EMBO/sd-character-level-ner huggingface dataset:
F) U2OS (EGFP-BIR-5085) cells expressing PIF1 shRNA or shRNA vector (Ctrl) (left) or expressing PIF1-WT or E307Q mutant with endogenous PIF1 depleted by shRNA (right) were infected by lentiviruses expressing I-SceI. The percentage of EGFP positive cells was assayed by FACS analysis 4 days post infection. PIF1 expression level was determined by qPCR (Appendix Fig S3A), and the expression of PIF1-WT or E307Q mutant is shown in Appendix Fig S3C. ata information: Error bars represent the standard deviation (SD) of at least three independent experiments. Signiﬁcance of the differences was assayed by Two-tailed non-paired parameters were applied in Student's t-test. The P value is indicated as **P < 0.01, ****P < 0.0001 and n.s. (not significant) P>0.05.
Reconstitution SUMO conjugation/de-conjugation reaction with purified SAE1/2, UBC9, SUMO protease SENP2364-489), free SUMO in equimolar amounts and 20-fold molar excess over TDG. TDG SUMOylation was performed in the presence or absence of AP-site containing synthetic DNA double-strands as (as indicated (G•AP). TDG and TDG-SUMO were detected by immunoblotting. SUMOylation of DNA (G•AP) bound TDG is strongly reduced but a 20-fold molar excess of free SUMO compensates the inhibitory effect of DNA.
C For two patient derived serum samples (#289, #265), differences in the NM1267-mediated displacement of IgGs binding the three spike-derived antigens (RBD, S1, spike) are shown.
(C) Representative immunoblotting of Lrp4, MuSK, CTGF, and TfR in whole tissue lysates and the plasma membrane fraction of lower limb muscles at E18.5 of wild-type (WT) and Ctgf-/- mice.
IF staining of late differentiation markers Loricrin and Filaggrin in uc.291-depleted, si-uc.291(1) and si-uc.291(2), organotypic human epidermis compared to scramble control one (SCR); haematoxylin/eosin (H&E) staining shows the organotypic epidermis structure (left panels); scale bars: 50μm. The magnified boxes show expression of Loricrin and Filaggrin in the granular layer; scale bars: 10μm. Dotted lines represent the insert border. One representative experiment of three is shown.
(B) Cartoon representations of the superimposed crystal structures of CrIFT81 and MmIFT54 CH-domains in two orientations differing by 180 degrees. The residues mediating tubulin-binding are shown in stick representation and are located on different surface areas in IFT81 and IFT54.
A SDS-PAGE gel showing rat brain cytoplasm incubated for 60 min with different fixatives. The graph shows the summed intensity of the bands in each lane. Fixed proteins either no longer run into the gel or form only smears. To compare the efficiency of fixation, the bands that survive fixation were summed and were expressed as % of an unfixed control. The intensity of PFA-fixed samples was significantly higher than that of glyoxal-fixed samples (N = 5 independent experiments). Glut = 0.2% glutaraldehyde.
B. Root-length measurements of 10-day-old bri1-116, bes1-D and pRP5SA:BRI:YFP;bri1-116 seedlings compared to the wild type. Symbols represent the mean of more than 20 plants, from 3 independent experiments. Bars show standard deviation. Straight lines represent the linear regression applied to each curve starting with day 4 post germination. In this way the root growth rate can be extracted for each phenotype (See Table EV7).
H&E staining of malignant and non-malignant sites from patient p4, separated by the white dashed line. Scale bar is 100µm. Non-malignant human liver lobule from patient p4 used for LCM stained with HistoGene Staining Solution (Methods). Top - sequential zones from the central vein (cv) to the portal node (pn) before microdissection. LCM captured zones marked by the black dashed line. White dashed line marks the boundaries of NPC (non-parenchymal cells) located in the pn and not included in the analysis. Bottom - Tissue after microdissection. Scale bar is 100µm.
Microscopic examination of cross sections of tomato leaves at the leading edge of the lesion following fungal inoculation.S. sclerotiorum A2 (A) and wild type (B) strains were inoculated onto tomato leaves using colonized agar plugs. 24 hours post inoculation; leaves were post-fixed in osmium tetroxide, and embedded in Spurr's epoxy resin. A microtome was used to cut 400 nm sections. Toluidine blue stain was used to reveal fungal hyphae. H = hyphae. The dotted line represents the leading edge of the visible lesion. Images were collected using an Olympus DP 70 camera and processed with Olympus DP Controller software, version 2.2.1.227.
B, C Immunofluorescent staining (B) and quantitation (C) confirmed the graded decrease in MeCP2 expression from control to 50% MECP2 mosaic to full MECP2-KO neurospheres. Scale bar = 50 µm.
(B and C) RAW264.7 cells were co-transfected with control or miR-155 mimic together with a control plasmid or a plasmid expressing Rheb for 24 h, and then infected with Texas Red-labeled BCG for 1 h. The co-localization of BCG and MDC-labeled autophagosome was detected by confocal microscopy. Arrows indicate Quantification of BCG co-localization with autophagosomes described in B is shown (C).
(E) A cell line derived from a mammary tumor spontaneously developed in a Wap-cre:Ptenfl/fl:Tp53fl/fl mouse was cloned and injected in the mammary fat pad of syngeneic C57BL6/J recipient mice. Tumours grew in 12 out of 35 transplanted mice and only these tumours were selected for the treatments described in the figure. When tumours reached an average volume of 100mm3, they were treated with vehicle or a combination of AZD8186 (150mg/kg, og once/day) and erlotinib (50mg/kg IP once/day). Tumours were then measured during the treatment (6 mice per group, mean±SEM). Statistical significance of two-way ANOVA statistical test ****P<0.0001.
(F) SDS-PAGE, Western blot and immunodetection, with the indicated specific antibodies, of ∆4-CYB and WT cells expressing an HA-tagged version of CYC1 and of cells transduced with the lentiviral expression vector without any cDNA insert (Empty).
Western blot showing relative mitochondrial mass in the total lysates of Atg5 KO MEF cells. n = 2. **P = 0.03; ***P = 0.02. Expression levels of Q23 or Q73 were detected with anti-His antibody.
Reduction in β-catenin in the electroporation site (white arrowheads) indicates loss of apical belt integrity and disruption of apico-basal polarity upon Ece2 KD.
FDG PET imaging of coronal views from WT and TetONYap transgenic mice, treated with doxycycline for 10 days. Arrow is pointing to the liver
(B) The upper panel showing qRT-PCR analysis of four identified LUAD-associated RBPs (ADARB1, CELF2, QKI and ZFP36) mRNA levels in 61 LUAD tissues and matched paracarcinoma tissues. The lower panel showing relative mRNA expression (T/N) of the four RBPs in metastatic (n = 28) and non-metastatic (n = 33) LUAD tissues. LUAD tissues were classified into metastatic and non-metastatic tissues as described in Materials and Methods. T, LUAD tissues; N, paracarcinoma tissues. Y axis represents the log10 transformed fold change of mRNA expression (T/N) of four RBPs.
(B) Western blot analysis of extracts of 107promastigotes at stationary phase of growth probed with α-HASPB. α-Cysteine Synthase was used as a loading control [56].
f) Images of WFA-labeled PNNs of scrambled treated visual cortex (left) and amiR-29a LNA (right) in adult mice. Scale bar 60 µm. (g,h) Quantification of PNN density (scr vs amiR-29a, N=3 mice per group; t-test, p=0.03) and intensity for each animal scr vs amiR-29a, N=3 mice per group; t-test, p=0.047. i) Cumulative frequency of PNNs intensity in scrambled and amiR-29a treated adult mice. scr N=1883 cells vs amiR-29a N=1937 cells, Kolmogorov-Smirnov test, p< 0.0001. j) PNN distribution in classes of intensity in mice treated with scrambled and amiR-29a.
A. Flow cytometry analysis of CTV dilution in splenic CD19+ cells sorted from non-immune Ahrfl/+mb1Cre+ (Ahr+/- B cells, solid grey) and Ahrfl/-mb1Cre+ (Ahr-/- B cells, black) mice stimulated for 72h as indicated. Treatment of Ahr+/- CD19+ cells with CH223191 is indicated in red. Representative data of n = 4-5 independent experiments.B-D. Flow cytometry analysis of expansion index (B), % of divided cells (C) and replication index (D) of splenic CD19+ cells sorted from non-immune Ahrfl/+mb1Cre+ (black) and Ahrfl/-mb1Cre+ (white) mice stimulated for 72h as indicated. Treatment of Ahr+/- CD19+ cells with CH223191 is indicated in red. n = 4-5 independent experiments; mean ± SEM; 2-way ANOVA, Sidak's multiple comparison test.
A, B. Tables showing top 20 down-regulated (A) genes in Ahr-/- B cells as compared to Ahr+/+ cells, after analysis by RNA sequencing. B cells were activated with 10 µg/ml α-IgM + 20 ng/ml IL-4 for 8h; 250 nM FICZ was added to the culture during the last 4h. The average read counts are directly proportional to the extent of expression of a given gene in Ahr+/+ or Ahr-/- cells. Data from n = 3 mice per group. Average read counts for the housekeeping gene Hprt1 in both Ahr+/+ and Ahr-/- B cells are indicated below the table in figure 6A.
(E) HeLa cells were depleted of endogenous PELP1 and reconstituted with siRNA resistant constructs expressing either wild‐type HA‐tagged PELP1 or a Flag‐tagged PELP1-SUMO2 fusion protein. The localization of the respective proteins was monitored by indirect immunofluorescence using either anti‐HA‐ or anti‐Flag‐antibodies.
(D) Quantification of CTL roundness for contacts in the three indicated categories. Each dot represents one CTL. Red bars represent mean values. Data information: Data were pooled from three independent experiments. (***p<0.001, ns, not significant, unpaired t‑test).
D. qRT-PCR based quantification of veal2 transcript across Prkcbb, Ephb3 and IgG immunoprecipitations. actb was used as normalization control. Data from three different biological replicates represented as mean fold change values ± standard deviation.
C. Submitochondrial localization of MDI. Mitochondria from cultured cells expressing an MDI-myc fusion protein were kept intact or subjected to swelling to disrupt their outer membranes, and digested or not with Protease K (PK). Protein extracts were subjected to western blot analysis. Tom20, cytochrome C (cyt.C) and SOD2 were used as markers of the outer membrane, inter-membrane space and matrix, respectively. MDI behaved like an outer-membrane protein.
Analysis of STED microscopy of mouse cortex tissue expressing mCherry in axonal projections after stereotaxic viral injections in the thalamus and post-hoc immunostained for ChgA as DCV marker. (H) Representative confocal (100x magnification) image of mCherry labeled axon (blue) with ChgA confocal signal (red) and corresponding super-resolution STED ChgA signal (green). Zoomed areas are indicated by arrows. Scale bar merged image (left): 1 µm, scale bars zooms: 100 nm. (I) Percentage of single ChgA puncta within mCherry labeled axons with corresponding number of overlaying STED puncta. Data shows average ± SEM. N = 2 mice (7 STED images, 70 single observations).
(C, D) Oxygen consumption rates (OCRs) of MEFs were measured on an XF24 Analyzer. (C) Oxygen consumption profiles for MEFs exposed sequentially to oligomycin (2 μg/mL) (Oligo), FCCP (2 μM), and rotenone (1 μM) plus actinomycin (2 μM) (R & A). (D) OCR (pmol O2/min) (n=8). Error bars represent ±SD from eight independent experiments. Data information: For graph the P values was determined by a Mann-Whitney U test. ns = not significant, *P < 0.05, **P < 0.01.
(B) Representative flow cytometry analysis of phenotypic HSCs [c-Kit+Sca-1+Lin- (KSL) CD135-CD48-CD150+] in the bone marrow of 4-month-old Ctrl (Npm1F/FVav1Cre-), 4-months old Npm1 cKO (Npm1F/FVav1Cre+) and 2-year Old WT mice (left). Mean percentages of the indicated fraction are shown (right, n = 4-9 mice per group).
B) HEK 293A cell lysates (from approximately 8 × 106 cells per construct) expressing the indicated GFP fusions were subjected to IP and immunoblotting for GFP, TRAPPC12 and TRAPPC4. Data are representative of 3 independent experiments.
Western-blot of CYLD (full length FL and cleaved c'd) in total protein lysates from GSC#9 after refreshing the medium (+), as compared to 3 days-old culture (-). GAPDH served as a loading control. Densitometric analysis of c'd/FL CYLD was performed. Data are presented as the mean + s.e.m. on 5 independent experiments.
c, HeLa cells transfected with control, caspase-3- or caspase-7-specific siRNAs were stimulated with 20 ng ml−1 TNF + 10 &amp;amp;mgr;g ml−1 CHX.
(C) A significant genotype x treatment interaction was detected for pup retrieval, two-way ANOVA, effect of genotype: P=0.187, effect of treatment: P=0.759, genotype x treatment interaction: *P=0.031. Shank2+/+ vehicle injected n = 6, Shank2-/- vehicle injected n = 6, Shank2+/+ CNO injected n = 6, Shank2-/- CNO injected n = 7. Data information: All data are presented as mean ± SEM, NS: not significant. AC, anterior commissure and MPOA, medial preoptic area.
qPCR measurements of the expressions of ISGs upon knock-down of HNRNPC in MCF7 and T47D cells using CRISPR-Cas9
Using CRISPR/Cas9, TLR2KO and AAVS1KO (control) pDCs were generated and cells were evaluated functionally by exposure to two different TLR2 agonists; Pam2CSK4 (5 ng/mL, yellow) and Pam3CSK4 (50 ng/mL, orange) Data information: Bars represent mean values and equal symbols represent equal donors (n=4). Statistical significance was determined using the ratio paired student T test for agonist or virus treated cells and compared to the mock treated condition, or by unpaired T test when comparing matched conditions between different KOs. *
(G) Representative images (top) and bar plot quantification (bottom) showing the adhesion of calcein-labeled U937 monocytes to ECs treated with or without TNF-α ± (siKDM7A+siUTX). Scale bar represents 250 μm. Graphs are representative of three independent experiments. Data are shown as means ± SD. *P < 0.05 compared to TNF-α (-) siKDM7A+siUTX (-). † P < 0.05 compared to TNF-α (+) siKDM7A+siUTX (-). Statistical differences were analyzed by the Tukey-Kramer test.
G) ROC curve for the ALDH1A3 score on 15 ccRCC patients. ROC variation method was used due to categorical predictor factor. AUC= 80.6±13.8, Sensitivity 83.3% [95%CI: 35.9-99.5], Specificity 33.3% [95%CI: 7.5-70.0], empirical p=0.008 by Bootstrapping method (n=1000).
A. mRNA levels of indicated RP transcripts determined by qRTPCR in MEFs transfected with Non-targeting control (NTC) mimics (white) or miR-132-3p mimics (grey). * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001.
Growth curves of the MCF7 (left) and T47D cells (right) upon gene silencing with siRNAs. siNC: non-targeting siRNA as a negative control, siHN-1: siRNA sequence 1 for HNRNPC, siHN-2: siRNA sequence 2 for HNRNPC, siLMNA: siRNA for LMNA as another negative control. Each sample has 3 replicates. Error bars represent mean ± SD.
(E and F) The mRNA stability of TGFβR1 was examined in QKI-5-overexpressing/-silenced and control A549 and H1299 cells. Cells were treated with actinomycin D (Act-D, 10 μg/ml) for 0, 2, 4 or 6 h, and mRNA levels of TGFβR1 were determined by qRT-PCR. The quantity value of qRT-PCR at 0 h was set 1.
D. MTT-proliferation assay of control (Scr) and MDGI-silenced (shMDGI1) BT12 and BT13 cells. The values of each cell line were normalized to the values at day 1 marked with a dashed line (n = 3). Data are represented as mean ± SD. ***P < 0.001, two-tailed, nonparametric Mann-Whitney's U-test.
(C) Confocal time-lapse microscopy frames of formaldehyde fixed GFP+ S. flexneri following admixture of 10 µM Alexa-Fluor647-labeled hGBP1F or hGBP1FR584-586A and 2 mM GTP. Binding of hGBP1F polymers to bacteria at 5 min and enclosure of bacteria with hGBP1F protein coats after 60 min were quantified. Mean frequencies ± SEM of combined data from at least three independent experiments are shown. Significance was determined by by unpaired t-tests, two-tailed. ***, P ≤ 0.001; ****, P ≤ 0.0001.
K Illustration of a cohort of patients (n=15) with available primary 2D PDAC cell lines. This cohort includes the ID188 (pre-FFX (FOLFIRINOX), red) and ID211 (post-FFX, blue) lines. These lines were screened for sensitivity towards three MEKi. L 15 primary human PDAC 2D cell lines were screened for MEKi (as indicated) sensitivity. The determined AUC was variance scaled and the z-scores are depicted. The ID188 and ID211 identity is color coded.
Representative images showing SA-β-gal staining in hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells at passage 7. Scale bar: 50 µm.
(F) Immunoblots for indicated proteins in skeletal muscle from 10‐mo‐old Con and KO mice.
F-I, 3D reconstruction of the membrane-proximal pool (top view) and J-M, the ribbon-associated pool of vesicles (front view). Active zone membrane is depicted in blue, presynaptic density in pink, and ribbons in red, scale bars 100nm.N-Q, Cumulative probability distribution of the diameter of round vesicles as well as the longest axis of flattened vesicles in the membrane-proximal pool (N-O) and ribbon-associated pool (P-Q). N-P, one way ANOVA followed by Tukey's test; Q, Kruskal-Wallis test. Round vesicles tested in both the pools appeared larger in OtofI515T/I515T IHC synapses but the long axis of flattened vesicles were comparable for both the genotypes (see also Table EV1).
MACS-purified CD34+ human cord-blood derived HSPC were treated with PF-477736 or CHIR-124 ± the caspase-inhibitor QVD (50 μM). Cell death was assessed using AnnexinV/7-AAD staining and flow cytometry.
ACE2 expression is upregulated in human airway epithelial cells in response to rhinovirus infection.Primary epithelial cells from 4 donors were exposed to rhinovirus or medium only (used as control). 24 hrs post-infection, gene expression was assessed using Affymetrix U133 plus 2.0 human GeneChips. ACE2 expression data was retrieved from GEO microarray database (NCBI Accession: PRJNA137767; GEO: GSE27973).
A, Sample collection procedure and labelling scheme using tandem mass tag (TMT) proteomics
PLSR-derived variable importance in the projection (VIP) scores predicting viability for each of the ten studied cell lines. VIP scores are shown for each cell line-specific model, each signal and measurement time point. The direction of the bars (left or right) shows whether the changes in signal correlated negatively or positively with relative viability. VIP scores of larger than one indicate important variables (signals and time points) that predict the responses (viability).
A. Immunoblot analysis of indicated proteins in control and siRNA treated cells.
(A) Targeting strategy for the Car7 locus. Endogenous Car7 locus (top). Targeting construct (middle). Targeted locus after Cre-mediated recombination (bottom). Exons are indicated as grey boxes and loxP sites as arrowheads.
Heat-map indicating DEG patterns comparing LPS or S-protein stimulation of SC-conv macrophages. Z-score is indicated in a color score.
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
C HeLa cells expressing Dox-inducible RIPK3 WT, 2xKR or 3xKR were treated with 1 µg/ml Dox overnight before pre-treatment with 20 µM zVAD.fmk, 5 µM BV6 for 1 h. After pre-treatment, 10 ng/ml TNFα were added for 2 h. Protein levels of inducible RIPK3 expression were analyzed by Western blotting. β-Actin served as loading control. D HeLa cells expressing Dox-inducible RIPK3 WT, K518R or 3xKR were treated with 1 µg/ml Dox overnight before pre-treatment with 20 µM zVAD.fmk, 5 µM BV6 for 1 h. After pre-treatment, 10 ng/ml TNFα were added for 2 h. Whole cell lysates were generated using RIPA lysis buffer containing 2% SDS. Protein levels of inducible RIPK3 expression were analyzed by Western blotting. β-Actin served as loading control.
(A, B) AP-2α levels normalized to GAPDH are significantly decreased in lysates of iPSC-derived neurons from late-onset AD patients carrying the TREM2 p.R47H (AD-TREM2-2 and AD-TREM2-4) variant compared to healthy controls (CON8 and CON9) set to 100% (ADAP-2α: 52.42±8.04%, p=0.020, N=3 biological replicates). Data information: All graphs show mean ± SEM, statistical analysis was performed by one-sample Student's t‐test n.s.-non-significant.* indicates p≤0.05, ** indicates p≤0.01, *** indicates p≤0.001.
(A) Schematic view of the constructs for genomically tagging Vam3 and Nyv1 at their C-termini.
(G) Representative pictures (right) and weights (left, n = 6-8 mice per group) of spleens of 4-month-old Ctrl and Npm1 cKO mice.
E Immunoblotting of UCP1 and Tubulin (control) (top) with relative quantification (bottom), using total cell lysates of BAT from 10-week-old male WT and FADD-D mice on a SD. Data are expressed as mean ± SEM from three independent experiments. *P = 0.0217 (Student's t-test).
DX neuroblastoma cells have MAM-replete mitochondria that are MOMP competent and sensitive to therapeutic stress. REL tumor cells have reduced MAMs (by number and/or proximity) and are relatively multidrug resistant due to attenuated MOMP (red box). Rare tumors at relapse retain MOMP competence and relative therapy sensitivity (green box). Ca2+ transfer may be reduced but is not essential for the multidrug resistant phenotype. Reduced transfer of sphingolipids such as ceramides (Cer) at MAMs is common in REL cells and contributes to attenuated MOMP via altered Bak/Bax oligomerization in response to stress.
B Immediately following heat shock at 43°C for 40 min, AMPK complexes were immunoprecipitated from HEK293 cells and in vitro kinase assays were performed as described in Figure 3D using recombinant human ACC1 proteins as substrates.
H and I. The effects of m6A modifications of LncBMP4 on the ceRNA system were detected by the luciferase reporting system (Data are shown as mean ± SEM, n =3 independent experiments, * p < 0.05, **** p < 0.0001, one-way ANOVA.).
C Close-up view of structure of H2A C-terminal regions shown in cartoon representation. Histones H2A, H3 and ROF region in H2A-NCP (PDB: 3LZ0) are colored in yellow, blue and red, respectively.
(I) NPM1 expression levels (relative quantitation, RQ) in MDS-L cells transfected with siNPM1 or control (siCTRL) (n = 3 mice per group).
(a) Cells were fixed and stained for anti-pTyr-416-Src (red) and co-stained for anti-LC3B, anti-Atg7 or anti-Atg12 (all green). Scale bars, 20 μm. (b) Higher-magnification images of the areas outlined in a. Solid arrows indicate co-localization in focal adhesions and dashed arrows show puncta in the cytoplasm.
(C) Aut2p shows weak similarities to part of tubulin α2 from maize ( Montoliu et al., 1990).
(B-E) SARS-CoV-2 viral RNA (B and D) or infectious virus (C and E) was detected in the lung (B and C) and nasal turbinates (D and E). The mean copy number or the mean infectious titer is shown, error bars represent s.e.m. (n = 5 biological replicates).
(a) The phenotype of non-colonized (Mock) and SA187-colonized (187) 5 d old wheat seedlings after HS treatment at 44°C for 2 h. Data information: All treatments are compared with direct 44°C heat stressed plants. Scale bars correspond to 1 cm.
Analysis of local coefficient of variation (LCOV) as a ratio between MBSm and CTRL; circles indicate median LCOV observed in MBSm cells divided by median LCOV observed in CTRL cells per experiment; bars indicate mean and SEM of LCOV ratios from 4 independent experiments.
Binding sites of mabs (highlighted with ovals) were mapped by mutational analysis (A1 and A2) or by neutralization escape (A3 and B4). The residues affecting binding are represented as white patches on the surface of the sE trimer (PDB 1URZ) color-coded as domains. The a-d surface segments identified by the HDX-MS experiments are shown as grey patches.
(C) Total SA levels were determined in the rosette leaves of 4-week-old plants with or without 1 µM flg22 application for 24 h. Data are averages (±SD) of material from three independent plants. The experiments were repeated twice, with similar results. (▲, p < 0.01 in two-tailed tests compared to the differences (± flg22) from the corresponding values of WT plants. Two independent experiments were combined for statistical analysis.)