EMBO/sd-character-level-ner huggingface dataset:
Neurodegeneration by mutations in Hippo pathway genes.Figure 5(A) Tangential eye sections through wtsX1 mutant fly eyes. In clones for the null wtsX1 allele, degeneration inside the clones is at severe stages at 14 days. (B) Tangential eye sections through sav3 clones. In sav3 after enclosure many photoreceptors are intact but after 14 days at 29°C most sav mutant photoreceptors have degenerated. (C) Histograms showing the quantification of ommatidia with the full complement of photoreceptors in hpo, wts and sav mutant clones. The progression of loss of photoreceptors is evident and statistically significant in all cases. Mutants for hpoBF33 do not survive for 14 days at 29oC and corresponding sections are shown in Supplementary Figure 12. N=195-268. ***P0.001, **P0.01; *P0.05 in two‐tailed t‐test.
Figure 4(A) Schematic of the experimental strategy to assess injections of COCO in the adult retinal vasculature. (B) Retinal flat mounts of adult mice injected with PBS or COCO for 5 days are stained with IB4 (negative images of the fluorescent signal). Scale bar, 100 μm. (C) Quantification of vascular length and number of branchpoints; (n=4). (D) Schematic of the experimental strategy to assess repeated injections of COCO in the adult retinal vasculature. (E) Retinal flat mounts of adult mice injected with PBS or COCO for 28 days are stained with IB4. Scale bar, 90 μm. (F) Quantification of vascular length and number of branchpoints; (n=4).
Figure 3A: Superposition of the SARS-CoV-2 N-NTD structure with other human-infecting CoV N-NTD structures. The ribbon representation of each structure is coloured separately (SARS-CoV, PDB: 2OFZ, cyan; HCoV-OC43, PDB: 4LI4, pink; MERS-CoV, PDB: 4UD1, orange; HCoV-NL63, PDB: 5N4K, blue) (Lin et al, 2014, Papageorgiou et al, 2016, Saikatendu et al, 2007, Szelazek et al, 2017). The loops that show significant differences are highlighted by dotted circles. The AMP ligand in the HCoV-OC43 N-NTD-AMP complex is shown as a stick structure. B: Structural superimposition of SARS-CoV-2, SARS-CoV and MERS-CoV N-NTDs with that of HCoV-OC43 bound to AMP to show the detailed interactions involved in AMP binding. C: Structural superimposition of HCoV-NL63 N-NTD with HCoV-OC43 N-NTD bound to AMP to show the detailed interactions involved in AMP binding. D-H: Comparison of the electrostatic surfaces with other human-infecting CoV N-NTD structures. The electrostatic surface of N-NTD from (D) SARS-CoV-2, (E) SARS-CoV, (F) HCoV-OC43 bound to AMP, (G) MERS-CoV, and (H) HCoV-NL63 are shown, and the AMP binding sites are highlighted in dotted circles. Red and blue colours indicate negative and positive potential, respectively.
Figure 8Iron loss induced by DFP is associated with HIF1α-SP1 axis-mediated regulation of FTMT expression. The FTMT accumulation across the outer membrane of defective mitochondria leads to induction of mitophagy through the specific interaction between FTMT and nuclear receptor coactivator 4 (NCOA4), autophagic cargo receptor. PHD; propyl hydrogenase domain protein. VHL; von Hippel-Lindau protein.
Reduced connectivity of ErbB4+ PV interneurons in Nrg3 mutants.Figure 5 A) Schematic outline of the connectivity analyses performed in hippocampal slices. PV inhibitory cells (shown in red) were identified using a genetically encoded fluorescence marker (ParvCre;Ai14flox) and recorded from. Neighboring pyramidal neurons were stimulated to probe for connectivity to the recorded interneuron  B) Quantification of the proportion of connected vs. unconnected pyramidal neurons in slices from wildtype (wt) and Nrg3 mutants. Data are presented as bars and the numbers of connected/tested neuron pairs from 20 wildtype and 30 mutant mice are displayed. Chi-square test was performed to assess statistical significance (****P<0.0001)  C) Example traces of evoked excitatory postsynaptic currents (eEPSCs) averaged over 50 sweeps. D, E) Quantification of the peak amplitude of the first eEPSC (D) and of the paired pulse ratio (E)  F-I) sEPSC recordings from CA1 pyramidal (F,H) and PV neurons (G, I) in acute slices. sEPSC frequencies (F,G) and amplitudes (H,I) are shown
Fig.Figure 8The NTF of WT GPR56 contains both PLL and GAIN domains. The S4 variant of GPR56 contains only the GAIN domain. (A) WT GPR56 participates in cortical patterning during brain development. Collagen III, secreted by meningeal fibroblasts, activates GPR56 by binding to its PLL domain and sends a stop signal to migrating neurons once they reached to the pial basement membrane (B) In oligodendrocyte progenitor cells (OPCs), WT GPR56 binds to microglia-secreted tissue transglutaminase-2 (TG2) in the presence of laminin-111 to promote OPC proliferation (C) In microglia, GPR56 S4 binds to externalized PS, which services as an "eat-me" signal for those synapses needed to be removed, and mediates the engulfment of synapses by microglia.
An SxIP motif located in the C-terminus of Duo1 is required for binding of Bim1 to Dam1c A: Scheme of the Duo1 subunit of the Dam1 complex.Figure 2A: Scheme of the Duo1 subunit of the Dam1 complex. Predicted helical regions are highlighted in red, blue regions are unstructured (top). The position of an SxIP motif is marked by a vertical line. The multiple sequence alignment of Duo1 sequences from various fungal species highlights the conservation of the SxIP motif (black box) and adjacent amino acids across species. Amino acids are colored according to the Clustal color scheme. B: Chromatogram and SDS-PAGE of elution fractions from gel filtration. Binding of Bim1 to Dam1∆SxIPc lacking the SxIP motif in the C-terminus of Duo1 was examined by analytical size exclusion chromatography. Elution fractions were analyzed by SDS-PAGE. C: Solid phase binding assay to test for binding of different Dam1 complexes to Bim1. Recombinant GST-Bim1185-344 was immobilized on glutathione sepharose beads and incubated with either recombinant Dam1WTc or Dam1∆SxIPc. Input and pull down samples were analyzed by SDS-PAGE. D: Pull down assay to compare binding of Dam1WTc and Dam1∆SxIPc to immobilized GST-Bim1185-344. Soluble cell lysates from yeast strains expressing the respective Duo1-6xFlag alleles were incubated with GST-Bim1185-344 immobilized on beads. Duo1-6xFlag bound to GST-Bim1185-344 was analyzed by western blot. An anti-Pgk1 antibody was used to confirm equal protein amounts in input samples.
Targeted systemic gene therapy against orthotopic primary HSJD-GBM-001 with RGD4C/AAVP-Grp78-HSVtk plus GCV and combination with TMZ.Figure 8BLI of luciferase of representative tumor-bearing mice from all experimental groups at day 19 post therapy initiation. Survival benefit for tumor-bearing mice from all treatment groups. Data shown are representative of two experiments, n=6. Statistical significance was determined by Kaplan-Meier method (Kaplan-Meier survival fractions). Log-rank (Mantel-Cox) test was used. H&E staining, Ki67 immunostaining, and evaluation of apoptosis in tumors by using an anti- caspase-3 antibody staining of representative tumor sections from all experimental groups. The low-magnification inserts represent negative controls with the secondary antibody alone on serial sections used for both Ki67 and caspase-3 immunostainings. Arrow points to apoptotic cells. Immunostaining of tumors with an antibody against CD133. Scale bars, 100 μm.
Figure 2A, B cRNA or water as a control was injected into oocytes and uptake was assessed two days after injection for 14h in N free MBS. Data information: biological replicates: n = 5 with 2 oocytes in each sample. Asterisks denote significant difference: **P<0.01, *P<0.05 (Student's t-test).
Figure 5(A) Exemplar image of EB3-tdTomatoHeLa cell used for kymograph analyses. To assess astral MT number and dynamics a line (blue) was added to images from the pole to the cortex. (B) Kymographs of pole (bottom)-to-cortex (top) line scans of control and CITK-depleted EB3-tdTomatoHeLa cells. The maximum projection of a 20-pixel-wide line (exemplified above) was plotted at 500 ms time intervals from left to right. MT growth results in diagonal lines. (C) Quantification of astral MT dynamics. MT stability, length, growth speed (n > 250 MT, 30 cells) and nucleation frequency were calculated (n > 30 cells, 3 independent experiments). (D) Immunofluorescence microscopy images showing MT growth at mitotic spindle poles 0, 1, and 2 min after nocodazole washout. Control and CITK-depleted cells were immunostained for α-tubulin (red) and DNA (blue).(E) Percentage of cells showing detectable MT nucleation (aster size > 1 µm) 0, 1, and 2 min after nocodazole washout (n > 100 cells, 4 independent experiments).(F) Quantification of aster size 2 min after nocodazole washout (n > 100 cells, 4 independent experiments).
Figure 2A - DAPI stain of sagittal sections through the rostral telencephalon of E17.5 control and Rx-Dicer mutant littermates showing the neocortex (NCx) and olfactory bulb (OB; dashed line). B - Expression pattern of Grm1 mRNA in OB (dotted line) of control and Rx-Dicer mutants. C - Quantification of OB perimeter (mean ± SEM; symbols indicate values for individual embryos); t-test, ***P < 0.001. N = 14 replicates per genotype. D - Immunostains of E17.5 control and Rx-Dicer mutant brains showing the distribution of progenitor cells (Ki67, red) and neurons (Tuj1, green). Arrowheads indicate rosettes. Sp, septum. E - Detail of a rosette from an E17.5 Rx-Dicer mutant embryo displaying typical features: closed apical surface (dotted line) with PH3+ apical mitoses (white arrowhead) and basal mitoses, surrounded by Tuj1+ neurons (green). Dashed line indicates the basal border of the rosette. F - Rostral half of an Rx-Dicer mutant E17.5 brain immunostained for Pax6, clarified and segmented to reveal rosettes (yellow). C, caudal; R, rostral. G,H - BrdU incorporation and cell cycle re-entry analysis with the progenitor cell marker Ki67 at E17.5, in the rostral cortex of control embryos compared to rostral rosettes of Rx-Dicer mutants. Dotted lines indicate apical surface, dashed lines indicate basal border of VZ. Arrowheads indicate double-positive cells. Data in histograms are mean ± SEM, symbols indicate values for individual embryos; n ≥ 3 embryos; X2-test, *P < 0.05, ***P < 0.001. I - Apical lumen of rosettes immunostained against apical complex proteins (Par3, β-Catenin), primary cilia (Arl13b), apical mitoses (PhVim) and neurons (Tuj1). J - Coronal section through the rostral telencephalon of an E14.5 Rx-Dicer mutant embryo illustrating the high abundance and location of rosettes (arrows), as revealed by the distribution of mitoses (PH3) and neurons (Tuj1). K-S - Analysis of the regional identity of rosettes in E14.5 Rx-Dicer mutants. (K) Schema of normal transcription factor expression patterns defining telencephalic regional identity. Expression of Ngn2, Tbr2 and Pax6 identifies rosettes in the rostro-dorsal telencephalon as having dorsal identity (L-N,P); Gsx2, Dlx2 and Dlx5 identify rosettes in the ventral telencephalon as having ventral identity (O,Q); Nkx2.1 identifies MGE rosettes as being normotopic (R); absence of Gsx2 in LGE rosette cells identifies them as ectopic (S). Tuj1 labels neurons. In (L,M), arrowheads indicate the border between dorsal and ventral territories, and dotted line indicates the outer border of the telencephalon. LGE, lateral ganglionic eminence; MGE, medial ganglionic eminence; P, pallium; SP, subpallium.
Figure 3Dose-dependent viability assays of BRCA2-deficient (Capan-1) or -proficient (MIA PaCa-2) human pancreatic carcinoma-derived cells treated with drugs at the indicated concentrations for six days. Dose-dependent viability assays of BRCA2-deficient (PEO1) or -proficient (C4-2) human ovarian tumour-derived cells treated with drugs at the indicated concentrations for six days. BRCA2-deficient (PEO1) or -proficient (C4-2) human ovarian tumour-derived cells were infected with lentiviruses expressing control or CHD4 shRNAs, followed by selection with puromycin for 72 hours. Dose-dependent viability assays were performed on cells treated with drugs at the indicated concentrations for six days.
Figure 5ST2 wild type or NEMO KO cells were stimulated for 15 minutes with SF-IL-17 (500 ng/ml), solubilized and IL-17RSC was isolated via consecutive Flag and Strep immunoprecipitation and analyzed by MS. (A) The heatmap shows the row-normalized Z-Score calculated from log2 transformed iBAQ values from two independent experiments. ST2 wild type or NEMO KO cells were stimulated for 15 minutes with SF-IL-17 (500 ng/ml), solubilized and IL-17RSC was isolated via consecutive Flag and Strep immunoprecipitation and analyzed by MS. (B) The ratio between iBAQ intensities of selected IL-17RSC components to iBAQ intensity of IL-17RC. Mean + SEM from two independent experiments is shown. ST2 wild type or NEMO KO cells were stimulated with SF-IL-17 (500 ng/ml) as indicated or were left unstimulated and IL-17 was added post lysis. Lysates were subjected to anti-Flag immunoprecipitation to isolate IL-17RSC (C) and analyzed by immunoblotting. ST2 wild type or NEMO KO cells were stimulated with SF-IL-17 (500 ng/ml) as indicated or were left unstimulated and IL-17 was added post lysis. Lysates were tested for activation of signaling pathways (D) and analyzed by immunoblotting. E. ST2 cells were pretreated with TBK1/IKKε inhibitor MRT67307 (2 µM) or IKKα/IKKβ inhibitor TPCA1 (10 µM), stimulated with IL-17 (500 ng/ml) as indicated and analyzed by immunoblotting. F. ST2 wild type or NEMO KO cells were stimulated with TNF (50 ng/ml) for indicated time points and lysates were analyzed by immunoblotting. G. Schematic model of the negative feedback loop mediated by NEMO-recruited TBK1/IKKε.
Figure 6(A) Representative images of livers from the different treatment groups, as indicated. The corresponding liver weights are shown below (n=6 mice per group). (B) Flow cytometry analysis of CD45+CD8+, CD11b+Gr1+ and CD4+CD25+FOXP3+ cell populations in the livers of the mice from the different treatment groups, as indicated (n=5 per group; (means ± SD, n=1, One-way ANOVA, Bonferroni test).
Segmentation of MERFISH data from the hippocampus using JSTA.Figure 3a. High resolution cell type map of 133 cell (sub) types segmented and annotated by JSTA. Colors match those defined by Neocortical Cell Type Taxonomy (NCTT). Scale bar is 500 microns. b. JSTA based classification of CA1 (green), CA3 (cyan), and DG (red) neurons matches their known domains. c. Correlation of the average expression of 163 genes across major cell types between MERFISH measurements to scRNAseq data from NCTT. d. Correlation of the average expression of the same genes as in c between expression of types in scRNAseq data from NCTT. The correlation structure in panel C closely mirrors the structure in panel D.
THEM6-mediated lipid remodelling is required for UPR activation.Figure 5A, Enriched biological processes commonly down-regulated in THEM6 KO 22rv1 cells (2 clones) when compared to CTL. B, Proteomic analysis highlighting proteins associated with the ER stress response significantly down-regulated in THEM6 KO 22rv1 cells when compared to CTL (p-value ≤ 0.05, FC = 1.3). Data information: Data are presented as mean values +/- SD. Data reproducibility: n = 3 independent biological experiments. C, Western blot analysis of BIP, XBP1s, ATF4, CHOP and THEM6 expression in CTL and THEM6 KO 22rv1 cells. Data information: HSC70 was used as a sample loading control. Data reproducibility: representative image from 3 independent biological experiments. D, Proliferation of CTL and THEM6 KO CRPC cells treated with tunicamycin (2.5 µg/ml) for 72 hours. Cell count is normalised to initial number of cells at T0. Data information: Data are presented as mean values +/- SD. Statistical analysis: 1-way ANOVA with a Dunnett's multiple comparisons test. Data reproducibility: n = 3 independent biological experiments. E, Proteomic analysis highlighting ATF4 targets significantly down-regulated in THEM6 KO LNCaP AI cells when compared to CTL (p-value ≤ 0.05, FC = 1.3). Data information: Data are presented as mean values +/- SD. Data reproducibility: n = 3 independent biological experiments. F, Western blot analysis of ATF4 and THEM6 expression in CTL and THEM6 KO LNCaP AI cells. Data information: HSC70 was used as a sample loading control. Data reproducibility: representative image from 3 independent biological experiments. G, Western blot analysis of ATF4, CHOP and THEM6 expression in PCa cells following THEM6 silencing. Data information: HSC70 was used as a sample loading control. Data reproducibility: representative image from 3 independent biological experiments. H, Differential expression of EIF4G1 and ASNS in high and low THEM6 tumours according to the PRAD TCGA dataset. Data information: Centre line corresponds to median of data, top and bottom of box correspond to 90th and 10th percentile, respectively. Whiskers extend to adjacent values (minimum and maximum data points not considered outliers). Statistical analysis: two-tailed Mann-Whitney U test. Data reproducibility: : n = 225 tumours for THEM6 low and n = 121 tumours for THEM6 high. I, Western blot analysis of ATF4 and CHOP expression in CTL and THEM6 KO 22rv1 cells treated with palmitic acid (200 µM) for 48 hours. Data information: HSC70 was used as a sample loading control. Data reproducibility: : representative image from 3 independent biological experiments. J, Western blot analysis of ATF4 and CHOP expression in CTL and THEM6 KO LNCaP AI cells treated with palmitic acid (200 µM) or hexadecylglycerol (50 µM) for 48 hours. Data information: HSC70 was used as a sample loading control. Data reproducibility: representative image from 3 independent biological experiments.
Knockdown of Acs2p Cures the Autophagy Defect in ach1 Mutants (A and B) Representative micrographs (A) and respective quantification (B) of wild-type and Δach1 cells expressing GFP-Atg8p chimera combined with or without knockdown of ACS2 (tet-ACS2).Figure 6(A and B) Representative micrographs (A) and respective quantification (B) of wild-type and Δach1 cells expressing GFP-Atg8p chimera combined with or without knockdown of ACS2 (tet-ACS2). Cells were chronologically aged to day 3 in the presence of 1 ng/ml doxycycline and PI counterstained prior to epifluorescence microscopy (see also Figure S6). (A and B) Representative micrographs (A) and respective quantification (B) of wild-type and Δach1 cells expressing GFP-Atg8p chimera combined with or without knockdown of ACS2(tet-ACS2). Cells were chronologically aged to day 3 in the presence of 1 ng/ml doxycycline and PI counterstained prior to epifluorescence microscopy (see also Figure S6).(C) Representative immunoblot analysis of cells shown in (A) aged until days 1, 2, and 3 to detect "free-GFP" indicative of autophagic flux (see Figure S6A for quantification). (D and E) Representative immunoblot analyses of GFP-Atg8p expressing wild-type (WT) and Δach1 cells either combined with deletion of SCH9 (D) and aged until indicated time points. Blots were probed with anti-GFP and anti-GAPDH (loading control) antibodies to detect "free-GFP" indicative of autophagic flux (see Figures S6B and S6C for quantification). (D and E) Representative immunoblot analyses of GFP-Atg8p expressing wild-type (WT) and Δach1 cells either combined with deletion of SCH9 (D) or supplemented with or without 20 nM rapamycin (Rapa) (E) and aged until indicated time points. Blots were probed with anti-GFP and anti-GAPDH(loading control) antibodies to detect "free-GFP" indicative of autophagic flux (see Figures S6B and S6C for quantification). (F and G) Representative micrographs (F) and respective quantification (G) of GFP-Atg8p expressing yeast cells ectopically overexpressing ACS2 (ACS2 overexp.) or carrying the empty vector (wild-type) during nutrient depletion (starved) compared to SC 2% galactose control conditions (control). Counterstaining of cells with propidium iodide was used to visualize dead cells.(H) Representative immunoblot analyses of the experiment shown in (F) to detect "free-GFP" indicative of autophagic flux.
Figure 7Analysis of TFEB binding and modulation of the MYO1C promoter in human ECs. (A) Representative snapshot of TFEB binding on MYO1C in human ECs. Analysis of TFEB binding and modulation of the MYO1C promoter in human ECs. ChIP was performed using digested chromatin from control ECs and TFEBS142A ECs incubated with IgG (indicated in the bar graph as "+IgG") or with Ab anti-TFEB (indicated in the bar graph as "+Ab anti-TFEB"), followed by qPCR for MYO1C. Bar graph shows the percent enrichment (n=3, mean±SD). Analysis of TFEB binding and modulation of the MYO1C promoter in human ECs. qPCR of MYO1C expression in scr-shRNA, sh-TFEB, sh-MYO1C and sh-TFEB+sh-MYO1C ECs. Data are expressed as relative fold change compared with the expression in scr-shRNA ECs after normalization to the housekeeping gene TBP MYO1C silencing reverses the effect of TFEB silencing on the up-regulation of PM VEGFR2. Analyses were performed on human ECs carrying appropriate scr-shRNA or sh-TFEB in the presence or absence of sh-MYO1C. Representative western blot of MYOC1, total and PM biotinylated VEGFR2 (representative experiment out of 4 with similar results). Representative immunostaining images of the vascular plexus of the retina (p5) (E) and glomerulus (p17)(F) of control and TfebiEC-/- mice with anti-CD31 and anti-MYO1C Abs (scale bars: 50 µm). Bar graphs indicate the Myo1C mean intensity only in vessel areas CD31+ Representative TIRF and epifluorescence images of VEGFR2 in scr-shRNA, sh-TFEB, sh-MYO1C and sh-TFEB+sh-MYO1C human ECs (scale bars: 10 µm). Bar graph shows the ratio between PM and total VEGFR2
increases lipid storage (A) Hepatocytes were treated with BSA, Palm or Palm+Rap for 24 h.Figure 2Hepatocytes were treated with BSA, Palm or Palm+Rap for 24 h. Cells were stained for lipid droplet accumulation (Bodipy 493/503, green) and nuclei (Hoechst, blue). Lipid accumulation was quantified using automated image-based analysis (n=4 biological replicates). Scale bar represents 100 µm. Shown is one representative Western blot from two independent experiments of hepatocytes transfected with siRNA targeting ASK1 (siASK1) or non-targeting siRNA control (siCtrl). Lipid accumulation was quantified using automated image-based analysis in ASK1 knockdown (siASK1; grey bars) or control (siCtrl; black bars) cells treated with BSA, Palm, Palm+Rap and stained as mentioned above (n=4 biological replicates). Shown is one representative Western blot from two independent experiments and quantification of LC3-II/I and p62 protein levels in siCtrl (n=4 biological replicates) or siASK1 (n=4 biological replicates) cells treated with Palm. Colocalization of LC3-II punctate (red; arrow) with lipid (BODIPY 493/503, green) and nuclei (Hoechst, blue) in siCtrl or siASK1 cells treated with BSA, Palm or Palm+Rap. Scale bar represents 100 µm. Colocalization of LC3-II punctate with lipid droplets (BODIPY 493/503, green) was quantified in hepatocytes transfected with siRNA targeting ASK1 (siASK1; grey bars) or non-targeting siRNA control (siCtrl; black bars) and treated with BSA or BSA+Baf for 24 hours (n=4 biological replicates). Lipid accumulation was quantified using automated image-based analysis in ASK1 knockdown (siASK1; grey bars) or control (siCtrl; black bars) cells treated with BSA, Palm or Palm+Baf and stained as mentioned above (n=4 biological replicates). Values are expressed as mean ± SEM. *