins10 and recombinant p-hydroxybenzoate hydroxylase using our previously developed approaches. Drosophila fascin (also known as singed) complementary DNA was inserted in a bacterial expression vector, and recombinant Drosophila fascin protein was purified. All F-actin and Mical co-sedimentation assays and G-actin/F-actin ratio experiments were performed using standard approaches, as were all pyrene-labelled actin polymerization and depolymerization assays, actin bundling assays, tubulin polymerization assays and microtubule co-sedimentation assays.
Publication 2010
Actins Adult Animals, Transgenic Bacteria Biological Assay Cloning Vectors Dissection DNA, Complementary Drosophila Electron Microscopy Embryo F-Actin fascin Fluorescence G-Actin Growth Cones Hydroxybenzoates Microscopy Microtubules Mixed Function Oxygenases Mutation Polymerization Protein Isoforms Proteins Pupa Pyrenes Reconstructive Surgical Procedures Sn protein, Drosophila Transmission Electron Microscopy Tubulin
While annotation alone is sufficient for certain types of cellular tomogram interpretation, subtomogram extraction and averaging remains a primary purpose for detailed annotation. To extract discrete objects like ribosomes or other macromolecules, we begin by identifying all connected voxels annotated as being the same feature. For each connected region, the maxima position in the annotation is used as the particle location. For continuous features like microtubules, we randomly seed points on the annotation output and use these points as box coordinates for particle extraction. In both cases, EMAN2 2D classification20 (link) is performed on a Z-axis projection of the particles in order to help identify and remove bad particles, in a similar fashion to single particle analysis. 3D alignment and averaging are performed using EMAN2 single particle tomography utilities2 (link).
Publication 2017
Cells Epistropheus Microtubules Ribosomes Single Molecule Analysis Tomography
The PHF and SF maps from the PT and FL data sets have complementary regions for model building. The β-helix motif at the tips of the C-shaped protofilaments is better ordered in the PHFs than in SFs, whereas the amino- and carboxy-terminal ends of the protofilament cores are best ordered in the SF map from the FL data set. Moreover, density for the cross-β structures near the termini of the PHFs is better defined in the PT reconstruction than in the FL reconstruction. Combined, the different maps allow for unambiguous main-chain tracing of the atomic models (Figure 2; Extended Data Figures 4 and 6). Initial model building started by fitting the L-type β-helix from the magic-angle spinning NMR-derived structure of filaments of the prion-forming domain HET-s218-289 (PDB-entry 2RNM) in the tip of the protofilaments of the PT PHF reconstruction. The sequence of only one of the four microtubule-binding repeats of Tau had a sequence that was compatible with the observed density in both PHFs and SFs (Extended Data Figure 4). Using the β-helix region as a starting point, we then built the remainder of the amino- and carboxy-terminal regions by manually adding amino acids and targeted real-space refinement in COOT54 (link).
Fourier-space refinement of the complete atomic model against the PHF and SF maps was performed in REFMAC55 (link). A stack of three consecutive monomers from each of the protofilaments was refined in order to preserve nearest-neighbour interactions for the middle chain. Local symmetry restraints were imposed in REFMAC to keep all β-strand rungs identical. Since most of the structure adopts a β-strand conformation, hydrogen-bond restraints were imposed to preserve a parallel, in-register hydrogen-bonding pattern in earlier stages of the model building process. In addition, ϕ/ψ angle restraints were imposed for the polyglycine II region, 333GGG335, and the three-residue β-arc, 347KDR349. The dihedral angles for polyglycine II were taken from Crick’s proposed fold27 (link) (ϕ = −80, ψ =150) and those for the three-residue β-arc from the crystal structure of PDB-entry 1QRE56 (link). Side-chain clashes were detected using MOLPROBITY57 (link) and corrected by iterative cycles of real-space refinement in COOT and Fourier-space refinement in REFMAC. Refinements of atomic models were performed for the FL and PT PHFs and for the FL SF. The refined model from the FL SF was rigid-body fitted into the PT SF map. For each refined structure, separate model refinements were performed against a single half-map, and the resulting model was compared to the other half-map to confirm the absence of overfitting. The final models were stable in refinements without additional restraints. Statistics for the final models are shown in Extended Data Table 1.
Publication 2017
Amino Acids Cytoskeletal Filaments Helix (Snails) Human Body Hydrogen Bonds Microtubule-Associated Proteins Microtubules Muscle Rigidity polyglycine Prions Reconstructive Surgical Procedures Repetitive Region

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Publication 2014
Fluorescence Microscopy Microtubules Proteins

Most recents protocols related to «Microtubules»

Cy5-labeled GDP-MT (10% labeled) was grown from Alexa Fluor 488–labeled GMPCPP-MT (2% labeled) in the same way as the microtubule expansion assay (see the Microtubule expansion assay section). After 30-min incubation to hydrolyze GTP completely, the chamber was washed with washout buffer (BRB80, 25% glycerol, and 2× blocking solution) with or without 4 μM D2 and incubated for 5 min. Subsequently, glycerol-free imaging buffer (BRB80, 1× blocking solution, 0.1% methylcellulose, 5 mM protocatechuic acid, 5 mM TSY, and 50 nM protocatechuate-3,4-dioxygenase) with or without 4 μM D2 was flowed into the chamber, and the image acquisition was started immediately. For experiments without D2, images were taken at 0.5-s intervals; for those with D2, images were taken at 5-s intervals. Signals from the mCherry channel were also taken for the experiments in Fig S4.
Instead of building kymographs, we measured the decrease in Cy5 total intensity to quantify the depolymerization rate. Areas that microtubules occupied during depolymerization were manually drawn using maximum projection as the reference. The total Cy5 intensity in the area was measured for every frame, and the values were converted into length using the ratio of the microtubule length to total Cy5 intensity of the first frame. The depolymerization rate was determined by a linear regression of data points that corresponded to microtubule lengths longer than 0.5 μm using the scikit-learn package (v1.0.1; Pedregosa et al, 2011 (link)). This workflow was applied to all microtubules independently.
Publication 2023
5'-guanylylmethylenebisphosphonate alexa fluor 488 Biological Assay Buffers Dioxygenases Glycerin Kymography Methylcellulose Microtubules protocatechuic acid Reading Frames
D2-mCherry in imaging buffer (BRB80, 25% glycerol 1× blocking solution, 0.1% methylcellulose, 5 mM protocatechuic acid (Pacific Bioscience), 5 mM TSY (Pacific Bioscience), and 50 nM protocatechuate-3,4-dioxygenase (Pacific Bioscience)) was applied to the microtubule-immobilized glass chamber (see the Preparation for binding assay section). After 5 min of incubation, image acquisition was conducted for all registered positions. To increase the signal-to-noise ratio, five frames were taken for every position and channel.
For assays in the presence of taxol, D2-mCherry in imaging buffer was supplemented with 20 μM taxol, and images were acquired the same way. Taxol depletion was conducted by exchanging the solution with a sample of same D2 concentration without taxol. Images were taken after 5-min incubation.
Because the binding activity of D2 was lost quickly after being thawed (<1 h), we prepared new samples every 30 min.
Publication 2023
Biological Assay Buffers Dioxygenases Glycerin Methylcellulose Microtubules protocatechuic acid Reading Frames Taxol
During this experiment, 1 μM D2-mCherry in imaging buffer was used for the D2-mCherry samples, and variable concentrations of KIF5C in BRB30 with 25% glycerol were used for the KIF5C pretreatment. A microtubule-immobilized glass chamber (see the Preparation for binding assay section) was first incubated with D2-mCherry for 5 min. As a no pretreatment control, microtubule-bound D2 was dissociated by 1-min incubation in high-salt buffer (7.5× PEM, 25% glycerol) followed by washout with BRB80 containing 25% glycerol. Again, D2-mCherry was applied, and the chamber was incubated for 5 min before the image acquisition.
For 0.1, 0.5, and 2.0 μM KIF5C pretreatment, the incubation/dissociation cycle described below was repeated in the same chamber after the previous image acquisition of D2-bound microtubules. First, D2 was dissociated and washed out by 1-min incubation in high-salt buffer and 30-s incubation in BRB80 containing 25% glycerol. Microtubules were subsequently expanded by the addition of KIF5C and incubated for 1 min. Next, KIF5C was dissociated and washed out by a 1-min incubation in high-salt buffer and 30-s incubation in BRB80 containing 25% glycerol. Finally, D2 was applied and incubated for 5 min before the image acquisition.
For the compaction experiment, pretreatment with 2.0 μM KIF5C was repeated as above except the buffer used for the KIF5C dissociation was ADP buffer (BRB80, 25% glycerol, and 1 mM ADP) and not a high-salt buffer.
Note that because this assay takes ∼1 h for each run, new D2 samples were prepared between 0 and 0.1 μM pretreatments in addition to the 0.5 and 2.0 μM pretreatments.
Publication 2023
Afterimage Biological Assay Buffers Glycerin Microtubules Sodium Chloride
Microtubule immobilization was carried out similar to the binding assay (see the Binding assay section) but slightly modified to fit the expansion assay. After GMPCPP-MT was added, 28 μM Cy5-labeled tubulin (10% labeled) was used for a 15-min polymerization period to lengthen and brighten the microtubules. Subsequently, 8 μM Alexa Fluor 488–labeled tubulin (2% labeled) with 1 mM GMPCPP was loaded into the chamber and polymerized for 20 min. Polymerization was terminated by washing free tubulin out with washout buffer. Images were acquired before and after 4 μM D2-mCherry in imaging buffer was added to the chamber followed by the dissociation of D2 by 1-min incubation in high-salt buffer and washout by imaging buffer for 30 s.
To calculate expansion, a background correction was performed in the same way as the data analysis for the binding assay (see the Data analysis of binding assays section). Microtubule lengths were measured using napari-filaments as follows (Fig S5): first, the Cy5 channel and Alexa Fluor 488 channel of the image were added with 1:1 weight to create a total intensity image. This image was used for 2D spline fitting as mentioned in the data analysis of the binding assay (see the Data analysis of binding assays section). Next, the spline curves were clipped at the Cy5-labeled microtubule edges by fitting to the error function: fx=a-b21+erfx-x02σ+b where: erfx=2π0xe-t2dt
The parameters of the error function indicate that intensity increases from b to a , where the inflection point of the intensity change is x0 . Cy5-labeled microtubule lengths were obtained by fragmenting the spline curve into 1,024 pieces and summing the lengths of all fragments.
Publication 2023
5'-guanylylmethylenebisphosphonate alexa fluor 488 Biological Assay Buffers Cytoskeletal Filaments Immobilization Microtubules Polymerization Sodium Chloride Tubulin
A PEG-biotin–coated glass chamber was made by silane coupling and a succinimidyl ester reaction. Cover glasses (C022221S; Matsunami Glass) were first subjected to sonication in 1 N KOH and plasma treatment. Glass surfaces were coated with an amino group by sandwiching N-2-(aminoethyl)-3-aminopropyl-triethoxysilane (KBE-603; Shin-Etsu Chemical) and incubation for 20 min at room temperature. These glasses were washed with deionized water 20 times and then incubated with 200 mg/ml of 0.5% biotinylated NHS-PEG (ME-050-TS and BI-050-TS; NOF) for 90 min at room temperature. Coated glasses were stuck to each other with 30-μm double-sided tape (5603; Nitto-Denko) to make an ∼2-mm wide flowing chamber. The glasses were sealed in a food saver in vacuo and stored at −80°C until use.
GMPCPP-bound tubulin labeled with Alexa Fluor 488 (2% labeled) and biotin (5% labeled) was incubated at 27°C for 1 h to promote nucleation, followed by 1 h of polymerization at 37°C. Polymerized microtubule samples were purified by centrifugation at 20,000g, 35°C for 25 min.
The glass chamber was treated as follows: first, 1 mg/ml NeutrAvidin was loaded into the chamber and incubated for 2 min to let it bind to biotin molecules covalently connected to the glass surface. The glass surface was subsequently deactivated by adding and incubating with 10× blocking solution (1 mg/ml casein and 1% pluronic F127) for 2 min. After washing them out with BRB80 containing 25% glycerol, GMPCPP-MT seeds were loaded into the chamber and incubated for 2 min to immobilize microtubules on the glass surface. Unbound microtubules were washed out with BRB80 containing 10x blocking solution and 1 mM GTP. To polymerize GDP-MT from the seeds, 28 μM Cy5-labeled tubulin (labeling rate 2%) in polymerization buffer (BRB80, 2× blocking solution, 1 mM GTP) was applied to the chamber, polymerized for 5 min, and terminated by washing free tubulin out with washout buffer (BRB80, 25% glycerol, and 2× blocking solution). To completely hydrolyze GTP, the chamber was incubated for more than 30 min before any subsequent experiments.
Publication 2023
3-(triethoxysilyl)propylamine 5'-guanylylmethylenebisphosphonate alexa fluor 488 Biotin Buffers Caseins Centrifugation Esters Eyeglasses Food Glycerin Immobilization Microtubules neutravidin Plant Embryos Plasma Pluronic F-127 Silanes Tubulin

Top products related to «Microtubules»

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Nocodazole is a synthetic compound that acts as a microtubule-destabilizing agent. It functions by binding to and disrupting the polymerization of microtubules, which are essential components of the cytoskeleton in eukaryotic cells. This property makes Nocodazole a valuable tool in cell biology research for studying cell division, cell motility, and other cellular processes that rely on the dynamics of the microtubule network.
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Paclitaxel is a pharmaceutical compound used in the production of various cancer treatment medications. It functions as a microtubule-stabilizing agent, which plays a crucial role in the development and regulation of cells. Paclitaxel is a key ingredient in the manufacture of certain anti-cancer drugs.
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Cytochalasin D is a laboratory reagent that inhibits actin polymerization. It is commonly used in cell biology research to disrupt the cytoskeleton and study its role in cellular processes.
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DAPI is a fluorescent dye that binds strongly to adenine-thymine (A-T) rich regions in DNA. It is commonly used as a nuclear counterstain in fluorescence microscopy to visualize and locate cell nuclei.
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Taxol is a laboratory product manufactured by Merck Group. It is a complex organic compound used in various research and analysis applications. The core function of Taxol is to facilitate the stabilization of microtubules, which are essential structural components within cells.
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Triton X-100 is a non-ionic surfactant commonly used in various laboratory applications. It functions as a detergent and solubilizing agent, facilitating the solubilization and extraction of proteins and other biomolecules from biological samples.

More about "Microtubules"

Microtubules are essential cytoskeletal structures found within the cytoplasm of eukaryotic cells.
These dynamic filaments, composed of tubulin dimers, play crucial roles in diverse cellular processes, including cell division, intracellular transport, and the maintenance of cell shape.
Studying the structure, function, and regulation of microtubules is vital for understanding fundamental mechanisms in cell biology and developing therapies for microtubule-related diseases, such as cancer and neurodegenerative disorders.
Researchers can optimize their microtubule studies by utilizing the power of PubCompare.ai, an AI-driven platform that helps locate the best protocols from literature, preprints, and patents, while comparing them to identify the most accurate and reproducible methods.
This tool can take your microtubule research to new heights and facilitate breakthroughs in this important field.
Microtubules are highly dynamic structures, undergoing constant assembly and disassembly, which is regulated by various cellular processes.
Modulators of microtubule dynamics, such as Nocodazole, Paclitaxel, Cytochalasin D, and Colchicine, are widely used in microtubule research to investigate their effects on cellular processes.
Fluorescent dyes, such as DAPI and Alexa Fluor 488, are commonly employed to visualize and study microtubule structures, often in combination with techniques like immunofluorescence and live-cell imaging.
The use of MATLAB, a powerful computational software, can aid in the analysis and quantification of microtubule dynamics and organization.
By leveraging the insights and resources provided by PubCompare.ai, researchers can optimize their microtubule studies, leading to a better understanding of this crucial cellular component and paving the way for advancements in the fields of cell biology and therapeutics.