EMBO/sd-character-level-ner huggingface dataset:
Figure 4A. Representative spinning disk confocal live-cell image series of MT-flux in U2OS cells stably co-expressing PA-GFP-α-tubulin (cyan) and mCherry-α-tubulin (red) treated with indicated siRNAs. White arrowheads highlight poleward motion of the photoactivated regions due to MT-flux. Scale bars, 10 µm. Time, min:sec. B. Quantification of the impact of the MT-crosslinking proteins on MT-flux in U2OS PA-GFP/mCherry-α-tubulin cells transfected with respective siRNAs. Graph represent MT-flux values with mean ± SD. N (number of cells, number of independent experiments): siControl (49, 5), siPRC1 (45, 3), siNuMA (40, 3), siHSET (37, 3), siHSET + siNuMA (39, 3). C. Quantification of the impact of the motor activity of HSET on MT-flux in U2OS cells stably expressing mEOS-α-tubulin treated with control or HSET 3′UTR siRNAs in presence or absence of the respective RNAi-resistant GFP-HSET constructs. Graph represent MT-flux values with mean ± SD. N (number of cells, number of independent experiments): siControl (23, 3), siHSET 3′UTR (33, 3), siHSET 3′UTR + HSET WT (29, 5), siHSET 3′UTR + HSET N593K (30, 4). D. Representative kymographs of the photoactivated spindles displaying asynchronous flux motion (split of the two red dashed lines towards individual poles) upon RNAi-mediated depletion of MT-crosslinkers. E. Percentage of cells with asynchronous flux movements F. Model illustrating the role of MT-crosslinking activities of NuMA and HSET in uniform distribution of poleward forces across the mitotic spindle.
Figure 5(A) Violin plot of Itgb1 expression levels in fibroblasts from murine wounds. Raw scRNA-seq data are derived from (Haensel et al., 2020, Data ref: Haensel et al 2020). (B) UMAP plots of ACTA2 and ITGB1 expression of fibroblasts in human wounds. Raw scRNA-data are derived from (Davis et al. 2020, Data ref: Davis et al, 2020). (C) IF for β1 integrin (red) and αSMA (green) on wound tissue sections at day 17 post-wounding. White boxes denote zoomed regions depicted in right panels. Scale bar: 20 μm. (D) Quantification of the number of αSMA+ β1 integrin+ cells. WT, N=3; TK, N=3 biological replicates. Unpaired t-test performed comparing WT to TK. (E) Wound area measurements in WT and Itgb1cKO mice. WT, N=5; Itgb1cKO, N=6 biological replicates. Two-way ANOVA performed comparing WT and Itgb1cKO mice. (F-K) Reepithelization, granulation tissue formation, and vascularization in WT and Itgb1cKO mice. (F) Representative images of keratin 5 (Krt5, red) stained wounds at day 14 post-wounding. White boxes denote zoomed regions depicted in right panels. Scale bar, 500 µm. (G) Quantification of epidermal thickness. WT, N=4; Itgb1cKO, N=6 biological replicates. (H) Immunofluorescent staining for CD31 (red) and nuclei (blue) on wound tissue sections at day 14 post-wounding. White boxes denote zoomed regions depicted in right panels. Scale bar, 20 μm. (I) Quantification of CD31+ area per visual field normalized to WT mice. WT, N=6; Itgb1cKO, N=6 biological replicates. (J) Polarized light images of picrosirius red stained wound tissues at day 14 post-wounding. Red: collagen fibers. White boxes denote zoomed regions depicted in right panels. Scale bar, 50 µm. (K) Quantification of collagen fiber percent area normalized to the average area in WT controls. WT, N=6; Itgb1cKO, N=6 biological replicates. (L) Quantification of collagen fiber width normalized to the average width in WT controls. WT, N=6; Itgb1cKO, N=6 biological replicates. D
miR-155-induced autophagy promotes the co-localization of BCG with autophagosomes by suppressing Rheb expression.Figure 9(A) RAW264.7 cells were transfected with a plasmid expressing Rheb for 24 h, and then incubated with DMSO or BafA. for 2 h. The expression levels of Rheb and LC3 were detected by Western-blot. Values of LC3-II/β-actin ratios are indicated below the representative blot. (B and C) RAW264.7 cells were co-transfected with control or miR-155 mimic together with a control plasmid or a plasmid expressing Rheb for 24 h, and then infected with Texas Red-labeled BCG for 1 h. The co-localization of BCG and MDC-labeled autophagosome was detected by confocal microscopy. Arrows indicate Quantification of BCG co-localization with autophagosomes described in B is shown (C). D) RAW264.7 cells were co-transfected with control or miR-155 mimic together with a control plasmid or a plasmid expressing Rheb for 24 h. Cells were infected with BCG for 1 h, and washed for three times to remove extracellular mycobacteria. Intracellular mycobacterial viability was determined by CFU assay at the indicated timepoints. Data are shown as the mean ± SEM of three independent experiments. *, p<0.05; **, p<0.01; NS, not significant.
Figure 2Influence of AK2 cysteines on the AK2 redox state. Cells expressing single cysteine to serine mutants of AK2-HA (isoform A) were lysed after NEM treatment, and analyzed by inverse redox shift assay using mmPEG12, SDS-PAGE and immunoblot against the HA tag. AK2C42S and AK2C92S are present in their completely reduced state indicating presence of a disulfide bond between both cysteines. Crystal structure of AK2 (pdb entry 2C9Y). In the crystal structure, a disulfide bond between C42 and C92 is visible with about 50 % occupancy, while 50 % of the Cys42/92 residues are in the reduced state. This disulfide bond is far away from the active site of AK2. The figure was created using PyMOL. Influence of AK2 cysteines on cellular localization. Cells expressing single cysteine to serine mutants of AK2-HA (isoform A) were fixed and analyzed by immunofluorescence. The colocalization of AK2-HA variants with Mitotracker was quantified using Cellprofiler (Pearson's correlation coefficient). C42 and C92 are critical for mitochondrial localization of AK2. The C40S mutant exhibits significantly decreased colocalization with mitochondria. A Kruskall-Wallis rank sum test/ Dunn-test was performed. Numbers of analysed cells are indicated in the plot. *** represents p-value <0.001 compared to wild-type. The black horizontal line represents the median. Data information: Scale bars: 10 μm. Model for AK2 import and oxidative folding.
Figure 3(A) 293T cells were co-transfected with HA-GRWD1 (1.6 ug) and RPL5-FLAG (2.4 ug) or RPL11-FLAG (2.4 ug) as indicated for 42h and subjected to immunoprecipitation with anti-FLAG antibody. Immunoprecipitates (IPs) and 3.125% of inputs were immunoblotted with the indicated antibodies. *, immunoglobulin light chains. (B) Lysates from untransfected 293T cells were immunoprecipitated with anti-GRWD1 antibody or control IgG. Immunoprecipitates (IPs) and 2.7% of inputs were immunoblotted with the indicated antibodies. (C) HCT116 cells were treated with 5nM actinomycin D for 12 h or left untreated and subjected to immunoprecipitation with anti-GRWD1 antibody or control IgG. Immunoprecipitates (IPs) and 3.5% of inputs were immunoblotted with the indicated antibodies. (D) GST-RPL11 or GST alone was incubated with purified GRWD1 and bound proteins analyzed by immunoblotting with the indicated antibodies. I, input. P, pull-down. (E) Cell lysates were prepared from 293T cells transfected with wild-type (WT) HA-GRWD1-FLAG (12 µg) or various N-terminal truncated mutants of HA-GRWD1-FLAG (12 µg) for 42h, and then subjected to GST pull-down assay with purified GST-RPL11 or GST. Bound proteins were analyzed by CBB staining (GST and GSR-RPL11) and immunoblotting with the indicated antibodies. *, non-specific bands. (F) Schematic representation of WT GRWD1 and N-terminal truncated mutants used in (D) and following studies. (G) HCT116 cells were transfected with RPL11-FLAG expression vector (0.56 ug) or empty vector (0.56 ug) for 24 h and then treated with 5 nM actinomycinD or vehicle (PBS) for 12 h. The cells were first extracted with Triton X-100 to remove nucleoplasmic proteins, double-immunostained with anti-GRWD1 antibody (green) and anti-FLAG M2 antibody (red), and counterstained with DAPI. Scale bar, 20 um.
a) Representative photographs of Bax/Bak−/− MEFs treated with etoposide.figf1(a) Representative photographs of Bax/Bak−/− MEFs treated with etoposide. Bax/Bak−/− MEFs were treated with 20 μM etoposide in the presence of PI (2 μM) for the indicated times, and were analysed under a phase-contrast and fluorescence (PI) microscope. (b, c) Reduced viability of Bax/Bak−/− MEFs after exposure to etoposide. WT (circles) and Bax/Bak−/− (squares) MEFs were treated with 20 μM etoposide in the presence (closed symbols) or absence (open symbols) of 100 μM zVAD-fmk. Then cell viability was measured by the PI staining (b) and CTB assay (c), and expressed as a percentage of the initial value without etoposide. Data are shown as mean ± s.d. (n = 4). (d) Reduced viability of etoposide-treated Bax/Bak−/− MEFs as assessed by proliferation assay. Bax/Bak−/− MEFs were either not treated (0 h) or were treated with 20 μM etoposide for 12 and 24 h, then all cells were recovered and 5,000 cells were reseeded. Viable cell numbers were measured on the indicated days by the CTB assay. Results were normalized by adjusting the day 0 value. n = 4. e) Reduced viability of Bax/Bak−/− MEFs after exposure to etoposide and staurosporine, as assessed by clonogenicity assay. MEFs were treated with etoposide (20 μM) or staurosporine (1 μM) at the indicated times, collected, and 2,000 cells were seeded in the normal medium. After 1 week, colonies were counted. n = 4 f-i) Induction of autophagy in Bax/Bak−/− MEFs by etoposide. (f) Electron micrograph (×14,800) of Bax/Bak−/− MEF treated with etoposide (20 μM) for 18 h. Representative features of Bax/Bak−/− MEFs that have received no treatment (NT; that is, are healthy) are also shown (NT: ×14,000). (g) In magnified photographs, a large number of autolysosomes/autophagosomes (left: ×26,000) were observed, but the mitochondria were unaffected (right: ×17,000). (h, i) Punctate GFP-LC3 fluorescence in Bax/Bak−/− MEFs treated with etoposide. GFP-LC3-transfected cells were incubated with and without etoposide (20 μM) for 24 h (h) or the indicated times (i), and then examined by fluorescent microscopy. (h) Representative photographs of healthy (NT) and etoposide-treated Bax/Bak−/− MEFs are shown. (i) The percentage of cells with punctate GFP-LC3 fluorescence was calculated relative to all GFP-positive cells. Data are shown as mean ± s.d. (n = 4).
Figure 42D-tSNE representation of 1,247 single cells isolated from naïve (blue) and LPS-treated mice showing two distinct subpopulations among the 770 cells isolated from LPS-injected mice (n = 703, red; n = 67, yellow). Venn diagram showing 732 genes uniquely upregulated in the "main LPS" cluster (red) and 241 genes exclusively increased in the "subset LPS" (yellow) compared to their corresponding controls (blue) (FDR<0.05). A total of 274 genes were shared between the two LPS populations. Venn diagram showing 1055 genes uniquely downregulated in the "main LPS" cluster (red) and 29 genes exclusively decreased in the "subset LPS" (yellow) compared to their corresponding controls (blue) (FDR<0.05). A total of 87 genes were shared between the two LPS populations. Heatmap showing examples of specific genes mainly up-regulated in "main LPS" (Manf) or "subset LPS" (Ash1l) and down-regulated in "main LPS" (Mef2c) or "subset LPS" (Lamp1) overlaid on the 2D-tSNE space. Bars represent log2 (Count+1). Gene set enrichment analysis (GO, top 10 biological processes) of 99 down-regulated and 397 up-regulated genes distinguishing cells in "subset LPS" versus "main LPS" (FDR<0.05).
Figure 8(A, B) Fibroblast proliferation was assessed by Edu incorporation assay. Endogenous Fstl1 was ablated by siRNA. NRCFbs were cultured in 0.5% FBS condition for 48 hours to synchronize the cell cycle. EdU (10μM as the final concentration) was added into media at 4 hours before harvest. Error bars represent mean ± SEM (n=5, each group). Statistical analysis was performed by unpaired t-test (2-tailed). Two independent experiments were performed. (B) Effect of exogenous Fstl1 on cardiac fibroblast proliferation. Cells were cultured in FBS 0.5% media for 24 hours. Recombinant Fstl1 (50ng/ml) or vehicle were added to 2% FBS-containing media and cultured for 48 hours. EdU was added into media at 4 hours before harvest. Error bars represent mean ± SEM (n=7, each group). Statistical analysis was performed by unpaired t-test (2-tailed). Two independent experiments were performed. (C) Fstl1 promoted fibroblasts proliferation was diminished by PD98059. PD98059 (5nM) was added 30 min prior to recombinant Fstl1 stimulation (50ng/ml). The cells were cultured for 48 hours, and EdU was added into media at 4 hours before harvest. Error bars represent mean ± SEM (n=4-10, per treatment group). Statistical analysis was performed by one-way ANOVA and Tukey multi comparison test. Two independent experiments were performed. (D) Schema of the role of Fstl1 in infarct repair. Fstl1 is upregulated by TGF-β1 in infarcted heart and it contributes to the proliferation and migration of fibroblasts into the infarcted site and border zone. These actions increase the number of myofibroblasts (MyoFB) in the infarcted lesion. In turn, fibroblasts and myofibroblasts synthesize ECM components including collagens and fibronectin, and protect the infarcted heart from rupture.
Figure 1Depiction of the experimental setting. A biotinylated DNA oligonucleotide is immobilised onto a surface plasmon resonance (SPR) CM5 chip via biotin-streptavidin interaction. RAD51 protein is injected over the DNA-coated SPR matrix to measure polymerisation kinetics. Throughout this period, association and dissociation of RAD51 take place simultaneously. Following protein injection (stop), running buffer is injected to measure dissociation kinetics. Wild-type (WT) RAD51 SPR curves for ssDNA dN-50 and dsDNA dN-50p. RAD51 was injected at 150 nM in the presence of 2.5 mM ATP (pH 7.5) and 10 mM CaCl2. The normalised mean number of WT RAD51 bound to respective DNA oligonucleotides (N) are plotted versus time, as measured by SPR, following the equation N = S / (L * (MRAD51 / MDNA)), where S is the signal in RU units (1 RU ~ 50 pg/mm2), L is the amount of DNA ligand immobilised onto the experimental flow cell (RU), MRAD51 is the molecular weight (kDa) of RAD51 (~ 37 kDa) and MDNA is the molecular weight (kDa) of the immobilised DNA molecule.
Figure 1(A) Acyl-RAC assay of HEK293T cells transfected with the indicated plasmids for 24 h. Data information: EtOH: ethanol; HAM: hydroxylamine; 2-BP: 2-bromopalmitate (B) Acyl-RAC assay of HEK293T cells transfected with the indicated plasmids for 24 h. Data information: FL: full length; N: N-terminal domain; C: C-terminal domain (C) Click chemistry was applied to detect endogenous cGAS palmitoylation in RAW264.7 cells. Data information: PA: palmitic acid; 17-ODYA: 17-octadecanoic acid. (D and E) In vitro palmitoylation assay for the indicated proteins. NBD-Palm-CoA: (N-[(7-nitro-2-1,3-benzoxadiazol-4-yl)-methyl] amino) palmitoyl-CoA. The recombinant cGAS protein used in the assay was indicated by Coomassie blue staining. (F) LC-MS/MS analysis of palmitoylated peptides of cGAS. (G) Acyl-RAC assay of HEK293T cells transfected with the indicated plasmids for 24 h. Data information: HAM: hydroxylamine (H-I) THP-1 cells were treated with DMSO or 2-BP (50 μM) (H) or palmitic acid (100 μM) (I) for 12 h. Six hours after transfection with HT-DNA (2 μg/mL), cGAMP was extracted and quantified by cGAMP ELISA. Data information: 2-BP: 2-bromopalmitate Data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; ns, not significant; **, P˂0.005; ***, P˂0.001 (J) THP-1 cells were treated with palmitic acid (0, 50 μM, or 100 μM) for 12 h before a cGAMP bioassay. Data information: Data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; ns, not significant; **, P˂0.005; ***, P˂0.001 BMDMs were treated with palmitic acid (0, 100 μM, or 200 μM) for 12 h and transfected with HT-DNA (2 μg/mL) for 6 h before RT-qPCR analysis of Ifna4 (K), IFNb1 (L) expression. Data information: Data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; ns, not significant; **, P˂0.005; ***, P˂0.001 BMDMs were treated with palmitic acid (0, 100 μM, or 200 μM) for 12 h and transfected with HT-DNA (2 μg/mL) for 6 h before RT-qPCR analysis of , Cxcl10 (M) and Rantes (N) expression. Data information: Data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; ns, not significant; **, P˂0.005; ***, P˂0.001 (O) L929 cells were treated with BSA and palmitic acid (100 μM) and transfected with HT-DNA (2 μg/mL) for the indicated times before immunoblotting analysis with the indicated antibodies.
Figure 7Wildtype myosin is phosphorylated in early sporozoites allowing the generation of optimal force transduction and gliding motility. Dephosphorylation is also important for optimal force generation as S19D shows lower force and speed. Non-phosphorylated myosin still allows sporozoite gliding but at reduced speed with too little force generated for efficient salivary gland invasion. Disruption of the interaction of the N-terminus with the Switch I and II (E6R mutation) has similar impact as constitutive phosphorylation as mimicked by S19D.
Figure 1A. Schematic representation of the type I IFN signaling pathway in human cells. B. Stimulation of A549/pr(ISRE).eGFP.A1 cells with 1000 IU/mL of IFN-α2 for 16h results in high and homogeneous expression of eGFP as determined by fluorescence microscopy (left panels, scale bars indicate 300μm), and flow cytometry (right panel). The FITC channel was used to monitor eGFP levels by flow cytometry, and AU refers to arbitrary units. Data are representative of at least two biological replicates. C. A549/pr(ISRE).eGFP.A1 cells were transduced for at least 10 days with lentivirus pools expressing Cas9 and sgRNAs targeting the indicated host genes. eGFP levels following 16h of IFN-α2 treatment (1000 IU/mL) or mock, were determined by flow cytometry. Data are representative of at least two biological replicates. D. Workflow overview of the genome-scale loss-of-function screen for essential IFN signaling components using the full GeCKOv2 CRISPR-Cas9 library. E. 1/αRRA scores from two biological replicates of the genome-scale screen. Dotted lines represent the significance cut-offs for each replicate. Genes identified as significant in both screens are highlighted.
Figure 1A. Experimental scheme of antagomiR-132 and miR-132 mimic injections into the lateral ventricle of 2-month old APPPS1 mice. B. Semi-quantitative PCR of miR-132 and negative control miRNAs in the hippocampus of antagomiR-132-injected mice (ant-132) in comparison to control-injected animals (aCSF and scramble) at six months of age. Sample size, n=9 per group. C. FISH of miR-132 and negative control miR-124 in the hippocampus of ant-132- and scramble-injected mice. Scramble probes were used as FISH negative controls. Scale bar, 500μm. D. Semi-quantitative PCR of miR-132 and miR-212 in the hippocampus of 3-month old miR-132 mimic-injected mice (miR-132) compared to animals injected with a negative control oligonucleotide (Ctr). Sample size, n=6 per group.
Figure 6Retinal slices from MOG/CFA-injected and CFA-injected SypHy mice were stimulated by applying a 25mM K+-containing depolarization solution for 1min (Fig. 6A). In response to depolarization, we observed a strong increase in fluorescence (Fig. 6A) that can be best fitted by a double-exponential curve (B). Amplitudes of fast and slow release (together with the respective time constants) of the first depolarization response are plotted in C)
Fig.Figure 5A. Survival curves of A53T α-synuclein TG mice, with LAG3 knockout, heterozygous LAG3 expression, or LAG3 WT. Median survival was shortest for α-synuclein TG LAG3‑/‑ at 239 d, followed by α-synuclein TG LAG3+/- at 260 d and α-synuclein TG LAG3+/+ at 268 d. The survivals of ASYNA53T LAG3‑/‑, LAG3+/- and LAG3+/+ mice were similar (Mantel-Cox log-rank test, p-value = 0.165). Mice were euthanized and dissected in the late-stage symptomatic phase, which would inevitably result in death within a week. None of the control LAG3‑/‑ α-synuclein WT mice died over the course of the experiment. B. Immunostaining for hyperphosphorylated α-synuclein aggregates (pS129) and aggregated protein (Thioflavin S) in sections of end-stage symptomatic mice; no obvious difference in terms of staining pattern or number of stained cells were apparent in midbrain or brain stem. Scale bars represent 1 mm (sagittal section) and 100 µm (panel). C. Immunofluorescence staining and quantification of pS129-positive α-synuclein inclusions in hippocampal slice cultures (HSCs) at 5 weeks post-seeding with 350 µM PFF. Scale bars represent 500 µm (overview), and 100 µm (insets). Shown is mean ± SEM and individual values are shown; n = 6 cultures per group; two-way-ANOVA revealed for LAG3 F(1, 20) = 0.0294; p = 0.8656; A53T F(1, 20) = 36.42, p < 0.0001; interaction F(1, 20) = 0.0062, p = 0.9382. Bonferroni's correction for multiple comparisons revealed p = 0.9973 for LAG3 WT vs. KO in A53T TG and p > 0.9808 for LAG3 WT vs. KO in A53T WT. D. Immunofluorescence staining and quantification of Thioflavin S-positive α-synuclein inclusions in HSCs at 5 weeks post-seeding. Scale bars represent 500 µm (overview), and 100 µm (insets). Shown is mean ± SEM and individual values are shown; n = 5-6 cultures per group; two-way-ANOVA revealed for LAG3 F(1, 19) = 1.972, p = 0.1763; A53T F(1, 19) = 62.49, p < 0.0001; interaction F(1, 19) = 1.586, p = 0.2231. Bonferroni's correction for multiple comparisons revealed p = 0.1373 for LAG3 WT vs. KO in A53T TG and p > 0.9999 for LAG3 WT vs. KO in A53T WT.
Figure 6A Left, time lapse confocal images of LimE in single cells following RacGEF1ΔN recruitment, induced by rapamycin addition at time 0. Right, temporal profile of normalized mean LimE intensity at cell cortex (mean±s.e.m., n=20 cells). B Time lapse confocal images of LimE at the basal surface of a giant cell, which recruits RacGEF1ΔN to membrane induced by rapamycin at time 0. C T-stack of LimE in the region outlined by the colored line box in B. D Right, kymographs of LimE along a line across giant cells after RacGEF1ΔN recruitment. Top left, confocal image with a dotted line as an example used to make kymographs. White arrows in image and kymographs point to examples of actin puncta. Bottom left, box plot of lifetime of puncta (red bar indicates median, n=100 puncta from 10 cells). All scale bars above represent 20 μm. E Cartoon highlighting positive feedbacks in CEN. F Simulations of the model in e, showing the CEN (top) and STEN (bottom) activity, before and after the feedback is altered (perturbation) at time 0. G The CEN activity stacked in time showing how the waves become diffuse after the perturbation is introduced.
Figure 2TUNEL assays on eye and brain sections of stage (st) 30 medakafish control and MO-injected embryos reveal a decrease in the number of apoptotic cells in both hccs-MO/miR-181a/b-MO- and cox7b-MO/miR-181a/b-MO-injected compared to hccs-MO- and cox7b-MO-injected embryos. Scale bars are 20μm. TUNEL-positive cells/eye. n≥5 eyes for each model. Caspase assays show restored levels of caspase-3 and caspase-9 activities in hccs-MO/miR-181a/b-MO- and cox7b-MO/miR-181a/b-MO-injected embryos with respect to hccs-MO- and cox7b-MO-injected embryos. n≥5 embryos for each model.