EMBO/sd-character-level-ner huggingface dataset:
(E) PASTAA ranking of the top 3 transcription factors involved in the regulation of the differentially expressed genes in ALSC9orf72 cultures. Significance was set with the algorithm published in Roider et al. (2009).
AGO6 relative enrichment of small RNAs (solid lines) and total small RNAs (dashed lines) are shown for each small RNA size class (21, 22 and 24nt) at four genomic loci.I A second biological replicate of the FLAG‐AGO6‐IP and no‐antigen control followed by deep sequencing shown for the Athila6A consensus element in ddm1 mutants. The transcriptional start sites of the LTR TSS‐ and IR‐driven transcripts are shown.
(A) The expression of FTCDwt-HA-MAO causes the aggregation of mitochondria. HeLa Tet-off cells inducibly expressing either FTCDwt-HA-MAO or FTCD(R382A)-HA-MAO were cultured in DOX-free medium for 48 hrs. Cells which were cultured in the DOX-containing medium were used as a control. The cells were fixed and stained with a monoclonal antibody to mitochondria and a polyclonal antibody to HA, followed by observation by confocal microscopy. Panels a-j display representative images. Scale bar = 10 μm. (B) The results of quantification of (A). Results are shown as the mean±SD of five sets of independent experiments, with 100 cells counted in each group in each independent experiment. An asterisk indicates a significant difference at P<0.01 compared with the others (Bonferroni method).
C-D. Density plots showing average ChIP-seq signals for (C) H3K9me3 or (D) H3K36me3 with 95% confidence intervals of the mean indicated in grey. Plots are shown for genes, which are down- or up-regulated according to the microarray analyses (FDR<0.05, absolute fold change log2(|FC|)>0.5) for both 2ac and 2abc KO ESCs (overlaps presented in Appendix Fig S6A), or do not show strong expression changes (log2(|FC|) < 0.2). Genes are further classified as "Bound" if containing binding sites for both Jmjd2a and Jmjd2c within +/- 1kb of a TSS.
C Quantified fluorescence of UbG76V-GFP normalized to mRFP in the hypodermis of animals of the indicated genotype at L4+48 hours. ****P<0.001, ANOVA with Dunnett's posthoc comparison to the wild-type control equivalent time point. N=20 animals per genotype and time point. Error bars indicate SEM.
Effect of HK2 targeting on in vitro tumorigenicity. Treatment with cl-HK2pep (50 µM, 6 h; C, scale bar: 100 µm) reverts formation of foci; dead cells are highlighted by Trypan Blue staining. Data information: Throughout the Figure, cl-SCRpep or SCRpep are used as peptide negative control.
Kugel diameter was not statistically significantly altered by ccbe1 MO knockdown (p = 0.8783; control MO n=21 kugeln from 22 embryos 7.75 ± 1.29 (mean ± s.e.m.), ccbe1 MO n=13 kugeln from 23 embryos 8.93 ± 2.35 (mean ± s.e.m.); 3dpf; 3 experimental repeats; Mann-Whitney U test).
(i) Immunoblot for Atg16 and Atg14 in immunoprecipitates (IP) of endogenous Cx43 from WT MEFs maintained in the absence of serum (4 h) or incubated in the presence of tamoxifen or lindane. I: input; FT: flow through. All values are mean + s.e.m and differences from untreated cells are significant for *P 0.01. Scale bars: 5 μm. Uncropped images of blots are shown in Supplementary Fig. 9.
Representative cells cultured on circular micropatterns with surfaces of 1500 and 500 µm2 and stained for p-Jun Ser63 (magenta), YAP (cyan) and for DNA (green). Additionally, cells were cultured on the micropatterns of 500 µm2 and an agarose pad was used to flatten their nuclei. Scale bar = 10 µm. Nuclear heights were measured using Hoechst staining. Corresponding quantifications of YAP activity (nucleo-cytoplasmic ratio) and p-Jun Ser63 nuclear intensity.
(A) RPE1 cells were transfected as indicated, followed by incubation in serum-starvation media in the presence or absence of cholesterol/MCD for 24 h, and then immunostained for Rab8 (red) and γ-tubulin (green). Scale bar, 10 μm. Representative magnified images are shown from cells labeled with white asterisks.
(H) Quantification of cystine levels (nmol/mg protein) by HPLC-MS/MS in cystinotic zebrafish after treatment with cysteamine (1000 µM), bicalutamide (10 µM), and a combination of cysteamine and bicalutamide (1000 µM and 10 µM, respectively) (n=40 embryos per group).
EM images of BC on liver tissue sections of untreated mice (left) and 1.8 d post sham OP (middle) or PH (right).
(G) Functional gene annotation of altered cellular pathways in TAM-MG vs. TAM-MDM. Left panel depicts pathways enriched in TAM-MG, right panel depicts pathways enriched in TAM-MDM. Adjusted p value (padj) were obtained by Wald test and corrected for multiple testing using the Benjamini and Hochberg method.
Immunolabeling of PDS5B (green) and ACA (pseudocolored in purple onto a spread pachytene spermatocyte. Data information: Sex chromosomes (X, Y) and bivalents (XY) are indicated.
B. Calibration curves of the nomogram in prediction of the 3-year and 5-year DFS. The 45-degree blue dotted line represents the reference line of an ideal nomogram. The error bars represent the 95% confidence intervals of the actual survival in the upper, middle, and lower textiles. NI, perineural invasion. VI, lymphatic or vascular invasion.
B Open field analysis of 2 month old animals show a significant decrease in ambulatory distance (cm) and ambulatory time (s) and a significant increase in resting time (s) (NT n=19, SCA8 BAC n=23, ** p<0.01, *** p<0.001; mean ± SEM; unpaired t test).
(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).
No incidence of spontaneous colitis observed in Ifih1-/- (n = 5) and Cd4cre A1fl/fl Ifih1-/- (n = 11) mice. For side-by-side comparison with Cd4cre A1fl/fl mice
F The ratio of the average number of NEAT1_2 per nuclei in each mutant cell line to that in the WT. Data are represented as mean ± SD (n = 3).
(A) Representative light microscopic images show that the in vitro cultured RPE cells exhibited a hexagonal shape. D3, D5 and D11, cultured for 3 days, 5 days and 11 days, respectively. Scale bars, 100 μm
(a) HUWE1 and MYC Western blot analysis of epithelial cell extractions from control and Huwe1 deficient intestines. Levels of MYC protein are significantly increased in normal intestines lacking HUWE1 (Mann Whitney, p = 0.04, n = 3).
B Typical dsDNA processing event. The dashed red line connects the minima at the end of the rewinding sections The inset shows a DNA unwinding event in the presence of nuclease-dead Dna2 E675A and RPA.
(D-F) Immunoblots of Gp96 and NMHCIIA levels from Gp96 IP of HeLa cells left untreated (U) or treated with: LLO (0.5 nM, 15 min) (LLO) and (F) LLO in the presence of 25 μM blebbistatin (BB).
B Hierarchical clustering of 15 TA and 12 SSA samples using a TGFβ response signature derived from TGFβ-treated TA organoids (log2FC > 3). Expression values were mean-centered (gene-wise) and cosine similarity was used as the distance measure.
(c) HA-GluN2Bct-CTM specifically and dose-dependently decreased the level of cDAPK1 (n = 4 independent experiments from 4 separate cell cultures and transfections; P 0.001; F(5,18) = 18.27) but not wtDAPK1
E. Cells were lysed with SDS-containing sample buffer before proteins were visualized by Western blotting. Insoluble aggregates migrate at the top of the gel between stacker and resolving gel. Tim17 served as loading control.
Uptake of radio-labeled 3H-2-deoxyglucose in siRNA-transfected Capan-1 cells (48 h post-transfection); n = 6 cell culture wells per group; statistically different (P < 0.05) from control (siNC #2) $P = 0.03; Welch's t-test.
(E and F) Top ten Wikipathway (WP) terms (Slenter et al., 2018) significantly enriched among proteins coded for by mRNAs that were decreased (E) or increased (F) in abundance in PABP-depleted cells relative to cells expressing PABP. The number above each column represents the number of genes associated with its corresponding term.
E STAT3 phosphorylation as assessed by Western blotting of CD126-proficient (WT) or -deficient (ko) RC-K8 cells, with and without 1h of exposure to 50ng/ml hIL-6.
(A) Scheme for the preparation of DY-635 targeted liposomes containing the PI3Kγ inhibitor AS605240 (T-LipoAS). LC-MS determined concentrations of AS605240 and DY-635 individually prepared batches used for all subsequent experiments. The graph depicts the mean ± SD from five different batches.
Time-lapse confocal imaging (at a rate of one image stack/min) was used to document dynamic behavior of ONLmicroglia in rd10retinal explants at ages P21-24. Amoeboid infiltrating microglia lacking extended processes were also observed to phagocytose photoreceptors via phagocytic cups formed at their cell body (red *).
(J) Representative western blot of DLL4 levels in scr or miR-30c antagomiR transfected TREx cells at 0, 24 and 48 hours post induction with GAPDH as a loading control. Densitometry analysis of n=3. Data information: data are presented as mean ± SD. *P<0.05, **P<0.01, ***P<0.001 (Unpaired Student's t-test). All repeats are biological.
A. Representative western blot demonstrating ABCB8 overexpression in H9c2 cells. EV = empty vector. N=3 independent samples for each group.
H Mutation of the SCR gene impairs the recruitment of SEU to the WOX5 promoter, as shown by ChIP-qPCR analysis. Chromatin was extracted from SEU-GFP and SEU-GFP scr-3 seedlings at 5 DAG and precipitated with anti-GFP antibody. ChIP signals were quantified by qPCR as a percentage of total input DNA. Data information: In (H) data represent mean ± SD of three independent replicates. **P < 0.01 (Student's t-test).
B. HEK293 cells were transfected with a pool of siRNA against p53 (sip53) or with control siRNA (siScr) for 24 h and treated for additional 24 h with 100 μM H2O2. Basal and phospho-active forms of ATM and CHK2, as well as p53 and GSNOR were assessed by Western blot. Phospho:basal level ratios of ATM and CHK2 (normalized to Vinculin), along with densitometry of GSNOR immunoreactive bands (normalized to GAPDH) are expressed as arbitrary units. Values shown represent the means ± SD of n = 3 independent experiments. *, p<0.05; **, p<0.01; n.s., not significant.
PHD1 mRNA levels in p53R248/− HCT116 silenced for PHD1. *P = 0.0005 toward scrambled control with a two-tailed unpaired t-test and n = 3/group.
Oscillations in aspartate (a) concentrations throughout the cell cycle when feeding [U-13C]-glutamine (representing oxidative TCA cycle activity).
ChIP-seq analyses identified the EGR family members as a functional partner of LDB2. Our study suggested that LDB2 suppresses (blue) and upregulates (red) EGR-mediated gene expression in a context-dependent manner. See the main text for more detailed information.
(D) Real-time PCR analysis of circLMP2A and LMP2A expression after treatment with actinomycin D at the indicated time points in SNU-4th cells.
G. Clone 1 was treated with DOX for 3 days and then transfected with the Tat-Flag cDNA (20 ug/150-mm dish). Two days later, NE and anti-FlagIP from NE were analyzed as in F.
Detection of nascent protein synthesis in the mitochondrial fraction of the ovary. C. Nascent protein synthesis of Tamas and TFAM was decreased in mdi1 ovary, whereas mtSSB was not affected. Tfamgfp, Tamasgfp and mtSSBgfp were expressed in wt or mdi1 background. Nascent proteins were labeled by AHA incorporation and then the GFP-tagged protein was immunopurified with a GFP antibody and the nascent protein synthesis was detected by anti-biotin antibody.
C. Genome browser visualization of different HA-IN occupancy for chromosome V (chrV:431129..443275). Occupancy of the indicated integrase is represented in each panel. Control, as panel 3D. The region contains tH(GUG) E2, tK(CUU) E2, tV(ACC) E1, tI(AAU) E1, SNR52 and SCR1, all transcribed by Pol III.
B Western blot analysis to detect HybA cleavage in S. sonneiΔrhom7 by wild-type (+) or inactive (S201A) GlpG expressed chromosomally (native) or from pUC19 (plasmid) with (+)/without (-) HybB. HybA was expressed from its native locus or a plasmid (pHybA). HybA that is uncleaved or cleaved by GlpG is marked by black and red arrows, respectively.
(A) Hypothetical model for C5 cleavage by the alternative pathway C5 convertase. The AP C5 convertase is a multimeric complex between a dimeric C3 convertase enzyme (comprised of surface-bound non-catalytic C3b in complex with protease Bb), together with additional surface-bound C3b molecules (not depicted here), which are required to strengthen the affinity for C5. Hypothetical model of C3bBb (surface representation, C3b in gray, Bb in orange) bound to substrate C5 (light green, C5d domain in dark green). C3bBb is derived from the dimeric C3bBb-SCIN complex (PDB 2WIN (Rooijakkers et al, 2009)), and C5 is modeled based on superposition of the CVF-C5 complex (PDB 3PVM (Laursen et al, 2011)) on the C3b molecule from C3bBb. The right panel shows C3bBb bound to C5b (light green, C5d in dark green). The structure of C5b is derived from the structure of the C5b6 complex (PDB 4A5W (Hadders et al, 2012)), and superimposed on C5 from the model in the left panel.
Representative images of mDia2 knockdown and control mouse fibroblasts stained for p53 (left), and quantification of cells showing accumulation of p53 in the nucleus (right). N=3.
(D) Quantitative real time PCR analysis showing dEsyt transcript level expression in head RNA samples from wild type and sOD. Y-axis indicates the dEsyt transcript level expression normalized to the loading control (RP49- Ribosomal protein 49), n=3 replicates (biological).
Data in this study support the existence of a YAP-LATS2 negative feedback loop consisting of oncogene YAP and its upstream suppressor LATS2. Under normal physiological condition, the feedback loop is functional, activation of YAP leads to increased expression of LATS2, which may inactivate YAP via phosphorylating YAP and retain YAP in the cytoplasm, leading to the blockage of its proliferative action on hOSE cells (A). Under certain circumstance, YAP protein may be over-activated by the intrinsic and extrinsic stresses (e.g. YAP gene amplification). If the Hippo pathway is still functional and the YAP-LATS2 negative feedback is still exist in these cells, hyperactivated YAP may induce cellular senescence via high expression of LATS2 (B). However, if the Hippo pathway is dysfunctional and the YAP-LATS2 feedback loop is deficient, YAP may induce transformation and carcinogenesis of OSE cells (C).
FST317 and FST344 overexpression resulted in significant increases of FST transcription by RT-qPCR and protein by Western Blot (B) Green, ML-2-GFP; Blue, ML-2-FST317; Red, ML-2-FST344. The RT-qPCR experiments were performed in triplicates (B). Data information: data were presented as mean ± SEM. *P<0.05, **P<0.01, ***P<0.001 (Student's t-test). ns: Not significant.
A) Structural comparison of the CA-CCCT with CENPN-NT (left) and CA-CCpep with CENPN-NT (right). The cryo-EM density maps of the CENPC-CT fragment, CM peptide, and CENPN-NT are indicated as a surface representation. The cryo-EM density maps indicate that the structure of the CENP-A nucleosomes bound with two CENPC-CT fragments symmetrically (CA-CCCT complex) comprised approximately 94% of total analyzed particles. The RG loopCENPA is occupied by CENPC-CT in the CA-CCCT complex, and thereby the CENPN-NT could not access the same side of the nucleosome. The minor fraction (approximately 6% of total analyzed particles) comprised asymmetric CA-CCCT-CNNT complexes, in which CENP-C weakly associates with CENP-A nucleosomes through the CENPC motif. In the structures of the CA-CCpep-CNNT (right), CM peptide and CENPN-NT simultaneously bind to the CENP-A nucleosome.
A Functional NEAT1_2 RNA domains for paraspeckle assembly and shell-localization of the 5′ and 3′ ends of the NEAT1_2 within the paraspeckles. Summary of the NEAT1_2 organization within the paraspeckle and the size of the paraspeckles in the representative NEAT1_2 mutants used in this study.
C. Ratios of IdU/CldU tracts length is plotted. The box extends from the 25th to the 75th percentile with the line in the box representing the median. Whiskers indicate the 10-90 percentiles with data outside this range for individual outliers being plotted as dots. Mean values of IdU/CldU ratios are indicated above the plot. At least 100 replication forks were analyzed for each condition.
Three orthogonal views of gp105 dimer. The uncleaved N-terminal tag is in cyan. Residue numbers are given in strategic positions. Three orthogonal views of T4 gp8 dimer extracted from the T4 baseplate structure in the same orientations as gp105 in panels (A through C). The fragment of T4 gp7 that spans the gp8 dimer is in magenta. Superposition of T4 gp8 and gp105 dimers. The color scheme is unchanged. Gp7 (magenta) nearly perfectly matches the gp105 N-terminal tag (cyan) upon the superposition of T4 gp8 and gp105 dimers.
Coomassie gel of recombinant ATG16L172-307 wild type and mutants. * indicates bacterial protein
B) Mean ratio of expression (fft2Δ fft3Δ /WT) for each of the following categories: non-coding with LTR (n=69) / without LTR (n=1665) (p=0.008); protein coding with LTR (n=246) / without LTR (n=4887) (p<0.001); Tf2s (n=13). A and B) Data shown as box plots, significance of difference between categories was assessed by Wilcoxon-Mann-Whitney test (** p<0.001).
(F) Volcano plot representing NTA analyses of nsi knockout lines (treated together) and wild type. For this analysis, the p-value was calculated using Excel's two-tailed t-test function, for two-sample with equal variance. The most impacted proteins are shown in green. N is related to the number of quantified N-termini.
Real Time PCR gene expression analysis of egl- genes, performed in wild-type animals fed bacteria transformed with either empty-vector (con) or with vector expressing dsRNA against frh-1 or isp-1 and left untreated or treated wit UV Data information: Data are presented as mean ± SE N= * p < 0.05, ** p < 0.01, *** p < 0.001 and **** p < 0.0001 vs untreated; # p < 0.05 and ## p < 0.01 vs con. Not significant if nothing is specified. 2-way ANOVA Tukey"s multiple comparisons
A) SPPL2c overexpression causes a decrease on SPPL3 levels. Endogenous levels of SPPL3 were assessed in cells ectopically expressing wild type SPPL2c (SPPL2c WT) or catalytically inactive SPPL2c (SPPL2c D/A) by Western Blot. Non-transfected cells (-) or stably transfected but non-induced SPPL2c wt cells (n/i) served as controls. Note that SPPL3 expression is reduced in cells expressing SPPL2c wt. Data information: Expression levels of the ectopically expressed SPPL proteases are shown and Calnexin serves as loading control
(E) Body temperature of AdRiKO and control mice housed at 30°C for 2 weeks (n=8/group).
(b) Densitometric analysis relative to actin of soluble EGFP-HDQ74 clearance in stable inducible PC12 cell line expressing EGFP-HDQ74. Transgene expression was induced with doxycycline for 8 h, and then switched off (by removing doxycycline) with drug (all 1 μM) or DMSO (control) treatment for 96 h. Control condition is set to 100%. Error bars show s.e.m.
The stability of the purified proteins was assessed via thermal denaturation by fluorescent CPM-adduct formation. The thermal denaturation profiles (left) were used to calculate the first derivative (right), which provides the apparent melting temperature, indicated with the same colour coding.
Sequence alignment of the PA-binding fragment of GID1 with that of the PA binding motifs in chicken Raf1, abscisic acid insensitive 1 (ABI1), constitutive triple response1 (CTR1) and werewolf (WER) from Arabidopsis. Residues in bold are basic, potentially involved in PA binding and were mutated to Ala in GID1.
D,E: Structure of the MSP domain of VAP-A in complex with a Phospho-FFAT motif. Ribbon diagram (D) and surface representation (E) of the MSP domain of VAP-A in complex with the Phospho-FFAT of STARD3 depicted in stick model. The protein surface is colored according to the YRB scheme, showing hydrophobic, negatively and positively charged atoms in yellow, red and blue, respectively; the other atoms are in white Data information: Phosphorous, nitrogen, oxygen, and sulfur atoms are colored in orange, blue, red, and yellow, respectively. Carbon atoms are shown in green and grey/pink in the MSP domain and the FFAT motif, respectively. The numbers of the peptide residues are noted in subscript.
D Heatmap showing the relative expression levels (row-wide Z score) of the 20 most significant markers for each cluster (rows) across cells in the 8 clusters (columns). Bars on the top were colored as in (C).
Representative images of the 2mt-GCaMP6m 474/410 ratio of ShMICU1 HeLa stable cells expressing an empty vector (ctrl) or the MICU1 WT, MICU1 SD, and MICU1 SA. Scale bar 10 μm
C. The ratio of the nanocluster and monomeric TCR in each lysis condition was quantified by densitometry from immunoblots as in B (n ≥ 4).
a, Ultrasonic vocalizations (USV) in isolated miR379-410 ko mouse pups emitted on postnatal day P3, P6, P9 and P12. Left panel: total number of ultrasonic vocalizations (USV) in isolated miR379-410 wt and ko mouse pups emitted on average (P 3, 6, 9 and 12) when isolated from the mother, wt n=13 (male n=9, female n=4), ko n=20 (male n=11, female n=9), t31=2.274, *p=0.0301, unpaired Student's t-test. Right panel: developmental course for total number of USV, wt n=13 (male n=9, female n=4), ko n=20 (male n=11, female n=9), (development: F3,87=25.463, p<0.001; genotype: F1,29=4.979, p=0.03; development x genotype: F3,87=1.403, p= 0.22, rm-ANOVA); P 9: t31=2.096, *p=0.044; unpaired Student`s t-test.
The 22G RNAs mapping to the 21U sensor transgene were identified from small RNA sequencing data, and read density was plotted over the transgene, which is schematically depicted at the bottom. The aggregated results of three replicates is shown for each indicated genotype in the different panels. The shading, in grey, represents the standard deviation of the read density from the three replicates. (+) means that the sensor was detectably expressed. (RNAe) means that the sensor was crossed into the respective mutant background in an RNAe state (i.e. its silencing was PRG-1-independent), and its expression remained undetectable by microscopy.
(g) NRK cells were starved for 0, 4 or 6 h and then subjected to cell fractionation. Fractions were analysed by western blotting with antibodies against LAMP2 and clathrin heavy chain. 1 is the top fraction. The outline indicates the Lamp2-positive fraction.
Volcano plot of differentially expressed brain mRNAs of 4.5-month-old mice (n = 3 biological replicates per genotype) detected by the Neuropathology panel of NanoString. Expression changes were only taken into consideration when the extent of change was above 20% as indicated by vertical lines for all volcano plots. Gliosis and Myelination related genes are highlighted if changes are above 20%. Fold changes are displayed after log2 transformation. (C) Volcano plot for Grn-/-/Tmem106b-/- and wild type mice. From 680 detected genes 79 are significantly upregulated, while 24 are significantly reduced.
HME control (vector) and KO1 cells were treated with H2O2 for the indicated times and stained with anti-2-5A and anti-PAR. Scale bar, 10μm.
C Quantitation of body weight (left) and gonadal fat pad mass normalized to total body weight (right) (mean ± SEM; 4 samples per genotype).
D. Representative confocal images of fixed HeLa cells ectopically expressing Myc-SKIP, KMI motif mutant (AAA) or RUN domain truncation mutant (∆RUN) (red) together with RFP-VPS39 (green), immunolabeled for endogenous VPS11 (eVPS11, blue).
ChIP-qPCR results show the association of HP1c with Notch target genes compared to RFP control. The amount of immunoprecipitated DNA in each sample is represented as signal relative to the total amount of input chromatin (equivalent to 1). Error bars indicate SEM. n=3 technical replicates. Data are evaluated with two-tailed Student's t-test (*p < 0.05, **p < 0.01, ***p < 0.001).