EMBO/sd-character-level-ner huggingface dataset:
Figure 3A, B The Na+ and K+ contents in the shoots and roots of DJ and osprr73 mutant plants with or without 180 mM NaCl treatment for 7 days. Na+ (A) and K+ (B) contents were measured with ICP method. Data represent means ± SD, (n = 3, biological replicates). (**) P ≤ 0.001 and (*) P ≤ 0.001 indicate significant difference by student t-test. The abbreviation of n.s. stands for no significant. C Ratio of Na+ to K+ was calculated with their respective content in (A) and (B). Data represent mean ± SD (n = 3, biological replicates). For each of biological replicates, 6 individual plants were measured. The asterisk represents significant difference among means by student's t-test with (*) P ≤0.05, and n.s. indicates no significant. D Four-weeks old seedlings of DJ and osprr73 were treated with 90 mM Na2SO4 for 14 d (middle panel) and recovered for additional 7 days (right panel). Scale bar, 5 cm. E Statistical analysis of survival rates with Na2SO4 treatment in (D). Data represent means ± SD. n = 3 biological replicates, 24 plants for each biological replicate. (***) P ≤ 0.001 indicates significant difference by student t-test. F The seedlings of DJ and osprr73 mutant were treated with 90 mM MgCl2 for 14 days (middle panel) and recovered for 7 days (right panel). Scale bar, 5 cm. G Statistical analysis of survival rates with MgCl2 treatment in (F). The survival rate of DJ and osprr73 plants in MgCl2 stress were calculated after recovery 7 days. Data represent means ± SD. n = 2 biological replicates, 24 plants of each replicate. H The seedlings of DJ and osprr73 mutant were treated with 180 mM mannitol for 36 days (middle panel) and recovered for 7 days (right panel). Scale bar, 5 cm. I The survival rate of DJ and osprr73 plants in mannitol stress. Data represent means ± SD. n = 3 biological replicates, 24 plants of each replicate. The abbreviation of n.s. stands for no significant generated by student t-test.
Figure 1A 58 Males were described in DECIPHER of which 24 carried a microdeletion, and 34 carried a microduplication. B Central nervous system (CNS) disease associations derived from the Open Target Platform. Association score ranges from 0 to 1, with 0 indicating no association, and 1 indicating full association. FXR2 has highest association with intellectual disability and epilepsy.
POLG mutations induced defects in respiratory chain complex I.Figure 7A: Complex I immunohistochemistry in the occipital cortex of a neurologically healthy control (a) and two patients with POLG-disease (b and c) (Scale bar, 20 µm). Patients have numerous complex-I negative neurons (examples marked by arrows). (d) mtDNA relative quantification in microdissected neurons from the occipital cortex of patients with POLG diseases (n=5) and neurologically healthy controls (n=5). Each point represents the mean value of three technical replicates from a pooled sample of 10 neurons. For the purposes of comparison, a control sample has been arbitrarily set to one. The medians of the two groups are compared by Mann-Whitney U test. Data are presented as mean (horizontal bars) ± SEM (vertical bars). B: Representative confocal images of immunostaining for mitocondrial complex I subunit NDUFB10 (green) and TOMM20 (red) in control, WS5A and CP2A NSCs (scale bars, 50 µm). Nuclei are stained with DAPI (blue). C-E: Flow cytometric measurements of mitochondrial complex I (C, n=4, technical replicates per clone), II (D, n=3, technical replicates per clone for control; n=4, technical replicates per clone for WS5A and CP2A) and IV (E, n=3, technical replicates per clone for control and CP2A; n=4, technical replicates per clone for WS5A) protein level in iPSC-derived NSCs. Expressed as specific complex I, II and IV level (total complex I, II, IV level/TOMM20). F-H: Flow cytometric measurements of mitochondrial complex I (F, n=4, technical replicates per clone), II (G, n=4, technical replicates per clone) and IV (H, n=4, technical replicates per clone) protein level in iPSCs. Expressed as specific complex I, II and IV level. I-K: Flow cytometric measurements of mitochondrial complex I (I, n=4, technical replicates), II (J, n=4, technical replicates) and IV (K, n=4, technical replicates) protein level in parental fibroblasts expressed as specific complex I, II and IV level.
Representative images for MLX immunofluorescence on C2C12 myotubes.Figure 4A Immunofluorescence for total MLX protein detection (red signal) performed on C2C12 cells treated with siRNAs against Mlx-γ (si-Mlx-γ), lnc-SMaRT (si-SMaRT), DHX36 (si-DHX36) or with a control siRNA (si-SCR). Cells were fixed two days after the switch to differentiation medium. Representative binary images of single confocal planes for MLX immunofluorescence are shown for each treatment. The inserts on the topside of the images sketch the MLX signal peaks in the nuclei (white stars) to highlight the variation of MLX staining in each condition. Dashed lines indicate the edge of the nucleus. B Histogram represents the fluorescence intensity ratio of the MLX protein signals in the nuclear (Nuc) and cytoplasmic (Cyt) compartment in the indicated conditions. About 50 cells from two independent experiments were analyzed Data are presented as the mean of two biological replicates (dots). C Venn diagram showing the overlap between genes deregulated upon lnc-SMaRT depletion and MLX targets [33], both in C2C12 samples. Genes at the intersection are those with opposite fold changes in the two depletion experiments. Only genes expressed in both systems were used to evaluate the overlap. Significance of overlap was evaluated using hypergeometric test.
Fig.Figure 4(A) Representative images of necrotic cell death (SYTOX orange) at 2-, 24- and 48-hours post exposure to 0.1μg/mL TcdB in HIOs. Scale bar = 250μm. (B) Quantification of necrotic cell death in HIOs. (C) Representative images of necrotic cell death (SYTOX orange) at 2-, 24- and 48-hours post exposure to 0.5μg/mL TcdB in kcHIEs. Scale bar = 250μm. (D) Quantification of necrotic cell death in kcHIEs. (E) Representative images of necrotic cell death (SYTOX orange) at 2-, 24- and 48-hours post exposure to 0.5μg/mL TcdB in bHIEs. Scale bar = 250μm. (F) Quantification of necrotic cell death in bHIEs.
IF1 is beneficial for ATP production even under OXPHOS conditions.Figure 9A) Mitochondrial ATP production rates in HeLa cells the presence and absence of IF1. Oxygen consumption rates (OCR) and extracellular acidification rates (ECAR) were determined with an automatic flux analyzer (Seahorse/Agilent). After monitoring basal respiration, oligomycin (1 µM), and rotenone plus antimycin A (Rot; 0.5 µM; AA, 0.5 µM) were added sequentially to determine glycolytic and mitochondrial ATP production rates. ~12 technical replicates per measurement, N=4 independent assays. B) Cytosolic ATP production rates. Each data point represents the mean ATP production rate of one well (~12 technical replicates per measurement, N=4 independent assays.). C) Determination of mitochondrial ATP levels with the fluorogenic dye ATP-red™ (5 µM, prestaining for 15 min). To normalize on mitochondrial mass, mitochondria were stained with MitoTracker™ Green (MTG, 100 nM for 30 min). Two technical replicates from same clones.
Figure 2(A) T6SS assembly in A. baylyi cells that are in contact with E. coli. T6SS+ A. baylyi cells lacking all known effectors (ΔEffectors tssB-sfGFP clpV-mCherry2) were mixed with E. coli cells (MG1655 Ptac-mRuby3) and incubated on LB agar plate for 2 h before imaging. Yellow arrows indicate sheath foci that are formed at the contact site with E. coli. Data information: Scale bars and time intervals are indicated. (B) Stable sheath foci formation in A. baylyi cells that are in contact with E. coli. A. baylyi cells lacking TagX (ΔtagX tssB-sfGFP) were mixed well with cells of E. coli (MG1655 Ptac-mRuby3) and incubated on an LB agar plate for at least 90 min before imaging. Yellow arrows indicate sheath foci that are stably present at the contact site with E. coli. Data information: Scale bars and time intervals are indicated. (C) Time-lapse 3D-SIM imaging of sheath dynamics (TssB-sfGFP) in capsulated A. baylyi BD4 cells. Data information: Scale bars and time intervals are indicated. (D) Time-lapse 3D-SIM imaging of sheath dynamics (TssB-sfGFP) in capsulated A. baylyi BD4 cells lacking TagX. Data information: Scale bars and time intervals are indicated.
Fig.Figure 6mRNA expression analysis of Il1b, Nlrp3 and Caspase1 (Casp1) of Gata6-WT and Gata6-KOmye pMФ stimulated for 3 h with 100 ng.ml-1 LPS, 10 µM beraprost, 10 ng.ml-1 IL-10, 5 µg.ml-1 αIL-10R or 5 µg.ml-1 isotype. Data are representative of at least 3 independent experiments. Western blot analysis (left) and quantification (right) of Gata6-WT and Gata6-KOmye pMФ stimulated for 6 h with 100 ng.ml-1 LPS, 10 µM beraprost, 10 ng.ml-1 IL-10 or 5 µg.ml-1 αIL-10R. Data are representative of 3 independent experiments. Caspase1 activity analysis of Gata6-WT and Gata6-KOmye pMФ stimulated for 16 h with 100 ng.ml-1 LPS, 10 µM beraprost, 10 ng.ml-1 IL-10, 5 µg.ml-1 αIL-10R or 5 µg.ml-1 isotype. n = 5 to 8 individual mice. Mean fluorescence intensity (MFI) of pro-IL-1β of Gata6-WT and Gata6-KOmye pMФ stimulated for 3 h with 100 ng.ml-1 LPS, 10 µM beraprost, 10 ng.ml-1 IL-10, 5 µg.ml-1 αIL-10R or 5 µg.ml-1 isotype for 16 h or freshly isolated. n = 6 to 13 individual mice. Data were log transformed before performing statistical analysis. mRNA expression analysis of Il10 and Tnf of Gata6-WT and Gata6-KOmye pMФ stimulated for 3 h with 100 ng.ml-1 LPS, 10 µM beraprost, 10 ng.ml-1 IL-10 or 5 µg.ml-1 αIL-10R. Data are representative of at least 3 independent experiments. Representation of the mechanism of action of the Gata6-PGI2-IL-10 active inhibitory signal on IL-1β processing.
Figure 3Top: same as the top part of Figure 2B. Middle/Bottom: Nuc/Cyto (middle) and IP/Input (bottom) ratios for variants of Jpx#9 in which the indicated sequence was introduced at the indicated position (aligned to the sequence on top) in either the WT or the mutated Jpx#9 context. Yellow, turquoise, and white arrows indicate the tiles mentioned in the text. The histograms on the right indicate the distributions of the values in each heatmap. Asterisks indicate positions where the Nuc/Cyto ratios of the mutated tiles are significantly different than those of the WT tile (Wilcoxon two-sided rank-sum test P<0.05). Nuc/Cyto and RIP/Input ratios for sequences containing the indicated number of changes in the overall number of CCC motifs relative to the WT Jpx#9 sequence, when considering all the Jpx#9 variants in NucLibC. Ratios computed based on three replicates. Boxplots are as in Figure 1C.
The formation of Bax-rings is strictly correlated to cytochrome c release in apoptotic wild type cells.Figure 3A, B Three-color images of mitochondria of unchallenged (A) and apoptotic (B) U2OS cells. From left to right: Tom22, Bax (recorded in the STED-mode), cytochrome c and an overlay of all three channels. The arrows denote Bax-rings. Scale bars: 2 µm.
Figure 6A) Src family kinase inhibition via Dasatinib treatment in control organoids enforces YAP cytoplasmic localisation after 4h of treatment in organoids cultured for 3d. n > 10 organoids in each experiment. B) Quantification of the percentage of nuclear YAP cells per control crypt bud as shown in panel (A), error bars show 1 SD (**** p <0.0001). n > 10 organoids per condition (top). Quantification of the nuclear/cytoplasmic ratio of YAP per cell in Apc5 mutant organoids as shown in panel (C). n > 10 organoids per condition (bottom). Statistical analysis was performed with an unpaired student's t-test. C C) Src family kinase inhibition via Dasatinib or eCF506 treatment in Apc5 organoids causes relocalisation of YAP to the cytoplasm. n > 10 organoids in each experiment. Q-PCR analysis of the YAP-TEAD target gene Ctgf reveals a strong inhibition of mRNA expression upon treatment with eCF506 (relative expression, error bars = 1 SD). Statistical analysis was performed with an unpaired student's t-test. D) Src family kinase inhibition via Dasatinib or eCF506 treatment in VillinCreERt Lats1/2 dKO organoids (induced in vitro with 4-OHT) fails to cause relocalisation of YAP to the cytoplasm after 4h treatment in culture. n > 10 organoids in each experiment.
a) Schematic representation of the rod and cone death kinetics found in the four mouse models of retinitis pigmentosa.figf3(a) Schematic representation of the rod and cone death kinetics found in the four mouse models of retinitis pigmentosa. The onset of cone death is set as time zero. The corresponding time windows on the x axis are given in weeks. The major cone death phase was the time period from onset until roughly 85% of cones had died. The end phase of cone death was the time period thereafter. (b) Summary of rod and cone death kinetics. Time is indicated in postnatal days or weeks. (c) Immunofluorescence microscopy on retinal flat mounts showing the ventral reduction of red/green opsin expression found in the four mutants during cone degeneration. Strain and time, in postnatal days, are indicated below each image (for higher magnification of wild type, see Fig. 2b).
Figure 2(A) Relative share of the three PIKKs in NCS-responsive phosphorylations. (B) Venn diagram depicting the relative share of the three PIKKs in NCS-induced phosphorylations occurring on S/TQ sites. (C) The profile of a group of substrates targeted by ATM 20 min after neocarzinostatin (NCS) addition and by ATR 1 hr after hydroxyurea (HU) addition. Box plots depict 23 phosphopeptides measured in two independent biological replicates. The box indicates the range from first to third quartiles, and the central band represents the median. Upper and lower whiskers extend to the maximum and minimum values which are not farther than 1.5 times the interquartile range (IQR). (D) Western blotting analysis confirming that the ATM substrate, pS824/KAP1 is targeted by ATR in response to HU. pS345/CHK1 - an established ATR substrate - served as a positive control for ATR activation.
PWP1 acts downstream of ERK7 to control growth and lipid storageA.Figure 6A. ERK7 overexpression leads to phosphorylation of PWP1, as shown by appearance of an extra band on Phos-tag Western blot (marked with red arrow). Insulin-inducible bands (dark blue) remain unresponsive to ERK7. B. Representative immunofluorescent images of PWP1 localization in fat bodies of ERK71 mutant and control third instar larvae. Scale bar: 20 µm. C. PWP1 localization displays increased nucleolar/nuclear ratio in ERK71 mutant fat bodies compared to control (N=20 cells from 5 independent fat bodies per genotype). D. Representative immunofluorescent images of PWP1 localization in fat bodies of third instar larvae. ERK7 overexpression (GFP marked clones) alters the subcellular localization of PWP1. Scale bar: 30 µm. E. PWP1 localization displays reduced nuclear/cytoplasmic ratio in ERK7 overexpressing clones, compared to control cells (N=10 cells from at least 8 different fat bodies per genotype). F. Fat body specific depletion of PWP1 by RNAi leads to decreased TAG levels (N=4 replicates of ≥10 larvae/replicate for each genotype). G. Representative immunofluorescent images of fat bodies in a genetic epistasis experiment using ERK7 and PWP1 fat body (CG-GAL4) knockdown with LipidTOX staining and DAPI to visualize lipid droplets and nucleus, respectively. Scale bar: 50 µm. H, I. Fat body specific knockdown of PWP1 suppresses increased lipid droplet number (H; N>30 cells per genotype) and increased nuclear area (I; N>45 cells per genotype) caused by ERK7 knockdown (BDSC 56939).
Generation of CRC single-cell RNA sequencing data and epithelial cell type census.Figure 1A Workflow of the Clinical Single Cell Sequencing pipeline. In short, CRC and adjacent non-tumor tissue was sampled from 12 patients. Single cell RNA sequencing data was generated using the 10x Genomics platform, as outlined in Materials and Methods. For histology, see Appendix Fig. S1. For patient characteristics, see Table EV1, for mutational data, see Table 2. UMAPs of single cell transcriptome data. (B) UMAPs of epithelial, immune, and stromal cell transcriptomes, color-coded by tissue origin as assessed by marker genes. For marker genes, see Table EV3. (C) UMAPs of epithelial cell transcriptomes, color-coded by patient identity or tissue of origin, as indicated. (D) UMAPs of epithelial cells, separated by tissue of origin (normal vs. tumor). Clusters are color-coded by cell identity, as inferred from marker genes as outlined in main text. E Relative fractions of epithelial cell states for all patients. F Identification of copy-number aberrant versus normal epithelial cells in tumor tissue. To the left: Cell cluster dendrogram, color-coded by patient and by copy-number-associated clusters (n=2 per patient, copy-number normal cluster: grey; copy number-aberrant cluster: red). To the right: Localization of SCN aberrant cells in the UMAP (red). G Relative fractions of epithelial cell states for SCN-normal versus -aberrant cells for all patients. For fractions by patient and copy number status, see Fig EV 2.
Figure 1A. Pull-down experiments using as a bait the biotinylated peptides mimicking the N-terminal cytosolic tail of glycoenzymes performed from the whole HeLa cells lysates (top blot) or purified His-tagged GOLPH3 protein (bottom blot). The N-terminal cytosolic tail sequence of each glycoenzyme is indicated on the top of the blot (LxxR motif in red, biotin at the C-terminus). Immunoblotting shows affinity-captured GOLPH3 (endogenous and recombinant). B. Control or GOLPH3-KD HeLa cells expressing luminal SI-GFP or the chimeras of sucrose-isomaltase containing the N-terminal cytosolic tails of LCS, Gb3S, GM3S and GD3S were fixed and labelled for surface localized GFP (red). Scale bar, 20 μm. C. Pull-down experiments of biotinylated LCS WT and LCS mutant cytosolic tails from HeLa cells lysates (top blot) or purified His-tagged GOLPH3 protein (bottom blot). The N-terminal cytosolic tail of LCS WT and LCS mutants (mut. 1, 2 and 3) is shown on the top of the blot (mutations are in blue, LxxR motif in red, biotin is at the C-terminus). D. HeLa cells expressing luminal SI-GFP chimeras of sucrose-isomaltase (SI-GFP, green) containing the WT and mutant N-terminal cytosolic tails of LCS, were fixed and labelled for surface localized GFP (red). Cells expressing LCS-SI-RxR and LCS-SI-LxxR chimeras shown PM staining. Scale bar, 20 μm, (left). PM (surface) fluorescence intensity (in Table S10 are listed the software used in this study) of each chimera is normalised on the LCS-SI-GFP surface intensity (data are means ± SEM derived from two biological replicates; n is indicated in the graph, ***p <0.001 [Student's t-test]) (right). E. Quantitative flow cytometry-based analysis of the experiment reported in D; n is indicated in the graph (left). Percentage of cells with plasma membrane staining (surface) is reported for each chimera (right). F. GOLPH3-KD or OE HeLa cells were processed for ShTxB (upper panels) or ChTxB (lower panels) staining followed by flow cytometry analysis. Flow cytometry distributions and the relative scatter plots reporting the percentage of positive cells are shown for each condition.
Figure 4Molecular dynamics simulations superimposing the cryo-EM-determined GSEC structure (PDB: 5FN3) with an NMR Aβ structure (PDB: 1IYT) on the co-purifying helical peptide (I), present hNCT- I242 and APPC99 -K28 at the NCT ectodomain-APP interface and modelling of the NCT I242E mutant suggests a direct (II) or indirect (bridged by H2O, III) interaction between the NCT -E242 and the APPC99 -K28 side chains. Aβ profiles (% contribution of individual Aβ37, Aβ38, Aβ40, and Aβ42 peptides to the total Aβ levels (Aβ37+38+40+42)) in the conditioned medium collected from WT or mutant (NCT) MEF cells lines co-expressing WT or mutant APPC99 substrates were assayed by ELISA. Schematic models of the tested GSEC-APP complexes are shown. To account for the increased production of Aβ37 and Aβ38 at the expense of Aβ40 and Aβ42 in the tested conditions, the ratio of ((Aβ 37/40) + (Aβ 38/42))/2 was determined and used to estimate GSEC processivity of APPC99. All the data are presented as mean ± SD, N ≥ 3, Unpaired, two-tailed Student's t-test was used to determine the statistical significance. **p > 0.01, ****p > 0.0001. Calculated T- and Df values were: T = 11,63; Df = 16 (I241-K28 vs I241E-K28), T = 11,37; Df = 14 (I241-K28 vs I241-K28E), T = 4,572; Df = 8 (I241E-K28 vs I241-K28E), T = 4,497; Df = 5 (I241-K28E vs I241K-K28E), T = 2,561; Df = 7.
Fig.Figure 1A: Relative expression of ELDR in OSCC patient samples compared to adjacent non-tumor tissues (N=20) analyzed by qRT-PCR. Technical triplicates were used from each sample. 18S rRNA was used as an internal control. Data were analyzed by Student's t test. Small bars indicate standard error (*, p<0.05, **, p<0.01; *** p<0.001). B: OSCC grade wise upregulation of ELDR expression was noted in the patient samples (N=20). Correlation analysis showed signification positive correlation of ELDR expression with tumor grade (R2= 0.926, significant P value = 0.01). Pearson correlation coefficient and p value was calculated using socscistatistics.com. Well: well differentiated, Mod: moderately differentiated, Poor: poorly differentiated carcinoma. Data are represented as the mean ± SD, C: Representative images of FISH analysis with an RNA probe of ELDR (red) and DAPI staining (blue) in formalin fixed paraffin embedded OSCC tissue. An unrelated probe was used as negative control. Magnification: 40X; inset magnification 100X and scale bar 10 µm. D: Relative expression of ELDR in OSCC cell lines compared to normal oral keratinocytes (NOK) analyzed by qRT-PCR. 18S was used as internal control. Data were analyzed by Student's t test. Small bars indicate standard error (**, p<0.01; *** p<0.001). n = 4 biological replicates. Data are represented as the mean ± SD,