Journal: Data in Brief

Article Title: Gene datasets associated with mouse cleft palate

doi: 10.1016/j.dib.2018.03.010

Figure Lengend Snippet: KEGG pathways enriched with a statistically significant number of genes involved in cleft palate.

Article Snippet: Regulation of actin cytoskeleton , Fgf8 Fgfr1 Itgb1 Egfr Itgb6 Pdgfc Sos1 Fgf18 Crk Itgav Fgf10 Rac1 Pdgfrb Fgf9.

Techniques:

Journal: Data in Brief

Article Title: Gene datasets associated with mouse cleft palate

doi: 10.1016/j.dib.2018.03.010

Figure Lengend Snippet: GO biological process terms enriched with a statistically significant number of genes involved in cleft palate.

Article Snippet: Regulation of actin cytoskeleton , Fgf8 Fgfr1 Itgb1 Egfr Itgb6 Pdgfc Sos1 Fgf18 Crk Itgav Fgf10 Rac1 Pdgfrb Fgf9.

Techniques: Cell Differentiation

Journal: Data in Brief

Article Title: Gene datasets associated with mouse cleft palate

doi: 10.1016/j.dib.2018.03.010

Figure Lengend Snippet: GO Molecular Function terms enriched with a statistically significant number of genes involved in cleft palate.

Article Snippet: Regulation of actin cytoskeleton , Fgf8 Fgfr1 Itgb1 Egfr Itgb6 Pdgfc Sos1 Fgf18 Crk Itgav Fgf10 Rac1 Pdgfrb Fgf9.

Techniques: Binding Assay, Protein Binding, Activity Assay, Sequencing

Journal: Data in Brief

Article Title: Gene datasets associated with mouse cleft palate

doi: 10.1016/j.dib.2018.03.010

Figure Lengend Snippet: GO cellular component terms enriched with a statistically significant number of genes involved in cleft palate.

Article Snippet: Regulation of actin cytoskeleton , Fgf8 Fgfr1 Itgb1 Egfr Itgb6 Pdgfc Sos1 Fgf18 Crk Itgav Fgf10 Rac1 Pdgfrb Fgf9.

Techniques:

Journal: Nature Communications

Article Title: Deconvolution of Buparlisib's mechanism of action defines specific PI3K and tubulin inhibitors for therapeutic intervention

doi: 10.1038/ncomms14683

Figure Lengend Snippet: ( a ) Backbone of the αβ-tubulin heterodimer (in cartoon representation) in complex with BKM120; GTP is shown in spheres representation (PDB ID 5M7E). ( b ) BKM120 binding site in tubulin. Relevant amino acids are labelled in single letter code; secondary structure elements (marine blue) are H: helix; S: β-sheet; T: T-loop, preceeded by the respective tubulin subunit, α or β. Resolved water molecules are indicated as red spheres; dashed lines denote hydrogen bonds or interactions discussed in the main text. ( c ) Overlay of BKM120 and MTD147 (PDB ID 5M7G) binding to the colchicine-binding pocket of tubulin in the T 2 R-TTL complex. None of the compounds affected the global conformation of tubulin in the complex (rmsd 0.290 Å; 1941 Cα atoms) compared to the non-ligated T 2 R-TTL complex (PDB ID: 4I55, refs , ). Residues of strands βS8 and βS9, loop βT7 and helices βH7 and βH8 of β-tubulin and of loop αT5 of α-tubulin form the boundaries of the binding site. For all investigated compounds, the trifluoromethyl substituted α-aminopyridine moiety pointed into the hydrophobic pocket outlined by side chains of βCys241, βLeu248, βAla250, βAla316, βIle318 and βAla354, with its amino group in H-bond distance to the βTyr202 OH and the βVal238 backbone carbonyl. The ring nitrogen is in H-bond contact to βGlu200 and βTyr202 through a water molecule. One morpholino group points towards the nucleotide-binding site, with the ether oxygen connected to two water molecules that establish an H-bond network to the side chains of Asn101 of α-tubulin, to Lys254 of β-tubulin, to the alpha and gamma-phosphates of the nucleotide and to the backbone carbonyl of Ser178 of α-tubulin. ( d ) Overlay of the BKM120 binding region in αβ-tubulin in the context of a microtubule (‘straight' tubulin conformation, grey; PDB ID: 1JFF ) and in αβ-tubulin bound to BKM120 (orange).

Article Snippet: Cell-free tubulin polymerization assays were carried out with kit #BK006P from Cytoskeleton (Denver, USA) according to the manufacturer's instructions.

Techniques: Binding Assay

Journal: Nature Communications

Article Title: Deconvolution of Buparlisib's mechanism of action defines specific PI3K and tubulin inhibitors for therapeutic intervention

doi: 10.1038/ncomms14683

Figure Lengend Snippet: ( a ) Chemical formulas and schematic orientation of BKM120 regioisomeric derivatives MTD265 (PDB ID 5M8G) and MTD265-R1 (PDB ID 5M8D) in tubulin. ( b ) Phospho-Histone H3-positive A2058 cells triggered by increasing concentrations of MTD265 (grey) or MTD265-R1 (blue; % of total cells, n =3, mean±s.e.m.). ( c , d ) Structural overlay of amino acid side chains relevant for pyrimidine core ring interactions with BKM120 (orange), MTD147 (red), MTD265 (grey) and MTD-265-R1 (sky blue) in stick representation. The indicated water molecule is oriented towards the GTP-binding site ( c ) Visualization of βMet259 and βAla316 interactions with the pyrimidine core of MTD265 and MTD-265-R1 (core C–H protons shown in black). ( d ) βLys352 cation in proximity to pyrimidine core π-system of MTD265 and MTD-265-R1. The βLys352 side chain is fully resolved in crystal structures of BKM120, MTD265 and MTD147, but is poorly defined in MTD265-R1 complex beyond the δCH2 of βLys352 (yellow spheres and cloud denote poorly defined atoms).

Article Snippet: Cell-free tubulin polymerization assays were carried out with kit #BK006P from Cytoskeleton (Denver, USA) according to the manufacturer's instructions.

Techniques: Binding Assay

Journal: Nature Communications

Article Title: Deconvolution of Buparlisib's mechanism of action defines specific PI3K and tubulin inhibitors for therapeutic intervention

doi: 10.1038/ncomms14683

Figure Lengend Snippet: ( a ) BKM120 targets PI3K and tubulin proportionally. A concentration increase of BKM120 does therefore not change PI3K/tubulin targeting ratios, while combinations of selective PI3K inhibitors (such as PQR309) and potent microtubule-targeting drugs (MTDs) allow a flexible access to PI3K inhibition and perturbation of microtubule dynamics. ( b ) PI3K inhibitors are typically administered daily (dosing schedule in green), while microtubule targeting drugs are usually given in 1–3 week intervals (dosing schedule in red) for a limited time only.

Article Snippet: Cell-free tubulin polymerization assays were carried out with kit #BK006P from Cytoskeleton (Denver, USA) according to the manufacturer's instructions.

Techniques: Concentration Assay, Inhibition

Journal: Cell reports

Article Title: The STRIPAK complex is required for radial sorting and laminin receptor expression in Schwann cells

doi: 10.1016/j.celrep.2025.115401

Figure Lengend Snippet:

Article Snippet: The following primary antibodies were used: mouse anti-β-Actin 1:1000 (Santa Cruz sc-47778), mouse anti-β-tubulin 1:2000 (Sigma-Aldrich T4026), mouse anti-β-dystroglycan 1:500 (Leica Biosystems NCL-β-DG), rabbit anti-Ccm3 1:250 (Proteintech 10294–2-AP), rabbit anti-Cdc42 1:250 (Cell Signaling 2462), rabbit anti-Egr2/Krox20 1:500 (kindly shared by D. Meijer), rabbit anti-GAPDH 1:10,000 (Sigma-Aldrich G9545), rabbit anti-GST tag 1:1000 (Proteintech 80006–1-RR), mouse anti-GST tag 1:1000 (Santa Cruz sc-138), rabbit anti-His tag 1:1000 (Cell Signaling 2365S), rabbit anti-His tag 1:50,000 (Cell Signaling 2366T), goat anti-integrin α6 1:250 (Santa Cruz sc-6597), rabbit anti-integrin b1 1:250 (Cell Signaling 4706), rat anti-integrin b4 1:250 (Abcam ab25254), mouse anti-Mob4/Phocein 1:250 (Santa Cruz sc-137229), rabbit anti-Mst1 1:500 (Cell Signaling 3682), rabbit anti-Mst2 1:500 (Abcam ab52641), rabbit anti-p-Mst1/2 1:250 (Proteintech 28953–1-AP), rabbit anti-NF2 1:500 (Cell Signaling 6995), rabbit anti-p-NF2 1:500 (Cell Signaling 1328), rabbit anti-Oct6/Pou3f1 1:500 (kindly shared by D. Meijer), rabbit anti-Pak1 1:500 (Cell Signaling 2602), rabbit anti-p-Pak1 1:500 (Cell Signaling 2601), mouse anti-Rac1 1:250 (EMD Millipore 05–389), mouse anti-Rac1 1:250 (Cytoskeleton, Inc. ARC03), rabbit anti-Rac1 1:500 (Thermo Fisher Scientific PA1–091), rabbit anti-Rac1 1:500 (Proteintech 24072–1-AP), rabbit anti-Sox10 1:250 (Cell Signaling 89356), mouse anti-StrepII tag 1:250 (Thermo Fisher Scientific MA5–37747), mouse anti-STRIP1 1:250 (Origene TA502314), mouse anti-striatin-1 (Santa Cruz sc-136084), rabbit anti-striatin-3 1:100 (Atlas Antibodies HPA004636), mouse anti-striatin-3 (Novus Biologicals NB110–74572), rabbit anti-striatin-4 (GeneTex GTX133282), rabbit anti-Yap 1:250 (Cell Signaling 4912), rabbit anti-Yap 1:250 (Cell Signaling 14074), rabbit anti-Yap/Taz 1:250 (Cell Signaling 8418), rabbit anti-p-Yap 1:250 (Cell Signaling 13008), rabbit anti-p-Taz 1:250 (Cell Signaling 59971).

Techniques: Generated, Virus, Recombinant, SYBR Green Assay, Protease Inhibitor, Plasmid Preparation, In Situ, BIA-KA, Mutagenesis, Software

Journal: bioRxiv

Article Title: Opposing motors provide mechanical and functional robustness in the human spindle

doi: 10.1101/2021.03.02.433652

Figure Lengend Snippet: (A) Schematic illustrations of contractile microtubule (gray filament) minus end clustering by dynein, dynactin, and NuMA (left, green), and extensile sliding of antiparallel microtubules by Eg5 (right, purple) in the human spindle. Dynein/dynactin, targeted to minus end cargoes by NuMA, walks towards microtubule minus ends (denoted by “-“). Eg5 walks towards microtubule plus ends (denoted by “+”). Direction of motor stepping is indicated by green and purple arrows, and contractile and extensile stresses are indicated by gray arrows. (B) Schematic diagram of opposing motor (NuMA/dynein and Eg5) inhibition experiment in human spindles. Cas9 expression was induced by doxycycline addition (+DOX) for 4 days to knock out dynein heavy chain or NuMA. Cells were synchronized in G2 (with Cdk1 inhibitor RO-3306) for 0.5 days before imaging, released into mitosis, and Eg5 was acutely inhibited during imaging with 5 µM STLC. See also . (C) Representative timelapse confocal images of an RPE1 DHC-KO cell stably expressing GFP-tubulin (gray, maximum intensity projection of 5 planes) with SiR-DNA labeling chromosomes (cyan, single plane), starting as a turbulent spindle. After 5 µM STLC addition to inhibit Eg5 (time 0:00), the turbulent spindle recovers bipolarity, but does not progress to anaphase. Scale bar = 5 µm. (D) Representative timelapse confocal images of an RPE1 NuMA-KO cell stably expressing GFP-tubulin (gray, maximum intensity projection of 5 planes) and mCherry-H2B (cyan, single plane), starting as a turbulent spindle. After 5 µM STLC addition to inhibit Eg5 (time 0:00), the turbulent spindle recovers bipolarity and progresses to anaphase. Scale bar = 5 µm. (E) Schematic illustration of spindle length and width measurements. (F) – (H) Length (F), width (G), and aspect ratio (length/width; (H)) of control (-DOX), turbulent NuMA-KO, and bipolar NuMA-KO+STLC spindles. Spindle dimensions were measured after establishment of bipolarity (control, NuMA-KO+STLC) or 45 min after the start of imaging (NuMA-KO). Data in (F)-(H) include the same 49 (control), 36 (NuMA-KO), and 75 (NuMA-KO+STLC) spindles pooled from ≥ 3 independent experiments. ****, p < 0.00005; n.s. = not significant, two-sample t-test. Lines represent mean ± s.d. (I) Outcomes 90 min post-STLC addition to NuMA- and DHC-KO turbulent spindles. Without STLC addition, DHC-KO and NuMA-KO spindles remain turbulent. After STLC addition, most spindles establish bipolarity. (J) Percentage of bipolar spindles entering anaphase within 90 min of STLC addition, with and without 500 nM of the MPS1 inhibitor reversine to bypass the SAC. DHC-KO+STLC cells enter anaphase after reversine addition, consistent with DHC-KO+STLC cells experiencing a SAC-dependent metaphase arrest. (K) Spindle outcomes in NuMA-KO cells 90 min after STLC addition, with luciferase (Control), Kif15, or HSET RNAi knockdown or 500 nM latrunculin A to disrupt actin. Kif15 and HSET are required for turbulent spindles to recover bipolarity in the absence of NuMA and Eg5, and F-actin is not. See also and . For (I)-(K), number of spindles is indicated on each bar; cells pooled from ≥3 independent experiments. ****, p < 0.00005, n.s. = not significant, Fisher’s exact test.

Article Snippet: Chromosomes were labeled in the inducible DHC-KO cell line ( ) by incubating cells in 1 µM SiR-DNA and 10 µM verapamil (CY-SC007, Cytoskeleton Inc.) for 60 min prior to imaging.

Techniques: Inhibition, Expressing, Knock-Out, Imaging, Stable Transfection, DNA Labeling, Luciferase