EMBO/sd-character-level-ner huggingface dataset:
NexCre cTKOs reveal severe impairments in basal synaptic transmission and synaptic plasticityA: mEPSC and mIPSC sample traces of recordings from deep CA1 pyramidal cells.Figure 4A: mEPSC and mIPSC sample traces of recordings from deep CA1 pyramidal cells. B - E: Bar graphs of mEPSC and mIPSC frequencies and amplitudes in deep CA1 pyramidal cells. mEPSC frequency was not different in deep CA1 pyramidal neurons of adult (4 months) NexCre cTKO versus littermate controls (B, p = 0.6415). mEPSC amplitude was increased in deep CA1 pyramidal cells of NexCre cTKO compared to LM control cells (C, *p = 0.0363). mIPSC frequency was not different in deep CA1 pyramidal neurons of adult (4 months) NexCre cTKO versus littermate controls (D, p = 0.0564) and mIPSC amplitude was increased in deep CA1 pyramidal cells of NexCre cTKO compared to LM (E, *p = 0.0356). F: mEPSC and mIPSC sample traces of recordings from superficial CA1 pyramidal cells. G G - J: mEPSC frequency was increased in superficial CA1 pyramidal neurons of adult (4 months) NexCre cTKO versus littermate controls (G, **p = 0.0052). mEPSC amplitude was not altered (H, p = 0.1579). mIPSC frequencies were not different in superficial CA1 pyramidal neurons of adult (4 months) NexCre cTKO versus littermate controls (I, p = 0.3831) and mIPSC amplitude was not altered in superficial CA1 pyramidal cells of NexCre cTKO mice compared to cells of LM (J, p = 0.3712). K: Sample traces of AMPA and NMDA receptor-mediated currents recorded from CA1 pyramidal cells. L: A/N ratio was not changed in CA1 pyramidal neurons of adult (4 months) cTKO (light blue, n=36) versus littermate controls (LM, grey, n=34) and wildype animals (white, n=22; Kruskal-Wallis-test: p = 0.2748). M: Paired-pulse stimulation revealed a significant defect of short-term plasticity at ISI 10 and 160 ms (unpaired Student's t-test, ∗p < 0.05). N: The correlation of given stimulus intensities to fEPSP slope revealed a highly significant deficit of NexCre cTKO (red) compared to LM (grey), (unpaired Student's t-test, ***p < 0.0001). O: The correlation of fEPSP slope to defined fiber volley amplitudes revealed a reduced IO strength in NexCre cTKO animals (unpaired Student's t-test, **p < 0.01, ***p < 0.001). P,Q: LTP was induced after 20 min baseline activity recording at hippocampal CA3-CA1 synapses (arrowhead, TBS). TBS led to an overall increase of synaptic efficacy in LM controls (145 ± 4.9%, gray), which was significantly reduced in NexCre cTKO (109 ± 3.4%, red) 60 min after TBS (t75-80; unpaired Student's t-test, ***p = 5.71562E-07). The insets show original traces of representative individual experiments.
Figure 4Mettl5 partners identified as significantly-enriched candidates in mass spectrometric analysis of Mettl5-FLAG-Myc affinity purifications (ribosomal proteins not listed for simplicity). Measurements of 2 biological replicates. Western blot validation of the co-immunoprecipitated proteins Mettl5-FLAG-Myc and Trmt112, bearing either a N-terminal HA tag (top) or a C-terminal GFP tag (bottom), in S2R+ cells. The arrows point at the indicated proteins. HA-Trmt12 migrates below the antibody light chains (top). Trmt112-eGFP migrates above the heavy chains indicated by an asterisk (bottom). Trmt112 depletion reduces m6A levels in total RNA from Drosophila S2R+ cells. Mean ± standard deviation of three technical measurements from three biological replicates. *P < 0.05 (two-tailed t-test). The sequences of D. melanogaster Mettl5 and Trmt112 were modelled in the experimentally-determined atomic resolution structure of the human METTL5-TRM112 complex (based on PDB model 6H2V), revealing high conservation and formation of a parallel ß-zipper involving main chain atoms at the complex interface. Mettl5 and Trmt112 are coloured light brown and blue, respectively. The NPPF signature, known to coordinate planar nitrogen groups to be methylated, is shown as sticks. The S-adenosyl-methionine (SAM) is shown in stick representation (yellow) with the methyl group to be transferred to the 18S rRNA represented as a black sphere. Important secondary structure elements, including ß3 on Mettl5 and ß4 on Trmt112, are indicated.
Figure 2(A) Left panel, Mice, treated as indicated, were sacrificed and the indicated tissues were collected and stained for PG (arrows) with PAS following diastase treatment. Scale bars, 200 µm (liver, muscle), 50 µm (cortex, heart, peripheral nerve). Right panel, PAS staining was quantified based on analysis of 4 sections from each tissue in n=3 wt, n=7 Gbeys/ys vehicle-treated, and n=9 144DG11-treated mice. (B) Total glycogen in the indicated tissues, collected from n=5 nine month old vehicle and 144DG11-treated mice, was quantified Repeated-measures 2-way ANOVA tests show that the pharmacokinetic profile of each tissue is significantly different from that of all other tissues (p<0.05). *, Significant difference (p<0.05) as determined by two-tailed t-tests. (C) 144DG11 Pharmacokinetics. Gbeys/ys mice injected with 144DG1 were sacrificed 30, 60, 90, and 210 min post injection and the indicated tissues were removed, as well as 200 uL of serum drawn. Graph shows means (+/- SEM) of 144DG11 levels in the different tissues determined by LC-MS/MS Results obtained from n = 3 mice at each time point.
Figure 2IE were isolated and binding to HBMEC and HDMEC was determined under flow conditions. Number of IE bound per mm2 EC surface was calculated and shown is the mean ± 95% CI for 26 CM and 33 UM cases on HBMEC and 21 CM and 35 UM cases on HDMEC on a log scale. P-value was calculated by two-tailed unpaired t-test. The dotted line is 20 IE/mm2, the cut-off value for inclusion of the inhibition data.
Figure 4Representative images of pADAM17-stained lung sections from KrasWT and KrasG12D (6 weeks post inhalation) mice. Scale bar, 100μm. Quantification of pADAM17-positive cells/high power field (HPF) in lungs of KrasWT and KrasG12D mice (n = 6 per genotype). Representative immunoblots of individual KrasWT and KrasG12D mouse lung lysates with the indicated antibodies. Semi-quantitative densitometry of pADAM17 in lung lysates (n = 6 per genotype). Representative immunoblots of individual KrasWT and KrasG12D lung lysates with the indicated antibodies. Semi-quantitative densitometry of pp38 and pERK1/2 MAPK protein levels in KrasWT and KrasG12D lung lysates (n = 6 per genotype). Representative images of pADAM17-stained lung sections from KrasG12D mice injected with a single dose of vehicle (control), SB203580 p38 MAPK or U0126 ERK1/2 inhibitors. Scale bar, 100μm. Quantification of pADAM17-positive cells/HPF in lungs of the indicated groups (n = 5 per group). Immunoblots with the indicated antibodies on lysates from A549 and NIH-H23 LAC cell lines treated with SB203580 for 24 hours. MTT viability assays of A549 and NCI-H23 LAC cells treated with SB203580. ATP proliferation (K) assays of A549 and NCI-H23 LAC cells treated with SB203580. Representative immunoblots of individual KrasG12D and KrasG12D:Adam17ex/ex lung lysates with the indicated antibodies. Representative images of pERK1/2-stained lung sections from the indicated genotypes. Scale bars, 100μm. Quantification of pERK1/2-positive cells/high power field (HPF) in lungs of the indicated genotypes (n = 6 per genotype).
A regulates ceRNA, in a dose-dependent manner, at the RRACH sites of LncBMP4.Figure 6A. The influence of m6A on the stability of LncBMP4 was detected by qRT-PCR (Data are shown as mean ± SEM, n =3 independent experiments, **** p < 0.0001, one-way ANOVA). B. The effects of m6A modification on the binding ability of LncBMP4 with gga-mir-12211 was detected using a luciferase reporting system (Data are shown as mean ± SEM, n =3 independent experiments, * p < 0.05, **** p < 0.0001, one-way ANOVA). C. Effect of NPC and MA treatment on the activity of Luc-LncBMP4 was detected using a luciferase reporting system (Data are shown as mean ± SEM, n =3 independent experiments, **** p < 0.0001, one-way ANOVA). D. The enrichment level of m6A, for LncBMP4 variants with the progressive accumulation of RRACH site mutations, was detected by RIP-qPCR (Data are shown as mean ± SEM, n =3 independent experiments, * p < 0.05, ** p < 0.01, one-way ANOVA). E. The ability of LncBMP4, modified with different levels of m6A, to bind gga-mir-12211 was detected by the luciferase reporting system (Data are shown as mean ± SEM, n =3 independent experiments, ** p < 0.01, **** p < 0.0001, one-way ANOVA.).
a, Current densities (mean ± s.figf2a, Current densities (mean ± s.e.m., n = 4-10) of IFe (30 mM Fe2+, pH 4.6) for TRPML1Va and ML4 mutant TRPML1Va channels. Asterisk indicates statistical difference (P < 0.01) compared to TRPML1Va. b, 55Fe2+uptake (normalized) in HEK293T cells transfected with vector control, with TRPML1Va, with F408D-TRPML1Va and with T232P-TRPML1Va constructs. Error bars indicate the standard deviation on the basis of two independent triplicate experiments. c, [Fe2+]o-dependent quenching of Fura-2 fluorescence in TRPML1Va-transfected cells (arrows), but not in non-transfected control cells (arrowheads) or T232P-TRPML1Va-transfected cells (bottom row). The fluorescence intensity was measured at an excitation wavelength of 360 nm (F360). The original magnification used for all micrographs was ×200. d, Average normalized responses of EGFP-positive TRPML1Va-transfected cells (typically n = 20-40 cells) to 1 or 10 mM Fe2+ (pH 4.6). e, No significant quenching was seen in T232P-TRPML1Va-transfected cells. f, Slightly less quenching was observed for the F408Dgr;-TRPML1Va-expressing cells. g, A small but significant quenching reaction was detected (with 10 mM Fe2+) in R403C-TRPML1Va-expressing cells.
Figure 5Scatter plots representing the association of CSF PGRN with temporo-parietal FDG-PET uptake within the subjects of the Alzheimer's continuum group (n = 474). Abbreviations: FDG-PET: Fludeoxyglucose positron emission tomography Scatter plots representing the association of CSF PGRN with total hippocampal volume (B) within the subjects of the Alzheimer's continuum group (n = 474).
Viability of FI, CI, PI and PI+MVF.Figure 2A Neutral red and trypan blue stainings of FI, CI, PI and PI+MVF. CI incubated for 24 h with 0.2% H2O2 served as control. Scale bar: 100 µm. B Representative flow cytometric scatterplots of propidium iodide / annexin V-stained cells from PI+MVF and CI+H2O2 (positive control). C Quantitative analysis of propidium iodide / annexin V-stained cells from FI, CI, PI, PI+MVF and CI+H2O2 subdivided in necrotic, necroptotic, apoptotic and vital cells in % of total cell number (n = 3 each). D Schematic illustration of the mitochondrial ROS-sensor mito-roGFP2-Orp1. The fluorescence maximum of this sensor shifts from 488 nm to 405 nm with increasing mitochondrial H2O2 levels, as shown by representative fluorescence images of FI. Scale bar: 70 µm. E Quantitative analysis of the ROS sensor ratio (405 nm / 488 nm) of FI, CI, PI and PI+MVF (n = 25 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. CI; +P < 0.05 vs. PI. F Representative Western blot analysis of β-actin and HO-1 in whole cell extracts from FI, CI, PI and PI+MVF. G Quantitative analysis of HO-1 expression in FI, CI, PI and PI+MVF (n = 3 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. CI; +P < 0.05 vs. PI. H Representative immunofluorescence stainings of HO-1 / insulin and HO-1 / CD31 in PI+MVF. Cell nuclei are stained with Hoechst 33342 (blue). Scale bar: 50 µm. I Representative Western blot analysis of β-actin and HO-1 in whole cell extracts from PI and MVF.
Fig.Figure 4(A) The overall structure of N-glycan on N58 of PD-1 is presented with N-glycans on N58 of PD-1 highlighted in sticks in green. The 2 Fo-Fc electron density map of the N58 N-glycans contoured at 1.0 sigma is represented in orange on the right. The β strands were labeled according to canonical IgV-strand designations. (B) Location of N58 glycosylation in the interaction with camrelizumab-scFv. VL of camrelizumab-scFv is colored in yellow and VH in deep salmon. (C) Detailed interactions of N-glycans on N58 of PD-1 with camrelizumab-scFv. The observed glycans on N58 of PD-1 are highlighted in sticks and colored in green. Residues with hydrogen bond and van der Waals force interaction are shown as sticks and labeled while Hydrogen bond and van der Waals force interaction are shown as dashed red lines. (D) Binding paratope on VH and VL of camrelizumab by PD-1 is presented with residues in contact with glycan of N58 highlighted in green. (E) SPR analysis of the binding of camrelizumab with N58A mutated PD-1 expressed in 293T cells. (F) The SPR analysis of the binding of camrelizumab with WT (upper) or PNGase F treated PD-1 proteins (lower) expressed in 293T cells. (G The SPR analysis of the binding of nivolumab with WT (upper) or N58A mutated (lower) PD-1 expressed in 293T cells H) The SPR analysis of the binding of pembrolizumab with WT (upper) or N58A mutated (lower) PD-1 proteins.
Figure 1 Figure 1. Symmetry breaking of Min protein patterns in vivo. A. Schematic showing Min protein patterns in a defined geometry originating from 1) a dynamic instability arising from an equilibrium state, or 2) dynamic transitions from a pre-existing pattern associated with cell growth. Green and red particles represent MinD and MinE proteins, respectively. The green gradient depicts the MinD concentration gradient. B-D. Examples of Min protein patterns emerging from nearly homogeneous initial conditions in E. coli cells of different sizes. Lateral dimensions (in µm) from top to bottom: 2x6.5, 2x8.8, and 5.2x8.8 respectively. The gray-scale images show cytosolic near-infrared fluorescence emitted by the protein eqFP670 at the first (left) and last (right) time points. The color montages show the sfGFP-MinD intensity (indicated by the color scale at the bottom right) over time. The scale bar in panel B corresponds to 5 μm. Red arrows show the oscillation mode at the respective time point. E. Two early and two late frames depicting sfGFP-MinD patterns in a cell exhibiting stable transverse oscillations. The images share the scale bar in B. F. Difference in sfGFP-MinD intensity between the top half and bottom half of the cell plotted against time.
Fig.Figure 7HEK293 cells were transiently transfected with hNrCAM, FLAG-tagged hTSPAN15, either plasmids or the empty vector. Detection of sAPPα and sNrCAM in the conditioned media and ADAM10 in the cell lysate. Densitometric quantification of the Western Blots are shown (** p < 0.01), (*** p < 0.001), (**** p < 0.0001), two-sided students t-test, or one-way ANOVA with post hoc Dunnett's test (n = 6). Given are mean +/- the standard error of them mean. The mean levels of solvent treated cells were set to 1. Representative Western Blots are shown.
NBS1 is not required for DNA cleavage opposite to a nick.Figure 7Representative nuclease assays with MRE11, MR, MRN and pCtIP, as indicated, on 5'-end labeled dsDNA with a single streptavidin-blocked end (S). The substrate contained 5 phosphorothioate bonds (PTO) at both 3'-ends to prevent exonucleolytic DNA degradation. Reactions were incubated for 2 h. Representative nuclease assays as in (A), but with a substrate containing a nick in the top oligonucleotide (20 nt away from the 3'-end, see cartoon). Quantitation of experiments such as shown in (A), with pCtIP. Averages shown; n ≥ 4; error bars, SEM. Quantitation of experiments such as shown in (B), with and without pCtIP. Averages shown; n = 3; error bars, SEM.
Loss of Sox9 improves liver fibrosis in vivo.Figure 3 A-J Representative images and quantification shown for olive oil treated (n=6) or chronic CCl4 (n=5 Sox9fl/fl;RosaCreER-; n=8 Sox9fl/fl;RosaCreER+) induced fibrosis or following sham operation (n=5) or BDL (n=7 Sox9fl/fl;RosaCreER-; n=5 Sox9fl/fl;RosaCreER+)) induced fibrosis. A Picrosirius red (PSR) staining (collagen deposition in red) counterstained with fast green (top row) and immunohistochemistry for α-SMA (brown staining bottom row; activated HSC / myofibroblast marker) in olive oil treated (left) or chronic CCl4 induced fibrosis (right) in control and Sox9-null mice. Size bar = 200 μm. B, C Quantification of surface area covered by the PSR staining or α-SMA in control (Cnt) and Sox9-null (Null) in (A). D PSR staining (red; top row) and immunohistochemistry for α-SMA (brown; middle row) and CK19 (brown; bottom row) in control and Sox9-null mice following sham operation (left) or BDL induced fibrosis (right). Size bar = 500 μm. E, F Quantification of surface area covered by the PSR staining or α-SMA in (D). G, H Liver function is improved in Sox9-null mice following CCl4 (G) or BDL (H) induced fibrosis compared to control mice. Reduction in serum alanine aminotransferase (ALT; G, H) and bilirubin (H) down to levels shown in non-fibrotic mice (olive oil treated groups; Oil). G, H Liver function is improved in Sox9-null mice following CCl4 (G) or BDL (H) induced fibrosis compared to control mice. Reduction in serum alanine aminotransferase (ALT; G, H) and bilirubin (H) down to levels shown in non-fibrotic mice (olive oil treated groups; Oil). I Sox9-loss improved severity of fibrosis compared to control mice indicated by quantification of bridging fibrosis in PSR sections following CCl4. Olive oil treated mice had no bridging fibrosis, in line with a non-fibrotic liver histology in (A). J Ductal hyperplasia as quantified by the surface area covered by CK19 positive ducts in (D) is reduced in Sox9-null mice compared to control following BDL. All mice were treated with tamoxifen (Tam) which did not induce ectopic expression of SOX9 in non-fibrotic livers (Figure 2A, E and Appendix Figure S3). All experiments are n≥5 as indicated. Two-tailed unpaired t-test was used for statistical analysis. Data in bar charts show means ± s.e.m. P values indicated.
Figure 6A) Vero cells were infected with SARS-CoV-2 and analysed as shown in the cartoon (see Methods). B) Reduction in SARS-CoV-2 induced cytopathic effect with rac5c, Remdesivir (RDV) and hydroxychloroquine (HCQ) treatment. DMSO 0.3% (v/v) was required to keep 33 µM rac5c in solution (see Fig EV6A, B). Mean (black line) is provided for 18 samples in each group, representing 3 independent experiments with 6 biological replicates per experiment across the different concentrations of rac5c. HCQ data is pooled from 2 independent experiments and RDV from 1 experiment using 6 biological repeats. P values were calculated using a one-way ANOVA, with regular Dunnet's post-hoc test for multiple comparisons between treatment arms and infected/vehicle treated control using a single pooled variance. C) TCID50 data, mean and SD, for one representative experiment from B with 6 technical replicates.
Depletion of ADAR1 in combination with epigenetic repressors trigger type I IFN induction in an LGP2-dependent manner.Figure 6A) HT29 cells were treated with or without 300 nM 5-AZA-CdR for 2 days and subsequently washed and transfected with the indicated siRNAs. Cells were harvested 72h post-transfection and the type I IFN response was analyzed by RT-qPCR analysis of IFN-β, IFIT1, and ISG15 transcript expression, normalized to ACTB. B) LIM1215 cells were treated with or without 300 nM 5-AZA-CdR for 2 days and subsequently washed and transfected with the indicated siRNAs. Cells were harvested 72h post-transfection and the type I IFN response was analyzed as in (A). C) LIM1215 cells were treated with 250 nM palbociclib or a DMSO control for 7 days. Three days after treatment initiation, cells were transfected with the indicated siRNAs and cultured for an additional 72h. The type I IFN response was monitored as in (A). Data information: Data from three biological independent experiments are shown with mean ± s.d.. Statistical analysis was performed using ordinary two-way ANOVA with Tukey's post hoc test. ns, not significant; *, p<0.05; **, p<0.01; ***, p<0.001; ****, p<0.0001.
Figure 4Differential interaction heatmap for Piwi- and Control (EGFP)-KD shown in log2 fold change. Hi-C data is shown with RNA levels (RNA-seq signal density), H3K9me3 association (H3K9me3 ChIP-seq signal density), H3K27Ac association (H3K27Ac ChIP-seq signal density), H3K4me3 association (H3K4me3 ChIP-seq signal density), H1 association (H1 ChIP-seq signal density), and lamin association (Lamin DamID-seq signal density). The genomic region flanking the gypsy insertion (red dashed line) is shown for OSCs with EGFP- and Piwi-KD. FlyBase protein-coding genes are indicated, together with chromosome position. Boxplots showing fold changes in the histone mark association of piRNA target or non-target TEs based on ChIP-seq upon Piwi-KD (Definition of piRNA target and non-target TEs are described in Fig EV1E). Boxplot whiskers, box, and central band show maximum, third quartile, median, first quartile, and minimum, respectively (n=10 for piRNA target TEs, n= 80 for non-piRNA target TEs). P-values were calculated by Wilcoxon rank-sum test. Dot plot showing the correlation between changes in Lamin DamID signal upon Piwi-KD (x-axis) and changes of indicated ChIP-seq signal in each LADs upon Piwi-KD (y-axis). The trend lines are in red. Spearman's rank correlation rho is indicated along with the p-value (algorithm AS 89). Dot plot showing the correlation between changes in intra-TAD interactions upon Piwi-KD (x-axis) and changes of indicated ChIP-seq signal in each TADs upon Piwi-KD (y-axis). The trend lines are in red. Spearman's rank correlation rho is indicated along with the p-value (algorithm AS 89). ChIP‐qPCR analysis of H3K27Ac and H3K4me3 occupancy on the reporter gene upon transfection of λN-Nxf2 expression vector or control EGFP expression vector. Bar graph shows the occupancy relative to that of the sample transfected with a control plasmid. Error bars indicate SD (n = 3), * = p-value<0.01 (t-test)..
Analysis of TFEB-mediated lysosomal gene activation in vivoGene set enrichment analysis (GSEA) of transcriptome changes in TFEB-injected vs.Figure 6A Gene set enrichment analysis (GSEA) of transcriptome changes in TFEB−injected vs. uninjected wild−type (WT + TFEB vs. WT) mice. GSEA of genes annotated as participating in the lysosomal function are reported. The upper panel shows the enrichment generated by GSEA of ranked gene expression data (left in upper panel and red in middle panel: upregulated; right in upper panel and blue in middle panel: downregulated). Peak value corresponds to the point (along the ranked microarray) where the enrichment score (ES) meets its highest value, while the zero value indicates the boundary (along the ranked microarray) between positive fold change and negative fold change. In the middle panel, vertical blue bars indicate the position of lysosomal genes within the ranked list. Lower panel shows the cumulative distribution of lysosomal genes within the ranked lists. The ranking positions that include 50% of lysosomal genes are indicated. The analysis shows that lysosomal genes have a significant global shift toward upregulated genes in TFEB−injected mice compared with uninjected littermates (ES = 0.56, P = 0.0029). n = 4 mice/group. B Representative image of Tau mice coinjected with TFEB‐FLAG/GFP and immunostained with anti‐FLAG and LAMP1 antibodies. Merge image highlights that nuclear TFEB‐FLAG is correlated with higher LAMP1. Scale bar: 10 μm. C Western blot analysis of TFEB, LAMP1 and CTSD expression in Tau mice with (+TFEB) or without AAV‐TFEB adult injection. D Quantification of relative band intensities of (C). n = 3 and 4 per group. TFEB protein levels are significantly increased in Tg + TFEB vs Tg (***P = 0.00013) along with LAMP1 protein levels (*P = 0.013) and CTSD protein levels (*P = 0.028), Student's t‐test. Each bar represents average ± s.e.m.