EMBO/sd-character-level-ner huggingface dataset:
Triple KD organoids show improved growth in ovarian cancer medium.Figure 4In long-term 3D culture triple KD organoids show loss of growth capacity and premature growth arrest compared to the controls as indicated by the representative growth curves of FT234. Scale bar: 500 µm. Growth curves and phase-contrast images of triple KD organoids grown in OCM compared to FTM reveal successful rescue of long-term growth capacity. Scale bar: 500 µm. Levels of DNA damage (yH2AX) and apoptosis (cleaved caspase-3, PARP1) do not differ among the different media as shown by representative western blots comparing triple KD organoids and their controls. Triple KD (p53/PTEN/RB) organoids are characterized by a HGSOC gene expression signature as revealed by microarray analysis comparing WT and KD organoids grown in either OCM or FTM. Differential expression determined by dual-color microarray for 2 biological replicates was significant for all genes with p < 0.00005. Differential expression of stemness- and differentiation-related genes of triple KD organoids grown in OCM vs. FTM. Fold-changes were derived from microarray data and indicate and an increase in stemness (CD133, SOX2, MYCN) and a drop in differentiation (OVGP1, PGR, FOXJ1) under OCM conditions. Differential expression determined by dual-color microarray for 2 biological replicates was significant for all genes with p < 0.05. FOXJ1 expression determined by qPCR was significantly diminished in triple KD organoids grown in OCM compared to FTM, suggesting a decrease in differentiation capacity. Data represent the mean ±SEM from technical triplicates for two independent knockdown cultures. Proportion of ciliated cells (detyrosinated Tubulin; dtyrTub) is significantly reduced in KD organoids under OCM growth conditions, confirming inhibition of differentiation as illustrated by confocal images (Scale bar: 50 µm). The quantification plot depicts the mean ±SEM from 3 independent biological replicates, based on quantification of the average number of ciliated cells per counted nuclei. 1000 cells were counted per individual experiment. *p < 0.05, two-sided Student's t-test.
Design and optimization of glucose, acetate, and oxygen sensors.Figure 1(a) Scheme for sensor design including (left to right): computational design and DNA chip oligo library synthesis, insertion into a plasmid reporter, FACS enrichment, and screening of select mutants in the presence (black) and absence (white) of stimulus. All three sensors were synthesized on a single chip (indicated by the colors) (b) Design of the promoter library. The location, number, and name of promoter elements are shown. The permutations included different constitutive core promoters (blue) flanked by random spacers (orange). Single operators (colored bars) were varied across the ranges shown with single nucleotide resolution. When two operators were included, they were inserted at multiple sites and the distance between them was varied by up to 6 bp from each site (c) Shown are the responses of the glucose sensor promoter (PgluA7), a negative control lacking the CRP operator (PgluA7*), and a constitutive promoter (BBa_J23101) to the presence (+) and absence (-) of glucose (d) Shown are the responses of the oxygen sensor promoter (PfnrF8), a negative control lacking the FNR operator (PfnrF8*), and a constitutive promoter (BBa_J23101) to the presence (+) and absence (-) of oxygen (e) The orthogonality of the sensors is shown. The averages and standard deviations for these data are provided in Appendix Figure S5 Shown are the schematics and responses for the glucose sensor The response functions (center) are shown for each sensor (black circles) compared to promoter variants where the operators are removed (PgluA7*, PfnrF8*) (open circles) text). Representative cytometry florescence distributions for Figures 1f Shown are the schematics and responses for th oxygen sensors Horizontal error bars in the PfnrF8 response reflect one standard deviation of three DO measurements Representative cytometry florescence distributions for Figure 1g Shown are the schematics and responses for th acetate sensors For the acetate sensor, the response of the sensor is shown in unmodified E. coli MG1655 with glnL intact (open diamonds). The dynamics of induction are shown (right graph) where cells are induced at the time indicated by the dashed line (see text). Representative cytometry florescence distributions for Figure 1h are shown i
ATG9A interacts with an ULK1-independent ATG13 complex that includes ATG101.Figure 2(A) Schematic representation of ATG13 mutations used in the study. (B) HA-ATG9A-BirA* was expressed in HCT-116 ATG13 WT, ATG13 KO or ATG13 KO cells reconstituted with WT ATG13 or ATG13 ∆HORMA. Cells were grown in full DMEM media, treated with 50 µM biotin for 12 hrs, followed by detergent lysis and incubation with streptavidin resin. The graph on right shows quantification of normalized ATG101 infrared signal. Mean ± SEM, n=3 (biological replicates). Significance measured using RM one-way ANOVA test followed by Fisher's LSD tests. (C) Cells were treated as in panel B but included reconstitution with ATG13 ∆2AA mutant. The graph on right shows quantification of normalized ATG101 infrared signal. Mean ± SEM, n=3 (biological replicates). Significance measured using RM one-way ANOVA test followed by Fisher's LSD tests. (right). (D) HA-ATG9A-BirA* was overexpressed in WT and ULK1/2 Double KO MEFs. Cells were subjected to streptavidin pulldown and immunoblotting with indicated antibodies. The graph on right shows quantification of normalized ATG13 infrared signal. Mean ± SEM. n=3 (biological replicates). Significance measured using one-sample t-test compared to hypothetical mean of 1 (right). ns=p>0.05, *=p≤0.05, **= p≤0.01, ***=p≤0.001, ****= p≤0.0001.
Figure 3A) Gene ontology (GO) analysis of tissue expression of up- and down-regulated genes in Id1KO ESCs as compared to wild-type ESCs. B) Western blot analysis of ID1 and ZRF1 expression in wild-type and Id1 KO ESCs upon Zrf1 depletion. C) Overlap between misregulated genes in Id1 KO ESCs, genes significantly affected by Zrf1 depletion in Id1KO ESCs (identified by gene expression analysis), and Polycomb bound-genes in ESC (identified by ChIP-sequencing analysis). D) GO analysis of tissue expression of 642 genes identified as Polycomb targets misregulated in Id1KO ESCs, which are significantly affected by Zrf1 depletion. E) Heatmap analysis of Zrf1-regulated Polycomb genes whose expression is significantly enriched in brain and spinal cord. F) mRNA fold-changes of Otx2, Pax6, Sox4 and Sox11 in Ctrl ESCs, Id1KO ESCs, and Zrf1-depleted Id1KO ESCs. SD is representative of three independent experiments. ** P < 0.01 (paired t-test) represents comparison with Ctrl ESCs at the corresponding time point. G) ZRF1 ChIPs at Otx2, Pax6, Sox4 and Sox11 promoters in Ctrl ESCs, Id1KO ESCs, and Zrf1-depleted Id1KO ESCs. SD is representative of three independent experiments. ** P < 0.01 (paired t-test).
Figure 4(a-c) Whole-population in situ structures of the 32-nm CPA repeat from pig (a), horse (b), and mouse (c) sperm. Panels (i), (ii), (iii), and (iv) are cut-through views of the lumens of the C1 (i and ii) and C2 (iii and iv) microtubules. Microtubules are shown in grey and microtubule protein densities are colored individually.
Actin filament oxidation removes their protections from cofilin-induced disassembly.Figure 5A. Time-lapse of actin filaments constantly exposed to nGr-Tpm1.8 (yellow), WT mCh-cofilin-1 (blue) and S3D-cofilin-1, and to MICAL1 from time t=100s onwards. Here we mixed WT with an excess of S3D-cofilin-1 to mimic cellular conditions in which most of cofilin-1 is inhibited by phosphorylation. While Tpm prevents cofilin from binding to non-oxidized filaments, MICAL1 rapidly oxidizes actin, allowing cofilin to bind and sever filaments. B. Summary of the results. Different mechanisms can simultaneously down regulate the activity of cofilin (here cofilin phosphorylation and protection by Tpm). Actin oxidation is a rapid means to cancel these protections without, for example, the need to activate a large concentration of cofilin.
Figure 6Localization of FUS in R495X_N2A cells (R495X), and wild-type N2A cells (WT). Cells were fractionated to separate nucleus and cytoplasm. Equal proportion of cell extracts from nuclear and cytoplasmic fractions were immunoblotted with indicated antibodies. Interactions between FUS and U1 snRNP in the R495X_N2A cells (R495X) and wild-type N2A cells (WT). Total cell lysates were immunoprecipitated with anti-U1-70K antibody or a control antibody (cont), and immunoblotted with indicated antibodies. Effects of the R495X mutation on four categories of polyA sites. Four categories of polyA sites are comprised of (1) FUS-repressed (rep) /U1-repressed sites, (2) FUS-activated (act) /U1-repressed sites, (3) FUS-repressed/U1-activated sites, and (4) FUS-activated/U1-activated sites, according to Fig 4A. Fold change of each polyA site usage by the R495X mutation (R495X/WT) is shown in violin plots. Bars indicate the median and 95% confidential intervals for each category. *** p < 0.001, **** p < 0.0001, based on the Steel-Dwass test for comparing all 6 pairs of categories. Change in polyA site usage by the R495X mutation. Fold change of polyA site usage by the R495X mutation (R495X/WT) on the relative positions of all mouse coding genes is plotted. The average is shown in blue line. The standard error of the mean is shown in semi-transparent blue shade.
a) Sequence alignment of the FLIP α2 and α4 peptide sequences.figf4(a) Sequence alignment of the FLIP α2 and α4 peptide sequences. The red letters correspond to hydrophobic core residues. (b) At 12-16 h post-transfection with GFP-LC3, TREX-BCBL vector and TREX-BCBL-vFLIP cells were treated with doxycycline for 24 h, followed by incubation with 30 μM of the TAT, K-α2 or K-α4 peptide (top left) or the TAT, C-α2, or C-α4 peptide (bottom left) for an additional 12 h. Subsequently, autophagy was quantified as means ± s.d. of the combined results from three independent experiments (2 μM rapamycin treatment was included as a control). TREX-BCBL vector and TREX-BCBL-vFLIP cells were treated with doxycycline for 24 h, followed by incubation with 0, 30, or 50 μM of the TAT, K-α2, or K-α4 peptide (top right) or the TAT, C-α2, or C-α4 peptide (bottom right) for an additional 12 h. Trypan blue staining was then used to determine cell death (as a percentage). Data are mean ± s.e.m.; n = 200-300; three independent experiments; *P 0.01; **P 0.05. (c) At 12-16 h post-transfection with GFP-LC3, TREX-BCBL vector and TREX-BCBL-vFLIP cells were treated with doxycycline for 24 h, followed by incubation with 30 μM of the TAT, K-α2 or K-α4 peptide (top left) or the TAT, C-α2, or C-α4 peptide (bottom left) for an additional 12 h. Subsequently, autophagy was quantified as means ± s.d. of the combined results from three independent experiments (2 μM rapamycin treatment was included as a control). TREX-BCBL vector and TREX-BCBL-vFLIP cells were treated with doxycycline for 24 h, followed by incubation with 0, 30, or 50 μM of the TAT, K-α2, or K-α4 peptide (top right) or the TAT, C-α2, or C-α4 peptide (bottom right) for an additional 12 h and GFP-LC3 puncta were subsequently detected using an inverted fluorescence microscope. Scale bar, 5 μm. (d) KSHV-infected BCBL1 cells were treated with 30 μM of the K-α2 or the K-α4 peptide for 12 h and subjected to scanning electron microscopy. Scale bar, 50 nm. (e) TREX-BCBL-Vector and TREX-BCBL-vFLIP cells were treated with the K-α2 and the K-α4 (30 μM each) peptide for 12 h, followed by immunoblotting (IB) with anti-LC3 and anti-actin antibody. (f) NOD/SCID mice received an injection of 5 × 106 BCBL1-Luc cells, followed by intraperitoneal injections with 300 μg the TAT, K-α2 or Kα-4 peptide for three weeks (top three panels). After three weeks, a group of three mice treated with the TAT peptide was challenged with 300 μg of the K-α2 or Kα-4 peptide for an additional three weeks (bottom panel, see Supplementary Information, Fig. S15). Tumours were measured by in vivo bioluminescence imaging.
WT UPF3A can rescue NMD in full extent.Figure 7A Schematic representation of the UPF3A and UPF3B protein domains. Below are the respective mutated rescue constructs. B Western blot analysis of WT and UPF3B KO clone 90 with Luciferase and UPF3A KDs respectively. Monitored expression of the FLAG-tagged UPF3A and UPF3B rescue construct shown in (A). Rescue construct protein levels were detected with anti-FLAG, anti-UPF3A and anti-UPF3B (AK-141) antibodies. Tubulin serves as control (n=1). The asterisk indicates unspecific bands. C Quantitative RT-PCR of the samples from (B). For RSRC2 and SRSF2 the ratio of NMD isoform to canonical isoform was calculated. Data points and means are plotted as log2 fold change (log2FC) (n=3).
Convergent alterations in the phosphoproteome status after resveratrol and/or spermidine treatment.Figure 4.Convergent alterations in the phosphoproteome status after resveratrol and/or spermidine treatment. (A-C) Human colon carcinoma HCT 116 cells were treated for 2 h with vehicle (Co, control), 100-µM resveratrol (Resv), and 100-µM spermidine (Spd), alone or in combination (Resv + Spd). (A) Representative phosphoprotein arrays are shown. (B) Clustering analysis for the effects on protein kinase phosphorylation. (C) Representative immunoblots of selected kinases whose phosphorylation status was unaffected (PRKAA1, RPS6KB1, and acetyl-CoA carboxylase a [ACACA]) or affected by resveratrol or/and spermidine treatment (PTKB, AKT1, MAPK8, and CDKN1B), validating phosphoprotein array data. (D) Human colorectal carcinoma HCT 116 cells were transfected with a GFP-LC3-encoding plasmid, cultured in complete medium for 24 h, and then treated with either vehicle or the indicated dose of resveratrol or spermidine, alone or in combination, for 2 h. Quantitative data. Bars depict the percentages (means ± SD; n = 3; *, P < 0.05) of cells showing the accumulation of GFP-LC3 in puncta (GFP-LC3vac). GAPDH, glyceraldehyde 3-phosphate dehydrogenase.
COUP-TFs regulate atrial-specific ion channel genes KCNA5 and KCNJ3.Figure 5A, B mRNA expression of COUP-TFI and COUP-TFII following shRNA-mediated knockdown of (A) COUP-TFI or (B) COUP-TFII in hESC-atrial cardiomyocytes (AM) at day 30. C, D mRNA expression of ion channel genes KCNA5, KCNJ3 and KCNJ5 after knockdown of (C) COUP-TFI or (D) COUP-TFII in AM at day 30. E, F Schematic of NR2F binding sites in (E) KCNA5 and (F) KCNJ3 promoters.G, H ChIP-qPCR analysis at day 30 shows enriched binding of COUP-TFI and COUP-TFII to the promoter region of (G) KCNA5 and (H) KCNJ3, compared to IgG in AM.
Figure 3(A) Schematic of the experimental strategy to assess early formation of the retinal vasculature (P1-P28). (B) Retinal flat mounts of P28 mice injected with PBS, COCO or Flt1Fc are stained with IB4 (negative images of the fluorescent signal). Scale bar, 100 μm. (C) Quantification of vascular length and number of branchpoints (p-values are versus PBS treatment). Vessel length: **P=0.0019 (PBS vs COCO); *P=0.0128 (PBS vs Flt1Fc). Vessel junctions: **P=0.0073 (PBS vs COCO); *P=0.0302 (PBS vs Flt1Fc); (n=4). (D) COCO injections (P1, P7 and P14) do not result in ONL thinning in P28 retinas. Scale bar, 40 μm. (E) Quantification of apoptotic cells (cleaved caspase-3; CC3) in control and COCO-injected mice (p-values are versus PBS treatment). (n=4).
Figure 2Quantitative RT-PCR for myogenin (A) and Myoparr (B) during myogenesis of C2C12 cells, primary mouse myoblasts (growth medium, GM), and mouse embryonic skeletal muscle (S.K.). The x-axis shows days after differentiation induction or embryonic days. n = 3, mean ± SD. qRT-PCR showing increased Myoparr expression by MyoD in C3H10T1/2 fibroblasts. n = 4, mean ± SD. **p < 0.01 (unpaired two-tailed Welch's t-test). Treatment of recombinant TGF-β for 24 h decreased Myoparr expression in differentiating C2C12 cells. n = 3, mean ± SD. *p < 0.05 (unpaired two-tailed Student's t-test). Schematic diagram of the constructs used for luciferase assays. Relative luciferase activities of the indicated promoter in differentiating C2C12 cells by exogenous MyoD. n = 3, mean ± SD. **p < 0.01. (unpaired two-tailed Student's t-test). Relative luciferase activities of the indicated promoter with/without E-box mutations in differentiating C2C12 cells. n = 3, mean ± SD. **p < 0.01. (unpaired two-tailed Student's t-test). Relative luciferase activities of the indicated promoter with/without E-box mutations in differentiating C2C12 cells by TGF-β treatment. n = 3, mean ± SD. *p < 0.05. **p < 0.01. n.s., not significant (unpaired two-tailed Student's t-test).
Figure 7(A-B) Lathosterol and 24OHC measured by mass spectrometry in the brain of WT (n=6), R6/2-untreated (n=7) and R6/2-Chol (n=5) mice. Data represent mean ± SEM. (C-D) mRNA levels of hmgcr and fdft1 in liver and lung of WT (n=7), R6/2-untreated (n=8) and R6/2-Chol (n=4) mice. As no differences were found between R6/2 mice treated with saline or treated with empty g7-NPs, data were pooled. (E-F) mRNA levels of inflammatory genes in liver and lung of the of WT (n=7), R6/2 (n=4), R6/2-emp (n=4) and R6/2-Chol (n=5) mice.
a) Southern blot analysis of genomic DNA isolated from wild-type (WT, mAtg14L+/+) , mAtg14L+/− and knockout (KO, mAtg14L−/−) ES cells after digestion with PstI.figf3(a) Southern blot analysis of genomic DNA isolated from wild-type (WT, mAtg14L+/+) , mAtg14L+/- and knockout (KO, mAtg14L-/-) ES cells after digestion with PstI. Details of the probe are shown in Supplementary Information, Fig. S3. (b) Analysis of Atg14L protein in knockout cells. Lysates from WT, mAtg14L−/− ES cells and mAtg5−/− mouse ES cells were subjected to western blotting with the antibodies indicated. (c) The effect of Atg14L knockout on p62 turnover. WT, mAtg14L−/−, mAtg14L−/− + Atg14L, and mAtg5−/− ES cells were cultured in nutrient-rich (N) or starvation medium (S) for 3 h. Cell lysates were subjected to western blotting with the antibodies indicated. (d) Degradation of long-lived proteins is reduced in Atg14L knockout cells. WT, mAtg14L−/−, and mAtg5−/− ES cells were cultured in N or S medium or S medium with wortmannin (W, 100 nM) for 3 h and degradation of long-lived proteins was measured. The data are the mean ± s.d. of three independent experiments. (e) The effect of Atg14L knockout on LC3 turnover. WT, mAtg14L−/− and mAtg5−/− ES cells were cultured in N or S medium for 3 h in the presence or absence of E64d (50 μg ml−1) and pepstatin A (50 μg ml−1). Cell lysates were subjected to western blotting with the antibodies indicated. Full scans of the blots in b, c and e are available in Supplementary Information, Fig. S6.
Figure 6The figure shows the degree to which each variable differs between heterozygous SCA3 mice and wildtype controls for a given age. For each variable, we quantified the deviation of hetero­zygous mice from controls of the same age by calculating the effect size r of the group comparison (independent t-tests). An effect size of 0 indicates that the value in heterozygous mice is not different from controls, while an effect size of 1 would indicate strong abnormality. Note that the drop in the effect size of Nf levels from 12 months to 18 months thus does not imply a putative reduction of Nf levels, but rather the loss of the effect in mutants relative to controls, as controls show strong age-related Nf increases at 18 months of age. Negative effect size values were set to 0.
Figure 6(A) Experimental design to evaluate the virucide effect of FD20, in the presence or not, of other antibodies. Different concentrations and 20-time dilution were used to achieve 70% inhibition when the antibody is provided alone. The comparisons of neutralization groups (3 to 5) relative to corresponding conditions without antibodies allow evaluating the irreversible effect of FD20 on particles. Group 4 is normalized using Group 1; Group 3 and 5 are normalized using Group 2. (B) FD20 acts irreversibly on particles in the presence or absence of other mAbs. As described in (A), 5 different conditions were used to evaluate the effect of SARS-CoV-2 pp pre-incubation with mAbs. In some experiments, FD20 was mixed with other mAbs and synergic effects were observed. Inhibition rate was calculated relatively to infection without antibodies at the similar SARS-CoV-2 pp input (diluted 20 times or not, Group 2/1 in A). Mean ± s.d. are plotted (n = 3 biological replicates). p < 0.0001 (****) unless specified otherwise (one-way ANOVA with Tukey's test); ns, not significant. Source data is available online. (C-F) The destruction of SARS-CoV-2 S by FD20. (C) Negative-stain of FD20. (D-F) Negative-stain image (i) and 2D class averages (ii) of S alone (D), and S incubated with FD20 (E) or 5E1 (F) which is an unrelated mAb targeting a protein called Hedgehog (Maun et al, 2010). Bar = 100 nm. In D and F, red circles indicate typical side views of S. Results are representative of two independent experiments with two different S purification batches.
Immunofluorescence-based visualization of cell-types surrounding zebrafish thyroid follicles (A-D) Images show immunofluorescence labeling of thyroid gland from adult zebrafish.Figure 4(A-D) Images show immunofluorescence labeling of thyroid gland from adult zebrafish. Transverse sections were utilized for imaging. The organ was isolated from tissue-specific transgenic lines to allow marking of a particular cell-type adjacent to the thyroid follicle. Blood vessels were marked using Tg(kdrl:EGFP) (A), macrophages using Tg(mpeg1.1:mCherry) (B) and stroma using Tg(col1a2:mCherry) (C). Thyrocytes were labeled with pax2amKO2 expression in (A) and Tg(tg:nls-EGFP) expression in (B - C). (D) NFE was labeled using antibody against TP63 in sections of the thyroid gland isolated from Tg(tg:nls-EGFP) animals. Gills are marked based on their morphological appearance. DAPI labels nuclei. Scale bars: 10 µm (A - B), 50 µm (C - D).
Figure 5A. The gene-specific correlation between protein copy number (x-axis) and predicted protein copy number based on the RNA levels (RNA-based prediction) is shown for all the 55 genes and all 20 cell lines and tissues. B. The Pearson correlation between RNA and protein levels for the 55 genes in the nine cell lines and eleven tissues are shown as a direct comparison of RNA and protein levels (purple, RNA vs protein) and after introducing the gene-specific correlation factor (blue, RNA-based prediction vs protein). C. Density plot for the direct comparison between RNA and protein levels before and after introducing the RTP-conversion factor. The Pearson correlation using the RTP-conversion factor is improved substantially for all cell lines and tissues with a median Pearson correlation of 0.93