EMBO/sd-character-level-ner huggingface dataset:
H Indicated parameters, following 5 days of treatment with dsRNA against CG2968, in cells grown in galactose‐containing (Gal) medium.
Phenotypic analysis. WT, GR-UVR8R338A/uvr8 and GR-UVR8W285F/uvr8 seedlings were grown in LD (16-h light/ 8-h dark) for 5 days, then transplanted to new medium with 0.4 μM NAA and with or without 20 μM DEX and kept in white light plus UV-B (1 W/m2) for 7 days. Images are shown in (A); scale bars = 2 mm. The lateral root density (number of lateral roots/length of primary root) (B) and average length of lateral roots (C) of indicated genotypes were measured. SDs (n > 8) are indicated.
D, E. C4-2 cells expressing EV, Q165 or F133V constructs were treated with 1 µM of NEO2734 for 4 days and cultured for another 8 days before harvesting. The number of colonies with more than 50 cells was counted. Representative images of colonies are shown in (D) with quantification data in (E). All data shown are means ± SEM. The P value was calculated by the unpaired two-tailed Student's t-test; * P < 0.05, *** P < 0.001.
(J) Lysates from MCF7 cells transfected with the CIP2A-FLAG construct (Junttila et al., 2007) and the indicated ubiquitin-HA constructs were subjected to anti-FLAG immunopurification in denaturing conditions with 0.1% SDS followed by immunoblotting with the indicated antibodies. Black lines indicate that intervening lanes have been spliced out. Ub, ubiquitin; WT, wild type.
Schematics for the requirement of Stx16 and Stx17 in autophagic clearance of damaged mitochondria, surplus peroxisomes and invaded bacterial pathogens.
E, Representative images of autonomous fluorescent signals of 4HRE-d2GFP (green) and immunofluorescent staining of the stem cell marker SOX2 (red) in xenografts derived from T387 GSCs transduced with 4HRE-d2GFP. More GFP signals were detected in the SOX2+ cells compared with the SOX2- cells, suggesting a stronger hypoxia response in GSCs relative to NSTCs. Scale bar, 200 μm.
A T-ALL cells of n=19 patients were engrafted into mice, cryopreserved after harvesting and enriched for viable cells after defrosting. Then, they were subjected to the ATAC-sequencing. Patients P7, P8, P10, P59 were published previously
E IF staining of the actin filaments (red) and nuclei (blue) of organoids in the left panel and H&E staining of embedded and sectioned organoids in the right panel (ID188 p30, ID211 p30).
B Haematoxylin and eosin (H&E) staining of skin biopsies from patient 1 and healthy controls. Scale bars: 200 µm.
(A) Distribution of GLT-1agold particles in PAP of saline-injected (Ctr KI, N=4) and Cef-treated KI mice (Cef KI, N=4) (P45-46). Cef treatment does not modify the density of total, cytoplasmic (arrows) and membrane-associated (arrowheads) gold particles in PAP of KI mice (cf Table II).
(E) Cell growth of MCF10A cells transiently transfected with a tRNATyrGUA overexpression vector relative to an empty control vector (n=3). A one-tailed Mann-Whitney test was used to test for significance at day 3.
(a) Structural model of the complex of TREM2-TMH wild-type and γ-secretase obtained by docking guided by the cryo-EM structure of the γ-secretase-NOTCH complex (Yang et al., 2019). Protein regions in γ-secretase that occlude the substrate binding site have been removed for clarity. (b, c) TREM2-TMH wild-type in the active site of γ-secretase in a register that would lead to cleavage between residues A192 and L193 (marked by spheres in red and purple), as detected by mass spectrometry (see Fig. 5). The K186 residue in TREM2 is also shown as well as the catalytically relevant residues in γ-secretase (D257 and D385). In TREM2-TMH K186A, the register of the helix moves upwards leading to positioning of A195 and A196 in the active site (c). The cleavage site needs to be unwound by γ-secretase, thus, the intrinsic stability of the helical substrate is a critical determinant of the cleavage position.
A Images show collagen matrix gel contraction by HDF (human dermal fibroblasts), skin-MAF (melanoma associated fibroblasts isolated from skin lesions), LN-FRC (lymph node fibroblast reticular cells), and LN-MAF (melanoma associated fibroblasts isolated from metastatic lymph node). Dashed circles represent the diameter of the gel. Data are representative of n = 3 independent experiments.
F. ELISA of IFN-β (upper), IL-6 (lower) levels in the supernatant of (D) and (E), and in HDAC6+/+ and HDAC6-/- MEFs transfected with poly(I:C) (1 µg/ml).
Confocal microscopy analysis of the subcellular localization of endogenous CK1α upon expression of WT or oncogenic RNF43 (R519X). Scale bars represent 10 μm. RNF43 is visualised by Flag-staining. Asterisks indicate RNF43-expressing cells.
(H) Whole blood Hb1Ac levels in 16 week old Abca12tm1d mice (mean±SEM, n=4-9 mice per group, **p<0.01 Students t-test).
(I) Respiration (VO2) of AdRiKO and control mice upon cold exposure (n=8/group). Data represent mean ± SEM. Statistically significant differences between AdRiKO and control mice were determined with unpaired Student's t-test and are indicated with asterisks (*=p<0.05; **=p<0.01, ***=p<0.001). Statistically significant differences between temperatures were determined with unpaired Student's t-test and are indicated with a number sign (#=p<0.05; ##=p<0.01; ###=p<0.001). The exact p-value for each significant difference can be found in Appendix Table S2.
Venn diagram displaying the number of TAD boundaries detected using EGFP- or Piwi-KD Hi-C interactions.
Splenocytes from mice of the indicated genotypes, (A) Ptenf/f, Ptenf/f x mb1-cre and Ptenf/f x mb1-cre 3-83ki mice on the respective backgrounds were analyzed by flow cytometry. B cells were pre-gated by B220 and CD19 expression and the IgM/IgD surface expression (dot plots, left) was determined. Histograms (right) show a comparison of intracellular IgD expression (Ig-δHC ic) between the splenic populations of B cells (orange, identified by B220 and CD19 expression) and non-B cells (gray). Numbers in the histograms indicate the percentages of the positive populations. Data are representative of 11 - 35 individual mice per genotype.
Splenocytes isolated from Ifih1-/- and Cd4cre A1fl/fl Ifih1-/- mice were stained with anti-IFNγ and anti-IL17 together with anti-CD4 antibodies and were gated on CD4+ cells. Representative flow cytometry images are shown (left panel). The percentages of IFNγ- and IL17-secreting CD4+ T cells were compared among Ifih1-/- (n = 4), Cd4cre A1fl/fl Ifih1-/- (n = 5) and Cd4cre A1fl/fl mice (n = 6) (right panel). The same data shown in Fig 4E was used for Cd4cre A1fl/fl mice.
E. Model: TLR3 and TLR4 signaling increase TBK1-mediated mTOR S2159 phosphorylation, resulting in increased mTORC1 catalytic activity, mTORC1 downstream signaling, IRF3 nuclear translocation, and IFNβ production.
A) Volcano plot shows significantly altered proteins in better responders before and after treatment. Samples are compared by paired student's t-test, FDR 5%. These proteins are not significantly altered in Poor responders. B) Same as (a) but comparing patients with and without relapse
Quantification of cardiomyocyte area of isolated adult cardiac myocytes (N=4 to 11 mice/group) of indicated mice 6 weeks after TAC or sham surgery. *P<0.05. One-way ANOVA with Sidak´s multiple comparisons test.
(C) The AVKA mutation has no discernible influence on Ras-induced paradoxical ERK activation triggered by the D594A mutation. Experimental set-up as in (A), shown are lysates from 4-HT treated MEFs. (D) Quantification of pMEK and pERK levels normed to HA expression. n = 3, mean + SEM, t-test, ** p < 0.01.
E SG recruitment of EGFP-TDP-43 NLS mutant variants (Wt, 12D, 12A) in primary hippocampal neurons. SG formation was induced by 1h heat shock at 42°C. SGs and TDP-43 were monitored by G3BP1 antibody staining and EGFP fluorescence, respectively. For clarity, signals were converted to grey values in the individual channels (first two columns). In the merge (third column), EGFP-TDP-43 shown in green, G3BP1 in red and nuclei (DAPI staining) in turquoise. Bar, 20 µm.
(D) Proteins from HEK293 cells transfected with empty plasmid or RESA1HIS were modified with PEG-PCMal. Control cells were pretreated with the thiol oxidizing agent diamide (DAM) or the reductant DTT. The samples were analyzed by SDS-PAGE and Western blot.
Representative immunofluorescence results (b) of longitudinal sections of VM mdx muscles for the CD146- and NG2-positive capillaries are shown.
F Left, Representative western blots showing H2AX-WT protein levels (revealed using Flag-specific antibody) from whole cell extracts in junD-/- fibroblasts co-transfected with Flag-tagged H2AX-WT construct and either non-targeting siRNA (siCtrl) or siRNA targeting RNF168 (siRNF168), RNF8 (siRNF8) or BMI1 (siBMI1). Efficiency of each siRNA has been verified and reached 60% of inhibition, in average, as shown for RNF168 (Up). Protein extracts were processed following cycloheximide (CHX) treatment for the indicated times (hours, h). Right, Bar graph showing the percentage (%) of decrease of H2AX-WT protein levels after 4h treatment with CHX (t=4) with respect to untreated conditions (t=0) in junD-/- fibroblasts transfected with specific siRNA, as indicated.
(M, N) Quantitation of gap closure assays of ovarian cancer cell lines PEO1, OVCA429, SKOV3, HEYA8 transduced with OPCML "O", or Empty vector control "E"; dashed white lines represent initial boundary and scale bars = 200μm
Rat hippocampal neurons at DIV3 were transduced with lentivirus coexpressing either hnRNPA3 targeting shRNA (shA3) or a control shRNA (shCtrl) and tag RFP. Three days after transduction (DIV3+3), neurons were transfected with (G4C2)80HIGH(+0) and analyzed at (DIV3+7). (C) Poly-GA aggregates were detected in a filter trap assay using an anti-Flag antibody. (D) The amounts of poly-GA aggregates were quantified and are presented as the fold change of signals from neurons treated with the control shRNA or the repeat construct. Means ± SD of three independent experiments are shown. * p<0.05 by a Student's t-test. n= 3 replicates.
C RNAs were prepared from cell lysates from wild‐type (W) or GIW1KO (∆) cells with ATP and the ATP regeneration system as in (A) but were separated in a native gel. The positions of double‐stranded 27‐nt RNAs (dsRNA) and each strand of RNA used to form the 27‐nt RNA duplex (ssRNA1 and ssRNA2) are indicated at the left.
(D) urface model of LC3(1-120) bound to HsAtg4B. Atom colouring is the same as in (A).
B) Activin/Nodal-induced gene responses are enhanced further in the absence of Wip1 as analyzed by RT-PCR. Animal caps in (B) were treated with Activin protein (5 ng/ml). (-), no injection of Co MO, Wip1 MO and/or Wip1 mRNA. The dose of reagent injected: Co MO (60 ng), Wip1 MO (60 ng) and Wip1 (1 ng).
The cartoon illustrates how too low membrane fluidity triggers large-scale lipid phase separation associated with both segregation and confined diffusion of membrane-integral proteins (left part). Too low membrane fluidity also results in dissipation of membrane potential likely due to a reduced electron transport chain activity (Budin et al, 2018). The core diffusion barrier function of the membrane, however, is maintained (right part).
A. Graphs show means of a- and b-waves of dark-adapted and light-adapted ERG responses (ERG intensities in μV) for both the left and the right eyes from 21-months old VEGF-Ahypermice, VEGF-Ahyper/CASP1-/-/CASP11-/-mice, CASP1-/-/CASP11-/-mice, VEGF-Ahyper/IL1R1-/-mice, IL1R1-/-mice, VEGF-Ahyper/IL18-/-mice, and IL18-/-mice. None of these mice had cataracts. Graphs show mean ± SEM.
(c) Footprint on the surface of LBD upon which Nix binds. Left, binding of THPN to Site C forms a fitting surface for the interaction with Nix. Right, THPN binding also results in a conformational change in residues Arg563 and Ser553 as compared to the apo structure.
d.p.i. I. 530 transcripts were examined at the endogenous mRNA levels by nanostring from young or aged lungs prior to (day 0), or 60 d.p.i. and displayed as a heatmap (purple = relatively low expression, orange = relatively high expression) following log2 transformation of raw expression data above detection threshold. Venn diagrams displaying data in both number of genes and % of total genes examined for the ratios infected versus not by age (top right panel) or aged to young by day post-infection (bottom right panel) from nanostring data. Groups from B & C are n=10 young and n=14 aged mice (2 experiments pooled). D is 6 BAL samples per group (2 experiments pooled) for days 9 & 15 and 3 each for day 30. D, E, G, and I are representatives of 2-4 experiments each; H is 1-2 independently significant replicates pooled. Scale bars on histology figures are 600 μm. * p<0.05 Student's two-tailed t-test with unequal variance.
Changes in relative ear thickness and body weight in vehicle- and MALT1 inhibitor-treated mice upon CARD14E138A induction. M1 inh= MALT1 inhibitor, WT = K14creERTg/+ Rosa26+/+, ieCARD14E138A = K14creERTg/+ Rosa26LSL-CARD14-E138A/+. Combined results of two independent experiments are shown (WT + vehicle: n=9, WT + M1 inh: n=8, ieCARD14E138A + vehicle: n=9, ieCARD14E138A + M1 inh: n=10).
SA‐β‐gal staining on spheres formed by control cells and those treated by the Shp2 inhibitor GS493 at 15 μM at day 7. Scale bar, 100 μm.Quantification of the numbers of senescent cells shown in (K). Error bars represent SEM (n = 3). **P 0.01.Quantification of the numbers of spheres formed by control cells and those treated by the Shp2 inhibitor GS493 at 15 μM. Error bars represent SEM (n = 3). **P 0.01. Statistical significance was assessed by Student's unpaired t‐test.
A. Second harmonic generation (SHG) and unfiltered multiphoton (MP) imaging of collagen fibres surrounding TEBs (dashed line) in 6-7 weeks old wt and Sharpincpdm mouse mammary glands (n = 6 - 9 mice, 5 - 13 TEBs analysed per mouse; scale bars represent 100 µm). Magnified images of collagen fibres are also shown (scale bars represent 50 µm). B. Frequency of clear collagen bundles around TEBs per mouse (Mean ± SEM, n = 6 - 9 mice).
C. Dot plots of known entry determinants across cell types. The dot size represents the percentage of cells expressing the gene; the color represents the average relative expression across the cell type. Data are from mock-infected colon (left) and ileum organoids (right).
Groups of BALB/c mice (n = 5) were inoculated three times, four weeks apart, with 20 µg of the postfusion F proteins indicated above each panel. One group (n = 5) was inoculated only with the CpG adjuvant, as indicated. Two other groups of mice (n = 8) were similarly inoculated with either F-415 or F-416, as indicated at top of the panels. A) Mouse sera, collected just before challenging with hRSV (A2 strain), were used in microneutralization assays against the viruses indicated at bottom. Statistical results are shown as in Fig. 3B. *P = 0.00085 and **P = 0.01986.
D, E RFP-p62 bodies exhibited fusion (D) and fission (E) characteristics of liquid droplets. WT and MOAP-1 KO LO2 cells were transfected with expression vector encoding RFP-tagged p62 and 14 hours later, cells were analyzed by live-imaging to visualize the dynamics of RFP-p62 bodies. Scale bar: 2 µm
Representative 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).
(d) Schematic representation of N-terminally FLAG-tagged WT Parkin and various mutants of Parkin. (e) The association of endogenous p53 with various Parkin mutants in DOX-treated HeLa cells. The immunoprecipitation assay revealed that the RING0 domain was essential for the interaction with p53.
E Confocal images of PHcrac (left) and PHcrac merged with LimE (middle, PHcrac as red, LimE as green) in a giant cell after steady PKBA recruitment. Right, intensity plots of PHcrac (red) and LimE (green) across the blue box.
J Axonal area occupied by mitochondria in Yme1l-/- neurons relative to WT controls. In total 120 axonal segments were analyzed for WT control neurons and 107 axonal segments for Yme1l-/- neurons at DIV10-14. Data are means of three independent experiments ± SEM. Unpaired t-test, ns = not significant, *P ≤ 0.05.
(D) CYLD-/- MEF were infected with retrovirus encoding FLAG-CYLD as indicated and CYLD was purified by FLAG-IP. The blot was probed with antibodies recognizing CYLD, SPATA2 and actin.
C IP of TRAF2 and TAK1 by GFP-tagged Mtb PknG or its truncated forms in transfected HEK293T cells.
(c) Only knockdown of eIF4A, but not of other genes involved in translation, causes elevated TORC1 upon amino acid withdrawal. S2 cells were treated with dsRNAs for 5 days and then incubated with medium containing or lacking amino acids for 30 minutes. After cell lysis, levels of S6K phosphorylation (T398) were measured by dot blot analysis and normalized to total S6K levels. Results are summarized here for all genes involved in translation, and provided in Dataset EV1.
D May-Gruenwald-Giemsa-stained pleural cells (macrophages, MΦ: black arrow; lymphocytes, LΦ: purple arrow; neutrophils, NΦ: green arrow; eosinophils, EΦ: orange arrow).
(F) Change of Aβ42/40 ratio for all participants with Aβ42/40 ≤ 0.09 at baseline; bars represent mean ± SD. Full circles: APOE4 carrier, open circles: APOE4 non-carrier.
A. IF staining of hnRNP U, FUBP1, ILF2, and SRSF1 in normal L2C, E4C, and embryos injected with Control-LNA or LincGET-LNA. The results show that hnRNP U, FUBP1, ILF2, and SRSF1 are present in the nuclei of 2- to 4-cell embryos, and the expression of hnRNP U, FUBP1, and ILF2 increased significantly after LincGET depletion. Normal L2C and 4-cell embryos were collected at phCG 48 hours and 54 hours, respectively. Embryos injected with LNA were collected at phCG 48 hours. Scale bar, 50 μm. Three experimental replicates were performed and about 15 embryos were used in each group.
I, J NHEJ repair assay using GFP expression-based reporter system in SirT7-depleted HT1080 cells (SirT7 Knockdown) versus control (Scramble Control). (I) Representative FACS dot plots. (J) Quantitation of (I); mean ± SEM of 3 independent clones per condition. Values are normalized to control (Scramble Control + I-SceI) mean.
(E) Raptor protein complexes immunoprecipitated from MCF7 cells treated with control (C) or PPP2R1A (R1A) siRNAs for 56 h were analyzed by immunoblotting with the indicated antibodies. Immunoblots of corresponding cell lysates are shown on the left.
C Statistical illustration of TMA analysis demonstrating NFATc1 strong nuclear positive tumors (n = 161 patients) with respect to functional status of p53 expression in human PDAC tissues.
C, D. Donor OT-I cells were enumerated in young and aged hosts in the lung vasculature (Cir) or parenchyma (Res) (C), or in spleens (D) at 50 d.p.i.
(E) Relative TCR abundance within all sequenced TCRs represented as small (0.01-0.1%), medium (0.1-1%) or large (1-10%) clusters. No hyperexpanded TCRs (>10% abundance) were detected.
(D) Representative images of RFP-GFP-LC3 assay in ARPE-19 cells transiently transfected with RFP-GFP-LC3 and treated with DMSO or NSC668394. Nuclei were counterstained with DAPI (blue). Scale bars: 5 μm. (E) Box plots showing quantitative analysis of RFP+GFP+ puncta (Autophagosome) and RFP+GFP- puncta (Autolysosome ) (n ≥ 100 cells) from 3 independent experiments. Box limits represent 25th percentile and 75th percentile; horizontal lines represent medians; whiskers display min. to max. values. Student's t-test (NSC668394 vs DMSO) *p ≤ 0.05.
b, HO was induced in G2 wild-type, hda1Δ, rpd3Δ and hda1Δ rpd3Δ cells and western and Southern blot analyses were performed.
(E) Cumulative mitotic entry of cells following washout from 0, 1, 4 or 7 days treated of palbociclib (1μM). 50 cells were quantified per experiments and graphs display mean -/+ SEM from 3 experiments.
(D) Immunofluorescence microscopy analysis of the mitochondrial network. Control and subject fibroblasts, overexpressing an EGFP-tagged version of the wild-type SLC25A46 protein (green) and control fibroblasts treated with an siRNA against SLC25A46 were stained with the mitochondrial marker TOMM20 (red) and the nuclear marker DAPI (blue). Scale bars: 10 µm. (E) Quantification of the effect of SLC25A46 on the mitochondrial network shape. In each experimental condition described in (D), 150 cells were analysed and the mitochondrial network organisation was classified as intermediate, fused or fragmented, in three independent experiments. Error bars represent mean +/- SEM and p-values were calculated using a t-test: Control vs patient, p=1.10x10-4. Control vs siRNA SLC25A46, p=1.16x10-4. Subject vs subject+SLC25A46-GFP, p=2.06x10-5.
(e) Four constructs expressing either: (1) no PGAM5 (empty vector) or (2) amino acids 1-98, (3) 1-110 and (4) 98-289 truncated versions of PGAM5 (left panel). Immunoblot of HEK293T cells expressing PINK1-GFP and myc-tagged PGAM5 truncation mutants as indicated with anti-PINK1 or anti-myc for the input proteins as well as the anti-GFP IP (right panel).
A. Representative maximum-intensity projected coherent-hybrid STED (CH-STED) images of mitotic spindles in U2OS cells treated with control and NDC80 siRNAs and stained for DNA (DAPI), KTs (CENP-C, magenta), α-tubulin (red) and CENP-E (green). Scale bar, 10 µm.
(B) Representative confocal micrographs (as maximum intensity projections) of wild-type K562 and ATG9AKO cells expressing tf-NBR1. Selected regions (white box) of micrographs are shown as single and merged channels from fluorescence and immunofluorescence microscopy against indicated proteins. In conditions where puncta were not observed, representative cytoplasmic regions were selected to showcase diffuseness of signal. TAX1BP1, SQSTM1, or NDP52, magenta; NBR1, green; Hoechst, blue.
(i) Immunoblot for Flag and Cx43 of immunoprecipitates (IP) of endogenous Cx43 in WT MEFs transfected with the indicated Flag-tagged constructs of truncated Atg16.
F) Schematic of the extreme C-terminal serine phosphorylation found in pathological TDP-43.
TNF measurement in the serum of GRwt/wt and GRdim/dim mice (n=4) treated with PBS or LPS (12.5 and 1.5 mg/kg in GRwt/wt and GRdim/dim mice respectively) with or without pretreatment with 10 mg/kg DEX. Blood was taken 2 hours after LPS challenge and TNF concentrations were measured with ELISA.
Representative dot-plot analysis showing CXCR4 and CD86 expression on B cells for Dark zone (DZ) and Light zone (LZ) analysis (gated on GC GL7+ Fas+ B cells). The graph shows the mean percentage of DZ (CXCR4+CD86-) and LZ (CXCR4-CD86+) populations from n ≥ 5 reconstituted mice ± SEM.
LPS-primed Brcc3+/+ and Brcc3−/− BMDMs were left unstimulated or stimulated with nigericin. Immunoblot analysis of NLRP3 ubiquitination (detected by mouse anti-ubiquitin antibody) in cell lysates immunoprecipitated with rabbit anti-NLRP3 antibody.
(I) EVs remaining in the FT, or EVs secreted by the same number of cells but not subjected to immuno-isolation (input) were used to infect a reporter cell line. Mean± SD of six independent experiments is shown.
LGN and Gαi3 protein levels are not affected by Elp3 loss. (B) Western blots on P0 WT and Elp3cKO cochlear extracts and corresponding quantifications of normalized LGN and Gαi3 levels (n=3, each lysate obtained from cochleae pooled from 2 animals; Unpaired two-tailed t-test, LGN: p=0.586, t=0.591, DF=4, Gαi3: p=0.963, t=0.0491, DF=4, mean±SEM).