EMBO/sd-character-level-ner huggingface dataset:
Scl binds to both its activated and repressed target genes in Flk1+ mesodermVenn diagram showing the number of Scl binding sites and overlap with Scl activated and repressed genes in Flk1+ MES (mesoderm) documents that Scl binds to both Scl‐dependent activated and repressed genes.Figure 1A Venn diagram showing the number of Scl binding sites and overlap with Scl activated and repressed genes in Flk1+MES (mesoderm) documents that Scl binds to both Scl‐dependent activated and repressed genes. B DAVID (Huang et al, ) GO enrichment analysis for Scl‐bound and activated or Scl‐bound and repressed genes shows enrichment of hematopoietic and heart‐related terms, respectively. C Gene expression heatmaps of selected genes from the bound and activated and bound and repressed groups show activation of key hematopoietic target genes and repression of key cardiac target genes in Scl‐expressing mesoderm as compared to Scl‐deficient mesoderm. Control [Scl+/hCD4, divided into Scl‐expressing (Scl+) and non‐expressing cells (Scl−)] and SclKOEBs are shown. D Scl and control IgGChIP‐seq tracks show examples of Scl binding sites near hematopoietic (Runx1 and Gata2) and cardiac (Gata4 and Gata6) genes in Flk1+mesoderm (MES). E Verification of Scl binding sites marked with asterisks in (D) using ChIP‐PCR, average enrichment of at least three independent biological experiments over negative control region (chr16: 92230219-92230338) with SEM are shown. F Verification of Scl‐dependent gene expression using qRT-PCR. Average of three biological replicates with SD are shown. G Venn diagrams show the number of potential 'extended activated' and 'extended repressed' Scl target genes by intersecting genes associated with Scl binding in Flk1+MES with Scl activated and repressed genes from day 4 EBs, E9.5 yolk sac, placenta and endocardium (Van Handel et al, ). H Heatmaps show Scl binding to majority of activated hematopoietic and repressed cardiac transcription factors and other proteins. See also Supplementary Fig S1 and Supplementary Table S1A-E.
uORFs and oORFs repress downstream reporter translation.Figure 5(A) Schematic displays uORF/oORF configurations for reporter experiments. GFP reporters contained variable uORF configurations: no uORFs, 1 uORF, 3 uORFs, 1 oORF, or 1 uORF in weak initiation context. TLS length (104nt) and polyA tail length (60A) was constant across all reporters, and TLS sequence differed only by single nucleotide changes at each uORF start codon (or two single nucleotide changes in the weak context reporter). Constructs (100pg) were coinjected with dsRed (150pg) into 1-cell-stage embryos and quantified at 24hpf. (B) Fluorescent microscopy images of representative embryos expressing each GFP reporter and the dsRed control 24 hours post injection. uORFs and oORFs repress downstream translation as predicted by analysis of endogeneous transcripts. Repression is observed in reporters with uORF/oORF-containing TLSs, but the effect is weaker for a uORF with a bad initiation context. Group pictures can be found in supplementary figure S2. (C) Barplot displays fluorescence quantification of 24h embryos injected with each reporter. GFP fluorescence intensity was normalized to dsRed intensity in each embryo, then mean fluorescence for each reporter was scaled relative to the no uORF reporter (the number of embryos measured for each reporter is displayed below the X-axis). Error bars display +/- 1 S.E.M. Reporter fluorescence was compared using unpaired two-tailed student's T-test and was significant for all comparisons: ** (p<0.01) - no uORFs vs. 1 weak context uORF (p=2.98e-3); **** (p<0.0001) - no uORF vs. 1 uORF (p=3.21e-9), 1 uORF vs. 3 uORFs (p=6.66e-5), 1 uORF vs. 1 oORF (p=7.65e-11), 1 uORF vs. 1 uORF weak context (p=3.24e-5)
Figure 5Left: Representative images of H1299 cells on 3D collagen wells with defined stiffness with NANOG (green) or DAPI (blue). Scale bars 10µm. Right: Quantification of NANOG:DAPI nuclear co-localization (upper graph) and total NANOG fluorescence intensity (bottom graph). Quantification of nuclear co-localization (n=300cells/experiment) is represented by Pearson's coefficient. Data information: Statistical significance was determined by Student's t-test (2-tailed) of n=3 experiments unless otherwise stated. Error bars represent the mean ± S.E.M. Representative immunofluorescence images show merge of NANOG (green), DAPI (blue) distribution in H1299control and H1299RASSF1A cells cultured on 2D glass. Scale bars 10µm. Right: Quantification of nuclear co-localization (n=200cells/experiment) is represented by Pearson's coefficient. Representative immunofluorescence images of CD133 in H1299control and H1299RASSF1A cells grown on 3D collagen wells with defined stiffness. Scale bars 10µm. Bottom: Quantification of n=200 cells/experiment. Data information: Statistical significance was determined by Student's t-test (2-tailed) of n=3 experiments unless otherwise stated. Error bars represent the mean ± S.E.M. Representative images of immunofluorescence staining for the pluripotency marker NANOG and β-catenin in three-dimensional spheroids embedded in collagen matrix (2mg/ml). Scale bars 50µm. Representative images of H&E and immunohistochemical staining for NANOG and YAP1 in primary lung tumours, (day 17). Scale bars 100µm. Right: Graph bars represent quantification of NANOG and YAP1 staining based on strong (3+, 2+) nuclear intensity (%) for at least 2 independent regions of n=4 H1299control and n=2 H1299RASSF1A primary tumours at day 17. Data information: Statistical significance was determined by Student's t-test (2-tailed) of n=3 experiments unless otherwise stated. Error bars represent the mean ± S.E.M.
ATP induces a gliosis in msEGCs A: Volcano plot showing significantly regulated genes between control and ATP-treated msEGCs.Figure 1A: Volcano plot showing significantly regulated genes between control and ATP-treated msEGCs. B: Visual representation of GO terms associated with enriched genes in ATP-treated msEGCs compared to control. C-F: Heat maps of indicated GO terms in ATP-treated msEGCs compared to control. G-I: qPCR analysis of indicated gliosis genes in ATP-treated EGCs. J: qPCR analysis of IL-6 in msEGCs that were treated for 6h with ATP. K: IL-6 protein levels in supernatants from msEGCs collected after 24h treatment with ATP.
Figure 73D reconstruction of representative images of ASM (A) or ceramide (B) staining in HeLa cells infected with Shigella WTor mock-treated, analyzed at 3 hpi. ASM, ceramide, Hoechst and Shigella staining were surface converted by voxel distance ASM enzymatic activity measurement in HeLa cells infected with Shigella-WT or mock-treated, analyzed at 3 hpi. The ASM enzymatic activity was determined in the membrane fraction corresponding to 3.0×105 cells per condition ceramide measurement in HeLa cells infected with Shigella-WT or mock-treated, analyzed at 3 hpi Ceramide is shown normalized to mock-treated cells Representative spinning-disk confocal images of colon tissue sections of non-infected (E and F) and Shigella infected (G and H) guinea pigs, collected at 4 hpi. E and G are montages of multiple image fields; dashed boxes in (E and G) are shown enlarged in (F and H), respectively Mean fluorescence intensity of ceramide signal in surface epithelial cells (outermost tissue layer) of non-infected or Shigella-infected guinea pig colon tissue sections Model depicting the effect of stress-induced host plasma membrane remodeling on infection by bacterial pathogens. Different stressors, including TNF-α stimulation and Shigella intracellular replication, induce the relocalization and activation of acid sphingomyelinase (ASM) to the host plasma membrane, leading to the conversion of sphingomyelin into ceramide. As a consequence of membrane remodeling, the binding of non-motile bacteria, such as Shigella, to host cells is inhibited. Motile bacteria, such as Salmonella, are able to scan the host membrane for the remaining permissive binding sites, and thus circumvent this defense mechanism
IL-1 signalling inhibition in MPSIIIA mice prevents memory deficits and hyperactivity.Figure 5Behavioural assessments and histological analysis of control and treated mice from figure 4 were carried out at 6 months of age in all groups, alongside WT x IL-1R1-/- and MPSIIIA x IL-1R1-/- mice Mice were placed in the centre of the Y-maze and allowed to explore freely for 10 minutes. The percentage of spontaneous alternations in the Y-maze were measured to assess working memory (n=10 mice per group). Data are expressed as mean ± STDEV and were tested by one-way ANOVA with Tukey's post-test; *P<0.05, **P<0.01 A one-hour open field test was performed and path length measured as an indicator of hyperactivity (n=10 mice per group). Data are expressed as mean ± STDEV and were tested by one-way ANOVA with Tukey's post-test; ***P<0.001. Symbols above bars are versus WT
Figure 1(A) Graph derived from two published data available in the PubMed GEO database (GSE6919 and GSE35988). The box charts depict the relative expression of ESM1 in benign, primary, and metastatic prostate cancer patients. The centre line donates the median value while the box contains the 25th to 75th percentiles of dataset. The whiskers mark the 5th and 95th percentiles, and values beyond these upper and lower bounds are considered outliers. (B) Relative ESM1 mRNA expression and ESM1 protein expression in two sets of human metastatic PCa cell lines. P: parental cells, M: metastatic cells. (C) Cell invasion assays of 22Rv1-M and PC3-M cells transfected with either Scramble-shRNA or ESM1-shRNA. The data are shown as the relative fold change of invasive cells compared with the shScramble group. Scale bar: 100 μm. (D) Representative images of lungs, livers, intestines, and kidneys from mice 8 weeks after orthotopical injection of 22Rv1-M cells transfected with either Scramble-shRNA or ESM1-shRNA. Scale bar: 0.5 cm. Tumors were removed and weighed. Quantitative summary of tumor luminescence in different metastases measured in photons/second are shown. (E) Formalin-fixed, paraffin-embedded tissue microarray sections of 59 normal prostate tissues and 65 prostate adenocarcinoma tissues with and without metastasis (n=16 and n=49, respectively) were stained with an anti-ESM1 antibody. Tissue-bound ESM1 is shown in brown. Scale bar: 50 μm. Arrowheads indicate positively stained nucleus of cancer cells. Plot representation of scores according to immunohistochemical expression of ESM1 in normal prostate tissue related to the prostate adenocarcinoma tissue with and without metastasis. The scores are calculated by intensity (score 1-3) x percentage (score 1-4) of stained cells. The line in the middle of the box is plotted at the median. The box extends from the 25th to 75th percentiles. Whiskers above and below the box indicate the 5th and 95th percentiles.
A stable TIP30/eEF1A1 ratio is maintained in homeostasis and compensated growth conditions.Figure 5Western blot analysis for TIP30, eEF1A1 and GAPDH in C57BL/6 WT mice 3 days (A, B), N=4 mice/group, 2 weeks (C, D), N=4 to 8 mice/group and 6 weeks (E, F), N=4 to 8 mice/group after TAC or sham surgery and their quantification. KO denotes TIP30 homozygous knock-out. (G, H) Western blot for TIP30, eEF1A1 and Actin in TIP30 Het mice 6 after TAC surgery and their quantification (N=4 mice/group). (I, J) Western blot for TIP30, eEF1A1 and Actin 2 weeks after sham or TAC surgery in AAV-Con or AAV-TIP30 treated C57BL/6 WT mice and their quantification (N=4 mice/group). A ratio of TIP30 and eEF1A1 expression was calculated for each condition.
Fig.Figure 2(A) Left: The ratio between the striatal and the cortical BDNF determined by quantifying the level of BDNF proteins at the cortex and the striatum of 55 day-old WT (n=8), Mecp2 KO (n=6), Mecp2 KO/HTTSD (mimicking the absence of phosphorylation) (n=4) and Mecp2 KO/HTTSA mice (mimicking constitutive phosphorylation) (n=5). Since striatal BDNF depends only on BDNF transport from the cortex, this ratio reflects BDNF transport through corticostriatal pathway (Mann Whitney test). Right: Quantitative analysis of phospho TrkB protein level in striatum of KO WT mice and KO HTTSD mice by immunoblotting. The relative expression levels of phospho TrkB were normalized against GAPDH and are presented as the ratio. (n = 6 mice per group) (Mann Whitney test) Middle: Quantitative analysis of PSD-95 protein level in striatum of Mecp2 KO/HTT WT mice and KO/HTTSD mice by immunoblotting. The relative expression levels of PSD-95 were normalized against GAPDH and are presented as the ratio. (n = 6 mice per group) (Mann Whitney test) Data information: Data are presented as the means ± SEM. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns = not significant. (B) Left: We investigated the behavior of Mecp2 KO mice at 35, 45, and 55 days of age and assessed their survival. Right: Mecp2 KO/HTTSD mice (n = 30) and WT mice (n = 17) had a significantly longer lifespan than KO (n=22) or KO/HTTSA mice (n = 21) (Kaplan-Meier survival test). Data information: Data are presented as the means ± SEM. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns = not significant. (C) Body weight of 10 WT, 24 KO, 32 KO/HTTSD, and 24 KO/HTTSA mice at P30 and P50 (one-way ANOVA with Tukey's comparison). Data information: Data are presented as the means ± SEM. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns = not significant. (D) Frequency of apnea of 9 WT, 10 KO, 14 KO/HTTSD, and 9 KO/HTTSA mice at P35 and P55. (Kruskal-Wallis test with Dunn's comparison). Data information: Data are presented as the means ± SEM. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns = not significant. (E) Mecp2 KO/HTTSD mice (n=19) performed as well as WT (n=17) at P35 on the accelerating rotarod test and continued to outperform Mecp2 KO (n=16) and Mecp2 KO/ HTTSA (n=13) at P55 (one-way ANOVA with Fisher's LSD test). Data information: Data are presented as the means ± SEM. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns = not significant. (F) Time before the onset of spontaneous locomotor activity of 17 WT, 20 KO, 19 KO/HTTSD, and 17 KO/HTTSA mice at P55. (Kruskal-Wallis test with Dunn's comparison). Data information: Data are presented as the means ± SEM. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001 ns = not significant.
Traction force maps and distributions of signaling components in amoeboid cells.Figure 4A: Sequence of snapshots of the LimE-GFP distribution and stress T for an amoeboid cell and the GFP-myo distribution for a separate amoeboid cell. Corresponding speeds are 7.4µm/min and 4.5µm/min. The sequences show both the phases of protrusion and retraction. White arrows represent the direction of motion. B: Spatially averaged LimE-GFP intensity as a function of time (green line), together with the basal area (black line) for the first cell in A. Inset: CF of the area and LimE-GFP intensity (blue) and of the area change rate and the LimE-GFP intensity (magenta). C: Basal area (black line) and total force F (blue line) as a function of time corresponding to the first cell in A. Inset: Temporal cross-correlation function (CF) of the area and the total force F (blue) and of the area change rate and F (magenta). The correlation within the shaded region is below the 95% confidence interval. D: Median shift in the CF of the area and F (blue symbols; N=66 biological replicates), the LimE-GFP intensity (brown symbols, N=18 biological replicates) and the GFP-myo intensity (yellow symbols, N=7 biological replicates). Values of these shifts were determined as 11.3 (3.8/15) s, -11.2 (-15.0/-7.5) s, and 7.5 (1.9/12.2) s. E: Median shift in the CF of the area change rate and F (blue symbols, N=52 biological replicates), the LimE-GFP intensity (brown symbols, N=17 biological replicates) and the GFP-myo intensity (yellow symbols, N=7 biological replicates). Data below the dashed line indicates cells for which no significant correlation was found. Shift values are -11.2 (-15.0/-9.4) s, 11.3 (7.5/11.3) s, and -26.3 (-30.0/-14.1) s. F, G and H: Kymographs for LimE-GFP intensity, T, and edge velocity along the cell outlines for the first cell of A. I, J and K: kymographs for GFP-myo intensity, T, and edge velocity along the cell outlines for the second cell of A. L and M: Time-averaged total force F as a function of the cell's area and time-averaged Fy as a function of time-averaged Fx (slope of fit shown as a dashed line: 0.86, r2=0.94). Markers indicate the different strains: AX2 LimE-GFP (>), AX2 GFP-myo (<), AX2 lifeAct-GFP (^) and engineered cells (o).
a,d)Venn diagram showing up or downregulated genes, (b,e) GO processes of open reading frames, (c,f) histogram of microarray data from Candida SC5314 cells exposed to IL-17A (10 ng) for 4 h (a–c) and 24 h (d–f).f2(a,d) Venn diagram showing up or downregulated genes, (b,e) GO processes of open reading frames, (c,f) histogram of microarray data from Candida SC5314 cells exposed to IL-17A (10 ng) for 4 h (a-c) and 24 h (d-f). Text and arrows: genes involved in TOR pathway at 4 h (c) and of hyphae-induced genes at 24 h (f). (g,h) TOR inhibition in cells treated with 10 ng ml−1 IL-17A, 15 nM rapamycin or vehicle (none) by western blotting after 4-h (g) or 24-h (h) exposure. i-n) Immunofluorescence of ATG8 in untreated (i-k) or IL-17A-treated (10 ng ml−1 for 4 h) (l-n) cells. Cells were red after TRITC-ATG8 staining (i,l), green after ConA staining (j,m), merged images (k,n). Mean values (% ATG8+ cells (merge); mean±s.d.): ATG8/none, 8.2±1.6; ATG8/IL-17A, 58.0±11.3 (P=0.002) (n=3). Scale bars, 10 μm. (o-r) Monodansilcadaverine (MDC) labelling performed on cells unexposed (o) or exposed to 1 (p) or 10 ng ml−1 (q) IL-17A for 4 h. Cells were magnified in the inset (r). Representative results from three independent experiments. The mean values (% hyphal cells with MDC-stained organelles (merge); mean±s.d.) were as follows: none, 9.5±3.2; 1 ng ml−1 IL-17A, 14.0±4.7; 10 ng ml−1 IL-17A, 56.2±18.71 (P=0.004, IL-17A 10 ng ml−1 versus none). Scale bars, 10 μm. (s,t) Quantitative real-time PCR of orfs. 19.4325, 19.130, RIC1 on cDNA from Candida SC5314 (s) or the TOR1-1/TOR1 mutant (t) strains exposed to vehicle (open column), 10 ng ml−1 IL-17A (black column) or 15 nM rapamycin (grey column) for 4 h. The actual P-values are indicated (two-tailed t-test) (n=3). (u,v) Intracellular (u) or extracellular (v) cAMP levels, vehicle (open circle), 10 ng ml−1 IL-17A (black square) or rapamycin (grey square). P0.05, IL-17A-treated versus untreated at 1 h and P0.01, IL-17A-treated versus untreated at 24 h (u), and P0.05, rapamycin-treated versus untreated at 6 h (v) (one-way analysis of variance Bonferroni post-test) (n=3). (w) orf. 19.5258 expression after 24-h Candida SC5314 exposure as in (n,o). Data are mean±s.d. (n=3). The actual P-values are indicated (two-tailed t-test).
Figure 6A-B. Immunohistochemistry of TH in coronal sections of the striatal region in mice treated with 6OH-DA and rIFN-β and quantification. C-D. Immunohistochemistry of TH in coronal sections of the substantia nigra in mice treated with 6OH-DA, with or without rIFN-β and quantification. E-K. Immunofluorescence in the striatal region in mice treated with 6OH-DA and rIFN-β for optineurin (E, quantified in F) and Tom20 (E), with quantification of individual mitochondrial size by mitochondrial section area (G). 8OHdG- (H-I), OxDJ1- (J-K), and DAPI-labeled nuclei. Scale bars equal 10 microns. L-M. PGAM5 and TH immunostaining (L) and quantification (M) in striatum from mice treated with 6OH-DA and rIFN-β. N. Percentage of right versus left forepaw use before and 21 days after injection with hSNCA (left hemisphere) and control lentivirus (CTL) or hSNCA and lenti-Ifnb (right hemisphere). Bars are mean + SEM. YYY p<0.001 by ANOVA and **p<0.01 by post hoc Tukey's multiple comparison correction. N=6/hSCNA-CTL and 8/hSCNA-Ifnb. O. Immunostaining of TH and human α-synuclein in SN. Scale bars equal 20 microns P. TH immunostaining in brains of rats injected with hSNCA (left hemisphere) and control lentivirus (CTL) or hSNCA and lenti-Ifnb (right hemisphere). Scale bar equals 1 mm. Q. Immunostaining of PGAM5 in brains of rats injected with hSCNA and control or hSCNA and Ifnb. Scale bars equal 100 microns. TH immunostaining in brains of rats injected with hSNCA (left hemisphere) and control lentivirus (CTL) or hSNCA and lenti-Ifnb (right hemisphere). Scale bar equals 1 mm. R. Quantification of P. Immunostaining of PGAM5 in brains of rats injected with hSCNA and control or hSCNA and Ifnb. Scale bars equal 100 microns. S. Quantification of Q. T. Correlation of levels of PGAM5 and TH in rat brains injected with hSNCA (left hemisphere) and control lentivirus (CTL) or hSNCA and lenti-Ifnb (right hemisphere) by Pearson correlation.
CN1.f5CN1.4mousecortical cells stably expressing inducible tau were treated with doxycycline (Dox, 1 μg ml−1) for 24 h. On the next day (a), the cells were washed twice with PBS and the media were replaced with Dox-deficient media with either vehicle, epoxomicin (12.5 nM, Epox), MG132 (7 μM) or 3-methyladenine (10 mM, 3-MA) for 24 h. Samples in first lane were from cells maintained in the presence of Dox without medium exchange. CN1.4 mouse cortical cells stably expressing inducible tau were treated with doxycycline (Dox, 1 μg ml−1) for 24 h. (b) Cells were treated with either chloroquine (50 μM, CQ) or bafilomycin A1 (10 nM, Baf A1) for 24 h. Samples in first lane were from cells maintained in the presence of Dox without medium exchange. (c) HEK293-TN cells were co-transfected with the plasmid expressing tau together either with siRNA of beclin-1 or scramble RNA as a control, which was kept for 48 h. (d) Stably transfected CN1.4 cortical cells were maintained in the presence of Dox (1 μg ml−1) to induce the expression of tau for 24 h, and subsequently treated with SFN (10 μM) for 12 h. The culture medium was exchanged for fresh media containing Dox (1 μg ml−1) but no SFN after washing with PBS. The cells were then incubated for an additional 18 h in the absence or presence of CQ (50 μM). The levels of tau phosphorylated at Ser262/Ser356 and Ser396/Ser404 were analysed by immunoblotting using the 12E8 and PHF1 antibodies, respectively. Tau, beclin-1 and LC3 were detected with the appropriate polyclonal antibodies. The relative molecular masses (kDa) are indicated to the left of each blot. (e) Bar graphs represent the relative optical density of phosphorylated tau, tau or LC3-II normalized with that of actin. n=4. Data shown are mean±s.e. and were analysed using Student's t-test. (*P0.05; **P0.01).