EMBO/sd-character-level-ner huggingface dataset:
(I) Left: PD-L1 surface histogram shows direct antibody treatment on DR5-KO cells. Right: PD-L1 surface histogram from DR5-KO cells after treatment (24 hrs) with ApoEVs isolated from DR5 sensitive cells after either Lexa or KMTR2 treatment.
Mice were infected with sub-lethal dose (25 pfu) of influenza virus and assessed as follows (B) Relative amount of PR8 viral NP mRNA, by qPCR Data information: Data are representative of three independent experiments with 3-5 mice per group and represented as mean ± S.E.M
(E) AUC of cytosolic Ca2+ flux from intracellular Ca2+ stores in (A). Two-tailed paired t test, *P < 0.05.
(M) Average of tumor weights (harvested at same time) from mice treated (i.p.) with IgG1, lexatumumab, avelumab, lexatumumab +avelumab and anti-CD8+ lexatumumab +avelumab (n=4-6).
E, F Effect of suppressing autophagy on wound healing and actin cable formation. Time-lapse series of single-cell wound healing in larvae expressing (E) Src-GFP (green) and DsRed2-Nuc (magenta) to mark cell membrane and nuclei and (F) endogenously GFP-tagged E-cadherin (DE-cad-GFP; green) and mCherry-marked myosin regulatory light chain (Sqh-mCherry; magenta) to visualize adherens junctions and actomyosin cables.
C Securin ubiquitination by APC/C and either UBE2C WT or K157E, resolved by SDS-PAGE and fluorescent scanning. Quantification of 4 or more ubiquitins added on the substrate (right) are calculated as a fraction of total ubiquitination and analyzed by an unpaired Welch's t-test (**** p ≤ 0.0001, n=5 independent, technical replicates). Error bars: SEM. D Similar to C, Ub-securin ubiquitination by APC/C and either UBE2D2 WT or charge-swap variants. Quantification of 4 or more ubiquitins (right) added on the substrate are calculated as a fraction of total ubiquitination and analyzed by one-way ANOVA (**** p ≤ 0.0001, n=4 independent, technical replicates). Error bars: SEM.
(A)-(C) The scattering profiles (A), the PDDFs (B) and the dimensionless Kratky plots (C) of xrRNA1-2s from DENV2 (cyan), ZIKV (red) and WNV (blue). The inset in (A) shows the guinier regions of the respective scattering profiles with linear fit lines. The dimensionless Kratky plot of ZIKV xrRNA1 (red dashed line) was included in (C) for comparison, indicating that the structures of xrRNA1-2s are all well folded.
H. Immunoblot analysis of SATB2, GSC marker SOX2 and differentiation marker GFAP expression during serum-induced GSC differentiation.
c, d, Average oxygen consumption rate (OCR, c) and extracellular acidification rate (ECAR,
G. Kaplan-Meier survival curves comparing mice treated with vehicle (CTRL), IBL-302, cisplatin, or the combination. Log-rank test was used to determine statistical significance. p=0.0014.
a) The number of somatic mutations discovered from each paired NPC case subjected to WES and key clinical parameters (Supplementary Table 2a) clustered according to the clinical stage. Indel, insertion or deletion. (b) Trinucleotide contexts of somatic mutations occurring at cytosine nucleotides in NPC. The font size of the nucleotides at the 3′ and 5′ positions is proportional to their frequencies (Supplementary Fig. 3b).
Knockdown of actin-related subunit, BAP55, reduces Su(H) recruitment in both Notch-OFF (PBS treatment) and Notch-ON (EGTA treatment) conditions. Fold enrichment of Su(H) occupancy at the indicated positions detected by ChIP, relative to input, in Kc167 cells treated with Bap55 or lacZ RNAi as a control. Mean +/- SEM; n = 3; * p<0.05 with one-tailed student's t-test compared to lacZ RNAi control.
(D) Immunoblot for Tcf7l1 in Ctnnb1 null cells during the first 3 days of differentiation in the absence (-) or presence (+) of 3 µM CH. Results from two independent, clonally-derived Ctnnb1 null ES cell lines are shown. Tubulin was used as a loading control.
(A) Representative western blots showing SQR, TST, ETHE1 and SUOX of two control fibroblasts treated with DMSO (-) or with DMSO+ 4-NB (+). (B) Quantification of proteins levels in fibroblasts treated with 4-NB relative to control.
(E) Sox17 immunostaining of FoxA2-Tet ES cells at day 7 of differentiation in the presence or absence of 10 ng/ml DOX and the presence and absence of 3 µM CH as indicated. Far right panel shows image to its left without DAPI.
C Cyto B inhibits TNT formation in the co-culture assay. The percentage of cells forming TNTs was quantified in co-cultured cells in the absence or presence of Cyto B. Three independent experiments were conducted. Data information: data were analyzed using two-way ANOVA with Bonferroni post-test and shown as mean ± SEM; * P < 0.05, ** P < 0.01, *** P < 0.001, ns, not significant.
(D) Experimental layout to compare the activities of TOP2 and Top2-∆83 on DNA and chromatin. Arrowheads indicate the extrachromosomal expression of TOP2 and Top2-∆83 under the inducible pGAL1 promoter.
Based on GSEA results, significantly changed genes due to depletion of HAND2-AS1 and INO80 were attributed to the BMP signaling in HCC primary cells. NES, normalized enrichment score; FWER, familywise error rate.
Application of yeast-based TAR cloning to generate viral cDNA clones and the recovery of recombinant MHV-GFP.a, Schematic representation of the general workflow of TAR cloning and virus rescue. In-yeast assembly require the delivery of overlapping DNA fragments covering the viral genome and a TAR vector into yeast in one transformation event. Transformed DNA fragments are joined by homologous recombination in yeast generating a YAC-cloned full-length viral genomic cDNA. The in vitro production of infectious capped viral RNA starts with the isolation of the YAC, followed by plasmid linearization to provide DNA template for run-off T7 polymerase-based transcription. Virus rescue starts with electroporation of BHK-21 and/or BHK-21 cells expressing the corresponding coronavirus N protein, followed by co-cultivation of electroporated cells with susceptible cell line for virus production and amplification.
(left) ChIP-qPCR of the 13myc-tagged RNAP3 subunit Rpc25 in the indicated strains at the indicated loci (mean ± standard deviation of 4 biological replicates). (right) Western blot analysis of Myc-tagged Rpc25 and Flag-tagged RnhA protein levels in the indicated strains. Tubulin was used as a loading control.
D. in vitro phosphorylation assay of ATOH1. GST-tagged full length ATOH1 (FL), N-terminus ATOH1 including the bHLH domain (N) and C-terminus of ATOH1 downstream of the bHLH domain (C) were purified from N2a cells using glutathione-beads. ATOH1 proteins were incubated with either Casaine kinase 1α (CK1α) or CCND1 and CDK4 in the presence of [γ-32P]-ATP. Phosphorylation signals detected with FL, N and C by the phosphorylation of CK1α (lanes 1, 2, 3) are indicated by white arrowheads. Phosphorylation signals were also detected with FL and C by the phosphorylation of CCND1-CDK4 (lanes 5, 6, 7). Phosphorylation signals of N with CCND1-CDK4 were not detected. Strong CK1α self-phosphorylation signals were observed (lane 4).
(A) Lysates from spleen-derived T cells of wild-type (Bim+/+) and Bim-knockout (Bim−/−) mice were immunoblotted and probed with indicated antibodies. Statistics were from three knockout and control mice. Data are shown as mean ± SD. ∗∗∗p < 0.001.
Mapping 3' termini of mitochondrial 7S RNA/early LSP transcripts in control (L/L) and Tefm knockout (L/L, cre) mouse hearts at the age of 8 weeks. A 3' RACE was performed using linker-ligated RNA and a forward primer corresponding to the first 45 bp from the transcription initiation site at LSP. CSB, conserved sequence block.
A Box and whiskers (from 5th to 95th percentile) plots depicting TINCR RNA levels in the TCGA SKCM RNA-seq dataset of melanoma samples. TINCR expression is higher in Primary A melanomas, and its reduction in Primary-B melanomas and all groups of metastatic samples is statistically significant (Mann-Whitney test, **p< 0.01). Median, minimum, maximum, 25th, 75th whiskers of expression values are shown.
(e) The heatmap shows the expression of genes most strongly associated with SSTR2 expression within the pericytes (left color bar indicates significant correlation or anti-correlation).
B: Ubc9 W103 mutants are H2O2 resistant but not fully active. Left panel: Recombinant Ubc9 W103R, W103A and W103F were purified (embedded panel). Resistance against oxidation was tested under conditions of limiting E1 enzyme: 21 nM Aos1/Uba2 and 73 nM Ubc9 were incubated with H2O2 prior to the addition of 160 nM each of YFP-SUMO1 and CFP-RanGAPtail. Right panel: To compare specific activities of wt and mutants in the absence of H2O2, sumoylation assays were carried out using limiting Ubc9 concentration. Reactions contained 35 nM Aos1/Uba2, 11 nM Ubc9, 85 nM each of YFP-SUMO1 and CFP-RanGAPtail and 1 mM ATP.
(E) Pacs1+/+ and Pacs1-/- NIH-3T3 cells (C1 and C2 from (A)) were transfected with ER-GCamP6-210. ER Ca2+ was measured before and after treatment with 10 µM ATP. Kinetic traces show the mean 488/405 nm excitation ratio of each cell line with error bars indicating SEM. N=30 cells (3T3), 16 cells (C1), 25 cells (C2). Data are representative of 2 independent experiments.
C) Gene ontology enrichment analysis of the telomere-sequence associated interactors. Analysis was performed using the PantherDB.org overrepresentation Test. Fisher's exact test was subjected to Bonferroni correction.
F Representative images of ZO-1, ZO-2, PLAKOGLOBIN and β-CATENIN immunofluorescent staining in the ileum tissue of male wildtype and Vil-Ogt KO mice. Arrow and arrowhead indicate ZO-1 and PLAKOGLOBIN, respectively. Scale bars = 10 μm
(C) Venn blot of the overlaps of the differential genes in mRNA and protein levels.
F. TAX1BP1 KO MEFs (clone sg1) in which ATG7 was knocked down were pretreated with 10 μg/ml FAC for 12 h and then cultured with 100 μM Dfo. Soluble lysates were analyzed by immunoblotting with the indicated antibodies.
C Boxplots showing the distributions of the normalized rank-sums of the up-regulated (left panel) and down-regulated (right panel) genes in the identified signature. Down-regulated genes in Primary-B melanomas better discriminate the two groups of primary melanoma samples (p=5.9e-15, Wilcoxon rank-sum test). Median, minimum, maximum, 25th, 75th whiskers of ranksum distribution are shown.
(C) A validation cohort of PDAC patients (n=21) that underwent direct resection was stained for CSF-1 (scale bar represents 100 µm), PSR (scale bar represents 500 µm) and α-SMA (scale bar represents 200 µm). OK8 is low in CSF-1 expression and high in PSR and α-SMA expression, while the opposite accounts for OK7. (D) Correlation of % of PSR in the tumor and CSF-1 expressing tumor cells, as indicated in panel C. R2 and P-value were analyzed with linear regression. n=21 primary PDAC samples (E) Correlation of % of α-SMA in the tumor and CSF-1 expressing tumor cells, as indicated in panel C, R2 and P-value were analyzed with linear regression. n=21 primary PDAC samples
Western blot of insoluble fraction and F quantification of insoluble full-length TDP-43, ratio paired-t-test,
Figure 6. 4D reorganization of the yeast genome.. (B) Illustration of the three chromatin folding states characteristic of each of the cell cycle phase. Establishment of sister-chromatid (SC) cohesion during S phase increases intra-SC long-range contacts and leads to the individualization of the replicated chromosomes. Then during M phase, the two sisters are segregated and each chromatid (C) individualized thanks to the action combination of cohesin cleavage, condensin loading and spindle elongation. The chromosomes display a stretched internal structure, which relaxed upon destabilization of the spindle with nocodazole.
(e) Survival determined by the age-specific number of dead individuals of female Drosophila with and without (control) supplementation of food with various concentrations of spermidine (as indicated). A representative ageing experiment of at least 50 flies per sample is shown.
(B) Gene expression levels of COL1A1 in PS-1 cells after treatment using qPCR. Graph shows n=3 technical replicates of an example experiment that was performed three times. Data information: data are represented as mean±SD, Student's t-test.
B Scatter-plot showing correlation between the expression of TINCR RNA and normalized rank-sums s of the down-regulated (upper panel) and up-regulated (lower panel) genes in the primary melanoma signature. TINCR expression strongly correlates (Spearman's correlation coefficient of 0.79, Spearman rank p-value: **p<0.01) with the expression of the down-regulated genes.
(c) Left: colocalization of LAMP1 (red) with GFP-p38 and -ANK1-p38 Agm in SY5Y cells maintained in the absence of serum. Arrows indicate colocalization. Right: percentage LAMP1 colocalization with p38 and ANK1-p38 Agm in cells maintained in the presence or absence of serum.
B. Opened view of the molecular footprint of the regulator-C3b interaction (as shown in Fig. 2A), highlighting the C3b domains on the regulator surface (top) and the regulator domains on C3b (bottom).
A, RB was efficiently deleted in the uterine epithelium of uterine epithelium-specific conditional knockout mice (Rb1 eKO mice). Scale bar = 100μm. Rb1 eKO mice, Rb1loxP/loxPLtfCre/+ mice; Rb1 eControl mice (littermate controls of Rb1 eKO mice), Rb1loxP/loxP mice; le, luminal epithelium; s, stroma.
F In-vitro translation of MT-CO1-TGA mRNA and MT-CO1-AGA mRNA using mutant A1555G mitohybrid ribosomes in the presence of tobramycin (0 - 20 µM). Autoradiography of immunoprecipitated MT-CO1 proteins; top: 35S-Met labelling, bottom: 14C-Lys labelling. In-organello translated 35S-Met labelled MT-CO1 was used as a marker. * MT-CO1, ** MT-CO1 extended by read-through, MT-CO1 AGA-polyA and MT-CO1 TGA-polyA constructs used for in-vitro translation are schematized.
Figure 5: Memory decline in 8-month old Fmn2 -/- mice correlates with deregulated transcriptome plasticityA. Volcano plot showing genes differentially expressed in the dentate gyrus of either 3- (red) or 8-month (black) old Fmn2 -/- mice compared to corresponding wild type control group (FDR < 0,05, log2 fold change < +/- 0,25). The upper panel depicts the number of altered genes.
) Time-lapse imaging of the first embryonic cell division in zygotes of the indicated genotypes and expressing the indicated fluorescent proteins. Pronuclear meeting (pnm) time is defined as 0min. Times are relative to pnm. Scale bar, 5μm.
(D) C4-2 cells were transfected control (siC) or EZH2-specific siRNA and lysed for polysome fractionation. RNA was extracted from even-number fractions followed by RT-qPCR analysis for p53 and GAPDH mRNA. The β-ACTIN mRNA was used as an internal control. Data shown as means±SD (n=3). Statistical significance was determined by two-tailed Student's t-test. * P<0.01; NS, no significance.
mRNA levels of Hes5 (n = 3) in DHT-treated NSC97Q cells treated with or without RG108.
Inhibitor dose-response curves of the two DOT1L inhibitors EPZ-5676 (Pinometostat) and SGC-0946 in Hdac1-proficient and -deficient cell lines. Cell viability was measured by a resazurin assay after three days of treatment and measurements were normalized to DMSO-treated cells. Two independent cell lines are plotted separately; error bars indicate the range of two biological replicates.
E. Immunofluorescenc of SATB2 (green) and SOX2 (red) in T3359 GSCs and matched NSTCs. Scale bar, 50 μm.
A. EGCG inhibited α-CD3/CD28 reactivation of latent HIV-1. Primary CD4+ T cells were isolated from HIV-1 positive patients on antiretroviral therapy (n=5, P1-P5). Primary CD4+ T cells were treated with α-CD3/CD28 alone or α-CD3/CD28 and 10 µM EGCG. Cell-associated RNA was extracted 7 days post-treatment. The transcription of HIV-1 was determined by real-time qPCR.
(I) After treatment with IgG1 control and indicated DR5 agonists (KMTR2, Lexa, Tigatuzumab) ± ROCK1 inhibitors (GSK269962A, GSK429286A) tumor cells were co-cultured with anti-CD3 stimulated PD1+ effector Jurkat cells (stably expressing luciferase under NFAT-RE promoter). Relative luciferase signal was quantified and plotted after subtraction of background signal from untreated cells.
(C) C4-2 cells were subjected to UV-RIP assay. RT-qPCR measurement of p53 mRNA immunoprecipitated by IgG or anti-EZH2 antibody. Data shown as means ± SD (n=3). Statistical significance was determined by two-tailed Student's t-test. ** P<0.01.
(F) Fraction of apoptotic B cells in the adoptively transferred B cell populations in the experiment in (C). Symbols represent individual recipient mice and data are from one adoptive transfer experiment. Two-tailed unpaired t test, ***P < 0.001.
(B) CK1α activity in MEF cell extracts was determined using ELISA kinase activity assay. The results are average of 3 experiments (mean +/- SD). *p<0.01 (Student's t test).
Sample recordings from 7-week-old hESC-derived Cerebral Organoids (COs). WWOX's coding sequence was re-introduced into week 6 WWOX-KO COs using lentiviral transduction (lenti-WWOX) (G) Normalized area under the curve of the mean spectral power of WT line, 2 KO lines and 2 KO lines infected with lenti-WWOX at week 7 in baseline condition, for the 0.25-1 Hz frequency range. Data represented by mean ± SEM. The numerals in all bars indicate the number of analyzed slices and organoids (i.e. slices (organoids)). Statistical significance was determined using one-way ANOVA with Tukey's multiple comparisons test. Data information: ***p ≤ 0.001, ****p ≤ 0.0001.
G Comparison of the cofactors bound at the active sites of SiaB/SiaC and BsSpoIIAB/SpoIIAA complexes. For SiaB/SiaC complex, ADP, TPO68 of SaiC and Asn65 of SiaB are all shown as sticks in atomic colors (O, red; N, blue), whereas their C-atoms are colored in cyan, yellow and light blue, respectively. For BsSpoIIAB/SpoIIAA complex, ATP, Ala58 (mutation of Ser58) of SpoIIAA and Asn50 of SpoIIAB are all colored in white. Mg2+ ion and its coordinating water molecules are shown as spheres in green and red, respectively.
I Representative image showing 8-week-old newborn granule neurons in the DG projecting axons through the mossy fiber tract into the CA3 field (indicated by a white square).
Representative images of hypothalamic cultures exposed to AβOs (500 nM, 3 h) and double-labeled with NU4 (oligomer-sensitive) and eIF2α-P antibodies. Arrow points to a neuron presenting high levels of eIF2α-P in the absence of AβO binding. Nuclear staining (DAPI) is shown in blue. Scale bar = 30 μm.
a, Electron microscopy analysis of wild-type (WT) and Smurf1-/- (KO) MEFs grown in normal media or EBSS (starvation) for 4 h. Arrowheads, representative autophagosomes; arrows, representative autolysosomes. Scale bars, 500 nm.
B Rounding pressure plots of MYH9 (positive control, n = 7), luc (negative control, n = 12), PCDH7 (n = 11), PCDH1 (n = 12), and PCDH1 and PCDH7 (n = 11) RNAi cells. Bars show mean ± SEM (left). Rounding pressure plots HeLa Kyoto cells stably expressing PCDH7‐LAP‐tagged BAC transgenes treated with MYH9 (positive control, n = 7), luc (negative control, n = 14), PCDH1 (n = 13) esiRNA. *P 0.05; **P 0.01; ***P 0.001; ns, P > 0.05 (non‐significant).
(B) NOESY spectrum recorded for a solution comprising tubulin (6.5µM), CPAP peptide (400µM) and CCB02.1 (200µM) with 70ms mixing time. The signals colored in green and (highlighted by boxes) correspond to inter-ligand trNOE signals arising due to protein-mediated spin-diffusion (INPHARMA NOEs), while the black peaks represent intra-ligand trNOE signals.
D-G. Atg9 is epistatic to Atg11 in macro-ER-phagy. ATG9 was deleted in wild type and atg11∆ mutant cells and the effects of overexpression of GFP-Snc1-PEM were determined in the single and double mutants as described in Fig 1 legend. D. Deletion of ATG9 in wild type (WT) or atg11∆ mutant cells results in an increase of GFP-Snc1-PEM protein level similar to the increase in atg11∆ mutant cells.
F. Spine/dendrite ratios showing enrichment of EGFP-GSK3α in wild-type or tauKO slices in 'baseline', 'cLTD' or 'recovery' conditions. Error bars represent SEM and statistical significance was calculated according to the Mann-Whitney U test.
Oxygen consumption rate (OCR) was measured in freshly isolated mitochondria from wild-type and mutant mouse cortex. D State 3 uncoupled OCR (state 3u after addition of FCCP), effect of genotype (p<0.0001) and age-genotype interaction (p<0.0001).
A) Sep+/+ or Sep-/- oocytes were matured in vitro until metaphase II. Sep-/- oocytes were injected with wild-type separase or cleavage mutant separase encoding mRNAs in metaphase II. Oocytes were either fixed in metaphase II or activated and fixed in anaphase II. Spreads were stained with Rec8 antibody (red), CREST serum (green), and DAPI (blue) to label DNA. n indicates the number of oocytes with the shown phenotype (e.g. in anaphase II, after successful activation) and the total number of oocytes analysed
A, hmCD40 mHEVc expressing LC3-EGFP were treated with or without CD154 followed by challenge with T. gondii-RFP in the presence or absence of EGF (50 ng/ml) or AG1478 (1 µM). LC3 accumulation around T. gondii was assessed by immunofluorescence. B, mHEVc-LC3-EGFP cells were infected with T. gondii-T. gondii. Cells were treated with vehicle or rapamycin (1 µM) 2 h after challenge with T. gondii in the presence or absent of EGF or AG1478. Recruitment of LC3 around the parasite was examined at 5 h after challenge with T. gondii.
Microvessels within the plugs stained against human-specific CD34. Cell nuclei were stained with DAPI. Scale bar, 100 μm.The area of CD34-positive microvessels was quantified and normalized to the total area of plug. Results represent the means ± s.e.m of 5 plugs (control) and 7 plugs (Sema3C), *P = 0.018.
(H) LC8 siRNA knockdown reduces the Bim-Beclin 1 interaction. Control siRNA or LC8 siRNA were transfected into HeLa cells. After 48 hr, HA-Bim(EL) EE/vector (IP negative control) or HA-Bim(EL) EE/Beclin 1-Flag was transfected into control siRNA transfected HeLa cells; HA-Bim(EL) EE/Beclin 1-Flag was transfected into LC8 siRNA-transfected HeLa cells. Anti-Flag (M2) was used for immunoprecipitation. Note that in the presence of BimEE, endogenous LC8 was pulled down by Beclin 1 when cells were treated with control siRNA. Data are shown as mean ± SD. ∗∗∗p < 0.001.
, C TNT formation was quantified in transfected cells following confocal microscopy. Expression of MICAL2PV mutants, #1, #2 or #4 significantly reduced TNT formation Three independent experiments were conducted. Data information: Data were analyzed using Student's t-test and shown as mean ± SEM; * P < 0.05, ** P < 0.01, *** P < 0.001, ns, not significant.
I. Late stage glioma growthvessels are leaky compared to early tumor growth (n=5 mice per group). Statistical analysis: D.E.G.I. one-way ANOVA followed by multiple comparisons Tukey's test. Error bars: meanSD. Scale bars: A: 250µm; B: 50µm; C-F: 150µm; G: 0,5cm.
Coomassie-stained SDS-PAGE gel showing purified protein from the predicted bacterial OTU constructs.
(D) Correlation graph of CSF1 expression in PANC-1 pLKOctrl or shCSF1 (#560-562) and how these various CM affect COL1A1 expression in PS-1 cells using qPCR, values were normalized for RPLPO expression. n=3 biological replicates for all individual experiments, error bars indicated SD. R2 and P-value were analyzed with linear regression.
(C) Fractions of cells containing centrosomes after siRNA treatment. 48 hours of siRNA treatment still contained a fraction of cells with extra centrosomes that were analyzed in the following experiments. Bar graph shows the percentage of cells with extra centrosomes in MCF10A (+Dox, extra centrosomes) in the presence of control siRNA or CPAP siRNA. Data represent mean ± SEM of three independent experiments. (N)=3, (n=300 cells per condition). p values were obtained using Ordinary One-way ANOVA test *P < 0.01, **P < 0.001
microscale thermophoresis (MST) analysis (B) of Alexa647-labeled C10-15 interaction with mTLR2-Fc Protein (n=4 each) I one representative of 'n' independent experiments is show