EMBO/sd-character-level-ner huggingface dataset:
(A) Representative confocal micrographs of BMMs infected with either wild type (2308), ∆bspF or or complemented ∆bspF (∆bspF::bspF) bacteria (red) for 24 h and immunostained for the TGN vesicular marker Stx6 (green) and GM130 (blue). Scale bars, 10 µm and 2 µm (insets). Magnified insets show the association between Stx6-positive vesicles and rBCVs.
H Knockdown of YTHDF1 but not YTHDF2 abolished the increase of FOXO3 protein level in METTL3-overexpressing Bel-7402 cells. Quantification of the protein optical density by Image J in H-1 and H-2. Data information: In all relevant panels, *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; Two-tailed t-test. Data are presented as mean ± SD and are representative of 3 independent experiments.
Heat map of the JNK signature composed of 68 genes that are induced by expression of MKK7-JNK and repressed by JNKi,
(B) Representative brightfield images of organoids generated from GFPhigh stem cells isolated from tamoxifen treated AhR WT mice (Lgr5-GFPCreERT2 X CDX2P-CreERT2 [GC]) and KO mice (AhRf/f X Lgr5-GFPCreERT2 X CDX2P-CreERT2 [HGC]), treated with DMSO (control) or TCDD for 5 d. Data are from ≥4 mice, scale bar 200 µm.
Average DNase-Seq tag density profile for the 1000 IL-2 pDHSs in both replicates of TB IL-2 and TB IL-2nil samples, and for naïve T cells (TN).
MUTYH initiates the excision of the misincorporated adenine opposite 8-oxo-dG. The resulting 1-nt gap is then filled by Pol λ in an error-free (C) or error-prone (A) manner. Completion of the canonical short-patch (SP) pathway is futile as DNA ligase III cannot seal an 8-oxo-dG:dC base pair at the primer terminus. Thus, Pol λ promotes the long-patch (LP) extension past a correct base pair to complete error-free BER. Conversely, Pol λ is capable of stalling ligation (SP) or extension (LP) of an 8-oxo-dG:dA mispair, thus promoting its excision by proofreading. The resulting intermediate can then proceed through the error-free pathway.
D Effect of rAAV9-CUEDC2 treatment on echocardiography indices of left ventricle function recovery post-I/R measured by fractional shortening (FS) and ejection fraction (EF). WT+ rAAV-GFP (n = 10); Cuedc2-/- + rAAV-GFP (n = 10); Cuedc2-/- + rAAV-CUEDC2 (Low dose) (n = 12); Cuedc2-/- + rAAV-CUEDC2 (High dose) (n = 12). ** p < 0.0001.
H&E stained sections of mouse ear from indicated mice. Bright-field images, Scale bar: 250 µm, Magnification: 10x.
(B) SCs from C57 mice were treated with 10mM 2-DG or 10mM NaN3 for 36 hrs before measurement of proliferation rate by MTS assay (n=3 mice, each).
A. Cryo-sections of human organoids were analyzed for the presence of enterocytes (E-cad), Goblet cells (Muc-2) and tight junctions (ZO-1) by indirect immunofluorescence. Nuclei are stained with DAPI. Scale bar 25 μm. Data information: Three biological replicates were performed for each experiment. Representative immunofluorescence images are shown. Error bars indicate the standard deviation. Statistics are from unpaired t-test.
C, Clongenic assay of KRAS-mutant lung and pancreatic cells (MIA PaCa-2, H2122, H2009, H23, H358 and A549) treated with control (DMSO), AZD4547 (5 µM) and BI2536 (5 nM), alone or combination.
, E Images of Plin2-GFP in 3rd instar larval fat body cells of different genotypes. Scale bar represents 25 µm. (E) The peripheral localization of Plin2-GFP is greatly reduced in fat body cells from ppl>DGAT1 larvae with CSN2 RNAi or RDH/CG2064 overexpression. Images were taken by focusing on the periphery of fat cells.
ChIP analysis of NF45 and NF90 binding to the H42.9 loci in CD3+ T cells stimulated with P/I for 6 h. (n=3)
A. DC domain binding footprints (residues within 4 Å distance) on MT lattice at GTP/GDP.Pi and GDP states. Interface areas were calculated using PDBePISA
e. SARS-CoV (I-II) and SARS-CoV-2 (III-IV) S-mediated syncytium formation on 293T/ACE2 cells at 48 h. f. SARS-CoV (I-II) and SARS-CoV-2 (III-IV) S-mediated syncytium formation on Huh-7 cells at 48 h. Scale bar equals 400 μm in d-f.
(b) SH-SY5Y cells were exposed to CCCP (10 μM) for the indicated times and then subjected to immunoblot analysis.
A The data were analyzed by categorizing the splice events into seven types: exon skip (ES), alternative 5' donor (AD), alternative 3' acceptor (AA), retained intron (RI), mutually exclusive exons (ME), alternative first exon (AP) and alternative last exon (AT). The analysis of splice events was performed using the following filter criteria: Min Gene RPKM>2, |dPSI|>0.1, p-value≤0.02, Min Group Obs % >.85; RPKM-reads per kilobase of transcript per million aligned reads; and |dPSI|-absolute changes in percent splicing (dPSI, ∆Ψ). The events are presented in Fig 6 Source data file 1 as differential expression of splice events between ESRP1_Low and ESRP1_High cases.
A. Unique residue pairs mapped to the OCCM complex (PDB|5udb) and the key link Mcm2 - Orc5 (Mcm2-850-Orc5-369).
MIAPaCa-2 cells were transfected with wild-type or mutated (Twist1 binding site) Twist1 luciferase reporters (TGTLuc) together with increasing amounts of Twist1 expression vector in the presence of empty vector (EV) or TGIF1 expression vector. Luciferase activity was measured 48 hr following transfection and normalized on the basis of co-transfected Renilla luciferase (n=6).
C, A Tetracycline (Tet)-inducible, shRNA-resistant USP22 transgene was stably introduced into HCT116 cells. Cells were treated as in A, with and without expression of the transgene via Tet treatment. Whole-cell lysates were subjected to immunoblotting with the indicated antibodies.
(D) Heat map of the row-wise z-scores of 11 genes associated with cisplatin resistance in MB002 expressing Sox9-WT or Sox9-T236/T240A. Heat map was generated using the GenePattern software.
Western Blot analysis of bone tumor protein lysates from H2-c-fosLTR and H2-c-fosLTR/ColAREG mice
B. Western blot of STAT3, PDK4 and β-TUBULIN proteins in 22Rv1 cells with or without knockdown of STAT3. Ctrl = scrambled control, shSTAT3 = short hairpin knockdown of STAT3.
(D) Quantification of HIS3 mRNA levels from strains used in (C). Cells were grown in liquid media with selection for the transformed plasmids (SC-Leu), harvested in logarithmic growth phase and total mRNA was prepared. After reverse transcription, HIS3 mRNA levels were quantified using qPCR (RT-qPCR), normalized first to ACT1 mRNA and then to the empty vector control strain. Data represent means ± SD (n = 4). p = 2.43*10-5 (Student's t-test).
(A) Representative images using in vivo bioluminescence of control or IBMPFD mutant RH-expressing mice (RH12) 2 d after electroporation (baseline) or after 24 h of nutrient deprivation (starvation) of polyQ80 (Q80)- or polyQ19-luciferase (Q19) in the right and left tibialis anterior, respectively. The ratio of polyQ80-luciferase/polyQ19-luciferase is indicated below each image set. Values are in ×104 photons per second per square centimeter per steradian. (B) Box and whisker plot of the change (Δ) in the ratio of polyQ80-luciferase/polyQ19-luciferase activity in the left and right tibialis anterior muscle of control, VCP-WT, or one of two VCP-RH (RH12 or RH9) transgenic mouse lines after 24 h of starvation. The graph is representative of three animals per group. The p-value for RH12 was 0.05 and 0.06 when compared with control animals or VCP-WT transgenic. The p-value for RH9 was 0.03 when compared with either control or VCP-WT transgenic. The p-value was 0.01 and 0.02 when combined RH12 and RH9 animals were compared with control or VCP-WT groups, respectively. There was no statistical difference between control or VCP-WT groups.
(A) Workflow to identify genes involved in tumor growth from BRAFi-persister cells. Cell populations were subcutaneously grafted on nude mice flanks (3x106 cells per mouse); Vem-persister cells (n=11 mice) and PLX8394 (PB)-persister cells (n=12 mice) (BRAFi for PBV
F Survival rates (left panel) until 72 hours and H&E staining (right panel) at 18 hours of the zebrafish larvae with indicated protein expression and VSV challenge. The arrows indicated the VSV-infected eye and skeletal muscle in zebrafish larvae. Bars, 100 μm. Data information: *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 and ns, not significant (P > 0.05); using a log-rank (Mantel-Cox) test Data are representative of three independent experiments
J. CCK-8 assay of inhibition ratio by L-OHP in HCT116 and SW480 cells with lnc-AP/pep-AP attenuation and restoration (n = 3, biological replicates, mean±SEM). Data information: * si-NC was the abbreviation of commercial normal control of siRNA.
(B) Cell proliferation and immunoblotting assays in MDA-MB-231 cells with Luciferase or MIG-6 knockdown.
C. Quantification of BrdU incorporation in shScr, sh1 and sh2 ESCs at the indicated days of EB differentiation. Data are relative to shScr.
Representative averaged traces of sAPs of the mHb neurons with the pipette solution (40 mM Cl- and 0.5 mM EGTA) from TMEM16A cKO mice and littermate controls.
Whole-mount immunofluorescence of P7 mesenteries, showing efficient FOXP2 depletion in Foxp2flox/-;Tie2-Cre vessels. Dotted line indicates vessel width. Quantification of mesenteric collecting lymphatic vessel width in P7 Foxp2flox/-;Tie2-Cre and littermate controls (n = vessels [mice], as indicated).
(B) Chart highlighting the expression of the homeodomain cluster genes Dfd, Scr and mirr as well as the Ig genes DIPgamma and DIPkappa in MN2a and MN3, showing that both Ig genes are only expressed in MN2a and not in MN3.
D 5 μm‐long profile of the parkin‐positive vesicle and adjacent mitochondrial tubule depicted in the antimycin A‐treated cell from (B) (left). Increasing position values on the x‐axis of the fluorescence intensity plot (right) correspond to moving from the top to the bottom of the profile. *MDV indicated by an arrow in (B).
Mouse YUMM1.7 melanoma cells were subcutaneously inoculated into C57BL/6 mice and when tumors reached 100 mm3 mice were treated with vehicle (Ctrl), Nintedanib/BIBF1120 (BIBF), MAPKi (BRAFi, Vemurafenib and MEKi, Trametinib) or BRAFi/MEKi plus BIBF (n=6). (D) Mouse body weight was measured at the indicated times. Data shown are mean±SD (n = 6).
(B) Bar graph representing the normalized average value of the neuronal ATP/ATP+ADP ratio on the basal condition, on glutamate stimulation for 5 minutes, on glutamate stimulation with anisomycin (25μM) and on glutamate stimulation with cycloheximide (350μM). Data presented as mean ± SEM with scattered data points. Values in all other groups were normalized to the basal group for the corresponding experiment. **p<0.01, ***p<0.001, ****p<0.0001, n=5 independent platings. One-way ANOVA followed by Bonferroni's multiple comparison test.
(a) mCherry-p62/GST-GFP-4xUb clusters were photobleached and fluorescence recovery in the bleached area was monitored. The mCherry-tagged low complexity domain (LCD) of hnRNPA1 (hnRNPA1LCD) was included as a reference for a liquid droplet-forming protein. Left: representative micrographs of bleached particles. White arrows indicate the position and orientation of the kymographs shown in Figure EV4a. Right: quantification of fluorescence recovery. Individual traces of all particles analyzed from three independent replicates are displayed
Tumor volume and metastasis in live KCLuc and KTCLuc mice were analyzed by IVIS bioluminescence. Following imaging live animals, pancreas, brain, liver and lung were dissected and analyzed again by IVIS bioluminescence (n= 6, 5 out of 6 mice developed metastasis to liver and lung).
WT-derived BMDMs were stimulated with C.albicans, curldan, or α-mannan in combination with or without 2-DG (2.5mM) for 24h. mRNA expression of Il-7 were detected by using qPCR. BMDMs were acquired from WT and HIF-1-/- mice and were stimulated with C.albicans, curldan, or α-mannan for 24h. mRNA expression of Il-7 were detected by using qPCR.
GFP-C. albicans (5×106) were added onto 1×106 BMDMs, and incubated at 37°C for 1h. Wells were washed and fresh media containing fluconazole (300 μg/ml) was added. At 6 hours and 18 hours, C. albicans CFU inside BMDMs were photographed and calculated by plating on YPD agar. Scale bars, 25 µm.
(B) Flow cytometric analysis of YY1 protein or IgG control in FACS-isolated SCs cultured for the designated time (0, 24 or 48hrs). YY1 protein level is normalized to IgG levels. The numbers indicate the normalized level of YY1 protein relative to that of FISCs.
Proteins associated with SPTAC1L, identified by LC-MS/MS analysis. Proteins immunoprecipitated by an anti-SPATC1L antibody were analyzed by LC-MS/MS. Spec., spectrum count; Seq., sequence count (number of non-redundant peptides identified for each protein); Seq. cov., sequence coverage calculated based on the amino acid count; MW, molecular weight calculated using TurboSEQUEST software.
(K) Tumor growth curves from 501Mel cells overexpressing SMAD3, BIRC3 or SLC9A5.
E. PCR and WB analysis of HEK293T cells transfected with either lnc-AP-Flag OE plasmid (n = 3, biological replicates, mean±SEM, Dunnett-t test). F. PCR and WB analysis of HCT116/L-OHP and SW480/L-OHP cells transfected with either lnc-AP-Flag OE plasmid (n = 3, biological replicates, mean±SEM, Dunnett-t test). Data information: * for P < 0.05; ** for P < 0.01; NS for no significance. Control referred to the corresponding plasmid vector.
J Working model. The molecular mechanisms of m6A-dependent sorafenib-resistance in liver cancer. The expression of METTL3 was down-regulated in sorafenib-resistant liver cancer, and caused decrease of FOXO3 by the m6A modification in an YTHDF1-dependent manner. Degradation of FOXO3 thus promoted autophagy-associated sorafenib-resistance in liver cancer.
C J774A.1 macrophages were stimulated with zymosan after FK506 (10 ng/ml) or control treatment, and macrophage nuclear extracts were probed by Western blot for NFATc2 and NF-κB translocation. NFATc2 and NF-κB nuclear translocation was observed, which was maximal at 1 h p.i., in stimulated macrophages. FK506 specifically inhibited NFATc2 translocation, but had no effect on NF-κB.
(E) Volcano plots of the differential gene expression analysis of n=51 SPF and 136 GF stromal cpMΦs (left) and n= 85 SPF and 134 GF Kolmer epiplexus cell (CPepi) cells (right) based on Wilcoxon Rank Sum tests. The shown genes are filtered based on an avg. log2FC > 0.2 and adjusted p-value < 0.05.
(L) Single EDL myofibers were cultured for 3 days, followed by immunostaining for Myogenin (red) and MyoD (green). Scale bar = 50 µm. Quantifications of the numbers of each population, MyoD+Myog+, MyoD-Myog+, or MyoD+Myog-, are shown on the right (n=3 mice, each).
During development the tissue scale behaviour of dermal fibroblasts is achieved and maintained by a feedback loop between ECM deposition and fibroblast switching from proliferating to quiescent. Upon wounding, quiescent cells re-enter the cell cycle and tissue regeneration occurs via the sequential coordination of proliferation, active migration and cell displacement in the wound bed.
Average JUNB ChIP-Seq signal at the 1000 IL-2 pDHSs in TB IL-2 and TB+ IL-2 (Bevington et al., 2016).
Overlap between proteins affected by Bortezomib treatment and aging in killifish brain. For all comparisons, only significantly affected proteins adj. p < 0.05 were considered. A significant overlap between Bortezomib and aging-affected proteins is detected (Fisher test, as indicated in the figure panel). Significantly enriched GO biological process terms in the subset of overlapping proteins are indicated (FDR < 0.05).
(D) Representation of the SNARE complex with Ile51 (upper) and Ser51 (lower) residues highlighted.
A-D Microtubule affinity measured by a cosedimentation assay in the apo state (full line) and in the presence of ATP (dashed line), and AMPPNP (dotted line) for wild-type (A), mutant 2 (B), mutant 5 (C), and mutant 13 (D).
(C). Frequency of colonies with distinct cell size 5 days after initiation of culture of individual LT-HSCs from septin 7fl/fl of septin 7∆/∆ mice (192 sorted HSCs were analysed, error bars indicate mean±SD).
(F) In vivo primary tumor growth derived from BT549 cells containing iNT-shRNA and iMIG-6-shRNA (n=7 per group). The arrow indicates the time point when the diet was given to induce MIG-6 knockdown in vivo. Volumes of iNT-shRNA and iMIG-6-shRNA BT549 tumors are presented as mean ± SEM.
(f, g) SCFAs and acetic acid content in dietary experiments. Faecal samples from mice on the indicated diets were analysed for SCFAs by gas chromatography. Data information: All data shown are representative of at least three independent biological replicates.Error bars indicate SD (n=3). ****P-value < 0.0001 ***P-value < 0.001; **P-value < 0.01; *P-value < 0.05; NS: no significance (One-way ANOVA).
hnRNPA2 interacts with transport granule components hnRNPF and ch-TOG in the phase separated state. Disease mutations (X) D290V and P298L induce aggregation of hnRNPA2 in vitro, while D290V induces tdp-1-dependent neurodegeneration in a C. elegans model. hnRNPA2 LC tyrosine phosphorylation alters hnRNPA2 LC LLPS in vitro, prevents interaction with hnRNPF and ch-TOG, reduces aggregation in vitro, and expression of an activated tyrosine kinase reduces D290V-associated neurodegeneration in the C. elegans model.
Human CD14+ monocytes were electroporated with plasmids encoding the nucleocapsid or control vector for 36 h, followed by stimulation with 10 μM nigericin for 30 min post pretreatment with 1 μg/ml LPS for 3 h. Supernatants and cell pellets were collected and The percentage of viable cells was determined through checking cellular ATP levels in cell pellets (H). The percentage of cells undergoing pyroptosis was calculated through checking released LDH in the supernatants (I). Student's t-test was used and data were shown as means±SD of three technical replicates. **, P<0.01; NS, non-significant. Data information: control vector used here was empty vector corresponded to the nucleocapsid-containing vector. Student's t-test was used and data were shown as means±SD of three technical replicates. **, P<0.01; NS, non-significant. Similar results were observed for at least three times.
(D) Genes with higher expression at different developmental stages were selected out from previously reported RNA-seq (Data ref: Bertone, 2015). "Mor", "ICM", "pre-EPI" and "post-EPI" represented genes that have high expression only in morula, inner cell mass, pre-implantation epiblast and post-implantation epiblast, respectively. "Mor+ICM", "ICM+pre", and "EPI" indicated genes that have high expression in both morula and inner cell mass, in both inner cell mass and pre-implantation epiblast, and in both pre-implantation and post-implantation epiblast, respectively. The results of previously reported RNA-seq were summarized in the left panel, while the expression of these genes in current RNA-seq was summarized in the right panel. Log2 values of FKPM were presented similarly as in (C).
A) Representation of the differential glutamylation of α- and β-tubulin, and which epitopes can be detected by the glutamylation-specific antibodies used in this study. The most prominent tubulin isotypes in brain, α1- and β2-tubulin are shown with their C-terminal tails represented as amino-acid sequences. The main modification sites, glutamates (E) 445 on α1-tubulin (Eddé et al, 1990) and E435 on β2-tubulin (Rüdiger et al, 1992) are indicated. However, all glutamate residues in these C-terminal tails (light grey circles) could potentially be glutamylated. Glutamylation generated by TTLL1 is colour-coded red, while TTLL7-catalysed glutamylation is orange. Note that under wild-type conditions, TTLL1 and TTLL7 exclusively modify α- and β-tubulin, respectively in brain tissue.
(B) The PSR activates RALF expression under LP conditions. Col-0 seedlings were grown in either HP or LP media for 5 days and roots were harvested. The relative expression of RALFs was quantified via RT-qPCR. The data shown indicate the means ± SDs (n = 3, n refers to technical replicates); n.s., not significant; *, p < 0.05; **, p < 0.01 (Student's t test). Data information: All experiments were repeated three times with similar results.
A Autoinhibition of the Munc18-1/Syx1 complex. The closed Syx1 linker region and the bent Munc18-1 domain 3a render this complex inactivate, inhibiting Syx1 association with SN25 and Syb2. B Activation of the Munc18-1/Syx1 complex by Munc13 MUN domain. The MUN domain catalyzes opening of the Syx1 linker region via binding to H11 of domain 3a and Syx1 linker region, leading to a conformational flexibility of domain 3a (between bend and extension). The open Syx1 linker region and putative unstructured N-terminal of Syx1-H3 are displayed by lemon green and blue dashed lines, respectively. C Templating function of domain 3a. Assisted with Munc13 MUN domain, the extended domain 3a serves as a template for Syx1-H3 and Syb2 simultaneously, awaiting SN25 entry and registering SNARE complex assembly at the N-terminus. Dashed lines indicate putative unstructured regions. D SNARE complex assembly. Proceeding of SNARE four-helix bundle inside the central cavity of Munc18-1 to complete SNARE complex formation and membrane fusion.
C. Metabolite profile following three cycles of rapamycin and glucosamine treatment. The abundance of isoprenoid biosynthestic intermediates (1-deoxy-xylulose-5-P (DOXP), methyl-erithritol-4-P (MEP), methyl-erithritol-cyclo-2,4-PP (MEcPP), and isopentyl-PP), and hemoglobin-like peptides are presented as the mean log2 fold change from four biological replicates (±SD).
B. CCK-8 assay of inhibition ratio by L-OHP in two groups of CRC cells with down- or up-regulation of lnc-AP (n = 3, biological replicates, mean±SEM). Data information: * si-NC was the abbreviation of commercial normal control of siRNA.
Constructs and isoforms transcribed from 35S:EVDmU1 (C). Probes for northern analysis of GAG exon 1 (GAG-ex1), intron (GAG-in), exon2 (GAG-ex2) and the POL region are depicted with black lines. Red squares: stop codons.
(c) The mean percentage (+ s.d.) of L1 larvae alive after 48 h fasting in minimum media shows that hlh-30 (tm1978) mutant animals are sensitive to starvation. n = 3 independent experiments. For L4 survival see Supplementary Fig. S6g.
(A) The number of receptor SSDs, segmented from the combined receptor clusters of GABAARs and GlyRs, was decreased after 4-AP treatment (MW test, p < 0.0001). (B) This was mostly due to the loss of GABAAR SSDs that were segmented from the rendered images of GABAAR detections only (MW, ****p < 0.0001). (C) The number of GlyR SSDs (based on GlyR detections) were only marginally reduced (MW, **p < 0.01). Data information: Number of synapses: n = 452 in TTX, n = 583 in 4-AP condition, from three independent experiments. Mean ± SEM.
(B) Quantification of Alizarin Red staining at 570 nm (A570). n=3, one‐way ANOVA, Bonferroni post hoc.
The amount of CAPZB in mature sperm from WT (+/+) and KO (-/-) mice. Graph shows densitometric analysis of CAPZB shown in immunoblot analyses (Figure 7F), expressed relative to WT as a percentage. The density of CAPZB in immunoblot analysis was calculated in relation to density of α-Tubulin.
(H) Schematic model showing how the CSN-RDH/CG2064-Plin2 axis inhibits Bmm and promotes the formation of large lipid droplets under high-fat/increased TAG conditions.
Overlap between the subsets of IL-2 pDHSs which are present in in vivo derived Th1, Th2 and Th17 cells.
(Q) Representative brightfield images of human colonic organoids treated with DMSO or FDI-6. FoxM1 inhibition suppressed human colonic organoid growth in a dose-dependent manner, scale bar 200 µm.
F. Quantification for TIFs in EdU positive and EdU negative cells upon POT1 removal in clone 35. The bars show percentage of cells containing more than 5 TIFs ± SD. Experiments were performed in triplicate. At least 120 cells were analyzed per condition per replicate. Significance was determined using two-way ANOVA. p-values are indicated on the graph.
Volcano plot of gene expression in Ronin del/del day 4 vs. Ronin fl/del (left panel) and Ronin del/del day 8 vs. Ronin fl/del ESC (right panel) with annotated naïve and primed pluripotency markers.
F Western blot analysis showing FBXW7 expression in Day7 KO, KO+HA-MT5WT, and KO+HA-MT5Mut EBs. GAPDH was used as a loading control.