EMBO/sd-character-level-ner huggingface dataset:
C qRT-PCR analysis of the Ifnb1 mRNA expression in the liver (n=8), spleen (n=7) and lung (n=7) of WT or Akt2 KO mice 6 hours after the injection of VSV (1 × 106 PFU/g, i.v.). Data information: *P < 0.05, **P < 0.01; using a paired t-test Data are representative of three independent experiments respectively , in which the different groups of mice were sacrificed and quantified for indicated experimental purposes
(F) Representative immunostaining images of D-CiPSCs expressing pluripotency markers. n = 5 biological replicates. Scale bar, 50 μm.
B. Single cell morphology of MCF7 and MDA-MB-231 cell lines, expressing or not a RASSF1C construct, cultured in 3D rat tail collagen I and analyzed for their rounded or elongated morphology 24 hours after seeding in 3D matrix. Data information: All data are from n=3 independent experiments. Data are analyzed by Student T-test and represented as mean ± SEM.* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001.
RNAPII CRAC were performed in the presence of the indicated versions of SEN1 expressed from its own promoter in a centromeric plasmid, upon depletion of the chromosomally-encoded version of Sen1 in a Sen1-AID strain. G-H) IGV screenshots of examples of CUTs displaying substantial termination defects in the mutants.
(B) Quantification of miniature EPSC amplitudes in mock- and PTX-treated hippocampal neurons. (n=10 neurons per condition from 3 independent experiments, independent two-sample Wilcoxon-Mann-Whitney-U test, *p<0.05).
(B) Incidence of ankle pathological new bone formation in DBA/1 model. n=9 per cage of total 3 cages per group, Fisher's exact test.
A-I. Dye release time courses from liposomes as a percentage of maximal release. D. Dye release at 20 minutes reaction as a function of GSDMD (dark orange) and caspase-1 (dark blue) concentrations. Errors bars for three independent experiments are shown.
C) Representative Western blot of in vitro translation analysis of folding-incompetent model constructs. Bands show Total (T) and Soluble (S) fractions after centrifugation at 21,000 g for 30 mins. "+ Dnak" indicates addition of either DnaK mix - containing DnaK, DnaJ and GrpE.
Isothermal Titration Calorimetry (ITC) assay of Mac2 binding Paip1M. The raw calorimetric curve is displayed on top while the fitted binding isotherm curve is at the bottom. The measured values are: N = 0.94 ± 0.01 (binding stoichiometry); Kd = 15.5 ± 1.5 μM (dissociation constant); ΔH = -6778 ± 149 cal/mol (standard molar enthalpy change for binding); ΔS = -0.716 cal/mol/K (standard molar entropy change).
A. Schematic diagram of Co-IP combined with LC-MS/MS to screen potential proteins interacted with pep-AP.
B. TEM analysis of SPBs. PHSL1-CDC20 ama1∆ cells containing SPC72 or spc72-7 were shifted from 24 to 36°C at 4 h in SPM. TEM samples were collected at 12 h in SPM. Spc72 inactivation causes MP formation at metaphase I (P < 0.0001, Fisher's exact test). Scale bar, 0.2 μm.
A Schematic diagram of the strategy to generate F9Y381D and F9Y381Smouse strains. Introduced mutant oligonucleotide is in red and the corresponding amino acids are in green.
(C) UMAP representation of the meningeal macrophages of SPF and GF mice color-coded for the clustering results of the Seurat algorithm. The mappings between colors and clusters are shown on the right. The cell type annotations are based on published gene expression profiles.
Structural alignment of 2019-nCoV RBD/ACE2 and SARS-CoV RBD/ACE2 complexes. 2019-nCoV RBD is colored cyan and red, its interacting ACE2 is colored green. SARS-CoV RBD is colored orange and blue, its interacting ACE2 is colored salmon. The PDB code for SARS-CoV RBD/ACE2 complex: 2AJF.
(B) Representative of three Western Blot analysis of endogenous p150Glued, HOOK3 and p50 (or Dynamitin) immunoprecipitated with KIFC1 in wild-type ECs. Negative control (CTL) was performed incubating cell lysate with protein A- or G-Sepharose and empty mouse IgG.
Flow cytometry analysis of CFSE-labeled CD3+ T cells in the presence of DMSO, FK506 and CX5461 for 0, 3 and 7 d.
D. Scheme depicts the in vitro MS2 system strategy. CMV promoter-driven expression of MCP-GFPnls and hHBB-24xMS2-tagged RAB13 3'UTR. The visualisation of MCP-GFPnls bound to 24xMS2 allows the identification of the minimal region in the 3'UTR of RAB13 necessary for its localisation.
Bar graph showing relative glial cell volume in larvae of the indicated genotypes. All values represent mean±SEM. Data points represent values from biological replicates. Statistical test employed was Student's t-test.
Levels of neurotransmitters in cerebrum of Coq9+/+ mice supplemented with the H2S donor GYY4137 (E).
(A) Twenty spinal cords of NF50 tadpoles were isolated at 0, 1 and 3 day post amputation (dpa) and pooled for RNA sequencing.
D. Western blot analysis of control or FAM111A-depleted U2OS cells transfected with SV40 LT variants. Cells were collected and lysed at indicated timepoints after SV40 transfection, immunoblotted with FAM111A, LT, or PARP antibodies. Cdc2-PSTAIR was used as a loading control.
I) Solubility analysis of the in vitro solubility screen performed by Niwa et al (Niwa et al, 2009). Left panel shows combined box- and violin plots depicting the solubility distributions of proteins containing at least one strong APR (TANGO score > 70) not protected by any negative GKs (red) versus proteins where all strong APRs are flanked by at least one negative charge (blue). The right panel shows a control analysis, in which proteins were classified by the occurrence of at least one strong APR (TANGO score > 70) not flanked by any positive GKs (red) versus proteins where all strong APRs are flanked by at least one positive charge (blue). The upper boxplot whiskers indicate the largest value no further than 1.5 times the Inter-Quartile Range (IQR) from the upper hinge, the lower whiskers show the smallest value at least 1.5 * IQR from the lower hinge. Notches extend 1.58 * IQR / sqrt(n) from either side of the median and represent a 95% confidence interval for the median value. Statistical significance was determined through Kruskal-Wallis test with a post-hoc Wilcoxon analysis for pairwise testing. P-values are indicated.
(I-M) The core Atg genes are required for starvation-induced autophagy in both wild-type and CQ-treated skeletal muscles. Dmef2-Gal4, UAS-GFP-Atg8/UAS-Atg1 larvae were starved on low-nutrient food for 6 h (I) or starved on low-nutrient food +2.5 mg/ml CQ for 6 h (J). Note that Atg1 knockdown completely abolished the formation of GFP-Atg8-labeled autophagosomes (compare I-J to C-D). (K-L) Dmef2-Gal4, UAS-GFP-Atg8, Atg1Δ3d larvae failed to form GFP-Atg8 vesicles when starved or starved and treated with CQ. (M) Quantification of autophagy changes due to Atg gene knockdown in Dmef2-Gal4, UAS-GFP-Atg8 larvae starved on low-nutrient food +2.5 mg/ml CQ for 6 h. Each of the 10 UAS-Atg RNAi transgenes tested caused a highly significant decrease (p<.01) in the total area of GFP-Atg8vesicles. SEM is indicated, with n = 5 ventral longitudinal muscles from individual animals.
Interactions of the linker helix (pink) with the cNMP sensor domain (dark/light blue in cAMP-bound form, yellow/orange in apo state, residues from the opposing monomer labeled by a '). (A) Sidechains along the full span of the linker helix contact those from both chains of the sensor dimer, forming both polar (S139, K145, E147, N148) and hydrophobic (A140, L141, I144) interfaces. The linker helix conformation in the bound state would be sterically incompatible with the position of the cNMP body in the apo state (transparent, overlaid). (B) The hydrophobic A140/L141/I144 triplet forms a "wedge" that inserts between two faces formed by the cNMP body (I28, I55, A80) and C-helix (V97', L100'). In the apo state this linker feature is absent, allowing direct contact of these faces (closure of cleft). (C) Analogous role of N3A motif (green) from the cNMP sensor of M. loti MloK (PDB 1vp6, main fold in white). The hydrophobic patch in Bd1971 linker helix formed by A140/L141/I144 is spatially equivalent to one from MloK (V233/F236/I247) despite a difference in secondary structure between the two proteins. Similarly to Bd1971, the MloK N3A hydrophobic patch contacts the fold at a region between the hinge and cNMP body (right).
(C) Chemical shift perturbation values and relative peak intensities for backbone resonances (15N and 1H) of YqgPNTD calculated for complexes of 400 μM YqgPNTD with 10 μM (light grey, light orange) or 40 μM MnCl2 (dark grey, dark orange bars). Only residues 20-100 of YqgP are displayed for simplicity. Residues identified as potential manganese-binding region based on their chemical shifts and intensity changes upon NMR titrations are depicted in orange. The X sign marks residues whose chemical shifts were not calculated due to the lack of resonance signal.
D. Model of HP1γ-dependent impact on splicing events via its binding to repeated intronic hexameric motifs (red arrows).
I. Schematic representation of Hsp70 control of DnaJC5-mediated tau release. When clients are unable to bind Hsc70, or ifHsc70 is inactive or knocked down, client proteins are sent for degradation instead of release. Thus, Hsc70 is important for upstream control of the DnaJC5-mediated extracellular release.
C-D. Affinity chromatography with immobilised NlpI. Membrane extracts from E. coli were incubated in low and high salt binding conditions (50 and 400 mM NaCl, respectively), and then eluted with 1 M NaCl or 2 M NaCl to identify possible interaction partners by label-free LC-MS analysis. The plot shows the log2 fold enriched proteins when compared to those eluted from a parallel empty column control, versus the log10 p-value, in low (4 replicates) (C) and high (2 replicates) (D) salt. Highlighted points are all interactions with PG enzymes and their regulators, as well as members of the divisome. All other proteins were colored grey and not labelled to increase the plot clarity; many were non-physiological interactions with abundant cytoplasmic proteins.
A particle-based model of subepidermal blister healing at the basal layer. Epidermal basal cells (colored in blue), which do not divide, are placed on the basement membrane (gray). Stem cells (SCs, green) give rise to progeny (simulating HF-derived cells; red) within epidermal defects or in the surrounding epidermis (IFE-derived cells; yellow). t: arbitrary time. See Movie EV1.
C) Average composite plots of MSL2 [Chromatin] profiles centered at MSL2 chromatin regions called in both early and late (left) or only in late stages (right). Graphs represent average IP/Input signal of 3 biological replicates. Shaded area indicates the 95% confidence interval across regions. Total number of early = 212 and late = 87.
Pearson correlation of relative SAMHD1 protein abundance and synergy delta scores for ara-C and HU or dF-dC in primary patient-derived AML blasts (n = 23).
A: Glial shNf-1/shTp53 control and sgAtg7 cells were serum starved 4 hr then stimulated with 20 ng/mL TexasRed-EGF (TxRed-EGF) for 30 min. Scale bar: 10 μm. B: Quantification of TxRed-EGF puncta per cell, relative to the number taken up by control cells (in A). Data information: Statistical analyses were performed on at least 3 independent experiments, where error bars represent SEM and p values represent a two-tailed Student's t test: NS p>0.05, * p<0.05, *** p<0.001.
(A) Profiling of RNA methylome by m6A-seq shows significant changes of lncRNA modifications upon epidermal differentiation in vitro.
E. Representative images displaying JC-1 monomers (green), aggregates (red) and bright filed images of GV and MII oocytes from wild-type (WT) and Erk1/2oo-/- oocytes (n=3 mice in each group). Erk1/2oo-/- oocytes exhibited big and multiple polar bodies. Scale bar=100 µm.
C. Bacterially expressed and purified His-PCM1 (a.a. 1-1128) was incubated with MBP alone or MBP-Plk4 (WT or KD) in vitro, and pulled down by magnetic beads coupled with an anti-MBP antibody, followed by staining with Coomassie Blue (left) or immunoblotting with an anti-His antibody (right). Asterisks show non-specific bands. The mobility difference between Plk4-WT and Plk4-KD was reported previously [43, 48]. We reproducibly observed the upward mobility shift of His-PCM1 upon binding to MBP-Plk4-WT, but not Plk4-KD.
BRAFi-resistant M238R cells overexpressing FSCN1 were obtained after transduction with a FSCN1 lentiviral construct. M238R transduced with a Ctrl lentivirus were used as control. (G) Western Blot analysis of FSCN1, phenotype switch markers and ECM remodeling markers on cell lysates from control and FSCN1 overexpressing cells.
H. Schematic diagram of two lnc-AP OE plasmids of HA-sORF fusion and the corresponding initiation codon mutant.
D Phospho‐flow cytometry analysis of pERK responses against titrated concentrations of 9V tetramer. Time point was fixed at 60 s. Data shown are representative of three independent experiments.E Quantification of pERK‐positive cells from (D). Data from three independent experiments were used in the analysis. n = 3, means ± SEM are shown.
(B) Venn diagram shows the number of vDNA foci and vRNA foci and the number of vDNA foci colocalizing with vRNA foci. The p-value indicates the significance of colocalization based on a jittering analysis (see Methods).
(A) ssDNA repair efficiency of the rev1∆ mutant treated with MMS only in G1 as determined from the maximal and final percentages of cells with Rad52 foci during the time course (right panel). Cells were synchronized in G1 and treated with 0.033% MMS for 1 hour; after that the MMS was inactivated with 2.5% sodium thiosulfate and cells were released into fresh medium in the absence of DNA damage. The percentage of cells with foci at each point was normalized to the highest value of the wild type, taken as 100 (middle panel). A scheme on the left shows the experimental set up followed in this (MMS in G1 only) and the other experiments (MMS in S/G2). An asterisk represents a blocking DNA lesion for the replicative polymerase. Data information: The mean and SEM of 4 independent experiments are shown. Statistically significant differences according to an unpaired two-tailed Student's t-test are shown, where one, two and three asterisks represent p-values <0.05, <0.01 and <0.001, respectively.
B. TEM analysis of SPBs. PHSL1-CDC20 ama1∆ cdc28-as2 cells were treated with 1Na-PP1 at 3 h in SPM. At 9 h in SPM, cells were washed with cSPM containing (top) or lacking 1Na-PP1 (washout, bottom). TEM samples were collected at 13 h in SPM. Washout of 1Na-PP1 causes MP formation (P < 0.0001, Fisher's exact test). Scale bar, 0.2 μm.
F. Cell viability. Mouse tumour derived cell lines #3540 (Rosa26_Alkal2;Th-MYCN) and #3456 (Alk-F1178S;Th-MYCN) were treated with brigatinib (125nM and 500nM) and viability was evaluated by using a resazurin-based assay. Data is presented as mean ± SEM from three independent experiments. *p<0.05, **p<0.005; two-tailed paired student t-test.
Total GSH in cytosol and mitochondria of cerebrum of Coq9+/+ and Coq9R239X mice(A).
(F) Western blot of SOX9, HA-SOX9, pSOX9-T236, SNAI2 (SLUG), VIM and POU3F1 (OCT6) in MB002 cells stably transduced with EV, SOX9-WT and SOX9-T236/240A. Cells were induced for 24 and 48 hours with doxycycline and GAPDH were used as a loading control.
RNAPII CRAC were performed in the presence of the indicated versions of SEN1 expressed from its own promoter in a centromeric plasmid, upon depletion of the chromosomally-encoded version of Sen1 in a Sen1-AID strain. Analysis of RNAPII occupancy around snoRNAs performed as for CUTs.
(D) In vitro PAR binding assay. THRAP3 binding to PAR was used as a positive control and BSA binding to PAR was used as a negative control.
Diagram showing the structure of truncated HOXA4 (H) and TEAD1 (I) constructs and possible protein-protein interactions between them. Conservation between human TEAD1, 2, 3, and 4 is shown (I).
B. 5dpf dlx5a/6a transgenic line showing GFP+ GABAergic neurons are reduced in chd7-/- mutants (bottom) in comparison to controls (top) in both dorsal (left) and ventral (right) view.
D. Top: representative Western blots assessing mTOR phosphorylation at S2448 and p70S6K phosphorylation at T389 in PFC of adult 5-HT6-/- mice are illustrated. Bottom: data represent the ratios of immunoreactive signals of the anti phospho-mTOR (S2448) or anti phospho-p70S6K (T389) antibodies to the immunoreactive signal of the anti-β-actin antibody and are expressed in % of values in vehicle-injected 5-HT6-/- mice. They are the means ± S.E.M. of results obtained in four mice per group. n.s. p > 0.05, one-way ANOVA followed by Newman-Keuls test.
(D) Representative images of limb muscles (Tibialis anterior, TA; Gastrocnemius, Gas; Quadruple, Quad) from Ctrl or YY1dKO mice. (E) Quantifications of muscle weight from three pairs of littermate mice.
C Removal of FBS from normal growth conditions (DMEM+10% FBS) results in MAGE-A3/6 protein degradation in HeLa cells.
Representative current traces from oocytes expressing wild-type (WT) and double cysteine mutant NMDARs before and after DTE treatment. For each mutant, traces are normalized (in height, not in current amplitude) to the maximal response obtained after DTE treatment on wild-type (WT) receptors
(A) Immunofluorescence analysis of spine in PGIS mice. Quantitative analysis of CaSR+ p-p65+ cells and CaSR+ p-Stat3+ cells number in pathological new bone formation of PGIS model. n = 5, one‐way ANOVA, Bonferroni post hoc. Data information: AF: Annulus fibrosus; GP: Growth plate; NB: New bone
(A) Western blot analysis of PARP1 in chromatin. Two Ewing Sarcoma cells (CHP100 and A4573) were treated with MMS (0.02%, 1 hour) with or without release (1 hour) from MMS (N.T: non treat, T: treat, R: release sample).
D. Proteoliposome with protein/lipid molar ratio of 1/100 at higher magnification. Scale bar = 80 nm.
D Half-life of FOXO3 mRNA in Bel-7402 cells and correspondent METTL3-knockdown Bel-7402 cells treated with actinomycin D.
A Protein proximity map of the endocytic coat-associated proteins. B Enlarged view of the map focused on selected proximities of clathrin subunits, End3, and Sla2 and Pan1 shortened and full-length proteins. C Enlarged view of the map focused on Gts1 proximity network.
Adaptation at the end of growth. When the nutrient concentration decreases, the nutrient uptake rate slows down with a Michaelis-Menten type kinetics (top). Depending on the uptake affinity, bacteria will experience either a sharp or smooth decrease of growth rate (bottom left, bright orange: 10 µM, dark orange: 1 mM). During this slow down, the proteome adapts (bottom center), with lower affinities (dark orange) showing a slight improvement of proteome adaptation, which results in a slightly lower death rate (bottom right).
D) EMSA based DNA binding experiment shows that USP1PIP1 and USP1WT has similar DNA binding capability while USP1DM1 has lost its ability to bind DNA.
B) Bar graphic showing that human breast cancers with deletion of the miR-424/503 locus have higher protein levels of β-catenin (RPPA). P-value is calculated based on one-sided Wilcoxon rank-sum test. In the box-plots in B and C the relative expression of β-catenin in the RPPA data from TCGA is shown. The yellow line indicates the median and the bars indicate the 75th percentile (Q3)+1.5 interquartile range (IQR).
S. Quantification of luciferase activity in Drosophila with indicated genotypes and applied manipulations. Error bars show the SD of six independent experiments. Data information: Error bars represent SDs. Student's t-tests, **p < 0.01, ***p < 0.001, ****p < 0.0001, and non-significant (NS) represents p > 0.05.
(d-f) Echocardiography analysis of cardiac dimensions and function in Sham-operated mice and mice treated with intravenous injection of either control (Scr) or miR-132 inhibitors (Ant-132) after TAC. These mice were analysed 3 weeks after TAC for (d) fractional shortening, (e) end-diastolic area and (f) end-systolic area (n=4-9).
E. Representative confocal images of Mtmr2-/- co-cultures transduced using LV expressing Nrg1 type III shRNA #1, with quantification of the percentage of myelin outfoldings, n= number of DRG/coverslips, n= 9, 382 fibers (SCR), n=9, 368 fibers (LV #sh1, 12.5%), n= 8, 327 fibers (LV #sh1, 25%). Asterisks indicate fibers with myelin outfoldings. Results are mean ± SEM, p<0.0001, nonparametric one-way ANOVA, followed by Dunn's post hoc test, representative of two independent experiments.
(C) ORF length of Ty1/Copia and Ty3/Gypsy elements expressed in ddm1 relative to their genomic length.
(C) MitoTracker (red) and LC3immunostaining (green) of myotubes at DM-2. Chloroquine and 3-MA (where indicated) were added 12 h before staining. Note the extensive overlap of MitoTracker and LC3 in Rb−/−myotubes (yellow), which is inhibited by 3-MA. (D) Mean percentage of MitoTracker (red) to LC3 (green) overlap in 25 myotubes from two independent cultures in control versus Rb−/−myotubes (total) or Rb−/−myotubes with perinuclear mitochondrial aggregation (high). *, P = 7 × 10−5 by Student's t test.
(D) Structural arrangement of COX subunits detected in association with SC I+III2. Upper illustrations depict lateral views of human SC I+III2+IV1, where CI (aquamarine) and CIII2 (light green) are positioned along the inner membrane plane (dots). CIV appears as a smooth backbone with the associated COX subunits highlighted to show their positions relative to SC I+III2: COX7A2 (blue) and COX5B (red) attach COX1 (yellow) to the concave surface formed by CIII2 and the CI membrane arm, interaction further stabilized by COX7C (green) binding to CI. COX4 (magenta) interacts with COX1 on the distal side of CIV. Medium illustrations: matrix (M) view. Lower illustrations: intermembrane space (IMS) view. The figure was created with USCF Chimera v.1.12 using the 5XTH structure (Guo et al., 2017) from the PDB database.
(E) Immunoblotting analysis for HIF1α protein expression in GFP and MIG-6 knockdown BT549 cells in the absence or presence of the proteasome inhibitor MG132.
(c) CSR complementation assay in Samhd1 KO cells. Data are shown as the % IgA switching relative to the IgA switching in WT cells transfected with empty vector, and are derived from three independent experiments (mean ± sd; two-tailed unpaired Student's t-test).
Figure 2. Mmi1 binding to nam1 lncRNA controls MAPK-mediated entry into sexual differentiation. (F) Mating assay showing the percentage of zygotes formed over time in WT and nam1-1 cells. Average fold enrichment is shown with error bars that indicate mean average deviations (n=3) (B, E and F).
H) Determination of ER Ca2+. WT and Mfn2 KO MEFs were transfected with plasmid encoding the ER-located Ca2+ sensor LAR-GECO1. After 48 h, fluorescence was recorded every 3 seconds. ER Ca2+ release was induced with caffeine (20 mM) as indicated (n= 30 cells from 3 independent experiments). Data are presented as mean ± SEM.
(D) Venn diagram showing the overlap of AS in sh1 and sh2. mouse ESCs according to the type of AS event.
Immunoblot analysis of whole cell lysate from untreated human THP-1 monocytes with stable expression of a non-targeting control shRNA or and shRNA targeting OTULIN. Data are representative of two independent experiments.
F, p27 suppresses BIR/RMD and SSA/RMD. U2OS (EGFP-SSA-3427-3) cells carrying the Tet-on-cyclin E allele were infected with and without p27 lentiviral viruses. RMD was determined before and after induction of cyclin E overexpression by DOX (0.5 µg/mL) added 24 hours before transfection with the indicated sgRNAs/Cas9. Cyclin E expression levels and cell cycle profiles are shown in Appendix Fig S6.
(D) Accumulation of p62/SQSTM1 was analyzed via immunoblotting. β-actin was used as a loading control.
(b) FACS profile of the percentage of WT and Samhd1 KO CH12F3-2A cells undergoing IgA switching following transfection with the indicated plasmids. The number in the FACS plot represents the percentage of cells expressing IgA on their surface. (c) Summary of the FACS data obtained from two independent experiments. The data are shown as percentage of IgA expressing cells upon CSR induced by blunt (left) or staggered (right) DSBs (n = 2; mean + sd; two-tailed unpaired Student's t-test); ns = not significant.