EMBO/sd-character-level-ner huggingface dataset:
Figure 3a, The CD loop sequences of PROPPINs from a wide variety of organisms. Potential amphipathic helices were predicted using the online tool Heliquest and are plotted in red. Amino acids removed in Atg18DLoop (aa 328-384) are printed in bold. b, Helical wheel projections of the red sequences from a. A schematic representation of the 7-bladed beta-propeller PROPPIN structure is also shown, illustrating the localisation of the putative amphipathic -helix (blue) of the CD loop between the two lipid binding sites for PI3P/PI(3,5) P2. Bold print marks phosphorylation sites in the loop of Pichia pastoris Atg18, which are relevant for its membrane insertion (Tamura et al, 2013).
Figure.Figure 8The 2 mature miRNAs generated from this cluster, miR-143-3p and miR-145-5p collaborate to mediate phenotypic transition towards a drug resistant undifferentiated mesenchymal-like state by targeting Fascin actin-bundling protein 1 (FSCN1), increasing focal adhesion signaling (FAs), cytoskeleton remodeling, YAP/MRTFA mechanotransduction pathways activation and ECM production. This mechanism leading to an undifferentiated fibrotic-like drug resistant phenotype can be targeted by the anti-fibrotic dru nintedanib.
Figure 7A, Genome browser image of ChIP-seq for middle and tail Mediator subunits and H3K4me3 HiChIP tracks before and after induction of ER stress at ER stress response gene BHLHE40. H3K4me1 and H3K27ac tracks are from the ENCODE Consortium (GEO accessions GSM945858 and GSM945853). ATF4/Xbp1s binding sites are from publicly available datasets (GEO accessions GSE69304 and GSE49952). B, H3K4me3 HiChIP signal (log2) at promoter-enhancer loops before and after induction of ER stress or USP22 depletion at indicated Bound group genes. C,D, Mean ChIP-seq signal MED1 and MED16 surrounding gene promoters from gene groups defined in Fig 4. E,F, Linear regression analysis of Mediator and USP22 recruitment to USP22-bound target gene promoters following induction of ER stress.
Figure 1Tau levels in the cortex (A, C-E) and hippocampus (B, F-H) of 4-10-month-old mice were determined by western blot analysis. (A, B) Representative western blots of cortical (A) and hippocampal (B) homogenates from mice of the indicated genotypes show levels of hTau (HT7) and total tau (Tau5). Actin served as a loading control. (C-H) Quantitation of western blot signals for full-length tau detected with the mTau/hTau cross-reactive antibodies Tau5 (C, F) or EP2456Y (D, G) or the hTau-specific antibody Tau12 (E, H). n = 3-8 mice per group. *P < 0.05, **P < 0.01, ***P < 0.001 by two-tailed unpaired t test (E, H) or by Welch's one-way ANOVA with post-hoc two-tailed Welch's t test (C, D, F, G). P values were Holm-adjusted for multiple comparisons. Values are means ± SEM.
a) Single-plane confocal microscopy images showing co-localization of the MBds and the autophagic receptor NBR1 in U2OS cells and.figf7(a) Single-plane confocal microscopy images showing co-localization of the MBds and the autophagic receptor NBR1 in U2OS cells and p62-deleted MEFs. MBd markers: MKLP1 or Cep55. Scale bar, 2 μm. (b) The percentage of MBd+ cells is significantly increased following the depletion of NBR1 (P=0.022, n=3), but not another autophagic receptor, p62. Co-depletion of NBR1 and p62 does not further increase MBd levels over NBR1 depletion alone. (c) Deletion of the p62 gene does not affect the percentage of MBd+ cells. For b and c, immunoblots verify protein loss. (d) Co-immunoprecipitation (IP) reveals that CEP55 and NBR1 form a complex. Precipitated proteins and 5% of the input material (Input) were analysed by immunoblotting (IB) with antibodies against NBR1 or CEP55. (e-g) Overexpression of CEP55-eGFP (enhanced green fluorescent protein) increases the percentage of MBd+ cells (e; P=0.0007, n=3) and the percentage of NBR1-negative MBds (f; P=0.0568, n=3), presumably by sequestering NBR1 (red) away from MBds in cells expressing CEP55-eGFP (green) as shown in g, and consequently preventing MBd degradation. The dotted box in g is enlarged (top right panel), and the labelling of NBR1 and CEP55-eGFP (middle and bottom right panels) are also presented. DAPI, DNA (blue). Scale bar, 5 μm. The data are presented as mean±s.d. (b,c,e,f). Uncropped images of blots are shown in Supplementary Fig. S6.
Figure 7Functional annotation of the significantly enriched (A) pAsp-containing proteins or (B) pGlu-containing proteins (ptmRS ≥ 0.90) using DAVID (q-value <0.05). BH: Benjamini-Hochberg.
Figure 6A-A" Staining of Drosophila indirect flight muscles at 25% pupal development with 22C10 antibody (myotube marker) and anti-Twist antibody (myoblast marker) indicates that in wild-type animals, indirect flight muscles are formed from 6 myotubes, and a large number of Twist+myoblasts are present.B-B" rumi79/79 mutants raised at 18C show no obvious defects in myoblast number or myotube morphology.C-D" rumi79/79 mutants exhibit decreased number of myoblasts at 25°-30°C and either an incomplete set of short myotubes when raised at 25C or aberrant morphology of myotubes when raised at 30C.E-E" rumi79/79 animals overexpressing FLAG-tagged POGLUT1WT in the muscle compartment using Mef2-GAL4 and raised at 25C during the pupal stage show a rescue of the rumi79/79 muscle phenotype.F-G" Overexpression of FLAG-tagged POGLUT1D233E only partially rescues the rumi79/79 muscle phenotype, with some variation in the myotube length and the number of restored Twist+cells (compare G and F). Note that the number of Twist+cells restored by POGLUT1D233E is much smaller than that restored by POGLUT1WT. Scale bar in A' is 50 µm and applies to A-G".H Quantification of myotube lengths in rumi79/79 mutants with or without POGLUT1 expression indicates a weak rescue of the phenotypes by POGLUT1D233E compared to POGLUT1WT. Mean ± standard deviation is shown. The differences in myotube lengths are statistically significant (n = 22-54). Mean ± standard deviation is shown; One-way Anova with Bonferroni´s multiple comparisons test.
A) The effects of 3-MA and NH4Cl on the accumulation of Htt-552.Figure 1 (B) The activations of macroautophagy induced by starvation as indicated by induction of Beclin 1. Starvation of PC12 cells were induced by removal of serum in the culture medium for indicated time. Values are the mean±SE of three independent experiments (*P<0.05; **P<0.01 vs 0 h). (C) The activations of CMA induced by starvation as indicated by induction of LAMP-2A. Values are the mean±SE of three independent experiments (**P<0.01 vs 0 h). (D) The relocation of CMA-active lysosomes toward the nuclear regions in PC12 cells. Cells were maintained in the presence or absence of serum. After 12 h, cells were fixed and subjected to immunofluorescence for LAMP-2A. Representative cells for each condition. N: nucleus. Thin arrows point to lysosomes. The scale bar represents 10 µm. (E) Effects of starvation for 6 or 12 h on the degradation of Htt-552 in PC12 cells. The effects of these starvations on protein levels of Htt-552 protein were determined with Western blot analysis. Values are the mean±SE of three independent experiments. **P<0.01 (compared with Htt-552-18Q without treatment); ##P<0.01, #P<0.05 (compared with Htt-552-100Q without treatment).
Figure 2A-F Shown are hypocotyl lengths of cRL-grown 4-day-old seedlings of toc1 complemented with wild-type TOC1 (A), 5X (B), T135A (C), S175A (D) driven by TOC1 native promoter and wild-type TOC1 (E), 5X (F) driven by 35S promoter at sequential fluent rates. Different letters indicate statistically significant differences between genotypes (p<0.01, one-way ANOVA followed by Tukey-Kramer HSD test), error bars indicate SEM. Data are representative of three biological trials with similar results.
Figure 5M-CSF induced mouse bone marrow derived macrophages (BMMs) were stimulated with 50 ng/mL mouse recombinant IFN-γ (A) in the absence or presence of PGE2 ± varying concentrations of TP-16 for 12 hr. The mRNA levels of selected M1 markers (Cxcl10 and Tnfa) were measured by q-PCR. Data are normalized to β-actin expression levels (n=3). B. M-CSF induced mouse bone marrow derived macrophages (BMMs) were stimulated with 20 ng/mL mouse recombinant IL-4 (B) in the absence or presence of PGE2 ± varying concentrations of TP-16 for 12 hr. The mRNA levels of selected M2 markers (Arg-1 and Ym-1) were measured by q-PCR. Data are normalized to β-actin expression levels (n=3). C. Bone marrow cells were cultured with 40 ng/mL GM-CSF/IL-6 or co-stimulated with PGE2 ± varying concentrations of TP-16 for 6 days. Representative quantification of Ly6C+Ly6G− monocytic myeloid-derived suppressor cells (mMDSCs) and Ly6CmidLy6G+ PMN-MDSCs (n = 3). D. Bone marrow cells were treated with GM-CSF/IL-6 for 6 days to induce MDSCs and thereafter, with PGE2 ± varying concentrations of TP-16 for 12 hr. The mRNA levels of selected MDSC markers (Arg-1, Ptgs2, Il-4, and Il-10) were measured by qPCR. Data are normalized to β-actin expression levels (n=3). E, F. In vitro T cell suppression activity of CT26-tumor infiltrating CD11b+ myeloid cells collected at 2 weeks post-treatment with vehicle or 75 mg/kg TP-16. CD8+ T cells were labeled with CFSE and then stimulated with CD3/CD28 antibodies for 3 days in the absence or presence of tumor-infiltrating CD11b+ myeloid cells from vehicle- or 75 mg/kg TP-16-treated CT26 tumors. Representative flow cytometry histograms (E) and percentages (F) of proliferating CD8+ T cells when plated in a ratio of 2:1, 1:1, and 1:2 CD8+ T cells to CD11b+ myeloid cells (n = 3).
Figure 4Schematic diagram of the Spatc1l gene coding region and region deleted using CRISPR/Cas9. The start codon sequence is labeled in red. Blue arrows indicate the forward and reverse primers used for genotyping. The numbers in boxes indicate exons, and filled boxes show Spatc1l coding regions. The 178-bp sequence deleted in the targeted allele of a Spatc1l-/- mouse (red dots) is indicated in partial sequencing results, shown below. PCR genotyping analysis of WT (Spatc1l+/+), heterozygous (Spatc1l+/-) and homozygous (Spatc1l-/-) mice. SPATC1L expression levels in testes obtained from WT, Spatc1l+/-, and Spatc1l-/- mice. An anti-GAPDH antibody was used as a control. Graph shows densitometric analysis of SPATC1L in relation to GAPDH in immunoblot analysis. Percentage of females that became pregnant after mating with WT (white bar), Spatc1l+/- (gray bar), and Spatc1l-/- (black bar) male mice. Male mice used: WT, n = 5; Spatc1l+/-, n = 6; Spatc1l-/-, n = 7. WT female mice used for mating with the indicated genotype: WT, n = 30; Spatc1l+/-, n = 36; Spatc1l-/-, n = 42. Vaginal plugs were observed in all mated females. Average litter size of pups produced by females mated with WT (white bar), Spatc1l+/- (gray bar), and Spatc1l-/- (black bar) male mice.
Figure 6A, Frequency of long-range RMD is increased by an additional DSB downstream of the 3' repeat. Illustrations show the GFP-RMD reporter, with sgRNAs/Cas9 cleavage sites indicated as red arrows (left). The frequency of BIR/SSA in mES cells carrying the RMD-GFP reporter was determined after cleavage of the reporter by the indicated sgRNAs/Cas9 (right). B and C, The effects of RAD52, POLD3, ATM and H2AX inactivation on BIR/RMD with cleavage at L17/D10k. The frequency of BIR/RMD in mES cells carrying the RMD-GFP reporter was determined using the sgRNAs/Cas9 at L17/D10k in RAD52 KO cells or after POLD3 depletion by siRNA (B), or after treatment with ATM inhibitor (ku55933, 15mM) or H2AX depletion by siRNA (C).
An autocrine stimulation by ActivinB in the 1603MED cell line.Figure 2The level of phosphorylated Smad2 (P-Smad2) and total Smad2 (Smad2) was assessed by immunoblotting and β-actin was used as a loading control. Lower bar graphs show WB quantification of P-Smad2 (P-S2) normalized to β-actin. (A) Activation of the pathway was assessed in non-Group 3 (blue) and Group 3 (yellow) MB cell lines in response to TGFβ or ActivinB stimulation for 1h. The level of phosphorylated Smad2 (P-Smad2) and total Smad2 (Smad2) was assessed by immunoblotting and β-actin was used as a loading control. Lower bar graphs show WB quantification of P-Smad2 (P-S2) normalized to β-actin. (B) 1603MED cells were treated with PBS (vehicle) or a blocking antibody targeting ActivinB (Ab α-ActB) or Follistatin. The p-values were determined by unpaired t-test. *p < 0.05, **p < 0.01, ***p < 0.001. Bars represent the mean ± SD. Number of replicates is n≥3. The level of phosphorylated Smad2 (P-Smad2) and total Smad2 (Smad2) was assessed by immunoblotting and β-actin was used as a loading control. Lower bar graphs show WB quantification of P-Smad2 (P-S2) normalized to β-actin. (C) Conditioned media experiments were performed on the HDMB03 MB cell line. Phosphorylation of Smad2 was analyzed by immunoblot upon treatment with either non conditioned media (NCM), media conditioned with HDMB03 cells (CM-HDMB03) or media conditioned with 1603MED cells (CM-1603). Pre-incubation with blocking antibody against ActivinB (Ab α-ActB) or vehicule (PBS) was performed before HDMB03 cell-line treatment as indicated. Relative level of P-Smad2 (P-S2) were quantified to β-actin (below). The p-values were determined by unpaired t-test. *p < 0.05, **p < 0.01, ***p < 0.001. Bars represent the mean ± SD. Number of replicates is n≥3. (D) RT-qPCR were performed on total RNA extracted from 1603MED cells 48 hours after transfection with siRNA targeting INHBB. Relative INHBB expression was assessed. siCTRL condition was set at 1. The p-values were determined by unpaired t-test. *p < 0.05, **p < 0.01, ***p < 0.001. Bars represent the mean ± SD. Number of replicates is n≥3. The level of phosphorylated Smad2 (P-Smad2) and total Smad2 (Smad2) was assessed by immunoblotting and β-actin was used as a loading control. Lower bar graphs show WB quantification of P-Smad2 (P-S2) normalized to β-actin. (E) 1603MED cells were transfected with the indicated control siRNA (siCTRL, blue) or targeting INHBB (siINHBB, red). Lysates were prepared 48 hours after transfection. Lower bar graphs represent the quantification of the relative level of P-Smad2 (P-S2) to β-actin. The p-values were determined by unpaired t-test. *p < 0.05, **p < 0.01, ***p < 0.001. Bars represent the mean ± SD. Number of replicates is n≥3. (F) Growth curve of 1603MED cells after transfection with either siCTRL (blue) or siINHBB (red). The p-values were determined by unpaired t-test. *p < 0.05, **p < 0.01, ***p < 0.001.
Figure 6A. Niaspan administration (daily i.p. injection of 160mg/Kg starting at P15 for 60 days) does not affect the growth of Mtmr2-/- mice. The growth rates of Mtmr2-/- and WT both saline-treated are significantly different, p<0.0001, Linear Mixed Effect (LME) models, as already reported (Bolino et al, 2004), n=8 animals per condition. B. Niaspan administration reduces the percentage of myelin outfoldings (red asterisks) in Mtmr2-/- sciatic nerves without affecting the number of myelinated fibers as assessed by semithin section analysis at P75, n= 8 mice per genotype, results are mean ± SEM, p=0.0093, two-tailed Mann Whitney U test, representative of three independent experiments. Niaspan treatment does not alter myelin thickness in WT or Mtmr2-/- mice as assessed by g-ratio analysis (WT saline-treated, 0.67 ± 0.003, 2014 fibers; Mtmr2-/- Niaspan-treated, 0.67 ± 0.007, 1924 fibers; Mtmr2-/- saline-treated, 0.68 ± 0.003, 2244 fibers; n=4 animals per condition).
Systematic assessment of genetic background dependencies of gene deletion phenotypes.Figure 2Average S-score Pearson's correlation between the same genes (orthologs, solid line) and random gene pairs (shaded distribution) across all the 38 conditions and four strains. Genes are stratified by the number of conditions in which they show a significant phenotype across the four strains. S-score scatterplots for each pairwise strain comparison, highlighting conserved phenotypes (black points), significant changes (red points) and gene-condition relationships for which no call can reliably be made (grey points). "r", pearson's r value. Fraction of deletion phenotypes in each strain conserved with other stains in pairwise, three-way and four-way comparisons. Error bars represent standard deviation for all pairwise and three-way comparisons. Only a four-way comparison is possible for each strain so no error bars are represented in these cases. Gene exclusiveness: a measure of each gene's propensity to change its chemical genomics profile across strains. The top 10 genes' names are reported. Genes with high exclusiveness (> 0) tend to have a higher number of negative genetic and physical interactions (as reported in the biogrid database).
Figure 3A) Experimental design. ESC cultures were supplemented with increasing concentrations (see Table EV1) of 20 distinct metabolites for 48 hours. The abundance of the Zscan4+ and 2-cell-like cells was quantified by FACS according to the reporters B) Heatmap showing the effect of the 20 metabolites tested on 2-cell-like cell levels. Percentage of 2-cell-like cells in cultures treated with increasing concentrations of sodium acetate, sodium L-lactate or D-ribose. Shown are the mean ± s.d. of 2 independent cell cultures, performed across 3 biological replicates. Boxes indicate the range between the first and third quantile, the band depicts the median and the whiskers extend no further than 1.5-times the interquartile range. Percentage of Zscan4+ cells in cultures treated with increasing concentrations of sodium acetate, sodium L-lactate or D-ribose. Shown are the mean ± s.d. of 2 independent cell cultures, performed across 3 biological replicates. Boxes indicate the range between the first and third quantile, the band depicts the median and the whiskers extend no further than 1.5-times the interquartile range. Percentage of Zscan4+ cells in cultures treated with varying combinations of sodium acetate, sodium L-lactate or D-ribose. Shown are the mean ± s.d. of 2 independent cell cultures, performed across biological replicates. Boxes indicate the range between the first and third quantile, the band depicts the median and the whiskers extend no further than 1.5-times the interquartile range. Percentage of 2-cell-like cells in cultures treated with varying combinations of sodium acetate, sodium L-lactate or D-ribose. Shown are the mean ± s.d. of 2 independent cell cultures, performed across biological replicates. Boxes indicate the range between the first and third quantile, the band depicts the median and the whiskers extend no further than 1.5-times the interquartile range.
Figure 1A) LN-229 CM stimulated growth of BCE cells, n=3. Data information: Bars and error bars represent mean ± SD. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test. ns, not statistically significant. B) VEGF neutralizing antibody (B20) failed to suppress BCE cell growth induced by LN-229 CM, n=3. Data information: Bars and error bars represent mean ± SD. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test. ns, not statistically significant. C) Reverse-phase fractions of LN-229 CM induced BCE cell growth. BCE cells were incubated with fractions (2 μl/well) as indicated in the Figure, n=3. Data information: Bars and error bars represent mean ± SD. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test. ns, not statistically significant. D) Candidate proteins generated from Mass-spectrometry analysis of LN-229 CM reverse-phase fractions. Candidates were identified by excluding intracellular proteins and proteins showing higher abundance in inactive fractions compared to those in mitogenic factions. Proteins were ranked for relative abundance as described in Materials and Methods. E) The anti-LIF neutralizing antibody abolished BCE cell growth induced by reverse-phase fractions, n=3. Data information: Bars and error bars represent mean ± SD. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test. ns, not statistically significant. F) Recombinant human LIF proteins stimulated growth of BCE cells in a dose-dependent manner. BCE cells were cultured in the presence of vehicle, VEGF (10 ng/ml) and the indicated concentrations of recombinant human LIF (rhLIF, Sigma), n=3. Data information: Bars and error bars represent mean ± SD. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test. ns, not statistically significant. G) LIF and VEGF synergistically stimulated BCE cell growth. Cell proliferation was analyzed after 6 days using alamar blue as described in Materials and Methods, n=3. Data information: Bars and error bars represent mean ± SD. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test. ns, not statistically significant.
Figure 3A, ColE9 residues 3-67 of the IUTD in the partial translocon structure pass through OmpF subunit 2 and then back up into subunit 1. As a result, OBS1 (gold) docks within subunit 1 and OBS2 (orange) within subunit 2. The ColE9 TBE motif (pink) interacts with TolB and is positioned below subunit 2, above which the ColE9 T-domain is located. B, Surface representation of OmpF subunit 1 (grey) and ColE9 residues 3-24 (gold) containing OBS1 sequence. ColE9 OBS1 binds the inner vestibule of OmpF subunit 1 such that it runs along the edge of the vestibule, stopping at the eyelet. C, ColE9 residues 45-67 (orange) encompassing OBS2, traverse the pore of OmpF subunit 2 (grey). After passing through the eyelet, OBS2 tracks more centrally in the inner vestibule unlike in panel c where residues 3-24 trail the side of the pore. D, OmpF subunit 1 displayed as an electrostatic surface (same cut-through as in b), revealing a patch of negative charge located on the extracellular side of the eyelet that interacts with OBS1, also shown as an electrostatic surface adjacent to the subunit. E, OmpF subunit 2 displayed as an electrostatic surface (same cut-through as in c), with OBS2 also shown as an electrostatic surface adjacent to the subunit. Projecting out of the page for OBS2 is a positively charged region flanked by negative charges. F, A zoom-in of grey box in panel a highlighting hydrogen bonding network between residues 3-7 of OBS1 (gold sticks) and nearby residues within OmpF subunit 1 (grey sticks). G, OBS1 residues 11-17 (gold sticks) also interact with the base of OmpF subunit 1 (grey sticks) in the periplasm. Region is a zoom-in of blue box in panel a. H, OmpF subunit 2 residues (grey sticks) form a hydrogen bond network with the backbone of residues of ColE9 OBS2. Region is a zoom-in of brown box in panel a. All electrostatic surfaces shown in panels d and e were calculated using the APBS plugin within Pymol.