EMBO/sd-character-level-ner huggingface dataset:
A HeLa cells stably expressing GFP alone or GFP-FXR1 were immunoprecipitated using GFP-Trap beads (GFP-IP), analysed by Western blot and quantified (mean, *P < 0.05; N = 3).
D. Quantification of the number of CETN3 foci per spermatocyte. n = 30 for each meiotic prophase substage.
(E) Immunostaining of reticulon 3 (RTN3), a marker of dystrophic neurites, and Aβ plaques in coronal sections through the hippocampus of 6 month old 5xFAD, 5xFAD/KO, 5xFAD/ΔDD and 5xFAD/C259A mice. Scale bar, 40μm. (F) Quantification of RTN3-positive dystrophic neurite area in the hippocampus of 5xFAD mouse strains carrying different p75NTR variants as indicated. Histogram shows the percentage of Aβ plaque area that overlapped with RTN3 immunostaining (mean ± SEM, N=5 mice per group).
A Schematic representation of p73 isoforms. TAD, transactivation domain; DBD, DNA-binding domain; OD, oligomerization domain; SAM, sterile alpha motif domain.
(c) Knockdown of EndoB1 or Cdk5 expression abolishes MPP+-induced neuronal death. Data are means ± s.e.m.; n=8.
(A) Sequences of the Nrxn1β mutants used, color-coded as in Fig 1A, with residues previously mapped to bind CA10 indicated. Right, table summarizing properties of the recombinant variants: 'HS?' indicates if HS-modified when expressed alone (Fig 1B), 'Binds CA10?', indicates if found to bind CA10, according to (et al,Sterky 2017), and whether the HS modification is blocked by CA10 (this figure). Asterisk denotes non-covalent interaction (see discussion).
(D) Microglia infiltration is not sufficient to induce PC degeneration. C1.4 demonstrates numerous microglia marked by anti-F4/80 (red) in all layers of the cerebellum, including immediately adjacent to wild-type (GFP-positive) PCs (arrows). Despite this close approximation, no loss of wild-type PCs was detected by cell counting. The GFP transgene is apparently poorly expressed in microglia, as all microglia appear GFP-negative regardless of their genotype.
Three independent Chk1fl/fl mT/mG (coloured) and mT/mG (grey) Hoxb8-FL progenitor cell lines were transduced with a retroviral construct carrying Cre (pMIP-CRE-IRES-PURO) and monitored over time for GFP-expression. Shown here are three technical replicates per genotype. Additionally, Chk1fl/fl mT/mG Hoxb8-FL progenitor cells were FACS-sorted for GFP+ and dsRED+ cells 48h after transduction with the Cre-construct. Sorted cells were processed for western blotting using the indicated antibodies.
Immunostaining for VEGFR2 on Npr3-sCreER;Kdrflox/flox heart section from mice without tamoxifen treatment (No Tam).
A. Scheme of the assay to determine shRNA strand activities in the absence or presence of specific TuDs. Huh7 cells were co-transfected with the shRNA and the TuD encoded on the same plasmid, and a luciferase reporter with appropriate shRNA strand binding sites. bs, binding site.
D) All constructs analyzed in (E) were stably expressed in CENP-C knockout cells.
ChIP-qPCR detection of Pol II occupancy and histone modification status at the myogenin locus in Myoparr-depleted differentiating C2C12 cells. The data were normalized to input values. n = 3, mean ± SD. *p < 0.05. **p < 0.01 (unpaired two-tailed Student's t-test or unpaired two-tailed Welch's t-test).
D Expression-modulating effect of each SNP [log2(OR)] as measured in MPRA and validation experiments. OR were calculated using the median activity of allelic constructs and are presented with respect to the risk allele (luciferase: n=5, MPRA: n=12).
Representative histological sections of indicated lungs with PAO1 infection (5 × 106 CFU) for 6 hours. H&E staining. Scale bar, 1000 μm (upper panel) and 50 μm (lower panel).
Representative immunofluorescence analysis of caspase 3/7 activation in DMKG (2 mM)-treated CTNSWT, CTNS‑/-, and CTNSPatient cells for 24 hrs (n = 3).
A-C Slices showing lateral association between two plates and the corresponding 3D segmentations. D. Edge-to-edge interactions form cylindrical structures. Data information: Scale bars: 50 nm.
A. Fe content of whole plants. Plants with reciprocal grafts of wild-type (WT), HY5-RNAi (hy5) and HY5-over expression (HY5) were hydroponically grown under white light conditions with either Fe-sufficient (20 µM, +Fe) or Fe-deficient (2 µM, -Fe) conditions for 7 d.
G The pASDOG1::LUC reporter is silenced by the application of ABA, while mutation of TATA elements in the asDOG1 promoter (pASDOG1∆TATA::LUC) leads to attenuation of expression in the presence and absence of ABA.
D. A feedback control of APC/C by Plx1 and PP2A-B56 on Apc1-loop500. CDK phosphorylates Apc1-loop500 at T539 and S558 and promotes Plx1-binding onto Apc1-loop500 via its PBD. Two PBD interactions, possibly dimerisation of Plx1, may stabilise the complex between Plx1 and Apc1-loop500. Plx1-binding blocks PP2A-B56 recruitment to Apc1-loop500 and stimulates Apc3-loop phosphorylation, which may induce Cdk1-CyclinB-p9/Cks2 recruitment and subsequent Apc1-loop300 phosphorylation. Cdk1 recruited onto phosphorylated Apc3-loop promotes phosphorylation of T532, a residue important for the recruitment of PP2A-B56 on Apc1-loop500. PP2A-B56 recruitment promotes dissociation of Plx1 by competitive binding and by dephosphorylation of T532 and T539, which diminishes Plx1-mediated phosphorylation of Apc3-loop. PP2A-B56 may quickly dissociate from Apc1-loop500 once T532 is dephosphorylated, but Apc1-loop500 is phosphorylated again by Cdk1 while Cdk1 is active. The dynamic phosphorylation-dephosphorylation cycle may continue until Cdk1 is inactivated, allowing swift response of the APC/C during the cell cycle.
G. Representation of the BFP+/RFP+ cells proportions for increasing drug concentrations of either JQ1 or Salinomycin alone, or in combination. Blue bars: BFP+ cells proportion, Red bars: RFP+ cells proportion.
Venn diagram representing the overlaps of the up/down DEGs and gene lists for the GO term 'DNA repair' (biological process, GO: 0006281), using DAVID and Metascape. Only the commonly matched genes are shown. The genes that positively and negatively regulate HR are underlined in red and blue, respectively.
A. Cycloheximide (CHX) chase experiments of RPE-1 cells treated with the indicated siRNA for 48 hours and then either grown further asynchronously or arrested in S phase with 2 mM hydroxyurea (HU) or in G2 with 10 µM RO-3306 for 18 hours. 50 µg/ml CHX was added to the cells, samples were harvested at the indicated time points and analysed via SDS-PAGE and western blotting using the indicated antibodies for detection. Bottom: Representative blots. Asterisks indicate an unspecific band detected by the Fbxw5 antibody. Top: Quantification of MCAK/Uba2 signal intensity ratios normalised to time point zero. Error bars show standard deviation of 4 independent experiments and asterisks indicate p-value of a two-tailed unpaired Student's t-test (*P < 0.05, **P < 0.01, ***P < 0.001).
C) Representative traces of hERG activation (left), inactivation (middle), and deactivation (right) measured in HEK293 hERG cells under baseline conditions (black) and in the presence of 3 µM LUF7346 (red). Insets: voltage clamp protocols.
(A) Representative confocal image of brain parenchyma, four hours after intracerebroventricular injection of PKH26 labelled EVs (red). Astrocytes are stained with GFAP (white), nuclei with Hoechst (blue), and pan-cytokeratin (panCK; green) was used to label the choroid plexus. The dotted line shows the ventricular border and the white arrow heads point to EVs that crossed the ependymal cell layer.
(E) 25HC does not inhibit SARS-CoV-2 pseudovirus receptor binding. Calu-3 cells were treated with EtOH or 25HC (2.5 or 5 µM) for 24h prior to challenge by SARS-CoV-2 pseudovirus at 4 °C for 1h. Total cellular RNA was extracted and quantified for VSV-N by qPCR.
(B and C) NO donors decreased EGFP-LC3 vesicles in EGFP-LC3-transfected WT Bcl-2 and AAA Bcl-2 MEFs (C). Images were acquired by a confocal microscope (B). WT Bcl-2 and AAA Bcl-2 MEFs were analyzed separately.
Representative two-dimensional scatter plots constructed with overlaid dPCR data of the reference (VIC) and cMet (FAM) from one tumour without cMet amplification and one with cMet amplified. Dots represent results of independent PCR reactions in the wells of a digital PCR chip. Reactions in the bottom left corner (yellow) are negative for both targets, while the ones in the top right corner (green) are double positives. Reactions in the top left (blue) and bottom right (red) corners are positive for cMet and the reference targets, respectively.
(A-J) The small 28S (A) and large 39S (D) subunits are found in control (143B, blue lines) but absent in ρ0 cells (red lines), while subassemblies highlighted in color in the structural surface model (PDB 3J9M; Amunts et al., 2015) persist in the absence of ribosomal RNA. The relative changes for the individual components of the 28S (B) and 39S (C) subunits and migration profiles of the subassemblies as averages of its components (E-J) are shown using the same color code. Note that peaks at 30 - 60 kDa result from individual proteins rather than subassemblies. In (B-C) data are presented as mean ± SD (n=4). *p<0.05, **p<0.01, ***p<0.001, ns, not significant (Student's t-test).
(F) Western blot for GalNAc-T2 specific target and hemidesmosome component COL17A1.
(H) UPLC-MS/MS analysis revealed a reduction in triacylglycerol (TAG) content in Tnfaip2-/- EBs compared to WT EBs at the indicated time points after differentiation induction [n=3 independent cultures of EBs per time point; data of EBs on day-0 to day-3 of differentiation were statistically analyzed; mean centered group data were normally distributed and (P>0.05 as per Shapiro-Wilk test) and analyzed by one-sided t-test with Holm Sidak correction for multiple testing].
G. Hierarchical clustering of embryonic F4/80hi and CD11bhi cells based on 43 DE-genes in embryonic cells visualized in F. Heat map exhibits z-transformed log2-expression values from red to blue via white.
C) Confocal imaging of dystrophic neurites found in a postmortem tissue of a patient with FTLD-TDP-C. Dystrophic neurites were identified using TDP-43 (cyan), and TDP-43pS403/404 (magenta). Neurite markers were used to visualize neuronal projections (MAP2 for dendrites, PNF for axons; yellow and orange, respectively). D) 2D TEM (first row) of dystrophic neurites from FTLD-TDP-C, localized in postmortem human brain by correlative light and electron microscopy (also shown in Fig. EV5D). 2D projections of the central slices of reconstructed 3D tomograms (middle row) taken at higher magnification from regions within each aggregate show a sparse arrangement of filaments which are interspersed with vesicles (white asterisk). A similar arrangement of sparse filaments and vesicles is seen in a cross-section of a dystrophic neurite from FTLD-TDP-C (cross-section, also shown in Fig. EV5G). The positions of filaments selected for subtomogram analysis are shown within a single orthoslice from the same tomogram (colored dots, last row).
(A) Changes of Aβ40 relative from baseline values up to 3 months of daily dosing. Shown are means ± SD, n = 21-25 for pre-dose and day 91, and n = 2 - 7 for the intermediate time points.
A Sgs1-Dna2 complex binds first to a 5' DNA overhang assisted by RPA. At the DNA junction both helicases start to move unidirectionally on either of the strands. Due to the faster movement of Sgs1, this helicase powers the unwinding of the DNA duplex and causes the formation of a ssDNA loop in front of Dna2. Upon an occasional strand switch of Sgs1, the protein rewinds the DNA and moves towards Dna2. This leads to shortening of the loop. Upon encounter of Dna2, Sgs1 switches back to the original strand to power further unwinding.
glucose uptake (C) in HUVECs treated with control siRNA or siRNA targeting LDLR or Scavenger receptor B1 (SCARB1, SRBI) followed by 15 min stimulation with VEGF-B186. Data presented as mean ± SEM from representative experiments performed in triplicates. Statistical evaluation using one-way ANOVA and Dunnett´s multiple comparisons test, p-value: * <0.05, ** <0.01, *** <0.001 (compared to respective control).
(A) MEK inhibitors block starvation-induced p-ERK and Bcl-2. HMGB1−/− and HMGB1+/+ MEFs were starved in the presence or absence of 10 µM U0126 and 20 µM PD98059 for 6 h. Protein expression levels were assessed as indicated by co-IP or Western blotting.
C. MvcA interferes with MavC-induced UBE2N ubiquitination. Reactions containing the indicated combinations of proteins were allowed to proceed for 30 min and samples resolved by SDS-PAGE were detected by Coomassie Brilliant blue (CBB) staining. Note that MvcA (inclusion of MvcA with MavC, 7th lane. Compare to MavC alone in 3rd lane) but not the MvcAC83A mutant (8th lane) abolished MavC-induced UBE2N modification.
(B) Schematic of IL-33 full length and IL-33 cytokine domain constructs (top). Venn diagram of differential genes shared between RNA-Seq and ChIP-Seq results (bottom). For ChIP-Seq, Pam212 cells transfected with IL-33 full length versus IL-33 cytokine domain were compared. Any gene with a peak in HA-empty vector control was excluded from the final analysis.
(D, E) Flow cytometry profiles representing the levels of MPM-2 (D) and H3S10P (E) in WT and CDK2/4/6 knockout MEF in control conditions (Control, black) and after treatment with 50 μM P22077 for 4 hrs (USP7i, red). The experiment was performed twice using two different wild type and CDK2/4/6 KO MEF and one representative result is shown.
Cell viability measurements using Propidium Iodide staining for HeLa and CCNF K/O cells after treatment with Chk1i (LY2603618).
(B) Side‐by‐side diagrams of a healthy cell and a starved/stressed cell, showing the respective distribution of mTORC1 and TFEB in relationship to lysosomes, cytoplasm, and nucleus.
(C) SipB-induced structures were labeled with the ER marker Sec-61. COS-2 cells were cotransfected with plasmids encoding SipB-YFP and Sec61-CFP, and transfected cells were examined by confocal microscopy.
B) Excitation of the GCaMP5 reporter in AWA neurons could be observed through both lateral and top views but the top view was clearer and more suitable for quantification. Arrowheads: AWA neurons. Scale bar = 50 μm.
g, h, Western blotting analysis of protein levels of indicated proteins in MEFs with indicated genotypes in normal medium or subjected to 24 h serum starvation (SS), 50 nM bafilomycin A1 (Baf), 20 µM chloroquine (CQ) or 1 µM MG132. Quantified OFD1 level was normalized with alpha-tubulin. Similar results were observed in three independent experiments.
F, G Growth assays of untreated and tunicamycin-treated WT, ∆atg39/40, ∆snf7 and ∆snf7 ∆atg39/40 cells. Numbers indicate growth relative to WT cells based on the areas under the curves. Mean ± SEM, n = 3.
A. Expression of all analyzed gene transcripts in GRN-/- hiMGL treated with control isotype antibody, Ab1 or Ab2 in comparison to WT hiMGL. Data show the mean of four individual treatments and NanoString measurements. The mRNA counts for each gene were normalized to the mean value of all WT samples followed by a log2 transformation.
HEK293T cells transfected with HA-E2F1 Wild Type (WT) and HA-E2F1 lacking a CY motif (∆RxL) harvested for immunoprecipitation using HA antibodies. Immunoprecipitates were immunoblotted as indicated.
(J) PI analysis of CTRL and CX cells treated with CX-5461 in the presence and absence of metformin for 48 hours as indicated.
D The HR-B proximal Hsc70 binding site is essential for Hsc70/DnaJB1-mediated dissociation of HSE-DNA bound Hsf1.
B. Cell lysates from GFP-TgAtg8 parasites were subjected to a centrifugation at 100,000 g to separate the soluble fraction (high speed supernatant, HSS) from the membrane fraction (high speed pellet, HSP). The faster migrating form of GFP-TgAtg8 is exclusively present in the membrane fraction as revealed by Western blot analysis after urea SDS-PAGE using anti-GFP
D RT-qPCR measurements of transposon RNA levels. Double: ago4‐6 ago6‐2 double mutant. Actin 2 was used as an internal control. RNA levels in the mutants are relative to those in the wild‐type (Col‐0). Means ± SD are shown, n = 3.
(B) Macrophages were electroporated with EGFP-Rab8A and RFP-Galectin-3. Cells were then treated with 1 mM of LLOMe and monitored by live cell imaging. Snapshots at the indicated time points after LLOMe addition are shown. Scale bar = 5 μm.
(D-G) DREADD activation by CNO injection selectively rescues major components of social attachment behavior in Shank2-/- mice: (D) grooming, two-way ANOVA, effect of genotype: *P=0.018, effect of treatment: **P=0.002, genotype x treatment interaction: ***P=0.001. (E) Crouching, two-way ANOVA, effect of genotype: P=0.091, effect of treatment: P=0.869, genotype x treatment interaction: P=0.663, (F) nest building, two-way ANOVA, effect of genotype: P=0.415, effect of treatment: P=0.341 genotype x treatment interaction: P=0.093, (G) Maternal interaction, two-way ANOVA, effect of genotype: *P=0.034, effect of treatment: P=0.149, genotype x treatment interaction: *P=0.045. Shank2+/+ vehicle injected n = 6, Shank2-/- vehicle injected n = 6, Shank2+/+ CNO injected n = 6, Shank2-/- CNO injected n = 7. Data information: All data are presented as mean ± SEM, NS: not significant.
The IgGsc-molecule was applied in escalating doses, with a starting dose of 20µg (patient 1) or 40µg (patients 2 and 3) to a maximum of approx. 2.6mg, as indicated. PSA values were monitored and T-cell activation was assessed by flow cytometry.
A-C Exponentially growing cell cultures were arrested in G1 with α-factor (αf) and released in YEPD supplemented with CPT (50 μM). (A) Western blot analysis with anti-Rad53 antibodies
(A) CRISPR-targeted follicular B cell proliferation after 3 days of CD40L stimulation. mCherry+ populations were quantified within individual DDAO peaks. N = 3 mice. P, statistical significance calculated by two-way ANOVA reached p<0.0001 for all proliferation peaks. Data information: All data show means ± SEM.
a) Gating strategy used for neuronal cell sorting. Live cells as determined by FSC/SSC gating were selected for CD184-APC-negative/low surface expression and subsequently separated for CD24-PE versus CD15/CD29/CD44 expression, detected in the FITC channel as indicated in the dot plots. Post-sort reanalysis shows representative samples of both fractions immediately after FACS enrichment, which were then plated for comparative in vitro analysis (phase contrast images. Bars, 50 μm).
(B) Decreased levels of Slc6a20a, but not Slc6a20b, mRNAs in the brain of Slc6a20a+/- (HT) and Slc6a20a-/- (KO) mice (P21-28), as shown by qRT-PCR analysis. (n = 4, 3, 3 mice for WT, HT, and KO; *P < 0.05, **P < 0.01, ns, not significant, one-way ANOVA with Bonferroni's test). The error bars represent SEM.
C. Active RAB13 pulldown assay from cells with CRISPR knockdown of RABIF using the indicated sgRNAs. n=3. Bars: mean ± s.e.m..
Reporter gene assays addressing expression of lacZ fusions under GlcN6P replete and depletion conditions. strains were grown in 96-well plates and exposed to various degrees of GlcN6P depletion elicited by Nva-FMDP. Cells were harvested at indicated times and the β-galactosidase activities were determined. Strains Z190 and the ∆qseF mutant Z196 are compared, both of which transcribe the glmY'-lacZ fusion solely from the σ54 promoter.
DNA-damage assessment in KSL from primary recipients and after two turns of replating. (D, F, H) Number of γH2AX foci in control-derived and Molm-14-xenograft-derived: (D) Primary recipient KSL, n=211 and 321, All cells were stained with phosphoH2axser139 and the nuclear stain Hoechst (blue), imaged using the GE/API DV widefield microscope (60X objective) to show the γH2AX foci (green) and counted using Imaris software.
E Average Ezh2 enrichment in WT (left) and SclKOmesoderm (right) for inactive enhancers (defined by having H3K4me1 and H3K27me3 modifications (Wamstad et al, ) and distance greater than 5 kb from TSS) and for Scl binding sites shows no Ezh2 enrichment at Scl binding sites.
D. Transmission electron microscopy images of H295R/TRSF-1 cells cultured in basal conditions or treated with Dox. ER-mitochondria contacts are indicated by white arrowheads. Scale bars, 200 nm. Right, quantification of the number of contacts normalized by the number of mitochondria and the percentage of mitochondria with ER contact sites is shown in basal conditions (white histograms) and after Dox treatment (black histograms) of cells (mean ± SEM; n=41 for basal and 42 for Dox-treated cells). ***p<0.001.
D. AURKA interacts with PCM1 in centriole-less cells. GFP-PCM1 or GFP-PCM1 was co-expressed with FLAG-AURKA in HEK293T cells treated with DMSO (control) or 500 nM centrinone B for 7 days. Complexes were precipitated with GFP-Trap beads. The initial sample and immunoprecipitated proteins were run on a gel and immunoblotted with antibodies against GFP and FLAG.
(G) Coomassie brilliant blue (CBB) staining and protein synthesis assays using the Cayman kit (601100) were performed in cells with or without GDH1. Western blotting (WB) was performed with the indicated antibodies. β-Actin was used as a loading control(left). The Click-iT HPG kit (C10428) is also used to detect newly synthesized proteins in cells with or without GDH1 (right). Data information: The data are represented as means ± SEM of three independent experiments and all statistical analyses were conducted using unpaired t-test. (**p < 0.01; ***p < 0.001.)
Analysis of the percentage of infolded nuclei in the hippocampus of Satb2flx/flx mice vs Satb2CamkCre mice. In Satb2flx/flx mice, the number of infolded nuclei was significantly higher in the CA1 area compared to the CA3 area (p = 0.000001) and DG (p = 1.8 E-12). In Satb2CamkCre mice, the number of infolded nuclei in the CA1 area was significantly reduced compared to the corresponding number in littermate controls (p = 1.9 E-09). No significant differences were observed in this number in the CA3 and DG between Satb2CamkCre mice and floxed controls (n = 4 mice, two-way ANOVA, significant interaction, F2,18 = 47.81, p = 0.00001, simple main effects analysis, CA1 area, Satb2flx/flx vs CKO mice p = 1.9 E-09, CA3 area, Satb2flx/flx vs CKO mice p = 0.909, DG, Satb2flx/flx vs CKO mice p = 0.262, adjustment for multiple comparisons: Bonferroni). Number of analyzed nuclei: Satb2flx/flx mice: 469 (CA1), 225 (CA3), 665 (DG); Satb2CamkCre: 508 (CA1), 224 (CA3), 575 (DG). Data are presented as mean ± SEM, ***p < 0.001.
(E, F) Images of colonic epithelial spheroids isolated from control and Atg5VC mice grown in 5% CM+DAPT and stained for Muc2 (green: E) or with the lectin, UEA (red: F). Bars=20 μm.
Longevity assays of (CGG)90-EGFP; Tub5-GS (Log-rank Mantel-Cox test with Bonferroni corrections for multiple comparisons; n=110-219/genotype) flies with belle knockdown. Data Information: For all panels, * P≤0.05, ** P≤0.01, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All data in all panels are presented as mean ± SD (compiled from ≥3 replicates).
(L) Pearson's colocalization coefficient for IL‐1β and LC3. Pearson's coefficient was derived from three independent experiments with five fields per experiment, for a total of 15 fields contributing to the cumulative result. Figure source data can be found in Supplementary data.
A Epo-induced signaling upon AKT or MEK inhibitor treatment. Growth-factor deprived cells were pretreated for half an hour with AKT VIII or U0126, respectively, and subsequently stimulated with 5 U/ml Epo. PDI served as loading control.
A working model. Cholesterol‐enriched regions accumulate in the endolysosomal membranes of LSDs sequestering SNAREs in defined domains. This locks SNAREs in assembled complexes and reduces their availability to interact with dedicated adaptor components of vesicle coat, a process needed for SNARE re‐distribution between membranes. Consequently, the dysfunction of SNARE cycle decreases the rate of new fusion events.
(D) APEX2:RAB biotinylated proteins (streptavidin) are partially colocalized with EEA1 in HeLa cells, n=2 independent experiments. Scale bars: 10µm or 5µm in enlarged views.